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

Author: pxlxingliang

source/module_cell/atom_spec.cpp

@@ -15,6 +15,9 @@ Atom::Atom()
     taud = new ModuleBase::Vector3<double>[1];
     vel = new ModuleBase::Vector3<double>[1];
     mag = new double[1];
+    angle1 = new double[1];
+    angle2 = new double[1];
+    m_loc_ = new ModuleBase::Vector3<double>[1];
     l_nchi = new int[1];
     iw2l = new int[1];
     iw2n = new int[1];
@@ -29,6 +32,9 @@ Atom::~Atom()
     delete[] taud;
     delete[] vel;
     delete[] mag;
+    delete[] angle1;
+    delete[] angle2;
+    delete[] m_loc_;
     delete[] l_nchi;
     delete[] iw2l;
     delete[] iw2n;
@@ -137,6 +143,9 @@ void Atom::bcast_atom(void)
 		delete[] taud;
 	    delete[] vel;
         delete[] mag;
+        delete[] angle1;
+        delete[] angle2;
+        delete[] m_loc_;
         tau = new ModuleBase::Vector3<double>[na];
 		taud = new ModuleBase::Vector3<double>[na];
 	    vel = new ModuleBase::Vector3<double>[na];

source/module_cell/read_atoms.cpp

@@ -570,6 +570,9 @@ bool UnitCell_pseudo::read_atom_positions(std::ifstream &ifpos, std::ofstream &o
 				delete[] atoms[it].vel;
        			delete[] atoms[it].mbl;
 				delete[] atoms[it].mag;
+                delete[] atoms[it].angle1;
+                delete[] atoms[it].angle2;
+                delete[] atoms[it].m_loc_;
        			atoms[it].tau = new ModuleBase::Vector3<double>[na];
        			atoms[it].taud = new ModuleBase::Vector3<double>[na];
 				atoms[it].vel = new ModuleBase::Vector3<double>[na];

source/module_cell/unitcell_pseudo.cpp

@@ -695,24 +695,11 @@ void UnitCell_pseudo::setup_cell_after_vc(std::ofstream &log)
         for(int ia =0;ia< atom->na;ia++)
         {
             atom->tau[ia] = atom->taud[ia] * latvec;
-/*
-#ifdef __MPI
-Parallel_Common::bcast_double( atom->tau[ia].x );
-Parallel_Common::bcast_double( atom->tau[ia].y );
-Parallel_Common::bcast_double( atom->tau[ia].z );
-Parallel_Common::bcast_double( atom->taud[ia].x );
-Parallel_Common::bcast_double( atom->taud[ia].y );
-Parallel_Common::bcast_double( atom->taud[ia].z );
-#endif
-*/
         }
     }
+    
 #ifdef __MPI
-    MPI_Barrier(MPI_COMM_WORLD);
-    for (int i=0;i<ntype;i++)
-    {
-        atoms[i].bcast_atom(); // bcast tau array
-    }
+    this->bcast_unitcell();
 #endif
 
     log << std::endl;

source/module_gint/gint_tools.cpp

@@ -39,7 +39,7 @@ namespace Gint_Tools
 		const int jby,
 		const int kbz)
 	{
-		int *vindex = (int*)malloc(GlobalC::bigpw->bxyz*sizeof(int));
+		int *vindex = new int[GlobalC::bigpw->bxyz];
 		int bindex=0;
 		// z is the fastest,
 		// ipart can be obtained by using a previously stored array
@@ -71,12 +71,12 @@ namespace Gint_Tools
 	{
 		// set the index for obtaining local potentials
 		int* vindex = Gint_Tools::get_vindex(ncyz, ibx, jby, kbz);	
-		double *vldr3 = (double*)malloc(GlobalC::bigpw->bxyz*sizeof(double));					
+		double *vldr3 = new double[GlobalC::bigpw->bxyz];
 		for(int ib=0; ib<GlobalC::bigpw->bxyz; ib++)
 		{
 			vldr3[ib]=vlocal[vindex[ib]] * dv;
 		}
-		free(vindex);	vindex=nullptr;
+		delete[] vindex;
 		return vldr3;
 	}
 
@@ -88,12 +88,12 @@ namespace Gint_Tools
 	{
 		// set the index for obtaining local potentials
 		int* vindex = Gint_Tools::get_vindex(start_ind, ncyz);	
-		double *vldr3 = (double*)malloc(GlobalC::bigpw->bxyz*sizeof(double));					
+		double *vldr3 = new double[GlobalC::bigpw->bxyz];
 		for(int ib=0; ib<GlobalC::bigpw->bxyz; ib++)
 		{
 			vldr3[ib]=vlocal[vindex[ib]] * dv;
 		}
-		free(vindex);	vindex=nullptr;
+		delete[] vindex;
 		return vldr3;
 	}
 

source/module_gint/gint_tools.h

@@ -243,8 +243,8 @@ namespace Gint_Tools
 	template<typename T>
 	Array_Pool<T>::Array_Pool(const int nr, const int nc)	// Attention: uninitialized
 	{
-		ptr_1D = (T*)malloc(nr*nc*sizeof(T));
-		ptr_2D = (T**)malloc(nr*sizeof(T*));
+		ptr_1D = new T[nr*nc];
+		ptr_2D = new T*[nr];
 		for (int ir=0; ir<nr; ++ir)
 			ptr_2D[ir] = &ptr_1D[ir*nc];
 	}
@@ -254,15 +254,15 @@ namespace Gint_Tools
 	{
 		ptr_1D = array.ptr_1D;
 		ptr_2D = array.ptr_2D;
-		free(array.ptr_2D);		array.ptr_2D=nullptr;
-		free(array.ptr_1D);		array.ptr_1D=nullptr;
+		delete[] array.ptr_2D;
+		delete[] array.ptr_1D;
 	}
 
 	template<typename T>
 	Array_Pool<T>::~Array_Pool()
 	{
-		free(ptr_2D);
-		free(ptr_1D);
+		delete[] ptr_2D;
+		delete[] ptr_1D;
 	}
 }
 

source/module_md/MSST.cpp

@@ -240,6 +240,9 @@ void MSST::rescale(double volume)
     ucell.latvec.e11 *= dilation[0];
     ucell.latvec.e22 *= dilation[1];
     ucell.latvec.e33 *= dilation[2];
+    ucell.a1 *= dilation[0];
+    ucell.a2 *= dilation[1];
+    ucell.a3 *= dilation[2];
 
     ucell.setup_cell_after_vc(GlobalV::ofs_running);
     MD_func::InitPos(ucell, pos);

tests/deepks/Autotest.sh

@@ -159,7 +159,7 @@ repo="$(realpath ..)/"
 if [ "$sanitize" == true ]; then
 	echo "Testing with Address Sanitizer..."
 	mkdir ../html
-	echo -e "# Address Sanitizer Diagnostics\n" > ../html/README.md
+	echo -e "# Address Sanitizer Diagnostics\n" >> ../html/README.md
 	report=$(realpath ../html/README.md)
 fi