Add test for AiiDA with masses

Fix masses creation for AiiDA StructureData to take concentration into account.
Materials-Consortia · Dec 21, 2020 · 8148ed8 · 8148ed8
1 parent 705533f
commit 8148ed8
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Showing 3 changed files with 98 additions and 5 deletions.
diff --git a/optimade/adapters/structures/aiida.py b/optimade/adapters/structures/aiida.py
@@ -49,8 +49,7 @@ def get_aiida_structure_data(optimade_structure: OptimadeStructure) -> Structure
     for kind in attributes.species:
         symbols = []
         concentration = []
-        masses = []
-        mass = 1.0
+        mass = 0.0
         for index, chemical_symbol in enumerate(kind.chemical_symbols):
             # NOTE: The non-chemical element identifier "X" is identical to how AiiDA handles this,
             # so it will be treated the same as any other true chemical identifier.
@@ -64,11 +63,13 @@ def get_aiida_structure_data(optimade_structure: OptimadeStructure) -> Structure
 
                 # AiiDA needs a definition for the mass, and for it to be > 0
                 # mass is OPTIONAL for OPTIMADE structures
-                masses.append(kind.mass[index] if kind.mass else mass)
-        mass = sum(masses) if masses else mass
+                if kind.mass:
+                    mass += kind.concentration[index] * kind.mass[index]
 
         structure.append_kind(
-            Kind(symbols=symbols, weights=concentration, mass=mass, name=kind.name)
+            Kind(
+                symbols=symbols, weights=concentration, mass=mass or 1.0, name=kind.name
+            )
         )
 
     # Add Sites

diff --git a/tests/adapters/structures/special_species.json b/tests/adapters/structures/special_species.json
@@ -208,5 +208,76 @@
         ]
         }
     }
+  },
+  {
+    "id": "mpf_1",
+    "type": "structures",
+    "attributes": {
+        "last_modified": "2019-06-08T05:13:37.331000",
+        "elements": [
+            "Ac", "O"
+        ],
+        "nelements": 1,
+        "elements_ratios": [
+        1
+        ],
+        "chemical_formula_descriptive": "AcO",
+        "chemical_formula_reduced": "AcO",
+        "chemical_formula_anonymous": "AB",
+        "dimension_types": [
+        1,
+        1,
+        1
+        ],
+        "nperiodic_dimensions": 3,
+        "lattice_vectors": [
+        [
+            1.2503264826932692,
+            0,
+            0
+        ],
+        [
+            0,
+            9.888509716321765,
+            0
+        ],
+        [
+            0,
+            0,
+            0.2972637673241818
+        ]
+        ],
+        "cartesian_site_positions": [
+        [
+            0.17570227444196573,
+            0.17570227444196573,
+            0.17570227444196573
+        ]
+        ],
+        "nsites": 1,
+        "species_at_sites": [
+        "AcO"
+        ],
+        "species": [
+        {
+            "name": "AcO",
+            "chemical_symbols": ["Ac", "O"],
+            "concentration": [0.9, 0.1],
+            "mass": [227.0, 15.999]
+        }
+        ],
+        "structure_features": ["disorder"],
+        "_exmpl_chemsys": "AcO"
+    },
+    "relationships": {
+        "references": {
+        "data": [
+            {
+            "id": "dijkstra1968",
+            "type": "references"
+            }
+        ]
+        }
+    }
   }
 ]
diff --git a/tests/adapters/structures/test_aiida.py b/tests/adapters/structures/test_aiida.py
@@ -44,6 +44,7 @@ def test_special_species(SPECIAL_SPECIES_STRUCTURES):
 
         assert isinstance(aiida_structure, StructureData)
 
+        # Test species.chemical_symbols
         if "vacancy" in structure.attributes.species[0].chemical_symbols:
             assert aiida_structure.has_vacancies
             assert not aiida_structure.is_alloy
@@ -53,3 +54,23 @@ def test_special_species(SPECIAL_SPECIES_STRUCTURES):
         else:
             assert not aiida_structure.has_vacancies
             assert not aiida_structure.is_alloy
+
+        # Test species.mass
+        if structure.attributes.species[0].mass:
+            if len(structure.attributes.species[0].mass) > 1:
+                assert aiida_structure.kinds[0].mass == sum(
+                    [
+                        conc * mass
+                        for conc, mass in zip(
+                            structure.attributes.species[0].concentration,
+                            structure.attributes.species[0].mass,
+                        )
+                    ]
+                )
+            else:
+                assert (
+                    aiida_structure.kinds[0].mass
+                    == structure.attributes.species[0].mass[0]
+                )
+        else:
+            assert aiida_structure.kinds[0].mass == 1.0