"""Tests of VASP calculator interface.""" import tarfile import tempfile from io import StringIO from pathlib import Path import numpy as np import pytest from phonopy.file_IO import parse_FORCE_SETS from phonopy.interface.phonopy_yaml import read_cell_yaml from phonopy.interface.vasp import ( Vasprun, VasprunxmlExpat, get_vasp_structure_lines, parse_force_constants, parse_set_of_forces, read_vasp, read_vasp_from_strings, read_XDATCAR, write_XDATCAR, ) cwd = Path(__file__).parent def test_read_vasp(): """Test read_vasp.""" cell = read_vasp(cwd / ".." / "POSCAR_NaCl") filename = cwd / "NaCl-vasp.yaml" cell_ref = read_cell_yaml(filename) assert (np.abs(cell.cell - cell_ref.cell) < 1e-5).all() diff_pos = cell.scaled_positions - cell_ref.scaled_positions diff_pos -= np.rint(diff_pos) assert (np.abs(diff_pos) < 1e-5).all() for s, s_r in zip(cell.symbols, cell_ref.symbols, strict=True): assert s == s_r @pytest.mark.parametrize( "first_line_str, is_vasp4", [(None, True), (None, False), ("my_comment", True), ("my_comment", False)], ) def test_get_vasp_structure_lines(helper_methods, is_vasp4, first_line_str): """Test get_vasp_structure_lines (almost write_vasp).""" filename = cwd / "NaCl-vasp.yaml" cell_ref = read_cell_yaml(filename) lines = get_vasp_structure_lines( cell_ref, direct=True, is_vasp4=is_vasp4, first_line_str=first_line_str ) cell = read_vasp_from_strings("\n".join(lines)) helper_methods.compare_cells_with_order(cell, cell_ref) if is_vasp4: # is_vasp4 is True, first_line_str is ignored. assert lines[0] == "Na Cl" elif first_line_str: assert lines[0] == first_line_str def test_get_vasp_structure_lines_shuffled_positions(helper_methods): """Test get_vasp_structure_lines with a cell having shuffled positions. Order of atoms is sorted by chemical symbols. Therefore, helper_methods.compare_cells_with_order fails. """ poscar_yaml = """lattice: - [ 5.690301476175672, 0.000000000000000, 0.000000000000000 ] # a - [ 0.000000000000000, 5.690301476175672, 0.000000000000000 ] # b - [ 0.000000000000000, 0.000000000000000, 5.690301476175672 ] # c points: - symbol: Na # 1 coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ] mass: 22.989769 - symbol: Cl # 2 coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ] mass: 35.453000 - symbol: Na # 3 coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ] mass: 22.989769 - symbol: Cl # 4 coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ] mass: 35.453000 - symbol: Na # 5 coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ] mass: 22.989769 - symbol: Cl # 6 coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ] mass: 35.453000 - symbol: Na # 7 coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ] mass: 22.989769 - symbol: Cl # 8 coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ] mass: 35.453000 """ cell_ref = read_cell_yaml(StringIO(poscar_yaml)) lines = get_vasp_structure_lines(cell_ref, direct=True) cell = read_vasp_from_strings("\n".join(lines)) with pytest.raises(AssertionError): helper_methods.compare_cells_with_order(cell, cell_ref) helper_methods.compare_cells(cell, cell_ref) perm = [] for p_i in cell.scaled_positions: diff = cell_ref.scaled_positions - p_i diff -= np.rint(diff) dists = np.linalg.norm(diff @ cell.cell, axis=1) perm.append(np.where(dists < 1e-8)[0][0]) np.testing.assert_array_equal(perm, [0, 2, 4, 6, 1, 3, 5, 7]) np.testing.assert_array_equal(cell.numbers, [11, 11, 11, 11, 17, 17, 17, 17]) def test_parse_vasprun_xml(): """Test parsing vasprun.xml with expat.""" filename_vasprun = cwd / "vasprun.xml.tar.bz2" _tar = tarfile.open(filename_vasprun) filename = cwd / ".." / "FORCE_SETS_NaCl" dataset = parse_FORCE_SETS(filename=filename) energy_ref = [-216.82820693, -216.82817843] for i, member in enumerate(_tar.getmembers()): vr = Vasprun(_tar.extractfile(member), use_expat=True) # for force in vr.read_forces(): # print("% 15.8f % 15.8f % 15.8f" % tuple(force)) # print("") ref = dataset["first_atoms"][i]["forces"] np.testing.assert_allclose(ref, vr.read_forces(), atol=1e-8) np.testing.assert_allclose(energy_ref[i], vr.read_energy(), atol=1e-8) def test_VasprunxmlExpat(): """Test VasprunxmlExpat.""" filename_vasprun = cwd / "vasprun.xml.tar.bz2" _tar = tarfile.open(filename_vasprun) for member in _tar.getmembers(): vasprun = VasprunxmlExpat(_tar.extractfile(member)) vasprun.parse() np.testing.assert_equal(vasprun.fft_grid, [64, 64, 64]) np.testing.assert_equal(vasprun.fft_fine_grid, [128, 128, 128]) assert vasprun.efermi is None assert vasprun.symbols == ["Na"] * 32 + ["Cl"] * 32 np.testing.assert_almost_equal(vasprun.NELECT, 448) np.testing.assert_almost_equal(vasprun.volume, 1473.99433936) break def test_parse_set_of_forces(): """Test parse_set_of_forces.""" filename_vasprun = cwd / "vasprun.xml.tar.bz2" _tar = tarfile.open(filename_vasprun) fps = [_tar.extractfile(member) for member in _tar.getmembers()] calc_dataset = parse_set_of_forces(64, fps) filename = cwd / ".." / "FORCE_SETS_NaCl" dataset = parse_FORCE_SETS(filename=filename) force_sets = [dataset["first_atoms"][i]["forces"] for i in (0, 1)] energy_ref = [-216.82820693, -216.82817843] np.testing.assert_allclose( calc_dataset["points"][0][0], [0.00087869, 0.0, 0.0], atol=1e-5 ) np.testing.assert_allclose( calc_dataset["points"][1][32], [0.25087869, 0.25, 0.25], atol=1e-5 ) np.testing.assert_allclose(force_sets, calc_dataset["forces"], atol=1e-8) np.testing.assert_allclose( energy_ref, calc_dataset["supercell_energies"], atol=1e-8 ) def test_read_XDATCAR(): """Test read_XDATCAR.""" filename_xdatcar = cwd / "XDATCAR-NaCl" lattice, positions = read_XDATCAR(filename_xdatcar) np.testing.assert_allclose(lattice, np.eye(3) * 22.562240, atol=1e-8) np.testing.assert_allclose( positions[0, 0], [0.99854664, 0.00265936, 0.00701660], atol=1e-8 ) np.testing.assert_allclose( positions[-1, -1], [0.75034458, 0.74972945, 0.87262656], atol=1e-8 ) def test_write_XDATCAR(): """Test write_XDATCAR.""" filename_vasprun = cwd / "vasprun.xml.tar.bz2" _tar = tarfile.open(filename_vasprun) for _, member in enumerate(_tar.getmembers()): vasprun = VasprunxmlExpat(_tar.extractfile(member)) vasprun.parse() break with tempfile.TemporaryFile() as fp: write_XDATCAR(vasprunxml_expat=vasprun, fileptr=fp) fp.seek(0) lattice, positions = read_XDATCAR(fileptr=fp) np.testing.assert_allclose(lattice, np.eye(3) * 11.38060295, atol=1e-8) np.testing.assert_allclose(positions[0, 0], [0.00087869, 0, 0], atol=1e-8) np.testing.assert_allclose(positions[-1, -1], [0.5, 0.5, 0.75], atol=1e-8) def test_read_force_constants_from_vasprun_xml(): """Test reading force constants from vasprun.xml.""" fc, symbols = parse_force_constants(cwd / "vasprun_fc.xml.xz") assert fc.shape == (64, 64, 3, 3) assert symbols == ["Na", "Cl"] assert fc[0, 1, 2, 2] == pytest.approx(0.0046225992999999995)