{"id":18091323,"url":"https://github.com/jamesetsmith/ppix_final","last_synced_at":"2025-06-11T07:32:53.847Z","repository":{"id":104005884,"uuid":"267915727","full_name":"jamesETsmith/ppix_final","owner":"jamesETsmith","description":"NEVPT2 Calculations on Protoporphyrin IX","archived":false,"fork":false,"pushed_at":"2021-02-10T17:24:53.000Z","size":113,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-06T02:43:00.273Z","etag":null,"topics":["chemistry","pyscf"],"latest_commit_sha":null,"homepage":"","language":"Python","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/jamesETsmith.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-05-29T17:24:11.000Z","updated_at":"2022-04-15T16:00:31.000Z","dependencies_parsed_at":null,"dependency_job_id":"bd99275b-c3ba-4621-9c99-80b92c527765","html_url":"https://github.com/jamesETsmith/ppix_final","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jamesETsmith%2Fppix_final","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jamesETsmith%2Fppix_final/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jamesETsmith%2Fppix_final/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jamesETsmith%2Fppix_final/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jamesETsmith","download_url":"https://codeload.github.com/jamesETsmith/ppix_final/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jamesETsmith%2Fppix_final/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":259222036,"owners_count":22824003,"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","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":["chemistry","pyscf"],"created_at":"2024-10-31T18:11:22.859Z","updated_at":"2025-06-11T07:32:53.802Z","avatar_url":"https://github.com/jamesETsmith.png","language":"Python","readme":"![](media/toc_figure.png)\n\n# Calculations for Protoporphyrin IX (PPIX) \n\nThis repository contains the input files to reproduce the NEVPT2 calculations from the following paper:\n\n\u003e Wyatt Zagorec-Marks, James E. T. Smith, Madison M. Foreman, Sandeep Sharma, J. Mathias Weber. ___Intrinsic Electronic Spectra of Cryogenically Prepared Protoporphyrin IX Ions in Vacuo – Deprotonation-Induced Stark Shifts___. __(Submitted)__.\n\nIf this work helped you in your research please cite us using one of the following:\n\n```\n@Article{D0CP03614E,\nauthor =\"Zagorec-Marks, Wyatt and Smith, James E. T. and Foreman, Madison M. and Sharma, Sandeep and Weber, J. Mathias\",\ntitle  =\"Intrinsic electronic spectra of cryogenically prepared protoporphyrin IX ions in vacuo – deprotonation-induced Stark shifts\",\njournal  =\"Phys. Chem. Chem. Phys.\",\nyear  =\"2020\",\nvolume  =\"22\",\nissue  =\"36\",\npages  =\"20295-20302\",\npublisher  =\"The Royal Society of Chemistry\",\ndoi  =\"10.1039/D0CP03614E\",\nurl  =\"http://dx.doi.org/10.1039/D0CP03614E\",\n}\n```\n\n## Software Details\n- [PySCF](https://github.com/pyscf/pyscf) v1.7.2\n  - git commit: [7ba318ff7cae650b255d5c5b90ed550521d324f0](https://github.com/pyscf/pyscf/commit/7ba318ff7cae650b255d5c5b90ed550521d324f0)\n\u003c!-- - [ORCA](https://orcaforum.kofo.mpg.de/app.php/portal) v 4.0.1.2 --\u003e\n\n\n## Reproducing the NEVPT2 Results\n\nA summary of our results in presented in [`./analysis/NEVPT2_summart.txt`](analysis/NEVPT2_summary.txt) along with a condensed version in `csv` format in [`./analysis/sa-3-mcscf_nevpt2.csv`](analysis/sa-3-mcscf_nevpt2.csv).\n\nTo reproduce our NEVPT2 results for a particular species, navigate to that directory, ensure your Python environment is properly set up for PySCF, then execute the following:\n\n```bash\nsh run_all.sh\n```\n\nEach directory contains one of these helper scripts to make workflow easy to reproduce. Below is an snippet showing the workflow in detail:\n\n```bash\n# Run RKS Calculation\npython dft.py\n\n# Run SA-MCSCF Calculation\npython sa_mcscf.py \u003e _logs/_sa_mcscf.out\n\n# Run PT2 Calculations on all Excited States\npython pt2.py 0 \u003e _logs/_pt2_0.out\npython pt2.py 1 \u003e _logs/_pt2_1.out\npython pt2.py 2 \u003e _logs/_pt2_2.out\n```\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjamesetsmith%2Fppix_final","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjamesetsmith%2Fppix_final","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjamesetsmith%2Fppix_final/lists"}