src/cats/configuration/configuration.c

@@ -301,6 +301,8 @@ void cleanup_configuration(struct cats_configuration **conf_orig)
         free(conf->global_stats.populated_by_classes);
         free_string_array(&conf->output.needed_output_directories);
         free_string_array(&conf->output.needed_module_output_directories);
+        free_string_array(&conf->overlays.registered_custom_overlay_names);
+
         free(conf->param);
         conf->param = NULL;
         free(conf->run_name);

src/cats/configuration/load_configuration.c

@@ -84,7 +84,7 @@ load_configuration_from_file(const char *filename, const struct program_options
 
         conf->command_line_options = *command_line_options;
         if (command_line_options->need_conf) {
-                conf->command_line_options.configuration_file = strdup(command_line_options->configuration_file);
+                //conf->command_line_options.configuration_file = strdup(command_line_options->configuration_file);
         } else {
                 conf->command_line_options.configuration_file = strdup("auto-generated");
         }

src/cats/configuration/load_configuration_overlays.c

@@ -102,6 +102,7 @@ void load_overlay_configuration(struct cats_configuration *conf, struct cats_ini
                                 exit(EXIT_FAILURE);
                 }
                 free(type_name);
+                free(overlay_name);
         }
 
         free_string_array(&overlay_names);

src/cats/data/cats_global.c

@@ -78,6 +78,7 @@ _Noreturn void exit_cats(int status)
 
         exit(status);
 
+
 }
 
 

src/cats/lambda/lambda.c

@@ -65,7 +65,7 @@ cats_dt_rates calculate_lambda(struct cats_configuration *conf, struct lambda_pa
         //
 
         double *matrix_copy = NULL;
-        matrix_copy = copy_matrix(matrix, N, N);
+
 
         if (silent == false || conf->command_line_options.debug_flags & DEBUG_LAMBDA) {
                 matrix_copy = copy_matrix(matrix, N, N);

src/modules/butterflies/butterflies_actions.c

@@ -183,14 +183,6 @@ void butterflies_area_dispersal(struct cats_grid *grid, struct cats_thread_info
                         butterflies_cell_dispersal(grid, ts, row, col, false, false);
                 }
         }
-
-        /*
-        if (ts->rw_debug_cells_with_adults) {
-                log_message(LOG_INFO, "thread %d: %ld cells with adults, %ld random walks, %ld deposits",
-                            ts->id, ts->rw_debug_cells_with_adults, ts->rw_debug_random_walks, ts->rw_debug_deposits);
-        }
-         */
-
 }
 
 
@@ -250,9 +242,10 @@ enum action_status bf_action_dispersal(struct cats_grid *grid, struct cats_confi
         threaded_action(&butterflies_area_dispersal, grid, conf, TS_DISPERSAL);
         struct conf_data_butterflies *module_conf = CATS_MODULE_DATA;
 
-        for (enum butterfly_stats which = BF_RANDOM_WALK_DEPOSIT_COUNT; which < BF_STAT_MAX; which++) {
+        for (enum butterfly_stats which = BF_RANDOM_WALK_DEPOSIT_COUNT; which < BF_OUTPUT_STAT_MAX; which++) {
                 int64_t stat_id = module_conf->stat_ids[which];
-                log_message(LOG_INFO, "STAT %s: %ld", bf_get_stats_field_name(which), grid->stats.stats[stat_id]);
+                log_message(LOG_INFO, "STAT %s (%ld): %ld", bf_get_stats_field_name(which), stat_id,
+                            grid->stats.custom_stats[stat_id]);
         }
 
         return ACTION_RUN;
@@ -300,8 +293,7 @@ enum action_status bf_action_generation_update(struct cats_grid *grid, struct ca
         int64_t cells_with_eggs_removed = grid->stats.custom_stats[egg_cells_removed_id];
         log_message(LOG_INFO, "%ld cells with eggs left, %ld cells with eggs removed", cells_with_eggs,
                     cells_with_eggs_removed);
-        grid->stats.custom_stats[egg_cells_id] = 0;
-        grid->stats.custom_stats[egg_cells_removed_id] = 0;
+
         return ACTION_RUN;
 }
 
@@ -312,7 +304,6 @@ enum action_status bf_action_overlay_update(struct cats_grid *grid, struct cats_
 }
 
 
-
 enum action_status bf_action_generation_finish(struct cats_grid *grid, struct cats_configuration *conf)
 {
         const int module_id = CATS_MODULE_ID;
@@ -322,7 +313,7 @@ enum action_status bf_action_generation_finish(struct cats_grid *grid, struct ca
 
         data->generation_current--;
         assert(data->generation_current >= 0);
-        // struct conf_data_butterflies *data = CATS_MODULE_DATA;
+
         return ACTION_RUN;
 }
 

src/modules/butterflies/butterflies_dispersal.c

@@ -42,6 +42,7 @@ static void inline single_random_walk(struct cats_thread_info *ts, struct cats_g
         const struct conf_data_butterflies *module_conf = CATS_MODULE_DATA;
         const bool debug_rw = module_conf->debug_rw;
         const int64_t stat_id_deposits = module_conf->stat_ids[BF_RANDOM_WALK_DEPOSIT_COUNT];
+        const int64_t stat_id_rw_steps = module_conf->stat_ids[BF_RANDOM_WALK_STEP_COUNT];
 
         int32_t eggs_left = eggs;
         const cats_dt_coord max_steps = module_conf->animal_dispersal_max_radius;
@@ -72,6 +73,8 @@ static void inline single_random_walk(struct cats_thread_info *ts, struct cats_g
                         return; // we escaped the simulation extent and got lost
                 }
 
+                increase_custom_stat(ts->stats, stat_id_rw_steps, 1);
+
 
                 // is the cell a valid dispersal target location?
                 if (!(data->info_layer[row][col] & BF_CELL_VALID_DISPERSAL_TARGET)) {
@@ -214,7 +217,6 @@ butterflies_cell_dispersal(struct cats_grid *grid, struct cats_thread_info *ts,
 
                 }
 
-
                 single_random_walk(ts, grid, row, col, eggs_to_disperse_per_female, egg_fraction_step, rw_number);
                 increase_custom_stat(ts->stats, stat_id_rw, 1);
 

src/modules/butterflies/butterflies_stats.c

@@ -26,12 +26,10 @@ const char *bf_get_stats_field_name(enum butterfly_stats which)
                         return "unpopulated_unfit";
                 case BF_STAT_EXCLUDED:
                         return "excluded";
-
                 case BF_RANDOM_WALK_DEPOSIT_COUNT:
                         return "random_walk_deposit_count";
                 case BF_RANDOM_WALK_COUNT:
                         return "random_walk_count";
-
                 case BF_RANDOM_WALK_STEP_COUNT:
                         return "random_walk_step_count";
                 case BF_OUTPUT_STAT_MAX:

src/modules/butterflies/butterflies_stats.h

@@ -16,9 +16,9 @@ enum butterfly_stats {
     BF_RANDOM_WALK_DEPOSIT_COUNT,
     BF_RANDOM_WALK_COUNT,
     BF_RANDOM_WALK_STEP_COUNT,
+    BF_OUTPUT_STAT_MAX,
     BF_CELLS_WITH_EGGS,
     BF_CELLS_WITH_EGGS_REMOVED,
-    BF_OUTPUT_STAT_MAX,
     BF_STAT_MAX
 };
 
@@ -31,7 +31,6 @@ static inline void increase_custom_stat(struct statistics *stats, int64_t stat_i
         assert(stats != NULL);
         assert(stat_id >= 0 && stat_id < stats->custom_stat_count);
         stats->custom_stats[stat_id] += by;
-
 }