Initial support for structural data extraction from a JARVIS database entry

express/parsers/structure.py

@@ -1,7 +1,11 @@
 import io
+import json
+
 import pymatgen as mg
 from pymatgen.core.structure import Structure
 from ase.io import read, write
+from jarvis.core.atoms import Atoms
+from jarvis.io.vasp.inputs import Poscar
 
 from express.parsers import BaseParser
 from express.parsers.mixins.ionic import IonicDataMixin
@@ -33,6 +37,11 @@ def __init__(self, *args, **kwargs):
             self.structure_format = "poscar"
             self.structure_string = self.espresso_input_to_poscar(self.structure_string)
 
+        # convert jarvis-db-entry JSON into poscar
+        if self.structure_format == "jarvis-db-entry":
+            self.structure_format = "poscar"
+            self.structure_string = self.jarvis_db_entry_json_to_poscar(self.structure_string)
+
         # cell_type is either original, primitive or conventional
         self.cell_type = kwargs["cell_type"]
         self.structure = Structure.from_str(self.structure_string, self.structure_format)
@@ -223,3 +232,19 @@ def espresso_input_to_poscar(self, espresso_input):
         input_.close()
         output_.close()
         return content
+
+    def jarvis_db_entry_json_to_poscar(self, jarvis_db_entry_json_str):
+        """
+        Extracts structure from jarvis atoms dictionary and returns in poscar format.
+
+        Args:
+            jarvis_atoms_json (dict): input content
+
+        Returns:
+            str: poscar
+        """
+        jarvis_db_entry = json.loads(jarvis_db_entry_json_str)
+        atoms = Atoms.from_dict(jarvis_db_entry["atoms"])
+        poscar = Poscar(atoms)
+        content = poscar.to_string()
+        return content

express/properties/material.py

@@ -4,7 +4,6 @@
 from express.parsers.apps.vasp.parser import VaspParser
 from express.parsers.crystal import CrystalParser
 from express.parsers.molecule import MoleculeParser
-from express.parsers.structure import StructureParser  # noqa: F401
 from express.parsers.utils import lattice_basis_to_poscar
 from express.properties import BaseProperty
 from express.properties.non_scalar.symmetry import Symmetry

requirements.txt

@@ -3,3 +3,4 @@ pymatgen==2023.8.10
 ase==3.17.0
 esse==2023.12.25.post0
 rdkit-pypi>=2022.3.5
+jarvis-tools==2023.12.12

tests/fixtures/structural/test-002/JVASP-677.json

@@ -0,0 +1,92 @@
+{
+    "phi": {
+        "nelect": 48,
+        "phi": 4.73414095269429,
+        "scf_vbm": -1.6519,
+        "scf_cbm": -1.6472,
+        "Ef": -1.97822464,
+        "scf_gap": 0.0,
+        "avg_max": 2.7559163126942896,
+        "scf_dir": false
+    },
+    "atoms": {
+        "lattice_mat": [
+            [
+                3.353617811446221,
+                0.0,
+                0.0
+            ],
+            [
+                0.0,
+                6.273423021773385,
+                0.0
+            ],
+            [
+                0.0,
+                0.0,
+                33.313518
+            ]
+        ],
+        "coords": [
+            [
+                0.0,
+                0.6004615456553349,
+                0.2002745956304112
+            ],
+            [
+                0.5,
+                0.9651745521229684,
+                0.205389889617873
+            ],
+            [
+                0.0,
+                0.8600702878546368,
+                0.2642586539633663
+            ],
+            [
+                0.5,
+                0.3508476059345406,
+                0.2471701152668883
+            ],
+            [
+                0.5,
+                0.7055702442093444,
+                0.1414059027438078
+            ],
+            [
+                0.0,
+                0.2147957642231673,
+                0.1584938427776558
+            ]
+        ],
+        "elements": [
+            "Mo",
+            "Mo",
+            "Te",
+            "Te",
+            "Te",
+            "Te"
+        ],
+        "abc": [
+            3.35362,
+            6.27342,
+            33.31352
+        ],
+        "angles": [
+            90.0,
+            90.0,
+            90.0
+        ],
+        "cartesian": false,
+        "props": [
+            "",
+            "",
+            "",
+            "",
+            "",
+            ""
+        ]
+    },
+    "jid": "JVASP-677",
+    "doi": "https://figshare.com/articles/dataset/Monolayer_data_for_heterostructure/22344571"
+}

tests/integration/parsers/test_structure.py

@@ -1,7 +1,7 @@
 import os
 
 from express.parsers.structure import StructureParser
-from tests.fixtures.data import SI
+from tests.fixtures.data import SI, JVASP_677
 from tests.integration import IntegrationTestBase
 
 
@@ -26,11 +26,17 @@ def parser(self):
     def test_structure_espresso_basis(self):
         self.assertDeepAlmostEqual(self.parser.basis(), SI["basis"], places=2)
 
-    def test_structure_vasp_basis(self):
-        self.assertDeepAlmostEqual(self.parser.basis(), SI["basis"], places=2)
-
     def test_structure_espresso_lattice_bravais(self):
         self.assertDeepAlmostEqual(self.parser.lattice_bravais(), SI["lattice"], places=2)
 
+    def test_structure_vasp_basis(self):
+        self.assertDeepAlmostEqual(self.parser.basis(), SI["basis"], places=2)
+
     def test_structure_vasp_lattice_bravais(self):
         self.assertDeepAlmostEqual(self.parser.lattice_bravais(), SI["lattice"], places=2)
+
+    def test_structure_jarvis_db_entry_basis(self):
+        self.assertDeepAlmostEqual(self.parser.basis(), JVASP_677["basis"], places=2)
+
+    def test_structure_jarvis_db_entry_lattice_bravais(self):
+        self.assertDeepAlmostEqual(self.parser.lattice_bravais(), JVASP_677["lattice"], places=2)

tests/manifest.yaml

@@ -212,6 +212,14 @@ test_structure_vasp_basis:
 test_structure_vasp_lattice_bravais:
   structurePath: fixtures/vasp/test-001/POSCAR
 
+test_structure_jarvis_db_entry_basis:
+  structurePath: fixtures/structural/test-002/JVASP-677.json
+  structureFormat: jarvis-db-entry
+
+test_structure_jarvis_db_entry_lattice_bravais:
+  structurePath: fixtures/structural/test-002/JVASP-677.json
+  structureFormat: jarvis-db-entry
+
 test_molecule_inchi:
   structurePath: fixtures/structural/test-001/POSCAR