Removing unused ToRORd model

Author: bergolho

.gitignore

@@ -186,6 +186,7 @@ sync_local.sh
 sync_outputs.sh
 private_configs/
 private_parameter_sets/
+private_src/
 /src/domains_library/custom_mesh_info_data.h
 retired_code/
 *.gcno
@@ -199,3 +200,4 @@ VV_49900.dat
 *.build_type*
 /ecg.txt
 __pycache__/
+backup/

ToDo

@@ -18,13 +18,4 @@
 #KNOW ISSUES:
 The logger symbols are only exported to an executable if an static library linked to a shared library uses then. For now this is ok. But I think it will be a pain in future releases.
 The GPU linear system solver is not working for purkinje-only simulations
-When the minimum number of PMJs is not reached the solver will be in an infinite loop
-
-Lucas ToDo list:
-
-0) Revise all the examples inside the example_configs/ folder.
-
-1) Purkinje coupling: 
-    - Find a better way to write the PMJ delay into a file for the propagation block cases.
-
-  
+When the minimum number of PMJs is not reached the solver will be in an infinite loop  

networks/simple_his_bundle_pmj_location.vtk

@@ -127,6 +127,10 @@ SET_SPATIAL_DOMAIN(initialize_grid_with_rabbit_mesh) {
     return num_loaded > 0;
 }
 
+/**
+ * Sets the current domain as a domain described in the N-version benchmark
+ * (http://rsta.royalsocietypublishing.org/content/369/1954/4331)
+ */
 SET_SPATIAL_DOMAIN(initialize_grid_with_benchmark_mesh) {
 
     real_cpu side_length;
@@ -137,6 +141,15 @@ SET_SPATIAL_DOMAIN(initialize_grid_with_benchmark_mesh) {
     real_cpu max_h = start_h;
     GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real_cpu, max_h, config, "maximum_discretization");
 
+    real_cpu side_length_x = 20000.0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, side_length_x, config, "side_length_x");
+
+    real_cpu side_length_y = 7000.0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, side_length_y, config, "side_length_y");
+
+    real_cpu side_length_z = 3000.0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, side_length_z, config, "side_length_z");
+
     log_info("Loading N-Version benchmark mesh using dx %lf um, dy %lf um, dz %lf um\n", start_h, start_h, start_h);
 
     side_length = start_h;
@@ -150,7 +163,7 @@ SET_SPATIAL_DOMAIN(initialize_grid_with_benchmark_mesh) {
     int num_steps = get_num_refinement_steps_to_discretization(side_length, start_h);
 
     refine_grid(the_grid, num_steps);
-    set_benchmark_domain(the_grid);
+    set_benchmark_domain(the_grid, side_length_x, side_length_y, side_length_z);
 
     log_info("Cleaning grid\n");
     int i;

src/domains_library/domain.c

@@ -445,13 +445,13 @@ int calculate_cuboid_side_lengths(real_cpu start_dx, real_cpu start_dy, real_cpu
  * (http://rsta.royalsocietypublishing.org/content/369/1954/4331)
  *
  */
-void set_benchmark_domain(struct grid *the_grid) {
+void set_benchmark_domain(struct grid *the_grid, real_cpu sx, real_cpu sy, real_cpu sz) {
     struct cell_node *grid_cell = the_grid->first_cell;
 
-    real_cpu sx, sy, sz;
-    sx = 20000;
-    sy = 7000;
-    sz = 3000;
+    //real_cpu sx, sy, sz;
+    //sx = 20000;
+    //sy = 7000;
+    //sz = 3000;
 
     while(grid_cell != 0) {
         grid_cell->active = (grid_cell->center.x < sx) && (grid_cell->center.y < sy) && (grid_cell->center.z < sz);

src/domains_library/domain_helpers.c

@@ -17,7 +17,7 @@ int set_cuboid_domain_mesh(struct grid *the_grid, real_cpu start_dx, real_cpu st
                            real_cpu side_length_z);
 int set_square_mesh(struct config *config, struct grid *the_grid);
 
-void set_benchmark_domain(struct grid *the_grid);
+void set_benchmark_domain(struct grid *the_grid, real_cpu sx, real_cpu sy, real_cpu sz);
 void set_cuboid_domain(struct grid *the_grid, real_cpu sizeX, real_cpu sizeY, real_cpu sizeZ);
 
 void set_custom_mesh(struct grid *the_grid, const char *file_name, size_t size, char *read_format);
@@ -58,7 +58,7 @@ void set_cube_sphere_fibrosis(struct grid *the_grid, real_cpu phi, real_cpu sphe
 
 void set_cuboid_sphere_fibrosis_with_conic_path (struct grid *the_grid, real_cpu phi, real_cpu plain_center, real_cpu sphere_radius, real_cpu bz_size, real_cpu bz_radius,
                                unsigned fib_seed, real_cpu cone_slope);
-                                                
+
 int calc_num_refs(real_cpu start_h, real_cpu desired_h);
 
-#endif // MONOALG3D_DOMAIN_HELPERS_H
+#endif // MONOALG3D_DOMAIN_HELPERS_H