def extract(filenames, equilibrium_length=None):
frequencies = []
intensities = []
geometry_params = dict()
geometry_params['geometry'] = []
geometry_params['l1'] = []
geometry_params['l2'] = []
geometry_params['l12'] = []
geometry_params['theta'] = []
if equilibrium_length:
geometry_params['l1_diff'] = []
geometry_params['l2_diff'] = []
geometry_params['l12_diff'] = []
geometry_params['o12_diff'] = []
for filename in filenames:
try:
job = ccopen(filename)
data = job.parse()
vibfreqs = data.vibfreqs
vibirs = data.vibirs
geometry = data.atomcoords[0]
assert len(vibfreqs) == len(vibirs) >= 3
frequencies.append(vibfreqs)
intensities.append(vibirs)
C, O1, O2 = 0, 1, 2
d_C_O1 = distance(geometry[C], geometry[O1])
d_C_O2 = distance(geometry[C], geometry[O2])
d_O1_O2 = distance(geometry[O1], geometry[O2])
bond_sum = d_C_O1 + d_C_O2
# bond_difference = abs(d_C_O1 - d_C_O2)
angle = bond_angle(geometry[O1], geometry[C], geometry[O2])
theta = 180.0 - angle
l1 = d_C_O1
l2 = d_C_O2
o12 = d_O1_O2
l12 = bond_sum
# dl = bond_difference
if equilibrium_length:
l1_diff = l1 - equilibrium_length
l2_diff = l2 - equilibrium_length
o12_diff = o12 - (2 * equilibrium_length)
l12_diff = l12 - (2 * equilibrium_length)
geometry_params['l1_diff'].append(l1_diff)
geometry_params['l2_diff'].append(l2_diff)
geometry_params['l12_diff'].append(l12_diff)
geometry_params['o12_diff'].append(o12_diff)
geometry_params['geometry'].append(geometry)
geometry_params['l1'].append(l1)
geometry_params['l2'].append(l2)
geometry_params['l12'].append(l12)
geometry_params['theta'].append(theta)
except:
pass
frequencies = make_numpy_array_from_ragged_list(frequencies)
intensities = make_numpy_array_from_ragged_list(intensities)
for k in geometry_params:
geometry_params[k] = np.array(geometry_params[k])
print("frequencies.shape:", frequencies.shape)
print("intensities.shape:", intensities.shape)
print("geometry_params['geometry'].shape:", geometry_params['geometry'].shape)
return frequencies, intensities, geometry_params
assert len(vibfreqs) == len(vibirs) == 3
frequencies.append(vibfreqs)
intensities.append(vibirs)
geometries.append(geometry)
C, O1, O2 = 0, 1, 2
d_C_O1 = distance(geometry[C], geometry[O1])
d_C_O2 = distance(geometry[C], geometry[O2])
d_O1_O2 = distance(geometry[O1], geometry[O2])
bond_sum = d_C_O1 + d_C_O2
bond_difference = abs(d_C_O1 - d_C_O2)
angle = bond_angle(geometry[O1], geometry[C], geometry[O2])
theta = 180.0 - angle
l1 = d_C_O1
l2 = d_C_O2
o12 = d_O1_O2
l12 = bond_sum
dl = bond_difference
geometry_params['l1'].append(l1)
geometry_params['l2'].append(l2)
geometry_params['l12'].append(l12)
import matplotlib as mpl
mpl.use("Agg")
import matplotlib.pyplot as plt
