Merge branch 'materialsproject:master' into beautifulsoup-optional

.coderabbit.yaml

@@ -0,0 +1,17 @@
+# yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json
+language: "en-US"
+early_access: false
+reviews:
+  request_changes_workflow: false
+  high_level_summary: false
+  poem: false
+  review_status: false
+  collapse_walkthrough: false
+  auto_review:
+    enabled: true
+    ignore_title_keywords:
+      - "WIP"
+      - "DO NOT MERGE"
+    drafts: false
+chat:
+  auto_reply: true

pymatgen/analysis/local_env.py

@@ -3794,6 +3794,10 @@ class CrystalNN(NearNeighbors):
     algorithm can also modify probability using smooth distance cutoffs as well as Pauling
     electronegativity differences. The output can either be the most probable coordination
     environment or a weighted list of coordination environments.
+    Please note that the default weights have been benchmarked for inorganic crystal structures.
+    For MOFs or molecular crystals, weights and cutoffs likely will need to be adapted.
+    A starting point could be:
+    CrystalNN(x_diff_weight = 1.5, search_cutoff = 4.5)
     """
 
     NNData = namedtuple("NNData", ["all_nninfo", "cn_weights", "cn_nninfo"])

pymatgen/io/vasp/inputs.py

@@ -584,6 +584,8 @@ def get_str(self, direct: bool = True, vasp4_compatible: bool = False, significa
 
         return "\n".join(lines) + "\n"
 
+    get_string = get_str
+
     def __repr__(self):
         return self.get_str()
 

pymatgen/phonon/gruneisen.py

@@ -75,10 +75,10 @@ def average_gruneisen(
         limit_frequencies: Literal["debye", "acoustic"] | None = None,
     ) -> float:
         """Calculates the average of the Gruneisen based on the values on the regular grid.
-        If squared is True the average will use the squared value of the Gruneisen and a squared root
+        If squared is True, the average will use the squared value of the Gruneisen and a squared root
         is performed on the final result.
-        Values associated to negative frequencies will be ignored.
-        See Scripta Materialia 129, 88 for definitions.
+        Values associated with negative frequencies will be ignored.
+        See Nath et al. _Scripta Materialia_ **2017**, _129_, 88 for the definitions.
         Adapted from classes in abipy that have been written by Guido Petretto (UCLouvain).
 
         Args:

pymatgen/util/testing/__init__.py

@@ -26,8 +26,8 @@
 MODULE_DIR = Path(__file__).absolute().parent
 STRUCTURES_DIR = MODULE_DIR / ".." / "structures"
 TEST_FILES_DIR = Path(SETTINGS.get("PMG_TEST_FILES_DIR", f"{ROOT}/tests/files"))
-VASP_IN_DIR = f"{TEST_FILES_DIR}/vasp/inputs"
-VASP_OUT_DIR = f"{TEST_FILES_DIR}/vasp/outputs"
+VASP_IN_DIR = f"{TEST_FILES_DIR}/io/vasp/inputs"
+VASP_OUT_DIR = f"{TEST_FILES_DIR}/io/vasp/outputs"
 # fake POTCARs have original header information, meaning properties like number of electrons,
 # nuclear charge, core radii, etc. are unchanged (important for testing) while values of the and
 # pseudopotential kinetic energy corrections are scrambled to avoid VASP copyright infringement

tests/alchemy/test_filters.py

@@ -72,7 +72,7 @@ def test_as_from_dict(self):
 
 class TestRemoveDuplicatesFilter(TestCase):
     def setUp(self):
-        with open(f"{TEST_FILES_DIR}/TiO2_entries.json") as file:
+        with open(f"{TEST_FILES_DIR}/entries/TiO2_entries.json") as file:
             entries = json.load(file, cls=MontyDecoder)
         self._struct_list = [entry.structure for entry in entries]
         self._sm = StructureMatcher()
@@ -91,7 +91,7 @@ def test_as_from_dict(self):
 
 class TestRemoveExistingFilter(TestCase):
     def setUp(self):
-        with open(f"{TEST_FILES_DIR}/TiO2_entries.json") as file:
+        with open(f"{TEST_FILES_DIR}/entries/TiO2_entries.json") as file:
             entries = json.load(file, cls=MontyDecoder)
         self._struct_list = [entry.structure for entry in entries]
         self._sm = StructureMatcher()

tests/alchemy/test_materials.py

@@ -18,6 +18,8 @@
 from pymatgen.util.provenance import StructureNL
 from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, PymatgenTest
 
+TEST_DIR = f"{TEST_FILES_DIR}/alchemy"
+
 
 class TestTransformedStructure(PymatgenTest):
     def setUp(self):
@@ -61,7 +63,7 @@ def test_final_structure(self):
         assert isinstance(deepcopy(self.trans), TransformedStructure)
 
     def test_from_dict(self):
-        with open(f"{TEST_FILES_DIR}/transformations.json") as file:
+        with open(f"{TEST_DIR}/transformations.json") as file:
             dct = json.load(file)
         dct["other_parameters"] = {"tags": ["test"]}
         ts = TransformedStructure.from_dict(dct)

tests/alchemy/test_transmuters.py

@@ -14,7 +14,7 @@
 class TestCifTransmuter(PymatgenTest):
     def test_init(self):
         trafos = [SubstitutionTransformation({"Fe": "Mn", "Fe2+": "Mn2+"})]
-        tsc = CifTransmuter.from_filenames([f"{TEST_FILES_DIR}/MultiStructure.cif"], trafos)
+        tsc = CifTransmuter.from_filenames([f"{TEST_FILES_DIR}/cif/MultiStructure.cif"], trafos)
         assert len(tsc) == 2
         expected = {"Mn", "O", "Li", "P"}
         for s in tsc:

tests/analysis/chemenv/connectivity/test_connected_components.py

@@ -760,7 +760,7 @@ def test_real_systems(self):
             assert cc.periodicity == "2D"
 
         # Connectivity of Li4Fe3Mn1(PO4)4
-        struct = Structure.from_file(f"{TEST_FILES_DIR}/Li4Fe3Mn1(PO4)4.cif")
+        struct = Structure.from_file(f"{TEST_FILES_DIR}/cif/Li4Fe3Mn1(PO4)4.cif")
         lgf.setup_structure(structure=struct)
         se = lgf.compute_structure_environments(only_atoms=["Li", "Fe", "Mn", "P"], maximum_distance_factor=1.2)
         lse = LightStructureEnvironments.from_structure_environments(strategy=strategy, structure_environments=se)
@@ -837,7 +837,7 @@ def test_real_systems(self):
         assert ccs_periodicities == {"0D", "2D"}
 
     def test_coordination_sequences(self):
-        BaTiO3_se_fpath = f"{TEST_FILES_DIR}/chemenv/structure_environments/se_mp-5020.json"
+        BaTiO3_se_fpath = f"{TEST_FILES_DIR}/analysis/chemenv/structure_environments/se_mp-5020.json"
         with open(BaTiO3_se_fpath) as file:
             dct = json.load(file)
         struct_envs = StructureEnvironments.from_dict(dct)

tests/analysis/chemenv/connectivity/test_structure_connectivity.py

@@ -16,7 +16,7 @@
 
 class TestStructureConnectivity(PymatgenTest):
     def test_serialization(self):
-        BaTiO3_se_fpath = f"{TEST_FILES_DIR}/chemenv/structure_environments/se_mp-5020.json"
+        BaTiO3_se_fpath = f"{TEST_FILES_DIR}/analysis/chemenv/structure_environments/se_mp-5020.json"
         with open(BaTiO3_se_fpath) as file:
             dd = json.load(file)
         struct_envs = StructureEnvironments.from_dict(dd)

tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py

@@ -16,7 +16,7 @@
 
 __author__ = "waroquiers"
 
-json_dir = f"{TEST_FILES_DIR}/chemenv/json"
+json_dir = f"{TEST_FILES_DIR}/analysis/chemenv/json"
 
 
 class TestCoordinationGeometryFinder(PymatgenTest):

tests/analysis/chemenv/coordination_environments/test_read_write.py

@@ -26,8 +26,8 @@
 
 __author__ = "waroquiers"
 
-json_dir = f"{TEST_FILES_DIR}/chemenv/json"
-struct_env_dir = f"{TEST_FILES_DIR}/chemenv/structure_environments"
+json_dir = f"{TEST_FILES_DIR}/analysis/chemenv/json"
+struct_env_dir = f"{TEST_FILES_DIR}/analysis/chemenv/structure_environments"
 
 
 class TestReadWriteChemenv(PymatgenTest):

tests/analysis/chemenv/coordination_environments/test_structure_environments.py

@@ -21,12 +21,12 @@
 
 __author__ = "waroquiers"
 
-struct_env_dir = f"{TEST_FILES_DIR}/chemenv/structure_environments"
+TEST_DIR = f"{TEST_FILES_DIR}/analysis/chemenv/structure_environments"
 
 
 class TestStructureEnvironments(PymatgenTest):
     def test_structure_environments(self):
-        with open(f"{struct_env_dir}/se_mp-7000.json") as file:
+        with open(f"{TEST_DIR}/se_mp-7000.json") as file:
             dct = json.load(file)
 
         struct_envs = StructureEnvironments.from_dict(dct)
@@ -119,7 +119,7 @@ def test_structure_environments(self):
         assert ce != ce2
 
     def test_light_structure_environments(self):
-        with open(f"{struct_env_dir}/se_mp-7000.json") as file:
+        with open(f"{TEST_DIR}/se_mp-7000.json") as file:
             dct = json.load(file)
 
         struct_envs = StructureEnvironments.from_dict(dct)
@@ -220,8 +220,7 @@ def test_light_structure_environments(self):
 
     def test_from_structure_environments(self):
         # https://github.com/materialsproject/pymatgen/issues/2756
-        mp_id = "mp-554015"
-        struct = Structure.from_file(f"{TEST_FILES_DIR}/{mp_id}.json.gz")
+        struct = Structure.from_file(f"{TEST_DIR}/mp-554015.json.gz")
         strategy = SimplestChemenvStrategy(distance_cutoff=1.4, angle_cutoff=0.3)
         local_geom_finder = LocalGeometryFinder()
         local_geom_finder.setup_structure(structure=struct)

tests/analysis/chemenv/coordination_environments/test_voronoi.py

@@ -11,7 +11,7 @@
 
 __author__ = "waroquiers"
 
-img_files_dir = f"{TEST_FILES_DIR}/chemenv/images"
+img_files_dir = f"{TEST_FILES_DIR}/analysis/chemenv/images"
 
 
 class TestVoronoiContainer(PymatgenTest):

tests/analysis/chemenv/coordination_environments/test_weights.py

@@ -20,7 +20,7 @@
 
 __author__ = "waroquiers"
 
-struct_env_dir = f"{TEST_FILES_DIR}/chemenv/structure_environments"
+struct_env_dir = f"{TEST_FILES_DIR}/analysis/chemenv/structure_environments"
 
 
 class FakeNbSet:

tests/analysis/chemenv/utils/test_chemenv_config.py

@@ -6,7 +6,7 @@
 
 __author__ = "waroquiers"
 
-config_file_dir = f"{TEST_FILES_DIR}/chemenv/config"
+config_file_dir = f"{TEST_FILES_DIR}/analysis/chemenv/config"
 
 
 class TestChemenvConfig(PymatgenTest):

tests/analysis/elasticity/test_elastic.py

@@ -30,6 +30,8 @@
 from pymatgen.core.units import FloatWithUnit
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
+TEST_DIR = f"{TEST_FILES_DIR}/analysis/elasticity"
+
 
 class TestElasticTensor(PymatgenTest):
     def setUp(self):
@@ -65,10 +67,10 @@ def setUp(self):
         )
 
         self.elastic_tensor_1 = ElasticTensor(self.ft)
-        filepath = f"{TEST_FILES_DIR}/Sn_def_stress.json"
+        filepath = f"{TEST_DIR}/Sn_def_stress.json"
         with open(filepath) as file:
             self.def_stress_dict = json.load(file)
-        with open(f"{TEST_FILES_DIR}/test_toec_data.json") as file:
+        with open(f"{TEST_DIR}/test_toec_data.json") as file:
             self.toec_dict = json.load(file)
         self.structure = self.get_structure("Sn")
 
@@ -256,7 +258,7 @@ def test_energy_density(self):
 
 class TestElasticTensorExpansion(PymatgenTest):
     def setUp(self):
-        with open(f"{TEST_FILES_DIR}/test_toec_data.json") as file:
+        with open(f"{TEST_DIR}/test_toec_data.json") as file:
             self.data_dict = json.load(file)
         self.strains = [Strain(sm) for sm in self.data_dict["strains"]]
         self.pk_stresses = [Stress(d) for d in self.data_dict["pk_stresses"]]
@@ -357,7 +359,7 @@ def test_get_yield_stress(self):
 
 class TestNthOrderElasticTensor(PymatgenTest):
     def setUp(self):
-        with open(f"{TEST_FILES_DIR}/test_toec_data.json") as file:
+        with open(f"{TEST_DIR}/test_toec_data.json") as file:
             self.data_dict = json.load(file)
         self.strains = [Strain(sm) for sm in self.data_dict["strains"]]
         self.pk_stresses = [Stress(d) for d in self.data_dict["pk_stresses"]]
@@ -396,7 +398,7 @@ class TestDiffFit(PymatgenTest):
     """Tests various functions related to diff fitting."""
 
     def setUp(self):
-        with open(f"{TEST_FILES_DIR}/test_toec_data.json") as file:
+        with open(f"{TEST_DIR}/test_toec_data.json") as file:
             self.data_dict = json.load(file)
         self.strains = [Strain(sm) for sm in self.data_dict["strains"]]
         self.pk_stresses = [Stress(d) for d in self.data_dict["pk_stresses"]]

tests/analysis/ferroelectricity/test_polarization.py

@@ -15,7 +15,7 @@
 from pymatgen.io.vasp.outputs import Outcar
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
-TEST_DIR = f"{TEST_FILES_DIR}/vasp/fixtures/BTO_221_99_polarization"
+TEST_DIR = f"{TEST_FILES_DIR}/io/vasp/fixtures/BTO_221_99_polarization"
 bto_folders = ["nonpolar_polarization"]
 bto_folders += [f"interpolation_{idx}_polarization" for idx in range(8, 0, -1)]
 bto_folders += ["polar_polarization"]

tests/analysis/magnetism/test_analyzer.py

@@ -17,26 +17,30 @@
 from pymatgen.core import Element, Lattice, Species, Structure
 from pymatgen.util.testing import TEST_FILES_DIR
 
+TEST_DIR = f"{TEST_FILES_DIR}/analysis/magnetic_orderings"
+
 enum_cmd = which("enum.x") or which("multienum.x")
 makestr_cmd = which("makestr.x") or which("makeStr.x") or which("makeStr.py")
 enumlib_present = enum_cmd and makestr_cmd
 
 
 class TestCollinearMagneticStructureAnalyzer(TestCase):
     def setUp(self):
-        self.Fe = Structure.from_file(f"{TEST_FILES_DIR}/Fe.cif", primitive=True)
+        self.Fe = Structure.from_file(f"{TEST_FILES_DIR}/cif/Fe.cif", primitive=True)
 
-        self.LiFePO4 = Structure.from_file(f"{TEST_FILES_DIR}/LiFePO4.cif", primitive=True)
+        self.LiFePO4 = Structure.from_file(f"{TEST_FILES_DIR}/cif/LiFePO4.cif", primitive=True)
 
-        self.Fe3O4 = Structure.from_file(f"{TEST_FILES_DIR}/Fe3O4.cif", primitive=True)
+        self.Fe3O4 = Structure.from_file(f"{TEST_FILES_DIR}/cif/Fe3O4.cif", primitive=True)
 
-        self.GdB4 = Structure.from_file(f"{TEST_FILES_DIR}/mcif/magnetic.ncl.example.GdB4.mcif", primitive=True)
+        self.GdB4 = Structure.from_file(f"{TEST_FILES_DIR}/io/cif/mcif/magnetic.ncl.example.GdB4.mcif", primitive=True)
 
-        self.NiO_expt = Structure.from_file(f"{TEST_FILES_DIR}/mcif/magnetic.example.NiO.mcif", primitive=True)
+        self.NiO_expt = Structure.from_file(f"{TEST_FILES_DIR}/io/cif/mcif/magnetic.example.NiO.mcif", primitive=True)
 
         # CuO.mcif sourced from https://www.cryst.ehu.es/magndata/index.php?index=1.62
         # doi: 10.1088/0022-3719/21/15/023
-        self.CuO_expt = Structure.from_file(f"{TEST_FILES_DIR}/mcif/magnetic.example.CuO.mcif.gz", primitive=True)
+        self.CuO_expt = Structure.from_file(
+            f"{TEST_FILES_DIR}/io/cif/mcif/magnetic.example.CuO.mcif.gz", primitive=True
+        )
 
         lattice = Lattice.cubic(4.17)
         species = ["Ni", "O"]
@@ -251,17 +255,17 @@ class TestMagneticStructureEnumerator:
     @pytest.mark.skipif(not enumlib_present, reason="enumlib not present")
     def test_ordering_enumeration(self):
         # simple afm
-        structure = Structure.from_file(f"{TEST_FILES_DIR}/magnetic_orderings/LaMnO3.json")
+        structure = Structure.from_file(f"{TEST_DIR}/LaMnO3.json")
         enumerator = MagneticStructureEnumerator(structure)
         assert enumerator.input_origin == "afm"
 
         # ferrimagnetic (Cr produces net spin)
-        structure = Structure.from_file(f"{TEST_FILES_DIR}/magnetic_orderings/Cr2NiO4.json")
+        structure = Structure.from_file(f"{TEST_DIR}/Cr2NiO4.json")
         enumerator = MagneticStructureEnumerator(structure)
         assert enumerator.input_origin == "ferri_by_Cr"
 
         # antiferromagnetic on single magnetic site
-        structure = Structure.from_file(f"{TEST_FILES_DIR}/magnetic_orderings/Cr2WO6.json")
+        structure = Structure.from_file(f"{TEST_DIR}/Cr2WO6.json")
         enumerator = MagneticStructureEnumerator(structure)
         assert enumerator.input_origin == "afm_by_Cr"
 
@@ -275,7 +279,7 @@ def test_ordering_enumeration(self):
         # assert enumerator.input_origin == "afm"
 
         # antiferromagnetic by structural motif
-        structure = Structure.from_file(f"{TEST_FILES_DIR}/magnetic_orderings/Ca3Co2O6.json")
+        structure = Structure.from_file(f"{TEST_DIR}/Ca3Co2O6.json")
         enumerator = MagneticStructureEnumerator(
             structure,
             strategies=("antiferromagnetic_by_motif",),
@@ -288,7 +292,7 @@ def test_ordering_enumeration(self):
 
 class TestMagneticDeformation:
     def test_magnetic_deformation(self):
-        test_structs = loadfn(f"{TEST_FILES_DIR}/magnetic_deformation.json")
+        test_structs = loadfn(f"{TEST_FILES_DIR}/analysis/magnetism/magnetic_deformation.json")
         mag_def = magnetic_deformation(test_structs[0], test_structs[1])
 
         assert mag_def.type == "NM-FM"

tests/analysis/magnetism/test_heisenberg.py

@@ -8,7 +8,7 @@
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import TEST_FILES_DIR
 
-TEST_DIR = f"{TEST_FILES_DIR}/magnetic_orderings"
+TEST_DIR = f"{TEST_FILES_DIR}/analysis/magnetic_orderings"
 
 
 class TestHeisenbergMapper(TestCase):

tests/analysis/magnetism/test_jahnteller.py

@@ -82,9 +82,9 @@ def test_jahn_teller_species_analysis(self):
         assert magnitude == "none"
 
     def test_jahn_teller_structure_analysis(self):
-        LiFePO4 = Structure.from_file(f"{TEST_FILES_DIR}/LiFePO4.cif", primitive=True)
+        LiFePO4 = Structure.from_file(f"{TEST_FILES_DIR}/cif/LiFePO4.cif", primitive=True)
 
-        Fe3O4 = Structure.from_file(f"{TEST_FILES_DIR}/Fe3O4.cif", primitive=True)
+        Fe3O4 = Structure.from_file(f"{TEST_FILES_DIR}/cif/Fe3O4.cif", primitive=True)
 
         assert self.jt.is_jahn_teller_active(LiFePO4)
         assert self.jt.is_jahn_teller_active(Fe3O4)

tests/analysis/solar/test_slme.py

@@ -1,16 +1,16 @@
 from __future__ import annotations
 
-import os
-
 from pytest import approx
 
 from pymatgen.analysis.solar.slme import optics, slme
-from pymatgen.util.testing import PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+
+TEST_DIR = f"{TEST_FILES_DIR}/analysis/solar"
 
 
 class TestSolar(PymatgenTest):
     def test_slme_from_vasprun(self):
-        en, abz, dir_gap, indir_gap = optics(f"{os.path.dirname(__file__)}/vasprun.xml")
+        en, abz, dir_gap, indir_gap = optics(f"{TEST_DIR}/vasprun.xml")
         abz = abz * 100.0
         eff = slme(en, abz, indir_gap, indir_gap, plot_current_voltage=False)
         assert eff == approx(27.729, abs=1e-2)