fix: export ABACUS structures for atomic LAMMPS

dpgen2/conf/conf_generator.py

@@ -59,9 +59,17 @@ def get_file_content(
         for ii in range(len(ms)):
             ss = ms[ii]
             for jj in range(ss.get_nframes()):
+                frame = ss[jj]
+                if fmt in {"lmp", "lammps/lmp"}:
+                    # Exploration inputs always declare ``atom_style atomic``.
+                    # dpdata serializes ABACUS magnetic moments as four extra
+                    # atom columns, which belong to LAMMPS's spin atom style and
+                    # make the resulting atomic-style data file unreadable.
+                    # Remove them only from this per-frame export copy.
+                    frame.data.pop("spins", None)
                 with tempfile.NamedTemporaryFile() as ft:
                     tf = Path(ft.name)
-                    ss[jj].to(fmt, tf)
+                    frame.to(fmt, tf)
                     ret.append(tf.read_text())
         return ret
 

tests/conf/test_file_conf.py

@@ -105,6 +105,29 @@
     + "Atoms # atomic\n\n     1      2    0.0000000000    0.0000000000    0.0000000000\n"
 )
 
+abacus_stru = """ATOMIC_SPECIES
+Si 28.085 Si.upf
+
+NUMERICAL_ORBITAL
+Si.orb
+
+LATTICE_CONSTANT
+1.0
+
+LATTICE_VECTORS
+10.0 0.0 0.0
+0.0 10.0 0.0
+0.0 0.0 10.0
+
+ATOMIC_POSITIONS
+Cartesian
+
+Si
+0.0
+1
+1.0 2.0 3.0 1 1 1 mag 0.0
+"""
+
 
 class TestFileConfGenerator(unittest.TestCase):
     def setUp(self):
@@ -205,6 +228,20 @@ def test_deepmd_mixed(self):
 
 
 class TestFileConfGeneratorContent(unittest.TestCase):
+    def test_abacus_spin_metadata_is_not_written_to_atomic_lammps_data(self):
+        stru = Path("STRU")
+        stru.write_text(abacus_stru)
+        self.addCleanup(stru.unlink, missing_ok=True)
+
+        content = FileConfGenerator(str(stru), fmt="abacus/stru").get_file_content(
+            type_map=["Si"]
+        )[0]
+        atom_section = content.split("Atoms # atomic", maxsplit=1)[1]
+        atom_line = next(line for line in atom_section.splitlines() if line.strip())
+
+        # Atomic style accepts only ID, type, and xyz coordinates.
+        self.assertEqual(len(atom_line.split()), 5)
+
     def test_list_1(self):
         f0 = Path("f0.POSCAR")
         f1 = Path("f1.POSCAR")