diff --git a/pyproject.toml b/pyproject.toml index 196c0b227f..269fb348d5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -108,7 +108,7 @@ strict = [ "numpy", "openmm-mdanalysis-reporter==0.1.0", "openmm==8.1.1", - "phonopy==2.27.0", + "phonopy==2.30.1", "pydantic-settings==2.6.1", "pydantic==2.9.2", "pymatgen-analysis-defects==2024.10.22", diff --git a/src/atomate2/common/schemas/gruneisen.py b/src/atomate2/common/schemas/gruneisen.py index b12f9c78a9..379dc173c2 100644 --- a/src/atomate2/common/schemas/gruneisen.py +++ b/src/atomate2/common/schemas/gruneisen.py @@ -4,12 +4,8 @@ from pathlib import Path from typing import Optional, Union -import matplotlib.pyplot as plt -import numpy as np import phonopy from emmet.core.structure import StructureMetadata -from matplotlib import colors -from matplotlib.colors import LinearSegmentedColormap from phonopy.api_gruneisen import PhonopyGruneisen from phonopy.phonon.band_structure import get_band_qpoints_and_path_connections from pydantic import BaseModel, Field @@ -24,12 +20,7 @@ GruneisenParameter, GruneisenPhononBandStructureSymmLine, ) -from pymatgen.phonon.plotter import ( - GruneisenPhononBSPlotter, - GruneisenPlotter, - freq_units, -) -from pymatgen.util.plotting import pretty_plot +from pymatgen.phonon.plotter import GruneisenPhononBSPlotter, GruneisenPlotter from typing_extensions import Self from atomate2.common.schemas.phonons import PhononBSDOSDoc @@ -164,7 +155,7 @@ def from_phonon_yamls( mesh=mesh, shift=compute_gruneisen_param_kwargs.get("shift"), is_gamma_center=compute_gruneisen_param_kwargs.get( - "is_gamma_center", True + "is_gamma_center", False ), is_time_reversal=compute_gruneisen_param_kwargs.get( "is_time_reversal", True @@ -184,7 +175,7 @@ def from_phonon_yamls( mesh=kpoint.kpts[0], shift=compute_gruneisen_param_kwargs.get("shift"), is_gamma_center=compute_gruneisen_param_kwargs.get( - "is_gamma_center", True + "is_gamma_center", False ), is_time_reversal=compute_gruneisen_param_kwargs.get( "is_time_reversal", True @@ -228,9 +219,14 @@ def from_phonon_yamls( labels_dict=kpath_dict, ) gp_bs_plot = GruneisenPhononBSPlotter(bs=gruneisen_band_structure) - GruneisenParameterDocument.get_gruneisen_weighted_bandstructure( - gruneisen_band_symline_plotter=gp_bs_plot, - save_fig=True, + + gruneisen_bs_plot = compute_gruneisen_param_kwargs.get( + "gruneisen_bs", "gruneisen_band.pdf" + ) + gp_bs_plot.save_plot_gs( + filename=gruneisen_bs_plot, + plot_ph_bs_with_gruneisen=True, + img_format=compute_gruneisen_param_kwargs.get("img_format", "pdf"), **compute_gruneisen_param_kwargs, ) gruneisen_parameter_inputs = { @@ -261,82 +257,3 @@ def from_phonon_yamls( gruneisen_band_structure=gruneisen_band_structure, derived_properties=derived_properties, ) - - @staticmethod - def get_gruneisen_weighted_bandstructure( - gruneisen_band_symline_plotter: GruneisenPhononBSPlotter, - save_fig: bool = True, - **kwargs, - ) -> None: - """Save a phonon band structure weighted with Grueneisen parameters. - - Parameters - ---------- - gruneisen_band_symline_plotter: GruneisenPhononBSPlotter - pymatgen GruneisenPhononBSPlotter obj - save_fig: bool - bool to save plots - kwargs: dict - keyword arguments to adjust plotter - - Returns - ------- - None - """ - u = freq_units(kwargs.get("units", "THz")) - ax = pretty_plot(12, 8) - gruneisen_band_symline_plotter._make_ticks(ax) # noqa: SLF001 - - # plot y=0 line - ax.axhline(0, linewidth=1, color="black") - - # Create custom colormap (default is red to blue) - cmap = LinearSegmentedColormap.from_list( - "mycmap", kwargs.get("mycmap", ["red", "blue"]) - ) - - data = gruneisen_band_symline_plotter.bs_plot_data() - - # extract min and max Grüneisen parameter values - max_gruneisen = np.array(data["gruneisen"]).max() - min_gruneisen = np.array(data["gruneisen"]).min() - - # LogNormalize colormap based on the min and max Grüneisen parameter values - norm = colors.SymLogNorm( - vmin=min_gruneisen, - vmax=max_gruneisen, - linthresh=1e-2, - linscale=1, - ) - - for (dists_inx, dists), (_, freqs) in zip( - enumerate(data["distances"]), enumerate(data["frequency"]), strict=True - ): - for band_idx in range(gruneisen_band_symline_plotter.n_bands): - ys = [freqs[band_idx][j] * u.factor for j in range(len(dists))] - ys_gru = [ - data["gruneisen"][dists_inx][band_idx][idx] - for idx in range(len(data["distances"][dists_inx])) - ] - sc = ax.scatter( - dists, ys, c=ys_gru, cmap=cmap, norm=norm, marker="o", s=1 - ) - - # Main X and Y Labels - ax.set_xlabel(r"$\mathrm{Wave\ Vector}$", fontsize=30) - units = kwargs.get("units", "THz") - ax.set_ylabel(f"Frequencies ({units})", fontsize=30) - # X range (K) - # last distance point - x_max = data["distances"][-1][-1] - ax.set_xlim(0, x_max) - - cbar = plt.colorbar(sc, ax=ax) - cbar.set_label(r"$\gamma \ \mathrm{(logarithmized)}$", fontsize=30) - plt.tight_layout() - gruneisen_band_plot = kwargs.get("gruneisen_bs", "gruneisen_band.pdf") - if save_fig: - plt.savefig(fname=gruneisen_band_plot) - plt.close() - else: - plt.close() diff --git a/tests/common/jobs/test_gruneisen.py b/tests/common/jobs/test_gruneisen.py index b93169968c..a4cbd95247 100644 --- a/tests/common/jobs/test_gruneisen.py +++ b/tests/common/jobs/test_gruneisen.py @@ -53,8 +53,8 @@ def test_compute_gruneisen_param(tmp_dir, test_dir): "minus": False, } assert gp_doc.derived_properties.average_gruneisen == pytest.approx( - 1.1882292157682082 + 1.1203420586842452, abs=1e-2 ) assert gp_doc.derived_properties.thermal_conductivity_slack == pytest.approx( - 38.861289530152796 + 44.078885068152346, abs=1e-2 ) diff --git a/tests/test_data/vasp/Si_phonons_4/dielectric/inputs/INCAR.gz b/tests/test_data/vasp/Si_phonons_3/dielectric/inputs/INCAR.gz similarity index 100% rename from tests/test_data/vasp/Si_phonons_4/dielectric/inputs/INCAR.gz rename to tests/test_data/vasp/Si_phonons_3/dielectric/inputs/INCAR.gz diff --git 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a/tests/vasp/flows/test_phonons.py +++ b/tests/vasp/flows/test_phonons.py @@ -123,8 +123,8 @@ def test_phonon_wf_vasp_only_displacements_no_structural_transformation( ): # mapping from job name to directory containing test files ref_paths = { - "phonon static 1/1": "Si_phonons_3/phonon_static_1_1", - "static": "Si_phonons_3/static", + "phonon static 1/1": "Si_phonons_2/phonon_static_1_1", + "static": "Si_phonons_2/static", } # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings @@ -145,33 +145,27 @@ def test_phonon_wf_vasp_only_displacements_no_structural_transformation( store_force_constants=False, prefer_90_degrees=False, generate_frequencies_eigenvectors_kwargs={"tstep": 100}, - ).make(si_structure) + ).make(si_structure.to_conventional()) # run the flow or job and ensure that it finished running successfully responses = run_locally(job, create_folders=True, ensure_success=True) - # validate the outputs - assert isinstance(responses[job.jobs[-1].uuid][1].output, PhononBSDOSDoc) - - assert_allclose( - responses[job.jobs[-1].uuid][1].output.free_energies, - [5927.157337, 5905.309813, 5439.530414, 4207.379685, 2297.576147], - ) - assert_allclose( - responses[job.jobs[-1].uuid][1].output.entropies, - [0.0, 1.256496, 8.511348, 15.928285, 22.063785], - atol=1e-6, - ) - assert_allclose( - responses[job.jobs[-1].uuid][1].output.heat_capacities, - [0.0, 4.958763, 15.893881, 20.311967, 22.196143], + # validate settings + assert responses[job.jobs[-1].uuid][1].output.code == "vasp" + assert isinstance( + responses[job.jobs[-1].uuid][1].output.phonopy_settings, + PhononComputationalSettings, ) - - assert_allclose( - responses[job.jobs[-1].uuid][1].output.internal_energies, - [5927.157337, 6030.959432, 7141.800004, 8985.865319, 11123.090225], + assert responses[job.jobs[-1].uuid][1].output.phonopy_settings.npoints_band == 101 + assert ( + responses[job.jobs[-1].uuid][1].output.phonopy_settings.kpath_scheme + == "seekpath" ) + phonopy_settings = responses[job.jobs[-1].uuid][1].output.phonopy_settings + assert phonopy_settings.kpoint_density_dos == 7_000 + # validate the outputs + assert isinstance(responses[job.jobs[-1].uuid][1].output, PhononBSDOSDoc) assert isinstance( responses[job.jobs[-1].uuid][1].output.phonon_bandstructure, PhononBandStructureSymmLine, @@ -187,7 +181,7 @@ def test_phonon_wf_vasp_only_displacements_no_structural_transformation( assert isinstance(responses[job.jobs[-1].uuid][1].output.jobdirs, PhononJobDirs) assert isinstance(responses[job.jobs[-1].uuid][1].output.uuids, PhononUUIDs) assert_allclose( - responses[job.jobs[-1].uuid][1].output.total_dft_energy, -5.74525804 + responses[job.jobs[-1].uuid][1].output.total_dft_energy, -5.74555232 ) assert responses[job.jobs[-1].uuid][1].output.born is None assert responses[job.jobs[-1].uuid][1].output.epsilon_static is None @@ -196,40 +190,25 @@ def test_phonon_wf_vasp_only_displacements_no_structural_transformation( ) assert_allclose( responses[job.jobs[-1].uuid][1].output.primitive_matrix, - ((0, 1, 0), (0, 0, 1), (1, 0, 0)), + ((0, 0.5, 0.5), (0.5, 0, 0.5), (0.5, 0.5, 0)), atol=1e-8, ) assert_allclose( - responses[job.jobs[-1].uuid][1].output.primitive_matrix, - ((0, 1, 0), (0, 0, 1), (1, 0, 0)), - ) - assert responses[job.jobs[-1].uuid][1].output.code == "vasp" - assert isinstance( - responses[job.jobs[-1].uuid][1].output.phonopy_settings, - PhononComputationalSettings, - ) - assert responses[job.jobs[-1].uuid][1].output.phonopy_settings.npoints_band == 101 - assert ( - responses[job.jobs[-1].uuid][1].output.phonopy_settings.kpath_scheme - == "seekpath" + responses[job.jobs[-1].uuid][1].output.free_energies, + [6115.980051, 6059.749756, 5490.929122, 4173.234384, 2194.164562], ) - phonopy_settings = responses[job.jobs[-1].uuid][1].output.phonopy_settings - assert phonopy_settings.kpoint_density_dos == 7_000 assert_allclose( responses[job.jobs[-1].uuid][1].output.entropies, - [0.0, 1.256496, 8.511348, 15.928285, 22.063785], + [0.0, 2.194216, 9.478603, 16.687079, 22.702177], atol=1e-6, ) assert_allclose( responses[job.jobs[-1].uuid][1].output.heat_capacities, - [0.0, 4.958763, 15.893881, 20.311967, 22.196143], - atol=1e-6, + [0.0, 5.750113, 15.408866, 19.832123, 21.842104], ) - assert_allclose( responses[job.jobs[-1].uuid][1].output.internal_energies, - [5927.157337, 6030.959432, 7141.800004, 8985.865319, 11123.090225], - atol=1e-6, + [6115.980051, 6279.17132, 7386.649622, 9179.358187, 11275.035523], ) @@ -542,11 +521,11 @@ def test_phonon_wf_vasp_only_displacements_optional_settings( def test_phonon_wf_vasp_all_steps(mock_vasp, clean_dir, si_structure: Structure): # mapping from job name to directory containing test files ref_paths = { - "phonon static 1/1": "Si_phonons_4/phonon_static_1_1", - "static": "Si_phonons_4/static", - "tight relax 1": "Si_phonons_4/tight_relax_1", - "tight relax 2": "Si_phonons_4/tight_relax_2", - "dielectric": "Si_phonons_4/dielectric", + "phonon static 1/1": "Si_phonons_3/phonon_static_1_1", + "static": "Si_phonons_3/static", + "tight relax 1": "Si_phonons_3/tight_relax_1", + "tight relax 2": "Si_phonons_3/tight_relax_2", + "dielectric": "Si_phonons_3/dielectric", } # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings