diff --git a/src/phelel/velph/cli/phono3py/__init__.py b/src/phelel/velph/cli/phono3py/__init__.py index 02664ae..4898b4b 100644 --- a/src/phelel/velph/cli/phono3py/__init__.py +++ b/src/phelel/velph/cli/phono3py/__init__.py @@ -3,6 +3,7 @@ from __future__ import annotations import pathlib +from typing import Optional import click import tomli @@ -29,13 +30,21 @@ def cmd_phono3py(): type=click.Path(), default="velph.toml", ) +@click.option( + "--rd", + "random_displacements", + nargs=1, + default=None, + type=int, + help="Number of snapshots of supercells with random directional displacement.", +) @click.help_option("-h", "--help") -def cmd_init(toml_filename: str): +def cmd_init(toml_filename: str, random_displacements: Optional[int]): """Generate displacements and write phelel_disp.yaml.""" with open(toml_filename, "rb") as f: toml_dict = tomli.load(f) - ph3py = run_init(toml_dict) + ph3py = run_init(toml_dict, number_of_snapshots=random_displacements) phono3py_yaml_filename = pathlib.Path("phono3py/phono3py_disp.yaml") phono3py_yaml_filename.parent.mkdir(parents=True, exist_ok=True) diff --git a/test/velph/cli/phono3py/init/test_phono3py_init.py b/test/velph/cli/phono3py/init/test_phono3py_init.py new file mode 100644 index 0000000..c512da9 --- /dev/null +++ b/test/velph/cli/phono3py/init/test_phono3py_init.py @@ -0,0 +1,58 @@ +"""Tests velph-phono3py-init.""" + +import numpy as np +import pytest +import tomli +from phelel.velph.cli.phono3py.init import run_init + + +@pytest.mark.parametrize("distance", [0.03, 0.05]) +def test_phono3py_init_random_displacements(distance: float): + """Test of plusminus and diagonal with Ti.""" + toml_str = f"""title = "VASP el-ph settings" + +[phelel] +supercell_dimension = [4, 4, 2] +amplitude = {distance} +fft_mesh = [18, 18, 28] +[vasp.supercell.incar] +lwap = true +isym = 0 +kpar = 2 +ncore = 24 +ismear = 0 +sigma = 0.2 +ediff = 1e-08 +encut = 329.532 +prec = "accurate" +lreal = false +lwave = false +lcharg = false +addgrid = true +lsorbit = true +[vasp.supercell.kpoints] +mesh = [6, 6, 7] + +[unitcell] +lattice = [ + [ 2.930720886111760, 0.000000000000000, 0.000000000000000 ], # a + [ -1.465360443055880, 2.538078738774425, 0.000000000000000 ], # b + [ 0.000000000000000, 0.000000000000000, 4.646120482318025 ], # c +] +[[unitcell.points]] # 1 +symbol = "Ti" +coordinates = [ 0.333333333333336, 0.666666666666664, 0.250000000000000 ] +magnetic_moment = [ 0.00000000, 0.00000000, 0.00000000 ] +[[unitcell.points]] # 2 +symbol = "Ti" +coordinates = [ 0.666666666666664, 0.333333333333336, 0.750000000000000 ] +magnetic_moment = [ 0.00000000, 0.00000000, 0.00000000 ] +""" + + toml_dict = tomli.loads(toml_str) + ph3 = run_init(toml_dict, number_of_snapshots=10) + np.testing.assert_array_equal(ph3.supercell_matrix, np.diag([4, 4, 2])) + natom = len(ph3.supercell) + assert natom == 64 + assert ph3.displacements.shape == (10, natom, 3) + np.testing.assert_allclose(np.linalg.norm(ph3.displacements, axis=2), distance)