Merge pull request #353 from arosen93/molecule

Add missing molecule field to cclib TaskDocument
materialsproject · May 23, 2023 · 236d471 · 236d471
2 parents 07073ca + 96fa4c7
commit 236d471
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Showing 2 changed files with 3 additions and 5 deletions.
diff --git a/src/atomate2/common/schemas/cclib.py b/src/atomate2/common/schemas/cclib.py
@@ -200,7 +200,6 @@ def from_logfile(
         initial_molecule = molecules[0]
         final_molecule = molecules[-1]
         attributes["molecule_initial"] = initial_molecule
-        attributes["molecule_final"] = final_molecule
         if store_trajectory:
             attributes["trajectory"] = molecules
 
@@ -249,6 +248,7 @@ def from_logfile(
             attributes=attributes,
             metadata=metadata,
         )
+        doc.molecule = final_molecule
         doc = doc.copy(update=additional_fields)
         return doc
 

diff --git a/tests/common/schemas/test_cclib.py b/tests/common/schemas/test_cclib.py
@@ -33,9 +33,7 @@ def test_cclib_taskdoc(test_dir):
     assert doc.get("metadata", None) is not None
     assert doc["metadata"]["success"] is True
     assert doc["attributes"]["molecule_initial"][0].coords == pytest.approx([0, 0, 0])
-    assert doc["attributes"]["molecule_final"][0].coords == pytest.approx(
-        [0.397382, 0.0, 0.0]
-    )
+    assert doc["molecule"][0].coords == pytest.approx([0.397382, 0.0, 0.0])
     assert doc["last_updated"] is not None
     assert doc["attributes"]["homo_energies"] == pytest.approx(
         [-7.054007346511501, -11.618445074798501]
@@ -85,7 +83,7 @@ def test_cclib_taskdoc(test_dir):
     doc = TaskDocument.from_logfile(p, ".log", store_trajectory=True).dict()
     assert len(doc["attributes"]["trajectory"]) == 7
     assert doc["attributes"]["trajectory"][0] == doc["attributes"]["molecule_initial"]
-    assert doc["attributes"]["trajectory"][-1] == doc["attributes"]["molecule_final"]
+    assert doc["attributes"]["trajectory"][-1] == doc["molecule"]
 
     # Make sure additional fields can be stored
     doc = TaskDocument.from_logfile(p, ".log", additional_fields={"test": "hi"})