Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/tilde-lab/pycrystal
Utilities for ab initio modeling suite CRYSTAL, developed in Turin University
https://github.com/tilde-lab/pycrystal
abinitio abinitio-simulations atomistic-simulations computational-chemistry computational-materials crystal crystal-ab-initio crystal-structure crystallography emsl first-principles gaussian gaussian-lcao materials-science
Last synced: 2 months ago
JSON representation
Utilities for ab initio modeling suite CRYSTAL, developed in Turin University
- Host: GitHub
- URL: https://github.com/tilde-lab/pycrystal
- Owner: tilde-lab
- License: other
- Created: 2018-12-03T18:41:15.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2024-04-01T19:55:40.000Z (9 months ago)
- Last Synced: 2024-10-18T17:01:42.379Z (3 months ago)
- Topics: abinitio, abinitio-simulations, atomistic-simulations, computational-chemistry, computational-materials, crystal, crystal-ab-initio, crystal-structure, crystallography, emsl, first-principles, gaussian, gaussian-lcao, materials-science
- Language: Python
- Homepage:
- Size: 310 KB
- Stars: 11
- Watchers: 2
- Forks: 1
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
CRYSTAL ab initio code utilities
==========
[](https://doi.org/10.5281/zenodo.7693500)
[](https://pypi.org/project/pycrystal)
Intro
------
The [CRYSTAL](http://www.crystal.unito.it) is an _ab initio_ solid state modeling suite employing the Gaussian basis sets in the LCAO framework. The `pycrystal` Python utilities are good for:
* quick logs parsing, getting the maximum information, and presenting it in a systematic machine-readable way
* preparing and handling the Gaussian LCAO basis sets, based on the EMSL and own CRYSTAL libraries
All the popular versions of the CRYSTAL code are supported (CRYSTAL03, CRYSTAL06, CRYSTAL09, CRYSTAL14, and CRYSTAL17).
The `pycrystal` was tested on about 20k in-house simulation logs for about 700 distinct materials systems, produced with the different CRYSTAL versions. Its development was initiated in 2009 by [Maxim Losev](https://github.com/mlosev) at the quantum chemistry chair, chemistry dept. of St. Petersburg State University (Russia) under supervision of Professor Robert Evarestov.
Installation
------
`pip install pycrystal`
Usage
------
Parsing is done as follows:
```python
import os, sys
from pprint import pprint
from pycrystal import CRYSTOUT
try:
sys.argv[1] and os.path.exists(sys.argv[1])
except (IndexError, OSError):
sys.exit("USAGE: <file>")
assert CRYSTOUT.acceptable(sys.argv[1])
result = CRYSTOUT(sys.argv[1])
pprint(result.info)
```
Also, for any basis set taken from [EMSL](https://bse.pnl.gov) in Gaussian'94 format:
```python
import os, sys
from pycrystal import parse_bs
try:
sys.argv[1] and os.path.exists(sys.argv[1])
except (IndexError, OSError):
sys.exit("USAGE: <script> <file>")
content = open(sys.argv[1]).read()
for atom in parse_bs(content):
print(atom.crystal_input())
```
To deal with the CRYSTAL (University of Turin) online BS library:
```python
from pycrystal import download_basis_library
library = download_basis_library()
print(library['Bi'])
```
Related work
------
There is another Python parser [ejplugins](https://github.com/chrisjsewell/ejplugins) for CRYSTAL14 and CRYSTAL17 by [Chris Sewell](https://github.com/chrisjsewell) (Imperial College London, UK). The comparison was done using `cmp_unito_crystal_parsers.py` script on the above-mentioned 20k logs, the results are as follows:
* the final total energies and atomic structures are the same in more than 99% cases
* `pycrystal` supports slightly more CRYSTAL features than `ejplugins`
* `pycrystal` is more lightweight than `ejplugins` and has less dependencies
* performance is nearly the same