Adding jarvis-tools structures

optimade/adapters/structures/__init__.py

@@ -6,6 +6,7 @@
 from .cif import get_cif
 from .proteindatabank import get_pdb, get_pdbx_mmcif
 from .pymatgen import get_pymatgen
+from .jarvis import get_jarvis_atoms
 
 
 __all__ = ("Structure",)
@@ -24,4 +25,5 @@ class Structure(EntryAdapter):
         "pdb": get_pdb,
         "pdbx_mmcif": get_pdbx_mmcif,
         "pymatgen": get_pymatgen,
+        "jarvis": get_jarvis_atoms,
     }

optimade/adapters/structures/jarvis.py

@@ -0,0 +1,43 @@
+from warnings import warn
+from optimade.models import StructureResource as OptimadeStructure
+from optimade.adapters.exceptions import ConversionError
+from optimade.adapters.structures.utils import pad_positions
+
+try:
+    from jarvis.core.atoms import Atoms
+except (ImportError, ModuleNotFoundError):
+    Atoms = None
+    JARVIS_NOT_FOUND = "jarvis-tools package not found, cannot convert structure to a JARVIS Atoms. Visit https://github.com/usnistgov/jarvis"
+
+
+__all__ = ("get_jarvis_atoms",)
+
+
+def get_jarvis_atoms(optimade_structure: OptimadeStructure) -> Atoms:
+    """ Get jarvis Atoms from OPTIMADE structure
+
+    NOTE: Cannot handle partial occupancies
+
+    :param optimade_structure: OPTIMADE structure
+    :return: jarvis.core.Atoms
+    """
+    if globals().get("Atoms", None) is None:
+        warn(JARVIS_NOT_FOUND)
+        return None
+
+    attributes = optimade_structure.attributes
+
+    # Cannot handle partial occupancies
+    if "disorder" in attributes.structure_features:
+        raise ConversionError(
+            "jarvis-tools cannot handle structures with partial occupancies."
+        )
+
+    cartesian_site_positions, _ = pad_positions(attributes.cartesian_site_positions)
+
+    return Atoms(
+        lattice_mat=attributes.lattice_vectors,
+        elements=[specie.name for specie in attributes.species],
+        coords=cartesian_site_positions,
+        cartesian=True,
+    )

setup.py

@@ -16,6 +16,7 @@
 cif_deps = ["numpy~=1.18"]
 pdb_deps = cif_deps
 pymatgen_deps = ["pymatgen~=2020.3"]
+jarvis_deps = ["jarvis-tools~=2020.6"]
 client_deps = cif_deps
 
 # General
@@ -27,7 +28,15 @@
     "jsondiff",
 ] + server_deps
 dev_deps = ["pylint", "black", "pre-commit", "invoke"] + testing_deps + client_deps
-all_deps = dev_deps + django_deps + elastic_deps + aiida_deps + ase_deps + pymatgen_deps
+all_deps = (
+    dev_deps
+    + django_deps
+    + elastic_deps
+    + aiida_deps
+    + ase_deps
+    + pymatgen_deps
+    + jarvis_deps
+)
 
 setup(
     name="optimade",
@@ -76,6 +85,7 @@
         "cif": cif_deps,
         "pdb": pdb_deps,
         "pymatgen": pymatgen_deps,
+        "jarvis": jarvis_deps,
     },
     entry_points={
         "console_scripts": ["optimade_validator=optimade.validator:validate"]

tests/adapters/structures/test_jarvis.py

@@ -0,0 +1,53 @@
+# pylint: disable=import-error
+import pytest
+
+from .utils import get_min_ver
+
+min_ver = get_min_ver("jarvis-tools")
+jarvis = pytest.importorskip(
+    "jarvis",
+    minversion=min_ver,
+    reason=f"jarvis-tools must be installed with minimum version {min_ver} for these tests to"
+    " be able to run",
+)
+
+from jarvis.core.atoms import Atoms
+from optimade.adapters import Structure
+from optimade.adapters.exceptions import ConversionError
+from optimade.adapters.structures.jarvis import get_jarvis_atoms
+
+
+def test_successful_conversion(RAW_STRUCTURES):
+    """Make sure its possible to convert"""
+    for structure in RAW_STRUCTURES:
+        assert isinstance(get_jarvis_atoms(Structure(structure)), Atoms)
+
+
+def test_null_positions(null_position_structure):
+    """Make sure null positions are handled"""
+    assert isinstance(get_jarvis_atoms(null_position_structure), Atoms)
+
+
+def test_null_lattice_vectors(null_lattice_vector_structure):
+    """Make sure null lattice vectors are handled"""
+    assert isinstance(get_jarvis_atoms(null_lattice_vector_structure), Atoms)
+
+
+def test_special_species(SPECIAL_SPECIES_STRUCTURES):
+    """Make sure vacancies and non-chemical symbols ("X") are handled"""
+    for special_structure in SPECIAL_SPECIES_STRUCTURES:
+        structure = Structure(special_structure)
+
+        # Since all the special species structure only have a single species, this works fine.
+        if len(structure.species[0].chemical_symbols) > 1:
+            # If the structure is disordered (has partial occupancies of any kind),
+            # jarvis-tools cannot convert the structure
+            with pytest.raises(
+                ConversionError,
+                match="jarvis-tools cannot handle structures with partial occupancies",
+            ):
+                get_jarvis_atoms(structure)
+        else:
+            # No partial occupancies, just special/non-standard species.
+            # jarvis-tools should convert these structure fine enough.
+            assert isinstance(get_jarvis_atoms(structure), Atoms)

tests/adapters/structures/test_structures.py

@@ -8,6 +8,7 @@
     import ase  # noqa: F401
     import numpy  # noqa: F401
     import pymatgen  # noqa: F401
+    import jarvis  # noqa: F401
 except ImportError:
     all_modules_found = False
 else:
@@ -107,10 +108,11 @@ def test_no_module_conversion(self, structure):
             "ase": ["ase"],
             "numpy": ["cif", "pdb", "pdbx_mmcif"],
             "pymatgen": ["pymatgen"],
+            "jarvis": ["jarvis"],
         }
 
         modules_to_test = []
-        for module in ("aiida", "ase", "numpy", "pymatgen"):
+        for module in ("aiida", "ase", "numpy", "pymatgen", "jarvis"):
             try:
                 importlib.import_module(module)
             except (ImportError, ModuleNotFoundError):