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Improve interface for getting parameters of NAC

This commit is contained in:
Atsushi Togo 2017-11-01 18:14:55 +09:00
parent 7e0fd74fc5
commit 1ad205d0f5
3 changed files with 95 additions and 99 deletions
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49
phonopy/interface/vasp.py
View File

@ -42,9 +42,7 @@ import numpy as np
from phonopy.structure.atoms import PhonopyAtoms as Atoms from phonopy.structure.atoms import PhonopyAtoms as Atoms
from phonopy.structure.atoms import symbol_map, atom_data from phonopy.structure.atoms import symbol_map, atom_data
from phonopy.structure.cells import get_primitive, get_supercell from phonopy.structure.cells import get_primitive, get_supercell
from phonopy.structure.symmetry import (Symmetry, get_site_symmetry, from phonopy.structure.symmetry import Symmetry, symmetrize_borns_and_epsilon
get_pointgroup_operations)
from phonopy.harmonic.force_constants import similarity_transformation
from phonopy.file_IO import (write_FORCE_SETS, write_force_constants_to_hdf5, from phonopy.file_IO import (write_FORCE_SETS, write_force_constants_to_hdf5,
write_FORCE_CONSTANTS) write_FORCE_CONSTANTS)
@ -397,51 +395,6 @@ def get_born_OUTCAR(poscar_filename="POSCAR",
symmetrize_tensors=symmetrize_tensors, symmetrize_tensors=symmetrize_tensors,
symprec=symprec) symprec=symprec)
def symmetrize_borns_and_epsilon(borns,
epsilon,
ucell,
symprec=1e-5,
is_symmetry=True):
lattice = ucell.get_cell()
positions = ucell.get_scaled_positions()
u_sym = Symmetry(ucell, is_symmetry=is_symmetry, symprec=symprec)
rotations = u_sym.get_symmetry_operations()['rotations']
translations = u_sym.get_symmetry_operations()['translations']
ptg_ops = get_pointgroup_operations(rotations)
epsilon_ = symmetrize_2nd_rank_tensor(epsilon, ptg_ops, lattice)
for i, Z in enumerate(borns):
site_sym = get_site_symmetry(i,
lattice,
positions,
rotations,
translations,
symprec)
Z = symmetrize_2nd_rank_tensor(Z, site_sym, lattice)
borns_ = np.zeros_like(borns)
for i in range(len(borns)):
count = 0
for r, t in zip(rotations, translations):
count += 1
diff = np.dot(positions, r.T) + t - positions[i]
diff -= np.rint(diff)
dist = np.sqrt(np.sum(np.dot(diff, lattice) ** 2, axis=1))
j = np.nonzero(dist < symprec)[0][0]
r_cart = similarity_transformation(lattice.T, r)
borns_[i] += similarity_transformation(r_cart, borns[j])
borns_[i] /= count
return borns_, epsilon_
def symmetrize_2nd_rank_tensor(tensor, symmetry_operations, lattice):
sym_cart = [similarity_transformation(lattice.T, r)
for r in symmetry_operations]
sum_tensor = np.zeros_like(tensor)
for sym in sym_cart:
sum_tensor += similarity_transformation(sym, tensor)
return sum_tensor / len(symmetry_operations)
def _get_indep_borns(ucell, def _get_indep_borns(ucell,
borns, borns,
epsilon, epsilon,

110
phonopy/structure/symmetry.py
View File

@ -36,6 +36,7 @@ import sys
import numpy as np import numpy as np
import phonopy.structure.spglib as spg import phonopy.structure.spglib as spg
from phonopy.structure.atoms import PhonopyAtoms as Atoms from phonopy.structure.atoms import PhonopyAtoms as Atoms
from phonopy.harmonic.force_constants import similarity_transformation
class Symmetry(object): class Symmetry(object):
def __init__(self, cell, symprec=1e-5, is_symmetry=True): def __init__(self, cell, symprec=1e-5, is_symmetry=True):
@ -110,12 +111,12 @@ class Symmetry(object):
rotations = self._symmetry_operations['rotations'] rotations = self._symmetry_operations['rotations']
translations = self._symmetry_operations['translations'] translations = self._symmetry_operations['translations']
return get_site_symmetry(atom_number, return self._get_site_symmetry(atom_number,
lattice, lattice,
positions, positions,
rotations, rotations,
translations, translations,
self._symprec) self._symprec)
def get_symmetry_tolerance(self): def get_symmetry_tolerance(self):
return self._symprec return self._symprec
@ -129,6 +130,39 @@ class Symmetry(object):
""" """
return self._reciprocal_operations return self._reciprocal_operations
def _get_pointgroup_operations(self, rotations):
ptg_ops = []
for rot in rotations:
is_same = False
for tmp_rot in ptg_ops:
if (tmp_rot == rot).all():
is_same = True
break
if not is_same:
ptg_ops.append(rot)
return ptg_ops
def _get_site_symmetry(self,
atom_number,
lattice,
positions,
rotations,
translations,
symprec):
pos = positions[atom_number]
site_symmetries = []
for r, t in zip(rotations, translations):
rot_pos = np.dot(pos, r.T) + t
diff = pos - rot_pos
diff -= np.rint(diff)
diff = np.dot(diff, lattice)
if np.linalg.norm(diff) < symprec:
site_symmetries.append(r)
return np.array(site_symmetries, dtype='intc')
def _set_symmetry_dataset(self): def _set_symmetry_dataset(self):
self._dataset = spg.get_symmetry_dataset(self._cell, self._symprec) self._dataset = spg.get_symmetry_dataset(self._cell, self._symprec)
self._symmetry_operations = { self._symmetry_operations = {
@ -180,7 +214,7 @@ class Symmetry(object):
def _set_pointgroup_operations(self): def _set_pointgroup_operations(self):
rotations = self._symmetry_operations['rotations'] rotations = self._symmetry_operations['rotations']
ptg_ops = get_pointgroup_operations(rotations) ptg_ops = self._get_pointgroup_operations(rotations)
reciprocal_rotations = [rot.T for rot in ptg_ops] reciprocal_rotations = [rot.T for rot in ptg_ops]
exist_r_inv = False exist_r_inv = False
for rot in ptg_ops: for rot in ptg_ops:
@ -285,34 +319,42 @@ def get_lattice_vector_equivalence(point_symmetry):
return equivalence return equivalence
def get_site_symmetry(atom_number, def symmetrize_borns_and_epsilon(borns,
lattice, epsilon,
positions, ucell,
rotations, symprec=1e-5,
translations, is_symmetry=True):
symprec): lattice = ucell.get_cell()
pos = positions[atom_number] positions = ucell.get_scaled_positions()
site_symmetries = [] u_sym = Symmetry(ucell, is_symmetry=is_symmetry, symprec=symprec)
rotations = u_sym.get_symmetry_operations()['rotations']
translations = u_sym.get_symmetry_operations()['translations']
ptg_ops = u_sym.get_pointgroup_operations()
epsilon_ = _symmetrize_2nd_rank_tensor(epsilon, ptg_ops, lattice)
for r, t in zip(rotations, translations): for i, Z in enumerate(borns):
rot_pos = np.dot(pos, r.T) + t site_sym = u_sym.get_site_symmetry(i)
diff = pos - rot_pos Z = _symmetrize_2nd_rank_tensor(Z, site_sym, lattice)
diff -= np.rint(diff)
diff = np.dot(diff, lattice)
if np.linalg.norm(diff) < symprec:
site_symmetries.append(r)
return np.array(site_symmetries, dtype='intc') borns_ = np.zeros_like(borns)
for i in range(len(borns)):
count = 0
for r, t in zip(rotations, translations):
count += 1
diff = np.dot(positions, r.T) + t - positions[i]
diff -= np.rint(diff)
dist = np.sqrt(np.sum(np.dot(diff, lattice) ** 2, axis=1))
j = np.nonzero(dist < symprec)[0][0]
r_cart = similarity_transformation(lattice.T, r)
borns_[i] += similarity_transformation(r_cart, borns[j])
borns_[i] /= count
def get_pointgroup_operations(rotations): return borns_, epsilon_
ptg_ops = []
for rot in rotations:
is_same = False
for tmp_rot in ptg_ops:
if (tmp_rot == rot).all():
is_same = True
break
if not is_same:
ptg_ops.append(rot)
return ptg_ops def _symmetrize_2nd_rank_tensor(tensor, symmetry_operations, lattice):
sym_cart = [similarity_transformation(lattice.T, r)
for r in symmetry_operations]
sum_tensor = np.zeros_like(tensor)
for sym in sym_cart:
sum_tensor += similarity_transformation(sym, tensor)
return sum_tensor / len(symmetry_operations)

35
scripts/phonopy-vasp-born
View File

@ -51,8 +51,8 @@ parser = OptionParser()
parser.set_defaults(num_atoms=None, parser.set_defaults(num_atoms=None,
primitive_axis =None, primitive_axis =None,
supercell_matrix=None, supercell_matrix=None,
symmetrize_tensors=False, symmetrize_tensors=True,
read_vasprunxml=False, read_outcar=False,
symprec=1e-5) symprec=1e-5)
parser.add_option("--dim", dest="supercell_matrix", parser.add_option("--dim", dest="supercell_matrix",
action="store", type="string", action="store", type="string",
@ -60,24 +60,25 @@ parser.add_option("--dim", dest="supercell_matrix",
parser.add_option("--pa", "--primitive_axis", dest="primitive_axis", parser.add_option("--pa", "--primitive_axis", dest="primitive_axis",
action="store", type="string", action="store", type="string",
help="Same as PRIMITIVE_AXIS tags") help="Same as PRIMITIVE_AXIS tags")
parser.add_option("--st", "--symmetrize_tensors", dest="symmetrize_tensors", parser.add_option("--nost", "--no_symmetrize_tensors",
action="store_true", dest="symmetrize_tensors",
help="Symmetrize tensors") action="store_false",
help="Prevent from symmetrizing tensors")
parser.add_option("--tolerance", dest="symprec", type="float", parser.add_option("--tolerance", dest="symprec", type="float",
help="Symmetry tolerance to search") help="Symmetry tolerance to search")
parser.add_option("--vasprunxml", dest="read_vasprunxml", parser.add_option("--outcar", dest="read_outcar",
action="store_true", action="store_true",
help=("Read vasprun.xml instead of OUTCAR. " help=("Read OUTCAR instead of vasprun.xml. "
"POSCAR is not necessary")) "POSCAR is necessary in this case."))
(options, args) = parser.parse_args() (options, args) = parser.parse_args()
if args: if args:
outcar_filename = args[0] outcar_filename = args[0]
else: else:
if options.read_vasprunxml: if options.read_outcar:
outcar_filename = "vasprun.xml"
else:
outcar_filename = "OUTCAR" outcar_filename = "OUTCAR"
else:
outcar_filename = "vasprun.xml"
if len(args) > 1: if len(args) > 1:
poscar_filename = args[1] poscar_filename = args[1]
@ -111,17 +112,17 @@ with warnings.catch_warnings() as w:
warnings.simplefilter("always") warnings.simplefilter("always")
try: try:
if options.read_vasprunxml: if options.read_outcar:
borns, epsilon, atom_indices = get_born_vasprunxml( borns, epsilon, atom_indices = get_born_OUTCAR(
filename=outcar_filename, poscar_filename=poscar_filename,
outcar_filename=outcar_filename,
primitive_matrix=primitive_axis, primitive_matrix=primitive_axis,
supercell_matrix=supercell_matrix, supercell_matrix=supercell_matrix,
symmetrize_tensors=options.symmetrize_tensors, symmetrize_tensors=options.symmetrize_tensors,
symprec=options.symprec) symprec=options.symprec)
else: else:
borns, epsilon, atom_indices = get_born_OUTCAR( borns, epsilon, atom_indices = get_born_vasprunxml(
poscar_filename=poscar_filename, filename=outcar_filename,
outcar_filename=outcar_filename,
primitive_matrix=primitive_axis, primitive_matrix=primitive_axis,
supercell_matrix=supercell_matrix, supercell_matrix=supercell_matrix,
symmetrize_tensors=options.symmetrize_tensors, symmetrize_tensors=options.symmetrize_tensors,