Refactor: refactor neighbour atom search but no change on algo (#5759)

* format file source/module_cell/module_neighbor/sltk_atom_arrange.cpp, remove some useless parameter in atom input

* rewrite module neighbour to parition atom into boxes

* merge atom input and grid

* replace some variable

* fresh unit test according to refactor

* add log

* add new find atom interface

* fix a atom self must on last bug

* fix unit test mask error

* fix a merge bug

* revert algo back to all 2 all search

* fix a unit test bug

Author: goodchong

source/Makefile.Objects

@@ -368,7 +368,6 @@ OBJS_MD=fire.o\
 
 OBJS_NEIGHBOR=sltk_atom.o\
     sltk_atom_arrange.o\
-    sltk_atom_input.o\
     sltk_grid.o\
     sltk_grid_driver.o\
 

source/module_cell/module_neighbor/CMakeLists.txt

@@ -3,7 +3,6 @@ add_library(
     OBJECT
     sltk_atom.cpp
     sltk_atom_arrange.cpp
-    sltk_atom_input.cpp
     sltk_grid.cpp
     sltk_grid_driver.cpp
 )

source/module_cell/module_neighbor/sltk_atom.cpp

@@ -4,9 +4,9 @@
 /*** Constructors and destructor ***/
 FAtom::FAtom()
 {
-	d_x = 0.0;	
-	d_y = 0.0;	
-	d_z = 0.0;	
-	type = 0;		
+	x = 0.0;
+	y = 0.0;
+	z = 0.0;
+	type = 0;
 	natom = 0;
 }

source/module_cell/module_neighbor/sltk_atom.h

@@ -10,31 +10,26 @@
 // the type and the index,
 class FAtom
 {
-private:
-	double d_x;
-	double d_y;
-	double d_z;
-	std::vector<FAtom *> adjacent;
+public:
+	double x;
+	double y;
+	double z;
 
 	int type;
 	int natom;
 
 	int cell_x;
 	int cell_y;
 	int cell_z;
-public:
-//==========================================================
-// Default Constructor and deconstructor
-//==========================================================
 
 	FAtom();
 	FAtom(const double& x_in, const double& y_in, const double& z_in, 
 			const int& type_in, const int& natom_in, 
 			const int& cell_x_in, const int& cell_y_in, const int& cell_z_in)
 	{
-		d_x = x_in;
-		d_y = y_in;
-		d_z = z_in;
+		x = x_in;
+		y = y_in;
+		z = z_in;
 		type = type_in;
 		natom = natom_in;
 		cell_x = cell_x_in;
@@ -43,27 +38,7 @@ class FAtom
 	}
 	~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
-//==========================================================
-	const double& x() const { return d_x; }
-	const double& y() const { return d_y; }
-	const double& z() const { return d_z; }
-	const int& getType() const { return type;}
-	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; }
 };
 
 #endif

source/module_cell/module_neighbor/sltk_atom_arrange.cpp

@@ -1,11 +1,11 @@
 #include "sltk_atom_arrange.h"
-#include "sltk_atom_input.h"
+
+#include "module_base/timer.h"
 #include "module_parameter/parameter.h"
 #include "sltk_grid.h"
 #include "sltk_grid_driver.h"
-#include "module_base/timer.h"
 
-// update the followig class in near future 
+// update the followig class in near future
 #include "module_cell/unitcell.h"
 
 atom_arrange::atom_arrange()
@@ -16,126 +16,92 @@ atom_arrange::~atom_arrange()
 {
 }
 
-double atom_arrange::set_sr_NL(
-	std::ofstream &ofs_in,
-	const std::string &output_level,
-	const double &rcutmax_Phi, 
-	const double &rcutmax_Beta, 
-	const bool gamma_only_local)
+double atom_arrange::set_sr_NL(std::ofstream& ofs_in,
+                               const std::string& output_level,
+                               const double& rcutmax_Phi,
+                               const double& rcutmax_Beta,
+                               const bool gamma_only_local)
 {
-	ModuleBase::TITLE("atom_arrange","set_sr_NL");
-
-	if(output_level != "m") //xiaohui add 'output_level', 2015-09-16
-	{
-		ofs_in << "\n\n\n\n";
-		ofs_in << " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" << std::endl;
-		ofs_in << " |                                                                    |" << std::endl;
-		ofs_in << " | Search adjacent atoms:                                             |" << std::endl;
-		ofs_in << " | Set the adjacent atoms for each atom and set the periodic boundary |" << std::endl;
-		ofs_in << " | condition for the atoms on real space FFT grid. For k-dependent    |" << std::endl;  
-		ofs_in << " | algorithm, we also need to set the sparse H and S matrix element   |" << std::endl;
-		ofs_in << " | for each atom.                                                     |" << std::endl; 
-		ofs_in << " |                                                                    |" << std::endl;
-		ofs_in << " <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<" << std::endl;
-		ofs_in << "\n\n\n\n";
-	}
+    ModuleBase::TITLE("atom_arrange", "set_sr_NL");
+    // check in use_overlap_matrix,
+    double sr = 0.0;
+    if (gamma_only_local)
+    {
+        sr = 2 * rcutmax_Phi + 0.001;
+    }
+    else
+    {
+        sr = 2 * (rcutmax_Phi + rcutmax_Beta) + 0.001; // 0.001 is added to make safe.
+                                                      // sr = 2 * longest_orb_rcut + 0.001;
+    }
 
-	
-	//xiaohui add 'output_level' line, 2015-09-16
-	if(output_level != "m") { ofs_in << "\n SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS" << std::endl;
-}
-	if(output_level != "m") { ofs_in << std::setprecision(3);
-}
-	if(output_level != "m") { ModuleBase::GlobalFunc::OUT(ofs_in,"longest orb rcut (Bohr)",rcutmax_Phi);
+    if (output_level != "m") // xiaohui add 'output_level', 2015-09-16
+    {
+        ofs_in << "\n\n\n\n";
+        ofs_in << " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" << std::endl;
+        ofs_in << " |                                                                    |" << std::endl;
+        ofs_in << " | Search adjacent atoms:                                             |" << std::endl;
+        ofs_in << " | Set the adjacent atoms for each atom and set the periodic boundary |" << std::endl;
+        ofs_in << " | condition for the atoms on real space FFT grid. For k-dependent    |" << std::endl;
+        ofs_in << " | algorithm, we also need to set the sparse H and S matrix element   |" << std::endl;
+        ofs_in << " | for each atom.                                                     |" << std::endl;
+        ofs_in << " |                                                                    |" << std::endl;
+        ofs_in << " <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<" << std::endl;
+        ofs_in << "\n\n\n\n";
+
+        ofs_in << "\n SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS" << std::endl;
+        ofs_in << std::setprecision(3);
+        ModuleBase::GlobalFunc::OUT(ofs_in, "longest orb rcut (Bohr)", rcutmax_Phi);
+        ModuleBase::GlobalFunc::OUT(ofs_in, "longest nonlocal projector rcut (Bohr)", rcutmax_Beta);
+        ModuleBase::GlobalFunc::OUT(ofs_in, "search radius (Bohr)", sr);
+	}
+    return sr;
 }
 
-//	std::cout << " LONGEST NL PROJ RCUT : " << longest_nl_proj_rcut << std::endl;
-	if(output_level != "m") { ModuleBase::GlobalFunc::OUT(ofs_in,"longest nonlocal projector rcut (Bohr)", rcutmax_Beta);
-}
+void atom_arrange::search(const bool pbc_flag,
+                          std::ofstream& ofs_in,
+                          Grid_Driver& grid_d,
+                          const UnitCell& ucell,
+                          const double& search_radius_bohr,
+                          const int& test_atom_in,
+                          const bool test_only)
+{
+    ModuleBase::TITLE("atom_arrange", "search");
+    ModuleBase::timer::tick("atom_arrange", "search");
 
-	// check in use_overlap_matrix, 
-	double sr = 0.0;
-	if(gamma_only_local)
-	{
-		sr = 2 * rcutmax_Phi + 0.01;
-	}
-	else
-	{
-		sr = 2 * (rcutmax_Phi +rcutmax_Beta) + 0.01; // 0.01 is added to make safe.
-		//sr = 2 * longest_orb_rcut + 0.01;
-	}
+    if (search_radius_bohr < 0.0)
+    {
+        ModuleBase::WARNING_QUIT("atom_arrange::search", " search_radius_bohr < 0,forbidden");
+    }
 
-	return sr;			
-}
+    ModuleBase::GlobalFunc::OUT(ofs_in, "searching radius is (Bohr))", search_radius_bohr);
+    ModuleBase::GlobalFunc::OUT(ofs_in, "searching radius unit is (Bohr))", ucell.lat0);
 
-void atom_arrange::search(
-	const bool pbc_flag,
-	std::ofstream &ofs_in,
-	Grid_Driver &grid_d, 
-	const UnitCell &ucell, 
-	const double &search_radius_bohr, 
-	const int &test_atom_in,
-	const bool test_only)
-{
-	ModuleBase::TITLE("atom_arrange", "search");
-	ModuleBase::timer::tick("atom_arrange","search");
-/* 	std::cout << "pbc_flag = " << pbc_flag << std::endl;
-	std::cout << "search_radius_bohr = " << search_radius_bohr << std::endl;
-	std::cout << "test_atom_in = " << test_atom_in << std::endl;
-	std::cout << "test_only = " << test_only << std::endl;
- */
-	assert( search_radius_bohr > 0.0 );
-
-//	OUT(ofs_in,"Atom coordinates reading from",PARAM.inp.stru_file);
-//	OUT(ofs_in,"The coordinate type",ucell.Coordinate);
-//	OUT(ofs_in,"Use cartesian(unit:lat0) coordinate","TRUE");
-//	if(PARAM.inp.out_level != "m") OUT(ofs_in,"searching radius is (Bohr))", search_radius_bohr);
-//	if(PARAM.inp.out_level != "m") OUT(ofs_in,"searching radius unit is (Bohr))",ucell.lat0);
-
-	ModuleBase::GlobalFunc::OUT(ofs_in,"searching radius is (Bohr))", search_radius_bohr);
-	ModuleBase::GlobalFunc::OUT(ofs_in,"searching radius unit is (Bohr))",ucell.lat0);
-
-	assert(ucell.nat > 0);
-	//=============================
-	// Initial Atom information
-	//=============================
-
-	const double radius_lat0unit = search_radius_bohr / ucell.lat0;
-    ModuleBase::timer::tick("atom_arrange", "Atom_input");
-
-	Atom_input at(
-		ofs_in,
-		ucell, 
-		ucell.nat, 
-		ucell.ntype, 
-		pbc_flag, 
-		radius_lat0unit, 
-		test_atom_in);
-    ModuleBase::timer::tick("atom_arrange", "Atom_input");
-
-	//===========================================
-	// Print important information in Atom_input
-	//===========================================
-//	at.print(std::cout);
-//	at.print_xyz_format("1.xyz");
-	//=========================================
-	// Construct Grid , Cells , Adjacent atoms
-	//=========================================
-
-    ModuleBase::timer::tick("atom_arrange", "grid_d.init");
-
-	grid_d.init(ofs_in, ucell, at);
-    ModuleBase::timer::tick("atom_arrange", "grid_d.init");
+    assert(ucell.nat > 0);
 
+    /*
+    2024-12-04 Zhang Haochong
+        The neighboring atom search module has been completely rewritten.
+        The new algorithm places atoms into boxes with an edge length of twice the atomic radius. The neighboring 
+    atom list stores the data using the atom's type and its index within that type.
+        By setting pbc_flag = false, periodic boundary conditions can be forcibly disabled. In this case, the search 
+    process will not expand the supercell, and the neighboring atoms will only consider those within the original unit cell.
+    */
+    const double radius_lat0unit = search_radius_bohr / ucell.lat0;
+
+    // Atom_input at(ofs_in, ucell, pbc_flag, radius_lat0unit, test_atom_in);
+
+    grid_d.init(ofs_in, ucell, radius_lat0unit, pbc_flag);
+
+	// The screen output is very time-consuming. To avoid interfering with the timing, we will insert logging here earlier.
     ModuleBase::timer::tick("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;
+    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;
+        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"
                   << std::endl;
@@ -147,19 +113,21 @@ void atom_arrange::search(
 
                 ofs_in << " " << std::setw(5) << it << std::setw(5) << ia << std::setw(8) << grid_d.getAdjacentNum() + 1
                        << std::endl;
-
+                std::cout << " adjacent atoms of " << ucell.atoms[it].label + std::to_string(ia + 1) << ":" << std::endl;
+                std::cout << "getAdjacentNum: " << grid_d.getAdjacentNum() + 1 << std::endl;
+                /*
                 for (int ad = 0; ad < grid_d.getAdjacentNum() + 1; ad++)
                 {
                     ModuleBase::Vector3<double> tau = grid_d.getAdjacentTau(ad);
                     ModuleBase::Vector3<int> box = grid_d.getBox(ad);
                     std::cout << std::setw(8) << ucell.atoms[it].label + std::to_string(ia + 1) << 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 << std::endl;
-                }
+                }*/
             }
         }
         ofs_in << "search neighboring atoms done." << std::endl;
     }
 
     return;
-}
+}

source/module_cell/module_neighbor/sltk_atom_arrange.h

@@ -3,7 +3,6 @@
 
 #include "sltk_grid.h"
 #include "sltk_grid_driver.h"
-#include "sltk_atom_input.h"
 
 
 class atom_arrange
@@ -29,7 +28,6 @@ class atom_arrange
 		const double& rcutmax_Phi, 
 		const double& rcutmax_Beta, 
 		const bool gamma_only_local);
-
 };
 
 #endif