def check_opts_set(file_pattern,
folder='',
server=None,
username=None,
passwrd=None):
analysis = pg.Analysis(folderpath=folder,
server=server,
username=username,
passwrd=passwrd)
files = analysis.folder.list_files(file_pattern)
if not files:
return None
for file_name in files:
analysis.add_run({'File': file_name},
opt_fname=file_name,
add_if_error=True)
analysis.add_basic_properties(['optimised'])
analysis.add_basic_properties(['opt_error'])
analysis.add_mol_property('E(au)', 'get_optimisation_E', units='hartree')
analysis.add_mol_property('allE',
'get_optimisation_E',
units='hartree',
final=False)
df = analysis.get_table(row_index='File')
df['Steps'] = df.allE.map(lambda x: x.shape[0])
df['Ediff'] = df.allE.map(lambda x: x[-1] - x[-2]
if x.shape[0] > 1 else np.nan)
return df.drop('allE', 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 test_add_runs_with_errors(self, add_if_error, count):
analysis = pg.Analysis(folder_obj=self.folder)
errors = analysis.add_runs(
headers=['Cation', 'Anion', 'Initial'],
values=[['emim'], ['cl'], ['B', 'Error']],
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',
add_if_error=add_if_error)
that.assert_equals(analysis.count_runs(), count)
def test_add_mol_property(self, name, prop, *args, **kwargs):
analysis = pg.Analysis(folder_obj=self.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]
})
analysis.add_mol_property(name, prop, *args, **kwargs)
def test_add_runs(self):
analysis = pg.Analysis(folder_obj=self.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]
})
that.assert_equals(analysis.count_runs(), 3)
def test_add_run_fails(self):
analysis = pg.Analysis(folder_obj=self.folder)
errors = analysis.add_run(
identifiers={'Test': 'test'},
init_fname='none.com',
opt_fname='*emim-cl_B_6-311+g-d-p-_gd3bj_opt*unfrz.log',
freq_fname='*emim-cl_B_6-311+g-d-p-_gd3bj_freq*.log',
nbo_fname='*emim-cl_B_6-311+g-d-p-_gd3bj_pop-nbo-full-*.log',
alignto=[3, 2, 1],
atom_groups={
'emim': list(range(20)),
'cl': [20]
})
that.assert_equals(len(errors), 1)
that.assert_equals(analysis.count_runs(), 0)
def check_freqs_set(file_pattern,
folder='',
server=None,
username=None,
passwrd=None):
analysis = pg.Analysis(folderpath=folder,
server=server,
username=username,
passwrd=passwrd)
files = analysis.folder.list_files(file_pattern)
if not files:
return None
for file_name in files:
analysis.add_run({'File': file_name},
freq_fname=file_name,
add_if_error=True)
analysis.add_basic_properties(['conformer'])
df = analysis.get_table(row_index='File')
return df
def test_tbl_images(self, mtype):
analysis = pg.Analysis(folder_obj=self.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_images(
mtype=mtype,
max_cols=2,
info_columns=['Cation', 'Anion', 'Initial'],
rotations=[[0, 0, 90]])
def test_initialises(self):
pg.Analysis(folder_obj=self.folder)