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"""Tests for lammps calculater interface."""
import io
from pathlib import Path
import numpy as np
import pytest
from phonopy.interface.lammps import (
LammpsForcesLoader,
LammpsStructureDumper,
LammpsStructureLoader,
)
from phonopy.interface.phonopy_yaml import read_phonopy_yaml
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.structure.cells import get_cell_matrix_from_lattice
from phonopy.structure.symmetry import Symmetry
cwd = Path(__file__).parent
phonopy_atoms = {
symbol: f"""lattice:
- [ 2.923479689273095, 0.000000000000000, 0.000000000000000 ] # a
- [ -1.461739844636547, 2.531807678358337, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 4.624022835916574 ] # c
points:
- symbol: {symbol} # 1
coordinates: [ 0.333333333333334, 0.666666666666667, 0.750000000000000 ]
- symbol: {symbol} # 2
coordinates: [ 0.666666666666667, 0.333333333333333, 0.250000000000000 ]
"""
for symbol in ["H", "Ti"]
}
@pytest.mark.parametrize("symbol", ["H", "Ti"])
def test_LammpsStructure(helper_methods, symbol):
"""Test of LammpsStructureLoader.load(stream)."""
with open(cwd / f"lammps_structure_{symbol}") as fp:
cell = LammpsStructureLoader().load(fp).cell
_assert_LammpsStructure(cell, symbol, helper_methods)
@pytest.mark.parametrize("symbol", ["H", "Ti"])
def test_LammpsStructure_from_file(helper_methods, symbol):
"""Test of LammpsStructureLoader.load(filename)."""
cell = LammpsStructureLoader().load(cwd / f"lammps_structure_{symbol}").cell
_assert_LammpsStructure(cell, symbol, helper_methods)
def _assert_LammpsStructure(cell: PhonopyAtoms, symbol: str, helper_methods):
phyml = read_phonopy_yaml(io.StringIO(phonopy_atoms[symbol]))
helper_methods.compare_cells_with_order(cell, phyml.unitcell)
symmetry = Symmetry(phyml.unitcell)
assert symmetry.dataset.number == 194
def test_LammpsStructureDumper(primcell_nacl: PhonopyAtoms, helper_methods):
"""Test of LammpsStructureDumper."""
lmpsd = LammpsStructureDumper(primcell_nacl)
cell_stream = io.StringIO("\n".join(lmpsd.get_lines()))
lmpsd_cell = LammpsStructureLoader().load(cell_stream).cell
pcell_rot = primcell_nacl.copy()
pcell_rot.cell = get_cell_matrix_from_lattice(pcell_rot.cell)
helper_methods.compare_cells_with_order(pcell_rot, lmpsd_cell)
@pytest.mark.parametrize("symbol", ["H", "Ti", "Ti_id"])
def test_LammpsStructureDumper_Ti(symbol, helper_methods):
"""Test of LammpsStructureDumper with Ti (with and without Atom Type Labels)."""
cell = LammpsStructureLoader().load(cwd / f"lammps_structure_{symbol}").cell
lmpsd = LammpsStructureDumper(cell)
cell_stream = io.StringIO("\n".join(lmpsd.get_lines()))
lmpsd_cell = LammpsStructureLoader().load(cell_stream).cell
helper_methods.compare_cells_with_order(cell, lmpsd_cell)
def test_LammpsForcesLoader():
"""Test of LammpsForcesLoader with HCP Ti.
This is forces of 4x4x3 supercell of lammps_structure_Ti with a displacement
[ 0.0064452834123435, 0.0000000000000000, 0.0076458041914876 ].
"""
forces = LammpsForcesLoader().load(cwd / "lammps_forces_Ti.0").forces
# print("%15.10f %15.10f %15.10f" % tuple(forces[0]))
# print("%15.10f %15.10f %15.10f" % tuple(forces[-1]))
np.testing.assert_allclose(
forces[0], [-0.0337045900, -0.0000210300, -0.0399063800], atol=1e-8
)
np.testing.assert_allclose(
forces[-1], [-0.0000369000, -0.0000003300, 0.0001166000], atol=1e-8
)
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