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import numpy as np
from ase.units import Bohr
from ase.data import atomic_numbers
def attach_charges(atoms, fileobj='ACF.dat', displacement=1e-4):
"""Attach the charges from the fileobj to the Atoms."""
if isinstance(fileobj, str):
with open(fileobj) as fd:
lines = fd.readlines()
else:
lines = fileobj
sep = '---------------'
i = 0 # Counter for the lines
k = 0 # Counter of sep
assume6columns = False
for line in lines:
if line[0] == '\n': # check if there is an empty line in the
i -= 1 # head of ACF.dat file
if i == 0:
headings = line
if 'BADER' in headings.split():
j = headings.split().index('BADER')
elif 'CHARGE' in headings.split():
j = headings.split().index('CHARGE')
else:
print('Can\'t find keyword "BADER" or "CHARGE".'
' Assuming the ACF.dat file has 6 columns.')
j = 4
assume6columns = True
if sep in line: # Stop at last separator line
if k == 1:
break
k += 1
if not i > 1:
pass
else:
words = line.split()
if assume6columns is True:
if len(words) != 6:
raise IOError('Number of columns in ACF file incorrect!\n'
'Check that Bader program version >= 0.25')
atom = atoms[int(words[0]) - 1]
atom.charge = atomic_numbers[atom.symbol] - float(words[j])
if displacement is not None: # check if the atom positions match
xyz = np.array([float(w) for w in words[1:4]])
# ACF.dat units could be Bohr or Angstrom
norm1 = np.linalg.norm(atom.position - xyz)
norm2 = np.linalg.norm(atom.position - xyz * Bohr)
assert norm1 < displacement or norm2 < displacement
i += 1
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