abacus: add checks on pp and orb in construction of STRU

dpdata/abacus/scf.py

@@ -628,6 +628,9 @@ def make_unlabeled_stru(
     link_file : bool, optional
         Whether to link the pseudo potential files and orbital files in the STRU file.
         If True, then only filename will be written in the STRU file, and make a soft link to the real file.
+    dest_dir : str, optional
+        The destination directory to make the soft link of the pseudo potential files and orbital files.
+        
     For velocity, mag, angle1, angle2, sc, and lambda_, if the value is None, then the corresponding information will not be written.
     ABACUS support defining "mag" and "angle1"/"angle2" at the same time, and in this case, the "mag" only define the norm of the magnetic moment, and "angle1" and "angle2" define the direction of the magnetic moment.
     If data has spins, then it will be written as mag to STRU file; while if mag is passed at the same time, then mag will be used.
@@ -682,6 +685,20 @@ def ndarray2list(i):
     out = "ATOMIC_SPECIES\n"
     if pp_file is not None:
         pp_file = ndarray2list(pp_file)
+        ppfiles = None
+        if isinstance(pp_file,(list, tuple)):
+            assert len(pp_file) == len(data["atom_names"]), "ERROR: make_unlabeled_stru: pp_file length is not equal to the number of atom types"
+            ppfiles = pp_file
+        elif isinstance(pp_file, dict):
+            for iele in data["atom_names"]:
+                if iele not in pp_file:
+                    raise RuntimeError(f"ERROR: make_unlabeled_stru: pp_file does not contain {iele}")
+            ppfiles = [pp_file[data["atom_names"][i]] for i in range(len(data["atom_names"]))]
+        else:
+            raise RuntimeError(f"ERROR: invalid pp_file: {pp_file}")
+    else:
+        ppfiles = None
+
     for iele in range(len(data["atom_names"])):
         if data["atom_numbs"][iele] == 0:
             continue
@@ -690,57 +707,42 @@ def ndarray2list(i):
             out += f"{mass[iele]:.3f} "
         else:
             out += "1 "
-        if pp_file is not None:
-            if isinstance(pp_file, (list, tuple)):
-                ipp_file = pp_file[iele]
-            elif isinstance(pp_file, dict):
-                if data["atom_names"][iele] not in pp_file:
-                    print(
-                        f"ERROR: make_unlabeled_stru: pp_file does not contain {data['atom_names'][iele]}"
-                    )
-                    ipp_file = None
-                else:
-                    ipp_file = pp_file[data["atom_names"][iele]]
-            else:
-                ipp_file = None
+        if ppfiles is not None:
+            ipp_file = ppfiles[iele]
             if ipp_file is not None:
                 if not link_file:
                     out += ipp_file
                 else:
                     out += os.path.basename(ipp_file.rstrip("/"))
                     if dest_dir is not None:
                         _link_file(dest_dir, ipp_file)
-
         out += "\n"
     out += "\n"
 
     # NUMERICAL_ORBITAL block
     if numerical_orbital is not None:
-        assert len(numerical_orbital) == len(data["atom_names"])
         numerical_orbital = ndarray2list(numerical_orbital)
+        orbfiles = []
+        if isinstance(numerical_orbital, (list, tuple)):
+            assert len(numerical_orbital) == len(data["atom_names"]), "ERROR: make_unlabeled_stru: numerical_orbital length is not equal to the number of atom types"
+            orbfiles = [numerical_orbital[i] for i in range(len(data["atom_names"])) if data["atom_numbs"][i] != 0]
+        elif isinstance(numerical_orbital, dict):
+            for iele in data["atom_names"]:
+                if iele not in numerical_orbital:
+                    raise RuntimeError(f"ERROR: make_unlabeled_stru: numerical_orbital does not contain {iele}")
+            orbfiles = [numerical_orbital[data["atom_names"][i]] for i in range(len(data["atom_names"])) if data["atom_numbs"][i] != 0]
+        else:
+            raise RuntimeError(f"ERROR: invalid numerical_orbital: {numerical_orbital}")
+
+
         out += "NUMERICAL_ORBITAL\n"
-        for iele in range(len(data["atom_names"])):
-            if data["atom_numbs"][iele] == 0:
-                continue
-            if isinstance(numerical_orbital, (list, tuple)):
-                inum_orbital = numerical_orbital[iele]
-            elif isinstance(numerical_orbital, dict):
-                if data["atom_names"][iele] not in numerical_orbital:
-                    print(
-                        f"ERROR: make_unlabeled_stru: numerical_orbital does not contain {data['atom_names'][iele]}"
-                    )
-                    inum_orbital = None
-                else:
-                    inum_orbital = numerical_orbital[data["atom_names"][iele]]
+        for iorb in orbfiles:
+            if not link_file:
+                out += iorb
             else:
-                inum_orbital = None
-            if inum_orbital is not None:
-                if not link_file:
-                    out += inum_orbital
-                else:
-                    out += os.path.basename(inum_orbital.rstrip("/"))
-                    if dest_dir is not None:
-                        _link_file(dest_dir, inum_orbital)
+                out += os.path.basename(iorb.rstrip("/"))
+                if dest_dir is not None:
+                    _link_file(dest_dir, iorb)
             out += "\n"
         out += "\n"