fix nopbc

dpdata/plugins/pymatgen.py

@@ -30,14 +30,15 @@ def to_system(self, data, **kwargs):
         """Convert System to Pymatgen Structure obj."""
         structures = []
         try:
-            from pymatgen.core import Structure
+            from pymatgen.core import Lattice, Structure
         except ModuleNotFoundError as e:
             raise ImportError("No module pymatgen.Structure") from e
 
         species = [data["atom_names"][tt] for tt in data["atom_types"]]
+        pbc = not (data.get("nopbc", False))
         for ii in range(data["coords"].shape[0]):
             structure = Structure(
-                data["cells"][ii],
+                Lattice(data["cells"][ii], pbc=[pbc] * 3),
                 species,
                 data["coords"][ii],
                 coords_are_cartesian=True,

tests/test_pymatgen_structure.py

@@ -3,7 +3,7 @@
 import os
 import unittest
 
-from comp_sys import CompSys, IsPBC
+from comp_sys import CompSys, IsNoPBC, IsPBC
 from context import dpdata
 
 try:
@@ -42,5 +42,20 @@ def setUp(self):
         self.v_places = 6
 
 
+@unittest.skipIf(not exist_module, "skip pymatgen")
+class TestFormToPytmatgenNopbc(unittest.TestCase, CompSys, IsNoPBC):
+    def setUp(self):
+        self.system = dpdata.System("pymatgen_data/deepmd/", fmt="deepmd/npy")
+        self.system.data["nopbc"] = True
+        self.system_1 = self.system
+        self.system_2 = dpdata.System().from_pymatgen_structure(
+            self.system.to("pymatgen/structure")[0]
+        )
+        self.places = 6
+        self.e_places = 6
+        self.f_places = 6
+        self.v_places = 6
+
+
 if __name__ == "__main__":
     unittest.main()