refactor: locate more functions into namespace ModuleIO (#1856)

* refactor: locate more functions into namespace ModuleIO

* restore files in src_ri

* remove charge_density.h

* locate write_HS and write_wfc_realspace into ModuleIO

* treat write_HS_R and rename psi to wfc

* build write_HS_sparse.h

* adjust header files

* build write_occ and write_orb_info

* locate write_dos_pw into ModuleIO

* locate write_dos_lcao into ModuleIO

* combine write_rho_cube with write_rho

* Fix CI err

* Fix CI err

Author: hongriTianqi

source/Makefile.Objects

@@ -336,7 +336,8 @@ OBJS_IO=input.o\
     berryphase.o\
     bessel_basis.o\
     cal_test.o\
-    energy_dos_pw.o\
+    write_occ.o\
+    write_dos_pw.o\
     dos.o\
     numerical_descriptor.o\
     numerical_basis.o\
@@ -347,24 +348,27 @@ OBJS_IO=input.o\
     rwstream.o\
     to_wannier90.o\
     unk_overlap_pw.o\
-    wf_io.o\
+    write_wfc_pw.o\
     winput.o\
     write_input.o\
     write_rho.o\
-    write_rho_cube.o\
-	write_wfc_realspace.o\
+    write_wfc_r.o\
 
 OBJS_IO_LCAO=cal_r_overlap_R.o\
-      energy_dos.o\
+      write_orb_info.o\
+      write_dos_lcao.o\
       istate_charge.o\
       istate_envelope.o\
       mulliken_charge.o\
       read_dm.o\
       unk_overlap_lcao.o\
-      wf_local.o\
+      read_wfc_nao.o\
+      write_wfc_nao.o\
       write_HS.o\
+      write_HS_sparse.o\
       write_HS_R.o\
       write_dm.o\
+      write_dm_sparse.o\
 
 OBJS_LCAO=DM_gamma.o\
       DM_k.o\

source/module_elecstate/energy.h

@@ -27,15 +27,6 @@ class energy
     energy();
     ~energy();
 
-	//calculate density of states(DOS) and partial density of states(PDOS) and mulliken charge for LCAO base
-	void perform_dos(
-		const psi::Psi<double> *psid,
-		const psi::Psi<std::complex<double>> *psi,
-		LCAO_Hamilt &uhm,
-		const elecstate::ElecState* pelec);
-	//calculate density of states(DOS) for PW base
-    void perform_dos_pw(const elecstate::ElecState* pelec);
-
     double etot;    	   // the total energy of the solid
     double ef;             // the fermi energy
     double ef_up;		   // spin up fermi energy
@@ -98,12 +89,8 @@ class energy
 	void print_etot(const bool converged, const int &iter,
 	const double &scf_thr, const double &duration, const double &pw_diag_thr=0, const double &avg_iter=0, bool print = true);
 
-	void print_occ(const elecstate::ElecState* pelec);
-
 	void print_format(const std::string &name, const double &value);
 
-	void print_orbital_file();
-
 	void calculate_harris(); //mohan add 2012-06-05
 
     double delta_e(const elecstate::ElecState* pelec);

source/module_elecstate/module_charge/charge.cpp

@@ -29,6 +29,7 @@
 #include <vector>
 #include "module_base/timer.h"
 #include "module_base/tool_threading.h"
+#include "module_io/rho_io.h"
 
 Charge::Charge()
 {
@@ -157,7 +158,7 @@ void Charge::init_rho()
             ssc << GlobalV::global_readin_dir << "SPIN" << is + 1 << "_CHG";
             GlobalV::ofs_running << ssc.str() << std::endl;
             // mohan update 2012-02-10
-            if (this->read_rho(is, ssc.str(), this->rho[is]))
+            if (ModuleIO::read_rho(is, ssc.str(), this->rho[is], this->prenspin))
             {
                 GlobalV::ofs_running << " Read in the charge density: " << ssc.str() << std::endl;
             }
@@ -212,7 +213,7 @@ void Charge::init_rho()
 				ssc << GlobalV::global_readin_dir << "SPIN" << is + 1 << "_TAU";
 				GlobalV::ofs_running << " try to read kinetic energy density from file : " << ssc.str() << std::endl;
 				// mohan update 2012-02-10
-				if (this->read_rho(is, ssc.str(), this->kin_r[is]))
+				if (ModuleIO::read_rho(is, ssc.str(), this->kin_r[is], this->prenspin))
 				{
 					GlobalV::ofs_running << " Read in the kinetic energy density: " << ssc.str() << std::endl;
 				}

source/module_elecstate/module_charge/charge.h

@@ -79,13 +79,6 @@ class Charge
 
 	public:
 
-    void write_rho(const double* rho_save, const int &is, const int &iter, const std::string &fn, 
-		const int &precision = 11, const bool for_plot = false);//mohan add 2007-10-17
-
-    void write_rho_cube(const double* rho_save, const int &is, const std::string &fn, 
-		const int &precision = 11);    
-
-    bool read_rho(const int &is, const std::string &fn, double* rho);//mohan add 2007-10-17
     void rho_mpi(void);
 
 	// mohan add 2021-02-20

source/module_elecstate/test/CMakeLists.txt

@@ -13,7 +13,7 @@ if(ENABLE_LCAO)
             ../module_charge/charge.cpp ../../src_parallel/parallel_reduce.cpp
             ../../module_hamilt_pw/hamilt_pwdft/structure_factor.cpp
             ../../module_cell/klist.cpp ../../src_parallel/parallel_kpoints.cpp ../occupy.cpp
-            ../kernels/elecstate_op.cpp ../../module_io/rwstream.cpp ../../module_io/wf_io.cpp
+            ../kernels/elecstate_op.cpp ../../module_io/rwstream.cpp ../../module_io/write_wfc_pw.cpp
   )
 
   install(DIRECTORY support DESTINATION ${CMAKE_CURRENT_BINARY_DIR})

source/module_elecstate/test/elecstate_lcao_test.cpp

@@ -74,12 +74,12 @@ XC_Functional::XC_Functional(){}
 XC_Functional::~XC_Functional(){}
 int XC_Functional::get_func_type(){return 0;}
 
-namespace WF_Local
+namespace ModuleIO
 {
-    int read_lowf(double** ctot, const int& is, const Parallel_Orbitals* ParaV, psi::Psi<double>*, elecstate::ElecState*) {return 1;};
-    int read_lowf_complex(std::complex<double>** ctot, const int& ik, const Parallel_Orbitals* ParaV, psi::Psi<std::complex<double> >*, elecstate::ElecState*) {return 1;}
-    void write_lowf(const std::string &name, double **ctot, const ModuleBase::matrix& ekb, const ModuleBase::matrix& wg) {}
-    void write_lowf_complex(const std::string &name, std::complex<double>** ctot, const int &ik, const ModuleBase::matrix& ekb, const ModuleBase::matrix& wg) {}
+    int read_wfc_nao(double** ctot, const int& is, const Parallel_Orbitals* ParaV, psi::Psi<double>*, elecstate::ElecState*) {return 1;};
+    int read_wfc_nao_complex(std::complex<double>** ctot, const int& ik, const Parallel_Orbitals* ParaV, psi::Psi<std::complex<double> >*, elecstate::ElecState*) {return 1;}
+    void write_wfc_nao(const std::string &name, double **ctot, const ModuleBase::matrix& ekb, const ModuleBase::matrix& wg) {}
+    void write_wfc_nao_complex(const std::string &name, std::complex<double>** ctot, const int &ik, const ModuleBase::matrix& ekb, const ModuleBase::matrix& wg) {}
 }
 
 //mock the unrelated functions in charge.cpp

source/module_elecstate/test/updaterhok_pw_test.cpp

@@ -13,7 +13,7 @@
 
 #include "updaterhok_pw_test.h"
 #include "module_io/berryphase.h"
-#include "module_io/wf_io.h"
+#include "module_io/write_wfc_pw.h"
 bool berryphase::berry_phase_flag;
 using::testing::AtLeast;
 using::testing::Assign;
@@ -146,6 +146,7 @@ struct ENVPrepare
     std::string init_wfc_;
     int out_wfc_pw_;
     std::string out_dir_;
+    int prenspin_;
     // default values
     ENVPrepare()
     {
@@ -180,7 +181,8 @@ struct ENVPrepare
         init_chg_ = "atomic";
         init_wfc_ = "atomic";
         out_wfc_pw_ = 1;
-	out_dir_="./support/";
+	    out_dir_="./support/";
+        prenspin_ = 1;
     }
 };
 
@@ -207,8 +209,8 @@ class ENVEnvironment : public ::testing::Environment
         GlobalV::stru_file = env->stru_file_;
         running_log = env->running_log_;
         // INPUT is an object of Input, and declared in input.h
-	GlobalC::ucell.latName = env->latname_;
-	GlobalC::ucell.ntype = env->ntype_;
+	    GlobalC::ucell.latName = env->latname_;
+	    GlobalC::ucell.ntype = env->ntype_;
         // important in pseudo_nc::set_pseudo_atom
         GlobalV::PSEUDORCUT = env->pseudo_rcut_;
         ModuleSymmetry::Symmetry::symm_flag = env->symm_flag_;
@@ -233,8 +235,9 @@ class ENVEnvironment : public ::testing::Environment
         INPUT.cell_factor = env->cell_factor_;
         GlobalV::init_chg = env->init_chg_;
         GlobalC::wf.init_wfc = env->init_wfc_;
-	GlobalC::wf.out_wfc_pw = env->out_wfc_pw_;
-	GlobalV::global_out_dir = env->out_dir_;
+	    GlobalC::wf.out_wfc_pw = env->out_wfc_pw_;
+	    GlobalV::global_out_dir = env->out_dir_;
+        GlobalC::CHR.prenspin = env->prenspin_;
     }
 
     void set_variables_in_set_up(ENVPrepare* envtmp)
@@ -326,8 +329,8 @@ TEST_F(EState,RhoPW)
     {
         std::stringstream ssw;
         ssw << "WFC";
-        WF_io::write_wfc(ssw.str(), psi[0], &GlobalC::kv, GlobalC::wfcpw);
-	remove("WFC1.dat");
+        ModuleIO::write_wfc_pw(ssw.str(), psi[0], &GlobalC::kv, GlobalC::wfcpw);
+	    remove("WFC1.dat");
     }
 
     // copy data from old wf.evc to new evc(an object of Psi)
@@ -370,7 +373,7 @@ TEST_F(EState,RhoPW)
         rho_for_compare[is] = new double[GlobalC::rhopw->nrxx];
         std::stringstream ssc;
         ssc <<GlobalV::global_out_dir<< "SPIN" << is + 1 << "_CHG";
-        GlobalC::CHR.read_rho(is, ssc.str(), rho_for_compare[is]);
+        ModuleIO::read_rho(is, ssc.str(), rho_for_compare[is],GlobalC::CHR.prenspin);
         for (int ix = 0; ix < GlobalC::rhopw->nrxx; ix++)
         //for (int ix = 0; ix < 5; ix++)
         {

source/module_elecstate/test/updaterhok_pw_test.h

@@ -21,6 +21,7 @@
 #include "module_hamilt_general/module_xc/xc_functional.h"
 #include "module_pw/pw_basis_k.h"
 #include "module_io/restart.h"
+#include "module_io/rho_io.h"
 
 int ModuleSymmetry::Symmetry::symm_flag;
 
@@ -103,7 +104,7 @@ psi::Psi<complex<double>>* wavefunc::allocate(const int nks)
 	return psi;
 }
 
-bool Charge::read_rho(const int &is, const std::string &fn, double* rho) //add by dwan
+bool ModuleIO::read_rho(const int &is, const std::string &fn, double* rho, int &prenspin) //add by dwan
 {
 	std::ifstream ifs(fn.c_str());
 
@@ -322,4 +323,4 @@ bool UnitCell::read_atom_positions(LCAO_Orbitals &orb, std::ifstream &ifpos, std
 void elecstate::Potential::init_pot(int istep, const Charge* chg)
 {
 	return;
-}
+}

source/module_esolver/Makefile.Objects

@@ -336,7 +336,7 @@ OBJS_IO=input.o\
     berryphase.o\
     bessel_basis.o\
     cal_test.o\
-    energy_dos_pw.o\
+    write_dos_pw.o\
     dos.o\
     numerical_descriptor.o\
     numerical_basis.o\
@@ -347,24 +347,26 @@ OBJS_IO=input.o\
     rwstream.o\
     to_wannier90.o\
     unk_overlap_pw.o\
-    wf_io.o\
+    write_wfc_pw.o\
     winput.o\
     write_input.o\
     write_rho.o\
-    write_rho_cube.o\
 	write_wfc_realspace.o\
 
 OBJS_IO_LCAO=cal_r_overlap_R.o\
-      energy_dos.o\
+      write_dos_lcao.o\
       istate_charge.o\
       istate_envelope.o\
       mulliken_charge.o\
       read_dm.o\
       unk_overlap_lcao.o\
-      wf_local.o\
+      read_wfc_nao.o\
+      write_wfc_nao.o\
       write_HS.o\
+      write_HS_sparse.o\
       write_HS_R.o\
       write_dm.o\
+      write_dm_sparse.o\
 
 OBJS_LCAO=DM_gamma.o\
       DM_k.o\

source/module_esolver/esolver_ks_lcao.cpp

@@ -1,6 +1,10 @@
 #include "esolver_ks_lcao.h"
 #include "module_io/cal_r_overlap_R.h"
-#include "module_io/density_matrix.h"
+#include "module_io/dm_io.h"
+#include "module_io/write_dm_sparse.h"
+#include "module_io/rho_io.h"
+#include "module_io/write_HS_R.h"
+#include "module_io/write_dos_lcao.h"
 
 //--------------temporary----------------------------
 #include "module_base/global_function.h"
@@ -227,7 +231,19 @@ void ESolver_KS_LCAO::postprocess()
     GlobalV::ofs_running << " !FINAL_ETOT_IS " << GlobalC::en.etot * ModuleBase::Ry_to_eV << " eV" << std::endl;
     GlobalV::ofs_running << " --------------------------------------------\n\n" << std::endl;
 
-    GlobalC::en.perform_dos(this->psid, this->psi, this->UHM, this->pelec);
+    ModuleIO::write_dos_lcao(this->psid, 
+        this->psi, 
+        this->UHM, 
+        this->pelec,
+        GlobalC::en.out_dos,
+        GlobalC::en.out_band,
+        GlobalC::en.out_proj_band,
+        GlobalC::en.dos_edelta_ev,
+        GlobalC::en.bcoeff,
+        GlobalC::en.dos_scale,
+        GlobalC::en.ef,
+        GlobalC::en.ef_up,
+        GlobalC::en.ef_dw);
 }
 
 void ESolver_KS_LCAO::Init_Basis_lcao(ORB_control& orb_con, Input& inp, UnitCell& ucell)
@@ -547,9 +563,7 @@ void ESolver_KS_LCAO::eachiterfinish(int iter)
         std::stringstream ss1;
         ssc << GlobalV::global_out_dir << "tmp"
             << "_SPIN" << is + 1 << "_CHG";
-        pelec->charge->write_rho(pelec->charge->rho_save[is], is, iter, ssc.str(), precision); // mohan add 2007-10-17
-        ss1 << GlobalV::global_out_dir << "tmp" << "_SPIN" << is + 1 << "_CHG.cube";
-        pelec->charge->write_rho_cube(pelec->charge->rho_save[is], is, ss1.str(), 3);
+        ModuleIO::write_rho(pelec->charge->rho_save[is], is, iter, ssc.str(), precision); // mohan add 2007-10-17
 
         std::stringstream ssd;
 
@@ -575,9 +589,7 @@ void ESolver_KS_LCAO::eachiterfinish(int iter)
             std::stringstream ss1;
             ssc << GlobalV::global_out_dir << "tmp"
                 << "_SPIN" << is + 1 << "_TAU";
-            pelec->charge->write_rho(pelec->charge->kin_r_save[is], is, iter, ssc.str(), precision); // mohan add 2007-10-17
-            ss1 << GlobalV::global_out_dir << "tmp" << "_SPIN" << is + 1 << "_TAU.cube";
-            pelec->charge->write_rho_cube(pelec->charge->kin_r_save[is], is, ss1.str(), 3);
+            ModuleIO::write_rho(pelec->charge->kin_r_save[is], is, iter, ssc.str(), precision); // mohan add 2007-10-17
         }
     }
 
@@ -616,9 +628,7 @@ void ESolver_KS_LCAO::afterscf(const int istep)
         std::stringstream ssc;
         std::stringstream ss1;
         ssc << GlobalV::global_out_dir << "SPIN" << is + 1 << "_CHG";
-        ss1 << GlobalV::global_out_dir << "SPIN" << is + 1 << "_CHG.cube";
-        pelec->charge->write_rho(pelec->charge->rho_save[is], is, 0, ssc.str()); // mohan add 2007-10-17
-        pelec->charge->write_rho_cube(pelec->charge->rho_save[is], is, ss1.str(), 3);
+        ModuleIO::write_rho(pelec->charge->rho_save[is], is, 0, ssc.str()); // mohan add 2007-10-17
 
         std::stringstream ssd;
         if (GlobalV::GAMMA_ONLY_LOCAL)
@@ -651,9 +661,7 @@ void ESolver_KS_LCAO::afterscf(const int istep)
             std::stringstream ssc;
             std::stringstream ss1;
             ssc << GlobalV::global_out_dir << "SPIN" << is + 1 << "_TAU";
-            ss1 << GlobalV::global_out_dir << "SPIN" << is + 1 << "_TAU.cube";
-            pelec->charge->write_rho(pelec->charge->kin_r_save[is], is, 0, ssc.str()); // mohan add 2007-10-17
-            pelec->charge->write_rho_cube(pelec->charge->kin_r_save[is], is, ss1.str(), 3);
+            ModuleIO::write_rho(pelec->charge->kin_r_save[is], is, 0, ssc.str()); // mohan add 2007-10-17
         }
     }
 
@@ -894,7 +902,7 @@ void ESolver_KS_LCAO::afterscf(const int istep)
     {
         if( !(GlobalV::CALCULATION=="md" && (istep%hsolver::HSolverLCAO::out_hsR_interval!=0)) )
         {
-            this->output_HS_R(istep, this->pelec->pot->get_effective_v()); // LiuXh add 2019-07-15
+            ModuleIO::output_HS_R(istep, this->pelec->pot->get_effective_v(), this->UHM); // LiuXh add 2019-07-15
         } // LiuXh add 2019-07-15
     }