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PYthon GAUSSian DFT output analysis

Project description

A layer on top of cclib (v1.3), chemlab (v0.4) and pandas (v0.15.2) for analysis of gaussian DFT output

The basic function of the API is to take in data files ouput from Gaussian for a particular system and analyse their outcome in terms of:

  • Geometry alignment and,

  • Electronic distribution

Example

import pygauss.analysis as pg
folder = pg.get_test_folder()

analysis = pg.Analysis(folder)
analysis.add_runs(headers=['Cation', 'Anion', 'Initial'],
                  values=[['emim'], ['cl'], ['B', 'F']],
    init_pattern='CJS1_{0}-{1}_{2}_init.com',
    opt_pattern='CJS1_{0}-{1}_{2}_6-311+g-d-p-_gd3bj_opt-modredundant_unfrz.log',
    freq_pattern='CJS1_{0}-{1}_{2}_6-311+g-d-p-_gd3bj_freq_unfrz.log',
    nbo_pattern='CJS1_{0}-{1}_{2}_6-311+g-d-p-_gd3bj_pop-nbo-full-_unfrz.log')
analysis
  Anion Cation Initial
0    cl   emim       B
1    cl   emim       F
analysis.add_basic_properties()
analysis.add_mol_property('Energy (au)', 'get_optimisation_E', units='hartree')
analysis
  Anion Cation Initial                  Basis  Nbasis Optimised Conformer  Energy (au)
0    cl   emim       B  6-311+G(d,p) (5D, 7F)     272      True      True     -805.105
1    cl   emim       F  6-311+G(d,p) (5D, 7F)     272      True      True     -805.118
from IPython.display import display
mols = analysis.yield_mol_images(mtype='optimised',
                    align_to=[3,2,1], axis_length=0.3,
                    rotations=[[0, 0, 90], [-90, 90, 0]])
for mol in mols: display(mol)
https://github.com/chrisjsewell/PyGauss/raw/master/readme/output_5_0.png

https://github.com/chrisjsewell/PyGauss/raw/master/readme/output_5_1.png
mols = analysis.yield_mol_images(mtype='nbo',
                    align_to=[3,2,1], axis_length=0.3,
                    rotations=[[0, 0, 90], [-90, 90, 0]])
for mol in mols: display(mol)
https://github.com/chrisjsewell/PyGauss/raw/master/readme/output_6_0.png

https://github.com/chrisjsewell/PyGauss/raw/master/readme/output_6_1.png

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