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"""Tests for routines in force_constants.py."""
import numpy as np
import pytest
from phonopy import Phonopy
from phonopy.harmonic.force_constants import (
cutoff_force_constants,
rearrange_force_constants_array,
)
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.structure.cells import get_primitive, isclose
def test_fc(ph_nacl: Phonopy):
"""Test of force constants calculation with fcsym by NaCl."""
fc_1_10_ref = [
-0.037549,
0.000000,
0.000000,
0.000000,
0.002415,
-0.001746,
0.000000,
-0.001746,
0.002415,
]
fc_1_10 = ph_nacl.force_constants[1, 10]
# print("".join(["%f, " % v for v in fc_1_10.ravel()]))
np.testing.assert_allclose(fc_1_10.ravel(), fc_1_10_ref, atol=1e-5)
def test_fc_nofcsym(ph_nacl_nofcsym: Phonopy):
"""Test of force constants calculation without fcsym by NaCl."""
fc_1_10_nofcsym_ref = [
-0.005051,
0.000000,
0.000000,
0.000000,
0.094457,
0.000000,
0.000000,
0.000000,
-0.020424,
]
fc_1_10 = ph_nacl_nofcsym.force_constants[1, 10]
# print("".join(["%f, " % v for v in fc_1_10.ravel()]))
np.testing.assert_allclose(fc_1_10.ravel(), fc_1_10_nofcsym_ref, atol=1e-5)
def test_fc_compact_fcsym(ph_nacl_compact_fcsym: Phonopy):
"""Test of force constants calculation in compact format with fcsym by NaCl."""
fc_1_10_compact_fcsym_ref = [
-0.004481,
0.000000,
0.000000,
0.000000,
0.095230,
0.000000,
0.000000,
0.000000,
-0.019893,
]
fc_1_10 = ph_nacl_compact_fcsym.force_constants[1, 10]
# print("".join(["%f, " % v for v in fc_1_10.ravel()]))
np.testing.assert_allclose(fc_1_10.ravel(), fc_1_10_compact_fcsym_ref, atol=1e-5)
def test_fc_compact_symfc(ph_nacl_rd_symfc: Phonopy):
"""Test of force constants calculation in compact format using symfc by NaCl."""
fc_1_10_compact_symfc_ref = [
-6.777705e-03,
0,
0,
0,
9.591639e-02,
0,
0,
0,
-2.087195e-02,
]
fc_1_10 = ph_nacl_rd_symfc.force_constants[1, 10]
# print("".join(["%f, " % v for v in fc_1_10.ravel()]))
np.testing.assert_allclose(fc_1_10.ravel(), fc_1_10_compact_symfc_ref, atol=1e-5)
@pytest.mark.parametrize("is_compact", [False, True])
def test_fc_cutoff_radius(ph_nacl: Phonopy, ph_nacl_compact_fcsym: Phonopy, is_compact):
"""Test of cutoff radius of force constants calculation by NaCl."""
if is_compact:
ph = ph_nacl_compact_fcsym
else:
ph = ph_nacl
# Need restore fc because fc are overwritten.
fc_orig = ph.force_constants.copy()
ph.set_force_constants_zero_with_radius(4.0)
changed = np.abs(fc_orig - ph.force_constants) > 1e-8
ph.force_constants = fc_orig
if is_compact:
assert np.sum(changed) == 534
else:
assert np.sum(changed) == 17088
@pytest.mark.parametrize(
"is_compact,store_dense_svecs",
[(False, False), (False, True), (True, False), (True, True)],
)
def test_fc_cutoff_radius_svecs(
ph_nacl: Phonopy, ph_nacl_compact_fcsym: Phonopy, is_compact, store_dense_svecs
):
"""Test of cutoff radius with dense-svecs format by NaCl."""
if is_compact:
ph = ph_nacl_compact_fcsym
else:
ph = ph_nacl
fc = ph.force_constants.copy()
primitive_matrix = np.dot(np.linalg.inv(ph.supercell_matrix), ph.primitive_matrix)
primitive = get_primitive(
ph.supercell, primitive_matrix, store_dense_svecs=store_dense_svecs
)
cutoff_force_constants(fc, ph.supercell, primitive, 4.0)
changed = np.abs(ph.force_constants - fc) > 1e-8
if is_compact:
assert np.sum(changed) == 534
else:
assert np.sum(changed) == 17088
def test_rearrange_force_constants_array(
nacl_unitcell_order1: PhonopyAtoms,
nacl_unitcell_order2: PhonopyAtoms,
ph_nacl: Phonopy,
):
"""Test of rearrange_force_constants_array."""
ph1 = ph_nacl
assert isclose(nacl_unitcell_order1, ph1.unitcell)
fc = ph1.force_constants
assert fc.shape[0] == fc.shape[1]
ph2 = Phonopy(
nacl_unitcell_order2,
supercell_matrix=[2, 2, 2],
primitive_matrix="F",
)
re_fc, indices = rearrange_force_constants_array(fc, ph1.supercell, ph2.supercell)
ph1.run_qpoints([[0.5, 0.5, 0.5]])
freq1 = ph1.get_qpoints_dict()["frequencies"]
ph2.force_constants = re_fc
ph2.run_qpoints([[0.5, 0.5, 0.5]])
freq2 = ph2.get_qpoints_dict()["frequencies"]
np.testing.assert_allclose(fc[indices[3], indices[3]], re_fc[3, 3])
np.testing.assert_allclose(freq1, freq2)
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