def extract_params_onetep(self):
"""
TODO Move this to file_handling.py
From ONETEP output files, extract the necessary parameters for calculation of L-J.
Insert data into ddec_data in standard format
This will exclusively be used by this class.
It will also give less information, hence why it is here, not in the helpers file.
"""
# Just fill in None values until they are known
ddec_data = {
i: CustomNamespace(atomic_symbol=atom.atomic_symbol,
charge=None,
volume=None,
r_aim=None,
b_i=None,
a_i=None)
for i, atom in enumerate(self.molecule.atoms)
}
# Second file contains the rest (charges, dipoles and volumes):
ddec_output_file = 'ddec.onetep' if os.path.exists(
'ddec.onetep') else 'iter_1/ddec.onetep'
with open(ddec_output_file, 'r') as file:
lines = file.readlines()
charge_pos, vol_pos = None, None
for pos, line in enumerate(lines):
# Charges marker in file:
if 'DDEC density' in line:
charge_pos = pos + 7
# Volumes marker in file:
if 'DDEC Radial' in line:
vol_pos = pos + 4
if any(position is None for position in [charge_pos, vol_pos]):
raise EOFError(
'Cannot locate charges and / or volumes in ddec.onetep file.')
charges = [
float(line.split()[-1])
for line in lines[charge_pos:charge_pos + len(self.molecule.atoms)]
]
# Add the AIM-Valence and the AIM-Core to get V^AIM
volumes = [
float(line.split()[2]) + float(line.split()[3])
for line in lines[vol_pos:vol_pos + len(self.molecule.atoms)]
]
for atom_index in ddec_data:
ddec_data[atom_index].charge = charges[atom_index]
ddec_data[atom_index].volume = volumes[atom_index]
return ddec_data
def _extract_charge_data_onetep(self):
"""
From ONETEP output files, extract the necessary parameters for calculation of L-J.
Insert data into ddec_data in standard format.
Used exclusively by LennardJones class.
"""
# Just fill in None values until they are known
ddec_data = {
i: CustomNamespace(
atomic_symbol=atom.atomic_symbol,
charge=None,
volume=None,
r_aim=None,
b_i=None,
a_i=None,
)
for i, atom in enumerate(self.molecule.atoms)
}
# Second file contains the rest (charges, dipoles and volumes):
ddec_output_file = ("ddec.onetep" if os.path.exists("ddec.onetep") else
"iter_1/ddec.onetep")
with open(ddec_output_file, "r") as file:
lines = file.readlines()
charge_pos, vol_pos = None, None
for pos, line in enumerate(lines):
# Charges marker in file:
if "DDEC density" in line:
charge_pos = pos + 7
# Volumes marker in file:
if "DDEC Radial" in line:
vol_pos = pos + 4
if any(position is None for position in [charge_pos, vol_pos]):
raise EOFError(
"Cannot locate charges and / or volumes in ddec.onetep file.")
charges = [
float(line.split()[-1])
for line in lines[charge_pos:charge_pos + len(self.molecule.atoms)]
]
# Add the AIM-Valence and the AIM-Core to get V^AIM
volumes = [
float(line.split()[2]) + float(line.split()[3])
for line in lines[vol_pos:vol_pos + len(self.molecule.atoms)]
]
for atom_index in ddec_data:
ddec_data[atom_index].charge = charges[atom_index]
ddec_data[atom_index].volume = volumes[atom_index]
self.molecule.ddec_data = ddec_data
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 mol():
"""
Initialise the Ligand molecule object with data for Chloromethane
"""
molecule = Ligand.from_file(file_name=get_data("chloromethane.pdb"))
molecule.ddec_data = {
0: CustomNamespace(
a_i=72461.2438863321,
atomic_symbol="C",
b_i=36.09781017184126,
charge=-0.220088,
r_aim=1.9933297947778903,
volume=30.276517,
),
1: CustomNamespace(
a_i=153692.84134145387,
atomic_symbol="Cl",
b_i=101.44341268889193,
charge=1.815899,
r_aim=1.9020122149415648,
volume=67.413573,
),
2: CustomNamespace(
a_i=149.1117208173859,
atomic_symbol="H",
b_i=1.247688109065071,
charge=0.13473,
r_aim=1.2455924332095252,
volume=3.329737,
),
3: CustomNamespace(
a_i=149.1117208173859,
atomic_symbol="H",
b_i=1.247688109065071,
charge=0.13473,
r_aim=1.2455924332095252,
volume=3.329737,
),
4: CustomNamespace(
a_i=149.1117208173859,
atomic_symbol="H",
b_i=1.247688109065071,
charge=0.134729,
r_aim=1.2455924332095252,
volume=3.329737,
),
}
molecule.dipole_moment_data = {
0: CustomNamespace(x_dipole=0.109154, y_dipole=0.006347, z_dipole=-0.000885),
1: CustomNamespace(x_dipole=-0.139599, y_dipole=-0.006372, z_dipole=0.000994),
2: CustomNamespace(x_dipole=-0.005778, y_dipole=-0.018142, z_dipole=-0.029462),
3: CustomNamespace(x_dipole=-0.00516, y_dipole=-0.016898, z_dipole=0.030335),
4: CustomNamespace(x_dipole=-0.00839, y_dipole=0.035106, z_dipole=-0.000628),
}
molecule.quadrupole_moment_data = {
0: CustomNamespace(
q_3z2_r2=-0.150042,
q_x2_y2=0.148149,
q_xy=0.007494,
q_xz=-0.001301,
q_yz=-0.000128,
),
1: CustomNamespace(
q_3z2_r2=-1.074695,
q_x2_y2=1.070914,
q_xy=0.052325,
q_xz=-0.006765,
q_yz=-0.000286,
),
2: CustomNamespace(
q_3z2_r2=0.013971,
q_x2_y2=0.011282,
q_xy=0.001128,
q_xz=0.000274,
q_yz=0.011593,
),
3: CustomNamespace(
q_3z2_r2=0.01544,
q_x2_y2=0.011683,
q_xy=0.001125,
q_xz=-0.000412,
q_yz=-0.01131,
),
4: CustomNamespace(
q_3z2_r2=-0.043386,
q_x2_y2=-0.007519,
q_xy=-0.001058,
q_xz=-5.4e-05,
q_yz=-0.000249,
),
}
molecule.cloud_pen_data = {
0: CustomNamespace(a=2.102843, atomic_symbol="C", b=2.40575),
1: CustomNamespace(a=7.939831, atomic_symbol="Cl", b=3.395079),
2: CustomNamespace(a=0.1242, atomic_symbol="H", b=2.533532),
3: CustomNamespace(a=0.123448, atomic_symbol="H", b=2.533309),
4: CustomNamespace(a=0.120282, atomic_symbol="H", b=2.533191),
}
print(f"mol coords: {molecule.coordinates}")
return molecule
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
def __init__(self):
self.name = "water"
self.atoms = [
Atom(8, "O", 0, -0.827099, [1, 2]),
Atom(1, "H", 1, 0.41355, [0]),
Atom(1, "H", 1, 0.41355, [0]),
]
self.coords = {
"qm":
np.array([
[-0.00191868, 0.38989824, 0.0],
[-0.7626204, -0.19870548, 0.0],
[0.76453909, -0.19119276, 0.0],
])
}
self.topology = nx.Graph()
self.topology.add_node(0)
self.topology.add_node(1)
self.topology.add_node(2)
self.topology.add_edge(0, 1)
self.topology.add_edge(0, 2)
self.ddec_data = {
0:
CustomNamespace(
a_i=44312.906375462444,
atomic_symbol="O",
b_i=47.04465571009466,
charge=-0.827099,
r_aim=1.7571614241044191,
volume=29.273005,
),
1:
CustomNamespace(
a_i=0.0,
atomic_symbol="H",
b_i=0,
charge=0.41355,
r_aim=0.6833737065249833,
volume=2.425428,
),
2:
CustomNamespace(
a_i=0.0,
atomic_symbol="H",
b_i=0,
charge=0.413549,
r_aim=0.6833737065249833,
volume=2.425428,
),
}
self.dipole_moment_data = {
0:
CustomNamespace(x_dipole=-0.000457,
y_dipole=0.021382,
z_dipole=0.0),
1:
CustomNamespace(x_dipole=-0.034451,
y_dipole=-0.010667,
z_dipole=0.0),
2:
CustomNamespace(x_dipole=0.03439,
y_dipole=-0.010372,
z_dipole=-0.0),
}
self.quadrupole_moment_data = {
0:
CustomNamespace(q_3z2_r2=-0.786822,
q_x2_y2=0.307273,
q_xy=0.001842,
q_xz=-0.0,
q_yz=0.0),
1:
CustomNamespace(q_3z2_r2=-0.097215,
q_x2_y2=0.018178,
q_xy=0.001573,
q_xz=0.0,
q_yz=0.0),
2:
CustomNamespace(
q_3z2_r2=-0.097264,
q_x2_y2=0.018224,
q_xy=-0.001287,
q_xz=-0.0,
q_yz=-0.0,
),
}
self.cloud_pen_data = {
0: CustomNamespace(a=-0.126185, atomic_symbol="O", b=2.066872),
1: CustomNamespace(a=-2.638211, atomic_symbol="H", b=1.917509),
2: CustomNamespace(a=-2.627835, atomic_symbol="H", b=1.920499),
}
self.enable_symmetry = True
self.v_site_error_factor = 1.005