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

Author: wenfei-li

source/Makefile.Objects

@@ -238,6 +238,7 @@ OBJS_ESOLVER=esolver.o\
 
 OBJS_SURCHEM=H_correction_pw.o\
     cal_epsilon.o\
+    surchem.o\
     cal_pseudo.o\
     cal_totn.o\
     cal_vcav.o\
@@ -413,7 +414,6 @@ pzt2s.o\
 pdtrsm.o\
 pzhtrsm.o\
 
-
 PDIAG_MR_0=dcopy.o\
 dlae2.o\
 dlaebz.o\

source/input.cpp

@@ -420,6 +420,11 @@ void Input::Default(void)
     sigma_k = 0.6;
     nc_k = 0.00037;
 
+    comp_q = 0.0;
+    comp_l = 1.0;
+    comp_center = 0.0;
+    comp_dim = 2;
+
     return;
 }
 
@@ -1495,6 +1500,22 @@ bool Input::Read(const std::string &fn)
         {
             read_value(ifs, nc_k);
         }
+        else if (strcmp("comp_q", word) == 0)
+        {
+            read_value(ifs, comp_q);
+        }
+        else if (strcmp("comp_l", word) == 0)
+        {
+            read_value(ifs, comp_l);
+        }
+        else if (strcmp("comp_center", word) == 0)
+        {
+            read_value(ifs, comp_center);
+        }
+        else if (strcmp("comp_dim", word) == 0)
+        {
+            read_value(ifs, comp_dim);
+        }
         //----------------------------------------------------------------------------------
         else
         {

source/input.h

@@ -399,6 +399,11 @@ class Input
     double tau;
     double sigma_k;
     double nc_k;
+    // gauss charge
+    double comp_q;
+    double comp_l;
+    double comp_center;
+    int comp_dim;
 
     //==========================================================
     // variables for test only

source/input_conv.cpp

@@ -14,6 +14,7 @@
 #include "src_ions/ions_move_basic.h"
 #include "src_pw/global.h"
 #include "src_pw/occupy.h"
+#include "module_surchem/surchem.h"
 #ifdef __EXX
 #include "src_ri/exx_abfs-jle.h"
 #endif
@@ -501,6 +502,11 @@ void Input_Conv::Convert(void)
     GlobalV::tau = INPUT.tau;
     GlobalV::sigma_k = INPUT.sigma_k;
     GlobalV::nc_k = INPUT.nc_k;
+
+    GlobalC::solvent_model.comp_q = INPUT.comp_q;
+    GlobalC::solvent_model.comp_l = INPUT.comp_l;
+    GlobalC::solvent_model.comp_center = INPUT.comp_center;
+    GlobalC::solvent_model.comp_dim = INPUT.comp_dim;
     ModuleBase::timer::tick("Input_Conv", "Convert");
     return;
 }

source/module_base/global_file.cpp

@@ -128,20 +128,20 @@ void ModuleBase::Global_File::make_dir_out(
     if(out_alllog)
     {
 	    ss << "running_" << calculation << "_" << rank + 1;
-	    open_log(GlobalV::ofs_running, ss.str(), restart);
+	    open_log(GlobalV::ofs_running, ss.str(), calculation, restart);
     }
     else
     {
 	    if(rank==0)
 	    {
 		    ss << "running_" << calculation;
-		    open_log(GlobalV::ofs_running, ss.str(), restart);
+		    open_log(GlobalV::ofs_running, ss.str(), calculation, restart);
 	    }
     }
 
     if(rank==0)
     {
-	    open_log(GlobalV::ofs_warning, "warning", restart);
+	    open_log(GlobalV::ofs_warning, "warning", calculation, restart);
     }
     return;
 }
@@ -159,7 +159,7 @@ void ModuleBase::Global_File::make_dir_atom(const std::string &label)
     return;
 }
 
-void ModuleBase::Global_File::open_log(std::ofstream &ofs, const std::string &fn, const bool &restart)
+void ModuleBase::Global_File::open_log(std::ofstream &ofs, const std::string &fn, const std::string &calculation, const bool &restart)
 {
 //----------------------------------------------------------
 // USE GLOBAL VARIABLE :
@@ -168,7 +168,7 @@ void ModuleBase::Global_File::open_log(std::ofstream &ofs, const std::string &fn
     std::stringstream ss;
     ss << GlobalV::global_out_dir << fn << ".log";
 
-    if(fn == "running_md" && restart)
+    if((calculation == "md" || calculation == "sto-md") && restart)
     {
         ofs.open( ss.str(), ios::app );
     }

source/module_base/global_file.h

@@ -30,7 +30,7 @@ namespace Global_File
 		//const bool out_alllog = false);
 
 	void make_dir_atom(const std::string &label);
-	void open_log ( std::ofstream &ofs, const std::string &fn, const bool &restart);
+	void open_log ( std::ofstream &ofs, const std::string &fn, const std::string &calculation, const bool &restart);
 	void close_log( std::ofstream &ofs, const std::string &fn);
 	void close_all_log(const int rank, const bool out_alllog = false);
 }

source/module_md/FIRE.cpp

@@ -64,6 +64,7 @@ void FIRE::first_half()
     }
 #ifdef __MPI
     MPI_Bcast(pos , ucell.nat*3,MPI_DOUBLE,0,MPI_COMM_WORLD);
+    MPI_Bcast(vel , ucell.nat*3,MPI_DOUBLE,0,MPI_COMM_WORLD);
 #endif
 
     ucell.update_pos_tau(pos);
@@ -85,9 +86,9 @@ void FIRE::second_half()
     ModuleBase::timer::tick("FIRE", "second_half");
 }
 
-void FIRE::outputMD(std::ofstream &ofs)
+void FIRE::outputMD(std::ofstream &ofs, bool cal_stress)
 {
-    Verlet::outputMD(ofs);
+    Verlet::outputMD(ofs, cal_stress);
 
     ofs << " LARGEST GRAD (eV/A)  : " 
         << max * ModuleBase::Hartree_to_eV * ModuleBase::ANGSTROM_AU << std::endl;

source/module_md/FIRE.h

@@ -12,7 +12,7 @@ class FIRE : public Verlet
     void setup(ModuleESolver::ESolver *p_ensolve);
     void first_half();
     void second_half();
-    void outputMD(std::ofstream &ofs);
+    void outputMD(std::ofstream &ofs, bool cal_stress);
     void write_restart();
     void restart();
     void check_force();

source/module_md/Langevin.cpp

@@ -45,9 +45,9 @@ void Langevin::second_half()
     ModuleBase::timer::tick("Langevin", "second_half");
 }
 
-void Langevin::outputMD(std::ofstream &ofs)
+void Langevin::outputMD(std::ofstream &ofs, bool cal_stress)
 {
-    Verlet::outputMD(ofs);
+    Verlet::outputMD(ofs, cal_stress);
 }
 
 void Langevin::write_restart()

source/module_md/Langevin.h

@@ -12,7 +12,7 @@ class Langevin : public Verlet
     void setup(ModuleESolver::ESolver *p_ensolve);
     void first_half();
     void second_half();
-    void outputMD(std::ofstream &ofs);
+    void outputMD(std::ofstream &ofs, bool cal_stress);
     void write_restart();
     void restart();
     void post_force();