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February 10, 2011 22:28
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| diff --git a/Makefile b/Makefile | |
| index 1084fa7..d70dfbd 100644 | |
| --- a/Makefile | |
| +++ b/Makefile | |
| @@ -16,21 +16,40 @@ BINDIR=$(CURDIR)/bin | |
| # The directory in which to run RMG (used for the test) | |
| RUNDIR=$(CURDIR)/run | |
| -# The Fortran 90 compiler to use and flags to use when compiling Fortran 90 | |
| -# code | |
| -F90=g95 | |
| -F90FLAGS=-fbounds-check -ftrace=full -fmod=$(BUILDDIR) -Wall -O3 | |
| -F90FLAGS_NDEBUG=-fmod=$(BUILDDIR) -ftrace=full | |
| -# these are added to the LDFLAGS of the subsidiary makefiles | |
| -#F90_EXTRA_LDFLAGS = -L/home/local/lib -lg2c # required for Monch | |
| -#F90_EXTRA_LDFLAGS = -framework vecLIB # for optimized blas and lapack on MacOS X, if they're not found automatically | |
| +# The Fortran 90 compiler to use and flags to use when compiling Fortran code | |
| +# Call with 'make F90=g95' if you want to use g95 | |
| +# or 'make F90=gfortran' for GNU Fortran (recommended) | |
| +# Here we set the default | |
| +#F90=g95 | |
| +F90=gfortran | |
| + | |
| +ifeq ($(F90),g95) | |
| +F90FLAGS = -fbounds-check -ftrace=full -fmod=$(BUILDDIR) -Wall -O3 | |
| +F90FLAGS_NDEBUG = -fmod=$(BUILDDIR) -ftrace=full # used for dassl and daspk | |
| +endif ###### END OF g95 SETTINGS | |
| + | |
| +ifeq ($(F90),gfortran) | |
| +# --fpe-trap=invalid,zero,underflow,overflow | |
| +# The above flag causes problems at least with fame. Maybe a bug in gfortran? (Maybe a bug in fame.) | |
| +F90FLAGS = -ftrapv -fbounds-check -frange-check \ | |
| + -ggdb -J""$(BUILDDIR)"" -O3 -Wall -Wno-unused | |
| +# if gfortran>4.3 then add -fbacktrace (it's not supported in earlier versions) | |
| +ifeq ($(shell gfortran --version 2>/dev/zero|grep -iqs '^GNU Fortran.* [4-9]\.[3-9]\.[0-9]' && echo "ok"), ok) | |
| +F90FLAGS += -fbacktrace | |
| +endif | |
| +F90FLAGS_NDEBUG = $(F90FLAGS) # used for dassl and daspk | |
| + | |
| +# call as `make MACOS=true F90=gfortran` if you want MacOS X 10.6+ 64-bit intel core2 features | |
| +ifdef MACOS | |
| +F90FLAGS += -arch x86_64 -march=core2 | |
| +F90_EXTRA_LDFLAGS += -framework vecLIB | |
| +endif | |
| + | |
| +endif ###### END OF gfortran SETTINGS | |
| -#F90=gfortran | |
| -#F90FLAGS=-fbounds-check -fbacktrace -Wall -O3 | |
| -#F90FLAGS_NDEBUG=-fbacktrace | |
| -#F90=gfortran | |
| -#F90FLAGS = -ffpe-trap=invalid,zero,overflow -ftrapv -fbounds-check -ggdb -J""$(BUILDDIR)"" -Wall -O3 | |
| +# these are added to the LDFLAGS of the subsidiary makefiles | |
| +#F90_EXTRA_LDFLAGS = -L/home/local/lib -lg2c # required for Monch | |
| ################################################################################ | |
| @@ -67,9 +86,6 @@ daspk: dirs | |
| GATPFit: dirs | |
| make -C $(SOURCEDIR)/GATPFit SOURCEDIR=$(SOURCEDIR)/GATPFit BUILDDIR=$(BUILDDIR)/GATPFit BINDIR=$(BINDIR) F90=$(F90) F90FLAGS="$(F90FLAGS)" F90_EXTRA_LDFLAGS="$(F90_EXTRA_LDFLAGS)" | |
| - | |
| - | |
| - | |
| dirs: | |
| mkdir -p $(BUILDDIR) | |
| mkdir -p $(BINDIR) | |
| @@ -89,7 +105,8 @@ clean: | |
| test: | |
| mkdir -p $(RUNDIR) | |
| cp examples/RMG/1,3-hexadiene/condition.txt $(RUNDIR) | |
| - export RMG=$(CURDIR); cd $(RUNDIR); java -jar $(BINDIR)/RMG.jar condition.txt | tee RMG.log | |
| + export RMG=$(CURDIR); cd $(RUNDIR); java -jar $(BINDIR)/RMG.jar condition.txt 2>&1 | tee RMG.log | |
| + echo "Results saved to $(RUNDIR)/RMG.log" | |
| help: | |
| @echo "" | |
| diff --git a/README.rst b/README.rst | |
| new file mode 100644 | |
| index 0000000..642405c | |
| --- /dev/null | |
| +++ b/README.rst | |
| @@ -0,0 +1,49 @@ | |
| +==================================== | |
| +RMG - Reaction Mechanism Generator | |
| +==================================== | |
| + | |
| +.. image:: https://github.com/GreenGroup/RMG-Java/raw/master/web/source/_static/rmg_logo.png | |
| + :align: right | |
| + | |
| +RMG is an automatic chemical reaction mechanism generator that constructs | |
| +kinetic models composed of elementary chemical reaction steps using a general | |
| +understanding of how molecules react. | |
| + | |
| +The easiest way to get started on Windows is to download the complete installer package | |
| +from over at http://rmg.sourceforge.net/, and read the documentation_ that's also hosted there. | |
| +If you want to use the cutting-edge development version that is hosted here at GitHub, | |
| +then you'll have to compile it yourself. | |
| + | |
| +.. _documentation: http://rmg.sourceforge.net/documentation/ | |
| + | |
| +Compiling from source | |
| +----------------------------- | |
| + | |
| +Linux | |
| +~~~~~ | |
| + | |
| +Mac | |
| +~~~~~ | |
| + | |
| +You will need the Java compiler, Apache ant, and GNU Make, but these are all provided by MacOS. | |
| +If you're missing these `developer tools <http://developer.apple.com/technologies/tools/>`_ you can download them from Apple. | |
| +You will also need a Fortran compiler. | |
| +We recommend gfortran_, but g95 can be used if you add the option `F90=g95` to the `make` command. | |
| +On MacOS X 10.6 (Snow Leopard) the gfortran compiler flags can be optimized with the make option `MACOS=true`. | |
| +One nice way to get gfortran is to install homebrew_ then then type `brew install gfortran`. | |
| + | |
| +.. _gfortran: http://r.research.att.com/tools/ | |
| +.. _homebrew: http://mxcl.github.com/homebrew/ | |
| + | |
| +The quick-start instructions in full: | |
| + | |
| +#. git clone git://github.com/GreenGroup/RMG-Java.git | |
| +#. cd RMG-Java | |
| +#. make MACOS=true | |
| +#. make test | |
| + | |
| +For more, refer to the documentation_. | |
| + | |
| + | |
| +Windows | |
| +~~~~~~~~ | |
| diff --git a/RMG-gui.bat b/RMG-gui.bat | |
| index 3bd84bb..4bb123b 100755 | |
| --- a/RMG-gui.bat | |
| +++ b/RMG-gui.bat | |
| @@ -4,13 +4,13 @@ if not defined RMG ( | |
| echo Error: RMG environment variable not defined; please set to the location of your RMG installation. | |
| goto end | |
| ) | |
| -if not exist %RMG%\bin\RMG.jar ( | |
| +if not exist "%RMG%\bin\RMG.jar" ( | |
| echo Error: RMG.jar not found; please compile using ant. | |
| goto end | |
| ) | |
| echo Starting RMG GUI... | |
| -java -Xmx500m -classpath %RMG%\bin\RMG.jar GUI | |
| +java -Xmx500m -classpath "%RMG%\bin\RMG.jar" GUI | |
| :end | |
| pause | |
| diff --git a/build.xml b/build.xml | |
| index 1f2c962..030d5c7 100755 | |
| --- a/build.xml | |
| +++ b/build.xml | |
| @@ -16,7 +16,7 @@ | |
| </target> | |
| <target name="clean" description="delete all compiled classes"> | |
| - <delete> | |
| + <delete failonerror="false"> | |
| <fileset dir="${build}"> | |
| <include name="**/*.class"/> | |
| <include name="*.class"/> | |
| diff --git a/databases/RMG_database/ForbiddenStructures.txt b/databases/RMG_database/ForbiddenStructures.txt | |
| index 50eafd0..da3901a 100644 | |
| --- a/databases/RMG_database/ForbiddenStructures.txt | |
| +++ b/databases/RMG_database/ForbiddenStructures.txt | |
| @@ -43,18 +43,24 @@ Carbene_D | |
| 1 C 2T {2,D} | |
| 2 C 0 {1,D} | |
| -CO3 | |
| -1 C 0 {2,D} {3,S} {4,S} | |
| -2 O 0 {1,D} | |
| -3 O 0 {1,S} | |
| -4 O 0 {1,S} | |
| - | |
| - | |
| -CO3. | |
| -1 C 0 {2,D} {3,S} {4,S} | |
| -2 O 0 {1,D} | |
| -3 O 1 {1,S} | |
| -4 O 0 {1,S} | |
| +// Cyclic C3O is a saddle point and immediately becomes | |
| +// linear C3O according to http://dx.doi.org/10.1039/b718817j | |
| +cyclic-C3O | |
| +1 C 0 {2,D} {3,S} {4,S} | |
| +2 O 0 {1,D} | |
| +3 C 0 {4,T} {1,S} | |
| +4 C 0 {3,T} {1,S} | |
| + | |
| +// Cyclopropyne is unstable according to http://dx.doi.org/10.1021/ja960762n | |
| +// but note that cyclopropene-1,2-diyl, which is the same geometry but with a | |
| +// double bond and 2 radicals instead of a triple bond, is stable and now in | |
| +// the primaryThermoLibrary. | |
| +cyclopropyne | |
| +1 C 0 {2,T} {3,S} | |
| +2 C 0 {1,T} {3,S} | |
| +3 C 0 {2,S} {4,S} {5,S} {1,S} | |
| +4 H 0 {3,S} | |
| +5 H 0 {3,S} | |
| //gmagoon 2/22/10: forbid physically unlikely cyclic cumulenic C3 species to prevent infinite recursion error in getToEndOfAxis; UPDATE: this issue should be fixed by my updates to ChemGraph, so we don't need to make this a forbiddenStructure | |
| //cC3 | |
| diff --git a/databases/RMG_database/frequencies_groups/Dictionary.txt b/databases/RMG_database/frequencies_groups/Dictionary.txt | |
| index c838492..5a83d17 100644 | |
| --- a/databases/RMG_database/frequencies_groups/Dictionary.txt | |
| +++ b/databases/RMG_database/frequencies_groups/Dictionary.txt | |
| @@ -1,6 +1,7 @@ | |
| //Frequency dictionary: devised by Franklin Goldsmith | |
| //implemented by Greg Magoon: 11/13/08 (based off Group_Dictionary.txt for Thermo) | |
| //"counting nodes" (those that are counted by Franklin's code) denoted by ### | |
| +//"potential counting nodes" (not currently handled by frankie, cf. https://github.com/GreenGroup/RMG-Java/commit/a171151e334dfa563f97632cb687347e314f8f9b) denoted by *** | |
| //modified 11/18/08 since {} notation for radicals doesn't seem to work | |
| R!H //L0 | |
| @@ -656,7 +657,7 @@ | |
| 2 R!H 2 {1,D} | |
| 3 H 0 {1,S} | |
| - CtCr //L2 Node: triple-bonded to one heavy atom (carbon) ### | |
| + CtCr //L2 Node: triple-bonded to one heavy atom (carbon) *** | |
| Union {CtCrx0, CtCrx1} | |
| CtCrx0 | |
| @@ -838,7 +839,7 @@ | |
| C_R2 // L1 Node: carbon, double radical | |
| 1 * C 2 | |
| - RsCHrr // L2 Node: single-bonded to exactly one heavy atom ### | |
| + RsCHrr // L2 Node: single-bonded to exactly one heavy atom *** | |
| Union {RsCHrrx0,RsCHrrx1,RsCHrrx2} | |
| RsCHrrx0 | |
| @@ -856,7 +857,7 @@ | |
| 2 R!H 2 {1,S} | |
| 3 H 0 {1,S} | |
| - RdCrr //L2 Node: double-bonded to one heavy atom (vinylic) ### | |
| + RdCrr //L2 Node: double-bonded to one heavy atom (vinylic) *** | |
| Union {RdCrrx0,RdCrrx1,RdCrrx2} | |
| RdCrrx0 | |
| @@ -871,7 +872,7 @@ | |
| 1 * C 2 {2,D} | |
| 2 R!H 2 {1,D} | |
| - RsCrrsR // L2 Node: single-bonded to exactly two heavy atoms ### | |
| + RsCrrsR // L2 Node: single-bonded to exactly two heavy atoms *** | |
| Union {RsCrrsRx00,RsCrrsRx01,RsCrrsRx11,RsCrrsRx02,RsCrrsRx12,RsCrrsRx22} | |
| RsCrrsRx00 | |
| @@ -1040,7 +1041,7 @@ | |
| 1 * O 1 | |
| - Oxy // L2 Node: bound to carbon ### | |
| + Oxy // L2 Node: bound to carbon *** | |
| Union {Oxyx0,Oxyx1,Oxyx2} | |
| Oxyx0 | |
| diff --git a/databases/RMG_database/frequencies_groups/Tree.txt b/databases/RMG_database/frequencies_groups/Tree.txt | |
| index fc1ed6c..93a4e32 100644 | |
| --- a/databases/RMG_database/frequencies_groups/Tree.txt | |
| +++ b/databases/RMG_database/frequencies_groups/Tree.txt | |
| @@ -27,7 +27,7 @@ L0: R!H | |
| L2: OdCrsR | |
| L2: CdCrsR | |
| L2: RsCrsR2 | |
| - L2: C_R2 | |
| + L1: C_R2 | |
| L2: RsCHrr | |
| L2: RdCrr | |
| L2: RsCrrsR | |
| diff --git a/databases/RMG_database/kinetics_groups/H_Abstraction/rateLibrary.txt b/databases/RMG_database/kinetics_groups/H_Abstraction/rateLibrary.txt | |
| old mode 100644 | |
| new mode 100755 | |
| index b801731..42918cc | |
| --- a/databases/RMG_database/kinetics_groups/H_Abstraction/rateLibrary.txt | |
| +++ b/databases/RMG_database/kinetics_groups/H_Abstraction/rateLibrary.txt | |
| @@ -1,361 +1,358 @@ | |
| -// rate library for f01: HAbstraction reaction | |
| -// original from rate library.txt, CDW 03/08/01 | |
| -// SR and JS rename some nodes according to the tree and dictionary correction, Nov., 20, 2002 | |
| -// JS, comment out 10th, change XH in 23 from C/Cd/H3 to C/H3/Cd | |
| -// JS, remove CO_birad to form a new family later: CO + RH -> HCO + R. Aug, 26, 2003 | |
| - | |
| -// JS, define key word for format of the rate: either Arrhenius or Arrhenius_EP | |
| -Arrhenius_EP | |
| - | |
| -// Catherina Wijaya thesis, pg 151 -154. | |
| - | |
| -//f01_intermolecular_HA | |
| -//No. XH Y_rad Temp. A n a E0 DA Dn Da DE0 Rank Comments | |
| -0. X_H_or_Xrad_H Y_rad_birad 300-1500 1E+05 0 0 10 0 0 0 0 0 Default | |
| -1. X_H Y_rad_birad 300-1500 1E+05 0 0 10 0 0 0 0 0 Default | |
| -2. X_H H_rad 300-1500 2.4E+08 1.5 0.65 9.4 0 0 0 0 5 Dean, A. M. [118] | |
| -3. X_H O_atom_triplet 300-1500 1.7E+08 1.5 0.75 6.6 0 0 0 0 5 Dean, A. M. [118] | |
| -4. X_H O_pri_rad 300-1500 1.2E+06 2.0 0.50 10.1 0 0 0 0 5 Dean, A. M. [118] | |
| -5. X_H O_sec_rad 300-1500 1.4E+04 2.69 0.60 11.3 0 0 0 0 5 Dean, A. M. [118] | |
| -6. X_H C_methyl 300-1500 8.1E+05 1.87 0.65 13.0 0 0 0 0 5 Dean, A. M. [118] | |
| -7. C/H/Cs3 C_rad/Cs3 300-1500 1.30E-01 3.71 0 6.85 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -8. C/H2/NonDeC C_rad/Cs3 300-1500 1.26E+00 3.55 0 8.31 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -9. C/H3/Cs C_rad/Cs3 300-1500 2.85E+00 3.62 0 11.20 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -10. C/H/Cs3 C_rad/H/NonDeC 300-1500 5.58E+01 3.01 0 7.34 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -11. C/H2/NonDeC C_rad/H/NonDeC 300-1500 1.52E+01 3.19 0 10.31 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -12. C/H3/Cs C_rad/H/NonDeC 300-1500 4.71E+01 3.23 0 12.27 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -13. C/H/Cs3 C_rad/H2/Cs 300-1500 4.22E+03 2.51 0 8.06 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -14. C/H2/NonDeC C_rad/H2/Cs 300-1500 1.54E+03 2.66 0 10.10 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -15. C/H3/Cs C_rad/H2/Cs 300-1500 6.59E+02 2.71 0 12.92 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -16. C/H/Cs3 C_methyl 300-1500 5.74E+05 1.83 0 6.94 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -17. C/H2/NonDeC C_methyl 300-1500 1.45E+06 1.77 0 8.53 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -18. C/H3/Cs C_methyl 300-1500 2.78E+05 1.9 0 11.05 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -19. C_methane C_methyl 300-1500 1.01E+04 2.47 0 13.96 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -20. C/H/Cs3 H_rad 300-1500 4.83E+08 1.54 0 2.98 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -21. C/H2/NonDeC H_rad 300-1500 1.30E+08 1.69 0 4.78 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -22. C/H3/Cs H_rad 300-1500 6.28E+07 1.75 0 7.51 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -23. C_methane H_rad 300-1500 3.06E+07 1.87 0 10.59 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -24. O/H/NonDeC H_rad 300-1500 8.70E+08 1.39 0 10.07 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -25. CO_pri H_rad 300-1500 5.48E+07 1.82 0 2.44 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -26. CO/H/NonDe H_rad 300-1500 8.07E+07 1.76 0 0.67 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -27. Cd_pri H_rad 300-1500 2.53E+07 1.98 0 11.78 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Primary vinylic {Cd/H2} | |
| -28. Cd_pri H_rad 300-1500 4.53E+03 2.43 0 8.85 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Ketene hydrogen {CCO/H2} | |
| -29. Cd_pri H_rad 300-1500 1.46E+07 2.09 0 5.49 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Allene hydrogen {Cd/H2/Ca} | |
| -30. Cd/H/NonDeC H_rad 300-1500 2.98E+07 1.95 0 8.65 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -31. C/H3/Cd H_rad 300-1500 4.33E+05 2.38 0 2.80 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -32. C/H2/OneDeC H_rad 300-1500 6.99E+05 2.36 0 1.11 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Primary allylic hydrogen {C/Cd/C/H2} | |
| -33. C/H2/OneDeC H_rad 300-1500 7.79E+07 1.78 0 2.11 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Primary propergylic {C/Ct/C/H2} | |
| -34. C/H/Cs2 H_rad 300-1500 3.02E+06 2.16 0 -0.45 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Secondary allylic hydrogen {C/Cd/C2/H} | |
| -35. C/H/Cs2 H_rad 300-1500 1.21E+08 1.72 0 -0.73 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Secondary propergylic {C/Ct/C2/H} | |
| -36. C/H2/TwoDe H_rad 300-1500 7.09E+03 2.85 0 -1.90 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -37. Cd/H/OneDe H_rad 300-1500 1.93E+08 1.74 0 10.28 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Dienylic {Cd/Cd/H} | |
| -38. Cd/H/OneDe H_rad 300-1500 2.18E+06 2.4 0 6.11 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Eneynic {Cd/Ct/H} | |
| -39. Ct_H H_rad 300-1500 1.65E+08 1.85 0 26.52 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -40. C/H3/Ct H_rad 300-1500 2.70E+07 1.91 0 5.99 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -41. Cd/H/NonDeO H_rad 300-1500 9.67E+09 1.23 0 11.69 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -42. O/H/OneDe H_rad 300-1500 1.30E+11 0.82 0 7.75 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -43. Cd_pri C_methyl 300-1500 3.24E+03 2.58 0 14.04 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -44. C/H3/Cd C_methyl 300-1500 8.04E+01 2.92 0 7.16 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -45. O/H/NonDeC C_methyl 300-1500 2.54E+05 1.89 0 8.97 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -46. CO/H/NonDe C_methyl 300-1500 2.92E+04 2.29 0 5.44 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -47. O/H/OneDe C_methyl 300-1500 9.07E+04 2.04 0 10.85 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Olefinic alcohol {O/Cd/H} | |
| -48. O/H/OneDe H_rad 300-1500 3.30E+08 1.56 0 13.94 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Acid O-H {O/CO/H} | |
| -49. CO/H/NonDe C_methyl 300-1500 4.53E+03 2.43 0 8.85 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| -50. C_methane C_methyl 300-1500 6.03E+13 0 0 19.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -51. C/H3/Cs C_methyl 300-1500 2.80E+14 0 0 16.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -52. C/H3/Cs C_methyl 300-1500 6.15E+13 0 0 15.9 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -53. C/H3/Cs C_methyl 300-1500 7.71E+12 0 0 13.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -54. C/H2/NonDeC C_methyl 300-1500 5.02E+13 0 0 13.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -55. C/H/Cs3 C_methyl 300-1500 5.02E+13 0 0 11.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -56. C/H/Cs3 C_methyl 300-1500 4.42E+13 0 0 11.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -57. C/H3/Cd C_methyl 300-1500 2.62E+13 0 0 12.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -58. C/H2/OneDeC C_methyl 300-1500 2.73E+13 0 0 10.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -59. C/H/Cs2 C_methyl 300-1500 2.73E+13 0 0 8.9 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -60. C/H2/TwoDe C_methyl 300-1500 7.54E+13 0 0 8.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -61. C/H/Cs C_methyl 300-1500 9.32E+12 0 0 7.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -62. C/H3/Cb C_methyl 300-1500 4.90E+12 0 0 13.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -63. C/H2/OneDeC C_methyl 300-1500 1.70E+13 0 0 11.8 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -64. C/H/Cs2 C_methyl 300-1500 1.17E+13 0 0 11.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -65. C/H3/Ct C_methyl 300-1500 6.60E+13 0 0 13.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -66. C/H2/OneDeC C_methyl 300-1500 2.81E+13 0 0 11.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -67. C/H2/TwoDe C_methyl 300-1500 1.38E+14 0 0 8.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -68. C/H/Cs C_methyl 300-1500 3.43E+13 0 0 7.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -69. C/H/Cs2 C_methyl 300-1500 5.03E+13 0 0 9.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -70. Cd_pri C_methyl 300-1500 1.88E+14 0 0 18.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -71. Cd/H/NonDeC C_methyl 300-1500 4.43E+13 0 0 16.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -72. Cd/H/OneDe C_methyl 300-1500 5.78E+13 0 0 16.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -73. Cd/H/OneDe C_methyl 300-1500 2.26E+13 0 0 15.9 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -74. Cd/H/OneDe C_methyl 300-1500 4.37E+13 0 0 13.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -75. Ct_H C_methyl 300-1500 3.33E+18 0 0 28.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -76. Cb_H C_methyl 300-1500 1.17E+15 0 0 19.9 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -77. C/H2/NonDeC C_methyl 300-1500 9.87E+14 0 0 13.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -78. C/H2/NonDeC C_methyl 300-1500 4.51E+12 0 0 12.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -79. C/H/Cs3 C_methyl 300-1500 2.46E+13 0 0 11.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -80. C/H2/OneDeC C_methyl 300-1500 5.98E+13 0 0 9.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -81. C_methane H_rad 300-1500 1.87E+14 0 0 14.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -82. C_methane C_methyl 300-1500 6.03E+13 0 0 19.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -83. C_methane C_rad/H2/Cd 300-1500 1.53E+14 0 0 30.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -84. C_methane Cd_pri_rad 300-1500 1.59E+14 0 0 13.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -85. C_methane C_rad/Cs3 300-1500 1.86E+13 0 0 20.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -86. C/H/Cs3 H_rad 300-1500 5.31E+13 0 0 5.9 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -87. C/H/Cs3 C_methyl 300-1500 5.02E+13 0 0 11.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -88. C/H/Cs3 C_rad/H2/Cd 300-1500 5.02E+13 0 0 20.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -89. C/H/Cs3 Cd_pri_rad 300-1500 8.95E+13 0 0 6.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -90. C/H/Cs3 C_rad/Cs3 300-1500 5.43E+11 0 0 11.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -91. C/H/Cs3 C_rad/H2/Cs 300-1500 3.03E+12 0 0 12.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -92. C/H/Cs3 C_rad/H/NonDeC 300-1500 2.44E+12 0 0 12.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -93. C/H/Cs3 C_rad/H/OneDeC 300-1500 5.46E+12 0 0 21.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -94. C/H/Cs3 C_rad/Cs2 300-1500 1.10E+12 0 0 21.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -95. C/H/Cs3 Cd_rad/NonDeC 300-1500 1.02E+11 0 0 5.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -96. C/H/Cs3 Cd_rad/OneDe 300-1500 4.16E+12 0 0 13.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -97. C/H/Cs3 C_rad/H2/Ct 300-1500 3.14E+13 0 0 17.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -98. C/H/Cs3 C_rad/H/OneDeC 300-1500 2.53E+12 0 0 18.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -99. C/H/Cs3 C_rad/Cs2 300-1500 9.78E+11 0 0 18.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -100. Cd_pri H_rad 300-1500 3.39E+14 0 0 15.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -101. Cd_pri C_methyl 300-1500 1.88E+14 0 0 18.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -102. Cd_pri C_rad/H2/Cd 300-1500 5.36E+13 0 0 30.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -103. Cd_pri Cd_pri_rad 300-1500 1.47E+13 0 0 13.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -104. Cd_pri C_rad/Cs3 300-1500 3.93E+13 0 0 20.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -105. Cd_pri C_rad/H2/Cs 300-1500 7.82E+12 0 0 19.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -106. Cd_pri C_rad/H/NonDeC 300-1500 3.25E+12 0 0 20.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -107. Cd_pri C_rad/H/OneDeC 300-1500 1.51E+13 0 0 31.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -108. Cd_pri C_rad/Cs2 300-1500 3.39E+12 0 0 38.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -109. Cd_pri Cd_rad/NonDeC 300-1500 6.04E+13 0 0 14.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -110. Cd_pri Cd_rad/OneDe 300-1500 1.30E+13 0 0 20.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -111. Cd_pri C_rad/H2/Ct 300-1500 2.55E+13 0 0 26.8 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -112. Cd_pri C_rad/H/OneDeC 300-1500 4.41E+12 0 0 28.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -113. Cd_pri C_rad/Cs2 300-1500 3.59E+12 0 0 35.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -114. C/H3/Cd H_rad 300-1500 3.13E+13 0 0 7.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -115. C/H3/Cd C_methyl 300-1500 2.62E+13 0 0 12.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -116. C/H3/Cd C_rad/H2/Cd 300-1500 5.78E+12 0 0 21.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -117. C/H3/Cd Cd_pri_rad 300-1500 7.73E+12 0 0 7.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -118. C/H3/Cd C_rad/Cs3 300-1500 3.18E+12 0 0 11.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -119. C/H3/Cd C_rad/H2/Cs 300-1500 5.60E+11 0 0 12.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -120. C/H3/Cd C_rad/H/NonDeC 300-1500 2.87E+11 0 0 12.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -121. C/H3/Cd C_rad/H/OneDeC 300-1500 1.52E+12 0 0 21.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -122. C/H3/Cd C_rad/Cs2 300-1500 4.13E+11 0 0 21.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -123. C/H3/Cd Cd_rad/NonDeC 300-1500 5.52E+12 0 0 7.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -124. C/H3/Cd Cd_rad/OneDe 300-1500 1.95E+12 0 0 14.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -125. C/H3/Cd C_rad/H2/Ct 300-1500 7.58E+12 0 0 18.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -126. C/H3/Cd C_rad/H/OneDeC 300-1500 5.09E+11 0 0 18.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -127. C/H3/Cd C_rad/Cs2 300-1500 3.32E+11 0 0 18.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -128. H2 H_rad 300-1500 2.37E+13 0 0 9.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -129. H2 C_methyl 300-1500 2.95E+12 0 0 14.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -130. H2 C_rad/H2/Cd 300-1500 2.87E+12 0 0 25.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -131. H2 Cd_pri_rad 300-1500 4.49E+12 0 0 10.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -132. H2 C_rad/Cs3 300-1500 3.08E+11 0 0 14.8 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -133. H2 C_rad/H2/Cs 300-1500 4.57E+11 0 0 14.8 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -134. H2 C_rad/H/NonDeC 300-1500 3.04E+11 0 0 15.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -135. H2 C_rad/H/OneDeC 300-1500 1.82E+12 0 0 27.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -136. H2 C_rad/Cs2 300-1500 4.30E+11 0 0 27.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -137. H2 Cd_rad/NonDeC 300-1500 3.01E+12 0 0 10.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -138. H2 Cd_rad/OneDe 300-1500 2.37E+12 0 0 18.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -139. H2 C_rad/H2/Ct 300-1500 2.91E+12 0 0 23.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -140. H2 C_rad/H/OneDeC 300-1500 5.34E+11 0 0 24.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -141. H2 C_rad/Cs2 300-1500 4.20E+11 0 0 24.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| -142. C/H3/Cs O_pri_rad 300-1500 5.93E+06 1.80 0 1.431 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. Fixed by RWest (changed to per H) | |
| -//142. C/H3/Cs O_pri_rad 300-1500 2.92E+06 1.80 0 0.278 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| -143. C/H2/NonDeC O_pri_rad 300-1500 4.50E+05 2.00 0 -1.133 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| -144. C/H/Cs3 O_pri_rad 300-1500 1.70E+06 1.90 0 -1.451 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. | |
| -145. C/H3/Cs O_atom_triplet 300-1500 9.50E+02 3.05 0 3.123 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| -146. C/H2/NonDeC O_atom_triplet 300-1500 2.39E+04 2.71 0 2.106 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| -147. C/H/Cs3 O_atom_triplet 300-1500 3.83E+05 2.41 0 1.140 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. | |
| -148. C/H3/Cs O_rad/NonDeO 300-1500 2.80E+12 0 0 20.435 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| -149. C/H2/NonDeC O_rad/NonDeO 300-1500 2.80E+12 0 0 17.686 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| -150. C/H/Cs3 O_rad/NonDeO 300-1500 2.80E+12 0 0 16.013 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. | |
| -151. C/H3/Cs O_rad/NonDeC 300-1500 5.27E+10 0 0 7.000 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| -152. C/H2/NonDeC O_rad/NonDeC 300-1500 5.50E+10 0 0 5.000 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| -153. C/H/Cs3 O_rad/NonDeC 300-1500 1.90E+10 0 0 2.800 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. | |
| -154. C/H3/Cs O2b 300-1500 7.00E+12 0 0 50.76 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| -155. C/H2/NonDeC O2b 300-1500 7.00E+12 0 0 48.21 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| -156. C/H/Cs3 O2b 300-1500 7.00E+12 0 0 46.06 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. | |
| -157. H2 O2b 300-800 7.25E+13 0 0 56.64 *5.0 0 0 0 4 Tsang et al. [89] literature review. | |
| -158. H2 Cd_pri_rad 200-3000 4.73E+03 2.56 0 5.03 0 0 0 0 3 Knyazev et al. [119] Transition state theory. | |
| -159. H2 Cd_pri_rad 300-3500 1.11E+04 2.48 0 7.13 0 0 0 0 3 Mebel et al. [120] Transition state theory. | |
| -160. H2 Cd_pri_rad 300-1500 1.58E+09 0.70 0 5.11 0 0 0 0 3 Weissman et al. [121] Transition state theory. | |
| -161. H2 Ct_rad 300-2500 5.4E+12 0 0 2.17 *3.16 0 0 0 4 Baulch et al. [94] literature review. | |
| -162. H2 Cb_rad 300-5000 2.86E+04 2.43 0 6.28 0 0 0 0 3 Mebel et al. [122] Transition state theory. | |
| -163. H2 CO_pri_rad 300-2500 9.0E+05 2.00 0 17.83 *5 0 0 0 4 Tsang et al. [89] literature review. | |
| -164. H2 CO_rad/NonDe 300-2500 2.06E+06 1.82 0 17.61 *3.0 0 0 0 4 Tsang et al. [89] literature review. | |
| -165. H2 O_pri_rad 200-2400 9.10E+08 1.21 0 4.71 0 0 0 0 3 Isaacson [123] Transition state theory. | |
| -166. H2 O_rad/NonDeC 300-2000 6.32E-02 4.00 0 4.91 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| -167. C_methane O2b 500-2000 9.925E+12 0 0 56.83 *10.0 0 0 0 4 Baulch et al. [95] literature review. | |
| -168. C_methane C_rad/H2/Cs 300-2500 2.16E-02 4.14 0 12.56 *2.0 0 0 0 4 Tsang et al. [89] literature review. | |
| -169. C_methane C_rad/H/NonDeC 300-2500 1.81E-04 4.40 0 10.79 *2.0 0 0 0 4 Tsang et al. [91] literature review. | |
| -170. C_methane Ct_rad 300-2500 4.53E+11 0 0 0.50 *10.0 0 0 0 4 Tsang et al. [89] literature review. | |
| -171. C_methane Cb_rad 560-1410 5.0E+11 0 0 8.60 0 0 0 0 2 Heckmann et al. [124] | |
| -172. C_methane CO_pri_rad 300-2500 1.82E+03 2.85 0 22.46 *5.0 0 0 0 4 Tsang et al. [89] literature review. | |
| -173. C_methane CO_rad/NonDe 300-2500 5.43E+02 2.88 0 21.46 *5.0 0 0 0 4 Tsang et al. [89] literature review. | |
| -174. C_methane O_pri_rad 223-2400 3.85E-01 3.95 0 0.55 0 0 0 0 3 Melissas and Truhlar [125] Transition state theory. | |
| -175. C_methane O_pri_rad 240-2500 3.93E+06 1.83 0 2.78 *1.41 0 0 0 4 Baulch et al. [95] literature review. | |
| -176. C_methane O_pri_rad 298-1510 2.55E+07 1.60 0 3.12 0 0 0 0 3 Cohen et al. [101] Transition state theory. | |
| -177. C_methane O_rad/NonDeC 300-2000 1.55E-04 5.00 0 5.58 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| -178. C_methane O_rad/NonDeO 300-2500 4.53E+10 0 0 18.58 *5.0 0 0 0 4 Tsang et al. [89] literature review. | |
| -179. C/H3/Cs O2b 500-2000 1.005E+13 0 0 51.87 *10.0 0 0 0 4 Baulch et al. [95] literature review. | |
| -180. C/H3/Cs Ct_rad 300-1500 6.02E+11 0 0 0 *3 0 0 0 4 Tsang et al. [89] literature review. | |
| -181. C/H3/Cs Cb_rad 565-1000 3.48E+10 0 0 4.44 *2.35 0 0 0.18 2 Park et al. [126] | |
| -182. C/H3/Cs CO_pri_rad 300-2500 7.82E+03 2.72 0 18.24 *5.0 0 0 0 4 Tsang et al. [89] literature review. | |
| -183. C/H3/Cs CO_rad/NonDe 300-2500 3.02E+03 2.75 0 17.53 *5.0 0 0 0 4 Tsang et al. [89] literature review. | |
| -184. C/H3/Cs O_pri_rad 250-2000 1.20E+06 2.00 0 0.86 *1.41 0 0 0 4 Baulch et al. [95] literature review. | |
| -185. C/H3/CO O_pri_rad 295-600 5.17E+05 2.20 0 1.00 0 0 0 0 3 Taylor et al. [127] Transition state theory. | |
| -186. C/H3/O C_methyl 300-2000 2.05E-04 4.90 0 6.72 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| -187. C/H3/O O_pri_rad 300-2000 8.14E+03 2.80 0 -0.42 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| -100_R2 C/H3/O H_rad 300-2000 4.51E+02 3.20 0 3.49 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. added by Greg Magoon 08/25/09 | |
| -188. C/H2/NonDeC O2b 300-2500 1.985E+13 0 0 47.69 *10.0 0 0 0 4 Tsang [91] literature review. | |
| -189. C/H2/NonDeC CH2_triplet 300-2500 7.55E-01 3.46 0 7.47 *10.0 0 0 0 4 Tsang [91] literature review. | |
| -190. C/H2/NonDeC O_atom_triplet 300-2500 2.39E+04 2.71 0 2.11 *2.0 0 0 0 4 Tsang [91] literature review. | |
| -191. C/H2/NonDeC C_rad/H2/O 300-2500 3.02E+01 2.95 0 11.98 *5.0 0 0 0 4 Tsang [91] literature review. | |
| -192. C/H2/NonDeC Cd_pri_rad 300-2500 5.10E+02 3.10 0 8.82 *10.0 0 0 0 4 Tsang [91] literature review. | |
| -193. C/H2/NonDeC Ct_rad 300-2500 6.05E+11 0 0 0 *3.0 0 0 0 4 Tsang [91] literature review. | |
| -194. C/H2/NonDeC CO_pri_rad 300-2500 5.4E+06 1.90 0 17.01 *3.0 0 0 0 4 Tsang [91] literature review. | |
| -195. C/H2/NonDeC CO_rad/NonDe 300-2500 2.65E+06 2.00 0 16.24 *3.0 0 0 0 4 Tsang [91] literature review. | |
| -196. C/H2/NonDeC O_pri_rad 295-1220 3.95E+06 1.90 0 0.16 0 0 0 0 3 Cohen et al. [101] Transition state theory. | |
| -197. C/H2/NonDeC O_rad/NonDeC 300-2500 7.25E+10 0 0 4.57 *5.0 0 0 0 4 Tsang [91] literature review. | |
| -198. C/H/Cs3 O2b 300-2500 3.97E+13 0 0 43.92 *3.0 0 0 0 4 Tsang [92] literature review. | |
| -199. C/H/Cs3 O_atom_triplet 300-2500 1.57E+05 2.50 0 1.11 *2.0 0 0 0 4 Tsang [92] literature review. | |
| -200. C/H/Cs3 CH2_triplet 300-2500 1.09E+12 0 0 4.91 *5.0 0 0 0 4 Tsang [92] literature review. | |
| -201. C/H/Cs3 Cd_pri_rad 300-2500 9.04E-01 3.46 0 2.60 *5.0 0 0 0 4 Tsang [92] literature review. | |
| -202. C/H/Cs3 Ct_rad 300-2500 6.62E+11 0 0 0 *3.0 0 0 0 4 Tsang [92] literature review. | |
| -203. C/H/Cs3 CO_pri_rad 300-2500 3.43E+04 2.50 0 13.51 *5.0 0 0 0 4 Tsang [92] literature review. | |
| -204. C/H/Cs3 CO_rad/NonDe 300-2500 3.43E+04 2.50 0 13.51 *10.0 0 0 0 4 Tsang [92] literature review. | |
| -205. C/H/Cs3 O_pri_rad 298-1150 2.57E+06 1.90 0 1.45 0 0 0 0 3 Cohen et al. [101] Transition state theory. | |
| -206. C/H/Cs3 O_rad/NonDeC 300-2500 2.29E+10 0 0 2.88 *10.0 0 0 0 4 Tsang [92] literature review. | |
| -207. Cd_pri O2b 300-2500 1.792E+13 0 0 60.01 0 0 0 0 4 Hua, Ruscic, and Wang 2005, transition state theory. | |
| -//208. Cd_pri CO_birad 300-2500 3.78E+13 0 0 90.62 *5.0 0 0 0 4 Tsang [89] literature review. | |
| -209. Cd_pri O_atom_triplet 290-1510 3.78E+06 1.91 0 3.74 0 0 0 0 3 Mahmud et al. [128] Transition state theory | |
| -210. Cd_pri C_rad/H2/Cs 300-2500 1.58E+02 3.13 0 18.00 *10.0 0 0 0 4 Tsang [89] literature review. | |
| -211. Cd_pri O_pri_rad 650-1500 5.13E+12 0 0 5.94 *3.16 0 0 0 4 Baulch et al. [95] literature review. | |
| -212. Cd/H/NonDeC O_atom_triplet 300-2500 6.02E+10 0.70 0 7.63 *3.0 0 0 0 4 Tsang [93] literature review. | |
| -//213. Cd/H/NonDeC H_rad 300-2500 2.37E+00 0 0 7.31 *5.0 0 0 0 4 Tsang [93] literature review. | |
| -213. Cd/H/NonDeC H_rad 300-2500 4.09e+05 2.5 0 9.79 *4.0 0.0 0.0 0.0 4 Tsang [93] literature review. | |
| -//214. Cd/H/NonDeC C_methyl 300-2500 3.8E-01 0 0 5.98 *100.0 0 0 0 4 Tsang [93] literature review. | |
| -214. Cd/H/NonDeC C_methyl 300-2500 0.842 3.5 0.0 11.66 *6.0 0.0 0.0 0.0 4 Tsang [93] literature review. | |
| -//215. Cd/H/NonDeC Cd_pri_rad 300-2500 3.8E-01 0 0 4.99 *10.0 0 0 0 4 Tsang [93] literature review. | |
| -215. Cd/H/NonDeC Cd_pri_rad 300-2500 0.842 3.5 0.0 9.67 *6.0 0.0 0.0 0.0 4 Tsang [93] literature review. | |
| -216. Cd/H/NonDeC Ct_rad 300-2500 1.21E+12 0 0 0 *5.0 0 0 0 4 Tsang [93] literature review. | |
| -//217. Cd/H/NonDeC O_pri_rad 300-2500 1.11E+06 2.00 0 1.45 0 0 0 0 4 Tsang [93] literature review. | |
| -217. Cd/H/NonDeC O_pri_rad 300-2500 1.11E+06 2.00 0 1.45 *2 0.0 0.0 0.0 4 Tsang [93] literature review. | |
| -218. Ct_H O2b 300-2500 6.05E+12 0 0 74.52 *10.0 0 0 0 4 Tsang [89] literature review. | |
| -//219. Ct_H CO_birad 300-2500 2.41E+14 0 0 107 *10.0 0 0 0 4 Tsang [89] literature review. | |
| -220. Ct_H C_rad/H2/Cs 300-2500 1.36E+11 0 0 23.45 *5.0 0 0 0 4 Tsang [89] literature review. | |
| -221. Ct_H O_pri_rad 300-2500 7.25E+03 2.68 0 12.04 *10.0 0 0 0 4 Tsang [89] literature review. | |
| -222. Cb_H O2b 1200-1700 1.052E+13 0 0 60.01 0 0 0 0 4 Asaba et al. [129]. Data are estimated. | |
| -223. Cb_H H_rad 500-800 1.00E+08 1.80 0 16.35 0 0 0 0 4 Mebel et al. [122] RRK(M) extrapolation. | |
| -224. Cb_H H_rad 298-1000 5.02E+11 0 0 8.11 0 0 0 0 5 Nicovich et al. [130] | |
| -225. Cb_H C_rad/H2/Cs 650-770 1.05E+11 0 0 14.86 *2.0 0 0 1.19 5 Zhang et al. [131] | |
| -226. Cb_H O_pri_rad 400-1500 2.72E+07 1.42 0 1.45 *2.0 0 0 0 4 Baulch et al. [95] literature review. | |
| -227. CO_pri O2b 300-2200 2.34E+07 2.05 0 37.93 0 0 0 0 3 Michael et al. [132] Transition state theory. | |
| -228. CO_pri O_atom_triplet 250-2200 2.08E+11 0.57 0 2.76 *2.0 0 0 0 4 Baulch et al. [95] literature review. | |
| -229. CO_pri CH2_triplet 300-2500 3.02E+09 0 0 0 0 0 0 0 4 Tsang [89] literature review. | |
| -230. CO_pri C_methyl 300-2000 3.89E-08 6.10 0 1.97 *1.58 0 0 0 4 Baulch et al. [94] literature review. | |
| -231. CO_pri C_rad/H2/Cs 300-2500 2.75E+03 2.81 0 5.86 *5.0 0 0 0 4 Tsang [89] literature review. | |
| -232. CO_pri C_rad/H/NonDeC 300-2500 5.40E+10 0 0 6.96 *2.5 0 0 0 4 Tsang [91] literature review. | |
| -233. CO_pri C_rad/Cs3 300-2500 1.63E+09 0 0 3.56 *5.0 0 0 0 4 Tsang [92] literature review. | |
| -234. CO_pri Cd_pri_rad 300-2500 2.71E+03 2.81 0 5.86 *5.0 0 0 0 4 Tsang [89] literature review. | |
| -235. CO_pri CO_rad/NonDe 300-2500 9.05E+10 0 0 12.92 *10.0 0 0 0 4 Tsang [89] literature review. | |
| -236. CO_pri O_pri_rad 300-3000 1.72E+09 1.18 0 -0.45 *5.0 0 0 0 4 Baulch et al. [95] literature review. | |
| -237. CO_pri O_rad/NonDeC 300-2500 5.10E+10 0 0 2.98 *3.0 0 0 0 4 Tsang [89] literature review. | |
| -238. CO_pri O_rad/NonDeO 641-1600 2.06E+04 2.50 0 10.21 0 0 0 0 4 Eiteneer et al. [133] literature review. | |
| -239. CO/H/NonDe O2b 600-1100 3.01E+13 0 0 39.15 *10.0 0 0 0 4 Baulch et al. [95] literature review. | |
| -240. CO/H/NonDe O_atom_triplet 300-2000 5.0E+12 0 0 1.79 *2.0 0 0 0 4 Warnatz [134] literature review | |
| -241. CO/H/NonDe H_rad 300-2000 4.0E+13 0 0 4.21 *2.0 0 0 0 4 Warnatz [134] literature review | |
| -242. CO/H/NonDe C_methyl 300-1250 1.99E-06 5.64 0 2.46 *2.0 0 0 0 4 Baulch et al. [95] literature review. | |
| -243. CO/H/NonDe C_rad/H2/Cd 790-810 3.8E+11 0 0 7.21 0 0 0 0 5 Loser et al. [135] bond strength-bond length method. | |
| -244. CO/H/NonDe Cd_pri_rad 480-520 8.13E+10 0 0 3.68 0 0 0 0 5 Scherzer et al. [136] bond energy-bond order method. | |
| -//245. CO/H/NonDe O_pri_rad 295-600 2.0E+06 1.80 0 1.30 0 0 0 0 3 Taylor et al. [127] Transition state theory. | |
| -245. CO/H/NonDe O_pri_rad 295-600 2.0E+06 1.80 0 -1.30 0 0 0 0 3 Taylor et al. [127] Transition state theory. | |
| -246. CO/H/NonDe O_pri_rad 300-2000 1.0E+13 0 0 0 *2.51 0 0 0 4 Warnatz [134] literature review | |
| -247. CO/H/NonDe O_rad/NonDeO 900-1200 3.01E+12 0 0 11.92 *5.0 0 0 0 4 Baulch et al. [95] literature review. | |
| -248. O_pri O2b 300-1000 2.325E+12 0 0 74.12 0 0 0 0 5 Mayer et al. [137] Bond energy-bond order. | |
| -249. O_pri O_atom_triplet 298-1000 2.63E+09 1.20 0 17.83 0 0 0 0 3 Karach et al. [138] Transition state theory. | |
| -250. O_pri O_atom_triplet 300-2000 7.40E+04 2.60 0 15.18 0 0 0 0 3 Harding et al. [139] Transition state theory. | |
| -251. O_pri H_rad 300-2500 2.26E+08 1.60 0 19.32 *1.6 0 0 0 4 Baulch et al. [95] literature review. | |
| -252. O_pri C_methyl 300-1500 3.20E+00 3.31 0 12.56 0 0 0 0 3 Ma et al. [140] Transition state theory. | |
| -253. O_pri C_methyl 300-2500 2.42E+02 2.90 0 14.86 *1.6 0 0 0 4 Tsang [89] literature review. | |
| -254. O_pri C_rad/H2/Cs 300-2500 1.70E+06 1.44 0 20.27 *2.0 0 0 0 4 Tsang [89] literature review. | |
| -255. O_pri Cd_pri_rad 300-2500 2.42E+02 2.90 0 14.86 *5.0 0 0 0 4 Tsang [89] literature review. | |
| -256. O_pri CO_pri_rad 300-2500 1.18E+08 1.35 0 26.03 *5.0 0 0 0 4 Tsang [89] literature review. | |
| -//257. O_pri O_pri_rad 200-700 6.45E-06 5.01 0 0.61 0 0 0 0 3 Masgrau et al. [141] Transition state theory w/tunneling correction. | |
| -257. O_pri O_pri_rad 200-700 2.417E-07 5.48 0 0.274 0.0 0.0 0.0 0.0 3 Masgrau et al. [141] Transition state theory. | |
| -258. O_pri O_rad/NonDeC 300-2000 1.74E-01 3.80 0 11.49 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| -259. O/H/NonDeC O_atom_triplet 300-1000 1.0E+13 0 0 4.69 *2.51 0 0 0 4 Warnatz [134] literature review | |
| -260. O/H/NonDeC CH2_triplet 300-2500 1.44E+01 3.10 0 6.94 *3.0 0 0 0 4 Tsang [90] literature review. | |
| -261. O/H/NonDeC C_methyl 300-2000 3.70E-04 4.70 0 5.78 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| -262. O/H/NonDeC C_rad/H2/Cs 300-2500 1.44E+01 3.10 0 8.94 *3.0 0 0 0 4 Tsang [90] literature review. | |
| -//263. O/H/NonDeC C_rad/H/NonDeC 300-2500 1.45E+01 3.10 0 10.33 *5.0 0 0 0 4 Tsang [90] literature review. | |
| -263. O/H/NonDeC C_rad/H/NonDeC 300-2500 1.45E+01 3.10 0 10.33 *5.0 0 0 0 4 Tsang [91] literature review. | |
| -//264. O/H/NonDeC C_rad/Cs3 300-2500 1.51E+03 1.80 0 9.36 *10.0 0 0 0 4 Tsang [90] literature review. | |
| -264. O/H/NonDeC C_rad/Cs3 300-2500 1.51E+03 1.80 0 9.36 *10.0 0 0 0 4 Tsang [92] literature review. | |
| -265. O/H/NonDeC Cd_pri_rad 300-2500 1.44E+01 3.10 0 6.94 *10.0 0 0 0 4 Tsang [90] literature review. | |
| -266. O/H/NonDeC Ct_rad 300-2500 1.21E+12 0 0 0 *5.0 0 0 0 4 Tsang [90] literature review. | |
| -267. O/H/NonDeC O_pri_rad 300-2000 1.73E+01 3.40 0 -1.14 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| -268. O/H/NonDeC O_pri_rad 300-2000 1.0E+13 0 0 1.70 *3.16 0 0 0 4 Warnatz [134] literature review | |
| -// (Reverse) Rates for nButanol+HO2=H2O2+radicals | |
| -301. H2O2 InChI=1/C4H9O/c1-2-3-4-5/h5H,1-4H2 600-2000 2.88E+00 3.16 0.0 0.75 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -302. H2O2 InChI=1/C4H9O/c1-2-3-4-5/h2,5H,3-4H2,1H3 600-2000 6.75E-01 3.42 0.0 1.43 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -303. H2O2 InChI=1/C4H9O/c1-2-3-4-5/h3,5H,2,4H2,1H3 600-2000 3.145E-01 3.52 0.0 1.61 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -304. H2O2 InChI=1/C4H9O/c1-2-3-4-5/h4-5H,2-3H2,1H3 600-2000 1.485E+00 3.39 0.0 1.40 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -// (Reverse) Rates for sButanol+HO2=H2O2+radicals | |
| -305. H2O2 InChI=1/C4H9O/c1-3-4(2)5/h4-5H,1,3H2,2H3 600-2000 5.75E+00 2.94 0.0 0.46 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -306. H2O2 InChI=1/C4H9O/c1-3-4(2)5/h3-5H,1-2H3 600-2000 8.75E-01 2.91 0.0 -0.41 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -307. H2O2 InChI=1/C4H9O/c1-3-4(2)5/h5H,3H2,1-2H3 600-2000 1.73E+01 3.05 0.0 1.02 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -308. H2O2 InChI=1/C4H9O/c1-3-4(2)5/h4-5H,2-3H2,1H3 600-2000 3.055E-01 3.53 0.0 1.52 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -// (Reverse) Rates for tButanol+HO2=H2O2+radicals | |
| -309. H2O2 InChI=1/C4H9O/c1-4(2,3)5/h5H,1H2,2-3H3 600-2000 2.100E-01 3.53 0.0 1.56 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -310. Cd_pri O2b 300-1500 7.00E+12 0 0 60.36 0 0 0 0 5 Increased rate 154 Ea by 9.6 kcal/mol (vinyl versus methyl) | |
| -311. Cd_pri O2b 500-2000 1.005E+13 0 0 61.47 *10.0 0 0 0 4 Increased rate 179 Ea by 9.6 kcal/mol (vinyl versus methyl) | |
| -312. Cd/H/NonDeC O2b 300-1500 7.00E+12 0 0 57.81 0 0 0 0 5 Increased rate 155 Ea by 9.6 kcal/mol (vinyl versus methyl) | |
| -313. Cd/H/NonDeC O2b 300-2500 1.985E+13 0 0 57.29 *10.0 0 0 0 4 Increased rate 188 Ea by 9.6 kcal/mol (vinyl versus methyl)486. Orad_O_H O_rad/NonDeO 300-1500 1.75E+10 0 0 -3.275 0 0 0 0 5 [8] Curran's estimation in reaction type 13, RO2 + HO2 --> RO2H + O2 | |
| -486. Orad_O_H O_rad/NonDeO 300-1500 1.75E+10 0 0 -3.275 0 0 0 0 5 [8] Curran's estimation in reaction type 13, RO2 + HO2 --> RO2H + O2 | |
| -500. CO_pri InChI=1/C4H7/c1-4(2)3/h1-2H2,3H3 600-2000 3.065e-02 3.95 0.0 12.22 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -501. InChI=1/C3H8/c1-3-2/h3H2,1-2H3 InChI=1/C4H9O/c1-4(2)3-5/h5H,3H2,1-2H3 300-2000 9.11e-07 5.11 0 5.69 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -501R. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/beta InChI=1/C3H7/c1-3-2/h3H,1-2H3 300-2000 2.35e-06 4.84 0 4.27 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -502. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/alpha InChI=1/C3H7/c1-3-2/h3H,1-2H3 300-2000 1.06e-06 5.06 0 4.89 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -503. InChI=1/C4H8/c1-4(2)3/h1H2,2-3H3 InChI=1/C4H9O/c1-4(2)3-5/h4-5H,1,3H2,2H3 300-2000 8.39e-06 4.89 0 4.32 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -504. InChI=1/C4H8/c1-4(2)3/h1H2,2-3H3 InChI=1/C4H9O/c1-4(2)3-5/h5H,3H2,1-2H3 300-2000 1.44e-05 4.52 0 1.46 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -505. InChI=1/C4H8/c1-4(2)3/h1H2,2-3H3 InChI=1/C4H9O/c1-4(2)3-5/h3-5H,1-2H3 300-2000 4.91e-06 5.07 0 3.66 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -506. InChI=1/C4H8/c1-4(2)3/h1H2,2-3H3 InChI=1/C4H9O/c1-4(2)3-5/h4H,3H2,1-2H3 300-2000 5.83e-01 3.74 0 1.45 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -507. InChI=1/C3H6/c1-3-2/h3H,1H2,2H3 InChI=1/C4H9O/c1-4(2)3-5/h4-5H,1,3H2,2H3 300-2000 3.36e-05 4.75 0 4.13 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -508. InChI=1/C3H6/c1-3-2/h3H,1H2,2H3 InChI=1/C4H9O/c1-4(2)3-5/h5H,3H2,1-2H3 300-2000 1.64e-06 4.98 0 3.18 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -509. InChI=1/C3H6/c1-3-2/h3H,1H2,2H3 InChI=1/C4H9O/c1-4(2)3-5/h3-5H,1-2H3 300-2000 3.11e-06 4.97 0 3.64 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -510. InChI=1/C3H6/c1-3-2/h3H,1H2,2H3 InChI=1/C4H9O/c1-4(2)3-5/h4H,3H2,1-2H3 300-2000 1.19e-01 3.90 0 1.81 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -511. InChI=1/C2H6/c1-2/h1-2H3 InChI=1/C4H9O/c1-4(2)3-5/h4-5H,1,3H2,2H3 300-2000 3.21e-06 5.28 0 7.78 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -512. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/beta InChI=1/C2H5/c1-2/h1H2,2H3 300-2000 1.41e-05 4.83 0 4.37 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -513. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/alpha InChI=1/C2H5/c1-2/h1H2,2H3 300-2000 4.25e-06 5.01 0 5.01 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -514. InChI=1/C2H6/c1-2/h1-2H3 InChI=1/C4H9O/c1-4(2)3-5/h4H,3H2,1-2H3 300-2000 5.07e-03 4.52 0 2.34 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -515. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/beta InChI=1/C2H3/c1-2/h1H,2H2 300-2000 5.49e+00 3.33 0 0.63 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -516. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/gamma InChI=1/C3H5/c1-3-2/h1H2,2H3 300-2000 3.11e-05 4.87 0 3.50 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -517. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/alpha InChI=1/C3H5/c1-3-2/h1H2,2H3 300-2000 1.28e-02 4.09 0 1.31 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -518. InChI=1/C3H6O/c1-2-3-4/h3H,2H2,1H3/beta InChI=1/C4H9O/c1-4(2)3-5/h4-5H,1,3H2,2H3 300-2000 1.56e-04 4.31 0 3.39 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -519. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/beta InChI=1/C3H5O/c1-2-3-4/h2-3H,1H3/c 300-2000 4.85e-04 4.37 0 9.66 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -520. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/alpha InChI=1/C3H5O/c1-2-3-4/h2-3H,1H3/c 300-2000 1.84e-03 4.02 0 7.92 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -521. InChI=1/C4H8O/c1-4(2)3-5/h3-4H,1-2H3 H_rad 300-2000 2.08e+07 1.84 0 3.03 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -522. InChI=1/C4H8/c1-4(2)3/h1H2,2-3H3 InChI=1/C3H5O/c1-2-3-4/h2-3H,1H3/o 300-2000 7.52e-08 5.77 0 12.04 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| -523. O/H/NonDeC O2b 300-2000 5e+10 0.0 1 0.0 0 0 0 0 1 Estimate [W.H. Green] | |
| - | |
| -// Added by AJ for autoxidation simulations | |
| -487. C/H2/NonDeC O2b 378-433 3.16E+14 0 0 43.30 0 0 0 0 4 ET Denisov, LN Denisova. Int J Chem Kinet 8:123-130, 1975 for BuCH2(CH-H)Me in benzene | |
| -//488. C/H3/Cs O_rad/NonDeO 300-1500 8.60E+3 0 0 16.02 0 0 0 0 4 Landolt Bornstein estimates for C16H33O2J + C16H34 | |
| -//489. C/H2/NonDeC O_rad/NonDeO 300-1500 8.60E+3 0 0 16.02 0 0 0 0 4 Landolt Bornstein estimates for C16H33O2J + C16H34 | |
| - | |
| -524. C/H3/Cd O_rad/NonDeO 300-1500 0.57833e-03 4.65 0 9.78 0 0 0 0 5 SSM due to lack of better value ref rate rule 525 | |
| -525. InChI=1/C4H8/c1-3-4-2/h3-4H,1-2H3/b4-3+ O_rad/NonDeO 300-1500 0.57833e-03 4.65 0 9.78 0 0 0 0 5 SSM CBS-QB3 calculations w/o HR corrections | |
| -526. H2O2 Cd_rad/NonDeC 300-1500 4.375e-01 3.59 0 -4.03 0 0 0 0 5 SSM due to lack of better value ref rate rule 527 | |
| -527. H2O2 InChI=1/C4H7/c1-3-4-2/h3H,1-2H3 300-1500 4.375e-01 3.59 0 -4.03 0 0 0 0 5 SSM CBS-QB3 calculations w/o HR corrections | |
| -528. C/H2/OneDeC O_rad/NonDeO 300-1500 2.54e-04 4.59 0 7.16 0 0 0 0 5 SSM due to lack of better value ref rate rule 529 | |
| -529. InChI=1/C4H8/c1-3-4-2/h3H,1,4H2,2H3 O_rad/NonDeO 300-1500 2.54e-04 4.59 0 7.16 0 0 0 0 5 SSM CBS-QB3 calculations w/o HR corrections | |
| -530. H2O2 Cd_pri_rad 300-1500 1.00e+00 3.52 0 -7.48 0 0 0 0 5 SSM due to lack of better value ref rate rule 531 | |
| -531. H2O2 InChI=1/C4H7/c1-3-4-2/h1,3H,4H2,2H3 300-1500 1.00e+00 3.52 0 -7.48 0 0 0 0 5 SSM CBS-QB3 calculations w/o HR corrections | |
| -532. X_H O2b 300-2000 5e+10 0.0 1 0.0 0 0 0 0 1 Estimate [W.H. Green] | |
| - | |
| -//Added by AJ for low temperature aromatic oxidation (given rank 1 so that RMG will presumably prefer these rates to others that it makes up) | |
| -//Notes: AJ did not find data for ethylbenzene + O2 or ethylbenzene + OH on the NIST Kinetics databasa, so values for toluene (per H) were used instead | |
| -533. C/H3/Cb O_pri_rad 500-1000 0.42e+13 0.0 0.0 2.59 0 0 0 0 1 Tully et al. experimental data (changed to per H) | |
| -534. C/H2/Cb O_pri_rad 500-1000 0.42e+13 0.0 0.0 2.59 0 0 0 0 1 Tully et al. experimental data (changed to per H) | |
| -535. C/H/Cb O_pri_rad 500-1000 0.42e+13 0.0 0.0 2.59 0 0 0 0 1 Tully et al. experimental data (changed to per H) | |
| -536. C/H3/Cb O_rad/NonDeO 600-1000 1.32e+11 0.0 0.0 14.08 0 0 0 0 1 Baulch et al. literature review (value for HO2 + toluene) (changed to per H) | |
| -537. C/H2/Cb O_rad/NonDeO 600-1000 1.33e+11 0.0 0.0 11.30 0 0 0 0 1 Baulch et al. literature review (value for HO2 + ethylbenzene) (changed to per H) | |
| -538. C/H/Cb O_rad/NonDeO 600-1000 1.33e+11 0.0 0.0 11.30 0 0 0 0 1 Baulch et al. literature review (value for HO2 + ethylbenzene) (changed to per H) | |
| -539. C/H3/Cb O2b 700-1200 0.6e+12 0.0 0.0 39.71 0 0 0 0 1 Baulch et al. literature review (value for HO2 + toluene entered here) (changed to per H) | |
| -540. C/H2/Cb O2b 700-1200 0.6e+12 0.0 0.0 39.71 0 0 0 0 1 Baulch et al. literature review (value for HO2 + toluene entered here) (changed to per H) | |
| -541. C/H/Cb O2b 700-1200 0.6e+12 0.0 0.0 39.71 0 0 0 0 1 Baulch et al. literature review (value for HO2 + toluene entered here) (changed to per H) | |
| \ No newline at end of file | |
| +// rate library for f01: HAbstraction reaction | |
| +// original from rate library.txt, CDW 03/08/01 | |
| +// SR and JS rename some nodes according to the tree and dictionary correction, Nov., 20, 2002 | |
| +// JS, comment out 10th, change XH in 23 from C/Cd/H3 to C/H3/Cd | |
| +// JS, remove CO_birad to form a new family later: CO + RH -> HCO + R. Aug, 26, 2003 | |
| + | |
| +// JS, define key word for format of the rate: either Arrhenius or Arrhenius_EP | |
| +Arrhenius_EP | |
| + | |
| +// Catherina Wijaya thesis, pg 151 -154. | |
| + | |
| +//f01_intermolecular_HA | |
| +//No. XH Y_rad Temp. A n a E0 DA Dn Da DE0 Rank Comments | |
| +0. X_H_or_Xrad_H Y_rad_birad 300-1500 1E+05 0 0 10 0 0 0 0 0 Default | |
| +1. X_H Y_rad_birad 300-1500 1E+05 0 0 10 0 0 0 0 0 Default | |
| +2. X_H H_rad 300-1500 2.4E+08 1.5 0.65 9.4 0 0 0 0 5 Dean, A. M. [118] | |
| +3. X_H O_atom_triplet 300-1500 1.7E+08 1.5 0.75 6.6 0 0 0 0 5 Dean, A. M. [118] | |
| +4. X_H O_pri_rad 300-1500 1.2E+06 2.0 0.50 10.1 0 0 0 0 5 Dean, A. M. [118] | |
| +5. X_H O_sec_rad 300-1500 1.4E+04 2.69 0.60 11.3 0 0 0 0 5 Dean, A. M. [118] | |
| +6. X_H C_methyl 300-1500 8.1E+05 1.87 0.65 13.0 0 0 0 0 5 Dean, A. M. [118] | |
| +7. C/H/Cs3 C_rad/Cs3 300-1500 1.30E-01 3.71 0 6.85 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +8. C/H2/NonDeC C_rad/Cs3 300-1500 1.26E+00 3.55 0 8.31 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +9. C/H3/Cs C_rad/Cs3 300-1500 2.85E+00 3.62 0 11.20 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +10. C/H/Cs3 C_rad/H/NonDeC 300-1500 5.58E+01 3.01 0 7.34 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +11. C/H2/NonDeC C_rad/H/NonDeC 300-1500 1.52E+01 3.19 0 10.31 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +12. C/H3/Cs C_rad/H/NonDeC 300-1500 4.71E+01 3.23 0 12.27 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +13. C/H/Cs3 C_rad/H2/Cs 300-1500 4.22E+03 2.51 0 8.06 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +14. C/H2/NonDeC C_rad/H2/Cs 300-1500 1.54E+03 2.66 0 10.10 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +15. C/H3/Cs C_rad/H2/Cs 300-1500 6.59E+02 2.71 0 12.92 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +16. C/H/Cs3 C_methyl 300-1500 5.74E+05 1.83 0 6.94 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +17. C/H2/NonDeC C_methyl 300-1500 1.45E+06 1.77 0 8.53 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +18. C/H3/Cs C_methyl 300-1500 2.78E+05 1.9 0 11.05 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +19. C_methane C_methyl 300-1500 1.01E+04 2.47 0 13.96 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +20. C/H/Cs3 H_rad 300-1500 4.83E+08 1.54 0 2.98 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +21. C/H2/NonDeC H_rad 300-1500 1.30E+08 1.69 0 4.78 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +22. C/H3/Cs H_rad 300-1500 6.28E+07 1.75 0 7.51 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +23. C_methane H_rad 300-1500 3.06E+07 1.87 0 10.59 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +24. O/H/NonDeC H_rad 300-1500 8.70E+08 1.39 0 10.07 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +25. CO_pri H_rad 300-1500 5.48E+07 1.82 0 2.44 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +26. CO/H/NonDe H_rad 300-1500 8.07E+07 1.76 0 0.67 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +27. Cd_pri H_rad 300-1500 2.53E+07 1.98 0 11.78 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Primary vinylic {Cd/H2} | |
| +28. Cd_pri H_rad 300-1500 4.53E+03 2.43 0 8.85 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Ketene hydrogen {CCO/H2} | |
| +29. Cd_pri H_rad 300-1500 1.46E+07 2.09 0 5.49 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Allene hydrogen {Cd/H2/Ca} | |
| +30. Cd/H/NonDeC H_rad 300-1500 2.98E+07 1.95 0 8.65 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +31. C/H3/Cd H_rad 300-1500 4.33E+05 2.38 0 2.80 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +32. C/H2/OneDeC H_rad 300-1500 6.99E+05 2.36 0 1.11 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Primary allylic hydrogen {C/Cd/C/H2} | |
| +33. C/H2/OneDeC H_rad 300-1500 7.79E+07 1.78 0 2.11 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Primary propergylic {C/Ct/C/H2} | |
| +34. C/H/Cs2 H_rad 300-1500 3.02E+06 2.16 0 -0.45 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Secondary allylic hydrogen {C/Cd/C2/H} | |
| +35. C/H/Cs2 H_rad 300-1500 1.21E+08 1.72 0 -0.73 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Secondary propergylic {C/Ct/C2/H} | |
| +36. C/H2/TwoDe H_rad 300-1500 7.09E+03 2.85 0 -1.90 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +37. Cd/H/OneDe H_rad 300-1500 1.93E+08 1.74 0 10.28 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Dienylic {Cd/Cd/H} | |
| +38. Cd/H/OneDe H_rad 300-1500 2.18E+06 2.4 0 6.11 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Eneynic {Cd/Ct/H} | |
| +39. Ct_H H_rad 300-1500 1.65E+08 1.85 0 26.52 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +40. C/H3/Ct H_rad 300-1500 2.70E+07 1.91 0 5.99 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +41. Cd/H/NonDeO H_rad 300-1500 9.67E+09 1.23 0 11.69 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +42. O/H/OneDe H_rad 300-1500 1.30E+11 0.82 0 7.75 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +43. Cd_pri C_methyl 300-1500 3.24E+03 2.58 0 14.04 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +44. C/H3/Cd C_methyl 300-1500 8.04E+01 2.92 0 7.16 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +45. O/H/NonDeC C_methyl 300-1500 2.54E+05 1.89 0 8.97 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +46. CO/H/NonDe C_methyl 300-1500 2.92E+04 2.29 0 5.44 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +47. O/H/OneDe C_methyl 300-1500 9.07E+04 2.04 0 10.85 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Olefinic alcohol {O/Cd/H} | |
| +48. O/H/OneDe H_rad 300-1500 3.30E+08 1.56 0 13.94 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. Acid O-H {O/CO/H} | |
| +49. CO/H/NonDe C_methyl 300-1500 4.53E+03 2.43 0 8.85 0 0 0 0 2 Sumathy CBS-Q calculations. Rate expression per H atom. | |
| +50. C_methane C_methyl 300-1500 6.03E+13 0 0 19.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +51. C/H3/Cs C_methyl 300-1500 2.80E+14 0 0 16.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +52. C/H3/Cs C_methyl 300-1500 6.15E+13 0 0 15.9 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +53. C/H3/Cs C_methyl 300-1500 7.71E+12 0 0 13.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +54. C/H2/NonDeC C_methyl 300-1500 5.02E+13 0 0 13.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +55. C/H/Cs3 C_methyl 300-1500 5.02E+13 0 0 11.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +56. C/H/Cs3 C_methyl 300-1500 4.42E+13 0 0 11.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +57. C/H3/Cd C_methyl 300-1500 2.62E+13 0 0 12.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +58. C/H2/OneDeC C_methyl 300-1500 2.73E+13 0 0 10.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +59. C/H/Cs2 C_methyl 300-1500 2.73E+13 0 0 8.9 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +60. C/H2/TwoDe C_methyl 300-1500 7.54E+13 0 0 8.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +61. C/H/Cs C_methyl 300-1500 9.32E+12 0 0 7.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +62. C/H3/Cb C_methyl 300-1500 4.90E+12 0 0 13.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +63. C/H2/OneDeC C_methyl 300-1500 1.70E+13 0 0 11.8 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +64. C/H/Cs2 C_methyl 300-1500 1.17E+13 0 0 11.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +65. C/H3/Ct C_methyl 300-1500 6.60E+13 0 0 13.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +66. C/H2/OneDeC C_methyl 300-1500 2.81E+13 0 0 11.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +67. C/H2/TwoDe C_methyl 300-1500 1.38E+14 0 0 8.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +68. C/H/Cs C_methyl 300-1500 3.43E+13 0 0 7.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +69. C/H/Cs2 C_methyl 300-1500 5.03E+13 0 0 9.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +70. Cd_pri C_methyl 300-1500 1.88E+14 0 0 18.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +71. Cd/H/NonDeC C_methyl 300-1500 4.43E+13 0 0 16.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +72. Cd/H/OneDe C_methyl 300-1500 5.78E+13 0 0 16.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +73. Cd/H/OneDe C_methyl 300-1500 2.26E+13 0 0 15.9 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +74. Cd/H/OneDe C_methyl 300-1500 4.37E+13 0 0 13.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +75. Ct_H C_methyl 300-1500 3.33E+18 0 0 28.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +76. Cb_H C_methyl 300-1500 1.17E+15 0 0 19.9 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +77. C/H2/NonDeC C_methyl 300-1500 9.87E+14 0 0 13.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +78. C/H2/NonDeC C_methyl 300-1500 4.51E+12 0 0 12.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +79. C/H/Cs3 C_methyl 300-1500 2.46E+13 0 0 11.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +80. C/H2/OneDeC C_methyl 300-1500 5.98E+13 0 0 9.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +81. C_methane H_rad 300-1500 1.87E+14 0 0 14.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +82. C_methane C_methyl 300-1500 6.03E+13 0 0 19.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +83. C_methane C_rad/H2/Cd 300-1500 1.53E+14 0 0 30.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +84. C_methane Cd_pri_rad 300-1500 1.59E+14 0 0 13.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +85. C_methane C_rad/Cs3 300-1500 1.86E+13 0 0 20.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +86. C/H/Cs3 H_rad 300-1500 5.31E+13 0 0 5.9 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +87. C/H/Cs3 C_methyl 300-1500 5.02E+13 0 0 11.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +88. C/H/Cs3 C_rad/H2/Cd 300-1500 5.02E+13 0 0 20.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +89. C/H/Cs3 Cd_pri_rad 300-1500 8.95E+13 0 0 6.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +90. C/H/Cs3 C_rad/Cs3 300-1500 5.43E+11 0 0 11.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +91. C/H/Cs3 C_rad/H2/Cs 300-1500 3.03E+12 0 0 12.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +92. C/H/Cs3 C_rad/H/NonDeC 300-1500 2.44E+12 0 0 12.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +93. C/H/Cs3 C_rad/H/OneDeC 300-1500 5.46E+12 0 0 21.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +94. C/H/Cs3 C_rad/Cs2 300-1500 1.10E+12 0 0 21.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +95. C/H/Cs3 Cd_rad/NonDeC 300-1500 1.02E+11 0 0 5.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +96. C/H/Cs3 Cd_rad/OneDe 300-1500 4.16E+12 0 0 13.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +97. C/H/Cs3 C_rad/H2/Ct 300-1500 3.14E+13 0 0 17.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +98. C/H/Cs3 C_rad/H/OneDeC 300-1500 2.53E+12 0 0 18.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +99. C/H/Cs3 C_rad/Cs2 300-1500 9.78E+11 0 0 18.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +100. Cd_pri H_rad 300-1500 3.39E+14 0 0 15.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +101. Cd_pri C_methyl 300-1500 1.88E+14 0 0 18.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +102. Cd_pri C_rad/H2/Cd 300-1500 5.36E+13 0 0 30.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +103. Cd_pri Cd_pri_rad 300-1500 1.47E+13 0 0 13.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +104. Cd_pri C_rad/Cs3 300-1500 3.93E+13 0 0 20.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +105. Cd_pri C_rad/H2/Cs 300-1500 7.82E+12 0 0 19.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +106. Cd_pri C_rad/H/NonDeC 300-1500 3.25E+12 0 0 20.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +107. Cd_pri C_rad/H/OneDeC 300-1500 1.51E+13 0 0 31.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +108. Cd_pri C_rad/Cs2 300-1500 3.39E+12 0 0 38.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +109. Cd_pri Cd_rad/NonDeC 300-1500 6.04E+13 0 0 14.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +110. Cd_pri Cd_rad/OneDe 300-1500 1.30E+13 0 0 20.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +111. Cd_pri C_rad/H2/Ct 300-1500 2.55E+13 0 0 26.8 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +112. Cd_pri C_rad/H/OneDeC 300-1500 4.41E+12 0 0 28.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +113. Cd_pri C_rad/Cs2 300-1500 3.59E+12 0 0 35.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +114. C/H3/Cd H_rad 300-1500 3.13E+13 0 0 7.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +115. C/H3/Cd C_methyl 300-1500 2.62E+13 0 0 12.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +116. C/H3/Cd C_rad/H2/Cd 300-1500 5.78E+12 0 0 21.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +117. C/H3/Cd Cd_pri_rad 300-1500 7.73E+12 0 0 7.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +118. C/H3/Cd C_rad/Cs3 300-1500 3.18E+12 0 0 11.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +119. C/H3/Cd C_rad/H2/Cs 300-1500 5.60E+11 0 0 12.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +120. C/H3/Cd C_rad/H/NonDeC 300-1500 2.87E+11 0 0 12.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +121. C/H3/Cd C_rad/H/OneDeC 300-1500 1.52E+12 0 0 21.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +122. C/H3/Cd C_rad/Cs2 300-1500 4.13E+11 0 0 21.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +123. C/H3/Cd Cd_rad/NonDeC 300-1500 5.52E+12 0 0 7.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +124. C/H3/Cd Cd_rad/OneDe 300-1500 1.95E+12 0 0 14.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +125. C/H3/Cd C_rad/H2/Ct 300-1500 7.58E+12 0 0 18.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +126. C/H3/Cd C_rad/H/OneDeC 300-1500 5.09E+11 0 0 18.5 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +127. C/H3/Cd C_rad/Cs2 300-1500 3.32E+11 0 0 18.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +128. H2 H_rad 300-1500 2.37E+13 0 0 9.4 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +129. H2 C_methyl 300-1500 2.95E+12 0 0 14.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +130. H2 C_rad/H2/Cd 300-1500 2.87E+12 0 0 25.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +131. H2 Cd_pri_rad 300-1500 4.49E+12 0 0 10.3 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +132. H2 C_rad/Cs3 300-1500 3.08E+11 0 0 14.8 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +133. H2 C_rad/H2/Cs 300-1500 4.57E+11 0 0 14.8 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +134. H2 C_rad/H/NonDeC 300-1500 3.04E+11 0 0 15.1 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +135. H2 C_rad/H/OneDeC 300-1500 1.82E+12 0 0 27.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +136. H2 C_rad/Cs2 300-1500 4.30E+11 0 0 27.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +137. H2 Cd_rad/NonDeC 300-1500 3.01E+12 0 0 10.6 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +138. H2 Cd_rad/OneDe 300-1500 2.37E+12 0 0 18.2 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +139. H2 C_rad/H2/Ct 300-1500 2.91E+12 0 0 23.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +140. H2 C_rad/H/OneDeC 300-1500 5.34E+11 0 0 24.0 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +141. H2 C_rad/Cs2 300-1500 4.20E+11 0 0 24.7 0 0 0 0 3 Mark Saeys, CBS-QB3 calculations, without hindered rotor treatment. Rate expression per H atom. | |
| +142. C/H3/Cs O_pri_rad 300-1500 5.93E+06 1.80 0 1.431 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. Fixed by RWest (changed to per H) | |
| +//142. C/H3/Cs O_pri_rad 300-1500 2.92E+06 1.80 0 0.278 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| +143. C/H2/NonDeC O_pri_rad 300-1500 4.50E+05 2.00 0 -1.133 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| +144. C/H/Cs3 O_pri_rad 300-1500 1.70E+06 1.90 0 -1.451 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. | |
| +145. C/H3/Cs O_atom_triplet 300-1500 9.50E+02 3.05 0 3.123 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| +146. C/H2/NonDeC O_atom_triplet 300-1500 2.39E+04 2.71 0 2.106 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| +147. C/H/Cs3 O_atom_triplet 300-1500 3.83E+05 2.41 0 1.140 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. | |
| +148. C/H3/Cs O_rad/NonDeO 300-1500 2.80E+12 0 0 20.435 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| +149. C/H2/NonDeC O_rad/NonDeO 300-1500 2.80E+12 0 0 17.686 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| +150. C/H/Cs3 O_rad/NonDeO 300-1500 2.80E+12 0 0 16.013 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. | |
| +151. C/H3/Cs O_rad/NonDeC 300-1500 5.27E+10 0 0 7.000 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| +152. C/H2/NonDeC O_rad/NonDeC 300-1500 5.50E+10 0 0 5.000 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| +153. C/H/Cs3 O_rad/NonDeC 300-1500 1.90E+10 0 0 2.800 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. | |
| +154. C/H3/Cs O2b 300-1500 7.00E+12 0 0 50.76 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| +155. C/H2/NonDeC O2b 300-1500 7.00E+12 0 0 48.21 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. (changed to per H) | |
| +156. C/H/Cs3 O2b 300-1500 7.00E+12 0 0 46.06 0 0 0 0 5 Curran et al. [8] Rate expressions for H atom abstraction from fuels. | |
| +157. H2 O2b 300-800 7.25E+13 0 0 56.64 *5.0 0 0 0 4 Tsang et al. [89] literature review. | |
| +158. H2 Cd_pri_rad 200-3000 4.73E+03 2.56 0 5.03 0 0 0 0 3 Knyazev et al. [119] Transition state theory. | |
| +159. H2 Cd_pri_rad 300-3500 1.11E+04 2.48 0 7.13 0 0 0 0 3 Mebel et al. [120] Transition state theory. | |
| +160. H2 Cd_pri_rad 300-1500 1.58E+09 0.70 0 5.11 0 0 0 0 3 Weissman et al. [121] Transition state theory. | |
| +161. H2 Ct_rad 300-2500 5.4E+12 0 0 2.17 *3.16 0 0 0 4 Baulch et al. [94] literature review. | |
| +162. H2 Cb_rad 300-5000 2.86E+04 2.43 0 6.28 0 0 0 0 3 Mebel et al. [122] Transition state theory. | |
| +163. H2 CO_pri_rad 300-2500 9.0E+05 2.00 0 17.83 *5 0 0 0 4 Tsang et al. [89] literature review. | |
| +164. H2 CO_rad/NonDe 300-2500 2.06E+06 1.82 0 17.61 *3.0 0 0 0 4 Tsang et al. [89] literature review. | |
| +165. H2 O_pri_rad 200-2400 9.10E+08 1.21 0 4.71 0 0 0 0 3 Isaacson [123] Transition state theory. | |
| +166. H2 O_rad/NonDeC 300-2000 6.32E-02 4.00 0 4.91 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| +167. C_methane O2b 500-2000 9.925E+12 0 0 56.83 *10.0 0 0 0 4 Baulch et al. [95] literature review. | |
| +168. C_methane C_rad/H2/Cs 300-2500 2.16E-02 4.14 0 12.56 *2.0 0 0 0 4 Tsang et al. [89] literature review. | |
| +169. C_methane C_rad/H/NonDeC 300-2500 1.81E-04 4.40 0 10.79 *2.0 0 0 0 4 Tsang et al. [91] literature review. | |
| +170. C_methane Ct_rad 300-2500 4.53E+11 0 0 0.50 *10.0 0 0 0 4 Tsang et al. [89] literature review. | |
| +171. C_methane Cb_rad 560-1410 5.0E+11 0 0 8.60 0 0 0 0 2 Heckmann et al. [124] | |
| +172. C_methane CO_pri_rad 300-2500 1.82E+03 2.85 0 22.46 *5.0 0 0 0 4 Tsang et al. [89] literature review. | |
| +173. C_methane CO_rad/NonDe 300-2500 5.43E+02 2.88 0 21.46 *5.0 0 0 0 4 Tsang et al. [89] literature review. | |
| +174. C_methane O_pri_rad 223-2400 3.85E-01 3.95 0 0.55 0 0 0 0 3 Melissas and Truhlar [125] Transition state theory. | |
| +175. C_methane O_pri_rad 240-2500 3.93E+06 1.83 0 2.78 *1.41 0 0 0 4 Baulch et al. [95] literature review. | |
| +176. C_methane O_pri_rad 298-1510 2.55E+07 1.60 0 3.12 0 0 0 0 3 Cohen et al. [101] Transition state theory. | |
| +177. C_methane O_rad/NonDeC 300-2000 1.55E-04 5.00 0 5.58 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| +178. C_methane O_rad/NonDeO 300-2500 4.53E+10 0 0 18.58 *5.0 0 0 0 4 Tsang et al. [89] literature review. | |
| +179. C/H3/Cs O2b 500-2000 1.005E+13 0 0 51.87 *10.0 0 0 0 4 Baulch et al. [95] literature review. | |
| +180. C/H3/Cs Ct_rad 300-1500 6.02E+11 0 0 0 *3 0 0 0 4 Tsang et al. [89] literature review. | |
| +181. C/H3/Cs Cb_rad 565-1000 3.48E+10 0 0 4.44 *2.35 0 0 0.18 2 Park et al. [126] | |
| +182. C/H3/Cs CO_pri_rad 300-2500 7.82E+03 2.72 0 18.24 *5.0 0 0 0 4 Tsang et al. [89] literature review. | |
| +183. C/H3/Cs CO_rad/NonDe 300-2500 3.02E+03 2.75 0 17.53 *5.0 0 0 0 4 Tsang et al. [89] literature review. | |
| +184. C/H3/Cs O_pri_rad 250-2000 1.20E+06 2.00 0 0.86 *1.41 0 0 0 4 Baulch et al. [95] literature review. | |
| +185. C/H3/CO O_pri_rad 295-600 5.17E+05 2.20 0 1.00 0 0 0 0 3 Taylor et al. [127] Transition state theory. | |
| +186. C/H3/O C_methyl 300-2000 2.05E-04 4.90 0 6.72 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| +187. C/H3/O O_pri_rad 300-2000 8.14E+03 2.80 0 -0.42 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| +100_R2 C/H3/O H_rad 300-2000 4.51E+02 3.20 0 3.49 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. added by Greg Magoon 08/25/09 | |
| +188. C/H2/NonDeC O2b 300-2500 1.985E+13 0 0 47.69 *10.0 0 0 0 4 Tsang [91] literature review. | |
| +189. C/H2/NonDeC CH2_triplet 300-2500 7.55E-01 3.46 0 7.47 *10.0 0 0 0 4 Tsang [91] literature review. | |
| +190. C/H2/NonDeC O_atom_triplet 300-2500 2.39E+04 2.71 0 2.11 *2.0 0 0 0 4 Tsang [91] literature review. | |
| +191. C/H2/NonDeC C_rad/H2/O 300-2500 3.02E+01 2.95 0 11.98 *5.0 0 0 0 4 Tsang [91] literature review. | |
| +192. C/H2/NonDeC Cd_pri_rad 300-2500 5.10E+02 3.10 0 8.82 *10.0 0 0 0 4 Tsang [91] literature review. | |
| +193. C/H2/NonDeC Ct_rad 300-2500 6.05E+11 0 0 0 *3.0 0 0 0 4 Tsang [91] literature review. | |
| +194. C/H2/NonDeC CO_pri_rad 300-2500 5.4E+06 1.90 0 17.01 *3.0 0 0 0 4 Tsang [91] literature review. | |
| +195. C/H2/NonDeC CO_rad/NonDe 300-2500 2.65E+06 2.00 0 16.24 *3.0 0 0 0 4 Tsang [91] literature review. | |
| +196. C/H2/NonDeC O_pri_rad 295-1220 3.95E+06 1.90 0 0.16 0 0 0 0 3 Cohen et al. [101] Transition state theory. | |
| +197. C/H2/NonDeC O_rad/NonDeC 300-2500 7.25E+10 0 0 4.57 *5.0 0 0 0 4 Tsang [91] literature review. | |
| +198. C/H/Cs3 O2b 300-2500 3.97E+13 0 0 43.92 *3.0 0 0 0 4 Tsang [92] literature review. | |
| +199. C/H/Cs3 O_atom_triplet 300-2500 1.57E+05 2.50 0 1.11 *2.0 0 0 0 4 Tsang [92] literature review. | |
| +200. C/H/Cs3 CH2_triplet 300-2500 1.09E+12 0 0 4.91 *5.0 0 0 0 4 Tsang [92] literature review. | |
| +201. C/H/Cs3 Cd_pri_rad 300-2500 9.04E-01 3.46 0 2.60 *5.0 0 0 0 4 Tsang [92] literature review. | |
| +202. C/H/Cs3 Ct_rad 300-2500 6.62E+11 0 0 0 *3.0 0 0 0 4 Tsang [92] literature review. | |
| +203. C/H/Cs3 CO_pri_rad 300-2500 3.43E+04 2.50 0 13.51 *5.0 0 0 0 4 Tsang [92] literature review. | |
| +204. C/H/Cs3 CO_rad/NonDe 300-2500 3.43E+04 2.50 0 13.51 *10.0 0 0 0 4 Tsang [92] literature review. | |
| +205. C/H/Cs3 O_pri_rad 298-1150 2.57E+06 1.90 0 1.45 0 0 0 0 3 Cohen et al. [101] Transition state theory. | |
| +206. C/H/Cs3 O_rad/NonDeC 300-2500 2.29E+10 0 0 2.88 *10.0 0 0 0 4 Tsang [92] literature review. | |
| +207. Cd_pri O2b 300-2500 1.792E+13 0 0 60.01 0 0 0 0 4 Hua, Ruscic, and Wang 2005, transition state theory. | |
| +//208. Cd_pri CO_birad 300-2500 3.78E+13 0 0 90.62 *5.0 0 0 0 4 Tsang [89] literature review. | |
| +209. Cd_pri O_atom_triplet 290-1510 3.78E+06 1.91 0 3.74 0 0 0 0 3 Mahmud et al. [128] Transition state theory | |
| +210. Cd_pri C_rad/H2/Cs 300-2500 1.58E+02 3.13 0 18.00 *10.0 0 0 0 4 Tsang [89] literature review. | |
| +211. Cd_pri O_pri_rad 650-1500 5.13E+12 0 0 5.94 *3.16 0 0 0 4 Baulch et al. [95] literature review. | |
| +212. Cd/H/NonDeC O_atom_triplet 300-2500 6.02E+10 0.70 0 7.63 *3.0 0 0 0 4 Tsang [93] literature review. | |
| +//213. Cd/H/NonDeC H_rad 300-2500 2.37E+00 0 0 7.31 *5.0 0 0 0 4 Tsang [93] literature review. | |
| +213. Cd/H/NonDeC H_rad 300-2500 4.09e+05 2.5 0 9.79 *4.0 0.0 0.0 0.0 4 Tsang [93] literature review. | |
| +//214. Cd/H/NonDeC C_methyl 300-2500 3.8E-01 0 0 5.98 *100.0 0 0 0 4 Tsang [93] literature review. | |
| +214. Cd/H/NonDeC C_methyl 300-2500 0.842 3.5 0.0 11.66 *6.0 0.0 0.0 0.0 4 Tsang [93] literature review. | |
| +//215. Cd/H/NonDeC Cd_pri_rad 300-2500 3.8E-01 0 0 4.99 *10.0 0 0 0 4 Tsang [93] literature review. | |
| +215. Cd/H/NonDeC Cd_pri_rad 300-2500 0.842 3.5 0.0 9.67 *6.0 0.0 0.0 0.0 4 Tsang [93] literature review. | |
| +216. Cd/H/NonDeC Ct_rad 300-2500 1.21E+12 0 0 0 *5.0 0 0 0 4 Tsang [93] literature review. | |
| +//217. Cd/H/NonDeC O_pri_rad 300-2500 1.11E+06 2.00 0 1.45 0 0 0 0 4 Tsang [93] literature review. | |
| +217. Cd/H/NonDeC O_pri_rad 300-2500 1.11E+06 2.00 0 1.45 *2 0.0 0.0 0.0 4 Tsang [93] literature review. | |
| +218. Ct_H O2b 300-2500 6.05E+12 0 0 74.52 *10.0 0 0 0 4 Tsang [89] literature review. | |
| +//219. Ct_H CO_birad 300-2500 2.41E+14 0 0 107 *10.0 0 0 0 4 Tsang [89] literature review. | |
| +220. Ct_H C_rad/H2/Cs 300-2500 1.36E+11 0 0 23.45 *5.0 0 0 0 4 Tsang [89] literature review. | |
| +221. Ct_H O_pri_rad 300-2500 7.25E+03 2.68 0 12.04 *10.0 0 0 0 4 Tsang [89] literature review. | |
| +222. Cb_H O2b 1200-1700 1.052E+13 0 0 60.01 0 0 0 0 4 Asaba et al. [129]. Data are estimated. | |
| +223. Cb_H H_rad 500-800 1.00E+08 1.80 0 16.35 0 0 0 0 4 Mebel et al. [122] RRK(M) extrapolation. | |
| +224. Cb_H H_rad 298-1000 5.02E+11 0 0 8.11 0 0 0 0 5 Nicovich et al. [130] | |
| +225. Cb_H C_rad/H2/Cs 650-770 1.05E+11 0 0 14.86 *2.0 0 0 1.19 5 Zhang et al. [131] | |
| +226. Cb_H O_pri_rad 400-1500 2.72E+07 1.42 0 1.45 *2.0 0 0 0 4 Baulch et al. [95] literature review. | |
| +227. CO_pri O2b 300-2200 2.34E+07 2.05 0 37.93 0 0 0 0 3 Michael et al. [132] Transition state theory. | |
| +228. CO_pri O_atom_triplet 250-2200 2.08E+11 0.57 0 2.76 *2.0 0 0 0 4 Baulch et al. [95] literature review. | |
| +229. CO_pri CH2_triplet 300-2500 3.02E+09 0 0 0 0 0 0 0 4 Tsang [89] literature review. | |
| +230. CO_pri C_methyl 300-2000 3.89E-08 6.10 0 1.97 *1.58 0 0 0 4 Baulch et al. [94] literature review. | |
| +231. CO_pri C_rad/H2/Cs 300-2500 2.75E+03 2.81 0 5.86 *5.0 0 0 0 4 Tsang [89] literature review. | |
| +232. CO_pri C_rad/H/NonDeC 300-2500 5.40E+10 0 0 6.96 *2.5 0 0 0 4 Tsang [91] literature review. | |
| +233. CO_pri C_rad/Cs3 300-2500 1.63E+09 0 0 3.56 *5.0 0 0 0 4 Tsang [92] literature review. | |
| +234. CO_pri Cd_pri_rad 300-2500 2.71E+03 2.81 0 5.86 *5.0 0 0 0 4 Tsang [89] literature review. | |
| +235. CO_pri CO_rad/NonDe 300-2500 9.05E+10 0 0 12.92 *10.0 0 0 0 4 Tsang [89] literature review. | |
| +236. CO_pri O_pri_rad 300-3000 1.72E+09 1.18 0 -0.45 *5.0 0 0 0 4 Baulch et al. [95] literature review. | |
| +237. CO_pri O_rad/NonDeC 300-2500 5.10E+10 0 0 2.98 *3.0 0 0 0 4 Tsang [89] literature review. | |
| +238. CO_pri O_rad/NonDeO 641-1600 2.06E+04 2.50 0 10.21 0 0 0 0 4 Eiteneer et al. [133] literature review. | |
| +239. CO/H/NonDe O2b 600-1100 3.01E+13 0 0 39.15 *10.0 0 0 0 4 Baulch et al. [95] literature review. | |
| +240. CO/H/NonDe O_atom_triplet 300-2000 5.0E+12 0 0 1.79 *2.0 0 0 0 4 Warnatz [134] literature review | |
| +241. CO/H/NonDe H_rad 300-2000 4.0E+13 0 0 4.21 *2.0 0 0 0 4 Warnatz [134] literature review | |
| +242. CO/H/NonDe C_methyl 300-1250 1.99E-06 5.64 0 2.46 *2.0 0 0 0 4 Baulch et al. [95] literature review. | |
| +243. CO/H/NonDe C_rad/H2/Cd 790-810 3.8E+11 0 0 7.21 0 0 0 0 5 Loser et al. [135] bond strength-bond length method. | |
| +244. CO/H/NonDe Cd_pri_rad 480-520 8.13E+10 0 0 3.68 0 0 0 0 5 Scherzer et al. [136] bond energy-bond order method. | |
| +//245. CO/H/NonDe O_pri_rad 295-600 2.0E+06 1.80 0 1.30 0 0 0 0 3 Taylor et al. [127] Transition state theory. | |
| +245. CO/H/NonDe O_pri_rad 295-600 2.0E+06 1.80 0 -1.30 0 0 0 0 3 Taylor et al. [127] Transition state theory. | |
| +246. CO/H/NonDe O_pri_rad 300-2000 1.0E+13 0 0 0 *2.51 0 0 0 4 Warnatz [134] literature review | |
| +247. CO/H/NonDe O_rad/NonDeO 900-1200 3.01E+12 0 0 11.92 *5.0 0 0 0 4 Baulch et al. [95] literature review. | |
| +248. O_pri O2b 300-1000 2.325E+12 0 0 74.12 0 0 0 0 5 Mayer et al. [137] Bond energy-bond order. | |
| +249. O_pri O_atom_triplet 298-1000 2.63E+09 1.20 0 17.83 0 0 0 0 3 Karach et al. [138] Transition state theory. | |
| +250. O_pri O_atom_triplet 300-2000 7.40E+04 2.60 0 15.18 0 0 0 0 3 Harding et al. [139] Transition state theory. | |
| +251. O_pri H_rad 300-2500 2.26E+08 1.60 0 19.32 *1.6 0 0 0 4 Baulch et al. [95] literature review. | |
| +252. O_pri C_methyl 300-1500 3.20E+00 3.31 0 12.56 0 0 0 0 3 Ma et al. [140] Transition state theory. | |
| +253. O_pri C_methyl 300-2500 2.42E+02 2.90 0 14.86 *1.6 0 0 0 4 Tsang [89] literature review. | |
| +254. O_pri C_rad/H2/Cs 300-2500 1.70E+06 1.44 0 20.27 *2.0 0 0 0 4 Tsang [89] literature review. | |
| +255. O_pri Cd_pri_rad 300-2500 2.42E+02 2.90 0 14.86 *5.0 0 0 0 4 Tsang [89] literature review. | |
| +256. O_pri CO_pri_rad 300-2500 1.18E+08 1.35 0 26.03 *5.0 0 0 0 4 Tsang [89] literature review. | |
| +//257. O_pri O_pri_rad 200-700 6.45E-06 5.01 0 0.61 0 0 0 0 3 Masgrau et al. [141] Transition state theory w/tunneling correction. | |
| +257. O_pri O_pri_rad 200-700 2.417E-07 5.48 0 0.274 0.0 0.0 0.0 0.0 3 Masgrau et al. [141] Transition state theory. | |
| +258. O_pri O_rad/NonDeC 300-2000 1.74E-01 3.80 0 11.49 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| +259. O/H/NonDeC O_atom_triplet 300-1000 1.0E+13 0 0 4.69 *2.51 0 0 0 4 Warnatz [134] literature review | |
| +260. O/H/NonDeC CH2_triplet 300-2500 1.44E+01 3.10 0 6.94 *3.0 0 0 0 4 Tsang [90] literature review. | |
| +261. O/H/NonDeC C_methyl 300-2000 3.70E-04 4.70 0 5.78 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| +262. O/H/NonDeC C_rad/H2/Cs 300-2500 1.44E+01 3.10 0 8.94 *3.0 0 0 0 4 Tsang [90] literature review. | |
| +//263. O/H/NonDeC C_rad/H/NonDeC 300-2500 1.45E+01 3.10 0 10.33 *5.0 0 0 0 4 Tsang [90] literature review. | |
| +263. O/H/NonDeC C_rad/H/NonDeC 300-2500 1.45E+01 3.10 0 10.33 *5.0 0 0 0 4 Tsang [91] literature review. | |
| +//264. O/H/NonDeC C_rad/Cs3 300-2500 1.51E+03 1.80 0 9.36 *10.0 0 0 0 4 Tsang [90] literature review. | |
| +264. O/H/NonDeC C_rad/Cs3 300-2500 1.51E+03 1.80 0 9.36 *10.0 0 0 0 4 Tsang [92] literature review. | |
| +265. O/H/NonDeC Cd_pri_rad 300-2500 1.44E+01 3.10 0 6.94 *10.0 0 0 0 4 Tsang [90] literature review. | |
| +266. O/H/NonDeC Ct_rad 300-2500 1.21E+12 0 0 0 *5.0 0 0 0 4 Tsang [90] literature review. | |
| +267. O/H/NonDeC O_pri_rad 300-2000 1.73E+01 3.40 0 -1.14 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. | |
| +268. O/H/NonDeC O_pri_rad 300-2000 1.0E+13 0 0 1.70 *3.16 0 0 0 4 Warnatz [134] literature review | |
| +// (Reverse) Rates for nButanol+HO2=H2O2+radicals | |
| +301. H2O2 InChI=1/C4H9O/c1-2-3-4-5/h5H,1-4H2 600-2000 2.88E+00 3.16 0.0 0.75 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +302. H2O2 InChI=1/C4H9O/c1-2-3-4-5/h2,5H,3-4H2,1H3 600-2000 6.75E-01 3.42 0.0 1.43 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +303. H2O2 InChI=1/C4H9O/c1-2-3-4-5/h3,5H,2,4H2,1H3 600-2000 3.145E-01 3.52 0.0 1.61 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +304. H2O2 InChI=1/C4H9O/c1-2-3-4-5/h4-5H,2-3H2,1H3 600-2000 1.485E+00 3.39 0.0 1.40 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +// (Reverse) Rates for sButanol+HO2=H2O2+radicals | |
| +305. H2O2 InChI=1/C4H9O/c1-3-4(2)5/h4-5H,1,3H2,2H3 600-2000 5.75E+00 2.94 0.0 0.46 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +306. H2O2 InChI=1/C4H9O/c1-3-4(2)5/h3-5H,1-2H3 600-2000 8.75E-01 2.91 0.0 -0.41 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +307. H2O2 InChI=1/C4H9O/c1-3-4(2)5/h5H,3H2,1-2H3 600-2000 1.73E+01 3.05 0.0 1.02 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +308. H2O2 InChI=1/C4H9O/c1-3-4(2)5/h4-5H,2-3H2,1H3 600-2000 3.055E-01 3.53 0.0 1.52 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +// (Reverse) Rates for tButanol+HO2=H2O2+radicals | |
| +309. H2O2 InChI=1/C4H9O/c1-4(2,3)5/h5H,1H2,2-3H3 600-2000 2.100E-01 3.53 0.0 1.56 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +310. Cd_pri O2b 300-1500 7.00E+12 0 0 60.36 0 0 0 0 5 Increased rate 154 Ea by 9.6 kcal/mol (vinyl versus methyl) | |
| +311. Cd_pri O2b 500-2000 1.005E+13 0 0 61.47 *10.0 0 0 0 4 Increased rate 179 Ea by 9.6 kcal/mol (vinyl versus methyl) | |
| +312. Cd/H/NonDeC O2b 300-1500 7.00E+12 0 0 57.81 0 0 0 0 5 Increased rate 155 Ea by 9.6 kcal/mol (vinyl versus methyl) | |
| +313. Cd/H/NonDeC O2b 300-2500 1.985E+13 0 0 57.29 *10.0 0 0 0 4 Increased rate 188 Ea by 9.6 kcal/mol (vinyl versus methyl)486. Orad_O_H O_rad/NonDeO 300-1500 1.75E+10 0 0 -3.275 0 0 0 0 5 [8] Curran's estimation in reaction type 13, RO2 + HO2 --> RO2H + O2 | |
| +486. Orad_O_H O_rad/NonDeO 300-1500 1.75E+10 0 0 -3.275 0 0 0 0 5 [8] Curran's estimation in reaction type 13, RO2 + HO2 --> RO2H + O2 | |
| +500. CO_pri InChI=1/C4H7/c1-4(2)3/h1-2H2,3H3 600-2000 3.065e-02 3.95 0.0 12.22 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +501. InChI=1/C3H8/c1-3-2/h3H2,1-2H3 InChI=1/C4H9O/c1-4(2)3-5/h5H,3H2,1-2H3 300-2000 9.11e-07 5.11 0 5.69 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +501R. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/beta InChI=1/C3H7/c1-3-2/h3H,1-2H3 300-2000 2.35e-06 4.84 0 4.27 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +502. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/alpha InChI=1/C3H7/c1-3-2/h3H,1-2H3 300-2000 1.06e-06 5.06 0 4.89 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +503. InChI=1/C4H8/c1-4(2)3/h1H2,2-3H3 InChI=1/C4H9O/c1-4(2)3-5/h4-5H,1,3H2,2H3 300-2000 8.39e-06 4.89 0 4.32 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +504. InChI=1/C4H8/c1-4(2)3/h1H2,2-3H3 InChI=1/C4H9O/c1-4(2)3-5/h5H,3H2,1-2H3 300-2000 1.44e-05 4.52 0 1.46 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +505. InChI=1/C4H8/c1-4(2)3/h1H2,2-3H3 InChI=1/C4H9O/c1-4(2)3-5/h3-5H,1-2H3 300-2000 4.91e-06 5.07 0 3.66 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +506. InChI=1/C4H8/c1-4(2)3/h1H2,2-3H3 InChI=1/C4H9O/c1-4(2)3-5/h4H,3H2,1-2H3 300-2000 5.83e-01 3.74 0 1.45 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +507. InChI=1/C3H6/c1-3-2/h3H,1H2,2H3 InChI=1/C4H9O/c1-4(2)3-5/h4-5H,1,3H2,2H3 300-2000 3.36e-05 4.75 0 4.13 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +508. InChI=1/C3H6/c1-3-2/h3H,1H2,2H3 InChI=1/C4H9O/c1-4(2)3-5/h5H,3H2,1-2H3 300-2000 1.64e-06 4.98 0 3.18 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +509. InChI=1/C3H6/c1-3-2/h3H,1H2,2H3 InChI=1/C4H9O/c1-4(2)3-5/h3-5H,1-2H3 300-2000 3.11e-06 4.97 0 3.64 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +510. InChI=1/C3H6/c1-3-2/h3H,1H2,2H3 InChI=1/C4H9O/c1-4(2)3-5/h4H,3H2,1-2H3 300-2000 1.19e-01 3.90 0 1.81 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +511. InChI=1/C2H6/c1-2/h1-2H3 InChI=1/C4H9O/c1-4(2)3-5/h4-5H,1,3H2,2H3 300-2000 3.21e-06 5.28 0 7.78 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +512. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/beta InChI=1/C2H5/c1-2/h1H2,2H3 300-2000 1.41e-05 4.83 0 4.37 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +513. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/alpha InChI=1/C2H5/c1-2/h1H2,2H3 300-2000 4.25e-06 5.01 0 5.01 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +514. InChI=1/C2H6/c1-2/h1-2H3 InChI=1/C4H9O/c1-4(2)3-5/h4H,3H2,1-2H3 300-2000 5.07e-03 4.52 0 2.34 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +515. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/beta InChI=1/C2H3/c1-2/h1H,2H2 300-2000 5.49e+00 3.33 0 0.63 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +516. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/gamma InChI=1/C3H5/c1-3-2/h1H2,2H3 300-2000 3.11e-05 4.87 0 3.50 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +517. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/alpha InChI=1/C3H5/c1-3-2/h1H2,2H3 300-2000 1.28e-02 4.09 0 1.31 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +518. InChI=1/C3H6O/c1-2-3-4/h3H,2H2,1H3/beta InChI=1/C4H9O/c1-4(2)3-5/h4-5H,1,3H2,2H3 300-2000 1.56e-04 4.31 0 3.39 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +519. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/beta InChI=1/C3H5O/c1-2-3-4/h2-3H,1H3/c 300-2000 4.85e-04 4.37 0 9.66 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +520. InChI=1/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3/alpha InChI=1/C3H5O/c1-2-3-4/h2-3H,1H3/c 300-2000 1.84e-03 4.02 0 7.92 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +521. InChI=1/C4H8O/c1-4(2)3-5/h3-4H,1-2H3 H_rad 300-2000 2.08e+07 1.84 0 3.03 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +522. InChI=1/C4H8/c1-4(2)3/h1H2,2-3H3 InChI=1/C3H5O/c1-2-3-4/h2-3H,1H3/o 300-2000 7.52e-08 5.77 0 12.04 0 0 0 0 3 MRH CBS-QB3 calculations w/o HR corrections | |
| +523. O/H/NonDeC O2b 300-2000 5e+10 0.0 1 0.0 0 0 0 0 1 Estimate [W.H. Green] | |
| +524. C/H3/Cd O_rad/NonDeO 300-1500 0.57833e-03 4.65 0 9.78 0 0 0 0 5 SSM due to lack of better value ref rate rule 525 | |
| +525. InChI=1/C4H8/c1-3-4-2/h3-4H,1-2H3/b4-3+ O_rad/NonDeO 300-1500 0.57833e-03 4.65 0 9.78 0 0 0 0 5 SSM CBS-QB3 calculations w/o HR corrections | |
| +526. H2O2 Cd_rad/NonDeC 300-1500 4.375e-01 3.59 0 -4.03 0 0 0 0 5 SSM due to lack of better value ref rate rule 527 | |
| +527. H2O2 InChI=1/C4H7/c1-3-4-2/h3H,1-2H3 300-1500 4.375e-01 3.59 0 -4.03 0 0 0 0 5 SSM CBS-QB3 calculations w/o HR corrections | |
| +528. C/H2/OneDeC O_rad/NonDeO 300-1500 2.54e-04 4.59 0 7.16 0 0 0 0 5 SSM due to lack of better value ref rate rule 529 | |
| +529. InChI=1/C4H8/c1-3-4-2/h3H,1,4H2,2H3 O_rad/NonDeO 300-1500 2.54e-04 4.59 0 7.16 0 0 0 0 5 SSM CBS-QB3 calculations w/o HR corrections | |
| +530. H2O2 Cd_pri_rad 300-1500 1.00e+00 3.52 0 -7.48 0 0 0 0 5 SSM due to lack of better value ref rate rule 531 | |
| +531. H2O2 InChI=1/C4H7/c1-3-4-2/h1,3H,4H2,2H3 300-1500 1.00e+00 3.52 0 -7.48 0 0 0 0 5 SSM CBS-QB3 calculations w/o HR corrections | |
| +532. X_H O2b 300-2000 5e+10 0.0 1 0.0 0 0 0 0 1 Estimate [W.H. Green] | |
| +// Added by AJ for autoxidation simulations | |
| +487. C/H2/NonDeC O2b 378-433 3.16E+14 0 0 43.30 0 0 0 0 4 ET Denisov, LN Denisova. Int J Chem Kinet 8:123-130, 1975 for BuCH2(CH-H)Me in benzene | |
| +//488. C/H3/Cs O_rad/NonDeO 300-1500 8.60E+3 0 0 16.02 0 0 0 0 4 Landolt Bornstein estimates for C16H33O2J + C16H34 | |
| +//489. C/H2/NonDeC O_rad/NonDeO 300-1500 8.60E+3 0 0 16.02 0 0 0 0 4 Landolt Bornstein estimates for C16H33O2J + C16H34 | |
| +//Added by AJ for low temperature aromatic oxidation (given rank 1 so that RMG will presumably prefer these rates to others that it makes up) | |
| +//Notes: AJ did not find data for ethylbenzene + O2 or ethylbenzene + OH on the NIST Kinetics databasa, so values for toluene (per H) were used instead | |
| +533. C/H3/Cb O_pri_rad 500-1000 0.42e+13 0.0 0.0 2.59 0 0 0 0 1 Tully et al. experimental data (changed to per H) | |
| +534. C/H2/Cb O_pri_rad 500-1000 0.42e+13 0.0 0.0 2.59 0 0 0 0 1 Tully et al. experimental data (changed to per H) | |
| +535. C/H/Cb O_pri_rad 500-1000 0.42e+13 0.0 0.0 2.59 0 0 0 0 1 Tully et al. experimental data (changed to per H) | |
| +536. C/H3/Cb O_rad/NonDeO 600-1000 1.32e+11 0.0 0.0 14.08 0 0 0 0 1 Baulch et al. literature review (value for HO2 + toluene) (changed to per H) | |
| +537. C/H2/Cb O_rad/NonDeO 600-1000 1.33e+11 0.0 0.0 11.30 0 0 0 0 1 Baulch et al. literature review (value for HO2 + ethylbenzene) (changed to per H) | |
| +538. C/H/Cb O_rad/NonDeO 600-1000 1.33e+11 0.0 0.0 11.30 0 0 0 0 1 Baulch et al. literature review (value for HO2 + ethylbenzene) (changed to per H) | |
| +539. C/H3/Cb O2b 700-1200 0.6e+12 0.0 0.0 39.71 0 0 0 0 1 Baulch et al. literature review (value for HO2 + toluene entered here) (changed to per H) | |
| +540. C/H2/Cb O2b 700-1200 0.6e+12 0.0 0.0 39.71 0 0 0 0 1 Baulch et al. literature review (value for HO2 + toluene entered here) (changed to per H) | |
| +541. C/H/Cb O2b 700-1200 0.6e+12 0.0 0.0 39.71 0 0 0 0 1 Baulch et al. literature review (value for HO2 + toluene entered here) (changed to per H) | |
| diff --git a/databases/RMG_database/thermo_libraries/QMcorrections/Dictionary.txt b/databases/RMG_database/thermo_libraries/QMcorrections/Dictionary.txt | |
| deleted file mode 100644 | |
| index a940962..0000000 | |
| --- a/databases/RMG_database/thermo_libraries/QMcorrections/Dictionary.txt | |
| +++ /dev/null | |
| @@ -1,7 +0,0 @@ | |
| -O2 | |
| -1 O 1 {2,S} | |
| -2 O 1 {1,S} | |
| - | |
| -OH | |
| -1 O 1 {2,S} | |
| -2 H 0 {1,S} | |
| \ No newline at end of file | |
| diff --git a/databases/RMG_database/thermo_libraries/QMcorrections/Library.txt b/databases/RMG_database/thermo_libraries/QMcorrections/Library.txt | |
| deleted file mode 100644 | |
| index 713cfcd..0000000 | |
| --- a/databases/RMG_database/thermo_libraries/QMcorrections/Library.txt | |
| +++ /dev/null | |
| @@ -1,2 +0,0 @@ | |
| -O2 -0.0010244 49.0236 7.0233 7.1986 7.4285 7.6673 8.0656 8.3363 8.7407 0.0 0.0 0.0 "gmagoon 072009: molecular oxygen (triplet) thermo data taken from GRI-Mech species s00010295 (RMG was considering at a singlet, which produced incorrect thermochemistry results when using quantum chemistry)" | |
| -OH 9.4021 43.9063 7.1402 7.0675 7.0458 7.0581 7.1493 7.3353 7.8741 0.0 0.0 0.0 "gmagoon 072509: OH thermo data taken from GRI-Mech species s00010102 (RMG would be off by factor of R*ln2 for entropy due to electronic degeneracy of 4 rather than 2 (due to spatial degeneracy in addition to spin degeneracy))" | |
| \ No newline at end of file | |
| diff --git a/databases/RMG_database/thermo_libraries/primaryThermoLibrary/Dictionary.txt b/databases/RMG_database/thermo_libraries/primaryThermoLibrary/Dictionary.txt | |
| index 50f1442..322cdcd 100644 | |
| --- a/databases/RMG_database/thermo_libraries/primaryThermoLibrary/Dictionary.txt | |
| +++ b/databases/RMG_database/thermo_libraries/primaryThermoLibrary/Dictionary.txt | |
| @@ -5,6 +5,54 @@ H2 | |
| H | |
| 1 H 1 | |
| +OCCO(S) | |
| +1 O 0 {2,D} | |
| +2 C 0 {1,D} {3,D} | |
| +3 C 0 {2,D} {4,D} | |
| +4 O 0 {3,D} | |
| + | |
| +OCCO | |
| +1 O 1 {2,S} | |
| +2 C 0 {1,S} {3,T} | |
| +3 C 0 {2,T} {4,S} | |
| +4 O 1 {3,S} | |
| + | |
| O2 | |
| 1 O 1 {2,S} | |
| 2 O 1 {1,S} | |
| + | |
| +OH | |
| +1 O 1 {2,S} | |
| +2 H 0 {1,S} | |
| + | |
| +CO3s1 | |
| +1 C 0 {2,D} {3,S} {4,S} | |
| +2 O 0 {1,D} | |
| +3 O 0 {4,S} {1,S} | |
| +4 O 0 {3,S} {1,S} | |
| + | |
| +CO3t1 | |
| +1 C 0 {2,D} {3,S} {4,S} | |
| +2 O 0 {1,D} | |
| +3 O 1 {1,S} | |
| +4 O 1 {1,S} | |
| + | |
| +CO3t2 | |
| +1 C 1 {2,D} {3,S} | |
| +2 O 0 {1,D} | |
| +3 O 0 {4,S} {1,S} | |
| +4 O 1 {3,S} | |
| + | |
| +cyclopropene12diyl | |
| +1 C 1 {2,D} {3,S} | |
| +2 C 1 {1,D} {3,S} | |
| +3 C 0 {1,S} {2,S} {4,S} {5,S} | |
| +4 H 0 {3,S} | |
| +5 H 0 {3,S} | |
| + | |
| +cyclopropynylidyne | |
| +1 C 0 {2,T} {3,S} | |
| +2 C 0 {1,T} {3,S} | |
| +3 C 1 {1,S} {2,S} {4,S} | |
| +4 H 0 {3,S} | |
| + | |
| diff --git a/databases/RMG_database/thermo_libraries/primaryThermoLibrary/Library.txt b/databases/RMG_database/thermo_libraries/primaryThermoLibrary/Library.txt | |
| index 835d8c5..f20ca5e 100644 | |
| --- a/databases/RMG_database/thermo_libraries/primaryThermoLibrary/Library.txt | |
| +++ b/databases/RMG_database/thermo_libraries/primaryThermoLibrary/Library.txt | |
| @@ -1,4 +1,12 @@ | |
| //Name H298 S298 Cp300 Cp400 Cp500 Cp600 Cp800 Cp1000 Cp1500 dH dS dCp Comments | |
| H2 0.000 31.233 6.895 6.975 6.994 7.009 7.081 7.219 7.720 0 0.0007 0 "library value for H2" | |
| -H 52.103 27.419 4.968 4.968 4.968 4.968 4.968 4.968 4.968 0.001 0.0005 0 "library value for H radical" | |
| +H 52.103 27.419 4.968 4.968 4.968 4.968 4.968 4.968 4.968 0.001 0.0005 0 "library value for H radical" | |
| O2 -0.0010244 49.0236 7.0233 7.1986 7.4285 7.6673 8.0656 8.3363 8.7407 0.0 0.0 0.0 "from GRI-Mech 3.0" | |
| +OH 9.4021 43.9063 7.1402 7.0675 7.0458 7.0581 7.1493 7.3353 7.8741 0.0 0.0 0.0 "taken from GRI-Mech 3.0 species s00010102" | |
| +CO3s1 -37.90 61.28 11.82 13.53 14.80 15.76 17.05 17.85 18.84 0.0 0.0 0.0 "Mebel et al (2004) http://dx.doi.org/10.1021/jp049315h" | |
| +CO3t1 -11.50 64.53 12.43 14.02 15.23 16.16 17.40 18.14 19.01 0.0 0.0 0.0 "Mebel et al (2004) http://dx.doi.org/10.1021/jp049315h" | |
| +CO3t2 28.70 67.06 13.48 14.83 15.83 16.59 17.62 18.26 19.05 0.0 0.0 0.0 "Mebel et al (2004) http://dx.doi.org/10.1021/jp049315h" | |
| +cyclopropene12diyl 188.13 59.26 11.32 13.42 15.16 16.58 18.74 20.29 22.63 0.0 0.0 0.0 "doi:10.1016/j.chemphys.2008.01.057 and doi:10.1021/jp003224c" | |
| +cyclopropynylidyne 169.80 57.47 10.43 11.93 13.18 14.18 15.61 16.59 17.99 0.0 0.0 0.0 "doi:10.1016/j.chemphys.2008.01.057 and doi:10.1021/jp003224c" | |
| +OCCO(S) 18.31 90.63 13.66 14.78 15.66 16.41 17.57 18.39 19.53 0.0 0.0 0.0 "QCI//DFT calculation by CFGoldsmith; Copied from DFT_QCI_thermo library" | |
| +OCCO 5.60 61.18 14.21 15.20 15.98 16.65 17.72 18.49 19.58 0.0 0.0 0.0 "QCI//DFT calculation by CFGoldsmith; Copied from DFT_QCI_thermo library" | |
| diff --git a/databases/RMG_database/thermo_libraries/primaryThermoLibrary/README.txt b/databases/RMG_database/thermo_libraries/primaryThermoLibrary/README.txt | |
| new file mode 100644 | |
| index 0000000..9ee1b13 | |
| --- /dev/null | |
| +++ b/databases/RMG_database/thermo_libraries/primaryThermoLibrary/README.txt | |
| @@ -0,0 +1,56 @@ | |
| +primaryThermoLibrary | |
| +==================== | |
| + | |
| +This thermochemistry library contains thermochemistry of a few small | |
| +molecules. Some of them, RMG may otherwise estimate poorly. In some instances | |
| +it would be OK estimating via group additivity, but if running with automatic | |
| +quantum calculations the calculations are likely to fail. | |
| + | |
| +It is recommended that this library is included in all calculations. (It is | |
| +advisable to use a much larger library, as many other small molecules will be | |
| +poorly estimated by RMG. This should be considered a bare minimum.) | |
| + | |
| +-------- | |
| +Sources: | |
| +-------- | |
| + | |
| +For CO3 isomers: | |
| +Data is from the paper by Mebel et al. [1]. | |
| +Geometries are from Figure 1. | |
| +Vibrational frequencies from the supplementary material. | |
| +H298 values are derived from the relative energies given in the paper. | |
| + | |
| +For C3Hn species: | |
| +Geometries from Aguilera-Iparraguirre [2] and frequencies from Nguyen [3]. | |
| +H298 values from a mixture of the two. | |
| + | |
| +For OCCO species: | |
| +QCI//DFT calculation by C.F. Goldsmith (2010): The lowest energy conformer | |
| +using CBS-QB3 method was selected, and this geometry was re-optimized using | |
| +the B3LYP functional with the larger 6-311++G(d,p) basis set. the DFT | |
| +equilibrium geometries were used for RQCISD(T)/cc-pVTZ and RQCISD(T)/cc-pVQZ | |
| +energies. To avoid spin contamination, all calculations were spin restricted. | |
| +The RQCISD(T) complete basis set limit was extrapolated from the triple and | |
| +quadruple zeta basis set calculations assuming an inverse power law. | |
| +Manuscript in preparation. | |
| + | |
| + | |
| +---------- | |
| +References | |
| +---------- | |
| + | |
| +[1] A. M. Mebel, M. Hayashi, V. V. Kislov, and S. H. Lin. Theoretical Study of | |
| +Oxygen Isotope Exchange and Quenching in the O(1D) + CO2 Reaction. The Journal | |
| +of Physical Chemistry A, 108(39):7983–7994, September 2004. | |
| +http://dx.doi.org/10.1021/jp049315h | |
| + | |
| +[2] J. Aguilera-Iparraguirre, A. Daniel Boese, W. Klopper, and B. Ruscic. | |
| +Accurate ab initio computation of thermochemical data for C3Hx | |
| +(x=0,...,4)(x=0,...,4) species. Chemical Physics, 346(1-3):56–68, May 2008. | |
| +http://dx.doi.org/10.1016/j.chemphys.2008.01.057 | |
| + | |
| +[3] T. L. Nguyen, A. M. Mebel, and R. I. Kaiser. A Theoretical Investigation | |
| +of the Triplet Carbon Atom C(3P) + Vinyl Radical C2H3(2A’) Reaction and | |
| +Thermochemistry of C3Hn (n = 14) Species. The Journal of Physical Chemistry A, | |
| +105(13):3284–3299, April 2001. | |
| +http://dx.doi.org/10.1021/jp003224c | |
| diff --git a/examples/CheckForwardAndReverseRateCoefficients/CheckForwardAndReverseRateCoefficients.bat b/examples/CheckForwardAndReverseRateCoefficients/CheckForwardAndReverseRateCoefficients.bat | |
| new file mode 100644 | |
| index 0000000..a93e934 | |
| --- /dev/null | |
| +++ b/examples/CheckForwardAndReverseRateCoefficients/CheckForwardAndReverseRateCoefficients.bat | |
| @@ -0,0 +1,28 @@ | |
| +@echo off | |
| + | |
| +REM RMG 3.2 Windows batch script for CheckForwardAndReverseRateCoefficient execution | |
| +REM Put me in the directory containing the chem.inp file and double-click to run. | |
| +REM This assumes that the input file is called chem.inp. | |
| +REM This script will check that the necessary setup has been done before running class. | |
| +REM Output from class will be logged to the file RMG.log. | |
| + | |
| +if not defined RMG ( | |
| +echo Error: RMG environment variable not defined; please set to the location of your RMG installation. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\RMG.jar" ( | |
| +echo Error: RMG.jar not found; please compile using ant. | |
| +goto end | |
| +) | |
| + | |
| +if not exist chem.inp ( | |
| +echo Error: chem.inp not found. Please create an input file before running. | |
| +goto end | |
| +) | |
| + | |
| +echo Running CheckForwardAndReverseRateCoefficients... | |
| +java -Xmx500m -classpath "%RMG%\bin\RMG.jar" CheckForwardAndReverseRateCoefficients chem.inp > RMG.log 2>&1 & | |
| +echo Job completed. | |
| + | |
| +:end | |
| +pause | |
| diff --git a/examples/PopulateReactions/PopulateReactions.bat b/examples/PopulateReactions/PopulateReactions.bat | |
| index 760edfe..34cca24 100755 | |
| --- a/examples/PopulateReactions/PopulateReactions.bat | |
| +++ b/examples/PopulateReactions/PopulateReactions.bat | |
| @@ -4,7 +4,7 @@ if not defined RMG ( | |
| echo Error: RMG variable not defined; please set to the location of your RMG installation. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\RMG.jar ( | |
| +if not exist "%RMG%\bin\RMG.jar" ( | |
| echo Error: RMG.jar not found; please compile using ant. | |
| goto end | |
| ) | |
| @@ -15,7 +15,7 @@ goto end | |
| ) | |
| echo Running PopulateReactions... | |
| -java -Xmx500m -classpath "%RMG%"\bin\RMG.jar PopulateReactions input.txt > RMG.log 2>&1 & | |
| +java -Xmx500m -classpath "%RMG%\bin\RMG.jar" PopulateReactions input.txt > RMG.log 2>&1 & | |
| echo PopulateReactions job completed. | |
| :end | |
| diff --git a/examples/PopulateReactions/input.txt b/examples/PopulateReactions/input.txt | |
| index ea397d4..dec373c 100644 | |
| --- a/examples/PopulateReactions/input.txt | |
| +++ b/examples/PopulateReactions/input.txt | |
| @@ -1,51 +1,53 @@ | |
| -// Sample input file for PopulateReactions module | |
| - | |
| -PrimaryThermoLibrary: | |
| -Name: RMG_Default | |
| -Location: primaryThermoLibrary | |
| -//Name: GRI-Mech3.0 | |
| -//Location: GRI-Mech3.0 | |
| -END | |
| - | |
| -PrimaryTransportLibrary: | |
| -Name: GRI-Mech-3 | |
| -Location: GRI-Mech3.0 | |
| -END | |
| - | |
| -TemperatureModel: Constant (K) 1200 | |
| -PressureModel: Constant (atm) 1 | |
| - | |
| -//Solvation: off | |
| - | |
| -SpeciesStatus: | |
| - | |
| -nButanol (molecule/cm3) 0.01 | |
| -1 C 0 {2,S} | |
| -2 C 0 {1,S} {3,S} | |
| -3 C 0 {2,S} {4,S} | |
| -4 C 0 {3,S} {5,S} | |
| -5 O 0 {4,S} | |
| - | |
| -CH3 (molecule/cm3) 0.01 | |
| -1 C 1 | |
| - | |
| -END | |
| - | |
| -BathGas: | |
| -N2 (molecule/cm3) 0.99 | |
| -END | |
| - | |
| -SpectroscopicDataEstimator: FrequencyGroups | |
| -PressureDependence: ReservoirState off ModifiedStrongCollision | |
| -PDepKineticsModel: Chebyshev | |
| -//DecreaseGrainSize: yes | |
| - | |
| +// Sample input file for PopulateReactions module | |
| + | |
| +Database: RMG_database | |
| + | |
| +PrimaryThermoLibrary: | |
| +Name: RMG_Default | |
| +Location: primaryThermoLibrary | |
| +//Name: GRI-Mech3.0 | |
| +//Location: GRI-Mech3.0 | |
| +END | |
| + | |
| +PrimaryTransportLibrary: | |
| +Name: GRI-Mech-3 | |
| +Location: GRI-Mech3.0 | |
| +END | |
| + | |
| +TemperatureModel: Constant (K) 1200 | |
| +PressureModel: Constant (atm) 1 | |
| + | |
| +//Solvation: off | |
| + | |
| +SpeciesStatus: | |
| + | |
| +nButanol (molecule/cm3) 0.01 | |
| +1 C 0 {2,S} | |
| +2 C 0 {1,S} {3,S} | |
| +3 C 0 {2,S} {4,S} | |
| +4 C 0 {3,S} {5,S} | |
| +5 O 0 {4,S} | |
| + | |
| +CH3 (molecule/cm3) 0.01 | |
| +1 C 1 | |
| + | |
| +END | |
| + | |
| +BathGas: | |
| +N2 (molecule/cm3) 0.99 | |
| +END | |
| + | |
| +SpectroscopicDataEstimator: FrequencyGroups | |
| +PressureDependence: ReservoirState off ModifiedStrongCollision | |
| +PDepKineticsModel: Chebyshev | |
| +//DecreaseGrainSize: yes | |
| + | |
| PrimaryKineticLibrary: | |
| -//Name: PrIMe-recommended | |
| +//Name: PrIMe-recommended | |
| //Location: GRI-Mech3.0 | |
| -END | |
| - | |
| -ReactionLibrary: | |
| -END | |
| - | |
| +END | |
| + | |
| +ReactionLibrary: | |
| +END | |
| + | |
| //Verbose: off | |
| \ No newline at end of file | |
| diff --git a/examples/RMG/1,3-hexadiene/RMG.bat b/examples/RMG/1,3-hexadiene/RMG.bat | |
| index bb76ff8..3c1adb7 100755 | |
| --- a/examples/RMG/1,3-hexadiene/RMG.bat | |
| +++ b/examples/RMG/1,3-hexadiene/RMG.bat | |
| @@ -10,31 +10,31 @@ if not defined RMG ( | |
| echo Error: RMG environment variable not defined; please set to the location of your RMG installation. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\RMG.jar ( | |
| +if not exist "%RMG%\bin\RMG.jar" ( | |
| echo Error: RMG.jar not found; please compile using ant. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\blas.dll ( | |
| +if not exist "%RMG%\bin\blas.dll" ( | |
| echo Error: blas.dll not found. A 32-bit version can be downloaded from http://github.com/GreenGroup/RMG-Java/downloads. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\lapack.dll ( | |
| +if not exist "%RMG%\bin\lapack.dll" ( | |
| echo Error: lapack.dll not found. A 32-bit version can be downloaded from http://github.com/GreenGroup/RMG-Java/downloads. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\dasslAUTO.exe ( | |
| +if not exist "%RMG%\bin\dasslAUTO.exe" ( | |
| echo Error: dasslAUTO.exe not found. Please run make.bat to compile DASSL. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\GATPFit.exe ( | |
| +if not exist "%RMG%\bin\GATPFit.exe" ( | |
| echo Error: GATPFit.exe not found. Please run make.bat to compile GATPFit. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\fame.exe ( | |
| +if not exist "%RMG%\bin\fame.exe" ( | |
| echo Error: fame.exe not found. Please run make.bat to compile fame. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\frankie.exe ( | |
| +if not exist "%RMG%\bin\frankie.exe" ( | |
| echo Error: frankie.exe not found. Please run make.bat to compile frankie. | |
| goto end | |
| ) | |
| @@ -45,7 +45,7 @@ goto end | |
| ) | |
| echo Running RMG... | |
| -java -Xmx500m -classpath "%RMG%"\bin\RMG.jar RMG condition.txt > RMG.log 2>&1 & | |
| +java -Xmx500m -classpath "%RMG%\bin\RMG.jar" RMG condition.txt > RMG.log 2>&1 & | |
| echo RMG job completed. | |
| :end | |
| diff --git a/examples/RMG/1,3-hexadiene/condition-wAllOptions.txt b/examples/RMG/1,3-hexadiene/condition-wAllOptions.txt | |
| index 66f8617..ed5e5d2 100644 | |
| --- a/examples/RMG/1,3-hexadiene/condition-wAllOptions.txt | |
| +++ b/examples/RMG/1,3-hexadiene/condition-wAllOptions.txt | |
| @@ -20,7 +20,7 @@ Database: RMG_database | |
| PrimaryThermoLibrary: | |
| Name: GRIMech3.0 | |
| Location: GRI-Mech3.0 | |
| -Name: RMG old | |
| +Name: RMG-minimal | |
| Location: primaryThermoLibrary | |
| END | |
| @@ -47,6 +47,7 @@ ReadRestart: no yes | |
| WriteRestart: no yes | |
| // Only temperature/pressure model currently supported is "Constant" | |
| +// Several temperatures and pressures may be specified. | |
| // Units for temperature: K, C, F | |
| // Units for pressure: atm, bar, Pa, torr | |
| TemperatureModel: Constant (K) 1350 | |
| @@ -74,13 +75,14 @@ InitialStatus: | |
| // A species' name cannot begin with a number | |
| // Concentration units available: mol/cm3, mol/m3, mol/l | |
| +// Several concentrations may be specified, but all species must have the same number. | |
| // The following options may follow a species' concentration units: | |
| // Unreactive: This species will not react against RMG's rxn families. | |
| // Furthermore, a file named IncludeSpecies.txt must be supplied by the user | |
| // ConstantConcentration: This species concentration will remain fixed throughout the simulation | |
| // *** This option is still under construction *** | |
| -HXD13 (mol/cm3) 6.829e-4 | |
| +HXD13 (mol/cm3) 6.829e-4 | |
| 1 C 0 {2,D} | |
| 2 C 0 {1,D} {3,S} | |
| 3 C 0 {2,S} {4,D} | |
| @@ -88,10 +90,10 @@ HXD13 (mol/cm3) 6.829e-4 | |
| 5 C 0 {4,S} {6,S} | |
| 6 C 0 {5,S} | |
| -CH4 (mol/cm3) 0.104 | |
| +CH4 (mol/cm3) 0.104 | |
| 1 C 0 | |
| -H2 (mol/cm3) 1.56e-2 | |
| +H2 (mol/cm3) 1.56e-2 | |
| 1 H 0 {2,S} | |
| 2 H 0 {1,S} | |
| @@ -101,10 +103,11 @@ END | |
| // However, RMG only has the Lennard-Jones parameters for N2, Ar, and He | |
| // hard-coded into BathGas.java. Furthermore, RMG only reports the | |
| // thermo for N2, Ar, and Ne in the chem.inp file | |
| -// The concentration units available are the same as before | |
| +// The concentration units available are the same as before. | |
| +// The number of concentrations must match the reactant species in the previous section. | |
| InertGas: | |
| -N2 (mol/cm3) 0.8797 | |
| -Ar (mol/cm3) 0.0e-6 | |
| +N2 (mol/cm3) 0.8797 | |
| +Ar (mol/cm3) 0.0e-6 | |
| END | |
| SpectroscopicDataEstimator: off/frequencygroups | |
| diff --git a/examples/RMG/1,3-hexadiene/condition.txt b/examples/RMG/1,3-hexadiene/condition.txt | |
| index b1a1704..754e3f5 100644 | |
| --- a/examples/RMG/1,3-hexadiene/condition.txt | |
| +++ b/examples/RMG/1,3-hexadiene/condition.txt | |
| @@ -3,7 +3,7 @@ | |
| //a oxidation mechanism. Also the sensitivity analysis section is missing | |
| //because we are using the dassl solver. | |
| -//This example should take roughly 15-20 minutes to run to completion. | |
| +//This example should take roughly 2-3 minutes to run to completion. | |
| Database: RMG_database | |
| @@ -18,7 +18,7 @@ Database: RMG_database | |
| PrimaryThermoLibrary: | |
| Name: GRIMech3.0 | |
| Location: GRI-Mech3.0 | |
| -Name: RMG-old | |
| +Name: RMG-minimal | |
| Location: primaryThermoLibrary | |
| END | |
| diff --git a/examples/RMG/butane_pruning/RMG.bat b/examples/RMG/butane_pruning/RMG.bat | |
| new file mode 100644 | |
| index 0000000..3c1adb7 | |
| --- /dev/null | |
| +++ b/examples/RMG/butane_pruning/RMG.bat | |
| @@ -0,0 +1,52 @@ | |
| +@echo off | |
| + | |
| +REM RMG 3.2 Windows batch script for RMG execution | |
| +REM Put me in the directory containing the condition file and double-click to run RMG. | |
| +REM This assumes that the condition file is called condition.txt. | |
| +REM This script will check that the necessary setup has been done before running RMG. | |
| +REM Output from RMG will be logged to the file RMG.log. | |
| + | |
| +if not defined RMG ( | |
| +echo Error: RMG environment variable not defined; please set to the location of your RMG installation. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\RMG.jar" ( | |
| +echo Error: RMG.jar not found; please compile using ant. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\blas.dll" ( | |
| +echo Error: blas.dll not found. A 32-bit version can be downloaded from http://github.com/GreenGroup/RMG-Java/downloads. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\lapack.dll" ( | |
| +echo Error: lapack.dll not found. A 32-bit version can be downloaded from http://github.com/GreenGroup/RMG-Java/downloads. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\dasslAUTO.exe" ( | |
| +echo Error: dasslAUTO.exe not found. Please run make.bat to compile DASSL. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\GATPFit.exe" ( | |
| +echo Error: GATPFit.exe not found. Please run make.bat to compile GATPFit. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\fame.exe" ( | |
| +echo Error: fame.exe not found. Please run make.bat to compile fame. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\frankie.exe" ( | |
| +echo Error: frankie.exe not found. Please run make.bat to compile frankie. | |
| +goto end | |
| +) | |
| + | |
| +if not exist condition.txt ( | |
| +echo Error: condition.txt not found. Please create an RMG condition file before running. | |
| +goto end | |
| +) | |
| + | |
| +echo Running RMG... | |
| +java -Xmx500m -classpath "%RMG%\bin\RMG.jar" RMG condition.txt > RMG.log 2>&1 & | |
| +echo RMG job completed. | |
| + | |
| +:end | |
| +pause | |
| diff --git a/examples/RMG/butane_pruning/condition.txt b/examples/RMG/butane_pruning/condition.txt | |
| index f2e9563..cd99cbd 100644 | |
| --- a/examples/RMG/butane_pruning/condition.txt | |
| +++ b/examples/RMG/butane_pruning/condition.txt | |
| @@ -17,7 +17,7 @@ Database: RMG_database | |
| PrimaryThermoLibrary: | |
| Name: GRIMech3.0 | |
| Location: GRI-Mech3.0 | |
| -Name: RMG-old | |
| +Name: RMG-minimal | |
| Location: primaryThermoLibrary | |
| END | |
| @@ -39,21 +39,21 @@ PressureModel: Constant (atm) 20 30 40 | |
| InitialStatus: | |
| -(1) C4H10 1 (mol/cm3) | |
| +C4H10 (mol/cm3) 1 2 | |
| 1 C 0 {2,S} | |
| 2 C 0 {1,S} {3,S} | |
| 3 C 0 {2,S} {4,S} | |
| 4 C 0 {3,S} | |
| -(2) O2 6.5 (mol/cm3) | |
| +O2 (mol/cm3) 6.5 5.5 | |
| 1 O 1 {2,S} | |
| 2 O 1 {1,S} | |
| END | |
| InertGas: | |
| -N2 24.399 (mol/cm3) | |
| -Ar 0 (mol/cm3) | |
| +N2 (mol/cm3) 24.399 24.399 | |
| +Ar (mol/cm3) 0 0 | |
| END | |
| SpectroscopicDataEstimator: off | |
| diff --git a/examples/RMG/cyclopropane_QM/RMG.bat b/examples/RMG/cyclopropane_QM/RMG.bat | |
| index bb76ff8..3c1adb7 100755 | |
| --- a/examples/RMG/cyclopropane_QM/RMG.bat | |
| +++ b/examples/RMG/cyclopropane_QM/RMG.bat | |
| @@ -10,31 +10,31 @@ if not defined RMG ( | |
| echo Error: RMG environment variable not defined; please set to the location of your RMG installation. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\RMG.jar ( | |
| +if not exist "%RMG%\bin\RMG.jar" ( | |
| echo Error: RMG.jar not found; please compile using ant. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\blas.dll ( | |
| +if not exist "%RMG%\bin\blas.dll" ( | |
| echo Error: blas.dll not found. A 32-bit version can be downloaded from http://github.com/GreenGroup/RMG-Java/downloads. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\lapack.dll ( | |
| +if not exist "%RMG%\bin\lapack.dll" ( | |
| echo Error: lapack.dll not found. A 32-bit version can be downloaded from http://github.com/GreenGroup/RMG-Java/downloads. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\dasslAUTO.exe ( | |
| +if not exist "%RMG%\bin\dasslAUTO.exe" ( | |
| echo Error: dasslAUTO.exe not found. Please run make.bat to compile DASSL. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\GATPFit.exe ( | |
| +if not exist "%RMG%\bin\GATPFit.exe" ( | |
| echo Error: GATPFit.exe not found. Please run make.bat to compile GATPFit. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\fame.exe ( | |
| +if not exist "%RMG%\bin\fame.exe" ( | |
| echo Error: fame.exe not found. Please run make.bat to compile fame. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\frankie.exe ( | |
| +if not exist "%RMG%\bin\frankie.exe" ( | |
| echo Error: frankie.exe not found. Please run make.bat to compile frankie. | |
| goto end | |
| ) | |
| @@ -45,7 +45,7 @@ goto end | |
| ) | |
| echo Running RMG... | |
| -java -Xmx500m -classpath "%RMG%"\bin\RMG.jar RMG condition.txt > RMG.log 2>&1 & | |
| +java -Xmx500m -classpath "%RMG%\bin\RMG.jar" RMG condition.txt > RMG.log 2>&1 & | |
| echo RMG job completed. | |
| :end | |
| diff --git a/examples/RMG/cyclopropane_QM/condition.txt b/examples/RMG/cyclopropane_QM/condition.txt | |
| index 77e34f3..c378ff1 100644 | |
| --- a/examples/RMG/cyclopropane_QM/condition.txt | |
| +++ b/examples/RMG/cyclopropane_QM/condition.txt | |
| @@ -21,7 +21,7 @@ Database: RMG_database | |
| PrimaryThermoLibrary: | |
| Name: GRIMech3.0 | |
| Location: GRI-Mech3.0 | |
| -Name: RMG-old | |
| +Name: RMG-minimal | |
| Location: primaryThermoLibrary | |
| END | |
| @@ -42,7 +42,7 @@ MaxRadNumForQM: 0 | |
| InitialStatus: | |
| -(1) Cyclopropane 6.829e-4 (mol/cm3) | |
| +Cyclopropane (mol/cm3) 6.829e-4 | |
| 1 C 0 {2,S} {3,S} | |
| 2 C 0 {1,S} {3,S} | |
| 3 C 0 {1,S} {2,S} | |
| @@ -50,13 +50,12 @@ InitialStatus: | |
| END | |
| InertGas: | |
| -N2 0.8797 (mol/cm3) | |
| -Ar 0.0e-6 (mol/cm3) | |
| +N2 (mol/cm3) 0.8797 | |
| +Ar (mol/cm3) 0.0e-6 | |
| END | |
| -SpectroscopicDataEstimator: off FrequencyGroups | |
| -PressureDependence: off ModifiedStrongCollision | |
| -//PDepKineticsModel: Chebyshev | |
| +SpectroscopicDataEstimator: off | |
| +PressureDependence: off | |
| FinishController: | |
| (1) Goal Conversion: Cyclopropane 0.9 | |
| @@ -68,22 +67,12 @@ Atol: 1e-18 | |
| Rtol: 1e-8 | |
| PrimaryKineticLibrary: | |
| -//Name: RMG-example | |
| -//Location: Example | |
| END | |
| ReactionLibrary: | |
| -//Name: RMG-example | |
| -//Location: RMG_database/primaryReactionLibrary/Example | |
| END | |
| SeedMechanism: | |
| -//Name: Leeds | |
| -//Location: RMG_database/SeedMechanisms/combustion_core/version5 | |
| -//GenerateReactions: yes | |
| -//Name: GRIMech3.0 | |
| -//Location: RMG_database/SeedMechanisms/GRI-Mech3.0 | |
| -//GenerateReactions: yes | |
| END | |
| ChemkinUnits: | |
| diff --git a/examples/RMG/minimal/RMG.bat b/examples/RMG/minimal/RMG.bat | |
| new file mode 100644 | |
| index 0000000..3c1adb7 | |
| --- /dev/null | |
| +++ b/examples/RMG/minimal/RMG.bat | |
| @@ -0,0 +1,52 @@ | |
| +@echo off | |
| + | |
| +REM RMG 3.2 Windows batch script for RMG execution | |
| +REM Put me in the directory containing the condition file and double-click to run RMG. | |
| +REM This assumes that the condition file is called condition.txt. | |
| +REM This script will check that the necessary setup has been done before running RMG. | |
| +REM Output from RMG will be logged to the file RMG.log. | |
| + | |
| +if not defined RMG ( | |
| +echo Error: RMG environment variable not defined; please set to the location of your RMG installation. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\RMG.jar" ( | |
| +echo Error: RMG.jar not found; please compile using ant. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\blas.dll" ( | |
| +echo Error: blas.dll not found. A 32-bit version can be downloaded from http://github.com/GreenGroup/RMG-Java/downloads. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\lapack.dll" ( | |
| +echo Error: lapack.dll not found. A 32-bit version can be downloaded from http://github.com/GreenGroup/RMG-Java/downloads. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\dasslAUTO.exe" ( | |
| +echo Error: dasslAUTO.exe not found. Please run make.bat to compile DASSL. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\GATPFit.exe" ( | |
| +echo Error: GATPFit.exe not found. Please run make.bat to compile GATPFit. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\fame.exe" ( | |
| +echo Error: fame.exe not found. Please run make.bat to compile fame. | |
| +goto end | |
| +) | |
| +if not exist "%RMG%\bin\frankie.exe" ( | |
| +echo Error: frankie.exe not found. Please run make.bat to compile frankie. | |
| +goto end | |
| +) | |
| + | |
| +if not exist condition.txt ( | |
| +echo Error: condition.txt not found. Please create an RMG condition file before running. | |
| +goto end | |
| +) | |
| + | |
| +echo Running RMG... | |
| +java -Xmx500m -classpath "%RMG%\bin\RMG.jar" RMG condition.txt > RMG.log 2>&1 & | |
| +echo RMG job completed. | |
| + | |
| +:end | |
| +pause | |
| diff --git a/examples/RMG/minimal/condition.txt b/examples/RMG/minimal/condition.txt | |
| index 2c07e4b..eca82df 100644 | |
| --- a/examples/RMG/minimal/condition.txt | |
| +++ b/examples/RMG/minimal/condition.txt | |
| @@ -20,15 +20,15 @@ PressureModel: Constant (atm) 1 | |
| InitialStatus: | |
| -(1) C2H6 1.0 (mol/cm3) | |
| +C2H6 (mol/cm3) 1.0 | |
| 1 C 0 {2,S} | |
| 2 C 0 {1,S} | |
| END | |
| InertGas: | |
| -N2 0.0 (mol/cm3) | |
| -Ar 0.0 (mol/cm3) | |
| +N2 (mol/cm3) 0.0 | |
| +Ar (mol/cm3) 0.0 | |
| END | |
| SpectroscopicDataEstimator: off | |
| diff --git a/examples/ThermoDataEstimator/ThermoDataEstimator.bat b/examples/ThermoDataEstimator/ThermoDataEstimator.bat | |
| index 36e6d84..5da3d98 100755 | |
| --- a/examples/ThermoDataEstimator/ThermoDataEstimator.bat | |
| +++ b/examples/ThermoDataEstimator/ThermoDataEstimator.bat | |
| @@ -4,7 +4,7 @@ if not defined RMG ( | |
| echo Error: RMG variable not defined; please set to the location of your RMG installation. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\RMG.jar ( | |
| +if not exist "%RMG%\bin\RMG.jar" ( | |
| echo Error: RMG.jar not found; please compile using ant. | |
| goto end | |
| ) | |
| @@ -15,7 +15,7 @@ goto end | |
| ) | |
| echo Running ThermoDataEstimator... | |
| -java -Xmx500m -classpath "%RMG%"\bin\RMG.jar ThermoDataEstimator input.txt > RMG.log 2>&1 & | |
| +java -Xmx500m -classpath "%RMG%\bin\RMG.jar" ThermoDataEstimator input.txt > RMG.log 2>&1 & | |
| echo ThermoDataEstimator job completed. | |
| :end | |
| diff --git a/examples/ThermoDataEstimator/ThermoDataEstimator.sh b/examples/ThermoDataEstimator/ThermoDataEstimator.sh | |
| new file mode 100755 | |
| index 0000000..08e9f87 | |
| --- /dev/null | |
| +++ b/examples/ThermoDataEstimator/ThermoDataEstimator.sh | |
| @@ -0,0 +1,23 @@ | |
| +#! /bin/bash | |
| + | |
| +if ($RMG) | |
| + then | |
| + echo "Environment variable \$RMG is not defined. Please set to the location of your RMG installation." | |
| + exit | |
| +fi | |
| + | |
| +if [ ! -e "$RMG/bin/RMG.jar" ] | |
| +then | |
| + echo "$RMG/bin/RMG.jar not found; please compile using ant."; | |
| + exit | |
| +fi | |
| + | |
| +if [ ! -e "input.txt" ] | |
| +then | |
| + echo "Error: input.txt not found. Please create an ThermoDataEstimator input file before running."; | |
| + exit | |
| +fi | |
| + | |
| +echo "Running TransportDataEstimator..." | |
| +java -Xmx500m -classpath $RMG/bin/RMG.jar ThermoDataEstimator input.txt 2>&1 | tee RMG.log | |
| +echo "TransportDataEstimator job completed." | |
| diff --git a/examples/ThermoDataEstimator/input.txt b/examples/ThermoDataEstimator/input.txt | |
| index 98773bd..37b38cf 100644 | |
| --- a/examples/ThermoDataEstimator/input.txt | |
| +++ b/examples/ThermoDataEstimator/input.txt | |
| @@ -1,68 +1,70 @@ | |
| -PrimaryThermoLibrary: | |
| -//Name: | |
| -//Location: | |
| -END | |
| - | |
| -1 C 0 {2,S} | |
| -2 C 0 {1,S} {3,S} | |
| -3 C 0 {2,S} {4,S} | |
| -4 C 0 {3,S} {5,S} | |
| -5 O 0 {4,S} | |
| - | |
| -1 C 1 {2,S} | |
| -2 C 0 {1,S} {3,S} | |
| -3 C 0 {2,S} {4,S} | |
| -4 C 0 {3,S} {5,S} | |
| -5 O 0 {4,S} | |
| - | |
| -1 C 0 {2,S} | |
| -2 C 1 {1,S} {3,S} | |
| -3 C 0 {2,S} {4,S} | |
| -4 C 0 {3,S} {5,S} | |
| -5 O 0 {4,S} | |
| - | |
| -1 C 0 {2,S} | |
| -2 C 0 {1,S} {3,S} | |
| -3 C 1 {2,S} {4,S} | |
| -4 C 0 {3,S} {5,S} | |
| -5 O 0 {4,S} | |
| - | |
| -1 C 0 {2,S} | |
| -2 C 0 {1,S} {3,S} | |
| -3 C 0 {2,S} {4,S} | |
| -4 C 1 {3,S} {5,S} | |
| -5 O 0 {4,S} | |
| - | |
| -1 C 0 {2,S} | |
| -2 C 0 {1,S} {3,S} | |
| -3 C 0 {2,S} {4,S} | |
| -4 C 0 {3,S} {5,S} | |
| -5 O 1 {4,S} | |
| - | |
| -1 C 1 | |
| - | |
| -1 C 1 {2,S} | |
| -2 C 0 {1,S} {3,S} | |
| -3 C 0 {2,S} {4,S} | |
| -4 O 0 {3,S} | |
| - | |
| -1 C 1 {2,S} | |
| -2 C 0 {1,S} | |
| - | |
| -1 C 1 {2,S} | |
| -2 C 0 {1,S} {3,S} | |
| -3 O 0 {2,S} | |
| - | |
| -1 C 1 {2,S} | |
| -2 C 0 {1,S} {3,S} | |
| -3 C 0 {2,S} | |
| - | |
| -1 C 1 {2,S} | |
| -2 O 0 {1,S} | |
| - | |
| -1 C 1 {2,S} | |
| -2 C 0 {1,S} {3,S} | |
| -3 C 0 {2,S} {4,S} | |
| -4 C 0 {3,S} | |
| +Database: RMG_database | |
| +PrimaryThermoLibrary: | |
| +Name: RMG-minimal | |
| +Location: primaryThermoLibrary | |
| +END | |
| + | |
| +1 C 0 {2,S} | |
| +2 C 0 {1,S} {3,S} | |
| +3 C 0 {2,S} {4,S} | |
| +4 C 0 {3,S} {5,S} | |
| +5 O 0 {4,S} | |
| + | |
| +1 C 1 {2,S} | |
| +2 C 0 {1,S} {3,S} | |
| +3 C 0 {2,S} {4,S} | |
| +4 C 0 {3,S} {5,S} | |
| +5 O 0 {4,S} | |
| + | |
| +1 C 0 {2,S} | |
| +2 C 1 {1,S} {3,S} | |
| +3 C 0 {2,S} {4,S} | |
| +4 C 0 {3,S} {5,S} | |
| +5 O 0 {4,S} | |
| + | |
| +1 C 0 {2,S} | |
| +2 C 0 {1,S} {3,S} | |
| +3 C 1 {2,S} {4,S} | |
| +4 C 0 {3,S} {5,S} | |
| +5 O 0 {4,S} | |
| + | |
| +1 C 0 {2,S} | |
| +2 C 0 {1,S} {3,S} | |
| +3 C 0 {2,S} {4,S} | |
| +4 C 1 {3,S} {5,S} | |
| +5 O 0 {4,S} | |
| + | |
| +1 C 0 {2,S} | |
| +2 C 0 {1,S} {3,S} | |
| +3 C 0 {2,S} {4,S} | |
| +4 C 0 {3,S} {5,S} | |
| +5 O 1 {4,S} | |
| + | |
| +1 C 1 | |
| + | |
| +1 C 1 {2,S} | |
| +2 C 0 {1,S} {3,S} | |
| +3 C 0 {2,S} {4,S} | |
| +4 O 0 {3,S} | |
| + | |
| +1 C 1 {2,S} | |
| +2 C 0 {1,S} | |
| + | |
| +1 C 1 {2,S} | |
| +2 C 0 {1,S} {3,S} | |
| +3 O 0 {2,S} | |
| + | |
| +1 C 1 {2,S} | |
| +2 C 0 {1,S} {3,S} | |
| +3 C 0 {2,S} | |
| + | |
| +1 C 1 {2,S} | |
| +2 O 0 {1,S} | |
| + | |
| +1 C 1 {2,S} | |
| +2 C 0 {1,S} {3,S} | |
| +3 C 0 {2,S} {4,S} | |
| +4 C 0 {3,S} | |
| + | |
| 1 O 1 | |
| \ No newline at end of file | |
| diff --git a/examples/TransportDataEstimator/TransportDataEstimator.bat b/examples/TransportDataEstimator/TransportDataEstimator.bat | |
| index df8df60..53847d7 100644 | |
| --- a/examples/TransportDataEstimator/TransportDataEstimator.bat | |
| +++ b/examples/TransportDataEstimator/TransportDataEstimator.bat | |
| @@ -4,18 +4,18 @@ if not defined RMG ( | |
| echo Error: RMG variable not defined; please set to the location of your RMG installation. | |
| goto end | |
| ) | |
| -if not exist "%RMG%"\bin\RMG.jar ( | |
| +if not exist "%RMG%\bin\RMG.jar" ( | |
| echo Error: RMG.jar not found; please compile using ant. | |
| goto end | |
| ) | |
| if not exist input.txt ( | |
| -echo Error: input.txt not found. Please create an ThermoDataEstimator input file before running. | |
| +echo Error: input.txt not found. Please create an TransportDataEstimator input file before running. | |
| goto end | |
| ) | |
| echo Running TransportDataEstimator... | |
| -java -Xmx500m -classpath "%RMG%"\bin\RMG.jar TransportDataEstimator input.txt > RMG.log 2>&1 & | |
| +java -Xmx500m -classpath "%RMG%\bin\RMG.jar" TransportDataEstimator input.txt > RMG.log 2>&1 & | |
| echo TransportDataEstimator job completed. | |
| :end | |
| diff --git a/examples/TransportDataEstimator/TransportDataEstimator.sh b/examples/TransportDataEstimator/TransportDataEstimator.sh | |
| new file mode 100755 | |
| index 0000000..01b9a27 | |
| --- /dev/null | |
| +++ b/examples/TransportDataEstimator/TransportDataEstimator.sh | |
| @@ -0,0 +1,23 @@ | |
| +#! /bin/bash | |
| + | |
| +if ($RMG) | |
| + then | |
| + echo "Environment variable \$RMG is not defined. Please set to the location of your RMG installation." | |
| + exit | |
| +fi | |
| + | |
| +if [ ! -e "$RMG/bin/RMG.jar" ] | |
| +then | |
| + echo "$RMG/bin/RMG.jar not found; please compile using ant."; | |
| + exit | |
| +fi | |
| + | |
| +if [ ! -e "input.txt" ] | |
| +then | |
| + echo "Error: input.txt not found. Please create an TransportDataEstimator input file before running."; | |
| + exit | |
| +fi | |
| + | |
| +echo "Running TransportDataEstimator..." | |
| +java -Xmx500m -classpath $RMG/bin/RMG.jar TransportDataEstimator input.txt 2>&1 | tee RMG.log | |
| +echo "TransportDataEstimator job completed." | |
| diff --git a/examples/TransportDataEstimator/input.txt b/examples/TransportDataEstimator/input.txt | |
| index ed7f346..092305e 100644 | |
| --- a/examples/TransportDataEstimator/input.txt | |
| +++ b/examples/TransportDataEstimator/input.txt | |
| @@ -1,6 +1,8 @@ | |
| +Database: RMG_database | |
| + | |
| PrimaryTransportLibrary: | |
| -//Name: GRI-Mech-3.0 | |
| -//Location: GRI-Mech3.0 | |
| +Name: RMG-minimal | |
| +Location: primaryTransportLibrary | |
| END | |
| Allene | |
| diff --git a/source/GATPFit/Makefile b/source/GATPFit/Makefile | |
| index 11201e9..35772b0 100644 | |
| --- a/source/GATPFit/Makefile | |
| +++ b/source/GATPFit/Makefile | |
| @@ -13,14 +13,40 @@ BUILDDIR=../../build/GATPFit | |
| # The directory in which to place compiled executables and JAR files | |
| BINDIR=../../bin | |
| -# The Fortran 90 compiler to use and flags to use when compiling Fortran 90 | |
| -# code | |
| -F90=g95 | |
| -F90FLAGS=-fmod=$(BUILDDIR) -ftrace=full | |
| +# The Fortran 90 compiler to use and flags to use when compiling Fortran code | |
| +# Call with 'make F90=g95' if you want to use g95 | |
| +# or 'make F90=gfortran' for GNU Fortran (recommended) | |
| +# Here we set the default | |
| +#F90=g95 | |
| +F90=gfortran | |
| + | |
| +ifeq ($(F90),g95) | |
| +F90FLAGS = -fbounds-check -ftrace=full -fmod=$(BUILDDIR) -Wall -O3 | |
| +F90FLAGS_NDEBUG = -fmod=$(BUILDDIR) -ftrace=full # used for dassl and daspk | |
| +endif ###### END OF g95 SETTINGS | |
| + | |
| +ifeq ($(F90),gfortran) | |
| +# --fpe-trap=invalid,zero,underflow,overflow | |
| +# The above flag causes problems at least with fame. Maybe a bug in gfortran? (Maybe a bug in fame.) | |
| +F90FLAGS = -ftrapv -fbounds-check -frange-check \ | |
| + -ggdb -J""$(BUILDDIR)"" -O3 -Wall -Wno-unused | |
| +# if gfortran>4.3 then add -fbacktrace (it's not supported in earlier versions) | |
| +ifeq ($(shell gfortran --version 2>/dev/zero|grep -iqs '^GNU Fortran.* [4-9]\.[3-9]\.[0-9]' && echo "ok"), ok) | |
| +F90FLAGS += -fbacktrace | |
| +endif | |
| +F90FLAGS_NDEBUG = $(F90FLAGS) # used for dassl and daspk | |
| + | |
| +# call as `make MACOS=true F90=gfortran` if you want MacOS X 10.6+ 64-bit intel core2 features | |
| +ifdef MACOS | |
| +F90FLAGS += -arch x86_64 -march=core2 | |
| +F90_EXTRA_LDFLAGS += -framework vecLIB | |
| +endif | |
| + | |
| +endif ###### END OF gfortran SETTINGS | |
| LDFLAGS= $(F90_EXTRA_LDFLAGS) -lblas -llapack | |
| -OBJ0=lsfp_chem1.o lsfp.f lsfp_nasa.f lsfp_nist1.f lsfp_wilh1.f | |
| +OBJ0=lsfp_chem1.o lsfp.o lsfp_nasa.o lsfp_nist1.o lsfp_wilh1.o | |
| OBJ=$(patsubst %.o,$(BUILDDIR)/%.o,$(OBJ0)) | |
| diff --git a/source/GATPFit/lsfp.f b/source/GATPFit/lsfp.f | |
| index 59e6191..cb0ec1e 100644 | |
| --- a/source/GATPFit/lsfp.f | |
| +++ b/source/GATPFit/lsfp.f | |
| @@ -25,37 +25,37 @@ C: M_in: the number of input thermo data, use 'DATAGROUP' to read the input data | |
| C*********************************************************************************** | |
| PROGRAM LSAP | |
| C | |
| - implicit none | |
| + implicit none | |
| C | |
| - INTEGER LIN,LOUT,I,J,J_elem,IJ | |
| + INTEGER LIN,LOUT,I,J,J_elem,IJ | |
| C max atoms number allowed in a species is 999 | |
| C max number of different atoms is 5 | |
| - integer indc_elno(5,3) | |
| - PARAMETER (LIN=5,LOUT=6) ! 5 is STDIN and 6 is STDOUT | |
| + integer indc_elno(5,3) | |
| + PARAMETER (LIN=5,LOUT=6) ! 5 is STDIN and 6 is STDOUT | |
| C For input file | |
| - CHARACTER(LEN=4) MARK, DATATYPE | |
| - CHARACTER(LEN=48) TEXT, SNAM ! beware truncation! | |
| - CHARACTER(LEN=9) STRUC_MOL | |
| - CHARACTER(LEN=3) ELNO(5) | |
| - CHARACTER(LEN=2) ENAM(5) | |
| - DOUBLE PRECISION ROL,H_298,DLTH,S_298,MW,T_int,TINT | |
| - DOUBLE PRECISION T_min,T_max,T_int1,TINT1,ATOMS,ROTORS | |
| + CHARACTER(LEN=4) MARK, DATATYPE | |
| + CHARACTER(LEN=48) TEXT, SNAM ! beware truncation! | |
| + CHARACTER(LEN=9) STRUC_MOL | |
| + CHARACTER(LEN=3) ELNO(5) | |
| + CHARACTER(LEN=2) ENAM(5) | |
| + DOUBLE PRECISION ROL,H_298,DLTH,S_298,MW,T_int,TINT | |
| + DOUBLE PRECISION T_min,T_max,T_int1,TINT1,ATOMS,ROTORS | |
| C | |
| C: 'M' is the size of sample dataset | |
| - INTEGER M_in | |
| -! PARAMETER (M_in=59) | |
| - PARAMETER (M_in=7) | |
| - DOUBLE PRECISION TEMP,CPT,CH,CS,TEMF,CPF,CHF,CSF | |
| - DIMENSION TEMP(M_in),CPT(M_in),CH(M_in),CS(M_in) | |
| - DIMENSION TEMF(101),CPF(101),CHF(101),CSF(101) | |
| + INTEGER M_in | |
| +! PARAMETER (M_in=59) | |
| + PARAMETER (M_in=7) | |
| + DOUBLE PRECISION TEMP,CPT,CH,CS,TEMF,CPF,CHF,CSF | |
| + DIMENSION TEMP(M_in),CPT(M_in),CH(M_in),CS(M_in) | |
| + DIMENSION TEMF(101),CPF(101),CHF(101),CSF(101) | |
| C | |
| C: THERMs contain the coefficients in different temperature ranges | |
| DOUBLE PRECISION THERM1,THERM2,THERM3 | |
| - DIMENSION THERM1(20),THERM2(20),THERM3(20) | |
| + DIMENSION THERM1(20),THERM2(20),THERM3(20) | |
| C | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| - COMMON /INDICTOR/INDC_ELNO | |
| - DATA ROL/1.9872D0/ | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| + COMMON /INDICTOR/INDC_ELNO | |
| + DATA ROL/1.9872D0/ | |
| C | |
| C: For the format of input file, please ref. a sample file. | |
| C This now commented out because LIN=5 is standard input | |
| @@ -65,1064 +65,1061 @@ C 1 FILE='INPUT.txt') | |
| C OPEN (LOUT, FORM='FORMATTED', STATUS='UNKNOWN', | |
| C 1 FILE='OUTPUT.txt') | |
| C | |
| - MARK='' | |
| - DATATYPE='' | |
| - TEXT='' | |
| - STRUC_MOL='' | |
| - DO I=1,5 | |
| - ENAM(I)='' | |
| - ELNO(I)='' | |
| - ENDDO | |
| + MARK='' | |
| + DATATYPE='' | |
| + TEXT='' | |
| + STRUC_MOL='' | |
| + DO I=1,5 | |
| + ENAM(I)='' | |
| + ELNO(I)='' | |
| + ENDDO | |
| C | |
| - IJ=0 | |
| + IJ=0 | |
| J_elem=0 | |
| - do i=1,5 | |
| - do j=1,3 | |
| - indc_elno(i,j)=0 | |
| - enddo | |
| - enddo | |
| + do i=1,5 | |
| + do j=1,3 | |
| + indc_elno(i,j)=0 | |
| + enddo | |
| + enddo | |
| c | |
| - DO I=1,8 | |
| - IJ=IJ+1 | |
| - READ (LIN, 100) MARK, TEXT | |
| - IF (MARK .EQ. 'SPEC') THEN | |
| -! WRITE(*,*) MARK | |
| -! WRITE(*,*) TEXT | |
| - SNAM=TEXT(1:16) | |
| -! WRITE(*,103) MARK,SNAM | |
| - ELSE IF (MARK .EQ. 'ELEM') THEN | |
| - J_elem=J_elem+1 | |
| -! WRITE(*,*) TEXT | |
| - ENAM(J_elem)=TEXT(1:(INDEX(TEXT,' ')-1)) | |
| - do J=1,3 | |
| - if (TEXT(INDEX(TEXT,' ')+J:INDEX(TEXT,' ')+J) .EQ. ' ') then | |
| - indc_elno(j_elem,J)=1 | |
| - endif | |
| - enddo | |
| + DO I=1,8 | |
| + IJ=IJ+1 | |
| + READ (LIN, 100) MARK, TEXT | |
| + IF (MARK .EQ. 'SPEC') THEN | |
| +! WRITE(*,*) MARK | |
| +! WRITE(*,*) TEXT | |
| + SNAM=TEXT(1:16) | |
| +! WRITE(*,103) MARK,SNAM | |
| + ELSE IF (MARK .EQ. 'ELEM') THEN | |
| + J_elem=J_elem+1 | |
| +! WRITE(*,*) TEXT | |
| + ENAM(J_elem)=TEXT(1:(INDEX(TEXT,' ')-1)) | |
| + do J=1,3 | |
| + if (TEXT(INDEX(TEXT,' ')+J:INDEX(TEXT,' ')+J) .EQ. ' ') then | |
| + indc_elno(j_elem,J)=1 | |
| + endif | |
| + enddo | |
| ! | |
| - ELNO(J_elem)=TEXT(INDEX(TEXT,' ')+1:INDEX(TEXT,' ')+4) | |
| -! WRITE(*,102) MARK,ENAM(J_ELEM),ELNO(J_ELEM) | |
| - ELSE IF (MARK .EQ. 'H298') THEN | |
| + ELNO(J_elem)=TEXT(INDEX(TEXT,' ')+1:INDEX(TEXT,' ')+4) | |
| +! WRITE(*,102) MARK,ENAM(J_ELEM),ELNO(J_ELEM) | |
| + ELSE IF (MARK .EQ. 'H298') THEN | |
| ! We've read beyond the end of the elements, so read TEXT | |
| ! as a double into H_298 and exit the loop | |
| ! WARNING: if the number in the input spans beyond the end of TEXT | |
| ! then it will be truncated, eg: 1.345678901234567E+012 | |
| ! ---------------####### | |
| ! this number could be read in as 10^12 too small! | |
| - READ(TEXT,*) H_298 | |
| - GOTO 200 | |
| - ENDIF | |
| - ENDDO | |
| - 100 FORMAT (A4,1X,A48) ! beware truncation | |
| - 200 CONTINUE | |
| -C | |
| - DO I=1,5 | |
| - IF (ELNO(I) .EQ. '') THEN | |
| - ELNO(I)='0' | |
| - ENDIF | |
| - ENDDO | |
| + READ(TEXT,*) H_298 | |
| + GOTO 200 | |
| + ENDIF | |
| + ENDDO | |
| + 100 FORMAT (A4,1X,A48) ! beware truncation | |
| + 200 CONTINUE | |
| +C | |
| + DO I=1,5 | |
| + IF (ELNO(I) .EQ. '') THEN | |
| + ELNO(I)='0' | |
| + ENDIF | |
| + ENDDO | |
| C | |
| ! We have already read H_298 line, so continue with S_298 | |
| -! READ (LIN, *) MARK, H_298 | |
| -! WRITE(*,*) MARK, H_298 | |
| - READ (LIN, *) MARK, S_298 | |
| -! WRITE(*,*) MARK, S_298 | |
| - READ (LIN, *) MARK, DLTH | |
| -! WRITE(*,*) 'HEAT OF FORMATION at 298K', DLTH | |
| - READ (LIN, *) MARK, MW | |
| -! WRITE(*,*) 'MOLAR WEIGHT', MW | |
| - READ (LIN, *) MARK, T_int | |
| -! WRITE(*,*) MARK, T_int | |
| - READ (LIN, *) MARK, T_min | |
| -! WRITE(*,*) MARK, T_min | |
| - READ (LIN, *) MARK, T_max | |
| -! WRITE(*,*) MARK, T_max | |
| - if (T_max .gt. 6000.0) then | |
| - write(*,*) 'Warning!!!' | |
| - write(*,*) 'The maximum T should be no greater than 6000K!' | |
| - endif | |
| - 101 FORMAT (A4,1X,F8.1) | |
| +! READ (LIN, *) MARK, H_298 | |
| +! WRITE(*,*) MARK, H_298 | |
| + READ (LIN, *) MARK, S_298 | |
| +! WRITE(*,*) MARK, S_298 | |
| + READ (LIN, *) MARK, DLTH | |
| +! WRITE(*,*) 'HEAT OF FORMATION at 298K', DLTH | |
| + READ (LIN, *) MARK, MW | |
| +! WRITE(*,*) 'MOLAR WEIGHT', MW | |
| + READ (LIN, *) MARK, T_int | |
| +! WRITE(*,*) MARK, T_int | |
| + READ (LIN, *) MARK, T_min | |
| +! WRITE(*,*) MARK, T_min | |
| + READ (LIN, *) MARK, T_max | |
| +! WRITE(*,*) MARK, T_max | |
| + if (T_max .gt. 6000.0) then | |
| + write(*,*) 'Warning!!!' | |
| + write(*,*) 'The maximum T should be no greater than 6000K!' | |
| + endif | |
| + 101 FORMAT (A4,1X,F8.1) | |
| 102 FORMAT (A5,1X,A2,1X,A4) | |
| 103 FORMAT (A5,1X,A8) | |
| - READ (LIN, *) DATATYPE | |
| -! WRITE(*,*) 'DATA FORMAT: ', DATATYPE | |
| -C | |
| - IF (DATATYPE .EQ. 'NASA') THEN | |
| - READ (LIN, *) MARK, T_int1 | |
| -! WRITE(*,*) MARK, T_int1 | |
| - ELSE | |
| - READ (LIN, 101) | |
| - T_int1=0.D0 | |
| - ENDIF | |
| -C | |
| - READ (LIN, *) STRUC_MOL | |
| -! WRITE(*,*) STRUC_MOL | |
| - READ (LIN, *) ATOMS | |
| -! WRITE(*,*) 'NO. OF ATOMS', ATOMS | |
| - READ (LIN, *) ROTORS | |
| -! WRITE(*,*) 'NO. OF ROTORS', ROTORS | |
| - 104 FORMAT(F8.1) | |
| + READ (LIN, *) DATATYPE | |
| +! WRITE(*,*) 'DATA FORMAT: ', DATATYPE | |
| +C | |
| + IF (DATATYPE .EQ. 'NASA') THEN | |
| + READ (LIN, *) MARK, T_int1 | |
| +! WRITE(*,*) MARK, T_int1 | |
| + ELSE | |
| + READ (LIN, 101) | |
| + T_int1=0.D0 | |
| + ENDIF | |
| +C | |
| + READ (LIN, *) STRUC_MOL | |
| +! WRITE(*,*) STRUC_MOL | |
| + READ (LIN, *) ATOMS | |
| +! WRITE(*,*) 'NO. OF ATOMS', ATOMS | |
| + READ (LIN, *) ROTORS | |
| +! WRITE(*,*) 'NO. OF ROTORS', ROTORS | |
| + 104 FORMAT(F8.1) | |
| ! CLOSE(LIN) | |
| -! PAUSE | |
| +! PAUSE | |
| C | |
| C: Keywords input over | |
| C | |
| C: INPUT the Cp, H, and S sample dataset | |
| -C: | |
| +C: | |
| C | |
| - DO I=1,M_in | |
| - TEMP(I)=0.D0 | |
| - CPT(I) =0.D0 | |
| - CH(I) =0.D0 | |
| - CS(I) =0.D0 | |
| - ENDDO | |
| + DO I=1,M_in | |
| + TEMP(I)=0.D0 | |
| + CPT(I) =0.D0 | |
| + CH(I) =0.D0 | |
| + CS(I) =0.D0 | |
| + ENDDO | |
| C | |
| ! CALL DATAINPUT (M_in,TEMP,CPT,CH,CS) | |
| CALL DATAGROUP (M_in,TEMP,CPT,CH,CS,LIN) | |
| C | |
| - TINT = 0.D0 | |
| - TINT1 = 0.D0 | |
| + TINT = 0.D0 | |
| + TINT1 = 0.D0 | |
| C | |
| ! SWILT uses the enthalpy in: cal/mol | |
| - DO I=1,M_in | |
| - CH(I) = CH(I)*1.D3 | |
| - ENDDO | |
| + DO I=1,M_in | |
| + CH(I) = CH(I)*1.D3 | |
| + ENDDO | |
| C | |
| ! First fit SWILT because it takes into account limits at 0 and infinite T | |
| - CALL SWILT(SNAM,ENAM,ELNO,STRUC_MOL,ATOMS,ROTORS,THERM1, | |
| - & TEMP,CPT,CH,CS,M_in) | |
| + CALL SWILT(SNAM,ENAM,ELNO,STRUC_MOL,ATOMS,ROTORS,THERM1, | |
| + & TEMP,CPT,CH,CS,M_in) | |
| C | |
| - IF (DATATYPE .EQ. 'WILH') GOTO 3000 | |
| + IF (DATATYPE .EQ. 'WILH') GOTO 3000 | |
| C | |
| C: INTERPOLATE ACCORDING TO THE SWILHOIT FORMAT | |
| C | |
| - DO I=1,11 | |
| + DO I=1,11 | |
| ! 10 points between 1 and 298 | |
| - TEMF(I) = 29.815D0*DFLOAT(I-1) | |
| - IF (TEMF(I) .EQ. 0.D0) TEMF(I)=1.0D0 | |
| + TEMF(I) = 29.815D0*DFLOAT(I-1) | |
| + IF (TEMF(I) .EQ. 0.D0) TEMF(I)=1.0D0 | |
| CALL DATAFIND(THERM1,TEMF(I),CPF(I),CHF(I),CSF(I)) | |
| - CHF(I) = CHF(I)/1.D3 | |
| - ENDDO | |
| + CHF(I) = CHF(I)/1.D3 | |
| + ENDDO | |
| ! | |
| - DO I=12,101 | |
| + DO I=12,101 | |
| ! 90 points between 298 and 6000 | |
| - TEMF(I)=298.15D0+(6000.D0-298.15D0)*DFLOAT(I-11)/90.D0 | |
| - CALL DATAFIND(THERM1,TEMF(I),CPF(I),CHF(I),CSF(I)) | |
| - CHF(I)=CHF(I)/1.D3 | |
| - ENDDO | |
| + TEMF(I)=298.15D0+(6000.D0-298.15D0)*DFLOAT(I-11)/90.D0 | |
| + CALL DATAFIND(THERM1,TEMF(I),CPF(I),CHF(I),CSF(I)) | |
| + CHF(I)=CHF(I)/1.D3 | |
| + ENDDO | |
| C | |
| ! Then re-fit the other formats to these data points | |
| C | |
| - IF (DATATYPE .EQ. 'CHEM') THEN | |
| - CALL CHEM(T_int,TINT,THERM1,THERM2,TEMF,CPF,CHF,CSF) | |
| - IF (TINT .NE. 0.D0 ) T_int =TINT | |
| + IF (DATATYPE .EQ. 'CHEM') THEN | |
| + CALL CHEM(T_int,TINT,THERM1,THERM2,TEMF,CPF,CHF,CSF) | |
| + IF (TINT .NE. 0.D0 ) T_int =TINT | |
| C | |
| - ELSEIF (DATATYPE .EQ. 'NASA') THEN | |
| - CALL NASA(T_int,TINT,T_int1,TINT1,THERM1,THERM2, | |
| - & THERM3,TEMF,CPF,CHF,CSF) | |
| - IF (TINT .NE. 0.D0 ) T_int =TINT | |
| - IF (TINT1 .NE. 0.D0 ) T_int1=TINT1 | |
| + ELSEIF (DATATYPE .EQ. 'NASA') THEN | |
| + CALL NASA(T_int,TINT,T_int1,TINT1,THERM1,THERM2, | |
| + & THERM3,TEMF,CPF,CHF,CSF) | |
| + IF (TINT .NE. 0.D0 ) T_int =TINT | |
| + IF (TINT1 .NE. 0.D0 ) T_int1=TINT1 | |
| C | |
| - ELSEIF (DATATYPE .EQ. 'NIST') THEN | |
| - CALL NIST(T_int,TINT,THERM1,THERM2,TEMF,CPF,CHF,CSF) | |
| - IF (TINT .NE. 0.D0 ) T_int =TINT | |
| + ELSEIF (DATATYPE .EQ. 'NIST') THEN | |
| + CALL NIST(T_int,TINT,THERM1,THERM2,TEMF,CPF,CHF,CSF) | |
| + IF (TINT .NE. 0.D0 ) T_int =TINT | |
| C | |
| - ENDIF | |
| + ENDIF | |
| C | |
| - 3000 CONTINUE | |
| + 3000 CONTINUE | |
| C | |
| - CALL PRINT_THERM(T_int,T_int1,SNAM,ENAM,ELNO,MW,H_298,DLTH, | |
| - & DATATYPE,LOUT,THERM1,THERM2,THERM3,J_elem, | |
| + CALL PRINT_THERM(T_int,T_int1,SNAM,ENAM,ELNO,MW,H_298,DLTH, | |
| + & DATATYPE,LOUT,THERM1,THERM2,THERM3,J_elem, | |
| & T_min,T_max) | |
| C | |
| - CLOSE(LOUT) | |
| + CLOSE(LOUT) | |
| C | |
| - END | |
| - | |
| + END | |
| C*********************************************************************** | |
| C | |
| SUBROUTINE DATAINPUT(M,TEMP,CPT,CH,CS) | |
| C | |
| - INTEGER M,I,LIN,IJ,IK,IM | |
| - CHARACTER(LEN=4) MARK | |
| - CHARACTER(LEN=40) TEXT | |
| - DOUBLE PRECISION TEMP,CPT,CH,CS | |
| - DIMENSION TEMP(*),CPT(*),CH(*),CS(*) | |
| - DOUBLE PRECISION TEMP1,C1,CH1,CS1 | |
| - DIMENSION TEMP1(7),C1(7),CH1(7),CS1(7) | |
| + INTEGER M,I,LIN,IJ,IK,IM | |
| + CHARACTER(LEN=4) MARK | |
| + CHARACTER(LEN=40) TEXT | |
| + DOUBLE PRECISION TEMP,CPT,CH,CS | |
| + DIMENSION TEMP(*),CPT(*),CH(*),CS(*) | |
| + DOUBLE PRECISION TEMP1,C1,CH1,CS1 | |
| + DIMENSION TEMP1(7),C1(7),CH1(7),CS1(7) | |
| C | |
| - DATA TEMP1/290.262D0, 393.258D0, 496.255D0, 589.888D0, 795.88D0, | |
| + DATA TEMP1/290.262D0, 393.258D0, 496.255D0, 589.888D0, 795.88D0, | |
| & 1001.87D0, 1488.76D0/ | |
| C | |
| - DATA C1/17.7725D0, 22.4645D0, 27.0142D0, 30.7109D0, 36.9668D0, | |
| - & 41.8009D0, 49.3365D0/ | |
| + DATA C1/17.7725D0, 22.4645D0, 27.0142D0, 30.7109D0, 36.9668D0, | |
| + & 41.8009D0, 49.3365D0/ | |
| C | |
| - DATA CH1/0.D0,0.D0,0.D0,0.D0,0.D0,0.D0,0.D0/ | |
| + DATA CH1/0.D0,0.D0,0.D0,0.D0,0.D0,0.D0,0.D0/ | |
| C | |
| - DATA CS1/0.D0,0.D0,0.D0,0.D0,0.D0,0.D0,0.D0/ | |
| + DATA CS1/0.D0,0.D0,0.D0,0.D0,0.D0,0.D0,0.D0/ | |
| C | |
| - DO I=1,M | |
| - TEMP(I)= TEMP1(I) | |
| - CPT(I) = C1(I) | |
| - CH(I) = CH1(I) | |
| - CS(I) = CS1(I) | |
| - ENDDO | |
| - RETURN | |
| + DO I=1,M | |
| + TEMP(I)= TEMP1(I) | |
| + CPT(I) = C1(I) | |
| + CH(I) = CH1(I) | |
| + CS(I) = CS1(I) | |
| + ENDDO | |
| + RETURN | |
| C | |
| - END | |
| - | |
| + END | |
| C*********************************************************************** | |
| C | |
| - SUBROUTINE PRINT_THERM(Tint,Tint1,SNAM,ENAM,ELNO,MW,H298,DLTH, | |
| + SUBROUTINE PRINT_THERM(Tint,Tint1,SNAM,ENAM,ELNO,MW,H298,DLTH, | |
| & DATATYPE,LOUT,THERM1,THERM2,THERM3,J_elem, | |
| & T_min,T_max) | |
| C | |
| - implicit none | |
| -C | |
| - INTEGER LOUT,J_elem | |
| - integer indc_elno(5,3) | |
| - CHARACTER(LEN=4) DATATYPE | |
| - CHARACTER(LEN=16) SNAM | |
| - CHARACTER(LEN=3) ELNO(5) | |
| - CHARACTER(LEN=2) ENAM(5) | |
| - DOUBLE PRECISION THERM1,THERM2,THERM3,Tint,Tint1,H298,DLTH,MW | |
| - DOUBLE PRECISION DLTH298,T_min,T_max | |
| - DIMENSION THERM1(*),THERM2(*),THERM3(*) | |
| - EXTERNAL DLTH298 | |
| - COMMON /INDICTOR/INDC_ELNO | |
| -C | |
| - IF (DATATYPE .EQ. 'WILH') THEN | |
| -! write(*,*) 'THE COEFFICIENTS OF WILHOIT FORM' | |
| -! write(*,*) THERM1(1:6) | |
| - WRITE(LOUT,*) 'The Wilhoit polynomial coefficients calculated:' | |
| - WRITE(LOUT,200) | |
| - WRITE(LOUT,201) THERM1(1:6) | |
| - 200 FORMAT(10X,'a1',15X,'a2',15X,'a3',15X,'a4',15X,'I',15X,'J') | |
| + implicit none | |
| +C | |
| + INTEGER LOUT,J_elem | |
| + integer indc_elno(5,3) | |
| + CHARACTER(LEN=4) DATATYPE | |
| + CHARACTER(LEN=16) SNAM | |
| + CHARACTER(LEN=3) ELNO(5) | |
| + CHARACTER(LEN=2) ENAM(5) | |
| + DOUBLE PRECISION THERM1,THERM2,THERM3,Tint,Tint1,H298,DLTH,MW | |
| + DOUBLE PRECISION DLTH298,T_min,T_max | |
| + DIMENSION THERM1(*),THERM2(*),THERM3(*) | |
| + EXTERNAL DLTH298 | |
| + COMMON /INDICTOR/INDC_ELNO | |
| +C | |
| + IF (DATATYPE .EQ. 'WILH') THEN | |
| +! write(*,*) 'THE COEFFICIENTS OF WILHOIT FORM' | |
| +! write(*,*) THERM1(1:6) | |
| + WRITE(LOUT,*) 'The Wilhoit polynomial coefficients calculated:' | |
| + WRITE(LOUT,200) | |
| + WRITE(LOUT,201) THERM1(1:6) | |
| + 200 FORMAT(10X,'a1',15X,'a2',15X,'a3',15X,'a4',15X,'I',15X,'J') | |
| 201 FORMAT(1X,E15.6,2X,E15.6,2X,E15.6,2X,E15.6,2X,E15.6,2X,E15.6) | |
| C | |
| - ELSEIF (DATATYPE .EQ. 'CHEM') THEN | |
| -! write(*,*) SNAM | |
| + ELSEIF (DATATYPE .EQ. 'CHEM') THEN | |
| +! write(*,*) SNAM | |
| C | |
| - WRITE(LOUT,*) 'The Chemkin polynomial coefficients calculated:' | |
| - if (J_elem .eq. 2) then | |
| + WRITE(LOUT,*) 'The Chemkin polynomial coefficients calculated:' | |
| + if (J_elem .eq. 2) then | |
| IF (INDC_ELNO(1,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| - WRITE(LOUT,330) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & 'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| - WRITE(LOUT,331) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & 'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,332) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & 'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(1,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| - WRITE(LOUT,333) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & 'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| - WRITE(LOUT,334) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & 'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,335) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & 'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| - WRITE(LOUT,336) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & 'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| - WRITE(LOUT,337) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & 'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,338) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & 'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ENDIF | |
| - ENDIF | |
| -C | |
| - if (J_elem .eq. 3) then | |
| + IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| + WRITE(LOUT,330) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & 'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| + WRITE(LOUT,331) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & 'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,332) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & 'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(1,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| + WRITE(LOUT,333) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & 'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| + WRITE(LOUT,334) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & 'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,335) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & 'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| + WRITE(LOUT,336) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & 'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| + WRITE(LOUT,337) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & 'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,338) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & 'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ENDIF | |
| + ENDIF | |
| +C | |
| + if (J_elem .eq. 3) then | |
| IF (INDC_ELNO(1,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - WRITE(LOUT,340) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - WRITE(LOUT,341) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,342) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - WRITE(LOUT,343) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - WRITE(LOUT,344) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,345) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - WRITE(LOUT,346) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - WRITE(LOUT,347) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,348) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(1,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - WRITE(LOUT,350) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - WRITE(LOUT,351) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,352) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - WRITE(LOUT,353) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - WRITE(LOUT,354) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,355) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - WRITE(LOUT,356) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - WRITE(LOUT,357) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,358) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - WRITE(LOUT,360) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - WRITE(LOUT,361) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,362) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - WRITE(LOUT,363) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - WRITE(LOUT,364) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,365) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - WRITE(LOUT,366) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - WRITE(LOUT,367) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,368) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ENDIF | |
| - ENDIF | |
| + IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + WRITE(LOUT,340) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + WRITE(LOUT,341) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,342) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + WRITE(LOUT,343) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + WRITE(LOUT,344) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,345) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + WRITE(LOUT,346) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + WRITE(LOUT,347) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,348) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(1,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + WRITE(LOUT,350) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + WRITE(LOUT,351) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,352) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + WRITE(LOUT,353) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + WRITE(LOUT,354) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,355) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + WRITE(LOUT,356) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + WRITE(LOUT,357) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,358) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + WRITE(LOUT,360) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + WRITE(LOUT,361) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,362) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + WRITE(LOUT,363) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + WRITE(LOUT,364) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,365) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + WRITE(LOUT,366) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + WRITE(LOUT,367) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,368) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ENDIF | |
| + ENDIF | |
| ENDIF | |
| if (J_elem .eq. 4) then | |
| IF (INDC_ELNO(1,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,370) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,371) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,372) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,373) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,374) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,375) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,376) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,377) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,378) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,380) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,381) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,382) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,383) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,384) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,385) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,386) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,387) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,388) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,390) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,391) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,392) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,393) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,394) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,395) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,396) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,397) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,398) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ENDIF | |
| - ENDIF | |
| + IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,370) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,371) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,372) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,373) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,374) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,375) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,376) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,377) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,378) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,380) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,381) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,382) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,383) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,384) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,385) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,386) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,387) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,388) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,390) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,391) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,392) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,393) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,394) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,395) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,396) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,397) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,398) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ENDIF | |
| + ENDIF | |
| ELSEIF (INDC_ELNO(1,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,470) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,471) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,472) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,473) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,474) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,475) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,476) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,477) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,478) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,480) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,481) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,482) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,483) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,484) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,485) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,486) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,487) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,488) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,490) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,491) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,492) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,493) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,494) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,495) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,496) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,497) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,498) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ENDIF | |
| - ENDIF | |
| + IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,470) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,471) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,472) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,473) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,474) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,475) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,476) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,477) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,478) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,480) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,481) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,482) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,483) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,484) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,485) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,486) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,487) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,488) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,490) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,491) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,492) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,493) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,494) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,495) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,496) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,497) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,498) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ENDIF | |
| + ENDIF | |
| ELSE | |
| - IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,570) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,571) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,572) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,573) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,574) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,575) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,576) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,577) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,578) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,580) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,581) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,582) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,583) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,584) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,585) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,586) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,587) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,588) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,590) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,591) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,592) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,593) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,594) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,595) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ELSE | |
| - IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| - WRITE(LOUT,596) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| - WRITE(LOUT,597) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ELSE | |
| - WRITE(LOUT,598) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| - ENDIF | |
| - ENDIF | |
| - ENDIF | |
| - ENDIF | |
| - ENDIF | |
| - IF (J_elem .eq. 5) THEN | |
| - WRITE(LOUT,601) SNAM,T_min,T_max,Tint | |
| - WRITE(LOUT,602) ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| - & ENAM(3),ELNO(3),ENAM(4),ELNO(4),ENAM(5),ELNO(5) | |
| - ENDIF | |
| - WRITE(LOUT,301) THERM2(1),THERM2(2),THERM2(3),THERM2(4),THERM2(5) | |
| + IF (INDC_ELNO(2,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,570) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,571) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,572) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,573) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,574) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,575) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,576) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,577) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,578) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(2,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,580) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,581) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,582) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,583) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,584) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,585) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,586) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,587) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,588) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(3,2) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,590) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,591) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,592) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSEIF (INDC_ELNO(3,3) .EQ. 1) THEN | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,593) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,594) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,595) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ELSE | |
| + IF (INDC_ELNO(4,2) .EQ. 1) THEN | |
| + WRITE(LOUT,596) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSEIF (INDC_ELNO(4,3) .EQ. 1) THEN | |
| + WRITE(LOUT,597) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ELSE | |
| + WRITE(LOUT,598) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),'G',T_min,T_max,Tint | |
| + ENDIF | |
| + ENDIF | |
| + ENDIF | |
| + ENDIF | |
| + ENDIF | |
| + IF (J_elem .eq. 5) THEN | |
| + WRITE(LOUT,601) SNAM,T_min,T_max,Tint | |
| + WRITE(LOUT,602) ENAM(1),ELNO(1),ENAM(2),ELNO(2), | |
| + & ENAM(3),ELNO(3),ENAM(4),ELNO(4),ENAM(5),ELNO(5) | |
| + ENDIF | |
| + WRITE(LOUT,301) THERM2(1),THERM2(2),THERM2(3),THERM2(4),THERM2(5) | |
| WRITE(LOUT,302) THERM2(6),THERM2(7),THERM1(1),THERM1(2),THERM1(3) | |
| WRITE(LOUT,303) THERM1(4),THERM1(5),THERM1(6),THERM1(7) | |
| C | |
| - 330 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| + 330 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| & '1') | |
| - 331 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| + 331 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| & '1') | |
| - 332 FORMAT(A16,8X,A2,2X,A1,A3,A2,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| + 332 FORMAT(A16,8X,A2,2X,A1,A3,A2,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| & '1') | |
| - 333 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| + 333 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| & '1') | |
| - 334 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| - & '1') | |
| - 335 FORMAT(A16,8X,A2,1X,A2,A3,A2,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| + 334 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| & '1') | |
| - 336 FORMAT(A16,8X,A2,A3,A2,2X,A1,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| + 335 FORMAT(A16,8X,A2,1X,A2,A3,A2,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| & '1') | |
| - 337 FORMAT(A16,8X,A2,A3,A2,1X,A2,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| - & '1') | |
| - 338 FORMAT(A16,8X,A2,A3,A3,A2,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| + 336 FORMAT(A16,8X,A2,A3,A2,2X,A1,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| & '1') | |
| - 340 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 337 FORMAT(A16,8X,A2,A3,A2,1X,A2,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| + & '1') | |
| + 338 FORMAT(A16,8X,A2,A3,A3,A2,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X, | |
| + & '1') | |
| + 340 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 341 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 341 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 342 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 342 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 343 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 343 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 344 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 344 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 345 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 345 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 346 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 346 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 347 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 347 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 348 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 348 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 350 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 350 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| 351 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 352 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 352 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 353 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 353 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 354 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 354 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 355 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 355 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 356 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 356 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 357 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 357 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 358 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 358 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 360 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 360 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| 361 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 362 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 362 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 363 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 363 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 364 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 364 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 365 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 365 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 366 FORMAT(A16,8X,A2,A3,A2,A3,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 366 FORMAT(A16,8X,A2,A3,A2,A3,A2,2X,A1,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 367 FORMAT(A16,8X,A2,A3,A2,A3,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 367 FORMAT(A16,8X,A2,A3,A2,A3,A2,1X,A2,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 368 FORMAT(A16,8X,A2,A3,A2,A3,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| + 368 FORMAT(A16,8X,A2,A3,A2,A3,A2,A3,5X,A1,3X,F7.3,2X,F8.3,2X, | |
| & F8.3,4X,'1') | |
| - 370 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 370 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 371 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 371 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 372 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 372 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 373 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 373 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 374 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 374 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 375 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 375 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 376 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 376 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 377 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 377 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 378 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 378 FORMAT(A16,8X,A2,2X,A1,A2,2X,A1,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 380 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 380 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 381 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 381 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 382 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 382 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 383 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 383 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 384 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 384 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 385 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 385 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 386 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 386 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 387 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 387 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 388 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 388 FORMAT(A16,8X,A2,2X,A1,A2,1X,A2,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 390 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 390 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 391 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 391 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 392 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 392 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 393 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 393 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 394 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 394 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 395 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 395 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 396 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 396 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 397 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 397 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 398 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 398 FORMAT(A16,8X,A2,2X,A1,A2,A3,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 470 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 470 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 471 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 471 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 472 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 472 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 473 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 473 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 474 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 474 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 475 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 475 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 476 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 476 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 477 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 477 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 478 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 478 FORMAT(A16,8X,A2,1X,A2,A2,2X,A1,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 480 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 480 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 481 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 481 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 482 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 482 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 483 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 483 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 484 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 484 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 485 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 485 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 486 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 486 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 487 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 487 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 488 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 488 FORMAT(A16,8X,A2,1X,A2,A2,1X,A2,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 490 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 490 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 491 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 491 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 492 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 492 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 493 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 493 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 494 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 494 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 495 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 495 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 496 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 496 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 497 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 497 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 498 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 498 FORMAT(A16,8X,A2,1X,A2,A2,A3,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 570 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 570 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 571 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 571 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 572 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 572 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 573 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 573 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 574 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 574 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 575 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 575 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 576 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 576 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 577 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 577 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 578 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 578 FORMAT(A16,8X,A2,A3,A2,2X,A1,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 580 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 580 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 581 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 581 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 582 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 582 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 583 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 583 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 584 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 584 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 585 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 585 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 586 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 586 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 587 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 587 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 588 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 588 FORMAT(A16,8X,A2,A3,A2,1X,A2,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 590 FORMAT(A16,8X,A2,A3,A2,A3,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 590 FORMAT(A16,8X,A2,A3,A2,A3,A2,2X,A1,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 591 FORMAT(A16,8X,A2,A3,A2,A3,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 591 FORMAT(A16,8X,A2,A3,A2,A3,A2,2X,A1,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 592 FORMAT(A16,8X,A2,A3,A2,A3,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 592 FORMAT(A16,8X,A2,A3,A2,A3,A2,2X,A1,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 593 FORMAT(A16,8X,A2,A3,A2,A3,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 593 FORMAT(A16,8X,A2,A3,A2,A3,A2,1X,A2,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 594 FORMAT(A16,8X,A2,A3,A2,A3,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 594 FORMAT(A16,8X,A2,A3,A2,A3,A2,1X,A2,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 595 FORMAT(A16,8X,A2,A3,A2,A3,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 595 FORMAT(A16,8X,A2,A3,A2,A3,A2,1X,A2,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 596 FORMAT(A16,8X,A2,A3,A2,A3,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| + 596 FORMAT(A16,8X,A2,A3,A2,A3,A2,A3,A2,2X,A1,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 597 FORMAT(A16,8X,A2,A3,A2,A3,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| + 597 FORMAT(A16,8X,A2,A3,A2,A3,A2,A3,A2,1X,A2,A1,3X,F7.3,2X, | |
| & F8.3,2X,F8.3,4X,'1') | |
| - 598 FORMAT(A16,8X,A2,A3,A2,A3,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| + 598 FORMAT(A16,8X,A2,A3,A2,A3,A2,A3,A2,A3,A1,3X,F7.3,2X,F8.3, | |
| & 2X,F8.3,4X,'1') | |
| - 601 FORMAT(A16,28X,'G',3X,F7.3,2X,F8.3,2X,F8.3,4X,'1&') | |
| + 601 FORMAT(A16,28X,'G',3X,F7.3,2X,F8.3,2X,F8.3,4X,'1&') | |
| !' | |
| - 602 FORMAT(A2,1X,A3,A2,1X,A3,A2,1X,A3,A2,1X,A3,A2,1X,A3) | |
| - 300 FORMAT(A16,8X,A4,A1,A4,A1,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X,'1') | |
| + 602 FORMAT(A2,1X,A3,A2,1X,A3,A2,1X,A3,A2,1X,A3,A2,1X,A3) | |
| + 300 FORMAT(A16,8X,A4,A1,A4,A1,10X,A1,3X,F7.3,2X,F8.3,2X,F8.3,4X,'1') | |
| 301 FORMAT(ES15.8,ES15.8,ES15.8,ES15.8,ES15.8,4X,'2') | |
| 302 FORMAT(ES15.8,ES15.8,ES15.8,ES15.8,ES15.8,4X,'3') | |
| 303 FORMAT(ES15.8,ES15.8,ES15.8,ES15.8,15X,4X,'4') | |
| C | |
| - ELSEIF (DATATYPE .EQ. 'NIST') THEN | |
| -! write(*,*) 'THE COEFFICIENTS OF NIST FORM' | |
| -! write(*,*) THERM1(1:7) | |
| -! write(*,*) THERM2(1:7) | |
| -C | |
| - WRITE(LOUT,*) 'The NIST polynomial coefficients calculated:' | |
| - WRITE(LOUT,*) 'H0-H0_298=A*t+B*t*t/2+C*t*t*t/3+D*t*t*t*t/4' | |
| - WRITE(LOUT,*) ' -E/t+F-H' | |
| - WRITE(LOUT,*) 'H=DLTH_formation=',DLTH | |
| - WRITE(LOUT,300) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2),'G', | |
| - & T_min,T_max,Tint | |
| - WRITE(LOUT,301) THERM1(1),THERM1(2),THERM1(3),THERM1(4),THERM1(5) | |
| + ELSEIF (DATATYPE .EQ. 'NIST') THEN | |
| +! write(*,*) 'THE COEFFICIENTS OF NIST FORM' | |
| +! write(*,*) THERM1(1:7) | |
| +! write(*,*) THERM2(1:7) | |
| +C | |
| + WRITE(LOUT,*) 'The NIST polynomial coefficients calculated:' | |
| + WRITE(LOUT,*) 'H0-H0_298=A*t+B*t*t/2+C*t*t*t/3+D*t*t*t*t/4' | |
| + WRITE(LOUT,*) ' -E/t+F-H' | |
| + WRITE(LOUT,*) 'H=DLTH_formation=',DLTH | |
| + WRITE(LOUT,300) SNAM,ENAM(1),ELNO(1),ENAM(2),ELNO(2),'G', | |
| + & T_min,T_max,Tint | |
| + WRITE(LOUT,301) THERM1(1),THERM1(2),THERM1(3),THERM1(4),THERM1(5) | |
| WRITE(LOUT,302) THERM1(6),THERM1(7),THERM2(1),THERM2(2),THERM2(3) | |
| WRITE(LOUT,303) THERM2(4),THERM2(5),THERM2(6),THERM2(7) | |
| C | |
| - ELSE IF (DATATYPE .EQ. 'NASA') THEN | |
| -! write(*,*) 'THE COEFFICIENTS OF NASA FORM' | |
| -! write(*,*) THERM1(1:9) | |
| -! write(*,*) THERM2(1:9) | |
| -! write(*,*) THERM3(1:9) | |
| + ELSE IF (DATATYPE .EQ. 'NASA') THEN | |
| +! write(*,*) 'THE COEFFICIENTS OF NASA FORM' | |
| +! write(*,*) THERM1(1:9) | |
| +! write(*,*) THERM2(1:9) | |
| +! write(*,*) THERM3(1:9) | |
| C | |
| - WRITE(LOUT,*) 'The NASA polynomial coefficients calculated:' | |
| - WRITE(LOUT,399) SNAM | |
| + WRITE(LOUT,*) 'The NASA polynomial coefficients calculated:' | |
| + WRITE(LOUT,399) SNAM | |
| ! HF_298 in 'J/mol' in NASA format: 1 cal = 4.184 J | |
| -! WRITE(*,*) MW | |
| -! WRITE(*,*) DLTH*4.184D0 | |
| - WRITE(LOUT,400) 3,ENAM(1),ELNO(1),'.00',ENAM(2),ELNO(2),'.00', | |
| - & ENAM(3),ELNO(3),'.00',ENAM(4),ELNO(4),'.00', | |
| +! WRITE(*,*) MW | |
| +! WRITE(*,*) DLTH*4.184D0 | |
| + WRITE(LOUT,400) 3,ENAM(1),ELNO(1),'.00',ENAM(2),ELNO(2),'.00', | |
| + & ENAM(3),ELNO(3),'.00',ENAM(4),ELNO(4),'.00', | |
| & ENAM(5),ELNO(5),'.00',MW,DLTH*4.184D0 | |
| - WRITE(LOUT,401) T_min,Tint,7,'-2.0','-1.0','0.0','1.0','2.0', | |
| - & '3.0','4.0','0.0',DLTH298(THERM1(1:7))*4.184D0 | |
| - WRITE(LOUT,404) THERM1(1),THERM1(2),THERM1(3),THERM1(4),THERM1(5) | |
| + WRITE(LOUT,401) T_min,Tint,7,'-2.0','-1.0','0.0','1.0','2.0', | |
| + & '3.0','4.0','0.0',DLTH298(THERM1(1:7))*4.184D0 | |
| + WRITE(LOUT,404) THERM1(1),THERM1(2),THERM1(3),THERM1(4),THERM1(5) | |
| WRITE(LOUT,404) THERM1(6),THERM1(7),0.D0,THERM1(8),THERM1(9) | |
| - WRITE(LOUT,402) Tint,Tint1,7,'-2.0','-1.0','0.0','1.0','2.0', | |
| - & '3.0','4.0','0.0',DLTH298(THERM1(1:7))*4.184D0 | |
| - WRITE(LOUT,404) THERM2(1),THERM2(2),THERM2(3),THERM2(4),THERM2(5) | |
| + WRITE(LOUT,402) Tint,Tint1,7,'-2.0','-1.0','0.0','1.0','2.0', | |
| + & '3.0','4.0','0.0',DLTH298(THERM1(1:7))*4.184D0 | |
| + WRITE(LOUT,404) THERM2(1),THERM2(2),THERM2(3),THERM2(4),THERM2(5) | |
| WRITE(LOUT,404) THERM2(6),THERM2(7),0.D0,THERM2(8),THERM2(9) | |
| - WRITE(LOUT,403) Tint1,T_max,7,'-2.0','-1.0','0.0','1.0','2.0', | |
| - & '3.0','4.0','0.0',DLTH298(THERM1(1:7))*4.184D0 | |
| - WRITE(LOUT,404) THERM3(1),THERM3(2),THERM3(3),THERM3(4),THERM3(5) | |
| + WRITE(LOUT,403) Tint1,T_max,7,'-2.0','-1.0','0.0','1.0','2.0', | |
| + & '3.0','4.0','0.0',DLTH298(THERM1(1:7))*4.184D0 | |
| + WRITE(LOUT,404) THERM3(1),THERM3(2),THERM3(3),THERM3(4),THERM3(5) | |
| WRITE(LOUT,404) THERM3(6),THERM3(7),0.D0,THERM3(8),THERM3(9) | |
| C | |
| - ENDIF | |
| + ENDIF | |
| C | |
| - 399 FORMAT(A16) | |
| - 400 FORMAT(1X,I1,8X,A4,A1,A3,A4,A1,A3,A4,A1,A3,A4,A1,A3,A4,A1,A3, | |
| + 399 FORMAT(A16) | |
| + 400 FORMAT(1X,I1,8X,A4,A1,A3,A4,A1,A3,A4,A1,A3,A4,A1,A3,A4,A1,A3, | |
| & 1X,'0',2X,F11.7,4X,F11.3) | |
| - 401 FORMAT(4X,F7.3,3X,F7.3,1X,I1,1X,A4,1X,A4,2X,A3,2X,A3,2X,A3,2X,A3, | |
| + 401 FORMAT(4X,F7.3,3X,F7.3,1X,I1,1X,A4,1X,A4,2X,A3,2X,A3,2X,A3,2X,A3, | |
| & 2X,A3,2X,A3,6X,F11.3) | |
| - 402 FORMAT(4X,F7.3,2X,F8.3,1X,I1,1X,A4,1X,A4,2X,A3,2X,A3,2X,A3,2X,A3, | |
| + 402 FORMAT(4X,F7.3,2X,F8.3,1X,I1,1X,A4,1X,A4,2X,A3,2X,A3,2X,A3,2X,A3, | |
| & 2X,A3,2X,A3,6X,F11.3) | |
| - 403 FORMAT(3X,F8.3,2X,F8.3,1X,I1,1X,A4,1X,A4,2X,A3,2X,A3,2X,A3,2X,A3, | |
| + 403 FORMAT(3X,F8.3,2X,F8.3,1X,I1,1X,A4,1X,A4,2X,A3,2X,A3,2X,A3,2X,A3, | |
| & 2X,A3,2X,A3,6X,F11.3) | |
| 404 FORMAT(5ES16.9) | |
| C | |
| - RETURN | |
| + RETURN | |
| C | |
| - END | |
| - | |
| + END | |
| C*********************************************************************** | |
| C | |
| SUBROUTINE DATAGROUP(M_in,TEMP,CPT,CH,CS,LIN) | |
| C | |
| - INTEGER M_in,I,LIN,IJ,IK,IM | |
| - CHARACTER(LEN=4) MARK | |
| - CHARACTER(LEN=40) TEXT | |
| - DOUBLE PRECISION TEMP,CPT,CH,CS | |
| - DIMENSION TEMP(*),CPT(*),CH(*),CS(*) | |
| - DOUBLE PRECISION TEMP1,C1,CH1,CS1 | |
| -! DIMENSION TEMP1(50),C1(50),CH1(50),CS1(50) | |
| + INTEGER M_in,I,LIN,IJ,IK,IM | |
| + CHARACTER(LEN=4) MARK | |
| + CHARACTER(LEN=40) TEXT | |
| + DOUBLE PRECISION TEMP,CPT,CH,CS | |
| + DIMENSION TEMP(*),CPT(*),CH(*),CS(*) | |
| + DOUBLE PRECISION TEMP1,C1,CH1,CS1 | |
| +! DIMENSION TEMP1(50),C1(50),CH1(50),CS1(50) | |
| C | |
| -! DATA TEMP1/290.262D0, 393.258D0, 496.255D0, 589.888D0, 795.88D0, | |
| +! DATA TEMP1/290.262D0, 393.258D0, 496.255D0, 589.888D0, 795.88D0, | |
| ! & 1001.87D0, 1488.76D0/ | |
| C | |
| -! DATA C1/17.7725D0, 22.4645D0, 27.0142D0, 30.7109D0, 36.9668D0, | |
| -! & 41.8009D0, 49.3365D0/ | |
| +! DATA C1/17.7725D0, 22.4645D0, 27.0142D0, 30.7109D0, 36.9668D0, | |
| +! & 41.8009D0, 49.3365D0/ | |
| C | |
| -! DATA CH1/0.D0,0.D0,0.D0,0.D0,0.D0,0.D0,0.D0/ | |
| +! DATA CH1/0.D0,0.D0,0.D0,0.D0,0.D0,0.D0,0.D0/ | |
| C | |
| -! DATA CS1/0.D0,0.D0,0.D0,0.D0,0.D0,0.D0,0.D0/ | |
| +! DATA CS1/0.D0,0.D0,0.D0,0.D0,0.D0,0.D0,0.D0/ | |
| C | |
| - MARK='' | |
| - TEXT='' | |
| - 100 FORMAT (A4,1X,A40) | |
| - 101 FORMAT (A4,1X,F4.0,1X,F8.1) | |
| + MARK='' | |
| + TEXT='' | |
| + 100 FORMAT (A4,1X,A40) | |
| + 101 FORMAT (A4,1X,F4.0,1X,F8.1) | |
| C | |
| C | |
| - DO I=1,M_in | |
| - READ(LIN, *) MARK, TEMP(I), CPT(I) | |
| - CH(I) = 0.0D0 | |
| - CS(I) = 0.0D0 | |
| - IF (MARK .NE. 'TECP') THEN | |
| - write(*,*) 'Error. Need more TECP' | |
| - GOTO 250 | |
| - ENDIF | |
| - ENDDO | |
| + DO I=1,M_in | |
| + READ(LIN, *) MARK, TEMP(I), CPT(I) | |
| + CH(I) = 0.0D0 | |
| + CS(I) = 0.0D0 | |
| + IF (MARK .NE. 'TECP') THEN | |
| + write(*,*) 'Error. Need more TECP' | |
| + GOTO 250 | |
| + ENDIF | |
| + ENDDO | |
| C | |
| 250 CONTINUE | |
| - RETURN | |
| + RETURN | |
| C | |
| - END | |
| \ No newline at end of file | |
| + END | |
| \ No newline at end of file | |
| diff --git a/source/GATPFit/lsfp_chem1.f b/source/GATPFit/lsfp_chem1.f | |
| index 6b9d183..4ecdb00 100644 | |
| --- a/source/GATPFit/lsfp_chem1.f | |
| +++ b/source/GATPFit/lsfp_chem1.f | |
| @@ -1,616 +1,599 @@ | |
| -C: Add the constrains to the first and second derivatives | |
| -C: Therefore, there are three constrains: Cp, DCp, and D2Cp | |
| -C: -------------------------------------------------------------- | |
| -C: For CHEMKIN | |
| -C: Use a single matrix to calculate all 10 coefficients | |
| -C: [A]: M x 10 | |
| -C: [X]: 10 x 1 (alpha1_low,alpha2_low,alpha3_low,alpha4_low,alpha5_low, | |
| -C: alpha1_hig,alpha2_hig,alpha3_hig,alpha4_hig,alpha5_hig) | |
| -C: [C]: M x 1 | |
| -C: Contrains: CP, dCP/dT, and d2CP/d2T | |
| -C: at the intermediate temperature Tint | |
| -C: [B]: 3 x 10 | |
| -C: [D]: 3 x 1 | |
| -C---------------------------------------------------------------- | |
| -C FOR CHEMKIN CHEMTHERMO DATA FORMAT | |
| -C number of coefficients: N=5 x 2 | |
| -C number of discrete data point: M>=N, i.e., M=102 | |
| -C | |
| -C use the DGGLSE to solve the linear least squares equality-constrained | |
| -C (LlSE) problem. | |
| -C%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| -C: Need to change the value of M according to the size of sample data | |
| -!******************************************************************** | |
| -! Programmed by John Z. Wen, MIT, June 2005 | |
| -!******************************************************************** | |
| -C | |
| - SUBROUTINE CHEM(Tint,TNEW,THERM1,THERM2,TEMP1,C1,CH1,CS1) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION Tint,TNEW,THERM1,THERM2 | |
| - DOUBLE PRECISION H_298,S_298,DLTH | |
| -C | |
| - INTEGER M,N,P,LDA,LDB,LWORK,INFO,M1 | |
| - INTEGER MH,NH,PH,LDAH,LDBH,LWORKH | |
| - INTEGER MS,NS,PS,LDAS,LDBS,LWORKS | |
| - DOUBLE PRECISION A1,B1,Bk,C1,D1,X1,WORK1 | |
| - DOUBLE PRECISION TEMP1,PHI_CHEM1,PHI_CHEM2,PHI_CHEM3, | |
| - & PHI_CHEM4,PHI_CHEM5,ROL | |
| - DOUBLE PRECISION PHI_CHEM_DCP1,PHI_CHEM_DCP2,PHI_CHEM_DCP3, | |
| - & PHI_CHEM_DCP4,PHI_CHEM_DCP5,PHI_CHEM_D2CP1, | |
| - & PHI_CHEM_D2CP2,PHI_CHEM_D2CP3,PHI_CHEM_D2CP4, | |
| - & PHI_CHEM_D2CP5 | |
| - DOUBLE PRECISION A_H1,A_S1,A_H2,A_S2 | |
| - DOUBLE PRECISION AH1,BH1,CH1,DH1,XH1,WORKH,BHk,CH,CH2 | |
| - DOUBLE PRECISION AS1,BS1,CS1,DS1,XS1,WORKS,BSk,CS,CS2 | |
| - DOUBLE PRECISION PHI_CHEM_H,PHI_CHEM_S | |
| - INTEGER MARK1 | |
| - DOUBLE PRECISION TEMP,C | |
| -C | |
| -C Required by LSEC solver: | |
| -! LDA >= MAX(1,M) | |
| -! LDB >= MAX(1,P) | |
| -! LWORK >= max(1,M+N+P) | |
| -! P=1 for only one constrain at the intermediate temp. | |
| -! P=3 for three constrains at the intermediate temp. | |
| -C | |
| -C CHANGE 'LWORK' if NECESSARY | |
| - PARAMETER (M=102) | |
| - PARAMETER (LDB=3,P=3) | |
| - PARAMETER (N=10) | |
| - DIMENSION A1(M,N),B1(LDB,N),C1(M-1),D1(P),X1(N),WORK1(M+N+P), | |
| - & Bk(LDB,N) | |
| - PARAMETER (LDBH=2,PH=2) | |
| - PARAMETER (NH=2) | |
| - PARAMETER (LDBS=2,PS=2) | |
| - PARAMETER (NS=2) | |
| - DIMENSION AH1(M,NH),BH1(LDBH,NH),CH1(M-1),DH1(PH),XH1(NH), | |
| - & WORKH(M+NH+PH),BHk(LDBH,NH),CH(M),CH2(M) | |
| - DIMENSION AS1(M,NS),BS1(LDBS,NS),CS1(M-1),DS1(PS),XS1(NS), | |
| - & WORKS(M+NS+PS),BSk(LDBS,NS),CS(M),CS2(M) | |
| - DIMENSION TEMP1(M-1),THERM1(7),THERM2(7) | |
| - DIMENSION TEMP(M),C(M) | |
| - INTEGER I,J | |
| -C | |
| -! GAS CONSTANT | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - EXTERNAL PHI_CHEM1,PHI_CHEM2,PHI_CHEM3,PHI_CHEM4,PHI_CHEM5, | |
| - & PHI_CHEM_DCP1,PHI_CHEM_DCP2,PHI_CHEM_DCP3, | |
| - & PHI_CHEM_DCP4,PHI_CHEM_DCP5,PHI_CHEM_D2CP1, | |
| - & PHI_CHEM_D2CP2,PHI_CHEM_D2CP3,PHI_CHEM_D2CP4, | |
| - & PHI_CHEM_D2CP5,PHI_CHEM_H,PHI_CHEM_S | |
| -C | |
| -! WRITE(*,*) 'CALLED CHEM' | |
| -C | |
| - LDA = M | |
| - LWORK = M+N+P | |
| - MH = M | |
| - LDAH = MH | |
| - LWORKH= MH+NH+PH | |
| - MS = M | |
| - LDAS = MS | |
| - LWORKS= MS+NS+PS | |
| -C | |
| -C FIND 'Tint' and 'Tint1' in sample data | |
| -C | |
| - DO I=1,M-1 | |
| - IF (TEMP1(I) .GT. Tint) THEN | |
| - MARK1=I-1 | |
| - IF (Tint .NE. TEMP1(I-1)) THEN | |
| - Tint=TEMP1(I-1) | |
| - TNEW=Tint | |
| -! WRITE(*,*) 'Tint has been replaced!' | |
| - ENDIF | |
| - GOTO 995 | |
| - ENDIF | |
| - ENDDO | |
| - 995 CONTINUE | |
| -! WRITE(*,*) 'MARK1=',MARK1 | |
| -C | |
| -C Rearrange the matrics | |
| -C | |
| - DO I=1,M | |
| - TEMP(I)=0.D0 | |
| - C (I)=0.D0 | |
| - CH (I)=0.D0 | |
| - CS (I)=0.D0 | |
| - CH2 (I)=0.D0 | |
| - CS2 (I)=0.D0 | |
| - ENDDO | |
| -C | |
| - DO I=1,MARK1 | |
| - TEMP(I)=TEMP1(I) | |
| - C (I)=C1(I) | |
| - CH(I)=CH1(I) | |
| - CS(I)=CS1(I) | |
| - ENDDO | |
| - TEMP(MARK1+1)=TEMP(MARK1) | |
| - C (MARK1+1)=C (MARK1) | |
| - CH(MARK1+1)=CH(MARK1) | |
| - CS(MARK1+1)=CS(MARK1) | |
| - DO I=MARK1+2,M | |
| - TEMP(I)=TEMP1(I-1) | |
| - C (I)=C1 (I-1) | |
| - CH(I)=CH1(I-1) | |
| - CS(I)=CS1(I-1) | |
| - ENDDO | |
| -C | |
| -! WRITE(*,*) 'Tint=', Tint | |
| -! WRITE(*,*) TEMP | |
| -! WRITE(*,*) C | |
| -! WRITE(*,*) CH | |
| -! WRITE(*,*) CS | |
| -! PAUSE | |
| -C | |
| - DO I=1,N | |
| - X1(I)=0.D0 | |
| - ENDDO | |
| - DO I=1,N | |
| - DO J=1,LDA | |
| - A1(J,I)=0.D0 | |
| - ENDDO | |
| - DO J=1,LDB | |
| - B1(J,I)=0.D0 | |
| - Bk(J,I)=0.D0 | |
| - ENDDO | |
| - ENDDO | |
| - DO I=1,LWORK | |
| - WORK1(I)=0.D0 | |
| - ENDDO | |
| -C | |
| -! For PHI matrix, first temperature range | |
| - DO I=1,MARK1 | |
| - A1(I,1)=PHI_CHEM1(TEMP(I)) | |
| - A1(I,2)=PHI_CHEM2(TEMP(I)) | |
| - A1(I,3)=PHI_CHEM3(TEMP(I)) | |
| - A1(I,4)=PHI_CHEM4(TEMP(I)) | |
| - A1(I,5)=PHI_CHEM5(TEMP(I)) | |
| - ENDDO | |
| -! For PHI matrix, second temperature range | |
| - DO I=MARK1+1,M | |
| - A1(I,6) =PHI_CHEM1(TEMP(I)) | |
| - A1(I,7) =PHI_CHEM2(TEMP(I)) | |
| - A1(I,8) =PHI_CHEM3(TEMP(I)) | |
| - A1(I,9) =PHI_CHEM4(TEMP(I)) | |
| - A1(I,10)=PHI_CHEM5(TEMP(I)) | |
| - ENDDO | |
| -C | |
| -! WRITE(*,*) TEMP1 | |
| -! WRITE(*,*) C1 | |
| -! PAUSE | |
| -C | |
| -C For Constrains at Tint ------------------------ | |
| -C | |
| -! For CP values | |
| - Bk(1,1) = PHI_CHEM1(Tint) | |
| - Bk(1,2) = PHI_CHEM2(Tint) | |
| - Bk(1,3) = PHI_CHEM3(Tint) | |
| - Bk(1,4) = PHI_CHEM4(Tint) | |
| - Bk(1,5) = PHI_CHEM5(Tint) | |
| - Bk(1,6) =-PHI_CHEM1(Tint) | |
| - Bk(1,7) =-PHI_CHEM2(Tint) | |
| - Bk(1,8) =-PHI_CHEM3(Tint) | |
| - Bk(1,9) =-PHI_CHEM4(Tint) | |
| - Bk(1,10)=-PHI_CHEM5(Tint) | |
| - D1(1)=0.D0 | |
| -C For DCp values | |
| - Bk(2,1) = PHI_CHEM_DCP1(Tint) | |
| - Bk(2,2) = PHI_CHEM_DCP2(Tint) | |
| - Bk(2,3) = PHI_CHEM_DCP3(Tint) | |
| - Bk(2,4) = PHI_CHEM_DCP4(Tint) | |
| - Bk(2,5) = PHI_CHEM_DCP5(Tint) | |
| - Bk(2,6) =-PHI_CHEM_DCP1(Tint) | |
| - Bk(2,7) =-PHI_CHEM_DCP2(Tint) | |
| - Bk(2,8) =-PHI_CHEM_DCP3(Tint) | |
| - Bk(2,9) =-PHI_CHEM_DCP4(Tint) | |
| - Bk(2,10)=-PHI_CHEM_DCP5(Tint) | |
| - D1(2)=0.D0 | |
| -C For D2Cp values | |
| - Bk(3,1) = PHI_CHEM_D2CP1(Tint) | |
| - Bk(3,2) = PHI_CHEM_D2CP2(Tint) | |
| - Bk(3,3) = PHI_CHEM_D2CP3(Tint) | |
| - Bk(3,4) = PHI_CHEM_D2CP4(Tint) | |
| - Bk(3,5) = PHI_CHEM_D2CP5(Tint) | |
| - Bk(3,6) =-PHI_CHEM_D2CP1(Tint) | |
| - Bk(3,7) =-PHI_CHEM_D2CP2(Tint) | |
| - Bk(3,8) =-PHI_CHEM_D2CP3(Tint) | |
| - Bk(3,9) =-PHI_CHEM_D2CP4(Tint) | |
| - Bk(3,10)=-PHI_CHEM_D2CP5(Tint) | |
| - D1(3)=0.D0 | |
| -C | |
| - DO I=1,N | |
| - DO J=1,LDB | |
| - B1(J,I)=Bk(J,I) | |
| - ENDDO | |
| - ENDDO | |
| -C | |
| -! CHEM FORMAT----------------------------------------- | |
| -C | |
| - call DGGLSE(M,N,P,A1,LDA,B1,LDB,C,D1,X1,WORK1,LWORK,INFO) | |
| -! WRITE(*,*) 'X1=',X1(1:10) | |
| -! pause | |
| -C | |
| -C For enthalpy, NEED define 2 coeffs, N=2 | |
| -C | |
| - DO I=1,NH | |
| - XH1(I)=0.D0 | |
| - ENDDO | |
| - DO I=1,NH | |
| - DO J=1,LDAH | |
| - AH1(J,I)=0.D0 | |
| - ENDDO | |
| - DO J=1,LDBH | |
| - BH1(J,I)=0.D0 | |
| - BHk(J,I)=0.D0 | |
| - ENDDO | |
| - ENDDO | |
| - DO I=1,LWORKH | |
| - WORKH(I)=0.D0 | |
| - ENDDO | |
| -C | |
| - DO I=1,MARK1 | |
| - CH2(I)=CH(I) - PHI_CHEM_H(TEMP(I),X1(1:5)) | |
| - ENDDO | |
| - DO I=MARK1+1,MH | |
| - CH2(I)=CH(I) - PHI_CHEM_H(TEMP(I),X1(6:10)) | |
| - ENDDO | |
| -C | |
| - DO I=1,MARK1 | |
| - AH1(I,1)=ROL/1000.d0 | |
| - ENDDO | |
| - DO I=MARK1+1,MH | |
| - AH1(I,2)=ROL/1000.d0 | |
| - ENDDO | |
| -C | |
| -C Contrain for H at Tint | |
| -C | |
| - BHk(1,1)=ROL/1000.d0 | |
| - BHk(1,2)=-ROL/1000.d0 | |
| - DH1(1)=PHI_CHEM_H(Tint,X1(6:10)) | |
| - & -PHI_CHEM_H(Tint,X1(1:5)) | |
| -C | |
| -C Contrain for H at 298.15K | |
| -C | |
| - BHk(2,1)=ROL/1000.d0 | |
| - BHk(2,2)=0.D0 | |
| - DH1(2)=DLTH - PHI_CHEM_H(298.15D0,X1(1:5)) | |
| -C | |
| - DO I=1,NH | |
| - DO J=1,LDBH | |
| - BH1(J,I)=BHk(J,I) | |
| - ENDDO | |
| - ENDDO | |
| -C | |
| - call DGGLSE(MH,NH,PH,AH1,LDAH,BH1,LDBH,CH2,DH1,XH1,WORKH, | |
| - & LWORKH,INFO) | |
| -! WRITE(*,*) 'H_CONST1=',XH1(1) | |
| -! WRITE(*,*) 'H_CONST2=',XH1(2) | |
| -C | |
| - A_H1=XH1(1) | |
| - A_H2=XH1(2) | |
| -C | |
| -C For entropy, NEED define 2 coeffs, N=2 | |
| - DO I=1,NS | |
| - XS1(I)=0.D0 | |
| - ENDDO | |
| - DO I=1,NS | |
| - DO J=1,LDAS | |
| - AS1(J,I)=0.D0 | |
| - ENDDO | |
| - DO J=1,LDBS | |
| - BS1(J,I)=0.D0 | |
| - BSk(J,I)=0.D0 | |
| - ENDDO | |
| - ENDDO | |
| - DO I=1,LWORKS | |
| - WORKS(I)=0.D0 | |
| - ENDDO | |
| -C | |
| - DO I=1,MARK1 | |
| - CS2(I)=CS(I) - PHI_CHEM_S(TEMP(I),X1(1:5)) | |
| - ENDDO | |
| - DO I=MARK1+1,MS | |
| - CS2(I)=CS(I) - PHI_CHEM_S(TEMP(I),X1(6:10)) | |
| - ENDDO | |
| - DO I=1,MARK1 | |
| - AS1(I,1)=ROL | |
| - ENDDO | |
| - DO I=MARK1+1,MS | |
| - AS1(I,2)=ROL | |
| - ENDDO | |
| -C | |
| -C Contrain for S at Tint | |
| -C | |
| - BSk(1,1)=ROL | |
| - BSk(1,2)=-ROL | |
| - DS1(1)=PHI_CHEM_S(Tint,X1(6:10)) | |
| - & -PHI_CHEM_S(Tint,X1(1:5)) | |
| -C | |
| -C Contrain for S at 298.15K | |
| -C | |
| - BSk(2,1)=ROL | |
| - BSk(2,2)=0.D0 | |
| - DS1(2)=S_298 - PHI_CHEM_S(298.15D0,X1(1:5)) | |
| -C | |
| - DO I=1,NS | |
| - DO J=1,LDBS | |
| - BS1(J,I)=BSk(J,I) | |
| - ENDDO | |
| - ENDDO | |
| -C | |
| - call DGGLSE(MS,NS,PS,AS1,LDAS,BS1,LDBS,CS2,DS1,XS1,WORKS, | |
| - & LWORKS,INFO) | |
| -! WRITE(*,*) XS1 | |
| -! WRITE(*,*) 'S_CONST1=',XS1(1) | |
| -! WRITE(*,*) 'S_CONST2=',XS1(2) | |
| -C | |
| - A_S1=XS1(1) | |
| - A_S2=XS1(2) | |
| -C | |
| -C | |
| - DO I=1,5 | |
| - THERM1(I)=X1(I) | |
| - ENDDO | |
| - THERM1(5+1)=A_H1 | |
| - THERM1(5+2)=A_S1 | |
| - DO I=1,5 | |
| - THERM2(I)=X1(I+5) | |
| - ENDDO | |
| - THERM2(5+1)=A_H2 | |
| - THERM2(5+2)=A_S2 | |
| -C | |
| -! WRITE(*,*) 'CHEM OVER' | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM1(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM1=ROL | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM2(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM2=ROL*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM3(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM3=ROL*TEM*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM4(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM4=ROL*TEM*TEM*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM5(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM5=ROL*TEM*TEM*TEM*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM_DCP1(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM_DCP1=0.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM_DCP2(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM_DCP2=ROL | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM_DCP3(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM_DCP3=2.D0*ROL*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM_DCP4(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM_DCP4=3.D0*ROL*TEM*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM_DCP5(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM_DCP5=4.D0*ROL*TEM*TEM*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM_D2CP1(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM_D2CP1=0.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM_D2CP2(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM_D2CP2=0.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM_D2CP3(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM_D2CP3=2.D0*ROL | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM_D2CP4(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM_D2CP4=6.D0*ROL*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM_D2CP5(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM_D2CP5=12.D0*ROL*TEM*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM_H(TEM,alpha) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH | |
| - DIMENSION alpha(5) | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_CHEM_H=(alpha(1)*TEM+alpha(2)*TEM*TEM/2.D0 | |
| - & +alpha(3)*TEM*TEM*TEM/3.D0+alpha(4)*TEM*TEM*TEM*TEM/4.D0 | |
| - & +alpha(5)*TEM*TEM*TEM*TEM*TEM/5.D0)*ROL/1000.d0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_CHEM_S(TEM,alpha) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH | |
| - DIMENSION alpha(5) | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| -! WRITE(*,*) ALPHA(1:5) | |
| -! WRITE(*,*) TEM | |
| - PHI_CHEM_S=(alpha(1)*DLOG(TEM)+alpha(2)*TEM | |
| - & +alpha(3)*TEM*TEM/2.D0+alpha(4)*TEM*TEM*TEM/3.D0 | |
| - & +alpha(5)*TEM*TEM*TEM*TEM/4.D0)*ROL | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| +C: Add the constrains to the first and second derivatives | |
| +C: Therefore, there are three constrains: Cp, DCp, and D2Cp | |
| +C: -------------------------------------------------------------- | |
| +C: For CHEMKIN | |
| +C: Use a single matrix to calculate all 10 coefficients | |
| +C: [A]: M x 10 | |
| +C: [X]: 10 x 1 (alpha1_low,alpha2_low,alpha3_low,alpha4_low,alpha5_low, | |
| +C: alpha1_hig,alpha2_hig,alpha3_hig,alpha4_hig,alpha5_hig) | |
| +C: [C]: M x 1 | |
| +C: Contrains: CP, dCP/dT, and d2CP/d2T | |
| +C: at the intermediate temperature Tint | |
| +C: [B]: 3 x 10 | |
| +C: [D]: 3 x 1 | |
| +C---------------------------------------------------------------- | |
| +C FOR CHEMKIN CHEMTHERMO DATA FORMAT | |
| +C number of coefficients: N=5 x 2 | |
| +C number of discrete data point: M>=N, i.e., M=102 | |
| +C | |
| +C use the DGGLSE to solve the linear least squares equality-constrained | |
| +C (LlSE) problem. | |
| +C%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| +C: Need to change the value of M according to the size of sample data | |
| +!******************************************************************** | |
| +! Programmed by John Z. Wen, MIT, June 2005 | |
| +!******************************************************************** | |
| +C | |
| + SUBROUTINE CHEM(Tint,TNEW,THERM1,THERM2,TEMP1,C1,CH1,CS1) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION Tint,TNEW,THERM1,THERM2 | |
| + DOUBLE PRECISION H_298,S_298,DLTH | |
| +C | |
| + INTEGER M,N,P,LDA,LDB,LWORK,INFO,M1 | |
| + INTEGER MH,NH,PH,LDAH,LDBH,LWORKH | |
| + INTEGER MS,NS,PS,LDAS,LDBS,LWORKS | |
| + DOUBLE PRECISION A1,B1,Bk,C1,D1,X1,WORK1 | |
| + DOUBLE PRECISION TEMP1,PHI_CHEM1,PHI_CHEM2,PHI_CHEM3, | |
| + & PHI_CHEM4,PHI_CHEM5,ROL | |
| + DOUBLE PRECISION PHI_CHEM_DCP1,PHI_CHEM_DCP2,PHI_CHEM_DCP3, | |
| + & PHI_CHEM_DCP4,PHI_CHEM_DCP5,PHI_CHEM_D2CP1, | |
| + & PHI_CHEM_D2CP2,PHI_CHEM_D2CP3,PHI_CHEM_D2CP4, | |
| + & PHI_CHEM_D2CP5 | |
| + DOUBLE PRECISION A_H1,A_S1,A_H2,A_S2 | |
| + DOUBLE PRECISION AH1,BH1,CH1,DH1,XH1,WORKH,BHk,CH,CH2 | |
| + DOUBLE PRECISION AS1,BS1,CS1,DS1,XS1,WORKS,BSk,CS,CS2 | |
| + DOUBLE PRECISION PHI_CHEM_H,PHI_CHEM_S | |
| + INTEGER MARK1 | |
| + DOUBLE PRECISION TEMP,C | |
| +C | |
| +C Required by LSEC solver: | |
| +! LDA >= MAX(1,M) | |
| +! LDB >= MAX(1,P) | |
| +! LWORK >= max(1,M+N+P) | |
| +! P=1 for only one constrain at the intermediate temp. | |
| +! P=3 for three constrains at the intermediate temp. | |
| +C | |
| +C CHANGE 'LWORK' if NECESSARY | |
| + PARAMETER (M=102) | |
| + PARAMETER (LDB=3,P=3) | |
| + PARAMETER (N=10) | |
| + DIMENSION A1(M,N),B1(LDB,N),C1(M-1),D1(P),X1(N),WORK1(M+N+P), | |
| + & Bk(LDB,N) | |
| + PARAMETER (LDBH=2,PH=2) | |
| + PARAMETER (NH=2) | |
| + PARAMETER (LDBS=2,PS=2) | |
| + PARAMETER (NS=2) | |
| + DIMENSION AH1(M,NH),BH1(LDBH,NH),CH1(M-1),DH1(PH),XH1(NH), | |
| + & WORKH(M+NH+PH),BHk(LDBH,NH),CH(M),CH2(M) | |
| + DIMENSION AS1(M,NS),BS1(LDBS,NS),CS1(M-1),DS1(PS),XS1(NS), | |
| + & WORKS(M+NS+PS),BSk(LDBS,NS),CS(M),CS2(M) | |
| + DIMENSION TEMP1(M-1),THERM1(7),THERM2(7) | |
| + DIMENSION TEMP(M),C(M) | |
| + INTEGER I,J | |
| +C | |
| +! GAS CONSTANT | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + EXTERNAL PHI_CHEM1,PHI_CHEM2,PHI_CHEM3,PHI_CHEM4,PHI_CHEM5, | |
| + & PHI_CHEM_DCP1,PHI_CHEM_DCP2,PHI_CHEM_DCP3, | |
| + & PHI_CHEM_DCP4,PHI_CHEM_DCP5,PHI_CHEM_D2CP1, | |
| + & PHI_CHEM_D2CP2,PHI_CHEM_D2CP3,PHI_CHEM_D2CP4, | |
| + & PHI_CHEM_D2CP5,PHI_CHEM_H,PHI_CHEM_S | |
| +C | |
| +! WRITE(*,*) 'CALLED CHEM' | |
| +C | |
| + LDA = M | |
| + LWORK = M+N+P | |
| + MH = M | |
| + LDAH = MH | |
| + LWORKH= MH+NH+PH | |
| + MS = M | |
| + LDAS = MS | |
| + LWORKS= MS+NS+PS | |
| +C | |
| +C FIND 'Tint' and 'Tint1' in sample data | |
| +C | |
| + MARK1 = 0 | |
| + DO I=1,M-1 | |
| + IF (TEMP1(I) .GT. Tint) THEN | |
| + MARK1=I-1 | |
| + IF (Tint .NE. TEMP1(I-1)) THEN | |
| + Tint=TEMP1(I-1) | |
| + TNEW=Tint | |
| +! WRITE(*,*) 'Tint has been replaced!' | |
| + ENDIF | |
| + GOTO 995 | |
| + ENDIF | |
| + ENDDO | |
| + 995 CONTINUE | |
| +! WRITE(*,*) 'MARK1=',MARK1 | |
| +C | |
| +C Rearrange the matrics | |
| +C | |
| + DO I=1,M | |
| + TEMP(I)=0.D0 | |
| + C (I)=0.D0 | |
| + CH (I)=0.D0 | |
| + CS (I)=0.D0 | |
| + CH2 (I)=0.D0 | |
| + CS2 (I)=0.D0 | |
| + ENDDO | |
| +C | |
| + DO I=1,MARK1 | |
| + TEMP(I)=TEMP1(I) | |
| + C (I)=C1(I) | |
| + CH(I)=CH1(I) | |
| + CS(I)=CS1(I) | |
| + ENDDO | |
| + TEMP(MARK1+1)=TEMP(MARK1) | |
| + C (MARK1+1)=C (MARK1) | |
| + CH(MARK1+1)=CH(MARK1) | |
| + CS(MARK1+1)=CS(MARK1) | |
| + DO I=MARK1+2,M | |
| + TEMP(I)=TEMP1(I-1) | |
| + C (I)=C1 (I-1) | |
| + CH(I)=CH1(I-1) | |
| + CS(I)=CS1(I-1) | |
| + ENDDO | |
| +C | |
| +! WRITE(*,*) 'Tint=', Tint | |
| +! WRITE(*,*) TEMP | |
| +! WRITE(*,*) C | |
| +! WRITE(*,*) CH | |
| +! WRITE(*,*) CS | |
| +! PAUSE | |
| +C | |
| + DO I=1,N | |
| + X1(I)=0.D0 | |
| + ENDDO | |
| + DO I=1,N | |
| + DO J=1,LDA | |
| + A1(J,I)=0.D0 | |
| + ENDDO | |
| + DO J=1,LDB | |
| + B1(J,I)=0.D0 | |
| + Bk(J,I)=0.D0 | |
| + ENDDO | |
| + ENDDO | |
| + DO I=1,LWORK | |
| + WORK1(I)=0.D0 | |
| + ENDDO | |
| +C | |
| +! For PHI matrix, first temperature range | |
| + DO I=1,MARK1 | |
| + A1(I,1)=PHI_CHEM1(TEMP(I)) | |
| + A1(I,2)=PHI_CHEM2(TEMP(I)) | |
| + A1(I,3)=PHI_CHEM3(TEMP(I)) | |
| + A1(I,4)=PHI_CHEM4(TEMP(I)) | |
| + A1(I,5)=PHI_CHEM5(TEMP(I)) | |
| + ENDDO | |
| +! For PHI matrix, second temperature range | |
| + DO I=MARK1+1,M | |
| + A1(I,6) =PHI_CHEM1(TEMP(I)) | |
| + A1(I,7) =PHI_CHEM2(TEMP(I)) | |
| + A1(I,8) =PHI_CHEM3(TEMP(I)) | |
| + A1(I,9) =PHI_CHEM4(TEMP(I)) | |
| + A1(I,10)=PHI_CHEM5(TEMP(I)) | |
| + ENDDO | |
| +C | |
| +! WRITE(*,*) TEMP1 | |
| +! WRITE(*,*) C1 | |
| +! PAUSE | |
| +C | |
| +C For Constrains at Tint ------------------------ | |
| +C | |
| +! For CP values | |
| + Bk(1,1) = PHI_CHEM1(Tint) | |
| + Bk(1,2) = PHI_CHEM2(Tint) | |
| + Bk(1,3) = PHI_CHEM3(Tint) | |
| + Bk(1,4) = PHI_CHEM4(Tint) | |
| + Bk(1,5) = PHI_CHEM5(Tint) | |
| + Bk(1,6) =-PHI_CHEM1(Tint) | |
| + Bk(1,7) =-PHI_CHEM2(Tint) | |
| + Bk(1,8) =-PHI_CHEM3(Tint) | |
| + Bk(1,9) =-PHI_CHEM4(Tint) | |
| + Bk(1,10)=-PHI_CHEM5(Tint) | |
| + D1(1)=0.D0 | |
| +C For DCp values | |
| + Bk(2,1) = PHI_CHEM_DCP1(Tint) | |
| + Bk(2,2) = PHI_CHEM_DCP2(Tint) | |
| + Bk(2,3) = PHI_CHEM_DCP3(Tint) | |
| + Bk(2,4) = PHI_CHEM_DCP4(Tint) | |
| + Bk(2,5) = PHI_CHEM_DCP5(Tint) | |
| + Bk(2,6) =-PHI_CHEM_DCP1(Tint) | |
| + Bk(2,7) =-PHI_CHEM_DCP2(Tint) | |
| + Bk(2,8) =-PHI_CHEM_DCP3(Tint) | |
| + Bk(2,9) =-PHI_CHEM_DCP4(Tint) | |
| + Bk(2,10)=-PHI_CHEM_DCP5(Tint) | |
| + D1(2)=0.D0 | |
| +C For D2Cp values | |
| + Bk(3,1) = PHI_CHEM_D2CP1(Tint) | |
| + Bk(3,2) = PHI_CHEM_D2CP2(Tint) | |
| + Bk(3,3) = PHI_CHEM_D2CP3(Tint) | |
| + Bk(3,4) = PHI_CHEM_D2CP4(Tint) | |
| + Bk(3,5) = PHI_CHEM_D2CP5(Tint) | |
| + Bk(3,6) =-PHI_CHEM_D2CP1(Tint) | |
| + Bk(3,7) =-PHI_CHEM_D2CP2(Tint) | |
| + Bk(3,8) =-PHI_CHEM_D2CP3(Tint) | |
| + Bk(3,9) =-PHI_CHEM_D2CP4(Tint) | |
| + Bk(3,10)=-PHI_CHEM_D2CP5(Tint) | |
| + D1(3)=0.D0 | |
| +C | |
| + DO I=1,N | |
| + DO J=1,LDB | |
| + B1(J,I)=Bk(J,I) | |
| + ENDDO | |
| + ENDDO | |
| +C | |
| +! CHEM FORMAT----------------------------------------- | |
| +C | |
| + call DGGLSE(M,N,P,A1,LDA,B1,LDB,C,D1,X1,WORK1,LWORK,INFO) | |
| +! WRITE(*,*) 'X1=',X1(1:10) | |
| +! pause | |
| +C | |
| +C For enthalpy, NEED define 2 coeffs, N=2 | |
| +C | |
| + DO I=1,NH | |
| + XH1(I)=0.D0 | |
| + ENDDO | |
| + DO I=1,NH | |
| + DO J=1,LDAH | |
| + AH1(J,I)=0.D0 | |
| + ENDDO | |
| + DO J=1,LDBH | |
| + BH1(J,I)=0.D0 | |
| + BHk(J,I)=0.D0 | |
| + ENDDO | |
| + ENDDO | |
| + DO I=1,LWORKH | |
| + WORKH(I)=0.D0 | |
| + ENDDO | |
| +C | |
| + DO I=1,MARK1 | |
| + CH2(I)=CH(I) - PHI_CHEM_H(TEMP(I),X1(1:5)) | |
| + ENDDO | |
| + DO I=MARK1+1,MH | |
| + CH2(I)=CH(I) - PHI_CHEM_H(TEMP(I),X1(6:10)) | |
| + ENDDO | |
| +C | |
| + DO I=1,MARK1 | |
| + AH1(I,1)=ROL/1000.d0 | |
| + ENDDO | |
| + DO I=MARK1+1,MH | |
| + AH1(I,2)=ROL/1000.d0 | |
| + ENDDO | |
| +C | |
| +C Contrain for H at Tint | |
| +C | |
| + BHk(1,1)=ROL/1000.d0 | |
| + BHk(1,2)=-ROL/1000.d0 | |
| + DH1(1)=PHI_CHEM_H(Tint,X1(6:10)) | |
| + & -PHI_CHEM_H(Tint,X1(1:5)) | |
| +C | |
| +C Contrain for H at 298.15K | |
| +C | |
| + BHk(2,1)=ROL/1000.d0 | |
| + BHk(2,2)=0.D0 | |
| + DH1(2)=DLTH - PHI_CHEM_H(298.15D0,X1(1:5)) | |
| +C | |
| + DO I=1,NH | |
| + DO J=1,LDBH | |
| + BH1(J,I)=BHk(J,I) | |
| + ENDDO | |
| + ENDDO | |
| +C | |
| + call DGGLSE(MH,NH,PH,AH1,LDAH,BH1,LDBH,CH2,DH1,XH1,WORKH, | |
| + & LWORKH,INFO) | |
| +! WRITE(*,*) 'H_CONST1=',XH1(1) | |
| +! WRITE(*,*) 'H_CONST2=',XH1(2) | |
| +C | |
| + A_H1=XH1(1) | |
| + A_H2=XH1(2) | |
| +C | |
| +C For entropy, NEED define 2 coeffs, N=2 | |
| + DO I=1,NS | |
| + XS1(I)=0.D0 | |
| + ENDDO | |
| + DO I=1,NS | |
| + DO J=1,LDAS | |
| + AS1(J,I)=0.D0 | |
| + ENDDO | |
| + DO J=1,LDBS | |
| + BS1(J,I)=0.D0 | |
| + BSk(J,I)=0.D0 | |
| + ENDDO | |
| + ENDDO | |
| + DO I=1,LWORKS | |
| + WORKS(I)=0.D0 | |
| + ENDDO | |
| +C | |
| + DO I=1,MARK1 | |
| + CS2(I)=CS(I) - PHI_CHEM_S(TEMP(I),X1(1:5)) | |
| + ENDDO | |
| + DO I=MARK1+1,MS | |
| + CS2(I)=CS(I) - PHI_CHEM_S(TEMP(I),X1(6:10)) | |
| + ENDDO | |
| + DO I=1,MARK1 | |
| + AS1(I,1)=ROL | |
| + ENDDO | |
| + DO I=MARK1+1,MS | |
| + AS1(I,2)=ROL | |
| + ENDDO | |
| +C | |
| +C Contrain for S at Tint | |
| +C | |
| + BSk(1,1)=ROL | |
| + BSk(1,2)=-ROL | |
| + DS1(1)=PHI_CHEM_S(Tint,X1(6:10)) | |
| + & -PHI_CHEM_S(Tint,X1(1:5)) | |
| +C | |
| +C Contrain for S at 298.15K | |
| +C | |
| + BSk(2,1)=ROL | |
| + BSk(2,2)=0.D0 | |
| + DS1(2)=S_298 - PHI_CHEM_S(298.15D0,X1(1:5)) | |
| +C | |
| + DO I=1,NS | |
| + DO J=1,LDBS | |
| + BS1(J,I)=BSk(J,I) | |
| + ENDDO | |
| + ENDDO | |
| +C | |
| + call DGGLSE(MS,NS,PS,AS1,LDAS,BS1,LDBS,CS2,DS1,XS1,WORKS, | |
| + & LWORKS,INFO) | |
| +! WRITE(*,*) XS1 | |
| +! WRITE(*,*) 'S_CONST1=',XS1(1) | |
| +! WRITE(*,*) 'S_CONST2=',XS1(2) | |
| +C | |
| + A_S1=XS1(1) | |
| + A_S2=XS1(2) | |
| +C | |
| +C | |
| + DO I=1,5 | |
| + THERM1(I)=X1(I) | |
| + ENDDO | |
| + THERM1(5+1)=A_H1 | |
| + THERM1(5+2)=A_S1 | |
| + DO I=1,5 | |
| + THERM2(I)=X1(I+5) | |
| + ENDDO | |
| + THERM2(5+1)=A_H2 | |
| + THERM2(5+2)=A_S2 | |
| +C | |
| +! WRITE(*,*) 'CHEM OVER' | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM1(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM1=ROL | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM2(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM2=ROL*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM3(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM3=ROL*TEM*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM4(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM4=ROL*TEM*TEM*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM5(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM5=ROL*TEM*TEM*TEM*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM_DCP1(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM_DCP1=0.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM_DCP2(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM_DCP2=ROL | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM_DCP3(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM_DCP3=2.D0*ROL*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM_DCP4(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM_DCP4=3.D0*ROL*TEM*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM_DCP5(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM_DCP5=4.D0*ROL*TEM*TEM*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM_D2CP1(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM_D2CP1=0.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM_D2CP2(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM_D2CP2=0.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM_D2CP3(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM_D2CP3=2.D0*ROL | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM_D2CP4(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM_D2CP4=6.D0*ROL*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM_D2CP5(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM_D2CP5=12.D0*ROL*TEM*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM_H(TEM,alpha) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH | |
| + DIMENSION alpha(5) | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_CHEM_H=(alpha(1)*TEM+alpha(2)*TEM*TEM/2.D0 | |
| + & +alpha(3)*TEM*TEM*TEM/3.D0+alpha(4)*TEM*TEM*TEM*TEM/4.D0 | |
| + & +alpha(5)*TEM*TEM*TEM*TEM*TEM/5.D0)*ROL/1000.d0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_CHEM_S(TEM,alpha) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH | |
| + DIMENSION alpha(5) | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| +! WRITE(*,*) ALPHA(1:5) | |
| +! WRITE(*,*) TEM | |
| + PHI_CHEM_S=(alpha(1)*DLOG(TEM)+alpha(2)*TEM | |
| + & +alpha(3)*TEM*TEM/2.D0+alpha(4)*TEM*TEM*TEM/3.D0 | |
| + & +alpha(5)*TEM*TEM*TEM*TEM/4.D0)*ROL | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| diff --git a/source/GATPFit/lsfp_nasa.f b/source/GATPFit/lsfp_nasa.f | |
| index 6081d16..0775c88 100644 | |
| --- a/source/GATPFit/lsfp_nasa.f | |
| +++ b/source/GATPFit/lsfp_nasa.f | |
| @@ -1,889 +1,866 @@ | |
| -C: Add the constrains to the first and second derivatives | |
| -C: Therefore, there are three constrains: Cp, DCp, and D2Cp | |
| -C: at each intermediate temperature | |
| -C: -------------------------------------------------------------- | |
| -C: For NASA | |
| -C: Use a single matrix to calculate all 21 coefficients | |
| -C: [A]: M x 21 | |
| -C: [X]: 21 x 1 | |
| -C: [alpha1_l,alpha2_l,alpha3_l,alpha4_l,alpha5_l,alpha6_l,alpha7_l, | |
| -C: [alpha1_m,alpha2_m,alpha3_m,alpha4_m,alpha5_m,alpha6_m,alpha7_m, | |
| -C: [alpha1_h,alpha2_h,alpha3_h,alpha4_h,alpha5_h,alpha6_h,alpha7_h] | |
| -C: [C]: M x 1 | |
| -C: Contrains at both temperatures: | |
| -C: [B]: 6 x 21 | |
| -C: [D]: 6 x 1 | |
| -C---------------------------------------------------------------- | |
| -C FOR NASA CHEMTHERMO DATA FORMAT | |
| -C number of coefficients: N=7 x 3 | |
| -C number of discrete data point: M>=N, i.e., M=103 | |
| -C | |
| -C use the DGGLSE to solve the linear least squares equality-constrained | |
| -C (LLSE) problem. | |
| -!**************************************************************** | |
| -! Programmed by John Z. Wen, MIT, June 2005 | |
| -!**************************************************************** | |
| -C | |
| - SUBROUTINE NASA(Tint,TNEW,Tint1,T1NEW, | |
| - & THERM1,THERM2,THERM3,TEMP1,C1,CH1,CS1) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION Tint,Tint1,THERM1,THERM2,THERM3,TNEW,T1NEW | |
| - DOUBLE PRECISION H_298,S_298,DLTH,ROL | |
| -C | |
| - INTEGER M,N,P,LDA,LDB,LWORK,INFO | |
| - INTEGER MH,NH,PH,LDAH,LDBH,LWORKH | |
| - INTEGER MS,NS,PS,LDAS,LDBS,LWORKS | |
| - DOUBLE PRECISION A1,B1,Bk,C1,D1,X1,WORK1 | |
| - DOUBLE PRECISION TEMP1,PHI_NASA1,PHI_NASA2,PHI_NASA3, | |
| - & PHI_NASA4,PHI_NASA5,PHI_NASA6,PHI_NASA7 | |
| - DOUBLE PRECISION PHI_NASA_DCP1,PHI_NASA_DCP2,PHI_NASA_DCP3, | |
| - & PHI_NASA_DCP4,PHI_NASA_DCP5,PHI_NASA_DCP6,PHI_NASA_DCP7, | |
| - & PHI_NASA_D2CP1,PHI_NASA_D2CP2,PHI_NASA_D2CP3, | |
| - & PHI_NASA_D2CP4,PHI_NASA_D2CP5,PHI_NASA_D2CP6, | |
| - & PHI_NASA_D2CP7 | |
| - DOUBLE PRECISION A_H1,A_S1,A_H2,A_S2,A_H3,A_S3 | |
| - DOUBLE PRECISION AH1,BH1,CH1,DH1,XH1,WORKH,BHk,CH,CH2 | |
| - DOUBLE PRECISION AS1,BS1,CS1,DS1,XS1,WORKS,BSk,CS,CS2 | |
| - DOUBLE PRECISION PHI_NASA_H,PHI_NASA_S | |
| - INTEGER MARK1,MARK2 | |
| - DOUBLE PRECISION TEMP,C | |
| -C: Required by llse solver: | |
| -! LDA >= MAX(1,M) | |
| -! LDB >= MAX(1,P) | |
| -! LWORK >= max(1,M+N+P) | |
| -! P=1 for only one constrain at the intermediate temp. | |
| -! P=3 for three constrains at the intermediate temp. | |
| - PARAMETER (M=103) | |
| - PARAMETER (LDB=6,P=6) | |
| - PARAMETER (N=21) | |
| - DIMENSION A1(M,N),B1(LDB,N),C1(M-2),D1(P),X1(N),WORK1(M+N+P), | |
| - & Bk(LDB,N) | |
| - PARAMETER (LDBH=3,PH=3) | |
| - PARAMETER (NH=3) | |
| - PARAMETER (LDBS=3,PS=3) | |
| - PARAMETER (NS=3) | |
| - DIMENSION AH1(M,NH),BH1(LDBH,NH),CH1(M-2),DH1(PH),XH1(NH), | |
| - & WORKH(M+NH+PH),BHk(LDBH,NH),CH(M),CH2(M) | |
| - DIMENSION AS1(M,NS),BS1(LDBS,NS),CS1(M-2),DS1(PS),XS1(NS), | |
| - & WORKS(M+NS+PS),BSk(LDBS,NS),CS(M),CS2(M) | |
| - DIMENSION TEMP1(M-2),THERM1(20),THERM2(20),THERM3(20) | |
| - DIMENSION TEMP(M),C(M) | |
| - INTEGER I,J | |
| -C | |
| -! GAS CONSTANT | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - EXTERNAL PHI_NASA1,PHI_NASA2,PHI_NASA3,PHI_NASA4,PHI_NASA5, | |
| - & PHI_NASA6,PHI_NASA7, | |
| - & PHI_NASA_DCP1,PHI_NASA_DCP2,PHI_NASA_DCP3, | |
| - & PHI_NASA_DCP4,PHI_NASA_DCP5,PHI_NASA_DCP6, | |
| - & PHI_NASA_DCP7, | |
| - & PHI_NASA_D2CP1,PHI_NASA_D2CP2,PHI_NASA_D2CP3, | |
| - & PHI_NASA_D2CP4,PHI_NASA_D2CP5,PHI_NASA_D2CP6, | |
| - & PHI_NASA_D2CP7, | |
| - & PHI_NASA_H,PHI_NASA_S | |
| -C | |
| -! WRITE(*,*) 'CALLED NASA' | |
| -C | |
| - LDA = M | |
| - LWORK = M+N+P | |
| - MH = M | |
| - LDAH = MH | |
| - LWORKH= MH+NH+PH | |
| - MS = M | |
| - LDAS = MS | |
| - LWORKS= MS+NS+PS | |
| -C | |
| -C FIND 'Tint' and 'Tint1' in sample data | |
| -C | |
| - DO I=1,M-2 | |
| - IF (TEMP1(I) .GT. Tint) THEN | |
| - MARK1=I-1 | |
| - IF (Tint .NE. TEMP1(I-1)) THEN | |
| - Tint=TEMP1(I-1) | |
| - TNEW=Tint | |
| -! WRITE(*,*) 'Tint has been replaced!' | |
| - ENDIF | |
| - GOTO 995 | |
| - ENDIF | |
| - ENDDO | |
| - 995 CONTINUE | |
| -! WRITE(*,*) 'MARK1=',MARK1 | |
| -C | |
| - DO I=1,M-2 | |
| - IF (TEMP1(I) .GT. Tint1) THEN | |
| - MARK2=I-1 | |
| - IF (Tint1 .NE. TEMP1(I-1)) THEN | |
| - Tint1=TEMP1(I-1) | |
| - T1NEW=Tint1 | |
| -! WRITE(*,*) 'Tint1 has been replaced!' | |
| - ENDIF | |
| - GOTO 996 | |
| - ENDIF | |
| - ENDDO | |
| - 996 CONTINUE | |
| -! WRITE(*,*) 'MARK2=',MARK2 | |
| -C | |
| -C Rearrange the matrics | |
| -C | |
| - DO I=1,M | |
| - TEMP(I)=0.D0 | |
| - C (I)=0.D0 | |
| - CH (I)=0.D0 | |
| - CS (I)=0.D0 | |
| - CH2 (I)=0.D0 | |
| - CS2 (I)=0.D0 | |
| - ENDDO | |
| -C | |
| - DO I=1,MARK1 | |
| - TEMP(I)=TEMP1(I) | |
| - C (I)=C1 (I) | |
| - CH (I)=CH1 (I) | |
| - CS (I)=CS1 (I) | |
| - ENDDO | |
| - TEMP(MARK1+1)=TEMP(MARK1) | |
| - C (MARK1+1)=C (MARK1) | |
| - CH (MARK1+1)=CH (MARK1) | |
| - CS (MARK1+1)=CS (MARK1) | |
| - DO I=MARK1+2,MARK2+1 | |
| - TEMP(I)=TEMP1(I-1) | |
| - C (I)=C1 (I-1) | |
| - CH (I)=CH1 (I-1) | |
| - CS (I)=CS1 (I-1) | |
| - ENDDO | |
| - TEMP(MARK2+2)=TEMP(MARK2+1) | |
| - C (MARK2+2)=C (MARK2+1) | |
| - CH (MARK2+2)=CH (MARK2+1) | |
| - CS (MARK2+2)=CS (MARK2+1) | |
| - DO I=MARK2+3,M | |
| - TEMP(I)=TEMP1(I-2) | |
| - C (I)=C1 (I-2) | |
| - CH (I)=CH1 (I-2) | |
| - CS (I)=CS1 (I-2) | |
| - ENDDO | |
| -! WRITE(*,*) 'Tint =', Tint | |
| -! WRITE(*,*) 'Tint1=', Tint1 | |
| -! WRITE(*,*) TEMP | |
| -! WRITE(*,*) C | |
| -! WRITE(*,*) CH | |
| -! WRITE(*,*) CS | |
| -C | |
| -C: Redefine the MARKS | |
| -C | |
| - DO I=1,M | |
| - IF (TEMP(I) .EQ. Tint ) THEN | |
| - MARK1=I | |
| - GOTO 997 | |
| - ENDIF | |
| - ENDDO | |
| - 997 CONTINUE | |
| - DO I=1,M | |
| - IF (TEMP(I) .EQ. Tint1) THEN | |
| - MARK2=I | |
| - GOTO 998 | |
| - ENDIF | |
| - ENDDO | |
| - 998 CONTINUE | |
| -! WRITE(*,*) 'MARK1 =', MARK1 | |
| -! WRITE(*,*) 'MARK2 =', MARK2 | |
| -! PAUSE | |
| -C | |
| - DO I=1,N | |
| - X1(I)=0.D0 | |
| - ENDDO | |
| - DO I=1,N | |
| - DO J=1,LDA | |
| - A1(J,I)=0.D0 | |
| - ENDDO | |
| - DO J=1,LDB | |
| - B1(J,I)=0.D0 | |
| - Bk(J,I)=0.D0 | |
| - ENDDO | |
| - ENDDO | |
| - DO I=1,LWORK | |
| - WORK1(I)=0.D0 | |
| - ENDDO | |
| -C | |
| -C For PHI matrix in FIRST temp range | |
| -C | |
| - DO I=1,MARK1 | |
| - A1(I,1)=PHI_NASA1(TEMP(I)) | |
| - A1(I,2)=PHI_NASA2(TEMP(I)) | |
| - A1(I,3)=PHI_NASA3(TEMP(I)) | |
| - A1(I,4)=PHI_NASA4(TEMP(I)) | |
| - A1(I,5)=PHI_NASA5(TEMP(I)) | |
| - A1(I,6)=PHI_NASA6(TEMP(I)) | |
| - A1(I,7)=PHI_NASA7(TEMP(I)) | |
| - ENDDO | |
| -C | |
| -C For PHI matrix in SECOND temp range | |
| -C | |
| - DO I=MARK1+1,MARK2 | |
| - A1(I,8) =PHI_NASA1(TEMP(I)) | |
| - A1(I,9) =PHI_NASA2(TEMP(I)) | |
| - A1(I,10)=PHI_NASA3(TEMP(I)) | |
| - A1(I,11)=PHI_NASA4(TEMP(I)) | |
| - A1(I,12)=PHI_NASA5(TEMP(I)) | |
| - A1(I,13)=PHI_NASA6(TEMP(I)) | |
| - A1(I,14)=PHI_NASA7(TEMP(I)) | |
| - ENDDO | |
| -C | |
| -C For PHI matrix in THIRD temp range | |
| -C | |
| - DO I=MARK2+1,M | |
| - A1(I,15)=PHI_NASA1(TEMP(I)) | |
| - A1(I,16)=PHI_NASA2(TEMP(I)) | |
| - A1(I,17)=PHI_NASA3(TEMP(I)) | |
| - A1(I,18)=PHI_NASA4(TEMP(I)) | |
| - A1(I,19)=PHI_NASA5(TEMP(I)) | |
| - A1(I,20)=PHI_NASA6(TEMP(I)) | |
| - A1(I,21)=PHI_NASA7(TEMP(I)) | |
| - ENDDO | |
| -C | |
| -C For Constrains at Tint------------------------- | |
| -C | |
| -C For CP values | |
| - Bk(1,1) = PHI_NASA1(Tint) | |
| - Bk(1,2) = PHI_NASA2(Tint) | |
| - Bk(1,3) = PHI_NASA3(Tint) | |
| - Bk(1,4) = PHI_NASA4(Tint) | |
| - Bk(1,5) = PHI_NASA5(Tint) | |
| - Bk(1,6) = PHI_NASA6(Tint) | |
| - Bk(1,7) = PHI_NASA7(Tint) | |
| - Bk(1,8) =-PHI_NASA1(Tint) | |
| - Bk(1,9) =-PHI_NASA2(Tint) | |
| - Bk(1,10)=-PHI_NASA3(Tint) | |
| - Bk(1,11)=-PHI_NASA4(Tint) | |
| - Bk(1,12)=-PHI_NASA5(Tint) | |
| - Bk(1,13)=-PHI_NASA6(Tint) | |
| - Bk(1,14)=-PHI_NASA7(Tint) | |
| - D1(1)=0.D0 | |
| -C For DCp values | |
| - Bk(2,1) = PHI_NASA_DCP1(Tint) | |
| - Bk(2,2) = PHI_NASA_DCP2(Tint) | |
| - Bk(2,3) = PHI_NASA_DCP3(Tint) | |
| - Bk(2,4) = PHI_NASA_DCP4(Tint) | |
| - Bk(2,5) = PHI_NASA_DCP5(Tint) | |
| - Bk(2,6) = PHI_NASA_DCP6(Tint) | |
| - Bk(2,7) = PHI_NASA_DCP7(Tint) | |
| - Bk(2,8) =-PHI_NASA_DCP1(Tint) | |
| - Bk(2,9) =-PHI_NASA_DCP2(Tint) | |
| - Bk(2,10)=-PHI_NASA_DCP3(Tint) | |
| - Bk(2,11)=-PHI_NASA_DCP4(Tint) | |
| - Bk(2,12)=-PHI_NASA_DCP5(Tint) | |
| - Bk(2,13)=-PHI_NASA_DCP6(Tint) | |
| - Bk(2,14)=-PHI_NASA_DCP7(Tint) | |
| - D1(2)=0.D0 | |
| -C For D2Cp values | |
| - Bk(3,1) = PHI_NASA_D2CP1(Tint) | |
| - Bk(3,2) = PHI_NASA_D2CP2(Tint) | |
| - Bk(3,3) = PHI_NASA_D2CP3(Tint) | |
| - Bk(3,4) = PHI_NASA_D2CP4(Tint) | |
| - Bk(3,5) = PHI_NASA_D2CP5(Tint) | |
| - Bk(3,6) = PHI_NASA_D2CP6(Tint) | |
| - Bk(3,7) = PHI_NASA_D2CP7(Tint) | |
| - Bk(3,8) =-PHI_NASA_D2CP1(Tint) | |
| - Bk(3,9) =-PHI_NASA_D2CP2(Tint) | |
| - Bk(3,10)=-PHI_NASA_D2CP3(Tint) | |
| - Bk(3,11)=-PHI_NASA_D2CP4(Tint) | |
| - Bk(3,12)=-PHI_NASA_D2CP5(Tint) | |
| - Bk(3,13)=-PHI_NASA_D2CP6(Tint) | |
| - Bk(3,14)=-PHI_NASA_D2CP7(Tint) | |
| - D1(3)=0.D0 | |
| -C | |
| -C For Constrains at Tint1---------------------------- | |
| -C | |
| -C For CP values | |
| - Bk(4,8) = PHI_NASA1(Tint1) | |
| - Bk(4,9) = PHI_NASA2(Tint1) | |
| - Bk(4,10)= PHI_NASA3(Tint1) | |
| - Bk(4,11)= PHI_NASA4(Tint1) | |
| - Bk(4,12)= PHI_NASA5(Tint1) | |
| - Bk(4,13)= PHI_NASA6(Tint1) | |
| - Bk(4,14)= PHI_NASA7(Tint1) | |
| - Bk(4,15)=-PHI_NASA1(Tint1) | |
| - Bk(4,16)=-PHI_NASA2(Tint1) | |
| - Bk(4,17)=-PHI_NASA3(Tint1) | |
| - Bk(4,18)=-PHI_NASA4(Tint1) | |
| - Bk(4,19)=-PHI_NASA5(Tint1) | |
| - Bk(4,20)=-PHI_NASA6(Tint1) | |
| - Bk(4,21)=-PHI_NASA7(Tint1) | |
| - D1(4)=0.D0 | |
| -C For DCp values | |
| - Bk(5,8) = PHI_NASA_DCP1(Tint1) | |
| - Bk(5,9) = PHI_NASA_DCP2(Tint1) | |
| - Bk(5,10)= PHI_NASA_DCP3(Tint1) | |
| - Bk(5,11)= PHI_NASA_DCP4(Tint1) | |
| - Bk(5,12)= PHI_NASA_DCP5(Tint1) | |
| - Bk(5,13)= PHI_NASA_DCP6(Tint1) | |
| - Bk(5,14)= PHI_NASA_DCP7(Tint1) | |
| - Bk(5,15)=-PHI_NASA_DCP1(Tint1) | |
| - Bk(5,16)=-PHI_NASA_DCP2(Tint1) | |
| - Bk(5,17)=-PHI_NASA_DCP3(Tint1) | |
| - Bk(5,18)=-PHI_NASA_DCP4(Tint1) | |
| - Bk(5,19)=-PHI_NASA_DCP5(Tint1) | |
| - Bk(5,20)=-PHI_NASA_DCP6(Tint1) | |
| - Bk(5,21)=-PHI_NASA_DCP7(Tint1) | |
| - D1(5)=0.D0 | |
| -C For D2Cp values | |
| - Bk(6,8) = PHI_NASA_D2CP1(Tint1) | |
| - Bk(6,9) = PHI_NASA_D2CP2(Tint1) | |
| - Bk(6,10)= PHI_NASA_D2CP3(Tint1) | |
| - Bk(6,11)= PHI_NASA_D2CP4(Tint1) | |
| - Bk(6,12)= PHI_NASA_D2CP5(Tint1) | |
| - Bk(6,13)= PHI_NASA_D2CP6(Tint1) | |
| - Bk(6,14)= PHI_NASA_D2CP7(Tint1) | |
| - Bk(6,15)=-PHI_NASA_D2CP1(Tint1) | |
| - Bk(6,16)=-PHI_NASA_D2CP2(Tint1) | |
| - Bk(6,17)=-PHI_NASA_D2CP3(Tint1) | |
| - Bk(6,18)=-PHI_NASA_D2CP4(Tint1) | |
| - Bk(6,19)=-PHI_NASA_D2CP5(Tint1) | |
| - Bk(6,20)=-PHI_NASA_D2CP6(Tint1) | |
| - Bk(6,21)=-PHI_NASA_D2CP7(Tint1) | |
| - D1(6)=0.D0 | |
| -C | |
| - DO I=1,N | |
| - DO J=1,LDB | |
| - B1(J,I)=Bk(J,I) | |
| - ENDDO | |
| - ENDDO | |
| -C | |
| -! NASA FORMAT | |
| -C | |
| - call DGGLSE(M,N,P,A1,LDA,B1,LDB,C,D1,X1,WORK1,LWORK,INFO) | |
| -! WRITE(*,*) 'X1=',X1(1:21) | |
| -! pause | |
| -C | |
| -C For enthalpy, NEED define 2 coeffs, N=3 | |
| - DO I=1,NH | |
| - XH1(I)=0.D0 | |
| - ENDDO | |
| - DO I=1,NH | |
| - DO J=1,LDAH | |
| - AH1(J,I)=0.D0 | |
| - ENDDO | |
| - DO J=1,LDBH | |
| - BH1(J,I)=0.D0 | |
| - BHk(J,I)=0.D0 | |
| - ENDDO | |
| - ENDDO | |
| - DO I=1,LWORKH | |
| - WORKH(I)=0.D0 | |
| - ENDDO | |
| -C | |
| - DO I=1,MARK1 | |
| - CH2(I)=CH(I) - PHI_NASA_H(TEMP(I),X1(1:7)) | |
| - ENDDO | |
| -C | |
| - DO I=MARK1+1,MARK2 | |
| - CH2(I)=CH(I) - PHI_NASA_H(TEMP(I),X1(8:14)) | |
| - ENDDO | |
| -C | |
| - DO I=MARK2+1,MH | |
| - CH2(I)=CH(I) - PHI_NASA_H(TEMP(I),X1(15:21)) | |
| - ENDDO | |
| -C | |
| - DO I=1,MARK1 | |
| - AH1(I,1)=ROL | |
| - ENDDO | |
| - DO I=MARK1+1,MARK2 | |
| - AH1(I,2)=ROL | |
| - ENDDO | |
| - DO I=MARK2+1,MH | |
| - AH1(I,3)=ROL | |
| - ENDDO | |
| -C | |
| -C Contrain for H at Tint | |
| - BHk(1,1)=ROL | |
| - BHk(1,2)=-ROL | |
| - DH1(1)=PHI_NASA_H(Tint,X1(8:14)) | |
| - & -PHI_NASA_H(Tint,X1(1:7)) | |
| -C | |
| -C Contrain for H at 298.15K | |
| - BHk(2,1)=ROL | |
| - BHk(2,2)=0.D0 | |
| -! DH1(2)=CH(1) - PHI_NASA_H(298.D0,X1(1:7)) | |
| - DH1(2)=DLTH - PHI_NASA_H(298.15D0,X1(1:7)) | |
| -C | |
| -C Contrain for H at Tint1 | |
| - BHk(3,2)=ROL | |
| - BHk(3,3)=-ROL | |
| - DH1(3)=PHI_NASA_H(Tint1,X1(15:21)) | |
| - & -PHI_NASA_H(Tint1,X1(8:14)) | |
| -C | |
| - DO I=1,NH | |
| - DO J=1,LDBH | |
| - BH1(J,I)=BHk(J,I) | |
| - ENDDO | |
| - ENDDO | |
| -C | |
| - call DGGLSE(MH,NH,PH,AH1,LDAH,BH1,LDBH,CH2,DH1,XH1,WORKH, | |
| - & LWORKH,INFO) | |
| -! WRITE(*,*) 'H_CONST1=',XH1(1) | |
| -! WRITE(*,*) 'H_CONST2=',XH1(2) | |
| -! WRITE(*,*) 'H_CONST3=',XH1(3) | |
| -C | |
| - A_H1=XH1(1) | |
| - A_H2=XH1(2) | |
| - A_H3=XH1(3) | |
| -C | |
| -C For entropy, NEED define 2 coeffs, N=2 | |
| - DO I=1,NS | |
| - XS1(I)=0.D0 | |
| - ENDDO | |
| - DO I=1,NS | |
| - DO J=1,LDAS | |
| - AS1(J,I)=0.D0 | |
| - ENDDO | |
| - DO J=1,LDBS | |
| - BS1(J,I)=0.D0 | |
| - BSk(J,I)=0.D0 | |
| - ENDDO | |
| - ENDDO | |
| - DO I=1,LWORKS | |
| - WORKS(I)=0.D0 | |
| - ENDDO | |
| -C | |
| - DO I=1,MARK1 | |
| - CS2(I)=CS(I) - PHI_NASA_S(TEMP(I),X1(1:7)) | |
| - ENDDO | |
| - DO I=MARK1+1,MARK2 | |
| - CS2(I)=CS(I) - PHI_NASA_S(TEMP(I),X1(8:14)) | |
| - ENDDO | |
| - DO I=MARK2+1,MS | |
| - CS2(I)=CS(I) - PHI_NASA_S(TEMP(I),X1(15:21)) | |
| - ENDDO | |
| -C | |
| - DO I=1,MARK1 | |
| - AS1(I,1)=ROL | |
| - ENDDO | |
| - DO I=MARK1+1,MARK2 | |
| - AS1(I,2)=ROL | |
| - ENDDO | |
| - DO I=MARK2+1,MS | |
| - AS1(I,3)=ROL | |
| - ENDDO | |
| -C | |
| -C Contrain for S at Tint | |
| - BSk(1,1)=ROL | |
| - BSk(1,2)=-ROL | |
| - DS1(1)=PHI_NASA_S(Tint,X1(8:14)) | |
| - & -PHI_NASA_S(Tint,X1(1:7)) | |
| -C | |
| -C Contrain for S at 298.15K | |
| - BSk(2,1)=ROL | |
| - BSk(2,2)=0.D0 | |
| -! DS1(2)=CS(1) - PHI_NASA_S(298.D0,X1(1:7)) | |
| - DS1(2)=S_298 - PHI_NASA_S(298.15D0,X1(1:7)) | |
| -C | |
| -C Contrain for S at Tint1 | |
| - BSk(3,2)=ROL | |
| - BSk(3,3)=-ROL | |
| - DS1(3)=PHI_NASA_S(Tint1,X1(15:21)) | |
| - & -PHI_NASA_S(Tint1,X1(8:14)) | |
| -C | |
| - DO I=1,NS | |
| - DO J=1,LDBS | |
| - BS1(J,I)=BSk(J,I) | |
| - ENDDO | |
| - ENDDO | |
| -C | |
| - call DGGLSE(MS,NS,PS,AS1,LDAS,BS1,LDBS,CS2,DS1,XS1,WORKS, | |
| - & LWORKS,INFO) | |
| -! WRITE(*,*) XS1 | |
| -! WRITE(*,*) 'S_CONST1=',XS1(1) | |
| -! WRITE(*,*) 'S_CONST2=',XS1(2) | |
| -! WRITE(*,*) 'S_CONST3=',XS1(3) | |
| -C | |
| - A_S1=XS1(1) | |
| - A_S2=XS1(2) | |
| - A_S3=XS1(3) | |
| -C | |
| -C | |
| -C | |
| - DO I=1,7 | |
| - THERM1(I)=X1(I) | |
| - ENDDO | |
| - THERM1(7+1)=A_H1 | |
| - THERM1(7+2)=A_S1 | |
| - DO I=1,7 | |
| - THERM2(I)=X1(I+7) | |
| - ENDDO | |
| - THERM2(7+1)=A_H2 | |
| - THERM2(7+2)=A_S2 | |
| - DO I=1,7 | |
| - THERM3(I)=X1(I+7*2) | |
| - ENDDO | |
| - THERM3(7+1)=A_H3 | |
| - THERM3(7+2)=A_S3 | |
| -! write(*,*) therm1(1:9) | |
| -! write(*,*) therm2(1:9) | |
| -! write(*,*) therm3(1:9) | |
| -C | |
| -! write(*,*) 'NASA OVER!' | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA1(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA1=ROL/(TEM*TEM) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA2(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA2=ROL/TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA3(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA3=ROL | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA4(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA4=ROL*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA5(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA5=ROL*TEM*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA6(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA6=ROL*TEM*TEM*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA7(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA7=ROL*TEM*TEM*TEM*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_DCP1(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_DCP1=-2.D0*ROL/(TEM*TEM*TEM) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_DCP2(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_DCP2=-ROL/(TEM*TEM) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_DCP3(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_DCP3=0.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_DCP4(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_DCP4=ROL | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_DCP5(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_DCP5=2.D0*ROL*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_DCP6(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_DCP6=3.D0*ROL*TEM*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_DCP7(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_DCP7=4.D0*ROL*TEM*TEM*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_D2CP1(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_D2CP1=6.D0*ROL/(TEM*TEM*TEM*TEM) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_D2CP2(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_D2CP2=2.D0*ROL/(TEM*TEM*TEM) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_D2CP3(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_D2CP3=0.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_D2CP4(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_D2CP4=0.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_D2CP5(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_D2CP5=2.D0*ROL | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_D2CP6(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_D2CP6=6.D0*ROL*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_D2CP7(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NASA_D2CP7=12.D0*ROL*TEM*TEM | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_H(TEM,alpha) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH | |
| - DIMENSION alpha(7) | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| -! WRITE(*,*) ALPHA | |
| -! WRITE(*,*) TEM | |
| -! WRITE(*,*) PHI_NASA_H | |
| - PHI_NASA_H=((-1.0D0)*alpha(1)/TEM+alpha(2)*DLOG(TEM)+alpha(3)*TEM | |
| - & +alpha(4)*TEM*TEM/2.D0+alpha(5)*TEM*TEM*TEM/3.D0 | |
| - & +alpha(6)*TEM*TEM*TEM*TEM/4.D0 | |
| - & +alpha(7)*TEM*TEM*TEM*TEM*TEM/5.D0)*ROL | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NASA_S(TEM,alpha) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH | |
| - DIMENSION alpha(7) | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| -! WRITE(*,*) ALPHA(1:7) | |
| -! WRITE(*,*) TEM | |
| - PHI_NASA_S=(-alpha(1)/TEM/TEM/2.D0-alpha(2)/TEM | |
| - & +alpha(3)*DLOG(TEM)+alpha(4)*TEM | |
| - & +alpha(5)*TEM*TEM/2.D0+alpha(6)*TEM*TEM*TEM/3.D0 | |
| - & +alpha(7)*TEM*TEM*TEM*TEM/4.D0)*ROL | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION DLTH298(alpha) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH | |
| - DIMENSION alpha(7) | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - TEM=298.15D0 | |
| - DLTH298=((-1.0D0)*alpha(1)/TEM+alpha(2)*DLOG(TEM)+alpha(3)*TEM | |
| - & +alpha(4)*TEM*TEM/2.D0+alpha(5)*TEM*TEM*TEM/3.D0 | |
| - & +alpha(6)*TEM*TEM*TEM*TEM/4.D0 | |
| - & +alpha(7)*TEM*TEM*TEM*TEM*TEM/5.D0)*ROL | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| +C: Add the constrains to the first and second derivatives | |
| +C: Therefore, there are three constrains: Cp, DCp, and D2Cp | |
| +C: at each intermediate temperature | |
| +C: -------------------------------------------------------------- | |
| +C: For NASA | |
| +C: Use a single matrix to calculate all 21 coefficients | |
| +C: [A]: M x 21 | |
| +C: [X]: 21 x 1 | |
| +C: [alpha1_l,alpha2_l,alpha3_l,alpha4_l,alpha5_l,alpha6_l,alpha7_l, | |
| +C: [alpha1_m,alpha2_m,alpha3_m,alpha4_m,alpha5_m,alpha6_m,alpha7_m, | |
| +C: [alpha1_h,alpha2_h,alpha3_h,alpha4_h,alpha5_h,alpha6_h,alpha7_h] | |
| +C: [C]: M x 1 | |
| +C: Contrains at both temperatures: | |
| +C: [B]: 6 x 21 | |
| +C: [D]: 6 x 1 | |
| +C---------------------------------------------------------------- | |
| +C FOR NASA CHEMTHERMO DATA FORMAT | |
| +C number of coefficients: N=7 x 3 | |
| +C number of discrete data point: M>=N, i.e., M=103 | |
| +C | |
| +C use the DGGLSE to solve the linear least squares equality-constrained | |
| +C (LLSE) problem. | |
| +!**************************************************************** | |
| +! Programmed by John Z. Wen, MIT, June 2005 | |
| +!**************************************************************** | |
| +C | |
| + SUBROUTINE NASA(Tint,TNEW,Tint1,T1NEW, | |
| + & THERM1,THERM2,THERM3,TEMP1,C1,CH1,CS1) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION Tint,Tint1,THERM1,THERM2,THERM3,TNEW,T1NEW | |
| + DOUBLE PRECISION H_298,S_298,DLTH,ROL | |
| +C | |
| + INTEGER M,N,P,LDA,LDB,LWORK,INFO | |
| + INTEGER MH,NH,PH,LDAH,LDBH,LWORKH | |
| + INTEGER MS,NS,PS,LDAS,LDBS,LWORKS | |
| + DOUBLE PRECISION A1,B1,Bk,C1,D1,X1,WORK1 | |
| + DOUBLE PRECISION TEMP1,PHI_NASA1,PHI_NASA2,PHI_NASA3, | |
| + & PHI_NASA4,PHI_NASA5,PHI_NASA6,PHI_NASA7 | |
| + DOUBLE PRECISION PHI_NASA_DCP1,PHI_NASA_DCP2,PHI_NASA_DCP3, | |
| + & PHI_NASA_DCP4,PHI_NASA_DCP5,PHI_NASA_DCP6,PHI_NASA_DCP7, | |
| + & PHI_NASA_D2CP1,PHI_NASA_D2CP2,PHI_NASA_D2CP3, | |
| + & PHI_NASA_D2CP4,PHI_NASA_D2CP5,PHI_NASA_D2CP6, | |
| + & PHI_NASA_D2CP7 | |
| + DOUBLE PRECISION A_H1,A_S1,A_H2,A_S2,A_H3,A_S3 | |
| + DOUBLE PRECISION AH1,BH1,CH1,DH1,XH1,WORKH,BHk,CH,CH2 | |
| + DOUBLE PRECISION AS1,BS1,CS1,DS1,XS1,WORKS,BSk,CS,CS2 | |
| + DOUBLE PRECISION PHI_NASA_H,PHI_NASA_S | |
| + INTEGER MARK1,MARK2 | |
| + DOUBLE PRECISION TEMP,C | |
| +C: Required by llse solver: | |
| +! LDA >= MAX(1,M) | |
| +! LDB >= MAX(1,P) | |
| +! LWORK >= max(1,M+N+P) | |
| +! P=1 for only one constrain at the intermediate temp. | |
| +! P=3 for three constrains at the intermediate temp. | |
| + PARAMETER (M=103) | |
| + PARAMETER (LDB=6,P=6) | |
| + PARAMETER (N=21) | |
| + DIMENSION A1(M,N),B1(LDB,N),C1(M-2),D1(P),X1(N),WORK1(M+N+P), | |
| + & Bk(LDB,N) | |
| + PARAMETER (LDBH=3,PH=3) | |
| + PARAMETER (NH=3) | |
| + PARAMETER (LDBS=3,PS=3) | |
| + PARAMETER (NS=3) | |
| + DIMENSION AH1(M,NH),BH1(LDBH,NH),CH1(M-2),DH1(PH),XH1(NH), | |
| + & WORKH(M+NH+PH),BHk(LDBH,NH),CH(M),CH2(M) | |
| + DIMENSION AS1(M,NS),BS1(LDBS,NS),CS1(M-2),DS1(PS),XS1(NS), | |
| + & WORKS(M+NS+PS),BSk(LDBS,NS),CS(M),CS2(M) | |
| + DIMENSION TEMP1(M-2),THERM1(20),THERM2(20),THERM3(20) | |
| + DIMENSION TEMP(M),C(M) | |
| + INTEGER I,J | |
| +C | |
| +! GAS CONSTANT | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + EXTERNAL PHI_NASA1,PHI_NASA2,PHI_NASA3,PHI_NASA4,PHI_NASA5, | |
| + & PHI_NASA6,PHI_NASA7, | |
| + & PHI_NASA_DCP1,PHI_NASA_DCP2,PHI_NASA_DCP3, | |
| + & PHI_NASA_DCP4,PHI_NASA_DCP5,PHI_NASA_DCP6, | |
| + & PHI_NASA_DCP7, | |
| + & PHI_NASA_D2CP1,PHI_NASA_D2CP2,PHI_NASA_D2CP3, | |
| + & PHI_NASA_D2CP4,PHI_NASA_D2CP5,PHI_NASA_D2CP6, | |
| + & PHI_NASA_D2CP7, | |
| + & PHI_NASA_H,PHI_NASA_S | |
| +C | |
| +! WRITE(*,*) 'CALLED NASA' | |
| +C | |
| + LDA = M | |
| + LWORK = M+N+P | |
| + MH = M | |
| + LDAH = MH | |
| + LWORKH= MH+NH+PH | |
| + MS = M | |
| + LDAS = MS | |
| + LWORKS= MS+NS+PS | |
| +C | |
| +C FIND 'Tint' and 'Tint1' in sample data | |
| +C | |
| + MARK1 = 0 | |
| + DO I=1,M-2 | |
| + IF (TEMP1(I) .GT. Tint) THEN | |
| + MARK1=I-1 | |
| + IF (Tint .NE. TEMP1(I-1)) THEN | |
| + Tint=TEMP1(I-1) | |
| + TNEW=Tint | |
| +! WRITE(*,*) 'Tint has been replaced!' | |
| + ENDIF | |
| + GOTO 995 | |
| + ENDIF | |
| + ENDDO | |
| + 995 CONTINUE | |
| +! WRITE(*,*) 'MARK1=',MARK1 | |
| +C | |
| + MARK2 = 0 | |
| + DO I=1,M-2 | |
| + IF (TEMP1(I) .GT. Tint1) THEN | |
| + MARK2=I-1 | |
| + IF (Tint1 .NE. TEMP1(I-1)) THEN | |
| + Tint1=TEMP1(I-1) | |
| + T1NEW=Tint1 | |
| +! WRITE(*,*) 'Tint1 has been replaced!' | |
| + ENDIF | |
| + GOTO 996 | |
| + ENDIF | |
| + ENDDO | |
| + 996 CONTINUE | |
| +! WRITE(*,*) 'MARK2=',MARK2 | |
| +C | |
| +C Rearrange the matrics | |
| +C | |
| + DO I=1,M | |
| + TEMP(I)=0.D0 | |
| + C (I)=0.D0 | |
| + CH (I)=0.D0 | |
| + CS (I)=0.D0 | |
| + CH2 (I)=0.D0 | |
| + CS2 (I)=0.D0 | |
| + ENDDO | |
| +C | |
| + DO I=1,MARK1 | |
| + TEMP(I)=TEMP1(I) | |
| + C (I)=C1 (I) | |
| + CH (I)=CH1 (I) | |
| + CS (I)=CS1 (I) | |
| + ENDDO | |
| + TEMP(MARK1+1)=TEMP(MARK1) | |
| + C (MARK1+1)=C (MARK1) | |
| + CH (MARK1+1)=CH (MARK1) | |
| + CS (MARK1+1)=CS (MARK1) | |
| + DO I=MARK1+2,MARK2+1 | |
| + TEMP(I)=TEMP1(I-1) | |
| + C (I)=C1 (I-1) | |
| + CH (I)=CH1 (I-1) | |
| + CS (I)=CS1 (I-1) | |
| + ENDDO | |
| + TEMP(MARK2+2)=TEMP(MARK2+1) | |
| + C (MARK2+2)=C (MARK2+1) | |
| + CH (MARK2+2)=CH (MARK2+1) | |
| + CS (MARK2+2)=CS (MARK2+1) | |
| + DO I=MARK2+3,M | |
| + TEMP(I)=TEMP1(I-2) | |
| + C (I)=C1 (I-2) | |
| + CH (I)=CH1 (I-2) | |
| + CS (I)=CS1 (I-2) | |
| + ENDDO | |
| +! WRITE(*,*) 'Tint =', Tint | |
| +! WRITE(*,*) 'Tint1=', Tint1 | |
| +! WRITE(*,*) TEMP | |
| +! WRITE(*,*) C | |
| +! WRITE(*,*) CH | |
| +! WRITE(*,*) CS | |
| +C | |
| +C: Redefine the MARKS | |
| +C | |
| + DO I=1,M | |
| + IF (TEMP(I) .EQ. Tint ) THEN | |
| + MARK1=I | |
| + GOTO 997 | |
| + ENDIF | |
| + ENDDO | |
| + 997 CONTINUE | |
| + DO I=1,M | |
| + IF (TEMP(I) .EQ. Tint1) THEN | |
| + MARK2=I | |
| + GOTO 998 | |
| + ENDIF | |
| + ENDDO | |
| + 998 CONTINUE | |
| +! WRITE(*,*) 'MARK1 =', MARK1 | |
| +! WRITE(*,*) 'MARK2 =', MARK2 | |
| +! PAUSE | |
| +C | |
| + DO I=1,N | |
| + X1(I)=0.D0 | |
| + ENDDO | |
| + DO I=1,N | |
| + DO J=1,LDA | |
| + A1(J,I)=0.D0 | |
| + ENDDO | |
| + DO J=1,LDB | |
| + B1(J,I)=0.D0 | |
| + Bk(J,I)=0.D0 | |
| + ENDDO | |
| + ENDDO | |
| + DO I=1,LWORK | |
| + WORK1(I)=0.D0 | |
| + ENDDO | |
| +C | |
| +C For PHI matrix in FIRST temp range | |
| +C | |
| + DO I=1,MARK1 | |
| + A1(I,1)=PHI_NASA1(TEMP(I)) | |
| + A1(I,2)=PHI_NASA2(TEMP(I)) | |
| + A1(I,3)=PHI_NASA3(TEMP(I)) | |
| + A1(I,4)=PHI_NASA4(TEMP(I)) | |
| + A1(I,5)=PHI_NASA5(TEMP(I)) | |
| + A1(I,6)=PHI_NASA6(TEMP(I)) | |
| + A1(I,7)=PHI_NASA7(TEMP(I)) | |
| + ENDDO | |
| +C | |
| +C For PHI matrix in SECOND temp range | |
| +C | |
| + DO I=MARK1+1,MARK2 | |
| + A1(I,8) =PHI_NASA1(TEMP(I)) | |
| + A1(I,9) =PHI_NASA2(TEMP(I)) | |
| + A1(I,10)=PHI_NASA3(TEMP(I)) | |
| + A1(I,11)=PHI_NASA4(TEMP(I)) | |
| + A1(I,12)=PHI_NASA5(TEMP(I)) | |
| + A1(I,13)=PHI_NASA6(TEMP(I)) | |
| + A1(I,14)=PHI_NASA7(TEMP(I)) | |
| + ENDDO | |
| +C | |
| +C For PHI matrix in THIRD temp range | |
| +C | |
| + DO I=MARK2+1,M | |
| + A1(I,15)=PHI_NASA1(TEMP(I)) | |
| + A1(I,16)=PHI_NASA2(TEMP(I)) | |
| + A1(I,17)=PHI_NASA3(TEMP(I)) | |
| + A1(I,18)=PHI_NASA4(TEMP(I)) | |
| + A1(I,19)=PHI_NASA5(TEMP(I)) | |
| + A1(I,20)=PHI_NASA6(TEMP(I)) | |
| + A1(I,21)=PHI_NASA7(TEMP(I)) | |
| + ENDDO | |
| +C | |
| +C For Constrains at Tint------------------------- | |
| +C | |
| +C For CP values | |
| + Bk(1,1) = PHI_NASA1(Tint) | |
| + Bk(1,2) = PHI_NASA2(Tint) | |
| + Bk(1,3) = PHI_NASA3(Tint) | |
| + Bk(1,4) = PHI_NASA4(Tint) | |
| + Bk(1,5) = PHI_NASA5(Tint) | |
| + Bk(1,6) = PHI_NASA6(Tint) | |
| + Bk(1,7) = PHI_NASA7(Tint) | |
| + Bk(1,8) =-PHI_NASA1(Tint) | |
| + Bk(1,9) =-PHI_NASA2(Tint) | |
| + Bk(1,10)=-PHI_NASA3(Tint) | |
| + Bk(1,11)=-PHI_NASA4(Tint) | |
| + Bk(1,12)=-PHI_NASA5(Tint) | |
| + Bk(1,13)=-PHI_NASA6(Tint) | |
| + Bk(1,14)=-PHI_NASA7(Tint) | |
| + D1(1)=0.D0 | |
| +C For DCp values | |
| + Bk(2,1) = PHI_NASA_DCP1(Tint) | |
| + Bk(2,2) = PHI_NASA_DCP2(Tint) | |
| + Bk(2,3) = PHI_NASA_DCP3(Tint) | |
| + Bk(2,4) = PHI_NASA_DCP4(Tint) | |
| + Bk(2,5) = PHI_NASA_DCP5(Tint) | |
| + Bk(2,6) = PHI_NASA_DCP6(Tint) | |
| + Bk(2,7) = PHI_NASA_DCP7(Tint) | |
| + Bk(2,8) =-PHI_NASA_DCP1(Tint) | |
| + Bk(2,9) =-PHI_NASA_DCP2(Tint) | |
| + Bk(2,10)=-PHI_NASA_DCP3(Tint) | |
| + Bk(2,11)=-PHI_NASA_DCP4(Tint) | |
| + Bk(2,12)=-PHI_NASA_DCP5(Tint) | |
| + Bk(2,13)=-PHI_NASA_DCP6(Tint) | |
| + Bk(2,14)=-PHI_NASA_DCP7(Tint) | |
| + D1(2)=0.D0 | |
| +C For D2Cp values | |
| + Bk(3,1) = PHI_NASA_D2CP1(Tint) | |
| + Bk(3,2) = PHI_NASA_D2CP2(Tint) | |
| + Bk(3,3) = PHI_NASA_D2CP3(Tint) | |
| + Bk(3,4) = PHI_NASA_D2CP4(Tint) | |
| + Bk(3,5) = PHI_NASA_D2CP5(Tint) | |
| + Bk(3,6) = PHI_NASA_D2CP6(Tint) | |
| + Bk(3,7) = PHI_NASA_D2CP7(Tint) | |
| + Bk(3,8) =-PHI_NASA_D2CP1(Tint) | |
| + Bk(3,9) =-PHI_NASA_D2CP2(Tint) | |
| + Bk(3,10)=-PHI_NASA_D2CP3(Tint) | |
| + Bk(3,11)=-PHI_NASA_D2CP4(Tint) | |
| + Bk(3,12)=-PHI_NASA_D2CP5(Tint) | |
| + Bk(3,13)=-PHI_NASA_D2CP6(Tint) | |
| + Bk(3,14)=-PHI_NASA_D2CP7(Tint) | |
| + D1(3)=0.D0 | |
| +C | |
| +C For Constrains at Tint1---------------------------- | |
| +C | |
| +C For CP values | |
| + Bk(4,8) = PHI_NASA1(Tint1) | |
| + Bk(4,9) = PHI_NASA2(Tint1) | |
| + Bk(4,10)= PHI_NASA3(Tint1) | |
| + Bk(4,11)= PHI_NASA4(Tint1) | |
| + Bk(4,12)= PHI_NASA5(Tint1) | |
| + Bk(4,13)= PHI_NASA6(Tint1) | |
| + Bk(4,14)= PHI_NASA7(Tint1) | |
| + Bk(4,15)=-PHI_NASA1(Tint1) | |
| + Bk(4,16)=-PHI_NASA2(Tint1) | |
| + Bk(4,17)=-PHI_NASA3(Tint1) | |
| + Bk(4,18)=-PHI_NASA4(Tint1) | |
| + Bk(4,19)=-PHI_NASA5(Tint1) | |
| + Bk(4,20)=-PHI_NASA6(Tint1) | |
| + Bk(4,21)=-PHI_NASA7(Tint1) | |
| + D1(4)=0.D0 | |
| +C For DCp values | |
| + Bk(5,8) = PHI_NASA_DCP1(Tint1) | |
| + Bk(5,9) = PHI_NASA_DCP2(Tint1) | |
| + Bk(5,10)= PHI_NASA_DCP3(Tint1) | |
| + Bk(5,11)= PHI_NASA_DCP4(Tint1) | |
| + Bk(5,12)= PHI_NASA_DCP5(Tint1) | |
| + Bk(5,13)= PHI_NASA_DCP6(Tint1) | |
| + Bk(5,14)= PHI_NASA_DCP7(Tint1) | |
| + Bk(5,15)=-PHI_NASA_DCP1(Tint1) | |
| + Bk(5,16)=-PHI_NASA_DCP2(Tint1) | |
| + Bk(5,17)=-PHI_NASA_DCP3(Tint1) | |
| + Bk(5,18)=-PHI_NASA_DCP4(Tint1) | |
| + Bk(5,19)=-PHI_NASA_DCP5(Tint1) | |
| + Bk(5,20)=-PHI_NASA_DCP6(Tint1) | |
| + Bk(5,21)=-PHI_NASA_DCP7(Tint1) | |
| + D1(5)=0.D0 | |
| +C For D2Cp values | |
| + Bk(6,8) = PHI_NASA_D2CP1(Tint1) | |
| + Bk(6,9) = PHI_NASA_D2CP2(Tint1) | |
| + Bk(6,10)= PHI_NASA_D2CP3(Tint1) | |
| + Bk(6,11)= PHI_NASA_D2CP4(Tint1) | |
| + Bk(6,12)= PHI_NASA_D2CP5(Tint1) | |
| + Bk(6,13)= PHI_NASA_D2CP6(Tint1) | |
| + Bk(6,14)= PHI_NASA_D2CP7(Tint1) | |
| + Bk(6,15)=-PHI_NASA_D2CP1(Tint1) | |
| + Bk(6,16)=-PHI_NASA_D2CP2(Tint1) | |
| + Bk(6,17)=-PHI_NASA_D2CP3(Tint1) | |
| + Bk(6,18)=-PHI_NASA_D2CP4(Tint1) | |
| + Bk(6,19)=-PHI_NASA_D2CP5(Tint1) | |
| + Bk(6,20)=-PHI_NASA_D2CP6(Tint1) | |
| + Bk(6,21)=-PHI_NASA_D2CP7(Tint1) | |
| + D1(6)=0.D0 | |
| +C | |
| + DO I=1,N | |
| + DO J=1,LDB | |
| + B1(J,I)=Bk(J,I) | |
| + ENDDO | |
| + ENDDO | |
| +C | |
| +! NASA FORMAT | |
| +C | |
| + call DGGLSE(M,N,P,A1,LDA,B1,LDB,C,D1,X1,WORK1,LWORK,INFO) | |
| +! WRITE(*,*) 'X1=',X1(1:21) | |
| +! pause | |
| +C | |
| +C For enthalpy, NEED define 2 coeffs, N=3 | |
| + DO I=1,NH | |
| + XH1(I)=0.D0 | |
| + ENDDO | |
| + DO I=1,NH | |
| + DO J=1,LDAH | |
| + AH1(J,I)=0.D0 | |
| + ENDDO | |
| + DO J=1,LDBH | |
| + BH1(J,I)=0.D0 | |
| + BHk(J,I)=0.D0 | |
| + ENDDO | |
| + ENDDO | |
| + DO I=1,LWORKH | |
| + WORKH(I)=0.D0 | |
| + ENDDO | |
| +C | |
| + DO I=1,MARK1 | |
| + CH2(I)=CH(I) - PHI_NASA_H(TEMP(I),X1(1:7)) | |
| + ENDDO | |
| +C | |
| + DO I=MARK1+1,MARK2 | |
| + CH2(I)=CH(I) - PHI_NASA_H(TEMP(I),X1(8:14)) | |
| + ENDDO | |
| +C | |
| + DO I=MARK2+1,MH | |
| + CH2(I)=CH(I) - PHI_NASA_H(TEMP(I),X1(15:21)) | |
| + ENDDO | |
| +C | |
| + DO I=1,MARK1 | |
| + AH1(I,1)=ROL | |
| + ENDDO | |
| + DO I=MARK1+1,MARK2 | |
| + AH1(I,2)=ROL | |
| + ENDDO | |
| + DO I=MARK2+1,MH | |
| + AH1(I,3)=ROL | |
| + ENDDO | |
| +C | |
| +C Contrain for H at Tint | |
| + BHk(1,1)=ROL | |
| + BHk(1,2)=-ROL | |
| + DH1(1)=PHI_NASA_H(Tint,X1(8:14)) | |
| + & -PHI_NASA_H(Tint,X1(1:7)) | |
| +C | |
| +C Contrain for H at 298.15K | |
| + BHk(2,1)=ROL | |
| + BHk(2,2)=0.D0 | |
| +! DH1(2)=CH(1) - PHI_NASA_H(298.D0,X1(1:7)) | |
| + DH1(2)=DLTH - PHI_NASA_H(298.15D0,X1(1:7)) | |
| +C | |
| +C Contrain for H at Tint1 | |
| + BHk(3,2)=ROL | |
| + BHk(3,3)=-ROL | |
| + DH1(3)=PHI_NASA_H(Tint1,X1(15:21)) | |
| + & -PHI_NASA_H(Tint1,X1(8:14)) | |
| +C | |
| + DO I=1,NH | |
| + DO J=1,LDBH | |
| + BH1(J,I)=BHk(J,I) | |
| + ENDDO | |
| + ENDDO | |
| +C | |
| + call DGGLSE(MH,NH,PH,AH1,LDAH,BH1,LDBH,CH2,DH1,XH1,WORKH, | |
| + & LWORKH,INFO) | |
| +! WRITE(*,*) 'H_CONST1=',XH1(1) | |
| +! WRITE(*,*) 'H_CONST2=',XH1(2) | |
| +! WRITE(*,*) 'H_CONST3=',XH1(3) | |
| +C | |
| + A_H1=XH1(1) | |
| + A_H2=XH1(2) | |
| + A_H3=XH1(3) | |
| +C | |
| +C For entropy, NEED define 2 coeffs, N=2 | |
| + DO I=1,NS | |
| + XS1(I)=0.D0 | |
| + ENDDO | |
| + DO I=1,NS | |
| + DO J=1,LDAS | |
| + AS1(J,I)=0.D0 | |
| + ENDDO | |
| + DO J=1,LDBS | |
| + BS1(J,I)=0.D0 | |
| + BSk(J,I)=0.D0 | |
| + ENDDO | |
| + ENDDO | |
| + DO I=1,LWORKS | |
| + WORKS(I)=0.D0 | |
| + ENDDO | |
| +C | |
| + DO I=1,MARK1 | |
| + CS2(I)=CS(I) - PHI_NASA_S(TEMP(I),X1(1:7)) | |
| + ENDDO | |
| + DO I=MARK1+1,MARK2 | |
| + CS2(I)=CS(I) - PHI_NASA_S(TEMP(I),X1(8:14)) | |
| + ENDDO | |
| + DO I=MARK2+1,MS | |
| + CS2(I)=CS(I) - PHI_NASA_S(TEMP(I),X1(15:21)) | |
| + ENDDO | |
| +C | |
| + DO I=1,MARK1 | |
| + AS1(I,1)=ROL | |
| + ENDDO | |
| + DO I=MARK1+1,MARK2 | |
| + AS1(I,2)=ROL | |
| + ENDDO | |
| + DO I=MARK2+1,MS | |
| + AS1(I,3)=ROL | |
| + ENDDO | |
| +C | |
| +C Contrain for S at Tint | |
| + BSk(1,1)=ROL | |
| + BSk(1,2)=-ROL | |
| + DS1(1)=PHI_NASA_S(Tint,X1(8:14)) | |
| + & -PHI_NASA_S(Tint,X1(1:7)) | |
| +C | |
| +C Contrain for S at 298.15K | |
| + BSk(2,1)=ROL | |
| + BSk(2,2)=0.D0 | |
| +! DS1(2)=CS(1) - PHI_NASA_S(298.D0,X1(1:7)) | |
| + DS1(2)=S_298 - PHI_NASA_S(298.15D0,X1(1:7)) | |
| +C | |
| +C Contrain for S at Tint1 | |
| + BSk(3,2)=ROL | |
| + BSk(3,3)=-ROL | |
| + DS1(3)=PHI_NASA_S(Tint1,X1(15:21)) | |
| + & -PHI_NASA_S(Tint1,X1(8:14)) | |
| +C | |
| + DO I=1,NS | |
| + DO J=1,LDBS | |
| + BS1(J,I)=BSk(J,I) | |
| + ENDDO | |
| + ENDDO | |
| +C | |
| + call DGGLSE(MS,NS,PS,AS1,LDAS,BS1,LDBS,CS2,DS1,XS1,WORKS, | |
| + & LWORKS,INFO) | |
| +! WRITE(*,*) XS1 | |
| +! WRITE(*,*) 'S_CONST1=',XS1(1) | |
| +! WRITE(*,*) 'S_CONST2=',XS1(2) | |
| +! WRITE(*,*) 'S_CONST3=',XS1(3) | |
| +C | |
| + A_S1=XS1(1) | |
| + A_S2=XS1(2) | |
| + A_S3=XS1(3) | |
| +C | |
| +C | |
| +C | |
| + DO I=1,7 | |
| + THERM1(I)=X1(I) | |
| + ENDDO | |
| + THERM1(7+1)=A_H1 | |
| + THERM1(7+2)=A_S1 | |
| + DO I=1,7 | |
| + THERM2(I)=X1(I+7) | |
| + ENDDO | |
| + THERM2(7+1)=A_H2 | |
| + THERM2(7+2)=A_S2 | |
| + DO I=1,7 | |
| + THERM3(I)=X1(I+7*2) | |
| + ENDDO | |
| + THERM3(7+1)=A_H3 | |
| + THERM3(7+2)=A_S3 | |
| +! write(*,*) therm1(1:9) | |
| +! write(*,*) therm2(1:9) | |
| +! write(*,*) therm3(1:9) | |
| +C | |
| +! write(*,*) 'NASA OVER!' | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA1(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA1=ROL/(TEM*TEM) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA2(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA2=ROL/TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA3(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA3=ROL | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA4(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA4=ROL*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA5(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA5=ROL*TEM*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA6(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA6=ROL*TEM*TEM*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA7(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA7=ROL*TEM*TEM*TEM*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_DCP1(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_DCP1=-2.D0*ROL/(TEM*TEM*TEM) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_DCP2(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_DCP2=-ROL/(TEM*TEM) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_DCP3(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_DCP3=0.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_DCP4(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_DCP4=ROL | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_DCP5(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_DCP5=2.D0*ROL*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_DCP6(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_DCP6=3.D0*ROL*TEM*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_DCP7(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_DCP7=4.D0*ROL*TEM*TEM*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_D2CP1(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_D2CP1=6.D0*ROL/(TEM*TEM*TEM*TEM) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_D2CP2(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_D2CP2=2.D0*ROL/(TEM*TEM*TEM) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_D2CP3(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_D2CP3=0.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_D2CP4(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_D2CP4=0.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_D2CP5(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_D2CP5=2.D0*ROL | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_D2CP6(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_D2CP6=6.D0*ROL*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_D2CP7(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NASA_D2CP7=12.D0*ROL*TEM*TEM | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_H(TEM,alpha) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH | |
| + DIMENSION alpha(7) | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| +! WRITE(*,*) ALPHA | |
| +! WRITE(*,*) TEM | |
| +! WRITE(*,*) PHI_NASA_H | |
| + PHI_NASA_H=((-1.0D0)*alpha(1)/TEM+alpha(2)*DLOG(TEM)+alpha(3)*TEM | |
| + & +alpha(4)*TEM*TEM/2.D0+alpha(5)*TEM*TEM*TEM/3.D0 | |
| + & +alpha(6)*TEM*TEM*TEM*TEM/4.D0 | |
| + & +alpha(7)*TEM*TEM*TEM*TEM*TEM/5.D0)*ROL | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NASA_S(TEM,alpha) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH | |
| + DIMENSION alpha(7) | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| +! WRITE(*,*) ALPHA(1:7) | |
| +! WRITE(*,*) TEM | |
| + PHI_NASA_S=(-alpha(1)/TEM/TEM/2.D0-alpha(2)/TEM | |
| + & +alpha(3)*DLOG(TEM)+alpha(4)*TEM | |
| + & +alpha(5)*TEM*TEM/2.D0+alpha(6)*TEM*TEM*TEM/3.D0 | |
| + & +alpha(7)*TEM*TEM*TEM*TEM/4.D0)*ROL | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION DLTH298(alpha) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH | |
| + DIMENSION alpha(7) | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + TEM=298.15D0 | |
| + DLTH298=((-1.0D0)*alpha(1)/TEM+alpha(2)*DLOG(TEM)+alpha(3)*TEM | |
| + & +alpha(4)*TEM*TEM/2.D0+alpha(5)*TEM*TEM*TEM/3.D0 | |
| + & +alpha(6)*TEM*TEM*TEM*TEM/4.D0 | |
| + & +alpha(7)*TEM*TEM*TEM*TEM*TEM/5.D0)*ROL | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| \ No newline at end of file | |
| diff --git a/source/GATPFit/lsfp_nist1.f b/source/GATPFit/lsfp_nist1.f | |
| index 750522b..802c3f2 100644 | |
| --- a/source/GATPFit/lsfp_nist1.f | |
| +++ b/source/GATPFit/lsfp_nist1.f | |
| @@ -1,625 +1,608 @@ | |
| -C: Add the constrains to the first and second derivatives | |
| -C: Therefore, there are three constrains: Cp, DCp, and D2Cp | |
| -C: -------------------------------------------------------------- | |
| -C: For NIST | |
| -C: Use a single matrix to calculate all 10 coefficients | |
| -C: [A]: M x 10 | |
| -C: [X]: 10 x 1 (alpha1_low,alpha2_low,alpha3_low,alpha4_low,alpha5_low, | |
| -C: alpha1_hig,alpha2_hig,alpha3_hig,alpha4_hig,alpha5_hig) | |
| -C: [C]: M x 1 | |
| -C: Contrains: CP, dCP/dT, and d2CP/d2T | |
| -C: at the intermediate temperature Tint | |
| -C: [B]: 3 x 10 | |
| -C: [D]: 3 x 1 | |
| -C---------------------------------------------------------------- | |
| -C FOR NIST CHEMTHERMO DATA FORMAT | |
| -C number of coefficients: N=5 x 2 | |
| -C number of discrete data point: M>=N, i.e., M=102 | |
| -C | |
| -C use the DGGLSE to solve the linear least squares equality-constrained | |
| -C (LlSE) problem. | |
| -!***************************A************************************* | |
| -! Programmed by John Z. Wen, MIT, June 2005 | |
| -!**************************************************************** | |
| -C | |
| - SUBROUTINE NIST(Tint,TNEW,THERM1,THERM2,TEMP1,C1,CH1,CS1) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION Tint,TNEW,THERM1,THERM2 | |
| - DOUBLE PRECISION H_298,S_298,DLTH | |
| -C | |
| - INTEGER M,N,P,LDA,LDB,LWORK,INFO | |
| - INTEGER MH,NH,PH,LDAH,LDBH,LWORKH | |
| - INTEGER MS,NS,PS,LDAS,LDBS,LWORKS | |
| - DOUBLE PRECISION A1,B1,Bk,C1,D1,X1,WORK1 | |
| - DOUBLE PRECISION TEMP1,PHI_NIST1,PHI_NIST2,PHI_NIST3, | |
| - & PHI_NIST4,PHI_NIST5,ROL | |
| - DOUBLE PRECISION PHI_NIST_DCP1,PHI_NIST_DCP2,PHI_NIST_DCP3, | |
| - & PHI_NIST_DCP4,PHI_NIST_DCP5,PHI_NIST_D2CP1, | |
| - & PHI_NIST_D2CP2,PHI_NIST_D2CP3,PHI_NIST_D2CP4, | |
| - & PHI_NIST_D2CP5 | |
| - DOUBLE PRECISION A_H1,A_S1,A_H2,A_S2 | |
| - DOUBLE PRECISION AH1,BH1,CH1,DH1,XH1,WORKH,BHk,CH,CH2 | |
| - DOUBLE PRECISION AS1,BS1,CS1,DS1,XS1,WORKS,BSk,CS,CS2 | |
| - DOUBLE PRECISION PHI_NIST_H,PHI_NIST_S | |
| - INTEGER MARK1 | |
| - DOUBLE PRECISION TEMP,C | |
| -C | |
| -C Required by LSEC solver: | |
| -! LDA >= MAX(1,M) | |
| -! LDB >= MAX(1,P) | |
| -! LWORK >= max(1,M+N+P) | |
| -! P=1 for only one constrain at the intermediate temp. | |
| -! P=3 for three constrains at the intermediate temp. | |
| -C | |
| -C CHANGE 'LWORK' if NECESSARY | |
| - PARAMETER (M=102) | |
| - PARAMETER (LDB=3,P=3) | |
| - PARAMETER (N=10) | |
| - DIMENSION A1(M,N),B1(LDB,N),C1(M-1),D1(P),X1(N),WORK1(M+N+P), | |
| - & Bk(LDB,N) | |
| - PARAMETER (LDBH=2,PH=2) | |
| - PARAMETER (NH=2) | |
| - PARAMETER (LDBS=2,PS=2) | |
| - PARAMETER (NS=2) | |
| - DIMENSION AH1(M,NH),BH1(LDBH,NH),CH1(M-1),DH1(PH),XH1(NH), | |
| - & WORKH(M+NH+PH),BHk(LDBH,NH),CH(M),CH2(M) | |
| - DIMENSION AS1(M,NS),BS1(LDBS,NS),CS1(M-1),DS1(PS),XS1(NS), | |
| - & WORKS(M+NS+PS),BSk(LDBS,NS),CS(M),CS2(M) | |
| - DIMENSION TEMP1(M-1),THERM1(7),THERM2(7) | |
| - DIMENSION TEMP(M),C(M) | |
| - INTEGER I,J | |
| -C | |
| -! GAS CONSTANT | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - EXTERNAL PHI_NIST1,PHI_NIST2,PHI_NIST3,PHI_NIST4,PHI_NIST5, | |
| - & PHI_NIST_DCP1,PHI_NIST_DCP2,PHI_NIST_DCP3, | |
| - & PHI_NIST_DCP4,PHI_NIST_DCP5,PHI_NIST_D2CP1, | |
| - & PHI_NIST_D2CP2,PHI_NIST_D2CP3,PHI_NIST_D2CP4, | |
| - & PHI_NIST_D2CP5,PHI_NIST_H,PHI_NIST_S | |
| -C | |
| -! WRITE(*,*) 'CALLED NIST' | |
| -C | |
| - LDA = M | |
| - LWORK = M+N+P | |
| - MH = M | |
| - LDAH = MH | |
| - LWORKH= MH+NH+PH | |
| - MS = M | |
| - LDAS = MS | |
| - LWORKS= MS+NS+PS | |
| -C | |
| -C FIND 'Tint' and 'Tint1' in sample data | |
| -C | |
| - DO I=1,M-1 | |
| - IF (TEMP1(I) .GT. Tint) THEN | |
| - MARK1=I-1 | |
| - IF (Tint .NE. TEMP1(I-1)) THEN | |
| - Tint=TEMP1(I-1) | |
| - TNEW=Tint | |
| -! WRITE(*,*) 'Tint has been replaced!' | |
| - ENDIF | |
| - GOTO 995 | |
| - ENDIF | |
| - ENDDO | |
| - 995 CONTINUE | |
| -! WRITE(*,*) 'MARK1=',MARK1 | |
| -C | |
| -C Rearrange the matrics | |
| -C | |
| - DO I=1,M | |
| - TEMP(I)=0.D0 | |
| - C (I)=0.D0 | |
| - CH (I)=0.D0 | |
| - CS (I)=0.D0 | |
| - CH2 (I)=0.D0 | |
| - CS2 (I)=0.D0 | |
| - ENDDO | |
| -C | |
| - DO I=1,MARK1 | |
| - TEMP(I)=TEMP1(I) | |
| - C (I)=C1(I) | |
| - CH(I)=CH1(I) | |
| - CS(I)=CS1(I) | |
| - ENDDO | |
| - TEMP(MARK1+1)=TEMP(MARK1) | |
| - C (MARK1+1)=C (MARK1) | |
| - CH(MARK1+1)=CH(MARK1) | |
| - CS(MARK1+1)=CS(MARK1) | |
| - DO I=MARK1+2,M | |
| - TEMP(I)=TEMP1(I-1) | |
| - C (I)=C1 (I-1) | |
| - CH(I)=CH1(I-1) | |
| - CS(I)=CS1(I-1) | |
| - ENDDO | |
| -C | |
| -! WRITE(*,*) 'Tint=', Tint | |
| -! WRITE(*,*) TEMP | |
| -! WRITE(*,*) C | |
| -! WRITE(*,*) CH | |
| -! WRITE(*,*) CS | |
| -! PAUSE | |
| -C | |
| - DO I=1,N | |
| - X1(I)=0.D0 | |
| - ENDDO | |
| - DO I=1,N | |
| - DO J=1,LDA | |
| - A1(J,I)=0.D0 | |
| - ENDDO | |
| - DO J=1,LDB | |
| - B1(J,I)=0.D0 | |
| - Bk(J,I)=0.D0 | |
| - ENDDO | |
| - ENDDO | |
| - DO I=1,LWORK | |
| - WORK1(I)=0.D0 | |
| - ENDDO | |
| -C | |
| -! For PHI matrix, first temperature range | |
| - DO I=1,MARK1 | |
| - A1(I,1)=PHI_NIST1(TEMP(I)) | |
| - A1(I,2)=PHI_NIST2(TEMP(I)) | |
| - A1(I,3)=PHI_NIST3(TEMP(I)) | |
| - A1(I,4)=PHI_NIST4(TEMP(I)) | |
| - A1(I,5)=PHI_NIST5(TEMP(I)) | |
| - ENDDO | |
| -! For PHI matrix, second temperature range | |
| - DO I=MARK1+1,M | |
| - A1(I,6) =PHI_NIST1(TEMP(I)) | |
| - A1(I,7) =PHI_NIST2(TEMP(I)) | |
| - A1(I,8) =PHI_NIST3(TEMP(I)) | |
| - A1(I,9) =PHI_NIST4(TEMP(I)) | |
| - A1(I,10)=PHI_NIST5(TEMP(I)) | |
| - ENDDO | |
| -C | |
| -! WRITE(*,*) TEMP1 | |
| -! WRITE(*,*) C1 | |
| -! PAUSE | |
| -C | |
| -C For Constrains at Tint ------------------------ | |
| -C | |
| -! For CP values | |
| - Bk(1,1) = PHI_NIST1(Tint) | |
| - Bk(1,2) = PHI_NIST2(Tint) | |
| - Bk(1,3) = PHI_NIST3(Tint) | |
| - Bk(1,4) = PHI_NIST4(Tint) | |
| - Bk(1,5) = PHI_NIST5(Tint) | |
| - Bk(1,6) =-PHI_NIST1(Tint) | |
| - Bk(1,7) =-PHI_NIST2(Tint) | |
| - Bk(1,8) =-PHI_NIST3(Tint) | |
| - Bk(1,9) =-PHI_NIST4(Tint) | |
| - Bk(1,10)=-PHI_NIST5(Tint) | |
| - D1(1)=0.D0 | |
| -C For DCp values | |
| - Bk(2,1) = PHI_NIST_DCP1(Tint) | |
| - Bk(2,2) = PHI_NIST_DCP2(Tint) | |
| - Bk(2,3) = PHI_NIST_DCP3(Tint) | |
| - Bk(2,4) = PHI_NIST_DCP4(Tint) | |
| - Bk(2,5) = PHI_NIST_DCP5(Tint) | |
| - Bk(2,6) =-PHI_NIST_DCP1(Tint) | |
| - Bk(2,7) =-PHI_NIST_DCP2(Tint) | |
| - Bk(2,8) =-PHI_NIST_DCP3(Tint) | |
| - Bk(2,9) =-PHI_NIST_DCP4(Tint) | |
| - Bk(2,10)=-PHI_NIST_DCP5(Tint) | |
| - D1(2)=0.D0 | |
| -C For D2Cp values | |
| - Bk(3,1) = PHI_NIST_D2CP1(Tint) | |
| - Bk(3,2) = PHI_NIST_D2CP2(Tint) | |
| - Bk(3,3) = PHI_NIST_D2CP3(Tint) | |
| - Bk(3,4) = PHI_NIST_D2CP4(Tint) | |
| - Bk(3,5) = PHI_NIST_D2CP5(Tint) | |
| - Bk(3,6) =-PHI_NIST_D2CP1(Tint) | |
| - Bk(3,7) =-PHI_NIST_D2CP2(Tint) | |
| - Bk(3,8) =-PHI_NIST_D2CP3(Tint) | |
| - Bk(3,9) =-PHI_NIST_D2CP4(Tint) | |
| - Bk(3,10)=-PHI_NIST_D2CP5(Tint) | |
| - D1(3)=0.D0 | |
| -C | |
| - DO I=1,N | |
| - DO J=1,LDB | |
| - B1(J,I)=Bk(J,I) | |
| - ENDDO | |
| - ENDDO | |
| -C | |
| -! NIST FORMAT----------------------------------------- | |
| -C | |
| - call DGGLSE(M,N,P,A1,LDA,B1,LDB,C,D1,X1,WORK1,LWORK,INFO) | |
| -! WRITE(*,*) 'X1=',X1(1:10) | |
| -! pause | |
| -C | |
| -C For enthalpy, NEED define 2 coeffs, N=2 | |
| -C | |
| - DO I=1,NH | |
| - XH1(I)=0.D0 | |
| - ENDDO | |
| - DO I=1,NH | |
| - DO J=1,LDAH | |
| - AH1(J,I)=0.D0 | |
| - ENDDO | |
| - DO J=1,LDBH | |
| - BH1(J,I)=0.D0 | |
| - BHk(J,I)=0.D0 | |
| - ENDDO | |
| - ENDDO | |
| - DO I=1,LWORKH | |
| - WORKH(I)=0.D0 | |
| - ENDDO | |
| -C | |
| - DO I=1,MARK1 | |
| - CH2(I)=CH(I)+ DLTH - H_298 - PHI_NIST_H(TEMP(I),X1(1:5)) | |
| - ENDDO | |
| - DO I=MARK1+1,MH | |
| - CH2(I)=CH(I)+ DLTH - H_298 - PHI_NIST_H(TEMP(I),X1(6:10)) | |
| - ENDDO | |
| -C | |
| - DO I=1,MARK1 | |
| - AH1(I,1)=1.0D0 | |
| - ENDDO | |
| - DO I=MARK1+1,MH | |
| - AH1(I,2)=1.0D0 | |
| - ENDDO | |
| -C | |
| -C Contrain for H at Tint | |
| -C | |
| - BHk(1,1)=1.0D0 | |
| - BHk(1,2)=-1.0D0 | |
| - DH1(1)=PHI_NIST_H(Tint,X1(6:10)) | |
| - & -PHI_NIST_H(Tint,X1(1:5)) | |
| -C | |
| -C Contrain for H at 298.15K | |
| -C | |
| - BHk(2,1)=1.0D0 | |
| - BHk(2,2)=0.D0 | |
| - DH1(2)=H_298 + DLTH - H_298 - PHI_NIST_H(298.15D0,X1(1:5)) | |
| -C | |
| - DO I=1,NH | |
| - DO J=1,LDBH | |
| - BH1(J,I)=BHk(J,I) | |
| - ENDDO | |
| - ENDDO | |
| -C | |
| - call DGGLSE(MH,NH,PH,AH1,LDAH,BH1,LDBH,CH2,DH1,XH1,WORKH, | |
| - & LWORKH,INFO) | |
| -! WRITE(*,*) 'H_CONST1=',XH1(1) | |
| -! WRITE(*,*) 'H_CONST2=',XH1(2) | |
| -C | |
| - A_H1=XH1(1) | |
| - A_H2=XH1(2) | |
| -C | |
| -C For entropy, NEED define 2 coeffs, N=2 | |
| - DO I=1,NS | |
| - XS1(I)=0.D0 | |
| - ENDDO | |
| - DO I=1,NS | |
| - DO J=1,LDAS | |
| - AS1(J,I)=0.D0 | |
| - ENDDO | |
| - DO J=1,LDBS | |
| - BS1(J,I)=0.D0 | |
| - BSk(J,I)=0.D0 | |
| - ENDDO | |
| - ENDDO | |
| - DO I=1,LWORKS | |
| - WORKS(I)=0.D0 | |
| - ENDDO | |
| -C | |
| - DO I=1,MARK1 | |
| - CS2(I)=CS(I) - PHI_NIST_S(TEMP(I),X1(1:5)) | |
| - ENDDO | |
| - DO I=MARK1+1,MS | |
| - CS2(I)=CS(I) - PHI_NIST_S(TEMP(I),X1(6:10)) | |
| - ENDDO | |
| - DO I=1,MARK1 | |
| - AS1(I,1)=1.0D0 | |
| - ENDDO | |
| - DO I=MARK1+1,MS | |
| - AS1(I,2)=1.0D0 | |
| - ENDDO | |
| -C | |
| -C Contrain for S at Tint | |
| -C | |
| - BSk(1,1)=1.0D0 | |
| - BSk(1,2)=-1.0D0 | |
| - DS1(1)=PHI_NIST_S(Tint,X1(6:10)) | |
| - & -PHI_NIST_S(Tint,X1(1:5)) | |
| -C | |
| -C Contrain for S at 298.15K | |
| -C | |
| - BSk(2,1)=1.0D0 | |
| - BSk(2,2)=0.0D0 | |
| -! DS1(2)=CS(1) - PHI_NIST_S(298.D0,X1(1:5)) | |
| - DS1(2)=S_298 - PHI_NIST_S(298.15D0,X1(1:5)) | |
| -C | |
| - DO I=1,NS | |
| - DO J=1,LDBS | |
| - BS1(J,I)=BSk(J,I) | |
| - ENDDO | |
| - ENDDO | |
| -C | |
| - call DGGLSE(MS,NS,PS,AS1,LDAS,BS1,LDBS,CS2,DS1,XS1,WORKS, | |
| - & LWORKS,INFO) | |
| -! WRITE(*,*) XS1 | |
| -! WRITE(*,*) 'S_CONST1=',XS1(1) | |
| -! WRITE(*,*) 'S_CONST2=',XS1(2) | |
| -C | |
| - A_S1=XS1(1) | |
| - A_S2=XS1(2) | |
| -C | |
| -C | |
| - DO I=1,5 | |
| - THERM1(I)=X1(I) | |
| - ENDDO | |
| - THERM1(5+1)=A_H1 | |
| - THERM1(5+2)=A_S1 | |
| - DO I=1,5 | |
| - THERM2(I)=X1(I+5) | |
| - ENDDO | |
| - THERM2(5+1)=A_H2 | |
| - THERM2(5+2)=A_S2 | |
| -C | |
| -! WRITE(*,*) THERM1(1:7) | |
| -! WRITE(*,*) THERM2(1:7) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST1(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST1=1.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST2(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST2=TEM/1000.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST3(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST3=(TEM/1000.D0)*(TEM/1000.D0) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST4(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST4=(TEM/1000.D0)*(TEM/1000.D0)*(TEM/1000.D0) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST5(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST5=1.0D0/(TEM/1000.D0)/(TEM/1000.D0) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST_DCP1(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST_DCP1=0.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST_DCP2(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST_DCP2=1.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST_DCP3(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST_DCP3=2.D0*(TEM/1000.D0) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST_DCP4(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST_DCP4=3.D0*(TEM/1000.D0)*(TEM/1000.D0) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST_DCP5(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST_DCP5=-2.D0/(TEM/1000.D0)/(TEM/1000.D0)/(TEM/1000.D0) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST_D2CP1(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST_D2CP1=0.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST_D2CP2(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST_D2CP2=0.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST_D2CP3(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST_D2CP3=2.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST_D2CP4(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST_D2CP4=6.D0*(TEM/1000.D0) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST_D2CP5(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - PHI_NIST_D2CP5=6.D0/(TEM/1000.D0)/(TEM/1000.D0) | |
| - & /(TEM/1000.D0)/(TEM/1000.D0) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST_H(TEM,alpha) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH,T1000 | |
| - DIMENSION alpha(5) | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| - T1000=TEM/1000.D0 | |
| - PHI_NIST_H=alpha(1)*T1000+alpha(2)*T1000*T1000/2.D0 | |
| - & +alpha(3)*T1000*T1000*T1000/3.D0 | |
| - & +alpha(4)*T1000*T1000*T1000*T1000/4.D0 | |
| - & -alpha(5)/T1000 | |
| -! WRITE(*,*) 'PHI_NIST_H=',PHI_NIST_H | |
| - WRITE(*,*) 'H calculated by Shomate is too small!' | |
| - WRITE(*,*) 'warning! warning! warning!' | |
| - PAUSE | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI_NIST_S(TEM,alpha) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH,T1000 | |
| - DIMENSION alpha(5) | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| -C | |
| -! WRITE(*,*) ALPHA(1:5) | |
| -! WRITE(*,*) TEM | |
| - T1000=TEM/1000.D0 | |
| - PHI_NIST_S=alpha(1)*DLOG(T1000)+alpha(2)*T1000 | |
| - & +alpha(3)*T1000*T1000/2.D0 | |
| - & +alpha(4)*T1000*T1000*T1000/3.D0 | |
| - & -alpha(5)/T1000/T1000/2.D0 | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| +C: Add the constrains to the first and second derivatives | |
| +C: Therefore, there are three constrains: Cp, DCp, and D2Cp | |
| +C: -------------------------------------------------------------- | |
| +C: For NIST | |
| +C: Use a single matrix to calculate all 10 coefficients | |
| +C: [A]: M x 10 | |
| +C: [X]: 10 x 1 (alpha1_low,alpha2_low,alpha3_low,alpha4_low,alpha5_low, | |
| +C: alpha1_hig,alpha2_hig,alpha3_hig,alpha4_hig,alpha5_hig) | |
| +C: [C]: M x 1 | |
| +C: Contrains: CP, dCP/dT, and d2CP/d2T | |
| +C: at the intermediate temperature Tint | |
| +C: [B]: 3 x 10 | |
| +C: [D]: 3 x 1 | |
| +C---------------------------------------------------------------- | |
| +C FOR NIST CHEMTHERMO DATA FORMAT | |
| +C number of coefficients: N=5 x 2 | |
| +C number of discrete data point: M>=N, i.e., M=102 | |
| +C | |
| +C use the DGGLSE to solve the linear least squares equality-constrained | |
| +C (LlSE) problem. | |
| +!***************************A************************************* | |
| +! Programmed by John Z. Wen, MIT, June 2005 | |
| +!**************************************************************** | |
| +C | |
| + SUBROUTINE NIST(Tint,TNEW,THERM1,THERM2,TEMP1,C1,CH1,CS1) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION Tint,TNEW,THERM1,THERM2 | |
| + DOUBLE PRECISION H_298,S_298,DLTH | |
| +C | |
| + INTEGER M,N,P,LDA,LDB,LWORK,INFO | |
| + INTEGER MH,NH,PH,LDAH,LDBH,LWORKH | |
| + INTEGER MS,NS,PS,LDAS,LDBS,LWORKS | |
| + DOUBLE PRECISION A1,B1,Bk,C1,D1,X1,WORK1 | |
| + DOUBLE PRECISION TEMP1,PHI_NIST1,PHI_NIST2,PHI_NIST3, | |
| + & PHI_NIST4,PHI_NIST5,ROL | |
| + DOUBLE PRECISION PHI_NIST_DCP1,PHI_NIST_DCP2,PHI_NIST_DCP3, | |
| + & PHI_NIST_DCP4,PHI_NIST_DCP5,PHI_NIST_D2CP1, | |
| + & PHI_NIST_D2CP2,PHI_NIST_D2CP3,PHI_NIST_D2CP4, | |
| + & PHI_NIST_D2CP5 | |
| + DOUBLE PRECISION A_H1,A_S1,A_H2,A_S2 | |
| + DOUBLE PRECISION AH1,BH1,CH1,DH1,XH1,WORKH,BHk,CH,CH2 | |
| + DOUBLE PRECISION AS1,BS1,CS1,DS1,XS1,WORKS,BSk,CS,CS2 | |
| + DOUBLE PRECISION PHI_NIST_H,PHI_NIST_S | |
| + INTEGER MARK1 | |
| + DOUBLE PRECISION TEMP,C | |
| +C | |
| +C Required by LSEC solver: | |
| +! LDA >= MAX(1,M) | |
| +! LDB >= MAX(1,P) | |
| +! LWORK >= max(1,M+N+P) | |
| +! P=1 for only one constrain at the intermediate temp. | |
| +! P=3 for three constrains at the intermediate temp. | |
| +C | |
| +C CHANGE 'LWORK' if NECESSARY | |
| + PARAMETER (M=102) | |
| + PARAMETER (LDB=3,P=3) | |
| + PARAMETER (N=10) | |
| + DIMENSION A1(M,N),B1(LDB,N),C1(M-1),D1(P),X1(N),WORK1(M+N+P), | |
| + & Bk(LDB,N) | |
| + PARAMETER (LDBH=2,PH=2) | |
| + PARAMETER (NH=2) | |
| + PARAMETER (LDBS=2,PS=2) | |
| + PARAMETER (NS=2) | |
| + DIMENSION AH1(M,NH),BH1(LDBH,NH),CH1(M-1),DH1(PH),XH1(NH), | |
| + & WORKH(M+NH+PH),BHk(LDBH,NH),CH(M),CH2(M) | |
| + DIMENSION AS1(M,NS),BS1(LDBS,NS),CS1(M-1),DS1(PS),XS1(NS), | |
| + & WORKS(M+NS+PS),BSk(LDBS,NS),CS(M),CS2(M) | |
| + DIMENSION TEMP1(M-1),THERM1(7),THERM2(7) | |
| + DIMENSION TEMP(M),C(M) | |
| + INTEGER I,J | |
| +C | |
| +! GAS CONSTANT | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + EXTERNAL PHI_NIST1,PHI_NIST2,PHI_NIST3,PHI_NIST4,PHI_NIST5, | |
| + & PHI_NIST_DCP1,PHI_NIST_DCP2,PHI_NIST_DCP3, | |
| + & PHI_NIST_DCP4,PHI_NIST_DCP5,PHI_NIST_D2CP1, | |
| + & PHI_NIST_D2CP2,PHI_NIST_D2CP3,PHI_NIST_D2CP4, | |
| + & PHI_NIST_D2CP5,PHI_NIST_H,PHI_NIST_S | |
| +C | |
| +! WRITE(*,*) 'CALLED NIST' | |
| +C | |
| + LDA = M | |
| + LWORK = M+N+P | |
| + MH = M | |
| + LDAH = MH | |
| + LWORKH= MH+NH+PH | |
| + MS = M | |
| + LDAS = MS | |
| + LWORKS= MS+NS+PS | |
| +C | |
| +C FIND 'Tint' and 'Tint1' in sample data | |
| +C | |
| + MARK1 = 0 | |
| + DO I=1,M-1 | |
| + IF (TEMP1(I) .GT. Tint) THEN | |
| + MARK1=I-1 | |
| + IF (Tint .NE. TEMP1(I-1)) THEN | |
| + Tint=TEMP1(I-1) | |
| + TNEW=Tint | |
| +! WRITE(*,*) 'Tint has been replaced!' | |
| + ENDIF | |
| + GOTO 995 | |
| + ENDIF | |
| + ENDDO | |
| + 995 CONTINUE | |
| +! WRITE(*,*) 'MARK1=',MARK1 | |
| +C | |
| +C Rearrange the matrics | |
| +C | |
| + DO I=1,M | |
| + TEMP(I)=0.D0 | |
| + C (I)=0.D0 | |
| + CH (I)=0.D0 | |
| + CS (I)=0.D0 | |
| + CH2 (I)=0.D0 | |
| + CS2 (I)=0.D0 | |
| + ENDDO | |
| +C | |
| + DO I=1,MARK1 | |
| + TEMP(I)=TEMP1(I) | |
| + C (I)=C1(I) | |
| + CH(I)=CH1(I) | |
| + CS(I)=CS1(I) | |
| + ENDDO | |
| + TEMP(MARK1+1)=TEMP(MARK1) | |
| + C (MARK1+1)=C (MARK1) | |
| + CH(MARK1+1)=CH(MARK1) | |
| + CS(MARK1+1)=CS(MARK1) | |
| + DO I=MARK1+2,M | |
| + TEMP(I)=TEMP1(I-1) | |
| + C (I)=C1 (I-1) | |
| + CH(I)=CH1(I-1) | |
| + CS(I)=CS1(I-1) | |
| + ENDDO | |
| +C | |
| +! WRITE(*,*) 'Tint=', Tint | |
| +! WRITE(*,*) TEMP | |
| +! WRITE(*,*) C | |
| +! WRITE(*,*) CH | |
| +! WRITE(*,*) CS | |
| +! PAUSE | |
| +C | |
| + DO I=1,N | |
| + X1(I)=0.D0 | |
| + ENDDO | |
| + DO I=1,N | |
| + DO J=1,LDA | |
| + A1(J,I)=0.D0 | |
| + ENDDO | |
| + DO J=1,LDB | |
| + B1(J,I)=0.D0 | |
| + Bk(J,I)=0.D0 | |
| + ENDDO | |
| + ENDDO | |
| + DO I=1,LWORK | |
| + WORK1(I)=0.D0 | |
| + ENDDO | |
| +C | |
| +! For PHI matrix, first temperature range | |
| + DO I=1,MARK1 | |
| + A1(I,1)=PHI_NIST1(TEMP(I)) | |
| + A1(I,2)=PHI_NIST2(TEMP(I)) | |
| + A1(I,3)=PHI_NIST3(TEMP(I)) | |
| + A1(I,4)=PHI_NIST4(TEMP(I)) | |
| + A1(I,5)=PHI_NIST5(TEMP(I)) | |
| + ENDDO | |
| +! For PHI matrix, second temperature range | |
| + DO I=MARK1+1,M | |
| + A1(I,6) =PHI_NIST1(TEMP(I)) | |
| + A1(I,7) =PHI_NIST2(TEMP(I)) | |
| + A1(I,8) =PHI_NIST3(TEMP(I)) | |
| + A1(I,9) =PHI_NIST4(TEMP(I)) | |
| + A1(I,10)=PHI_NIST5(TEMP(I)) | |
| + ENDDO | |
| +C | |
| +! WRITE(*,*) TEMP1 | |
| +! WRITE(*,*) C1 | |
| +! PAUSE | |
| +C | |
| +C For Constrains at Tint ------------------------ | |
| +C | |
| +! For CP values | |
| + Bk(1,1) = PHI_NIST1(Tint) | |
| + Bk(1,2) = PHI_NIST2(Tint) | |
| + Bk(1,3) = PHI_NIST3(Tint) | |
| + Bk(1,4) = PHI_NIST4(Tint) | |
| + Bk(1,5) = PHI_NIST5(Tint) | |
| + Bk(1,6) =-PHI_NIST1(Tint) | |
| + Bk(1,7) =-PHI_NIST2(Tint) | |
| + Bk(1,8) =-PHI_NIST3(Tint) | |
| + Bk(1,9) =-PHI_NIST4(Tint) | |
| + Bk(1,10)=-PHI_NIST5(Tint) | |
| + D1(1)=0.D0 | |
| +C For DCp values | |
| + Bk(2,1) = PHI_NIST_DCP1(Tint) | |
| + Bk(2,2) = PHI_NIST_DCP2(Tint) | |
| + Bk(2,3) = PHI_NIST_DCP3(Tint) | |
| + Bk(2,4) = PHI_NIST_DCP4(Tint) | |
| + Bk(2,5) = PHI_NIST_DCP5(Tint) | |
| + Bk(2,6) =-PHI_NIST_DCP1(Tint) | |
| + Bk(2,7) =-PHI_NIST_DCP2(Tint) | |
| + Bk(2,8) =-PHI_NIST_DCP3(Tint) | |
| + Bk(2,9) =-PHI_NIST_DCP4(Tint) | |
| + Bk(2,10)=-PHI_NIST_DCP5(Tint) | |
| + D1(2)=0.D0 | |
| +C For D2Cp values | |
| + Bk(3,1) = PHI_NIST_D2CP1(Tint) | |
| + Bk(3,2) = PHI_NIST_D2CP2(Tint) | |
| + Bk(3,3) = PHI_NIST_D2CP3(Tint) | |
| + Bk(3,4) = PHI_NIST_D2CP4(Tint) | |
| + Bk(3,5) = PHI_NIST_D2CP5(Tint) | |
| + Bk(3,6) =-PHI_NIST_D2CP1(Tint) | |
| + Bk(3,7) =-PHI_NIST_D2CP2(Tint) | |
| + Bk(3,8) =-PHI_NIST_D2CP3(Tint) | |
| + Bk(3,9) =-PHI_NIST_D2CP4(Tint) | |
| + Bk(3,10)=-PHI_NIST_D2CP5(Tint) | |
| + D1(3)=0.D0 | |
| +C | |
| + DO I=1,N | |
| + DO J=1,LDB | |
| + B1(J,I)=Bk(J,I) | |
| + ENDDO | |
| + ENDDO | |
| +C | |
| +! NIST FORMAT----------------------------------------- | |
| +C | |
| + call DGGLSE(M,N,P,A1,LDA,B1,LDB,C,D1,X1,WORK1,LWORK,INFO) | |
| +! WRITE(*,*) 'X1=',X1(1:10) | |
| +! pause | |
| +C | |
| +C For enthalpy, NEED define 2 coeffs, N=2 | |
| +C | |
| + DO I=1,NH | |
| + XH1(I)=0.D0 | |
| + ENDDO | |
| + DO I=1,NH | |
| + DO J=1,LDAH | |
| + AH1(J,I)=0.D0 | |
| + ENDDO | |
| + DO J=1,LDBH | |
| + BH1(J,I)=0.D0 | |
| + BHk(J,I)=0.D0 | |
| + ENDDO | |
| + ENDDO | |
| + DO I=1,LWORKH | |
| + WORKH(I)=0.D0 | |
| + ENDDO | |
| +C | |
| + DO I=1,MARK1 | |
| + CH2(I)=CH(I)+ DLTH - H_298 - PHI_NIST_H(TEMP(I),X1(1:5)) | |
| + ENDDO | |
| + DO I=MARK1+1,MH | |
| + CH2(I)=CH(I)+ DLTH - H_298 - PHI_NIST_H(TEMP(I),X1(6:10)) | |
| + ENDDO | |
| +C | |
| + DO I=1,MARK1 | |
| + AH1(I,1)=1.0D0 | |
| + ENDDO | |
| + DO I=MARK1+1,MH | |
| + AH1(I,2)=1.0D0 | |
| + ENDDO | |
| +C | |
| +C Contrain for H at Tint | |
| +C | |
| + BHk(1,1)=1.0D0 | |
| + BHk(1,2)=-1.0D0 | |
| + DH1(1)=PHI_NIST_H(Tint,X1(6:10)) | |
| + & -PHI_NIST_H(Tint,X1(1:5)) | |
| +C | |
| +C Contrain for H at 298.15K | |
| +C | |
| + BHk(2,1)=1.0D0 | |
| + BHk(2,2)=0.D0 | |
| + DH1(2)=H_298 + DLTH - H_298 - PHI_NIST_H(298.15D0,X1(1:5)) | |
| +C | |
| + DO I=1,NH | |
| + DO J=1,LDBH | |
| + BH1(J,I)=BHk(J,I) | |
| + ENDDO | |
| + ENDDO | |
| +C | |
| + call DGGLSE(MH,NH,PH,AH1,LDAH,BH1,LDBH,CH2,DH1,XH1,WORKH, | |
| + & LWORKH,INFO) | |
| +! WRITE(*,*) 'H_CONST1=',XH1(1) | |
| +! WRITE(*,*) 'H_CONST2=',XH1(2) | |
| +C | |
| + A_H1=XH1(1) | |
| + A_H2=XH1(2) | |
| +C | |
| +C For entropy, NEED define 2 coeffs, N=2 | |
| + DO I=1,NS | |
| + XS1(I)=0.D0 | |
| + ENDDO | |
| + DO I=1,NS | |
| + DO J=1,LDAS | |
| + AS1(J,I)=0.D0 | |
| + ENDDO | |
| + DO J=1,LDBS | |
| + BS1(J,I)=0.D0 | |
| + BSk(J,I)=0.D0 | |
| + ENDDO | |
| + ENDDO | |
| + DO I=1,LWORKS | |
| + WORKS(I)=0.D0 | |
| + ENDDO | |
| +C | |
| + DO I=1,MARK1 | |
| + CS2(I)=CS(I) - PHI_NIST_S(TEMP(I),X1(1:5)) | |
| + ENDDO | |
| + DO I=MARK1+1,MS | |
| + CS2(I)=CS(I) - PHI_NIST_S(TEMP(I),X1(6:10)) | |
| + ENDDO | |
| + DO I=1,MARK1 | |
| + AS1(I,1)=1.0D0 | |
| + ENDDO | |
| + DO I=MARK1+1,MS | |
| + AS1(I,2)=1.0D0 | |
| + ENDDO | |
| +C | |
| +C Contrain for S at Tint | |
| +C | |
| + BSk(1,1)=1.0D0 | |
| + BSk(1,2)=-1.0D0 | |
| + DS1(1)=PHI_NIST_S(Tint,X1(6:10)) | |
| + & -PHI_NIST_S(Tint,X1(1:5)) | |
| +C | |
| +C Contrain for S at 298.15K | |
| +C | |
| + BSk(2,1)=1.0D0 | |
| + BSk(2,2)=0.0D0 | |
| +! DS1(2)=CS(1) - PHI_NIST_S(298.D0,X1(1:5)) | |
| + DS1(2)=S_298 - PHI_NIST_S(298.15D0,X1(1:5)) | |
| +C | |
| + DO I=1,NS | |
| + DO J=1,LDBS | |
| + BS1(J,I)=BSk(J,I) | |
| + ENDDO | |
| + ENDDO | |
| +C | |
| + call DGGLSE(MS,NS,PS,AS1,LDAS,BS1,LDBS,CS2,DS1,XS1,WORKS, | |
| + & LWORKS,INFO) | |
| +! WRITE(*,*) XS1 | |
| +! WRITE(*,*) 'S_CONST1=',XS1(1) | |
| +! WRITE(*,*) 'S_CONST2=',XS1(2) | |
| +C | |
| + A_S1=XS1(1) | |
| + A_S2=XS1(2) | |
| +C | |
| +C | |
| + DO I=1,5 | |
| + THERM1(I)=X1(I) | |
| + ENDDO | |
| + THERM1(5+1)=A_H1 | |
| + THERM1(5+2)=A_S1 | |
| + DO I=1,5 | |
| + THERM2(I)=X1(I+5) | |
| + ENDDO | |
| + THERM2(5+1)=A_H2 | |
| + THERM2(5+2)=A_S2 | |
| +C | |
| +! WRITE(*,*) THERM1(1:7) | |
| +! WRITE(*,*) THERM2(1:7) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST1(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST1=1.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST2(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST2=TEM/1000.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST3(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST3=(TEM/1000.D0)*(TEM/1000.D0) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST4(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST4=(TEM/1000.D0)*(TEM/1000.D0)*(TEM/1000.D0) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST5(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST5=1.0D0/(TEM/1000.D0)/(TEM/1000.D0) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST_DCP1(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST_DCP1=0.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST_DCP2(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST_DCP2=1.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST_DCP3(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST_DCP3=2.D0*(TEM/1000.D0) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST_DCP4(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST_DCP4=3.D0*(TEM/1000.D0)*(TEM/1000.D0) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST_DCP5(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST_DCP5=-2.D0/(TEM/1000.D0)/(TEM/1000.D0)/(TEM/1000.D0) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST_D2CP1(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST_D2CP1=0.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST_D2CP2(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST_D2CP2=0.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST_D2CP3(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST_D2CP3=2.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST_D2CP4(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST_D2CP4=6.D0*(TEM/1000.D0) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST_D2CP5(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,H_298,S_298,DLTH | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + PHI_NIST_D2CP5=6.D0/(TEM/1000.D0)/(TEM/1000.D0) | |
| + & /(TEM/1000.D0)/(TEM/1000.D0) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST_H(TEM,alpha) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH,T1000 | |
| + DIMENSION alpha(5) | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| + T1000=TEM/1000.D0 | |
| + PHI_NIST_H=alpha(1)*T1000+alpha(2)*T1000*T1000/2.D0 | |
| + & +alpha(3)*T1000*T1000*T1000/3.D0 | |
| + & +alpha(4)*T1000*T1000*T1000*T1000/4.D0 | |
| + & -alpha(5)/T1000 | |
| +! WRITE(*,*) 'PHI_NIST_H=',PHI_NIST_H | |
| + WRITE(*,*) 'H calculated by Shomate is too small!' | |
| + WRITE(*,*) 'warning! warning! warning!' | |
| + PAUSE | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI_NIST_S(TEM,alpha) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ROL,alpha,H_298,S_298,DLTH,T1000 | |
| + DIMENSION alpha(5) | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| +C | |
| +! WRITE(*,*) ALPHA(1:5) | |
| +! WRITE(*,*) TEM | |
| + T1000=TEM/1000.D0 | |
| + PHI_NIST_S=alpha(1)*DLOG(T1000)+alpha(2)*T1000 | |
| + & +alpha(3)*T1000*T1000/2.D0 | |
| + & +alpha(4)*T1000*T1000*T1000/3.D0 | |
| + & -alpha(5)/T1000/T1000/2.D0 | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| \ No newline at end of file | |
| diff --git a/source/GATPFit/lsfp_wilh1.f b/source/GATPFit/lsfp_wilh1.f | |
| index 4598023..b661fc2 100644 | |
| --- a/source/GATPFit/lsfp_wilh1.f | |
| +++ b/source/GATPFit/lsfp_wilh1.f | |
| @@ -1,357 +1,345 @@ | |
| -C WEN, August 2005, | |
| -C add the Cp for 0K | |
| -C********************************************************************** | |
| -C FOR WILHOID CHEMTHERMO DATE FORMAT, N=4, M>=4 | |
| -C | |
| - SUBROUTINE SWILT(SNAM,ENAM,ELNO,STRUC_MOL,ATOMS, | |
| - & ROTORS,THERM1,TEMP,CPT,CH,CS,M) | |
| -C | |
| - implicit none | |
| -C | |
| - CHARACTER(LEN=4) ENAM(5) | |
| - CHARACTER(LEN=16) SNAM | |
| - CHARACTER(LEN=9) STRUC_MOL | |
| - CHARACTER(LEN=1) ELNO(5) | |
| - DOUBLE PRECISION ROL,H_298,S_298,DLTH | |
| - DOUBLE PRECISION TEMP,CPT,CH,CS,PHI1,PHI2,PHI3,PHI4,B_WILH, | |
| - & CP_INF,CP_0,ATOMS,ROTORS | |
| - DOUBLE PRECISION CPT2,TEM2 | |
| - DOUBLE PRECISION Y_H,A_H,A_S,FUN_H,FUN_S | |
| - DOUBLE PRECISION THERM1 | |
| -C | |
| - CHARACTER TRANS | |
| - INTEGER M,N,NRHS,LDA,LDB,LWORK,INFO | |
| - DOUBLE PRECISION A,B,WORK | |
| - PARAMETER (N=4, NRHS=1) | |
| -C | |
| -C REQUIRED BY dgels: | |
| -! LDA >= MAX(1,M) | |
| -! LDB >= MAX(1,M,N) | |
| -! LWORK >= max( 1, MN + max( MN, NRHS ) ) | |
| -! MN= MIN( M, N ) | |
| -C | |
| - PARAMETER (LWORK=8) | |
| - DIMENSION A(M+1,N),B(M+1,NRHS),WORK(LWORK) | |
| - DIMENSION TEMP(M),CPT(M),CH(M),CS(M),THERM1(6) | |
| - DIMENSION TEM2(M+1),CPT2(M+1) | |
| -C | |
| - INTEGER I,J | |
| -C | |
| - COMMON /GAS/ROL,H_298,S_298,DLTH | |
| - COMMON /CP/CP_INF,CP_0 | |
| -C | |
| - EXTERNAL PHI1,PHI2,PHI3,PHI4,B_WILH,FUN_H | |
| -C | |
| -C Input 100 temperature data | |
| -! TEMP(1:M) from group additivity | |
| -! DATA TEMP/300.D0,400.D0,500.D0,600.D0, | |
| -! & 800.D0,1000.D0,1500.D0/ | |
| -! DATA CPT/17.7725D0,22.4645D0,27.0142D0,30.7109D0, | |
| -! & 36.9668D0,41.8009D0,49.3365D0/ | |
| -C | |
| -! DEFINE THE TOTAL NUMBER OF DISCRETE DATA****************** | |
| -! | |
| -! WRITE(*,*) 'CALLED WILH' | |
| -C | |
| - LDA=M+1 | |
| - LDB=M+1 | |
| - TRANS ='N' | |
| -C | |
| - DO I=1,N | |
| - DO J=1,LDA | |
| - A(J,I)=0.D0 | |
| - ENDDO | |
| - ENDDO | |
| -C | |
| - DO I=1,NRHS | |
| - DO J=1,LDB | |
| - B(J,I)=0.D0 | |
| - ENDDO | |
| - ENDDO | |
| -C | |
| - DO I=1,LWORK | |
| - WORK(I)=0.D0 | |
| - ENDDO | |
| -C | |
| -C Calculate the Cp_0 and Cp_int, here ******************* | |
| - | |
| +C WEN, August 2005, | |
| +C add the Cp for 0K | |
| +C********************************************************************** | |
| +C FOR WILHOID CHEMTHERMO DATE FORMAT, N=4, M>=4 | |
| +C | |
| + SUBROUTINE SWILT(SNAM,ENAM,ELNO,STRUC_MOL,ATOMS, | |
| + & ROTORS,THERM1,TEMP,CPT,CH,CS,M) | |
| +C | |
| + implicit none | |
| +C | |
| + CHARACTER(LEN=4) ENAM(5) | |
| + CHARACTER(LEN=16) SNAM | |
| + CHARACTER(LEN=9) STRUC_MOL | |
| + CHARACTER(LEN=1) ELNO(5) | |
| + DOUBLE PRECISION ROL,H_298,S_298,DLTH | |
| + DOUBLE PRECISION TEMP,CPT,CH,CS,PHI1,PHI2,PHI3,PHI4,B_WILH, | |
| + & CP_INF,CP_0,ATOMS,ROTORS | |
| + DOUBLE PRECISION CPT2,TEM2 | |
| + DOUBLE PRECISION Y_H,A_H,A_S,FUN_H,FUN_S | |
| + DOUBLE PRECISION THERM1 | |
| +C | |
| + CHARACTER TRANS | |
| + INTEGER M,N,NRHS,LDA,LDB,LWORK,INFO | |
| + DOUBLE PRECISION A,B,WORK | |
| + PARAMETER (N=4, NRHS=1) | |
| +C | |
| +C REQUIRED BY dgels: | |
| +! LDA >= MAX(1,M) | |
| +! LDB >= MAX(1,M,N) | |
| +! LWORK >= max( 1, MN + max( MN, NRHS ) ) | |
| +! MN= MIN( M, N ) | |
| +C | |
| + PARAMETER (LWORK=8) | |
| + DIMENSION A(M+1,N),B(M+1,NRHS),WORK(LWORK) | |
| + DIMENSION TEMP(M),CPT(M),CH(M),CS(M),THERM1(6) | |
| + DIMENSION TEM2(M+1),CPT2(M+1) | |
| +C | |
| + INTEGER I,J | |
| +C | |
| + COMMON /GAS/ROL,H_298,S_298,DLTH | |
| + COMMON /CP/CP_INF,CP_0 | |
| +C | |
| + EXTERNAL PHI1,PHI2,PHI3,PHI4,B_WILH,FUN_H | |
| +C | |
| +C Input 100 temperature data | |
| +! TEMP(1:M) from group additivity | |
| +! DATA TEMP/300.D0,400.D0,500.D0,600.D0, | |
| +! & 800.D0,1000.D0,1500.D0/ | |
| +! DATA CPT/17.7725D0,22.4645D0,27.0142D0,30.7109D0, | |
| +! & 36.9668D0,41.8009D0,49.3365D0/ | |
| +C | |
| +! DEFINE THE TOTAL NUMBER OF DISCRETE DATA****************** | |
| +! | |
| +! WRITE(*,*) 'CALLED WILH' | |
| +C | |
| + LDA=M+1 | |
| + LDB=M+1 | |
| + TRANS ='N' | |
| +C | |
| + DO I=1,N | |
| + DO J=1,LDA | |
| + A(J,I)=0.D0 | |
| + ENDDO | |
| + ENDDO | |
| +C | |
| + DO I=1,NRHS | |
| + DO J=1,LDB | |
| + B(J,I)=0.D0 | |
| + ENDDO | |
| + ENDDO | |
| +C | |
| + DO I=1,LWORK | |
| + WORK(I)=0.D0 | |
| + ENDDO | |
| +C | |
| +C Calculate the Cp_0 and Cp_int, here ******************* | |
| C gmagoon 10/2/09: added monoatomic case; this needs to be considered separately | |
| C and was causing problems for H radical (presumably similar for O atom) | |
| IF (ATOMS .EQ. 1) THEN | |
| CP_0 = 2.5D0*1.9872D0 | |
| CP_INF = 2.5D0*1.9872D0 | |
| - ELSE IF (STRUC_MOL .EQ. 'NONLINEAR') THEN | |
| - CP_0 =4.0D0*1.9872D0 | |
| - CP_INF=(3.0D0*ATOMS-(2.D0+0.5D0*ROTORS))*1.9872D0 | |
| - ELSE | |
| - CP_0 =3.5D0*1.9872D0 | |
| - CP_INF=(3.0D0*ATOMS-1.5D0)*1.9872D0 | |
| - ENDIF | |
| -! WRITE(*,*) 'CP_INF=', CP_INF | |
| -! WRITE(*,*) 'CP_0 =', CP_0 | |
| -! PAUSE | |
| -C******************************************************** | |
| -C RESET 'TEMP' AND 'CPT' | |
| - DO I=1,M+1 | |
| - TEM2(I)=0.D0 | |
| - CPT2(I)=0.D0 | |
| - ENDDO | |
| -! | |
| - TEM2(1) = 0.D0 | |
| - CPT2(1) = CP_0 | |
| -! | |
| - DO I=1,M | |
| - TEM2(I+1)=TEMP(I) | |
| - CPT2(I+1)=CPT(I) | |
| - ENDDO | |
| -! A(1:N,1:M+1) | |
| - DO I=1,M+1 | |
| - A(I,1)=PHI1(TEM2(I)) | |
| - A(I,2)=PHI2(TEM2(I)) | |
| - A(I,3)=PHI3(TEM2(I)) | |
| - A(I,4)=PHI4(TEM2(I)) | |
| - ENDDO | |
| -! C(1:M+1), C(1:M+1,1)=CP(T)-CP_0-(CP_INF-CP_0)*Y*Y | |
| - B(1,1) = 0.D0 | |
| - DO I=1,M | |
| - B(I+1,1)=B_WILH(TEM2(I+1),CPT2(I+1)) | |
| - ENDDO | |
| -! | |
| -C Contrain for Cp at 0K | |
| -! | |
| -! B(1,1) = PHI1(0.D0) | |
| -! B(1,2) = PHI2(0.D0) | |
| -! B(1,3) = PHI3(0.D0) | |
| -! B(1,4) = PHI4(0.D0) | |
| -! WRITE(*,*) 'B=', B | |
| -! PAUSE | |
| -! | |
| -! D(1) = 0.D0 | |
| -! | |
| -C: Call LS solver wihtout contrains | |
| -C: Solver A*X=B | |
| -C | |
| - call dgels(trans,m+1,n,nrhs,a,lda,b,ldb,work,lwork,info) | |
| -! call DGGLSE(M+1,N,P,A,LDA,B,LDB,C,D,X1,WORK, | |
| -! & LWORK,INFO) | |
| -C | |
| -C The alpha coefficients are stored in b(1:4,1) | |
| -! WRITE(*,*) B(1:4) | |
| -C | |
| -C Calculate the constant 'I' for Enthalpy | |
| -C | |
| - Y_H=298.15D0/(298.15D0+500.D0) | |
| -C | |
| - A_H=DLTH*1000.d0-(CP_0*298.15D0)+(CP_INF-CP_0)*298.15D0 | |
| - & *FUN_H(298.15D0,B(1:4,1)) | |
| -C | |
| -C Calculate the constant 'J' for Entropy | |
| -C | |
| - A_S=S_298 - CP_INF*DLOG(298.15D0) + (CP_INF-CP_0)* | |
| - & FUN_S(298.15D0,B(1:4,1)) | |
| -C | |
| -C | |
| - DO I=1,4 | |
| - THERM1(I)=B(I,1) | |
| - ENDDO | |
| - THERM1(4+1)=A_H | |
| - THERM1(4+2)=A_S | |
| -! WRITE(*,*) THERM1(1:6) | |
| -C | |
| -! WRITE(*,*) 'WILH OVER' | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| -C************************************************************************ | |
| - DOUBLE PRECISION FUNCTION PHI1(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,Y,CP_INF,CP_0 | |
| - COMMON /CP/CP_INF,CP_0 | |
| -C | |
| - Y=TEM/(TEM+500.D0) | |
| - PHI1=1.0D0*(CP_INF-CP_0)*Y*Y*(Y-1) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI2(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,Y,CP_INF,CP_0 | |
| - COMMON /CP/CP_INF,CP_0 | |
| -C | |
| - Y=TEM/(TEM+500.D0) | |
| - PHI2=Y*(CP_INF-CP_0)*Y*Y*(Y-1) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI3(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,Y,CP_INF,CP_0 | |
| - COMMON /CP/CP_INF,CP_0 | |
| -C | |
| - Y=TEM/(TEM+500.D0) | |
| - PHI3=Y*Y*(CP_INF-CP_0)*Y*Y*(Y-1) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| -C | |
| - DOUBLE PRECISION FUNCTION PHI4(TEM) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,Y,CP_INF,CP_0 | |
| - COMMON /CP/CP_INF,CP_0 | |
| -C | |
| - Y=TEM/(TEM+500.D0) | |
| - PHI4=Y*Y*Y*(CP_INF-CP_0)*Y*Y*(Y-1) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION B_WILH(TEM,CP) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,Y,CP_INF,CP_0,CP | |
| - COMMON /CP/CP_INF,CP_0 | |
| -C | |
| - Y=TEM/(TEM+500.D0) | |
| - B_WILH=CP-CP_0-Y*Y*(CP_INF-CP_0) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION FUN_H(TEM,ALPHA) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ALPHA,Y | |
| - DOUBLE PRECISION FUN1,FUN2,FUN3,FUN4,FUN5 | |
| - DIMENSION alpha(4) | |
| -C | |
| - Y=TEM/(TEM+500.D0) | |
| - IF (Y .EQ. 0.D0) Y=1.0D0 | |
| - FUN1=(2.D0+ALPHA(1)+ALPHA(2)+ALPHA(3)+ALPHA(4))* | |
| - & (Y/2.D0-1+(1.D0/Y-1)*DLOG(TEM+500.D0)) | |
| - FUN2=(1.D0/6.D0)*(3.D0*ALPHA(1)+ALPHA(2)+ALPHA(3)+ALPHA(4)) | |
| - FUN3=(Y/12.D0)*(4.D0*ALPHA(2)+ALPHA(3)+ALPHA(4)) | |
| - FUN4=(Y*Y/20.D0)*(5.D0*ALPHA(3)+ALPHA(4)) | |
| - FUN5=(Y*Y*Y/30.D0)*6.D0*ALPHA(4) | |
| -C | |
| - FUN_H=FUN1+Y*Y*(FUN2+FUN3+FUN4+FUN5) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| - DOUBLE PRECISION FUNCTION FUN_S(TEM,ALPHA) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,ALPHA,Y | |
| - DIMENSION alpha(4) | |
| -C | |
| - Y=TEM/(TEM+500.D0) | |
| - IF (Y .EQ. 0.D0) Y=1.0D0 | |
| -C | |
| - FUN_S=DLOG(Y)+ | |
| - & (1.D0+Y*(ALPHA(1)/2.D0+ALPHA(2)*Y/3.D0+ALPHA(3)*Y*Y/4.D0 | |
| - & +ALPHA(4)*Y*Y*Y/5.D0))*Y | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| -C | |
| - | |
| - DOUBLE PRECISION FUNCTION CP_WILH(TEM,BETA) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,BETA,Y,CP_INF,CP_0 | |
| - DIMENSION BETA(6) | |
| - COMMON /CP/CP_INF,CP_0 | |
| -C | |
| - Y=TEM/(TEM+500.D0) | |
| - CP_WILH=CP_0+(CP_INF-CP_0)*Y*Y | |
| - & *(1.D0+(Y-1.D0)*(BETA(1)+BETA(2)*Y+BETA(3)*Y*Y | |
| - & +BETA(4)*Y*Y*Y)) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION H_WILH(TEM,BETA) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,BETA,Y,CP_INF,CP_0,FUN_H | |
| - DIMENSION BETA(6) | |
| - EXTERNAL FUN_H | |
| - COMMON /CP/CP_INF,CP_0 | |
| -C | |
| - Y=TEM/(TEM+500.D0) | |
| - H_WILH=BETA(5) | |
| - & +(CP_0*TEM)-(CP_INF-CP_0)*TEM* | |
| - & FUN_H(TEM,BETA(1:4)) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| -C | |
| - DOUBLE PRECISION FUNCTION S_WILH(TEM,BETA) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION TEM,BETA,Y,CP_INF,CP_0,FUN_S | |
| - DIMENSION BETA(6) | |
| - COMMON /CP/CP_INF,CP_0 | |
| - EXTERNAL FUN_S | |
| -C | |
| - Y=TEM/(TEM+500.D0) | |
| - IF (TEM .EQ. 0.D0) TEM = 1.0D0 | |
| - S_WILH=BETA(6) | |
| - & +CP_INF*DLOG(TEM) - (CP_INF-CP_0)* | |
| - & FUN_S(TEM,BETA(1:4)) | |
| -C | |
| - RETURN | |
| -C | |
| - END | |
| - | |
| - SUBROUTINE DATAFIND(BETA,TEM,CP,CH,CS) | |
| -C | |
| - implicit none | |
| -C | |
| - DOUBLE PRECISION BETA,TEM,CP,CH,CS | |
| - DOUBLE PRECISION CP_WILH,H_WILH,S_WILH | |
| - DIMENSION BETA(6) | |
| -C | |
| - EXTERNAL CP_WILH,H_WILH,S_WILH | |
| -C | |
| - CP=CP_WILH(TEM,BETA) | |
| - CH=H_WILH(TEM,BETA) | |
| - CS=S_WILH(TEM,BETA) | |
| - RETURN | |
| -C | |
| - END | |
| + ELSE IF (STRUC_MOL .EQ. 'NONLINEAR') THEN | |
| + CP_0 =4.0D0*1.9872D0 | |
| + CP_INF=(3.0D0*ATOMS-(2.D0+0.5D0*ROTORS))*1.9872D0 | |
| + ELSE | |
| + CP_0 =3.5D0*1.9872D0 | |
| + CP_INF=(3.0D0*ATOMS-1.5D0)*1.9872D0 | |
| + ENDIF | |
| +! WRITE(*,*) 'CP_INF=', CP_INF | |
| +! WRITE(*,*) 'CP_0 =', CP_0 | |
| +! PAUSE | |
| +C******************************************************** | |
| +C RESET 'TEMP' AND 'CPT' | |
| + DO I=1,M+1 | |
| + TEM2(I)=0.D0 | |
| + CPT2(I)=0.D0 | |
| + ENDDO | |
| +! | |
| + TEM2(1) = 0.D0 | |
| + CPT2(1) = CP_0 | |
| +! | |
| + DO I=1,M | |
| + TEM2(I+1)=TEMP(I) | |
| + CPT2(I+1)=CPT(I) | |
| + ENDDO | |
| +! A(1:N,1:M+1) | |
| + DO I=1,M+1 | |
| + A(I,1)=PHI1(TEM2(I)) | |
| + A(I,2)=PHI2(TEM2(I)) | |
| + A(I,3)=PHI3(TEM2(I)) | |
| + A(I,4)=PHI4(TEM2(I)) | |
| + ENDDO | |
| +! C(1:M+1), C(1:M+1,1)=CP(T)-CP_0-(CP_INF-CP_0)*Y*Y | |
| + B(1,1) = 0.D0 | |
| + DO I=1,M | |
| + B(I+1,1)=B_WILH(TEM2(I+1),CPT2(I+1)) | |
| + ENDDO | |
| +! | |
| +C Contrain for Cp at 0K | |
| +! | |
| +! B(1,1) = PHI1(0.D0) | |
| +! B(1,2) = PHI2(0.D0) | |
| +! B(1,3) = PHI3(0.D0) | |
| +! B(1,4) = PHI4(0.D0) | |
| +! WRITE(*,*) 'B=', B | |
| +! PAUSE | |
| +! | |
| +! D(1) = 0.D0 | |
| +! | |
| +C: Call LS solver wihtout contrains | |
| +C: Solver A*X=B | |
| +C | |
| + call dgels(trans,m+1,n,nrhs,a,lda,b,ldb,work,lwork,info) | |
| +! call DGGLSE(M+1,N,P,A,LDA,B,LDB,C,D,X1,WORK, | |
| +! & LWORK,INFO) | |
| +C | |
| +C The alpha coefficients are stored in b(1:4,1) | |
| +! WRITE(*,*) B(1:4) | |
| +C | |
| +C Calculate the constant 'I' for Enthalpy | |
| +C | |
| + Y_H=298.15D0/(298.15D0+500.D0) | |
| +C | |
| + A_H=DLTH*1000.d0-(CP_0*298.15D0)+(CP_INF-CP_0)*298.15D0 | |
| + & *FUN_H(298.15D0,B(1:4,1)) | |
| +C | |
| +C Calculate the constant 'J' for Entropy | |
| +C | |
| + A_S=S_298 - CP_INF*DLOG(298.15D0) + (CP_INF-CP_0)* | |
| + & FUN_S(298.15D0,B(1:4,1)) | |
| +C | |
| +C | |
| + DO I=1,4 | |
| + THERM1(I)=B(I,1) | |
| + ENDDO | |
| + THERM1(4+1)=A_H | |
| + THERM1(4+2)=A_S | |
| +! WRITE(*,*) THERM1(1:6) | |
| +C | |
| +! WRITE(*,*) 'WILH OVER' | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| +C************************************************************************ | |
| + DOUBLE PRECISION FUNCTION PHI1(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,Y,CP_INF,CP_0 | |
| + COMMON /CP/CP_INF,CP_0 | |
| +C | |
| + Y=TEM/(TEM+500.D0) | |
| + PHI1=1.0D0*(CP_INF-CP_0)*Y*Y*(Y-1) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI2(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,Y,CP_INF,CP_0 | |
| + COMMON /CP/CP_INF,CP_0 | |
| +C | |
| + Y=TEM/(TEM+500.D0) | |
| + PHI2=Y*(CP_INF-CP_0)*Y*Y*(Y-1) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI3(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,Y,CP_INF,CP_0 | |
| + COMMON /CP/CP_INF,CP_0 | |
| +C | |
| + Y=TEM/(TEM+500.D0) | |
| + PHI3=Y*Y*(CP_INF-CP_0)*Y*Y*(Y-1) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| +C | |
| + DOUBLE PRECISION FUNCTION PHI4(TEM) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,Y,CP_INF,CP_0 | |
| + COMMON /CP/CP_INF,CP_0 | |
| +C | |
| + Y=TEM/(TEM+500.D0) | |
| + PHI4=Y*Y*Y*(CP_INF-CP_0)*Y*Y*(Y-1) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION B_WILH(TEM,CP) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,Y,CP_INF,CP_0,CP | |
| + COMMON /CP/CP_INF,CP_0 | |
| +C | |
| + Y=TEM/(TEM+500.D0) | |
| + B_WILH=CP-CP_0-Y*Y*(CP_INF-CP_0) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION FUN_H(TEM,ALPHA) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ALPHA,Y | |
| + DOUBLE PRECISION FUN1,FUN2,FUN3,FUN4,FUN5 | |
| + DIMENSION alpha(4) | |
| +C | |
| + Y=TEM/(TEM+500.D0) | |
| + IF (Y .EQ. 0.D0) Y=1.0D0 | |
| + FUN1=(2.D0+ALPHA(1)+ALPHA(2)+ALPHA(3)+ALPHA(4))* | |
| + & (Y/2.D0-1+(1.D0/Y-1)*DLOG(TEM+500.D0)) | |
| + FUN2=(1.D0/6.D0)*(3.D0*ALPHA(1)+ALPHA(2)+ALPHA(3)+ALPHA(4)) | |
| + FUN3=(Y/12.D0)*(4.D0*ALPHA(2)+ALPHA(3)+ALPHA(4)) | |
| + FUN4=(Y*Y/20.D0)*(5.D0*ALPHA(3)+ALPHA(4)) | |
| + FUN5=(Y*Y*Y/30.D0)*6.D0*ALPHA(4) | |
| +C | |
| + FUN_H=FUN1+Y*Y*(FUN2+FUN3+FUN4+FUN5) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| + DOUBLE PRECISION FUNCTION FUN_S(TEM,ALPHA) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,ALPHA,Y | |
| + DIMENSION alpha(4) | |
| +C | |
| + Y=TEM/(TEM+500.D0) | |
| + IF (Y .EQ. 0.D0) Y=1.0D0 | |
| +C | |
| + FUN_S=DLOG(Y)+ | |
| + & (1.D0+Y*(ALPHA(1)/2.D0+ALPHA(2)*Y/3.D0+ALPHA(3)*Y*Y/4.D0 | |
| + & +ALPHA(4)*Y*Y*Y/5.D0))*Y | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION CP_WILH(TEM,BETA) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,BETA,Y,CP_INF,CP_0 | |
| + DIMENSION BETA(6) | |
| + COMMON /CP/CP_INF,CP_0 | |
| +C | |
| + Y=TEM/(TEM+500.D0) | |
| + CP_WILH=CP_0+(CP_INF-CP_0)*Y*Y | |
| + & *(1.D0+(Y-1.D0)*(BETA(1)+BETA(2)*Y+BETA(3)*Y*Y | |
| + & +BETA(4)*Y*Y*Y)) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION H_WILH(TEM,BETA) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,BETA,Y,CP_INF,CP_0,FUN_H | |
| + DIMENSION BETA(6) | |
| + EXTERNAL FUN_H | |
| + COMMON /CP/CP_INF,CP_0 | |
| +C | |
| + Y=TEM/(TEM+500.D0) | |
| + H_WILH=BETA(5) | |
| + & +(CP_0*TEM)-(CP_INF-CP_0)*TEM* | |
| + & FUN_H(TEM,BETA(1:4)) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| +C | |
| + DOUBLE PRECISION FUNCTION S_WILH(TEM,BETA) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION TEM,BETA,Y,CP_INF,CP_0,FUN_S | |
| + DIMENSION BETA(6) | |
| + COMMON /CP/CP_INF,CP_0 | |
| + EXTERNAL FUN_S | |
| +C | |
| + Y=TEM/(TEM+500.D0) | |
| + IF (TEM .EQ. 0.D0) TEM = 1.0D0 | |
| + S_WILH=BETA(6) | |
| + & +CP_INF*DLOG(TEM) - (CP_INF-CP_0)* | |
| + & FUN_S(TEM,BETA(1:4)) | |
| +C | |
| + RETURN | |
| +C | |
| + END | |
| + SUBROUTINE DATAFIND(BETA,TEM,CP,CH,CS) | |
| +C | |
| + implicit none | |
| +C | |
| + DOUBLE PRECISION BETA,TEM,CP,CH,CS | |
| + DOUBLE PRECISION CP_WILH,H_WILH,S_WILH | |
| + DIMENSION BETA(6) | |
| +C | |
| + EXTERNAL CP_WILH,H_WILH,S_WILH | |
| +C | |
| + CP=CP_WILH(TEM,BETA) | |
| + CH=H_WILH(TEM,BETA) | |
| + CS=S_WILH(TEM,BETA) | |
| + RETURN | |
| +C | |
| + END | |
| \ No newline at end of file | |
| diff --git a/source/RMG/CheckForwardAndReverseRateCoefficients.java b/source/RMG/CheckForwardAndReverseRateCoefficients.java | |
| index 2ecb408..933b21a 100644 | |
| --- a/source/RMG/CheckForwardAndReverseRateCoefficients.java | |
| +++ b/source/RMG/CheckForwardAndReverseRateCoefficients.java | |
| @@ -1,6 +1,9 @@ | |
| import java.io.BufferedReader; | |
| +import java.io.File; | |
| import java.io.FileNotFoundException; | |
| import java.io.FileReader; | |
| +import java.io.FileWriter; | |
| +import java.io.IOException; | |
| import java.util.StringTokenizer; | |
| import jing.chemParser.ChemParser; | |
| @@ -15,11 +18,15 @@ public class CheckForwardAndReverseRateCoefficients { | |
| public static void main(String args[]) { | |
| // Temperature is assumed to have units in Kelvin | |
| + StringBuilder reverseRateCoefficients = new StringBuilder(); | |
| + String temperatureString = ""; | |
| double[] T = new double [10]; | |
| for (int i=0; i<10; i++) { | |
| double temp = (1000.0/3000.0) + ((double)i/9.0) * (1000.0/300.0 - 1000.0/3000.0); | |
| T[i] = 1000.0 / temp; | |
| + temperatureString += Double.toString(T[i])+"\t"; | |
| } | |
| + reverseRateCoefficients.append(temperatureString+"\n"); | |
| // double[] T = {614.0,614.0,614.0,614.0,614.0,629.0,643.0,678.0,713.0,749.0,784.0,854.0,930.0,1010.0,1100.0,1250.0,1350.0,1440.0,1510.0,1570.0,1640.0,1790.0,1970.0,2030.0,2090.0,2110.0,2130.0,2170.0,2180.0,2210.0,2220.0,2220.0,2220.0,2220.0,2210.0,2210.0,2210.0,2200.0,2190.0,2180.0,2170.0,2160.0,2150.0,2150.0,2140.0,2140.0,2140.0,2140.0,2130.0,2130.0,2130.0,2120.0,2120.0,2120.0,2120.0,2110.0,2110.0,2110.0,2110.0,2110.0,2100.0,2100.0,2100.0,2090.0,2080.0,2080.0,2070.0,2060.0,2050.0,2050.0,2040.0,2030.0,2030.0,2020.0,2010.0,2000.0,2000.0,1990.0,1980.0,1970.0,1970.0,1960.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0,1950.0}; | |
| // double[] T = {681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,681.0,682.0,683.0,684.0,687.0,693.0,703.0,712.0,730.0,749.0,767.0,786.0,823.0,860.0,897.0,934.0,1000.0,1060.0,1120.0,1170.0,1230.0,1320.0,1370.0,1410.0,1440.0,1480.0,1550.0,1660.0,1760.0,1850.0,1920.0,1960.0,2060.0,2110.0,2150.0,2200.0,2240.0,2260.0,2260.0,2250.0,2250.0,2240.0,2240.0,2230.0,2220.0,2210.0,2200.0,2190.0,2180.0,2180.0,2180.0,2180.0,2180.0,2180.0,2170.0,2170.0,2170.0,2170.0,2170.0,2170.0,2160.0,2160.0,2150.0,2150.0,2140.0,2140.0,2130.0,2130.0,2120.0,2120.0,2110.0,2110.0,2100.0,2100.0,2090.0,2090.0,2080.0,2080.0,2070.0,2070.0,2060.0,2050.0,2050.0,2040.0,2030.0,2030.0,2020.0,2010.0,2010.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0,2000.0}; | |
| @@ -293,6 +300,7 @@ public class CheckForwardAndReverseRateCoefficients { | |
| output += (logk[iii] - logKeq[iii]) + "\t"; | |
| } | |
| // System.out.println(output + shortRxnString); | |
| + reverseRateCoefficients.append(output + shortRxnString + "\n"); | |
| } | |
| } | |
| line = ChemParser.readMeaningfulLine(br_thermodat, true); | |
| @@ -300,6 +308,17 @@ public class CheckForwardAndReverseRateCoefficients { | |
| } catch (FileNotFoundException e) { | |
| System.err.println("File was not found: " + args[0] + "\n"); | |
| } | |
| + | |
| + try { | |
| + File reversek = new File("reverseRateCoefficients.txt"); | |
| + FileWriter fw_rxns = new FileWriter(reversek); | |
| + fw_rxns.write(reverseRateCoefficients.toString()); | |
| + fw_rxns.close(); | |
| + } | |
| + catch (IOException e) { | |
| + System.out.println("Could not write reverseRateCoefficients.txt files"); | |
| + System.exit(0); | |
| + } | |
| } | |
| public static int[] determineSpeciesIndex(String reactsORprods) { | |
| diff --git a/source/RMG/GUI.java b/source/RMG/GUI.java | |
| index 536f3f7..27d5246 100644 | |
| --- a/source/RMG/GUI.java | |
| +++ b/source/RMG/GUI.java | |
| @@ -68,9 +68,7 @@ import javax.swing.JButton; | |
| import javax.swing.JComboBox; | |
| import javax.swing.JComponent; | |
| import javax.swing.JFileChooser; | |
| -import javax.swing.JFormattedTextField; | |
| import javax.swing.JLabel; | |
| -import javax.swing.JOptionPane; | |
| import javax.swing.JPanel; | |
| import javax.swing.JScrollPane; | |
| import javax.swing.JTabbedPane; | |
| @@ -80,6 +78,7 @@ import javax.swing.JTextField; | |
| import javax.swing.ListCellRenderer; | |
| import javax.swing.table.TableCellRenderer; | |
| import javax.swing.table.TableColumn; | |
| +import javax.swing.text.JTextComponent; | |
| import java.awt.Dimension; | |
| import java.awt.GridLayout; | |
| @@ -1959,16 +1958,7 @@ public class GUI extends JPanel implements ActionListener { | |
| return; | |
| } | |
| else { | |
| - String[] tempLines = tempConstant.getText().split("[\n]"); | |
| - StringTokenizer st = null; | |
| - for (int i=0; i<tempLines.length; i++) { | |
| - st = new StringTokenizer(tempLines[i]); | |
| - while (st.hasMoreTokens()) { | |
| - String line = st.nextToken(); | |
| - if (line.endsWith(",")) line = line.substring(0,line.length()-1).trim(); | |
| - conditionFile += " " + line; | |
| - } | |
| - } | |
| + conditionFile += extractListOfValuesFromGUIInput(tempConstant); | |
| } | |
| conditionFile += "\r"; | |
| @@ -1980,16 +1970,7 @@ public class GUI extends JPanel implements ActionListener { | |
| return; | |
| } | |
| else { | |
| - String[] pressLines = pressConstant.getText().split("[\n]"); | |
| - StringTokenizer st = null; | |
| - for (int i=0; i<pressLines.length; i++) { | |
| - st = new StringTokenizer(pressLines[i]); | |
| - while (st.hasMoreTokens()) { | |
| - String line = st.nextToken(); | |
| - if (line.endsWith(",")) line = line.substring(0,line.length()-1).trim(); | |
| - conditionFile += " " + line; | |
| - } | |
| - } | |
| + conditionFile += extractListOfValuesFromGUIInput(pressConstant); | |
| } | |
| conditionFile += "\r\r"; | |
| @@ -2005,9 +1986,18 @@ public class GUI extends JPanel implements ActionListener { | |
| // Add whether to turn solvation on or not | |
| // Add whether to run on-the-fly quantum jobs or not | |
| + if (thermomethod.getSelectedItem().equals("QM")) { | |
| + conditionFile += "ThermoMethod: QM " + qmSoftware.getSelectedItem().toString() + "\r" + | |
| + "QMForCyclicsOnly: "; | |
| + if (cyclicsOnly.getSelectedItem().equals("Yes")) { | |
| + conditionFile += "on"; | |
| + } else { | |
| + conditionFile += "off"; | |
| + } | |
| + conditionFile += "\rMaxRadNumForQM: " + maxRadNumQM.getText() + "\r\r"; | |
| + } | |
| // Determine if each species is reactive, unreactive, or inert | |
| - int nonInertCount = 0; | |
| boolean unreactiveStatus = false; | |
| String reactiveSpecies = ""; | |
| String inertSpecies = ""; | |
| @@ -2018,23 +2008,22 @@ public class GUI extends JPanel implements ActionListener { | |
| else { | |
| for (int i=0; i<tableInput.getRowCount(); i++) { | |
| if (tableInput.getValueAt(i,3).equals("Inert")) { | |
| - inertSpecies += tableInput.getValueAt(i,0) + " " + | |
| - tableInput.getValueAt(i,1) + " (" + | |
| - tableInput.getValueAt(i,2) + ")\r"; | |
| + inertSpecies += tableInput.getValueAt(i,0) + " (" + | |
| + tableInput.getValueAt(i,2) + ")" + | |
| + extractListOfValuesFromGUIInput(tableInput.getValueAt(i,1)) + "\r"; | |
| } else if (tableInput.getValueAt(i,3).equals("Reactive-RMG")) { | |
| - ++nonInertCount; | |
| - reactiveSpecies += "(" + nonInertCount + ") " + | |
| - tableInput.getValueAt(i,0) + " " + | |
| - tableInput.getValueAt(i,1) + " (" + | |
| - tableInput.getValueAt(i,2) + ")\r" + | |
| + reactiveSpecies += | |
| + tableInput.getValueAt(i,0) + " (" + | |
| + tableInput.getValueAt(i,2) + ")" + | |
| + extractListOfValuesFromGUIInput(tableInput.getValueAt(i,1)) + "\r" + | |
| tableInput.getValueAt(i,4) + "\r\r"; | |
| } else if (tableInput.getValueAt(i,3).equals("Reactive-User")) { | |
| unreactiveStatus = true; | |
| - ++nonInertCount; | |
| - reactiveSpecies += "(" + nonInertCount + ") " + | |
| - tableInput.getValueAt(i,0) + " " + | |
| - tableInput.getValueAt(i,1) + " (" + | |
| - tableInput.getValueAt(i,2) + ") unreactive\r" + | |
| + reactiveSpecies += | |
| + tableInput.getValueAt(i,0) + " (" + | |
| + tableInput.getValueAt(i,2) + ")" + | |
| + extractListOfValuesFromGUIInput(tableInput.getValueAt(i,1)) + | |
| + " unreactive\r" + | |
| tableInput.getValueAt(i,4) + "\r\r"; | |
| } | |
| } | |
| @@ -2557,6 +2546,41 @@ public class GUI extends JPanel implements ActionListener { | |
| } | |
| } | |
| + else if (line.startsWith("ThermoMethod")) { | |
| + st = new StringTokenizer(line); | |
| + tempString = st.nextToken(); // Skip over "ThermoMethod:" | |
| + String method = st.nextToken(); | |
| + if (method.toLowerCase().equals("qm")) { | |
| + thermomethod.setSelectedItem("QM"); | |
| + } else { | |
| + thermomethod.setSelectedItem("Group Additivity"); | |
| + } | |
| + qmSoftware.setSelectedItem("Both"); | |
| + if (st.hasMoreTokens()) { | |
| + method = st.nextToken().toLowerCase(); | |
| + if (method.equals("gaussian03")) qmSoftware.setSelectedItem("Gaussian03"); | |
| + else if (method.equals("mopac")) qmSoftware.setSelectedItem("MOPAC"); | |
| + else if (method.equals("both")) qmSoftware.setSelectedItem("Both"); | |
| + else System.out.println("GUI did not recognize the software package option " + method + " supplied to the ThermoMethod field."); | |
| + } | |
| + } | |
| + | |
| + else if (line.startsWith("QMForCyclicsOnly")) { | |
| + st = new StringTokenizer(line); | |
| + tempString = st.nextToken(); // Skip over "QMForCyclicsOnly:" | |
| + String yesno = st.nextToken(); | |
| + if (yesno.toLowerCase().equals("on")) | |
| + cyclicsOnly.setSelectedItem("Yes"); | |
| + else | |
| + cyclicsOnly.setSelectedItem("No"); | |
| + } | |
| + | |
| + else if (line.startsWith("MaxRadNumForQM")) { | |
| + st = new StringTokenizer(line); | |
| + tempString = st.nextToken(); // Skip over "MaxRadNumForQM:" | |
| + maxRadNumQM.setText(st.nextToken()); | |
| + } | |
| + | |
| else if (line.toLowerCase().startsWith("readrestart")) { | |
| st = new StringTokenizer(line); | |
| tempString = st.nextToken(); // Skip over "ReadRestart:" | |
| @@ -2606,16 +2630,17 @@ public class GUI extends JPanel implements ActionListener { | |
| String reactivity = ""; | |
| line = ChemParser.readMeaningfulLine(reader, true); | |
| while (!line.startsWith("END")) { | |
| - if (line.startsWith("(")) { | |
| + if (line.contains("(")) { | |
| ++numSpecies; | |
| st = new StringTokenizer(line); | |
| - tempString = st.nextToken(); // Skip over (#) | |
| name = st.nextToken(); | |
| - conc = st.nextToken(); | |
| unit = st.nextToken(); | |
| + conc = ""; | |
| reactivity = "Reactive-RMG"; | |
| - if (st.hasMoreTokens()) { | |
| - reactivity = "Reactive-User"; | |
| + while (st.hasMoreTokens()) { | |
| + String temporaryString = st.nextToken(); | |
| + if (temporaryString.equals("unreactive")) reactivity = "Reactive-User"; | |
| + else conc += temporaryString + " "; | |
| } | |
| } else { | |
| adjList += line + "\r"; | |
| @@ -2623,7 +2648,7 @@ public class GUI extends JPanel implements ActionListener { | |
| line = ChemParser.readMeaningfulLine(reader, true); | |
| - if (line.startsWith("(") || line.startsWith("END")) { | |
| + if (line.contains("(") || line.startsWith("END")) { | |
| ICVector icEntry = new ICVector(numSpecies-1,name,conc,unit.substring(1,unit.length()-1),reactivity,adjList); | |
| tmodelInput.updateIC(icEntry); | |
| adjList = ""; | |
| @@ -2644,8 +2669,9 @@ public class GUI extends JPanel implements ActionListener { | |
| ++numSpecies; | |
| st = new StringTokenizer(line); | |
| name = st.nextToken(); | |
| - conc = st.nextToken(); | |
| unit = st.nextToken(); | |
| + conc = ""; | |
| + while (st.hasMoreTokens()) conc += st.nextToken() + " "; | |
| reactivity = "Inert"; | |
| if (name.equals("Ar") || name.equals("Ne") || name.equals("N2") || name.equals("He")) { | |
| ICVector icEntry = new ICVector(numSpecies-1,name,conc,unit.substring(1,unit.length()-1),reactivity,adjList); | |
| @@ -3101,6 +3127,25 @@ public class GUI extends JPanel implements ActionListener { | |
| } | |
| } | |
| + public String extractListOfValuesFromGUIInput(Object guiInput) { | |
| + String string2return = ""; | |
| + String[] tempLines = null; | |
| + if (guiInput instanceof JTextComponent) | |
| + tempLines = ((JTextComponent) guiInput).getText().split("[\n]"); | |
| + else if (guiInput instanceof String) | |
| + tempLines = ((String) guiInput).split("[\n]"); | |
| + StringTokenizer st = null; | |
| + for (int i=0; i<tempLines.length; i++) { | |
| + st = new StringTokenizer(tempLines[i]); | |
| + while (st.hasMoreTokens()) { | |
| + String line = st.nextToken(); | |
| + if (line.endsWith(",")) line = line.substring(0,line.length()-1).trim(); | |
| + string2return += " " + line; | |
| + } | |
| + } | |
| + return string2return; | |
| + } | |
| + | |
| public JComponent createTabOptions() { | |
| // Create cellrenderers for JComboBox/JTable - CENTER text | |
| ListCellRenderer centerJComboBoxRenderer = new CenterJCBRenderer(); | |
| @@ -3255,6 +3300,46 @@ public class GUI extends JPanel implements ActionListener { | |
| chemkinPanel.add(chemkinProps); | |
| + // Create the thermomethod_QM options subpanel | |
| + JPanel qmPanel = new JPanel(); | |
| + qmPanel.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder("QM thermo method"), | |
| + BorderFactory.createEmptyBorder(5,5,5,5))); | |
| + // Populate the subpanel | |
| + JPanel thermomethodPanel = new JPanel(); | |
| + thermomethodPanel.setBorder(BorderFactory.createEmptyBorder(5,5,5,5)); | |
| + JLabel thermomethodLabel = new JLabel("Method for estimating thermo:"); | |
| + thermomethodPanel.add(thermomethodLabel); | |
| + thermomethodPanel.add(thermomethod = new JComboBox(thermomethodOptions)); | |
| + thermomethodPanel.add(qmSoftware = new JComboBox(softwareOptions)); | |
| + thermomethod.setActionCommand("QM"); | |
| + thermomethod.addActionListener(this); | |
| + qmSoftware.addActionListener(this); | |
| + qmSoftware.setEnabled(false); | |
| + | |
| + JPanel thermocyclicsPanel = new JPanel(); | |
| + thermocyclicsPanel.setBorder(BorderFactory.createEmptyBorder(5,5,5,5)); | |
| + JLabel thermocyclicsLabel = new JLabel("Use QM only for cyclic species?"); | |
| + thermocyclicsPanel.add(thermocyclicsLabel); | |
| + thermocyclicsPanel.add(cyclicsOnly = new JComboBox(yesnoOptions)); | |
| + cyclicsOnly.addActionListener(this); | |
| + cyclicsOnly.setEnabled(false); | |
| + | |
| + JPanel thermoMaxRadPanel = new JPanel(); | |
| + thermoMaxRadPanel.setBorder(BorderFactory.createEmptyBorder(5,5,5,5)); | |
| + JLabel thermoMaxRadLabel = new JLabel("Maximum radicals for QM species:"); | |
| + thermoMaxRadPanel.add(thermoMaxRadLabel); | |
| + thermoMaxRadPanel.add(maxRadNumQM = new JTextField()); | |
| + maxRadNumQM.setPreferredSize(new Dimension (75,25)); | |
| + maxRadNumQM.setHorizontalAlignment(JTextField.CENTER); | |
| + maxRadNumQM.setEnabled(false); | |
| + | |
| + Box qmProps = Box.createVerticalBox(); | |
| + qmProps.add(thermomethodPanel); | |
| + qmProps.add(thermocyclicsPanel); | |
| + qmProps.add(thermoMaxRadPanel); | |
| + | |
| + qmPanel.add(qmProps); | |
| + | |
| // Create the Equation Of State (EOS) subpanel | |
| JPanel EOS = new JPanel(); | |
| EOS.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder("Equation of State"), | |
| @@ -3333,20 +3418,24 @@ public class GUI extends JPanel implements ActionListener { | |
| Box totalOptionsBox = Box.createVerticalBox(); | |
| Box horizontalBox1 = Box.createHorizontalBox(); | |
| Box verticalBox1 = Box.createVerticalBox(); | |
| + Box verticalBox2 = Box.createVerticalBox(); | |
| totalOptionsBox.add(restartPanel); | |
| totalOptionsBox.add(maxPanel); | |
| - horizontalBox1.add(chemkinPanel); | |
| + verticalBox1.add(chemkinPanel); | |
| verticalBox1.add(inchiPanel); | |
| - verticalBox1.add(EOS); | |
| + verticalBox2.add(qmPanel); | |
| + verticalBox2.add(EOS); | |
| horizontalBox1.add(verticalBox1); | |
| + horizontalBox1.add(verticalBox2); | |
| totalOptionsBox.add(horizontalBox1); | |
| totalOptionsBox.add(forbiddenStructures); | |
| Options.add(totalOptionsBox); | |
| JComboBox[] allTab = {eosCombo, inchiCombo, chemkinAUnits, | |
| - chemkinEaUnits, chemkinVerbosity, chemkinSMILES}; | |
| + chemkinEaUnits, chemkinVerbosity, chemkinSMILES, thermomethod, | |
| + cyclicsOnly, qmSoftware}; | |
| initializeJCB(allTab); | |
| JScrollPane scrolltab = new JScrollPane(Options); | |
| @@ -3520,6 +3609,14 @@ public class GUI extends JPanel implements ActionListener { | |
| disableComponents(pruneComps); | |
| } | |
| } | |
| + // QM options | |
| + else if ("QM".equals(event.getActionCommand())) { | |
| + JComponent[] qmComps = {qmSoftware,cyclicsOnly,maxRadNumQM}; | |
| + if (thermomethod.getSelectedItem().equals("QM")) { | |
| + enableComponents(qmComps); | |
| + } else | |
| + disableComponents(qmComps); | |
| + } | |
| // Save the condition.txt file | |
| else if ("saveCondition".equals(event.getActionCommand())) { | |
| createConditionFile(false); | |
| @@ -3558,6 +3655,8 @@ public class GUI extends JPanel implements ActionListener { | |
| String[] AUnitsOptions = {"moles", "molecules"}; | |
| String[] EaUnitsOptions = {"kcal/mol", "cal/mol", "kJ/mol", "J/mol", "Kelvins"}; | |
| String[] eosOptions = {"Ideal Gas"}; // "Liquid" | |
| + String[] thermomethodOptions = {"Group Additivity", "QM"}; | |
| + String[] softwareOptions = {"Gaussian03", "MOPAC", "Both"}; | |
| JPanel | |
| // Main Panel | |
| @@ -3578,7 +3677,8 @@ public class GUI extends JPanel implements ActionListener { | |
| interCombo, | |
| // Tab : Additional Options | |
| eosCombo, inchiCombo, chemkinAUnits, chemkinEaUnits, chemkinVerbosity, | |
| - readRestartOnOff, writeRestartOnOff, chemkinSMILES, | |
| + readRestartOnOff, writeRestartOnOff, chemkinSMILES, thermomethod, | |
| + qmSoftware, cyclicsOnly, | |
| // | |
| chebyTUnits, chebyPUnits; | |
| @@ -3595,7 +3695,7 @@ public class GUI extends JPanel implements ActionListener { | |
| scName, | |
| // Tab : Additional Options | |
| maxCarbonNum, maxOxygenNum, maxRadicalNum, maxSulfurNum, maxSiliconNum, | |
| - maxHeavyAtom, FSName, | |
| + maxHeavyAtom, FSName, maxRadNumQM, | |
| // | |
| chebyTMin, chebyTMax, chebyPMin, chebyPMax, chebyTGen, chebyTRep, | |
| chebyPGen, chebyPRep, chebyT, chebyP, | |
| diff --git a/source/RMG/PopulateReactions.java b/source/RMG/PopulateReactions.java | |
| index 7e2f8d2..5756dcf 100644 | |
| --- a/source/RMG/PopulateReactions.java | |
| +++ b/source/RMG/PopulateReactions.java | |
| @@ -143,10 +143,22 @@ public class PopulateReactions { | |
| try { | |
| FileReader fr_input = new FileReader(args[0]); | |
| BufferedReader br_input = new BufferedReader(fr_input); | |
| + | |
| + // Read in the Database field | |
| + String line = ChemParser.readMeaningfulLine(br_input, true); | |
| + if (line.toLowerCase().startsWith("database")) { | |
| + RMG.extractAndSetDatabasePath(line); | |
| + } | |
| + else { | |
| + System.err.println("PopulateReactions: Could not" | |
| + + " locate the Database field"); | |
| + System.exit(0); | |
| + } | |
| + | |
| // Read in the first line of the input file | |
| // This line should hold the temperature of the system, e.g. | |
| // Temperature: 500 (K) | |
| - String line = ChemParser.readMeaningfulLine(br_input, true); | |
| + line = ChemParser.readMeaningfulLine(br_input, true); | |
| /* | |
| * Read max atom types (if they exist) | |
| @@ -376,7 +388,7 @@ public class PopulateReactions { | |
| for (int numSpecies=0; numSpecies<species.size(); ++numSpecies) { | |
| Species currentSpec = (Species)species.get(numSpecies); | |
| if (!allSpeciesInNetwork.contains(currentSpec)) { | |
| - listOfReactions += "!\t" + String.format(formatSpeciesName,currentSpec.getName()+"("+currentSpec.getID()+")") + currentSpec.getThermoData().toString() + currentSpec.getThermoData().getComments() + "\n"; | |
| + listOfReactions += "!\t" + String.format(formatSpeciesName,currentSpec.getFullName()) + currentSpec.getThermoData().toString() + currentSpec.getThermoData().getComments() + "\n"; | |
| allSpeciesInNetwork.add(currentSpec); | |
| } | |
| } | |
| @@ -456,7 +468,7 @@ public class PopulateReactions { | |
| int i = 0; | |
| while (iter_species.hasNext()) { | |
| Species species = (Species)iter_species.next(); | |
| - listOfSpecies += species.getName()+"("+species.getID()+")\n" + | |
| + listOfSpecies += species.getFullName()+"\n" + | |
| species.getChemGraph().toStringWithoutH(i) + "\n"; | |
| } | |
| diff --git a/source/RMG/RMG.java b/source/RMG/RMG.java | |
| index fea0990..ca7b892 100644 | |
| --- a/source/RMG/RMG.java | |
| +++ b/source/RMG/RMG.java | |
| @@ -147,7 +147,6 @@ public class RMG { | |
| public static void initializeSystemProperties(String inputfile) { | |
| globalInitializeSystemProperties(); | |
| - String workingDir = System.getProperty("RMG.workingDirectory"); | |
| File f = new File("."); | |
| String dir = f.getAbsolutePath(); | |
| @@ -291,12 +290,7 @@ public class RMG { | |
| //line = ChemParser.readMeaningfulLine(reader); | |
| if (line.startsWith("Database")){ | |
| - StringTokenizer st = new StringTokenizer(line); | |
| - String next = st.nextToken(); | |
| - String database_name = st.nextToken().trim(); | |
| - | |
| - String database_path = workingDir + "/databases/" + database_name; | |
| - setDatabasePaths(database_path); | |
| + extractAndSetDatabasePath(line); | |
| } | |
| } | |
| catch (IOException e) { | |
| @@ -304,6 +298,15 @@ public class RMG { | |
| } | |
| } | |
| + public static void extractAndSetDatabasePath(String line) { | |
| + StringTokenizer st = new StringTokenizer(line); | |
| + String next = st.nextToken(); | |
| + String database_name = st.nextToken().trim(); | |
| + String workingDir = System.getProperty("RMG.workingDirectory"); | |
| + String database_path = workingDir + "/databases/" + database_name; | |
| + setDatabasePaths(database_path); | |
| + } | |
| + | |
| /* this function is not used, has not been maintained, and is now out of date. | |
| private static void writeThermoFile() { | |
| diff --git a/source/RMG/ThermoDataEstimator.java b/source/RMG/ThermoDataEstimator.java | |
| index 1d767a4..236efa6 100644 | |
| --- a/source/RMG/ThermoDataEstimator.java | |
| +++ b/source/RMG/ThermoDataEstimator.java | |
| @@ -33,9 +33,7 @@ import jing.chemParser.*; | |
| import jing.param.*; | |
| import jing.chemUtil.*; | |
| //import bondGroups.*; | |
| -import jing.rxn.*; | |
| import jing.rxnSys.*; | |
| -import jing.mathTool.*; | |
| public class ThermoDataEstimator {//gmagoon 7/24/09: based off of Thermo.java rev. 1.6; this performs original functionality described in the manual | |
| @@ -58,11 +56,21 @@ public static void main(String[] args) { | |
| try { | |
| BufferedReader reader = new BufferedReader(new FileReader(file)); | |
| + String line = ChemParser.readMeaningfulLine(reader, true); | |
| + if (line.toLowerCase().startsWith("database")) { | |
| + RMG.extractAndSetDatabasePath(line); | |
| + } | |
| + else { | |
| + System.err.println("ThermoDataEstimator: Could not" | |
| + + " locate the Database field"); | |
| + System.exit(0); | |
| + } | |
| + | |
| /* | |
| * 14MAR2010: Allowing ThermoDataEstimator to read from Primary Reaction Library | |
| */ | |
| ReactionModelGenerator rmg = new ReactionModelGenerator(); | |
| - String line = ChemParser.readMeaningfulLine(reader, true); | |
| + line = ChemParser.readMeaningfulLine(reader, true); | |
| if (line.toLowerCase().startsWith("primarythermolibrary")) { | |
| rmg.readAndMakePTL(reader); | |
| } | |
| diff --git a/source/RMG/TransportDataEstimator.java b/source/RMG/TransportDataEstimator.java | |
| index 7232422..ed3697a 100644 | |
| --- a/source/RMG/TransportDataEstimator.java | |
| +++ b/source/RMG/TransportDataEstimator.java | |
| @@ -30,9 +30,21 @@ public class TransportDataEstimator { | |
| try { | |
| BufferedReader reader = new BufferedReader(new FileReader(new File(args[0]))); | |
| - // Read in the Primary Transport Library, if it exists | |
| ReactionModelGenerator rmg = new ReactionModelGenerator(); | |
| String line = ChemParser.readMeaningfulLine(reader, true); | |
| + | |
| + // Read in the Database field | |
| + if (line.toLowerCase().startsWith("database")) { | |
| + RMG.extractAndSetDatabasePath(line); | |
| + } | |
| + else { | |
| + System.err.println("TransportDataEstimator: Could not" | |
| + + " locate the Database field"); | |
| + System.exit(0); | |
| + } | |
| + line = ChemParser.readMeaningfulLine(reader, true); | |
| + | |
| + // Read in the Primary Transport Library, if it exists | |
| if (line.toLowerCase().startsWith("primarytransportlibrary")) { | |
| rmg.readAndMakePTransL(reader); | |
| } | |
| diff --git a/source/RMG/jing/chem/ChemGraph.java b/source/RMG/jing/chem/ChemGraph.java | |
| index bf23496..559408f 100644 | |
| --- a/source/RMG/jing/chem/ChemGraph.java | |
| +++ b/source/RMG/jing/chem/ChemGraph.java | |
| @@ -123,8 +123,8 @@ public class ChemGraph implements Matchable { | |
| if (isForbiddenStructure(p_graph,getRadicalNumber(),getOxygenNumber(),getCarbonNumber()) || getRadicalNumber() > MAX_RADICAL_NUM || getOxygenNumber() > MAX_OXYGEN_NUM || getCycleNumber() > MAX_CYCLE_NUM) { | |
| //if (getRadicalNumber() > MAX_RADICAL_NUM || getOxygenNumber() > MAX_OXYGEN_NUM || getCycleNumber() > MAX_CYCLE_NUM) { | |
| + String message = p_graph.toString() + " is forbidden by "+whichForbiddenStructures(p_graph, getRadicalNumber(), getOxygenNumber(), getCycleNumber()) +"and not allowed."; | |
| graph = null; | |
| - String message = p_graph.toString() + " is forbidden by "+whichForbiddenStructures(p_graph) +"and not allowed."; | |
| throw new ForbiddenStructureException(message); | |
| } | |
| } | |
| @@ -1547,21 +1547,8 @@ return sn; | |
| String newInChI=null; | |
| int radicalNumber = this.getUnpairedRadicalNumber(); | |
| // System.out.println("Radical number:"+radicalNumber);//for debugging purposes | |
| - if (radicalNumber == 2){ | |
| - newInChI = InChI.concat("/mult3"); | |
| - } | |
| - else if (radicalNumber == 3){ | |
| - newInChI = InChI.concat("/mult4"); | |
| - } | |
| - else if (radicalNumber == 4){ | |
| - newInChI = InChI.concat("/mult5"); | |
| - } | |
| - else if (radicalNumber == 5){ | |
| - newInChI = InChI.concat("/mult6"); | |
| - } | |
| - else if (radicalNumber > 5){ | |
| - System.out.println("Unexpectedly high multiplicity ("+ (radicalNumber+1)+ ") for " + InChI); | |
| - System.exit(0); | |
| + if (radicalNumber >= 2){ | |
| + newInChI = InChI.concat("/mult"+(radicalNumber+1)); | |
| } | |
| else{ | |
| newInChI = InChI; | |
| @@ -1575,21 +1562,8 @@ return sn; | |
| String newInChIKey=null; | |
| int radicalNumber = this.getUnpairedRadicalNumber(); | |
| // System.out.println("Radical number:"+radicalNumber);//for debugging purposes | |
| - if (radicalNumber == 2){ | |
| - newInChIKey = InChIKey.concat("mult3"); | |
| - } | |
| - else if (radicalNumber == 3){ | |
| - newInChIKey = InChIKey.concat("mult4"); | |
| - } | |
| - else if (radicalNumber == 4){ | |
| - newInChIKey = InChIKey.concat("mult5"); | |
| - } | |
| - else if (radicalNumber == 5){ | |
| - newInChIKey = InChIKey.concat("mult6"); | |
| - } | |
| - else if (radicalNumber > 5){ | |
| - System.out.println("Unexpectedly high multiplicity ("+ (radicalNumber+1)+ ") for " + InChI); | |
| - System.exit(0); | |
| + if (radicalNumber >= 2){ | |
| + newInChIKey = InChIKey.concat("mult"+(radicalNumber+1)); | |
| } | |
| else{ | |
| newInChIKey= InChIKey; | |
| @@ -2126,7 +2100,7 @@ return sn; | |
| // Which forbidden structure forbade this chemgraph? | |
| // returns the names of forbidden structures. | |
| - public static String whichForbiddenStructures(Graph p_graph) { | |
| + public static String whichForbiddenStructures(Graph p_graph, int radNumber, int oxygenNumber, int cycleNumber) { | |
| String forbidden_by = ""; | |
| for (Iterator iter = forbiddenStructure.iterator(); iter.hasNext(); ) { | |
| FunctionalGroup fg = (FunctionalGroup)iter.next(); | |
| @@ -2135,7 +2109,16 @@ return sn; | |
| forbidden_by += fg.getName() +", "; | |
| } | |
| } | |
| - if (forbidden_by=="") return "no forbidden structures, "; | |
| + if (forbidden_by=="") { | |
| + if (radNumber > MAX_RADICAL_NUM) | |
| + return "the maximum number of radicals per species (check the condition.txt file), "; | |
| + else if (oxygenNumber > MAX_OXYGEN_NUM) | |
| + return "the maximum number of oxygens per species (check the condition.txt file), "; | |
| + else if (cycleNumber > MAX_CYCLE_NUM) | |
| + return "the maximum number of cycles per species (check the condition.txt file), "; | |
| + else | |
| + return "no forbidden structures, "; | |
| + } | |
| return forbidden_by; | |
| } | |
| diff --git a/source/RMG/jing/chem/FrequencyGroups.java b/source/RMG/jing/chem/FrequencyGroups.java | |
| index 737981a..57f1071 100644 | |
| --- a/source/RMG/jing/chem/FrequencyGroups.java | |
| +++ b/source/RMG/jing/chem/FrequencyGroups.java | |
| @@ -80,8 +80,8 @@ public class FrequencyGroups{//gmagoon 111708: removed "implements GeneralGAPP" | |
| int nFreq = 3 * atoms - 5 - rotor - degeneracy - linearity; | |
| if (nFreq < 0) { | |
| - System.out.println(species.getName() + "(" + Integer.toString(species.getID()) + | |
| - ") is overspecified: " + | |
| + System.out.println(species.getFullName() + | |
| + " is overspecified: " + | |
| Integer.toString(degeneracy) + " harmonic oscillators and " + | |
| Integer.toString(rotor) + " internal rotors are specified, but only " + | |
| Integer.toString(3 * atoms - 5 - linearity) + " modes are allowed."); | |
| @@ -191,7 +191,7 @@ public class FrequencyGroups{//gmagoon 111708: removed "implements GeneralGAPP" | |
| // If the output file is empty, then an error occurred | |
| if (franklOutput.length() == 0) | |
| throw new IOException("Error: FrequencyGroups estimation for " + | |
| - species.getName() + "(" + Integer.toString(species.getID()) + ") failed."); | |
| + species.getFullName() + " failed."); | |
| // Read information about molecule (numuber of atoms, number of rotors, linearity) | |
| atoms = Integer.parseInt(br.readLine().trim()); | |
| @@ -259,7 +259,7 @@ public class FrequencyGroups{//gmagoon 111708: removed "implements GeneralGAPP" | |
| } | |
| // Rename input and output files | |
| - /*String newName = species.getName()+"("+String.valueOf(species.getID())+")"; | |
| + /*String newName = species.getFullName(); | |
| File f = new File("frankie/dat"); | |
| File newFile = new File("frankie/"+newName+"_input"); | |
| f.renameTo(newFile); | |
| diff --git a/source/RMG/jing/chem/FunctionalGroupCollection.java b/source/RMG/jing/chem/FunctionalGroupCollection.java | |
| index 3a4512b..dd83c90 100644 | |
| --- a/source/RMG/jing/chem/FunctionalGroupCollection.java | |
| +++ b/source/RMG/jing/chem/FunctionalGroupCollection.java | |
| @@ -111,7 +111,22 @@ public class FunctionalGroupCollection implements Matchable { | |
| public boolean isSubAtCentralNodes(Matchable p_functional) { | |
| //#[ operation isSubAtCentralNodes(Matchable) | |
| if (this == p_functional) return false; | |
| - if (!(p_functional instanceof FunctionalGroupCollection)) return false; | |
| + if (!(p_functional instanceof FunctionalGroupCollection)) { | |
| + boolean found = false; | |
| + Iterator iter1 = functionalGroups.iterator(); | |
| + while (iter1.hasNext()) { | |
| + FunctionalGroup fg1 = (FunctionalGroup)iter1.next(); | |
| + if (fg1.equals(p_functional) || fg1.isSubAtCentralNodes(p_functional)) { | |
| + found = true; | |
| + } | |
| + else { | |
| + found = false; | |
| + break; | |
| + } | |
| + } | |
| + if (!found) return false; | |
| + return true; | |
| + } | |
| Collection c1 = functionalGroups; | |
| Collection c2 = ((FunctionalGroupCollection)p_functional).functionalGroups; | |
| diff --git a/source/RMG/jing/chem/GATPFit.java b/source/RMG/jing/chem/GATPFit.java | |
| index 6a24e96..cb8b68a 100644 | |
| --- a/source/RMG/jing/chem/GATPFit.java | |
| +++ b/source/RMG/jing/chem/GATPFit.java | |
| @@ -111,7 +111,11 @@ public class GATPFit { | |
| // write MW, temperature, ouput format, etc | |
| //result.append( "MWEI " + MathTool.formatDouble(species.getMolecularWeight(), 6, 1).trim() + ls ); | |
| result.append( "TEMP 1000.0" + ls ); | |
| - result.append( "TMIN 300.0"+ls ); | |
| + //note:the TMIN and TMAX values below only affect the valid range in the CHEMKIN output file; | |
| + // the points used to deteremine the NASA-to-Wilhoit fit are determined independently inside the GATPFit fortran code. | |
| + // Too large a range causes problems fitting the transport data when pre-processing in CHEMKIN. | |
| + // (see https://github.com/GreenGroup/RMG-Java/issues/issue/18) | |
| + result.append( "TMIN 250.0"+ls ); | |
| result.append( "TMAX 5000.0" + ls ); | |
| result.append( "CHEM" + ls ); | |
| result.append( "TEM2 2000.0" + ls ); | |
| diff --git a/source/RMG/jing/chem/QMTP.java b/source/RMG/jing/chem/QMTP.java | |
| index 2374d9e..47e7b14 100644 | |
| --- a/source/RMG/jing/chem/QMTP.java | |
| +++ b/source/RMG/jing/chem/QMTP.java | |
| @@ -466,6 +466,9 @@ public class QMTP implements GeneralGAPP { | |
| int exitValue = pythonProc.waitFor(); | |
| if(timeoutThread.isAlive())//if the timeout thread is still alive (indicating that the process has completed in a timely manner), stop the timeout thread | |
| timeoutThread.interrupt(); | |
| + br.close(); | |
| + isr.close(); | |
| + is.close(); | |
| } | |
| catch (Exception e) { | |
| String err = "Error in running RDKit Python process \n"; | |
| @@ -614,6 +617,9 @@ public class QMTP implements GeneralGAPP { | |
| //do nothing | |
| } | |
| int exitValue = babelProc.waitFor(); | |
| + br.close(); | |
| + isr.close(); | |
| + is.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in running OpenBabel MOL to GJF process \n"; | |
| @@ -715,6 +721,9 @@ public class QMTP implements GeneralGAPP { | |
| //do nothing | |
| } | |
| int exitValue = molecoorProc.waitFor(); | |
| + br.close(); | |
| + isr.close(); | |
| + is.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in running MoleCoor MOL to .MM4 process \n"; | |
| @@ -743,6 +752,7 @@ public class QMTP implements GeneralGAPP { | |
| line=reader.readLine(); | |
| lineIndex++; | |
| } | |
| + reader.close(); | |
| mm4opt.close(); | |
| } | |
| catch(Exception e){ | |
| @@ -991,6 +1001,9 @@ public class QMTP implements GeneralGAPP { | |
| //do nothing | |
| } | |
| int exitValue = babelProc.waitFor(); | |
| + br.close(); | |
| + isr.close(); | |
| + is.close(); | |
| //append the final keywords to the end of the file just written | |
| // File mopacInpFile = new File(directory+"/"+name+".mop"); | |
| @@ -1034,6 +1047,9 @@ public class QMTP implements GeneralGAPP { | |
| System.out.println("Gaussian process received error (see above) on " + name); | |
| } | |
| int exitValue = gaussianProc.waitFor(); | |
| + br.close(); | |
| + isr.close(); | |
| + is.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in running Gaussian process \n"; | |
| @@ -1069,6 +1085,8 @@ public class QMTP implements GeneralGAPP { | |
| } | |
| line=reader.readLine(); | |
| } | |
| + reader.close(); | |
| + in.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in reading Gaussian log file \n"; | |
| @@ -1125,6 +1143,9 @@ public class QMTP implements GeneralGAPP { | |
| int exitValue = mm4Proc.waitFor(); | |
| + br.close(); | |
| + isr.close(); | |
| + is.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in running MM4 process \n"; | |
| @@ -1164,6 +1185,8 @@ public class QMTP implements GeneralGAPP { | |
| } | |
| line=reader.readLine(); | |
| } | |
| + reader.close(); | |
| + in.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in reading MM4 output file \n"; | |
| @@ -1219,6 +1242,9 @@ public class QMTP implements GeneralGAPP { | |
| int exitValue = mm4Proc.waitFor(); | |
| + br.close(); | |
| + isr.close(); | |
| + is.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in running MM4 rotor process \n"; | |
| @@ -1258,6 +1284,9 @@ public class QMTP implements GeneralGAPP { | |
| System.out.println("MOPAC process received error (see above) on " + name); | |
| } | |
| int exitValue = mopacProc.waitFor(); | |
| + br.close(); | |
| + isr.close(); | |
| + is.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in running MOPAC process \n"; | |
| @@ -1296,6 +1325,8 @@ public class QMTP implements GeneralGAPP { | |
| } | |
| line=reader.readLine(); | |
| } | |
| + reader.close(); | |
| + in.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in reading MOPAC output file \n"; | |
| @@ -1566,6 +1597,9 @@ public class QMTP implements GeneralGAPP { | |
| } | |
| int exitValue = canProc.waitFor(); | |
| + br.close(); | |
| + isr.close(); | |
| + is.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in running CanTherm process \n"; | |
| @@ -1606,6 +1640,7 @@ public class QMTP implements GeneralGAPP { | |
| Cp1000 = Double.parseDouble(split[9]); | |
| Cp1500 = Double.parseDouble(split[14]); | |
| reader.close(); | |
| + in.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in reading CanTherm .canout file \n"; | |
| @@ -1751,6 +1786,9 @@ public class QMTP implements GeneralGAPP { | |
| //do nothing (there shouldn't be any more information, but this is included to get all the output) | |
| } | |
| int exitValue = cclibProc.waitFor(); | |
| + br.close(); | |
| + isr.close(); | |
| + is.close(); | |
| } | |
| catch (Exception e) { | |
| String err = "Error in running ccLib Python process \n"; | |
| @@ -1948,6 +1986,9 @@ public class QMTP implements GeneralGAPP { | |
| } | |
| } | |
| int exitValue = symmProc.waitFor(); | |
| + br.close(); | |
| + isr.close(); | |
| + is.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in running point group calculation process using SYMMETRY \n"; | |
| @@ -2074,6 +2115,8 @@ public class QMTP implements GeneralGAPP { | |
| } | |
| line=reader.readLine(); | |
| } | |
| + reader.close(); | |
| + in.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in reading preexisting Gaussian log file \n"; | |
| @@ -2103,6 +2146,8 @@ public class QMTP implements GeneralGAPP { | |
| } | |
| lineI=readerI.readLine(); | |
| } | |
| + readerI.close(); | |
| + inI.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in reading preexisting Gaussian gjf file \n"; | |
| @@ -2204,6 +2249,8 @@ public class QMTP implements GeneralGAPP { | |
| } | |
| line=reader.readLine(); | |
| } | |
| + reader.close(); | |
| + in.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in reading preexisting MOPAC output file \n"; | |
| @@ -2233,6 +2280,8 @@ public class QMTP implements GeneralGAPP { | |
| } | |
| lineI=readerI.readLine(); | |
| } | |
| + readerI.close(); | |
| + inI.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in reading preexisting MOPAC input file \n"; | |
| @@ -2333,6 +2382,8 @@ public class QMTP implements GeneralGAPP { | |
| } | |
| line=reader.readLine(); | |
| } | |
| + reader.close(); | |
| + in.close(); | |
| } | |
| catch(Exception e){ | |
| String err = "Error in reading preexisting MM4 output file \n"; | |
| @@ -2357,7 +2408,9 @@ public class QMTP implements GeneralGAPP { | |
| String lineI=readerI.readLine(); | |
| //InChI should be repeated after in the first line of the input file | |
| inputFileInChI = lineI.trim().substring(80);//extract the string starting with character 81 | |
| - } | |
| + readerI.close(); | |
| + inI.close(); | |
| + } | |
| catch(Exception e){ | |
| String err = "Error in reading preexisting MM4 .mm4 file \n"; | |
| err += e.toString(); | |
| @@ -2668,6 +2721,9 @@ public class QMTP implements GeneralGAPP { | |
| //do nothing (there shouldn't be any more information, but this is included to get all the output) | |
| } | |
| int exitValue = cclibProc.waitFor(); | |
| + br.close(); | |
| + isr.close(); | |
| + is.close(); | |
| } | |
| catch (Exception e) { | |
| String err = "Error in running ccLib Python process \n"; | |
| diff --git a/source/RMG/jing/chem/Species.java b/source/RMG/jing/chem/Species.java | |
| index c18ef59..1f91c74 100644 | |
| --- a/source/RMG/jing/chem/Species.java | |
| +++ b/source/RMG/jing/chem/Species.java | |
| @@ -337,7 +337,7 @@ public class Species { | |
| //#[ operation findStablestThermoData() | |
| double H = chemGraph.getThermoData().getH298(); | |
| ChemGraph stablest = chemGraph; | |
| - if (resonanceIsomers != null) { | |
| + if (!resonanceIsomers.isEmpty()) { | |
| Iterator iter = resonanceIsomers.iterator(); | |
| while (iter.hasNext()) { | |
| ChemGraph g = (ChemGraph)iter.next(); | |
| @@ -727,11 +727,21 @@ public class Species { | |
| therfitExecuted = (threeFrequencyModel != null); | |
| } | |
| - | |
| + | |
| + //## operation getFullName() | |
| + public String getFullName() { | |
| + // get the full name with the ID appended. | |
| + // the chemkin name is a shortened version of this | |
| + if (addID){ | |
| + return String.format("%s(%d)",getName(),getID()); | |
| + } | |
| + else | |
| + return getName(); | |
| + } | |
| + | |
| + //## operation getChemkinName() | |
| public String getChemkinName() { | |
| - //#[ operation getChemkinName() | |
| - if (addID){ | |
| - String chemkinName = getName() + "(" + getID() + ")"; | |
| + String chemkinName = getFullName(); | |
| /* Updated by MRH on 1-Jun-2008 | |
| If statement used to check if chemkinName length was greater than 16 | |
| I've changed it to length 10. Chemkin format dictates that any | |
| @@ -746,11 +756,7 @@ public class Species { | |
| if (chemkinName.length() > 10) chemkinName = "SPC(" + getID() + ")"; | |
| return chemkinName; | |
| - } | |
| - else | |
| - return getName(); | |
| - //#] | |
| } | |
| //## operation getInternalRotor() | |
| @@ -874,7 +880,7 @@ public class Species { | |
| dictionary.putSpecies(spe, true); | |
| // DEBUG: Tell console I made this species | |
| - System.out.println("Created new species: " + spe.getName() + "(" + spe.getID() + ")"); | |
| + System.out.println("Created new species: " + spe.getFullName() ); | |
| } | |
| else { | |
| @@ -987,7 +993,7 @@ public class Species { | |
| p_chemGraph.setSpecies(spe); | |
| // DEBUG: Tell console I made this species | |
| - System.out.println("Created new species: " + spe.getName() + "(" + spe.getID() + ")"); | |
| + System.out.println("Created new species: " + spe.getFullName() ); | |
| return spe; | |
| } | |
| @@ -1285,6 +1291,14 @@ public class Species { | |
| } | |
| result[0]=InChIstring; | |
| result[1]=InChIKeystring; | |
| + try { | |
| + reader.close(); | |
| + in.close(); | |
| + } catch (Exception e) { | |
| + String err = "Error closing InChI output reader for " + p_chemGraph.chemicalFormula + " : "; | |
| + err += e.toString(); | |
| + System.out.println(err); | |
| + } | |
| } | |
| else { | |
| result[0] = ""; | |
| @@ -1354,8 +1368,7 @@ public class Species { | |
| int mRad = 1; | |
| int radCount = 0; | |
| - // Assume the species does not contain > 4 radicals | |
| - int maxRad = 4; | |
| + int maxRad = ChemGraph.MAX_RADICAL_NUM; | |
| int[] radLocation = new int[maxRad]; | |
| int[] radType = new int[maxRad]; | |
| for (int numRads=0; numRads<(atomCount-1); numRads++) { | |
| @@ -1647,7 +1660,7 @@ public class Species { | |
| String line = ChemParser.readMeaningfulLine(reader, true); | |
| while (!line.toUpperCase().endsWith("V2000")) { | |
| - line = ChemParser.readMeaningfulLine(reader, true); | |
| + line = ChemParser.readMeaningfulLine(reader, false); | |
| } | |
| String molFile = ""; | |
| @@ -1664,19 +1677,19 @@ public class Species { | |
| // Extract the information in the first line (Count Line) of the .mol file | |
| st = new StringTokenizer(molFileLines[0]); | |
| - int numOfAtoms = Integer.parseInt(st.nextToken()); | |
| - int numOfBonds = Integer.parseInt(st.nextToken()); | |
| + int numOfAtoms = Integer.parseInt(molFileLines[0].substring(0,3).trim()); | |
| + int numOfBonds = Integer.parseInt(molFileLines[0].substring(3,6).trim()); | |
| // Next few are irrelevant for RMG (as of 10-Feb-2009) | |
| - int numOfAtomLists = Integer.parseInt(st.nextToken()); | |
| - String obsoleteString1 = st.nextToken(); | |
| - String chiralFlag = st.nextToken(); | |
| - int stextEntries = Integer.parseInt(st.nextToken()); | |
| - String obsoleteString2 = st.nextToken(); | |
| - String obsoleteString3 = st.nextToken(); | |
| - String obsoleteString4 = st.nextToken(); | |
| - String obsoleteString5 = st.nextToken(); | |
| + int numOfAtomLists = Integer.parseInt(molFileLines[0].substring(6,9).trim()); | |
| + String obsoleteString1 = molFileLines[0].substring(9,12); | |
| + String chiralFlag = molFileLines[0].substring(12,15); | |
| + int stextEntries = Integer.parseInt(molFileLines[0].substring(15,18).trim()); | |
| + String obsoleteString2 = molFileLines[0].substring(18,21); | |
| + String obsoleteString3 = molFileLines[0].substring(21,24); | |
| + String obsoleteString4 = molFileLines[0].substring(24,27); | |
| + String obsoleteString5 = molFileLines[0].substring(27,30); | |
| // Extract the number of M lines | |
| - int numOfMLines = Integer.parseInt(st.nextToken()); | |
| + int numOfMLines = Integer.parseInt(molFileLines[0].substring(30,33).trim()); | |
| // Construct each individual line of the adjacency list | |
| String[] adjListElement = new String[numOfAtoms]; | |
| diff --git a/source/RMG/jing/chem/SpeciesDictionary.java b/source/RMG/jing/chem/SpeciesDictionary.java | |
| index 741dae9..6ef64aa 100644 | |
| --- a/source/RMG/jing/chem/SpeciesDictionary.java | |
| +++ b/source/RMG/jing/chem/SpeciesDictionary.java | |
| @@ -186,7 +186,7 @@ public class SpeciesDictionary { | |
| Iterator iter = dictionary.values().iterator(); | |
| while (iter.hasNext()) { | |
| Species spe = (Species)iter.next(); | |
| - if ((spe.getName()+"("+spe.getID()+")").compareToIgnoreCase(p_name) == 0) { | |
| + if ((spe.getFullName()).compareToIgnoreCase(p_name) == 0) { | |
| return spe; | |
| } | |
| } | |
| diff --git a/source/RMG/jing/chemParser/ChemParser.java b/source/RMG/jing/chemParser/ChemParser.java | |
| index 5d33774..19b41b3 100644 | |
| --- a/source/RMG/jing/chemParser/ChemParser.java | |
| +++ b/source/RMG/jing/chemParser/ChemParser.java | |
| @@ -63,13 +63,10 @@ public class ChemParser { | |
| //## operation ChemParser() | |
| private ChemParser() { | |
| - //#[ operation ChemParser() | |
| - //#] | |
| } | |
| //## operation extractReactionSeperator(String) | |
| public static final String extractReactionSeperator(String p_string) { | |
| - //#[ operation extractReactionSeperator(String) | |
| if (p_string == null) throw new NullPointerException(); | |
| StringTokenizer st = new StringTokenizer(p_string); | |
| @@ -81,7 +78,6 @@ public class ChemParser { | |
| else if (s.equals("->")) return "->"; | |
| } | |
| return null; | |
| - //#] | |
| } | |
| /** | |
| @@ -97,26 +93,14 @@ public class ChemParser { | |
| } | |
| } | |
| } | |
| - | |
| // The directory is now empty so delete it | |
| return dir.delete(); | |
| } | |
| - // Argument Stringp_name : | |
| - /** | |
| - the name of union | |
| - */ | |
| - // Argument HashMapp_unRead : | |
| - /** | |
| - the map including all the union, each mapping maps the unread union group's name with their union components' names. | |
| - */ | |
| - // Argument HashMapp_dictionary : | |
| - /** | |
| - The real dicationary where we can find the graph information from the name. | |
| - */ | |
| - //## operation findUnion(String,HashMap,HashMap) | |
| + // Argument Stringp_name : the name of union | |
| + // Argument HashMapp_unRead : the map including all the union, each mapping maps the unread union group's name with their union components' names. | |
| + // Argument HashMapp_dictionary : The real dicationary where we can find the graph information from the name. | |
| public static void findUnion(String p_name, HashMap p_unRead, HashMap p_dictionary) { | |
| - //#[ operation findUnion(String,HashMap,HashMap) | |
| FunctionalGroupCollection fgc = new FunctionalGroupCollection(p_name); | |
| // get the union set according to the p_name | |
| @@ -136,15 +120,10 @@ public class ChemParser { | |
| p_dictionary.put(p_name,fgc); | |
| p_unRead.remove(p_name); | |
| return; | |
| - | |
| - | |
| - | |
| - //#] | |
| } | |
| - //## operation parseArrheniusEPKinetics(String) | |
| + | |
| /** | |
| - * Input parameters updated by MRH on 8-Jun-2009 | |
| * This function is called when reading a kinetics Library.txt file, | |
| * if the kinetics tag is Arrhenius_EP. As of today, all rxn families | |
| * in the RMG database are labeled Arrhenius_EP. Instead of passing only | |
| @@ -156,22 +135,12 @@ public class ChemParser { | |
| * nodes associated with this data entry (e.g. 1 for Beta_Scission, 2 for | |
| * H_Abstraction, 3 for Diels_Alder_Addition, etc.). | |
| * | |
| - * The output is of type ArrheniusEPKinetics. The difference is that the | |
| - * "comments" and "source" fields are no longer null. The "source" contains | |
| + * The output is of type ArrheniusEPKinetics. The "source" contains | |
| * the set of nodes associated with this data, and the "comments" are | |
| * the end-of-line comments, hopefully denoting where this data came from. | |
| **/ | |
| public static ArrheniusEPKinetics parseArrheniusEPKinetics(String p_string, int p_keyNum) { | |
| - //#[ operation parseArrheniusEPKinetics(String) | |
| StringTokenizer token = new StringTokenizer(p_string); | |
| - //if (token.countTokens() != 10) throw new InvalidKineticsFormatException(); | |
| - /* | |
| - * If statement commented out by MRH on 8-Jun-2009 | |
| - * The if statement existed because RMG was looking for 10 tokens: | |
| - * (Trange, A, n, alpha, E0, dA, dn, dalpha, dE0, and Rank). | |
| - * RMG now has no limit on the number of tokens, which allows | |
| - * a RMG user/developer to put comments after the rank | |
| - */ | |
| String dummyCounter = token.nextToken(); // This should be the #. associated with the data | |
| // Set the source of this data as the set of nodes | |
| String source = ""; | |
| @@ -219,24 +188,15 @@ public class ChemParser { | |
| while (token.hasMoreTokens()) | |
| comments += token.nextToken() + " "; | |
| - /*if (token.hasMoreTokens()) { | |
| - String beginningOfComments = token.nextToken(); | |
| - String[] splitString = p_string.split(beginningOfComments); | |
| - comments = beginningOfComments + splitString[1]; | |
| - }*/ | |
| ArrheniusEPKinetics k = new ArrheniusEPKinetics(ua, un, ualpha, ue, TRange, rank, source, comments); | |
| -// ArrheniusEPKinetics k = new ArrheniusEPKinetics(ua, un, ualpha, ue, TRange, rank, null, null); | |
| return k; | |
| - | |
| - | |
| - //#] | |
| } | |
| //## operation parseArrheniusKinetics(String) | |
| /** | |
| - * Input parameters updated by MRH on 11-Jun-2009 | |
| + * | |
| * This function is called when reading a kinetics Library.txt file, | |
| * if the kinetics tag is Arrhenius. As of today, no rxn families | |
| * in the RMG database are labeled Arrhenius. Instead of passing only | |
| @@ -248,22 +208,12 @@ public class ChemParser { | |
| * nodes associated with this data entry (e.g. 1 for Beta_Scission, 2 for | |
| * H_Abstraction, 3 for Diels_Alder_Addition, etc.). | |
| * | |
| - * The output is of type ArrheniusKinetics. The difference is that the | |
| - * "comments" and "source" fields are no longer null. The "source" contains | |
| + * The output is of type ArrheniusKinetics. The "source" contains | |
| * the set of nodes associated with this data, and the "comments" are | |
| * the end-of-line comments, hopefully denoting where this data came from. | |
| **/ | |
| public static ArrheniusKinetics parseArrheniusKinetics(String p_string, int p_keyNum) { | |
| - //#[ operation parseArrheniusKinetics(String) | |
| StringTokenizer token = new StringTokenizer(p_string); | |
| - /* | |
| - * If statement commented out by MRH on 11-Jun-2009 | |
| - * The if statement existed because RMG was looking for 8 tokens: | |
| - * (Trange, A, n, Ea, dA, dn, dEa, and Rank). | |
| - * RMG now has no limit on the number of tokens, which allows | |
| - * a RMG user/developer to put comments after the rank | |
| - */ | |
| -// if (token.countTokens() != 8) throw new InvalidKineticsFormatException(); | |
| String dummyCounter = token.nextToken(); // This should be the #. associated with the data | |
| // Set the source of this data as the set of nodes | |
| String source = ""; | |
| @@ -305,19 +255,13 @@ public class ChemParser { | |
| // Set the comments of this data to whatever (if anything) follows the rank | |
| String comments = ""; | |
| - if (token.hasMoreTokens()) { | |
| - String beginningOfComments = token.nextToken(); | |
| - String[] splitString = p_string.split(beginningOfComments); | |
| - comments = beginningOfComments + splitString[1]; | |
| - } | |
| + while (token.hasMoreTokens()) | |
| + comments += token.nextToken() + " "; | |
| + | |
| ArrheniusKinetics k = new ArrheniusKinetics(ua, un, ue, TRange, rank, source, comments); | |
| -// ArrheniusKinetics k = new ArrheniusKinetics(ua, un, ue, TRange, rank, null, null); | |
| return k; | |
| - | |
| - | |
| - //#] | |
| } | |
| /* | |
| @@ -615,17 +559,12 @@ public class ChemParser { | |
| UncertainDouble un = new UncertainDouble(rxn_n,0.0,"A"); | |
| UncertainDouble uE = new UncertainDouble(rxn_E,0.0,"A"); | |
| - // The remaining tokens are comments | |
| - String comments = ""; | |
| - if (st.hasMoreTokens()) { | |
| - String beginningOfComments = st.nextToken(); | |
| - int startIndex = p_rxnString.indexOf(beginningOfComments); | |
| - comments = p_rxnString.substring(startIndex); | |
| - } | |
| + // The remaining tokens are comments, which may start with a ! | |
| + String comments = ""; | |
| + while (st.hasMoreTokens()) | |
| + comments += st.nextToken() + " "; | |
| if (comments.startsWith("!")) comments = comments.substring(1); | |
| -// while (st.hasMoreTokens()) { | |
| -// comments += st.nextToken(); | |
| -// } | |
| + | |
| // Generate the kinetics (assuming a rank of 1 ... as of 7/Sept/2009, the rank | |
| // of Kinetics should not be important at this stage of the mechanism | |
| @@ -771,9 +710,6 @@ public class ChemParser { | |
| return k; | |
| - | |
| - | |
| - //#] | |
| } | |
| @@ -843,7 +779,6 @@ public class ChemParser { | |
| } | |
| return reactionSpe; | |
| - //#] | |
| } | |
| //## operation parseSimpleArrheniusKinetics(String,double,double) | |
| @@ -884,9 +819,6 @@ public class ChemParser { | |
| return k; | |
| - | |
| - | |
| - //#] | |
| } | |
| //## operation parseThermoFromLibrary(String) | |
| @@ -982,7 +914,6 @@ public class ChemParser { | |
| //## operation parseAbrahamGAValue(String) | |
| public static UnifacGAValue parseUnifacGAValue(String p_string) { | |
| - //#[ operation parseThermoGAValue(String) | |
| String s = p_string.trim(); | |
| StringTokenizer token = new StringTokenizer(s); | |
| @@ -995,17 +926,10 @@ public class ChemParser { | |
| return new UnifacGAValue(R,Q); | |
| - | |
| - | |
| - | |
| - //#] | |
| } | |
| - | |
| - | |
| - | |
| //## operation parseThirdBodyList(String) | |
| public static HashMap parseThirdBodyList(String p_string, HashMap speciesList) { | |
| //#[ operation parseThirdBodyList(String) | |
| @@ -1142,14 +1066,10 @@ public class ChemParser { | |
| } | |
| return action; | |
| - | |
| - | |
| - //#] | |
| } | |
| //## operation readBond(String) | |
| public static Object readBond(String p_name) throws InvalidGraphFormatException { | |
| - //#[ operation readBond(String) | |
| String bondType = removeBrace(p_name); | |
| StringTokenizer bondToken = new StringTokenizer(bondType, ","); | |
| int bondNum = bondToken.countTokens(); | |
| @@ -1176,10 +1096,6 @@ public class ChemParser { | |
| throw new InvalidGraphFormatException("bond: " + bondType); | |
| } | |
| - | |
| - | |
| - | |
| - //#] | |
| } | |
| //## operation readChemGraph(BufferedReader) | |
| diff --git a/source/RMG/jing/mathTool/UncertainDouble.java b/source/RMG/jing/mathTool/UncertainDouble.java | |
| index 5c4e8ec..bb93a59 100644 | |
| --- a/source/RMG/jing/mathTool/UncertainDouble.java | |
| +++ b/source/RMG/jing/mathTool/UncertainDouble.java | |
| @@ -130,10 +130,32 @@ public class UncertainDouble { | |
| public UncertainDouble plus(double p_adder) { | |
| //#[ operation plus(double) | |
| return new UncertainDouble(value+p_adder,uncertainty,type); | |
| - | |
| - | |
| //#] | |
| } | |
| + | |
| + //## operation plus(UncertainDouble) | |
| + public UncertainDouble plus(UncertainDouble p_adder) { | |
| + double newUncertainty = getAddingUncertainty() + p_adder.getAddingUncertainty(); | |
| + double newValue = value + p_adder.getValue(); | |
| + return new UncertainDouble(newValue,newUncertainty,"Adder"); | |
| + | |
| + } | |
| + | |
| + //## operation getAddingUncertainty() | |
| + public double getAddingUncertainty() { | |
| + // return the uncertainty in an adding type | |
| + // i.e. if it's a multiplying type, subtract one and multiply it by 'value'. | |
| + // This exaggerates how low the lower bound will be. | |
| + // (e.g. 10*/2 will become 10+-10. | |
| + if (isAddingUncertainty()) { | |
| + return getUncertainty(); | |
| + } | |
| + else if (isMultiplyingUncertainty()){ | |
| + return getUncertainty() * ((double)getValue() - 1.0); | |
| + } | |
| + else throw new InvalidUncertaintyTypeException(); | |
| + } | |
| + | |
| //## operation toString() | |
| public String toString() { | |
| diff --git a/source/RMG/jing/rxn/ArrheniusEPKinetics.java b/source/RMG/jing/rxn/ArrheniusEPKinetics.java | |
| index f621ca1..3a87d5f 100644 | |
| --- a/source/RMG/jing/rxn/ArrheniusEPKinetics.java | |
| +++ b/source/RMG/jing/rxn/ArrheniusEPKinetics.java | |
| @@ -50,86 +50,23 @@ public class ArrheniusEPKinetics extends ArrheniusKinetics { | |
| //## operation ArrheniusEPKinetics(UncertainDouble,UncertainDouble,UncertainDouble,UncertainDouble,String,int,String,String) | |
| public ArrheniusEPKinetics(UncertainDouble p_A, UncertainDouble p_n, UncertainDouble p_alpha, UncertainDouble p_E, String p_TRange, int p_rank, String p_source, String p_comment) { | |
| - //#[ operation ArrheniusEPKinetics(UncertainDouble,UncertainDouble,UncertainDouble,UncertainDouble,String,int,String,String) | |
| super(p_A, p_n, p_E, p_TRange, p_rank, p_source, p_comment); | |
| alpha = p_alpha; | |
| - | |
| - //#] | |
| } | |
| + | |
| public ArrheniusEPKinetics() { | |
| } | |
| - /////////////////////////////////////// | |
| - // Notice that we don't redefine getEValue() here but instead inherit it from ArrheniusKinetics | |
| - // which means that if we imagine | |
| - // Ea = Eo + alpha * Hrxn | |
| - // then getEValue() returns Eo NOT Ea | |
| - // (notice the additional method getEaValue() which does return Ea) | |
| - // but we DO redefine toChemkinString to return the Ea | |
| - /////////////////////////////////////// | |
| - | |
| + //## operation toChemkinString(double, Temperature, boolean) | |
| public String toChemkinString(double p_Hrxn, Temperature p_temperature, boolean includeComments){ | |
| - double Ea = getEaValue(p_Hrxn); | |
| - // If reported Arrhenius Ea value was computed using Evans-Polanyi relationship, | |
| - // inform user (in chem.inp file) of what deltaHrxn(T) was used. | |
| - if ((double)alpha.getValue() != 0.0) { | |
| - comment += " (Ea computed using deltaHrxn(T=298K) of " + p_Hrxn + " kcal/mol)"; | |
| - } | |
| - if (Ea < p_Hrxn) { | |
| - comment += String.format("Warning: Ea=%.1f < dHrxn(298K)=%.1f by %.1f kcal/mol",Ea, p_Hrxn, p_Hrxn-Ea); | |
| - } | |
| - Object [] formatString = new Object[5]; | |
| - | |
| -// formatString[0] = new Double(getAValue()); | |
| - double tempDouble = new Double(getAValue()); | |
| - if (AUnits.equals("moles")) { | |
| - formatString[0] = tempDouble; | |
| - } else if (AUnits.equals("molecules")) { | |
| - formatString[0] = tempDouble / 6.022e23; | |
| - } | |
| - | |
| - formatString[1] = new Double(getNValue()); | |
| - | |
| - if (EaUnits.equals("kcal/mol")) { | |
| - formatString[2] = Ea; | |
| - } | |
| - else if (EaUnits.equals("cal/mol")) { | |
| - formatString[2] = Ea * 1000.0; | |
| - } | |
| - else if (EaUnits.equals("kJ/mol")) { | |
| - formatString[2] = Ea * 4.184; | |
| - } | |
| - else if (EaUnits.equals("J/mol")) { | |
| - formatString[2] = Ea * 4184.0; | |
| - } | |
| - else if (EaUnits.equals("Kelvins")) { | |
| - formatString[2] = Ea / 1.987e-3; | |
| - } | |
| - | |
| - formatString[3] = source; formatString[4] = comment; | |
| - | |
| - if (includeComments){ | |
| - return String.format("%1.7e \t %2.5f \t %1.7e \t !%s %s", formatString); | |
| - } | |
| - else | |
| - return String.format("%1.7e \t %2.5f \t %1.7e \t ", formatString); | |
| - | |
| - //return String.valueOf(getAValue()) + '\t' + String.valueOf(getNValue()) + '\t' + Ea + "\t!" + source + " "+comment; | |
| - | |
| + ArrheniusKinetics arrhenius = fixBarrier(p_Hrxn); | |
| + return arrhenius.toChemkinString(p_Hrxn, p_temperature, includeComments); | |
| } | |
| //## operation calculateRate(Temperature,double) | |
| public double calculateRate(Temperature p_temperature, double p_Hrxn) { | |
| - //#[ operation calculateRate(Temperature,double) | |
| - double T = p_temperature.getStandard(); | |
| - double R = GasConstant.getKcalMolK(); | |
| - | |
| - double Ea = E.getValue() + alpha.getValue()*p_Hrxn; | |
| - //if (Ea<0) throw new NegativeEnergyBarrierException(); | |
| - double rate = A.getValue() * Math.pow(T, n.getValue()) * Math.exp(-Ea/R/T); | |
| - return rate; | |
| - | |
| - //#] | |
| + ArrheniusKinetics arrhenius = fixBarrier(p_Hrxn); | |
| + return arrhenius.calculateRate(p_temperature); | |
| } | |
| //## operation getAlphaUncertainty() | |
| @@ -168,11 +105,52 @@ public class ArrheniusEPKinetics extends ArrheniusKinetics { | |
| public UncertainDouble getAlpha() { | |
| return alpha; | |
| } | |
| - //gmagoon 05/19/10: it looks like in rest of code, Hrxn at 298 K is used, so this temperature should be used elsewhere for consistency | |
| - public double getEaValue(double p_Hrxn) { | |
| - return E.getValue()+alpha.getValue()*p_Hrxn; | |
| - } | |
| + | |
| + public double getEValue() { | |
| + throw new InvalidKineticsTypeException("Convert ArrheniusEPKinetics to ArrheniusKinetics with fixBarrier(Hrxn)."); | |
| + } | |
| + public double getEaValue(double p_Hrxn) { | |
| + ArrheniusKinetics arrhenius = fixBarrier(p_Hrxn); | |
| + return arrhenius.getEValue(); | |
| + } | |
| + | |
| + public ArrheniusKinetics fixBarrier(double p_Hrxn){ | |
| + // create a new ArrheniusKinetics object with a corrected barrier and return it. | |
| + double al = alpha.getValue(); | |
| + double Eo = E.getValue(); | |
| + double Ea = Eo + al * p_Hrxn; | |
| + | |
| + UncertainDouble newEa = getE(); | |
| + String newComment = getComment(); | |
| + String warning = ""; | |
| + if (al != 0.0){ | |
| + warning = String.format("Ea computed using Evans-Polanyi dHrxn(298K)=%.1f kcal/mol and alpha=%.2f.", p_Hrxn, al ); | |
| + newComment += " " + warning; | |
| + System.out.println(warning); | |
| + newEa = newEa.plus((UncertainDouble)getAlpha().multiply(p_Hrxn)); | |
| + } | |
| + | |
| + if (Eo>0 && Ea<0) { | |
| + // Negative barrier estimated by Evans-Polanyi, despite positive intrinsic barrier. | |
| + warning = String.format("Ea raised from %.1f kcal/mol to 0.0.", Ea); | |
| + newComment += " Warning: " + warning; | |
| + System.out.println(warning); | |
| + newEa = newEa.plus((-Ea)); | |
| + Ea = 0.0; | |
| + } | |
| + if (p_Hrxn>0 && Ea<p_Hrxn){ | |
| + // Reaction is endothermic and the barrier is less than the endothermicity. | |
| + warning = String.format("Ea raised by %.1f from %.1f to dHrxn(298K)=%.1f kcal/mol.",p_Hrxn-Ea, Ea, p_Hrxn ); | |
| + newComment += " Warning: " + warning; | |
| + System.out.println(warning); | |
| + newEa = newEa.plus((p_Hrxn-Ea)); | |
| + Ea = p_Hrxn; | |
| + } | |
| + assert (Ea == newEa.getValue()) : String.format("Something wrong with Ea calculation. %e != %e",Ea,newEa.getValue()); | |
| + ArrheniusKinetics newK = new ArrheniusKinetics(getA(),getN(),newEa,getTRange(),getRank(),getSource(),newComment); | |
| + return newK; | |
| + } | |
| } | |
| /********************************************************************* | |
| File Path : RMG\RMG\jing\rxn\ArrheniusEPKinetics.java | |
| diff --git a/source/RMG/jing/rxn/ArrheniusKinetics.java b/source/RMG/jing/rxn/ArrheniusKinetics.java | |
| index 906edad..b84d7c4 100644 | |
| --- a/source/RMG/jing/rxn/ArrheniusKinetics.java | |
| +++ b/source/RMG/jing/rxn/ArrheniusKinetics.java | |
| @@ -89,8 +89,6 @@ public class ArrheniusKinetics implements Kinetics { | |
| source = p_source; | |
| comment = p_comment; | |
| - | |
| - //#] | |
| } | |
| public ArrheniusKinetics() { | |
| } | |
| @@ -213,19 +211,11 @@ public class ArrheniusKinetics implements Kinetics { | |
| //## operation calculateRate(Temperature,double) | |
| public double calculateRate(Temperature p_temperature, double p_Hrxn) { | |
| - //#[ operation calculateRate(Temperature,double) | |
| - double T = p_temperature.getStandard(); | |
| - double R = GasConstant.getKcalMolK(); | |
| - | |
| - //if (E.getValue() < 0) throw new NegativeEnergyBarrierException(); | |
| - double rate = A.getValue() * Math.pow(T, n.getValue()) * Math.exp(-E.getValue()/R/T); | |
| - return rate; | |
| - | |
| - | |
| - //#] | |
| + // ignore the Hrxn because we don't need it. | |
| + return calculateRate(p_temperature); | |
| } | |
| -// ## operation calculateRate(Temperature,double) | |
| + //## operation calculateRate(Temperature) | |
| public double calculateRate(Temperature p_temperature) { | |
| //#[ operation calculateRate(Temperature,double) | |
| double T = p_temperature.getStandard(); | |
| @@ -234,9 +224,7 @@ public class ArrheniusKinetics implements Kinetics { | |
| //if (E.getValue() < 0) throw new NegativeEnergyBarrierException(); | |
| double rate = A.getValue() * Math.pow(T, n.getValue()) * Math.exp(-E.getValue()/R/T); | |
| return rate; | |
| - | |
| - | |
| - //#] | |
| + | |
| } | |
| public boolean equals(Kinetics p_k){ | |
| @@ -271,6 +259,27 @@ public class ArrheniusKinetics implements Kinetics { | |
| return n.getValue(); | |
| //#] | |
| } | |
| + | |
| + public ArrheniusKinetics fixBarrier(double p_Hrxn){ | |
| + // Return an ArrheniusKinetics object with a corrected barrier. | |
| + double Ea = E.getValue(); | |
| + | |
| + if (p_Hrxn>0 && Ea<p_Hrxn){ | |
| + // Reaction is endothermic and the barrier is less than the endothermicity. | |
| + String newComment = getComment(); | |
| + String warning = String.format("Ea raised by %.1f from %.1f to dHrxn(298K)=%.1f kcal/mol",p_Hrxn-Ea, Ea, p_Hrxn ); | |
| + System.out.println(warning); | |
| + newComment += " Warning: " + warning; | |
| + UncertainDouble newEa = E.plus((p_Hrxn-Ea)); | |
| + Ea = p_Hrxn; | |
| + ArrheniusKinetics newK = new ArrheniusKinetics(getA(),getN(),newEa,getTRange(),getRank(),getSource(),newComment); | |
| + return newK; | |
| + } | |
| + else { | |
| + // return it without changes. | |
| + return this; | |
| + } | |
| + } | |
| //## operation multiply(double) | |
| public Kinetics multiply(double p_multiple) { | |
| @@ -292,9 +301,9 @@ public class ArrheniusKinetics implements Kinetics { | |
| //## operation toChemkinString() | |
| public String toChemkinString(double Hrxn, Temperature p_temperature, boolean includeComments) { | |
| //#[ operation toChemkinString() | |
| + | |
| Object [] formatString = new Object[5]; | |
| -// formatString[0] = new Double(getAValue()); | |
| double tempDouble = new Double(getAValue()); | |
| if (AUnits.equals("moles")) { | |
| formatString[0] = tempDouble; | |
| @@ -304,33 +313,32 @@ public class ArrheniusKinetics implements Kinetics { | |
| formatString[1] = new Double(getNValue()); | |
| -// formatString[2] = new Double(E.getValue()); | |
| - tempDouble = E.getValue(); | |
| + double Ea = E.getValue(); | |
| if (EaUnits.equals("kcal/mol")) { | |
| - formatString[2] = tempDouble; | |
| + formatString[2] = Ea; | |
| } | |
| else if (EaUnits.equals("cal/mol")) { | |
| - formatString[2] = tempDouble * 1000.0; | |
| + formatString[2] = Ea * 1000.0; | |
| } | |
| else if (EaUnits.equals("kJ/mol")) { | |
| - formatString[2] = tempDouble * 4.184; | |
| + formatString[2] = Ea * 4.184; | |
| } | |
| else if (EaUnits.equals("J/mol")) { | |
| - formatString[2] = tempDouble * 4184.0; | |
| + formatString[2] = Ea * 4184.0; | |
| } | |
| else if (EaUnits.equals("Kelvins")) { | |
| - formatString[2] = tempDouble / 1.987e-3; | |
| + formatString[2] = Ea / 1.987e-3; | |
| } | |
| - | |
| - formatString[3] = source; formatString[4] = comment; | |
| - | |
| + | |
| if (includeComments) | |
| - return String.format("%1.3e \t %2.2f \t %3.2f \t !%s %s", formatString); | |
| - else | |
| - return String.format("%1.3e \t %2.2f \t %3.2f \t ", formatString); | |
| - | |
| - //String.valueOf(getAValue()) + '\t' + String.valueOf(getNValue()) + '\t' + String.valueOf(getEValue() + "\t!" + source + " "+comment); | |
| - //#] | |
| + { | |
| + formatString[3] = source; | |
| + formatString[4] = comment; | |
| + return String.format("%1.3e \t %2.2f \t %3.2f \t!%s %s", formatString); | |
| + } | |
| + else | |
| + return String.format("%1.3e \t %2.2f \t %3.2f", formatString); | |
| + | |
| } | |
| //## operation toString() | |
| diff --git a/source/RMG/jing/rxn/FastMasterEqn.java b/source/RMG/jing/rxn/FastMasterEqn.java | |
| index ea2d5fc..f177933 100644 | |
| --- a/source/RMG/jing/rxn/FastMasterEqn.java | |
| +++ b/source/RMG/jing/rxn/FastMasterEqn.java | |
| @@ -614,7 +614,7 @@ public class FastMasterEqn implements PDepKineticsEstimator { | |
| spec.calculateTransportParameters(); | |
| input.append( "# Species identifier (128 characters or less, no spaces)\n" ); | |
| - input.append( spec.getName() + "(" + Integer.toString(spec.getID()) + ")\n" ); | |
| + input.append( spec.getFullName() + "\n" ); | |
| input.append( "# Ground-state energy; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1\n" ); | |
| input.append( "J/mol " + Double.toString(spec.calculateH(stdTemp) * 4184) + "\n" ); | |
| @@ -682,7 +682,7 @@ public class FastMasterEqn implements PDepKineticsEstimator { | |
| input.append( Integer.toString(isomer.getNumSpecies()) ); | |
| for (int j = 0; j < isomer.getNumSpecies(); j++) { | |
| Species spec = isomer.getSpecies(j); | |
| - input.append( " " + spec.getName() + "(" + Integer.toString(spec.getID()) + ")" ); | |
| + input.append( " " + spec.getFullName() ); | |
| } | |
| input.append( "\n\n" ); | |
| } | |
| @@ -969,12 +969,13 @@ public class FastMasterEqn implements PDepKineticsEstimator { | |
| */ | |
| LinkedList pathReactionList = pdn.getPathReactions(); | |
| boolean foundHighPLimitRxn = false; | |
| + Temperature stdtemp = new Temperature(298,"K"); | |
| + double Hrxn; | |
| for (int HighPRxNum = 0; HighPRxNum < pathReactionList.size(); HighPRxNum++) { | |
| PDepReaction rxnWHighPLimit = (PDepReaction)pathReactionList.get(HighPRxNum); | |
| - Temperature stdtemp = new Temperature(298,"K"); | |
| - double Hrxn = rxnWHighPLimit.calculateHrxn(stdtemp); | |
| if (rxn.getStructure().equals(rxnWHighPLimit.getStructure())) { | |
| foundHighPLimitRxn = true; | |
| + Hrxn = rxnWHighPLimit.calculateHrxn(stdtemp); | |
| double A = 0.0, Ea = 0.0, n = 0.0; | |
| if (rxnWHighPLimit.isForward()) { | |
| Kinetics[] k_array = rxnWHighPLimit.getKinetics(); | |
| @@ -1220,16 +1221,11 @@ public class FastMasterEqn implements PDepKineticsEstimator { | |
| double[] k_total = new double[5]; | |
| for (int numKinetics=0; numKinetics<k_array.length; ++numKinetics) { | |
| for (int numTemperatures=0; numTemperatures<T.length; ++numTemperatures) { | |
| - double Ea = 0.0; | |
| - if (k_array[numKinetics] instanceof ArrheniusEPKinetics){ | |
| - Ea = ((ArrheniusEPKinetics)k_array[numKinetics]).getEaValue(Hrxn); | |
| - } | |
| - else{ | |
| - Ea = k_array[numKinetics].getEValue(); | |
| - } | |
| + double Ea = 0.0; | |
| + Ea = ((ArrheniusKinetics)k_array[numKinetics]).getEValue(); | |
| k_total[numTemperatures] += k_array[numKinetics].getAValue() * | |
| - Math.pow(T[numTemperatures], k_array[numKinetics].getNValue()) * | |
| - Math.exp(-Ea/GasConstant.getKcalMolK()/T[numTemperatures]); | |
| + Math.pow(T[numTemperatures], k_array[numKinetics].getNValue()) * | |
| + Math.exp(-Ea/GasConstant.getKcalMolK()/T[numTemperatures]); | |
| } | |
| } | |
| // Construct matrix X and vector y | |
| diff --git a/source/RMG/jing/rxn/Kinetics.java b/source/RMG/jing/rxn/Kinetics.java | |
| index 555b5b7..89338e9 100644 | |
| --- a/source/RMG/jing/rxn/Kinetics.java | |
| +++ b/source/RMG/jing/rxn/Kinetics.java | |
| @@ -109,6 +109,8 @@ public interface Kinetics { | |
| String toString(); | |
| boolean equals(Kinetics p_k); | |
| + | |
| + ArrheniusKinetics fixBarrier(double p_Hrxn); | |
| } | |
| /********************************************************************* | |
| diff --git a/source/RMG/jing/rxn/PDepNetwork.java b/source/RMG/jing/rxn/PDepNetwork.java | |
| index 2e83f8f..0f31925 100644 | |
| --- a/source/RMG/jing/rxn/PDepNetwork.java | |
| +++ b/source/RMG/jing/rxn/PDepNetwork.java | |
| @@ -523,6 +523,43 @@ public class PDepNetwork { | |
| return rLeak; | |
| } | |
| + public static double[] getSpeciesLeakFluxes(SystemSnapshot ss, CoreEdgeReactionModel cerm) { | |
| + | |
| + int len = cerm.getMaxSpeciesID() + 1; | |
| + double[] leakFlux = new double[len]; | |
| + for (int n = 0; n < len; n++) | |
| + leakFlux[n] = 0.0; | |
| + | |
| + for (ListIterator<PDepNetwork> iter0 = networks.listIterator(); iter0.hasNext(); ) { | |
| + PDepNetwork pdn = iter0.next(); | |
| + | |
| + // If there is only one path reaction (and thus only one nonincluded | |
| + // reaction), use the high-pressure limit rate as the flux rather than | |
| + // the k(T,P) value to ensure that we are considering the maximum | |
| + // possible flux entering the network | |
| + if (pdn.getPathReactions().size() == 1 && pdn.getNetReactions().size() == 0) { | |
| + PDepReaction rxn = pdn.getPathReactions().get(0); | |
| + if (!rxn.getProduct().getIncluded()) | |
| + leakFlux[rxn.getProduct().getSpecies(0).getID()] += rxn.calculateForwardFlux(ss); | |
| + else if (!rxn.getReactant().getIncluded()) | |
| + leakFlux[rxn.getReactant().getSpecies(0).getID()] += rxn.calculateReverseFlux(ss); | |
| + } | |
| + // Otherwise use the set of k(T,P) values | |
| + else { | |
| + for (ListIterator<PDepReaction> iter = pdn.getNonincludedReactions().listIterator(); iter.hasNext(); ) { | |
| + PDepReaction rxn = iter.next(); | |
| + if (rxn.getReactant().getIncluded() && !rxn.getProduct().getIncluded()) | |
| + leakFlux[rxn.getProduct().getSpecies(0).getID()] += rxn.calculateForwardFlux(ss); | |
| + else if (!rxn.getReactant().getIncluded() && rxn.getProduct().getIncluded()) | |
| + leakFlux[rxn.getReactant().getSpecies(0).getID()] += rxn.calculateReverseFlux(ss); | |
| + } | |
| + } | |
| + } | |
| + | |
| + return leakFlux; | |
| + | |
| + } | |
| + | |
| /** | |
| * Calculates the isomer with the largest leak flux for this network. The | |
| * reaction with the maximum flux is used to select the isomer. This isomer | |
| diff --git a/source/RMG/jing/rxn/PDepReaction.java b/source/RMG/jing/rxn/PDepReaction.java | |
| index f09fff2..42fdebd 100644 | |
| --- a/source/RMG/jing/rxn/PDepReaction.java | |
| +++ b/source/RMG/jing/rxn/PDepReaction.java | |
| @@ -395,9 +395,9 @@ public class PDepReaction extends Reaction { | |
| if (conc < 0) { | |
| double aTol = ReactionModelGenerator.getAtol(); | |
| //if (Math.abs(conc) < aTol) conc = 0; | |
| - //else throw new NegativeConcentrationException(spe.getName() + ": " + String.valueOf(conc)); | |
| + //else throw new NegativeConcentrationException(spe.getFullName() + ": " + String.valueOf(conc)); | |
| if (conc < -100.0 * aTol) | |
| - throw new NegativeConcentrationException("Species " + spe.getName() + " has negative concentration: " + String.valueOf(conc)); | |
| + throw new NegativeConcentrationException("Species " + spe.getFullName() + " has negative concentration: " + String.valueOf(conc)); | |
| } | |
| forwardFlux *= conc; | |
| } | |
| @@ -424,9 +424,9 @@ public class PDepReaction extends Reaction { | |
| if (conc < 0) { | |
| double aTol = ReactionModelGenerator.getAtol(); | |
| //if (Math.abs(conc) < aTol) conc = 0; | |
| - //else throw new NegativeConcentrationException(spe.getName() + ": " + String.valueOf(conc)); | |
| + //else throw new NegativeConcentrationException(spe.getFullName() + ": " + String.valueOf(conc)); | |
| if (conc < -100.0 * aTol) | |
| - throw new NegativeConcentrationException("Species " + spe.getName() + " has negative concentration: " + String.valueOf(conc)); | |
| + throw new NegativeConcentrationException("Species " + spe.getFullName() + " has negative concentration: " + String.valueOf(conc)); | |
| } | |
| reverseFlux *= conc; | |
| } | |
| @@ -518,7 +518,8 @@ public class PDepReaction extends Reaction { | |
| String result = getStructure().toChemkinString(true).toString(); | |
| if (PDepRateConstant.getMode() == PDepRateConstant.Mode.CHEBYSHEV) | |
| result = formPDepSign(result); | |
| - result += '\t' + "1.0E0 0.0 0.0" ; | |
| + result = String.format("%-52s",result); | |
| + result += "\t1.0E0 0.0 0.0" ; | |
| result += "\t!" + getComments().toString() + '\n'; | |
| if (PDepRateConstant.getMode() == PDepRateConstant.Mode.CHEBYSHEV) | |
| result += pDepRate.getChebyshev().toChemkinString() + '\n'; | |
| @@ -545,7 +546,8 @@ public class PDepReaction extends Reaction { | |
| String result = getStructure().toRestartString(true).toString(); | |
| if (PDepRateConstant.getMode() == PDepRateConstant.Mode.CHEBYSHEV) | |
| result = formPDepSign(result); | |
| - result += '\t' + "1.0E0 0.0 0.0" ; | |
| + result = String.format("%-52s",result); | |
| + result += "\t1.0E0 0.0 0.0" ; | |
| result += "\t!" + getComments().toString() + | |
| "\tdeltaHrxn(T=298K) = " + | |
| calculateHrxn(new Temperature(298.0,"K")) + " kcal/mol\n"; | |
| @@ -575,17 +577,21 @@ public class PDepReaction extends Reaction { | |
| @Override | |
| public String toChemkinString(Temperature t, Pressure p) { | |
| if (pDepRate != null) { | |
| - | |
| String result = getStructure().toChemkinString(true).toString(); | |
| - if (PDepRateConstant.getMode() == PDepRateConstant.Mode.CHEBYSHEV) | |
| - result = formPDepSign(result); | |
| + | |
| if (PDepRateConstant.getMode() == PDepRateConstant.Mode.RATE) { | |
| - result = formPDepSign(result) + "\t" + calculateRate(t,p) + " 0.0 0.0"; | |
| - result += "\t!" + getComments().toString() + '\n'; | |
| + result = String.format(result = formPDepSign(result)); | |
| + result += String.format("\t%.3e 0.0 0.0",calculateRate(t,p)); | |
| + result += "\t!" + getComments().toString() + '\n'; | |
| return result; | |
| } | |
| - result += '\t' + "1.0E0 0.0 0.0"; | |
| - result += "\t!" + getComments().toString() + '\n'; | |
| + | |
| + if (PDepRateConstant.getMode() == PDepRateConstant.Mode.CHEBYSHEV) | |
| + result = formPDepSign(result); | |
| + result = String.format("%-52s",result); | |
| + | |
| + result += "\t1.0E0 0.0 0.0"; | |
| + result += "\t!" + getComments().toString() + '\n'; | |
| if (PDepRateConstant.getMode() == PDepRateConstant.Mode.CHEBYSHEV) | |
| result += pDepRate.getChebyshev().toChemkinString() + '\n'; | |
| diff --git a/source/RMG/jing/rxn/RateConstant.java b/source/RMG/jing/rxn/RateConstant.java | |
| index 23275df..1df1894 100644 | |
| --- a/source/RMG/jing/rxn/RateConstant.java | |
| +++ b/source/RMG/jing/rxn/RateConstant.java | |
| @@ -109,8 +109,6 @@ public class RateConstant { | |
| public String printKey() { | |
| //#[ operation printKey() | |
| return kineticsTemplate.printKey(); | |
| - | |
| - | |
| //#] | |
| } | |
| @@ -118,8 +116,6 @@ public class RateConstant { | |
| public boolean repOk() { | |
| //#[ operation repOk() | |
| return kineticsTemplate.repOk(); | |
| - | |
| - | |
| //#] | |
| } | |
| diff --git a/source/RMG/jing/rxn/Reaction.java b/source/RMG/jing/rxn/Reaction.java | |
| index 0593310..200ef2b 100644 | |
| --- a/source/RMG/jing/rxn/Reaction.java | |
| +++ b/source/RMG/jing/rxn/Reaction.java | |
| @@ -79,8 +79,7 @@ public class Reaction { | |
| protected boolean kineticsFromPrimaryKineticLibrary = false; | |
| protected ReactionTemplate rxnTemplate; | |
| - | |
| - // Constructors | |
| + // Constructors | |
| //## operation Reaction() | |
| public Reaction() { | |
| @@ -180,7 +179,7 @@ public class Reaction { | |
| double rate =0; | |
| Temperature stdtemp = new Temperature(298,"K"); | |
| double Hrxn = calculateHrxn(stdtemp); | |
| - Temperature sys_temp = ReactionModelGenerator.getTemp4BestKinetics(); | |
| + Temperature sys_temp = ReactionModelGenerator.getTemp4BestKinetics(); | |
| /* AJ 12JULY2010: | |
| * Added diffusive limits from previous RMG version by replacing function calculateTotalRate | |
| @@ -206,22 +205,18 @@ public class Reaction { | |
| Kinetics[] k_All = kinetics; | |
| for (int numKinetics=0; numKinetics<kinetics.length; numKinetics++) { | |
| Kinetics k = k_All[numKinetics]; | |
| - if (k instanceof ArrheniusEPKinetics) | |
| - rate += k.calculateRate(p_temperature,Hrxn); | |
| - else | |
| - rate += k.calculateRate(p_temperature); | |
| - | |
| + rate += k.calculateRate(p_temperature,Hrxn); | |
| } | |
| return rate; | |
| } | |
| else if (isForward()){ | |
| Kinetics[] k_All = kinetics; | |
| for (int numKinetics=0; numKinetics<kinetics.length; numKinetics++) { | |
| - Kinetics k = k_All[numKinetics].multiply(structure.redundancy); | |
| - if (k instanceof ArrheniusEPKinetics) | |
| - rate += k.calculateRate(p_temperature,Hrxn); | |
| - else | |
| - rate += k.calculateRate(p_temperature); | |
| + Kinetics k = k_All[numKinetics]; | |
| + if ((int)structure.redundancy != 1){ | |
| + k = k.multiply(structure.redundancy); | |
| + } | |
| + rate += k.calculateRate(p_temperature,Hrxn); | |
| } | |
| /* Amrit Jalan, November 29, 2010 | |
| @@ -413,9 +408,9 @@ public class Reaction { | |
| else { | |
| throw new InvalidReactionDirectionException(); | |
| } | |
| - | |
| } | |
| - | |
| + | |
| + //## operation calculatediff(LinkedList) | |
| public double calculatediff(LinkedList p_struct) { | |
| if (p_struct.size()!=2){ | |
| @@ -688,8 +683,6 @@ public class Reaction { | |
| //#[ operation contains(Species) | |
| if (containsAsReactant(p_species) || containsAsProduct(p_species)) return true; | |
| else return false; | |
| - | |
| - | |
| //#] | |
| } | |
| @@ -729,17 +722,11 @@ public class Reaction { | |
| public boolean equals(Object p_reaction) { | |
| //#[ operation equals(Object) | |
| if (this == p_reaction) return true; | |
| - | |
| if (!(p_reaction instanceof Reaction)) return false; | |
| - | |
| Reaction r = (Reaction)p_reaction; | |
| - | |
| if (!getStructure().equals(r.getStructure())) return false; | |
| - | |
| return true; | |
| - | |
| - //#] | |
| } | |
| /* | |
| @@ -970,9 +957,7 @@ public class Reaction { | |
| fittedReverseKinetics = null; | |
| } | |
| else { | |
| - //double temp = 715; | |
| - // double temp = 298.15; //10/29/07 gmagoon: Sandeep made change to temp = 298 on his computer locally | |
| - // double temp = 1350; //11/6/07 gmagoon:**** changed to actual temperature in my condition file to create agreement with old version; apparently, choice of temp has large effect; //11/9/07 gmagoon: commented out | |
| + //double temp = 715; | |
| double temp = 298.15; //11/9/07 gmagoon: restored use of 298.15 per discussion with Sandeep | |
| //double temp = Global.temperature.getK(); | |
| Kinetics[] k = getKinetics(); | |
| @@ -1088,6 +1073,7 @@ public class Reaction { | |
| } | |
| if (isForward()) { | |
| int red = structure.getRedundancy(); | |
| + if (red==1) return kinetics; // Don't waste time multiplying by 1 | |
| Kinetics[] kinetics2return = new Kinetics[kinetics.length]; | |
| for (int numKinetics=0; numKinetics<kinetics.length; ++numKinetics) { | |
| kinetics2return[numKinetics] = kinetics[numKinetics].multiply(red); | |
| @@ -1109,9 +1095,6 @@ public class Reaction { | |
| else | |
| throw new InvalidReactionDirectionException(structure.toString()); | |
| - | |
| - | |
| - //#] | |
| } | |
| public void setKineticsComments(String p_string, int num_k){ | |
| @@ -1420,7 +1403,7 @@ public class Reaction { | |
| if (ChemkinString != null) | |
| return ChemkinString; | |
| StringBuilder result = new StringBuilder(); | |
| - StringBuilder strucString = getStructure().toChemkinString(hasReverseReaction()); | |
| + String strucString = String.format("%-52s",getStructure().toChemkinString(hasReverseReaction())); | |
| Temperature stdtemp = new Temperature(298,"K"); | |
| double Hrxn = calculateHrxn(stdtemp); | |
| Kinetics[] allKinetics = getKinetics(); | |
| @@ -1462,7 +1445,7 @@ public class Reaction { | |
| * when writing the Restart files, to account for this bug. | |
| */ | |
| - String result = getStructure().toRestartString(hasReverseReaction()).toString(); //+ " "+getStructure().direction + " "+getStructure().redundancy; | |
| + String result = String.format("%-52s",getStructure().toRestartString(hasReverseReaction())); //+ " "+getStructure().direction + " "+getStructure().redundancy; | |
| // MRH 18Jan2010: Restart files do not look for direction/redundancy | |
| /* | |
| * MRH 14Feb2010: Handle reactions with multiple kinetics | |
| @@ -1772,17 +1755,17 @@ public class Reaction { | |
| String rxn = ""; | |
| Species species = (Species) structure.getReactantList().get(0); | |
| - rxn = rxn + species.getName() + "(" + Integer.toString(species.getID()) + ")"; | |
| + rxn = rxn + species.getFullName() ; | |
| for (int i = 1; i < getReactantNumber(); i++) { | |
| species = (Species) structure.getReactantList().get(i); | |
| - rxn += " + " + species.getName() + "(" + Integer.toString(species.getID()) + ")"; | |
| + rxn += " + " + species.getFullName() ; | |
| } | |
| rxn += " --> "; | |
| species = (Species) structure.getProductList().get(0); | |
| - rxn = rxn + species.getName() + "(" + Integer.toString(species.getID()) + ")"; | |
| + rxn = rxn + species.getFullName() ; | |
| for (int i = 1; i < getProductNumber(); i++) { | |
| species = (Species) structure.getProductList().get(i); | |
| - rxn += " + " + species.getName() + "(" + Integer.toString(species.getID()) + ")"; | |
| + rxn += " + " + species.getFullName() ; | |
| } | |
| return rxn; | |
| @@ -1839,9 +1822,9 @@ public class Reaction { | |
| if (conc < 0) { | |
| double aTol = ReactionModelGenerator.getAtol(); | |
| //if (Math.abs(conc) < aTol) conc = 0; | |
| - //else throw new NegativeConcentrationException(spe.getName() + ": " + String.valueOf(conc)); | |
| + //else throw new NegativeConcentrationException(spe.getFullName() + ": " + String.valueOf(conc)); | |
| if (conc < -100.0 * aTol) | |
| - throw new NegativeConcentrationException("Species " + spe.getName() + " has negative concentration: " + String.valueOf(conc)); | |
| + throw new NegativeConcentrationException("Species " + spe.getFullName() + " has negative concentration: " + String.valueOf(conc)); | |
| } | |
| forwardFlux *= conc; | |
| } | |
| diff --git a/source/RMG/jing/rxn/ReactionTemplate.java b/source/RMG/jing/rxn/ReactionTemplate.java | |
| index f46ace4..6fce3ee 100644 | |
| --- a/source/RMG/jing/rxn/ReactionTemplate.java | |
| +++ b/source/RMG/jing/rxn/ReactionTemplate.java | |
| @@ -252,7 +252,7 @@ public class ReactionTemplate { | |
| } | |
| //## operation findClosestRateConstant(Collection) | |
| - public Kinetics[] findClosestRateConstant(LinkedList p_matchedPathSet) { | |
| + public Kinetics findClosestRateConstant(LinkedList p_matchedPathSet) { | |
| //#[ operation findClosestRateConstant(Collection) | |
| LinkedHashSet exactTreeNode = new LinkedHashSet(); | |
| LinkedHashSet exactKey = new LinkedHashSet(); | |
| @@ -277,10 +277,7 @@ public class ReactionTemplate { | |
| KineticsTemplate kt = kineticsTemplateLibrary.getKineticsTemplate(exactKey); | |
| int rNum = getReactantNumber(); | |
| if (kt!=null) { | |
| - Kinetics[] k_closest = new Kinetics[1]; | |
| - k_closest[0] = kt.kinetics; | |
| - return k_closest; | |
| -// return kt.kinetics; | |
| + return kt.kinetics; | |
| } | |
| Collection allPossibleTreeNodeSet = MathTool.expand(p_matchedPathSet.iterator()); | |
| @@ -319,20 +316,12 @@ public class ReactionTemplate { | |
| // get averaged k with the closest distance | |
| Kinetics newK = ArrheniusKinetics.average(bestKineticsSet); | |
| - //KineticsTemplate newKT = kineticsTemplateLibrary.addKinetics(exactKey, newK); | |
| - //RateConstant rc = new RateConstant(newKT, bestKineticsTemplateSet, closest); | |
| - Kinetics[] k_closest = new Kinetics[1]; | |
| - k_closest[0] = newK; | |
| - return k_closest; | |
| -// return newK; | |
| + return newK; | |
| - | |
| - | |
| - //#] | |
| } | |
| //## operation findExactRateConstant(Collection) | |
| - public Kinetics[] findExactRateConstant(Collection p_matchedPathSet) { | |
| + public Kinetics findExactRateConstant(Collection p_matchedPathSet) { | |
| //#[ operation findExactRateConstant(Collection) \ | |
| LinkedHashSet fgc = new LinkedHashSet(); | |
| @@ -349,14 +338,7 @@ public class ReactionTemplate { | |
| KineticsTemplate kt = kineticsTemplateLibrary.getKineticsTemplate(fgc); | |
| if (kt==null) return null; | |
| - else { | |
| - //kt.kinetics.setSource(kt.kinetics.toChemkinString()); | |
| - Kinetics[] k_exact = new Kinetics[1]; | |
| - k_exact[0] = kt.kinetics; | |
| - return k_exact; | |
| -// return kt.kinetics; | |
| - } | |
| - | |
| + else return kt.kinetics; | |
| } | |
| /** | |
| @@ -413,6 +395,11 @@ public class ReactionTemplate { | |
| * for the R. + HOO. --> .OO. + RH direction are not very accurate (ignition delays | |
| * change drastically, running the same condition.txt file). | |
| */ | |
| + /* 17-JAN-2011 | |
| + * Once again removing the "H_Abstraction" code so that the exothermic direction is always favored. | |
| + * The observation of 24-SEPT-2010 that the ignition delays change drastically could have been due | |
| + * to some other change. | |
| + | |
| if (name.equals("H_Abstraction")) { | |
| boolean polyRadicalReactant = false; | |
| boolean polyRadicalProduct = false; | |
| @@ -445,6 +432,7 @@ public class ReactionTemplate { | |
| p_structure.setDirection(-1); | |
| } | |
| } | |
| + */ | |
| if (thermoConsistence) { | |
| Temperature T = new Temperature(298, "K"); | |
| @@ -489,20 +477,29 @@ public class ReactionTemplate { | |
| } | |
| if (p_structure.isForward()) { | |
| + Kinetics kf = null; | |
| LinkedList fg = structureTemplate.getMatchedFunctionalGroup(reactants); | |
| if (fg == null) { | |
| Global.RT_findRateConstant += (System.currentTimeMillis()-pT)/1000/60; | |
| return null; | |
| } | |
| String comments = getKineticsComments(fg); | |
| - k = findExactRateConstant(fg); | |
| - if (k==null) { | |
| - k = findClosestRateConstant(fg); | |
| - k[0].setSource(name + " estimate: (" + k[0].getSource() + ")"); | |
| + kf = findExactRateConstant(fg); | |
| + if (kf==null) { | |
| + kf = findClosestRateConstant(fg); | |
| + kf.setSource(name + " estimate: (" + kf.getSource() + ")"); | |
| } | |
| - else k[0].setSource(name + " exact: "); | |
| - k[0].setComments(comments); | |
| + else kf.setSource(name + " exact: "); | |
| + kf.setComments(comments); | |
| Global.RT_findRateConstant += (System.currentTimeMillis()-pT)/1000/60; | |
| + | |
| + // fix rate constant here | |
| + double Hrxn = p_structure.calculateHrxn(new Temperature(298, "K")); | |
| + ArrheniusKinetics k_fixed = kf.fixBarrier(Hrxn); | |
| + | |
| + // We must return a list (with one element). | |
| + k = new Kinetics[1]; | |
| + k[0] = k_fixed; | |
| return k; | |
| } | |
| else { | |
| @@ -608,20 +605,22 @@ public class ReactionTemplate { | |
| } | |
| private String getKineticsComments(Collection p_matchedPathSet) { | |
| - StringBuilder comment = new StringBuilder(); | |
| - for (Iterator iter = p_matchedPathSet.iterator(); iter.hasNext();) { | |
| + StringBuilder comment = new StringBuilder("[ "); | |
| + for (Iterator iter = p_matchedPathSet.iterator(); iter.hasNext();) { | |
| Stack s = (Stack)iter.next(); | |
| HierarchyTreeNode node = (HierarchyTreeNode)s.peek(); | |
| - if (node.hasDummyChild()) comment.append((node.getDummyChild().getName()+" ")); | |
| + if (node.hasDummyChild()) comment.append((node.getDummyChild().getName() + " , ")); | |
| else { | |
| if (node.getElement() instanceof FunctionalGroup) | |
| - comment.append(((FunctionalGroup)node.getElement()).getName() + " "); | |
| + comment.append(((FunctionalGroup)node.getElement()).getName() + " , "); | |
| else | |
| - comment.append(((FunctionalGroupCollection)node.getElement()).getName() + " "); | |
| + comment.append(((FunctionalGroupCollection)node.getElement()).getName() + " , "); | |
| } | |
| - } | |
| - return comment.toString(); | |
| - } | |
| + } | |
| + comment.delete(comment.length()-2, comment.length()); // remove the final comma | |
| + comment.append("]"); | |
| + return comment.toString(); | |
| + } | |
| //## operation findUnion(String,HashMap) | |
| private void findUnion(String p_name, HashMap p_unRead) { | |
| @@ -1484,22 +1483,8 @@ public class ReactionTemplate { | |
| } | |
| else fgc.add(fg); | |
| } | |
| - // read in the | |
| - /* | |
| - * Commented out by MRH 15-Jun-2009 | |
| - * We used to pass only the TRange, modified Arrhenius parameters, | |
| - * their uncertainties, and the data's rank to parseArrheniusKinetics. | |
| - * Now, pass the entire line of data, so that any comments | |
| - * written after the rank may be read in | |
| - */ | |
| -// String kinetics = token.nextToken(); | |
| -// while (token.hasMoreTokens()) { | |
| -// kinetics = kinetics + " " + token.nextToken(); | |
| -// } | |
| + // read in the kinetics | |
| Kinetics k; | |
| -// if (format.equals("Arrhenius")) k = ChemParser.parseArrheniusKinetics(kinetics); | |
| -// else if (format.equals("Arrhenius_EP")) k = ChemParser.parseArrheniusEPKinetics(kinetics); | |
| -// else throw new InvalidKineticsFormatException("Invalid rate constant format: " + kinetics); | |
| if (format.equals("Arrhenius")) k = ChemParser.parseArrheniusKinetics(line,keyNum); | |
| else if (format.equals("Arrhenius_EP")) k = ChemParser.parseArrheniusEPKinetics(line,keyNum); | |
| else throw new InvalidKineticsFormatException("Invalid rate constant format: " + line); | |
| diff --git a/source/RMG/jing/rxn/ReactionTemplateLibrary.java b/source/RMG/jing/rxn/ReactionTemplateLibrary.java | |
| index 2403917..11ea839 100644 | |
| --- a/source/RMG/jing/rxn/ReactionTemplateLibrary.java | |
| +++ b/source/RMG/jing/rxn/ReactionTemplateLibrary.java | |
| @@ -67,6 +67,7 @@ public class ReactionTemplateLibrary { | |
| // Read the file families.txt | |
| try { | |
| + System.out.println("\nReading kinetics groups database from: " + kineticsDirectory + "\n"); | |
| String familiesPath = kineticsDirectory + "families.txt"; | |
| FileReader in = new FileReader(familiesPath); | |
| BufferedReader data = new BufferedReader(in); | |
| diff --git a/source/RMG/jing/rxn/Structure.java b/source/RMG/jing/rxn/Structure.java | |
| index b850b20..159c659 100644 | |
| --- a/source/RMG/jing/rxn/Structure.java | |
| +++ b/source/RMG/jing/rxn/Structure.java | |
| @@ -935,8 +935,8 @@ public class Structure { | |
| while (iter1.hasNext()) { | |
| index++; | |
| Species spe = (Species)iter1.next(); | |
| - if (index < r_num) s = s + spe.getName()+"("+spe.getID()+")" + "+"; | |
| - else s += spe.getName()+"("+spe.getID()+")"; | |
| + if (index < r_num) s = s + spe.getFullName() + "+"; | |
| + else s += spe.getFullName(); | |
| } | |
| if (p_includeReverse) | |
| s += "="; | |
| @@ -948,8 +948,8 @@ public class Structure { | |
| while (iter2.hasNext()) { | |
| index++; | |
| Species spe = (Species)iter2.next(); | |
| - if (index < p_num) s = s + spe.getName()+"("+spe.getID()+")" + "+"; | |
| - else s += spe.getName()+"("+spe.getID()+")"; | |
| + if (index < p_num) s = s + spe.getFullName() + "+"; | |
| + else s += spe.getFullName(); | |
| } | |
| StringBuilder sb = new StringBuilder(s); | |
| diff --git a/source/RMG/jing/rxn/TROEReaction.java b/source/RMG/jing/rxn/TROEReaction.java | |
| index dfd08c3..a131728 100644 | |
| --- a/source/RMG/jing/rxn/TROEReaction.java | |
| +++ b/source/RMG/jing/rxn/TROEReaction.java | |
| @@ -69,12 +69,8 @@ public class TROEReaction extends ThirdBodyReaction { | |
| public double calculateRate(SystemSnapshot p_presentStatus) { | |
| //#[ operation calculateRate(SystemSnapshot) | |
| Temperature temp = p_presentStatus.getTemperature(); | |
| - | |
| - //Kinetics k = getKinetics(); | |
| - //double rate = k.calculateRate(temp, calculateHrxn(temp)); | |
| double rate = super.calculateTotalRate(temp); | |
| rate *= calculateTroeFallOff(p_presentStatus); | |
| - | |
| return rate; | |
| //#] | |
| } | |
| diff --git a/source/RMG/jing/rxn/TemplateReaction.java b/source/RMG/jing/rxn/TemplateReaction.java | |
| index 02969d2..c21e464 100644 | |
| --- a/source/RMG/jing/rxn/TemplateReaction.java | |
| +++ b/source/RMG/jing/rxn/TemplateReaction.java | |
| @@ -64,9 +64,8 @@ public class TemplateReaction extends Reaction { | |
| reactionTemplate = p_template; | |
| if (kinetics != null) | |
| kineticsFromPrimaryKineticLibrary = p_kinetics[0].getFromPrimaryKineticLibrary(); | |
| - | |
| - //#] | |
| } | |
| + | |
| public TemplateReaction() { | |
| } | |
| @@ -350,8 +349,15 @@ public class TemplateReaction extends Reaction { | |
| TemplateReaction reaction = p_template.getReactionFromStructure(p_structureSp); | |
| Global.getReacFromStruc = Global.getReacFromStruc + (System.currentTimeMillis() - PT) / 1000 / 60; | |
| - if (reaction == null) { | |
| - | |
| + if (reaction != null){ | |
| + // the same identity of p_structure already exists, clear p_structure to release mem | |
| + Structure st = reaction.getStructure(); | |
| + if (st != p_structure) { | |
| + p_structure = null; | |
| + } | |
| + } | |
| + else { | |
| + // Create a new reaction. | |
| reaction = new TemplateReaction(p_structureSp, p_kinetics, p_template); | |
| // DEBUG: Tell console I made this reaction | |
| System.out.println("Created new reaction: " + reaction.toString()); | |
| @@ -385,12 +391,6 @@ public class TemplateReaction extends Reaction { | |
| if (!reaction.repOk()) { | |
| throw new InvalidTemplateReactionException(); | |
| } | |
| - } else { | |
| - // the same identity of p_structure already exists, clear p_structure to release mem | |
| - Structure st = reaction.getStructure(); | |
| - if (st != p_structure) { | |
| - p_structure = null; | |
| - } | |
| } | |
| Global.makeTR += (System.currentTimeMillis() - PT) / 1000 / 60; | |
| return reaction; | |
| diff --git a/source/RMG/jing/rxn/TemplateReactionGenerator.java b/source/RMG/jing/rxn/TemplateReactionGenerator.java | |
| index 1849108..21e0f65 100644 | |
| --- a/source/RMG/jing/rxn/TemplateReactionGenerator.java | |
| +++ b/source/RMG/jing/rxn/TemplateReactionGenerator.java | |
| @@ -102,18 +102,8 @@ public class TemplateReactionGenerator implements ReactionGenerator { | |
| } | |
| } | |
| Runtime runTime = Runtime.getRuntime(); | |
| - System.out.print("Memory used: "); | |
| - System.out.println(runTime.totalMemory()); | |
| - System.out.print("Free memory: "); | |
| - System.out.println(runTime.freeMemory()); | |
| - if (runTime.freeMemory() < runTime.totalMemory()/3) { | |
| + if (runTime.freeMemory() < runTime.totalMemory()/3) | |
| runTime.gc(); | |
| - System.out.println("After garbage collection:"); | |
| - System.out.print("Memory used: "); | |
| - System.out.println(runTime.totalMemory()); | |
| - System.out.print("Free memory: "); | |
| - System.out.println(runTime.freeMemory()); | |
| - } | |
| return pdepReactionSet; | |
| } | |
| @@ -267,18 +257,8 @@ public class TemplateReactionGenerator implements ReactionGenerator { | |
| //PDepNetwork.completeNetwork(p_species); | |
| Runtime runTime = Runtime.getRuntime(); | |
| - System.out.print("Memory used: "); | |
| - System.out.println(runTime.totalMemory()); | |
| - System.out.print("Free memory: "); | |
| - System.out.println(runTime.freeMemory()); | |
| - if (runTime.freeMemory() < runTime.totalMemory()/3) { | |
| + if (runTime.freeMemory() < runTime.totalMemory()/3) | |
| runTime.gc(); | |
| - System.out.println("After garbage collection:"); | |
| - System.out.print("Memory used: "); | |
| - System.out.println(runTime.totalMemory()); | |
| - System.out.print("Free memory: "); | |
| - System.out.println(runTime.freeMemory()); | |
| - } | |
| // double t = (System.currentTimeMillis()-pT)/1000/60; | |
| // Global.RT_reactTwoReactants += t; | |
| diff --git a/source/RMG/jing/rxn/ThirdBodyReaction.java b/source/RMG/jing/rxn/ThirdBodyReaction.java | |
| index 25a99ae..99e1346 100644 | |
| --- a/source/RMG/jing/rxn/ThirdBodyReaction.java | |
| +++ b/source/RMG/jing/rxn/ThirdBodyReaction.java | |
| @@ -58,14 +58,10 @@ public class ThirdBodyReaction extends Reaction { | |
| //## operation calculateRate(SystemSnapshot) | |
| public double calculateRate(SystemSnapshot p_systemSnapshot) { | |
| - //#[ operation calculateRate(SystemSnapshot) | |
| Temperature temp = p_systemSnapshot.getTemperature(); | |
| - //Kinetics k = getKinetics(); | |
| - //double rate = k.calculateRate(temp, calculateHrxn(temp)); | |
| double rate = super.calculateTotalRate(temp); | |
| rate *= calculateThirdBodyCoefficient(p_systemSnapshot); | |
| return rate; | |
| - //#] | |
| } | |
| public HashMap getWeightMap(){ | |
| @@ -219,6 +215,7 @@ public class ThirdBodyReaction extends Reaction { | |
| //#[ operation toChemkinString() | |
| StringBuilder s = getStructure().toChemkinString(true); | |
| s = formPDepSign(s); | |
| + s = new StringBuilder(String.format("%-52s",s)); // pad it to 52 characters | |
| for (int i=0; i<getKinetics().length; i++) { | |
| s.append("\t" + getKinetics()[i].toChemkinString(calculateHrxn(p_temperature),p_temperature, true) + '\n'); | |
| } | |
| @@ -253,6 +250,7 @@ public class ThirdBodyReaction extends Reaction { | |
| public String toRestartString(Temperature t) { | |
| StringBuilder s = getStructure().toRestartString(true); | |
| s = formPDepSignForRestart(s); | |
| + s = new StringBuilder(String.format("%-52s",s)); // pad it to 52 characters | |
| for (int i=0; i<getKinetics().length; i++) { | |
| s.append("\t" + getKinetics()[i].toChemkinString(calculateHrxn(t),t,false) + " 0.0 0.0 0.0\n"); | |
| } | |
| diff --git a/source/RMG/jing/rxnSys/Chemkin.java b/source/RMG/jing/rxnSys/Chemkin.java | |
| index d9ec16a..d019f99 100644 | |
| --- a/source/RMG/jing/rxnSys/Chemkin.java | |
| +++ b/source/RMG/jing/rxnSys/Chemkin.java | |
| @@ -173,14 +173,14 @@ public Chemkin() { | |
| double conc = ((Double)p_speciesConc.get(i)).doubleValue(); | |
| double flux = ((Double)p_speciesFlux.get(i)).doubleValue(); | |
| - System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); | |
| + System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getFullName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); | |
| if (conc < 0) { | |
| double aTol = ReactionModelGenerator.getAtol(); | |
| //if (Math.abs(conc) < aTol) conc = 0; | |
| - //else throw new NegativeConcentrationException("species " + spe.getName() + " has negative conc: " + String.valueOf(conc)); | |
| + //else throw new NegativeConcentrationException("species " + spe.getFullName() + " has negative conc: " + String.valueOf(conc)); | |
| if (conc < -100.0 * aTol) | |
| - throw new NegativeConcentrationException("Species " + spe.getName() + " has negative concentration: " + String.valueOf(conc)); | |
| + throw new NegativeConcentrationException("Species " + spe.getFullName() + " has negative concentration: " + String.valueOf(conc)); | |
| } | |
| SpeciesStatus ss = new SpeciesStatus(spe, 1, conc, flux); | |
| @@ -415,9 +415,9 @@ public Chemkin() { | |
| } | |
| //## operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,boolean) | |
| - public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, final ReactionTime p_beginTime, ReactionTime p_endTime, boolean p_conditionChanged) { | |
| + public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, final ReactionTime p_beginTime, ReactionTime p_endTime, boolean p_conditionChanged, LinkedHashSet nonpdep_from_seed) { | |
| //#[ operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,boolean) | |
| - writeChemkinInputFile(p_reactionModel, p_beginStatus); | |
| + writeChemkinInputFile(p_reactionModel, p_beginStatus, nonpdep_from_seed); | |
| runChemkin(); | |
| checkChemkinMessage(); | |
| @@ -461,7 +461,7 @@ public Chemkin() { | |
| } | |
| //## operation writeChemkinInputFile(ReactionModel,SystemSnapshot) | |
| - public static void writeChemkinInputFile(final ReactionModel p_reactionModel, SystemSnapshot p_beginStatus) { | |
| + public static void writeChemkinInputFile(final ReactionModel p_reactionModel, SystemSnapshot p_beginStatus, LinkedHashSet nonpdep_from_seed) { | |
| //String dir = System.getProperty("RMG.workingDirectory"); | |
| //if (!dir.endsWith("/")) dir += "/"; | |
| @@ -485,7 +485,7 @@ public Chemkin() { | |
| bufferedWriter.write(writeChemkinElement()); | |
| bufferedWriter.write(writeChemkinSpecies(p_reactionModel, p_beginStatus)); | |
| bufferedWriter.write(writeChemkinThermo(p_reactionModel)); | |
| - bufferedWriter = writeChemkinPdepReactions(p_reactionModel, p_beginStatus,bufferedWriter); | |
| + bufferedWriter = writeChemkinPdepReactions(p_reactionModel, p_beginStatus,bufferedWriter,nonpdep_from_seed); | |
| } catch (FileNotFoundException ex) { | |
| ex.printStackTrace(); | |
| } catch (IOException ex) { | |
| @@ -542,14 +542,14 @@ public Chemkin() { | |
| } | |
| - public static void writeChemkinInputFile(ReactionSystem rs) { | |
| + public static void writeChemkinInputFile(ReactionSystem rs, LinkedHashSet nonpdep_from_seed) { | |
| // call the above writeChemkinInputFile method, with the appropriate parameters | |
| - writeChemkinInputFile(rs.reactionModel, rs.initialStatus); | |
| + writeChemkinInputFile(rs.reactionModel, rs.initialStatus, nonpdep_from_seed); | |
| } | |
| //## operation writeChemkinPdepReactions(ReactionModel, SystemSnapshot) | |
| - public static BufferedWriter writeChemkinPdepReactions(ReactionModel p_reactionModel, SystemSnapshot p_beginStatus, BufferedWriter bufferedWriter) throws IOException { | |
| + public static BufferedWriter writeChemkinPdepReactions(ReactionModel p_reactionModel, SystemSnapshot p_beginStatus, BufferedWriter bufferedWriter, LinkedHashSet nonpdep_from_seed) throws IOException { | |
| /* | |
| Writes all reactions, not just the P-dep ones. | |
| Returns the result as a string. | |
| @@ -606,7 +606,8 @@ public Chemkin() { | |
| if (rxn.getReverseReaction() == null) | |
| rxn.generateReverseReaction(); | |
| - if (!rxn.reactantEqualsProduct() && !pDepList.contains(rxn) && !pDepList.contains(rxn.getReverseReaction()) ) { | |
| + if (!rxn.reactantEqualsProduct() && !pDepList.contains(rxn) && !pDepList.contains(rxn.getReverseReaction()) && | |
| + !nonpdep_from_seed.contains(rxn) && !nonpdep_from_seed.contains(rxn.getReverseReaction())) { | |
| pDepList.add(rxn); | |
| } | |
| } | |
| @@ -660,7 +661,7 @@ public Chemkin() { | |
| for (Iterator iter = cerm.getSpecies(); iter.hasNext(); ) { | |
| Species spe = (Species)iter.next(); | |
| if (spe.getChemkinName().startsWith("SPC")) | |
| - result.append("\t" + spe.getChemkinName() + "\t!" + spe.getName() + "\n"); | |
| + result.append("\t" + spe.getChemkinName() + "\t! " + spe.getFullName() + "\n"); | |
| else | |
| result.append('\t' + spe.getChemkinName() + '\n'); | |
| } | |
| @@ -894,7 +895,7 @@ public Chemkin() { | |
| } | |
| -public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged, TerminationTester tt, int iternum) { | |
| +public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged, TerminationTester tt, int iternum, LinkedHashSet nonpdep_from_seed) { | |
| //writeChemkinInputFile(p_reactionModel, p_beginStatus); | |
| diff --git a/source/RMG/jing/rxnSys/CoreEdgeReactionModel.java b/source/RMG/jing/rxnSys/CoreEdgeReactionModel.java | |
| index 90565c0..250505d 100644 | |
| --- a/source/RMG/jing/rxnSys/CoreEdgeReactionModel.java | |
| +++ b/source/RMG/jing/rxnSys/CoreEdgeReactionModel.java | |
| @@ -324,7 +324,7 @@ public class CoreEdgeReactionModel implements ReactionModel { | |
| //#[ operation addUnreactedSpecies(Species) | |
| if (containsAsReactedSpecies(p_species)) { | |
| // this is not a unreacted species | |
| - System.out.println("This is a reacted species " + p_species.getName()); | |
| + System.out.println("This is a reacted species " + p_species.getFullName()); | |
| System.out.println("Can't add it into unreacted species set!"); | |
| } | |
| else { | |
| @@ -341,7 +341,7 @@ public class CoreEdgeReactionModel implements ReactionModel { | |
| Species species = (Species)speciesIter.next(); | |
| if (containsAsReactedSpecies(species)) { | |
| // this is not a unreacted species | |
| - System.out.println("This is a reacted species " + species.getName()); | |
| + System.out.println("This is a reacted species " + species.getFullName()); | |
| System.out.println("Can't add it into unreacted species set!"); | |
| } | |
| else { | |
| @@ -797,7 +797,7 @@ public class CoreEdgeReactionModel implements ReactionModel { | |
| getReactedSpeciesSet().add(p_species); | |
| return; | |
| } | |
| - else throw new InvalidCoreEdgeRelationException(p_species.getName()); | |
| + else throw new InvalidCoreEdgeRelationException(p_species.getFullName()); | |
| //#] | |
| } | |
| @@ -839,7 +839,7 @@ public class CoreEdgeReactionModel implements ReactionModel { | |
| System.out.println("SpeciesID\tNamw\tH298\tS298\tCp300\tCp400\tCp500\tCp600\tCp800\tCp1000\tCp1500"); | |
| for (int i=0; i<sortedSpeList.size(); i++) { | |
| Species spe = (Species)sortedSpeList.get(i); | |
| - System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + spe.getThermoData().toString()); | |
| + System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getFullName() + '\t' + spe.getThermoData().toString()); | |
| }*/ | |
| LinkedList nonPDepList = new LinkedList(); | |
| @@ -926,7 +926,7 @@ public class CoreEdgeReactionModel implements ReactionModel { | |
| System.out.println("SpeciesID\tNamw\tH298\tS298\tCp300\tCp400\tCp500\tCp600\tCp800\tCp1000\tCp1500"); | |
| for (int i=0; i<sortedSpeList.size(); i++) { | |
| Species spe = (Species)sortedSpeList.get(i); | |
| - System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + spe.getThermoData().toString()); | |
| + System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getFullName() + '\t' + spe.getThermoData().toString()); | |
| }*/ | |
| LinkedList nonPDepList = new LinkedList(); | |
| diff --git a/source/RMG/jing/rxnSys/DynamicSimulator.java b/source/RMG/jing/rxnSys/DynamicSimulator.java | |
| index d6adbb8..95f1c8e 100644 | |
| --- a/source/RMG/jing/rxnSys/DynamicSimulator.java | |
| +++ b/source/RMG/jing/rxnSys/DynamicSimulator.java | |
| @@ -47,7 +47,7 @@ public interface DynamicSimulator { | |
| //void clean(); | |
| //## operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) | |
| - SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure,boolean p_conditionChanged, TerminationTester tt, int p_iterationNum); | |
| + SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure,boolean p_conditionChanged, TerminationTester tt, int p_iterationNum, LinkedHashSet nonpdep_from_seed); | |
| void addConversion(double [] p_conversion, int p_numConversiosn); | |
| double[] getConversion(); | |
| diff --git a/source/RMG/jing/rxnSys/JDAS.java b/source/RMG/jing/rxnSys/JDAS.java | |
| index 275b4f5..586295b 100644 | |
| --- a/source/RMG/jing/rxnSys/JDAS.java | |
| +++ b/source/RMG/jing/rxnSys/JDAS.java | |
| @@ -93,6 +93,7 @@ public abstract class JDAS implements DAESolver { | |
| protected double endTime; | |
| protected StringBuilder thermoString = new StringBuilder(); | |
| protected static HashMap edgeID; | |
| + protected static HashMap edgeLeakID; | |
| protected double[] maxEdgeFluxRatio; | |
| protected boolean[] prunableSpecies; | |
| protected double termTol; | |
| @@ -142,7 +143,8 @@ public abstract class JDAS implements DAESolver { | |
| } | |
| public StringBuilder generatePDepODEReactionList(ReactionModel p_reactionModel, | |
| - SystemSnapshot p_beginStatus, Temperature p_temperature, Pressure p_pressure) { | |
| + SystemSnapshot p_beginStatus, Temperature p_temperature, Pressure p_pressure, | |
| + LinkedHashSet nonpdep_from_seed) { | |
| StringBuilder rString = new StringBuilder(); | |
| StringBuilder arrayString = new StringBuilder(); | |
| @@ -154,7 +156,7 @@ public abstract class JDAS implements DAESolver { | |
| LinkedList nonPDepList = new LinkedList(); | |
| LinkedList pDepList = new LinkedList(); | |
| - generatePDepReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure, nonPDepList, pDepList); | |
| + generatePDepReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure, nonPDepList, pDepList, nonpdep_from_seed); | |
| int size = nonPDepList.size() + pDepList.size() + duplicates.size(); | |
| @@ -259,7 +261,7 @@ public abstract class JDAS implements DAESolver { | |
| public void generatePDepReactionList(ReactionModel p_reactionModel, | |
| SystemSnapshot p_beginStatus, Temperature p_temperature, Pressure p_pressure, | |
| - LinkedList nonPDepList, LinkedList pDepList) { | |
| + LinkedList nonPDepList, LinkedList pDepList, LinkedHashSet nonpdep_from_seed) { | |
| CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel; | |
| @@ -274,7 +276,10 @@ public abstract class JDAS implements DAESolver { | |
| rxn.generateReverseReaction(); | |
| } | |
| - if (!rxn.reactantEqualsProduct() && !troeList.contains(rxn) && !troeList.contains(rxn.getReverseReaction()) && !thirdBodyList.contains(rxn) && !thirdBodyList.contains(rxn.getReverseReaction()) && !lindemannList.contains(rxn) && !lindemannList.contains(rxn.getReverseReaction())) { | |
| + if (!rxn.reactantEqualsProduct() && !troeList.contains(rxn) && !troeList.contains(rxn.getReverseReaction()) && | |
| + !thirdBodyList.contains(rxn) && !thirdBodyList.contains(rxn.getReverseReaction()) && | |
| + !lindemannList.contains(rxn) && !lindemannList.contains(rxn.getReverseReaction()) && | |
| + !nonpdep_from_seed.contains(rxn) && !nonpdep_from_seed.contains(rxn.getReverseReaction())) { | |
| if (!pDepList.contains(rxn) && !pDepList.contains(rxn.getReverseReaction())) { | |
| pDepList.add(rxn); | |
| } else if (pDepList.contains(rxn) && !pDepList.contains(rxn.getReverseReaction())) { | |
| @@ -319,18 +324,18 @@ public abstract class JDAS implements DAESolver { | |
| Species spe = (Species) iter.next(); | |
| int id = getRealID(spe); | |
| if (id > p_y.length) { | |
| - throw new UnknownReactedSpeciesException(spe.getName()); | |
| + throw new UnknownReactedSpeciesException(spe.getFullName()); | |
| } | |
| double conc = p_y[id - 1]; | |
| double flux = p_yprime[id - 1]; | |
| - System.out.println(String.format("%1$4d\t%2$-13s\t%3$ 6E \t%4$ 6E", spe.getID(), spe.getName(), conc, flux)); | |
| + System.out.println(String.format("%1$4d\t%2$-13s\t%3$ 6E \t%4$ 6E", spe.getID(), spe.getFullName(), conc, flux)); | |
| if (conc < 0) { | |
| double aTol = ReactionModelGenerator.getAtol(); | |
| //if (Math.abs(conc) < aTol) conc = 0; | |
| - //else throw new NegativeConcentrationException("Species " + spe.getName() + " has negative conc: " + String.valueOf(conc)); | |
| + //else throw new NegativeConcentrationException("Species " + spe.getFullName() + " has negative conc: " + String.valueOf(conc)); | |
| if (conc < -100.0 * aTol) { | |
| - throw new NegativeConcentrationException("Species " + spe.getName() + " has negative concentration: " + String.valueOf(conc)); | |
| + throw new NegativeConcentrationException("Species " + spe.getFullName() + " has negative concentration: " + String.valueOf(conc)); | |
| } | |
| } | |
| SpeciesStatus ss = new SpeciesStatus(spe, 1, conc, flux); | |
| @@ -574,7 +579,7 @@ public abstract class JDAS implements DAESolver { | |
| Species spe = ss.getSpecies(); | |
| int id = getRealID(spe); | |
| - //System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); | |
| + //System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getFullName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); | |
| y[id - 1] = conc; | |
| yprime[id - 1] = flux; | |
| @@ -751,10 +756,10 @@ public abstract class JDAS implements DAESolver { | |
| return rtol; | |
| } | |
| - public String getEdgeReactionString(CoreEdgeReactionModel model, HashMap edgeID, | |
| - Reaction r, Temperature temperature, Pressure pressure) { | |
| + public String getEdgeReactionString(CoreEdgeReactionModel model, HashMap IDmap, | |
| + Reaction r, Temperature temperature, Pressure pressure, int offset) { | |
| - int edgeSpeciesCounter = edgeID.size(); | |
| + int edgeSpeciesCounter = IDmap.size() + offset; | |
| // Find the rate coefficient | |
| double k; | |
| @@ -782,11 +787,11 @@ public abstract class JDAS implements DAESolver { | |
| Species spe = (Species) pIter.next(); | |
| if (model.containsAsUnreactedSpecies(spe)) { | |
| prodCount++; | |
| - Integer id = (Integer) edgeID.get(spe); | |
| + Integer id = (Integer) IDmap.get(spe); | |
| if (id == null) { | |
| edgeSpeciesCounter++; | |
| id = new Integer(edgeSpeciesCounter); | |
| - edgeID.put(spe, id); | |
| + IDmap.put(spe, id); | |
| } | |
| tempProdArray[prodCount - 1] = id; | |
| } | |
| @@ -811,12 +816,13 @@ public abstract class JDAS implements DAESolver { | |
| // First use reactions in unreacted reaction set, which is valid for both RateBasedRME and RateBasedPDepRME | |
| edgeID = new HashMap(); | |
| + edgeLeakID = new HashMap(); | |
| LinkedHashSet ur = model.getUnreactedReactionSet(); | |
| for (Iterator iur = ur.iterator(); iur.hasNext();) { | |
| Reaction r = (Reaction) iur.next(); | |
| if (((CoreEdgeReactionModel) model).reactantsInCoreQ(r.getStructure())) { | |
| edgeReactionCounter++; | |
| - String str = getEdgeReactionString(model, edgeID, r, p_temperature, p_pressure);//this line is needed even when not writing to file because it will update edgeID | |
| + String str = getEdgeReactionString(model, edgeID, r, p_temperature, p_pressure, 0);//this line is needed even when not writing to file because it will update edgeID | |
| // edgeReacInfoString.append("\n" + str); | |
| } | |
| } | |
| @@ -868,13 +874,13 @@ public abstract class JDAS implements DAESolver { | |
| if (edgeReaction) { | |
| if (forwardFlag) { | |
| edgeReactionCounter++; | |
| - String str = getEdgeReactionString(model, edgeID, rxn, p_temperature, p_pressure);//use the forward reaction | |
| + String str = getEdgeReactionString(model, edgeID, rxn, p_temperature, p_pressure, 0);//use the forward reaction | |
| // edgeReacInfoString.append("\n" + str); | |
| } else { | |
| PDepReaction rxn_r = (PDepReaction) rxn.getReverseReaction(); | |
| if (rxn_r != null) {//make sure the reverse is not null | |
| edgeReactionCounter++; | |
| - String str = getEdgeReactionString(model, edgeID, rxn_r, p_temperature, p_pressure);//use the reverse reaction | |
| + String str = getEdgeReactionString(model, edgeID, rxn_r, p_temperature, p_pressure, 0);//use the reverse reaction | |
| // edgeReacInfoString.append("\n" + str); | |
| } | |
| } | |
| @@ -884,107 +890,92 @@ public abstract class JDAS implements DAESolver { | |
| //second, consider kLeak of each reaction network so that the validity of each reaction network may be tested | |
| //in the original CHEMDIS approach, we included a reaction and pseudospecies for each kleak/P-dep network | |
| - //with the FAME approach we still consider each P-dep network as a pseudospecies, but we have multiple reactions contributing to this pseudo-species, with each reaction having different reactants | |
| + //with the FAME approach we still group all the wells from separate networks together in a new construct, edgeLeakID, analogous to edge ID | |
| + //edgeLeakID may include some of the same species as edgeID, as well as some new species | |
| + //the IDs used in edgeID and edgeLeakID will be consecutive; i.e. edgeID will go from 1 to N and edgeFluxID will go from N+1 to N+M | |
| edgeSpeciesCounter = edgeID.size();//above functions use getEdgeReactionString, which only uses edgeSpeciesCounter locally; we need to update it for the current context | |
| for (Iterator iter1 = PDepNetwork.getNetworks().iterator(); iter1.hasNext();) { | |
| PDepNetwork pdn = (PDepNetwork) iter1.next(); | |
| - //account for pseudo-edge species product by incrementing the edgeSpeciesCounter and storing the ID in the tempProdArray; each of these ID's will occur once and only once; thus, note that the corresponding PDepNetwork is NOT stored to the HashMap | |
| - int prodCount = 1;//prodCount will not be modified as each PDepNetwork will be treated as a pseudo-edge species product | |
| - int[] tempProdArray = {0, 0, 0}; | |
| - edgeSpeciesCounter++; | |
| - tempProdArray[0] = edgeSpeciesCounter;//note that if there are no non-included reactions that have all core reactants for a particular P-dep network, then the ID will be allocated, but not used...hopefully this would not cause problems with the Fortran code | |
| double k = 0.0; | |
| boolean allCoreReac = false; | |
| - // double k = pdn.getKLeak(index);//index in DASSL should correspond to the same (reactionSystem/TPcondition) index as used by kLeak | |
| - // if (!pdn.isActive() && pdn.getIsChemAct()) { | |
| - // k = pdn.getEntryReaction().calculateTotalRate(p_temperature); | |
| - // } | |
| - if (pdn.getPathReactions().size() == 1 && pdn.getNetReactions().size() == 0) {//// If there is only one path reaction (and thus only one nonincluded reaction), use the high-pressure limit rate as the flux rather than the k(T,P) value (cf. PDepNetwork.getLeakFlux()) | |
| + if (pdn.getPathReactions().size() == 1 && pdn.getNetReactions().size() == 0) {// If there is only one path reaction and no net reactions (i.e. the network is A + B --> C*), use the high-pressure limit rate as the flux rather than the k(T,P) value (cf. PDepNetwork.getLeakFlux()) | |
| PDepReaction rxn = pdn.getPathReactions().get(0); | |
| - int reacCount = 0; | |
| - int[] tempReacArray = {0, 0, 0}; | |
| allCoreReac = false;//allCoreReac will be used to track whether all reactant species are in the core | |
| if (!rxn.getProduct().getIncluded()) { | |
| - k = rxn.calculateRate(p_temperature, p_pressure); | |
| allCoreReac = true; | |
| //iterate over the reactants, counting and storing IDs in tempReacArray, up to a maximum of 3 reactants | |
| for (ListIterator<Species> rIter = rxn.getReactant().getSpeciesListIterator(); rIter.hasNext();) { | |
| - reacCount++; | |
| Species spe = (Species) rIter.next(); | |
| - if (model.containsAsReactedSpecies(spe)) { | |
| - tempReacArray[reacCount - 1] = getRealID(spe); | |
| - } else { | |
| + if (!model.containsAsReactedSpecies(spe)) { | |
| allCoreReac = false; | |
| } | |
| } | |
| + if (allCoreReac) {//only consider cases where all reactants are in the core | |
| + edgeReactionCounter++; | |
| + ////update the output string with info for kLeak for one PDepNetwork | |
| + String str = getEdgeReactionString(model, edgeLeakID, rxn, p_temperature, p_pressure, edgeID.size());//use the forward reaction | |
| + //bw.write("\n" + str); | |
| + } | |
| } else { | |
| PDepReaction rxnReverse = (PDepReaction) rxn.getReverseReaction(); | |
| if (rxnReverse != null) { | |
| - k = rxnReverse.calculateRate(p_temperature, p_pressure); | |
| allCoreReac = true; | |
| //iterate over the products, counting and storing IDs in tempReacArray, up to a maximum of 3 reactants | |
| for (ListIterator<Species> rIter = rxn.getProduct().getSpeciesListIterator(); rIter.hasNext();) { | |
| - | |
| - reacCount++; | |
| Species spe = (Species) rIter.next(); | |
| - if (model.containsAsReactedSpecies(spe)) { | |
| - tempReacArray[reacCount - 1] = getRealID(spe); | |
| - } else { | |
| + if (!model.containsAsReactedSpecies(spe)) { | |
| allCoreReac = false; | |
| } | |
| } | |
| } | |
| - } | |
| - if (allCoreReac) {//only consider cases where all reactants are in the core | |
| - edgeReactionCounter++; | |
| - ////update the output string with info for kLeak for one PDepNetwork | |
| - //bw.write("\n" + reacCount + " " + prodCount + " " + tempReacArray[0] + " " + tempReacArray[1] + " " + tempReacArray[2] + " " + tempProdArray[0] + " " + tempProdArray[1] + " " + tempProdArray[2] + " " + k); | |
| + if (allCoreReac) {//only consider cases where all reactants are in the core | |
| + edgeReactionCounter++; | |
| + ////update the output string with info for kLeak for one PDepNetwork | |
| + String str = getEdgeReactionString(model, edgeLeakID, rxnReverse, p_temperature, p_pressure, edgeID.size());//use the reverse reaction | |
| + //bw.write("\n" + str); | |
| + } | |
| } | |
| } else { | |
| for (ListIterator<PDepReaction> iter = pdn.getNonincludedReactions().listIterator(); iter.hasNext();) {//cf. getLeakFlux in PDepNetwork | |
| PDepReaction rxn = iter.next(); | |
| - int reacCount = 0; | |
| - int[] tempReacArray = {0, 0, 0}; | |
| allCoreReac = false;//allCoreReac will be used to track whether all reactant species are in the core | |
| if (rxn.getReactant().getIncluded() && !rxn.getProduct().getIncluded()) { | |
| - k = rxn.calculateRate(p_temperature, p_pressure); | |
| allCoreReac = true; | |
| //iterate over the reactants, counting and storing IDs in tempReacArray, up to a maximum of 3 reactants | |
| for (ListIterator<Species> rIter = rxn.getReactant().getSpeciesListIterator(); rIter.hasNext();) { | |
| - reacCount++; | |
| Species spe = (Species) rIter.next(); | |
| - if (model.containsAsReactedSpecies(spe)) { | |
| - tempReacArray[reacCount - 1] = getRealID(spe); | |
| - } else { | |
| + if (!model.containsAsReactedSpecies(spe)) { | |
| allCoreReac = false; | |
| } | |
| } | |
| + if (allCoreReac) {//only consider cases where all reactants are in the core | |
| + edgeReactionCounter++; | |
| + ////update the output string with info for kLeak for one PDepNetwork | |
| + String str = getEdgeReactionString(model, edgeLeakID, rxn, p_temperature, p_pressure, edgeID.size());//use the forward reaction | |
| + //bw.write("\n" + str); | |
| + } | |
| } else if (!rxn.getReactant().getIncluded() && rxn.getProduct().getIncluded()) { | |
| PDepReaction rxnReverse = (PDepReaction) rxn.getReverseReaction(); | |
| - k = rxnReverse.calculateRate(p_temperature, p_pressure); | |
| allCoreReac = true; | |
| //iterate over the products, counting and storing IDs in tempReacArray, up to a maximum of 3 reactants | |
| for (ListIterator<Species> rIter = rxn.getProduct().getSpeciesListIterator(); rIter.hasNext();) { | |
| - | |
| - reacCount++; | |
| Species spe = (Species) rIter.next(); | |
| - if (model.containsAsReactedSpecies(spe)) { | |
| - tempReacArray[reacCount - 1] = getRealID(spe); | |
| - } else { | |
| + if (!model.containsAsReactedSpecies(spe)) { | |
| allCoreReac = false; | |
| } | |
| } | |
| - } | |
| - if (allCoreReac) {//only consider cases where all reactants are in the core | |
| - edgeReactionCounter++; | |
| - ////update the output string with info for kLeak for one PDepNetwork | |
| - //bw.write("\n" + reacCount + " " + prodCount + " " + tempReacArray[0] + " " + tempReacArray[1] + " " + tempReacArray[2] + " " + tempProdArray[0] + " " + tempProdArray[1] + " " + tempProdArray[2] + " " + k); | |
| + if (allCoreReac) {//only consider cases where all reactants are in the core | |
| + edgeReactionCounter++; | |
| + ////update the output string with info for kLeak for one PDepNetwork | |
| + String str = getEdgeReactionString(model, edgeLeakID, rxnReverse, p_temperature, p_pressure, edgeID.size());//use the reverse reaction | |
| + //bw.write("\n" + str); | |
| + } | |
| } | |
| } | |
| } | |
| - | |
| } | |
| } | |
| + edgeSpeciesCounter = edgeID.size() + edgeLeakID.size(); | |
| @@ -1000,12 +991,13 @@ public abstract class JDAS implements DAESolver { | |
| // First use reactions in unreacted reaction set, which is valid for both RateBasedRME and RateBasedPDepRME | |
| edgeID = new HashMap(); | |
| + edgeLeakID = new HashMap(); | |
| ur = model.getUnreactedReactionSet(); | |
| for (Iterator iur = ur.iterator(); iur.hasNext();) { | |
| Reaction r = (Reaction) iur.next(); | |
| if (((CoreEdgeReactionModel) model).reactantsInCoreQ(r.getStructure())) { | |
| edgeReactionCounter++; | |
| - String str = getEdgeReactionString(model, edgeID, r, p_temperature, p_pressure);//this line is needed even when not writing to file because it will update edgeID | |
| + String str = getEdgeReactionString(model, edgeID, r, p_temperature, p_pressure, 0);//this line is needed even when not writing to file because it will update edgeID | |
| bw.write("\n" + str); | |
| } | |
| @@ -1058,13 +1050,13 @@ public abstract class JDAS implements DAESolver { | |
| if (edgeReaction) { | |
| if (forwardFlag) { | |
| edgeReactionCounter++; | |
| - String str = getEdgeReactionString(model, edgeID, rxn, p_temperature, p_pressure);//use the forward reaction | |
| + String str = getEdgeReactionString(model, edgeID, rxn, p_temperature, p_pressure, 0);//use the forward reaction | |
| bw.write("\n" + str); | |
| } else { | |
| PDepReaction rxn_r = (PDepReaction) rxn.getReverseReaction(); | |
| if (rxn_r != null) {//make sure the reverse is not null | |
| edgeReactionCounter++; | |
| - String str = getEdgeReactionString(model, edgeID, rxn_r, p_temperature, p_pressure);//use the reverse reaction | |
| + String str = getEdgeReactionString(model, edgeID, rxn_r, p_temperature, p_pressure, 0);//use the reverse reaction | |
| bw.write("\n" + str); | |
| } | |
| } | |
| @@ -1072,127 +1064,95 @@ public abstract class JDAS implements DAESolver { | |
| } | |
| } | |
| - //6/19/09 gmagoon: original code below; with new P-dep implementation, it would only take into account forward reactions | |
| - //if (rxn.isEdgeReaction(model)) { | |
| - // edgeReactionCounter++; | |
| - // String str = getEdgeReactionString(model, edgeID, rxn, p_temperature, p_pressure); | |
| - // edgeReacInfoString.append("\n" + str); | |
| - //} | |
| - //a potentially simpler approach based on the original approach (however, it seems like isEdgeReaction may return false even if there are some core products along with edge products): | |
| - // PDepReaction rxnReverse = (PDepReaction)rxn.getReverseReaction(); | |
| - // if (rxn.isEdgeReaction(model)) { | |
| - // edgeReactionCounter++; | |
| - // String str = getEdgeReactionString(model, edgeID, rxn, p_temperature, p_pressure); | |
| - // edgeReacInfoString.append("\n" + str); | |
| - // } | |
| - // else if (rxnReverse.isEdgeReaction(model)){ | |
| - // edgeReactionCounter++; | |
| - // String str = getEdgeReactionString(model, edgeID, rxn, p_temperature, p_pressure); | |
| - // edgeReacInfoString.append("\n" + str); | |
| - // } | |
| //second, consider kLeak of each reaction network so that the validity of each reaction network may be tested | |
| //in the original CHEMDIS approach, we included a reaction and pseudospecies for each kleak/P-dep network | |
| - //with the FAME approach we still consider each P-dep network as a pseudospecies, but we have multiple reactions contributing to this pseudo-species, with each reaction having different reactants | |
| + //with the FAME approach we still group all the wells from separate networks together in a new construct, edgeLeakID, analogous to edge ID | |
| + //edgeLeakID may include some of the same species as edgeID, as well as some new species | |
| + //the IDs used in edgeID and edgeLeakID will be consecutive; i.e. edgeID will go from 1 to N and edgeFluxID will go from N+1 to N+M | |
| edgeSpeciesCounter = edgeID.size();//above functions use getEdgeReactionString, which only uses edgeSpeciesCounter locally; we need to update it for the current context | |
| for (Iterator iter1 = PDepNetwork.getNetworks().iterator(); iter1.hasNext();) { | |
| PDepNetwork pdn = (PDepNetwork) iter1.next(); | |
| - //account for pseudo-edge species product by incrementing the edgeSpeciesCounter and storing the ID in the tempProdArray; each of these ID's will occur once and only once; thus, note that the corresponding PDepNetwork is NOT stored to the HashMap | |
| - int prodCount = 1;//prodCount will not be modified as each PDepNetwork will be treated as a pseudo-edge species product | |
| - int[] tempProdArray = {0, 0, 0}; | |
| - edgeSpeciesCounter++; | |
| - tempProdArray[0] = edgeSpeciesCounter;//note that if there are no non-included reactions that have all core reactants for a particular P-dep network, then the ID will be allocated, but not used...hopefully this would not cause problems with the Fortran code | |
| double k = 0.0; | |
| boolean allCoreReac = false; | |
| - // double k = pdn.getKLeak(index);//index in DASSL should correspond to the same (reactionSystem/TPcondition) index as used by kLeak | |
| - // if (!pdn.isActive() && pdn.getIsChemAct()) { | |
| - // k = pdn.getEntryReaction().calculateTotalRate(p_temperature); | |
| - // } | |
| - if (pdn.getPathReactions().size() == 1 && pdn.getNetReactions().size() == 0) {//// If there is only one path reaction (and thus only one nonincluded reaction), use the high-pressure limit rate as the flux rather than the k(T,P) value (cf. PDepNetwork.getLeakFlux()) | |
| + if (pdn.getPathReactions().size() == 1 && pdn.getNetReactions().size() == 0) {// If there is only one path reaction and no net reactions (i.e. the network is A + B --> C*), use the high-pressure limit rate as the flux rather than the k(T,P) value (cf. PDepNetwork.getLeakFlux()) | |
| PDepReaction rxn = pdn.getPathReactions().get(0); | |
| - int reacCount = 0; | |
| - int[] tempReacArray = {0, 0, 0}; | |
| allCoreReac = false;//allCoreReac will be used to track whether all reactant species are in the core | |
| if (!rxn.getProduct().getIncluded()) { | |
| - k = rxn.calculateRate(p_temperature, p_pressure); | |
| allCoreReac = true; | |
| //iterate over the reactants, counting and storing IDs in tempReacArray, up to a maximum of 3 reactants | |
| for (ListIterator<Species> rIter = rxn.getReactant().getSpeciesListIterator(); rIter.hasNext();) { | |
| - reacCount++; | |
| Species spe = (Species) rIter.next(); | |
| - if (model.containsAsReactedSpecies(spe)) { | |
| - tempReacArray[reacCount - 1] = getRealID(spe); | |
| - } else { | |
| + if (!model.containsAsReactedSpecies(spe)) { | |
| allCoreReac = false; | |
| } | |
| } | |
| + if (allCoreReac) {//only consider cases where all reactants are in the core | |
| + edgeReactionCounter++; | |
| + ////update the output string with info for kLeak for one PDepNetwork | |
| + String str = getEdgeReactionString(model, edgeLeakID, rxn, p_temperature, p_pressure, edgeID.size());//use the forward reaction | |
| + bw.write("\n" + str); | |
| + } | |
| } else { | |
| PDepReaction rxnReverse = (PDepReaction) rxn.getReverseReaction(); | |
| if (rxnReverse != null) { | |
| - k = rxnReverse.calculateRate(p_temperature, p_pressure); | |
| allCoreReac = true; | |
| //iterate over the products, counting and storing IDs in tempReacArray, up to a maximum of 3 reactants | |
| for (ListIterator<Species> rIter = rxn.getProduct().getSpeciesListIterator(); rIter.hasNext();) { | |
| - | |
| - reacCount++; | |
| Species spe = (Species) rIter.next(); | |
| - if (model.containsAsReactedSpecies(spe)) { | |
| - tempReacArray[reacCount - 1] = getRealID(spe); | |
| - } else { | |
| + if (!model.containsAsReactedSpecies(spe)) { | |
| allCoreReac = false; | |
| } | |
| } | |
| } | |
| - } | |
| - if (allCoreReac) {//only consider cases where all reactants are in the core | |
| - edgeReactionCounter++; | |
| - //update the output string with info for kLeak for one PDepNetwork | |
| - bw.write("\n" + reacCount + " " + prodCount + " " + tempReacArray[0] + " " + tempReacArray[1] + " " + tempReacArray[2] + " " + tempProdArray[0] + " " + tempProdArray[1] + " " + tempProdArray[2] + " " + k); | |
| + if (allCoreReac) {//only consider cases where all reactants are in the core | |
| + edgeReactionCounter++; | |
| + ////update the output string with info for kLeak for one PDepNetwork | |
| + String str = getEdgeReactionString(model, edgeLeakID, rxnReverse, p_temperature, p_pressure, edgeID.size());//use the reverse reaction | |
| + bw.write("\n" + str); | |
| + } | |
| } | |
| } else { | |
| for (ListIterator<PDepReaction> iter = pdn.getNonincludedReactions().listIterator(); iter.hasNext();) {//cf. getLeakFlux in PDepNetwork | |
| PDepReaction rxn = iter.next(); | |
| - int reacCount = 0; | |
| - int[] tempReacArray = {0, 0, 0}; | |
| allCoreReac = false;//allCoreReac will be used to track whether all reactant species are in the core | |
| if (rxn.getReactant().getIncluded() && !rxn.getProduct().getIncluded()) { | |
| - k = rxn.calculateRate(p_temperature, p_pressure); | |
| allCoreReac = true; | |
| //iterate over the reactants, counting and storing IDs in tempReacArray, up to a maximum of 3 reactants | |
| for (ListIterator<Species> rIter = rxn.getReactant().getSpeciesListIterator(); rIter.hasNext();) { | |
| - reacCount++; | |
| Species spe = (Species) rIter.next(); | |
| - if (model.containsAsReactedSpecies(spe)) { | |
| - tempReacArray[reacCount - 1] = getRealID(spe); | |
| - } else { | |
| + if (!model.containsAsReactedSpecies(spe)) { | |
| allCoreReac = false; | |
| } | |
| } | |
| + if (allCoreReac) {//only consider cases where all reactants are in the core | |
| + edgeReactionCounter++; | |
| + ////update the output string with info for kLeak for one PDepNetwork | |
| + String str = getEdgeReactionString(model, edgeLeakID, rxn, p_temperature, p_pressure, edgeID.size());//use the forward reaction | |
| + bw.write("\n" + str); | |
| + } | |
| } else if (!rxn.getReactant().getIncluded() && rxn.getProduct().getIncluded()) { | |
| PDepReaction rxnReverse = (PDepReaction) rxn.getReverseReaction(); | |
| - k = rxnReverse.calculateRate(p_temperature, p_pressure); | |
| allCoreReac = true; | |
| //iterate over the products, counting and storing IDs in tempReacArray, up to a maximum of 3 reactants | |
| for (ListIterator<Species> rIter = rxn.getProduct().getSpeciesListIterator(); rIter.hasNext();) { | |
| - | |
| - reacCount++; | |
| Species spe = (Species) rIter.next(); | |
| - if (model.containsAsReactedSpecies(spe)) { | |
| - tempReacArray[reacCount - 1] = getRealID(spe); | |
| - } else { | |
| + if (!model.containsAsReactedSpecies(spe)) { | |
| allCoreReac = false; | |
| } | |
| } | |
| - } | |
| - if (allCoreReac) {//only consider cases where all reactants are in the core | |
| - edgeReactionCounter++; | |
| - //update the output string with info for kLeak for one PDepNetwork | |
| - bw.write("\n" + reacCount + " " + prodCount + " " + tempReacArray[0] + " " + tempReacArray[1] + " " + tempReacArray[2] + " " + tempProdArray[0] + " " + tempProdArray[1] + " " + tempProdArray[2] + " " + k); | |
| + if (allCoreReac) {//only consider cases where all reactants are in the core | |
| + edgeReactionCounter++; | |
| + ////update the output string with info for kLeak for one PDepNetwork | |
| + String str = getEdgeReactionString(model, edgeLeakID, rxnReverse, p_temperature, p_pressure, edgeID.size());//use the reverse reaction | |
| + bw.write("\n" + str); | |
| + } | |
| } | |
| } | |
| } | |
| } | |
| } | |
| + edgeSpeciesCounter = edgeID.size() + edgeLeakID.size();//this line is not needed here, but it is included for consistency with the first pass | |
| } catch (IOException e) { | |
| System.err.println("Problem writing Solver Input File!"); | |
| e.printStackTrace(); | |
| diff --git a/source/RMG/jing/rxnSys/JDASPK.java b/source/RMG/jing/rxnSys/JDASPK.java | |
| index 3021258..b092fbc 100644 | |
| --- a/source/RMG/jing/rxnSys/JDASPK.java | |
| +++ b/source/RMG/jing/rxnSys/JDASPK.java | |
| @@ -98,7 +98,7 @@ public class JDASPK extends JDAS { | |
| } | |
| //## operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) | |
| - public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged,TerminationTester tt, int p_iterationNum) { | |
| + public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged,TerminationTester tt, int p_iterationNum, LinkedHashSet nonpdep_from_seed) { | |
| // set up the input file | |
| setupInputFile(); | |
| //outputString = new StringBuilder(); | |
| @@ -141,7 +141,7 @@ public class JDASPK extends JDAS { | |
| //rString is a combination of a integer and a real array | |
| //real array format: rate, A, n, Ea, Keq | |
| //int array format : nReac, nProd, r1, r2, r3, p1, p2, p3, HASrev(T=1 or F=0) | |
| - rString = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); | |
| + rString = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure, nonpdep_from_seed); | |
| nParameter = 0; | |
| if (parameterInfor != 0) { | |
| @@ -426,8 +426,8 @@ public class JDASPK extends JDAS { | |
| } | |
| //for autoflag cases, there will be additional information which may be used for pruning | |
| if (autoflag){ | |
| - prunableSpecies = new boolean[edgeID.size()]; | |
| - maxEdgeFluxRatio = new double[edgeID.size()]; | |
| + prunableSpecies = new boolean[edgeID.size()+edgeLeakID.size()]; | |
| + maxEdgeFluxRatio = new double[edgeID.size()+edgeLeakID.size()]; | |
| line=br.readLine();//read volume; (this is actually in the output even if AUTO is off, but is not used) | |
| line=br.readLine();//read the edgeflag | |
| Integer edgeflag = Integer.parseInt(line.trim()); | |
| @@ -440,10 +440,8 @@ public class JDASPK extends JDAS { | |
| line=br.readLine();//read the time integrated to | |
| double finalTime = Double.parseDouble(line.trim()); | |
| System.out.println("ODE solver integrated to "+ finalTime+" sec."); | |
| - // read the "prunability index" (0 or 1) and maximum ratio (edge flux/Rchar) for each edge species; | |
| - // note that edgeID only contains species, not P-dep networks, so we will not be reading in all the output from DASSL, | |
| - // only the flux ratio to actual edge species (vs. P-dep network pseudospecies) | |
| - for (int i=0; i<edgeID.size(); i++){ | |
| + // read the "prunability index" (0 or 1) and maximum ratio (edge flux/Rchar) for each edge species; vector index + 1 corresponds to ID value in edgeID and edgeLeakID | |
| + for (int i=0; i<(edgeID.size()+edgeLeakID.size()); i++){ | |
| line = br.readLine().trim(); //read the prunability index | |
| int q = Integer.parseInt(line); //q should be 1 or 0 | |
| if (q == 1) {prunableSpecies[i]=true;} | |
| @@ -469,7 +467,7 @@ public class JDASPK extends JDAS { | |
| return 1; | |
| } | |
| - public LinkedList solveSEN(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged,TerminationTester tt) { | |
| + public LinkedList solveSEN(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged,TerminationTester tt, LinkedHashSet nonpdep_from_seed) { | |
| setupInputFile(); | |
| // outputString = new StringBuilder(); | |
| Iterator spe_iter = p_reactionModel.getSpecies(); | |
| @@ -510,7 +508,7 @@ public class JDASPK extends JDAS { | |
| //rString is a combination of a integer and a real array | |
| //real array format: rate, A, n, Ea, Keq | |
| //int array format : nReac, nProd, r1, r2, r3, p1, p2, p3, HASrev(T=1 or F=0) | |
| - rString = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); | |
| + rString = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure, nonpdep_from_seed); | |
| nParameter = 0; | |
| if (parameterInfor != 0) { | |
| diff --git a/source/RMG/jing/rxnSys/JDASSL.java b/source/RMG/jing/rxnSys/JDASSL.java | |
| index 07197ef..0292c89 100644 | |
| --- a/source/RMG/jing/rxnSys/JDASSL.java | |
| +++ b/source/RMG/jing/rxnSys/JDASSL.java | |
| @@ -101,7 +101,7 @@ public class JDASSL extends JDAS { | |
| }*/ | |
| //## operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) | |
| - public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged, TerminationTester tt, int p_iterationNum) { | |
| + public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged, TerminationTester tt, int p_iterationNum, LinkedHashSet nonpdep_from_seed) { | |
| // set up the input file | |
| setupInputFile(); | |
| @@ -158,7 +158,7 @@ public class JDASSL extends JDAS { | |
| //rString is a combination of a integer and a real array | |
| //real array format: rate, A, n, Ea, Keq | |
| //int array format : nReac, nProd, r1, r2, r3, p1, p2, p3, rev(=1 or -1) | |
| - rString = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); | |
| + rString = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure,nonpdep_from_seed); | |
| initializeWorkSpace(); | |
| initializeConcentrations(p_beginStatus, p_reactionModel, p_beginTime, p_endTime, initialSpecies); | |
| @@ -387,7 +387,7 @@ public class JDASSL extends JDAS { | |
| line = br.readLine(); | |
| if (Double.parseDouble(line.trim()) != neq) { | |
| - System.out.println("ODESolver didnt generate all species result"); | |
| + System.out.println("ODESolver didnt generate all species results"); | |
| System.exit(0); | |
| } | |
| endTime = Double.parseDouble(br.readLine().trim()); | |
| @@ -407,8 +407,8 @@ public class JDASSL extends JDAS { | |
| } | |
| //for autoflag cases, there will be additional information which may be used for pruning | |
| if (autoflag){ | |
| - prunableSpecies = new boolean[edgeID.size()]; | |
| - maxEdgeFluxRatio = new double[edgeID.size()]; | |
| + prunableSpecies = new boolean[edgeID.size()+edgeLeakID.size()]; | |
| + maxEdgeFluxRatio = new double[edgeID.size()+edgeLeakID.size()]; | |
| line=br.readLine();//read volume; (this is actually in the output even if AUTO is off, but is not used) | |
| line=br.readLine();//read the edgeflag | |
| Integer edgeflag = Integer.parseInt(line.trim()); | |
| @@ -416,16 +416,13 @@ public class JDASSL extends JDAS { | |
| targetReached = true; | |
| } | |
| else{ | |
| - System.out.println("DEBUG: DASSL Fortran code found that edge entity "+ edgeflag+ " exceeded the model enlargement criterion."); | |
| targetReached = false; | |
| } | |
| line=br.readLine();//read the time integrated to | |
| double finalTime = Double.parseDouble(line.trim()); | |
| - // read the "prunability index" (0 or 1) and maximum ratio (edge flux/Rchar) for each edge species; | |
| - // note that edgeID only contains species, not P-dep networks, so we will not be reading in all the output from DASSL, | |
| - // only the flux ratio to actual edge species (vs. P-dep network pseudospecies) | |
| + // read the "prunability index" (0 or 1) and maximum ratio (edge flux/Rchar) for each edge species; vector index + 1 corresponds to ID value in edgeID and edgeLeakID | |
| System.out.println("ODE solver integrated to "+ finalTime+" sec."); | |
| - for (int i=0; i<edgeID.size(); i++){ | |
| + for (int i=0; i<(edgeID.size()+edgeLeakID.size()); i++){ | |
| line = br.readLine().trim(); //read the prunability index | |
| int q = Integer.parseInt(line); //q should be 1 or 0 | |
| if (q == 1) { prunableSpecies[i] = true; } | |
| @@ -474,7 +471,7 @@ public class JDASSL extends JDAS { | |
| spe = (Species)iter.next(); | |
| if((Integer)(IDTranslator.get(spe))==i+1) break; | |
| } | |
| - String name = spe.getName(); | |
| + String name = spe.getFullName(); | |
| fw.write(name + "\t"); | |
| } | |
| fw.write("\n"); | |
| diff --git a/source/RMG/jing/rxnSys/RateBasedPDepRME.java b/source/RMG/jing/rxnSys/RateBasedPDepRME.java | |
| index 5bc631f..4eaca67 100644 | |
| --- a/source/RMG/jing/rxnSys/RateBasedPDepRME.java | |
| +++ b/source/RMG/jing/rxnSys/RateBasedPDepRME.java | |
| @@ -107,14 +107,29 @@ public class RateBasedPDepRME implements ReactionModelEnlarger { | |
| CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) rm; | |
| - // Iterate over reaction systems, enlarging each individually | |
| - LinkedList updateList = new LinkedList(); | |
| - for (int i = 0; i < rxnSystemList.size(); i++) { | |
| + // Lists of species to add to the core or to explore in PDepNetworks | |
| + // These lists will be of the same length as rxnSystemList, and will | |
| + // contain null where there is no corresponding species; this is done | |
| + // so that we know which reaction system corresponds with each update | |
| + // (although it doesn't matter very much, since they all share the same | |
| + // model core and edge anyway) | |
| + // They should also not contain duplicates, i.e. each candidate species | |
| + // should only appear in one of the two lists, and only once in that | |
| + // list; since adding to core is a superset of making included, species | |
| + // that would be in both lists are placed in coreUpdateList | |
| + LinkedList coreUpdateList = new LinkedList(); | |
| + LinkedList leakUpdateList = new LinkedList(); | |
| + | |
| + // Iterate over reaction systems, enlarging each individually | |
| + for (int i = 0; i < rxnSystemList.size(); i++) { | |
| // Don't need to enlarge if the system is already valid | |
| - if ((Boolean) validList.get(i)) | |
| - continue; | |
| - | |
| + if ((Boolean) validList.get(i)) { | |
| + coreUpdateList.add(null); | |
| + leakUpdateList.add(null); | |
| + continue; | |
| + } | |
| + | |
| ReactionSystem rxnSystem = (ReactionSystem) rxnSystemList.get(i); | |
| PresentStatus ps = rxnSystem.getPresentStatus(); | |
| @@ -138,27 +153,6 @@ public class RateBasedPDepRME implements ReactionModelEnlarger { | |
| us.getName() + "(" + us.getID() + "), but there are only " + | |
| unreactedSpeciesFlux.length + " fluxes."); | |
| } | |
| - | |
| - // Flux from pDep reactions //gmagoon 61709: ...is already taken into account above (the unreactedSpeciesFlux is also used by the validityTester | |
| -// for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) { | |
| -// PDepNetwork pdn = (PDepNetwork) iter.next(); | |
| -// for (Iterator iter2 = pdn.getNetReactions().iterator(); iter2.hasNext(); ) { | |
| -// PDepReaction rxn = (PDepReaction) iter2.next(); | |
| -// double forwardFlux = rxn.calculateForwardFlux(ps); | |
| -// double reverseFlux = rxn.calculateReverseFlux(ps); | |
| -// //System.out.println(rxn.toString() + ": " + forwardFlux + " " + reverseFlux); | |
| -// for (int j = 0; j < rxn.getReactantNumber(); j++) { | |
| -// Species species = (Species) rxn.getReactantList().get(j); | |
| -// if (cerm.containsAsUnreactedSpecies(species)) | |
| -// flux[species.getID()] += reverseFlux; | |
| -// } | |
| -// for (int j = 0; j < rxn.getProductNumber(); j++) { | |
| -// Species species = (Species) rxn.getProductList().get(j); | |
| -// if (cerm.containsAsUnreactedSpecies(species)) | |
| -// flux[species.getID()] += forwardFlux; | |
| -// } | |
| -// } | |
| -// } | |
| // Determine species with maximum flux and its flux | |
| Species maxSpecies = null; | |
| @@ -172,215 +166,240 @@ public class RateBasedPDepRME implements ReactionModelEnlarger { | |
| } | |
| if (maxSpecies == null) throw new NullPointerException(); | |
| - // Determine network with maximum leak flux and its flux | |
| - PDepNetwork maxNetwork = null; | |
| - double maxLeak = 0; | |
| - for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) { | |
| - PDepNetwork pdn = (PDepNetwork) iter.next(); | |
| - if (Math.abs(pdn.getLeakFlux(ps)) >= maxLeak) { | |
| - maxLeak = Math.abs(pdn.getLeakFlux(ps)); | |
| - maxNetwork = pdn; | |
| + // Determine species with maximum leak flux and its flux | |
| + Species maxLeakSpecies = null; | |
| + double maxLeakFlux = 0; | |
| + double[] leakFlux = PDepNetwork.getSpeciesLeakFluxes(ps, cerm); | |
| + for (Iterator iter = cerm.getUnreactedSpeciesSet().iterator(); iter.hasNext(); ) { | |
| + Species us = (Species) iter.next(); | |
| + if (Math.abs(leakFlux[us.getID()]) >= maxLeakFlux) { | |
| + maxLeakFlux = Math.abs(leakFlux[us.getID()]); | |
| + maxLeakSpecies = us; | |
| } | |
| } | |
| - if (maxNetwork == null) throw new NullPointerException(); | |
| + if (maxLeakSpecies == null) throw new NullPointerException(); | |
| // Output results of above calculations to console | |
| System.out.print("Time: "); | |
| System.out.println(ps.getTime()); | |
| System.out.println("Rmin: " + String.valueOf(Rmin)); | |
| - System.out.println("Unreacted species " + maxSpecies.getName() + " has highest flux: " + String.valueOf(maxFlux)); | |
| - System.out.println("Network " + maxNetwork.getID() + " has highest leak flux: " + String.valueOf(maxLeak)); | |
| + System.out.println("Unreacted species " + maxSpecies.getFullName() + " has highest flux: " + String.valueOf(maxFlux)); | |
| + System.out.println("Unreacted species " + maxLeakSpecies.getFullName() + " has highest leak flux: " + String.valueOf(maxLeakFlux)); | |
| - //if (maxFlux > Rmin) | |
| - if (maxFlux > maxLeak && maxFlux > Rmin) { | |
| - if (!updateList.contains(maxSpecies)) | |
| - updateList.add(maxSpecies); | |
| - else | |
| - updateList.add(null); | |
| - } | |
| - else if (maxLeak > Rmin) { | |
| - if (!updateList.contains(maxNetwork)) | |
| - updateList.add(maxNetwork); | |
| - else | |
| - updateList.add(null); | |
| + | |
| + if (maxFlux > maxLeakFlux && maxFlux > Rmin) { | |
| + // Flux is greater than leakFlux, and big enough to matter. | |
| + if (!coreUpdateList.contains(maxSpecies)) | |
| + coreUpdateList.add(maxSpecies); | |
| + else | |
| + coreUpdateList.add(null); | |
| + leakUpdateList.add(null); | |
| + } | |
| + else if (maxLeakFlux > Rmin) { | |
| + // leakFlux is greater than Flux, and big enough to matter. | |
| + if (!leakUpdateList.contains(maxLeakSpecies)) | |
| + leakUpdateList.add(maxLeakSpecies); | |
| + else | |
| + leakUpdateList.add(null); | |
| + coreUpdateList.add(null); | |
| + } | |
| + else { | |
| + // neither leakFlux nor Flux is big enough to matter | |
| + leakUpdateList.add(null); | |
| + coreUpdateList.add(null); | |
| } | |
| - else | |
| - updateList.add(null); | |
| + } | |
| - } | |
| + // Check that species don't exist in both coreUpdateList and leakUpdateList | |
| + // If any are in both lists, then remove from leakUpdateList | |
| + for (int i = 0; i < rxnSystemList.size(); i++) { | |
| + if (leakUpdateList.get(i) != null && coreUpdateList.contains(leakUpdateList.get(i))) | |
| + leakUpdateList.set(i, null); | |
| + } | |
| - for (int i = 0; i < updateList.size(); i++) { | |
| + // Make sure we're about to do something to the reaction model | |
| + boolean found = false; | |
| + for (int i = 0; i < rxnSystemList.size(); i++) { | |
| + if (coreUpdateList.get(i) != null || leakUpdateList.get(i) != null) | |
| + found = true; | |
| + } | |
| + if (!found) { | |
| + System.out.println("Could not find any species to add to core or leak species to explore. Stopping to avoid infinite loop."); | |
| + System.exit(0); | |
| + } | |
| + | |
| + // Update the reaction model | |
| + for (int i = 0; i < rxnSystemList.size(); i++) { | |
| + // Add species to core | |
| + if (coreUpdateList.get(i) != null) | |
| + addSpeciesToCore((Species) coreUpdateList.get(i), cerm, (ReactionSystem) rxnSystemList.get(i)); | |
| + // Explore species in networks | |
| + else if (leakUpdateList.get(i) != null) | |
| + makeSpeciesIncluded((Species) leakUpdateList.get(i), cerm, (ReactionSystem) rxnSystemList.get(i)); | |
| + } | |
| + } | |
| - Object object = updateList.get(i); | |
| - ReactionSystem rxnSystem = (ReactionSystem) rxnSystemList.get(i); | |
| - PresentStatus ps = rxnSystem.getPresentStatus(); | |
| - | |
| - if (object == null) | |
| - continue; | |
| - else if (object instanceof Species) { | |
| - | |
| - Species maxSpecies = (Species) object; | |
| - | |
| - // Add a species to the core | |
| - System.out.print("\nAdd a new reacted Species: "); | |
| - System.out.println(maxSpecies.getChemkinName()); | |
| - System.out.println(maxSpecies.toStringWithoutH()); | |
| - Temperature temp = new Temperature(715, "K"); | |
| - double H = maxSpecies.calculateH(temp); | |
| - double S = maxSpecies.calculateS(temp); | |
| - double G = maxSpecies.calculateG(temp); | |
| - double Cp = maxSpecies.calculateCp(temp); | |
| - System.out.println("Thermo of species at 715K (H, S, G, Cp, respectively)\t" + String.valueOf(H) + '\t' + String.valueOf(S) + '\t' + String.valueOf(G) + '\t' + String.valueOf(Cp)); | |
| - | |
| - if (cerm.containsAsReactedSpecies(maxSpecies)) | |
| - System.out.println("Species " + maxSpecies.getName() + "(" + | |
| - Integer.toString(maxSpecies.getID()) + | |
| - ") is already present in reaction model"); | |
| - else { | |
| - | |
| - // Move the species and appropriate reactions from the edge to the core | |
| - cerm.moveFromUnreactedToReactedSpecies(maxSpecies); | |
| - cerm.moveFromUnreactedToReactedReaction(); | |
| - | |
| - // Adding a species to the core automatically makes it | |
| - // included in all networks it is contained in | |
| - // Therefore we need to merge all networks containing that | |
| - // species as a unimolecular isomer together | |
| - PDepNetwork network = null; | |
| - LinkedList<PDepNetwork> networksToRemove = new LinkedList<PDepNetwork>(); | |
| - for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) { | |
| - PDepNetwork pdn = (PDepNetwork) iter.next(); | |
| - if (pdn.contains(maxSpecies)) { | |
| - if (network == null) | |
| - network = pdn; // first pdn to contain maxSpecies | |
| - else { // second or later pdn to contain maxSpecies. merge it with network | |
| - for (int j = 0; j < pdn.getIsomers().size(); j++) | |
| - network.addIsomer(pdn.getIsomers().get(j)); | |
| - for (int j = 0; j < pdn.getPathReactions().size(); j++) | |
| - network.addReaction(pdn.getPathReactions().get(j),false); | |
| - networksToRemove.add(pdn); | |
| - } | |
| - } | |
| - } | |
| - if (network != null) { | |
| - network.getIsomer(maxSpecies).setIncluded(true); | |
| - try { | |
| - network.updateReactionLists(cerm); | |
| - } catch (PDepException e) { | |
| - e.printStackTrace(); | |
| - System.out.println(e.getMessage()); | |
| - System.err.println("WARNING: Attempt to update reaction list failed " + | |
| - "for the following network:\n" + network.toString()); | |
| - System.exit(0); | |
| - } | |
| - } | |
| - | |
| - // Generate new reaction set; partition into core and edge | |
| - LinkedHashSet newReactionSet_nodup; | |
| - if(rxnSystem.getLibraryReactionGenerator().getReactionLibrary() != null){ | |
| - | |
| - System.out.println("Checking Reaction Library "+rxnSystem.getLibraryReactionGenerator().getReactionLibrary().getName()+" for reactions of "+maxSpecies.getName()+" with the core."); | |
| - // At this point the core (cerm.getReactedSpeciesSet()) already contains maxSpecies, so we can just react the entire core. | |
| - LinkedHashSet newReactionSet = rxnSystem.getLibraryReactionGenerator().react(cerm.getReactedSpeciesSet()); | |
| - //LinkedHashSet newReactionSet = rxnSystem.getLibraryReactionGenerator().react(cerm.getReactedSpeciesSet(),maxSpecies,"All"); | |
| - | |
| - // Report only those that contain the new species (maxSpecies) | |
| - Iterator ReactionIter = newReactionSet.iterator(); | |
| - while(ReactionIter.hasNext()){ | |
| - Reaction current_reaction = (Reaction)ReactionIter.next(); | |
| - if (current_reaction.contains(maxSpecies)) { | |
| - System.out.println("Library Reaction: " + current_reaction.toString() ); | |
| - } | |
| - } | |
| - | |
| - System.out.println("Generating reactions using reaction family templates."); | |
| - // Iterate through the reaction templates | |
| - newReactionSet.addAll(rxnSystem.getReactionGenerator().react(cerm.getReactedSpeciesSet(),maxSpecies,"All")); | |
| - | |
| - // To remove the duplicates that are found in Reaction Library and Reaction Template | |
| - // Preference given to Reaction Library over Template Reaction | |
| - newReactionSet_nodup = rxnSystem.getLibraryReactionGenerator().RemoveDuplicateReac(newReactionSet); | |
| - } | |
| - else{ | |
| - // When no Reaction Library is present | |
| - System.out.println("Generating reactions using reaction family templates."); | |
| - newReactionSet_nodup = rxnSystem.getReactionGenerator().react(cerm.getReactedSpeciesSet(),maxSpecies,"All"); | |
| - } | |
| - // shamel 6/22/2010 Suppressed output , line is only for debugging | |
| - // System.out.println("Reaction Set For Pdep PdepRME "+newReactionSet_nodup); | |
| - | |
| - Iterator rxnIter = newReactionSet_nodup.iterator(); | |
| - while (rxnIter.hasNext()){ | |
| - Reaction r = (Reaction) rxnIter.next(); | |
| - if (r.getReactantNumber() > 1 && r.getProductNumber() > 1) | |
| - cerm.addReaction(r); | |
| - else { | |
| - cerm.categorizeReaction(r.getStructure()); | |
| - PDepNetwork.addReactionToNetworks(r); | |
| - } | |
| - } | |
| + public void addSpeciesToCore(Species maxSpecies, CoreEdgeReactionModel cerm, ReactionSystem rxnSystem) { | |
| - } | |
| + // Add a species to the core | |
| + System.out.print("\nAdd a new reacted Species to the core: "); | |
| + System.out.println(maxSpecies.getFullName()); | |
| + System.out.println(maxSpecies.toStringWithoutH()); | |
| + Temperature temp = new Temperature(715, "K"); | |
| + double H = maxSpecies.calculateH(temp); | |
| + double S = maxSpecies.calculateS(temp); | |
| + double G = maxSpecies.calculateG(temp); | |
| + double Cp = maxSpecies.calculateCp(temp); | |
| + System.out.println("Thermo of species at 715K (H, S, G, Cp, respectively)\t" + String.valueOf(H) + '\t' + String.valueOf(S) + '\t' + String.valueOf(G) + '\t' + String.valueOf(Cp)); | |
| - } | |
| - else if (object instanceof PDepNetwork) { | |
| + if (cerm.containsAsReactedSpecies(maxSpecies)) | |
| + System.out.println("Species " + maxSpecies.getFullName() + | |
| + " is already present in reaction model"); | |
| + else { | |
| - PDepNetwork maxNetwork = (PDepNetwork) object; | |
| - if ( maxNetwork.getAltered() ) { | |
| - System.out.println("\nNetwork " + maxNetwork.getID() + " has been altered already this step, so will not be expanded until next step."); | |
| - } | |
| - else { | |
| - try { | |
| - PDepIsomer isomer = maxNetwork.getMaxLeakIsomer(ps); | |
| - System.out.println("\nAdd a new included Species: " + isomer.toString() + | |
| - " to network " + maxNetwork.getID()); | |
| - | |
| - // Debug by Mike | |
| - System.out.println("Here's the # of networks: " + PDepNetwork.getNetworks().size()); | |
| - // Making a species included in one network automatically | |
| - // makes it included in all networks it is contained in | |
| - // Therefore we need to merge all networks containing that | |
| - // species as a unimolecular isomer together | |
| - LinkedList<PDepNetwork> networksToRemove = new LinkedList<PDepNetwork>(); | |
| - for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) { | |
| - PDepNetwork pdn = (PDepNetwork) iter.next(); | |
| - if (pdn.contains(isomer.getSpecies(0)) && pdn != maxNetwork) { | |
| - for (int j = 0; j < pdn.getIsomers().size(); j++) | |
| - maxNetwork.addIsomer(pdn.getIsomers().get(j)); | |
| - for (int j = 0; j < pdn.getPathReactions().size(); j++) | |
| - maxNetwork.addReaction(pdn.getPathReactions().get(j),false); | |
| - networksToRemove.add(pdn); | |
| - } | |
| - } | |
| - for (Iterator iter = networksToRemove.iterator(); iter.hasNext(); ) { | |
| - PDepNetwork pdn = (PDepNetwork) iter.next(); | |
| - PDepNetwork.getNetworks().remove(pdn); | |
| - } | |
| - | |
| - // Make the isomer included | |
| - // This will cause any other reactions of the form | |
| - // isomer -> products that don't yet exist to be created | |
| - maxNetwork.makeIsomerIncluded(isomer); | |
| - maxNetwork.updateReactionLists(cerm); | |
| - System.out.println("Here's the # of networks: " + PDepNetwork.getNetworks().size()); | |
| - } | |
| - catch (PDepException e) { | |
| - e.printStackTrace(); | |
| - System.out.println(e.getMessage()); | |
| - System.out.println(maxNetwork.toString()); | |
| - System.exit(0); | |
| - } | |
| - } | |
| + // Move the species and appropriate reactions from the edge to the core | |
| + cerm.moveFromUnreactedToReactedSpecies(maxSpecies); | |
| + cerm.moveFromUnreactedToReactedReaction(); | |
| + | |
| + // Adding a species to the core automatically makes it | |
| + // included in all networks it is contained in | |
| + // Therefore we need to merge all networks containing that | |
| + // species as a unimolecular isomer together | |
| + PDepNetwork network = null; | |
| + LinkedList<PDepNetwork> networksToRemove = new LinkedList<PDepNetwork>(); | |
| + for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) { | |
| + PDepNetwork pdn = (PDepNetwork) iter.next(); | |
| + if (pdn.contains(maxSpecies)) { | |
| + if (network == null) | |
| + network = pdn; // first pdn to contain maxSpecies | |
| + else { // second or later pdn to contain maxSpecies. merge it with network | |
| + for (int j = 0; j < pdn.getIsomers().size(); j++) | |
| + network.addIsomer(pdn.getIsomers().get(j)); | |
| + for (int j = 0; j < pdn.getPathReactions().size(); j++) | |
| + network.addReaction(pdn.getPathReactions().get(j),false); | |
| + networksToRemove.add(pdn); | |
| + } | |
| + } | |
| + } | |
| + if (network != null) { | |
| + network.getIsomer(maxSpecies).setIncluded(true); | |
| + try { | |
| + network.updateReactionLists(cerm); | |
| + } catch (PDepException e) { | |
| + e.printStackTrace(); | |
| + System.out.println(e.getMessage()); | |
| + System.err.println("WARNING: Attempt to update reaction list failed " + | |
| + "for the following network:\n" + network.toString()); | |
| + System.exit(0); | |
| + } | |
| + } | |
| + | |
| + // Generate new reaction set; partition into core and edge | |
| + LinkedHashSet newReactionSet_nodup; | |
| + if(rxnSystem.getLibraryReactionGenerator().getReactionLibrary() != null){ | |
| + | |
| + System.out.println("Checking Reaction Library "+rxnSystem.getLibraryReactionGenerator().getReactionLibrary().getName()+" for reactions of "+maxSpecies.getFullName()+" with the core."); | |
| + // At this point the core (cerm.getReactedSpeciesSet()) already contains maxSpecies, so we can just react the entire core. | |
| + LinkedHashSet newReactionSet = rxnSystem.getLibraryReactionGenerator().react(cerm.getReactedSpeciesSet()); | |
| + //LinkedHashSet newReactionSet = rxnSystem.getLibraryReactionGenerator().react(cerm.getReactedSpeciesSet(),maxSpecies,"All"); | |
| + | |
| + // Report only those that contain the new species (maxSpecies) | |
| + Iterator ReactionIter = newReactionSet.iterator(); | |
| + while(ReactionIter.hasNext()){ | |
| + Reaction current_reaction = (Reaction)ReactionIter.next(); | |
| + if (current_reaction.contains(maxSpecies)) { | |
| + System.out.println("Library Reaction: " + current_reaction.toString() ); | |
| + } | |
| + } | |
| + | |
| + System.out.println("Generating reactions using reaction family templates."); | |
| + // Iterate through the reaction templates | |
| + newReactionSet.addAll(rxnSystem.getReactionGenerator().react(cerm.getReactedSpeciesSet(),maxSpecies,"All")); | |
| + | |
| + // To remove the duplicates that are found in Reaction Library and Reaction Template | |
| + // Preference given to Reaction Library over Template Reaction | |
| + newReactionSet_nodup = rxnSystem.getLibraryReactionGenerator().RemoveDuplicateReac(newReactionSet); | |
| + } | |
| + else{ | |
| + // When no Reaction Library is present | |
| + System.out.println("Generating reactions using reaction family templates."); | |
| + newReactionSet_nodup = rxnSystem.getReactionGenerator().react(cerm.getReactedSpeciesSet(),maxSpecies,"All"); | |
| + } | |
| + // shamel 6/22/2010 Suppressed output , line is only for debugging | |
| + // System.out.println("Reaction Set For Pdep PdepRME "+newReactionSet_nodup); | |
| + | |
| + Iterator rxnIter = newReactionSet_nodup.iterator(); | |
| + while (rxnIter.hasNext()){ | |
| + Reaction r = (Reaction) rxnIter.next(); | |
| + if (r.getReactantNumber() > 1 && r.getProductNumber() > 1) | |
| + cerm.addReaction(r); | |
| + else { | |
| + cerm.categorizeReaction(r.getStructure()); | |
| + PDepNetwork.addReactionToNetworks(r); | |
| + } | |
| + } | |
| + | |
| + } | |
| + | |
| + System.out.println(""); | |
| + | |
| + } | |
| + | |
| + public void makeSpeciesIncluded(Species species, CoreEdgeReactionModel cerm, ReactionSystem rxnSystem) { | |
| + | |
| + LinkedList<PDepNetwork> networksToRemove = new LinkedList<PDepNetwork>(); | |
| + | |
| + // Find the networks that this species occurs in as a nonincluded isomer | |
| + // There should be at least one | |
| + for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) { | |
| + PDepNetwork network = (PDepNetwork) iter.next(); | |
| + if (network.contains(species)) { | |
| + PDepIsomer isomer = network.getIsomer(species); | |
| + if (isomer.isUnimolecular() && !isomer.getIncluded()) { | |
| + networksToRemove.add(network); | |
| + if (network.getAltered()) { | |
| + System.out.println("\nNetwork " + network.getID() + " has been altered already this step, so will not be expanded until next step."); | |
| + return; | |
| + } | |
| + } else { | |
| + System.out.println("Isomer " + species.toString() + " is in network #" + network.getID() + | |
| + ", but is not unimolecular AND nonIncluded,\n\tso RMG will not remove this network."); | |
| + } | |
| } | |
| - else | |
| - continue; | |
| - | |
| - System.out.println(""); | |
| + } | |
| + | |
| + // Keep the first identified network; remove the others | |
| + PDepNetwork maxNetwork = networksToRemove.get(0); | |
| + networksToRemove.remove(0); | |
| + | |
| + try { | |
| + | |
| + // Debug by Mike | |
| + System.out.println("Here's the # of networks: " + PDepNetwork.getNetworks().size()); | |
| + // Making a species included in one network automatically | |
| + // makes it included in all networks it is contained in | |
| + // Therefore we need to merge all networks containing that | |
| + // species as a unimolecular isomer together | |
| + for (Iterator iter = networksToRemove.iterator(); iter.hasNext(); ) { | |
| + PDepNetwork pdn = (PDepNetwork) iter.next(); | |
| + PDepNetwork.getNetworks().remove(pdn); | |
| + } | |
| + | |
| + // Make the isomer included | |
| + // This will cause any other reactions of the form | |
| + // isomer -> products that don't yet exist to be created | |
| + maxNetwork.makeIsomerIncluded(maxNetwork.getIsomer(species)); | |
| + maxNetwork.updateReactionLists(cerm); | |
| + System.out.println("Here's the # of networks: " + PDepNetwork.getNetworks().size()); | |
| + } | |
| + catch (PDepException e) { | |
| + e.printStackTrace(); | |
| + System.out.println(e.getMessage()); | |
| + System.out.println(maxNetwork.toString()); | |
| + System.exit(0); | |
| } | |
| - | |
| - } | |
| - | |
| - | |
| + System.out.println(""); | |
| + } | |
| } | |
| diff --git a/source/RMG/jing/rxnSys/RateBasedPDepVT.java b/source/RMG/jing/rxnSys/RateBasedPDepVT.java | |
| index dfbdd1e..28c8395 100644 | |
| --- a/source/RMG/jing/rxnSys/RateBasedPDepVT.java | |
| +++ b/source/RMG/jing/rxnSys/RateBasedPDepVT.java | |
| @@ -67,14 +67,14 @@ public class RateBasedPDepVT extends RateBasedVT { | |
| PresentStatus ps = p_reactionSystem.getPresentStatus(); | |
| calculateRmin(ps); | |
| - for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) { | |
| - PDepNetwork pdn = (PDepNetwork )iter.next(); | |
| - if (pdn.getLeakFlux(ps) > Rmin) | |
| - { | |
| - System.out.println("Exceeded largest permitted flux for convergence (tolerance="+tolerance+"): " + Rmin); | |
| + CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionSystem.getReactionModel(); | |
| + double[] leakFlux = PDepNetwork.getSpeciesLeakFluxes(ps, cerm); | |
| + for (Iterator iter = cerm.getUnreactedSpeciesSet().iterator(); iter.hasNext(); ) { | |
| + Species us = (Species) iter.next(); | |
| + if (leakFlux[us.getID()] > Rmin) { | |
| + System.out.println("Leak flux exceeded largest permitted flux for convergence (tolerance="+tolerance+"): " + Rmin); | |
| return false; | |
| } | |
| - | |
| } | |
| return true; | |
| diff --git a/source/RMG/jing/rxnSys/RateBasedRME.java b/source/RMG/jing/rxnSys/RateBasedRME.java | |
| index 41d4fe5..d151359 100644 | |
| --- a/source/RMG/jing/rxnSys/RateBasedRME.java | |
| +++ b/source/RMG/jing/rxnSys/RateBasedRME.java | |
| @@ -112,9 +112,8 @@ public class RateBasedRME implements ReactionModelEnlarger { | |
| Species newCoreSpecies = (Species) nextList.get(i); | |
| if (cerm.containsAsReactedSpecies(newCoreSpecies)) //throw new InvalidNextCandidateSpeciesException(); | |
| { | |
| - System.out.println("Species " + newCoreSpecies.getName() + "(" + | |
| - Integer.toString(newCoreSpecies.getID()) + | |
| - ") is already present in reaction model"); | |
| + System.out.println("Species " + newCoreSpecies.getFullName() + | |
| + " is already present in reaction model"); | |
| } else { | |
| double findSpeciesTime = (System.currentTimeMillis() - startTime) / 1000 / 60; | |
| @@ -123,7 +122,7 @@ public class RateBasedRME implements ReactionModelEnlarger { | |
| //Global.diagnosticInfo.append(next.getChemkinName() + "\t" + maxflux + "\t" + ((RateBasedVT) ((ReactionSystem) p_reactionSystemList.get(i)).finishController.validityTester).Rmin + "\t" + findSpeciesTime + "\t"); | |
| System.out.print("\nAdd a new reacted Species:"); | |
| - System.out.println(newCoreSpecies.getName()); | |
| + System.out.println(newCoreSpecies.getFullName()); | |
| Temperature temp = new Temperature(298, "K"); | |
| double H = newCoreSpecies.calculateH(temp); | |
| double S = newCoreSpecies.calculateS(temp); | |
| @@ -151,7 +150,7 @@ public class RateBasedRME implements ReactionModelEnlarger { | |
| ReactionSystem rxnSystem = (ReactionSystem) p_reactionSystemList.get(i); | |
| // Check Reaction Library | |
| if(rxnSystem.getLibraryReactionGenerator().getReactionLibrary() != null){ | |
| - System.out.println("Checking Reaction Library "+rxnSystem.getLibraryReactionGenerator().getReactionLibrary().getName()+" for reactions of "+newCoreSpecies.getName()+" with the core."); | |
| + System.out.println("Checking Reaction Library "+rxnSystem.getLibraryReactionGenerator().getReactionLibrary().getName()+" for reactions of "+newCoreSpecies.getFullName()+" with the core."); | |
| // At this point the core (cerm.getReactedSpeciesSet()) already contains newCoreSpecies, so we can just react the entire core. | |
| LinkedHashSet newReactionSet = rxnSystem.getLibraryReactionGenerator().react(cerm.getReactedSpeciesSet()); | |
| @@ -301,9 +300,9 @@ public class RateBasedRME implements ReactionModelEnlarger { | |
| if (conc<0) { | |
| double aTol = ReactionModelGenerator.getAtol(); | |
| //if (Math.abs(conc) < aTol) conc = 0; | |
| - //else throw new NegativeConcentrationException(spe.getName() + ": " + String.valueOf(conc)); | |
| + //else throw new NegativeConcentrationException(spe.getFullName() + ": " + String.valueOf(conc)); | |
| if (conc < -100.0 * aTol) | |
| - throw new NegativeConcentrationException("Species " + spe.getName() + " has negative concentration: " + String.valueOf(conc)); | |
| + throw new NegativeConcentrationException("Species " + spe.getFullName() + " has negative concentration: " + String.valueOf(conc)); | |
| } | |
| flux *= conc; | |
| } | |
| @@ -324,7 +323,7 @@ public class RateBasedRME implements ReactionModelEnlarger { | |
| System.out.print("Time: "); | |
| System.out.println(p_presentStatus.getTime()); | |
| - System.out.println("Unreacted species " + maxSpecies.getName() + " has highest flux: " + String.valueOf(maxFlux)); | |
| + System.out.println("Unreacted species " + maxSpecies.getFullName() + " has highest flux: " + String.valueOf(maxFlux)); | |
| System.out.println("The total number of unreacted reactions with this species is "+reactionWithSpecies+". Significant ones are:"); | |
| Iterator reactionIter = significantReactions.keySet().iterator(); | |
| while (reactionIter.hasNext()){ | |
| diff --git a/source/RMG/jing/rxnSys/ReactionModelGenerator.java b/source/RMG/jing/rxnSys/ReactionModelGenerator.java | |
| index 4329dab..03e62b0 100644 | |
| --- a/source/RMG/jing/rxnSys/ReactionModelGenerator.java | |
| +++ b/source/RMG/jing/rxnSys/ReactionModelGenerator.java | |
| @@ -133,6 +133,7 @@ public class ReactionModelGenerator { | |
| protected static int maxEdgeSpeciesAfterPruning; | |
| public int limitingReactantID = 1; | |
| + public int numberOfEquivalenceRatios = 0; | |
| //## operation ReactionModelGenerator() | |
| public ReactionModelGenerator() { | |
| @@ -740,8 +741,8 @@ public class ReactionModelGenerator { | |
| while (st.hasMoreTokens()) { | |
| String name = st.nextToken(); | |
| Species spe = (Species)speciesSet.get(name); | |
| + if (spe == null) throw new InvalidConversionException("Unknown reactant in 'Goal Conversion' field of input file : " + name); | |
| setLimitingReactantID(spe.getID()); | |
| - if (spe == null) throw new InvalidConversionException("Unknown reactant: " + name); | |
| String conv = st.nextToken(); | |
| double conversion; | |
| try { | |
| @@ -1399,8 +1400,9 @@ public class ReactionModelGenerator { | |
| ReactionSystem rs = (ReactionSystem)reactionSystemList.get(i); | |
| ReactionTime begin = (ReactionTime)beginList.get(i); | |
| ReactionTime end = (ReactionTime)endList.get(i); | |
| - endList.set(i,rs.solveReactionSystem(begin, end, true, true, true, iterationNumber-1)); | |
| - Chemkin.writeChemkinInputFile(rs); | |
| + LinkedHashSet seedmechnonpdeprxns = extractSeedMechRxnsIfTheyExist(); | |
| + endList.set(i,rs.solveReactionSystem(begin, end, true, true, true, iterationNumber-1,seedmechnonpdeprxns)); | |
| + Chemkin.writeChemkinInputFile(rs, seedmechnonpdeprxns); | |
| boolean terminated = rs.isReactionTerminated(); | |
| terminatedList.add(terminated); | |
| if(!terminated) | |
| @@ -1530,7 +1532,8 @@ public class ReactionModelGenerator { | |
| boolean conditionChanged = (Boolean)conditionChangedList.get(i); | |
| ReactionTime begin = (ReactionTime)beginList.get(i); | |
| ReactionTime end = (ReactionTime)endList.get(i); | |
| - endList.set(i,rs.solveReactionSystem(begin, end, false, reactionChanged, conditionChanged, iterationNumber-1)); | |
| + LinkedHashSet seedmechnonpdeprxns = extractSeedMechRxnsIfTheyExist(); | |
| + endList.set(i,rs.solveReactionSystem(begin, end, false, reactionChanged, conditionChanged, iterationNumber-1,seedmechnonpdeprxns)); | |
| //end = reactionSystem.solveReactionSystem(begin, end, false, reactionChanged, conditionChanged, iterationNumber-1); | |
| } | |
| solverMin = solverMin + (System.currentTimeMillis()-startTime)/1000/60; | |
| @@ -1540,7 +1543,8 @@ public class ReactionModelGenerator { | |
| // we over-write the chemkin file each time, so only the LAST reaction system is saved | |
| // i.e. if you are using RATE for pdep, only the LAST pressure is used. | |
| ReactionSystem rs = (ReactionSystem)reactionSystemList.get(i); | |
| - Chemkin.writeChemkinInputFile(rs); | |
| + LinkedHashSet seedmechnonpdeprxns = extractSeedMechRxnsIfTheyExist(); | |
| + Chemkin.writeChemkinInputFile(rs,seedmechnonpdeprxns); | |
| } | |
| //9/1/09 gmagoon: if we are using QM, output a file with the CHEMKIN name, the RMG name, the (modified) InChI, and the (modified) InChIKey | |
| if (ChemGraph.useQM){ | |
| @@ -1579,15 +1583,16 @@ public class ReactionModelGenerator { | |
| System.out.println("At this time: " + ((ReactionTime)endList.get(i)).toString()); | |
| Species spe = SpeciesDictionary.getSpeciesFromID(getLimitingReactantID()); | |
| double conv = rs.getPresentConversion(spe); | |
| - System.out.print("Conversion of " + spe.getName() + " is:"); | |
| + System.out.print("Conversion of " + spe.getFullName() + " is:"); | |
| System.out.println(conv); | |
| } | |
| System.out.println("Running Time is: " + String.valueOf((System.currentTimeMillis()-tAtInitialization)/1000/60) + " minutes."); | |
| printModelSize(); | |
| - | |
| + printMemoryUsed(); | |
| + | |
| startTime = System.currentTimeMillis(); | |
| - double mU = memoryUsed(); | |
| + double mU = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); | |
| double gc = (System.currentTimeMillis()-startTime)/1000/60; | |
| startTime = System.currentTimeMillis(); | |
| @@ -1660,7 +1665,8 @@ public class ReactionModelGenerator { | |
| boolean conditionChanged = (Boolean)conditionChangedList.get(i); | |
| ReactionTime begin = (ReactionTime)beginList.get(i); | |
| ReactionTime end = (ReactionTime)endList.get(i); | |
| - endList.set(i,rs.solveReactionSystem(begin, end, false, reactionChanged, false, iterationNumber-1)); | |
| + LinkedHashSet seedmechnonpdeprxns = extractSeedMechRxnsIfTheyExist(); | |
| + endList.set(i,rs.solveReactionSystem(begin, end, false, reactionChanged, false, iterationNumber-1,seedmechnonpdeprxns)); | |
| // end = reactionSystem.solveReactionSystem(begin, end, false, reactionChanged, false, iterationNumber-1); | |
| } | |
| solverMin = solverMin + (System.currentTimeMillis()-startTime)/1000/60; | |
| @@ -1720,7 +1726,7 @@ public class ReactionModelGenerator { | |
| System.out.println("At this reaction time: " + ((ReactionTime)endList.get(i)).toString()); | |
| Species spe = SpeciesDictionary.getSpeciesFromID(getLimitingReactantID()); | |
| double conv = rs.getPresentConversion(spe); | |
| - System.out.print("Conversion of " + spe.getName() + " is:"); | |
| + System.out.print("Conversion of " + spe.getFullName() + " is:"); | |
| System.out.println(conv); | |
| } | |
| //System.out.println("At this time: " + end.toString()); | |
| @@ -1729,21 +1735,8 @@ public class ReactionModelGenerator { | |
| //System.out.print("current conversion = "); | |
| //System.out.println(conv); | |
| - Runtime runTime = Runtime.getRuntime(); | |
| - System.out.print("Memory used: "); | |
| - System.out.println(runTime.totalMemory()); | |
| - System.out.print("Free memory: "); | |
| - System.out.println(runTime.freeMemory()); | |
| + printMemoryUsed(); | |
| - //runTime.gc(); | |
| - /* if we're not calling runTime.gc() then don't bother printing this: | |
| - System.out.println("After garbage collection:"); | |
| - System.out.print("Memory used: "); | |
| - System.out.println(runTime.totalMemory()); | |
| - System.out.print("Free memory: "); | |
| - System.out.println(runTime.freeMemory()); | |
| - */ | |
| - | |
| printModelSize(); | |
| } | |
| @@ -1785,7 +1778,8 @@ public class ReactionModelGenerator { | |
| //terminated = false; | |
| ReactionTime begin = (ReactionTime)beginList.get(i); | |
| ReactionTime end = (ReactionTime)endList.get(i); | |
| - rs.solveReactionSystemwithSEN(begin, end, true, false, false); | |
| + LinkedHashSet seedmechnonpdeprxns = extractSeedMechRxnsIfTheyExist(); | |
| + rs.solveReactionSystemwithSEN(begin, end, true, false, false, seedmechnonpdeprxns); | |
| //reactionSystem.solveReactionSystemwithSEN(begin, end, true, false, false); | |
| } | |
| @@ -1794,7 +1788,8 @@ public class ReactionModelGenerator { | |
| // All of the reaction systems are the same, so just write the chemkin | |
| // file for the first reaction system | |
| ReactionSystem rs = (ReactionSystem)reactionSystemList.get(0); | |
| - Chemkin.writeChemkinInputFile(getReactionModel(),rs.getPresentStatus()); | |
| + LinkedHashSet seedmechnonpdeprxns = extractSeedMechRxnsIfTheyExist(); | |
| + Chemkin.writeChemkinInputFile(getReactionModel(),rs.getPresentStatus(),seedmechnonpdeprxns); | |
| //9/1/09 gmagoon: if we are using QM, output a file with the CHEMKIN name, the RMG name, the (modified) InChI, and the (modified) InChIKey | |
| if (ChemGraph.useQM){ | |
| @@ -2187,7 +2182,7 @@ public class ReactionModelGenerator { | |
| System.gc(); | |
| } | |
| - public static long memoryUsed(){ | |
| + public static void printMemoryUsed(){ | |
| garbageCollect(); | |
| Runtime rT = Runtime.getRuntime(); | |
| long uM, tM, fM; | |
| @@ -2196,11 +2191,9 @@ public class ReactionModelGenerator { | |
| uM = tM - fM; | |
| System.out.println("After garbage collection:"); | |
| System.out.print("Memory used: "); | |
| - System.out.println(tM); | |
| + System.out.println(uM); | |
| System.out.print("Free memory: "); | |
| System.out.println(fM); | |
| - | |
| - return uM; | |
| } | |
| private HashSet readIncludeSpecies(String fileName) { | |
| @@ -2565,7 +2558,7 @@ public class ReactionModelGenerator { | |
| bw = new BufferedWriter(new FileWriter("Restart/edgeSpecies.txt")); | |
| for(Iterator iter=((CoreEdgeReactionModel)getReactionModel()).getUnreactedSpeciesSet().iterator();iter.hasNext();){ | |
| Species species = (Species) iter.next(); | |
| - bw.write(species.getName()+"("+species.getID()+")"); | |
| + bw.write(species.getFullName()); | |
| bw.newLine(); | |
| int dummyInt = 0; | |
| bw.write(species.getChemGraph().toString(dummyInt)); | |
| @@ -2651,7 +2644,7 @@ public class ReactionModelGenerator { | |
| bw = new BufferedWriter(new FileWriter("Restart/coreSpecies.txt")); | |
| for(Iterator iter=getReactionModel().getSpecies();iter.hasNext();){ | |
| Species species = (Species) iter.next(); | |
| - bw.write(species.getName()+"("+species.getID()+")"); | |
| + bw.write(species.getFullName()); | |
| bw.newLine(); | |
| int dummyInt = 0; | |
| bw.write(species.getChemGraph().toString(dummyInt)); | |
| @@ -2837,12 +2830,10 @@ public class ReactionModelGenerator { | |
| LinkedList allNets = PDepNetwork.getNetworks(); | |
| - int netCounter = 0; | |
| for(Iterator iter=allNets.iterator(); iter.hasNext();){ | |
| PDepNetwork pdepnet = (PDepNetwork) iter.next(); | |
| - ++netCounter; | |
| - bw.write("PDepNetwork #" + netCounter); | |
| + bw.write("PDepNetwork #" + pdepnet.getID()); | |
| bw.newLine(); | |
| // Write netReactionList | |
| @@ -4026,9 +4017,9 @@ public class ReactionModelGenerator { | |
| (((CoreEdgeReactionModel)reactionModel).getEdge().getSpeciesNumber()+reactionModel.getSpeciesNumber())>= minSpeciesForPruning){ | |
| int numberToBePruned = ((CoreEdgeReactionModel)reactionModel).getEdge().getSpeciesNumber() - maxEdgeSpeciesAfterPruning; | |
| - System.out.println("PDep Pruning DEBUG:\nThe number of species in the model's edge, before pruning: " + ((CoreEdgeReactionModel)reactionModel).getEdge().getSpeciesNumber()); | |
| - System.out.println("PDep Pruning DEBUG:\nRMG thinks the following number of species" + | |
| - " needs to be pruned: " + numberToBePruned); | |
| + //System.out.println("PDep Pruning DEBUG:\nThe number of species in the model's edge, before pruning: " + ((CoreEdgeReactionModel)reactionModel).getEdge().getSpeciesNumber()); | |
| + //System.out.println("PDep Pruning DEBUG:\nRMG thinks the following number of species" + | |
| + // " needs to be pruned: " + numberToBePruned); | |
| Iterator iter = JDAS.edgeID.keySet().iterator();//determine the maximum edge flux ratio for each edge species | |
| while(iter.hasNext()){ | |
| Species spe = (Species)iter.next(); | |
| @@ -4046,10 +4037,51 @@ public class ReactionModelGenerator { | |
| prunableSpeciesMap.put(spe, maxmaxRatio); | |
| } | |
| } | |
| + //repeat with the edgeLeakID; if a species appears in both lists, it will be prunable only if it is prunable in both cases, and the sum of maximum edgeFlux + maximum edgeLeakFlux (for each reaction system) will be considered; this will be a conservative overestimate of maximum (edgeFlux+edgeLeakFlux) | |
| + iter = JDAS.edgeLeakID.keySet().iterator(); | |
| + while(iter.hasNext()){ | |
| + Species spe = (Species)iter.next(); | |
| + Integer id = (Integer)JDAS.edgeLeakID.get(spe); | |
| + //check whether the same species is in edgeID | |
| + if(JDAS.edgeID.containsKey(spe)){//the species exists in edgeID | |
| + if(prunableSpeciesMap.containsKey(spe)){//the species was determined to be "prunable" based on edgeID | |
| + Integer idEdge=(Integer)JDAS.edgeID.get(spe); | |
| + double maxmaxRatio = ds0.maxEdgeFluxRatio[id-1]+ds0.maxEdgeFluxRatio[idEdge-1]; | |
| + boolean prunable = ds0.prunableSpecies[id-1]; | |
| + //go through the rest of the reaction systems to see if there are higher max flux ratios | |
| + for (Integer i = 1; i < reactionSystemList.size(); i++) { | |
| + JDAS ds = (JDAS)((ReactionSystem) reactionSystemList.get(i)).getDynamicSimulator(); | |
| + if(ds.maxEdgeFluxRatio[id-1]+ds.maxEdgeFluxRatio[idEdge-1] > maxmaxRatio) maxmaxRatio = ds.maxEdgeFluxRatio[id-1]+ds.maxEdgeFluxRatio[idEdge-1]; | |
| + if(!ds.prunableSpecies[id-1]) prunable = false;// probably redundant: if the conc. is zero in one system, it should be zero in all systems, but it is included for completeness | |
| + } | |
| + if( prunable){//if the species is "prunable" (i.e. it doesn't have any reactions producing it with zero flux), replace with the newly determined maxmaxRatio | |
| + prunableSpeciesMap.remove(spe); | |
| + prunableSpeciesMap.put(spe, maxmaxRatio); | |
| + } | |
| + else{//otherwise, the species is not prunable in both edgeID and edgeLeakID and should be removed from the prunable species map | |
| + prunableSpeciesMap.remove(spe); | |
| + } | |
| + } | |
| + } | |
| + else{//the species is new | |
| + double maxmaxRatio = ds0.maxEdgeFluxRatio[id-1]; | |
| + boolean prunable = ds0.prunableSpecies[id-1]; | |
| + //go through the rest of the reaction systems to see if there are higher max flux ratios | |
| + for (Integer i = 1; i < reactionSystemList.size(); i++) { | |
| + JDAS ds = (JDAS)((ReactionSystem) reactionSystemList.get(i)).getDynamicSimulator(); | |
| + if(ds.maxEdgeFluxRatio[id-1] > maxmaxRatio) maxmaxRatio = ds.maxEdgeFluxRatio[id-1]; | |
| + if(!ds.prunableSpecies[id-1]) prunable = false;// probably redundant: if the conc. is zero in one system, it should be zero in all systems, but it is included for completeness | |
| + } | |
| + //if the species is "prunable" (i.e. it doesn't have any reactions producing it with zero flux), add it to the prunableSpeciesMap | |
| + if( prunable){ | |
| + prunableSpeciesMap.put(spe, maxmaxRatio); | |
| + } | |
| + } | |
| + } | |
| // at this point prunableSpeciesMap includes ALL prunable species, no matter how large their flux | |
| - System.out.println("PDep Pruning DEBUG:\nRMG has marked the following number of species" + | |
| - " as prunable, before checking against explored (included) species: " + prunableSpeciesMap.size()); | |
| + //System.out.println("PDep Pruning DEBUG:\nRMG has marked the following number of species" + | |
| + // " as prunable, before checking against explored (included) species: " + prunableSpeciesMap.size()); | |
| // Pressure dependence only: Species that are included in any | |
| // PDepNetwork are not eligible for pruning, so they must be removed | |
| @@ -4066,8 +4098,8 @@ public class ReactionModelGenerator { | |
| } | |
| } | |
| - System.out.println("PDep Pruning DEBUG:\nRMG now reduced the number of prunable species," + | |
| - " after checking against explored (included) species, to: " + prunableSpeciesMap.size()); | |
| + //System.out.println("PDep Pruning DEBUG:\nRMG now reduced the number of prunable species," + | |
| + // " after checking against explored (included) species, to: " + prunableSpeciesMap.size()); | |
| // sort the prunableSpecies by maxmaxRatio | |
| // i.e. sort the map by values | |
| @@ -4099,10 +4131,10 @@ public class ReactionModelGenerator { | |
| else break; // no more to be pruned | |
| } | |
| - System.out.println("PDep Pruning DEBUG:\nRMG has marked the following number of species" + | |
| - " to be pruned due to max flux ratio lower than threshold: " + belowThreshold); | |
| - System.out.println("PDep Pruning DEBUG:\nRMG has marked the following number of species" + | |
| - " to be pruned due to low max flux ratio : " + lowMaxFlux); | |
| + //System.out.println("PDep Pruning DEBUG:\nRMG has marked the following number of species" + | |
| + // " to be pruned due to max flux ratio lower than threshold: " + belowThreshold); | |
| + //System.out.println("PDep Pruning DEBUG:\nRMG has marked the following number of species" + | |
| + // " to be pruned due to low max flux ratio : " + lowMaxFlux); | |
| //now, speciesToPrune has been filled with species that should be pruned from the edge | |
| System.out.println("Pruning..."); | |
| @@ -4286,7 +4318,7 @@ public class ReactionModelGenerator { | |
| } | |
| } | |
| } | |
| - System.out.println("PDep Pruning DEBUG:\nThe number of species in the model's edge, after pruning: " + ((CoreEdgeReactionModel)reactionModel).getEdge().getSpeciesNumber()); | |
| + //System.out.println("PDep Pruning DEBUG:\nThe number of species in the model's edge, after pruning: " + ((CoreEdgeReactionModel)reactionModel).getEdge().getSpeciesNumber()); | |
| return; | |
| } | |
| @@ -4890,6 +4922,7 @@ public class ReactionModelGenerator { | |
| } | |
| //System.out.println(name); | |
| Species species = Species.make(name,cg); | |
| + int numConcentrations = 0; // The number of concentrations read-in for each species | |
| // The remaining tokens are either: | |
| // The desired concentrations | |
| @@ -4923,14 +4956,26 @@ public class ReactionModelGenerator { | |
| else if (!unit.equals("mole/cm3") && !unit.equals("mol/cm3")) { | |
| throw new InvalidUnitException("Species Concentration in condition.txt!"); | |
| } | |
| + SpeciesStatus ss = new SpeciesStatus(species,1,concentration,0.0); | |
| + speciesStatus.put(numSpeciesStatus, ss); | |
| + ++numSpeciesStatus; | |
| + ++numConcentrations; | |
| } | |
| } | |
| + // Check if the number of concentrations read in is consistent with all previous | |
| + // concentration counts. The first time this function is called, the variable | |
| + // numberOfEquivalenceRatios will be initialized. | |
| + boolean goodToGo = areTheNumberOfConcentrationsConsistent(numConcentrations); | |
| + if (!goodToGo) { | |
| + System.out.println("\n\nThe number of concentrations (" + numConcentrations + ") supplied for species " + species.getName() + | |
| + "\nis not consistent with the number of concentrations (" + numberOfEquivalenceRatios + ") " + | |
| + "supplied for all previously read-in species \n\n" + | |
| + "Terminating RMG simulation."); | |
| + System.exit(0); | |
| + } | |
| // Make a SpeciesStatus and store it in the LinkedHashMap | |
| // double flux = 0; | |
| -// int species_type = 1; // reacted species | |
| - SpeciesStatus ss = new SpeciesStatus(species,1,concentration,0.0); | |
| - speciesStatus.put(numSpeciesStatus, ss); | |
| - ++numSpeciesStatus; | |
| +// int species_type = 1; // reacted species | |
| species.setReactivity(IsReactive); // GJB | |
| species.setConstantConcentration(IsConstantConcentration); | |
| @@ -4977,6 +5022,7 @@ public class ReactionModelGenerator { | |
| // The remaining tokens are concentrations | |
| double inertConc = 0.0; | |
| int counter = 0; | |
| + int numberOfConcentrations = 0; | |
| while (st.hasMoreTokens()) { | |
| String conc = st.nextToken(); | |
| inertConc = Double.parseDouble(conc); | |
| @@ -5006,6 +5052,19 @@ public class ReactionModelGenerator { | |
| ((InitialStatus)initialStatusList.get(isIndex)).putInertGas(name,inertConc); | |
| } | |
| ++counter; | |
| + ++numberOfConcentrations; | |
| + } | |
| + | |
| + // Check if the number of concentrations read in is consistent with all previous | |
| + // concentration counts. The first time this function is called, the variable | |
| + // numberOfEquivalenceRatios will be initialized. | |
| + boolean goodToGo = areTheNumberOfConcentrationsConsistent(numberOfConcentrations); | |
| + if (!goodToGo) { | |
| + System.out.println("\n\nThe number of concentrations (" + numberOfConcentrations + ") supplied for species " + name + | |
| + "\nis not consistent with the number of concentrations (" + numberOfEquivalenceRatios + ") " + | |
| + "supplied for all previously read-in species \n\n" + | |
| + "Terminating RMG simulation."); | |
| + System.exit(0); | |
| } | |
| line = ChemParser.readMeaningfulLine(reader, true); | |
| @@ -5225,6 +5284,21 @@ public class ReactionModelGenerator { | |
| System.out.println("The model edge has " + Integer.toString(numberOfEdgeReactions) + " reactions and "+ Integer.toString(numberOfEdgeSpecies) + " species."); | |
| } | |
| + | |
| + public boolean areTheNumberOfConcentrationsConsistent(int number) { | |
| + if (numberOfEquivalenceRatios == 0) numberOfEquivalenceRatios = number; | |
| + else { | |
| + if (number == numberOfEquivalenceRatios) return true; | |
| + else return false; | |
| + } | |
| + return true; | |
| + } | |
| + | |
| + public LinkedHashSet extractSeedMechRxnsIfTheyExist() { | |
| + LinkedHashSet seedmechnonpdeprxns = new LinkedHashSet(); | |
| + if (seedMechanism != null) seedmechnonpdeprxns = seedMechanism.getReactionSet(); | |
| + return seedmechnonpdeprxns; | |
| + } | |
| } | |
| /********************************************************************* | |
| File Path : RMG\RMG\jing\rxnSys\ReactionModelGenerator.java | |
| diff --git a/source/RMG/jing/rxnSys/ReactionSystem.java b/source/RMG/jing/rxnSys/ReactionSystem.java | |
| index 82d14f9..b2a22ea 100644 | |
| --- a/source/RMG/jing/rxnSys/ReactionSystem.java | |
| +++ b/source/RMG/jing/rxnSys/ReactionSystem.java | |
| @@ -244,7 +244,7 @@ public class ReactionSystem { | |
| // if (p_systemSnapshot.getSpeciesStatus(spe) != null) | |
| // conc = (p_systemSnapshot.getSpeciesStatus(spe)).getConcentration(); | |
| // if (conc<0) | |
| -// throw new NegativeConcentrationException(spe.getName() + ": " + String.valueOf(conc)); | |
| +// throw new NegativeConcentrationException(spe.getFullName() + ": " + String.valueOf(conc)); | |
| // flux *= conc; | |
| // | |
| // } | |
| @@ -281,9 +281,9 @@ public class ReactionSystem { | |
| if (conc<0) { | |
| double aTol = ReactionModelGenerator.getAtol(); | |
| //if (Math.abs(conc) < aTol) conc = 0; | |
| - //else throw new NegativeConcentrationException(spe.getName() + ": " + String.valueOf(conc)); | |
| + //else throw new NegativeConcentrationException(spe.getFullName() + ": " + String.valueOf(conc)); | |
| if (conc < -100.0 * aTol) | |
| - throw new NegativeConcentrationException("Species " + spe.getName() + " has negative concentration: " + String.valueOf(conc)); | |
| + throw new NegativeConcentrationException("Species " + spe.getFullName() + " has negative concentration: " + String.valueOf(conc)); | |
| } | |
| flux *= conc; | |
| @@ -392,7 +392,7 @@ public class ReactionSystem { | |
| } | |
| } | |
| - System.out.println("The main pathway to generate " + p_species.getName() + " is "); | |
| + System.out.println("The main pathway to generate " + p_species.getFullName() + " is "); | |
| System.out.println(maxReaction); | |
| System.out.println("The max flux is " + String.valueOf(maxFlux)); | |
| @@ -584,7 +584,7 @@ public class ReactionSystem { | |
| double maxFlux = 0; | |
| Reaction maxReaction = null; | |
| - System.out.println("the consumption paths for " + p_species.getName()); | |
| + System.out.println("the consumption paths for " + p_species.getFullName()); | |
| for (Iterator iter = p_reactionList.iterator(); iter.hasNext(); ) { | |
| Reaction rxn = (Reaction)iter.next(); | |
| if (rxn.containsAsReactant(p_species)) { | |
| @@ -614,7 +614,7 @@ public class ReactionSystem { | |
| } | |
| } | |
| - System.out.println("the formationtion paths for " + p_species.getName()); | |
| + System.out.println("the formationtion paths for " + p_species.getFullName()); | |
| for (Iterator iter = p_reactionList.iterator(); iter.hasNext(); ) { | |
| Reaction rxn = (Reaction)iter.next(); | |
| if (rxn.containsAsProduct(p_species)) { | |
| @@ -690,7 +690,7 @@ public class ReactionSystem { | |
| for (Iterator iter = speSet.iterator(); iter.hasNext(); ) { | |
| Species spe = (Species)iter.next(); | |
| - System.out.println(spe.getName()+"("+String.valueOf(spe.getID())+"): " + spe.getThermoData().toString()); | |
| + System.out.println(spe.getFullName()+": " + spe.getThermoData().toString()); | |
| } | |
| @@ -1478,7 +1478,7 @@ public String printLowerBoundConcentrations(LinkedList p_speciesList) { | |
| //## operation solveReactionSystem(ReactionTime,ReactionTime,boolean,boolean,boolean) | |
| //9/24/07 gmagoon: added p_reactionModel as parameter; subsequently removed | |
| - public ReactionTime solveReactionSystem(ReactionTime p_beginTime, ReactionTime p_endTime, boolean p_initialization, boolean p_reactionChanged, boolean p_conditionChanged, int iterationNum) { | |
| + public ReactionTime solveReactionSystem(ReactionTime p_beginTime, ReactionTime p_endTime, boolean p_initialization, boolean p_reactionChanged, boolean p_conditionChanged, int iterationNum, LinkedHashSet nonpdep_from_seed) { | |
| //#[ operation solveReactionSystem(ReactionTime,ReactionTime,boolean,boolean,boolean) | |
| Temperature t = getTemperatureModel().getTemperature(p_beginTime); | |
| @@ -1497,7 +1497,7 @@ public String printLowerBoundConcentrations(LinkedList p_speciesList) { | |
| if (!beginStatus.getTime().equals(p_beginTime)) throw new InvalidBeginStatusException(); | |
| System.out.println("Solving reaction system..."); | |
| - SystemSnapshot present = getDynamicSimulator().solve(p_initialization, getReactionModel(), p_reactionChanged, beginStatus, p_beginTime, p_endTime,t,p, p_conditionChanged, finishController.terminationTester, iterationNum); | |
| + SystemSnapshot present = getDynamicSimulator().solve(p_initialization, getReactionModel(), p_reactionChanged, beginStatus, p_beginTime, p_endTime,t,p, p_conditionChanged, finishController.terminationTester, iterationNum, nonpdep_from_seed); | |
| appendUnreactedSpeciesStatus(present, t); | |
| @@ -1506,7 +1506,7 @@ public String printLowerBoundConcentrations(LinkedList p_speciesList) { | |
| //#] | |
| } | |
| - public void solveReactionSystemwithSEN(ReactionTime p_beginTime, ReactionTime p_endTime, boolean p_initialization, boolean p_reactionChanged, boolean p_conditionChanged) { | |
| + public void solveReactionSystemwithSEN(ReactionTime p_beginTime, ReactionTime p_endTime, boolean p_initialization, boolean p_reactionChanged, boolean p_conditionChanged, LinkedHashSet nonpdep_from_seed) { | |
| Temperature t = getTemperatureModel().getTemperature(p_beginTime); | |
| Pressure p = getPressureModel().getPressure(p_beginTime); | |
| @@ -1523,7 +1523,7 @@ public String printLowerBoundConcentrations(LinkedList p_speciesList) { | |
| if (!beginStatus.getTime().equals(p_beginTime)) throw new InvalidBeginStatusException(); | |
| System.out.println("Solving reaction system..."); | |
| - LinkedList sS = ((JDASPK)getDynamicSimulator()).solveSEN(p_initialization, getReactionModel(), p_reactionChanged, beginStatus, p_beginTime, p_endTime,t,p, p_conditionChanged, finishController.terminationTester); | |
| + LinkedList sS = ((JDASPK)getDynamicSimulator()).solveSEN(p_initialization, getReactionModel(), p_reactionChanged, beginStatus, p_beginTime, p_endTime,t,p, p_conditionChanged, finishController.terminationTester, nonpdep_from_seed); | |
| for (int i=0; i< sS.size(); i++){ | |
| systemSnapshot.add(sS.get(i)); | |
| diff --git a/source/RMG/jing/rxnSys/SeedMechanism.java b/source/RMG/jing/rxnSys/SeedMechanism.java | |
| index 713314d..a9db16d 100644 | |
| --- a/source/RMG/jing/rxnSys/SeedMechanism.java | |
| +++ b/source/RMG/jing/rxnSys/SeedMechanism.java | |
| @@ -285,139 +285,139 @@ public class SeedMechanism { | |
| if (nextLine == null) { | |
| continueToReadRxn = false; | |
| } else if (nextLine.toLowerCase().contains("troe")) { | |
| - // read in troe parameters | |
| - StringTokenizer st = new StringTokenizer(nextLine, "/"); | |
| - String temp = st.nextToken().trim(); // TROE | |
| - String troeString = st.nextToken().trim(); // List of troe parameters | |
| - st = new StringTokenizer(troeString); | |
| - int n = st.countTokens(); | |
| - if (n != 3 && n != 4) throw new InvalidKineticsFormatException("Troe parameter number = "+n + " for reaction: " + r.toString()); | |
| - | |
| - a = Double.parseDouble(st.nextToken().trim()); | |
| - T3star = Double.parseDouble(st.nextToken().trim()); | |
| - Tstar = Double.parseDouble(st.nextToken().trim()); | |
| + // read in troe parameters | |
| + StringTokenizer st = new StringTokenizer(nextLine, "/"); | |
| + String temp = st.nextToken().trim(); // TROE | |
| + String troeString = st.nextToken().trim(); // List of troe parameters | |
| + st = new StringTokenizer(troeString); | |
| + int n = st.countTokens(); | |
| + if (n != 3 && n != 4) throw new InvalidKineticsFormatException("Troe parameter number = "+n + " for reaction: " + r.toString()); | |
| + | |
| + a = Double.parseDouble(st.nextToken().trim()); | |
| + T3star = Double.parseDouble(st.nextToken().trim()); | |
| + Tstar = Double.parseDouble(st.nextToken().trim()); | |
| + | |
| + if (st.hasMoreTokens()) { | |
| + troe7 = true; | |
| + T2star = Double.parseDouble(st.nextToken().trim()); | |
| + } | |
| + nextLine = ChemParser.readMeaningfulLine(data, true); | |
| + } else if (nextLine.toLowerCase().contains("low")) { | |
| + // read in lindemann parameters | |
| + StringTokenizer st = new StringTokenizer(nextLine, "/"); | |
| + String temp = st.nextToken().trim(); // LOW | |
| + String lowString = st.nextToken().trim(); // Modified Arrhenius parameters | |
| + /* | |
| + * MRH 17Feb2010: | |
| + * The units of the k_zero (LOW) Arrhenius parameters are different from the units of | |
| + * k_inf Arrhenius parameters by a factor of cm3/mol, hence the getReactantNumber()+1 | |
| + */ | |
| + low = ChemParser.parseSimpleArrheniusKinetics(lowString, A_multiplier, E_multiplier, r.getReactantNumber()+1); | |
| + nextLine = ChemParser.readMeaningfulLine(data, true); | |
| + } else if (nextLine.contains("CHEB")) { | |
| + // Read in the Tmin/Tmax and Pmin/Pmax information | |
| + StringTokenizer st_cheb = new StringTokenizer(nextLine,"/"); | |
| + String nextToken = st_cheb.nextToken(); // Should be TCHEB or PCHEB | |
| + StringTokenizer st_minmax = new StringTokenizer(st_cheb.nextToken()); | |
| + double Tmin = 0.0; double Tmax = 0.0; double Pmin = 0.0; double Pmax = 0.0; | |
| + if (nextToken.trim().equals("TCHEB")) { | |
| + Tmin = Double.parseDouble(st_minmax.nextToken()); | |
| + Tmax = Double.parseDouble(st_minmax.nextToken()); | |
| + } else { | |
| + Pmin = Double.parseDouble(st_minmax.nextToken()); | |
| + Pmax = Double.parseDouble(st_minmax.nextToken()); | |
| + } | |
| + nextToken = st_cheb.nextToken(); // Should be PCHEB or TCHEB | |
| + st_minmax = new StringTokenizer(st_cheb.nextToken()); | |
| + if (nextToken.trim().equals("TCHEB")) { | |
| + Tmin = Double.parseDouble(st_minmax.nextToken()); | |
| + Tmax = Double.parseDouble(st_minmax.nextToken()); | |
| + } else { | |
| + Pmin = Double.parseDouble(st_minmax.nextToken()); | |
| + Pmax = Double.parseDouble(st_minmax.nextToken()); | |
| + } | |
| + // Read in the N/M values (number of polynomials in the Temp and Press domain) | |
| + nextLine = ChemParser.readMeaningfulLine(data, true); | |
| + st_cheb = new StringTokenizer(nextLine,"/"); | |
| + nextToken = st_cheb.nextToken(); // Should be CHEB | |
| + st_minmax = new StringTokenizer(st_cheb.nextToken()); | |
| + int numN = Integer.parseInt(st_minmax.nextToken()); | |
| + int numM = Integer.parseInt(st_minmax.nextToken()); | |
| + // Read in the coefficients | |
| + nextLine = ChemParser.readMeaningfulLine(data, true); | |
| + double[] unorderedChebyCoeffs = new double[numN*numM]; | |
| + int chebyCoeffCounter = 0; | |
| + while (nextLine != null && nextLine.contains("CHEB")) { | |
| + st_cheb = new StringTokenizer(nextLine,"/"); | |
| + nextToken = st_cheb.nextToken(); // Should be CHEB | |
| + st_minmax = new StringTokenizer(st_cheb.nextToken()); | |
| + while (st_minmax.hasMoreTokens()) { | |
| + unorderedChebyCoeffs[chebyCoeffCounter] = Double.parseDouble(st_minmax.nextToken()); | |
| + ++chebyCoeffCounter; | |
| + } | |
| + nextLine = ChemParser.readMeaningfulLine(data, true); | |
| + } | |
| + // Order the chebyshev coefficients | |
| + double[][] chebyCoeffs = new double[numN][numM]; | |
| + for (int numRows=0; numRows<numN; numRows++) { | |
| + for (int numCols=0; numCols<numM; numCols++) { | |
| + chebyCoeffs[numRows][numCols] = unorderedChebyCoeffs[numM*numRows+numCols]; | |
| + } | |
| + } | |
| + // Make the ChebyshevPolynomials, PDepReaction, and add to list of PDepReactions | |
| + ChebyshevPolynomials coeffs = new ChebyshevPolynomials( | |
| + numN,new Temperature(Tmin,"K"),new Temperature(Tmax,"K"), | |
| + numM,new Pressure(Pmin,"bar"),new Pressure(Pmax,"bar"), | |
| + chebyCoeffs); | |
| + PDepIsomer reactants = new PDepIsomer(r.getStructure().getReactantList()); | |
| + PDepIsomer products = new PDepIsomer(r.getStructure().getProductList()); | |
| + PDepRateConstant pdepRC = new PDepRateConstant(coeffs); | |
| + PDepReaction pdeprxn = new PDepReaction(reactants,products,pdepRC); | |
| + allPdepNetworks.add(pdeprxn); | |
| + continueToReadRxn = false; | |
| + } else if (nextLine.contains("PLOG")) { | |
| + while (nextLine != null && nextLine.contains("PLOG")) { | |
| + // Increase the PLOG counter | |
| + ++numPLOGs; | |
| + // Store the previous PLOG information in temporary arrays | |
| + Pressure[] previousPressures = new Pressure[numPLOGs]; | |
| + ArrheniusKinetics[] previousKinetics = new ArrheniusKinetics[numPLOGs]; | |
| + for (int previousNumPLOG=0; previousNumPLOG<numPLOGs-1; ++previousNumPLOG) { | |
| + previousPressures[previousNumPLOG] = pdepkineticsPLOG.getPressures(previousNumPLOG); | |
| + previousKinetics[previousNumPLOG] = pdepkineticsPLOG.getKinetics(previousNumPLOG); | |
| + } | |
| + // Read in the new PLOG information, and add this to the temporary array | |
| + PDepArrheniusKinetics newpdepkinetics = parsePLOGline(nextLine); | |
| + previousPressures[numPLOGs-1] = newpdepkinetics.getPressures(0); | |
| + previousKinetics[numPLOGs-1] = newpdepkinetics.getKinetics(0); | |
| + // Re-initialize pdepkinetics and populate with stored information | |
| + pdepkineticsPLOG = new PDepArrheniusKinetics(numPLOGs); | |
| + pdepkineticsPLOG.setPressures(previousPressures); | |
| + pdepkineticsPLOG.setRateCoefficients(previousKinetics); | |
| + // Read the next line | |
| + nextLine = ChemParser.readMeaningfulLine(data, true); | |
| + } | |
| + // Make the PDepReaction | |
| + PDepIsomer reactants = new PDepIsomer(r.getStructure().getReactantList()); | |
| + PDepIsomer products = new PDepIsomer(r.getStructure().getProductList()); | |
| + PDepRateConstant pdepRC = new PDepRateConstant(pdepkineticsPLOG); | |
| + PDepReaction pdeprxn = new PDepReaction(reactants,products,pdepRC); | |
| + // Add to the list of PDepReactions | |
| + allPdepNetworks.add(pdeprxn); | |
| + // Re-initialize the pdepkinetics variable | |
| + numPLOGs = 0; | |
| + pdepkineticsPLOG = new PDepArrheniusKinetics(numPLOGs); | |
| + continueToReadRxn = false; | |
| + } else if (nextLine.contains("/")) { | |
| + // read in third body colliders + efficiencies | |
| + thirdBodyList.putAll(ChemParser.parseThirdBodyList(nextLine,allSpecies)); | |
| + nextLine = ChemParser.readMeaningfulLine(data, true); | |
| + } else { | |
| + // the nextLine is a "new" reaction, hence we need to exit the while loop | |
| + continueToReadRxn = false; | |
| + } | |
| + } | |
| - if (st.hasMoreTokens()) { | |
| - troe7 = true; | |
| - T2star = Double.parseDouble(st.nextToken().trim()); | |
| - } | |
| - nextLine = ChemParser.readMeaningfulLine(data, true); | |
| - } else if (nextLine.toLowerCase().contains("low")) { | |
| - // read in lindemann parameters | |
| - StringTokenizer st = new StringTokenizer(nextLine, "/"); | |
| - String temp = st.nextToken().trim(); // LOW | |
| - String lowString = st.nextToken().trim(); // Modified Arrhenius parameters | |
| - /* | |
| - * MRH 17Feb2010: | |
| - * The units of the k_zero (LOW) Arrhenius parameters are different from the units of | |
| - * k_inf Arrhenius parameters by a factor of cm3/mol, hence the getReactantNumber()+1 | |
| - */ | |
| - low = ChemParser.parseSimpleArrheniusKinetics(lowString, A_multiplier, E_multiplier, r.getReactantNumber()+1); | |
| - nextLine = ChemParser.readMeaningfulLine(data, true); | |
| - } else if (nextLine.contains("CHEB")) { | |
| - // Read in the Tmin/Tmax and Pmin/Pmax information | |
| - StringTokenizer st_cheb = new StringTokenizer(nextLine,"/"); | |
| - String nextToken = st_cheb.nextToken(); // Should be TCHEB or PCHEB | |
| - StringTokenizer st_minmax = new StringTokenizer(st_cheb.nextToken()); | |
| - double Tmin = 0.0; double Tmax = 0.0; double Pmin = 0.0; double Pmax = 0.0; | |
| - if (nextToken.trim().equals("TCHEB")) { | |
| - Tmin = Double.parseDouble(st_minmax.nextToken()); | |
| - Tmax = Double.parseDouble(st_minmax.nextToken()); | |
| - } else { | |
| - Pmin = Double.parseDouble(st_minmax.nextToken()); | |
| - Pmax = Double.parseDouble(st_minmax.nextToken()); | |
| - } | |
| - nextToken = st_cheb.nextToken(); // Should be PCHEB or TCHEB | |
| - st_minmax = new StringTokenizer(st_cheb.nextToken()); | |
| - if (nextToken.trim().equals("TCHEB")) { | |
| - Tmin = Double.parseDouble(st_minmax.nextToken()); | |
| - Tmax = Double.parseDouble(st_minmax.nextToken()); | |
| - } else { | |
| - Pmin = Double.parseDouble(st_minmax.nextToken()); | |
| - Pmax = Double.parseDouble(st_minmax.nextToken()); | |
| - } | |
| - // Read in the N/M values (number of polynomials in the Temp and Press domain) | |
| - nextLine = ChemParser.readMeaningfulLine(data, true); | |
| - st_cheb = new StringTokenizer(nextLine,"/"); | |
| - nextToken = st_cheb.nextToken(); // Should be CHEB | |
| - st_minmax = new StringTokenizer(st_cheb.nextToken()); | |
| - int numN = Integer.parseInt(st_minmax.nextToken()); | |
| - int numM = Integer.parseInt(st_minmax.nextToken()); | |
| - // Read in the coefficients | |
| - nextLine = ChemParser.readMeaningfulLine(data, true); | |
| - double[] unorderedChebyCoeffs = new double[numN*numM]; | |
| - int chebyCoeffCounter = 0; | |
| - while (nextLine != null && nextLine.contains("CHEB")) { | |
| - st_cheb = new StringTokenizer(nextLine,"/"); | |
| - nextToken = st_cheb.nextToken(); // Should be CHEB | |
| - st_minmax = new StringTokenizer(st_cheb.nextToken()); | |
| - while (st_minmax.hasMoreTokens()) { | |
| - unorderedChebyCoeffs[chebyCoeffCounter] = Double.parseDouble(st_minmax.nextToken()); | |
| - ++chebyCoeffCounter; | |
| - } | |
| - nextLine = ChemParser.readMeaningfulLine(data, true); | |
| - } | |
| - // Order the chebyshev coefficients | |
| - double[][] chebyCoeffs = new double[numN][numM]; | |
| - for (int numRows=0; numRows<numN; numRows++) { | |
| - for (int numCols=0; numCols<numM; numCols++) { | |
| - chebyCoeffs[numRows][numCols] = unorderedChebyCoeffs[numM*numRows+numCols]; | |
| - } | |
| - } | |
| - // Make the ChebyshevPolynomials, PDepReaction, and add to list of PDepReactions | |
| - ChebyshevPolynomials coeffs = new ChebyshevPolynomials( | |
| - numN,new Temperature(Tmin,"K"),new Temperature(Tmax,"K"), | |
| - numM,new Pressure(Pmin,"bar"),new Pressure(Pmax,"bar"), | |
| - chebyCoeffs); | |
| - PDepIsomer reactants = new PDepIsomer(r.getStructure().getReactantList()); | |
| - PDepIsomer products = new PDepIsomer(r.getStructure().getProductList()); | |
| - PDepRateConstant pdepRC = new PDepRateConstant(coeffs); | |
| - PDepReaction pdeprxn = new PDepReaction(reactants,products,pdepRC); | |
| - allPdepNetworks.add(pdeprxn); | |
| - continueToReadRxn = false; | |
| - } else if (nextLine.contains("PLOG")) { | |
| - while (nextLine != null && nextLine.contains("PLOG")) { | |
| - // Increase the PLOG counter | |
| - ++numPLOGs; | |
| - // Store the previous PLOG information in temporary arrays | |
| - Pressure[] previousPressures = new Pressure[numPLOGs]; | |
| - ArrheniusKinetics[] previousKinetics = new ArrheniusKinetics[numPLOGs]; | |
| - for (int previousNumPLOG=0; previousNumPLOG<numPLOGs-1; ++previousNumPLOG) { | |
| - previousPressures[previousNumPLOG] = pdepkineticsPLOG.getPressures(previousNumPLOG); | |
| - previousKinetics[previousNumPLOG] = pdepkineticsPLOG.getKinetics(previousNumPLOG); | |
| - } | |
| - // Read in the new PLOG information, and add this to the temporary array | |
| - PDepArrheniusKinetics newpdepkinetics = parsePLOGline(nextLine); | |
| - previousPressures[numPLOGs-1] = newpdepkinetics.getPressures(0); | |
| - previousKinetics[numPLOGs-1] = newpdepkinetics.getKinetics(0); | |
| - // Re-initialize pdepkinetics and populate with stored information | |
| - pdepkineticsPLOG = new PDepArrheniusKinetics(numPLOGs); | |
| - pdepkineticsPLOG.setPressures(previousPressures); | |
| - pdepkineticsPLOG.setRateCoefficients(previousKinetics); | |
| - // Read the next line | |
| - nextLine = ChemParser.readMeaningfulLine(data, true); | |
| - } | |
| - // Make the PDepReaction | |
| - PDepIsomer reactants = new PDepIsomer(r.getStructure().getReactantList()); | |
| - PDepIsomer products = new PDepIsomer(r.getStructure().getProductList()); | |
| - PDepRateConstant pdepRC = new PDepRateConstant(pdepkineticsPLOG); | |
| - PDepReaction pdeprxn = new PDepReaction(reactants,products,pdepRC); | |
| - // Add to the list of PDepReactions | |
| - allPdepNetworks.add(pdeprxn); | |
| - // Re-initialize the pdepkinetics variable | |
| - numPLOGs = 0; | |
| - pdepkineticsPLOG = new PDepArrheniusKinetics(numPLOGs); | |
| - continueToReadRxn = false; | |
| - } else if (nextLine.contains("/")) { | |
| - // read in third body colliders + efficiencies | |
| - thirdBodyList = ChemParser.parseThirdBodyList(nextLine,allSpecies); | |
| - nextLine = ChemParser.readMeaningfulLine(data, true); | |
| - } else { | |
| - // the nextLine is a "new" reaction, hence we need to exit the while loop | |
| - continueToReadRxn = false; | |
| - } | |
| - } | |
| - | |
| /* | |
| * Make the pdep reaction, according to which parameters | |
| * are present | |
| @@ -475,9 +475,9 @@ public class SeedMechanism { | |
| * troe reactions. In the instance that no "troeReactions.txt" file exists, inform | |
| * user of this but continue simulation. | |
| */ | |
| - System.out.println("RMG did not find/read pressure-dependent reactions (pdepreactions.txt) " + | |
| - "in the " + source + p_name + "\n" + e.getMessage()); | |
| - return new LinkedHashSet(); | |
| + System.err.println("RMG could not find, or read in its entirety, the pressure-dependent reactions file (pdepreactions.txt)" + | |
| + "\n\tin the " + source + p_name + "\n" + e.getMessage()); | |
| + return null; | |
| } | |
| } | |
| diff --git a/source/daspk/Makefile b/source/daspk/Makefile | |
| index b6090fa..acbcb47 100644 | |
| --- a/source/daspk/Makefile | |
| +++ b/source/daspk/Makefile | |
| @@ -13,10 +13,40 @@ BUILDDIR=../../build/daspk | |
| # The directory in which to place compiled executables and JAR files | |
| BINDIR=../../bin | |
| -# The Fortran 90 compiler to use and flags to use when compiling Fortran 90 | |
| -# code | |
| -F90=g95 | |
| -F90FLAGS=-fmod=$(BUILDDIR) -ftrace=full | |
| +# The Fortran 90 compiler to use and flags to use when compiling Fortran code | |
| +# Call with 'make F90=g95' if you want to use g95 | |
| +# or 'make F90=gfortran' for GNU Fortran (recommended) | |
| +# Here we set the default | |
| +#F90=g95 | |
| +F90=gfortran | |
| + | |
| +ifeq ($(F90),g95) | |
| +F90FLAGS = -fmod=$(BUILDDIR) -ftrace=full # used for dassl and daspk | |
| +endif ###### END OF g95 SETTINGS | |
| + | |
| +ifeq ($(F90),gfortran) | |
| +# --fpe-trap=invalid,zero,underflow,overflow | |
| +# The above flag causes problems at least with fame. Maybe a bug in gfortran? (Maybe a bug in fame.) | |
| +F90FLAGS = -ftrapv -fbounds-check -frange-check \ | |
| + -ggdb -J""$(BUILDDIR)"" -O3 -Wall -Wno-unused | |
| +# if gfortran>4.3 then add -fbacktrace (it's not supported in earlier versions) | |
| +ifeq ($(shell gfortran --version 2>/dev/zero|grep -iqs '^GNU Fortran.* [4-9]\.[3-9]\.[0-9]' && echo "ok"), ok) | |
| +F90FLAGS += -fbacktrace | |
| +endif | |
| +F90FLAGS_NDEBUG = $(F90FLAGS) # used for dassl and daspk | |
| + | |
| +# call as `make MACOS=true F90=gfortran` if you want MacOS X 10.6+ 64-bit intel core2 features | |
| +ifdef MACOS | |
| +F90FLAGS += -arch x86_64 -march=core2 | |
| +F90_EXTRA_LDFLAGS += -framework vecLIB | |
| +endif | |
| + | |
| +# Special flags for daspk files | |
| +# Don't check for bounds on arrays beacuse dlinpk breaks them on purpose. | |
| +# Don't warn about tab characters or uninitialized variables. | |
| +DASPK_FFLAGS = -fno-bounds-check -Wtabs -Wno-uninitialized | |
| +endif ###### END OF gfortran SETTINGS | |
| + | |
| LDFLAGS= $(F90_EXTRA_LDFLAGS) -lblas -llapack -ldaepack | |
| @@ -40,10 +70,11 @@ $(BUILDDIR)/%.o: %.f90 | |
| # the files in the private folder are not part of the base RMG distribution | |
| # because we are not licensed to distribute them | |
| +# NB. they are also compiled with extra special flags | |
| $(BUILDDIR)/%.o: private/%.f | |
| mkdir -p $(BUILDDIR) | |
| - $(F90) $(F90FLAGS) -c $< -o $@ | |
| - | |
| + $(F90) $(F90FLAGS) $(DASPK_FFLAGS) -c $< -o $@ | |
| + | |
| clean: | |
| rm -rf $(BUILDDIR) | |
| rm -rf $(BINDIR)/daspkAUTO.exe | |
| diff --git a/source/daspk/call_daspkAUTO.f90 b/source/daspk/call_daspkAUTO.f90 | |
| index 7482a6c..efc4ef9 100644 | |
| --- a/source/daspk/call_daspkAUTO.f90 | |
| +++ b/source/daspk/call_daspkAUTO.f90 | |
| @@ -1,5 +1,5 @@ | |
| ! 9-Jul-2009 mrharper: | |
| -! Added Lindemann reactions | |
| +! Added Lindemann reactions | |
| ! 6/26/08 gmagoon: | |
| ! filename: call_daspkAUTO.f90; | |
| ! changed name from CALL_DASPK to CALL_DASPKLAUTO | |
| @@ -106,59 +106,59 @@ PROGRAM CALL_DASPKAUTO | |
| ! READ INFORMATION ABOUT LINDEREACTIONS | |
| READ(12,*) LINDEREACTIONSIZE | |
| - READ(12,*)(LINDEREACTIONARRAY(I),I=1,20*LINDEREACTIONSIZE) | |
| - READ(12,*)(LINDEREACTIONRATEARRAY(I),I=1,17*LINDEREACTIONSIZE) | |
| + READ(12,*)(LINDEREACTIONARRAY(I),I=1,20*LINDEREACTIONSIZE) | |
| + READ(12,*)(LINDEREACTIONRATEARRAY(I),I=1,17*LINDEREACTIONSIZE) | |
| ! 6/26/08 gmagoon: if autoFlag = 1, read in additional information | |
| ! specific to automatic time stepping | |
| - IF (AUTOFLAG .EQ. 1) THEN | |
| - ! read the threshhold, corresponding to the value of | |
| - ! termination tolerance specified in condition.txt input file | |
| - !CORETHRESH is the threshhold for moving something from edge to core, | |
| - !whereas THRESH is the threshhold for terminating the run before the end | |
| - !THRESH >= CORETHRESH | |
| - READ(12,*) THRESH, CORETHRESH | |
| - ! read the number of edge species and edge reactions | |
| - READ(12,*) ESPECIES, EREACTIONSIZE | |
| - ! allocate memory for arrays | |
| - ALLOCATE(NEREAC(EREACTIONSIZE), NEPROD(EREACTIONSIZE),& | |
| - & IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3),& | |
| - & KVEC(EREACTIONSIZE)) | |
| - ! read in the reaction parameters for each reaction; | |
| - ! a maximum of 3 products and 3 reactants is assumed | |
| - ! for each reaction; parameters read for each reaction | |
| - ! are: number of reactants, number of products, | |
| - ! three reactant ID's (integers from 1 to NSTATE-1), | |
| - ! three product ID's (integers from 1 to ESPECIES), | |
| - ! and the rate coefficient k, such that dCi/dt=k*Ca*Cb; | |
| - ! note that cases where abs. value of stoic. coeff. | |
| - ! does not equal one are handled by using repeated | |
| - ! reactant/product IDs | |
| - ! note: use of KVEC rather than Arrhenius parameters | |
| - ! requires assumption that system is isothermal | |
| - ! (and isobaric for pressure dependence) | |
| - DO I=1, EREACTIONSIZE | |
| - READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| - & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| - & IDEPROD(I,2), IDEPROD(I,3), KVEC(I) | |
| - ! alternative for reading Arrhenius parameters instead | |
| - ! of k values; this allows easier extention to | |
| - ! non-isothermal systems in the future | |
| - ! form: k=A*T^n*e^(Ea/(RT)) *? | |
| - ! units: A[=], n[=]dimensionless, Ea[=] | |
| - ! READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| + IF (AUTOFLAG .EQ. 1) THEN | |
| + ! read the threshhold, corresponding to the value of | |
| + ! termination tolerance specified in condition.txt input file | |
| + !CORETHRESH is the threshhold for moving something from edge to core, | |
| + !whereas THRESH is the threshhold for terminating the run before the end | |
| + !THRESH >= CORETHRESH | |
| + READ(12,*) THRESH, CORETHRESH | |
| + ! read the number of edge species and edge reactions | |
| + READ(12,*) ESPECIES, EREACTIONSIZE | |
| + ! allocate memory for arrays | |
| + ALLOCATE(NEREAC(EREACTIONSIZE), NEPROD(EREACTIONSIZE),& | |
| + & IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3),& | |
| + & KVEC(EREACTIONSIZE)) | |
| + ! read in the reaction parameters for each reaction; | |
| + ! a maximum of 3 products and 3 reactants is assumed | |
| + ! for each reaction; parameters read for each reaction | |
| + ! are: number of reactants, number of products, | |
| + ! three reactant ID's (integers from 1 to NSTATE-1), | |
| + ! three product ID's (integers from 1 to ESPECIES), | |
| + ! and the rate coefficient k, such that dCi/dt=k*Ca*Cb; | |
| + ! note that cases where abs. value of stoic. coeff. | |
| + ! does not equal one are handled by using repeated | |
| + ! reactant/product IDs | |
| + ! note: use of KVEC rather than Arrhenius parameters | |
| + ! requires assumption that system is isothermal | |
| + ! (and isobaric for pressure dependence) | |
| + DO I=1, EREACTIONSIZE | |
| + READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| + & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| + & IDEPROD(I,2), IDEPROD(I,3), KVEC(I) | |
| + ! alternative for reading Arrhenius parameters instead | |
| + ! of k values; this allows easier extention to | |
| + ! non-isothermal systems in the future | |
| + ! form: k=A*T^n*e^(Ea/(RT)) *? | |
| + ! units: A[=], n[=]dimensionless, Ea[=] | |
| + ! READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| ! & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| ! & IDEPROD(I,2),IDEPROD(I,3), AVEC(I), NVEC(I), & | |
| ! & EAVEC(I) | |
| - ! for isothermal, isobaric systems, (or just isothermal | |
| - ! systems if pressure dependence is not considered) | |
| + ! for isothermal, isobaric systems, (or just isothermal | |
| + ! systems if pressure dependence is not considered) | |
| ! the following may be calculated here once | |
| - ! (versus calculating at every timestep) | |
| - ! ...units may need adjustment: | |
| - ! KVEC(I)=AVEC(I)*TEMPERATURE**NVEC(I)*EXP(EAVEC(I) & | |
| - ! & /(8.314*TEMPERATURE)) | |
| - END DO | |
| - END IF | |
| + ! (versus calculating at every timestep) | |
| + ! ...units may need adjustment: | |
| + ! KVEC(I)=AVEC(I)*TEMPERATURE**NVEC(I)*EXP(EAVEC(I) & | |
| + ! & /(8.314*TEMPERATURE)) | |
| + END DO | |
| + END IF | |
| ! read constantConcentration data (if flag = 1 then the concentration of that species will not be integrated) | |
| ! there is one integer for each species (up to nstate-1), then the last one is for the VOLUME | |
| READ(12,*) (ConstantConcentration(I), i=1,nstate) | |
| @@ -211,13 +211,13 @@ PROGRAM CALL_DASPKAUTO | |
| read(13) troereactionratearray(i) | |
| end do | |
| - READ(13) LINDEREACTIONSIZE | |
| - DO I=1,20*LINDEREACTIONSIZE | |
| - READ(13) LINDEREACTIONARRAY(I) | |
| - END DO | |
| - DO I=1,17*LINDEREACTIONSIZE | |
| - READ(13) LINDEREACTIONRATEARRAY(I) | |
| - END DO | |
| + READ(13) LINDEREACTIONSIZE | |
| + DO I=1,20*LINDEREACTIONSIZE | |
| + READ(13) LINDEREACTIONARRAY(I) | |
| + END DO | |
| + DO I=1,17*LINDEREACTIONSIZE | |
| + READ(13) LINDEREACTIONRATEARRAY(I) | |
| + END DO | |
| do i=1,nstate-1 | |
| read(13) thermo(i) | |
| @@ -260,8 +260,8 @@ PROGRAM CALL_DASPKAUTO | |
| ! 6/26/08 gmagoon: deallocate memory from allocatable arrays | |
| ! (may or may not be useful) | |
| IF (AUTOFLAG .EQ. 1) THEN | |
| - DEALLOCATE (NEREAC, NEPROD, KVEC, & | |
| - & IDEREAC, IDEPROD) | |
| + DEALLOCATE (NEREAC, NEPROD, KVEC, & | |
| + & IDEREAC, IDEPROD) | |
| END IF | |
| END PROGRAM CALL_DASPKAUTO | |
| @@ -366,10 +366,10 @@ PROGRAM CALL_DASPKAUTO | |
| & TROEREACTIONRATEARRAY(21*I+1) | |
| END DO | |
| - DO I=0,LINDEREACTIONSIZE-1 | |
| - RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+I+1) = & | |
| - & LINDEREACTIONRATEARRAY(17*I+1) | |
| - END DO | |
| + DO I=0,LINDEREACTIONSIZE-1 | |
| + RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+I+1) = & | |
| + & LINDEREACTIONRATEARRAY(17*I+1) | |
| + END DO | |
| DO I=0,NSTATE-2 | |
| RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+ & | |
| @@ -398,55 +398,55 @@ PROGRAM CALL_DASPKAUTO | |
| ! 6/26/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| ! determine EDGEFLAG and EDGEFLAGCORE (-1 if flux threshhold has not yet been met, | |
| ! positive integer otherwise) | |
| - EDGEFLAG = -1 | |
| - EDGEFLAGCORE = -1 | |
| - !initialize flag CORESTORED to -1 indicating that the output values (when core inclusion threshold is exceeded) have not been stored yet; this will be set to 1 once the values are stored | |
| - CORESTORED = -1 | |
| - !initialize MAXRATIO to a vector of all zeroes; | |
| - !this variable will track the maxiumum | |
| - !of rate(i)/Rchar for each edge species i, with respect to time | |
| - MAXRATIO = 0 | |
| - !initialize HIGHESTRATIO to 0; this variable (a scalar) | |
| - !tracks the maximum of maxratio; when a new maximum is | |
| - !attained, the present time step creating the new maximum | |
| - !will be stored for output from the ODE solver to the Java code | |
| - HIGHESTRATIO = 0 | |
| - IF (AUTOFLAG.eq.1) THEN | |
| - CALL EDGEFLUX(EDGEFLAG,EDGEFLAGCORE,Y,YPRIME,THRESH,CORETHRESH,ESPECIES, & | |
| + EDGEFLAG = -1 | |
| + EDGEFLAGCORE = -1 | |
| + !initialize flag CORESTORED to -1 indicating that the output values (when core inclusion threshold is exceeded) have not been stored yet; this will be set to 1 once the values are stored | |
| + CORESTORED = -1 | |
| + !initialize MAXRATIO to a vector of all zeroes; | |
| + !this variable will track the maxiumum | |
| + !of rate(i)/Rchar for each edge species i, with respect to time | |
| + MAXRATIO = 0 | |
| + !initialize HIGHESTRATIO to 0; this variable (a scalar) | |
| + !tracks the maximum of maxratio; when a new maximum is | |
| + !attained, the present time step creating the new maximum | |
| + !will be stored for output from the ODE solver to the Java code | |
| + HIGHESTRATIO = 0 | |
| + IF (AUTOFLAG.eq.1) THEN | |
| + CALL EDGEFLUX(EDGEFLAG,EDGEFLAGCORE,Y,YPRIME,THRESH,CORETHRESH,ESPECIES, & | |
| & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| & MAXRATIO,PRUNEVEC,NSTATE) | |
| - !update HIGHESTRATIO | |
| - !note that we cannot exit the do loop once the IF statement is | |
| - !caught because the HIGHESTRATIO will not necessarily have the highest value | |
| - DO I=1, ESPECIES | |
| - IF (MAXRATIO(I) .GT. HIGHESTRATIO) THEN | |
| - HIGHESTRATIO = MAXRATIO(I) | |
| - END IF | |
| - END DO | |
| - !when core flux threshold is exceeded for the first time, store the values for output | |
| - !we want to use the first point of exceeding the core inclusion threshold | |
| - !(aka error tolerance) to determine which species to add to the core | |
| - !note: TOTALREACTIONFLUX apparently tracks integrated flux, not | |
| - !instantaneous flux, so setting value to be zero here should be OK... | |
| - !in any case, the result doesn't seem to be used by the Java code | |
| - IF(EDGEFLAGCORE .GT. 0 .AND. CORESTORED .EQ. -1) THEN | |
| - ITER_OUTPT=0 | |
| - TIME_OUTPT=TIME | |
| - Y_OUTPT = Y | |
| - YPRIME_OUTPT = YPRIME | |
| - !IWORK_OUTPT = IWORK | |
| - !RWORK_OUTPT = RWORK | |
| - TOTALREACTIONFLUX_OUTPT = 0 | |
| - !PRUNEVEC_OUTPT = PRUNEVEC !note that we do not copy prunevec for the output value; this will be based on the final time integrated to (in case core threshold, but not termination threshold, is exceeded at t=0...it is ok to prune species that have zero flux at t=0 | |
| - CORESTORED = 1 | |
| - END IF | |
| - | |
| - ENDIF | |
| + !update HIGHESTRATIO | |
| + !note that we cannot exit the do loop once the IF statement is | |
| + !caught because the HIGHESTRATIO will not necessarily have the highest value | |
| + DO I=1, ESPECIES | |
| + IF (MAXRATIO(I) .GT. HIGHESTRATIO) THEN | |
| + HIGHESTRATIO = MAXRATIO(I) | |
| + END IF | |
| + END DO | |
| + !when core flux threshold is exceeded for the first time, store the values for output | |
| + !we want to use the first point of exceeding the core inclusion threshold | |
| + !(aka error tolerance) to determine which species to add to the core | |
| + !note: TOTALREACTIONFLUX apparently tracks integrated flux, not | |
| + !instantaneous flux, so setting value to be zero here should be OK... | |
| + !in any case, the result doesn't seem to be used by the Java code | |
| + IF(EDGEFLAGCORE .GT. 0 .AND. CORESTORED .EQ. -1) THEN | |
| + ITER_OUTPT=0 | |
| + TIME_OUTPT=TIME | |
| + Y_OUTPT = Y | |
| + YPRIME_OUTPT = YPRIME | |
| + !IWORK_OUTPT = IWORK | |
| + !RWORK_OUTPT = RWORK | |
| + TOTALREACTIONFLUX_OUTPT = 0 | |
| + !PRUNEVEC_OUTPT = PRUNEVEC !note that we do not copy prunevec for the output value; this will be based on the final time integrated to (in case core threshold, but not termination threshold, is exceeded at t=0...it is ok to prune species that have zero flux at t=0 | |
| + CORESTORED = 1 | |
| + END IF | |
| + | |
| + ENDIF | |
| iter =0 | |
| PREVTIME = TIME | |
| DO I=1,REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+ & | |
| - & LINDEREACTIONSIZE | |
| + & LINDEREACTIONSIZE | |
| PREVREACTIONFLUX(I) = 0 | |
| TOTALREACTIONFLUX(I) = 0 | |
| CURRENTREACTIONFLUX(I) = 0 | |
| @@ -481,28 +481,28 @@ PROGRAM CALL_DASPKAUTO | |
| PREVTIME = TIME | |
| ! 6/26/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| ! determine EDGEFLAG | |
| - IF (AUTOFLAG.eq.1) THEN | |
| - CALL EDGEFLUX(EDGEFLAG,EDGEFLAGCORE,Y,YPRIME,THRESH,CORETHRESH,ESPECIES, & | |
| - & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| - & MAXRATIO,PRUNEVEC,NSTATE) | |
| - !update HIGHESTRATIO | |
| - DO I=1, ESPECIES | |
| - IF (MAXRATIO(I) .GT. HIGHESTRATIO) THEN | |
| - HIGHESTRATIO = MAXRATIO(I) | |
| - END IF | |
| - END DO | |
| - !when core flux threshold is exceeded for the first time, store the values for output | |
| - IF(EDGEFLAGCORE .GT. 0 .AND. CORESTORED .EQ. -1) THEN | |
| - ITER_OUTPT=ITER | |
| - TIME_OUTPT=TIME | |
| - Y_OUTPT = Y | |
| - YPRIME_OUTPT = YPRIME | |
| - !IWORK_OUTPT = IWORK | |
| - !RWORK_OUTPT = RWORK | |
| - TOTALREACTIONFLUX_OUTPT = TOTALREACTIONFLUX | |
| - CORESTORED=1 | |
| - END IF | |
| - END IF | |
| + IF (AUTOFLAG.eq.1) THEN | |
| + CALL EDGEFLUX(EDGEFLAG,EDGEFLAGCORE,Y,YPRIME,THRESH,CORETHRESH,ESPECIES, & | |
| + & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| + & MAXRATIO,PRUNEVEC,NSTATE) | |
| + !update HIGHESTRATIO | |
| + DO I=1, ESPECIES | |
| + IF (MAXRATIO(I) .GT. HIGHESTRATIO) THEN | |
| + HIGHESTRATIO = MAXRATIO(I) | |
| + END IF | |
| + END DO | |
| + !when core flux threshold is exceeded for the first time, store the values for output | |
| + IF(EDGEFLAGCORE .GT. 0 .AND. CORESTORED .EQ. -1) THEN | |
| + ITER_OUTPT=ITER | |
| + TIME_OUTPT=TIME | |
| + Y_OUTPT = Y | |
| + YPRIME_OUTPT = YPRIME | |
| + !IWORK_OUTPT = IWORK | |
| + !RWORK_OUTPT = RWORK | |
| + TOTALREACTIONFLUX_OUTPT = TOTALREACTIONFLUX | |
| + CORESTORED=1 | |
| + END IF | |
| + END IF | |
| go to 1 | |
| END IF | |
| @@ -538,28 +538,28 @@ PROGRAM CALL_DASPKAUTO | |
| end if | |
| ! 6/26/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| ! determine EDGEFLAG | |
| - IF (AUTOFLAG.eq.1) THEN | |
| - CALL EDGEFLUX(EDGEFLAG,EDGEFLAGCORE,Y,YPRIME,THRESH,CORETHRESH,ESPECIES, & | |
| - & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| - & MAXRATIO,PRUNEVEC,NSTATE) | |
| - !update HIGHESTRATIO | |
| - DO I=1, ESPECIES | |
| - IF (MAXRATIO(I) .GT. HIGHESTRATIO) THEN | |
| - HIGHESTRATIO = MAXRATIO(I) | |
| - END IF | |
| - END DO | |
| - !when core flux threshold is exceeded for the first time, store the values for output | |
| - IF(EDGEFLAGCORE .GT. 0 .AND. CORESTORED .EQ. -1) THEN | |
| - ITER_OUTPT=ITER | |
| - TIME_OUTPT=TIME | |
| - Y_OUTPT = Y | |
| - YPRIME_OUTPT = YPRIME | |
| - !IWORK_OUTPT = IWORK | |
| - !RWORK_OUTPT = RWORK | |
| - TOTALREACTIONFLUX_OUTPT = TOTALREACTIONFLUX | |
| - CORESTORED=1 | |
| - END IF | |
| - END IF | |
| + IF (AUTOFLAG.eq.1) THEN | |
| + CALL EDGEFLUX(EDGEFLAG,EDGEFLAGCORE,Y,YPRIME,THRESH,CORETHRESH,ESPECIES, & | |
| + & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| + & MAXRATIO,PRUNEVEC,NSTATE) | |
| + !update HIGHESTRATIO | |
| + DO I=1, ESPECIES | |
| + IF (MAXRATIO(I) .GT. HIGHESTRATIO) THEN | |
| + HIGHESTRATIO = MAXRATIO(I) | |
| + END IF | |
| + END DO | |
| + !when core flux threshold is exceeded for the first time, store the values for output | |
| + IF(EDGEFLAGCORE .GT. 0 .AND. CORESTORED .EQ. -1) THEN | |
| + ITER_OUTPT=ITER | |
| + TIME_OUTPT=TIME | |
| + Y_OUTPT = Y | |
| + YPRIME_OUTPT = YPRIME | |
| + !IWORK_OUTPT = IWORK | |
| + !RWORK_OUTPT = RWORK | |
| + TOTALREACTIONFLUX_OUTPT = TOTALREACTIONFLUX | |
| + CORESTORED=1 | |
| + END IF | |
| + END IF | |
| go to 2 | |
| END IF | |
| END IF | |
| @@ -574,13 +574,13 @@ PROGRAM CALL_DASPKAUTO | |
| !target time/conversion has been reached | |
| !in either case, CORESTORED should be -1 | |
| IF (CORESTORED .EQ. -1) THEN | |
| - ITER_OUTPT=ITER | |
| - TIME_OUTPT=TIME | |
| - Y_OUTPT = Y | |
| - YPRIME_OUTPT = YPRIME | |
| - !IWORK_OUTPT = IWORK | |
| - !RWORK_OUTPT = RWORK | |
| - TOTALREACTIONFLUX_OUTPT = TOTALREACTIONFLUX | |
| + ITER_OUTPT=ITER | |
| + TIME_OUTPT=TIME | |
| + Y_OUTPT = Y | |
| + YPRIME_OUTPT = YPRIME | |
| + !IWORK_OUTPT = IWORK | |
| + !RWORK_OUTPT = RWORK | |
| + TOTALREACTIONFLUX_OUTPT = TOTALREACTIONFLUX | |
| END IF | |
| IWORK_OUTPT = IWORK | |
| RWORK_OUTPT = RWORK | |
| @@ -605,8 +605,8 @@ PROGRAM CALL_DASPKAUTO | |
| DO j=1,NSTATE | |
| !WRITE(15,*) Yprime(I*nstate+j)/Y(NSTATE) | |
| WRITE(15,*) (Y_OUTPT(NSTATE)*YPRIME_OUTPT(I*nstate+j)- & | |
| - & Y_OUTPT(I*nstate+j)*YPRIME_OUTPT(NSTATE)) & | |
| - & /(Y_OUTPT(NSTATE)**2) | |
| + & Y_OUTPT(I*nstate+j)*YPRIME_OUTPT(NSTATE)) & | |
| + & /(Y_OUTPT(NSTATE)**2) | |
| END DO | |
| end do | |
| @@ -625,12 +625,12 @@ PROGRAM CALL_DASPKAUTO | |
| !, the final time integrated to, | |
| !along with pruning information | |
| IF (AUTOFLAG .EQ. 1) THEN | |
| - WRITE(15,*) EDGEFLAG | |
| - WRITE(15,*) TIME | |
| - DO I=1, ESPECIES | |
| - WRITE(15,*) PRUNEVEC(I) | |
| - WRITE(15,*) MAXRATIO(I) | |
| - END DO | |
| + WRITE(15,*) EDGEFLAG | |
| + WRITE(15,*) TIME | |
| + DO I=1, ESPECIES | |
| + WRITE(15,*) PRUNEVEC(I) | |
| + WRITE(15,*) MAXRATIO(I) | |
| + END DO | |
| END IF | |
| CLOSE(15) | |
| @@ -781,10 +781,10 @@ PROGRAM CALL_DASPKAUTO | |
| & TROEREACTIONRATEARRAY(21*I+1) | |
| END DO | |
| - DO I=0,LINDEREACTIONSIZE-1 | |
| - RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+I+1) = & | |
| - & LINDEREACTIONRATEARRAY(17*I+1) | |
| - END DO | |
| + DO I=0,LINDEREACTIONSIZE-1 | |
| + RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+I+1) = & | |
| + & LINDEREACTIONRATEARRAY(17*I+1) | |
| + END DO | |
| DO I=0,NSTATE-2 | |
| RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+LINDEREACTIONSIZE+i+1) = & | |
| @@ -905,71 +905,71 @@ PROGRAM CALL_DASPKAUTO | |
| ! if edgeflux also exceeds the termination threshold flux, edgeflag is set to the offending species ID | |
| SUBROUTINE EDGEFLUX(EDGEFLAG,EDGEFLAGCORE,Y,YPRIME,THRESH,CORETHRESH,ESPECIES, & | |
| - & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD, & | |
| - & KVEC, MAXRATIO,PRUNEVEC,NSTATE) | |
| - IMPLICIT NONE | |
| - INTEGER EDGEFLAG, EDGEFLAGCORE, ESPECIES, EREACTIONSIZE, NSTATE, I, J, K | |
| - DOUBLE PRECISION THRESH,CORETHRESH,FLUXRC, RFLUX, Y(NSTATE), YPRIME(NSTATE) | |
| - DOUBLE PRECISION, DIMENSION(:), ALLOCATABLE :: RATE | |
| - INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| + & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD, & | |
| + & KVEC, MAXRATIO,PRUNEVEC,NSTATE) | |
| + IMPLICIT NONE | |
| + INTEGER EDGEFLAG, EDGEFLAGCORE, ESPECIES, EREACTIONSIZE, NSTATE, I, J, K | |
| + DOUBLE PRECISION THRESH,CORETHRESH,FLUXRC, RFLUX, Y(NSTATE), YPRIME(NSTATE) | |
| + DOUBLE PRECISION, DIMENSION(:), ALLOCATABLE :: RATE | |
| + INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| INTEGER IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3) | |
| - INTEGER PRUNEVEC(ESPECIES) | |
| + INTEGER PRUNEVEC(ESPECIES) | |
| DOUBLE PRECISION KVEC(EREACTIONSIZE),RATIO, MAXRATIO(ESPECIES) | |
| - | |
| - ALLOCATE(RATE(ESPECIES)) | |
| - ! initialize array to have all zeroes | |
| - RATE=0 | |
| - ! it is assumed edgeflag = -1 at this point, since | |
| + | |
| + ALLOCATE(RATE(ESPECIES)) | |
| + ! initialize array to have all zeroes | |
| + RATE=0 | |
| + ! it is assumed edgeflag = -1 at this point, since | |
| ! this should be the only way to access this subroutine | |
| ! calculate characteristic flux, FLUXRC | |
| - CALL RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| - | |
| - !initialize PRUNEVEC; at first, assume everything is prunable | |
| - PRUNEVEC=1 | |
| - | |
| - ! calculate the vector of fluxes for each species | |
| - ! by summing contributions from each reaction | |
| - ILOOP: DO I=1, EREACTIONSIZE | |
| - ! calculate reaction flux by multiplying k | |
| - ! by concentration(s) | |
| - RFLUX = KVEC(I) | |
| - KLOOP: DO K=1, NEREAC(I) | |
| - RFLUX = RFLUX*Y(IDEREAC(I,K))/Y(NSTATE) | |
| - END DO KLOOP | |
| - ! loop over reaction products, adding RFLUX | |
| - JLOOP: DO J=1, NEPROD(I) | |
| - RATE(IDEPROD(I,J))=RATE(IDEPROD(I,J))+ RFLUX | |
| - !if RFLUX is zero, then presumably one of the | |
| - !reactant concentrations is zero (it is assumed | |
| - !that k != 0), and therefore, we don't want to | |
| - !prune the species yet | |
| - IF(RFLUX .EQ. 0.0) THEN | |
| - PRUNEVEC(IDEPROD(I,J)) = 0 | |
| - END IF | |
| - END DO JLOOP | |
| - END DO ILOOP | |
| - | |
| - | |
| - ! check if any of the edge species fluxes exceed | |
| - ! the threshhold and update the MAXRATIO vector | |
| - FLOOP: DO I=1, ESPECIES | |
| - RATIO = RATE(I)/FLUXRC | |
| - !if we reach the error tolerance (aka core tolerance), | |
| - !set EDGEFLAGCORE to the species ID | |
| - !if we also reach the termination tolerance, set EDGEFLAG to the species ID | |
| - IF (RATIO .GE. CORETHRESH) THEN | |
| - EDGEFLAGCORE = I | |
| - IF(RATIO .GE. THRESH) THEN | |
| - EDGEFLAG = I | |
| - END IF | |
| - END IF | |
| - !update the MAXRATIO vector | |
| - IF(RATIO .GT. MAXRATIO(I)) THEN | |
| - MAXRATIO(I) = RATIO | |
| - END IF | |
| - END DO FLOOP | |
| - DEALLOCATE(RATE) | |
| + CALL RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| + | |
| + !initialize PRUNEVEC; at first, assume everything is prunable | |
| + PRUNEVEC=1 | |
| + | |
| + ! calculate the vector of fluxes for each species | |
| + ! by summing contributions from each reaction | |
| + ILOOP: DO I=1, EREACTIONSIZE | |
| + ! calculate reaction flux by multiplying k | |
| + ! by concentration(s) | |
| + RFLUX = KVEC(I) | |
| + KLOOP: DO K=1, NEREAC(I) | |
| + RFLUX = RFLUX*Y(IDEREAC(I,K))/Y(NSTATE) | |
| + END DO KLOOP | |
| + ! loop over reaction products, adding RFLUX | |
| + JLOOP: DO J=1, NEPROD(I) | |
| + RATE(IDEPROD(I,J))=RATE(IDEPROD(I,J))+ RFLUX | |
| + !if RFLUX is zero, then presumably one of the | |
| + !reactant concentrations is zero (it is assumed | |
| + !that k != 0), and therefore, we don't want to | |
| + !prune the species yet | |
| + IF(RFLUX .EQ. 0.0) THEN | |
| + PRUNEVEC(IDEPROD(I,J)) = 0 | |
| + END IF | |
| + END DO JLOOP | |
| + END DO ILOOP | |
| + | |
| + | |
| + ! check if any of the edge species fluxes exceed | |
| + ! the threshhold and update the MAXRATIO vector | |
| + FLOOP: DO I=1, ESPECIES | |
| + RATIO = RATE(I)/FLUXRC | |
| + !if we reach the error tolerance (aka core tolerance), | |
| + !set EDGEFLAGCORE to the species ID | |
| + !if we also reach the termination tolerance, set EDGEFLAG to the species ID | |
| + IF (RATIO .GE. CORETHRESH) THEN | |
| + EDGEFLAGCORE = I | |
| + IF(RATIO .GE. THRESH) THEN | |
| + EDGEFLAG = I | |
| + END IF | |
| + END IF | |
| + !update the MAXRATIO vector | |
| + IF(RATIO .GT. MAXRATIO(I)) THEN | |
| + MAXRATIO(I) = RATIO | |
| + END IF | |
| + END DO FLOOP | |
| + DEALLOCATE(RATE) | |
| END SUBROUTINE EDGEFLUX | |
| ! RCHAR calculates the characteristic flux (i.e. the | |
| @@ -984,24 +984,24 @@ END SUBROUTINE EDGEFLUX | |
| ! plus one) | |
| SUBROUTINE RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| IMPLICIT NONE | |
| - INTEGER NSTATE, I | |
| - DOUBLE PRECISION SSF, FLUXRC, Y(NSTATE), YPRIME(NSTATE) | |
| - ! compute the sum of squared fluxes | |
| - SSF=0.0 | |
| + INTEGER NSTATE, I | |
| + DOUBLE PRECISION SSF, FLUXRC, Y(NSTATE), YPRIME(NSTATE) | |
| + ! compute the sum of squared fluxes | |
| + SSF=0.0 | |
| !6/26/08 gmagoon: note that we are implicitly treating only indexing | |
| !first NSTATE elements of array (i.e. nparam=0) since we do not care | |
| !about sensitivity here | |
| - DO I=1, NSTATE-1 | |
| - ! add (dCi/dt)^2 with dCi/dt computed based on | |
| + DO I=1, NSTATE-1 | |
| + ! add (dCi/dt)^2 with dCi/dt computed based on | |
| ! quotient rule...dCi/dt=d(Ni/V)/dt | |
| - ! =(V*dNi/dt-Ni*dV/dt)/V^2 | |
| - SSF=SSF+((Y(NSTATE)*YPRIME(I)-Y(I)*YPRIME(NSTATE)) & | |
| + ! =(V*dNi/dt-Ni*dV/dt)/V^2 | |
| + SSF=SSF+((Y(NSTATE)*YPRIME(I)-Y(I)*YPRIME(NSTATE)) & | |
| & /(Y(NSTATE)**2))**2 | |
| - END DO | |
| - ! compute the square root, corresponding to | |
| + END DO | |
| + ! compute the square root, corresponding to | |
| ! L2 norm | |
| - FLUXRC = SSF**0.5 | |
| + FLUXRC = SSF**0.5 | |
| END SUBROUTINE RCHAR | |
| diff --git a/source/daspk/private b/source/daspk/private | |
| index 7b246f0..168c901 160000 | |
| --- a/source/daspk/private | |
| +++ b/source/daspk/private | |
| @@ -1 +1 @@ | |
| -Subproject commit 7b246f0a33ef61c4df873c2979de720c9338dd65 | |
| +Subproject commit 168c9010767d8260b3914c6ad336de1f0d2bdf01 | |
| diff --git a/source/daspk/reaction_flux.f b/source/daspk/reaction_flux.f | |
| index 3a8ad72..691cb7d 100644 | |
| --- a/source/daspk/reaction_flux.f | |
| +++ b/source/daspk/reaction_flux.f | |
| @@ -16,7 +16,7 @@ C ************************************************ | |
| DO I=1,REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+ | |
| - $ LINDEREACTIONSIZE | |
| + $ LINDEREACTIONSIZE | |
| reactionflux(I) = 0 | |
| END DO | |
| @@ -193,11 +193,11 @@ c write(*,*) temperature | |
| LOGF = LOGFCENT/(1 + INSIDE**2) | |
| F = 10**LOGF | |
| - IF (RNUM .GT. 1 .AND. PNUM .GT. 1) THEN | |
| - FRATE = LOWRATE * (1/(1+PR)) * F | |
| - ELSE | |
| - FRATE = RATE * (PR/(1+PR)) * F | |
| - END IF | |
| + IF (RNUM .GT. 1 .AND. PNUM .GT. 1) THEN | |
| + FRATE = LOWRATE * (1/(1+PR)) * F | |
| + ELSE | |
| + FRATE = RATE * (PR/(1+PR)) * F | |
| + END IF | |
| IF (TROEREACTIONARRAY(21*I+9) .EQ. 1) THEN | |
| RRATE = fRATE/KEQ | |
| @@ -258,13 +258,13 @@ c write(*,*) temperature | |
| PR = LOWRATE * M/RATE | |
| - IF (RNUM .GT. 1 .AND. PNUM .GT. 1) THEN | |
| - FRATE = LOWRATE * (1/(1+PR)) | |
| - ELSE | |
| - FRATE = RATE * (PR/(1+PR)) | |
| - END IF | |
| + IF (RNUM .GT. 1 .AND. PNUM .GT. 1) THEN | |
| + FRATE = LOWRATE * (1/(1+PR)) | |
| + ELSE | |
| + FRATE = RATE * (PR/(1+PR)) | |
| + END IF | |
| - IF (LINDEREACTIONARRAY(20*I+9) .EQ. 1) THEN | |
| + IF (LINDEREACTIONARRAY(20*I+9) .EQ. 1) THEN | |
| RRATE = fRATE/KEQ | |
| ELSE | |
| RRATE = 0 | |
| @@ -282,7 +282,7 @@ C ********************************** | |
| END DO | |
| REACTIONFLUX(I+1+REACTIONSIZE+THIRDBODYREACTIONSIZE | |
| - $ +TROEREACTIONSIZE) = FRATE - RRATE | |
| + $ +TROEREACTIONSIZE) = FRATE - RRATE | |
| END DO | |
| diff --git a/source/daspk/res_rpar.f b/source/daspk/res_rpar.f | |
| index 6ea9079..afba886 100644 | |
| --- a/source/daspk/res_rpar.f | |
| +++ b/source/daspk/res_rpar.f | |
| @@ -19,8 +19,8 @@ C - GENERATED: Wed Jan 31 02:09:44 2007 | |
| parameter(tbrmax=50) | |
| integer troemax | |
| parameter(troemax=50) | |
| - integer lindemax | |
| - parameter(lindemax=50) | |
| + integer lindemax | |
| + parameter(lindemax=50) | |
| integer i | |
| integer j | |
| integer k | |
| @@ -29,7 +29,7 @@ C - GENERATED: Wed Jan 31 02:09:44 2007 | |
| integer nstate | |
| double precision pressure | |
| integer troereactionsize | |
| - integer lindereactionsize | |
| + integer lindereactionsize | |
| integer ires | |
| double precision cj | |
| integer ijac | |
| @@ -49,9 +49,9 @@ C - GENERATED: Wed Jan 31 02:09:44 2007 | |
| $ troereactionsize+lindereactionsize+nstate-1) | |
| integer reactionarray | |
| integer troereactionarray | |
| - integer lindereactionarray | |
| + integer lindereactionarray | |
| double precision troereactionratearray | |
| - double precision lindereactionratearray | |
| + double precision lindereactionratearray | |
| common /size/ nstate,neq,nparam,reactionsize,troereactionsize, | |
| $ thirdbodyreactionsize,lindereactionsize | |
| common /reac/ reactionratearray(5*rmax), | |
| @@ -83,7 +83,7 @@ C Active variable offsets and counters | |
| integer reactionratearrayoft | |
| integer thirdbodyreactionratearrayoft | |
| integer troereactionratearrayoft | |
| - integer lindereactionratearrayoft | |
| + integer lindereactionratearrayoft | |
| integer temperatureoft | |
| integer pressureoft | |
| integer zzzindx | |
| @@ -102,7 +102,7 @@ C Variable offsets for COMMON BLOCK reac | |
| reactionratearrayoft=0 | |
| thirdbodyreactionratearrayoft=reactionratearrayoft+(5*rmax) | |
| troereactionratearrayoft=thirdbodyreactionratearrayoft+(16*tbrmax) | |
| - lindereactionratearrayoft=troereactionratearrayoft+(21*troemax) | |
| + lindereactionratearrayoft=troereactionratearrayoft+(21*troemax) | |
| temperatureoft=lindereactionratearrayoft+(17*lindemax) | |
| pressureoft=temperatureoft+1 | |
| C Number of independent and dependent variables. | |
| @@ -178,8 +178,8 @@ C Done | |
| parameter(tbrmax=50) | |
| integer troemax | |
| parameter(troemax=50) | |
| - integer lindemax | |
| - parameter(lindemax=50) | |
| + integer lindemax | |
| + parameter(lindemax=50) | |
| integer numcollider | |
| double precision logpr | |
| double precision lowrate | |
| @@ -197,7 +197,7 @@ C Done | |
| double precision pressure | |
| double precision pr | |
| integer troereactionsize | |
| - integer lindereactionsize | |
| + integer lindereactionsize | |
| double precision dg | |
| integer thirdbodyreactionsize | |
| integer nparam | |
| @@ -230,9 +230,9 @@ C Done | |
| double precision rpar(*) | |
| integer reactionarray | |
| integer troereactionarray | |
| - integer lindereactionarray | |
| + integer lindereactionarray | |
| double precision troereactionratearray | |
| - double precision lindereactionratearray | |
| + double precision lindereactionratearray | |
| common /size/ nstate,neq,nparam,reactionsize,troereactionsize, | |
| $ thirdbodyreactionsize,lindereactionsize | |
| common /reac/ reactionratearray(5*rmax), | |
| @@ -275,7 +275,7 @@ C Active variable offsets and counters | |
| integer reactionratearrayoft | |
| integer thirdbodyreactionratearrayoft | |
| integer troereactionratearrayoft | |
| - integer lindereactionratearrayoft | |
| + integer lindereactionratearrayoft | |
| integer temperatureoft | |
| integer pressureoft | |
| integer thermooft | |
| @@ -341,7 +341,7 @@ C Variable offsets for COMMON BLOCK reac | |
| reactionratearrayoft=0 | |
| thirdbodyreactionratearrayoft=reactionratearrayoft+(5*rmax) | |
| troereactionratearrayoft=thirdbodyreactionratearrayoft+(16*tbrmax) | |
| - lindereactionratearrayoft=troereactionratearrayoft+(21*troemax) | |
| + lindereactionratearrayoft=troereactionratearrayoft+(21*troemax) | |
| temperatureoft=lindereactionratearrayoft+(17*lindemax) | |
| pressureoft=temperatureoft+1 | |
| C | |
| @@ -840,8 +840,8 @@ C | |
| f=zzzv3 | |
| call DSVM1(foft+1,2,zzzvbar2,logfoft+1,2) | |
| C | |
| - IF (RNUM .GT. 1 .AND. PNUM .GT. 1) THEN | |
| - zzzv4=1+pr | |
| + IF (RNUM .GT. 1 .AND. PNUM .GT. 1) THEN | |
| + zzzv4=1+pr | |
| zzzv5=1.0d0/zzzv4 | |
| zzzv6=lowrate*zzzv5 | |
| zzzv8=zzzv6*f | |
| @@ -854,8 +854,8 @@ C | |
| frate=zzzv8 | |
| call DSVM3(frateoft+1,2,zzzvbar7,foft+1,2,zzzvbar2, | |
| $ proft+1,2,zzzvbar1,lowrateoft+1,2) | |
| - ELSE | |
| - zzzv4=1+pr | |
| + ELSE | |
| + zzzv4=1+pr | |
| zzzv5=pr/zzzv4 | |
| zzzv6=rate*zzzv5 | |
| zzzv8=zzzv6*f | |
| @@ -868,7 +868,7 @@ C | |
| frate=zzzv8 | |
| call DSVM3(frateoft+1,2,zzzvbar7,foft+1,2,zzzvbar2, | |
| $ proft+1,2,zzzvbar1,rateoft+1,2) | |
| - END IF | |
| + END IF | |
| zzzv4=1+pr | |
| zzzv5=pr/zzzv4 | |
| @@ -1031,27 +1031,27 @@ C | |
| call DSVM3(proft+1,2,zzzvbar4,rateoft+1,2,zzzvbar2,moft+1,2, | |
| $ zzzvbar1,lowrateoft+1,2) | |
| C | |
| - IF (RNUM .GT. 1 .AND. PNUM .GT. 1) THEN | |
| + IF (RNUM .GT. 1 .AND. PNUM .GT. 1) THEN | |
| zzzv4=1+pr | |
| zzzv5=1.0d0/zzzv4 | |
| zzzvbar5=lowrate | |
| zzzvbar4=-zzzv5/zzzv4*zzzvbar5 | |
| zzzvbar2=zzzvbar4 | |
| zzzvbar1=zzzv5 | |
| - frate=zzzv5*zzzvbar5 | |
| + frate=zzzv5*zzzvbar5 | |
| call DSVM2(frateoft+1,2,zzzvbar2,proft+1,2, | |
| $ zzzvbar1,lowrateoft+1,2) | |
| - ELSE | |
| + ELSE | |
| zzzv4=1+pr | |
| zzzv5=pr/zzzv4 | |
| zzzvbar5=rate | |
| zzzvbar4=-zzzv5/zzzv4*zzzvbar5 | |
| zzzvbar2=1.0d0/zzzv4*zzzvbar5+zzzvbar4 | |
| zzzvbar1=zzzv5 | |
| - frate=zzzv5*zzzvbar5 | |
| + frate=zzzv5*zzzvbar5 | |
| call DSVM2(frateoft+1,2,zzzvbar2,proft+1,2, | |
| $ zzzvbar1,rateoft+1,2) | |
| - END IF | |
| + END IF | |
| C | |
| if(lindereactionarray(20*i+9)==1) then | |
| zzzv3=frate/keq | |
| diff --git a/source/daspk/resad.f b/source/daspk/resad.f | |
| index 955a0ab..97675db 100644 | |
| --- a/source/daspk/resad.f | |
| +++ b/source/daspk/resad.f | |
| @@ -19,8 +19,8 @@ C - GENERATED: Wed Jan 31 02:02:16 2007 | |
| parameter(tbrmax=50) | |
| integer troemax | |
| parameter(troemax=50) | |
| - integer lindemax | |
| - parameter(lindemax=50) | |
| + integer lindemax | |
| + parameter(lindemax=50) | |
| integer i | |
| integer j | |
| integer k | |
| @@ -29,7 +29,7 @@ C - GENERATED: Wed Jan 31 02:02:16 2007 | |
| integer nstate | |
| double precision pressure | |
| integer troereactionsize | |
| - integer lindereactionsize | |
| + integer lindereactionsize | |
| integer ires | |
| double precision cj | |
| integer ijac | |
| @@ -49,9 +49,9 @@ C - GENERATED: Wed Jan 31 02:02:16 2007 | |
| $ troereactionsize+lindereactionsize+nstate-1) | |
| integer reactionarray | |
| integer troereactionarray | |
| - integer lindereactionarray | |
| + integer lindereactionarray | |
| double precision troereactionratearray | |
| - double precision lindereactionratearray | |
| + double precision lindereactionratearray | |
| common /size/ nstate,neq,nparam,reactionsize,troereactionsize, | |
| $ thirdbodyreactionsize,lindereactionsize | |
| common /reac/ reactionratearray(5*rmax), | |
| @@ -83,7 +83,7 @@ C Active variable offsets and counters | |
| integer reactionratearrayoft | |
| integer thirdbodyreactionratearrayoft | |
| integer troereactionratearrayoft | |
| - integer lindereactionratearrayoft | |
| + integer lindereactionratearrayoft | |
| integer temperatureoft | |
| integer pressureoft | |
| integer zzzindx | |
| @@ -102,7 +102,7 @@ C Variable offsets for COMMON BLOCK reac | |
| reactionratearrayoft=0 | |
| thirdbodyreactionratearrayoft=reactionratearrayoft+(5*rmax) | |
| troereactionratearrayoft=thirdbodyreactionratearrayoft+(16*tbrmax) | |
| - lindereactionratearrayoft=troereactionratearrayoft+(21*troemax) | |
| + lindereactionratearrayoft=troereactionratearrayoft+(21*troemax) | |
| temperatureoft=lindereactionratearrayoft+(17*lindemax) | |
| pressureoft=temperatureoft+1 | |
| C Number of independent and dependent variables. | |
| @@ -176,8 +176,8 @@ C Done | |
| parameter(tbrmax=50) | |
| integer troemax | |
| parameter(troemax=50) | |
| - integer lindemax | |
| - parameter(lindemax=50) | |
| + integer lindemax | |
| + parameter(lindemax=50) | |
| integer numcollider | |
| double precision logpr | |
| double precision lowrate | |
| @@ -195,7 +195,7 @@ C Done | |
| double precision pressure | |
| double precision pr | |
| integer troereactionsize | |
| - integer lindereactionsize | |
| + integer lindereactionsize | |
| double precision dg | |
| integer thirdbodyreactionsize | |
| integer nparam | |
| @@ -228,9 +228,9 @@ C Done | |
| double precision rpar(*) | |
| integer reactionarray | |
| integer troereactionarray | |
| - integer lindereactionarray | |
| + integer lindereactionarray | |
| double precision troereactionratearray | |
| - double precision lindereactionratearray | |
| + double precision lindereactionratearray | |
| common /size/ nstate,neq,nparam,reactionsize,troereactionsize, | |
| $ thirdbodyreactionsize,lindereactionsize | |
| common /reac/ reactionratearray(5*rmax), | |
| @@ -273,7 +273,7 @@ C Active variable offsets and counters | |
| integer reactionratearrayoft | |
| integer thirdbodyreactionratearrayoft | |
| integer troereactionratearrayoft | |
| - integer lindereactionratearrayoft | |
| + integer lindereactionratearrayoft | |
| integer temperatureoft | |
| integer pressureoft | |
| integer yoft | |
| @@ -335,7 +335,7 @@ C Variable offsets for COMMON BLOCK reac | |
| reactionratearrayoft=0 | |
| thirdbodyreactionratearrayoft=reactionratearrayoft+(5*rmax) | |
| troereactionratearrayoft=thirdbodyreactionratearrayoft+(16*tbrmax) | |
| - lindereactionratearrayoft=troereactionratearrayoft+(21*troemax) | |
| + lindereactionratearrayoft=troereactionratearrayoft+(21*troemax) | |
| temperatureoft=lindereactionratearrayoft+(17*lindemax) | |
| pressureoft=temperatureoft+1 | |
| C | |
| @@ -785,7 +785,7 @@ C | |
| f=zzzv3 | |
| call DSVM1(foft+1,2,zzzvbar2,logfoft+1,2) | |
| C | |
| - if (rnum .gt. 1 .and. pnum .gt. 1) then | |
| + if (rnum .gt. 1 .and. pnum .gt. 1) then | |
| zzzv4=1+pr | |
| zzzv5=1.0d0/zzzv4 | |
| zzzv6=lowrate*zzzv5 | |
| @@ -798,7 +798,7 @@ C | |
| frate=zzzv8 | |
| call DSVM2(frateoft+1,2,zzzvbar7,foft+1,2, | |
| $ zzzvbar2,proft+1,2) | |
| - else | |
| + else | |
| zzzv4=1+pr | |
| zzzv5=pr/zzzv4 | |
| zzzv6=rate*zzzv5 | |
| @@ -811,7 +811,7 @@ C | |
| frate=zzzv8 | |
| call DSVM2(frateoft+1,2,zzzvbar7,foft+1,2, | |
| $ zzzvbar2,proft+1,2) | |
| - end if | |
| + end if | |
| C | |
| if(troereactionarray(21*i+9)==1) then | |
| zzzv3=frate/keq | |
| @@ -933,7 +933,7 @@ C | |
| $ +i+1) | |
| direction=lindereactionarray(20*i+9) | |
| C | |
| - if (rnum .gt. 1 .and. pnum .gt. 1) then | |
| + if (rnum .gt. 1 .and. pnum .gt. 1) then | |
| zzzv4=1+pr | |
| zzzv5=1.0d0/zzzv4 | |
| zzzvbar5=lowrate | |
| @@ -941,7 +941,7 @@ C | |
| zzzvbar2=zzzvbar4 | |
| frate=zzzv8 | |
| call DSVM1(frateoft+1,2,zzzvbar2,proft+1,2) | |
| - else | |
| + else | |
| zzzv4=1+pr | |
| zzzv5=pr/zzzv4 | |
| zzzvbar5=rate | |
| @@ -949,7 +949,7 @@ C | |
| zzzvbar2=1.0d0/zzzv4*zzzvbar5+zzzvbar4 | |
| frate=zzzv8 | |
| call DSVM1(frateoft+1,2,zzzvbar2,proft+1,2) | |
| - end if | |
| + end if | |
| C | |
| if(lindereactionarray(20*i+9)==1) then | |
| zzzv3=frate/keq | |
| diff --git a/source/dassl/Makefile b/source/dassl/Makefile | |
| index 2a035cd..182bfbd 100644 | |
| --- a/source/dassl/Makefile | |
| +++ b/source/dassl/Makefile | |
| @@ -13,10 +13,40 @@ BUILDDIR=../../build/dassl | |
| # The directory in which to place compiled executables and JAR files | |
| BINDIR=../../bin | |
| -# The Fortran 90 compiler to use and flags to use when compiling Fortran 90 | |
| -# code | |
| -F90=g95 | |
| -F90FLAGS=-fmod=$(BUILDDIR) -ftrace=full | |
| +# The Fortran 90 compiler to use and flags to use when compiling Fortran code | |
| +# Call with 'make F90=g95' if you want to use g95 | |
| +# or 'make F90=gfortran' for GNU Fortran (recommended) | |
| +# Here we set the default | |
| +#F90=g95 | |
| +F90=gfortran | |
| + | |
| +ifeq ($(F90),g95) | |
| +F90FLAGS = -fmod=$(BUILDDIR) -ftrace=full # used for dassl and daspk | |
| +endif ###### END OF g95 SETTINGS | |
| + | |
| +ifeq ($(F90),gfortran) | |
| +# --fpe-trap=invalid,zero,underflow,overflow | |
| +# The above flag causes problems at least with fame. Maybe a bug in gfortran? (Maybe a bug in fame.) | |
| +F90FLAGS = -ftrapv -fbounds-check -frange-check \ | |
| + -ggdb -J""$(BUILDDIR)"" -O3 -Wall -Wno-unused | |
| +# if gfortran>4.3 then add -fbacktrace (it's not supported in earlier versions) | |
| +ifeq ($(shell gfortran --version 2>/dev/zero|grep -iqs '^GNU Fortran.* [4-9]\.[3-9]\.[0-9]' && echo "ok"), ok) | |
| +F90FLAGS += -fbacktrace | |
| +endif | |
| +F90FLAGS_NDEBUG = $(F90FLAGS) # used for dassl and daspk | |
| + | |
| +# call as `make MACOS=true F90=gfortran` if you want MacOS X 10.6+ 64-bit intel core2 features | |
| +ifdef MACOS | |
| +F90FLAGS += -arch x86_64 -march=core2 | |
| +F90_EXTRA_LDFLAGS += -framework vecLIB | |
| +endif | |
| + | |
| +# Special flags for dassl d*.f files | |
| +# Don't check for bounds on arrays beacuse dlinpk breaks them on purpose. | |
| +# Don't warn about tab characters | |
| +DASSL_FFLAGS = -fno-bounds-check -Wtabs | |
| +endif ###### END OF gfortran SETTINGS | |
| + | |
| LDFLAGS= $(F90_EXTRA_LDFLAGS) | |
| @@ -30,6 +60,11 @@ $(BINDIR)/dasslAUTO.exe: $(OBJ) | |
| mkdir -p $(BINDIR) | |
| $(F90) $(LDFLAGS) $(OBJ) -o $(BINDIR)/dasslAUTO.exe | |
| +# only .f files that begin with a d (eg. daux.f, dassl.f, dlinpk.f) | |
| +$(BUILDDIR)/d%.o: d%.f | |
| + mkdir -p $(BUILDDIR) | |
| + $(F90) $(F90FLAGS) $(DASSL_FFLAGS) -c $< -o $@ | |
| + | |
| $(BUILDDIR)/%.o: %.f | |
| mkdir -p $(BUILDDIR) | |
| $(F90) $(F90FLAGS) -c $< -o $@ | |
| diff --git a/source/dassl/call_dasslAUTO.f90 b/source/dassl/call_dasslAUTO.f90 | |
| index df74600..535fae6 100644 | |
| --- a/source/dassl/call_dasslAUTO.f90 | |
| +++ b/source/dassl/call_dasslAUTO.f90 | |
| @@ -26,14 +26,14 @@ | |
| & REACTIONARRAY(9*RMAX), THIRDBODYREACTIONARRAY(20*TBRMAX), & | |
| & TROEREACTIONARRAY(21*TROEMAX), I, J, IDID, impspecies, & | |
| & AUTOFLAG, ESPECIES, EREACTIONSIZE, ConstantConcentration(SPMAX+1), & | |
| - & LINDEREACTIONSIZE, LINDEREACTIONARRAY(20*LINDEMAX) | |
| + & LINDEREACTIONSIZE, LINDEREACTIONARRAY(20*LINDEMAX) | |
| DOUBLE PRECISION Y(SPMAX), YPRIME(SPMAX), T, TOUT, RTOL, ATOL,& | |
| & RWORK(51+9*SPMAX+SPMAX**2), TEMPERATURE, PRESSURE,& | |
| & REACTIONRATEARRAY(5*rmax),& | |
| & THIRDBODYREACTIONRATEARRAY(16*Tbrmax),& | |
| & TROEREACTIONRATEARRAY(21*TROemax), targetconc, THRESH, & | |
| - & CORETHRESH, LINDEREACTIONRATEARRAY(17*LINDEMAX) | |
| + & CORETHRESH, LINDEREACTIONRATEARRAY(17*LINDEMAX) | |
| ! 4/25/08 gmagoon:make auto arrays allocatable and double | |
| ! precision for KVEC | |
| INTEGER, DIMENSION(:), ALLOCATABLE :: NEREAC,NEPROD | |
| @@ -47,7 +47,7 @@ | |
| & TROEREACTIONRATEARRAY, temperature, pressure,& | |
| & REACTIONARRAY, THIRDBODYREACTIONARRAY,& | |
| & TROEREACTIONARRAY, ConstantConcentration, & | |
| - & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| + & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| !5/12/08 gmagoon: added timing (cf. http://beige.ucs.indiana.edu/B673/node105.html) | |
| ! integer count_0, count_1, count_rate, count_max | |
| ! double precision start, finish | |
| @@ -100,7 +100,7 @@ | |
| READ(12,*) THIRDBODYREACTIONSIZE | |
| READ(12,*)(THIRDBODYREACTIONARRAY(I),I=1,20*THIRDBODYREACTIONSIZE) | |
| READ(12,*)(THIRDBODYREACTIONRATEARRAY(I),I=1, & | |
| - & 16*THIRDBODYREACTIONSIZE) | |
| + & 16*THIRDBODYREACTIONSIZE) | |
| ! READ INFORMATION ABOUT TROEREACTIONS | |
| READ(12,*) TROEREACTIONSIZE | |
| @@ -109,59 +109,59 @@ | |
| ! READ INFORMATION ABOUT LINDEMANNREACTIONS | |
| READ(12,*) LINDEREACTIONSIZE | |
| - READ(12,*)(LINDEREACTIONARRAY(I),I=1,20*LINDEREACTIONSIZE) | |
| - READ(12,*)(LINDEREACTIONRATEARRAY(I),I=1,17*LINDEREACTIONSIZE) | |
| + READ(12,*)(LINDEREACTIONARRAY(I),I=1,20*LINDEREACTIONSIZE) | |
| + READ(12,*)(LINDEREACTIONRATEARRAY(I),I=1,17*LINDEREACTIONSIZE) | |
| ! 4/24/08 gmagoon: if autoFlag = 1, read in additional information | |
| ! specific to automatic time stepping | |
| - IF (AUTOFLAG .EQ. 1) THEN | |
| - ! read the threshhold, corresponding to the value of | |
| - ! termination tolerance specified in condition.txt input file | |
| - !CORETHRESH is the threshhold for moving something from edge to core, | |
| - !whereas THRESH is the threshhold for terminating the run before the end | |
| - !THRESH >= CORETHRESH | |
| - READ(12,*) THRESH, CORETHRESH | |
| - ! read the number of edge species and edge reactions | |
| - READ(12,*) ESPECIES, EREACTIONSIZE | |
| - ! allocate memory for arrays | |
| - ALLOCATE(NEREAC(EREACTIONSIZE), NEPROD(EREACTIONSIZE),& | |
| - & IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3),& | |
| - & KVEC(EREACTIONSIZE)) | |
| - ! read in the reaction parameters for each reaction; | |
| - ! a maximum of 3 products and 3 reactants is assumed | |
| - ! for each reaction; parameters read for each reaction | |
| - ! are: number of reactants, number of products, | |
| - ! three reactant ID's (integers from 1 to NSTATE-1), | |
| - ! three product ID's (integers from 1 to ESPECIES), | |
| - ! and the rate coefficient k, such that dCi/dt=k*Ca*Cb; | |
| - ! note that cases where abs. value of stoic. coeff. | |
| - ! does not equal one are handled by using repeated | |
| - ! reactant/product IDs | |
| - ! note: use of KVEC rather than Arrhenius parameters | |
| - ! requires assumption that system is isothermal | |
| - ! (and isobaric for pressure dependence) | |
| - DO I=1, EREACTIONSIZE | |
| - READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| - & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| - & IDEPROD(I,2), IDEPROD(I,3), KVEC(I) | |
| - ! alternative for reading Arrhenius parameters instead | |
| - ! of k values; this allows easier extention to | |
| - ! non-isothermal systems in the future | |
| - ! form: k=A*T^n*e^(Ea/(RT)) *? | |
| - ! units: A[=], n[=]dimensionless, Ea[=] | |
| - ! READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| + IF (AUTOFLAG .EQ. 1) THEN | |
| + ! read the threshhold, corresponding to the value of | |
| + ! termination tolerance specified in condition.txt input file | |
| + !CORETHRESH is the threshhold for moving something from edge to core, | |
| + !whereas THRESH is the threshhold for terminating the run before the end | |
| + !THRESH >= CORETHRESH | |
| + READ(12,*) THRESH, CORETHRESH | |
| + ! read the number of edge species and edge reactions | |
| + READ(12,*) ESPECIES, EREACTIONSIZE | |
| + ! allocate memory for arrays | |
| + ALLOCATE(NEREAC(EREACTIONSIZE), NEPROD(EREACTIONSIZE),& | |
| + & IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3),& | |
| + & KVEC(EREACTIONSIZE)) | |
| + ! read in the reaction parameters for each reaction; | |
| + ! a maximum of 3 products and 3 reactants is assumed | |
| + ! for each reaction; parameters read for each reaction | |
| + ! are: number of reactants, number of products, | |
| + ! three reactant ID's (integers from 1 to NSTATE-1), | |
| + ! three product ID's (integers from 1 to ESPECIES), | |
| + ! and the rate coefficient k, such that dCi/dt=k*Ca*Cb; | |
| + ! note that cases where abs. value of stoic. coeff. | |
| + ! does not equal one are handled by using repeated | |
| + ! reactant/product IDs | |
| + ! note: use of KVEC rather than Arrhenius parameters | |
| + ! requires assumption that system is isothermal | |
| + ! (and isobaric for pressure dependence) | |
| + DO I=1, EREACTIONSIZE | |
| + READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| + & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| + & IDEPROD(I,2), IDEPROD(I,3), KVEC(I) | |
| + ! alternative for reading Arrhenius parameters instead | |
| + ! of k values; this allows easier extention to | |
| + ! non-isothermal systems in the future | |
| + ! form: k=A*T^n*e^(Ea/(RT)) *? | |
| + ! units: A[=], n[=]dimensionless, Ea[=] | |
| + ! READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| ! & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| ! & IDEPROD(I,2),IDEPROD(I,3), AVEC(I), NVEC(I), & | |
| ! & EAVEC(I) | |
| - ! for isothermal, isobaric systems, (or just isothermal | |
| - ! systems if pressure dependence is not considered) | |
| + ! for isothermal, isobaric systems, (or just isothermal | |
| + ! systems if pressure dependence is not considered) | |
| ! the following may be calculated here once | |
| - ! (versus calculating at every timestep) | |
| - ! ...units may need adjustment: | |
| - ! KVEC(I)=AVEC(I)*TEMPERATURE**NVEC(I)*EXP(EAVEC(I) & | |
| - ! & /(8.314*TEMPERATURE)) | |
| - END DO | |
| - END IF | |
| + ! (versus calculating at every timestep) | |
| + ! ...units may need adjustment: | |
| + ! KVEC(I)=AVEC(I)*TEMPERATURE**NVEC(I)*EXP(EAVEC(I) & | |
| + ! & /(8.314*TEMPERATURE)) | |
| + END DO | |
| + END IF | |
| ! read constantConcentration data (if flag = 1 then the concentration of that species will not be integrated) | |
| ! there is one integer for each species (up to nstate-1), then the last one is for the VOLUME | |
| @@ -183,7 +183,7 @@ | |
| ! Fortran90 vs. Fortran 77; perhaps it was a problem with | |
| ! non-auto cases after my modifications and I just didn't | |
| ! notice it | |
| - CLOSE(13) | |
| + CLOSE(13) | |
| CLOSE(14) | |
| CALL SOLVEODE(Y, YPRIME, T, TOUT, INFO, RTOL, ATOL, IDID, & | |
| @@ -197,8 +197,8 @@ | |
| ! this should prevent "deallocated a bad pointer" error when | |
| ! autoflag is not 1 | |
| IF (AUTOFLAG .EQ. 1) THEN | |
| - DEALLOCATE (NEREAC, NEPROD, KVEC, & | |
| - & IDEREAC, IDEPROD) | |
| + DEALLOCATE (NEREAC, NEPROD, KVEC, & | |
| + & IDEREAC, IDEPROD) | |
| END IF | |
| !5/12/08 gmagoon: added timing (see above) | |
| @@ -226,20 +226,20 @@ | |
| ! INITIALIZE VARIABLES IN COMMON BLOC | |
| INTEGER SPMAX, RMAX, TBRMAX, TROEMAX, AUTOFLAG, ESPECIES, & | |
| - & EREACTIONSIZE, LINDEMAX | |
| + & EREACTIONSIZE, LINDEMAX | |
| INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| INTEGER IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3) | |
| DOUBLE PRECISION KVEC(EREACTIONSIZE),MAXRATIO(ESPECIES), & | |
| - & HIGHESTRATIO | |
| + & HIGHESTRATIO | |
| PARAMETER (SPMAX = 1500, RMAX = 100000, TBRMAX=100, TROEMAX=100, & | |
| - & LINDEMAX=100) | |
| + & LINDEMAX=100) | |
| INTEGER REACTIONSIZE, THIRDBODYREACTIONSIZE, TROEREACTIONSIZE, & | |
| & REACTIONARRAY(9*RMAX), THIRDBODYREACTIONARRAY(20*TBRMAX), & | |
| & TROEREACTIONARRAY(21*TROEMAX), I, J, NSTATE, EDGEFLAG, & | |
| & EDGEFLAGCORE, CORESTORED, ConstantConcentration(SPMAX+1), & | |
| - & LINDEREACTIONSIZE, LINDEREACTIONARRAY(20*LINDEMAX) | |
| + & LINDEREACTIONSIZE, LINDEREACTIONARRAY(20*LINDEMAX) | |
| DOUBLE PRECISION REACTIONRATEARRAY(5*rmax), & | |
| & THIRDBODYREACTIONRATEARRAY(16*Tbrmax), & | |
| @@ -253,7 +253,7 @@ | |
| & TROEREACTIONRATEARRAY, temperature, pressure,& | |
| & REACTIONARRAY, THIRDBODYREACTIONARRAY,& | |
| & TROEREACTIONARRAY, ConstantConcentration, & | |
| - & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| + & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| INTEGER INFO(30), LIW, LRW, IWORK(41 + NSTATE), IPAR(1),IDID, iter, & | |
| & IMPSPECIES, conc, ITER_OUTPT, IWORK_OUTPT(41 + NSTATE) | |
| @@ -299,10 +299,10 @@ | |
| & TROEREACTIONRATEARRAY(21*I+1) | |
| END DO | |
| - DO I=0,LINDEREACTIONSIZE-1 | |
| - RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+I+1) = & | |
| - & LINDEREACTIONRATEARRAY(17*I+1) | |
| - END DO | |
| + DO I=0,LINDEREACTIONSIZE-1 | |
| + RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+I+1) = & | |
| + & LINDEREACTIONRATEARRAY(17*I+1) | |
| + END DO | |
| ! ********************************** | |
| ! 5/13/08 gmagoon: added time stepping timing | |
| ! call system_clock(count_0T, count_rateT, count_maxT) | |
| @@ -310,53 +310,53 @@ | |
| CALL GETFLUX(Y, YPRIME, RPAR) | |
| - | |
| + | |
| ! 4/24/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| ! determine EDGEFLAG and EDGEFLAGCORE (-1 if flux threshhold has not yet been met, | |
| ! positive integer otherwise) | |
| - EDGEFLAG = -1 | |
| - EDGEFLAGCORE = -1 | |
| - !initialize flag CORESTORED to -1 indicating that the output values (when core inclusion threshold is exceeded) have not been stored yet; this will be set to 1 once the values are stored | |
| - CORESTORED = -1 | |
| - !initialize MAXRATIO to a vector of all zeroes; | |
| - !this variable will track the maxiumum | |
| - !of rate(i)/Rchar for each edge species i, with respect to time | |
| - MAXRATIO = 0 | |
| - !initialize HIGHESTRATIO to 0; this variable (a scalar) | |
| - !tracks the maximum of maxratio; when a new maximum is | |
| - !attained, the present time step creating the new maximum | |
| - !will be stored for output from the ODE solver to the Java code | |
| - HIGHESTRATIO = 0 | |
| - IF (AUTOFLAG.eq.1) THEN | |
| - CALL EDGEFLUX(EDGEFLAG,EDGEFLAGCORE,Y,YPRIME,THRESH,CORETHRESH,ESPECIES, & | |
| + EDGEFLAG = -1 | |
| + EDGEFLAGCORE = -1 | |
| + !initialize flag CORESTORED to -1 indicating that the output values (when core inclusion threshold is exceeded) have not been stored yet; this will be set to 1 once the values are stored | |
| + CORESTORED = -1 | |
| + !initialize MAXRATIO to a vector of all zeroes; | |
| + !this variable will track the maxiumum | |
| + !of rate(i)/Rchar for each edge species i, with respect to time | |
| + MAXRATIO = 0 | |
| + !initialize HIGHESTRATIO to 0; this variable (a scalar) | |
| + !tracks the maximum of maxratio; when a new maximum is | |
| + !attained, the present time step creating the new maximum | |
| + !will be stored for output from the ODE solver to the Java code | |
| + HIGHESTRATIO = 0 | |
| + IF (AUTOFLAG.eq.1) THEN | |
| + CALL EDGEFLUX(EDGEFLAG,EDGEFLAGCORE,Y,YPRIME,THRESH,CORETHRESH,ESPECIES, & | |
| & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| & MAXRATIO,PRUNEVEC,NSTATE) | |
| - !update HIGHESTRATIO | |
| - !note that we cannot exit the do loop once the IF statement is | |
| - !caught because the HIGHESTRATIO will not necessarily have the highest value | |
| - DO I=1, ESPECIES | |
| - IF (MAXRATIO(I) .GT. HIGHESTRATIO) THEN | |
| - HIGHESTRATIO = MAXRATIO(I) | |
| - END IF | |
| - END DO | |
| - !when core flux threshold is exceeded for the first time, store the values for output | |
| - !we want to use the first point of exceeding the core inclusion threshold | |
| - !(aka error tolerance) to determine which species to add to the core | |
| - !note: TOTALREACTIONFLUX apparently tracks integrated flux, not | |
| - !instantaneous flux, so setting value to be zero here should be OK... | |
| - !in any case, the result doesn't seem to be used by the Java code | |
| - IF(EDGEFLAGCORE .GT. 0 .AND. CORESTORED .EQ. -1) THEN | |
| - ITER_OUTPT=0 | |
| - TIME_OUTPT=TIME | |
| - Y_OUTPT = Y | |
| - YPRIME_OUTPT = YPRIME | |
| - !IWORK_OUTPT = IWORK | |
| - !RWORK_OUTPT = RWORK | |
| - TOTALREACTIONFLUX_OUTPT = 0 | |
| - !PRUNEVEC_OUTPT = PRUNEVEC !note that we do not copy prunevec for the output value; this will be based on the final time integrated to (in case core threshold, but not termination threshold, is exceeded at t=0...it is ok to prune species that have zero flux at t=0 | |
| - CORESTORED = 1 | |
| - END IF | |
| - ENDIF | |
| + !update HIGHESTRATIO | |
| + !note that we cannot exit the do loop once the IF statement is | |
| + !caught because the HIGHESTRATIO will not necessarily have the highest value | |
| + DO I=1, ESPECIES | |
| + IF (MAXRATIO(I) .GT. HIGHESTRATIO) THEN | |
| + HIGHESTRATIO = MAXRATIO(I) | |
| + END IF | |
| + END DO | |
| + !when core flux threshold is exceeded for the first time, store the values for output | |
| + !we want to use the first point of exceeding the core inclusion threshold | |
| + !(aka error tolerance) to determine which species to add to the core | |
| + !note: TOTALREACTIONFLUX apparently tracks integrated flux, not | |
| + !instantaneous flux, so setting value to be zero here should be OK... | |
| + !in any case, the result doesn't seem to be used by the Java code | |
| + IF(EDGEFLAGCORE .GT. 0 .AND. CORESTORED .EQ. -1) THEN | |
| + ITER_OUTPT=0 | |
| + TIME_OUTPT=TIME | |
| + Y_OUTPT = Y | |
| + YPRIME_OUTPT = YPRIME | |
| + !IWORK_OUTPT = IWORK | |
| + !RWORK_OUTPT = RWORK | |
| + TOTALREACTIONFLUX_OUTPT = 0 | |
| + !PRUNEVEC_OUTPT = PRUNEVEC !note that we do not copy prunevec for the output value; this will be based on the final time integrated to (in case core threshold, but not termination threshold, is exceeded at t=0...it is ok to prune species that have zero flux at t=0 | |
| + CORESTORED = 1 | |
| + END IF | |
| + ENDIF | |
| @@ -374,7 +374,7 @@ | |
| IMPSPECIES = 1 | |
| conc = -1 | |
| END IF | |
| - | |
| + | |
| ! open 'SpeciesProfiles.txt' output file to append to | |
| OPEN(UNIT=17, FILE='SpeciesProfiles.txt', ACCESS = 'APPEND') | |
| @@ -408,34 +408,34 @@ | |
| tout = 200*time | |
| end if | |
| ! write(*,*) time, y(impspecies), targetConc*y(nstate) | |
| - ! 4/24/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| - ! determine EDGEFLAG | |
| - IF (AUTOFLAG.eq.1) THEN | |
| - CALL EDGEFLUX(EDGEFLAG,EDGEFLAGCORE,Y, YPRIME,THRESH,CORETHRESH,ESPECIES, & | |
| - & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| - & MAXRATIO,PRUNEVEC,NSTATE) | |
| - !update HIGHESTRATIO | |
| - DO I=1, ESPECIES | |
| - IF (MAXRATIO(I) .GT. HIGHESTRATIO) THEN | |
| - HIGHESTRATIO = MAXRATIO(I) | |
| - END IF | |
| - END DO | |
| - !when core flux threshold is exceeded for the first time, store the values for output | |
| - IF(EDGEFLAGCORE .GT. 0 .AND. CORESTORED .EQ. -1) THEN | |
| - ITER_OUTPT=ITER | |
| - TIME_OUTPT=TIME | |
| - Y_OUTPT = Y | |
| - YPRIME_OUTPT = YPRIME | |
| - !IWORK_OUTPT = IWORK | |
| - !RWORK_OUTPT = RWORK | |
| - TOTALREACTIONFLUX_OUTPT = TOTALREACTIONFLUX | |
| - CORESTORED = 1 | |
| - END IF | |
| - END IF | |
| + ! 4/24/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| + ! determine EDGEFLAG | |
| + IF (AUTOFLAG.eq.1) THEN | |
| + CALL EDGEFLUX(EDGEFLAG,EDGEFLAGCORE,Y, YPRIME,THRESH,CORETHRESH,ESPECIES, & | |
| + & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| + & MAXRATIO,PRUNEVEC,NSTATE) | |
| + !update HIGHESTRATIO | |
| + DO I=1, ESPECIES | |
| + IF (MAXRATIO(I) .GT. HIGHESTRATIO) THEN | |
| + HIGHESTRATIO = MAXRATIO(I) | |
| + END IF | |
| + END DO | |
| + !when core flux threshold is exceeded for the first time, store the values for output | |
| + IF(EDGEFLAGCORE .GT. 0 .AND. CORESTORED .EQ. -1) THEN | |
| + ITER_OUTPT=ITER | |
| + TIME_OUTPT=TIME | |
| + Y_OUTPT = Y | |
| + YPRIME_OUTPT = YPRIME | |
| + !IWORK_OUTPT = IWORK | |
| + !RWORK_OUTPT = RWORK | |
| + TOTALREACTIONFLUX_OUTPT = TOTALREACTIONFLUX | |
| + CORESTORED = 1 | |
| + END IF | |
| + END IF | |
| ! save time and concentrations to 'SpeciesProfiles.txt' | |
| WRITE(17,1700) TIME, ( Y(I)/Y(NSTATE), I=1, NSTATE-1) | |
| -1700 FORMAT(99999(G12.5,' ')) ! there should be a tab character between the quotes | |
| +1700 FORMAT(99999(G12.5,' ')) ! there should be a tab character between the quotes | |
| GO TO 1 | |
| END IF | |
| @@ -457,13 +457,13 @@ | |
| !target time/conversion has been reached | |
| !in either case, CORESTORED should be -1 | |
| IF (CORESTORED .EQ. -1) THEN | |
| - ITER_OUTPT=ITER | |
| - TIME_OUTPT=TIME | |
| - Y_OUTPT = Y | |
| - YPRIME_OUTPT = YPRIME | |
| - !IWORK_OUTPT = IWORK | |
| - !RWORK_OUTPT = RWORK | |
| - TOTALREACTIONFLUX_OUTPT = TOTALREACTIONFLUX | |
| + ITER_OUTPT=ITER | |
| + TIME_OUTPT=TIME | |
| + Y_OUTPT = Y | |
| + YPRIME_OUTPT = YPRIME | |
| + !IWORK_OUTPT = IWORK | |
| + !RWORK_OUTPT = RWORK | |
| + TOTALREACTIONFLUX_OUTPT = TOTALREACTIONFLUX | |
| END IF | |
| IWORK_OUTPT = IWORK | |
| RWORK_OUTPT = RWORK | |
| @@ -495,12 +495,12 @@ | |
| !, the final time integrated to, | |
| !along with pruning information | |
| IF (AUTOFLAG .EQ. 1) THEN | |
| - WRITE(16,*) EDGEFLAG | |
| - WRITE(16,*) TIME | |
| - DO I=1, ESPECIES | |
| - WRITE(16,*) PRUNEVEC(I) | |
| - WRITE(16,*) MAXRATIO(I) | |
| - END DO | |
| + WRITE(16,*) EDGEFLAG | |
| + WRITE(16,*) TIME | |
| + DO I=1, ESPECIES | |
| + WRITE(16,*) PRUNEVEC(I) | |
| + WRITE(16,*) MAXRATIO(I) | |
| + END DO | |
| END IF | |
| CLOSE(16) | |
| @@ -532,71 +532,71 @@ | |
| ! when edgeflux exceeds core threshold, edgeflagcore is set to the offending species ID | |
| ! if edgeflux also exceeds the termination threshold flux, edgeflag is set to the offending species ID | |
| SUBROUTINE EDGEFLUX(EDGEFLAG,EDGEFLAGCORE,Y,YPRIME,THRESH,CORETHRESH,ESPECIES, & | |
| - & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD, & | |
| - & KVEC,MAXRATIO,PRUNEVEC,NSTATE) | |
| - IMPLICIT NONE | |
| - INTEGER EDGEFLAG, EDGEFLAGCORE, ESPECIES, EREACTIONSIZE, NSTATE, I, J, K | |
| - DOUBLE PRECISION THRESH, CORETHRESH, FLUXRC, RFLUX, Y(NSTATE), YPRIME(NSTATE) | |
| - DOUBLE PRECISION, DIMENSION(:), ALLOCATABLE :: RATE | |
| - INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| + & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD, & | |
| + & KVEC,MAXRATIO,PRUNEVEC,NSTATE) | |
| + IMPLICIT NONE | |
| + INTEGER EDGEFLAG, EDGEFLAGCORE, ESPECIES, EREACTIONSIZE, NSTATE, I, J, K | |
| + DOUBLE PRECISION THRESH, CORETHRESH, FLUXRC, RFLUX, Y(NSTATE), YPRIME(NSTATE) | |
| + DOUBLE PRECISION, DIMENSION(:), ALLOCATABLE :: RATE | |
| + INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| INTEGER IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3) | |
| - INTEGER PRUNEVEC(ESPECIES) | |
| + INTEGER PRUNEVEC(ESPECIES) | |
| DOUBLE PRECISION KVEC(EREACTIONSIZE), RATIO, MAXRATIO(ESPECIES) | |
| - | |
| - ALLOCATE(RATE(ESPECIES)) | |
| - ! initialize array to have all zeroes | |
| - RATE=0 | |
| - ! it is assumed edgeflag = -1 at this point, since | |
| + | |
| + ALLOCATE(RATE(ESPECIES)) | |
| + ! initialize array to have all zeroes | |
| + RATE=0 | |
| + ! it is assumed edgeflag = -1 at this point, since | |
| ! this should be the only way to access this subroutine | |
| ! calculate characteristic flux, FLUXRC | |
| - CALL RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| - | |
| - !initialize PRUNEVEC; at first, assume everything is prunable | |
| - PRUNEVEC=1 | |
| - | |
| - ! calculate the vector of fluxes for each species | |
| - ! by summing contributions from each reaction | |
| - ILOOP: DO I=1, EREACTIONSIZE | |
| - ! calculate reaction flux by multiplying k | |
| - ! by concentration(s) | |
| - RFLUX = KVEC(I) | |
| - KLOOP: DO K=1, NEREAC(I) | |
| - RFLUX = RFLUX*Y(IDEREAC(I,K))/Y(NSTATE) | |
| - END DO KLOOP | |
| - ! loop over reaction products, adding RFLUX | |
| - JLOOP: DO J=1, NEPROD(I) | |
| - RATE(IDEPROD(I,J))=RATE(IDEPROD(I,J))+ RFLUX | |
| - !if RFLUX is zero, then presumably one of the | |
| - !reactant concentrations is zero (it is assumed | |
| - !that k != 0), and therefore, we don't want to | |
| - !prune the species yet | |
| - IF(RFLUX .EQ. 0.0) THEN | |
| - PRUNEVEC(IDEPROD(I,J)) = 0 | |
| - END IF | |
| - END DO JLOOP | |
| - END DO ILOOP | |
| - | |
| - | |
| - ! check if any of the edge species fluxes exceed | |
| - ! the threshhold and update the MAXRATIO vector | |
| - FLOOP: DO I=1, ESPECIES | |
| - RATIO = RATE(I)/FLUXRC | |
| - !if we reach the error tolerance (aka core tolerance), | |
| - !set EDGEFLAGCORE to the species ID | |
| - !if we also reach the termination tolerance, set EDGEFLAG to the species ID | |
| - IF (RATIO .GE. CORETHRESH) THEN | |
| - EDGEFLAGCORE = I | |
| - IF(RATIO .GE. THRESH) THEN | |
| - EDGEFLAG = I | |
| - END IF | |
| - END IF | |
| - !update the MAXRATIO vector | |
| - IF(RATIO .GT. MAXRATIO(I)) THEN | |
| - MAXRATIO(I) = RATIO | |
| - END IF | |
| - END DO FLOOP | |
| - DEALLOCATE(RATE) | |
| + CALL RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| + | |
| + !initialize PRUNEVEC; at first, assume everything is prunable | |
| + PRUNEVEC=1 | |
| + | |
| + ! calculate the vector of fluxes for each species | |
| + ! by summing contributions from each reaction | |
| + ILOOP: DO I=1, EREACTIONSIZE | |
| + ! calculate reaction flux by multiplying k | |
| + ! by concentration(s) | |
| + RFLUX = KVEC(I) | |
| + KLOOP: DO K=1, NEREAC(I) | |
| + RFLUX = RFLUX*Y(IDEREAC(I,K))/Y(NSTATE) | |
| + END DO KLOOP | |
| + ! loop over reaction products, adding RFLUX | |
| + JLOOP: DO J=1, NEPROD(I) | |
| + RATE(IDEPROD(I,J))=RATE(IDEPROD(I,J))+ RFLUX | |
| + !if RFLUX is zero, then presumably one of the | |
| + !reactant concentrations is zero (it is assumed | |
| + !that k != 0), and therefore, we don't want to | |
| + !prune the species yet | |
| + IF(RFLUX .EQ. 0.0) THEN | |
| + PRUNEVEC(IDEPROD(I,J)) = 0 | |
| + END IF | |
| + END DO JLOOP | |
| + END DO ILOOP | |
| + | |
| + | |
| + ! check if any of the edge species fluxes exceed | |
| + ! the threshhold and update the MAXRATIO vector | |
| + FLOOP: DO I=1, ESPECIES | |
| + RATIO = RATE(I)/FLUXRC | |
| + !if we reach the error tolerance (aka core tolerance), | |
| + !set EDGEFLAGCORE to the species ID | |
| + !if we also reach the termination tolerance, set EDGEFLAG to the species ID | |
| + IF (RATIO .GE. CORETHRESH) THEN | |
| + EDGEFLAGCORE = I | |
| + IF(RATIO .GE. THRESH) THEN | |
| + EDGEFLAG = I | |
| + END IF | |
| + END IF | |
| + !update the MAXRATIO vector | |
| + IF(RATIO .GT. MAXRATIO(I)) THEN | |
| + MAXRATIO(I) = RATIO | |
| + END IF | |
| + END DO FLOOP | |
| + DEALLOCATE(RATE) | |
| END SUBROUTINE EDGEFLUX | |
| ! RCHAR calculates the characteristic flux (i.e. the | |
| @@ -611,18 +611,18 @@ END SUBROUTINE EDGEFLUX | |
| ! plus one) | |
| SUBROUTINE RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| IMPLICIT NONE | |
| - INTEGER NSTATE, I | |
| - DOUBLE PRECISION SSF, FLUXRC, Y(NSTATE), YPRIME(NSTATE) | |
| - ! compute the sum of squared fluxes | |
| - SSF=0.0 | |
| - DO I=1, NSTATE-1 | |
| - ! add (dCi/dt)^2 with dCi/dt computed based on | |
| + INTEGER NSTATE, I | |
| + DOUBLE PRECISION SSF, FLUXRC, Y(NSTATE), YPRIME(NSTATE) | |
| + ! compute the sum of squared fluxes | |
| + SSF=0.0 | |
| + DO I=1, NSTATE-1 | |
| + ! add (dCi/dt)^2 with dCi/dt computed based on | |
| ! quotient rule...dCi/dt=d(Ni/V)/dt | |
| - ! =(V*dNi/dt-Ni*dV/dt)/V^2 | |
| - SSF=SSF+((Y(NSTATE)*YPRIME(I)-Y(I)*YPRIME(NSTATE)) & | |
| + ! =(V*dNi/dt-Ni*dV/dt)/V^2 | |
| + SSF=SSF+((Y(NSTATE)*YPRIME(I)-Y(I)*YPRIME(NSTATE)) & | |
| & /(Y(NSTATE)**2))**2 | |
| - END DO | |
| - ! compute the square root, corresponding to | |
| + END DO | |
| + ! compute the square root, corresponding to | |
| ! L2 norm | |
| - FLUXRC = SSF**0.5 | |
| + FLUXRC = SSF**0.5 | |
| END SUBROUTINE RCHAR | |
| diff --git a/source/dassl/call_dasslAUTOdebug3.f90 b/source/dassl/call_dasslAUTOdebug3.f90 | |
| index 30f9590..9899816 100644 | |
| --- a/source/dassl/call_dasslAUTOdebug3.f90 | |
| +++ b/source/dassl/call_dasslAUTOdebug3.f90 | |
| @@ -26,14 +26,14 @@ | |
| & REACTIONARRAY(9*RMAX), THIRDBODYREACTIONARRAY(20*TBRMAX), & | |
| & TROEREACTIONARRAY(21*TROEMAX), I, J, IDID, impspecies, & | |
| & AUTOFLAG, ESPECIES, EREACTIONSIZE, ConstantConcentration(SPMAX+1), & | |
| - & LINDEREACTIONSIZE, LINDEREACTIONARRAY(20*LINDEMAX) | |
| + & LINDEREACTIONSIZE, LINDEREACTIONARRAY(20*LINDEMAX) | |
| DOUBLE PRECISION Y(SPMAX), YPRIME(SPMAX), T, TOUT, RTOL, ATOL,& | |
| & RWORK(51+9*SPMAX+SPMAX**2), TEMPERATURE, PRESSURE,& | |
| & REACTIONRATEARRAY(5*rmax),& | |
| & THIRDBODYREACTIONRATEARRAY(16*Tbrmax),& | |
| & TROEREACTIONRATEARRAY(21*TROemax), targetconc, THRESH, & | |
| - & LINDEREACTIONRATEARRAY(17*LINDEMAX) | |
| + & LINDEREACTIONRATEARRAY(17*LINDEMAX) | |
| ! 4/25/08 gmagoon:make auto arrays allocatable and double | |
| ! precision for KVEC | |
| INTEGER, DIMENSION(:), ALLOCATABLE :: NEREAC,NEPROD | |
| @@ -47,7 +47,7 @@ | |
| & TROEREACTIONRATEARRAY, temperature, pressure,& | |
| & REACTIONARRAY, THIRDBODYREACTIONARRAY,& | |
| & TROEREACTIONARRAY, ConstantConcentration, & | |
| - & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| + & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| !5/12/08 gmagoon: added timing (cf. http://beige.ucs.indiana.edu/B673/node105.html) | |
| ! integer count_0, count_1, count_rate, count_max | |
| ! double precision start, finish | |
| @@ -99,7 +99,7 @@ | |
| READ(12,*) THIRDBODYREACTIONSIZE | |
| READ(12,*)(THIRDBODYREACTIONARRAY(I),I=1,20*THIRDBODYREACTIONSIZE) | |
| READ(12,*)(THIRDBODYREACTIONRATEARRAY(I),I=1, & | |
| - & 16*THIRDBODYREACTIONSIZE) | |
| + & 16*THIRDBODYREACTIONSIZE) | |
| ! READ INFORMATION ABOUT TROEREACTIONS | |
| READ(12,*) TROEREACTIONSIZE | |
| @@ -108,56 +108,56 @@ | |
| ! READ INFORMATION ABOUT LINDEMANNREACTIONS | |
| READ(12,*) LINDEREACTIONSIZE | |
| - READ(12,*)(LINDEREACTIONARRAY(I),I=1,20*LINDEREACTIONSIZE) | |
| - READ(12,*)(LINDEREACTIONRATEARRAY(I),I=1,17*LINDEREACTIONSIZE) | |
| + READ(12,*)(LINDEREACTIONARRAY(I),I=1,20*LINDEREACTIONSIZE) | |
| + READ(12,*)(LINDEREACTIONRATEARRAY(I),I=1,17*LINDEREACTIONSIZE) | |
| ! 4/24/08 gmagoon: if autoFlag = 1, read in additional information | |
| ! specific to automatic time stepping | |
| - IF (AUTOFLAG .EQ. 1) THEN | |
| - ! read the threshhold, corresponding to the value | |
| - ! specified in condition.txt input file | |
| - READ(12,*) THRESH | |
| - ! read the number of edge species and edge reactions | |
| - READ(12,*) ESPECIES, EREACTIONSIZE | |
| - ! allocate memory for arrays | |
| - ALLOCATE(NEREAC(EREACTIONSIZE), NEPROD(EREACTIONSIZE),& | |
| - & IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3),& | |
| - & KVEC(EREACTIONSIZE)) | |
| - ! read in the reaction parameters for each reaction; | |
| - ! a maximum of 3 products and 3 reactants is assumed | |
| - ! for each reaction; parameters read for each reaction | |
| - ! are: number of reactants, number of products, | |
| - ! three reactant ID's (integers from 1 to NSTATE-1), | |
| - ! three product ID's (integers from 1 to ESPECIES), | |
| - ! and the rate coefficient k, such that dCi/dt=k*Ca*Cb; | |
| - ! note that cases where abs. value of stoic. coeff. | |
| - ! does not equal one are handled by using repeated | |
| - ! reactant/product IDs | |
| - ! note: use of KVEC rather than Arrhenius parameters | |
| - ! requires assumption that system is isothermal | |
| - ! (and isobaric for pressure dependence) | |
| - DO I=1, EREACTIONSIZE | |
| - READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| - & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| - & IDEPROD(I,2), IDEPROD(I,3), KVEC(I) | |
| - ! alternative for reading Arrhenius parameters instead | |
| - ! of k values; this allows easier extention to | |
| - ! non-isothermal systems in the future | |
| - ! form: k=A*T^n*e^(Ea/(RT)) *? | |
| - ! units: A[=], n[=]dimensionless, Ea[=] | |
| - ! READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| + IF (AUTOFLAG .EQ. 1) THEN | |
| + ! read the threshhold, corresponding to the value | |
| + ! specified in condition.txt input file | |
| + READ(12,*) THRESH | |
| + ! read the number of edge species and edge reactions | |
| + READ(12,*) ESPECIES, EREACTIONSIZE | |
| + ! allocate memory for arrays | |
| + ALLOCATE(NEREAC(EREACTIONSIZE), NEPROD(EREACTIONSIZE),& | |
| + & IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3),& | |
| + & KVEC(EREACTIONSIZE)) | |
| + ! read in the reaction parameters for each reaction; | |
| + ! a maximum of 3 products and 3 reactants is assumed | |
| + ! for each reaction; parameters read for each reaction | |
| + ! are: number of reactants, number of products, | |
| + ! three reactant ID's (integers from 1 to NSTATE-1), | |
| + ! three product ID's (integers from 1 to ESPECIES), | |
| + ! and the rate coefficient k, such that dCi/dt=k*Ca*Cb; | |
| + ! note that cases where abs. value of stoic. coeff. | |
| + ! does not equal one are handled by using repeated | |
| + ! reactant/product IDs | |
| + ! note: use of KVEC rather than Arrhenius parameters | |
| + ! requires assumption that system is isothermal | |
| + ! (and isobaric for pressure dependence) | |
| + DO I=1, EREACTIONSIZE | |
| + READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| + & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| + & IDEPROD(I,2), IDEPROD(I,3), KVEC(I) | |
| + ! alternative for reading Arrhenius parameters instead | |
| + ! of k values; this allows easier extention to | |
| + ! non-isothermal systems in the future | |
| + ! form: k=A*T^n*e^(Ea/(RT)) *? | |
| + ! units: A[=], n[=]dimensionless, Ea[=] | |
| + ! READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| ! & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| ! & IDEPROD(I,2),IDEPROD(I,3), AVEC(I), NVEC(I), & | |
| ! & EAVEC(I) | |
| - ! for isothermal, isobaric systems, (or just isothermal | |
| - ! systems if pressure dependence is not considered) | |
| + ! for isothermal, isobaric systems, (or just isothermal | |
| + ! systems if pressure dependence is not considered) | |
| ! the following may be calculated here once | |
| - ! (versus calculating at every timestep) | |
| - ! ...units may need adjustment: | |
| - ! KVEC(I)=AVEC(I)*TEMPERATURE**NVEC(I)*EXP(EAVEC(I) & | |
| - ! & /(8.314*TEMPERATURE)) | |
| - END DO | |
| - END IF | |
| + ! (versus calculating at every timestep) | |
| + ! ...units may need adjustment: | |
| + ! KVEC(I)=AVEC(I)*TEMPERATURE**NVEC(I)*EXP(EAVEC(I) & | |
| + ! & /(8.314*TEMPERATURE)) | |
| + END DO | |
| + END IF | |
| ! read constantConcentration data (if flag = 1 then the concentration of that species will not be integrated) | |
| ! there is one integer for each species (up to nstate-1), then the last one is for the VOLUME | |
| @@ -179,7 +179,7 @@ | |
| ! Fortran90 vs. Fortran 77; perhaps it was a problem with | |
| ! non-auto cases after my modifications and I just didn't | |
| ! notice it | |
| - CLOSE(13) | |
| + CLOSE(13) | |
| CLOSE(14) | |
| CALL SOLVEODE(Y, YPRIME, T, TOUT, INFO, RTOL, ATOL, IDID, & | |
| @@ -193,8 +193,8 @@ | |
| ! this should prevent "deallocated a bad pointer" error when | |
| ! autoflag is not 1 | |
| IF (AUTOFLAG .EQ. 1) THEN | |
| - DEALLOCATE (NEREAC, NEPROD, KVEC, & | |
| - & IDEREAC, IDEPROD) | |
| + DEALLOCATE (NEREAC, NEPROD, KVEC, & | |
| + & IDEREAC, IDEPROD) | |
| END IF | |
| !5/12/08 gmagoon: added timing (see above) | |
| @@ -222,19 +222,19 @@ | |
| ! INITIALIZE VARIABLES IN COMMON BLOC | |
| INTEGER SPMAX, RMAX, TBRMAX, TROEMAX, AUTOFLAG, ESPECIES, & | |
| - & EREACTIONSIZE, LINDEMAX | |
| + & EREACTIONSIZE, LINDEMAX | |
| INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| INTEGER IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3) | |
| DOUBLE PRECISION KVEC(EREACTIONSIZE) | |
| PARAMETER (SPMAX = 1500, RMAX = 100000, TBRMAX=100, TROEMAX=100, & | |
| - & LINDEMAX=100) | |
| + & LINDEMAX=100) | |
| INTEGER REACTIONSIZE, THIRDBODYREACTIONSIZE, TROEREACTIONSIZE, & | |
| & REACTIONARRAY(9*RMAX), THIRDBODYREACTIONARRAY(20*TBRMAX), & | |
| & TROEREACTIONARRAY(21*TROEMAX), I, J, NSTATE, EDGEFLAG, & | |
| & ConstantConcentration(SPMAX+1), LINDEREACTIONSIZE, & | |
| - & LINDEREACTIONARRAY(20*LINDEMAX) | |
| + & LINDEREACTIONARRAY(20*LINDEMAX) | |
| DOUBLE PRECISION REACTIONRATEARRAY(5*rmax), & | |
| & THIRDBODYREACTIONRATEARRAY(16*Tbrmax), & | |
| @@ -248,7 +248,7 @@ | |
| & TROEREACTIONRATEARRAY, temperature, pressure,& | |
| & REACTIONARRAY, THIRDBODYREACTIONARRAY,& | |
| & TROEREACTIONARRAY, ConstantConcentration, & | |
| - & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| + & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| INTEGER INFO(30), LIW, LRW, IWORK(*), IPAR(1),IDID, iter, & | |
| & IMPSPECIES, conc | |
| @@ -289,10 +289,10 @@ | |
| & TROEREACTIONRATEARRAY(21*I+1) | |
| END DO | |
| - DO I=0,LINDEREACTIONSIZE-1 | |
| - RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+I+1) = & | |
| - & LINDEREACTIONRATEARRAY(17*I+1) | |
| - END DO | |
| + DO I=0,LINDEREACTIONSIZE-1 | |
| + RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+I+1) = & | |
| + & LINDEREACTIONRATEARRAY(17*I+1) | |
| + END DO | |
| ! ********************************** | |
| ! 5/13/08 gmagoon: added time stepping timing | |
| ! call system_clock(count_0T, count_rateT, count_maxT) | |
| @@ -300,16 +300,16 @@ | |
| CALL GETFLUX(Y, YPRIME, RPAR) | |
| - | |
| + | |
| ! 4/24/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| ! determine EDGEFLAG (-1 if flux threshhold has not been met, | |
| ! positive integer otherwise) | |
| - EDGEFLAG = -1 | |
| - IF (AUTOFLAG.eq.1) THEN | |
| - CALL EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| + EDGEFLAG = -1 | |
| + IF (AUTOFLAG.eq.1) THEN | |
| + CALL EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| & NSTATE) | |
| - ENDIF | |
| + ENDIF | |
| iter = 0; | |
| PREVTIME = TIME | |
| @@ -325,7 +325,7 @@ | |
| IMPSPECIES = 1 | |
| conc = -1 | |
| END IF | |
| - | |
| + | |
| ! 4/24/08 gmagoon: added criteria that edgeflag = -1 for loop to | |
| ! continue; calls to DASSL will stop once EDGEFLAG takes on a | |
| @@ -357,13 +357,13 @@ | |
| tout = 200*time | |
| end if | |
| ! write(*,*) time, y(impspecies), targetConc*y(nstate) | |
| - ! 4/24/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| - ! determine EDGEFLAG | |
| - IF (AUTOFLAG.eq.1) THEN | |
| - CALL EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| - & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| - & NSTATE) | |
| - ENDIF | |
| + ! 4/24/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| + ! determine EDGEFLAG | |
| + IF (AUTOFLAG.eq.1) THEN | |
| + CALL EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| + & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| + & NSTATE) | |
| + ENDIF | |
| GO TO 1 | |
| END IF | |
| END IF | |
| @@ -422,58 +422,58 @@ | |
| ! value besides -1; otherwise, EDGEFLAG remains -1; | |
| ! EDGEFLUX also calls RCHAR | |
| SUBROUTINE EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| - & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD, & | |
| - & KVEC, NSTATE) | |
| - IMPLICIT NONE | |
| - INTEGER EDGEFLAG, ESPECIES, EREACTIONSIZE, NSTATE, I, J, K | |
| - DOUBLE PRECISION THRESH, FLUXRC, RFLUX, Y(NSTATE), YPRIME(NSTATE) | |
| - DOUBLE PRECISION, DIMENSION(:), ALLOCATABLE :: RATE | |
| - INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| + & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD, & | |
| + & KVEC, NSTATE) | |
| + IMPLICIT NONE | |
| + INTEGER EDGEFLAG, ESPECIES, EREACTIONSIZE, NSTATE, I, J, K | |
| + DOUBLE PRECISION THRESH, FLUXRC, RFLUX, Y(NSTATE), YPRIME(NSTATE) | |
| + DOUBLE PRECISION, DIMENSION(:), ALLOCATABLE :: RATE | |
| + INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| INTEGER IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3) | |
| DOUBLE PRECISION KVEC(EREACTIONSIZE) | |
| - | |
| - ALLOCATE(RATE(ESPECIES)) | |
| - ! initialize array to have all zeroes | |
| - RATE=0 | |
| - ! it is assumed edgeflag = -1 at this point, since | |
| + | |
| + ALLOCATE(RATE(ESPECIES)) | |
| + ! initialize array to have all zeroes | |
| + RATE=0 | |
| + ! it is assumed edgeflag = -1 at this point, since | |
| ! this should be the only way to access this subroutine | |
| ! calculate characteristic flux, FLUXRC | |
| - CALL RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| - | |
| - ! calculate the vector of fluxes for each species | |
| - ! by summing contributions from each reaction | |
| - ILoOP: DO I=1, EREACTIONSIZE | |
| - ! calculate reaction flux by multiplying k | |
| - ! by concentration(s) | |
| - RFLUX = KVEC(I) | |
| - KLOOP: DO K=1, NEREAC(I) | |
| - RFLUX = RFLUX*Y(IDEREAC(I,K))/Y(NSTATE) | |
| - END DO KLOOP | |
| - ! loop over reaction products, adding RFLUX | |
| - JLOOP: DO J=1, NEPROD(I) | |
| - RATE(IDEPROD(I,J))=RATE(IDEPROD(I,J))+ RFLUX | |
| - END DO JLOOP | |
| - END DO ILOOP | |
| - | |
| - | |
| - ! check if any of the edge species fluxes exceed | |
| - ! the threshhold; if so, set edgeflag equal to | |
| - ! the index of the first species found and exit | |
| - ! the loop | |
| - ! 5/7/08 gmagoon: added write statements for debugging purposes | |
| -! OPEN (UNIT=20, FILE = 'debug.txt') | |
| -! WRITE(20,*) FLUXRC | |
| - FLOOP: DO I=1, ESPECIES | |
| -! WRITE(20,*) I, RATE(I) | |
| - IF(RATE(I) .GE. THRESH*FLUXRC) THEN | |
| + CALL RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| + | |
| + ! calculate the vector of fluxes for each species | |
| + ! by summing contributions from each reaction | |
| + ILoOP: DO I=1, EREACTIONSIZE | |
| + ! calculate reaction flux by multiplying k | |
| + ! by concentration(s) | |
| + RFLUX = KVEC(I) | |
| + KLOOP: DO K=1, NEREAC(I) | |
| + RFLUX = RFLUX*Y(IDEREAC(I,K))/Y(NSTATE) | |
| + END DO KLOOP | |
| + ! loop over reaction products, adding RFLUX | |
| + JLOOP: DO J=1, NEPROD(I) | |
| + RATE(IDEPROD(I,J))=RATE(IDEPROD(I,J))+ RFLUX | |
| + END DO JLOOP | |
| + END DO ILOOP | |
| + | |
| + | |
| + ! check if any of the edge species fluxes exceed | |
| + ! the threshhold; if so, set edgeflag equal to | |
| + ! the index of the first species found and exit | |
| + ! the loop | |
| + ! 5/7/08 gmagoon: added write statements for debugging purposes | |
| +! OPEN (UNIT=20, FILE = 'debug.txt') | |
| +! WRITE(20,*) FLUXRC | |
| + FLOOP: DO I=1, ESPECIES | |
| +! WRITE(20,*) I, RATE(I) | |
| + IF(RATE(I) .GE. THRESH*FLUXRC) THEN | |
| ! line below added for call_dasslAUTOdebug3.f90 7/28/09 | |
| WRITE(*,*) I, RATE(I), FLUXRC | |
| - EDGEFLAG = I | |
| - EXIT FLOOP | |
| - END IF | |
| - END DO FLOOP | |
| - DEALLOCATE(RATE) | |
| + EDGEFLAG = I | |
| + EXIT FLOOP | |
| + END IF | |
| + END DO FLOOP | |
| + DEALLOCATE(RATE) | |
| END SUBROUTINE EDGEFLUX | |
| ! RCHAR calculates the characteristic flux (i.e. the | |
| @@ -488,18 +488,18 @@ END SUBROUTINE EDGEFLUX | |
| ! plus one) | |
| SUBROUTINE RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| IMPLICIT NONE | |
| - INTEGER NSTATE, I | |
| - DOUBLE PRECISION SSF, FLUXRC, Y(NSTATE), YPRIME(NSTATE) | |
| - ! compute the sum of squared fluxes | |
| - SSF=0.0 | |
| - DO I=1, NSTATE-1 | |
| - ! add (dCi/dt)^2 with dCi/dt computed based on | |
| + INTEGER NSTATE, I | |
| + DOUBLE PRECISION SSF, FLUXRC, Y(NSTATE), YPRIME(NSTATE) | |
| + ! compute the sum of squared fluxes | |
| + SSF=0.0 | |
| + DO I=1, NSTATE-1 | |
| + ! add (dCi/dt)^2 with dCi/dt computed based on | |
| ! quotient rule...dCi/dt=d(Ni/V)/dt | |
| - ! =(V*dNi/dt-Ni*dV/dt)/V^2 | |
| - SSF=SSF+((Y(NSTATE)*YPRIME(I)-Y(I)*YPRIME(NSTATE)) & | |
| + ! =(V*dNi/dt-Ni*dV/dt)/V^2 | |
| + SSF=SSF+((Y(NSTATE)*YPRIME(I)-Y(I)*YPRIME(NSTATE)) & | |
| & /(Y(NSTATE)**2))**2 | |
| - END DO | |
| - ! compute the square root, corresponding to | |
| + END DO | |
| + ! compute the square root, corresponding to | |
| ! L2 norm | |
| - FLUXRC = SSF**0.5 | |
| + FLUXRC = SSF**0.5 | |
| END SUBROUTINE RCHAR | |
| diff --git a/source/dassl/call_dasslAUTOinfo.f90 b/source/dassl/call_dasslAUTOinfo.f90 | |
| index ce3e206..42483dc 100644 | |
| --- a/source/dassl/call_dasslAUTOinfo.f90 | |
| +++ b/source/dassl/call_dasslAUTOinfo.f90 | |
| @@ -26,14 +26,14 @@ | |
| & REACTIONARRAY(9*RMAX), THIRDBODYREACTIONARRAY(20*TBRMAX), & | |
| & TROEREACTIONARRAY(21*TROEMAX), I, J, IDID, impspecies, & | |
| & AUTOFLAG, ESPECIES, EREACTIONSIZE, ConstantConcentration(SPMAX+1), & | |
| - & LINDEREACTIONSIZE, LINDEREACTIONARRAY(20*LINDEMAX) | |
| + & LINDEREACTIONSIZE, LINDEREACTIONARRAY(20*LINDEMAX) | |
| DOUBLE PRECISION Y(SPMAX), YPRIME(SPMAX), T, TOUT, RTOL, ATOL,& | |
| & RWORK(51+9*SPMAX+SPMAX**2), TEMPERATURE, PRESSURE,& | |
| & REACTIONRATEARRAY(5*rmax),& | |
| & THIRDBODYREACTIONRATEARRAY(16*Tbrmax),& | |
| & TROEREACTIONRATEARRAY(21*TROemax), targetconc, THRESH, & | |
| - & LINDEREACTIONRATEARRAY(17*LINDEMAX) | |
| + & LINDEREACTIONRATEARRAY(17*LINDEMAX) | |
| ! 4/25/08 gmagoon:make auto arrays allocatable and double | |
| ! precision for KVEC | |
| INTEGER, DIMENSION(:), ALLOCATABLE :: NEREAC,NEPROD | |
| @@ -47,7 +47,7 @@ | |
| & TROEREACTIONRATEARRAY, temperature, pressure,& | |
| & REACTIONARRAY, THIRDBODYREACTIONARRAY,& | |
| & TROEREACTIONARRAY, ConstantConcentration, & | |
| - & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| + & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| !5/12/08 gmagoon: added timing (cf. http://beige.ucs.indiana.edu/B673/node105.html) | |
| ! integer count_0, count_1, count_rate, count_max | |
| ! double precision start, finish | |
| @@ -102,7 +102,7 @@ | |
| READ(12,*) THIRDBODYREACTIONSIZE | |
| READ(12,*)(THIRDBODYREACTIONARRAY(I),I=1,20*THIRDBODYREACTIONSIZE) | |
| READ(12,*)(THIRDBODYREACTIONRATEARRAY(I),I=1, & | |
| - & 16*THIRDBODYREACTIONSIZE) | |
| + & 16*THIRDBODYREACTIONSIZE) | |
| ! READ INFORMATION ABOUT TROEREACTIONS | |
| READ(12,*) TROEREACTIONSIZE | |
| @@ -111,56 +111,56 @@ | |
| ! READ INFORMATION ABOUT LINDEMANNREACTIONS | |
| READ(12,*) LINDEREACTIONSIZE | |
| - READ(12,*)(LINDEREACTIONARRAY(I),I=1,20*LINDEREACTIONSIZE) | |
| - READ(12,*)(LINDEREACTIONRATEARRAY(I),I=1,17*LINDEREACTIONSIZE) | |
| + READ(12,*)(LINDEREACTIONARRAY(I),I=1,20*LINDEREACTIONSIZE) | |
| + READ(12,*)(LINDEREACTIONRATEARRAY(I),I=1,17*LINDEREACTIONSIZE) | |
| ! 4/24/08 gmagoon: if autoFlag = 1, read in additional information | |
| ! specific to automatic time stepping | |
| - IF (AUTOFLAG .EQ. 1) THEN | |
| - ! read the threshhold, corresponding to the value | |
| - ! specified in condition.txt input file | |
| - READ(12,*) THRESH | |
| - ! read the number of edge species and edge reactions | |
| - READ(12,*) ESPECIES, EREACTIONSIZE | |
| - ! allocate memory for arrays | |
| - ALLOCATE(NEREAC(EREACTIONSIZE), NEPROD(EREACTIONSIZE),& | |
| - & IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3),& | |
| - & KVEC(EREACTIONSIZE)) | |
| - ! read in the reaction parameters for each reaction; | |
| - ! a maximum of 3 products and 3 reactants is assumed | |
| - ! for each reaction; parameters read for each reaction | |
| - ! are: number of reactants, number of products, | |
| - ! three reactant ID's (integers from 1 to NSTATE-1), | |
| - ! three product ID's (integers from 1 to ESPECIES), | |
| - ! and the rate coefficient k, such that dCi/dt=k*Ca*Cb; | |
| - ! note that cases where abs. value of stoic. coeff. | |
| - ! does not equal one are handled by using repeated | |
| - ! reactant/product IDs | |
| - ! note: use of KVEC rather than Arrhenius parameters | |
| - ! requires assumption that system is isothermal | |
| - ! (and isobaric for pressure dependence) | |
| - DO I=1, EREACTIONSIZE | |
| - READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| - & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| - & IDEPROD(I,2), IDEPROD(I,3), KVEC(I) | |
| - ! alternative for reading Arrhenius parameters instead | |
| - ! of k values; this allows easier extention to | |
| - ! non-isothermal systems in the future | |
| - ! form: k=A*T^n*e^(Ea/(RT)) *? | |
| - ! units: A[=], n[=]dimensionless, Ea[=] | |
| - ! READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| + IF (AUTOFLAG .EQ. 1) THEN | |
| + ! read the threshhold, corresponding to the value | |
| + ! specified in condition.txt input file | |
| + READ(12,*) THRESH | |
| + ! read the number of edge species and edge reactions | |
| + READ(12,*) ESPECIES, EREACTIONSIZE | |
| + ! allocate memory for arrays | |
| + ALLOCATE(NEREAC(EREACTIONSIZE), NEPROD(EREACTIONSIZE),& | |
| + & IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3),& | |
| + & KVEC(EREACTIONSIZE)) | |
| + ! read in the reaction parameters for each reaction; | |
| + ! a maximum of 3 products and 3 reactants is assumed | |
| + ! for each reaction; parameters read for each reaction | |
| + ! are: number of reactants, number of products, | |
| + ! three reactant ID's (integers from 1 to NSTATE-1), | |
| + ! three product ID's (integers from 1 to ESPECIES), | |
| + ! and the rate coefficient k, such that dCi/dt=k*Ca*Cb; | |
| + ! note that cases where abs. value of stoic. coeff. | |
| + ! does not equal one are handled by using repeated | |
| + ! reactant/product IDs | |
| + ! note: use of KVEC rather than Arrhenius parameters | |
| + ! requires assumption that system is isothermal | |
| + ! (and isobaric for pressure dependence) | |
| + DO I=1, EREACTIONSIZE | |
| + READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| + & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| + & IDEPROD(I,2), IDEPROD(I,3), KVEC(I) | |
| + ! alternative for reading Arrhenius parameters instead | |
| + ! of k values; this allows easier extention to | |
| + ! non-isothermal systems in the future | |
| + ! form: k=A*T^n*e^(Ea/(RT)) *? | |
| + ! units: A[=], n[=]dimensionless, Ea[=] | |
| + ! READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| ! & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| ! & IDEPROD(I,2),IDEPROD(I,3), AVEC(I), NVEC(I), & | |
| ! & EAVEC(I) | |
| - ! for isothermal, isobaric systems, (or just isothermal | |
| - ! systems if pressure dependence is not considered) | |
| + ! for isothermal, isobaric systems, (or just isothermal | |
| + ! systems if pressure dependence is not considered) | |
| ! the following may be calculated here once | |
| - ! (versus calculating at every timestep) | |
| - ! ...units may need adjustment: | |
| - ! KVEC(I)=AVEC(I)*TEMPERATURE**NVEC(I)*EXP(EAVEC(I) & | |
| - ! & /(8.314*TEMPERATURE)) | |
| - END DO | |
| - END IF | |
| + ! (versus calculating at every timestep) | |
| + ! ...units may need adjustment: | |
| + ! KVEC(I)=AVEC(I)*TEMPERATURE**NVEC(I)*EXP(EAVEC(I) & | |
| + ! & /(8.314*TEMPERATURE)) | |
| + END DO | |
| + END IF | |
| ! read constantConcentration data (if flag = 1 then the concentration of that species will not be integrated) | |
| ! there is one integer for each species (up to nstate-1), then the last one is for the VOLUME | |
| @@ -182,7 +182,7 @@ | |
| ! Fortran90 vs. Fortran 77; perhaps it was a problem with | |
| ! non-auto cases after my modifications and I just didn't | |
| ! notice it | |
| - CLOSE(13) | |
| + CLOSE(13) | |
| CLOSE(14) | |
| CALL SOLVEODE(Y, YPRIME, T, TOUT, INFO, RTOL, ATOL, IDID, & | |
| @@ -196,8 +196,8 @@ | |
| ! this should prevent "deallocated a bad pointer" error when | |
| ! autoflag is not 1 | |
| IF (AUTOFLAG .EQ. 1) THEN | |
| - DEALLOCATE (NEREAC, NEPROD, KVEC, & | |
| - & IDEREAC, IDEPROD) | |
| + DEALLOCATE (NEREAC, NEPROD, KVEC, & | |
| + & IDEREAC, IDEPROD) | |
| END IF | |
| !5/12/08 gmagoon: added timing (see above) | |
| @@ -228,19 +228,19 @@ | |
| ! INITIALIZE VARIABLES IN COMMON BLOC | |
| INTEGER SPMAX, RMAX, TBRMAX, TROEMAX, AUTOFLAG, ESPECIES, & | |
| - & EREACTIONSIZE, LINDEMAX | |
| + & EREACTIONSIZE, LINDEMAX | |
| INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| INTEGER IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3) | |
| DOUBLE PRECISION KVEC(EREACTIONSIZE) | |
| PARAMETER (SPMAX = 1500, RMAX = 100000, TBRMAX=100, TROEMAX=100, & | |
| - & LINDEMAX=100) | |
| + & LINDEMAX=100) | |
| INTEGER REACTIONSIZE, THIRDBODYREACTIONSIZE, TROEREACTIONSIZE, & | |
| & REACTIONARRAY(9*RMAX), THIRDBODYREACTIONARRAY(20*TBRMAX), & | |
| & TROEREACTIONARRAY(21*TROEMAX), I, J, NSTATE, EDGEFLAG, & | |
| & ConstantConcentration(SPMAX+1), LINDEREACTIONSIZE, & | |
| - & LINDEREACTIONARRAY(20*LINDEMAX) | |
| + & LINDEREACTIONARRAY(20*LINDEMAX) | |
| DOUBLE PRECISION REACTIONRATEARRAY(5*rmax), & | |
| & THIRDBODYREACTIONRATEARRAY(16*Tbrmax), & | |
| @@ -254,7 +254,7 @@ | |
| & TROEREACTIONRATEARRAY, temperature, pressure,& | |
| & REACTIONARRAY, THIRDBODYREACTIONARRAY,& | |
| & TROEREACTIONARRAY, ConstantConcentration, & | |
| - & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| + & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| INTEGER INFO(30), LIW, LRW, IWORK(*), IPAR(1),IDID, iter, & | |
| & IMPSPECIES, conc | |
| @@ -295,10 +295,10 @@ | |
| & TROEREACTIONRATEARRAY(21*I+1) | |
| END DO | |
| - DO I=0,LINDEREACTIONSIZE-1 | |
| - RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+I+1) = & | |
| - & LINDEREACTIONRATEARRAY(17*I+1) | |
| - END DO | |
| + DO I=0,LINDEREACTIONSIZE-1 | |
| + RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+I+1) = & | |
| + & LINDEREACTIONRATEARRAY(17*I+1) | |
| + END DO | |
| ! ********************************** | |
| ! 5/13/08 gmagoon: added time stepping timing | |
| ! call system_clock(count_0T, count_rateT, count_maxT) | |
| @@ -306,16 +306,16 @@ | |
| CALL GETFLUX(Y, YPRIME, RPAR) | |
| - | |
| + | |
| ! 4/24/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| ! determine EDGEFLAG (-1 if flux threshhold has not been met, | |
| ! positive integer otherwise) | |
| - EDGEFLAG = -1 | |
| - IF (AUTOFLAG.eq.1) THEN | |
| - CALL EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| + EDGEFLAG = -1 | |
| + IF (AUTOFLAG.eq.1) THEN | |
| + CALL EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| & NSTATE,time) | |
| - ENDIF | |
| + ENDIF | |
| iter = 0; | |
| PREVTIME = TIME | |
| @@ -331,7 +331,7 @@ | |
| IMPSPECIES = 1 | |
| conc = -1 | |
| END IF | |
| - | |
| + | |
| ! 4/24/08 gmagoon: added criteria that edgeflag = -1 for loop to | |
| ! continue; calls to DASSL will stop once EDGEFLAG takes on a | |
| @@ -363,13 +363,13 @@ | |
| tout = 200*time | |
| end if | |
| ! write(*,*) time, y(impspecies), targetConc*y(nstate) | |
| - ! 4/24/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| - ! determine EDGEFLAG | |
| - IF (AUTOFLAG.eq.1) THEN | |
| - CALL EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| - & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| - & NSTATE,time) | |
| - ENDIF | |
| + ! 4/24/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| + ! determine EDGEFLAG | |
| + IF (AUTOFLAG.eq.1) THEN | |
| + CALL EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| + & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| + & NSTATE,time) | |
| + ENDIF | |
| GO TO 1 | |
| END IF | |
| END IF | |
| @@ -428,63 +428,63 @@ | |
| ! value besides -1; otherwise, EDGEFLAG remains -1; | |
| ! EDGEFLUX also calls RCHAR | |
| SUBROUTINE EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| - & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD, & | |
| - & KVEC, NSTATE,T) | |
| - IMPLICIT NONE | |
| - INTEGER EDGEFLAG, ESPECIES, EREACTIONSIZE, NSTATE, I, J, K | |
| - DOUBLE PRECISION THRESH, FLUXRC, RFLUX, Y(NSTATE), YPRIME(NSTATE), T | |
| - DOUBLE PRECISION, DIMENSION(:), ALLOCATABLE :: RATE | |
| - INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| + & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD, & | |
| + & KVEC, NSTATE,T) | |
| + IMPLICIT NONE | |
| + INTEGER EDGEFLAG, ESPECIES, EREACTIONSIZE, NSTATE, I, J, K | |
| + DOUBLE PRECISION THRESH, FLUXRC, RFLUX, Y(NSTATE), YPRIME(NSTATE), T | |
| + DOUBLE PRECISION, DIMENSION(:), ALLOCATABLE :: RATE | |
| + INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| INTEGER IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3) | |
| DOUBLE PRECISION KVEC(EREACTIONSIZE) | |
| - | |
| - ALLOCATE(RATE(ESPECIES)) | |
| - ! initialize array to have all zeroes | |
| - RATE=0 | |
| - ! it is assumed edgeflag = -1 at this point, since | |
| + | |
| + ALLOCATE(RATE(ESPECIES)) | |
| + ! initialize array to have all zeroes | |
| + RATE=0 | |
| + ! it is assumed edgeflag = -1 at this point, since | |
| ! this should be the only way to access this subroutine | |
| ! calculate characteristic flux, FLUXRC | |
| - CALL RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| - | |
| - ! calculate the vector of fluxes for each species | |
| - ! by summing contributions from each reaction | |
| - ILOOP: DO I=1, EREACTIONSIZE | |
| - ! calculate reaction flux by multiplying k | |
| - ! by concentration(s) | |
| - RFLUX = KVEC(I) | |
| - KLOOP: DO K=1, NEREAC(I) | |
| - RFLUX = RFLUX*Y(IDEREAC(I,K))/Y(NSTATE) | |
| - END DO KLOOP | |
| + CALL RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| + | |
| + ! calculate the vector of fluxes for each species | |
| + ! by summing contributions from each reaction | |
| + ILOOP: DO I=1, EREACTIONSIZE | |
| + ! calculate reaction flux by multiplying k | |
| + ! by concentration(s) | |
| + RFLUX = KVEC(I) | |
| + KLOOP: DO K=1, NEREAC(I) | |
| + RFLUX = RFLUX*Y(IDEREAC(I,K))/Y(NSTATE) | |
| + END DO KLOOP | |
| WRITE(40,*) I, T, RFLUX/(THRESH*FLUXRC) | |
| - ! loop over reaction products, adding RFLUX | |
| - JLOOP: DO J=1, NEPROD(I) | |
| - RATE(IDEPROD(I,J))=RATE(IDEPROD(I,J))+ RFLUX | |
| - END DO JLOOP | |
| - END DO ILOOP | |
| - | |
| - | |
| - ! check if any of the edge species fluxes exceed | |
| - ! the threshhold; if so, set edgeflag equal to | |
| - ! the index of the first species found and exit | |
| - ! the loop | |
| - ! 5/7/08 gmagoon: added write statements for debugging purposes | |
| -! OPEN (UNIT=20, FILE = 'debug.txt') | |
| -! WRITE(20,*) FLUXRC | |
| + ! loop over reaction products, adding RFLUX | |
| + JLOOP: DO J=1, NEPROD(I) | |
| + RATE(IDEPROD(I,J))=RATE(IDEPROD(I,J))+ RFLUX | |
| + END DO JLOOP | |
| + END DO ILOOP | |
| + | |
| + | |
| + ! check if any of the edge species fluxes exceed | |
| + ! the threshhold; if so, set edgeflag equal to | |
| + ! the index of the first species found and exit | |
| + ! the loop | |
| + ! 5/7/08 gmagoon: added write statements for debugging purposes | |
| +! OPEN (UNIT=20, FILE = 'debug.txt') | |
| +! WRITE(20,*) FLUXRC | |
| do i=1,nstate-1 | |
| write(25,*) i, T, y(i)/y(nstate) | |
| end do | |
| - FLOOP: DO I=1, ESPECIES | |
| -! WRITE(20,*) I, RATE(I) | |
| + FLOOP: DO I=1, ESPECIES | |
| +! WRITE(20,*) I, RATE(I) | |
| WRITE(30,*) I, T, RATE(I)/(THRESH*FLUXRC) | |
| - IF(RATE(I) .GE. THRESH*FLUXRC) THEN | |
| - EDGEFLAG = I | |
| -! EXIT FLOOP | |
| - END IF | |
| - END DO FLOOP | |
| + IF(RATE(I) .GE. THRESH*FLUXRC) THEN | |
| + EDGEFLAG = I | |
| +! EXIT FLOOP | |
| + END IF | |
| + END DO FLOOP | |
| - DEALLOCATE(RATE) | |
| + DEALLOCATE(RATE) | |
| END SUBROUTINE EDGEFLUX | |
| ! RCHAR calculates the characteristic flux (i.e. the | |
| @@ -499,18 +499,18 @@ END SUBROUTINE EDGEFLUX | |
| ! plus one) | |
| SUBROUTINE RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| IMPLICIT NONE | |
| - INTEGER NSTATE, I | |
| - DOUBLE PRECISION SSF, FLUXRC, Y(NSTATE), YPRIME(NSTATE) | |
| - ! compute the sum of squared fluxes | |
| - SSF=0.0 | |
| - DO I=1, NSTATE-1 | |
| - ! add (dCi/dt)^2 with dCi/dt computed based on | |
| + INTEGER NSTATE, I | |
| + DOUBLE PRECISION SSF, FLUXRC, Y(NSTATE), YPRIME(NSTATE) | |
| + ! compute the sum of squared fluxes | |
| + SSF=0.0 | |
| + DO I=1, NSTATE-1 | |
| + ! add (dCi/dt)^2 with dCi/dt computed based on | |
| ! quotient rule...dCi/dt=d(Ni/V)/dt | |
| - ! =(V*dNi/dt-Ni*dV/dt)/V^2 | |
| - SSF=SSF+((Y(NSTATE)*YPRIME(I)-Y(I)*YPRIME(NSTATE)) & | |
| + ! =(V*dNi/dt-Ni*dV/dt)/V^2 | |
| + SSF=SSF+((Y(NSTATE)*YPRIME(I)-Y(I)*YPRIME(NSTATE)) & | |
| & /(Y(NSTATE)**2))**2 | |
| - END DO | |
| - ! compute the square root, corresponding to | |
| + END DO | |
| + ! compute the square root, corresponding to | |
| ! L2 norm | |
| - FLUXRC = SSF**0.5 | |
| + FLUXRC = SSF**0.5 | |
| END SUBROUTINE RCHAR | |
| diff --git a/source/dassl/call_dasslAUTOinfoFirst.f90 b/source/dassl/call_dasslAUTOinfoFirst.f90 | |
| index fb98e93..d9a529e 100644 | |
| --- a/source/dassl/call_dasslAUTOinfoFirst.f90 | |
| +++ b/source/dassl/call_dasslAUTOinfoFirst.f90 | |
| @@ -26,14 +26,14 @@ | |
| & REACTIONARRAY(9*RMAX), THIRDBODYREACTIONARRAY(20*TBRMAX), & | |
| & TROEREACTIONARRAY(21*TROEMAX), I, J, IDID, impspecies, & | |
| & AUTOFLAG, ESPECIES, EREACTIONSIZE, ConstantConcentration(SPMAX+1), & | |
| - & LINDEREACTIONSIZE, LINDEREACTIONARRAY(20*LINDEMAX) | |
| + & LINDEREACTIONSIZE, LINDEREACTIONARRAY(20*LINDEMAX) | |
| DOUBLE PRECISION Y(SPMAX), YPRIME(SPMAX), T, TOUT, RTOL, ATOL,& | |
| & RWORK(51+9*SPMAX+SPMAX**2), TEMPERATURE, PRESSURE,& | |
| & REACTIONRATEARRAY(5*rmax),& | |
| & THIRDBODYREACTIONRATEARRAY(16*Tbrmax),& | |
| & TROEREACTIONRATEARRAY(21*TROemax), targetconc, THRESH, & | |
| - & LINDEREACTIONRATEARRAY(17*LINDEMAX) | |
| + & LINDEREACTIONRATEARRAY(17*LINDEMAX) | |
| ! 4/25/08 gmagoon:make auto arrays allocatable and double | |
| ! precision for KVEC | |
| INTEGER, DIMENSION(:), ALLOCATABLE :: NEREAC,NEPROD | |
| @@ -47,7 +47,7 @@ | |
| & TROEREACTIONRATEARRAY, temperature, pressure,& | |
| & REACTIONARRAY, THIRDBODYREACTIONARRAY,& | |
| & TROEREACTIONARRAY, ConstantConcentration, & | |
| - & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| + & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| !5/12/08 gmagoon: added timing (cf. http://beige.ucs.indiana.edu/B673/node105.html) | |
| ! integer count_0, count_1, count_rate, count_max | |
| ! double precision start, finish | |
| @@ -102,7 +102,7 @@ | |
| READ(12,*) THIRDBODYREACTIONSIZE | |
| READ(12,*)(THIRDBODYREACTIONARRAY(I),I=1,20*THIRDBODYREACTIONSIZE) | |
| READ(12,*)(THIRDBODYREACTIONRATEARRAY(I),I=1, & | |
| - & 16*THIRDBODYREACTIONSIZE) | |
| + & 16*THIRDBODYREACTIONSIZE) | |
| ! READ INFORMATION ABOUT TROEREACTIONS | |
| READ(12,*) TROEREACTIONSIZE | |
| @@ -111,56 +111,56 @@ | |
| ! READ INFORMATION ABOUT LINDEMANNREACTIONS | |
| READ(12,*) LINDEREACTIONSIZE | |
| - READ(12,*)(LINDEREACTIONARRAY(I),I=1,20*LINDEREACTIONSIZE) | |
| - READ(12,*)(LINDEREACTIONRATEARRAY(I),I=1,17*LINDEREACTIONSIZE) | |
| + READ(12,*)(LINDEREACTIONARRAY(I),I=1,20*LINDEREACTIONSIZE) | |
| + READ(12,*)(LINDEREACTIONRATEARRAY(I),I=1,17*LINDEREACTIONSIZE) | |
| ! 4/24/08 gmagoon: if autoFlag = 1, read in additional information | |
| ! specific to automatic time stepping | |
| - IF (AUTOFLAG .EQ. 1) THEN | |
| - ! read the threshhold, corresponding to the value | |
| - ! specified in condition.txt input file | |
| - READ(12,*) THRESH | |
| - ! read the number of edge species and edge reactions | |
| - READ(12,*) ESPECIES, EREACTIONSIZE | |
| - ! allocate memory for arrays | |
| - ALLOCATE(NEREAC(EREACTIONSIZE), NEPROD(EREACTIONSIZE),& | |
| - & IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3),& | |
| - & KVEC(EREACTIONSIZE)) | |
| - ! read in the reaction parameters for each reaction; | |
| - ! a maximum of 3 products and 3 reactants is assumed | |
| - ! for each reaction; parameters read for each reaction | |
| - ! are: number of reactants, number of products, | |
| - ! three reactant ID's (integers from 1 to NSTATE-1), | |
| - ! three product ID's (integers from 1 to ESPECIES), | |
| - ! and the rate coefficient k, such that dCi/dt=k*Ca*Cb; | |
| - ! note that cases where abs. value of stoic. coeff. | |
| - ! does not equal one are handled by using repeated | |
| - ! reactant/product IDs | |
| - ! note: use of KVEC rather than Arrhenius parameters | |
| - ! requires assumption that system is isothermal | |
| - ! (and isobaric for pressure dependence) | |
| - DO I=1, EREACTIONSIZE | |
| - READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| - & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| - & IDEPROD(I,2), IDEPROD(I,3), KVEC(I) | |
| - ! alternative for reading Arrhenius parameters instead | |
| - ! of k values; this allows easier extention to | |
| - ! non-isothermal systems in the future | |
| - ! form: k=A*T^n*e^(Ea/(RT)) *? | |
| - ! units: A[=], n[=]dimensionless, Ea[=] | |
| - ! READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| + IF (AUTOFLAG .EQ. 1) THEN | |
| + ! read the threshhold, corresponding to the value | |
| + ! specified in condition.txt input file | |
| + READ(12,*) THRESH | |
| + ! read the number of edge species and edge reactions | |
| + READ(12,*) ESPECIES, EREACTIONSIZE | |
| + ! allocate memory for arrays | |
| + ALLOCATE(NEREAC(EREACTIONSIZE), NEPROD(EREACTIONSIZE),& | |
| + & IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3),& | |
| + & KVEC(EREACTIONSIZE)) | |
| + ! read in the reaction parameters for each reaction; | |
| + ! a maximum of 3 products and 3 reactants is assumed | |
| + ! for each reaction; parameters read for each reaction | |
| + ! are: number of reactants, number of products, | |
| + ! three reactant ID's (integers from 1 to NSTATE-1), | |
| + ! three product ID's (integers from 1 to ESPECIES), | |
| + ! and the rate coefficient k, such that dCi/dt=k*Ca*Cb; | |
| + ! note that cases where abs. value of stoic. coeff. | |
| + ! does not equal one are handled by using repeated | |
| + ! reactant/product IDs | |
| + ! note: use of KVEC rather than Arrhenius parameters | |
| + ! requires assumption that system is isothermal | |
| + ! (and isobaric for pressure dependence) | |
| + DO I=1, EREACTIONSIZE | |
| + READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| + & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| + & IDEPROD(I,2), IDEPROD(I,3), KVEC(I) | |
| + ! alternative for reading Arrhenius parameters instead | |
| + ! of k values; this allows easier extention to | |
| + ! non-isothermal systems in the future | |
| + ! form: k=A*T^n*e^(Ea/(RT)) *? | |
| + ! units: A[=], n[=]dimensionless, Ea[=] | |
| + ! READ(12,*) NEREAC(I),NEPROD(I),IDEREAC(I,1), & | |
| ! & IDEREAC(I,2),IDEREAC(I,3),IDEPROD(I,1), & | |
| ! & IDEPROD(I,2),IDEPROD(I,3), AVEC(I), NVEC(I), & | |
| ! & EAVEC(I) | |
| - ! for isothermal, isobaric systems, (or just isothermal | |
| - ! systems if pressure dependence is not considered) | |
| + ! for isothermal, isobaric systems, (or just isothermal | |
| + ! systems if pressure dependence is not considered) | |
| ! the following may be calculated here once | |
| - ! (versus calculating at every timestep) | |
| - ! ...units may need adjustment: | |
| - ! KVEC(I)=AVEC(I)*TEMPERATURE**NVEC(I)*EXP(EAVEC(I) & | |
| - ! & /(8.314*TEMPERATURE)) | |
| - END DO | |
| - END IF | |
| + ! (versus calculating at every timestep) | |
| + ! ...units may need adjustment: | |
| + ! KVEC(I)=AVEC(I)*TEMPERATURE**NVEC(I)*EXP(EAVEC(I) & | |
| + ! & /(8.314*TEMPERATURE)) | |
| + END DO | |
| + END IF | |
| ! read constantConcentration data (if flag = 1 then the concentration of that species will not be integrated) | |
| ! there is one integer for each species (up to nstate-1), then the last one is for the VOLUME | |
| @@ -182,7 +182,7 @@ | |
| ! Fortran90 vs. Fortran 77; perhaps it was a problem with | |
| ! non-auto cases after my modifications and I just didn't | |
| ! notice it | |
| - CLOSE(13) | |
| + CLOSE(13) | |
| CLOSE(14) | |
| CALL SOLVEODE(Y, YPRIME, T, TOUT, INFO, RTOL, ATOL, IDID, & | |
| @@ -196,8 +196,8 @@ | |
| ! this should prevent "deallocated a bad pointer" error when | |
| ! autoflag is not 1 | |
| IF (AUTOFLAG .EQ. 1) THEN | |
| - DEALLOCATE (NEREAC, NEPROD, KVEC, & | |
| - & IDEREAC, IDEPROD) | |
| + DEALLOCATE (NEREAC, NEPROD, KVEC, & | |
| + & IDEREAC, IDEPROD) | |
| END IF | |
| !5/12/08 gmagoon: added timing (see above) | |
| @@ -228,19 +228,19 @@ | |
| ! INITIALIZE VARIABLES IN COMMON BLOC | |
| INTEGER SPMAX, RMAX, TBRMAX, TROEMAX, AUTOFLAG, ESPECIES, & | |
| - & EREACTIONSIZE, LINDEMAX | |
| + & EREACTIONSIZE, LINDEMAX | |
| INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| INTEGER IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3) | |
| DOUBLE PRECISION KVEC(EREACTIONSIZE) | |
| PARAMETER (SPMAX = 1500, RMAX = 100000, TBRMAX=100, TROEMAX=100, & | |
| - & LINDEMAX=100) | |
| + & LINDEMAX=100) | |
| INTEGER REACTIONSIZE, THIRDBODYREACTIONSIZE, TROEREACTIONSIZE, & | |
| & REACTIONARRAY(9*RMAX), THIRDBODYREACTIONARRAY(20*TBRMAX), & | |
| & TROEREACTIONARRAY(21*TROEMAX), I, J, NSTATE, EDGEFLAG, & | |
| & ConstantConcentration(SPMAX+1), LINDEREACTIONSIZE, & | |
| - & LINDEREACTIONARRAY(20*LINDEMAX) | |
| + & LINDEREACTIONARRAY(20*LINDEMAX) | |
| DOUBLE PRECISION REACTIONRATEARRAY(5*rmax), & | |
| & THIRDBODYREACTIONRATEARRAY(16*Tbrmax), & | |
| @@ -254,7 +254,7 @@ | |
| & TROEREACTIONRATEARRAY, temperature, pressure,& | |
| & REACTIONARRAY, THIRDBODYREACTIONARRAY,& | |
| & TROEREACTIONARRAY, ConstantConcentration, & | |
| - & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| + & LINDEREACTIONRATEARRAY, LINDEREACTIONARRAY | |
| INTEGER INFO(30), LIW, LRW, IWORK(*), IPAR(1),IDID, iter, & | |
| & IMPSPECIES, conc | |
| @@ -295,10 +295,10 @@ | |
| & TROEREACTIONRATEARRAY(21*I+1) | |
| END DO | |
| - DO I=0,LINDEREACTIONSIZE-1 | |
| - RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+I+1) = & | |
| - & LINDEREACTIONRATEARRAY(17*I+1) | |
| - END DO | |
| + DO I=0,LINDEREACTIONSIZE-1 | |
| + RPAR(REACTIONSIZE+THIRDBODYREACTIONSIZE+TROEREACTIONSIZE+I+1) = & | |
| + & LINDEREACTIONRATEARRAY(17*I+1) | |
| + END DO | |
| ! ********************************** | |
| ! 5/13/08 gmagoon: added time stepping timing | |
| ! call system_clock(count_0T, count_rateT, count_maxT) | |
| @@ -306,16 +306,16 @@ | |
| CALL GETFLUX(Y, YPRIME, RPAR) | |
| - | |
| + | |
| ! 4/24/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| ! determine EDGEFLAG (-1 if flux threshhold has not been met, | |
| ! positive integer otherwise) | |
| - EDGEFLAG = -1 | |
| - IF (AUTOFLAG.eq.1) THEN | |
| - CALL EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| + EDGEFLAG = -1 | |
| + IF (AUTOFLAG.eq.1) THEN | |
| + CALL EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| & NSTATE,time) | |
| - ENDIF | |
| + ENDIF | |
| iter = 0; | |
| PREVTIME = TIME | |
| @@ -331,7 +331,7 @@ | |
| IMPSPECIES = 1 | |
| conc = -1 | |
| END IF | |
| - | |
| + | |
| ! 4/24/08 gmagoon: added criteria that edgeflag = -1 for loop to | |
| ! continue; calls to DASSL will stop once EDGEFLAG takes on a | |
| @@ -363,13 +363,13 @@ | |
| tout = 200*time | |
| end if | |
| ! write(*,*) time, y(impspecies), targetConc*y(nstate) | |
| - ! 4/24/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| - ! determine EDGEFLAG | |
| - IF (AUTOFLAG.eq.1) THEN | |
| - CALL EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| - & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| - & NSTATE,time) | |
| - ENDIF | |
| + ! 4/24/08 gmagoon: call EdgeFlux if AUTOFLAG is 1 to | |
| + ! determine EDGEFLAG | |
| + IF (AUTOFLAG.eq.1) THEN | |
| + CALL EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| + & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD,KVEC, & | |
| + & NSTATE,time) | |
| + ENDIF | |
| GO TO 1 | |
| END IF | |
| END IF | |
| @@ -428,65 +428,65 @@ | |
| ! value besides -1; otherwise, EDGEFLAG remains -1; | |
| ! EDGEFLUX also calls RCHAR | |
| SUBROUTINE EDGEFLUX(EDGEFLAG, Y, YPRIME,THRESH,ESPECIES, & | |
| - & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD, & | |
| - & KVEC, NSTATE,T) | |
| - IMPLICIT NONE | |
| - INTEGER EDGEFLAG, ESPECIES, EREACTIONSIZE, NSTATE, I, J, K | |
| - DOUBLE PRECISION THRESH, FLUXRC, RFLUX, Y(NSTATE), YPRIME(NSTATE), T | |
| - DOUBLE PRECISION, DIMENSION(:), ALLOCATABLE :: RATE | |
| - INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| + & EREACTIONSIZE,NEREAC,NEPROD,IDEREAC,IDEPROD, & | |
| + & KVEC, NSTATE,T) | |
| + IMPLICIT NONE | |
| + INTEGER EDGEFLAG, ESPECIES, EREACTIONSIZE, NSTATE, I, J, K | |
| + DOUBLE PRECISION THRESH, FLUXRC, RFLUX, Y(NSTATE), YPRIME(NSTATE), T | |
| + DOUBLE PRECISION, DIMENSION(:), ALLOCATABLE :: RATE | |
| + INTEGER NEREAC(EREACTIONSIZE),NEPROD(EREACTIONSIZE) | |
| INTEGER IDEREAC(EREACTIONSIZE,3), IDEPROD(EREACTIONSIZE,3) | |
| DOUBLE PRECISION KVEC(EREACTIONSIZE) | |
| - | |
| - ALLOCATE(RATE(ESPECIES)) | |
| - ! initialize array to have all zeroes | |
| - RATE=0 | |
| - ! it is assumed edgeflag = -1 at this point, since | |
| + | |
| + ALLOCATE(RATE(ESPECIES)) | |
| + ! initialize array to have all zeroes | |
| + RATE=0 | |
| + ! it is assumed edgeflag = -1 at this point, since | |
| ! this should be the only way to access this subroutine | |
| ! calculate characteristic flux, FLUXRC | |
| - CALL RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| - | |
| - ! calculate the vector of fluxes for each species | |
| - ! by summing contributions from each reaction | |
| - ILOOP: DO I=1, EREACTIONSIZE | |
| - ! calculate reaction flux by multiplying k | |
| - ! by concentration(s) | |
| - RFLUX = KVEC(I) | |
| - KLOOP: DO K=1, NEREAC(I) | |
| - RFLUX = RFLUX*Y(IDEREAC(I,K))/Y(NSTATE) | |
| - END DO KLOOP | |
| + CALL RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| + | |
| + ! calculate the vector of fluxes for each species | |
| + ! by summing contributions from each reaction | |
| + ILOOP: DO I=1, EREACTIONSIZE | |
| + ! calculate reaction flux by multiplying k | |
| + ! by concentration(s) | |
| + RFLUX = KVEC(I) | |
| + KLOOP: DO K=1, NEREAC(I) | |
| + RFLUX = RFLUX*Y(IDEREAC(I,K))/Y(NSTATE) | |
| + END DO KLOOP | |
| ! WRITE(40,*) I, T, RFLUX/(THRESH*FLUXRC) | |
| WRITE(40,*) I, T, RFLUX | |
| - ! loop over reaction products, adding RFLUX | |
| - JLOOP: DO J=1, NEPROD(I) | |
| - RATE(IDEPROD(I,J))=RATE(IDEPROD(I,J))+ RFLUX | |
| - END DO JLOOP | |
| - END DO ILOOP | |
| - | |
| - | |
| - ! check if any of the edge species fluxes exceed | |
| - ! the threshhold; if so, set edgeflag equal to | |
| - ! the index of the first species found and exit | |
| - ! the loop | |
| - ! 5/7/08 gmagoon: added write statements for debugging purposes | |
| -! OPEN (UNIT=20, FILE = 'debug.txt') | |
| -! WRITE(20,*) FLUXRC | |
| + ! loop over reaction products, adding RFLUX | |
| + JLOOP: DO J=1, NEPROD(I) | |
| + RATE(IDEPROD(I,J))=RATE(IDEPROD(I,J))+ RFLUX | |
| + END DO JLOOP | |
| + END DO ILOOP | |
| + | |
| + | |
| + ! check if any of the edge species fluxes exceed | |
| + ! the threshhold; if so, set edgeflag equal to | |
| + ! the index of the first species found and exit | |
| + ! the loop | |
| + ! 5/7/08 gmagoon: added write statements for debugging purposes | |
| +! OPEN (UNIT=20, FILE = 'debug.txt') | |
| +! WRITE(20,*) FLUXRC | |
| do i=1,nstate-1 | |
| write(25,*) i, T, y(i)/y(nstate) | |
| end do | |
| - FLOOP: DO I=1, ESPECIES | |
| -! WRITE(20,*) I, RATE(I) | |
| + FLOOP: DO I=1, ESPECIES | |
| +! WRITE(20,*) I, RATE(I) | |
| ! WRITE(30,*) I, T, RATE(I)/(THRESH*FLUXRC) | |
| WRITE(30,*) I, T, RATE(I) | |
| - IF(RATE(I) .GE. THRESH*FLUXRC) THEN | |
| - EDGEFLAG = I | |
| -! EXIT FLOOP | |
| - END IF | |
| - END DO FLOOP | |
| + IF(RATE(I) .GE. THRESH*FLUXRC) THEN | |
| + EDGEFLAG = I | |
| +! EXIT FLOOP | |
| + END IF | |
| + END DO FLOOP | |
| - DEALLOCATE(RATE) | |
| + DEALLOCATE(RATE) | |
| END SUBROUTINE EDGEFLUX | |
| ! RCHAR calculates the characteristic flux (i.e. the | |
| @@ -501,18 +501,18 @@ END SUBROUTINE EDGEFLUX | |
| ! plus one) | |
| SUBROUTINE RCHAR(FLUXRC, Y, YPRIME, NSTATE) | |
| IMPLICIT NONE | |
| - INTEGER NSTATE, I | |
| - DOUBLE PRECISION SSF, FLUXRC, Y(NSTATE), YPRIME(NSTATE) | |
| - ! compute the sum of squared fluxes | |
| - SSF=0.0 | |
| - DO I=1, NSTATE-1 | |
| - ! add (dCi/dt)^2 with dCi/dt computed based on | |
| + INTEGER NSTATE, I | |
| + DOUBLE PRECISION SSF, FLUXRC, Y(NSTATE), YPRIME(NSTATE) | |
| + ! compute the sum of squared fluxes | |
| + SSF=0.0 | |
| + DO I=1, NSTATE-1 | |
| + ! add (dCi/dt)^2 with dCi/dt computed based on | |
| ! quotient rule...dCi/dt=d(Ni/V)/dt | |
| - ! =(V*dNi/dt-Ni*dV/dt)/V^2 | |
| - SSF=SSF+((Y(NSTATE)*YPRIME(I)-Y(I)*YPRIME(NSTATE)) & | |
| + ! =(V*dNi/dt-Ni*dV/dt)/V^2 | |
| + SSF=SSF+((Y(NSTATE)*YPRIME(I)-Y(I)*YPRIME(NSTATE)) & | |
| & /(Y(NSTATE)**2))**2 | |
| - END DO | |
| - ! compute the square root, corresponding to | |
| + END DO | |
| + ! compute the square root, corresponding to | |
| ! L2 norm | |
| - FLUXRC = SSF**0.5 | |
| + FLUXRC = SSF**0.5 | |
| END SUBROUTINE RCHAR | |
| diff --git a/source/dassl/getflux.f b/source/dassl/getflux.f | |
| index 1d3b1bb..3792b86 100644 | |
| --- a/source/dassl/getflux.f | |
| +++ b/source/dassl/getflux.f | |
| @@ -181,17 +181,17 @@ c write(*,*) temperature | |
| LOGF = LOGFCENT/(1 + INSIDE**2) | |
| F = 10**LOGF | |
| -C 9-Jul-2009: MRH | |
| -C For unimolecular/recombination rxns, effective rate constant is | |
| -C keff = kinf * (Pr/(1+Pr)) * F | |
| -C For chemically-activated bimolecular rxns, effective rate constant is | |
| -C keff = kzero * (1/(1+Pr)) * F | |
| - IF (TROEREACTIONARRAY(I*21+1) .GT. 1 .AND. | |
| - $ TROEREACTIONARRAY(I*21+2) .GT. 1) THEN | |
| - FRATE = LOWRATE * (1/(1+PR)) * F | |
| - ELSE | |
| - FRATE = RATE * (PR/(1+PR)) * F | |
| - END IF | |
| +C 9-Jul-2009: MRH | |
| +C For unimolecular/recombination rxns, effective rate constant is | |
| +C keff = kinf * (Pr/(1+Pr)) * F | |
| +C For chemically-activated bimolecular rxns, effective rate constant is | |
| +C keff = kzero * (1/(1+Pr)) * F | |
| + IF (TROEREACTIONARRAY(I*21+1) .GT. 1 .AND. | |
| + $ TROEREACTIONARRAY(I*21+2) .GT. 1) THEN | |
| + FRATE = LOWRATE * (1/(1+PR)) * F | |
| + ELSE | |
| + FRATE = RATE * (PR/(1+PR)) * F | |
| + END IF | |
| IF (TROEREACTIONARRAY(21*I+9) .EQ. 1) THEN | |
| RRATE = fRATE/TROEREACTIONRATEARRAY(21*I+5) | |
| @@ -244,17 +244,17 @@ c write(*,*) temperature | |
| PR = LOWRATE * M/RATE | |
| -C 9-Jul-2009: MRH | |
| -C For unimolecular/recombination rxns, effective rate constant is | |
| -C keff = kinf * (Pr/(1+Pr)) * F | |
| -C For chemically-activated bimolecular rxns, effective rate constant is | |
| -C keff = kzero * (1/(1+Pr)) * F | |
| - IF (LINDEREACTIONARRAY(I*20+1) .GT. 1 .AND. | |
| - $ LINDEREACTIONARRAY(I*20+2) .GT. 1) THEN | |
| - FRATE = LOWRATE * (1/(1+PR)) | |
| - ELSE | |
| - FRATE = RATE * (PR/(1+PR)) | |
| - END IF | |
| +C 9-Jul-2009: MRH | |
| +C For unimolecular/recombination rxns, effective rate constant is | |
| +C keff = kinf * (Pr/(1+Pr)) * F | |
| +C For chemically-activated bimolecular rxns, effective rate constant is | |
| +C keff = kzero * (1/(1+Pr)) * F | |
| + IF (LINDEREACTIONARRAY(I*20+1) .GT. 1 .AND. | |
| + $ LINDEREACTIONARRAY(I*20+2) .GT. 1) THEN | |
| + FRATE = LOWRATE * (1/(1+PR)) | |
| + ELSE | |
| + FRATE = RATE * (PR/(1+PR)) | |
| + END IF | |
| IF (LINDEREACTIONARRAY(20*I+9) .EQ. 1) THEN | |
| RRATE = fRATE/LINDEREACTIONRATEARRAY(17*I+5) | |
| diff --git a/source/dassl/reaction_flux.f b/source/dassl/reaction_flux.f | |
| index 99b0161..739d977 100644 | |
| --- a/source/dassl/reaction_flux.f | |
| +++ b/source/dassl/reaction_flux.f | |
| @@ -165,17 +165,17 @@ c write(*,*) temperature | |
| LOGF = LOGFCENT/(1 + INSIDE**2) | |
| F = 10**LOGF | |
| -C 9-Jul-2009: MRH | |
| -C For unimolecular/recombination rxns, effective rate constant is | |
| -C keff = kinf * (Pr/(1+Pr)) * F | |
| -C For chemically-activated bimolecular rxns, effective rate constant is | |
| -C keff = kzero * (1/(1+Pr)) * F | |
| - IF (TROEREACTIONARRAY(I*21+1) .GT. 1 .AND. | |
| - $ TROEREACTIONARRAY(I*21+2) .GT. 1) THEN | |
| - FRATE = LOWRATE * (1/(1+PR)) * F | |
| - ELSE | |
| - FRATE = RATE * (PR/(1+PR)) * F | |
| - END IF | |
| +C 9-Jul-2009: MRH | |
| +C For unimolecular/recombination rxns, effective rate constant is | |
| +C keff = kinf * (Pr/(1+Pr)) * F | |
| +C For chemically-activated bimolecular rxns, effective rate constant is | |
| +C keff = kzero * (1/(1+Pr)) * F | |
| + IF (TROEREACTIONARRAY(I*21+1) .GT. 1 .AND. | |
| + $ TROEREACTIONARRAY(I*21+2) .GT. 1) THEN | |
| + FRATE = LOWRATE * (1/(1+PR)) * F | |
| + ELSE | |
| + FRATE = RATE * (PR/(1+PR)) * F | |
| + END IF | |
| IF (TROEREACTIONARRAY(21*I+9) .EQ. 1) THEN | |
| RRATE = fRATE/TROEREACTIONRATEARRAY(21*I+5) | |
| @@ -221,17 +221,17 @@ c write(*,*) temperature | |
| PR = LOWRATE * M/RATE | |
| -C 9-Jul-2009: MRH | |
| -C For unimolecular/recombination rxns, effective rate constant is | |
| -C keff = kinf * (Pr/(1+Pr)) * F | |
| -C For chemically-activated bimolecular rxns, effective rate constant is | |
| -C keff = kzero * (1/(1+Pr)) * F | |
| - IF (LINDEREACTIONARRAY(I*20+1) .GT. 1 .AND. | |
| - $ LINDEREACTIONARRAY(I*20+2) .GT. 1) THEN | |
| - FRATE = LOWRATE * (1/(1+PR)) | |
| - ELSE | |
| - FRATE = RATE * (PR/(1+PR)) | |
| - END IF | |
| +C 9-Jul-2009: MRH | |
| +C For unimolecular/recombination rxns, effective rate constant is | |
| +C keff = kinf * (Pr/(1+Pr)) * F | |
| +C For chemically-activated bimolecular rxns, effective rate constant is | |
| +C keff = kzero * (1/(1+Pr)) * F | |
| + IF (LINDEREACTIONARRAY(I*20+1) .GT. 1 .AND. | |
| + $ LINDEREACTIONARRAY(I*20+2) .GT. 1) THEN | |
| + FRATE = LOWRATE * (1/(1+PR)) | |
| + ELSE | |
| + FRATE = RATE * (PR/(1+PR)) | |
| + END IF | |
| IF (LINDEREACTIONARRAY(20*I+9) .EQ. 1) THEN | |
| RRATE = fRATE/LINDEREACTIONRATEARRAY(17*I+5) | |
| diff --git a/source/fame/Makefile b/source/fame/Makefile | |
| index 8f98fc2..e1684e6 100755 | |
| --- a/source/fame/Makefile | |
| +++ b/source/fame/Makefile | |
| @@ -13,10 +13,35 @@ BUILDDIR=../../build/fame | |
| # The directory in which to place compiled executables and JAR files | |
| BINDIR=../../bin | |
| -# The Fortran 90 compiler to use and flags to use when compiling Fortran 90 | |
| -# code | |
| -F90=g95 | |
| -F90FLAGS=-fmod=$(BUILDDIR) -ftrace=full | |
| +# The Fortran 90 compiler to use and flags to use when compiling Fortran code | |
| +# Call with 'make F90=g95' if you want to use g95 | |
| +# or 'make F90=gfortran' for GNU Fortran (recommended) | |
| +# Here we set the default | |
| +#F90=g95 | |
| +F90=gfortran | |
| + | |
| +ifeq ($(F90),g95) | |
| +F90FLAGS = -fbounds-check -ftrace=full -fmod=$(BUILDDIR) -Wall -O3 | |
| +endif ###### END OF g95 SETTINGS | |
| + | |
| +ifeq ($(F90),gfortran) | |
| +# --fpe-trap=invalid,zero,underflow,overflow | |
| +# The above flag causes problems at least with fame. Maybe a bug in gfortran? (Maybe a bug in fame.) | |
| +F90FLAGS = -ftrapv -fbounds-check -frange-check \ | |
| + -ggdb -J""$(BUILDDIR)"" -O3 -Wall -Wno-unused | |
| +# if gfortran>4.3 then add -fbacktrace (it's not supported in earlier versions) | |
| +ifeq ($(shell gfortran --version 2>/dev/zero|grep -iqs '^GNU Fortran.* [4-9]\.[3-9]\.[0-9]' && echo "ok"), ok) | |
| +F90FLAGS += -fbacktrace | |
| +endif | |
| +F90FLAGS_NDEBUG = $(F90FLAGS) # used for dassl and daspk | |
| + | |
| +# call as `make MACOS=true F90=gfortran` if you want MacOS X 10.6+ 64-bit intel core2 features | |
| +ifdef MACOS | |
| +F90FLAGS += -arch x86_64 -march=core2 | |
| +F90_EXTRA_LDFLAGS += -framework vecLIB | |
| +endif | |
| + | |
| +endif ###### END OF gfortran SETTINGS | |
| LDFLAGS= $(F90_EXTRA_LDFLAGS) -lpthread -lblas -llapack | |
| diff --git a/source/fame/fame.f90 b/source/fame/fame.f90 | |
| index 65cb1b1..a989f0a 100755 | |
| --- a/source/fame/fame.f90 | |
| +++ b/source/fame/fame.f90 | |
| @@ -137,7 +137,7 @@ program fame | |
| do t = 1, nT | |
| write (1,fmt=*) K(t,:,prod,reac) | |
| end do | |
| - stop | |
| + go to 99 | |
| end if | |
| write (*, fmt='(A)'), '# The reactant and product isomers' | |
| @@ -171,7 +171,7 @@ program fame | |
| end do | |
| ! Close log file | |
| - close(1) | |
| +99 close(1) | |
| deallocate(K, chebyshevCoeffs, pDepArrhenius) | |
| diff --git a/source/fame/io.f90 b/source/fame/io.f90 | |
| index c70e867..79a9166 100644 | |
| --- a/source/fame/io.f90 | |
| +++ b/source/fame/io.f90 | |
| @@ -656,7 +656,7 @@ contains | |
| read(token, *), numValues | |
| call getFirstToken(string, token) | |
| - units = token | |
| + units = token(1:64) | |
| allocate(values(1:numValues)) | |
| do n = 1, numValues | |
| @@ -688,7 +688,7 @@ contains | |
| read(token, *), numValues | |
| call getFirstToken(string, token) | |
| - units = token | |
| + units = token(1:64) | |
| call getFirstToken(string, token) | |
| read(token, *), Nmin | |
| @@ -714,7 +714,7 @@ contains | |
| character(len=256) token | |
| call getFirstToken(string, token) | |
| - units = token | |
| + units = token(1:64) | |
| call getFirstToken(string, token) | |
| read(token, *), value | |
| diff --git a/source/fame/network.f90 b/source/fame/network.f90 | |
| index cf42d42..270f956 100644 | |
| --- a/source/fame/network.f90 | |
| +++ b/source/fame/network.f90 | |
| @@ -308,16 +308,20 @@ contains | |
| integer linear, symm | |
| character(len=128) msg | |
| - integer i | |
| + integer Nvib, Nrot, Nhind, i | |
| + | |
| + Nvib = size(spec%spectral%vibFreq) | |
| + Nrot = size(spec%spectral%rotFreq) | |
| + Nhind = size(spec%spectral%hindFreq) | |
| ! Prepare inputs for density of states function | |
| - do i = 1, size(spec%spectral%vibFreq) | |
| + do i = 1, Nvib | |
| vib(i) = spec%spectral%vibFreq(i) | |
| end do | |
| - do i = 1, size(spec%spectral%rotFreq) | |
| + do i = 1, Nrot | |
| rot(i) = spec%spectral%rotFreq(i) | |
| end do | |
| - do i = 1, size(spec%spectral%hindFreq) | |
| + do i = 1, Nhind | |
| hind(i,1) = spec%spectral%hindFreq(i) | |
| hind(i,2) = spec%spectral%hindBarrier(i) | |
| end do | |
| @@ -328,8 +332,8 @@ contains | |
| symm = spec%spectral%symmNum | |
| ! Calculate the density of states | |
| - call densityOfStates(Elist, nGrains, vib, size(vib), rot, size(rot), & | |
| - hind, size(hind), symm, linear, densStates, msg) | |
| + call densityOfStates(Elist, nGrains, vib, Nvib, rot, Nrot, & | |
| + hind, Nhind, symm, linear, densStates, msg) | |
| end subroutine | |
| @@ -543,7 +547,7 @@ contains | |
| do r = 1, nGrains | |
| if (isom%E0 < Elist(r) .and. index == 0) index = r | |
| end do | |
| - isom%densStates(index:nGrains) = densStates(1:nGrains-index) | |
| + isom%densStates(index:nGrains) = densStates(1:nGrains-index+1) | |
| end subroutine | |
| @@ -988,7 +992,7 @@ contains | |
| real(8) dE, dEdown | |
| character(len=128) :: msg | |
| - integer i, j, r | |
| + integer i, j, r, s | |
| write(1,*) 'Applying method at', T, 'K,', P/1e5, 'bar...' | |
| @@ -1000,12 +1004,19 @@ contains | |
| densStates(i,:) = net%isomers(i)%densStates * dE / net%isomers(i)%Q | |
| end do | |
| - | |
| ! Active-state energy of each isomer | |
| do i = 1, nIsom+nReac+nProd | |
| Eres(i) = isomer_getActiveSpaceEnergy(i, net%reactions) | |
| end do | |
| + ! Zero collision matrix | |
| + do i = 1, nIsom | |
| + do r = 1, Ngrains | |
| + do s = 1, Ngrains | |
| + Mcoll(i,r,s) = 0.0 | |
| + end do | |
| + end do | |
| + end do | |
| ! Zero rate coefficient matrices | |
| do r = 1, nGrains | |
| do i = 1, nIsom | |
| diff --git a/source/fame/rs.f90 b/source/fame/rs.f90 | |
| index f84c57a..13730de 100644 | |
| --- a/source/fame/rs.f90 | |
| +++ b/source/fame/rs.f90 | |
| @@ -105,6 +105,15 @@ Kij, Fim, Gnj, dEdown, nIsom, nReac, nProd, nGrains, K, msg) | |
| bres(i) = sum(eqDist(i,1:nRes(i))) | |
| end do | |
| + ! Zero pseudo-steady state vector array | |
| + do i = 1, nIsom | |
| + do n = 1, nIsom+nReac | |
| + do r = nRes(i), nGrains | |
| + pa(r,n,i) = 0.0 | |
| + end do | |
| + end do | |
| + end do | |
| + | |
| ! Determine pseudo-steady state populations of active state | |
| if (nIsom == 1) then | |
| ! Not worth it to call banded solver when only one well | |
| diff --git a/source/frankie/Makefile b/source/frankie/Makefile | |
| index aba3c40..1a1aa38 100755 | |
| --- a/source/frankie/Makefile | |
| +++ b/source/frankie/Makefile | |
| @@ -13,10 +13,36 @@ BUILDDIR=../../build/frankie | |
| # The directory in which to place compiled executables and JAR files | |
| BINDIR=../../bin | |
| -# The Fortran 90 compiler to use and flags to use when compiling Fortran 90 | |
| -# code | |
| -F90=g95 | |
| -F90FLAGS=-fmod=$(BUILDDIR) -ftrace=full | |
| +# The Fortran 90 compiler to use and flags to use when compiling Fortran code | |
| +# Call with 'make F90=g95' if you want to use g95 | |
| +# or 'make F90=gfortran' for GNU Fortran (recommended) | |
| +# Here we set the default | |
| +#F90=g95 | |
| +F90=gfortran | |
| + | |
| +ifeq ($(F90),g95) | |
| +F90FLAGS = -fbounds-check -ftrace=full -fmod=$(BUILDDIR) -Wall -O3 | |
| +F90FLAGS_NDEBUG = -fmod=$(BUILDDIR) -ftrace=full # used for dassl and daspk | |
| +endif ###### END OF g95 SETTINGS | |
| + | |
| +ifeq ($(F90),gfortran) | |
| +# --fpe-trap=invalid,zero,underflow,overflow | |
| +# The above flag causes problems at least with fame. Maybe a bug in gfortran? (Maybe a bug in fame.) | |
| +F90FLAGS = -ftrapv -fbounds-check -frange-check \ | |
| + -ggdb -J""$(BUILDDIR)"" -O3 -Wall -Wno-unused | |
| +# if gfortran>4.3 then add -fbacktrace (it's not supported in earlier versions) | |
| +ifeq ($(shell gfortran --version 2>/dev/zero|grep -iqs '^GNU Fortran.* [4-9]\.[3-9]\.[0-9]' && echo "ok"), ok) | |
| +F90FLAGS += -fbacktrace | |
| +endif | |
| +F90FLAGS_NDEBUG = $(F90FLAGS) # used for dassl and daspk | |
| + | |
| +# call as `make MACOS=true F90=gfortran` if you want MacOS X 10.6+ 64-bit intel core2 features | |
| +ifdef MACOS | |
| +F90FLAGS += -arch x86_64 -march=core2 | |
| +F90_EXTRA_LDFLAGS += -framework vecLIB | |
| +endif | |
| + | |
| +endif ###### END OF gfortran SETTINGS | |
| LDFLAGS= $(F90_EXTRA_LDFLAGS) -lpthread | |
| diff --git a/source/frankie/calc_freq_code.f90 b/source/frankie/calc_freq_code.f90 | |
| index f4d8c5a..b343f87 100755 | |
| --- a/source/frankie/calc_freq_code.f90 | |
| +++ b/source/frankie/calc_freq_code.f90 | |
| @@ -1155,7 +1155,7 @@ SUBROUTINE Bond_avg_8x3_2_1 (Number_of_bonds, & | |
| INTEGER :: i,j, k | |
| IF (Number_of_bonds == 0 ) THEN | |
| - predicted_frequencies = (/ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 /) | |
| + ! predicted_frequencies has DIMENSION(0) so we can't assign anything to it | |
| ELSEIF (Number_of_bonds == 1) THEN | |
| call linspace(typical_frequencies(1),typical_frequencies(2), & | |
| @@ -1201,7 +1201,7 @@ SUBROUTINE Bond_avg_5x2_1 (Number_of_bonds, & | |
| INTEGER :: i,j, k | |
| IF (Number_of_bonds == 0 ) THEN | |
| - predicted_frequencies = (/ 0.0, 0.0, 0.0, 0.0, 0.0 /) | |
| + ! predicted_frequencies has DIMENSION(0) so we can't assign anything to it | |
| ELSEIF (Number_of_bonds == 1) THEN | |
| predicted_frequencies(1) = typical_frequencies(1) | |
| @@ -1240,7 +1240,7 @@ SUBROUTINE Bond_avg_3x2_1 (Number_of_bonds, & | |
| INTEGER :: i,j, k | |
| IF (Number_of_bonds == 0 ) THEN | |
| - predicted_frequencies = (/ 0.0, 0.0, 0.0 /) | |
| + ! predicted_frequencies has DIMENSION(0) so we can't assign anything to it | |
| ELSEIF (Number_of_bonds == 1) THEN | |
| predicted_frequencies(1) = typical_frequencies(1) | |
| @@ -1271,7 +1271,7 @@ SUBROUTINE Bond_avg_7x2_1 (Number_of_bonds, & | |
| INTEGER :: i,j, k | |
| IF (Number_of_bonds == 0 ) THEN | |
| - predicted_frequencies = (/ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 /) | |
| + !! predicted_frequencies has DIMENSION(0) so we can't assign anything to it | |
| ELSEIF (Number_of_bonds == 1) THEN | |
| predicted_frequencies(1) = typical_frequencies(1) | |
| @@ -1318,7 +1318,7 @@ SUBROUTINE Bond_avg_5x1 (Number_of_bonds, & | |
| INTEGER :: i,j, k | |
| IF (Number_of_bonds == 0 ) THEN | |
| - predicted_frequencies = (/ 0.0, 0.0, 0.0, 0.0, 0.0 /) | |
| + ! predicted_frequencies has DIMENSION(0) so we can't assign anything to it | |
| ELSEIF (Number_of_bonds == 1) THEN | |
| @@ -1362,7 +1362,7 @@ SUBROUTINE Bond_avg_3x1 (Number_of_bonds, & | |
| INTEGER :: i,j, k | |
| IF (Number_of_bonds == 0 ) THEN | |
| - predicted_frequencies = (/ 0.0, 0.0, 0.0 /) | |
| + ! predicted_frequencies has DIMENSION(0) so we can't assign anything to it | |
| ELSEIF (Number_of_bonds == 1) THEN | |
| @@ -1400,7 +1400,7 @@ SUBROUTINE Bond_avg_6x2_2_1 (Number_of_bonds, & | |
| IF (Number_of_bonds == 0 ) THEN | |
| ! WRITE (*,*) 'N = 0' | |
| - predicted_frequencies = (/ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 /) | |
| + ! predicted_frequencies has DIMENSION(0) so we can't assign anything to it | |
| ELSEIF (Number_of_bonds == 1) THEN | |
| @@ -1441,7 +1441,7 @@ SUBROUTINE Bond_avg_4x1 (Number_of_bonds, & | |
| INTEGER :: i,j, k | |
| IF (Number_of_bonds == 0 ) THEN | |
| - predicted_frequencies = (/ 0.0, 0.0, 0.0, 0.0 /) | |
| + ! predicted_frequencies has DIMENSION(0) so we can't assign anything to it | |
| ELSEIF (Number_of_bonds == 1) THEN | |
| @@ -1484,7 +1484,7 @@ SUBROUTINE Bond_avg_5x2_2_1 (Number_of_bonds, & | |
| IF (Number_of_bonds == 0 ) THEN | |
| ! WRITE (*,*) 'N = 0' | |
| - predicted_frequencies = (/ 0.0, 0.0, 0.0, 0.0, 0.0 /) | |
| + ! predicted_frequencies has DIMENSION(0) so we can't assign anything to it | |
| ELSEIF (Number_of_bonds == 1) THEN | |
| @@ -1521,7 +1521,7 @@ SUBROUTINE Bond_avg_6x2_1 (Number_of_bonds, & | |
| INTEGER :: i,j, k | |
| IF (Number_of_bonds == 0 ) THEN | |
| - predicted_frequencies = (/ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 /) | |
| + ! predicted_frequencies has DIMENSION(0) so we can't assign anything to it | |
| ELSEIF (Number_of_bonds == 1) THEN | |
| predicted_frequencies(1) = typical_frequencies(1) | |
| @@ -1564,7 +1564,7 @@ SUBROUTINE Bond_avg_2x1 (Number_of_bonds, & | |
| INTEGER :: i,j, k | |
| IF (Number_of_bonds == 0 ) THEN | |
| - predicted_frequencies = (/ 0.0, 0.0 /) | |
| + ! predicted_frequencies has DIMENSION(0) so we can't assign anything to it | |
| ELSEIF (Number_of_bonds == 1) THEN | |
| @@ -1595,7 +1595,7 @@ SUBROUTINE Bond_avg_1x1 (Number_of_bonds, & | |
| INTEGER :: i,j, k | |
| IF (Number_of_bonds == 0 ) THEN | |
| - predicted_frequencies = (/ 0.0 /) | |
| + ! predicted_frequencies has DIMENSION(0) so we can't assign anything to it | |
| ELSEIF (Number_of_bonds == 1) THEN | |
| @@ -1622,7 +1622,7 @@ SUBROUTINE Bond_avg_4x2_1 (Number_of_bonds, & | |
| INTEGER :: i,j, k | |
| IF (Number_of_bonds == 0 ) THEN | |
| - predicted_frequencies = (/ 0.0, 0.0, 0.0, 0.0 /) | |
| + ! predicted_frequencies has DIMENSION(0) so we can't assign anything to it | |
| ELSEIF (Number_of_bonds == 1) THEN | |
| predicted_frequencies(1) = typical_frequencies(1) | |
| @@ -7658,7 +7658,7 @@ IMPLICIT NONE | |
| WRITE(*,*) 'Nonlinear molecule' | |
| trans_rot_cp_to_cv = 4.0 | |
| N_vib = 3 * (N_atoms) - 6 - (N_rot) - (degeneracy) | |
| - IF (N_vib < 0) THEN | |
| + IF (N_vib < 0) THEN | |
| WRITE(*,*) 'Something is wrong. The system is over specified.' | |
| WRITE(*,*) 'Either reduce the number of rotors or reduce the number of bond types.' | |
| WRITE(*,*) 'Program will now exit to avoid crashing.' | |
| diff --git a/web/source/documentation/faq.txt b/web/source/documentation/faq.txt | |
| index 02befdc..f01907f 100644 | |
| --- a/web/source/documentation/faq.txt | |
| +++ b/web/source/documentation/faq.txt | |
| @@ -1,123 +1,123 @@ | |
| -.. _faq: | |
| - | |
| -******************************** | |
| -FAQ (Frequently-Asked Questions) | |
| -******************************** | |
| - | |
| -Questions | |
| ---------- | |
| - | |
| - | |
| -How do I represent molecular oxygen? | |
| -==================================== | |
| - | |
| -Use the ground electronic state of molecular oxygen, which contains a single | |
| -bond and a diradical. The adjacency list should be :: | |
| - | |
| - (1) O2 0.1 (mol/cm3) | |
| - 1 O 1 {2,S} | |
| - 2 O 1 {1,S} | |
| - | |
| -For more information, please see :ref:`Representing oxygen <oxygen>`. | |
| - | |
| -.. _Q3: | |
| - | |
| -My RMG run runs out of memory. How should I proceed? | |
| -==================================================================================================================================== | |
| -This type of error will probably look something like ``Exception in thread "main" java.lang.OutOfMemoryError: Java heap space``. | |
| -Species take up a large amount of memory, and when the combined edge plus core gets into the range of tens of thousands | |
| -of species, the run will typically crash even with around 1500 MB of RAM. | |
| -If you haven't already done so, we recommend allocating as much memory as possible | |
| -when executing the RMG job (for example, using the option -Xmx1600m will allocate 1600 MB of memory. See the section on :ref:`running RMG <running>`). If this still fails, there are several additional options: | |
| - | |
| -1) Use the pruning feature introduced in RMG 3.2. | |
| - | |
| -2) Use tighter bounds for MaxCarbonNumber, MaxRadicalNumber, etc. as appropriate for your system. | |
| - By reducing these values, RMG will generate fewer edge species. The idea is to intelligently choose the bounds to | |
| - exclude species that shouldn't be relevant for your particular system. | |
| - | |
| -3) Relax the error tolerance (i.e. make it larger). RMG keeps expanding the reaction mechanism | |
| - until the flux to 'edge' species is below the tolerance you specify. Increasing this tolerance | |
| - means RMG will build a smaller mechanism (though it may be | |
| - missing some important reaction pathways). For more details see http://rmg.sourceforge.net/documentation/theory/enlarger.html and the reference on that page. | |
| - | |
| -.. _Q4: | |
| - | |
| -RMG has been running for multiple days and hasn't finished. Is there any way to make it run faster? | |
| -=================================================================================================== | |
| -Getting RMG to converge in a reasonable time, especially for large starting species, can be tricky. Depending on the options specified, the RMG developers | |
| -have seen mechanism generation runs as long as ~10 days. During this time, RMG is running hundreds of reaction model simulations and considering tens of thousands of species, and perhaps over a million possible reactions. As such, it can be inconvenient to have it running for a long time on your personal single-core machine or laptop. So, if you have access to a computing cluster where you can run RMG, that can ease the burden. Some "tricks" that could be helpful in reducing time requirements for model generation (in no particular order): | |
| - | |
| -1) Relax the error tolerance (i.e. make it larger). RMG keeps expanding the reaction mechanism | |
| - until the flux to 'edge' species is below the tolerance you specify. Increasing this tolerance | |
| - means RMG will stop sooner; it will take less time, but the model will be smaller and may be | |
| - missing some important reaction pathways. For more details see http://rmg.sourceforge.net/documentation/theory/enlarger.html and the reference on that page. | |
| - | |
| -2) Setting the maximum number of carbons (or oxygens, heavy atoms, etc.) in a species, | |
| - if you're focusing on the species decomposition. | |
| - | |
| -3) Run RMG for a single temperature / pressure (TemperatureModel, PressureModel). | |
| - | |
| -4) If you are running RMG with pressure dependence, consider trying the less accurate | |
| - (but faster) ModifiedStrongCollision option. | |
| - | |
| -5) If you are using a Seed Mechanism, set the GenerateReactions field to off. | |
| - | |
| -.. _Q5: | |
| - | |
| -How do I use the DASPK dynamic solver? | |
| -====================================== | |
| -RMG uses DASPK in a manner that requires a proprietary library known as DAEPACK, | |
| -and unfortunately, we cannot distribute this library. If you acquire this | |
| -library (for example, possibly through the Jacobian program from Numerica) we | |
| -will be able to help you compile the Linux version of daspkAUTO.exe, but | |
| -compiling in Windows has been tricky in our experience. | |
| - | |
| -Hopefully, DASSL will meet your needs as it should provide all the functionality | |
| -of DASPK, with the exception of sensitivity analysis (which you could do in | |
| -Chemkin with the final model). | |
| - | |
| -.. _Q6: | |
| - | |
| -During the RMG run, I see the warning: "Frankie exceeded maximum number of iterations...". Is this normal? | |
| -============================================================================================================ | |
| -This occurs when the optimization algorithm for the frequency estimation code | |
| -"Frankie" fails to converge. In these cases, the frequencies (used to calculate | |
| -density of states in master equation calculations to account for pressure dependence) | |
| -may not be as accurate as they could be. It is typical for some fraction of Frankie | |
| -jobs to fail in this fashion. | |
| - | |
| -.. _Q7: | |
| - | |
| -During the RMG run, I see the warning: "fitted Er < 0 ...". Is this normal? | |
| -=============================================================================== | |
| -This occurs when the fitted activation energy for reverse reaction rate coefficients | |
| -(based on equilibrium considerations) turns out to be negative. In these cases, the | |
| -activation energy for the reverse reaction is adjusted to zero, with corresponding | |
| -adjustment to the A-factor to ensure accurate equilibrium constant is maintained. | |
| -It is typical for some fraction of the large number of reactions considered to | |
| -produce this output. | |
| - | |
| -.. _Q8: | |
| - | |
| -I encounter a NegativeConcentrationException, causing the RMG run to fail. How should I proceed? | |
| -============================================================================================================================================================================== | |
| -The error message will read something like ``Exception in thread "main" jing.rxnSys.NegativeConcentrationException...``. | |
| -The issue here is that the ODE simulator reached a slightly negative concentration, which RMG consequently interpreted as erroneous and stopped. It is basically a numerical | |
| -artifact, as the equations should not allow a negative concentration. There are two options for dealing with this: | |
| - | |
| -1. Play around with the value for Atol in the DynamicSimulator block in your | |
| - condition file...for example, maybe try tightening it (i.e. reduce the value) by a few orders of | |
| - magnitude. | |
| - | |
| -2. Specify the non-negativity option (introduced in version 3.2). (This could cause other solver errors, so use this as a last-resort.) | |
| - To use this option with the DASSL solver, specify non-negative in the condition.txt input file as follows: "DynamicSimulator: | |
| - DASSL: non-negative". | |
| - | |
| -.. _Q2: | |
| - | |
| -During the RMG run, I see the warning: "Negative Steady State populations encountered during reservoir state method, falling back to Modified Strong Collision". Is this normal? | |
| -================================================================================================================================================================================ | |
| -This is a normal numerical error in the matrix algebra. It occurs sometimes | |
| -with the reservoir state method due to the larger size of the matrices. RMG | |
| -recovers from the error by trying the Modified Strong Collision method. | |
| +.. _faq: | |
| + | |
| +******************************** | |
| +FAQ (Frequently-Asked Questions) | |
| +******************************** | |
| + | |
| +Questions | |
| +--------- | |
| + | |
| + | |
| +How do I represent molecular oxygen? | |
| +==================================== | |
| + | |
| +Use the ground electronic state of molecular oxygen, which contains a single | |
| +bond and a diradical. The adjacency list should be :: | |
| + | |
| + (1) O2 0.1 (mol/cm3) | |
| + 1 O 1 {2,S} | |
| + 2 O 1 {1,S} | |
| + | |
| +For more information, please see :ref:`Representing oxygen <oxygen>`. | |
| + | |
| +.. _Q3: | |
| + | |
| +My RMG run runs out of memory. How should I proceed? | |
| +==================================================================================================================================== | |
| +This type of error will probably look something like ``Exception in thread "main" java.lang.OutOfMemoryError: Java heap space``. | |
| +Species take up a large amount of memory, and when the combined edge plus core gets into the range of tens of thousands | |
| +of species, the run will typically crash even with around 1500 MB of RAM. | |
| +If you haven't already done so, we recommend allocating as much memory as possible | |
| +when executing the RMG job (for example, using the option -Xmx1600m will allocate 1600 MB of memory. See the section on :ref:`running RMG <running>`). If this still fails, there are several additional options: | |
| + | |
| +1) Use the pruning feature introduced in RMG 3.2. | |
| + | |
| +2) Use tighter bounds for MaxCarbonNumber, MaxRadicalNumber, etc. as appropriate for your system. | |
| + By reducing these values, RMG will generate fewer edge species. The idea is to intelligently choose the bounds to | |
| + exclude species that shouldn't be relevant for your particular system. | |
| + | |
| +3) Relax the error tolerance (i.e. make it larger). RMG keeps expanding the reaction mechanism | |
| + until the flux to 'edge' species is below the tolerance you specify. Increasing this tolerance | |
| + means RMG will build a smaller mechanism (though it may be | |
| + missing some important reaction pathways). For more details see http://rmg.sourceforge.net/documentation/theory/enlarger.html and the reference on that page. | |
| + | |
| +.. _Q4: | |
| + | |
| +RMG has been running for multiple days and hasn't finished. Is there any way to make it run faster? | |
| +=================================================================================================== | |
| +Getting RMG to converge in a reasonable time, especially for large starting species, can be tricky. Depending on the options specified, the RMG developers | |
| +have seen mechanism generation runs as long as ~10 days. During this time, RMG is running hundreds of reaction model simulations and considering tens of thousands of species, and perhaps over a million possible reactions. As such, it can be inconvenient to have it running for a long time on your personal single-core machine or laptop. So, if you have access to a computing cluster where you can run RMG, that can ease the burden. Some "tricks" that could be helpful in reducing time requirements for model generation (in no particular order): | |
| + | |
| +1) Relax the error tolerance (i.e. make it larger). RMG keeps expanding the reaction mechanism | |
| + until the flux to 'edge' species is below the tolerance you specify. Increasing this tolerance | |
| + means RMG will stop sooner; it will take less time, but the model will be smaller and may be | |
| + missing some important reaction pathways. For more details see http://rmg.sourceforge.net/documentation/theory/enlarger.html and the reference on that page. | |
| + | |
| +2) Setting the maximum number of carbons (or oxygens, heavy atoms, etc.) in a species, | |
| + if you're focusing on the species decomposition. | |
| + | |
| +3) Run RMG for a single temperature / pressure (TemperatureModel, PressureModel). | |
| + | |
| +4) If you are running RMG with pressure dependence, consider trying the less accurate | |
| + (but faster) ModifiedStrongCollision option. | |
| + | |
| +5) If you are using a Seed Mechanism, set the GenerateReactions field to off. | |
| + | |
| +.. _Q5: | |
| + | |
| +How do I use the DASPK dynamic solver? | |
| +====================================== | |
| +RMG uses DASPK in a manner that requires a proprietary library known as DAEPACK, | |
| +and unfortunately, we cannot distribute this library. If you acquire this | |
| +library (for example, possibly through the Jacobian program from Numerica) we | |
| +will be able to help you compile the Linux version of daspkAUTO.exe, but | |
| +compiling in Windows has been tricky in our experience. | |
| + | |
| +Hopefully, DASSL will meet your needs as it should provide all the functionality | |
| +of DASPK, with the exception of sensitivity analysis (which you could do in | |
| +Chemkin with the final model). | |
| + | |
| +.. _Q6: | |
| + | |
| +During the RMG run, I see the warning: "Frankie exceeded maximum number of iterations...". Is this normal? | |
| +============================================================================================================ | |
| +This occurs when the optimization algorithm for the frequency estimation code | |
| +"Frankie" fails to converge. In these cases, the frequencies (used to calculate | |
| +density of states in master equation calculations to account for pressure dependence) | |
| +may not be as accurate as they could be. It is typical for some fraction of Frankie | |
| +jobs to fail in this fashion. | |
| + | |
| +.. _Q7: | |
| + | |
| +During the RMG run, I see the warning: "fitted Er < 0 ...". Is this normal? | |
| +=============================================================================== | |
| +This occurs when the fitted activation energy for reverse reaction rate coefficients | |
| +(based on equilibrium considerations) turns out to be negative. In these cases, the | |
| +activation energy for the reverse reaction is adjusted to zero, with corresponding | |
| +adjustment to the A-factor to ensure accurate equilibrium constant is maintained. | |
| +It is typical for some fraction of the large number of reactions considered to | |
| +produce this output. | |
| + | |
| +.. _Q8: | |
| + | |
| +I encounter a NegativeConcentrationException, causing the RMG run to fail. How should I proceed? | |
| +============================================================================================================================================================================== | |
| +The error message will read something like ``Exception in thread "main" jing.rxnSys.NegativeConcentrationException...``. | |
| +The issue here is that the ODE simulator reached a slightly negative concentration, which RMG consequently interpreted as erroneous and stopped. It is basically a numerical | |
| +artifact, as the equations should not allow a negative concentration. There are two options for dealing with this: | |
| + | |
| +1. Play around with the value for Atol in the DynamicSimulator block in your | |
| + condition file...for example, maybe try tightening it (i.e. reduce the value) by a few orders of | |
| + magnitude. | |
| + | |
| +2. Specify the non-negativity option (introduced in version 3.2). (This could cause other solver errors, so use this as a last-resort.) | |
| + To use this option with the DASSL solver, specify non-negative in the condition.txt input file as follows: "DynamicSimulator: | |
| + DASSL: non-negative". | |
| + | |
| +.. _Q2: | |
| + | |
| +During the RMG run, I see the warning: "Negative Steady State populations encountered during reservoir state method, falling back to Modified Strong Collision". Is this normal? | |
| +================================================================================================================================================================================ | |
| +This is a normal numerical error in the matrix algebra. It occurs sometimes | |
| +with the reservoir state method due to the larger size of the matrices. RMG | |
| +recovers from the error by trying the Modified Strong Collision method. |
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