https://github.com/jarvist/polaron-lambda
Inner-sphere polaron reorgnisation energy (Lambda) from a 4-point calculation; with Gaussian
https://github.com/jarvist/polaron-lambda
checkpoint density-functional-theory gaussian lambda
Last synced: 8 months ago
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Inner-sphere polaron reorgnisation energy (Lambda) from a 4-point calculation; with Gaussian
- Host: GitHub
- URL: https://github.com/jarvist/polaron-lambda
- Owner: jarvist
- Created: 2014-02-05T13:17:58.000Z (over 12 years ago)
- Default Branch: master
- Last Pushed: 2022-01-12T12:31:08.000Z (over 4 years ago)
- Last Synced: 2025-04-14T10:52:28.948Z (about 1 year ago)
- Topics: checkpoint, density-functional-theory, gaussian, lambda
- Language: Shell
- Size: 5.86 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
Scripts to generate the 4-Gaussian jobs from an input molecule to calculate the
'inner sphere' reorganisation energy.
This follows the roughly nomenclature and working of JKP's thesis.
'we follow the method of Sakanou' - JKP Thesis 2.2 Reorganisation Energy
This is useful as an input into the Marcus equation for electron / hole
transport in organic semiconducting materials.
These calculations are pretty trivial and can be created by hand, but I wrote
these scripts to allow the automatic calculation of many lambdas of different fullerenes / oligomers (in
particular, when seeing whether you could vary lambda by chemical design to
induce better charge transport).
The scripts are very hairy.
# Using these Scripts
* Start with either Gaussian Checkpoints (.chk) or Log Files (.log) of the structures you want to calculate the inner-sphere reorganisation of.
* Run ./polaron_reorg_optimisation_jobs_from_chk.sh or ./polaron_reorg_optimisation_jobs_from_log.sh
````
>ls
mylovelymolecule.chk
>./polaron_reorg_optimisation_jobs_from_chk.sh *.chk
>ls
mylovelymolecule.chk mylovelymolecule_ion_opt.chk mylovelymolecule_ion_opt.com mylovelymolecule_neutral_opt.chk mylovelymolecule_neutral_opt.com
````
--> generates two geometry opt jobs (neutral + charged)
* Run these jobs, retaining the checkpoints.
* Generate the energy jobs (Nb: you could use a different / higher level of theory here, in particular you might want to think of expanding the basis set for an Anion calculation and/or increasing the convergence)
````
>./polaron_reorg_energy_jobs_from_geom_chks.sh *_opt.chk
````
--> generates 4 energy jobs "*_ion_E.chk" / "_neutral_E.chk"
* Run these *_E.com jobs...
* Have a tasty look at the reorganisation energies with the handy ./calc_reorg_energy.sh script
````
>./calc_reorg_energy.sh C60_b3lypopt [here's one I made earlier...]
C60_b3lypopt
N_ion: -2286.24731990 N_neu: -2286.17409196 I_ion: -2286.24982989 I_neu: -2286.17154854
Neutral transition (I_new-N_neu) in eV: .06920900162
Ion transition (N_ion - I_ion) in eV: .06829933789
.13750833951
````
--> C60 has an inner sphere reorganisation energy of 138 meV at b3lyp/6-31g*.