mech grid size in xml

Author: rheiland

core/PhysiCell_cell.cpp

@@ -1330,6 +1330,67 @@ bool is_neighbor_voxel(Cell* pCell, std::vector<double> my_voxel_center, std::ve
 	return true;
 }
 
+// bool is_neighbor_voxel_original(Cell* pCell, std::vector<double> my_voxel_center, std::vector<double> other_voxel_center, int other_voxel_index)
+// bool is_neighbor_voxel_Claude(Cell* pCell, const std::vector<double>& my_voxel_center, 
+//                        const std::vector<double>& other_voxel_center, int other_voxel_index)
+// {
+//     // Cache frequently used values
+//     const double max_interactive_distance = pCell->phenotype.mechanics.relative_maximum_adhesion_distance * 
+//                                            pCell->phenotype.geometry.radius + 
+//                                            pCell->get_container()->max_cell_interactive_distance_in_voxel[other_voxel_index];
+//     const double max_distance_squared = max_interactive_distance * max_interactive_distance;
+//     const auto& pos = pCell->position;
+    
+//     // Helper lambda to compute squared distance
+//     auto squared_distance = [](double dx, double dy, double dz = 0.0) {
+//         return dx * dx + dy * dy + dz * dz;
+//     };
+    
+//     // Count matching dimensions to determine neighbor type
+//     int matching_dims = 0;
+//     int differing_dim = -1;
+    
+//     for (int i = 0; i < 3; ++i) {
+//         if (my_voxel_center[i] == other_voxel_center[i]) {
+//             matching_dims++;
+//         } else {
+//             differing_dim = i;
+//         }
+//     }
+    
+//     // Case 1: Face neighbor (2 matching dimensions)
+//     if (matching_dims == 2) {
+//         const double surface_coord = 0.5 * (my_voxel_center[differing_dim] + other_voxel_center[differing_dim]);
+//         return std::fabs(pos[differing_dim] - surface_coord) <= max_interactive_distance;
+//     }
+    
+//     // Case 2: Edge neighbor (1 matching dimension)
+//     if (matching_dims == 1) {
+//         int dim1 = -1, dim2 = -1;
+//         for (int i = 0, count = 0; i < 3; ++i) {
+//             if (my_voxel_center[i] != other_voxel_center[i]) {
+//                 if (count == 0) dim1 = i;
+//                 else dim2 = i;
+//                 count++;
+//             }
+//         }
+        
+//         const double line_coord1 = 0.5 * (my_voxel_center[dim1] + other_voxel_center[dim1]);
+//         const double line_coord2 = 0.5 * (my_voxel_center[dim2] + other_voxel_center[dim2]);
+//         const double dist_sq = squared_distance(pos[dim1] - line_coord1, pos[dim2] - line_coord2);
+        
+//         return dist_sq <= max_distance_squared;
+//     }
+    
+//     // Case 3: Corner neighbor (0 matching dimensions)
+//     const double corner_x = 0.5 * (my_voxel_center[0] + other_voxel_center[0]);
+//     const double corner_y = 0.5 * (my_voxel_center[1] + other_voxel_center[1]);
+//     const double corner_z = 0.5 * (my_voxel_center[2] + other_voxel_center[2]);
+//     const double dist_sq = squared_distance(pos[0] - corner_x, pos[1] - corner_y, pos[2] - corner_z);
+    
+//     return dist_sq <= max_distance_squared;
+// }
+
 std::vector<Cell*>& Cell::cells_in_my_container( void )
 {
 	return get_container()->agent_grid[get_current_mechanics_voxel_index()];

core/PhysiCell_cell.h

@@ -262,6 +262,7 @@ void save_all_cells_to_matlab( std::string filename );
 
 //function to check if a neighbor voxel contains any cell that can interact with me
 bool is_neighbor_voxel(Cell* pCell, std::vector<double> myVoxelCenter, std::vector<double> otherVoxelCenter, int otherVoxelIndex);  
+// bool is_neighbor_voxel(Cell* pCell, const std::vector<double>& myVoxelCenter, const std::vector<double>& otherVoxelCenter, int otherVoxelIndex);    // Claude
 
 
 extern std::unordered_map<std::string,Cell_Definition*> cell_definitions_by_name; 

core/PhysiCell_constants.cpp

@@ -76,6 +76,7 @@ double mechanics_dt = 0.1;
 double phenotype_dt = 6.0;
 double intracellular_dt = 0.01;
 
+double mechanics_voxel_size = 30.0;
 
 // currently recognized cell cycle models 
 const int PhysiCell_constants::advanced_Ki67_cycle_model= 0;

core/PhysiCell_constants.h

@@ -157,6 +157,7 @@ extern double diffusion_dt;
 extern double mechanics_dt;
 extern double phenotype_dt;
 extern double intracellular_dt;
+extern double mechanics_voxel_size;
 
 
 extern std::unordered_map<std::string,int> cycle_model_codes;