fix: support shuffle_poscar for other formats (#1610)

Fix #1570.

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

## Summary by CodeRabbit

- **New Features**
- Enhanced efficiency in handling atomic configurations by directly
modifying coordinates in memory, eliminating the need for intermediate
files.
	- Simplified logic for shuffling atomic indices.

- **Bug Fixes**
- Removed obsolete function that may have caused confusion in the
workflow related to POSCAR file management.

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

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

Author: njzjz

dpgen/generator/run.py

@@ -216,19 +216,6 @@ def poscar_natoms(lines):
     return numb_atoms
 
 
-def poscar_shuffle(poscar_in, poscar_out):
-    with open(poscar_in) as fin:
-        lines = list(fin)
-    numb_atoms = poscar_natoms(lines)
-    idx = np.arange(8, 8 + numb_atoms)
-    np.random.shuffle(idx)
-    out_lines = lines[0:8]
-    for ii in range(numb_atoms):
-        out_lines.append(lines[idx[ii]])
-    with open(poscar_out, "w") as fout:
-        fout.write("".join(out_lines))
-
-
 def expand_idx(in_list):
     ret = []
     for ii in in_list:
@@ -1272,24 +1259,17 @@ def make_model_devi(iter_index, jdata, mdata):
     conf_path = os.path.join(work_path, "confs")
     create_path(conf_path)
     sys_counter = 0
+    rng = np.random.default_rng()
     for ss in conf_systems:
         conf_counter = 0
         for cc in ss:
             if model_devi_engine == "lammps":
                 conf_name = make_model_devi_conf_name(
                     sys_idx[sys_counter], conf_counter
                 )
-                orig_poscar_name = conf_name + ".orig.poscar"
                 poscar_name = conf_name + ".poscar"
                 lmp_name = conf_name + ".lmp"
-                if shuffle_poscar:
-                    os.symlink(cc, os.path.join(conf_path, orig_poscar_name))
-                    poscar_shuffle(
-                        os.path.join(conf_path, orig_poscar_name),
-                        os.path.join(conf_path, poscar_name),
-                    )
-                else:
-                    os.symlink(cc, os.path.join(conf_path, poscar_name))
+                os.symlink(cc, os.path.join(conf_path, poscar_name))
                 if "sys_format" in jdata:
                     fmt = jdata["sys_format"]
                 else:
@@ -1299,6 +1279,8 @@ def make_model_devi(iter_index, jdata, mdata):
                     fmt=fmt,
                     type_map=jdata["type_map"],
                 )
+                if shuffle_poscar:
+                    system.data["coords"] = rng.permuted(system.data["coords"], axis=1)
                 if jdata.get("model_devi_nopbc", False):
                     system.remove_pbc()
                 system.to_lammps_lmp(os.path.join(conf_path, lmp_name))