Merge branch 'main' into main

Author: esoteric-ephemera

pyproject.toml

@@ -51,7 +51,7 @@ defects = [
 ]
 forcefields = [
     "ase>=3.23.0",
-    "calorine<=2.2.1",
+    "calorine>=3.0",
     "chgnet>=0.2.2",
     "mace-torch>=0.3.3",
     "matgl>=1.1.3",
@@ -74,7 +74,7 @@ docs = [
     "FireWorks==2.0.3",
     "autodoc_pydantic==2.2.0",
     "furo==2024.8.6",
-    "ipython==8.29.0",
+    "ipython==8.30.0",
     "jsonschema[format]",
     "myst_parser==4.0.0",
     "numpydoc==1.8.0",
@@ -89,7 +89,7 @@ tests = [
     "pytest-cov==6.0.0",
     "pytest-mock==3.14.0",
     "pytest-split==0.10.0",
-    "pytest==8.3.3",
+    "pytest==8.3.4",
 ]
 strict = [
     "PyYAML==6.0.2",
@@ -98,17 +98,17 @@ strict = [
     "click==8.1.7",
     "custodian==2024.10.16",
     "dscribe==2.1.1",
-    "emmet-core==0.84.3rc4",
+    "emmet-core==0.84.3rc6",
     "ijson==3.3.0",
     "jobflow==0.1.19",
     "lobsterpy==0.4.9",
     "mdanalysis==2.7.0",
     "monty==2024.10.21",
-    "mp-api==0.42.2",
+    "mp-api==0.43.0",
     "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",
@@ -124,7 +124,7 @@ strict-forcefields = [
     "mace-torch>=0.3.6",
     "matgl==1.1.3",
     "quippy-ase==0.9.14; python_version < '3.12'",
-    "sevenn==0.10.1",
+    "sevenn==0.10.2",
     "torch==2.5.1",
     "torchdata==0.7.1",                            # TODO: remove when issue fixed
 ]

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()

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
     )

tests/test_data/vasp/Si_phonons_4/dielectric/inputs/INCAR.gz renamed to tests/test_data/vasp/Si_phonons_3/dielectric/inputs/INCAR.gz

@@ -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