fix a adj set clear bug and add self to adj list

Author: goodchong

source/module_cell/module_neighbor/sltk_grid_driver.cpp

@@ -38,6 +38,7 @@ void Grid_Driver::Find_atom(
 
 	// store result in member adj_info when parameter adjs is NULL
 	AdjacentAtomInfo* local_adjs = adjs == nullptr ? &this->adj_info : adjs;
+	local_adjs->clear();
 	const std::list<FAtom *> & all_atom = Cell[this->true_cell_x][this->true_cell_y][this->true_cell_z].atom_map[std::make_tuple(cartesian_pos.x, cartesian_pos.y, cartesian_pos.z)].getAdjacent();
 	//std::cout << "ntype = "<< ntype << "  atom size = " << all_atom.size() << std::endl;
 	for(const FAtom * atom : all_atom)
@@ -53,30 +54,34 @@ void Grid_Driver::Find_atom(
 		}
 		else
 		{
-			local_adjs->adjacent_tau.push_back(Calculate_adjacent_site(*atom,
+			local_adjs->adjacent_tau.push_back(Calculate_adjacent_site(atom->x(), atom->y(), atom->z(),
 			                  vec1[0], vec2[0], vec3[0],
 			                  vec1[1], vec2[1], vec3[1],
 			                  vec1[2], vec2[2], vec3[2],
 			                  atom->getCellX(), atom->getCellY(), atom->getCellZ()));
 		}//end if expand_flag
 		local_adjs->adj_num++;
 	}
-	local_adjs->adj_num--;
+	local_adjs->ntype.push_back(ntype);
+	local_adjs->natom.push_back(nnumber);
+	local_adjs->box.push_back(ModuleBase::Vector3<int>(0, 0, 0));
+	local_adjs->adjacent_tau.push_back(ModuleBase::Vector3<double>(cartesian_pos.x, cartesian_pos.y, cartesian_pos.z));
+
 
 	ModuleBase::timer::tick("Grid_Driver","Find_atom");
 	return;
 }
 
-ModuleBase::Vector3<double> Grid_Driver::Calculate_adjacent_site(const FAtom &atom,
+ModuleBase::Vector3<double> Grid_Driver::Calculate_adjacent_site(const double x, const double y, const double z,
 																	const double &box11, const double &box12, const double &box13,
 																	const double &box21, const double &box22, const double &box23,
 																	const double &box31, const double &box32, const double &box33,
 																	const short box_x, const short box_y, const short box_z) const
 {
 	ModuleBase::Vector3<double> adjacent_site(0, 0, 0);
-	adjacent_site.x = atom.x() + box_x * box11 + box_y * box12 + box_z * box13;
-	adjacent_site.y = atom.y() + box_x * box21 + box_y * box22 + box_z * box23;
-	adjacent_site.z = atom.z() + box_x * box31 + box_y * box32 + box_z * box33;
+	adjacent_site.x = x + box_x * box11 + box_y * box12 + box_z * box13;
+	adjacent_site.y = y + box_x * box21 + box_y * box22 + box_z * box23;
+	adjacent_site.z = z + box_x * box31 + box_y * box32 + box_z * box33;
 
 	return adjacent_site;
 }

source/module_cell/module_neighbor/sltk_grid_driver.h

@@ -25,6 +25,14 @@ class AdjacentAtomInfo
 	std::vector<int> natom;
 	std::vector<ModuleBase::Vector3<double>> adjacent_tau;
 	std::vector<ModuleBase::Vector3<int>> box;
+	void clear()
+	{
+		adj_num = 0;
+		ntype.clear();
+		natom.clear();
+		adjacent_tau.clear();
+		box.clear();
+	}
 };
 
 void filter_adjs(const std::vector<bool>& is_adj, AdjacentAtomInfo& adjs);
@@ -88,7 +96,7 @@ class Grid_Driver : public Grid
 // MEMBER FUNCTIONS :
 // NAME : Calculate_adjacent_site
 //==========================================================
-	ModuleBase::Vector3<double> Calculate_adjacent_site(const FAtom &atom,
+	ModuleBase::Vector3<double> Calculate_adjacent_site(const double x, const double y, const double z,
 							const double &box11, const double &box12, const double &box13,
 							const double &box21, const double &box22, const double &box23,
 							const double &box31, const double &box32, const double &box33,