PoSym Normal Modes

A point symmetry analysis tool written in python designed for theoretical chemistry. This tool makes use of continuous symmetry ideas to provide a robust implementation to compute the symmetry of different objects. This library is designed to be easily extendable to other objects by subclassing the SymmetryBase class.

Features

Use as simple calculator for irreducible representations supporting direct sum and product
Continuous symmetry measures (CSM) expressed in the basis or irreducible representation
Determine symmetry of:
- normal modes
Autogenerated high precision symmetry tables
Compatibility with PyQchem (http://www.github.com/abelcarreras/pyqchem)

Requisites

numpy
scipy
pandas

Use as a simple symmetry calculation

Posym allows to create basic continuous symmetry python objects that can be operated using direct sum (+) and direct product (*).

from posym_normal_modes import PointGroup, SymmetryBase

pg = PointGroup(group='Td')
print(pg)

a1 = SymmetryBase(group='Td', rep='A1')
a2 = SymmetryBase(group='Td', rep='A2')
e = SymmetryBase(group='Td', rep='E')
t1 = SymmetryBase(group='Td', rep='T1')

print('t1 * t1:', t1 * t1)
print('t1 * e:', t1 * e)
print('e * (e + a1):', e * (e + a1))

Determine the symmetry of normal modes

Symmetry objects can be obtained from normal modes using SymmetryModes.

from posym_normal_modes import SymmetryModes

coordinates = [[0.00000, 0.0000000, -0.0808819],
               [-1.43262, 0.0000000, -1.2823700],
               [1.43262, 0.0000000, -1.2823700]]

symbols = ['O', 'H', 'H']

normal_modes = [[[0., 0., -0.075],
                 [-0.381, -0., 0.593],
                 [0.381, -0., 0.593]],  # mode 1

                [[-0., -0., 0.044],
                 [-0.613, -0., -0.35],
                 [0.613, 0., -0.35]],  # mode 2

                [[-0.073, -0., -0.],
                 [0.583, 0., 0.397],
                 [0.583, 0., -0.397]]]  # mode 3

frequencies = [1737.01, 3988.5, 4145.43]

sym_modes_gs = SymmetryModes(group='c2v', coordinates=coordinates, modes=normal_modes, symbols=symbols)
for i in range(len(normal_modes)):
  print('Mode {:2}: {:8.3f} :'.format(i + 1, frequencies[i]), sym_modes_gs.get_state_mode(i))

print('Total symmetry: ', sym_modes_gs)

Determine the symmetry of a molecular geometry

Continuous symmetry measure (CSM) is obtained using measure method.

from posym_normal_modes import SymmetryMoleculeBase

coordinates = [[0.0000000000, 0.0000000000, 0.0000000000],
               [0.5541000000, 0.7996000000, 0.4965000000],
               [0.6833000000, -0.8134000000, -0.2536000000],
               [-0.7782000000, -0.3735000000, 0.6692000000],
               [-0.4593000000, 0.3874000000, -0.9121000000]]

symbols = ['C', 'H', 'H', 'H', 'H']

sym_geom = SymmetryMoleculeBase(group='Td', coordinates=coordinates, symbols=symbols)
print('Symmetry measure Td : ', sym_geom.measure)

sym_geom = SymmetryMoleculeBase(group='C3v', coordinates=coordinates, symbols=symbols)
print('Symmetry measure C3v : ', sym_geom.measure)

sym_geom = SymmetryMoleculeBase(group='C4v', coordinates=coordinates, symbols=symbols)
print('Symmetry measure C4v : ', sym_geom.measure)

Try an interactive example in Google Colab

Contact info

Abel Carreras
abelcarreras83@gmail.com

Donostia International Physics Center (DIPC)
Donostia-San Sebastian (Spain)