Refactor: replaced the original atomlink data structure with the Standard Template Library (#5642)

* A highly aggressive change: replaced the original atomlink data structure with the Standard Template Library.

* fix unittest errors

* [pre-commit.ci lite] apply automatic fixes

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

* use vector to refactor Cellset varible

* remove adjacent set, replaced by std list

* remove set fatom

* [pre-commit.ci lite] apply automatic fixes

* use 2 layers vector replace undered_map to improve perfermance

* remove a lot useless variable

* remove some useless variables

* refresh unit test to code logic

* [pre-commit.ci lite] apply automatic fixes

* fix a bug to force quit when test

* fresh unit test according to latest code logic

---------

Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>

Author: goodchong

source/Makefile.Objects

@@ -366,8 +366,7 @@ OBJS_MD=fire.o\
     run_md.o\
     verlet.o\
 
-OBJS_NEIGHBOR=sltk_adjacent_set.o\
-    sltk_atom.o\
+OBJS_NEIGHBOR=sltk_atom.o\
     sltk_atom_arrange.o\
     sltk_atom_input.o\
     sltk_grid.o\

source/module_cell/module_neighbor/CMakeLists.txt

@@ -1,7 +1,6 @@
 add_library(
     neighbor
     OBJECT
-    sltk_adjacent_set.cpp
     sltk_atom.cpp
     sltk_atom_arrange.cpp
     sltk_atom_input.cpp

source/module_cell/module_neighbor/sltk_adjacent_set.cpp

@@ -1,27 +1,12 @@
 #include "sltk_atom.h"
 #include <iostream>
 
-class AdjacentSet;
-
-//int FAtom::count1 = 0;
-//int FAtom::count2 = 0;
-
 /*** Constructors and destructor ***/
 FAtom::FAtom()
 {
 	d_x = 0.0;	
 	d_y = 0.0;	
 	d_z = 0.0;	
-	as = nullptr;
 	type = 0;		
 	natom = 0;
 }
-
-FAtom::~FAtom()
-{
-}
-
-void FAtom::delete_vector(void)
-{
-	if (as) { as->delete_vector(); }
-}

source/module_cell/module_neighbor/sltk_adjacent_set.h

@@ -3,9 +3,8 @@
 
 #include <memory>
 #include "sltk_util.h"
-#include "sltk_adjacent_set.h"
-
-class AdjacentSet;
+#include "module_base/timer.h"
+#include <vector>
 
 // a class contains the atom position, 
 // the type and the index,
@@ -15,7 +14,7 @@ class FAtom
 	double d_x;
 	double d_y;
 	double d_z;
-	std::shared_ptr<AdjacentSet> as;
+	std::vector<FAtom *> adjacent;
 
 	int type;
 	int natom;
@@ -42,30 +41,17 @@ class FAtom
 		cell_y = cell_y_in;
 		cell_z = cell_z_in;
 	}
-	~FAtom();
-//2015-05-07
-	void delete_vector();
-
-//	static int count1;
-//	static int count2;
-
-//==========================================================
-// MEMBER FUNCTION :
-// NAME : setAdjacent
-// Dangerous but high performance interface function!
-// no exception test.
-//
-// NAME : getAdjacentSet
-//
-// NAME : setAdjacentSet
-//==========================================================
-
-	std::shared_ptr<AdjacentSet> getAdjacentSet() const
-	{ return this->as; }
-
-	void allocate_AdjacentSet()
-	{ this->as = std::make_shared<AdjacentSet>(); }
+	~FAtom()
+	{
+		adjacent.clear();
+	}
 
+	void addAdjacent(FAtom& atom_in)
+	{
+		adjacent.push_back( &atom_in);
+	}
+	const std::vector<FAtom *>& getAdjacent() const { return adjacent; }
+	void clearAdjacent() { adjacent.clear(); }
 //==========================================================
 // MEMBER FUNCTION :
 // EXPLAIN : get value
@@ -77,7 +63,7 @@ class FAtom
 	const int& getNatom() const { return natom;}
 	const int& getCellX() const { return cell_x; }
 	const int& getCellY() const { return cell_y; }
-	const int& getCellZ() const { return cell_z; }	
+	const int& getCellZ() const { return cell_z; }
 };
 
 #endif