{"id":27423104,"url":"https://github.com/jarvist/polaron-lambda","last_synced_at":"2025-10-25T23:39:16.921Z","repository":{"id":13847973,"uuid":"16545248","full_name":"jarvist/polaron-lambda","owner":"jarvist","description":"Inner-sphere polaron reorgnisation energy (Lambda) from a 4-point calculation; with Gaussian","archived":false,"fork":false,"pushed_at":"2022-01-12T12:31:08.000Z","size":6,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-14T10:52:28.948Z","etag":null,"topics":["checkpoint","density-functional-theory","gaussian","lambda"],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/jarvist.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-02-05T13:17:58.000Z","updated_at":"2022-01-11T20:26:16.000Z","dependencies_parsed_at":"2022-07-21T13:02:17.859Z","dependency_job_id":null,"html_url":"https://github.com/jarvist/polaron-lambda","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/jarvist/polaron-lambda","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jarvist%2Fpolaron-lambda","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jarvist%2Fpolaron-lambda/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jarvist%2Fpolaron-lambda/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jarvist%2Fpolaron-lambda/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jarvist","download_url":"https://codeload.github.com/jarvist/polaron-lambda/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jarvist%2Fpolaron-lambda/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270625154,"owners_count":24618332,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-15T02:00:12.559Z","response_time":110,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["checkpoint","density-functional-theory","gaussian","lambda"],"created_at":"2025-04-14T10:44:46.271Z","updated_at":"2025-10-25T23:39:16.831Z","avatar_url":"https://github.com/jarvist.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"Scripts to generate the 4-Gaussian jobs from an input molecule to calculate the\n'inner sphere' reorganisation energy.\n\nThis follows the roughly nomenclature and working of JKP's thesis.\n'we follow the method of Sakanou' - JKP Thesis 2.2 Reorganisation Energy\n\nThis is useful as an input into the Marcus equation for electron / hole\ntransport in organic semiconducting materials.\n\nThese calculations are pretty trivial and can be created by hand, but I wrote\nthese scripts to allow the automatic calculation of many lambdas of different fullerenes / oligomers (in\nparticular, when seeing whether you could vary lambda by chemical design to\ninduce better charge transport).\n\nThe scripts are very hairy.\n\n# Using these Scripts\n\n* Start with either Gaussian Checkpoints (.chk) or Log Files (.log) of the structures you want to calculate the inner-sphere reorganisation of.\n\n* Run ./polaron_reorg_optimisation_jobs_from_chk.sh or ./polaron_reorg_optimisation_jobs_from_log.sh\n\n````\n    \u003els\n    mylovelymolecule.chk \n    \u003e./polaron_reorg_optimisation_jobs_from_chk.sh *.chk\n    \u003els\n    mylovelymolecule.chk mylovelymolecule_ion_opt.chk mylovelymolecule_ion_opt.com mylovelymolecule_neutral_opt.chk mylovelymolecule_neutral_opt.com \n````\n --\u003e generates two geometry opt jobs (neutral + charged)\n\n* Run these jobs, retaining the checkpoints.\n\n* 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)\n````\n    \u003e./polaron_reorg_energy_jobs_from_geom_chks.sh *_opt.chk\n````\n --\u003e generates 4 energy jobs \"*_ion_E.chk\" / \"_neutral_E.chk\"\n\n* Run these *_E.com jobs...\n\n* Have a tasty look at the reorganisation energies with the handy ./calc_reorg_energy.sh script\n````\n    \u003e./calc_reorg_energy.sh C60_b3lypopt [here's one I made earlier...]\n    C60_b3lypopt\n    N_ion:  -2286.24731990 N_neu:  -2286.17409196 I_ion:  -2286.24982989 I_neu:  -2286.17154854\n    Neutral transition (I_new-N_neu) in eV: .06920900162\n    Ion transition (N_ion - I_ion) in eV: .06829933789\n    .13750833951\n````\n--\u003e C60 has an inner sphere reorganisation energy of 138 meV at b3lyp/6-31g*.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjarvist%2Fpolaron-lambda","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjarvist%2Fpolaron-lambda","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjarvist%2Fpolaron-lambda/lists"}