dist = ed_cube.field.distance_transform(isoval)
exclusion_dist = 0
rand_skim = 1
axes_limits = [[0, 4]]
charge_types = {'aim': '.sumviz',
# 'aim': 'ACF.dat',
'mulliken': '.log',
'chelpg': '_chelpg.log',
'mk': '_mk.log',
'nbo': '_nbo.log',
}
# Use the same color span in all plots (true ESP doesn't depend on charges so
# common to all charge_types and can be outside of loop):
_dist, esp_values = filter_by_dist(exclusion_dist, dist, esp_cube.field)
color_span = [np.nanmin(esp_values), np.nanmax(esp_values)]
# A symmetric span can also be used:
# color_limit = max(abs(np.nanmin(esp_values)), abs(np.nanmax(esp_values)))
# color_span = [-color_limit, color_limit]
# Note that the y-axis is not set for different charge_types! If this is
# desired behaviour, it could be set in a similar manner here.
for charge_type in charge_types.keys():
charge_dir = output_path + charge_type
# raises OSError if directory exists
os.mkdir(charge_dir)
if charge_types[charge_type][0] in ['.', '_']:
filename = path + molecule_name + charge_types[charge_type]
else:
exclusion_dist = 0
rand_skim = 1
axes_limits = [[0, 4]]
charge_types = {
'aim': '.sumviz',
# 'aim': 'ACF.dat',
'mulliken': '.log',
'chelpg': '_chelpg.log',
'mk': '_mk.log',
'nbo': '_nbo.log',
}
# Use the same color span in all plots (true ESP doesn't depend on charges so
# common to all charge_types and can be outside of loop):
_dist, esp_values = filter_by_dist(exclusion_dist, dist, esp_cube.field)
color_span = [np.nanmin(esp_values), np.nanmax(esp_values)]
# A symmetric span can also be used:
# color_limit = max(abs(np.nanmin(esp_values)), abs(np.nanmax(esp_values)))
# color_span = [-color_limit, color_limit]
# Note that the y-axis is not set for different charge_types! If this is
# desired behaviour, it could be set in a similar manner here.
for charge_type in charge_types.keys():
charge_dir = output_path + charge_type
# raises OSError if directory exists
os.mkdir(charge_dir)
if charge_types[charge_type][0] in ['.', '_']:
filename = path + molecule_name + charge_types[charge_type]
else:
charges = [atom.charges['nbo_equiv'] for atom in pickled_mol]
_update_molecule_with_charges(molecule, charges, 'nbo_equiv')
all_charges = [
'chelpg_equiv', 'mk_equiv', 'nbo_equiv', 'compr_chelpg', 'compr_mk'
]
for charge_type in all_charges:
print('\n', charge_type.upper())
for atom in molecule:
atom.print_with_charge(charge_type)
sys.stdout.flush()
rep = calc_grid_field(molecule, esp_cube.field.grid, 'rep_esp',
[charge_type])[0]
# Change details of calculating difference here (absolute, relative)
diff = difference(esp_cube.field, rep)
# Write cube
diff.write_cube(output_path + charge_type + '_diff.cub', molecule,
charge_type)
# and with elements within the ED isosurface excluded
diff_filtered = copy.deepcopy(diff)
diff_filtered.check_nans = False
_dist, diff_filtered.values = filter_by_dist(exclusion_dist, dist, diff)
diff_filtered.write_cube(
output_path + charge_type + '_diff_filtered-iso_' + str(isoval) +
'.cub', molecule, charge_type)
ed_cube, isoval, excl_dist = args.exclude
ed_cube = Cube(ed_cube)
isoval = float(isoval)
excl_dist = float(excl_dist)
elif filetype == '.esp':
esp_file1 = resp_helpers.G09_esp(args.field1)
esp_file2 = resp_helpers.G09_esp(args.field2)
# TODO: Molecules not cross-checked. They should be because .esp files in
# Antechamber format produced by repESP will have no identitity info. This
# is fine for now for the difference (actual - reproduced), because actual
# will be Gaussian .esp but not the other way round.
molecule = esp_file1.molecule
field1 = esp_file1.field
field2 = esp_file2.field
diff = difference(field1, field2, relative=args.relative,
absolute=args.absolute)
if filetype == '.cub':
if args.exclude:
diff.check_nans = False
dist = ed_cube.field.distance_transform(isoval)
assign_val = 0 if args.exclusion_as_zero else None
_dist, diff.values = filter_by_dist(excl_dist, dist, diff,
assign_val=assign_val)
diff.write_cube(args.output + '.cub', molecule)
elif filetype == '.esp':
diff.write_to_file(args.output + '.esp', molecule)
