posym 0.2.0

posym module

PoSym

A simple point symmetry analysis tool written in python.
This tool is mainly designed for theoretical chemistry but can be used in general for other objects by defining subclasses of the SymmetryBase class. At this point SymmetryModes and SymmetryFunction subclasses are defined for the analysis of vibrational normal modes and molecular orbitals respectively.

Features

• Use as simple calculator for irreducible representations supporting direct sum and product
• Handles pseudosymmetry
• Determine point symmetry from normal modes
• Determine point symmetry functions defined in gaussian basis
• Compatibility with PyQchem (http://www.github.com/abelcarreras/pyqchem)

Requisites

• numpy
• scipy
• pandas
• yaml

Use as a simple symmetry calculation

posym allows to create symmetry python objects that can be operated using usual operators

from posym 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('e*e + a1:', e * (e + a1))

Determine the symmetry of normal modes

Symmetry objects can be obtained from normal modes

from posym 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)

Define basis set functions in gaussian basis

define basis function as linear combination of gaussian that act as normal python functions

from posym.basis import PrimitiveGaussian, BasisFunction

# Oxigen atom
sa = PrimitiveGaussian(alpha=130.70932)
sb = PrimitiveGaussian(alpha=23.808861)
sc = PrimitiveGaussian(alpha=6.4436083)
s_O = BasisFunction([sa, sb, sc],
                    [0.154328969, 0.535328136, 0.444634536],
                    center=[0.0000000000, 0.000000000, -0.0808819]) # Bohr

sa = PrimitiveGaussian(alpha=5.03315132)
sb = PrimitiveGaussian(alpha=1.1695961)
sc = PrimitiveGaussian(alpha=0.3803890)
s2_O = BasisFunction([sa, sb, sc],
                     [-0.099967228, 0.399512825, 0.700115461],
                     center=[0.0000000000, 0.000000000, -0.0808819])

pxa = PrimitiveGaussian(alpha=5.0331513, l=[1, 0, 0])
pxb = PrimitiveGaussian(alpha=1.1695961, l=[1, 0, 0])
pxc = PrimitiveGaussian(alpha=0.3803890, l=[1, 0, 0])

pya = PrimitiveGaussian(alpha=5.0331513, l=[0, 1, 0])
pyb = PrimitiveGaussian(alpha=1.1695961, l=[0, 1, 0])
pyc = PrimitiveGaussian(alpha=0.3803890, l=[0, 1, 0])

pza = PrimitiveGaussian(alpha=5.0331513, l=[0, 0, 1])
pzb = PrimitiveGaussian(alpha=1.1695961, l=[0, 0, 1])
pzc = PrimitiveGaussian(alpha=0.3803890, l=[0, 0, 1])

px_O = BasisFunction([pxa, pxb, pxc],
                     [0.155916268, 0.6076837186, 0.3919573931],
                     center=[0.0000000000, 0.000000000, -0.0808819])
py_O = BasisFunction([pya, pyb, pyc],
                     [0.155916268, 0.6076837186, 0.3919573931],
                     center=[0.0000000000, 0.000000000, -0.0808819])
pz_O = BasisFunction([pza, pzb, pzc],
                     [0.155916268, 0.6076837186, 0.3919573931],
                     center=[0.0000000000, 0.000000000, -0.0808819])

# Hydrogen atoms
sa = PrimitiveGaussian(alpha=3.42525091)
sb = PrimitiveGaussian(alpha=0.62391373)
sc = PrimitiveGaussian(alpha=0.1688554)
s_H = BasisFunction([sa, sb, sc],
                    [0.154328971, 0.535328142, 0.444634542],
                    center=[-1.43262, 0.000000000, -1.28237])

s2_H = BasisFunction([sa, sb, sc],
                     [0.154328971, 0.535328142, 0.444634542],
                     center=[1.43262, 0.000000000, -1.28237])

basis_set = [s_O, s2_O, px_O, py_O, pz_O, s_H, s2_H]

# Operate with basis functions in analytic form

px_O2 = px_O * px_O
print('integral from -inf to inf:', px_O2.integrate)

# plot functions
from matplotlib import pyplot as plt
import numpy as np

xrange = np.linspace(-5, 5, 100)
plt.plot(xrange, [s_O(x, 0, 0) for x in xrange] , label='s_O')
plt.plot(xrange, [px_O(x, 0, 0) for x in xrange] , label='px_O')
plt.legend()

Create molecular orbitals from basis set

Define molecular orbitals straightforwardly from molecular orbitals coefficients using usual operators

# Orbital 1
o1 = s_O * 0.994216442 + s2_O * 0.025846814 + px_O * 0.0 + py_O * 0.0 + pz_O * -0.004164076 + s_H * -0.005583712 + s2_H * -0.005583712

# Orbital 2
o2 = s_O * 0.23376666 + s2_O * -0.844456594 + px_O * 0.0 + py_O * 0.0 + pz_O * 0.122829781 + s_H * -0.155593214 + s2_H * -0.155593214

# Orbital 3
o3 = s_O * 0.0 + s2_O * 0.0 + px_O * 0.612692349 + py_O * 0.0 + pz_O * 0.0 + s_H * -0.44922168 + s2_H * 0.449221684

# Orbital 4
o4 = s_O * -0.104033343 + s2_O * 0.538153649 + px_O * 0.0 + py_O * 0.0 + pz_O * 0.755880259 + s_H * -0.295107107 + s2_H * -0.2951071074

# Orbital 5
o5 = s_O * 0.0 + s2_O * 0.0 + px_O * 0.0 + py_O * -1.0 + pz_O * 0.0 + s_H * 0.0 + s2_H * 0.0

# Orbital 6
o6 = s_O * -0.125818566 + s2_O * 0.820120983 + px_O * 0.0 + py_O * 0.0 + pz_O * -0.763538862 + s_H * -0.769155124 + s2_H * -0.769155124


# Check orthogonality
print('<o1|o1>: ', (o1*o1).integrate)
print('<o2|o2>: ', (o2*o2).integrate)
print('<o1|o2>: ', (o1*o2).integrate)

Analyze symmetry of molecular orbitals

Get symmetry objects from PrimitiveGaussian/BasisFunction type objects

from posym import SymmetryFunction

sym_o1 = SymmetryFunction('c2v', o1)
sym_o2 = SymmetryFunction('c2v', o2)
sym_o3 = SymmetryFunction('c2v', o3)
sym_o4 = SymmetryFunction('c2v', o4)
sym_o5 = SymmetryFunction('c2v', o5)
sym_o6 = SymmetryFunction('c2v', o6)

print('Symmetry O1: ', sym_o1)
print('Symmetry O2: ', sym_o2)
print('Symmetry O3: ', sym_o3)
print('Symmetry O4: ', sym_o4)
print('Symmetry O5: ', sym_o5)
print('Symmetry O6: ', sym_o6)

# Operate molecular orbitals symmetries to get the symmetry of wave functions

# restricted close shell
sym_wf_gs = sym_o1*sym_o1 * sym_o2*sym_o2 * sym_o3*sym_o3 * sym_o4*sym_o4 * sym_o5*sym_o5
print('Symmetry WF (ground state): ', sym_wf_gs)

# restricted open shell
sym_wf_excited_1 = sym_o1*sym_o1 * sym_o2*sym_o2 * sym_o3*sym_o3 * sym_o4*sym_o4 * sym_o5*sym_o6
print('Symmetry WF (excited state 1): ', sym_wf_excited_1)

# restricted close shell
sym_wf_excited_2 = sym_o1*sym_o1 * sym_o2*sym_o2 * sym_o3*sym_o3 * sym_o4*sym_o4 * sym_o6*sym_o6
print('Symmetry WF (excited state 2): ', sym_wf_excited_2)

Combine with PyQchem to create useful automations

from pyqchem import get_output_from_qchem, QchemInput, Structure
from pyqchem.parsers.basic import basic_parser_qchem
from posym import SymmetryFunction
# convenient functions to connect pyqchem - posym
from posym.tools import get_basis_set, build_orbital 

# define molecules
butadiene_cis = Structure(coordinates=[[ -1.07076839,   -2.13175980,    0.03234382],
                                       [ -0.53741536,   -3.05918866,    0.04995793],
                                       [ -2.14073783,   -2.12969357,    0.04016267],
                                       [ -0.39112115,   -0.95974916,    0.00012984],
                                       [  0.67884827,   -0.96181542,   -0.00769025],
                                       [ -1.15875076,    0.37505495,   -0.02522296],
                                       [ -0.62213437,    1.30041753,   -0.05065831],
                                       [ -2.51391203,    0.37767199,   -0.01531698],
                                       [ -3.04726506,    1.30510083,   -0.03293196],
                                       [ -3.05052841,   -0.54769055,    0.01011971]],
                          symbols=['C', 'H', 'H', 'C', 'H', 'C', 'H', 'C', 'H', 'H'])


# create qchem input
qc_input = QchemInput(butadiene_cis,
                      jobtype='sp',
                      exchange='hf',
                      basis='sto-3g',
                      )

# calculate and parse qchem output
data_cis, ee_cis = get_output_from_qchem(qc_input,
                                         read_fchk=True,
                                         processors=4,
                                         parser=basic_parser_qchem)

# extract required information from Q-Chem calculation
coordinates = ee_cis['structure'].get_coordinates()
mo_coefficients = ee_cis['coefficients']
basis = ee_cis['basis']

# print results
print('Molecular orbitals (alpha) symmetry')
basis_set = get_basis_set(coordinates, basis)
for i, orbital_coeff in enumerate(mo_coefficients['alpha']):
    orbital = build_orbital(basis_set, orbital_coeff)
    sym_orbital = SymmetryFunction('c2v', orbital)
    print('Symmetry O{}: '.format(i+1), sym_orbital)
    

Try an interactive example in Google Colab

Contact info

Abel Carreras
[e-mail]

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