remove set fatom

Author: goodchong

source/module_cell/module_neighbor/sltk_atom_arrange.cpp

@@ -75,7 +75,11 @@ void atom_arrange::search(
 {
 	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);
@@ -93,6 +97,7 @@ void atom_arrange::search(
 	//=============================
 
 	const double radius_lat0unit = search_radius_bohr / ucell.lat0;
+    ModuleBase::timer::tick("atom_arrange", "Atom_input");
 
 	Atom_input at(
 		ofs_in,
@@ -102,6 +107,7 @@ void atom_arrange::search(
 		pbc_flag, 
 		radius_lat0unit, 
 		test_atom_in);
+    ModuleBase::timer::tick("atom_arrange", "Atom_input");
 
 	//===========================================
 	// Print important information in Atom_input
@@ -111,7 +117,13 @@ void atom_arrange::search(
 	//=========================================
 	// 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");
+
+    ModuleBase::timer::tick("atom_arrange", "search");
 
 	// test the adjacent atoms and the box.
 	if(test_only)
@@ -142,7 +154,6 @@ void atom_arrange::search(
         ofs_in << "search neighboring atoms done." << std::endl;
     }
 
-    ModuleBase::timer::tick("atom_arrange", "search");
     return;
 }
 

source/module_cell/module_neighbor/sltk_atom_input.cpp

@@ -6,16 +6,13 @@
 //==========================================================
 // define constructor and deconstructor
 //==========================================================
-Atom_input::Atom_input
-(
-	std::ofstream &ofs_in,
-	const UnitCell &ucell,
-	const int amount,
-	const int ntype,
-    const bool boundary_in,
-	const double radius_in,
-	const int &test_atom_in
-)
+Atom_input::Atom_input(std::ofstream &ofs_in,
+						const UnitCell &ucell,
+						const int amount,
+						const int ntype,
+						const bool boundary_in,
+						const double radius_in,
+						const int &test_atom_in)
 		:d_amount(amount),
 		d_amount_expand(amount),
 		periodic_boundary(boundary_in),
@@ -33,17 +30,7 @@ Atom_input::Atom_input
 		x_max_expand(0),
 		y_max_expand(0),
 		z_max_expand(0),
-		d_current(0),
-		test_atom_input(test_atom_in),
-
-//----------------------------------------------------------
-// WARNING :
-// Please be very very careful!
-// Here type = 0 ,and natom = -1 is a initial value,
-// don't change it !!
-//----------------------------------------------------------
-		type(0),
-		natom(-1)
+		test_atom_input(test_atom_in)
 {
 	ModuleBase::TITLE("Atom_input", "Atom_input");
 
@@ -530,40 +517,3 @@ void Atom_input::calculate_cells(void)
 	//=======================================
 	return;
 }
-
-void Atom_input::set_FAtom(const UnitCell &ucell, FAtom &a)const
-{
-//----------------------------------------------------------
-// EXPLAIN : if expand grid , set from array
-//----------------------------------------------------------
-	if (expand_flag)
-	{
-		a = fake_atoms[d_current];
-		++ d_current;
-	}
-
-//----------------------------------------------------------
-// CALL MEMBER FUNCTION :
-// NAME : load_atom
-//
-// EXPLAIN : if not expand grid , set directly
-//----------------------------------------------------------
-	else
-	{
-		natom++;
-
-		if (natom >= ucell.atoms[type].na)
-		{
-			type ++;
-			natom = 0;
-		}
-		FAtom temp(ucell.atoms[type].tau[natom].x,
-				   ucell.atoms[type].tau[natom].y,
-				   ucell.atoms[type].tau[natom].z,
-				   type, natom,
-				   0, 0, 0);
-		a = temp;
-	}
-
-	return;
-}

source/module_cell/module_neighbor/sltk_atom_input.h

@@ -21,10 +21,6 @@ class Atom_input
 		const int &test_atom_in = 0	//caoyu reconst 2021-05-24
 	);
 	~Atom_input();
-//==========================================================
-// Manipulators
-//==========================================================
-	void set_FAtom(const UnitCell &ucell, FAtom& a)const ;
 
 	double vec1[3];
 	double vec2[3];

source/module_cell/module_neighbor/test/sltk_atom_input_test.cpp

@@ -229,9 +229,6 @@ TEST_F(SltkAtomInputTest, ConstructorNoExpand)
     radius = 0;
     Atom_input Atom_inp(ofs, *ucell, ucell->nat, ucell->ntype, pbc, radius, test_atom_in);
     EXPECT_FALSE(Atom_inp.getExpandFlag());
-    // call set_FAtom and Load_atom
-    FAtom fa;
-    EXPECT_NO_THROW(Atom_inp.set_FAtom(*ucell, fa));
     ofs.close();
     ifs.open("test.out");
     std::string str((std::istreambuf_iterator<char>(ifs)), std::istreambuf_iterator<char>());
@@ -257,9 +254,6 @@ TEST_F(SltkAtomInputTest, ConstructorSmallSearchRadius)
     radius = 0.5;
     Atom_input Atom_inp(ofs, *ucell, ucell->nat, ucell->ntype, pbc, radius, test_atom_in);
     EXPECT_TRUE(Atom_inp.getExpandFlag());
-    // call set_FAtom and Load_atom
-    FAtom fa;
-    EXPECT_NO_THROW(Atom_inp.set_FAtom(*ucell, fa));
     ofs.close();
     ifs.open("test.out");
     std::string str((std::istreambuf_iterator<char>(ifs)), std::istreambuf_iterator<char>());