scnc
/
phonopy
mirror of https://github.com/phonopy/phonopy.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Move compare_cells methods to be shared

This commit is contained in:
Atsushi Togo 2020-11-16 14:18:36 +09:00
parent e150388222
commit 727623e0bb
12 changed files with 153 additions and 51 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

0
test/__init__.py
View File

36
test/conftest.py
View File

@ -1,6 +1,7 @@
import os
import pytest
import phonopy
import numpy as np
from phonopy.structure.atoms import PhonopyAtoms
current_dir = os.path.dirname(os.path.abspath(__file__))
@ -121,3 +122,38 @@ def convcell_cr():
return PhonopyAtoms(cell=lattice,
scaled_positions=points,
symbols=symbols)
@pytest.fixture(scope='session')
def helper_methods():
class HelperMethods(object):
@staticmethod
def compare_cells_with_order(cell, cell_ref):
np.testing.assert_allclose(cell.cell, cell_ref.cell, atol=1e-5)
diff = cell.scaled_positions - cell_ref.scaled_positions
diff -= np.rint(diff)
dist = (np.dot(diff, cell.cell) ** 2).sum(axis=1)
assert (dist < 1e-5).all()
np.testing.assert_array_equal(cell.numbers, cell_ref.numbers)
np.testing.assert_allclose(cell.masses, cell_ref.masses, atol=1e-5)
@staticmethod
def compare_cells(cell, cell_ref):
np.testing.assert_allclose(cell.cell, cell_ref.cell, atol=1e-5)
indices = []
for pos in cell.scaled_positions:
diff = cell_ref.scaled_positions - pos
diff -= np.rint(diff)
dist = (np.dot(diff, cell.cell) ** 2).sum(axis=1)
matches = np.where(dist < 1e-5)[0]
assert len(matches) == 1
indices.append(matches[0])
np.testing.assert_array_equal(cell.numbers,
cell_ref.numbers[indices])
np.testing.assert_allclose(cell.masses, cell_ref.masses[indices],
atol=1e-5)
return HelperMethods

0
test/harmonic/__init__.py
View File

0
test/interface/__init__.py
View File

0
test/phonon/__init__.py
View File

0
test/qha/__init__.py
View File

0
test/spectrum/__init__.py
View File

0
test/structure/__init__.py
View File

80
test/structure/test_cells.py
View File

@ -1,4 +1,5 @@
import os
import pytest
import numpy as np
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.structure.cells import (
@ -38,60 +39,64 @@ def _test_compute_permutation(ph):
assert ((np.dot(diff, plat) ** 2).sum(axis=1) < symprec).all()
def test_get_supercell_convcell_sio2(convcell_sio2):
_test_get_supercell_convcell_sio2(convcell_sio2, is_old_style=True)
@pytest.mark.parametrize("nosnf", [True, False])
def test_get_supercell_convcell_sio2(convcell_sio2, nosnf, helper_methods):
_test_get_supercell_convcell_sio2(convcell_sio2,
helper_methods,
is_old_style=nosnf)
def test_get_supercell_convcell_sio2_snf(convcell_sio2):
_test_get_supercell_convcell_sio2(convcell_sio2, is_old_style=False)
@pytest.mark.parametrize("nosnf", [True, False])
def test_get_supercell_primcell_si(primcell_si, nosnf, helper_methods):
_test_get_supercell_primcell_si(primcell_si,
helper_methods,
is_old_style=nosnf)
def test_get_supercell_primcell_si(primcell_si):
_test_get_supercell_primcell_si(primcell_si, is_old_style=True)
def test_get_supercell_primcell_si_snf(primcell_si):
_test_get_supercell_primcell_si(primcell_si, is_old_style=False)
def test_get_supercell_nacl_snf(convcell_nacl):
def test_get_supercell_nacl_snf(convcell_nacl, helper_methods):
cell = convcell_nacl
smat = [[-1, 1, 1], [1, -1, 1], [1, 1, -1]]
scell = get_supercell(cell, smat, is_old_style=True)
scell_snf = get_supercell(cell, smat, is_old_style=False)
_compare_cells(scell, scell_snf)
helper_methods.compare_cells(scell, scell_snf)
def _test_get_supercell_convcell_sio2(convcell_sio2, is_old_style=True):
def _test_get_supercell_convcell_sio2(convcell_sio2,
helper_methods,
is_old_style=True):
smat = np.diag([1, 2, 3])
fname = "SiO2-123.yaml"
scell = get_supercell(convcell_sio2, smat, is_old_style=is_old_style)
cell_ref = read_cell_yaml(os.path.join(data_dir, fname))
if is_old_style is True:
_compare_cells_with_order(scell, cell_ref)
helper_methods.compare_cells_with_order(scell, cell_ref)
else:
_compare_cells(scell, cell_ref)
helper_methods.compare_cells(scell, cell_ref)
def _test_get_supercell_primcell_si(primcell_si, is_old_style=True):
def _test_get_supercell_primcell_si(primcell_si,
helper_methods,
is_old_style=True):
smat = [[-1, 1, 1], [1, -1, 1], [1, 1, -1]]
fname = "Si-conv.yaml"
scell = get_supercell(primcell_si, smat, is_old_style=is_old_style)
cell_ref = read_cell_yaml(os.path.join(data_dir, fname))
if is_old_style is True:
_compare_cells_with_order(scell, cell_ref)
helper_methods.compare_cells_with_order(scell, cell_ref)
else:
_compare_cells(scell, cell_ref)
helper_methods.compare_cells(scell, cell_ref)
def test_get_primitive_convcell_nacl(convcell_nacl, primcell_nacl):
def test_get_primitive_convcell_nacl(convcell_nacl,
primcell_nacl,
helper_methods):
pcell = get_primitive(convcell_nacl, [[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]])
_compare_cells_with_order(pcell, primcell_nacl)
helper_methods.compare_cells_with_order(pcell, primcell_nacl)
def test_TrimmedCell(convcell_nacl):
def test_TrimmedCell(convcell_nacl, helper_methods):
pmat = [[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]]
@ -113,31 +118,4 @@ def test_TrimmedCell(convcell_nacl):
tcell2 = TrimmedCell(pmat2, scell2)
tcell3 = TrimmedCell(pmat3, scell3_swap,
positions_to_reorder=tcell2.scaled_positions)
_compare_cells_with_order(tcell2, tcell3)
def _compare_cells_with_order(cell, cell_ref):
np.testing.assert_allclose(cell.cell, cell_ref.cell, atol=1e-5)
diff = cell.scaled_positions - cell_ref.scaled_positions
diff -= np.rint(diff)
dist = (np.dot(diff, cell.cell) ** 2).sum(axis=1)
assert (dist < 1e-5).all()
np.testing.assert_array_equal(cell.numbers, cell_ref.numbers)
np.testing.assert_allclose(cell.masses, cell_ref.masses, atol=1e-5)
def _compare_cells(cell, cell_ref):
np.testing.assert_allclose(cell.cell, cell_ref.cell, atol=1e-5)
indices = []
for pos in cell.scaled_positions:
diff = cell_ref.scaled_positions - pos
diff -= np.rint(diff)
dist = (np.dot(diff, cell.cell) ** 2).sum(axis=1)
matches = np.where(dist < 1e-5)[0]
assert len(matches) == 1
indices.append(matches[0])
np.testing.assert_array_equal(cell.numbers, cell_ref.numbers[indices])
np.testing.assert_allclose(cell.masses, cell_ref.masses[indices],
atol=1e-5)
helper_methods.compare_cells_with_order(tcell2, tcell3)

22
test/structure/test_grid_points.py
View File

@ -1,8 +1,12 @@
import os
import pytest
import numpy as np
from phonopy.structure.grid_points import (
GridPoints, GeneralizedRegularGridPoints)
current_dir = os.path.dirname(os.path.abspath(__file__))
ga234 = [[0, 0, 0],
[1, 0, 0],
[0, 1, 0],
@ -196,3 +200,21 @@ def test_GeneralizedRegularGridPoints(ph_tio2, suggest):
assert (grgp.grid_address[253] == [0, 5, 13]).all()
np.testing.assert_allclose(grgp.qpoints[253],
[-0.4375, -0.3125, -0.16666667])
def test_watch_GeneralizedRegularGridPoints(ph_tio2, helper_methods):
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.interface.phonopy_yaml import read_cell_yaml
grgp = GeneralizedRegularGridPoints(ph_tio2.unitcell, 10)
tmat = grgp.matrix_to_primitive
# direct basis vectors in row vectors
plat = np.dot(tmat.T, ph_tio2.unitcell.cell)
# reciprocal basis vectors in row vectors (10 times magnified)
rec_plat = np.linalg.inv(plat).T * 10
nums = [1, ] * len(grgp.qpoints)
cell = PhonopyAtoms(cell=rec_plat,
scaled_positions=grgp.qpoints,
numbers=nums)
yaml_filename = os.path.join(current_dir, "tio2_qpoints.yaml")
cell_ref = read_cell_yaml(yaml_filename)
helper_methods.compare_cells(cell, cell_ref)

66
test/structure/tio2_qpoints.yaml Normal file
View File

@ -0,0 +1,66 @@
phonopy:
version: 2.8.1
physical_unit:
atomic_mass: "AMU"
unit_cell:
lattice:
- [ 0.000000000000001, 2.648206303003766, 1.043788351328262 ] # a
- [ 2.648206303003766, 0.000000000000000, 1.043788351328262 ] # b
- [ 2.648206303003766, 2.648206303003766, -0.000000000000000 ] # c
points:
- symbol: H # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 1.007940
- symbol: H # 2
coordinates: [ 0.166666666666667, -0.166666666666667, -0.166666666666667 ]
mass: 1.007940
- symbol: H # 3
coordinates: [ 0.333333333333333, -0.333333333333333, -0.333333333333333 ]
mass: 1.007940
- symbol: H # 4
coordinates: [ 0.500000000000000, -0.500000000000000, -0.500000000000000 ]
mass: 1.007940
- symbol: H # 5
coordinates: [ -0.333333333333333, 0.333333333333333, 0.333333333333333 ]
mass: 1.007940
- symbol: H # 6
coordinates: [ -0.166666666666667, 0.166666666666667, 0.166666666666667 ]
mass: 1.007940
- symbol: H # 7
coordinates: [ 0.000000000000000, 0.000000000000000, 0.333333333333333 ]
mass: 1.007940
- symbol: H # 8
coordinates: [ 0.166666666666667, -0.166666666666667, 0.166666666666667 ]
mass: 1.007940
- symbol: H # 9
coordinates: [ 0.333333333333333, -0.333333333333333, 0.000000000000000 ]
mass: 1.007940
- symbol: H # 10
coordinates: [ 0.500000000000000, -0.500000000000000, -0.166666666666667 ]
mass: 1.007940
- symbol: H # 11
coordinates: [ -0.333333333333333, 0.333333333333333, -0.333333333333333 ]
mass: 1.007940
- symbol: H # 12
coordinates: [ -0.166666666666667, 0.166666666666667, -0.500000000000000 ]
mass: 1.007940
- symbol: H # 13
coordinates: [ 0.000000000000000, 0.000000000000000, -0.333333333333333 ]
mass: 1.007940
- symbol: H # 14
coordinates: [ 0.166666666666667, -0.166666666666667, 0.500000000000000 ]
mass: 1.007940
- symbol: H # 15
coordinates: [ 0.333333333333333, -0.333333333333333, 0.333333333333333 ]
mass: 1.007940
- symbol: H # 16
coordinates: [ 0.500000000000000, -0.500000000000000, 0.166666666666667 ]
mass: 1.007940
- symbol: H # 17
coordinates: [ -0.333333333333333, 0.333333333333333, 0.000000000000000 ]
mass: 1.007940
- symbol: H # 18
coordinates: [ -0.166666666666667, 0.166666666666667, -0.166666666666667 ]
mass: 1.007940

0
test/unfolding/__init__.py
View File