https://github.com/jamesetsmith/ppix_final

NEVPT2 Calculations on Protoporphyrin IX
https://github.com/jamesetsmith/ppix_final

chemistry pyscf

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NEVPT2 Calculations on Protoporphyrin IX

• Host: GitHub
• URL: https://github.com/jamesetsmith/ppix_final
• Owner: jamesETsmith
• Created: 2020-05-29T17:24:11.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2021-02-10T17:24:53.000Z (almost 4 years ago)
• Last Synced: 2024-10-31T18:12:11.837Z (3 months ago)
• Topics: chemistry, pyscf
• Language: Python
• Homepage:
• Size: 110 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
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# Calculations for Protoporphyrin IX (PPIX) 

This repository contains the input files to reproduce the NEVPT2 calculations from the following paper:

> 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)__.

If this work helped you in your research please cite us using one of the following:

```

@Article{D0CP03614E,

author ="Zagorec-Marks, Wyatt and Smith, James E. T. and Foreman, Madison M. and Sharma, Sandeep and Weber, J. Mathias",

title  ="Intrinsic electronic spectra of cryogenically prepared protoporphyrin IX ions in vacuo – deprotonation-induced Stark shifts",

journal  ="Phys. Chem. Chem. Phys.",

year  ="2020",

volume  ="22",

issue  ="36",

pages  ="20295-20302",

publisher  ="The Royal Society of Chemistry",

doi  ="10.1039/D0CP03614E",

url  ="http://dx.doi.org/10.1039/D0CP03614E",

}

```

## Software Details

- [PySCF](https://github.com/pyscf/pyscf) v1.7.2

  - git commit: [7ba318ff7cae650b255d5c5b90ed550521d324f0](https://github.com/pyscf/pyscf/commit/7ba318ff7cae650b255d5c5b90ed550521d324f0)

## Reproducing the NEVPT2 Results

A 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).

To 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:

```bash

sh run_all.sh

```

Each directory contains one of these helper scripts to make workflow easy to reproduce. Below is an snippet showing the workflow in detail:

```bash

# Run RKS Calculation

python dft.py

# Run SA-MCSCF Calculation

python sa_mcscf.py > _logs/_sa_mcscf.out

# Run PT2 Calculations on all Excited States

python pt2.py 0 > _logs/_pt2_0.out

python pt2.py 1 > _logs/_pt2_1.out

python pt2.py 2 > _logs/_pt2_2.out

```