fix: 781 pymatgen structure bug (#782)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
	- Enhanced support for PyMatGen structure format conversion
	- Improved handling of periodic boundary conditions (PBC)

- **Tests**
	- Added new test class for PyMatGen structure conversion
	- Expanded test data with additional element types (Fe, Li, O, P)

- **Bug Fixes**
	- Refined atomic species list generation
	- Improved error handling for structure periodicity

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: Han Wang <[email protected]>

dpdata/plugins/pymatgen.py

@@ -30,16 +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 = []
-        for name, numb in zip(data["atom_names"], data["atom_numbs"]):
-            species.extend([name] * numb)
+        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,

dpdata/pymatgen/structure.py

@@ -4,18 +4,27 @@
 
 
 def from_system_data(structure) -> dict:
-    symbols = [site.species_string for site in structure]
+    """Convert one pymatgen structure to dpdata's datadict."""
+    symbols = [ii.specie.symbol for ii in structure]
     atom_names = list(structure.symbol_set)
     atom_numbs = [symbols.count(symbol) for symbol in atom_names]
     atom_types = np.array([atom_names.index(symbol) for symbol in symbols]).astype(int)
     coords = structure.cart_coords
     cells = structure.lattice.matrix
+    if all(structure.pbc):
+        pbc = True
+    elif not any(structure.pbc):
+        pbc = False
+    else:
+        raise ValueError(f"Partial pbc condition {structure.pbc} is not supported")
 
     info_dict = {
         "atom_names": atom_names,
         "atom_numbs": atom_numbs,
         "atom_types": atom_types,
         "coords": np.array([coords]),
         "cells": np.array([cells]),
+        "orig": np.zeros(3),
+        "nopbc": not pbc,
     }
     return info_dict

tests/pymatgen_data/deepmd/type.raw

@@ -0,0 +1,98 @@
+1
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tests/pymatgen_data/deepmd/type_map.raw

@@ -0,0 +1,4 @@
+Fe
+Li
+O
+P

tests/test_pymatgen_structure.py

@@ -0,0 +1,61 @@
+from __future__ import annotations
+
+import os
+import unittest
+
+from comp_sys import CompSys, IsNoPBC, IsPBC
+from context import dpdata
+
+try:
+    from pymatgen.core import Structure  # noqa: F401
+
+    exist_module = True
+except Exception:
+    exist_module = False
+
+
+@unittest.skipIf(not exist_module, "skip pymatgen")
+class TestFormPytmatgen(unittest.TestCase, CompSys):
+    def setUp(self):
+        structure = Structure.from_file(os.path.join("poscars", "POSCAR.P42nmc"))
+        self.system_1 = dpdata.System(structure, fmt="pymatgen/structure")
+        self.system_2 = dpdata.System(
+            os.path.join("poscars", "POSCAR.P42nmc"), fmt="poscar"
+        )
+        self.places = 6
+        self.e_places = 6
+        self.f_places = 6
+        self.v_places = 6
+
+
+@unittest.skipIf(not exist_module, "skip pymatgen")
+class TestFormToPytmatgen(unittest.TestCase, CompSys, IsPBC):
+    def setUp(self):
+        self.system = dpdata.System("pymatgen_data/deepmd/", fmt="deepmd/npy")
+        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
+
+
+@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()