abacus/stru: return spins only when atomic magnetic moment is specified (#800)

The old version will induce a bug that dpdata will always store the spin
information, and when dpdata save it to lammps format, the spin
information will also be written, which is invalid for a non-spin lammps
job.
Now, the spin information is saved to dpdata only when the magnetic
moment of one atom is specified, which is necessary for a spin job.

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

- **New Features**
- Spin data is now processed to include only explicitly defined moments,
ensuring accurate output.
- **Documentation**
- User-facing documentation has been updated to clarify when spin
information appears.
- **Tests**
- Test entries for atomic positions have been streamlined by removing
redundant markers.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: root <pxlxingliang>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: pxlxingliang

dpdata/abacus/stru.py

@@ -362,6 +362,7 @@ def parse_pos(coords_lines, atom_names, celldm, cell):
 
     ntype = len(atom_names)
     line_idx = 1  # starting line of first element
+    define_atom_mag = False
     for it in range(ntype):
         atom_name = coords_lines[line_idx].split()[0]
         if atom_name != atom_names[it]:
@@ -390,6 +391,9 @@ def parse_pos(coords_lines, atom_names, celldm, cell):
                 mag = [0, 0, atom_type_mag]
             mags.append(mag)
 
+            if imagmom is not None:
+                define_atom_mag = True
+
             line_idx += 1
     coords = np.array(coords)  # need transformation!!!
 
@@ -409,7 +413,11 @@ def parse_pos(coords_lines, atom_names, celldm, cell):
     if all([i is None for i in lambda_]):
         lambda_ = []
 
-    mags = np.array(mags)
+    # here return the magnetic moment only when the atom magnetic moment is specified.
+    if not define_atom_mag:
+        mags = []
+    else:
+        mags = np.array(mags)
 
     return atom_numbs, coords, move, mags, velocity, sc, lambda_
 
@@ -438,10 +446,13 @@ def get_frame_from_stru(stru):
 
         "cells": list of cell vectors,
         "coords": list of atomic coordinates,
-        "spins": list of magnetic moments,
+        "spins": list of magnetic moments, # return only when set "mag xxx" for each atom in STRU file
         "moves": list of move flags,
     }
     For some keys, if the information is not provided in the STRU file, then it will not be included in the dictionary.
+    "spins" is designed for delta spin calculation, and when dpdata.System is write to lmp format, the spin will be written as magmom.
+    But we should note that this file format is valid only for a spin lammps job, not for a normal job.
+    If you want to use dpgen to run the non-spin job, then you should not define "mag x x x" in the STRU file.
     """
     if not os.path.isfile(stru):
         raise FileNotFoundError(f"ABACUS STRU file {stru} not found!!!")
@@ -472,8 +483,9 @@ def get_frame_from_stru(stru):
         "pp_files": pp_files,
         "cells": np.array([cell]),
         "coords": np.array([coords]),
-        "spins": np.array([mags]),
     }
+    if len(mags) > 0:
+        data["spins"] = np.array([mags])
     if len(orb_files) > 0:
         data["orb_files"] = orb_files
     if len(dpks_descriptor) > 0:

tests/abacus.scf/stru_test

@@ -22,11 +22,11 @@ Cartesian    # Cartesian(Unit is LATTICE_CONSTANT)
 C
 0.0
 1
-5.192682633809 4.557725978258 4.436846615358 1 1 1 mag 0.000000000000 0.000000000000 0.000000000000
+5.192682633809 4.557725978258 4.436846615358 1 1 1
 H
 0.0
 4
-5.416431453540 4.011298860305 3.511161492417 0 0 0 mag 0.000000000000 0.000000000000 0.000000000000
-4.131588222365 4.706745191323 4.431136645083 1 0 1 mag 0.000000000000 0.000000000000 0.000000000000
-5.630930319126 5.521640894956 4.450356541303 1 0 1 mag 0.000000000000 0.000000000000 0.000000000000
-5.499851012568 4.003388899277 5.342621842622 0 1 1 mag 0.000000000000 0.000000000000 0.000000000000
+5.416431453540 4.011298860305 3.511161492417 0 0 0
+4.131588222365 4.706745191323 4.431136645083 1 0 1
+5.630930319126 5.521640894956 4.450356541303 1 0 1
+5.499851012568 4.003388899277 5.342621842622 0 1 1