Vague notes written on upload - scripts to calculate Reorganisation Energies with Gaussian

a-Overview

This follows the roughly nomenclature and working of JKP's thesis.

'we follow the method of Sakanou' - JKP Thesis 2.2 Reorganisation Energy

1) Run 'polaron_reorg_optimisation_jobs_from_chk.sh' on a checkpoint for an arb molecule
 --> generates two geometry opt jobs (neutral + charged)

2) Once complete, run 'polaron_reorg_energy_jobs_from_geom_chks.sh' on the two checkpoints returned.
 --> generates 4 energy jobs "*_ion_E.chk" / "_neutral_E.chk"

3) Once everything's returned, run 'calc_reorg_energy.sh' on the root of the file names to calculate your energy in eV.

Nb: you can of course use your first calculation for the Neutral-struct-neutral-energy value, and also avoid doing 2 redundant energy calculations in part 2. Just copy the files rather than run more jobs.

However, this also allows you to do energy calculations at higher level of theory / basis than the geom optimisation (for which b3lyp/6-31g* should be fine).

AAA - Update 2014

Forgot about this gist, and made a full blown GitHub repo separately:- https://github.com/jarvist/polaron-lambda

Slight edits to allow more easy Method for the E calculations, a version to work from .log files rather than checkpoints, and a better description (perhaps).

Consider this Gist obsolete.

calc_reorg_energy.sh

for i
do
 N_ion=` grep "SCF Done" "${i}"*neutral_opt_ion_E.log | awk '{print $5}' `
 N_neu=` grep "SCF Done" "${i}"*neutral_opt_neutral_E.log |  awk '{print $5}' `
 I_ion=` grep "SCF Done" "${i}"*ion_opt_ion_E.log | awk '{print $5}' `
 I_neu=` grep "SCF Done" "${i}"*ion_opt_neutral_E.log | awk '{print $5}' `

 echo "N_ion: " $N_ion "N_neu: " $N_neu "I_ion: " $I_ion "I_neu: " $I_neu

# 'we follow the method of Sakanou' - JKP Thesis 2.2 Reorganisation Energy
 echo "(($I_neu - $N_neu) + ($N_ion - $I_ion) ) * 27.211 " | bc -l

done

polaron_reorg_energy_jobs_from_geom_chks.sh

#Jarv ~ 26-4-12
#Generate .com files from a base .chk file for the necessary jobs to calc polaron reorg energy

echo "WARNING: Be careful, don't run these jobs till you actually have the checkpoints returned!"

CHARGE="-1" #holes...
METHOD="b3lyp/6-31g*"

for i
do
#OK; Need: Geom opts in the neutral and charged state
#SP energy calcs for each of these in n + c state

cp "${i}" "${i%.*}_ion_E.chk"
cp "${i}" "${i%.*}_neutral_E.chk"

cat > "${i%.*}_ion_E.com" << EOF
%chk=${i%.*}_ion_E.chk
%Mem=8Gb
%nproc=8
#p geom=check guess=read sp ${METHOD}

B3lyp auto opt job - neutral state

${CHARGE} 2

EOF

cat > "${i%.*}_neutral_E.com" << EOF
%chk=${i%.*}_neutral_E.chk
%Mem=8Gb
%nproc=8
#p geom=check guess=read sp ${METHOD}

B3lyp auto opt job - neutral state

0 1

EOF

done

polaron_reorg_optimisation_jobs_from_chk.sh

#Jarv ~ 26-4-12
#Generate .com files from a base .chk file for the necessary jobs to calc polaron reorg energy

CHARGE="-1" #holes...

for i
do
#OK; Need: Geom opts in the neutral and charged state
#SP energy calcs for each of these in n + c state

cp "${i}" "${i%.*}_ion_opt.chk"
cp "${i}" "${i%.*}_neutral_opt.chk"

cat > "${i%.*}_ion_opt.com" << EOF
%chk=${i%.*}_ion_opt.chk
%Mem=8Gb
%nproc=8
#p geom=check guess=read opt b3lyp/6-31g*

B3lyp auto opt job - neutral state

${CHARGE} 2

EOF

cat > "${i%.*}_neutral_opt.com" << EOF
%chk=${i%.*}_neutral_opt.chk
%Mem=8Gb
%nproc=8
#p geom=check guess=read opt b3lyp/6-31g*

B3lyp auto opt job - neutral state

0 1

EOF

done