mirror of https://github.com/phonopy/phonopy.git
Improve interface for getting parameters of NAC
This commit is contained in:
Atsushi Togo
parent
7e0fd74fc5
commit
1ad205d0f5
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@ -42,9 +42,7 @@ import numpy as np
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from phonopy.structure.atoms import PhonopyAtoms as Atoms
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from phonopy.structure.atoms import symbol_map, atom_data
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from phonopy.structure.cells import get_primitive, get_supercell
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from phonopy.structure.symmetry import (Symmetry, get_site_symmetry,
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get_pointgroup_operations)
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from phonopy.harmonic.force_constants import similarity_transformation
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from phonopy.structure.symmetry import Symmetry, symmetrize_borns_and_epsilon
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from phonopy.file_IO import (write_FORCE_SETS, write_force_constants_to_hdf5,
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write_FORCE_CONSTANTS)
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@ -397,51 +395,6 @@ def get_born_OUTCAR(poscar_filename="POSCAR",
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symmetrize_tensors=symmetrize_tensors,
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symprec=symprec)
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def symmetrize_borns_and_epsilon(borns,
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epsilon,
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ucell,
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symprec=1e-5,
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is_symmetry=True):
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lattice = ucell.get_cell()
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positions = ucell.get_scaled_positions()
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u_sym = Symmetry(ucell, is_symmetry=is_symmetry, symprec=symprec)
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rotations = u_sym.get_symmetry_operations()['rotations']
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translations = u_sym.get_symmetry_operations()['translations']
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ptg_ops = get_pointgroup_operations(rotations)
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epsilon_ = symmetrize_2nd_rank_tensor(epsilon, ptg_ops, lattice)
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for i, Z in enumerate(borns):
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site_sym = get_site_symmetry(i,
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lattice,
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positions,
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rotations,
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translations,
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symprec)
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Z = symmetrize_2nd_rank_tensor(Z, site_sym, lattice)
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borns_ = np.zeros_like(borns)
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for i in range(len(borns)):
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count = 0
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for r, t in zip(rotations, translations):
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count += 1
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diff = np.dot(positions, r.T) + t - positions[i]
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diff -= np.rint(diff)
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dist = np.sqrt(np.sum(np.dot(diff, lattice) ** 2, axis=1))
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j = np.nonzero(dist < symprec)[0][0]
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r_cart = similarity_transformation(lattice.T, r)
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borns_[i] += similarity_transformation(r_cart, borns[j])
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borns_[i] /= count
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return borns_, epsilon_
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def symmetrize_2nd_rank_tensor(tensor, symmetry_operations, lattice):
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sym_cart = [similarity_transformation(lattice.T, r)
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for r in symmetry_operations]
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sum_tensor = np.zeros_like(tensor)
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for sym in sym_cart:
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sum_tensor += similarity_transformation(sym, tensor)
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return sum_tensor / len(symmetry_operations)
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def _get_indep_borns(ucell,
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borns,
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epsilon,
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@ -36,6 +36,7 @@ import sys
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import numpy as np
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import phonopy.structure.spglib as spg
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from phonopy.structure.atoms import PhonopyAtoms as Atoms
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from phonopy.harmonic.force_constants import similarity_transformation
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class Symmetry(object):
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def __init__(self, cell, symprec=1e-5, is_symmetry=True):
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@ -110,7 +111,7 @@ class Symmetry(object):
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rotations = self._symmetry_operations['rotations']
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translations = self._symmetry_operations['translations']
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return get_site_symmetry(atom_number,
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return self._get_site_symmetry(atom_number,
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lattice,
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positions,
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rotations,
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@ -129,6 +130,39 @@ class Symmetry(object):
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"""
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return self._reciprocal_operations
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def _get_pointgroup_operations(self, rotations):
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ptg_ops = []
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for rot in rotations:
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is_same = False
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for tmp_rot in ptg_ops:
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if (tmp_rot == rot).all():
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is_same = True
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break
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if not is_same:
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ptg_ops.append(rot)
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return ptg_ops
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def _get_site_symmetry(self,
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atom_number,
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lattice,
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positions,
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rotations,
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translations,
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symprec):
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pos = positions[atom_number]
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site_symmetries = []
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for r, t in zip(rotations, translations):
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rot_pos = np.dot(pos, r.T) + t
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diff = pos - rot_pos
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diff -= np.rint(diff)
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diff = np.dot(diff, lattice)
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if np.linalg.norm(diff) < symprec:
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site_symmetries.append(r)
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return np.array(site_symmetries, dtype='intc')
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def _set_symmetry_dataset(self):
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self._dataset = spg.get_symmetry_dataset(self._cell, self._symprec)
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self._symmetry_operations = {
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@ -180,7 +214,7 @@ class Symmetry(object):
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def _set_pointgroup_operations(self):
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rotations = self._symmetry_operations['rotations']
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ptg_ops = get_pointgroup_operations(rotations)
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ptg_ops = self._get_pointgroup_operations(rotations)
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reciprocal_rotations = [rot.T for rot in ptg_ops]
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exist_r_inv = False
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for rot in ptg_ops:
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@ -285,34 +319,42 @@ def get_lattice_vector_equivalence(point_symmetry):
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return equivalence
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def get_site_symmetry(atom_number,
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lattice,
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positions,
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rotations,
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translations,
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symprec):
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pos = positions[atom_number]
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site_symmetries = []
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def symmetrize_borns_and_epsilon(borns,
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epsilon,
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ucell,
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symprec=1e-5,
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is_symmetry=True):
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lattice = ucell.get_cell()
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positions = ucell.get_scaled_positions()
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u_sym = Symmetry(ucell, is_symmetry=is_symmetry, symprec=symprec)
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rotations = u_sym.get_symmetry_operations()['rotations']
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translations = u_sym.get_symmetry_operations()['translations']
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ptg_ops = u_sym.get_pointgroup_operations()
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epsilon_ = _symmetrize_2nd_rank_tensor(epsilon, ptg_ops, lattice)
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for i, Z in enumerate(borns):
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site_sym = u_sym.get_site_symmetry(i)
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Z = _symmetrize_2nd_rank_tensor(Z, site_sym, lattice)
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borns_ = np.zeros_like(borns)
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for i in range(len(borns)):
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count = 0
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for r, t in zip(rotations, translations):
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rot_pos = np.dot(pos, r.T) + t
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diff = pos - rot_pos
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count += 1
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diff = np.dot(positions, r.T) + t - positions[i]
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diff -= np.rint(diff)
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diff = np.dot(diff, lattice)
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if np.linalg.norm(diff) < symprec:
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site_symmetries.append(r)
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dist = np.sqrt(np.sum(np.dot(diff, lattice) ** 2, axis=1))
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j = np.nonzero(dist < symprec)[0][0]
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r_cart = similarity_transformation(lattice.T, r)
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borns_[i] += similarity_transformation(r_cart, borns[j])
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borns_[i] /= count
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return np.array(site_symmetries, dtype='intc')
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return borns_, epsilon_
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def get_pointgroup_operations(rotations):
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ptg_ops = []
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for rot in rotations:
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is_same = False
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for tmp_rot in ptg_ops:
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if (tmp_rot == rot).all():
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is_same = True
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break
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if not is_same:
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ptg_ops.append(rot)
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return ptg_ops
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def _symmetrize_2nd_rank_tensor(tensor, symmetry_operations, lattice):
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sym_cart = [similarity_transformation(lattice.T, r)
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for r in symmetry_operations]
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sum_tensor = np.zeros_like(tensor)
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for sym in sym_cart:
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sum_tensor += similarity_transformation(sym, tensor)
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return sum_tensor / len(symmetry_operations)
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@ -51,8 +51,8 @@ parser = OptionParser()
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parser.set_defaults(num_atoms=None,
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primitive_axis =None,
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supercell_matrix=None,
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symmetrize_tensors=False,
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read_vasprunxml=False,
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symmetrize_tensors=True,
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read_outcar=False,
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symprec=1e-5)
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parser.add_option("--dim", dest="supercell_matrix",
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action="store", type="string",
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@ -60,24 +60,25 @@ parser.add_option("--dim", dest="supercell_matrix",
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parser.add_option("--pa", "--primitive_axis", dest="primitive_axis",
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action="store", type="string",
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help="Same as PRIMITIVE_AXIS tags")
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parser.add_option("--st", "--symmetrize_tensors", dest="symmetrize_tensors",
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action="store_true",
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help="Symmetrize tensors")
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parser.add_option("--nost", "--no_symmetrize_tensors",
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dest="symmetrize_tensors",
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action="store_false",
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help="Prevent from symmetrizing tensors")
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parser.add_option("--tolerance", dest="symprec", type="float",
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help="Symmetry tolerance to search")
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parser.add_option("--vasprunxml", dest="read_vasprunxml",
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parser.add_option("--outcar", dest="read_outcar",
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action="store_true",
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help=("Read vasprun.xml instead of OUTCAR. "
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"POSCAR is not necessary"))
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help=("Read OUTCAR instead of vasprun.xml. "
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"POSCAR is necessary in this case."))
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(options, args) = parser.parse_args()
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if args:
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outcar_filename = args[0]
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else:
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if options.read_vasprunxml:
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outcar_filename = "vasprun.xml"
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else:
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if options.read_outcar:
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outcar_filename = "OUTCAR"
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else:
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outcar_filename = "vasprun.xml"
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if len(args) > 1:
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poscar_filename = args[1]
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@ -111,17 +112,17 @@ with warnings.catch_warnings() as w:
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warnings.simplefilter("always")
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try:
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if options.read_vasprunxml:
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borns, epsilon, atom_indices = get_born_vasprunxml(
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filename=outcar_filename,
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if options.read_outcar:
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borns, epsilon, atom_indices = get_born_OUTCAR(
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poscar_filename=poscar_filename,
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outcar_filename=outcar_filename,
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primitive_matrix=primitive_axis,
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supercell_matrix=supercell_matrix,
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symmetrize_tensors=options.symmetrize_tensors,
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symprec=options.symprec)
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else:
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borns, epsilon, atom_indices = get_born_OUTCAR(
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poscar_filename=poscar_filename,
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outcar_filename=outcar_filename,
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borns, epsilon, atom_indices = get_born_vasprunxml(
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filename=outcar_filename,
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primitive_matrix=primitive_axis,
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supercell_matrix=supercell_matrix,
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symmetrize_tensors=options.symmetrize_tensors,
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