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Update of tools around nac params symmetrization

This commit is contained in:
Atsushi Togo 2020-10-27 18:11:08 +09:00
parent a00493b140
commit 429d902a6a
9 changed files with 1292 additions and 33 deletions
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5
phonopy/cui/load.py
View File

@ -37,6 +37,7 @@ from phonopy.api_phonopy import Phonopy
from phonopy.interface.phonopy_yaml import PhonopyYaml
from phonopy.interface.calculator import get_default_physical_units
import phonopy.cui.load_helper as load_helper
from phonopy.structure.cells import get_primitive_matrix
def load(phonopy_yaml=None, # phonopy.yaml-like must be the first argument.
@ -219,8 +220,8 @@ def load(phonopy_yaml=None, # phonopy.yaml-like must be the first argument.
smat = phpy_yaml.supercell_matrix
if smat is None:
smat = np.eye(3, dtype='intc', order='C')
if primitive_matrix == 'auto':
pmat = 'auto'
if primitive_matrix is not None:
pmat = get_primitive_matrix(primitive_matrix, symprec=symprec)
else:
pmat = phpy_yaml.primitive_matrix
if nac_params is not None:

3
phonopy/cui/load_helper.py
View File

@ -35,8 +35,7 @@
import os
import numpy as np
from phonopy.interface.calculator import read_crystal_structure
from phonopy.structure.cells import (
get_primitive_matrix_by_centring, get_primitive_matrix)
from phonopy.structure.cells import get_primitive_matrix
from phonopy.file_IO import (
parse_BORN, read_force_constants_hdf5, parse_FORCE_SETS,
parse_FORCE_CONSTANTS)

56
phonopy/structure/symmetry.py
View File

@ -379,9 +379,8 @@ def elaborate_borns_and_epsilon(ucell,
"""
assert len(borns) == ucell.get_number_of_atoms(), \
"num_atom %d != len(borns) %d" % (ucell.get_number_of_atoms(),
len(borns))
assert len(borns) == len(ucell), \
"num_atom %d != len(borns) %d" % (len(ucell), len(borns))
if symmetrize_tensors:
borns_, epsilon_ = symmetrize_borns_and_epsilon(
@ -453,38 +452,19 @@ def symmetrize_borns_and_epsilon(borns,
"""
lattice = ucell.get_cell()
positions = ucell.get_scaled_positions()
lattice = ucell.cell
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 i, Z in enumerate(borns):
site_sym = u_sym.get_site_symmetry(i)
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
sum_born = borns_.sum(axis=0) / len(borns_)
borns_ -= sum_born
borns_ = _take_average_of_borns(borns, rotations, translations, ucell,
symprec)
if (abs(borns - borns_) > 0.1).any():
lines = ["Born effective charge symmetry is largely broken. "
"Largest different among elements: "
"%s" % np.amax(abs(borns - borns_))]
lines = ["Symmetry of Born effective charge is largely broken. "
"The difference is:",
"%s" % (borns - borns_)]
import warnings
warnings.warn("\n".join(lines))
@ -512,6 +492,26 @@ def symmetrize_borns_and_epsilon(borns,
return borns_in_prim[idx2].copy(), epsilon_
def _take_average_of_borns(borns, rotations, translations, cell, symprec):
lattice = cell.cell
positions = cell.scaled_positions
borns_ = np.zeros_like(borns)
for i in range(len(borns)):
for r, t in zip(rotations, translations):
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] /= len(rotations)
sum_born = borns_.sum(axis=0) / len(borns_)
borns_ -= sum_born
return borns_
def _get_mapping_between_cells(cell_from, cell_to, symprec=1e-5):
indices = []
lattice = cell_from.cell

4
test/BORN_TiO2 Normal file
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@ -0,0 +1,4 @@
# epsilon and Z* of atoms 1 9
7.10729047 0.00000000 0.00000000 0.00000000 7.10729047 0.00000000 0.00000000 0.00000000 6.41993410
-5.54435990 0.00000000 0.00000000 0.00000000 -1.11960146 -0.00000000 0.00000000 0.00000000 -2.89515567
6.66396136 0.00000000 0.00000000 0.00000000 6.66396136 -0.00000000 0.00000000 0.00000000 5.79031133

668
test/FORCE_SETS_TiO2 Normal file
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@ -0,0 +1,668 @@
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12
test/conftest.py
View File

@ -41,6 +41,18 @@ def ph_sno2():
log_level=1, produce_fc=True)
@pytest.fixture(scope='session')
def ph_tio2():
yaml_filename = os.path.join(current_dir, "phonopy_disp_TiO2.yaml")
force_sets_filename = os.path.join(current_dir, "FORCE_SETS_TiO2")
born_filename = os.path.join(current_dir, "BORN_SnO2")
return phonopy.load(yaml_filename,
force_sets_filename=force_sets_filename,
born_filename=born_filename,
is_compact_fc=False,
log_level=1, produce_fc=True)
@pytest.fixture(scope='session')
def convcell_sio2():
symbols = ['Si'] * 2 + ['O'] * 4

563
test/phonopy_disp_TiO2.yaml Normal file
View File

@ -0,0 +1,563 @@
phonopy:
version: 2.8.1
frequency_unit_conversion_factor: 15.633302
symmetry_tolerance: 1.00000e-05
configuration:
create_displacements: ".true."
physical_unit:
atomic_mass: "AMU"
length: "angstrom"
force_constants: "eV/angstrom^2"
space_group:
type: "I4_1/amd"
number: 141
Hall_symbol: "I 4bw 2bw -1bw"
primitive_matrix:
- [ -0.500000000000000, 0.500000000000000, 0.500000000000000 ]
- [ 0.500000000000000, -0.500000000000000, 0.500000000000000 ]
- [ 0.500000000000000, 0.500000000000000, -0.500000000000000 ]
supercell_matrix:
- [ 3, 0, 0 ]
- [ 0, 3, 0 ]
- [ 0, 0, 1 ]
primitive_cell:
lattice:
- [ -1.888070425000000, 1.888070425000000, 4.790243149999999 ] # a
- [ 1.888070425000000, -1.888070424999999, 4.790243149999999 ] # b
- [ 1.888070425000000, 1.888070424999999, -4.790243149999999 ] # c
points:
- symbol: O # 1
coordinates: [ 0.457386310000000, 0.957386310000000, 0.500000000000000 ]
mass: 15.999400
- symbol: O # 2
coordinates: [ 0.707386310000000, 0.707386310000000, 1.000000000000000 ]
mass: 15.999400
- symbol: O # 3
coordinates: [ 0.042613690000000, 0.542613690000000, 0.500000000000000 ]
mass: 15.999400
- symbol: O # 4
coordinates: [ 0.292613690000000, 0.292613690000000, 1.000000000000000 ]
mass: 15.999400
- symbol: Ti # 5
coordinates: [ 0.500000000000000, 0.500000000000000, 1.000000000000000 ]
mass: 47.867000
- symbol: Ti # 6
coordinates: [ 0.250000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 47.867000
reciprocal_lattice: # without 2pi
- [ 0.000000000000000, 0.264820630300377, 0.104378835132826 ] # a*
- [ 0.264820630300377, 0.000000000000000, 0.104378835132826 ] # b*
- [ 0.264820630300377, 0.264820630300377, -0.000000000000000 ] # c*
unit_cell:
lattice:
- [ 3.776140850000000, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 3.776140850000000, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 9.580486300000000 ] # c
points:
- symbol: O # 1
coordinates: [ 0.500000000000000, 0.000000000000000, 0.457386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 2
coordinates: [ 0.000000000000000, 0.000000000000000, 0.707386310000000 ]
mass: 15.999400
reduced_to: 2
- symbol: O # 3
coordinates: [ 0.000000000000000, 0.500000000000000, 0.542613690000000 ]
mass: 15.999400
reduced_to: 3
- symbol: O # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.792613690000000 ]
mass: 15.999400
reduced_to: 4
- symbol: O # 5
coordinates: [ 0.000000000000000, 0.500000000000000, 0.957386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 6
coordinates: [ 0.500000000000000, 0.500000000000000, 0.207386310000000 ]
mass: 15.999400
reduced_to: 2
- symbol: O # 7
coordinates: [ 0.500000000000000, 0.000000000000000, 0.042613690000000 ]
mass: 15.999400
reduced_to: 3
- symbol: O # 8
coordinates: [ 0.000000000000000, 0.000000000000000, 0.292613690000000 ]
mass: 15.999400
reduced_to: 4
- symbol: Ti # 9
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 47.867000
reduced_to: 9
- symbol: Ti # 10
coordinates: [ 0.000000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 47.867000
reduced_to: 10
- symbol: Ti # 11
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 47.867000
reduced_to: 9
- symbol: Ti # 12
coordinates: [ 0.500000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 47.867000
reduced_to: 10
supercell:
lattice:
- [ 11.328422549999999, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 11.328422549999999, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 9.580486300000000 ] # c
points:
- symbol: O # 1
coordinates: [ 0.166666666666667, 0.000000000000000, 0.457386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 2
coordinates: [ 0.500000000000000, 0.000000000000000, 0.457386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 3
coordinates: [ 0.833333333333333, 0.000000000000000, 0.457386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 4
coordinates: [ 0.166666666666667, 0.333333333333333, 0.457386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 5
coordinates: [ 0.500000000000000, 0.333333333333333, 0.457386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 6
coordinates: [ 0.833333333333333, 0.333333333333333, 0.457386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 7
coordinates: [ 0.166666666666667, 0.666666666666667, 0.457386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 8
coordinates: [ 0.500000000000000, 0.666666666666667, 0.457386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 9
coordinates: [ 0.833333333333333, 0.666666666666667, 0.457386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 10
coordinates: [ 0.000000000000000, 0.000000000000000, 0.707386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 11
coordinates: [ 0.333333333333333, 0.000000000000000, 0.707386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 12
coordinates: [ 0.666666666666667, 0.000000000000000, 0.707386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 13
coordinates: [ 0.000000000000000, 0.333333333333333, 0.707386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 14
coordinates: [ 0.333333333333333, 0.333333333333333, 0.707386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 15
coordinates: [ 0.666666666666667, 0.333333333333333, 0.707386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 16
coordinates: [ 0.000000000000000, 0.666666666666667, 0.707386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 17
coordinates: [ 0.333333333333333, 0.666666666666667, 0.707386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 18
coordinates: [ 0.666666666666667, 0.666666666666667, 0.707386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 19
coordinates: [ 0.000000000000000, 0.166666666666667, 0.542613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 20
coordinates: [ 0.333333333333333, 0.166666666666667, 0.542613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 21
coordinates: [ 0.666666666666667, 0.166666666666667, 0.542613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 22
coordinates: [ 0.000000000000000, 0.500000000000000, 0.542613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 23
coordinates: [ 0.333333333333333, 0.500000000000000, 0.542613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 24
coordinates: [ 0.666666666666667, 0.500000000000000, 0.542613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 25
coordinates: [ 0.000000000000000, 0.833333333333333, 0.542613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 26
coordinates: [ 0.333333333333333, 0.833333333333333, 0.542613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 27
coordinates: [ 0.666666666666667, 0.833333333333333, 0.542613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 28
coordinates: [ 0.166666666666667, 0.166666666666667, 0.792613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 29
coordinates: [ 0.500000000000000, 0.166666666666667, 0.792613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 30
coordinates: [ 0.833333333333333, 0.166666666666667, 0.792613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 31
coordinates: [ 0.166666666666667, 0.500000000000000, 0.792613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 32
coordinates: [ 0.500000000000000, 0.500000000000000, 0.792613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 33
coordinates: [ 0.833333333333333, 0.500000000000000, 0.792613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 34
coordinates: [ 0.166666666666667, 0.833333333333333, 0.792613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 35
coordinates: [ 0.500000000000000, 0.833333333333333, 0.792613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 36
coordinates: [ 0.833333333333333, 0.833333333333333, 0.792613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 37
coordinates: [ 0.000000000000000, 0.166666666666667, 0.957386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 38
coordinates: [ 0.333333333333333, 0.166666666666667, 0.957386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 39
coordinates: [ 0.666666666666667, 0.166666666666667, 0.957386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 40
coordinates: [ 0.000000000000000, 0.500000000000000, 0.957386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 41
coordinates: [ 0.333333333333333, 0.500000000000000, 0.957386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 42
coordinates: [ 0.666666666666667, 0.500000000000000, 0.957386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 43
coordinates: [ 0.000000000000000, 0.833333333333333, 0.957386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 44
coordinates: [ 0.333333333333333, 0.833333333333333, 0.957386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 45
coordinates: [ 0.666666666666667, 0.833333333333333, 0.957386310000000 ]
mass: 15.999400
reduced_to: 1
- symbol: O # 46
coordinates: [ 0.166666666666667, 0.166666666666667, 0.207386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 47
coordinates: [ 0.500000000000000, 0.166666666666667, 0.207386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 48
coordinates: [ 0.833333333333333, 0.166666666666667, 0.207386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 49
coordinates: [ 0.166666666666667, 0.500000000000000, 0.207386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 50
coordinates: [ 0.500000000000000, 0.500000000000000, 0.207386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 51
coordinates: [ 0.833333333333333, 0.500000000000000, 0.207386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 52
coordinates: [ 0.166666666666667, 0.833333333333333, 0.207386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 53
coordinates: [ 0.500000000000000, 0.833333333333333, 0.207386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 54
coordinates: [ 0.833333333333333, 0.833333333333333, 0.207386310000000 ]
mass: 15.999400
reduced_to: 10
- symbol: O # 55
coordinates: [ 0.166666666666667, 0.000000000000000, 0.042613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 56
coordinates: [ 0.500000000000000, 0.000000000000000, 0.042613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 57
coordinates: [ 0.833333333333333, 0.000000000000000, 0.042613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 58
coordinates: [ 0.166666666666667, 0.333333333333333, 0.042613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 59
coordinates: [ 0.500000000000000, 0.333333333333333, 0.042613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 60
coordinates: [ 0.833333333333333, 0.333333333333333, 0.042613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 61
coordinates: [ 0.166666666666667, 0.666666666666667, 0.042613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 62
coordinates: [ 0.500000000000000, 0.666666666666667, 0.042613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 63
coordinates: [ 0.833333333333333, 0.666666666666667, 0.042613690000000 ]
mass: 15.999400
reduced_to: 19
- symbol: O # 64
coordinates: [ 0.000000000000000, 0.000000000000000, 0.292613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 65
coordinates: [ 0.333333333333333, 0.000000000000000, 0.292613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 66
coordinates: [ 0.666666666666667, 0.000000000000000, 0.292613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 67
coordinates: [ 0.000000000000000, 0.333333333333333, 0.292613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 68
coordinates: [ 0.333333333333333, 0.333333333333333, 0.292613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 69
coordinates: [ 0.666666666666667, 0.333333333333333, 0.292613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 70
coordinates: [ 0.000000000000000, 0.666666666666667, 0.292613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 71
coordinates: [ 0.333333333333333, 0.666666666666667, 0.292613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: O # 72
coordinates: [ 0.666666666666667, 0.666666666666667, 0.292613690000000 ]
mass: 15.999400
reduced_to: 28
- symbol: Ti # 73
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 74
coordinates: [ 0.333333333333333, 0.000000000000000, 0.500000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 75
coordinates: [ 0.666666666666667, 0.000000000000000, 0.500000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 76
coordinates: [ 0.000000000000000, 0.333333333333333, 0.500000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 77
coordinates: [ 0.333333333333333, 0.333333333333333, 0.500000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 78
coordinates: [ 0.666666666666667, 0.333333333333333, 0.500000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 79
coordinates: [ 0.000000000000000, 0.666666666666667, 0.500000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 80
coordinates: [ 0.333333333333333, 0.666666666666667, 0.500000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 81
coordinates: [ 0.666666666666667, 0.666666666666667, 0.500000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 82
coordinates: [ 0.000000000000000, 0.166666666666667, 0.750000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 83
coordinates: [ 0.333333333333333, 0.166666666666667, 0.750000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 84
coordinates: [ 0.666666666666667, 0.166666666666667, 0.750000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 85
coordinates: [ 0.000000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 86
coordinates: [ 0.333333333333333, 0.500000000000000, 0.750000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 87
coordinates: [ 0.666666666666667, 0.500000000000000, 0.750000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 88
coordinates: [ 0.000000000000000, 0.833333333333333, 0.750000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 89
coordinates: [ 0.333333333333333, 0.833333333333333, 0.750000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 90
coordinates: [ 0.666666666666667, 0.833333333333333, 0.750000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 91
coordinates: [ 0.166666666666667, 0.166666666666667, 0.000000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 92
coordinates: [ 0.500000000000000, 0.166666666666667, 0.000000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 93
coordinates: [ 0.833333333333333, 0.166666666666667, 0.000000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 94
coordinates: [ 0.166666666666667, 0.500000000000000, 0.000000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 95
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 96
coordinates: [ 0.833333333333333, 0.500000000000000, 0.000000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 97
coordinates: [ 0.166666666666667, 0.833333333333333, 0.000000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 98
coordinates: [ 0.500000000000000, 0.833333333333333, 0.000000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 99
coordinates: [ 0.833333333333333, 0.833333333333333, 0.000000000000000 ]
mass: 47.867000
reduced_to: 73
- symbol: Ti # 100
coordinates: [ 0.166666666666667, 0.000000000000000, 0.250000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 101
coordinates: [ 0.500000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 102
coordinates: [ 0.833333333333333, 0.000000000000000, 0.250000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 103
coordinates: [ 0.166666666666667, 0.333333333333333, 0.250000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 104
coordinates: [ 0.500000000000000, 0.333333333333333, 0.250000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 105
coordinates: [ 0.833333333333333, 0.333333333333333, 0.250000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 106
coordinates: [ 0.166666666666667, 0.666666666666667, 0.250000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 107
coordinates: [ 0.500000000000000, 0.666666666666667, 0.250000000000000 ]
mass: 47.867000
reduced_to: 82
- symbol: Ti # 108
coordinates: [ 0.833333333333333, 0.666666666666667, 0.250000000000000 ]
mass: 47.867000
reduced_to: 82
displacements:
- atom: 1
displacement:
[ 0.0060687317141537, 0.0060687317141537, 0.0051323474905008 ]
- atom: 1
displacement:
[ -0.0060687317141537, -0.0060687317141537, -0.0051323474905008 ]
- atom: 73
displacement:
[ 0.0076355582977273, 0.0000000000000000, 0.0064574181746273 ]
- atom: 73
displacement:
[ -0.0076355582977273, 0.0000000000000000, -0.0064574181746273 ]

4
test/structure/test_grid_points.py
View File

@ -160,3 +160,7 @@ def test_GridPoints_SnO2_with_rotations_MP(ph_sno2):
[0.125, 0.125, 0.375],
[0.375, 0.125, 0.375],
[0.375, 0.375, 0.375]], atol=1e-8)
def test_GeneralizedRegularGridPoints(ph_tio2):
pass

10
test/structure/test_symmetry.py
View File

@ -59,7 +59,7 @@ def test_magmom(convcell_cr):
assert len_sym_nonspin != len_sym_brokenspin
def test_symmetrize_borns_and_epsilon(ph_nacl):
def test_symmetrize_borns_and_epsilon_nacl(ph_nacl):
nac_params = ph_nacl.nac_params
borns, epsilon = symmetrize_borns_and_epsilon(
nac_params['born'], nac_params['dielectric'], ph_nacl.primitive)
@ -67,6 +67,14 @@ def test_symmetrize_borns_and_epsilon(ph_nacl):
np.testing.assert_allclose(epsilon, nac_params['dielectric'], atol=1e-8)
def test_symmetrize_borns_and_epsilon_tio2(ph_tio2):
nac_params = ph_tio2.nac_params
borns, epsilon = symmetrize_borns_and_epsilon(
nac_params['born'], nac_params['dielectric'], ph_tio2.primitive)
# np.testing.assert_allclose(borns, nac_params['born'], atol=1e-8)
np.testing.assert_allclose(epsilon, nac_params['dielectric'], atol=1e-8)
def test_with_pmat_and_smat(ph_nacl):
pcell = ph_nacl.primitive
scell = ph_nacl.supercell