Software to calculate continuous symmetry measures of molecular structures
- 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 install2b. Compile as a python module
cd python
python setup.py install --user2c. Obtain from PyPi repository
pip install symgroupy --user./symgroupy input.zdatfor further information check the manual at:
https://symgroup.readthedocs.io
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)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)
