update docs and remove the parameter wannier_card

Author: kirk0830

docs/advanced/input_files/input-main.md

@@ -31,6 +31,7 @@
     - [read\_file\_dir](#read_file_dir)
     - [restart\_load](#restart_load)
     - [wannier\_card](#wannier_card)
+    - [spillage\_outdir](#spillage_outdir)
   - [Plane Wave](#plane-wave-related-variables)
     - [ecutwfc](#ecutwfc)
     - [ecutrho](#ecutrho)
@@ -172,6 +173,7 @@
     - [out\_wfc_re_im](#out_wfc_re_im)
     - [if\_separate\_k](#if_separate_k)
     - [out\_elf](#out_elf)
+    - [out\_spillage](#out_spillage)
   - [Density of States](#density-of-states)
     - [dos\_edelta\_ev](#dos_edelta_ev)
     - [dos\_sigma](#dos_sigma)
@@ -780,6 +782,13 @@ These variables are used to control parameters related to input files.
 - **Description**: The name of the input file related to Wannier90.
 - **Default**: "none"
 
+### spillage_outdir
+
+- **Type**: String
+- **Availability**: Used only for plane wave basis set.
+- **Description**: The directory to save the spillage files.
+- **Default**: "./"
+
 [back to top](#full-list-of-input-keywords)
 
 ## Plane wave related variables
@@ -2026,6 +2035,13 @@ These variables are used to control the output of properties.
   In molecular dynamics calculations, the output frequency is controlled by [out_interval](#out_interval).
 - **Default**: 0 3
 
+### out_spillage
+
+- **Type**: Integer
+- **Availability**: Only for Kohn-Sham DFT with plane-wave basis.
+- **Description**: This output is only intentively needed by the ABACUS numerical atomic orbital generation workflow. This parameter is used to control whether to output the overlap integrals between truncated spherical Bessel functions (TSBFs) and plane-wave basis expanded wavefunctions (named as `OVERLAP_Q`), and between TSBFs (named as `OVERLAP_Sq`), also their first order derivatives. The output files are named starting with `orb_matrix`. A value of `2` would enable the output.
+- **Default**: 0 
+
 [back to top](#full-list-of-input-keywords)
 
 ## Density of states

source/source_io/module_parameter/input_parameter.h

@@ -59,7 +59,6 @@ struct Input_para
     std::string orbital_dir = "";       ///< directory of orbital file
     std::string read_file_dir = "auto"; ///< directory of files for reading
     bool restart_load = false;
-    std::string wannier_card = "none";              ///< input card for wannier functions.
     int mem_saver = 0;                              ///< 1: save psi when nscf calculation.
     int diago_proc = 0;                             ///< the number of procs used to diag. mohan add 2012-01-13
     int nbspline = -1;                              ///< the order of B-spline basis(>=0) if it is -1 (default)

source/source_io/read_input_item_system.cpp

@@ -695,12 +695,6 @@ void ReadInput::item_system()
         read_sync_bool(input.restart_load);
         this->add_item(item);
     }
-    {
-        Input_Item item("wannier_card");
-        item.annotation = "input card for wannier functions";
-        read_sync_string(input.wannier_card);
-        this->add_item(item);
-    }
     {
         Input_Item item("mem_saver");
         item.annotation = "Only for nscf calculations. if set to 1, then a "

source/source_io/test/read_input_ptest.cpp

@@ -41,7 +41,6 @@ TEST_F(InputParaTest, ParaRead)
     EXPECT_EQ(param.inp.pseudo_dir, "../../PP_ORB/");
     EXPECT_EQ(param.inp.orbital_dir, "../../PP_ORB/");
     EXPECT_EQ(param.inp.read_file_dir, "OUT.autotest/");
-    EXPECT_EQ(param.inp.wannier_card, "none");
     EXPECT_EQ(param.inp.latname, "none");
     EXPECT_EQ(param.inp.calculation, "scf");
     EXPECT_EQ(param.inp.esolver_type, "ksdft");