def single_sc_loop(self, sc_loop, initial_bg):
"""Run a single iteration of the sc loop, with or without Ewald"""
sc_name = "sc_" + self.inputs["name"]
# Initial charges in mol
old_charges = self.region_1.charges()
# if sc_eec then there is no initial_bg so it needs to be computed
if self.mode == "ew_sc":
points = self.run_ewald(calc_name=sc_name)
initial_bg = points
ef.write_gauss(sc_name + ".com", self.region_1, initial_bg,
self.inputs["sc_temp"])
subprocess.call("${FRO_GAUSS} " + sc_name + ".com", shell=True)
# Calculate new charges
intact_charges, new_energy, char_self, char_int = rf.read_g_char(
sc_name + ".log", self.inputs["high_pop_method"], debug=True)
# Correct charges if they are not perfectly neutral
if sum(intact_charges) != 0.0:
temp_correct = sum(intact_charges) / len(intact_charges)
intact_charges = [i - temp_correct for i in intact_charges]
dummy_mol = self.region_1.copy()
dummy_mol.raw_assign_charges(intact_charges)
self.region_1.populate(dummy_mol)
# Damp the change in charges
new_charges = [
new * (1 - self.inputs["damping"]) + old * self.inputs["damping"]
for new, old in zip(self.region_1.charges(), old_charges)
]
# Correct charges again (due to damping)
if sum(new_charges) != 0.0:
temp_correct = sum(new_charges) / len(new_charges)
new_charges = [i - temp_correct for i in new_charges]
# assign damped charges
self.region_1.raw_assign_charges(new_charges)
self.cell.populate(self.region_1)
if self.mode == "noew_sc":
assign_charges(self.region_1, initial_bg)
# Calculate deviation between initial and new charges
deviation = sum([
abs(i - j) for (i, j) in zip(self.region_1.charges(), old_charges)
]) / len(self.region_1)
out_str = ("Iteration:", sc_loop, "Deviation:", deviation, "Energy:",
new_energy, "Charge self energy:", char_self,
"Total - charge self:", new_energy - char_self)
self.write_out(
"{:<6} {:<5} {:<6} {:10.6f} {:<6} {:10.6f} {:<6} {:10.6f} {:<6} {:10.6f}\n"
.format(*out_str))
return deviation
def populate(self, reference_mol):
"""
Assign charges to the Mol by comparing to the connectivity of a
reference
Parameters
----------
reference_mol : Mol object
Charged molecule or cell
"""
# This is a naughty in-function import to prevent a circular dependency.
# The reason is that assign_charges functions are grouped up with the
# executable script which needs to read_file and in turn use mol.py
# Some careful refactoring should fix this
import fromage.scripts.fro_assign_charges as ac
ac.assign_charges(reference_mol, self)
return
def benz_clust_char(benz_solo):
"""Return a Mol object of a charged benzene cluster"""
out_char_clust = rf.mol_from_file("benzene_clust.xyz")
ac.assign_charges(benz_solo, out_char_clust)
return out_char_clust
def pery_cell_char(pery_cell, pery_solo):
"""Return a Mol object of a charged perylene cell"""
out_char_cell = deepcopy(pery_cell)
ac.assign_charges(pery_solo, out_char_cell)
return out_char_cell
def benz_cell_char(benz_cell, benz_solo):
"""Return a Mol object of a charged benzene cell"""
out_char_cell = deepcopy(benz_cell)
ac.assign_charges(benz_solo, out_char_cell)
return out_char_cell