def _extract_charge_data_chargemol(self):
"""
From Chargemol output files, extract the necessary parameters for calculation of L-J.
:returns: 3 CustomNamespaces, ddec_data; dipole_moment_data; and quadrupole_moment_data
ddec_data used for calculating monopole esp and L-J values (used by both LennardJones and Charges classes)
dipole_moment_data used for calculating dipole esp
quadrupole_moment_data used for calculating quadrupole esp
"""
if self.molecule.ddec_version == 6:
net_charge_file_name = "DDEC6_even_tempered_net_atomic_charges.xyz"
elif self.molecule.ddec_version == 3:
net_charge_file_name = "DDEC3_net_atomic_charges.xyz"
else:
raise ValueError(
"Unsupported DDEC version; please use version 3 or 6.")
if not os.path.exists(net_charge_file_name):
raise FileNotFoundError(
"Cannot find the DDEC output file.\nThis could be indicative of several issues.\n"
"Please check Chargemol is installed in the correct location and that the configs"
" point to that location.")
with open(net_charge_file_name, "r+") as charge_file:
lines = charge_file.readlines()
# Find number of atoms
atom_total = int(lines[0])
# Find data markers:
ddec_start_pos, cloud_pen_pos = 0, 0
for pos, row in enumerate(lines):
if "The following XYZ" in row:
ddec_start_pos = pos + 2
# [sic]
elif "The sperically averaged" in row:
cloud_pen_pos = pos + 2
if ddec_start_pos and cloud_pen_pos:
break
else:
raise EOFError(
f"Cannot find charge or cloud penetration data in {net_charge_file_name}."
)
ddec_data = {}
dipole_moment_data = {}
quadrupole_moment_data = {}
cloud_pen_data = {}
for line in lines[ddec_start_pos:ddec_start_pos + atom_total]:
# _'s are the xyz coords, then the quadrupole moment tensor eigenvalues.
(
atom_count,
atomic_symbol,
_,
_,
_,
charge,
x_dipole,
y_dipole,
z_dipole,
_,
q_xy,
q_xz,
q_yz,
q_x2_y2,
q_3z2_r2,
*_,
) = line.split()
# File counts from 1 not 0; thereby requiring -1 to get the index.
atom_index = int(atom_count) - 1
ddec_data[atom_index] = CustomNamespace(
atomic_symbol=atomic_symbol,
charge=float(charge),
volume=None,
r_aim=None,
b_i=None,
a_i=None,
)
dipole_moment_data[atom_index] = CustomNamespace(
x_dipole=float(x_dipole),
y_dipole=float(y_dipole),
z_dipole=float(z_dipole),
)
quadrupole_moment_data[atom_index] = CustomNamespace(
q_xy=float(q_xy),
q_xz=float(q_xz),
q_yz=float(q_yz),
q_x2_y2=float(q_x2_y2),
q_3z2_r2=float(q_3z2_r2),
)
for line in lines[cloud_pen_pos:cloud_pen_pos + atom_total]:
# _'s are the xyz coords and the r_squared.
atom_count, atomic_symbol, _, _, _, a, b, _ = line.split()
atom_index = int(atom_count) - 1
cloud_pen_data[atom_index] = CustomNamespace(
atomic_symbol=atomic_symbol, a=float(a), b=float(b))
r_cubed_file_name = "DDEC_atomic_Rcubed_moments.xyz"
with open(r_cubed_file_name, "r+") as vol_file:
lines = vol_file.readlines()
vols = [float(line.split()[-1]) for line in lines[2:atom_total + 2]]
for atom_index in ddec_data:
ddec_data[atom_index].volume = vols[atom_index]
self.molecule.ddec_data = ddec_data
self.molecule.dipole_moment_data = dipole_moment_data
self.molecule.quadrupole_moment_data = quadrupole_moment_data
self.molecule.cloud_pen_data = cloud_pen_data
def extract_charge_data(ddec_version=6):
"""
From Chargemol output files, extract the necessary parameters for calculation of L-J.
:returns: 3 CustomNamespaces, ddec_data; dipole_moment_data; and quadrupole_moment_data
ddec_data used for calculating monopole esp and L-J values (used by both LennardJones and Charges classes)
dipole_moment_data used for calculating dipole esp
quadrupole_moment_data used for calculating quadrupole esp
"""
if ddec_version == 6:
net_charge_file_name = 'DDEC6_even_tempered_net_atomic_charges.xyz'
elif ddec_version == 3:
net_charge_file_name = 'DDEC3_net_atomic_charges.xyz'
else:
raise ValueError(
'Unsupported DDEC version; please use version 3 or 6.')
if not os.path.exists(net_charge_file_name):
raise FileNotFoundError(
'Cannot find the DDEC output file.\nThis could be indicative of several issues.\n'
'Please check Chargemol is installed in the correct location and that the configs'
' point to that location.')
with open(net_charge_file_name, 'r+') as charge_file:
lines = charge_file.readlines()
# Find number of atoms
atom_total = int(lines[0])
for pos, row in enumerate(lines):
# Data marker:
if 'The following XYZ' in row:
start_pos = pos + 2
break
else:
raise EOFError(f'Cannot find charge data in {net_charge_file_name}.')
ddec_data = {}
dipole_moment_data = {}
quadrupole_moment_data = {}
for line in lines[start_pos:start_pos + atom_total]:
# _s are the xyz coords, then the quadrupole moment tensor eigenvalues
atom_count, atomic_symbol, _, _, _, charge, x_dipole, y_dipole, z_dipole, _, q_xy, q_xz, q_yz, q_x2_y2, q_3z2_r2, *_ = line.split(
)
# File counts from 1 not 0; thereby requiring -1 to get the index
atom_index = int(atom_count) - 1
ddec_data[atom_index] = CustomNamespace(atomic_symbol=atomic_symbol,
charge=float(charge),
volume=None,
r_aim=None,
b_i=None,
a_i=None)
dipole_moment_data[atom_index] = CustomNamespace(
x_dipole=float(x_dipole),
y_dipole=float(y_dipole),
z_dipole=float(z_dipole))
quadrupole_moment_data[atom_index] = CustomNamespace(
q_xy=float(q_xy),
q_xz=float(q_xz),
q_yz=float(q_yz),
q_x2_y2=float(q_x2_y2),
q_3z2_r2=float(q_3z2_r2))
r_cubed_file_name = 'DDEC_atomic_Rcubed_moments.xyz'
with open(r_cubed_file_name, 'r+') as vol_file:
lines = vol_file.readlines()
vols = [float(line.split()[-1]) for line in lines[2:atom_total + 2]]
for atom_index in ddec_data:
ddec_data[atom_index].volume = vols[atom_index]
return ddec_data, dipole_moment_data, quadrupole_moment_data