fix(lammps): emit valid spin atom style sections

dpdata/formats/lammps/lmp.py

@@ -20,6 +20,9 @@
     "molecular": (0, 2, 3, 4, 5, True, False, None),
     "dipole": (0, 1, 3, 4, 5, False, True, 2),
     "sphere": (0, 1, 4, 5, 6, False, False, None),
+    # LAMMPS ``atom_style spin`` stores x/y/z in the same columns as atomic
+    # style, followed by a unit spin direction and its magnetic moment.
+    "spin": (0, 1, 2, 3, 4, False, False, None),
 }
 
 
@@ -327,6 +330,10 @@ def get_charges(lines: list[str], atom_style: str = "atomic") -> np.ndarray | No
 
 
 def get_spins(lines: list[str], atom_style: str = "atomic") -> np.ndarray | None:
+    if atom_style not in {"atomic", "spin"}:
+        # Extra columns in dipole/sphere/etc. styles describe those styles'
+        # own properties and must never be reinterpreted as magnetic spins.
+        return None
     atom_lines = get_atoms(lines)
     if len(atom_lines[0].split()) < 8:
         return None
@@ -567,7 +574,11 @@ def from_system_data(system, f_idx=0):
             ret += mass_fmt % (ii + 1, mass, atom_name)
         ret += "\n"
 
-    ret += "Atoms # atomic\n"
+    # The extra direction/magnitude columns have an official LAMMPS layout:
+    # they belong to ``atom_style spin``, not ``atom_style atomic``.  Using the
+    # matching section annotation lets ``read_data`` validate the rows.
+    atom_style = "spin" if "spins" in system else "atomic"
+    ret += f"Atoms # {atom_style}\n"
     ret += "\n"
     coord_fmt = (
         ptr_int_fmt

dpdata/plugins/lammps.py

@@ -60,7 +60,7 @@ def from_system(
         atom_style : str, optional
             The LAMMPS atom style. Default is "auto" which attempts to detect
             the style automatically from the file. Can also be explicitly set to:
-            atomic, full, charge, bond, angle, molecular, dipole, sphere
+            atomic, full, charge, bond, angle, molecular, dipole, sphere, spin
         **kwargs : dict
             Other parameters
 
@@ -100,6 +100,7 @@ def from_system(
         - molecular: atom-ID molecule-ID atom-type x y z
         - dipole: atom-ID atom-type charge x y z mux muy muz
         - sphere: atom-ID atom-type diameter density x y z
+        - spin: atom-ID atom-type x y z spx spy spz sp
         """
         with open_file(file_name) as fp:
             lines = [line.rstrip("\n") for line in fp]

tests/test_lammps_spin.py

@@ -2,6 +2,7 @@
 
 import os
 import shutil
+import subprocess
 import unittest
 
 import numpy as np
@@ -54,10 +55,20 @@ def test_dump_input(self):
         with open(self.lmp_coord_name) as f:
             c = f.read()
 
+        self.assertIn("Atoms # spin", c)
         coord_ref = """     1      1    0.0000000000    0.0000000000    0.0000000000    0.6000000000    0.8000000000    0.0000000000    5.0000000000
      2      2    1.2621856000    0.7018028000    0.5513885000    0.0000000000    0.8000000000    0.6000000000    5.0000000000"""
         self.assertTrue(coord_ref in c)
 
+        # Auto-detection must understand the official spin annotation and
+        # reconstruct the original vectors, including their magnitudes.
+        roundtrip = dpdata.System(
+            self.lmp_coord_name, fmt="lammps/lmp", type_map=["O", "H"]
+        )
+        np.testing.assert_allclose(
+            roundtrip.data["spins"], self.tmp_system.data["spins"]
+        )
+
     def test_dump_input_zero_spin(self):
         self.tmp_system.data["spins"] = [[[0, 0, 0], [0, 0, 0]]]
         self.tmp_system.to("lammps/lmp", self.lmp_coord_name)
@@ -68,6 +79,28 @@ def test_dump_input_zero_spin(self):
      2      2    1.2621856000    0.7018028000    0.5513885000    0.0000000000    0.0000000000    1.0000000000    0.0000000000"""
         self.assertTrue(coord_ref in c)
 
+    def test_dump_input_is_accepted_by_lammps(self):
+        """The generated spin section must be valid for LAMMPS itself."""
+        lmp = shutil.which("lmp")
+        if lmp is None:
+            self.skipTest("LAMMPS executable is not installed")
+        self.tmp_system.to("lammps/lmp", self.lmp_coord_name)
+        result = subprocess.run(
+            [lmp, "-log", "none", "-screen", "none"],
+            input=(
+                "units metal\n"
+                "atom_style spin\n"
+                f"read_data {self.lmp_coord_name}\n"
+                "run 0\n"
+            ),
+            text=True,
+            capture_output=True,
+            check=False,
+        )
+        if result.returncode and "Unrecognized atom style" in result.stderr:
+            self.skipTest("LAMMPS was built without the SPIN package")
+        self.assertEqual(result.returncode, 0, result.stderr)
+
     def test_read_input(self):
         # check if dpdata can read the spins
         tmp_system = dpdata.System(