fix: preserve all VASP database frames

dpgen/database/run.py

@@ -73,9 +73,9 @@ def parsing_vasp(path, config_info_dict, skip_init, output=OUTPUT, id_prefix=Non
 def _parsing_vasp(paths, config_info_dict, id_prefix, iters=True):
     entries = []
     icount = 0
+    iter_record = []
+    iter_record_new = []
     if iters:
-        iter_record = []
-        iter_record_new = []
         try:
             with open("record.database") as f_record:
                 iter_record = [i.split()[0] for i in f_record.readlines()]
@@ -89,9 +89,9 @@ def _parsing_vasp(paths, config_info_dict, id_prefix, iters=True):
             f_outcar = os.path.join(path, "OUTCAR")
             f_job = os.path.join(path, "job.json")
             tmp_iter = path.split("/")[-3]
-            if (tmp_iter in iter_record) and (tmp_iter != iter_record[-1]):
+            if iters and (tmp_iter in iter_record) and (tmp_iter != iter_record[-1]):
                 continue
-            if tmp_iter not in iter_record_new:
+            if iters and tmp_iter not in iter_record_new:
                 iter_record_new.append(tmp_iter)
             vi = VaspInput.from_directory(path)
             if os.path.isfile(f_job):
@@ -135,11 +135,16 @@ def _parsing_vasp(paths, config_info_dict, id_prefix, iters=True):
                     eid = id_prefix + "_" + str(icount)
                 else:
                     eid = str(uuid4())
-            entry = Entry(
-                comp, "vasp", vi.as_dict(), ls.as_dict(), attribute=attrib, entry_id=eid
-            )
-            entries.append(entry)
-            icount += 1
+                entry = Entry(
+                    comp,
+                    "vasp",
+                    vi.as_dict(),
+                    ls.as_dict(),
+                    attribute=attrib,
+                    entry_id=eid,
+                )
+                entries.append(entry)
+                icount += 1
         except Exception:
             # dlog.info(str(Exception))
             dlog.info(f"failed for {path}")

tests/database/test_database_frames.py

@@ -0,0 +1,38 @@
+import unittest
+from types import SimpleNamespace
+from unittest.mock import MagicMock, patch
+
+from dpgen.database.run import _parsing_vasp
+
+
+class TestVaspDatabaseFrames(unittest.TestCase):
+    @patch("dpgen.database.run.Entry", side_effect=lambda *args, **kwargs: kwargs)
+    @patch("dpgen.database.run.LabeledSystem")
+    @patch("dpgen.database.run.VaspInput.from_directory")
+    def test_each_outcar_frame_becomes_an_entry(
+        self, from_directory, labeled_system, _entry
+    ):
+        vasp_input = MagicMock()
+        vasp_input.__getitem__.return_value = SimpleNamespace(
+            structure=SimpleNamespace(composition="H2")
+        )
+        vasp_input.as_dict.return_value = {"input": "vasp"}
+        from_directory.return_value = vasp_input
+
+        frames = [MagicMock(), MagicMock()]
+        frames[0].as_dict.return_value = {"frame": 0}
+        frames[1].as_dict.return_value = {"frame": 1}
+        labeled_system.return_value.to_list.return_value = frames
+
+        entries = _parsing_vasp(
+            ["init/system/02.md/task.000"], {}, "dpgen", iters=False
+        )
+
+        self.assertEqual(len(entries), 2)
+        self.assertEqual(
+            [entry["entry_id"] for entry in entries], ["dpgen_0", "dpgen_1"]
+        )
+
+
+if __name__ == "__main__":
+    unittest.main()