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]>

Author: wanghan-iapcm

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/set.000/box.npy

@@ -0,0 +1,98 @@
+1
+1
+0
+0
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+0
+0
+0
+0
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+0
+0
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tests/pymatgen_data/deepmd/set.000/coord.npy

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