def get_mulliken_charges(self, initial: Atoms, verbose=True):
'''
This function is used to retrieve atomic charges using Mulliken charge
decomposition as implemented in FHI-aims. A new trajectory file containing
the charges
Args:
initial: Atoms
Atoms object containing structural information for the calculation
verbose: bool
Flag for turning off printouts in the code
Returns:
Atoms object with charges appended
'''
from ase.io.trajectory import Trajectory
from carmm.analyse.mulliken import extract_mulliken_charge
'''Setup initial parameters'''
params = self.params
hpc = self.hpc
basis_set = self.basis_set
self.initial = initial
dimensions = sum(self.initial.pbc)
'''Parent directory'''
parent_dir = os.getcwd()
'''Read the geometry'''
if not self.filename:
self.filename = self.initial.get_chemical_formula()
filename = self.filename
assert type(filename) == str, "Invalid type, filename should be string"
counter, subdirectory_name = self._restart_setup(
"Charges", self.filename)
'''Check for previously completed calculation'''
if os.path.exists(
os.path.join(subdirectory_name[:-1] + str(counter - 1),
filename + "_charges.traj")):
file_location = os.path.join(
subdirectory_name[:-1] + str(counter - 1),
filename + "_charges.traj")
self.initial = read(file_location)
if verbose:
print("Previously calculated structure has been found at",
file_location)
return self.initial
out = str(counter) + "_" + str(filename) + ".out"
'''Set the environment variables for geometry optimisation'''
set_aims_command(hpc=hpc, basis_set=basis_set, defaults=2020)
'''Request Mulliken charge decomposition'''
params["output"] = ["Mulliken_summary"]
os.makedirs(subdirectory_name, exist_ok=True)
os.chdir(subdirectory_name)
with _calc_generator(params,
out_fn=out,
dimensions=dimensions,
forces=False)[0] as calculator:
if not self.dry_run:
self.initial.calc = calculator
else:
self.initial.calc = EMT()
self.initial.get_potential_energy()
if not self.dry_run:
charges = extract_mulliken_charge(out, len(self.initial))
else:
charges = initial.get_charges()
self.initial.set_initial_charges(charges)
traj = Trajectory(filename + "_charges.traj", 'w')
traj.write(self.initial)
traj.close()
os.chdir(parent_dir)
return self.initial
nf = len(y)
pos.append([float(x) for x in y[nf - 4:nf - 1]])
syms += y[1].strip('0123456789')
y = s.readline().split()
pos = np.array(pos) * alat
natoms = len(pos)
# create atoms object with coordinates and unit cell
# as specified in the initial ionic step in log
atoms = Atoms(syms, pos, cell=cell * alat, pbc=(1, 1, 1))
atoms.get_calculator = calc.get_calculator
atoms.get_potential_energy = calc.get_potential_energy
atoms.get_forces = calc.notimpl
atoms.get_stress = calc.notimpl
atoms.get_charges = calc.notimpl
# get total energy at first ionic step
en = get_total_energy(s)
if en is not None:
calc.set_energy(en)
else:
print >>stderr, 'no total energy found'
exit(3)
print(atoms)
traj = PickleTrajectory(argv[2], 'w')
traj.write(atoms)
