Refactor:Remove GlobalC::ucell in module_io (#5677)

* change ucell in module_io

* change ucell in module_io/cal_r_overlap.cpp

* change ucell in module_io/cal_test.cpp

* change ucell in module_io/get_wf_lcao.cpp

* change ucell in module_io/numerical_desciptor.cpp

* change ucell in module_io/read_wfc_to_rho.cpp

* change ucell in module_io/td_current_io.cpp

* change ucell in module_io/to_wannier90_lcao_in_pw.cpp

* change ucell in module_io/to_wannier90_pw.cpp

* change ucell in module_io/to_wannier90_lcao.cpp

* change ucell in module_io/to_wannier90.cpp

* change ucell in module_io/write_vxc_lip.hpp.cpp

* change ucell in module_io/unk_overlap_lcao.cpp

* change ucell in module_io/write_dipole.cpp

* change ucell in module_io/write_dmr.cpp

* change ucell in module_io/write_dos_lcao.cpp

* change ucell in module_io/write_elecstat_pot.cpp

* change ucell in module_io/write_wfc_r.cpp

* change ucell in bessel_basis_test.cpp

* change ucell in read_wfc_to_rho_test.cpp

Author: A-006

source/module_esolver/esolver_gets.cpp

@@ -136,8 +136,8 @@ void ESolver_GetS::runner(UnitCell& ucell, const int istep)
     if (PARAM.inp.out_mat_r)
     {
         cal_r_overlap_R r_matrix;
-        r_matrix.init(pv, orb_);
-        r_matrix.out_rR(istep);
+        r_matrix.init(ucell,pv, orb_);
+        r_matrix.out_rR(ucell,istep);
     }
 
     ModuleBase::timer::tick("ESolver_GetS", "runner");

source/module_esolver/esolver_ks_lcao.cpp

@@ -991,6 +991,8 @@ void ESolver_KS_LCAO<TK, TR>::after_scf(UnitCell& ucell, const int istep)
                         PARAM.inp.out_dm1,
                         false,
                         PARAM.inp.out_app_flag,
+                        ucell.get_iat2iwt(),
+                        &ucell.nat,
                         istep);
 
     //! 7) write density matrix
@@ -1232,7 +1234,8 @@ void ESolver_KS_LCAO<TK, TR>::after_scf(UnitCell& ucell, const int istep)
                                              PARAM.inp.nnkpfile,
                                              PARAM.inp.wannier_spin);
 
-            myWannier.calculate(this->pelec->ekb, 
+            myWannier.calculate(ucell,
+                                this->pelec->ekb, 
                                 this->pw_wfc, 
                                 this->pw_big, 
                                 this->sf, 
@@ -1251,7 +1254,7 @@ void ESolver_KS_LCAO<TK, TR>::after_scf(UnitCell& ucell, const int istep)
                                        PARAM.inp.wannier_spin,
                                        orb_);
 
-            myWannier.calculate(this->pelec->ekb, this->kv, *(this->psi), &(this->pv));
+            myWannier.calculate(ucell,this->pelec->ekb, this->kv, *(this->psi), &(this->pv));
         }
         std::cout << FmtCore::format(" >> Finish %s.\n * * * * * *\n", "Wave function to Wannier90");
     }
@@ -1263,12 +1266,13 @@ void ESolver_KS_LCAO<TK, TR>::after_scf(UnitCell& ucell, const int istep)
     {
         std::cout << FmtCore::format("\n * * * * * *\n << Start %s.\n", "Berry phase calculation");
         berryphase bp(&(this->pv));
-        bp.lcao_init(this->kv,
+        bp.lcao_init(ucell,
+                     this->kv,
                      this->GridT,
                      orb_); // additional step before calling
                             // macroscopic_polarization (why capitalize
                             // the function name?)
-        bp.Macroscopic_polarization(this->pw_wfc->npwk_max, this->psi, this->pw_rho, this->pw_wfc, this->kv);
+        bp.Macroscopic_polarization(ucell,this->pw_wfc->npwk_max, this->psi, this->pw_rho, this->pw_wfc, this->kv);
         std::cout << FmtCore::format(" >> Finish %s.\n * * * * * *\n", "Berry phase calculation");
     }
 }

source/module_esolver/esolver_ks_lcao_tddft.cpp

@@ -349,15 +349,16 @@ void ESolver_KS_LCAO_TDDFT::after_scf(UnitCell& ucell, const int istep)
         {
             std::stringstream ss_dipole;
             ss_dipole << PARAM.globalv.global_out_dir << "SPIN" << is + 1 << "_DIPOLE";
-            ModuleIO::write_dipole(pelec->charge->rho_save[is], pelec->charge->rhopw, is, istep, ss_dipole.str());
+            ModuleIO::write_dipole(ucell,pelec->charge->rho_save[is], pelec->charge->rhopw, is, istep, ss_dipole.str());
         }
     }
     if (TD_Velocity::out_current == true)
     {
         elecstate::DensityMatrix<std::complex<double>, double>* tmp_DM
             = dynamic_cast<elecstate::ElecStateLCAO<std::complex<double>>*>(this->pelec)->get_DM();
 
-        ModuleIO::write_current(istep,
+        ModuleIO::write_current(ucell,
+                                istep,
                                 this->psi,
                                 pelec,
                                 kv,

source/module_esolver/esolver_ks_pw.cpp

@@ -585,8 +585,8 @@ void ESolver_KS_PW<T, Device>::after_scf(UnitCell& ucell, const int istep)
                            PARAM.inp.out_wannier_wvfn_formatted,
                            PARAM.inp.nnkpfile,
                            PARAM.inp.wannier_spin);
-
-        wan.calculate(this->pelec->ekb, this->pw_wfc, this->pw_big, this->kv, this->psi);
+        wan.set_tpiba_omega(ucell.tpiba, ucell.omega);
+        wan.calculate(ucell,this->pelec->ekb, this->pw_wfc, this->pw_big, this->kv, this->psi);
         std::cout << FmtCore::format(" >> Finish %s.\n * * * * * *\n", "Wannier functions calculation");
     }
 
@@ -595,7 +595,7 @@ void ESolver_KS_PW<T, Device>::after_scf(UnitCell& ucell, const int istep)
     {
         std::cout << FmtCore::format("\n * * * * * *\n << Start %s.\n", "Berry phase polarization");
         berryphase bp;
-        bp.Macroscopic_polarization(this->pw_wfc->npwk_max, this->psi, this->pw_rho, this->pw_wfc, this->kv);
+        bp.Macroscopic_polarization(ucell,this->pw_wfc->npwk_max, this->psi, this->pw_rho, this->pw_wfc, this->kv);
         std::cout << FmtCore::format(" >> Finish %s.\n * * * * * *\n", "Berry phase polarization");
     }
 }
@@ -783,7 +783,7 @@ void ESolver_KS_PW<T, Device>::after_all_runners(UnitCell& ucell)
     //! 6) Print out electronic wave functions in real space
     if (PARAM.inp.out_wfc_r == 1) // Peize Lin add 2021.11.21
     {
-        ModuleIO::write_psi_r_1(this->psi[0], this->pw_wfc, "wfc_realspace", true, this->kv);
+        ModuleIO::write_psi_r_1(ucell,this->psi[0], this->pw_wfc, "wfc_realspace", true, this->kv);
     }
 
     //! 7) Use Kubo-Greenwood method to compute conductivities

source/module_esolver/lcao_others.cpp

@@ -48,7 +48,10 @@ void ESolver_KS_LCAO<TK, TR>::others(UnitCell& ucell, const int istep)
     if (cal_type == "test_memory")
     {
         std::cout << FmtCore::format("\n * * * * * *\n << Start %s.\n", "testing memory");
-        Cal_Test::test_memory(this->pw_rho,
+        Cal_Test::test_memory(ucell.nat,
+                              ucell.ntype,
+                              ucell.GGT,
+                              this->pw_rho,
                               this->pw_wfc,
                               this->p_chgmix->get_mixing_mode(),
                               this->p_chgmix->get_mixing_ndim());
@@ -324,7 +327,8 @@ void ESolver_KS_LCAO<TK, TR>::others(UnitCell& ucell, const int istep)
         IState_Envelope IEP(this->pelec);
         if (PARAM.globalv.gamma_only_local)
         {
-            IEP.begin(this->psi,
+            IEP.begin(ucell,
+                      this->psi,
                       this->pw_rhod,
                       this->pw_wfc,
                       this->pw_big,
@@ -344,7 +348,8 @@ void ESolver_KS_LCAO<TK, TR>::others(UnitCell& ucell, const int istep)
         }
         else
         {
-            IEP.begin(this->psi,
+            IEP.begin(ucell,
+                      this->psi,
                       this->pw_rhod,
                       this->pw_wfc,
                       this->pw_big,

source/module_esolver/pw_others.cpp

@@ -56,13 +56,17 @@ void ESolver_KS_PW<T, Device>::others(UnitCell& ucell, const int istep)
     const std::string cal_type = PARAM.inp.calculation;
 
     if (cal_type == "test_memory") {
-        Cal_Test::test_memory(this->pw_rho,
+        Cal_Test::test_memory(ucell.nat,
+                              ucell.ntype,
+                              ucell.GGT,
+                              this->pw_rho,
                               this->pw_wfc,
                               this->p_chgmix->get_mixing_mode(),
                               this->p_chgmix->get_mixing_ndim());
     } else if (cal_type == "gen_bessel") {
         Numerical_Descriptor nc;
-        nc.output_descriptor(this->psi[0],
+        nc.output_descriptor(ucell,
+                             this->psi[0],
                              PARAM.inp.bessel_descriptor_lmax,
                              PARAM.inp.bessel_descriptor_rcut,
                              PARAM.inp.bessel_descriptor_tolerence,

source/module_hamilt_lcao/module_gint/gint_gamma.h

@@ -36,7 +36,7 @@ class Gint_Gamma : public Gint
 
     //! in gint_gamma_env.cpp 
 	//! calcualte the electronic wave functions via grid integral
-	void cal_env(const double* wfc, double* rho,UnitCell &ucell);
+	void cal_env(const double* wfc, double* rho,const UnitCell &ucell);
 
     //! transfer this->hRGint to Veff::hR
     void transfer_pvpR(hamilt::HContainer<double>* hR,const UnitCell* ucell);

source/module_hamilt_lcao/module_gint/gint_gamma_env.cpp

@@ -6,7 +6,7 @@
 #include "module_basis/module_ao/ORB_read.h"
 #include "module_hamilt_pw/hamilt_pwdft/global.h"
 
-void Gint_Gamma::cal_env(const double* wfc, double* rho, UnitCell& ucell)
+void Gint_Gamma::cal_env(const double* wfc, double* rho,const UnitCell& ucell)
 {
     ModuleBase::TITLE("Grid_Integral", "cal_env");
 

source/module_hamilt_lcao/module_gint/gint_k.h

@@ -65,7 +65,7 @@ class Gint_k : public Gint {
                    double* rho,
                    const std::vector<ModuleBase::Vector3<double>>& kvec_c,
                    const std::vector<ModuleBase::Vector3<double>>& kvec_d,
-                   UnitCell& ucell);
+                   const UnitCell& ucell);
 
     //------------------------------------------------------
     // in gint_k_sparse1.cpp

source/module_hamilt_lcao/module_gint/gint_k_env.cpp

@@ -13,7 +13,7 @@ void Gint_k::cal_env_k(int ik,
                        double* rho,
                        const std::vector<ModuleBase::Vector3<double>>& kvec_c,
                        const std::vector<ModuleBase::Vector3<double>>& kvec_d,
-                       UnitCell& ucell)
+                       const UnitCell& ucell)
 {
     ModuleBase::TITLE("Gint_k", "cal_env_k");
     ModuleBase::timer::tick("Gint_k", "cal_env_k");