Merge branch 'develop' of https://github.com/mohanchen/abacus-mc into develop

Author: mohanchen

docs/advanced/input_files/input-main.md

@@ -30,7 +30,7 @@
     - [orbital\_dir](#orbital_dir)
     - [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 +172,7 @@
     - [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)
@@ -773,12 +774,12 @@ These variables are used to control parameters related to input files.
   If EXX(exact exchange) is calculated (i.e. *[dft_fuctional](#dft_functional)==hse/hf/pbe0/scan0* or *[rpa](#rpa)==True*), the Hexx(R) files in the same folder for each processor will also be read.
 - **Default**: False
 
-### wannier_card
+### spillage_outdir
 
 - **Type**: String
-- **Availability**: Using ABACUS with Wannier90.
-- **Description**: The name of the input file related to Wannier90.
-- **Default**: "none"
+- **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)
 
@@ -2026,6 +2027,13 @@ 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
@@ -2258,7 +2266,7 @@ Warning: this function is not robust enough for the current version. Please try
 
 - **Type**: int
 - **Availability**: Numerical atomic orbital basis
-- **Description**: Include V_delta/V_delta_R (Hamiltonian in k/real space) label for DeePKS training. When `deepks_out_labels` is true and `deepks_v_delta` > 0 (k space), ABACUS will output `deepks_hbase.npy`, `deepks_vdelta.npy` and `deepks_htot.npy`(htot=hbase+vdelta). When `deepks_out_labels` is true and `deepks_v_delta` < 0 (real space), ABACUS will output `deepks_hrtot.csr`, `deepks_hrdelta.csr`. Some more files output for different settings.
+- **Description**: Include V_delta/V_delta_R (Hamiltonian in k/real space) label for DeePKS training. When `deepks_out_labels` is true and `deepks_v_delta` > 0 (k space), ABACUS will output `deepks_hbase.npy`, `deepks_vdelta.npy` and `deepks_htot.npy`(htot=hbase+vdelta). When `deepks_out_labels` is true and `deepks_v_delta` < 0 (real space), ABACUS will output `deepks_hrtot.csr`, `deepks_hrdelta.csr`. Some more files output for different settings. *NOTICE: To match the unit Normally used in DeePKS, the unit of Hamiltonian in k space is Hartree. However, currently in R space the unit is still Ry.*
   - `deepks_v_delta` = 1: `deepks_vdpre.npy`, which is used to calculate V_delta during DeePKS training.
   - `deepks_v_delta` = 2: `deepks_phialpha.npy` and `deepks_gevdm.npy`, which can be used to calculate `deepks_vdpre.npy`. A recommanded method for memory saving.
   - `deepks_v_delta` = -1: `deepks_vdrpre.npy`, which is used to calculate V_delta_R during DeePKS training.

source/Makefile.Objects

@@ -563,7 +563,6 @@ OBJS_IO=input_conv.o\
     unk_overlap_pw.o\
     write_pao.o\
     write_wfc_pw.o\
-    winput.o\
     write_cube.o\
     write_elecstat_pot.o\
     write_elf.o\

source/source_esolver/esolver_ks_lcaopw.cpp

@@ -29,7 +29,6 @@
 #include "source_io/numerical_basis.h"
 #include "source_io/numerical_descriptor.h"
 #include "source_io/to_wannier90_pw.h"
-#include "source_io/winput.h"
 #include "source_io/write_elecstat_pot.h"
 #include "source_io/module_parameter/parameter.h"
 

source/source_esolver/esolver_ks_pw.cpp

@@ -22,7 +22,6 @@
 #include "source_io/numerical_basis.h"
 #include "source_io/numerical_descriptor.h"
 #include "source_io/to_wannier90_pw.h"
-#include "source_io/winput.h"
 #include "source_io/write_dos_pw.h"
 #include "source_io/write_wfc_pw.h"
 #include "source_lcao/module_deltaspin/spin_constrain.h"
@@ -931,10 +930,10 @@ void ESolver_KS_PW<T, Device>::after_all_runners(UnitCell& ucell)
     //! 4) Calculate the spillage value,
     //! which are used to generate numerical atomic orbitals
     //----------------------------------------------------------
-    if (PARAM.inp.basis_type == "pw" && winput::out_spillage)
+    if (PARAM.inp.basis_type == "pw" && PARAM.inp.out_spillage)
     {
         // ! Print out overlap matrices
-        if (winput::out_spillage <= 2)
+        if (PARAM.inp.out_spillage <= 2)
         {
             for (int i = 0; i < PARAM.inp.bessel_nao_rcuts.size(); i++)
             {

source/source_esolver/pw_others.cpp

@@ -31,7 +31,6 @@
 #include "source_io/numerical_basis.h"
 #include "source_io/numerical_descriptor.h"
 #include "source_io/to_wannier90_pw.h"
-#include "source_io/winput.h"
 #include "source_io/write_elecstat_pot.h"
 #include "source_io/module_parameter/parameter.h"
 

source/source_io/CMakeLists.txt

@@ -46,7 +46,6 @@ list(APPEND objects_advanced
     to_wannier90_lcao_in_pw.cpp
     to_wannier90_lcao.cpp
     fR_overlap.cpp
-    winput.cpp
 )
 
 if(ENABLE_LCAO)

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)
@@ -408,6 +407,8 @@ struct Input_para
     bool if_separate_k = false;           ///< whether to write partial charge for all k-points to individual files or merge them
     std::vector<int> out_elf = {0, 3};    ///< output the electron localization function (ELF). 0: no; 1: yes
     std::vector<int> cal_symm_repr = {0, 3}; ///< output the symmetry representation matrix
+    int out_spillage = 0; ///< output the spillage of the wave function
+    std::string spillage_outdir = "./";  ///< output directory for spillage
 
     // ==============   #Parameters (12.Postprocess) ===========================
     double dos_emin_ev = -15.0;

source/source_io/numerical_basis.cpp

@@ -11,7 +11,6 @@
 #include "source_cell/module_symmetry/symmetry.h"
 #include "source_pw/module_pwdft/global.h"
 #include "source_io/numerical_basis_jyjy.h"
-#include "winput.h"
 
 #include <algorithm>
 #include <cstring>
@@ -82,13 +81,12 @@ void Numerical_Basis::output_overlap(const psi::Psi<std::complex<double>>& psi,
         this->mu_index = this->init_mu_index(ucell);
         this->init_label = true;
     }
-    ModuleBase::GlobalFunc::MAKE_DIR(winput::spillage_outdir);
+    ModuleBase::GlobalFunc::MAKE_DIR(PARAM.inp.spillage_outdir);
     for (int derivative_order = 0; derivative_order <= 1; ++derivative_order) // Peize Lin add 2020.04.23
     {
         std::ofstream ofs;
         std::stringstream ss;
-        // the parameter 'winput::spillage_outdir' is read from INPUTw.
-        ss << winput::spillage_outdir << "/";
+        ss << PARAM.inp.spillage_outdir << "/";
 
         if (PARAM.inp.bessel_nao_rcuts.size() > 1)
         {
@@ -134,7 +132,7 @@ void Numerical_Basis::output_overlap(const psi::Psi<std::complex<double>>& psi,
             ModuleBase::GlobalFunc::DONE(GlobalV::ofs_running, "cal_overlap_Q");
 
             // (2) generate Sq matrix if necessary.
-            if (winput::out_spillage == 2)
+            if (PARAM.inp.out_spillage == 2)
             {
 #ifndef __LCAO
                 // compute <jY|jY> in plane-wave basis
@@ -197,7 +195,7 @@ void Numerical_Basis::output_overlap(const psi::Psi<std::complex<double>>& psi,
             ModuleBase::WARNING_QUIT("Numerical_Basis", "Failed to write overlap Q to file.");
 }
         // because one stage of file io complete, re-check the file status.
-        if (winput::out_spillage == 2)
+        if (PARAM.inp.out_spillage == 2)
         {
             // caution: this is the largest matrix to be output, always flush
             if (ofs.good()) {

source/source_io/numerical_descriptor.cpp

@@ -2,7 +2,6 @@
 #include "source_pw/module_pwdft/global.h"
 #include "source_io/module_parameter/parameter.h"
 #include "source_cell/module_symmetry/symmetry.h"
-#include "winput.h"
 #include "source_base/math_ylmreal.h"
 #include "source_base/parallel_reduce.h"
 #include "source_base/timer.h"
@@ -75,8 +74,7 @@ void Numerical_Descriptor::output_descriptor(const UnitCell& ucell, const psi::P
 	//-----------------------------------
     std::ofstream ofs;
     std::stringstream ss;
-    // the parameter 'winput::spillage_outdir' is read from INPUTw.
-    ss << winput::spillage_outdir << "/" << "descriptor.dat";
+    ss << PARAM.inp.spillage_outdir << "/" << "descriptor.dat";
     if (GlobalV::MY_RANK==0)
     {
         ofs.open(ss.str().c_str());

source/source_io/read_input_item_output.cpp

@@ -572,5 +572,19 @@ void ReadInput::item_output()
         sync_intvec(input.cal_symm_repr, 2, 0);
         this->add_item(item);
     }
+    {
+        // refactored from the removal of wannier input file, ISSUE 6469
+        Input_Item item("out_spillage");
+        item.annotation = "output spillage of wavefunctions. This parameter only accepts 0 or 2.";
+        read_sync_int(input.out_spillage);
+        this->add_item(item);
+    }
+    {
+        // refactored from the removal of wannier input file, ISSUE 6469
+        Input_Item item("spillage_outdir");
+        item.annotation = "output directory for spillage of wavefunctions.";
+        read_sync_string(input.spillage_outdir);
+        this->add_item(item);
+    }
 }
 } // namespace ModuleIO