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*.