Merge branch 'develop' of https://github.com/deepmodeling/abacus-develop into refactor

Author: YuLiu98

source/driver.cpp

@@ -43,9 +43,6 @@ void Driver::init()
     // (4) close all of the running logs
     ModuleBase::Global_File::close_all_log(GlobalV::MY_RANK, PARAM.inp.out_alllog,PARAM.inp.calculation);
 
-    // (5) output the json file
-    // Json::create_Json(&GlobalC::ucell.symm,GlobalC::ucell.atoms,&INPUT);
-    Json::create_Json(&GlobalC::ucell, PARAM);
 }
 
 void Driver::print_start_info()
@@ -180,7 +177,7 @@ void Driver::atomic_world()
     //--------------------------------------------------
 
     // where the actual stuff is done
-    this->driver_run(GlobalC::ucell);
+    this->driver_run();
 
     ModuleBase::timer::finish(GlobalV::ofs_running);
     ModuleBase::Memory::print_all(GlobalV::ofs_running);

source/driver.h

@@ -36,7 +36,7 @@ class Driver
     void atomic_world();
 
     // the actual calculations
-    void driver_run(UnitCell& ucell);
+    void driver_run();
 };
 
 #endif

source/driver_run.cpp

@@ -24,13 +24,12 @@
  * the configuration-changing subroutine takes force and stress and updates the
  * configuration
  */
-void Driver::driver_run(UnitCell& ucell)
+void Driver::driver_run()
 {
     ModuleBase::TITLE("Driver", "driver_line");
     ModuleBase::timer::tick("Driver", "driver_line");
 
     //! 1: setup cell and atom information
-
     // this warning should not be here, mohan 2024-05-22
 #ifndef __LCAO
     if (PARAM.inp.basis_type == "lcao_in_pw" || PARAM.inp.basis_type == "lcao") {
@@ -40,6 +39,13 @@ void Driver::driver_run(UnitCell& ucell)
 #endif
 
     // the life of ucell should begin here, mohan 2024-05-12
+    UnitCell ucell;
+    ucell.setup(PARAM.inp.latname,
+                    PARAM.inp.ntype,
+                    PARAM.inp.lmaxmax,
+                    PARAM.inp.init_vel,
+                    PARAM.inp.fixed_axes);
+
     ucell.setup_cell(PARAM.globalv.global_in_stru, GlobalV::ofs_running);
     Check_Atomic_Stru::check_atomic_stru(ucell, PARAM.inp.min_dist_coef);
 
@@ -86,6 +92,8 @@ void Driver::driver_run(UnitCell& ucell)
 
     ModuleESolver::clean_esolver(p_esolver);
 
+    //! 6: output the json file
+    Json::create_Json(&ucell, PARAM);
     ModuleBase::timer::tick("Driver", "driver_line");
     return;
 }

source/module_elecstate/elecstate.cpp

@@ -208,6 +208,7 @@ void ElecState::calEBand()
 
 void ElecState::init_scf(const int istep, 
                          const UnitCell& ucell,
+                         const Parallel_Grid& pgrid,
                          const ModuleBase::ComplexMatrix& strucfac, 
                          const bool* numeric,
                          ModuleSymmetry::Symmetry& symm, 
@@ -227,7 +228,7 @@ void ElecState::init_scf(const int istep,
     // choose charge density from ionic step 0.
     if (istep == 0)
     {
-        this->charge->init_rho(this->eferm,ucell, strucfac, symm, (const void*)this->klist, wfcpw);
+        this->charge->init_rho(this->eferm,ucell, pgrid, strucfac, symm, (const void*)this->klist, wfcpw);
         this->charge->check_rho(); // check the rho
     }
 

source/module_elecstate/elecstate.h

@@ -111,6 +111,7 @@ class ElecState
      */
     void init_scf(const int istep,
                   const UnitCell& ucell,
+                  const Parallel_Grid& pgrid,
                   const ModuleBase::ComplexMatrix& strucfac,
                   const bool* numeric,
                   ModuleSymmetry::Symmetry& symm,

source/module_elecstate/module_charge/charge.h

@@ -6,8 +6,9 @@
 #include "module_base/global_variable.h"
 #include "module_base/parallel_global.h"
 #include "module_basis/module_pw/pw_basis.h"
-#include "module_elecstate/fp_energy.h"
 #include "module_cell/module_symmetry/symmetry.h"
+#include "module_elecstate/fp_energy.h"
+#include "module_hamilt_pw/hamilt_pwdft/parallel_grid.h"
 
 //a forward declaration of UnitCell
 class UnitCell;
@@ -43,6 +44,7 @@ class Charge
     double **kin_r = nullptr; // kinetic energy density in real space, for meta-GGA
     double **kin_r_save = nullptr; // kinetic energy density in real space, for meta-GGA
                                    // wenfei 2021-07-28
+    const Parallel_Grid* pgrid = nullptr;
   private:
     //temporary
     double *_space_rho = nullptr, *_space_rho_save = nullptr;
@@ -73,6 +75,7 @@ class Charge
      */
     void init_rho(elecstate::efermi& eferm_iout,
                   const UnitCell& ucell,
+                  const Parallel_Grid& pgrid,
                   const ModuleBase::ComplexMatrix& strucFac,
                   ModuleSymmetry::Symmetry& symm,
                   const void* klist = nullptr,

source/module_elecstate/module_charge/charge_extra.cpp

@@ -75,9 +75,7 @@ void Charge_Extra::Init_CE(const int& nspin, const int& natom, const int& nrxx,
 }
 
 void Charge_Extra::extrapolate_charge(
-#ifdef __MPI
     Parallel_Grid* Pgrid,
-#endif
     UnitCell& ucell,
     Charge* chr,
     Structure_Factor* sf,
@@ -109,7 +107,7 @@ void Charge_Extra::extrapolate_charge(
     rho_extr = std::min(istep, pot_order);
     if(rho_extr == 0)
     {
-        sf->setup_structure_factor(&ucell, chr->rhopw);
+        sf->setup_structure_factor(&ucell, *Pgrid, chr->rhopw);
         ofs_running << " charge density from previous step !" << std::endl;
         return;
     }
@@ -171,7 +169,7 @@ void Charge_Extra::extrapolate_charge(
         }
     }
 
-    sf->setup_structure_factor(&ucell, chr->rhopw);
+    sf->setup_structure_factor(&ucell, *Pgrid, chr->rhopw);
     double** rho_atom = new double*[this->nspin];
     for (int is = 0; is < this->nspin; is++)
     {

source/module_elecstate/module_charge/charge_extra.h

@@ -63,9 +63,7 @@ class Charge_Extra
      * @param ofs_warning the output stream
      */
     void extrapolate_charge(
-#ifdef __MPI
         Parallel_Grid* Pgrid,
-#endif
         UnitCell& ucell,
         Charge* chr,
         Structure_Factor* sf,

source/module_elecstate/module_charge/charge_init.cpp

@@ -23,6 +23,7 @@
 
 void Charge::init_rho(elecstate::efermi& eferm_iout,
                       const UnitCell& ucell,
+                      const Parallel_Grid& pgrid,
                       const ModuleBase::ComplexMatrix& strucFac,
                       ModuleSymmetry::Symmetry& symm,
                       const void* klist,
@@ -33,7 +34,8 @@ void Charge::init_rho(elecstate::efermi& eferm_iout,
     std::cout << " START CHARGE      : " << PARAM.inp.init_chg << std::endl;
     //here we need to set the omega for the charge density
     set_omega(&ucell.omega);
-    
+    this->pgrid = &pgrid;
+
     bool read_error = false;
     if (PARAM.inp.init_chg == "file" || PARAM.inp.init_chg == "auto")
     {
@@ -57,7 +59,7 @@ void Charge::init_rho(elecstate::efermi& eferm_iout,
             {
                 std::stringstream ssc;
                 ssc << PARAM.globalv.global_readin_dir << "SPIN" << is + 1 << "_CHG.cube";
-                if (ModuleIO::read_vdata_palgrid(GlobalC::Pgrid,
+                if (ModuleIO::read_vdata_palgrid(pgrid,
                     (PARAM.inp.esolver_type == "sdft" ? GlobalV::RANK_IN_STOGROUP : GlobalV::MY_RANK),
                     GlobalV::ofs_running,
                     ssc.str(),
@@ -107,7 +109,7 @@ void Charge::init_rho(elecstate::efermi& eferm_iout,
                     GlobalV::ofs_running << " try to read kinetic energy density from file : " << ssc.str()
                                          << std::endl;
                     // mohan update 2012-02-10, sunliang update 2023-03-09
-                    if (ModuleIO::read_vdata_palgrid(GlobalC::Pgrid,
+                    if (ModuleIO::read_vdata_palgrid(pgrid,
                         (PARAM.inp.esolver_type == "sdft" ? GlobalV::RANK_IN_STOGROUP : GlobalV::MY_RANK),
                         GlobalV::ofs_running,
                         ssc.str(),
@@ -170,7 +172,7 @@ void Charge::init_rho(elecstate::efermi& eferm_iout,
                 // try to load from the output of `out_chg` 
                 std::stringstream ssc;
                 ssc << PARAM.globalv.global_readin_dir << "SPIN" << is + 1 << "_CHG.cube";
-                if (ModuleIO::read_vdata_palgrid(GlobalC::Pgrid,
+                if (ModuleIO::read_vdata_palgrid(pgrid,
                     (PARAM.inp.esolver_type == "sdft" ? GlobalV::RANK_IN_STOGROUP : GlobalV::MY_RANK),
                     GlobalV::ofs_running,
                     ssc.str(),

source/module_elecstate/potentials/pot_surchem.hpp

@@ -40,6 +40,7 @@ class PotSurChem : public PotBase
         }
 
         v_eff += this->surchem_->v_correction(*ucell,
+                                              *chg->pgrid,
                                               const_cast<ModulePW::PW_Basis*>(this->rho_basis_),
                                               v_eff.nr,
                                               chg->rho,