def setUp(self):
self.mol1 = pg.Molecule(folder_obj=pg.get_test_folder(),
opt_fname='CJS1_emim-cl_F_6-311+g-d-p-_gd3bj_opt-modredundant_unfrz.log',
atom_groups={'emim':range(1,20), 'cl':[20]},
alignto=[3,2,1])
self.mol2 = pg.Molecule(folder_obj=pg.get_test_folder(),
opt_fname='CJS1_emim-cl_F_6-311+g-d-p-_gd3bj_opt-modredundant_unfrz.log',
atom_groups={'emim':range(1,20), 'cl':[20]},
alignto=[3,2,1])
def test_tbl_graphs(self, gtype, share_plot, **kwargs):
analysis = pg.Analysis(folder_obj=pg.get_test_folder())
analysis.add_runs(
headers=['Cation', 'Anion', 'Initial'],
values=[['emim'], ['cl'], ['B', 'F', 'FE']],
init_pattern='*{0}-{1}_{2}_init.com',
opt_pattern='*{0}-{1}_{2}_6-311+g-d-p-_gd3bj_opt*unfrz.log',
freq_pattern='*{0}-{1}_{2}_6-311+g-d-p-_gd3bj_freq*.log',
nbo_pattern='*{0}-{1}_{2}_6-311+g-d-p-_gd3bj_pop-nbo-full-*.log',
alignto=[3, 2, 1],
atom_groups={
'emim': list(range(20)),
'cl': [20]
})
fig, caption = analysis.plot_mol_graphs(
gtype=gtype,
share_plot=share_plot,
info_columns=['Cation', 'Anion', 'Initial'],
max_cols=2,
info_incl_id=True,
tick_rotation=45,
**kwargs)
that.assert_equal(type(caption), str)
def setUp(self):
self.mol = pg.Molecule(
folder_obj=pg.get_test_folder(),
init_fname='CJS1_emim-cl_B_init.com',
opt_fname=
'CJS1_emim-cl_B_6-311+g-d-p-_gd3bj_opt-modredundant_unfrz.log',
nbo_fname=
'CJS1_emim-cl_B_6-311+g-d-p-_gd3bj_pop-nbo-full-_unfrz.log')
def test_plot_pes(self, img_pos):
mol2 = pg.molecule.Molecule(folder_obj=pg.get_test_folder(),
alignto=[3, 2, 1],
pes_fname=[
'CJS_emim_6311_plus_d3_scan.log',
'CJS_emim_6311_plus_d3_scan_bck.log'
])
ax = mol2.plot_pes_scans([1, 4, 9, 10],
rotation=[0, 0, 90],
img_pos=img_pos,
zoom=0.5)
# -*- coding: utf-8 -*-
"""
Created on Fri May 01 04:11:16 2015
@author: chris
"""
import pygauss as pg
folder = pg.get_test_folder()
analysis = pg.analysis.Analysis(folder)
analysis.add_run({'Cation': 'emim'},
init_fname='CJS1_emim_-_init.com',
opt_fname='CJS1_emim_-_6-311+g-d-p-_gd3bj_opt_.log',
freq_fname='CJS1_emim_-_6-311+g-d-p-_gd3bj_freq_.log',
nbo_fname='CJS1_emim_-_6-311+g-d-p-_gd3bj_pop-nbo-full-_.log')
df, errors = analysis.add_runs(
headers=['Cation', 'Anion', 'Initial'],
values=[['emim'], ['cl'], ['B', 'BE', 'BM', 'F', 'FE', 'FM', 'T']],
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')
print 'Read Errors:', errors
analysis.add_basic_properties()
analysis.add_mol_property('Energy (au)', 'get_optimisation_E', units='hartree')
analysis.add_mol_property('Cation chain, $\\psi$', 'calc_dihedral_angle',
def setUp(self):
self.mol = pg.Molecule(
folder_obj=pg.get_test_folder(),
opt_fname=
'CJS1_emim-cl_B_6-311+g-d-p-_gd3bj_opt-modredundant_unfrz.log')
def setUp(self):
self.mol = pg.Molecule(folder_obj=pg.get_test_folder(),
nbo_fname='test_3h2o_pop.log')
def setUp(self):
self.folder = pg.get_test_folder()
def setUp(self):
self.mol = pg.Molecule(
folder_obj=pg.get_test_folder(),
freq_fname='CJS1_emim-cl_B_6-311+g-d-p-_gd3bj_freq_unfrz.log')