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

./configure (see --help for available options)
cd build
make install

2b. Compile as a python module

cd python
python setup.py install --user

2c. Obtain from PyPi repository

pip install symgroupy --user

Usage

./symgroupy input.zdat

for further information check the manual at:
https://symgroup.readthedocs.io

Python API

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)