def get_born_OUTCAR(poscar_filename="POSCAR",
outcar_filename="OUTCAR",
primitive_axis=np.eye(3),
is_symmetry=True,
symmetrize_tensors=False):
cell = read_vasp(poscar_filename)
primitive = Primitive(cell, primitive_axis)
p2p = primitive.get_primitive_to_primitive_map()
symmetry = Symmetry(primitive, is_symmetry=is_symmetry)
independent_atoms = symmetry.get_independent_atoms()
prim_lat = primitive.get_cell().T
outcar = open(outcar_filename)
borns = []
while True:
line = outcar.readline()
if not line:
break
if "NIONS" in line:
num_atom = int(line.split()[11])
if "MACROSCOPIC STATIC DIELECTRIC TENSOR" in line:
epsilon = []
outcar.readline()
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
if "BORN" in line:
outcar.readline()
line = outcar.readline()
if "ion" in line:
for i in range(num_atom):
born = []
born.append([float(x) for x in outcar.readline().split()][1:])
born.append([float(x) for x in outcar.readline().split()][1:])
born.append([float(x) for x in outcar.readline().split()][1:])
outcar.readline()
borns.append(born)
reduced_borns = []
for p_i, u_i in enumerate(p2p):
if p_i in independent_atoms:
if symmetrize_tensors:
site_sym = [similarity_transformation(prim_lat, rot)
for rot in symmetry.get_site_symmetry(p_i)]
reduced_borns.append(symmetrize_tensor(borns[u_i], site_sym))
else:
reduced_borns.append(borns[u_i])
if symmetrize_tensors:
point_sym = [similarity_transformation(prim_lat, rot)
for rot in symmetry.get_pointgroup_operations()]
epsilon = symmetrize_tensor(epsilon, point_sym)
else:
epsilon = np.array(epsilon)
return np.array(reduced_borns), epsilon
def get_born_OUTCAR(poscar_filename="POSCAR",
outcar_filename="OUTCAR",
primitive_axis=np.eye(3),
is_symmetry=True,
symmetrize_tensors=False):
cell = read_vasp(poscar_filename)
primitive = Primitive(cell, primitive_axis)
p2p = primitive.get_primitive_to_primitive_map()
symmetry = Symmetry(primitive, is_symmetry=is_symmetry)
independent_atoms = symmetry.get_independent_atoms()
prim_lat = primitive.get_cell().T
outcar = open(outcar_filename)
borns = []
while True:
line = outcar.readline()
if not line:
break
if "NIONS" in line:
num_atom = int(line.split()[11])
if "MACROSCOPIC STATIC DIELECTRIC TENSOR" in line:
epsilon = []
outcar.readline()
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
if "BORN" in line:
outcar.readline()
line = outcar.readline()
if "ion" in line:
for i in range(num_atom):
born = []
born.append([float(x)
for x in outcar.readline().split()][1:])
born.append([float(x)
for x in outcar.readline().split()][1:])
born.append([float(x)
for x in outcar.readline().split()][1:])
outcar.readline()
borns.append(born)
reduced_borns = []
for p_i, u_i in enumerate(p2p):
if p_i in independent_atoms:
if symmetrize_tensors:
site_sym = [
similarity_transformation(prim_lat, rot)
for rot in symmetry.get_site_symmetry(p_i)
]
reduced_borns.append(symmetrize_tensor(borns[u_i], site_sym))
else:
reduced_borns.append(borns[u_i])
if symmetrize_tensors:
point_sym = [
similarity_transformation(prim_lat, rot)
for rot in symmetry.get_pointgroup_operations()
]
epsilon = symmetrize_tensor(epsilon, point_sym)
else:
epsilon = np.array(epsilon)
return np.array(reduced_borns), epsilon
def _get_fc3_done(supercell: PhonopyAtoms, disp_dataset, symmetry: Symmetry,
array_shape):
num_atom = len(supercell)
fc3_done = np.zeros(array_shape, dtype="byte")
symprec = symmetry.tolerance
lattice = supercell.cell.T
positions = supercell.scaled_positions
rotations = symmetry.symmetry_operations["rotations"]
translations = symmetry.symmetry_operations["translations"]
atom_mapping = []
for rot, trans in zip(rotations, translations):
atom_indices = [
_get_atom_by_symmetry(lattice, positions, rot, trans, i, symprec)
for i in range(num_atom)
]
atom_mapping.append(atom_indices)
for dataset_first_atom in disp_dataset["first_atoms"]:
first_atom_num = dataset_first_atom["number"]
site_symmetry = symmetry.get_site_symmetry(first_atom_num)
direction = np.dot(dataset_first_atom["displacement"],
np.linalg.inv(supercell.cell))
reduced_site_sym = get_reduced_site_symmetry(site_symmetry, direction,
symprec)
least_second_atom_nums = []
for second_atoms in dataset_first_atom["second_atoms"]:
if "included" in second_atoms:
if second_atoms["included"]:
least_second_atom_nums.append(second_atoms["number"])
elif "cutoff_distance" in disp_dataset:
min_vec = get_smallest_vector_of_atom_pair(
first_atom_num, second_atoms["number"], supercell, symprec)
min_distance = np.linalg.norm(np.dot(lattice, min_vec))
if "pair_distance" in second_atoms:
assert abs(min_distance -
second_atoms["pair_distance"]) < 1e-4
if min_distance < disp_dataset["cutoff_distance"]:
least_second_atom_nums.append(second_atoms["number"])
positions_shifted = positions - positions[first_atom_num]
least_second_atom_nums = np.unique(least_second_atom_nums)
for red_rot in reduced_site_sym:
second_atom_nums = [
_get_atom_by_symmetry(
lattice,
positions_shifted,
red_rot,
np.zeros(3, dtype="double"),
i,
symprec,
) for i in least_second_atom_nums
]
second_atom_nums = np.unique(second_atom_nums)
for i in range(len(rotations)):
rotated_atom1 = atom_mapping[i][first_atom_num]
for j in second_atom_nums:
fc3_done[rotated_atom1, atom_mapping[i][j]] = 1
return fc3_done
def get_born_OUTCAR(poscar_filename="POSCAR",
outcar_filename="OUTCAR",
primitive_axis=np.eye(3),
supercell_matrix=np.eye(3, dtype='intc'),
is_symmetry=True,
symmetrize_tensors=False):
ucell = read_vasp(poscar_filename)
scell = get_supercell(ucell, supercell_matrix)
inv_smat = np.linalg.inv(supercell_matrix)
pcell = get_primitive(scell, np.dot(inv_smat, primitive_axis))
u_sym = Symmetry(ucell, is_symmetry=is_symmetry)
p_sym = Symmetry(pcell, is_symmetry=is_symmetry)
lattice = ucell.get_cell().T
outcar = open(outcar_filename)
borns = []
while True:
line = outcar.readline()
if not line:
break
if "NIONS" in line:
num_atom = int(line.split()[11])
if "MACROSCOPIC STATIC DIELECTRIC TENSOR" in line:
epsilon = []
outcar.readline()
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
if "BORN" in line:
outcar.readline()
line = outcar.readline()
if "ion" in line:
for i in range(num_atom):
born = []
born.append([float(x)
for x in outcar.readline().split()][1:])
born.append([float(x)
for x in outcar.readline().split()][1:])
born.append([float(x)
for x in outcar.readline().split()][1:])
outcar.readline()
borns.append(born)
borns = np.array(borns, dtype='double')
epsilon = np.array(epsilon, dtype='double')
if symmetrize_tensors:
borns_orig = borns.copy()
point_sym = [similarity_transformation(lattice, r)
for r in u_sym.get_pointgroup_operations()]
epsilon = symmetrize_tensor(epsilon, point_sym)
for i in range(num_atom):
z = borns[i]
site_sym = [similarity_transformation(lattice, r)
for r in u_sym.get_site_symmetry(i)]
borns[i] = symmetrize_tensor(z, site_sym)
rotations = u_sym.get_symmetry_operations()['rotations']
map_atoms = u_sym.get_map_atoms()
borns_copy = np.zeros_like(borns)
for i, m_i in enumerate(map_atoms):
count = 0
for j, r_j in enumerate(u_sym.get_map_operations()):
if map_atoms[j] == m_i:
count += 1
r_cart = similarity_transformation(lattice, rotations[r_j])
borns_copy[i] += similarity_transformation(r_cart, borns[j])
borns_copy[i] /= count
borns = borns_copy
sum_born = borns.sum(axis=0) / len(borns)
borns -= sum_born
if (np.abs(borns_orig - borns) > 0.1).any():
sys.stderr.write(
"Born effective charge symmetrization might go wrong.\n")
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = borns[u_indep_atoms].copy()
return reduced_borns, epsilon
def get_third_order_displacements(cell: PhonopyAtoms,
symmetry: Symmetry,
is_plusminus="auto",
is_diagonal=False):
"""Create dispalcement dataset.
Note
----
Atoms 1, 2, and 3 are defined as follows:
Atom 1: The first displaced atom. Third order force constant
between Atoms 1, 2, and 3 is calculated.
Atom 2: The second displaced atom. Second order force constant
between Atoms 2 and 3 is calculated.
Atom 3: Force is mesuared on this atom.
Parameters
----------
cell : PhonopyAtoms
Supercell
symmetry : Symmetry
Symmetry of supercell
is_plusminus : str or bool, optional
Type of displacements, plus only (False), always plus and minus (True),
and plus and minus depending on site symmetry ('auto').
is_diagonal : bool, optional
Whether allow diagonal displacements of Atom 2 or not
Returns
-------
[{'number': atom1,
'direction': [1, 0, 0], # int
'second_atoms': [ {'number': atom2,
'directions': [ [1, 0, 0], [-1, 0, 0], ... ]
'distance': distance-between-atom1-and-atom2},
{'number': ... }, ... ] },
{'number': atom1, ... } ]
"""
positions = cell.scaled_positions
lattice = cell.cell.T
# Least displacements of first atoms (Atom 1) are searched by
# using respective site symmetries of the original crystal.
# 'is_diagonal=False' below is made intentionally to expect
# better accuracy.
disps_first = get_least_displacements(symmetry,
is_plusminus=is_plusminus,
is_diagonal=False)
symprec = symmetry.tolerance
dds = []
for disp in disps_first:
atom1 = disp[0]
disp1 = disp[1:4]
site_sym = symmetry.get_site_symmetry(atom1)
dds_atom1 = {"number": atom1, "direction": disp1, "second_atoms": []}
# Reduced site symmetry at the first atom with respect to
# the displacement of the first atoms.
reduced_site_sym = get_reduced_site_symmetry(site_sym, disp1, symprec)
# Searching orbits (second atoms) with respect to
# the first atom and its reduced site symmetry.
second_atoms = get_least_orbits(atom1, cell, reduced_site_sym, symprec)
for atom2 in second_atoms:
dds_atom2 = _get_next_displacements(atom1, atom2, reduced_site_sym,
lattice, positions, symprec,
is_diagonal)
min_vec = get_smallest_vector_of_atom_pair(atom1, atom2, cell,
symprec)
min_distance = np.linalg.norm(np.dot(lattice, min_vec))
dds_atom2["distance"] = min_distance
dds_atom1["second_atoms"].append(dds_atom2)
dds.append(dds_atom1)
return dds
