def get_dipole_moment(self, atoms=None):
'''Tries to return the dipole vector of the unit cell in atomic units.
Returns None when CHG file is empty/not-present.
To get the dipole moment, use this formula:
dipole_moment = ((dipole_vector**2).sum())**0.5/Debye
'''
if atoms is None:
atoms = self.get_atoms()
try:
x, y, z, cd = self.get_charge_density()
except (IOError, IndexError):
# IOError: no CHG file, function called outside context manager
# IndexError: Empty CHG file, Vasp run with lcharg=False
return None
n0, n1, n2 = cd.shape
nelements = n0 * n1 * n2
voxel_volume = atoms.get_volume() / nelements
total_electron_charge = -cd.sum() * voxel_volume
electron_density_center = np.array([(cd*x).sum(),
(cd*y).sum(),
(cd*z).sum()])
electron_density_center *= voxel_volume
electron_density_center /= total_electron_charge
electron_dipole_moment = electron_density_center * total_electron_charge
electron_dipole_moment *= -1.0
# now the ion charge center
LOP = self.get_pseudopotentials()
ppp = os.environ['VASP_PP_PATH']
# make dictionary for ease of use
zval = {}
for sym, ppath, hash in LOP:
# out a bug above. os.path.join discards the root if the
# second path starts with /, which makes it look like an
# absolute path. the get_pseudopotentials code returns a path
# with a / in the beginning.
fullpath = ppp + ppath
z = get_ZVAL(fullpath)
zval[sym] = z
ion_charge_center = np.array([0.0, 0.0, 0.0])
total_ion_charge = 0.0
for atom in atoms:
Z = zval[atom.symbol]
total_ion_charge += Z
pos = atom.position
ion_charge_center += Z*pos
ion_charge_center /= total_ion_charge
ion_dipole_moment = ion_charge_center * total_ion_charge
dipole_vector = (ion_dipole_moment + electron_dipole_moment)
return dipole_vector
def get_dipole_vector(self, atoms=None):
"""Tries to return the dipole vector of the unit cell in atomic units.
Returns None when CHG file is empty/not-present.
"""
self.update()
from POTCAR import get_ZVAL
if atoms is None:
atoms = self.get_atoms()
try:
x, y, z, cd = self.get_charge_density()
except (IOError, IndexError):
# IOError: no CHG file, function called outside context manager
# IndexError: Empty CHG file, Vasp run with lcharg=False
return None
n0, n1, n2 = cd.shape
nelements = n0 * n1 * n2
voxel_volume = atoms.get_volume() / nelements
total_electron_charge = -cd.sum() * voxel_volume
electron_density_center = np.array([(cd * x).sum(),
(cd * y).sum(),
(cd * z).sum()])
electron_density_center *= voxel_volume
electron_density_center /= total_electron_charge
electron_dipole_moment = electron_density_center * total_electron_charge
electron_dipole_moment *= -1.0
# now the ion charge center
LOP = self.get_pseudopotentials()
ppp = os.environ['VASP_PP_PATH']
# make dictionary for ease of use
zval = {}
for sym, ppath, hash in LOP:
fullpath = os.path.join(ppp, ppath)
z = get_ZVAL(fullpath)
zval[sym] = z
ion_charge_center = np.array([0.0, 0.0, 0.0])
total_ion_charge = 0.0
for atom in atoms:
Z = zval[atom.symbol]
total_ion_charge += Z
pos = atom.position
ion_charge_center += Z * pos
ion_charge_center /= total_ion_charge
ion_dipole_moment = ion_charge_center * total_ion_charge
dipole_vector = (ion_dipole_moment + electron_dipole_moment)
return dipole_vector
def get_dipole_moment(self, atoms=None):
'''Tries to return the dipole vector of the unit cell in atomic units.
Returns None when CHG file is empty/not-present.
To get the dipole moment, use this formula:
dipole_moment = ((dipole_vector**2).sum())**0.5/Debye
'''
if atoms is None:
atoms = self.get_atoms()
try:
x, y, z, cd = self.get_charge_density()
except (IOError, IndexError):
# IOError: no CHG file, function called outside context manager
# IndexError: Empty CHG file, Vasp run with lcharg=False
return None
n0, n1, n2 = cd.shape
nelements = n0 * n1 * n2
voxel_volume = atoms.get_volume() / nelements
total_electron_charge = -cd.sum() * voxel_volume
electron_density_center = np.array([(cd * x).sum(), (cd * y).sum(),
(cd * z).sum()])
electron_density_center *= voxel_volume
electron_density_center /= total_electron_charge
electron_dipole_moment = electron_density_center * total_electron_charge
electron_dipole_moment *= -1.0
# now the ion charge center
LOP = self.get_pseudopotentials()
ppp = os.environ['VASP_PP_PATH']
# make dictionary for ease of use
zval = {}
for sym, ppath, hash in LOP:
# out a bug above. os.path.join discards the root if the
# second path starts with /, which makes it look like an
# absolute path. the get_pseudopotentials code returns a path
# with a / in the beginning.
fullpath = ppp + ppath
z = get_ZVAL(fullpath)
zval[sym] = z
ion_charge_center = np.array([0.0, 0.0, 0.0])
total_ion_charge = 0.0
for atom in atoms:
Z = zval[atom.symbol]
total_ion_charge += Z
pos = atom.position
ion_charge_center += Z * pos
ion_charge_center /= total_ion_charge
ion_dipole_moment = ion_charge_center * total_ion_charge
dipole_vector = (ion_dipole_moment + electron_dipole_moment)
return dipole_vector
def get_dipole_moment(self):
"""Return dipole moment (vector) of unit cell in atomic units.
:returns: a vector of the dipole moment
:rtype: :class:`numpy.array`
dipole_moment = ((dipole_vector**2).sum())**0.5/Debye
"""
atoms = self.get_atoms()
x, y, z, cd = self.get_charge_density()
n0, n1, n2 = cd.shape
nelements = n0 * n1 * n2
voxel_volume = atoms.get_volume() / nelements
total_electron_charge = -cd.sum() * voxel_volume
electron_density_center = np.array([(cd * x).sum(),
(cd * y).sum(),
(cd * z).sum()])
electron_density_center *= voxel_volume
electron_density_center /= total_electron_charge
electron_dipole_moment = electron_density_center * total_electron_charge
electron_dipole_moment *= -1.0
# now the ion charge center
LOP = self.get_pseudopotentials()
ppp = os.environ['VASP_PP_PATH']
# make dictionary for ease of use
zval = {}
for sym, ppath, hash in LOP:
fullpath = os.path.join(ppp, ppath)
z = get_ZVAL(fullpath)
zval[sym] = z
ion_charge_center = np.array([0.0, 0.0, 0.0])
total_ion_charge = 0.0
for atom in atoms:
Z = zval[atom.symbol]
total_ion_charge += Z
pos = atom.position
ion_charge_center += Z*pos
ion_charge_center /= total_ion_charge
ion_dipole_moment = ion_charge_center * total_ion_charge
dipole_vector = (ion_dipole_moment + electron_dipole_moment)
return dipole_vector
def get_dipole_moment(self):
"""Return dipole moment (vector) of unit cell in atomic units.
:returns: a vector of the dipole moment
:rtype: :class:`numpy.array`
dipole_moment = ((dipole_vector**2).sum())**0.5/Debye
"""
atoms = self.get_atoms()
x, y, z, cd = self.get_charge_density()
n0, n1, n2 = cd.shape
nelements = n0 * n1 * n2
voxel_volume = atoms.get_volume() / nelements
total_electron_charge = -cd.sum() * voxel_volume
electron_density_center = np.array([(cd * x).sum(), (cd * y).sum(),
(cd * z).sum()])
electron_density_center *= voxel_volume
electron_density_center /= total_electron_charge
electron_dipole_moment = electron_density_center * total_electron_charge
electron_dipole_moment *= -1.0
# now the ion charge center
LOP = self.get_pseudopotentials()
ppp = os.environ['VASP_PP_PATH']
# make dictionary for ease of use
zval = {}
for sym, ppath, hash in LOP:
fullpath = os.path.join(ppp, ppath)
z = get_ZVAL(fullpath)
zval[sym] = z
ion_charge_center = np.array([0.0, 0.0, 0.0])
total_ion_charge = 0.0
for atom in atoms:
Z = zval[atom.symbol]
total_ion_charge += Z
pos = atom.position
ion_charge_center += Z * pos
ion_charge_center /= total_ion_charge
ion_dipole_moment = ion_charge_center * total_ion_charge
dipole_vector = (ion_dipole_moment + electron_dipole_moment)
return dipole_vector
def get_dipole_moment(self):
'''
dipole_moment = ((dipole_vector**2).sum())**0.5/Debye
'''
atoms = self.get_atoms()
x,y,z,cd = self.get_charge_density()
n0, n1, n2 = cd.shape
nelements = n0*n1*n2
voxel_volume = atoms.get_volume()/nelements
total_electron_charge = -cd.sum()*voxel_volume
electron_density_center = np.array([(cd*x).sum(),
(cd*y).sum(),
(cd*z).sum()])
electron_density_center *= voxel_volume
electron_density_center /= total_electron_charge
electron_dipole_moment = electron_density_center*total_electron_charge
electron_dipole_moment *= -1.0 #we need the - here so the two
#negatives don't cancel
# now the ion charge center
LOP = self.get_pseudopotentials()
ppp = os.environ['VASP_PP_PATH']
# make dictionary for ease of use
zval = {}
for sym, ppath, hash in LOP:
fullpath = os.path.join(ppp, ppath)
z = get_ZVAL(fullpath)
zval[sym] = z
ion_charge_center = np.array([0.0, 0.0, 0.0])
total_ion_charge = 0.0
for atom in atoms:
Z = zval[atom.symbol]
total_ion_charge += Z
pos = atom.position
ion_charge_center += Z*pos
ion_charge_center /= total_ion_charge
ion_dipole_moment = ion_charge_center*total_ion_charge
dipole_vector = (ion_dipole_moment + electron_dipole_moment)
return dipole_vector
def attach_charges(self, fileobj='ACF.dat', displacement=1e-4):
'''
Attach the charges from the fileobj to the Atoms.
This is a modified version of the attach_charges function in
ase.io.bader to work better with VASP.
Does not require the atom positions to be in Bohr and references
the charge to the ZVAL in the POTCAR
'''
calc = self.get_calculator()
# Get the sorting and resorting lists
sort = calc.sort
resort = calc.resort
if isinstance(fileobj, str):
fileobj = open(fileobj)
f_open = True
# First get a dictionary of ZVALS from the pseudopotentials
LOP = calc.get_pseudopotentials()
ppp = os.environ['VASP_PP_PATH']
zval = {}
for sym, ppath, hash in LOP:
fullpath = ppp + ppath
z = get_ZVAL(fullpath)
zval[sym] = z
# Get sorted symbols and positions according to POSCAR and ACF.dat
symbols = np.array(self.get_chemical_symbols())[sort]
positions = self.get_positions()[sort]
charges = []
sep = '---------------'
i = 0 # Counter for the lines
k = 0 # Counter of sep
assume6columns = False
for line in fileobj:
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 seperator 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')
sym = symbols[int(words[0]) - 1]
charges.append(zval[sym] - 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]])
assert np.linalg.norm(positions[int(words[0]) - 1] - xyz) < displacement
i += 1
if f_open:
fileobj.close()
# Now attach the resorted charges to the atom
charges = np.array(charges)[resort]
for atom in self:
atom.charge = charges[atom.index]
def attach_charges(self, fileobj=None, displacement=1e-4):
"""Attach the charges from the fileobj to the atoms on the calculator.
This is a modified version of the attach_charges function in
ase.io.bader to work better with VASP.
Does not require the atom positions to be in Bohr and references
the charge to the ZVAL in the POTCAR
"""
if fileobj is None:
fileobj = os.path.join(self.directory, 'ACF.dat')
if isinstance(fileobj, str):
fileobj = open(fileobj)
f_open = True
# First get a dictionary of ZVALS from the pseudopotentials
LOP = self.get_pseudopotentials()
ppp = os.environ['VASP_PP_PATH']
zval = {}
for sym, ppath, hash in LOP:
fullpath = os.path.join(ppp, ppath)
z = get_ZVAL(fullpath)
zval[sym] = z
atoms = self.atoms
# Get sorted symbols and positions according to POSCAR and ACF.dat
symbols = np.array(atoms.get_chemical_symbols())[self.resort]
positions = atoms.get_positions()[self.resort]
charges = []
sep = '---------------'
i = 0 # Counter for the lines
k = 0 # Counter of sep
assume6columns = False
for line in fileobj:
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 seperator 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')
sym = symbols[int(words[0]) - 1]
charges.append(zval[sym] - 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]])
assert (np.linalg.norm(positions[int(words[0]) - 1] - xyz) <
displacement)
i += 1
if f_open:
fileobj.close()
# Now attach the resorted charges to the atom
charges = np.array(charges)[self.resort]
for atom in self.atoms:
atom.charge = charges[atom.index]