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speth/co2_RK.cti

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Cantera CTML writer
Raw
co2_RK.cti
units(length = "cm", time = "s", quantity = "mol", act_energy = "cal/mol")
RedlichKwongMFTP(name = "carbondioxide",
elements = " C O H ",
species = """ CO2 H2O """,
activity_coefficients = (pureFluidParameters(species="CO2", a_coeff = [7.54e12, -4.13e9], b_coeff = 27.80),
pureFluidParameters(species="H2O", a_coeff = [1.7458E13, -8.0E9], b_coeff = 18.18),
crossFluidParameters(species="CO2 H2O", a_coeff = [7.897e12, 0]) ),
initial_state = state(temperature = 300.0,
pressure = OneAtm,
mole_fractions = 'CO2:0.9999, H2O:0.0001') )
#-------------------------------------------------------------------------------
# Species data
#-------------------------------------------------------------------------------
species(name = "CO2",
atoms = " C:1 O:2 ",
thermo = (
NASA( [ 200.00, 1000.00], [ 2.356773520E+00, 8.984596770E-03,
-7.123562690E-06, 2.459190220E-09, -1.436995480E-13,
-4.837196970E+04, 9.901052220E+00] ),
NASA( [ 1000.00, 3500.00], [ 3.857460290E+00, 4.414370260E-03,
-2.214814040E-06, 5.234901880E-10, -4.720841640E-14,
-4.875916600E+04, 2.271638060E+00] )
),
)
species(name = "H2O",
atoms = " H:2 O:1 ",
thermo = (
NASA( [ 273.00, 1000.00], [ 4.198640560E+00, -2.036434100E-03,
6.520402110E-06, -5.487970620E-09, 1.771978170E-12,
-3.029372670E+04, -8.490322080E-01] ),
NASA( [ 1000.00, 1600.00], [ 3.033992490E+00, 2.176918040E-03,
-1.640725180E-07, -9.704198700E-11, 1.682009920E-14,
-3.000429710E+04, 4.966770100E+00] )
),
)
Raw
ctml_writer.py
#!/usr/bin/env python
##
# @file ctml_writer.py
#
# Cantera .cti input file processor
# @defgroup pygroup Cantera Python Interface
#
# The functions and classes in this module process Cantera .cti input
# files and produce CTML files. It can be imported as a module, or used
# as a script.
#
# script usage:
#
# python ctml_writer.py infile.cti
#
# This will produce CTML file 'infile.xml'
from __future__ import print_function
class CTI_Error(Exception):
"""Exception raised if an error is encountered while
parsing the input file.
@ingroup pygroup"""
def __init__(self, msg):
print('\n\n***** Error parsing input file *****\n\n')
print(msg)
print()
indent = ['',
' ',
' ',
' ',
' ',
' ',
' ',
' ',
' ',
' ',
' ',
' ',
' ',
' ',
' ',
' ']
#-----------------------------------------------------
class XMLnode(object):
"""This is a minimal class to allow easy creation of an XML tree
from Python. It can write XML, but cannot read it."""
def __init__(self, name="--", value = ""):
"""Create a new node. Usually this only needs to be explicitly
called to create the root element. Method addChild calls this
constructor to create the new child node."""
self._name = name
# convert 'value' to a string if it is not already, and
# strip leading whitespace
if not isinstance(value, str):
self._value = repr(value).lstrip()
else:
self._value = value.lstrip()
self._attribs = {} # dictionary of attributes
self._children = [] # list of child nodes
self._childmap = {} # dictionary of child nodes
def name(self):
"""The tag name of the node."""
return self._name
def nChildren(self):
"""Number of child elements."""
return len(self._children)
def addChild(self, name, value=""):
"""Add a child with tag 'name', and set its value if the value
parameter is supplied."""
# create a new node for the child
c = XMLnode(name = name, value = value)
# add it to the list of children, and to the dictionary
# of children
self._children.append(c)
self._childmap[name] = c
return c
def addComment(self, comment):
"""Add a comment."""
self.addChild(name = '_comment_', value = comment)
def value(self):
"""A string containing the element value."""
return self._value
def child(self, name=""):
"""The child node with specified name."""
return self._childmap[name]
def children(self):
""" An iterator over the child nodes """
for c in self._children:
yield c
def __getitem__(self, key):
"""Get an attribute using the syntax node[key]"""
return self._attribs[key]
def __setitem__(self, key, value):
"""Set a new attribute using the syntax node[key] = value."""
self._attribs[key] = value
def __call__(self):
"""Allows getting the value using the syntax 'node()'"""
return self._value
def write(self, filename):
"""Write out the XML tree to a file."""
f = open(filename, 'w')
f.write('<?xml version="1.0"?>\n')
self._write(f, 0)
f.write('\n')
def _write(self, f, level = 0):
"""Internal method used to write the XML representation of
each node."""
if self._name == "": return
indnt = indent[level]
# handle comments
if self._name == '_comment_':
f.write('\n'+indnt+'<!--')
if len(self._value) > 0:
if self._value[0] != ' ':
self._value = ' '+self._value
if self._value[-1] != ' ':
self._value = self._value+' '
f.write(self._value+'-->')
return
# write the opening tag and attributes
f.write(indnt + '<' + self._name)
for a in self._attribs.keys():
f.write(' '+a+'="'+self._attribs[a]+'"')
if (self._value == "" and self.nChildren() == 0):
f.write('/>')
else:
f.write('>')
if self._value != "":
vv = self._value.lstrip()
ieol = vv.find('\n')
if ieol >= 0:
while 1 > 0:
ieol = vv.find('\n')
if ieol >= 0:
f.write('\n '+indnt+vv[:ieol])
vv = vv[ieol+1:].lstrip()
else:
f.write('\n '+indnt+vv)
break
else:
f.write(self._value)
for c in self._children:
f.write('\n')
c._write(f, level + 2)
if (self.nChildren() > 0):
f.write('\n'+indnt)
f.write('</'+self._name+'>')
#--------------------------------------------------
# constants that can be used in .cti files
OneAtm = 1.01325e5
OneBar = 1.0e5
# Conversion from eV to J/kmol (electronCharge * Navrog)
eV = 9.64853364595687e7
# Electron Mass in kg
ElectronMass = 9.10938291e-31
import math, copy
# default units
_ulen = 'm'
_umol = 'kmol'
_umass = 'kg'
_utime = 's'
_ue = 'J/kmol'
_uenergy = 'J'
_upres = 'Pa'
# used to convert reaction pre-exponentials
_length = {'cm':0.01, 'm':1.0, 'mm':0.001}
_moles = {'kmol':1.0, 'mol':0.001, 'molec':1.0/6.02214129e26}
_time = {'s':1.0, 'min':60.0, 'hr':3600.0}
# default std state pressure
_pref = 1.0e5 # 1 bar
_name = 'noname'
# these lists store top-level entries
_elements = []
_species = []
_speciesnames = []
_phases = []
_reactions = []
_atw = {}
_enames = {}
_valsp = ''
_valrxn = ''
_valexport = ''
_valfmt = ''
def export_species(filename, fmt = 'CSV'):
global _valexport
global _valfmt
_valexport = filename
_valfmt = fmt
def validate(species = 'yes', reactions = 'yes'):
global _valsp
global _valrxn
_valsp = species
_valrxn = reactions
def isnum(a):
"""True if a is an integer or floating-point number."""
if isinstance(a, (int, float)):
return 1
else:
return 0
def is_local_species(name):
"""true if the species named 'name' is defined in this file"""
if name in _speciesnames:
return 1
return 0
def dataset(nm):
"Set the dataset name. Invoke this to change the name of the xml file."
global _name
_name = nm
def standard_pressure(p0):
"""Set the default standard-state pressure."""
global _pref
_pref = p0
def units(length = '', quantity = '', mass = '', time = '',
act_energy = '', energy = '', pressure = ''):
"""
Set the default units.
:param length:
The default units for length. Default: ``'m'``
:param mass:
The default units for mass. Default: ``'kg'``
:param quantity:
The default units to specify number of molecules. Default: ``'kmol'``
:param time:
The default units for time. Default: ``'s'``
:param energy:
The default units for energies. Default: ``'J'``
:param act_energy:
The default units for activation energies. Default: ``'K'``
:param pressure:
The default units for pressure. Default: ``'Pa'``
"""
global _ulen, _umol, _ue, _utime, _umass, _uenergy, _upres
if length: _ulen = length
if quantity: _umol = quantity
if act_energy: _ue = act_energy
if time: _utime = time
if mass: _umass = mass
if energy: _uenergy = energy
if pressure: _upres = pressure
def ufmt(base, n):
"""return a string representing a unit to a power n."""
if n == 0: return ''
if n == 1: return '-'+base
if n == -1: return '/'+base
if n > 0: return '-'+base+str(n)
if n < 0: return '/'+base+str(-n)
def write(outName=None):
"""write the CTML file."""
x = XMLnode("ctml")
v = x.addChild("validate")
v["species"] = _valsp
v["reactions"] = _valrxn
if _elements:
ed = x.addChild("elementData")
for e in _elements:
e.build(ed)
for ph in _phases:
ph.build(x)
s = species_set(name = _name, species = _species)
s.build(x)
r = x.addChild('reactionData')
r['id'] = 'reaction_data'
for rx in _reactions:
rx.build(r)
if outName is not None:
x.write(outName)
elif _name != 'noname':
x.write(_name+'.xml')
else:
print(x)
if _valexport:
f = open(_valexport,'w')
for s in _species:
s.export(f, _valfmt)
f.close()
def addFloat(x, nm, val, fmt='', defunits=''):
"""
Add a child element to XML element x representing a
floating-point number.
"""
u = ''
s = ''
if isnum(val):
fval = float(val)
if fmt:
s = fmt % fval
else:
s = repr(fval)
xc = x.addChild(nm, s)
if defunits:
xc['units'] = defunits
else:
v = val[0]
u = val[1]
if fmt:
s = fmt % v
else:
s = repr(v)
xc = x.addChild(nm, s)
xc['units'] = u
def getAtomicComp(atoms):
if isinstance(atoms, dict): return atoms
a = atoms.replace(',',' ')
toks = a.split()
d = {}
for t in toks:
b = t.split(':')
d[b[0]] = int(b[1])
return d
def getReactionSpecies(s):
"""Take a reaction string and return a
dictionary mapping species names to stoichiometric
coefficients. If any species appears more than once,
the returned stoichiometric coefficient is the sum.
>>> s = 'CH3 + 3 H + 5.2 O2 + 0.7 H'
>>> getReactionSpecies(s)
>>> {'CH3':1, 'H':3.7, 'O2':5.2}
"""
# get rid of the '+' signs separating species. Only plus signs
# surrounded by spaces are replaced, so that plus signs may be
# used in species names (e.g. 'Ar3+')
toks = s.replace(' + ',' ').split()
d = {}
n = 1.0
for t in toks:
# try to convert the token to a number.
try:
n = float(t)
if n < 0.0:
raise CTI_Error("negative stoichiometric coefficient:"
+s)
#if t > '0' and t < '9':
# n = int(t)
#else:
# token isn't a number, so it must be a species name
except:
# already seen this token so increment its value by the last
# value of n
if t in d:
d[t] += n
else:
# first time this token has been seen, so set its value to n
d[t] = n
# reset n to 1.0 for species that do not specify a stoichiometric
# coefficient
n = 1
return d
class element(object):
""" An atomic element or isotope. """
def __init__(self, symbol = '',
atomic_mass = 0.01,
atomic_number = 0):
"""
:param symbol:
The symbol for the element or isotope.
:param atomic_mass:
The atomic mass in amu.
"""
self._sym = symbol
self._atw = atomic_mass
self._num = atomic_number
global _elements
_elements.append(self)
def build(self, db):
e = db.addChild("element")
e["name"] = self._sym
e["atomicWt"] = repr(self._atw)
e["atomicNumber"] = repr(self._num)
class species_set(object):
def __init__(self, name = '', species = []):
self._s = species
self._name = name
#self.type = SPECIES_SET
def build(self, p):
p.addComment(' species definitions ')
sd = p.addChild("speciesData")
sd["id"] = "species_data"
for s in self._s:
#if s.type == SPECIES:
s.build(sd)
#else:
# raise 'wrong object type in species_set: '+s.__class__
class species(object):
"""A constituent of a phase or interface."""
def __init__(self,
name = 'missing name!',
atoms = '',
note = '',
thermo = None,
transport = None,
charge = -999,
size = 1.0):
"""
:param name:
The species name (or formula). The name may be arbitrarily long,
although usually a relatively short, abbreviated name is most
convenient. Required parameter.
:param atoms:
The atomic composition, specified by a string containing
space-delimited <element>:<atoms> pairs. The number of atoms may be
either an integer or a floating-point number.
:param thermo:
The parameterization to use to compute the reference-state
thermodynamic properties. This must be one of the entry types
described in :ref:`sec-thermo-models`. To specify multiple
parameterizations, each for a different temperature range,
group them in parentheses.
:param transport:
An entry specifying parameters to compute this species'
contribution to the transport properties. This must be one of the
entry types described in :ref:`sec-species-transport-models`, and
must be consistent with the transport model of the phase into which
the species is imported. To specify parameters for multiple
transport models, group the entries in parentheses.
:param size:
The species "size". Currently used only for surface species,
where it represents the number of sites occupied.
:param charge:
The charge, in multiples of :math:`|e|`. If not specified, the
charge will be calculated from the number of "atoms" of element
``E``, which represents an electron.
"""
self._name = name
self._atoms = getAtomicComp(atoms)
self._comment = note
if thermo:
self._thermo = thermo
else:
self._thermo = const_cp()
self._transport = transport
chrg = 0
self._charge = charge
if 'E' in self._atoms:
chrg = -self._atoms['E']
if self._charge != -999:
if self._charge != chrg:
raise CTI_Error('specified charge inconsistent with number of electrons')
else:
self._charge = chrg
self._size = size
global _species
global _enames
_species.append(self)
global _speciesnames
if name in _speciesnames:
raise CTI_Error('species '+name+' multiply defined.')
_speciesnames.append(name)
for e in self._atoms.keys():
_enames[e] = 1
def export(self, f, fmt = 'CSV'):
global _enames
if fmt == 'CSV':
s = self._name+','
for e in _enames:
if e in self._atoms:
s += repr(self._atoms[e])+','
else:
s += '0,'
f.write(s)
if isinstance(self._thermo, thermo):
self._thermo.export(f, fmt)
else:
nt = len(self._thermo)
for n in range(nt):
self._thermo[n].export(f, fmt)
f.write('\n')
def build(self, p):
hdr = ' species '+self._name+' '
p.addComment(hdr)
s = p.addChild("species")
s["name"] = self._name
a = ''
for e in self._atoms.keys():
a += e+':'+str(self._atoms[e])+' '
s.addChild("atomArray",a)
if self._comment:
s.addChild("note",self._comment)
if self._charge != -999:
s.addChild("charge",self._charge)
if self._size != 1.0:
s.addChild("size",self._size)
if self._thermo:
t = s.addChild("thermo")
if isinstance(self._thermo, thermo):
self._thermo.build(t)
else:
nt = len(self._thermo)
for n in range(nt):
self._thermo[n].build(t)
if self._transport:
t = s.addChild("transport")
if isinstance(self._transport, transport):
self._transport.build(t)
else:
nt = len(self._transport)
for n in range(nt):
self._transport[n].build(t)
class thermo(object):
"""Base class for species standard-state thermodynamic properties."""
def _build(self, p):
return p.addChild("thermo")
def export(self, f, fmt = 'CSV'):
pass
class Mu0_table(thermo):
"""Properties are computed by specifying a table of standard
chemical potentials vs. T."""
def __init__(self, Trange = (0.0, 0.0),
h298 = 0.0,
mu0 = None,
p0 = -1.0):
self._t = Trange
self._h298 = h298
self._mu0 = mu0
self._pref = p0
def build(self, t):
n = t.addChild("Mu0")
n['Tmin'] = repr(self._t[0])
n['Tmax'] = repr(self._t[1])
if self._pref <= 0.0:
n['P0'] = repr(_pref)
else:
n['P0'] = repr(self._pref)
energy_units = _uenergy+'/'+_umol
addFloat(n,"H298", self._h298, defunits = energy_units)
n.addChild("numPoints", len(self._mu0))
mustr = ''
tstr = ''
col = 0
for v in self._mu0:
mu0 = v[1]
t = v[0]
tstr += '%17.9E, ' % t
mustr += '%17.9E, ' % mu0
col += 1
if col == 3:
tstr = tstr[:-2]+'\n'
mustr = mustr[:-2]+'\n'
col = 0
u = n.addChild("floatArray", mustr)
u["size"] = "numPoints"
u["name"] = "Mu0Values"
u = n.addChild("floatArray", tstr)
u["size"] = "numPoints"
u["name"] = "Mu0Temperatures"
class NASA(thermo):
"""The 7-coefficient NASA polynomial parameterization."""
def __init__(self, Trange = (0.0, 0.0), coeffs = [], p0 = -1.0):
r"""
:param Trange:
The temperature range over which the parameterization is valid.
This must be entered as a sequence of two temperature values.
Required.
:param coeffs:
Array of seven coefficients :math:`(a_0, \ldots , a_6)`
:param p0:
The reference-state pressure, usually 1 atm or 1 bar. If omitted,
the default value is used, which is set by the ``standard_pressure``
directive.
"""
self._t = Trange
self._pref = p0
if len(coeffs) != 7:
raise CTI_Error('NASA coefficient list must have length = 7')
self._coeffs = coeffs
def export(self, f, fmt='CSV'):
if fmt == 'CSV':
s = 'NASA,'+str(self._t[0])+','+str(self._t[1])+','
for i in range(7):
s += '%17.9E, ' % self._coeffs[i]
f.write(s)
def build(self, t):
n = t.addChild("NASA")
n['Tmin'] = repr(self._t[0])
#n['Tmid'] = repr(self._t[1])
n['Tmax'] = repr(self._t[1])
if self._pref <= 0.0:
n['P0'] = repr(_pref)
else:
n['P0'] = repr(self._pref)
s = ''
for i in range(4):
s += '%17.9E, ' % self._coeffs[i]
s += '\n'
s += '%17.9E, %17.9E, %17.9E' % (self._coeffs[4],
self._coeffs[5], self._coeffs[6])
#if i > 0 and 3*((i+1)/3) == i: s += '\n'
#s = s[:-2]
u = n.addChild("floatArray", s)
u["size"] = "7"
u["name"] = "coeffs"
class NASA9(thermo):
"""NASA9 polynomial parameterization for a single temperature region."""
def __init__(self, Trange = (0.0, 0.0),
coeffs = [], p0 = -1.0):
self._t = Trange # Range of the polynomial representation
self._pref = p0 # Reference pressure
if len(coeffs) != 9:
raise CTI_Error('NASA9 coefficient list must have length = 9')
self._coeffs = coeffs
def export(self, f, fmt='CSV'):
if fmt == 'CSV':
s = 'NASA9,'+str(self._t[0])+','+str(self._t[1])+','
for i in range(9):
s += '%17.9E, ' % self._coeffs[i]
f.write(s)
def build(self, t):
n = t.addChild("NASA9")
n['Tmin'] = repr(self._t[0])
n['Tmax'] = repr(self._t[1])
if self._pref <= 0.0:
n['P0'] = repr(_pref)
else:
n['P0'] = repr(self._pref)
s = ''
for i in range(4):
s += '%17.9E, ' % self._coeffs[i]
s += '\n'
s += '%17.9E, %17.9E, %17.9E, %17.9E,' % (self._coeffs[4], self._coeffs[5],
self._coeffs[6], self._coeffs[7])
s += '\n'
s += '%17.9E' % (self._coeffs[8])
u = n.addChild("floatArray", s)
u["size"] = "9"
u["name"] = "coeffs"
class activityCoefficients(object):
pass
class pureFluidParameters(activityCoefficients):
"""
"""
def __init__(self, species = None, a_coeff = [], b_coeff = 0):
"""
"""
self._species = species
self._acoeff = a_coeff
self._bcoeff = b_coeff
def build(self,a):
f= a.addChild("pureFluidParameters")
f['species'] = self._species
s = '%10.4E, %10.4E \n' % (self._acoeff[0], self._acoeff[1])
ac = f.addChild("a_coeff",s)
ac["units"] = _upres+'-'+_ulen+'6/'+_umol+'2'
ac["model"] = "linear_a"
s = '%0.2f \n' % self._bcoeff
bc = f.addChild("b_coeff",s)
bc["units"] = _ulen+'3/'+_umol
class crossFluidParameters(activityCoefficients):
def __init__(self, species = None, a_coeff = [], b_coeff = []):
self._species1, self._species2 = species.split(' ')
self._acoeff = a_coeff
self._bcoeff = b_coeff
def build(self,a):
f= a.addChild("crossFluidParameters")
f["species2"] = self._species2
f["species1"] = self._species1
s = '%10.4E, %10.4E \n' % (self._acoeff[0], self._acoeff[1])
ac = f.addChild("a_coeff",s)
ac["units"] = _upres+'-'+_ulen+'6/'+_umol+'2'
ac["model"] = "linear_a"
if self._bcoeff:
s = '%0.2f \n' % self._bcoeff
bc = f.addChild("b_coeff",s)
bc["units"] = _ulen+'3/'+_umol
class Shomate(thermo):
"""Shomate polynomial parameterization."""
def __init__(self, Trange = (0.0, 0.0), coeffs = [], p0 = -1.0):
r"""
:param Trange:
The temperature range over which the parameterization is valid.
This must be entered as a sequence of two temperature values.
Required input.
:param coeffs:
Sequence of seven coefficients :math:`(A, \ldots ,G)`
:param p0:
The reference-state pressure, usually 1 atm or 1 bar. If omitted,
the default value set by the ``standard_pressure`` directive is used.
"""
self._t = Trange
self._pref = p0
if len(coeffs) != 7:
raise CTI_Error('Shomate coefficient list must have length = 7')
self._coeffs = coeffs
def build(self, t):
n = t.addChild("Shomate")
n['Tmin'] = repr(self._t[0])
n['Tmax'] = repr(self._t[1])
if self._pref <= 0.0:
n['P0'] = repr(_pref)
else:
n['P0'] = repr(self._pref)
s = ''
for i in range(4):
s += '%17.9E, ' % self._coeffs[i]
s += '\n'
s += '%17.9E, %17.9E, %17.9E' % (self._coeffs[4],
self._coeffs[5], self._coeffs[6])
u = n.addChild("floatArray", s)
u["size"] = "7"
u["name"] = "coeffs"
class Adsorbate(thermo):
"""Adsorbed species characterized by a binding energy and a set of
vibrational frequencies."""
def __init__(self, Trange = (0.0, 0.0),
binding_energy = 0.0,
frequencies = [], p0 = -1.0):
self._t = Trange
self._pref = p0
self._freqs = frequencies
self._be = binding_energy
def build(self, t):
n = t.addChild("adsorbate")
n['Tmin'] = repr(self._t[0])
n['Tmax'] = repr(self._t[1])
if self._pref <= 0.0:
n['P0'] = repr(_pref)
else:
n['P0'] = repr(self._pref)
energy_units = _uenergy+'/'+_umol
addFloat(n,'binding_energy',self._be, defunits = energy_units)
s = ""
nfreq = len(self._freqs)
for i in range(nfreq):
s += '%17.9E, ' % self._freqs[i]
s += '\n'
u = n.addChild("floatArray", s)
u["size"] = repr(nfreq)
u["name"] = "freqs"
class const_cp(thermo):
"""Constant specific heat."""
def __init__(self,
t0 = 298.15, cp0 = 0.0, h0 = 0.0, s0 = 0.0,
tmax = 5000.0, tmin = 100.0):
"""
:param t0:
Temperature parameter T0. Default: 298.15 K.
:param cp0:
Reference-state molar heat capacity (constant). Default: 0.0.
:param h0:
Reference-state molar enthalpy at temperature T0. Default: 0.0.
:param s0:
Reference-state molar entropy at temperature T0. Default: 0.0.
"""
self._t = [tmin, tmax]
self._c = [t0, h0, s0, cp0]
def build(self, t):
#t = self._build(p)
c = t.addChild('const_cp')
if self._t[0] >= 0.0: c['Tmin'] = repr(self._t[0])
if self._t[1] >= 0.0: c['Tmax'] = repr(self._t[1])
energy_units = _uenergy+'/'+_umol
addFloat(c,'t0',self._c[0], defunits = 'K')
addFloat(c,'h0',self._c[1], defunits = energy_units)
addFloat(c,'s0',self._c[2], defunits = energy_units+'/K')
addFloat(c,'cp0',self._c[3], defunits = energy_units+'/K')
class transport(object):
pass
class gas_transport(transport):
"""
Species-specific Transport coefficients for ideal gas transport models.
"""
def __init__(self, geom = 'nonlin',
diam = 0.0, well_depth = 0.0, dipole = 0.0,
polar = 0.0, rot_relax = 0.0):
"""
:param geom:
A string specifying the molecular geometry. One of ``atom``,
``linear``, or ``nonlin``. Required.
:param diam:
The Lennard-Jones collision diameter in Angstroms. Required.
:param well_depth:
The Lennard-Jones well depth in Kelvin. Required.
:param dipole:
The permanent dipole moment in Debye. Default: 0.0
:param polar:
The polarizability in A^3. Default: 0.0
:param rot_relax:
The rotational relaxation collision number at 298 K. Dimensionless.
Default: 0.0
"""
self._geom = geom
self._diam = diam
self._well_depth = well_depth
self._dipole = dipole
self._polar = polar
self._rot_relax = rot_relax
def build(self, t):
#t = s.addChild("transport")
t['model'] = 'gas_transport'
# t.addChild("geometry", self._geom)
tg = t.addChild('string',self._geom)
tg['title'] = 'geometry'
addFloat(t, "LJ_welldepth", (self._well_depth, 'K'), '%8.3f')
addFloat(t, "LJ_diameter", (self._diam, 'A'),'%8.3f')
addFloat(t, "dipoleMoment", (self._dipole, 'Debye'),'%8.3f')
addFloat(t, "polarizability", (self._polar, 'A3'),'%8.3f')
addFloat(t, "rotRelax", self._rot_relax,'%8.3f')
class rate_expression(object):
pass
class Arrhenius(rate_expression):
def __init__(self,
A = 0.0,
n = 0.0,
E = 0.0,
coverage = [],
rate_type = ''):
"""
:param A:
The pre-exponential coefficient. Required input. If entered without
units, the units will be computed considering all factors that
affect the units. The resulting units string is written to the CTML
file individually for each reaction pre-exponential coefficient.
:param n:
The temperature exponent. Dimensionless. Default: 0.0.
:param E:
Activation energy. Default: 0.0.
"""
self._c = [A, n, E]
self._type = rate_type
if coverage:
if isinstance(coverage[0], str):
self._cov = [coverage]
else:
self._cov = coverage
else:
self._cov = None
def build(self, p, units_factor = 1.0,
gas_species = [], name = '', rxn_phase = None):
a = p.addChild('Arrhenius')
if name: a['name'] = name
# check for sticking probability
if self._type:
a['type'] = self._type
if self._type == 'stick':
ngas = len(gas_species)
if ngas != 1:
raise CTI_Error("""
Sticking probabilities can only be used for reactions with one gas-phase
reactant, but this reaction has """+str(ngas)+': '+str(gas_species))
else:
a['species'] = gas_species[0]
units_factor = 1.0
# if a pure number is entered for A, multiply by the conversion
# factor to SI and write it to CTML as a pure number. Otherwise,
# pass it as-is through to CTML with the unit string.
if isnum(self._c[0]):
addFloat(a,'A',self._c[0]*units_factor, fmt = '%14.6E')
elif len(self._c[0]) == 2 and self._c[0][1] == '/site':
addFloat(a,'A',self._c[0][0]/rxn_phase._sitedens,
fmt = '%14.6E')
else:
addFloat(a,'A',self._c[0], fmt = '%14.6E')
# The b coefficient should be dimensionless, so there is no
# need to use 'addFloat'
a.addChild('b', repr(self._c[1]))
# If a pure number is entered for the activation energy,
# add the default units, otherwise use the supplied units.
addFloat(a,'E', self._c[2], fmt = '%f', defunits = _ue)
# for surface reactions, a coverage dependence may be specified.
if self._cov:
for cov in self._cov:
c = a.addChild('coverage')
c['species'] = cov[0]
addFloat(c, 'a', cov[1], fmt = '%f')
c.addChild('m', repr(cov[2]))
addFloat(c, 'e', cov[3], fmt = '%f', defunits = _ue)
def stick(A = 0.0, n = 0.0, E = 0.0, coverage = []):
return Arrhenius(A = A, n = n, E = E, coverage = coverage, rate_type = 'stick')
def getPairs(s):
toks = s.split()
m = {}
for t in toks:
key, val = t.split(':')
m[key] = float(val)
return m
class reaction(object):
"""
A homogeneous chemical reaction with pressure-independent rate coefficient
and mass-action kinetics.
"""
def __init__(self,
equation = '',
kf = None,
id = '',
order = '',
options = []):
"""
:param equation:
A string specifying the chemical equation.
:param rate_coeff:
The rate coefficient for the forward direction. If a sequence of
three numbers is given, these will be interpreted as [A, n,E] in
the modified Arrhenius function :math:`A T^n exp(-E/\hat{R}T)`.
:param id:
An optional identification string. If omitted, it defaults to a
four-digit numeric string beginning with 0001 for the first
reaction in the file.
:param options:
Processing options, as described in :ref:`sec-phase-options`.
"""
self._id = id
self._e = equation
self._order = order
if isinstance(options, str):
self._options = [options]
else:
self._options = options
global _reactions
self._num = len(_reactions)+1
r = ''
p = ''
for e in ['<=>', '=>', '=']:
if self._e.find(e) >= 0:
r, p = self._e.split(e)
if e in ['<=>','=']: self.rev = 1
else: self.rev = 0
break
self._r = getReactionSpecies(r)
self._p = getReactionSpecies(p)
self._rxnorder = copy.copy(self._r)
if self._order:
order = getPairs(self._order)
for o in order.keys():
if o in self._rxnorder:
self._rxnorder[o] = order[o]
else:
raise CTI_Error("order specified for non-reactant: "+o)
self._kf = kf
self._igspecies = []
self._dims = [0]*4
self._rxnphase = None
self._type = ''
_reactions.append(self)
def unit_factor(self):
"""
Conversion factor from given rate constant units to the MKS (+kmol)
used internally by Cantera, taking into account the reaction order.
"""
return (math.pow(_length[_ulen], -self.ldim) *
math.pow(_moles[_umol], -self.mdim) / _time[_utime])
def build(self, p):
if self._id:
id = self._id
else:
if self._num < 10:
nstr = '000'+str(self._num)
elif self._num < 100:
nstr = '00'+str(self._num)
elif self._num < 1000:
nstr = '0'+str(self._num)
else:
nstr = str(self._num)
id = nstr
self.mdim = 0
self.ldim = 0
rstr = ''
rxnph = []
for s in self._r.keys():
ns = self._rxnorder[s]
nm = -999
nl = -999
rstr += s+':'+str(self._r[s])+' '
mindim = 4
for ph in _phases:
if ph.has_species(s):
nm, nl = ph.conc_dim()
if ph.is_ideal_gas():
self._igspecies.append(s)
if not ph in rxnph:
rxnph.append(ph)
self._dims[ph._dim] += 1
if ph._dim < mindim:
self._rxnphase = ph
mindim = ph._dim
break
if nm == -999:
raise CTI_Error("species "+s+" not found")
self.mdim += nm*ns
self.ldim += nl*ns
p.addComment(" reaction "+id+" ")
r = p.addChild('reaction')
r['id'] = id
if self.rev:
r['reversible'] = 'yes'
else:
r['reversible'] = 'no'
noptions = len(self._options)
for nss in range(noptions):
s = self._options[nss]
if s == 'duplicate':
r['duplicate'] = 'yes'
elif s == 'negative_A':
r['negative_A'] = 'yes'
ee = self._e.replace('<','[')
ee = ee.replace('>',']')
r.addChild('equation',ee)
if self._order:
for osp in self._rxnorder.keys():
o = r.addChild('order',self._rxnorder[osp])
o['species'] = osp
# adjust the moles and length powers based on the dimensions of
# the rate of progress (moles/length^2 or moles/length^3)
if self._type == 'surface':
self.mdim += -1
self.ldim += 2
p = self._dims[:3]
if p[0] != 0 or p[1] != 0 or p[2] > 1:
raise CTI_Error(self._e +'\nA surface reaction may contain at most '+
'one surface phase.')
elif self._type == 'edge':
self.mdim += -1
self.ldim += 1
p = self._dims[:2]
if p[0] != 0 or p[1] > 1:
raise CTI_Error(self._e+'\nAn edge reaction may contain at most '+
'one edge phase.')
else:
self.mdim += -1
self.ldim += 3
# add the reaction type as an attribute if it has been specified.
if self._type:
r['type'] = self._type
# The default rate coefficient type is Arrhenius. If the rate
# coefficient has been specified as a sequence of three
# numbers, then create a new Arrhenius instance for it;
# otherwise, just use the supplied instance.
nm = ''
kfnode = r.addChild('rateCoeff')
if self._type == '':
self._kf = [self._kf]
elif self._type == 'surface':
self._kf = [self._kf]
elif self._type == 'edge':
self._kf = [self._kf]
elif self._type == 'threeBody':
self._kf = [self._kf]
self.mdim += 1
self.ldim -= 3
elif self._type == 'chebyshev':
self._kf = []
if self._type == 'edge':
if self._beta > 0:
electro = kfnode.addChild('electrochem')
electro['beta'] = repr(self._beta)
for kf in self._kf:
if isinstance(kf, rate_expression):
k = kf
else:
k = Arrhenius(A = kf[0], n = kf[1], E = kf[2])
k.build(kfnode, self.unit_factor(), gas_species = self._igspecies,
name = nm, rxn_phase = self._rxnphase)
if self._type == 'falloff':
# set values for low-pressure rate coeff if falloff rxn
self.mdim += 1
self.ldim -= 3
nm = 'k0'
rstr = rstr[:-1]
r.addChild('reactants',rstr)
pstr = ''
for s in self._p.keys():
ns = self._p[s]
pstr += s+':'+repr(ns)+' '
pstr = pstr[:-1]
r.addChild('products',pstr)
return r
#-------------------
class three_body_reaction(reaction):
"""
A three-body reaction.
"""
def __init__(self,
equation = '',
kf = None,
efficiencies = '',
id = '',
options = []
):
"""
:param equation:
A string specifying the chemical equation. The reaction can be
written in either the association or dissociation directions, and
may be reversible or irreversible.
:param rate_coeff:
The rate coefficient for the forward direction. If a sequence of
three numbers is given, these will be interpreted as [A,n,E] in
the modified Arrhenius function.
:param efficiencies:
A string specifying the third-body collision efficiencies.
The efficiencies for unspecified species are set to 1.0.
:param id:
An optional identification string. If omitted, it defaults to a
four-digit numeric string beginning with 0001 for the first
reaction in the file.
:param options:
Processing options, as described in :ref:`sec-phase-options`.
"""
reaction.__init__(self, equation, kf, id, '', options)
self._type = 'threeBody'
self._effm = 1.0
self._eff = efficiencies
# clean up reactant and product lists
for r in list(self._r.keys()):
if r == 'M' or r == 'm':
del self._r[r]
for p in list(self._p.keys()):
if p == 'M' or p == 'm':
del self._p[p]
def build(self, p):
r = reaction.build(self, p)
if r == 0: return
kfnode = r.child('rateCoeff')
if self._eff:
eff = kfnode.addChild('efficiencies',self._eff)
eff['default'] = repr(self._effm)
#---------------
class falloff_reaction(reaction):
""" A gas-phase falloff reaction. """
def __init__(self, equation, kf0, kf,
efficiencies='', falloff=None, id='', options=[]):
"""
:param equation:
A string specifying the chemical equation.
:param rate_coeff_inf:
The rate coefficient for the forward direction in the high-pressure
limit. If a sequence of three numbers is given, these will be
interpreted as [A, n,E] in the modified Arrhenius function.
:param rate_coeff_0:
The rate coefficient for the forward direction in the low-pressure
limit. If a sequence of three numbers is given, these will be
interpreted as [A, n,E] in the modified Arrhenius function.
:param efficiencies:
A string specifying the third-body collision efficiencies. The
efficiency for unspecified species is set to 1.0.
:param falloff:
An embedded entry specifying a falloff function. If omitted, a
unity falloff function (Lindemann form) will be used.
:param id:
An optional identification string. If omitted, it defaults to a
four-digit numeric string beginning with 0001 for the first
reaction in the file.
:param options:
Processing options, as described in :ref:`sec-phase-options`.
"""
kf2 = (kf, kf0)
reaction.__init__(self, equation, kf2, id, '', options)
self._type = 'falloff'
# use a Lindemann falloff function by default
self._falloff = falloff
if self._falloff == None:
self._falloff = Lindemann()
self._effm = 1.0
self._eff = efficiencies
# clean up reactant and product lists
del self._r['(+']
del self._p['(+']
if 'M)' in self._r:
del self._r['M)']
del self._p['M)']
elif 'm)' in self._r:
del self._r['m)']
del self._p['m)']
else:
for r in list(self._r.keys()):
if r[-1] == ')' and r.find('(') < 0:
species = r[:-1]
if self._eff:
raise CTI_Error('(+ '+species+') and '+self._eff+' cannot both be specified')
self._eff = species+':1.0'
self._effm = 0.0
del self._r[r]
del self._p[r]
def build(self, p):
r = reaction.build(self, p)
if r == 0: return
kfnode = r.child('rateCoeff')
if self._eff and self._effm >= 0.0:
eff = kfnode.addChild('efficiencies',self._eff)
eff['default'] = repr(self._effm)
if self._falloff:
self._falloff.build(kfnode)
class pdep_arrhenius(reaction):
"""
Pressure-dependent rate calculated by interpolating between Arrhenius
expressions at different pressures.
:param equation:
A string specifying the chemical equation.
:param args:
Each additiona argument is a sequence of four elements specifying the
pressure and the Arrhenius parameters at that pressure.
"""
def __init__(self, equation='', *args, **kwargs):
self.pressures = []
self.arrhenius = []
for p, A, n, Ea in args:
self.pressures.append(p)
self.arrhenius.append((A, n, Ea))
reaction.__init__(self, equation, self.arrhenius, **kwargs)
self._type = 'plog'
def build(self, p):
r = reaction.build(self, p)
kfnode = r.child('rateCoeff')
for i,c in enumerate(kfnode.children()):
assert c.name() == 'Arrhenius'
addFloat(c, 'P', self.pressures[i])
class chebyshev_reaction(reaction):
"""
Pressure-dependent rate calculated in terms of a bivariate Chebyshev
polynomial.
:param equation:
A string specifying the chemical equation.
:param Tmin:
The minimum temperature at which the rate expression is defined
:param Tmax:
the maximum temperature at which the rate expression is defined
:param Pmin:
The minimum pressure at which the rate expression is defined
:param Pmax:
The maximum pressure at which the rate expression is defined
:param coeffs:
A 2D array of the coefficients defining the rate expression. For a
polynomial with M points in temperature and N points in pressure, this
should be a list of M lists each with N elements.
"""
def __init__(self, equation='', Tmin=300.0, Tmax=2500.0,
Pmin=(0.001, 'atm'), Pmax=(100.0, 'atm'),
coeffs=[[]], **kwargs):
reaction.__init__(self, equation, **kwargs)
self._type = 'chebyshev'
self.Pmin = Pmin
self.Pmax = Pmax
self.Tmin = Tmin
self.Tmax = Tmax
self.coeffs = coeffs
# clean up reactant and product lists
del self._r['(+']
del self._p['(+']
if 'M)' in self._r:
del self._r['M)']
del self._p['M)']
if 'm)' in self._r:
del self._r['m)']
del self._p['m)']
def build(self, p):
r = reaction.build(self, p)
kfnode = r.child('rateCoeff')
addFloat(kfnode, 'Tmin', self.Tmin)
addFloat(kfnode, 'Tmax', self.Tmax)
addFloat(kfnode, 'Pmin', self.Pmin)
addFloat(kfnode, 'Pmax', self.Pmax)
self.coeffs[0][0] += math.log10(self.unit_factor());
lines = []
for line in self.coeffs:
lines.append(', '.join('{0:12.5e}'.format(val)
for val in line))
coeffNode = kfnode.addChild('floatArray', ',\n'.join(lines))
coeffNode['name'] = 'coeffs'
coeffNode['degreeT'] = str(len(self.coeffs))
coeffNode['degreeP'] = str(len(self.coeffs[0]))
class surface_reaction(reaction):
"""
A heterogeneous chemical reaction with pressure-independent rate
coefficient and mass-action kinetics.
"""
def __init__(self, equation='', kf=None, id='', order='', options=[]):
"""
:param equation:
A string specifying the chemical equation.
:param rate_coeff:
The rate coefficient for the forward direction. If a sequence of
three numbers is given, these will be interpreted as [A, n,E] in
the modified Arrhenius function.
:param sticking_prob:
The reactive sticking probability for the forward direction. This
can only be specified if there is only one bulk-phase reactant and
it belongs to an ideal gas phase. If a sequence of three numbers is
given, these will be interpreted as [A, n,E] in the modified
Arrhenius function.
:param id:
An optional identification string. If omitted, it defaults to a
four-digit numeric string beginning with 0001 for the first
reaction in the file.
:param options:
Processing options, as described in :ref:`sec-phase-options`.
"""
reaction.__init__(self, equation, kf, id, order, options)
self._type = 'surface'
class edge_reaction(reaction):
def __init__(self,
equation = '',
kf = None,
id = '',
order = '',
beta = 0.0,
options = []):
reaction.__init__(self, equation, kf, id, order, options)
self._type = 'edge'
self._beta = beta
#--------------
class state(object):
"""
An embedded entry that specifies the thermodynamic state of a phase
or interface.
"""
def __init__(self,
temperature = None,
pressure = None,
mole_fractions = None,
mass_fractions = None,
density = None,
coverages = None,
solute_molalities = None):
"""
:param temperature:
The temperature.
:param pressure:
The pressure.
:param density:
The density. Cannot be specified if the phase is incompressible.
:param mole_fractions:
A string specifying the species mole fractions. Unspecified species
are set to zero.
:param mass_fractions:
A string specifying the species mass fractions. Unspecified species
are set to zero.
:param coverages:
A string specifying the species coverages. Unspecified species are
set to zero. Can only be specified for interfaces.
"""
self._t = temperature
self._p = pressure
self._rho = density
self._x = mole_fractions
self._y = mass_fractions
self._c = coverages
self._m = solute_molalities
def build(self, ph):
st = ph.addChild('state')
if self._t: addFloat(st, 'temperature', self._t, defunits = 'K')
if self._p: addFloat(st, 'pressure', self._p, defunits = _upres)
if self._rho: addFloat(st, 'density', self._rho, defunits = _umass+'/'+_ulen+'3')
if self._x: st.addChild('moleFractions', self._x)
if self._y: st.addChild('massFractions', self._y)
if self._c: st.addChild('coverages', self._c)
if self._m: st.addChild('soluteMolalities', self._m)
class phase(object):
"""Base class for phases of matter."""
def __init__(self,
name = '',
dim = 3,
elements = '',
species = '',
reactions = 'none',
initial_state = None,
options = []):
"""
:param name:
A string to identify the phase. Must be unique among the phase
names within the file.
:param elements:
The elements. A string of element symbols.
:param species:
The species. A string or sequence of strings in the format
described in :ref:`sec-defining-species`.
:param reactions:
The homogeneous reactions. If omitted, no reactions will be
included. A string or sequence of strings in the format described
in :ref:`sec-declaring-reactions`. This field is not allowed for
stoichiometric_solid and stoichiometric_liquid entries.
:param kinetics:
The kinetics model. Optional; if omitted, the default model for the
phase type will be used.
:param transport:
The transport property model. Optional. If omitted, transport
property calculation will be disabled.
:param initial_state:
Initial thermodynamic state, specified with an embedded state entry.
:param options:
Special processing options. Optional.
"""
self._name = name
self._dim = dim
self._el = elements
self._sp = []
self._rx = []
if isinstance(options, str):
self._options = [options]
else:
self._options = options
self.debug = 0
if 'debug' in options:
self.debug = 1
#--------------------------------
# process species
#--------------------------------
# if a single string is entered, make it a list
if isinstance(species, str):
self._species = [species]
else:
self._species = species
self._skip = 0
# dictionary of species names
self._spmap = {}
# for each species string, check whether or not the species
# are imported or defined locally. If imported, the string
# contains a colon (:)
for sp in self._species:
icolon = sp.find(':')
if icolon > 0:
#datasrc, spnames = sp.split(':')
datasrc = sp[:icolon].strip()
spnames = sp[icolon+1:]
self._sp.append((datasrc+'.xml', spnames))
else:
spnames = sp
self._sp.append(('', spnames))
# strip the commas, and make the list of species names
# 10/31/03: commented out the next line, so that species names may contain commas
#sptoks = spnames.replace(',',' ').split()
sptoks = spnames.split()
for s in sptoks:
# check for stray commas
if s != ',':
if s[0] == ',': s = s[1:]
if s[-1] == ',': s = s[:-1]
if s != 'all' and s in self._spmap:
raise CTI_Error('Multiply-declared species '+s+' in phase '+self._name)
self._spmap[s] = self._dim
self._rxns = reactions
# check that species have been declared
if len(self._spmap) == 0:
raise CTI_Error('No species declared for phase '+self._name)
# and that only one species is declared if it is a pure phase
if self.is_pure() and len(self._spmap) > 1:
raise CTI_Error('Stoichiometric phases must declare exactly one species, \n'+
'but phase '+self._name+' declares '+str(len(self._spmap))+'.')
self._initial = initial_state
# add this phase to the global phase list
global _phases
_phases.append(self)
def is_ideal_gas(self):
"""True if the entry represents an ideal gas."""
return 0
def is_pure(self):
return 0
def has_species(self, s):
"""Return 1 is a species with name 's' belongs to the phase,
or 0 otherwise."""
if s in self._spmap: return 1
return 0
def conc_dim(self):
"""Concentration dimensions. Used in computing the units for reaction
rate coefficients."""
return (1, -self._dim)
def buildrxns(self, p):
if isinstance(self._rxns, str):
self._rxns = [self._rxns]
# for each reaction string, check whether or not the reactions
# are imported or defined locally. If imported, the string
# contains a colon (:)
for r in self._rxns:
icolon = r.find(':')
if icolon > 0:
#datasrc, rnum = r.split(':')
datasrc = r[:icolon].strip()
rnum = r[icolon+1:]
self._rx.append((datasrc+'.xml', rnum))
else:
rnum = r
self._rx.append(('', rnum))
for r in self._rx:
datasrc = r[0]
ra = p.addChild('reactionArray')
ra['datasrc'] = datasrc+'#reaction_data'
rk = None
if 'skip_undeclared_species' in self._options:
rk = ra.addChild('skip')
rk['species'] = 'undeclared'
if 'skip_undeclared_third_bodies' in self._options:
if not rk:
rk = ra.addChild('skip')
rk['third_bodies'] = 'undeclared'
rtoks = r[1].split()
if rtoks[0] != 'all':
i = ra.addChild('include')
#i['prefix'] = 'reaction_'
i['min'] = rtoks[0]
if len(rtoks) > 2 and (rtoks[1] == 'to' or rtoks[1] == '-'):
i['max'] = rtoks[2]
else:
i['max'] = rtoks[0]
def build(self, p):
p.addComment(' phase '+self._name+' ')
ph = p.addChild('phase')
ph['id'] = self._name
ph['dim'] = repr(self._dim)
# ------- error tests -------
#err = ph.addChild('validation')
#err.addChild('duplicateReactions','halt')
#err.addChild('thermo','warn')
e = ph.addChild('elementArray',self._el)
e['datasrc'] = 'elements.xml'
for s in self._sp:
datasrc, names = s
sa = ph.addChild('speciesArray',names)
sa['datasrc'] = datasrc+'#species_data'
if 'skip_undeclared_elements' in self._options:
sk = sa.addChild('skip')
sk['element'] = 'undeclared'
if self._rxns != 'none':
self.buildrxns(ph)
#self._eos.build(ph)
if self._initial:
self._initial.build(ph)
return ph
class ideal_gas(phase):
"""An ideal gas mixture."""
def __init__(self,
name = '',
elements = '',
species = '',
reactions = 'none',
kinetics = 'GasKinetics',
transport = 'None',
initial_state = None,
options = []):
"""
The parameters correspond to those of :class:`.phase`, with the
following modifications:
:param kinetics:
The kinetics model. Usually this field is omitted, in which case
kinetics model GasKinetics, appropriate for reactions in ideal gas
mixtures, is used.
:param transport:
The transport property model. One of the strings ``'none'``,
``'multi'``, or ``'mix'``. Default: ``'none'``.
"""
phase.__init__(self, name, 3, elements, species, reactions,
initial_state, options)
self._pure = 0
self._kin = kinetics
self._tr = transport
if self.debug:
print('Read ideal_gas entry '+self._name)
try:
print('in file '+__name__)
except:
pass
def build(self, p):
ph = phase.build(self, p)
e = ph.addChild("thermo")
e['model'] = 'IdealGas'
k = ph.addChild("kinetics")
k['model'] = self._kin
t = ph.addChild('transport')
t['model'] = self._tr
def is_ideal_gas(self):
return 1
class stoichiometric_solid(phase):
"""
A solid compound or pure element. Stoichiometric solid phases contain
exactly one species, which always has unit activity. The solid is assumed
to have constant density. Therefore the rates of reactions involving these
phases do not contain any concentration terms for the (one) species in the
phase, since the concentration is always the same."""
def __init__(self,
name = '',
elements = '',
species = '',
density = None,
transport = 'None',
initial_state = None,
options = []):
"""
See :class:`.phase` for descriptions of the parameters.
"""
phase.__init__(self, name, 3, elements, species, 'none',
initial_state, options)
self._dens = density
self._pure = 1
if self._dens is None:
raise CTI_Error('density must be specified.')
self._tr = transport
def conc_dim(self):
"""A stoichiometric solid always has unit activity, so the
generalized concentration is 1 (dimensionless)."""
return (0,0)
def build(self, p):
ph = phase.build(self, p)
e = ph.addChild("thermo")
e['model'] = 'StoichSubstance'
addFloat(e, 'density', self._dens, defunits = _umass+'/'+_ulen+'3')
if self._tr:
t = ph.addChild('transport')
t['model'] = self._tr
k = ph.addChild("kinetics")
k['model'] = 'none'
class stoichiometric_liquid(stoichiometric_solid):
"""
An incompressible stoichiometric liquid. Currently, there is no
distinction between stoichiometric liquids and solids.
"""
def __init__(self,
name = '',
elements = '',
species = '',
density = -1.0,
transport = 'None',
initial_state = None,
options = []):
"""
See :class:`.phase` for descriptions of the parameters.
"""
stoichiometric_solid.__init__(self, name, elements,
species, density, transport,
initial_state, options)
class metal(phase):
"""A metal."""
def __init__(self,
name = '',
elements = '',
species = '',
density = -1.0,
transport = 'None',
initial_state = None,
options = []):
phase.__init__(self, name, 3, elements, species, 'none',
initial_state, options)
self._dens = density
self._pure = 0
self._tr = transport
def conc_dim(self):
return (0,0)
def build(self, p):
ph = phase.build(self, p)
e = ph.addChild("thermo")
e['model'] = 'Metal'
addFloat(e, 'density', self._dens, defunits = _umass+'/'+_ulen+'3')
if self._tr:
t = ph.addChild('transport')
t['model'] = self._tr
k = ph.addChild("kinetics")
k['model'] = 'none'
class semiconductor(phase):
"""A semiconductor."""
def __init__(self,
name = '',
elements = '',
species = '',
density = -1.0,
bandgap = 1.0 * eV,
effectiveMass_e = 1.0 * ElectronMass,
effectiveMass_h = 1.0 * ElectronMass,
transport = 'None',
initial_state = None,
options = []):
phase.__init__(self, name, 3, elements, species, 'none',
initial_state, options)
self._dens = density
self._pure = 0
self._tr = transport
self._emass = effectiveMass_e
self._hmass = effectiveMass_h
self._bandgap = bandgap
def conc_dim(self):
return (1,-3)
def build(self, p):
ph = phase.build(self, p)
e = ph.addChild("thermo")
e['model'] = 'Semiconductor'
addFloat(e, 'density', self._dens, defunits = _umass+'/'+_ulen+'3')
addFloat(e, 'effectiveMass_e', self._emass, defunits = _umass)
addFloat(e, 'effectiveMass_h', self._hmass, defunits = _umass)
addFloat(e, 'bandgap', self._bandgap, defunits = 'eV')
if self._tr:
t = ph.addChild('transport')
t['model'] = self._tr
k = ph.addChild("kinetics")
k['model'] = 'none'
class incompressible_solid(phase):
"""An incompressible solid."""
def __init__(self,
name = '',
elements = '',
species = '',
density = -1.0,
transport = 'None',
initial_state = None,
options = []):
phase.__init__(self, name, 3, elements, species, 'none',
initial_state, options)
self._dens = density
self._pure = 0
if self._dens < 0.0:
raise CTI_Error('density must be specified.')
self._tr = transport
def conc_dim(self):
return (1,-3)
def build(self, p):
ph = phase.build(self, p)
e = ph.addChild("thermo")
e['model'] = 'Incompressible'
addFloat(e, 'density', self._dens, defunits = _umass+'/'+_ulen+'3')
if self._tr:
t = ph.addChild('transport')
t['model'] = self._tr
k = ph.addChild("kinetics")
k['model'] = 'none'
class lattice(phase):
def __init__(self, name = '',
elements = '',
species = '',
reactions = 'none',
transport = 'None',
initial_state = None,
options = [],
site_density = -1.0,
vacancy_species = ''):
phase.__init__(self, name, 3, elements, species, 'none',
initial_state, options)
self._tr = transport
self._n = site_density
self._vac = vacancy_species
self._species = species
if name == '':
raise CTI_Error('sublattice name must be specified')
if species == '':
raise CTI_Error('sublattice species must be specified')
if site_density < 0.0:
raise CTI_Error('sublattice '+name
+' site density must be specified')
def build(self,p, visible = 0):
#if visible == 0:
# return
ph = phase.build(self, p)
e = ph.addChild('thermo')
e['model'] = 'Lattice'
addFloat(e, 'site_density', self._n, defunits = _umol+'/'+_ulen+'3')
if self._vac:
e.addChild('vacancy_species',self._vac)
if self._tr:
t = ph.addChild('transport')
t['model'] = self._tr
k = ph.addChild("kinetics")
k['model'] = 'none'
class lattice_solid(phase):
"""A solid crystal consisting of one or more sublattices."""
def __init__(self,
name = '',
elements = '',
species = '',
lattices = [],
transport = 'None',
initial_state = None,
options = []):
# find elements
elist = []
for lat in lattices:
e = lat._el.split()
for el in e:
if not el in elist:
elist.append(el)
elements = ' '.join(elist)
# find species
slist = []
for lat in lattices:
_sp = ""
for spp in lat._species:
_sp = _sp + spp
s = _sp.split()
for sp in s:
if not sp in slist:
slist.append(sp)
species = ' '.join(slist)
phase.__init__(self, name, 3, elements, species, 'none',
initial_state, options)
self._lattices = lattices
if lattices == []:
raise CTI_Error('One or more sublattices must be specified.')
self._pure = 0
self._tr = transport
def conc_dim(self):
return (0,0)
def build(self, p):
ph = phase.build(self, p)
e = ph.addChild("thermo")
e['model'] = 'LatticeSolid'
if self._lattices:
lat = e.addChild('LatticeArray')
for n in self._lattices:
n.build(lat, visible = 1)
if self._tr:
t = ph.addChild('transport')
t['model'] = self._tr
k = ph.addChild("kinetics")
k['model'] = 'none'
class liquid_vapor(phase):
"""A fluid with a complete liquid/vapor equation of state.
This entry type selects one of a set of predefined fluids with
built-in liquid/vapor equations of state. The substance_flag
parameter selects the fluid. See purefluids.py for the usage
of this entry type."""
def __init__(self,
name = '',
elements = '',
species = '',
substance_flag = 0,
initial_state = None,
options = []):
phase.__init__(self, name, 3, elements, species, 'none',
initial_state, options)
self._subflag = substance_flag
self._pure = 1
def conc_dim(self):
return (0,0)
def build(self, p):
ph = phase.build(self, p)
e = ph.addChild("thermo")
e['model'] = 'PureFluid'
e['fluid_type'] = repr(self._subflag)
k = ph.addChild("kinetics")
k['model'] = 'none'
class RedlichKwongMFTP(phase):
"""A fluid with a complete liqui/vapor equation of state.
This entry type selects one of a set of predefined fluids with
built-in liquid/vapor equations of state. The substance_flag
parameter selects the fluid. See purefluids.py for the usage
of this entry type."""
def __init__(self,
name = '',
elements = '',
species = '',
initial_state = None,
activity_coefficients = None,
options = []):
phase.__init__(self,name, 3, elements, species, 'none',
initial_state,options)
self._pure = 0
self._activityCoefficients = activity_coefficients
def conc_dim(self):
return (0,0)
def build(self, p):
ph = phase.build(self,p)
e = ph.addChild("thermo")
e['model'] = 'RedlichKwongMFTP'
if self._activityCoefficients:
a = e.addChild("activityCoefficients")
if isinstance(self._activityCoefficients, activityCoefficients):
self._activityCoefficients.build(a)
else:
na = len(self._activityCoefficients)
for n in range(na):
self._activityCoefficients[n].build(a)
k = ph.addChild("kinetics")
k['model'] = 'none'
class redlich_kwong(phase):
"""A fluid with a complete liquid/vapor equation of state.
This entry type selects one of a set of predefined fluids with
built-in liquid/vapor equations of state. The substance_flag
parameter selects the fluid. See purefluids.py for the usage
of this entry type."""
def __init__(self,
name = '',
elements = '',
species = '',
substance_flag = 7,
initial_state = None,
Tcrit = 1.0,
Pcrit = 1.0,
options = []):
phase.__init__(self, name, 3, elements, species, 'none',
initial_state, options)
self._subflag = 7
self._pure = 1
self._tc = 1
self._pc = 1
def conc_dim(self):
return (0,0)
def build(self, p):
ph = phase.build(self, p)
e = ph.addChild("thermo")
e['model'] = 'PureFluid'
e['fluid_type'] = repr(self._subflag)
addFloat(e, 'Tc', self._tc, defunits = "K")
addFloat(e, 'Pc', self._pc, defunits = "Pa")
addFloat(e, 'MolWt', self._mw, defunits = _umass+"/"+_umol)
ph.addChild("kinetics")
k['model'] = 'none'
class ideal_interface(phase):
"""A chemically-reacting ideal surface solution of multiple species."""
def __init__(self,
name = '',
elements = '',
species = '',
reactions = 'none',
site_density = 0.0,
phases = [],
kinetics = 'Interface',
transport = 'None',
initial_state = None,
options = []):
"""
The parameters correspond to those of :class:`.phase`, with the
following modifications:
:param reactions:
The heterogeneous reactions at this interface. If omitted, no
reactions will be included. A string or sequence of strings in the
format described in :ref:`sec-declaring-reactions`.
:param site_density:
The number of adsorption sites per unit area.
:param phases:
A string listing the bulk phases that participate in reactions
at this interface.
"""
self._type = 'surface'
phase.__init__(self, name, 2, elements, species, reactions,
initial_state, options)
self._pure = 0
self._kin = kinetics
self._tr = transport
self._phases = phases
self._sitedens = site_density
def build(self, p):
ph = phase.build(self, p)
e = ph.addChild("thermo")
e['model'] = 'Surface'
addFloat(e, 'site_density', self._sitedens, defunits = _umol+'/'+_ulen+'2')
k = ph.addChild("kinetics")
k['model'] = self._kin
t = ph.addChild('transport')
t['model'] = self._tr
p = ph.addChild('phaseArray',self._phases)
def conc_dim(self):
return (1, -2)
class edge(phase):
"""A 1D boundary between two surface phases."""
def __init__(self,
name = '',
elements = '',
species = '',
reactions = 'none',
site_density = 0.0,
phases = [],
kinetics = 'Edge',
transport = 'None',
initial_state = None,
options = []):
self._type = 'edge'
phase.__init__(self, name, 1, elements, species, reactions,
initial_state, options)
self._pure = 0
self._kin = kinetics
self._tr = transport
self._phases = phases
self._sitedens = site_density
def build(self, p):
ph = phase.build(self, p)
e = ph.addChild("thermo")
e['model'] = 'Edge'
addFloat(e, 'site_density', self._sitedens, defunits = _umol+'/'+_ulen)
k = ph.addChild("kinetics")
k['model'] = self._kin
t = ph.addChild('transport')
t['model'] = self._tr
p = ph.addChild('phaseArray',self._phases)
def conc_dim(self):
return (1, -1)
## class binary_salt_parameters:
## def __init__(self,
## cation = "",
## anion = "",
## beta0 = None,
## beta1 = None,
## beta2 = None,
## Cphi = None,
## Alpha1 = -1.0):
## self._cation = cation
## self._anion = anion
## self._beta0 = beta0
## self._beta1 = beta1
## self._Cphi = Cphi
## self._Alpha1 = Alpha1
## def build(self, a):
## s = a.addChild("binarySaltParameters")
## s["cation"] = self._cation
## s["anion"] = self._anion
## s.addChild("beta0", self._beta0)
## s.addChild("beta1", self._beta1)
## s.addChild("beta2", self._beta2)
## s.addChild("Cphi", self._Cphi)
## s.addChild("Alpha1", self._Alpha1)
## class theta_anion:
## def __init__(self,
## anions = None,
## theta = 0.0):
## self._anions = anions
## self._theta = theta
## def build(self, a):
## s = a.addChild("thetaAnion")
## s["anion1"] = self._anions[0]
## s["anion2"] = self._anions[1]
## s.addChild("Theta", self._theta)
## class psi_common_cation:
## def __init__(self,
## anions = None,
## cation = '',
## theta = 0.0,
## psi = 0.0):
## self._anions = anions
## self._cation = cation
## self._theta = theta
## self._psi = psi
## def build(self, a):
## s = a.addChild("psiCommonCation")
## s["anion1"] = self._anions[0]
## s["anion2"] = self._anions[1]
## s["cation"] = self._cation
## s.addChild("Theta", self._theta)
## s.addChild("Psi", self._psi)
## class psi_common_anion:
## def __init__(self,
## anion = '',
## cations = None,
## theta = 0.0,
## psi = 0.0):
## self._anion = anion
## self._cations = cations
## self._theta = theta
## self._psi = psi
## def build(self, a):
## s = a.addChild("psiCommonAnion")
## s["anion1"] = self._cations[0]
## s["anion2"] = self._cations[1]
## s["cation"] = self._anion
## s.addChild("Theta", self._theta)
## s.addChild("Psi", self._psi)
## class theta_cation:
## def __init__(self,
## cations = None,
## theta = 0.0):
## self._cations = cations
## self._theta = theta
## def build(self, a):
## s = a.addChild("thetaCation")
## s["cation1"] = self._anions[0]
## s["cation2"] = self._anions[1]
## s.addChild("Theta", self._theta)
## class pitzer:
## def __init__(self,
## temp_model = "",
## A_Debye = "",
## default_ionic_radius = -1.0,
## class electrolyte(phase):
## """An electrolye solution obeying the HMW model."""
## def __init__(self,
## name = '',
## elements = '',
## species = '',
## transport = 'None',
## initial_state = None,
## solvent = '',
## standard_concentration = '',
## activity_coefficients = None,
## options = []):
## phase.__init__(self, name, 3, elements, species, 'none',
## initial_state, options)
## self._pure = 0
## self._solvent = solvent
## self._stdconc = standard_concentration
## def conc_dim(self):
## return (1,-3)
## def build(self, p):
## ph = phase.build(self, p)
## e = ph.addChild("thermo")
## sc = e.addChild("standardConc")
## sc['model'] = self._stdconc
## e['model'] = 'HMW'
## e.addChild("activity_coefficients")
## addFloat(e, 'density', self._dens, defunits = _umass+'/'+_ulen+'3')
## if self._tr:
## t = ph.addChild('transport')
## t['model'] = self._tr
## k = ph.addChild("kinetics")
## k['model'] = 'none'
#-------------------------------------------------------------------
# falloff parameterizations
class Troe(object):
"""The Troe falloff function."""
def __init__(self, A = 0.0, T3 = 0.0, T1 = 0.0, T2 = -999.9):
"""
Parameters: *A*, *T3*, *T1*, *T2*. These must be entered as pure
numbers with no attached dimensions.
"""
if T2 != -999.9:
self._c = (A, T3, T1, T2)
else:
self._c = (A, T3, T1)
def build(self, p):
s = ''
for num in self._c:
s += '%g ' % num
f = p.addChild('falloff', s)
f['type'] = 'Troe'
class SRI(object):
""" The SRI falloff function."""
def __init__(self, A = 0.0, B = 0.0, C = 0.0, D = -999.9, E=-999.9):
"""
Parameters: *A*, *B*, *C*, *D*, *E*. These must be entered as
pure numbers without attached dimensions.
"""
if D != -999.9 and E != -999.9:
self._c = (A, B, C, D, E)
else:
self._c = (A, B, C)
def build(self, p):
s = ''
for num in self._c:
s += '%g ' % num
f = p.addChild('falloff', s)
f['type'] = 'SRI'
class Lindemann(object):
"""The Lindemann falloff function."""
def __init__(self):
""" This falloff function takes no parameters."""
pass
def build(self, p):
f = p.addChild('falloff')
f['type'] = 'Lindemann'
#get_atomic_wts()
validate()
def convert(filename, outName=None):
import os, sys
base = os.path.basename(filename)
root, _ = os.path.splitext(base)
dataset(root)
try:
with open(filename) as f:
code = compile(f.read(), filename, 'exec')
exec(code)
except SyntaxError as err:
# Show more context than the default SyntaxError message
# to help see problems in multi-line statements
text = open(filename).readlines()
print('%s in "%s" on line %i:\n' % (err.__class__.__name__,
err.filename,
err.lineno))
print('| Line |')
for i in range(max(err.lineno-6, 0),
min(err.lineno+3, len(text))):
print('| % 5i |' % (i+1), text[i].rstrip())
if i == err.lineno-1:
print(' '* (err.offset+9) + '^')
print()
sys.exit(3)
except TypeError as err:
import traceback
text = open(filename).readlines()
tb = traceback.extract_tb(sys.exc_info()[2])
lineno = tb[-1][1]
print('%s on line %i of %s:' % (err.__class__.__name__, lineno, filename))
print(err)
print('\n| Line |')
for i in range(max(lineno-6, 0),
min(lineno+3, len(text))):
if i == lineno-1:
print('> % 4i >' % (i+1), text[i].rstrip())
else:
print('| % 4i |' % (i+1), text[i].rstrip())
sys.exit(4)
write(outName)
if __name__ == "__main__":
import sys
if len(sys.argv) not in (2,3):
raise ValueError('Incorrect number of command line arguments.')
convert(*sys.argv[1:])
@speth
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Author

speth commented Jun 17, 2013

Starting from version from Cantera trunk as of Subversion revision 2391

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