diff --git a/source/source_lcao/module_deepks/LCAO_deepks_interface.cpp b/source/source_lcao/module_deepks/LCAO_deepks_interface.cpp
index 04eb0cffc2..3e450221bb 100644
--- a/source/source_lcao/module_deepks/LCAO_deepks_interface.cpp
+++ b/source/source_lcao/module_deepks/LCAO_deepks_interface.cpp
@@ -618,6 +618,24 @@ void LCAO_Deepks_Interface<TK, TR>::out_deepks_labels(const double& etot,
 // 7. atom.npy, box.npy, overlap.npy
 //================================================================================
 
+    if(  ((PARAM.inp.deepks_out_labels == 2) && is_after_scf )
+      || ( PARAM.inp.deepks_out_freq_elec ) )// need overlap when deepks_out_freq_elec
+    {
+        if (PARAM.inp.deepks_v_delta > 0)
+        {
+            // prepare for overlap.npy, very much like h_tot except for p_ham->getSk()
+            std::vector<TH> s_tot(nks);
+            DeePKS_domain::get_h_tot<TK, TH, TR>(*ParaV, p_ham, s_tot, nlocal, nks, 'S');
+            const std::string file_stot = get_filename("overlap", PARAM.inp.deepks_out_labels, iter);
+            LCAO_deepks_io::save_npy_h<TK, TH>(s_tot,
+                                            file_stot,
+                                            nlocal,
+                                            nks,
+                                            rank,
+                                            1.0); // don't need unit_scale for overlap
+        }
+    }
+
     if ( is_after_scf ) // don't need to output in multiple electronic steps
     {
         if (PARAM.inp.deepks_out_labels == 2)
@@ -632,20 +650,6 @@ void LCAO_Deepks_Interface<TK, TR>::out_deepks_labels(const double& etot,
             DeePKS_domain::prepare_box(ucell, box_out);
             const std::string file_box = PARAM.globalv.global_out_dir + "deepks_box.npy";
             LCAO_deepks_io::save_tensor2npy<double>(file_box, box_out, rank);
-
-            if (PARAM.inp.deepks_v_delta > 0)
-            {
-                // prepare for overlap.npy, very much like h_tot except for p_ham->getSk()
-                std::vector<TH> s_tot(nks);
-                DeePKS_domain::get_h_tot<TK, TH, TR>(*ParaV, p_ham, s_tot, nlocal, nks, 'S');
-                const std::string file_stot = PARAM.globalv.global_out_dir + "deepks_overlap.npy";
-                LCAO_deepks_io::save_npy_h<TK, TH>(s_tot,
-                                                file_stot,
-                                                nlocal,
-                                                nks,
-                                                rank,
-                                                1.0); // don't need unit_scale for overlap
-            }
         }
 
 //================================================================================
diff --git a/tests/09_DeePKS/103_NO_GO_deepks_out_freq_elec/result.ref b/tests/09_DeePKS/103_NO_GO_deepks_out_freq_elec/result.ref
index 5c61657bb1..4707e8c814 100644
--- a/tests/09_DeePKS/103_NO_GO_deepks_out_freq_elec/result.ref
+++ b/tests/09_DeePKS/103_NO_GO_deepks_out_freq_elec/result.ref
@@ -22,4 +22,6 @@ deepks_f_label_elec .06676003678176294
 deepks_fdelta_elec .017979102769780632
 deepks_s_label_elec .06851710382835817
 deepks_sdelta_elec .013725178909672755
+deepks_overlap 61.931587180384426
+deepks_overlap_elec 309.657935901922130
 totaltimeref 3.76
diff --git a/tests/09_DeePKS/103_NO_KP_deepks_out_freq_elec/result.ref b/tests/09_DeePKS/103_NO_KP_deepks_out_freq_elec/result.ref
index bc76b36bcc..996128b56d 100644
--- a/tests/09_DeePKS/103_NO_KP_deepks_out_freq_elec/result.ref
+++ b/tests/09_DeePKS/103_NO_KP_deepks_out_freq_elec/result.ref
@@ -22,4 +22,6 @@ deepks_f_label_elec .0667600367817765
 deepks_fdelta_elec .017979102769778977
 deepks_s_label_elec .06851710382837811
 deepks_sdelta_elec .013725178909649378
+deepks_overlap 61.931587180384426
+deepks_overlap_elec 309.657935901922130
 totaltimeref 3.52
diff --git a/tests/integrate/tools/catch_deepks_properties.sh b/tests/integrate/tools/catch_deepks_properties.sh
index f8bd7cbf0d..74b66f7dc5 100644
--- a/tests/integrate/tools/catch_deepks_properties.sh
+++ b/tests/integrate/tools/catch_deepks_properties.sh
@@ -203,6 +203,11 @@ if ! test -z "$deepks_out_labels" && [ $deepks_out_labels == 1 ]; then
     # Process deepks_out_freq_elec > 0
     if [ ! -z "$deepks_out_freq_elec" ] && [ $deepks_out_freq_elec -gt 0 ]; then
         process_many_npys "multi" "_elec" "$1"
+        if ! test -z "$deepks_v_delta" && [[ $deepks_v_delta -gt 0 ]]; then
+            process_npy "single" "abs" "overlap" "" "deepks_overlap" "$1"
+            process_npy "multi" "abs" "overlap" "" "deepks_overlap_elec" "$1"
+            
+        fi
     fi
 fi