New 'evaluateBenchmarkCV' script

bergolho · Jun 2, 2024 · 736bf15 · 736bf15
2 parents 0008f6e + 82a5e32
commit 736bf15
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Showing 13 changed files with 3,846 additions and 31 deletions.
diff --git a/src/domains_library/domain.c b/src/domains_library/domain.c
@@ -127,10 +127,6 @@ 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;
@@ -141,15 +137,6 @@ 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;
@@ -163,7 +150,7 @@ 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, side_length_x, side_length_y, side_length_z);
+    set_benchmark_domain(the_grid);
 
     log_info("Cleaning grid\n");
     int i;

diff --git a/src/domains_library/domain_helpers.c b/src/domains_library/domain_helpers.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, real_cpu sx, real_cpu sy, real_cpu sz) {
+void set_benchmark_domain(struct grid *the_grid) {
     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);
@@ -1013,7 +1013,7 @@ int calc_num_refs(real_cpu start_h, real_cpu desired_h) {
 void set_cuboid_sphere_fibrosis_with_conic_path(struct grid *the_grid, real_cpu phi, real_cpu plain_center_x, real_cpu plain_center_y, \
                                                 real_cpu sphere_radius, real_cpu bz_size, real_cpu bz_radius, unsigned fib_seed, real_cpu cone_slope) {
 
-    log_info("Making %.2lf %% of cells inactive\n", phi * 100.0f);
+    struct cell_node *grid_cell;
 
     if(fib_seed == 0)
         fib_seed = (unsigned)time(NULL) + getpid();
@@ -1022,9 +1022,10 @@ void set_cuboid_sphere_fibrosis_with_conic_path(struct grid *the_grid, real_cpu
 
     log_info("Using %u as seed\n", fib_seed);
 
-    real_cpu bz_radius_2 = pow(bz_radius, 2.0);
-    real_cpu sphere_radius_2 = pow(sphere_radius, 2.0);
-    struct cell_node *grid_cell;
+    real_cpu a1 = (2.0*side_length) / (side_length - 2*source_sink_min_x);
+    real_cpu b1 = -source_sink_min_x*a1;
+    real_cpu a2 = (2.0*side_length) / (side_length - 2*source_sink_max_x);
+    real_cpu b2 = -source_sink_max_x*a2;
 
     grid_cell = the_grid->first_cell;
     while(grid_cell != 0) {
@@ -1073,11 +1074,15 @@ void set_cuboid_sphere_fibrosis_with_conic_path(struct grid *the_grid, real_cpu
                 distance_from_center = (distance_from_center - sphere_radius) / bz_size;
                 real_cpu phi_local = phi - phi * distance_from_center;
                 real_cpu p = (real_cpu)(rand()) / (RAND_MAX);
-                if(p < phi_local)
+                if(p < phi) {
                     grid_cell->active = false;
-                grid_cell->can_change = false;
+                }
+
+                INITIALIZE_FIBROTIC_INFO(grid_cell);
+                FIBROTIC(grid_cell) = true;
             }
         }
+
         grid_cell = grid_cell->next;
     }
-}
+}
diff --git a/src/domains_library/domain_helpers.h b/src/domains_library/domain_helpers.h
@@ -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, real_cpu sx, real_cpu sy, real_cpu sz);
+void set_benchmark_domain(struct grid *the_grid);
 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);

diff --git a/src/extra_data_library/extra_data.c b/src/extra_data_library/extra_data.c
@@ -626,4 +626,27 @@ SET_EXTRA_DATA(set_extra_data_trovato) {
 
     return (void*)extra_data;
 
-}
+}
+
+// For cable simulations for tuneCV
+SET_EXTRA_DATA(set_extra_data_for_cable_ToRORd_Land_mixed_endo_mid_epi_IKs) { 
+	uint32_t num_active_cells = the_grid->num_active_cells;
+    struct cell_node ** ac = the_grid->active_cells;
+
+    struct extra_data_for_torord_land_twave *extra_data = NULL;
+    extra_data = set_common_torord_Land_twave_data(config, num_active_cells);
+
+    // All cells will be the same type
+    OMP(parallel for)
+    for (int i = 0; i < num_active_cells; i++) {
+        // ENDO
+        extra_data->transmurality[i] = 0.0;
+		extra_data->sf_IKs[i] = 1.0;
+    }
+
+    SET_EXTRA_DATA_SIZE(sizeof(struct extra_data_for_torord_land_twave));
+
+    return (void*)extra_data;
+
+
+}