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Fix ddm with Wang's NAC method

This commit is contained in:
Atsushi Togo 2024-07-16 18:04:59 +09:00
parent 984914ca4d
commit 7152c9cb18
10 changed files with 274 additions and 143 deletions
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24
c/_phonopy.cpp
View File

@ -247,15 +247,17 @@ void py_get_recip_dipole_dipole_q0(nb::ndarray<> py_dd_q0,
void py_get_derivative_dynmat(
nb::ndarray<> py_derivative_dynmat, nb::ndarray<> py_force_constants,
nb::ndarray<> py_q_vector, nb::ndarray<> py_lattice, nb::ndarray<> py_svecs,
nb::ndarray<> py_multi, nb::ndarray<> py_masses, nb::ndarray<> py_s2p_map,
nb::ndarray<> py_p2s_map, double nac_factor, nb::ndarray<> py_born,
nb::ndarray<> py_dielectric, nb::ndarray<> py_q_direction, long is_nac,
long is_nac_q_zero, long use_openmp) {
nb::ndarray<> py_q_vector, nb::ndarray<> py_lattice,
nb::ndarray<> py_reclat, nb::ndarray<> py_svecs, nb::ndarray<> py_multi,
nb::ndarray<> py_masses, nb::ndarray<> py_s2p_map, nb::ndarray<> py_p2s_map,
double nac_factor, nb::ndarray<> py_born, nb::ndarray<> py_dielectric,
nb::ndarray<> py_q_direction, long is_nac, long is_nac_q_zero,
long use_openmp) {
double(*ddm)[2];
double *fc;
double *q_vector;
double *lat;
double *lattice;
double *reclat;
double(*svecs)[3];
double *masses;
long(*multi)[2];
@ -271,7 +273,8 @@ void py_get_derivative_dynmat(
ddm = (double(*)[2])py_derivative_dynmat.data();
fc = (double *)py_force_constants.data();
q_vector = (double *)py_q_vector.data();
lat = (double *)py_lattice.data();
lattice = (double *)py_lattice.data();
reclat = (double *)py_reclat.data();
svecs = (double(*)[3])py_svecs.data();
masses = (double *)py_masses.data();
multi = (long(*)[2])py_multi.data();
@ -288,9 +291,10 @@ void py_get_derivative_dynmat(
q_dir = (double *)py_q_direction.data();
}
phpy_get_derivative_dynmat_at_q(
ddm, num_patom, num_satom, fc, q_vector, lat, svecs, multi, masses,
s2p_map, p2s_map, nac_factor, born, epsilon, q_dir, is_nac, use_openmp);
phpy_get_derivative_dynmat_at_q(ddm, num_patom, num_satom, fc, q_vector,
lattice, reclat, svecs, multi, masses,
s2p_map, p2s_map, nac_factor, born, epsilon,
q_dir, is_nac, use_openmp);
}
void py_get_thermal_properties(nb::ndarray<> py_thermal_props,

60
c/derivative_dynmat.c
View File

@ -35,6 +35,7 @@
#include "derivative_dynmat.h"
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#define PI 3.14159265358979323846
@ -44,8 +45,7 @@ static void get_derivative_dynmat_at_q(
const long num_patom, const long num_satom, const double *fc,
const double *q, const double *lattice, /* column vector */
const double (*svecs)[3], const long (*multi)[2], const double *mass,
const long *s2p_map, const long *p2s_map, const double nac_factor,
const double *born, const double *dielectric);
const long *s2p_map, const long *p2s_map);
static void get_derivative_nac(double *ddnac, double *dnac,
const long num_patom, const double *lattice,
const double *mass, const double *q,
@ -63,6 +63,7 @@ void ddm_get_derivative_dynmat_at_q(
double (*derivative_dynmat)[2], const long num_patom, const long num_satom,
const double *fc, const double *q,
const double *lattice, /* column vector */
const double *reclat, /* column vector */
const double (*svecs)[3], const long (*multi)[2], const double *mass,
const long *s2p_map, const long *p2s_map, const double nac_factor,
const double *born, const double *dielectric, const double *q_direction,
@ -74,8 +75,8 @@ void ddm_get_derivative_dynmat_at_q(
if (is_nac) {
ddnac = (double *)malloc(sizeof(double) * num_patom * num_patom * 27);
dnac = (double *)malloc(sizeof(double) * num_patom * num_patom * 9);
factor = nac_factor * num_patom / num_satom;
get_derivative_nac(ddnac, dnac, num_patom, lattice, mass, q, born,
factor = (nac_factor * num_patom) / num_satom;
get_derivative_nac(ddnac, dnac, num_patom, reclat, mass, q, born,
dielectric, q_direction, factor);
}
@ -89,15 +90,15 @@ void ddm_get_derivative_dynmat_at_q(
get_derivative_dynmat_at_q(derivative_dynmat, i, j, ddnac, dnac,
is_nac, num_patom, num_satom, fc, q,
lattice, svecs, multi, mass, s2p_map,
p2s_map, nac_factor, born, dielectric);
p2s_map);
}
} else {
for (i = 0; i < num_patom; i++) {
for (j = 0; j < num_patom; j++) {
get_derivative_dynmat_at_q(
derivative_dynmat, i, j, ddnac, dnac, is_nac, num_patom,
num_satom, fc, q, lattice, svecs, multi, mass, s2p_map,
p2s_map, nac_factor, born, dielectric);
get_derivative_dynmat_at_q(derivative_dynmat, i, j, ddnac, dnac,
is_nac, num_patom, num_satom, fc, q,
lattice, svecs, multi, mass, s2p_map,
p2s_map);
}
}
}
@ -126,14 +127,15 @@ void ddm_get_derivative_dynmat_at_q(
}
}
void get_derivative_dynmat_at_q(
double (*derivative_dynmat)[2], const long i, const long j,
const double *ddnac, const double *dnac, const long is_nac,
const long num_patom, const long num_satom, const double *fc,
const double *q, const double *lattice, /* column vector */
const double (*svecs)[3], const long (*multi)[2], const double *mass,
const long *s2p_map, const long *p2s_map, const double nac_factor,
const double *born, const double *dielectric) {
void get_derivative_dynmat_at_q(double (*derivative_dynmat)[2], const long i,
const long j, const double *ddnac,
const double *dnac, const long is_nac,
const long num_patom, const long num_satom,
const double *fc, const double *q,
const double *lattice, /* column vector */
const double (*svecs)[3],
const long (*multi)[2], const double *mass,
const long *s2p_map, const long *p2s_map) {
long k, l, m, n, adrs, m_pair, i_pair, svecs_adrs;
double coef[3], real_coef[3], imag_coef[3];
double c, s, phase, mass_sqrt, fc_elem, real_phase, imag_phase;
@ -237,35 +239,21 @@ void get_derivative_dynmat_at_q(
/* D_nac = a * AB/C */
/* dD_nac = a * D_nac * (A'/A + B'/B - C'/C) */
static void get_derivative_nac(double *ddnac, double *dnac,
const long num_patom, const double *lattice,
const long num_patom, const double *reclat,
const double *mass, const double *q,
const double *born, const double *dielectric,
const double *q_direction, const double factor) {
long i, j, k, l, m;
double a, b, c, da, db, dc, volume, mass_sqrt;
double q_cart[3], rec_lat[9];
volume = lattice[0] * (lattice[4] * lattice[8] - lattice[5] * lattice[7]) +
lattice[1] * (lattice[5] * lattice[6] - lattice[3] * lattice[8]) +
lattice[2] * (lattice[3] * lattice[7] - lattice[4] * lattice[6]);
rec_lat[0] = (lattice[4] * lattice[8] - lattice[5] * lattice[7]) / volume;
rec_lat[1] = (lattice[5] * lattice[6] - lattice[3] * lattice[8]) / volume;
rec_lat[2] = (lattice[3] * lattice[7] - lattice[4] * lattice[6]) / volume;
rec_lat[3] = (lattice[7] * lattice[2] - lattice[8] * lattice[1]) / volume;
rec_lat[4] = (lattice[8] * lattice[0] - lattice[6] * lattice[2]) / volume;
rec_lat[5] = (lattice[6] * lattice[1] - lattice[7] * lattice[0]) / volume;
rec_lat[6] = (lattice[1] * lattice[5] - lattice[2] * lattice[4]) / volume;
rec_lat[7] = (lattice[2] * lattice[3] - lattice[0] * lattice[5]) / volume;
rec_lat[8] = (lattice[0] * lattice[4] - lattice[1] * lattice[3]) / volume;
double a, b, c, da, db, dc, mass_sqrt;
double q_cart[3];
for (i = 0; i < 3; i++) {
q_cart[i] = 0;
for (j = 0; j < 3; j++) {
if (q_direction) {
q_cart[i] += rec_lat[i * 3 + j] * q_direction[j];
q_cart[i] += reclat[i * 3 + j] * q_direction[j];
} else {
q_cart[i] += rec_lat[i * 3 + j] * q[j];
q_cart[i] += reclat[i * 3 + j] * q[j];
}
}
}

1
c/derivative_dynmat.h
View File

@ -39,6 +39,7 @@ void ddm_get_derivative_dynmat_at_q(
double (*derivative_dynmat)[2], const long num_patom, const long num_satom,
const double *fc, const double *q,
const double *lattice, /* column vector */
const double *reclat, /* column vector */
const double (*svecs)[3], const long (*multi)[2], const double *mass,
const long *s2p_map, const long *p2s_map, const double nac_factor,
const double *born, const double *dielectric, const double *q_direction,

7
c/phonopy.c
View File

@ -134,14 +134,15 @@ void phpy_get_derivative_dynmat_at_q(
double (*derivative_dynmat)[2], const long num_patom, const long num_satom,
const double *fc, const double *q,
const double *lattice, /* column vector */
const double *reclat, /* column vector */
const double (*svecs)[3], const long (*multi)[2], const double *mass,
const long *s2p_map, const long *p2s_map, const double nac_factor,
const double *born, const double *dielectric, const double *q_direction,
const long is_nac, const long use_openmp) {
ddm_get_derivative_dynmat_at_q(derivative_dynmat, num_patom, num_satom, fc,
q, lattice, svecs, multi, mass, s2p_map,
p2s_map, nac_factor, born, dielectric,
q_direction, is_nac, use_openmp);
q, lattice, reclat, svecs, multi, mass,
s2p_map, p2s_map, nac_factor, born,
dielectric, q_direction, is_nac, use_openmp);
}
void phpy_get_relative_grid_address(long relative_grid_address[24][4][3],

1
c/phonopy.h
View File

@ -82,6 +82,7 @@ void phpy_get_derivative_dynmat_at_q(
double (*derivative_dynmat)[2], const long num_patom, const long num_satom,
const double *fc, const double *q,
const double *lattice, /* column vector */
const double *reclat, /* column vector */
const double (*svecs)[3], const long (*multi)[2], const double *mass,
const long *s2p_map, const long *p2s_map, const double nac_factor,
const double *born, const double *dielectric, const double *q_direction,

35
phonopy/harmonic/derivative_dynmat.py
View File

@ -55,6 +55,8 @@ class DerivativeOfDynamicalMatrix:
"""
Q_DIRECTION_TOLERANCE = 1e-5
def __init__(self, dynamical_matrix: Union[DynamicalMatrix, DynamicalMatrixNAC]):
"""Init method.
@ -83,7 +85,6 @@ class DerivativeOfDynamicalMatrix:
self._multi = multi
else:
self._svecs, self._multi = sparse_to_dense_svecs(svecs, multi)
# self._svecs, self._multi = self._pcell.get_smallest_vectors()
self._ddm = None
@ -134,30 +135,34 @@ class DerivativeOfDynamicalMatrix:
import phonopy._phonopy as phonoc
num_patom = len(self._p2s_map)
fc = self._force_constants
ddm = np.zeros(
(3, num_patom * 3, num_patom * 3),
dtype=("c%d" % (np.dtype("double").itemsize * 2)),
)
reclat = np.array(np.linalg.inv(self._pcell.cell), dtype="double", order="C")
is_nac = False
is_nac_q_zero = True
born = np.zeros(9) # dummy value
dielectric = np.zeros(9) # dummy value
nac_factor = 0 # dummy value
q_dir = np.zeros(3) # dummy value
if isinstance(self._dynmat, DynamicalMatrixNAC):
is_nac = True
born = self._dynmat.born
dielectric = self._dynmat.dielectric_constant
nac_factor = self._dynmat.nac_factor
if q_direction is None:
q_dir = np.zeros(3)
is_nac_q_zero = True
q_norm = np.linalg.norm(reclat @ q)
if q_norm < self.Q_DIRECTION_TOLERANCE:
is_nac = False
else:
is_nac_q_zero = True
else:
q_dir = np.array(q_direction, dtype="double", order="C")
q_dir = np.array(q_direction, dtype="double")
is_nac_q_zero = False
else:
born = np.zeros(0) # dummy value
dielectric = np.zeros(0) # dummy value
nac_factor = 0 # dummy value
q_dir = np.zeros(3) # dummy value
is_nac = False
is_nac_q_zero = True
if fc.shape[0] == fc.shape[1]: # full fc
phonoc.derivative_dynmat(
@ -165,6 +170,7 @@ class DerivativeOfDynamicalMatrix:
fc,
np.array(q, dtype="double"),
np.array(self._pcell.cell.T, dtype="double", order="C"),
reclat,
self._svecs,
self._multi,
self._pcell.masses,
@ -184,6 +190,7 @@ class DerivativeOfDynamicalMatrix:
fc,
np.array(q, dtype="double"),
np.array(self._pcell.cell.T, dtype="double", order="C"),
np.array(np.linalg.inv(self._pcell.cell), dtype="double", order="C"),
self._svecs,
self._multi,
self._pcell.masses,
@ -236,7 +243,7 @@ class DerivativeOfDynamicalMatrix:
continue
multi = multiplicity[k, i]
vecs_multi = vecs[k, i, :multi]
vecs_multi = vecs[multi[1] : multi[1] + multi[0]]
phase_multi = np.exp(
[np.vdot(vec, q) * 2j * np.pi for vec in vecs_multi]
)
@ -263,7 +270,7 @@ class DerivativeOfDynamicalMatrix:
):
ddm_elem += d_nac[ll, i, j] * phase_multi.sum()
ddm_local[ll] += ddm_elem / mass / multi
ddm_local[ll] += ddm_elem / mass / multi[0]
ddm[:, (i * 3) : (i * 3 + 3), (j * 3) : (j * 3 + 3)] = ddm_local

20
test/conftest.py
View File

@ -43,6 +43,26 @@ def ph_nacl() -> Phonopy:
)
@pytest.fixture(scope="session")
def ph_nacl_wang() -> Phonopy:
"""Return Phonopy class instance of NaCl 2x2x2."""
yaml_filename = cwd / "phonopy_disp_NaCl.yaml"
force_sets_filename = cwd / "FORCE_SETS_NaCl"
born_filename = cwd / "BORN_NaCl"
ph = phonopy.load(
yaml_filename,
force_sets_filename=force_sets_filename,
born_filename=born_filename,
is_compact_fc=False,
log_level=1,
produce_fc=True,
)
nac_params = ph.nac_params
nac_params["method"] = "wang"
ph.nac_params = nac_params
return ph
@pytest.fixture(scope="session")
def ph_nacl_nofcsym() -> Phonopy:
"""Return Phonopy class instance of NaCl 2x2x2 without symmetrizing fc2."""

197
test/harmonic/test_derivative_dynmat.py
View File

@ -6,65 +6,129 @@ from phonopy import Phonopy
from phonopy.harmonic.derivative_dynmat import DerivativeOfDynamicalMatrix
ddm_ph_nacl = [
-0.2568036,
0.6947168,
0.0337825,
0.0342511,
0.0337825,
0.0342511,
0.6947168,
0.0561427,
0.0342511,
0.1430624,
0.0342511,
0.1430624,
2.0750808,
-1.5152406,
2.0750808,
-1.5152406,
-1.5152406,
1.3859454,
-1.5152406,
1.3859454,
2.0750808,
-1.5152406,
2.0750808,
-1.5152406,
-1.5152406,
1.3859454,
-1.5152406,
1.3859454,
[
-0.2568036,
0.6947168,
0.0337825,
0.0342511,
0.0337825,
0.0342511,
0.6947168,
0.0561427,
0.0342511,
0.1430624,
0.0342511,
0.1430624,
2.0750808,
-1.5152406,
2.0750808,
-1.5152406,
-1.5152406,
1.3859454,
-1.5152406,
1.3859454,
2.0750808,
-1.5152406,
2.0750808,
-1.5152406,
-1.5152406,
1.3859454,
-1.5152406,
1.3859454,
],
[
-0.4582279,
1.1733186,
0.0783508,
0.0543731,
0.0783508,
0.0543731,
1.1733186,
0.0724132,
0.0543731,
0.2215595,
0.0543731,
0.2215595,
0.5943896,
-0.2136538,
0.5943896,
-0.2136538,
-0.2136538,
0.4540728,
-0.2136538,
0.4540728,
0.5943896,
-0.2136538,
0.5943896,
-0.2136538,
-0.2136538,
0.4540728,
-0.2136538,
0.4540728,
],
]
ddm_ph_nacl_nonac = [
0.8832905,
-0.2233653,
0.0337825,
0.0342511,
0.0337825,
0.0342511,
-0.2233653,
0.7954454,
0.0342511,
0.1430624,
0.0342511,
0.1430624,
0.3493735,
-0.1255825,
0.3493735,
-0.1255825,
-0.1255825,
0.2668973,
-0.1255825,
0.2668973,
0.3493735,
-0.1255825,
0.3493735,
-0.1255825,
-0.1255825,
0.2668973,
-0.1255825,
0.2668973,
[
0.8832905,
-0.2233653,
0.0337825,
0.0342511,
0.0337825,
0.0342511,
-0.2233653,
0.7954454,
0.0342511,
0.1430624,
0.0342511,
0.1430624,
0.3493735,
-0.1255825,
0.3493735,
-0.1255825,
-0.1255825,
0.2668973,
-0.1255825,
0.2668973,
0.3493735,
-0.1255825,
0.3493735,
-0.1255825,
-0.1255825,
0.2668973,
-0.1255825,
0.2668973,
],
[
0.2826501,
0.5767127,
0.0783508,
0.0543731,
0.0783508,
0.0543731,
0.5767127,
0.5528413,
0.0543731,
0.2215595,
0.0543731,
0.2215595,
0.5943896,
-0.2136538,
0.5943896,
-0.2136538,
-0.2136538,
0.4540728,
-0.2136538,
0.4540728,
0.5943896,
-0.2136538,
0.5943896,
-0.2136538,
-0.2136538,
0.4540728,
-0.2136538,
0.4540728,
],
]
@ -73,6 +137,11 @@ def test_ddm_nac(ph_nacl: Phonopy):
_assert(ph_nacl, ddm_ph_nacl)
def test_ddm_nac_wang(ph_nacl_wang: Phonopy):
"""Test by NaCl with Wang's NAC."""
_assert(ph_nacl_wang, ddm_ph_nacl, show=True)
def test_ddm_nac_compact(ph_nacl_compact_fcsym: Phonopy):
"""Test by NaCl with compact fc."""
_assert(ph_nacl_compact_fcsym, ddm_ph_nacl)
@ -91,13 +160,14 @@ def test_ddm_nonac_compact(ph_nacl_nonac_compact_fc: Phonopy):
def _assert(ph: Phonopy, ref_vals, show=False):
dynmat = ph.dynamical_matrix
ddynmat = DerivativeOfDynamicalMatrix(dynmat)
ddynmat.run([0, 0.1, 0.1])
ddm = ddynmat.d_dynamical_matrix
condition = np.abs(ddm) > 1e-8
vals = np.extract(condition, ddm).real
if show:
_show(vals)
np.testing.assert_allclose(vals, ref_vals, rtol=0, atol=1e-7)
for i, q in enumerate(([0, 0.1, 0.1], [0, 0.25, 0.25])):
ddynmat.run(q)
ddm = ddynmat.d_dynamical_matrix
condition = np.abs(ddm) > 1e-8
vals = np.extract(condition, ddm).real
if show:
_show(vals)
np.testing.assert_allclose(vals, ref_vals[i], rtol=0, atol=1e-7)
def _show(vals):
@ -105,3 +175,4 @@ def _show(vals):
print("%.7f, " % v, end="")
if (i + 1) % 5 == 0:
print("")
print("")

37
test/harmonic/test_dynamical_matrix.py
View File

@ -1,10 +1,12 @@
"""Tests for dynamical matrix classes."""
from __future__ import annotations
import numpy as np
import pytest
from phonopy import Phonopy
from phonopy.harmonic.dynamical_matrix import DynamicalMatrixGL
from phonopy.harmonic.dynamical_matrix import DynamicalMatrix, DynamicalMatrixGL
dynmat_ref_000 = [
0.052897,
@ -461,7 +463,12 @@ dynmat_ref_555 = [
@pytest.mark.parametrize(
"is_compact_fc,lang", [(True, "C"), (False, "C"), (True, "Py"), (False, "Py")]
)
def test_dynmat(ph_nacl_nonac, ph_nacl_nonac_compact_fc, is_compact_fc, lang):
def test_dynmat(
ph_nacl_nonac: Phonopy,
ph_nacl_nonac_compact_fc: Phonopy,
is_compact_fc: bool,
lang: str,
):
"""Test dynamical matrix of NaCl in C and python implementations.
1. Without NAC.
@ -478,7 +485,7 @@ def test_dynmat(ph_nacl_nonac, ph_nacl_nonac_compact_fc, is_compact_fc, lang):
@pytest.mark.parametrize("lang", ["C", "Py"])
def test_dynmat_dense_svecs(ph_nacl_nonac_dense_svecs: Phonopy, lang):
def test_dynmat_dense_svecs(ph_nacl_nonac_dense_svecs: Phonopy, lang: str):
"""Test with dense svecs."""
ph = ph_nacl_nonac_dense_svecs
dynmat = ph.dynamical_matrix
@ -563,7 +570,7 @@ def test_dynmat_gonze_lee_short_range_fc(ph_nacl: Phonopy):
)
def test_dynmat_gonze_lee_full_term(ph_nacl):
def test_dynmat_gonze_lee_full_term(ph_nacl: Phonopy):
"""Test with NAC by Gonze and Lee."""
dynmat = ph_nacl.dynamical_matrix
_dynmat = DynamicalMatrixGL(
@ -576,19 +583,13 @@ def test_dynmat_gonze_lee_full_term(ph_nacl):
_test_dynmat_252525(_dynmat, dynmat_gonze_lee_full_ref_252525)
def test_dynmat_wang(ph_nacl):
def test_dynmat_wang(ph_nacl_wang: Phonopy):
"""Test with NAC by Wang et al."""
nac_params = ph_nacl.nac_params
nac_params["method"] = "wang"
ph_nacl.nac_params = nac_params
dynmat = ph_nacl.dynamical_matrix
dynmat = ph_nacl_wang.dynamical_matrix
_test_dynmat_252525(dynmat, dynmat_wang_ref_252525)
# Reset nac_params['method']
nac_params.pop("method")
ph_nacl.nac_params = nac_params
def _test_dynmat(dynmat, lang=None):
def _test_dynmat(dynmat: DynamicalMatrix, lang=None):
dtype_complex = "c%d" % (np.dtype("double").itemsize * 2)
if lang:
dynmat.run([0, 0, 0], lang=lang)
@ -609,7 +610,7 @@ def _test_dynmat(dynmat, lang=None):
np.testing.assert_allclose(dynmat.dynamical_matrix, dynmat_ref, atol=1e-5)
def _test_dynmat_252525(dynmat, dynmat_ref, lang=None):
def _test_dynmat_252525(dynmat: DynamicalMatrix, dynmat_ref: list, lang=None):
dtype_complex = "c%d" % (np.dtype("double").itemsize * 2)
if lang:
dynmat.run([0.25, 0.25, 0.25], lang=lang)
@ -617,7 +618,9 @@ def _test_dynmat_252525(dynmat, dynmat_ref, lang=None):
dynmat.run([0.25, 0.25, 0.25])
# for row in dynmat.dynamical_matrix:
# print("".join(["%f, %f, " % (c.real, c.imag) for c in row]))
dynmat_ref = (
np.array(dynmat_ref, dtype="double").view(dtype=dtype_complex).reshape(6, 6)
np.testing.assert_allclose(
dynmat.dynamical_matrix,
np.array(dynmat_ref, dtype="double").view(dtype=dtype_complex).reshape(6, 6),
atol=1e-5,
)
np.testing.assert_allclose(dynmat.dynamical_matrix, dynmat_ref, atol=1e-5)

35
test/phonon/test_group_velocity.py
View File

@ -39,6 +39,41 @@ def test_gv_nacl(ph_nacl: Phonopy):
# print("".join(["%.8f, " % v for v in line]))
def test_gv_nacl_wang(ph_nacl_wang: Phonopy):
"""Test of GroupVelocity by NaCl with Wang's NAC method.
This test should pass _get_dD_analytical.
"""
gv_ref = [
14.56800976,
14.56800976,
14.56800976,
14.56800976,
14.56800976,
14.56800976,
25.16351730,
25.16351730,
25.16351730,
1.51378156,
1.51378156,
1.51378156,
1.51378156,
1.51378156,
1.51378156,
-7.84946438,
-7.84946438,
-7.84946438,
]
gv = GroupVelocity(
ph_nacl_wang.dynamical_matrix, symmetry=ph_nacl_wang.primitive_symmetry
)
gv.run([[0.1, 0.1, 0.1]])
# for line in gv.group_velocities[0]:
# print("".join(["%.8f, " % v for v in line]))
np.testing.assert_allclose(gv.group_velocities[0].ravel(), gv_ref, atol=1e-5)
def test_gv_si(ph_si: Phonopy):
"""Test of GroupVelocity by Si.