use 2 layers vector replace undered_map to improve perfermance

Author: goodchong

source/module_cell/module_neighbor/sltk_atom.h

@@ -4,7 +4,7 @@
 #include <memory>
 #include "sltk_util.h"
 #include "module_base/timer.h"
-#include <list>
+#include <vector>
 
 // a class contains the atom position, 
 // the type and the index,
@@ -14,7 +14,7 @@ class FAtom
 	double d_x;
 	double d_y;
 	double d_z;
-	std::list<FAtom *> adjacent;
+	std::vector<FAtom *> adjacent;
 
 	int type;
 	int natom;
@@ -50,7 +50,7 @@ class FAtom
 	{
 		adjacent.push_back( &atom_in);
 	}
-	const std::list<FAtom *>& getAdjacent() const { return adjacent; }
+	const std::vector<FAtom *>& getAdjacent() const { return adjacent; }
 	void clearAdjacent() { adjacent.clear(); }
 //==========================================================
 // MEMBER FUNCTION :

source/module_cell/module_neighbor/sltk_atom_arrange.cpp

@@ -128,6 +128,9 @@ void atom_arrange::search(
 	// test the adjacent atoms and the box.
 	if(test_only)
 	{
+		std::cout << "radius_lat0unit = " << radius_lat0unit << std::endl;
+		std::cout << "search_radius_bohr = " << search_radius_bohr << std::endl;
+
 		ofs_in << " " << std::setw(5) << "Type" << std::setw(5) << "Atom" << std::setw(8) << "AdjNum" << std::endl;
         std::cout << std::setw(8) << "Labels" << std::setw(15) << "tau.x" << std::setw(15) << "tau.y" << std::setw(15)
                   << "tau.z" << std::setw(8) << "box.x" << std::setw(8) << "box.y" << std::setw(8) << "box.z"