Refactor: remove LCAO_Matrix from several class (#4645)

* remove lm from clear_zero_elements

* remove lm from save_HSR_sparse

* remove lm from cal_HR_exx

* remove lm from output_dHR

* remove lm from output_dHR 2

* remove lm from output_dHR 3

* remove lm from output_TR

* remove lm from output_TR 2

* remove lm from output_SR

* remove lm from out_dos_nao/out_dos_lcao

* remove lm from write_proj_band_lcao

* remove lm from Output_Sk

* fix bug

* fix build error of ouput_sk

source/module_esolver/esolver_ks_lcao.cpp

@@ -466,13 +466,12 @@ void ESolver_KS_LCAO<TK, TR>::after_all_runners()
 
     if (INPUT.out_proj_band) // Projeced band structure added by jiyy-2022-4-20
     {
-        ModuleIO::write_proj_band_lcao(this->psi, this->LM, this->pelec, this->kv, GlobalC::ucell, this->p_hamilt);
+        ModuleIO::write_proj_band_lcao(this->psi, this->ParaV, this->pelec, this->kv, GlobalC::ucell, this->p_hamilt);
     }
 
     if (INPUT.out_dos)
     {
         ModuleIO::out_dos_nao(this->psi,
-                              this->LM,
                               this->ParaV,
                               this->pelec->ekb,
                               this->pelec->wg,
@@ -1408,8 +1407,7 @@ void ESolver_KS_LCAO<TK, TR>::cal_mag(const int istep, const bool print)
                                 GlobalC::ucell.get_atomCounts(),
                                 GlobalC::ucell.get_lnchiCounts(),
                                 GlobalV::NSPIN);
-    auto out_sk = ModuleIO::Output_Sk<TK>(&(this->LM),
-                                          this->p_hamilt,
+    auto out_sk = ModuleIO::Output_Sk<TK>(this->p_hamilt,
                                           &(this->ParaV),
                                           GlobalV::NSPIN,
                                           this->kv.get_nks());

source/module_esolver/esolver_ks_lcao_elec.cpp

@@ -559,7 +559,7 @@ void ESolver_KS_LCAO<std::complex<double>, double>::get_S(void)
 
     std::cout << " The file is saved in " << fn << std::endl;
 
-    ModuleIO::output_SR(ParaV, this->LM, GlobalC::GridD, this->p_hamilt, fn);
+    ModuleIO::output_SR(ParaV, GlobalC::GridD, this->p_hamilt, fn);
 
     return;
 }
@@ -601,7 +601,7 @@ void ESolver_KS_LCAO<std::complex<double>, std::complex<double>>::get_S(void)
 
     std::cout << " The file is saved in " << fn << std::endl;
 
-    ModuleIO::output_SR(ParaV, this->LM, GlobalC::GridD, this->p_hamilt, fn);
+    ModuleIO::output_SR(ParaV, GlobalC::GridD, this->p_hamilt, fn);
 
     return;
 }

source/module_hamilt_lcao/hamilt_lcaodft/LCAO_allocate.cpp

@@ -7,7 +7,7 @@ namespace LCAO_domain
 {
 
 void divide_HS_in_frag(const bool isGamma, Parallel_Orbitals& pv,const int& nks) {
-    ModuleBase::TITLE("LCAO_Matrix", "divide_HS_in_frag");
+    ModuleBase::TITLE("LCAO_domain", "divide_HS_in_frag");
 
     //(1), (2): set up matrix division have been moved into ESolver_KS_LCAO::init_basis_lcao
     // just pass `ParaV` as pointer is enough

source/module_hamilt_lcao/hamilt_lcaodft/LCAO_hamilt.hpp

@@ -11,8 +11,6 @@
 #include "module_base/timer.h"
 #include "module_hamilt_lcao/hamilt_lcaodft/spar_exx.h"
 #include "module_ri/RI_2D_Comm.h"
-// use LCAO_Matrix
-#include "module_hamilt_lcao/hamilt_lcaodft/LCAO_matrix.h"
 
 #include <RI/global/Global_Func-2.h>
 #include <RI/ri/Cell_Nearest.h>
@@ -26,7 +24,7 @@
 // Peize Lin add 2022.09.13
 template <typename Tdata>
 void sparse_format::cal_HR_exx(
-    LCAO_Matrix& lm, // mohan add 2024-04-06
+    const Parallel_Orbitals& pv,
     LCAO_HS_Arrays& HS_Arrays,
     const int& current_spin,
     const double& sparse_threshold,
@@ -84,15 +82,15 @@ void sparse_format::cal_HR_exx(
 
                 for (size_t iw0 = 0; iw0 < Hexx.shape[0]; ++iw0) {
                     const int iwt0 = RI_2D_Comm::get_iwt(iat0, iw0, is0_b);
-                    const int iwt0_local = lm.ParaV->global2local_row(iwt0);
+                    const int iwt0_local = pv.global2local_row(iwt0);
 
                     if (iwt0_local < 0) {
                         continue;
                     }
 
                     for (size_t iw1 = 0; iw1 < Hexx.shape[1]; ++iw1) {
                         const int iwt1 = RI_2D_Comm::get_iwt(iat1, iw1, is1_b);
-                        const int iwt1_local = lm.ParaV->global2local_col(iwt1);
+                        const int iwt1_local = pv.global2local_col(iwt1);
 
                         if (iwt1_local < 0) {
                             continue;

source/module_hamilt_lcao/hamilt_lcaodft/spar_dh.cpp

@@ -2,7 +2,7 @@
 
 #include "module_hamilt_lcao/hamilt_lcaodft/LCAO_domain.h"
 
-void sparse_format::cal_dH(LCAO_Matrix& lm,
+void sparse_format::cal_dH(const Parallel_Orbitals& pv,
                            LCAO_HS_Arrays& HS_Arrays,
                            Grid_Driver& grid,
                            const TwoCenterBundle& two_center_bundle,
@@ -14,17 +14,17 @@ void sparse_format::cal_dH(LCAO_Matrix& lm,
 
     sparse_format::set_R_range(HS_Arrays.all_R_coor, grid);
 
-    const int nnr = lm.ParaV->nnr;
+    const int nnr = pv.nnr;
 
     ForceStressArrays fsr_dh;
 
     fsr_dh.DHloc_fixedR_x = new double[nnr];
     fsr_dh.DHloc_fixedR_y = new double[nnr];
     fsr_dh.DHloc_fixedR_z = new double[nnr];
 
-    ModuleBase::GlobalFunc::ZEROS(fsr_dh.DHloc_fixedR_x, lm.ParaV->nloc);
-    ModuleBase::GlobalFunc::ZEROS(fsr_dh.DHloc_fixedR_y, lm.ParaV->nloc);
-    ModuleBase::GlobalFunc::ZEROS(fsr_dh.DHloc_fixedR_z, lm.ParaV->nloc);
+    ModuleBase::GlobalFunc::ZEROS(fsr_dh.DHloc_fixedR_x, pv.nloc);
+    ModuleBase::GlobalFunc::ZEROS(fsr_dh.DHloc_fixedR_y, pv.nloc);
+    ModuleBase::GlobalFunc::ZEROS(fsr_dh.DHloc_fixedR_z, pv.nloc);
     // cal dT=<phi|kin|dphi> in LCAO
     // cal T + VNL(P1) in LCAO basis
     if (GlobalV::CAL_STRESS)
@@ -36,7 +36,7 @@ void sparse_format::cal_dH(LCAO_Matrix& lm,
                                   true,
                                   GlobalC::ucell,
                                   GlobalC::ORB,
-                                  *lm.ParaV,
+                                  pv,
                                   two_center_bundle,
                                   &GlobalC::GridD,
                                   nullptr); // delete unused parameter lm.Hloc_fixedR
@@ -50,13 +50,13 @@ void sparse_format::cal_dH(LCAO_Matrix& lm,
                                   true,
                                   GlobalC::ucell,
                                   GlobalC::ORB,
-                                  *lm.ParaV,
+                                  pv,
                                   two_center_bundle,
                                   &GlobalC::GridD,
                                   nullptr); // delete unused parameter lm.Hloc_fixedR
     }
 
-    LCAO_domain::build_Nonlocal_mu_new(*lm.ParaV,
+    LCAO_domain::build_Nonlocal_mu_new(pv,
                                        fsr_dh,
                                        nullptr,
                                        true,
@@ -65,14 +65,14 @@ void sparse_format::cal_dH(LCAO_Matrix& lm,
                                        *(two_center_bundle.overlap_orb_beta),
                                        &GlobalC::GridD);
 
-    sparse_format::cal_dSTN_R(lm, HS_Arrays, fsr_dh, grid, current_spin, sparse_thr);
+    sparse_format::cal_dSTN_R(pv, HS_Arrays, fsr_dh, grid, current_spin, sparse_thr);
 
     delete[] fsr_dh.DHloc_fixedR_x;
     delete[] fsr_dh.DHloc_fixedR_y;
     delete[] fsr_dh.DHloc_fixedR_z;
 
     gint_k
-        .cal_dvlocal_R_sparseMatrix(current_spin, sparse_thr, HS_Arrays, lm.ParaV, GlobalC::ucell, GlobalC::GridD);
+        .cal_dvlocal_R_sparseMatrix(current_spin, sparse_thr, HS_Arrays, &pv, GlobalC::ucell, GlobalC::GridD);
 
     return;
 }
@@ -102,7 +102,7 @@ void sparse_format::set_R_range(std::set<Abfs::Vector3_Order<int>>& all_R_coor,
     return;
 }
 
-void sparse_format::cal_dSTN_R(LCAO_Matrix& lm,
+void sparse_format::cal_dSTN_R(const Parallel_Orbitals& pv,
                                LCAO_HS_Arrays& HS_Arrays,
                                ForceStressArrays& fsr,
                                Grid_Driver& grid,
@@ -178,7 +178,7 @@ void sparse_format::cal_dSTN_R(LCAO_Matrix& lm,
                     for (int ii = 0; ii < atom1->nw * GlobalV::NPOL; ii++)
                     {
                         const int iw1_all = start + ii;
-                        const int mu = lm.ParaV->global2local_row(iw1_all);
+                        const int mu = pv.global2local_row(iw1_all);
 
                         if (mu < 0)
                         {
@@ -188,7 +188,7 @@ void sparse_format::cal_dSTN_R(LCAO_Matrix& lm,
                         for (int jj = 0; jj < atom2->nw * GlobalV::NPOL; jj++)
                         {
                             int iw2_all = start2 + jj;
-                            const int nu = lm.ParaV->global2local_col(iw2_all);
+                            const int nu = pv.global2local_col(iw2_all);
 
                             if (nu < 0)
                             {
@@ -230,7 +230,7 @@ void sparse_format::cal_dSTN_R(LCAO_Matrix& lm,
 
 void sparse_format::destroy_dH_R_sparse(LCAO_HS_Arrays& HS_Arrays)
 {
-    ModuleBase::TITLE("LCAO_Matrix", "destroy_dH_R_sparse");
+    ModuleBase::TITLE("LCAO_domain", "destroy_dH_R_sparse");
 
     if (GlobalV::NSPIN != 4)
     {

source/module_hamilt_lcao/hamilt_lcaodft/spar_dh.h

@@ -10,7 +10,7 @@
 
 namespace sparse_format
 {
-void cal_dH(LCAO_Matrix& lm,
+void cal_dH(const Parallel_Orbitals& pv,
             LCAO_HS_Arrays& HS_Arrays,
             Grid_Driver& grid,
             const TwoCenterBundle& two_center_bundle,
@@ -22,7 +22,7 @@ void cal_dH(LCAO_Matrix& lm,
 void set_R_range(std::set<Abfs::Vector3_Order<int>>& all_R_coor, Grid_Driver& grid);
 
 // be called by 'cal_dH_sparse'
-void cal_dSTN_R(LCAO_Matrix& lm,
+void cal_dSTN_R(const Parallel_Orbitals& pv,
                 LCAO_HS_Arrays& HS_Arrays,
                 ForceStressArrays& fsr, // mohan add 2024-06-16
                 Grid_Driver& grid,

source/module_hamilt_lcao/hamilt_lcaodft/spar_exx.h

@@ -9,16 +9,15 @@
 #include <map>
 #include <vector>
 
-// use LCAO_Matrix
 #include "module_hamilt_lcao/hamilt_lcaodft/LCAO_HS_arrays.hpp"
-#include "module_hamilt_lcao/hamilt_lcaodft/LCAO_matrix.h"
+#include "module_basis/module_ao/parallel_orbitals.h"
 
 namespace sparse_format
 {
 
 template <typename Tdata>
 void cal_HR_exx(
-    LCAO_Matrix& lm,
+    const Parallel_Orbitals& pv,
     LCAO_HS_Arrays& HS_Arrays,
     const int& current_spin,
     const double& sparse_thr,

source/module_hamilt_lcao/hamilt_lcaodft/spar_hsr.cpp

@@ -93,14 +93,14 @@ void sparse_format::cal_HSR(const Parallel_Orbitals& pv,
     // if EXX is considered
     if (GlobalC::exx_info.info_global.cal_exx) {
         if (GlobalC::exx_info.info_ri.real_number) {
-            sparse_format::cal_HR_exx(lm,
+            sparse_format::cal_HR_exx(pv,
                                       HS_Arrays,
                                       current_spin,
                                       sparse_thr,
                                       nmp,
                                       *lm.Hexxd);
         } else {
-            sparse_format::cal_HR_exx(lm,
+            sparse_format::cal_HR_exx(pv,
                                       HS_Arrays,
                                       current_spin,
                                       sparse_thr,
@@ -111,7 +111,7 @@ void sparse_format::cal_HSR(const Parallel_Orbitals& pv,
 #endif // __MPI
 #endif // __EXX
 
-    sparse_format::clear_zero_elements(lm, HS_Arrays, current_spin, sparse_thr);
+    sparse_format::clear_zero_elements(HS_Arrays, current_spin, sparse_thr);
 
     return;
 }
@@ -237,8 +237,7 @@ void sparse_format::cal_HContainer_td(
 }
 
 // in case there are elements smaller than the threshold
-void sparse_format::clear_zero_elements(LCAO_Matrix& lm,
-                                        LCAO_HS_Arrays& HS_Arrays,
+void sparse_format::clear_zero_elements(LCAO_HS_Arrays& HS_Arrays,
                                         const int& current_spin,
                                         const double& sparse_thr) {
     ModuleBase::TITLE("sparse_format", "clear_zero_elements");

source/module_hamilt_lcao/hamilt_lcaodft/spar_hsr.h

@@ -39,8 +39,7 @@ void cal_HContainer_td(
     std::map<Abfs::Vector3_Order<int>,
              std::map<size_t, std::map<size_t, std::complex<double>>>>& target);
 
-void clear_zero_elements(LCAO_Matrix& lm,
-                         LCAO_HS_Arrays& HS_Arrays,
+void clear_zero_elements(LCAO_HS_Arrays& HS_Arrays,
                          const int& current_spin,
                          const double& sparse_thr);
 

source/module_hamilt_lcao/hamilt_lcaodft/spar_st.cpp

@@ -54,15 +54,14 @@ void sparse_format::cal_SR(
 
 void sparse_format::cal_TR(const UnitCell& ucell,
                            const Parallel_Orbitals& pv,
-                           LCAO_Matrix& lm,
                            LCAO_HS_Arrays& HS_Arrays,
                            Grid_Driver& grid,
                            const TwoCenterBundle& two_center_bundle,
                            const double& sparse_thr) {
     ModuleBase::TITLE("sparse_format", "cal_TR");
 
     // need to rebuild T(R)
-    HS_Arrays.Hloc_fixedR.resize(lm.ParaV->nnr);
+    HS_Arrays.Hloc_fixedR.resize(pv.nnr);
 
     LCAO_domain::zeros_HSR('T', HS_Arrays);
 
@@ -82,14 +81,13 @@ void sparse_format::cal_TR(const UnitCell& ucell,
 
     sparse_format::set_R_range(HS_Arrays.all_R_coor, grid);
 
-    sparse_format::cal_STN_R_for_T(ucell, pv, lm, HS_Arrays, grid, sparse_thr);
+    sparse_format::cal_STN_R_for_T(ucell, pv, HS_Arrays, grid, sparse_thr);
 
     return;
 }
 
 void sparse_format::cal_STN_R_for_T(const UnitCell& ucell,
                                     const Parallel_Orbitals& pv,
-                                    LCAO_Matrix& lm,
                                     LCAO_HS_Arrays& HS_arrays,
                                     Grid_Driver& grid,
                                     const double& sparse_thr) {

source/module_hamilt_lcao/hamilt_lcaodft/spar_st.h

@@ -2,7 +2,6 @@
 #define SPARSE_FORMAT_ST_H
 
 #include "module_hamilt_lcao/hamilt_lcaodft/LCAO_HS_arrays.hpp"
-#include "module_hamilt_lcao/hamilt_lcaodft/LCAO_matrix.h"
 #include "module_hamilt_lcao/hamilt_lcaodft/hamilt_lcao.h"
 
 namespace sparse_format {
@@ -21,7 +20,6 @@ void cal_SR(const Parallel_Orbitals& pv,
 //! calculate kinetic matrix with lattice vector R
 void cal_TR(const UnitCell& ucell,
             const Parallel_Orbitals& pv,
-            LCAO_Matrix& lm,
             LCAO_HS_Arrays& HS_arrays,
             Grid_Driver& grid,
             const TwoCenterBundle& two_center_bundle,
@@ -30,7 +28,6 @@ void cal_TR(const UnitCell& ucell,
 //! cal_STN_R_for_T is only called by cal_TR
 void cal_STN_R_for_T(const UnitCell& ucell,
                      const Parallel_Orbitals& pv,
-                     LCAO_Matrix& lm,
                      LCAO_HS_Arrays& HS_arrays,
                      Grid_Driver& grid,
                      const double& sparse_thr);

source/module_hamilt_lcao/module_gint/gint_k.h

@@ -83,7 +83,7 @@ class Gint_k : public Gint {
                        std::map<size_t, std::map<size_t, double>>>&
             pvdpR_sparseMatrix,
         LCAO_HS_Arrays& HS_Arrays,
-        Parallel_Orbitals* pv);
+        const Parallel_Orbitals* pv);
 
     void distribute_pvdpR_soc_sparseMatrix(
         const int dim,
@@ -93,12 +93,12 @@ class Gint_k : public Gint {
             std::map<size_t, std::map<size_t, std::complex<double>>>>&
             pvdpR_soc_sparseMatrix,
         LCAO_HS_Arrays& HS_Arrays,
-        Parallel_Orbitals* pv);
+        const Parallel_Orbitals* pv);
 
     void cal_dvlocal_R_sparseMatrix(const int& current_spin,
                                     const double& sparse_threshold,
                                     LCAO_HS_Arrays& HS_Arrays,
-                                    Parallel_Orbitals* pv,
+                                    const Parallel_Orbitals* pv,
                                     UnitCell& ucell,
                                     Grid_Driver& gdriver);
 

source/module_hamilt_lcao/module_gint/gint_k_sparse1.cpp

@@ -16,7 +16,7 @@ void Gint_k::distribute_pvdpR_sparseMatrix(
     const double& sparse_threshold,
     const std::map<Abfs::Vector3_Order<int>, std::map<size_t, std::map<size_t, double>>>& pvdpR_sparseMatrix,
     LCAO_HS_Arrays& HS_Arrays,
-    Parallel_Orbitals* pv)
+    const Parallel_Orbitals* pv)
 {
     ModuleBase::TITLE("Gint_k", "distribute_pvdpR_sparseMatrix");
 
@@ -170,7 +170,7 @@ void Gint_k::distribute_pvdpR_soc_sparseMatrix(
     const std::map<Abfs::Vector3_Order<int>, std::map<size_t, std::map<size_t, std::complex<double>>>>&
         pvdpR_soc_sparseMatrix,
     LCAO_HS_Arrays& HS_Arrays,
-    Parallel_Orbitals* pv)
+    const Parallel_Orbitals* pv)
 {
     ModuleBase::TITLE("Gint_k", "distribute_pvdpR_soc_sparseMatrix");
 
@@ -320,7 +320,7 @@ void Gint_k::distribute_pvdpR_soc_sparseMatrix(
 void Gint_k::cal_dvlocal_R_sparseMatrix(const int& current_spin,
                                         const double& sparse_threshold,
                                         LCAO_HS_Arrays& HS_Arrays,
-                                        Parallel_Orbitals* pv,
+                                        const Parallel_Orbitals* pv,
                                         UnitCell& ucell,
                                         Grid_Driver& gdriver)
 {