phono3py/test/sscha/test_sscha.py

"""Tests for SSCHA routines."""
import pytest
import numpy as np
from phono3py.sscha.sscha import (
    DispCorrMatrix,
    DispCorrMatrixMesh,
    SupercellPhonon,
    ThirdOrderFC,
)
from phonopy.phonon.qpoints import QpointsPhonon
from phonopy.phonon.random_displacements import RandomDisplacements

try:
    ModuleNotFoundError
except NameError:
    ModuleNotFoundError = ImportError

si_pbesol_upsilon0_0 = [[3.849187e02, 0, 0], [0, 3.849187e02, 0], [0, 0, 3.849187e02]]
si_pbesol_upsilon1_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):
    """Return SupercellPhonon class instance."""
    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, frequency_factor_to_THz=factor)


def mass_sand(matrix, mass):
    """Calculate mass sandwich."""
    return ((matrix * mass).T * mass).T


def mass_inv(matrix, mass):
    """Calculate inverse mass sandwich."""
    bare = mass_sand(matrix, mass)
    inv_bare = np.linalg.pinv(bare)
    return mass_sand(inv_bare, mass)


def test_SupercellPhonon(si_pbesol_111):
    """Test of SupercellPhonon class."""
    sph = get_supercell_phonon(si_pbesol_111)
    np.testing.assert_allclose(si_pbesol_111_freqs, sph.frequencies, atol=1e-4)


def test_disp_corr_matrix_mesh(si_pbesol):
    """Test of DispCorrMatrixMesh class."""
    si_pbesol.mesh_numbers = [9, 9, 9]
    si_pbesol.init_phph_interaction()
    dynmat = si_pbesol.dynamical_matrix
    uu = DispCorrMatrixMesh(dynmat.primitive, dynmat.supercell)
    qpoints_phonon = QpointsPhonon(
        uu.commensurate_points, dynmat, with_eigenvectors=True
    )
    freqs = qpoints_phonon.frequencies
    eigvecs = qpoints_phonon.eigenvectors
    uu.run(freqs, eigvecs, 300.0)
    np.testing.assert_allclose(
        si_pbesol_upsilon0_0, uu.upsilon_matrix[0:3, 0:3], atol=1e-4
    )
    np.testing.assert_allclose(
        si_pbesol_upsilon1_34,
        uu.upsilon_matrix[1 * 3 : 2 * 3, 34 * 3 : 35 * 3],
        atol=1e-4,
    )

    sqrt_masses = np.repeat(np.sqrt(si_pbesol.supercell.masses), 3)
    uu_inv = mass_inv(uu.psi_matrix, sqrt_masses)
    np.testing.assert_allclose(uu.upsilon_matrix, uu_inv, atol=1e-8, rtol=0)


def test_disp_corr_matrix(si_pbesol):
    """Test of DispCorrMatrix class."""
    supercell_phonon = get_supercell_phonon(si_pbesol)
    uu = DispCorrMatrix(supercell_phonon)
    uu.run(300.0)
    np.testing.assert_allclose(
        si_pbesol_upsilon0_0, uu.upsilon_matrix[0:3, 0:3], atol=1e-4
    )
    np.testing.assert_allclose(
        si_pbesol_upsilon1_34,
        uu.upsilon_matrix[1 * 3 : 2 * 3, 34 * 3 : 35 * 3],
        atol=1e-4,
    )


def test_disp_corr_matrix_si(si_pbesol):
    """Test of DispCorrMatrix class with Si."""
    _test_disp_corr_matrix(si_pbesol)


def test_disp_corr_matrix_nacl(nacl_pbe):
    """Test of DispCorrMatrix class with NaCl."""
    _test_disp_corr_matrix(nacl_pbe)


def _test_disp_corr_matrix(ph3):
    supercell_phonon = get_supercell_phonon(ph3)
    uu = DispCorrMatrix(supercell_phonon)
    uu.run(300.0)

    sqrt_masses = np.repeat(np.sqrt(ph3.supercell.masses), 3)
    uu_inv = mass_inv(uu.psi_matrix, sqrt_masses)
    np.testing.assert_allclose(uu.upsilon_matrix, uu_inv, atol=1e-8, rtol=0)

    rd = RandomDisplacements(ph3.supercell, ph3.primitive, ph3.fc2)
    rd.run_correlation_matrix(300)
    rd_uu_inv = np.transpose(rd.uu_inv, axes=[0, 2, 1, 3]).reshape(uu_inv.shape)
    np.testing.assert_allclose(uu.upsilon_matrix, rd_uu_inv, atol=1e-8, rtol=0)


def test_fc3(si_pbesol_iterha_111):
    """Test of ThirdOrderFC class."""
    try:
        import alm  # noqa F401
    except ModuleNotFoundError:
        pytest.skip("Skip this test because ALM module was not found.")

    ph = si_pbesol_iterha_111
    ph.produce_force_constants(calculate_full_force_constants=True, fc_calculator="alm")
    supercell_phonon = SupercellPhonon(
        ph.supercell,
        ph.force_constants,
        frequency_factor_to_THz=ph.unit_conversion_factor,
    )
    fc3 = ThirdOrderFC(ph.displacements, ph.forces, supercell_phonon)
    fc3.run(T=300)