abacus: fix bug in make_abacus_scf_stru (#1755)

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

- **Bug Fixes**
- Improved the selection of pseudopotential and orbital files to ensure
only relevant files for the atoms present in the system are included.
<!-- 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

dpgen/generator/lib/abacus_scf.py

@@ -213,9 +213,38 @@ def make_abacus_scf_stru(
 ):
     sys_data_copy = copy.deepcopy(sys_data)
     # re-construct the path of files by pporb + file name
-    fp_pp_files = [os.path.join(pporb, i) for i in fp_pp_files]
+    # when element in sys_data is part of type_map/fp_pp_files
+    # we need to only pass the pp_file in sys_data, but not all pp_files
+    if type_map is None:
+        type_map = sys_data_copy["atom_names"]
+
+    missing_atoms = set(sys_data_copy["atom_names"]) - set(type_map)
+    if len(missing_atoms) > 0:
+        raise ValueError(
+            f"Some atoms in sys_data are not in type_map: {missing_atoms}. "
+            "Please provide a valid type_map."
+        )
+
+    if len(fp_pp_files) != len(type_map):
+        raise ValueError(
+            "The length of fp_pp_files should be equal to the length of type_map."
+        )
+    if fp_orb_files is not None and len(fp_orb_files) != len(type_map):
+        raise ValueError(
+            "The length of fp_orb_files should be equal to the length of type_map."
+        )
+
+    fp_pp_files = [
+        os.path.join(pporb, fp_pp_files[type_map.index(atom_name)])
+        for atom_name in sys_data_copy["atom_names"]
+    ]
+
     if fp_orb_files is not None:
-        fp_orb_files = [os.path.join(pporb, i) for i in fp_orb_files]
+        fp_orb_files = [
+            os.path.join(pporb, fp_orb_files[type_map.index(atom_name)])
+            for atom_name in sys_data_copy["atom_names"]
+        ]
+
     if fp_dpks_descriptor is not None:
         fp_dpks_descriptor = os.path.join(pporb, fp_dpks_descriptor)
 

tests/data/test_gen_bulk_abacus.py

@@ -76,7 +76,6 @@ def test(self):
     def testSTRU(self):
         jdata = self.jdata
         jdata["from_poscar_path"] = "./Cu.STRU"
-        jdata["potcars"] = ["abacus.in/Cu_ONCV_PBE-1.0.upf"]
         make_super_cell_STRU(jdata)
         make_abacus_relax(jdata, {"fp_resources": {}})
         make_scale_ABACUS(jdata)