revert algo back to all 2 all search

Author: goodchong

source/module_cell/module_neighbor/sltk_grid.cpp

@@ -194,6 +194,7 @@ void Grid::setMemberVariables(std::ofstream& ofs_in, //  output data to ofs
 
     this->box_edge_length = sradius + 0.1; // To avoid edge cases, the size of the box is slightly increased.
 
+/*  warning box algorithm   
     this->box_nx = std::ceil((this->x_max - this->x_min) / box_edge_length) + 1;
     this->box_ny = std::ceil((this->y_max - this->y_min) / box_edge_length) + 1;
     this->box_nz = std::ceil((this->z_max - this->z_min) / box_edge_length) + 1;
@@ -208,8 +209,21 @@ void Grid::setMemberVariables(std::ofstream& ofs_in, //  output data to ofs
             atoms_in_box[i][j].resize(this->box_nz);
         }
     }
+ */
+    this->box_nx = glayerX + glayerX_minus;
+    this->box_ny = glayerY + glayerY_minus;
+    this->box_nz = glayerZ + glayerZ_minus;
+    ModuleBase::GlobalFunc::OUT(ofs_in, "BoxNumber", box_nx, box_ny, box_nz);
 
-
+    atoms_in_box.resize(this->box_nx);
+    for (int i = 0; i < this->box_nx; i++)
+    {
+        atoms_in_box[i].resize(this->box_ny);
+        for (int j = 0; j < this->box_ny; j++)
+        {
+            atoms_in_box[i][j].resize(this->box_nz);
+        }
+    }
     for (int ix = -glayerX_minus; ix < glayerX; ix++)
     {
         for (int iy = -glayerY_minus; iy < glayerY; iy++)
@@ -225,7 +239,10 @@ void Grid::setMemberVariables(std::ofstream& ofs_in, //  output data to ofs
                         double z = ucell.atoms[i].tau[j].z + vec1[2] * ix + vec2[2] * iy + vec3[2] * iz;
                         FAtom atom(x, y, z, i, j, ix, iy, iz);
                         int box_i_x, box_i_y, box_i_z;
-                        this->getBox(box_i_x, box_i_y, box_i_z, x, y, z);
+                        //this->getBox(box_i_x, box_i_y, box_i_z, x, y, z);
+                        box_i_x = ix + glayerX_minus;
+                        box_i_y = iy + glayerY_minus;
+                        box_i_z = iz + glayerZ_minus;
                         this->atoms_in_box[box_i_x][box_i_y][box_i_z].push_back(atom);
                     }
                 }
@@ -269,12 +286,19 @@ void Grid::Construct_Adjacent_near_box(const FAtom& fatom)
     int box_i_x, box_i_y, box_i_z;
     this->getBox(box_i_x, box_i_y, box_i_z, fatom.x, fatom.y, fatom.z);
 
-    for (int box_i_x_adj = std::max(box_i_x - 1, 0); box_i_x_adj <= std::min(box_i_x + 1, box_nx - 1); box_i_x_adj++)
+/*     for (int box_i_x_adj = std::max(box_i_x - 1, 0); box_i_x_adj <= std::min(box_i_x + 1, box_nx - 1); box_i_x_adj++)
     {
         for (int box_i_y_adj = std::max(box_i_y - 1, 0); box_i_y_adj <= std::min(box_i_y + 1, box_ny - 1); box_i_y_adj++)
         {
             for (int box_i_z_adj = std::max(box_i_z - 1, 0); box_i_z_adj <= std::min(box_i_z + 1, box_nz - 1); box_i_z_adj++)
             {
+ */             
+    for (int box_i_x_adj = 0; box_i_x_adj < glayerX + glayerX_minus; box_i_x_adj++)
+    {
+        for (int box_i_y_adj = 0; box_i_y_adj < glayerY + glayerY_minus; box_i_y_adj++)
+        {
+            for (int box_i_z_adj = 0; box_i_z_adj < glayerZ + glayerZ_minus; box_i_z_adj++)
+            {
                 for (auto &fatom2 : this->atoms_in_box[box_i_x_adj][box_i_y_adj][box_i_z_adj])
                 {
                     this->Construct_Adjacent_final(fatom, &fatom2);