def main(in_xyz, in_log, target, output, bonding, thresh, kind):
if (in_xyz):
mol = rf.mol_from_file(in_xyz)
else:
mol = rf.mol_from_gauss(in_log)
charges = rf.read_g_char(in_log, kind)[0]
cluster = rf.mol_from_file(target)
mol.set_bonding(bonding=bonding, thresh=thresh)
cluster.set_bonding(bonding=bonding, thresh=thresh)
for atom, char in zip(mol, charges):
atom.q = char
assign_charges(mol, cluster)
# warning if some atoms have not been assigned or if some original charges
# were 0
bad_atoms = []
for atom in cluster:
if abs(atom.q) <= 0.000:
bad_atoms.append(atom)
if len(bad_atoms) > 0:
print("WARNING: " + str(len(bad_atoms)) + " atoms have null charge!")
print(bad_atoms)
out_file = open(output, "w")
out_file.write(str(len(cluster)) + "\n\n")
for atom in cluster:
out_file.write(str(atom) + "\n")
out_file.close()
def read_out_mol(self, pop="EPS"):
"""Read the output log file and return Mol"""
gauss_path = os.path.join(self.here, self.calc_name)
os.chdir(gauss_path)
out_mol = rf.mol_from_gauss(self.calc_name + ".log")
os.chdir(self.here)
return out_mol
def populate_cell(in_mol, program, pop_file, method):
"""
Assign charge to the atoms from a unit cell
Don't import this.
If you want to assign charges go straign to assign_charges.py and use
those utilities.
Parameters
----------
in_mol : Mol object
Make sure these atoms form a unit cell.
program : str
Make it "gaussian" or "cp2k"
pop_file : str
The corresponding file to read charges from
method : str
Acceptable strings are "esp", "mulliken" and "hirshfeld"
"""
output_file = open(here + "/prep.out", "a")
if program.lower() == "cp2k":
charges = rf.read_cp2k(pop_file, method)[0]
output_file.write("Read " + str(len(in_mol)) +
" charges in cp2k_file\n")
# in case there are more charges than atoms
charges = charges[:len(in_mol)]
# correct charges if they are not perfectly neutral
if sum(charges) != 0.0:
output_file.write("Charge correction: " + str(sum(charges)) +
"\n")
charges[-1] -= sum(charges)
if program.lower() == "gaussian":
mol_char = rf.mol_from_gauss(pop_file, pop=method)
mol_char.bonding = in_mol.bonding
mol_char.thresh = in_mol.thresh
charges = [i.q for i in mol_char]
# correct charges if they are not perfectly neutral
if sum(charges) != 0.0:
output_file.write("Charge correction: " + str(sum(charges)) +
"\n")
mol_char[-1].q -= sum(charges)
# assign charges to the rest of the cell
in_mol.populate(mol_char)
output_file.close()
return
def make_region_2(self):
"""
Get region 2 Mols with different charges
Returns
-------
shell_high : Mol object
Region 2 molecules with high level of theory charges
shell_low : Mole object
Region 2 molecules with low level of theory charges
"""
if self.inputs["target_shell"]:
shell_high = rf.mol_from_file(self.inputs["target_shell"])
self.write_out("Outer region read in with " +
str(len(shell_high)) + " atoms.\n")
high_level_pop_mol = rf.mol_from_gauss(
self.inputs["high_pop_file"],
pop=self.inputs["high_pop_method"])
shell_high.populate(high_level_pop_mol)
else:
shell_high = self.cell.make_cluster(self.inputs["clust_rad"],
central_mol=self.region_1,
mode=self.inputs["clust_mode"])
for atom_i in self.region_1:
for atom_j in shell_high:
if atom_i.very_close(atom_j):
shell_high.remove(atom_j)
break
self.write_out("Outer region generated with " +
str(len(shell_high)) + " atoms.\n")
low_level_pop_mol = rf.mol_from_gauss(
self.inputs["low_pop_file"], pop=self.inputs["low_pop_method"])
shell_low = shell_high.copy()
shell_low.populate(low_level_pop_mol)
return shell_low, shell_high
def pery_solo():
"""Return a Mol object of a charged perylene"""
out_mol = rf.mol_from_gauss("perylene_pop.log")
return out_mol
def benz_solo():
"""Return a Mol object of a charged benzene"""
out_mol = rf.mol_from_gauss("benzene_pop.log")
return out_mol