https://github.com/abelcarreras/symgroup

Continuous symmetry measures of molecular structures
https://github.com/abelcarreras/symgroup

chemistry csm molecule symmetry

Last synced: 11 days ago
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Continuous symmetry measures of molecular structures

• Host: GitHub
• URL: https://github.com/abelcarreras/symgroup
• Owner: abelcarreras
• License: mit
• Created: 2018-09-20T22:44:37.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2023-10-03T07:49:23.000Z (about 1 year ago)
• Last Synced: 2024-04-27T03:42:56.598Z (6 months ago)
• Topics: chemistry, csm, molecule, symmetry
• Language: Fortran
• Homepage: https://symgroup.readthedocs.io
• Size: 149 KB
• Stars: 7
• Watchers: 4
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: readme.md
  • License: LICENSE

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README

        
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SymGroup

=========

Software to calculate continuous symmetry measures of 

molecular structures

Installation instructions

---------------------------------------------------------

1. Requirements

  - Lapack & Blas libraries

  - Fortran77 compiler

  - cmake 2.6

  - (optional) MKL

2a. Install as standalone binary

   ```shell

   ./configure (see --help for available options)

   cd build

   make install

   ```

2b. Compile as a python module

   ```shell

   cd python

   python setup.py install --user

   ```

2c. Obtain from PyPi repository

```shell

pip install symgroupy --user

```

Usage

-----

```shell

./symgroupy input.zdat

```

for further information check the manual at:  

https://symgroup.readthedocs.io

Python API

----------

```python

from symgroupy import Symgroupy

fen4 = Symgroupy(coordinates=[[15.5182, -1.68040, 22.81703],

                              [6.78978, -3.22298, 23.08474],

                              [6.27712, -0.12712, 21.76775],

                              [4.24692, -3.22298, 22.54931],

                              [4.75958, -0.12712, 23.86630]],

                 group='c3',

                 multi=8,

                 labels=['Fe', 'N', 'N', 'N', 'N'],

                 central_atom=1)

print('CSM: {}'.format(fen4.csm))

print('Optimum axis: {}'.format(fen4.optimum_axis))

print('Optimum permutation: {}'.format(fen4.optimum_permutation))

print('Nearest structure')

print(fen4.nearest_structure)

print('Reference axis')

print(fen4.reference_axis)

print('multi CSM')

print(fen4.csm_multi)

print('multi axis')

print(fen4.axis_multi)

```

Authors

--------------------------------------------------------

This software has been developed by David Casanova


Python module by Abel Carreras

The theoretical background implemented in this software is described in:


Pinsky M, Dryzun C, Casanova D, Alemany P, Avnir D, J Comput Chem. 29:2712-21 (2008)


Pinsky M, Casanova D, Alemany P, Alvarez S, Avnir D, Dryzun C, Kizner Z, Sterkin A.  J Comput Chem. 29:190-7 (2008)