From e623b91aebb4e8422fe6243391b631016ed96bfe Mon Sep 17 00:00:00 2001
From: root <pxlxingliang>
Date: Fri, 8 Nov 2024 10:26:09 +0800
Subject: [PATCH 1/4] Adjust pp_file as an unnessary parameter in save to
 abacus/stru

---
 dpdata/abacus/scf.py | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py
index c144a4db..f3daa030 100644
--- a/dpdata/abacus/scf.py
+++ b/dpdata/abacus/scf.py
@@ -635,7 +635,7 @@ def get_frame_from_stru(fname):
 def make_unlabeled_stru(
     data,
     frame_idx,
-    pp_file,
+    pp_file=None,
     numerical_orbital=None,
     numerical_descriptor=None,
     mass=None,
@@ -759,7 +759,11 @@ def process_file_input(file_input, atom_names, input_name):
 
     # ATOMIC_SPECIES block
     out = "ATOMIC_SPECIES\n"
-    ppfiles = process_file_input(ndarray2list(pp_file), data["atom_names"], "pp_file")
+    if pp_file is not None:
+        ppfiles = process_file_input(ndarray2list(pp_file), data["atom_names"], "pp_file")
+    else:
+        warnings.warn("pp_file is not provided, will use empty string for pseudo potential file.")
+        ppfiles = [""] * len(data["atom_names"])
 
     for iele in range(len(data["atom_names"])):
         if data["atom_numbs"][iele] == 0:
@@ -771,12 +775,13 @@ def process_file_input(file_input, atom_names, input_name):
             out += "1 "
 
         ipp_file = ppfiles[iele]
-        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)
+        if ipp_file != "":
+            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"
 

From 50c138e078967facedd233565d78ef4a6680cfec Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 8 Nov 2024 02:28:42 +0000
Subject: [PATCH 2/4] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 dpdata/abacus/scf.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py
index f3daa030..e623f022 100644
--- a/dpdata/abacus/scf.py
+++ b/dpdata/abacus/scf.py
@@ -760,9 +760,13 @@ def process_file_input(file_input, atom_names, input_name):
     # ATOMIC_SPECIES block
     out = "ATOMIC_SPECIES\n"
     if pp_file is not None:
-        ppfiles = process_file_input(ndarray2list(pp_file), data["atom_names"], "pp_file")
+        ppfiles = process_file_input(
+            ndarray2list(pp_file), data["atom_names"], "pp_file"
+        )
     else:
-        warnings.warn("pp_file is not provided, will use empty string for pseudo potential file.")
+        warnings.warn(
+            "pp_file is not provided, will use empty string for pseudo potential file."
+        )
         ppfiles = [""] * len(data["atom_names"])
 
     for iele in range(len(data["atom_names"])):

From d5f23ce3f21b9bbf63cce959eaf54438b11af513 Mon Sep 17 00:00:00 2001
From: root <pxlxingliang>
Date: Fri, 8 Nov 2024 12:59:21 +0800
Subject: [PATCH 3/4] add test

---
 tests/test_abacus_stru_dump.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/test_abacus_stru_dump.py b/tests/test_abacus_stru_dump.py
index 8891dee3..1de852c5 100644
--- a/tests/test_abacus_stru_dump.py
+++ b/tests/test_abacus_stru_dump.py
@@ -29,6 +29,10 @@ def test_dump_stru(self):
         )
         myfilecmp(self, "abacus.scf/stru_test", "STRU_tmp")
 
+    def test_dump_stru_without_pporb(self):
+        self.system_ch4.to("stru", "STRU_tmp", mass=[12, 1])
+        self.assertTrue(os.path.isfile("STRU_tmp"))
+    
     def test_dumpStruLinkFile(self):
         os.makedirs("abacus.scf/tmp", exist_ok=True)
         self.system_ch4.to(

From aaa12e69272baaa9704b95fda28617c1646ccd22 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 8 Nov 2024 04:59:54 +0000
Subject: [PATCH 4/4] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/test_abacus_stru_dump.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_abacus_stru_dump.py b/tests/test_abacus_stru_dump.py
index 1de852c5..ee0a3082 100644
--- a/tests/test_abacus_stru_dump.py
+++ b/tests/test_abacus_stru_dump.py
@@ -32,7 +32,7 @@ def test_dump_stru(self):
     def test_dump_stru_without_pporb(self):
         self.system_ch4.to("stru", "STRU_tmp", mass=[12, 1])
         self.assertTrue(os.path.isfile("STRU_tmp"))
-    
+
     def test_dumpStruLinkFile(self):
         os.makedirs("abacus.scf/tmp", exist_ok=True)
         self.system_ch4.to(