Merge pull request #150 from Exabyte-io/feature/pymatgen.core.structure

feature: pymatgen.core.structure

Author: timurbazhirov

express/parsers/structure.py

@@ -51,12 +51,19 @@ def __init__(self, *args, **kwargs):
 
         # cell_type is either original, primitive or conventional
         self.cell_type = kwargs.get("cell_type", "original")
-        self.structure = Structure.from_str(self.structure_string, self.structure_format)
+
+        # Initialize structure class
+        if self.structure_format == "pymatgen.core.structure":
+            structure_as_dict = json.loads(self.structure_string)
+            self.structure = Structure.from_dict(structure_as_dict)
+        else:
+            self.structure = Structure.from_str(self.structure_string, self.structure_format)
+
         if self.cell_type != "original":
             self.structure = STRUCTURE_MAP[self.cell_type](self.structure)
 
         # keep only one atom inside the basis in order to have the original lattice type
-        self.lattice_only_structure = Structure.from_str(self.structure_string, self.structure_format)  # deepcopy
+        self.lattice_only_structure = self.structure.copy() # deepcopy
         self.lattice_only_structure.remove_sites(range(1, len(self.structure.sites)))
 
     def lattice_vectors(self):

tests/fixtures/data.py

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:1856a70b24c1282e38835fbfdcdcdcb2ec4dac9cd0081bf88b66141412eeacf1
-size 24072
+oid sha256:b43ccbf21870a847e8f01e1aa733605294e04332b3f12946526360a6811c14fb
+size 24827

tests/fixtures/structural/test-002/mp-32.json

@@ -0,0 +1,83 @@
+{
+    "@module": "pymatgen.core.structure",
+    "@class": "Structure",
+    "charge": 0,
+    "lattice": {
+        "matrix": [
+            [
+                3.47512448,
+                0.0,
+                2.00636466
+            ],
+            [
+                1.15837483,
+                3.2763781,
+                2.00636466
+            ],
+            [
+                0.0,
+                0.0,
+                4.01272831
+            ]
+        ],
+        "pbc": [
+            true,
+            true,
+            true
+        ],
+        "a": 4.012728410993222,
+        "b": 4.012727856438068,
+        "c": 4.01272831,
+        "alpha": 59.99998793483045,
+        "beta": 59.99999250641951,
+        "gamma": 59.999990385095536,
+        "volume": 45.68820923290832
+    },
+    "properties": {},
+    "sites": [
+        {
+            "species": [
+                {
+                    "element": "Ge",
+                    "occu": 1
+                }
+            ],
+            "abc": [
+                0.875,
+                0.875,
+                0.875
+            ],
+            "properties": {
+                "magmom": -0.0
+            },
+            "label": "Ge",
+            "xyz": [
+                4.05431189625,
+                2.8668308375000002,
+                7.02227542625
+            ]
+        },
+        {
+            "species": [
+                {
+                    "element": "Ge",
+                    "occu": 1
+                }
+            ],
+            "abc": [
+                0.125,
+                0.125,
+                0.125
+            ],
+            "properties": {
+                "magmom": -0.0
+            },
+            "label": "Ge",
+            "xyz": [
+                0.579187413749999,
+                0.4095472625,
+                1.00318220375
+            ]
+        }
+    ]
+}

tests/integration/parsers/test_structure.py

@@ -1,7 +1,7 @@
 import os
 
 from express.parsers.structure import StructureParser
-from tests.fixtures.data import JVASP_677, SI, SiC
+from tests.fixtures.data import JVASP_677, SI, SiC, GE
 from tests.integration import IntegrationTestBase
 
 
@@ -41,5 +41,11 @@ def test_structure_jarvis_db_entry_basis(self):
     def test_structure_jarvis_db_entry_lattice_bravais(self):
         self.assertDeepAlmostEqual(self.parser.lattice_bravais(), JVASP_677["lattice"], places=2)
 
+    def test_structure_pymatgen_core_structure_basis(self):
+        self.assertDeepAlmostEqual(self.parser.basis(), GE["basis"], places=2)
+
+    def test_structure_pymatgen_core_structure_lattice_bravais(self):
+        self.assertDeepAlmostEqual(self.parser.lattice_bravais(), GE["lattice"], places=2)
+
     def test_material_vasp_structure_order_of_elements(self):
         self.assertDeepAlmostEqual(self.parser.basis(), SiC["basis"], places=2)

tests/manifest.yaml

@@ -174,6 +174,14 @@ test_structure_jarvis_db_entry_lattice_bravais:
   structurePath: fixtures/structural/test-002/JVASP-677.json
   structureFormat: jarvis-db-entry
 
+test_structure_pymatgen_core_structure_basis:
+  structurePath: fixtures/structural/test-002/mp-32.json
+  structureFormat: pymatgen.core.structure
+
+test_structure_pymatgen_core_structure_lattice_bravais:
+  structurePath: fixtures/structural/test-002/mp-32.json
+  structureFormat: pymatgen.core.structure
+
 test_molecule_inchi:
   structurePath: fixtures/structural/test-001/POSCAR