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phono3py
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Add test for SupercellPhonon

This commit is contained in:
Atsushi Togo 2020-08-25 07:24:35 +09:00
parent 35e210eca9
commit 8514c42a63
3 changed files with 43 additions and 29 deletions
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11
phono3py/sscha/sscha.py
View File

@ -172,11 +172,10 @@ class SupercellPhonon(object):
def __init__(self, supercell, force_constants, factor=VaspToTHz):
self._supercell = supercell
_fc2 = np.swapaxes(force_constants, 1, 2)
self._force_constants = np.array(
_fc2.reshape(-1, np.prod(_fc2.shape[-2:])),
dtype='double', order='C')
_fc2 = _fc2.reshape(-1, np.prod(_fc2.shape[-2:]))
masses = np.repeat(supercell.masses, 3)
dynmat = self._force_constants / np.sqrt(np.outer(masses, masses))
dynmat = np.array(_fc2 / np.sqrt(np.outer(masses, masses)),
dtype='double', order='C')
eigvals, eigvecs = np.linalg.eigh(dynmat)
freqs = np.sqrt(np.abs(eigvals)) * np.sign(eigvals) * factor
self._eigenvalues = np.array(eigvals, dtype='double', order='C')
@ -204,10 +203,6 @@ class SupercellPhonon(object):
def supercell(self):
return self._supercell
@property
def force_constants(self):
return self._force_constants
class DispCorrMatrixMesh(object):
"""Calculate gamma matrix

6
test/conftest.py
View File

@ -12,3 +12,9 @@ def si_pbesol():
return phono3py.load(yaml_filename,
forces_fc3_filename=forces_fc3_filename,
log_level=1)
@pytest.fixture(scope='session')
def si_pbesol_111():
yaml_filename = os.path.join(current_dir, "phono3py_params_Si111.yaml")
return phono3py.load(yaml_filename, log_level=1)

53
test/sscha/test_sscha.py
View File

@ -1,6 +1,6 @@
import numpy as np
from phono3py.sscha.sscha import (
DispCorrMatrix, DispCorrMatrixMesh, SupercellPhonon)
DispCorrMatrix, DispCorrMatrixMesh, SupercellPhonon, LambdaTensor)
from phonopy.phonon.qpoints import QpointsPhonon
@ -10,6 +10,29 @@ si_pbesol_gamma0_0 = [[3.849187e+02, 0, 0],
si_pbesol_gamma1_34 = [[1.886404, -1.549705, -1.126055],
[-1.549705, 1.886404, -1.126055],
[-1.126055, -1.126055, -0.006187]]
si_pbesol_111_freqs = [
0.00000, 0.00000, 0.00000, 4.02839, 4.02839, 4.02839,
4.02839, 4.02839, 4.02839, 12.13724, 12.13724, 12.13724,
12.13724, 12.13724, 12.13724, 13.71746, 13.71746, 13.71746,
13.71746, 13.71746, 13.71746, 15.24974, 15.24974, 15.24974]
def get_supercell_phonon(ph3):
ph3.mesh_numbers = [1, 1, 1]
ph3.init_phph_interaction()
fc2 = ph3.dynamical_matrix.force_constants
supercell = ph3.phonon_supercell
factor = ph3.unit_conversion_factor
return SupercellPhonon(supercell, fc2, factor=factor)
# def test_run_Lambda(si_pbesol_111):
# lt = LambdaTensor()
def test_SupercellPhonon(si_pbesol_111):
sph = get_supercell_phonon(si_pbesol_111)
np.testing.assert_allclose(
si_pbesol_111_freqs, sph.frequencies, atol=1e-4)
def test_gamma_matrix_mesh(si_pbesol):
@ -24,28 +47,18 @@ def test_gamma_matrix_mesh(si_pbesol):
eigvecs = qpoints_phonon.eigenvectors
gmat.create_gamma_matrix(freqs, eigvecs, 300.0)
gmat.run()
np.testing.assert_allclose(si_pbesol_gamma0_0,
gmat.gamma_matrix[0, 0],
atol=1e-4)
np.testing.assert_allclose(si_pbesol_gamma1_34,
gmat.gamma_matrix[1, 34],
atol=1e-4)
print(gmat.gamma_matrix[1, 2])
np.testing.assert_allclose(
si_pbesol_gamma0_0, gmat.gamma_matrix[0, 0], atol=1e-4)
np.testing.assert_allclose(
si_pbesol_gamma1_34, gmat.gamma_matrix[1, 34], atol=1e-4)
def test_gamma_matrix(si_pbesol):
si_pbesol.mesh_numbers = [1, 1, 1]
si_pbesol.init_phph_interaction()
fc2 = si_pbesol.dynamical_matrix.force_constants
supercell = si_pbesol.phonon_supercell
factor = si_pbesol.unit_conversion_factor
supercell_phonon = SupercellPhonon(supercell, fc2, factor=factor)
supercell_phonon = get_supercell_phonon(si_pbesol)
gmat = DispCorrMatrix(supercell_phonon)
gmat.run(300.0)
np.testing.assert_allclose(si_pbesol_gamma0_0,
gmat.gamma_matrix[0:3, 0:3],
np.testing.assert_allclose(
si_pbesol_gamma0_0, gmat.gamma_matrix[0:3, 0:3], atol=1e-4)
np.testing.assert_allclose(
si_pbesol_gamma1_34, gmat.gamma_matrix[1 * 3: 2 * 3, 34 * 3: 35 * 3],
atol=1e-4)
np.testing.assert_allclose(si_pbesol_gamma1_34,
gmat.gamma_matrix[1 * 3: 2 * 3, 34 * 3: 35 * 3],
atol=1e-4)
print(gmat.gamma_matrix[1 * 3: 2 * 3, 34 * 3: 35 * 3])