diff --git a/src/cats/actions/setup_actions.c b/src/cats/actions/setup_actions.c
index 478dc9c9e61211e5195cc79ddd8fddb955b965af..5902def2fe0ca9b9d66fab8a3e208f9ab20c34ca 100644
--- a/src/cats/actions/setup_actions.c
+++ b/src/cats/actions/setup_actions.c
@@ -52,7 +52,7 @@ const char *ACTION_DEFAULT = "_default";
void add_default_actions(struct cats_configuration *conf)
{
assert(conf != NULL);
- register_default_functions(conf);
+ //register_default_action_functions(conf);
log_message(LOG_INFO, "setting up default actions");
append_action(conf, action_grid_stats_reset, ALL_STAGES, "statistics reset", ACTION_ALWAYS);
@@ -158,6 +158,41 @@ append_action(struct cats_configuration *conf, action_function action, enum cats
return conf->cycle.num_actions;
}
+void list_actions_full(struct cats_configuration *conf)
+{
+ log_message(LOG_INFO, "Action functions: %d", conf->action_functions.count);
+ for (int32_t i = 0; i < conf->action_functions.count; i++) {
+ log_message(LOG_INFO, "%d: %s %p ", i, conf->action_functions.names[i],
+ conf->action_functions.functions[i]);
+ }
+}
+
+
+action_function get_action_by_name(struct cats_configuration *conf, const char *name)
+{
+ for (int32_t i = 0; i < conf->action_functions.count; i++) {
+ if (!strcmp(conf->action_functions.names[i], name)) return conf->action_functions.functions[i];
+ }
+ return NULL;
+}
+
+int32_t
+append_action_by_name(struct cats_configuration *conf, const char *action_name, enum cats_simulation_stages when,
+ const char *name, const char *module_name)
+{
+ int32_t n = conf->cycle.num_actions;
+ conf->cycle.actions = realloc_or_die(conf->cycle.actions, (n + 1) * sizeof(struct cats_action));
+ conf->cycle.num_actions++;
+ action_function action = get_action_by_name(conf, action_name);
+ if (action == NULL) {
+ log_message(LOG_ERROR, "%s: could not find action '%s'", __func__, action_name);
+ exit_cats(EXIT_FAILURE);
+ }
+ add_action_at(conf, n, action, when, name, module_name);
+
+ return conf->cycle.num_actions;
+}
+
void shift_action_functions_down_by_one(struct cats_configuration *conf, int32_t from)
{
@@ -258,7 +293,7 @@ bool action_is_registered(const struct cats_configuration *conf, const action_fu
const struct action_function_registry *registry = &conf->action_functions;
for (int32_t i = 0; i < registry->count; i++) {
- if (registry->functions[i] == function) return true;
+ if (*(registry->functions[i]) == function) return true;
}
return false;
@@ -266,7 +301,7 @@ bool action_is_registered(const struct cats_configuration *conf, const action_fu
}
-void register_default_functions(struct cats_configuration *conf)
+void register_default_action_functions(struct cats_configuration *conf)
{
register_action_function(conf, action_grid_stats_reset, "action_reset_grid_stats", "resetting stats");
diff --git a/src/cats/actions/setup_actions.h b/src/cats/actions/setup_actions.h
index 6712074330c6d3717f3b3a666bd4fcabdf5ae26a..242c4746268403c9eb661d8dad5f40c336aee79d 100644
--- a/src/cats/actions/setup_actions.h
+++ b/src/cats/actions/setup_actions.h
@@ -41,7 +41,7 @@ int32_t append_action(struct cats_configuration *conf, action_function action, e
action_function get_action_function(const struct cats_configuration *conf, const char *name);
-void register_default_functions(struct cats_configuration *conf);
+void register_default_action_functions(struct cats_configuration *conf);
int32_t
add_action_after_function(struct cats_configuration *conf, action_function function, enum cats_simulation_stages when,
@@ -54,4 +54,14 @@ void replace_function(struct cats_configuration *conf, action_function function,
void cleanup_action_functions(struct action_function_registry *registry);
+void list_actions(const struct cats_configuration *conf);
+
+void list_actions_full(struct cats_configuration *conf);
+
+void register_action_function(struct cats_configuration *conf, action_function function, const char *name,
+ const char *message);
+
+int32_t append_action_by_name(struct cats_configuration *conf, const char *action_name, enum cats_simulation_stages when,
+ const char *name, const char *module_name);
+
#endif //CATS_SETUP_ACTIONS_H
diff --git a/src/cats/cats.c b/src/cats/cats.c
index be52637b132cd097f9e68f31f8ca0ccb726e3372..9cbc75a925df860a35ab8e5cf8adb37a3d5a9bb0 100644
--- a/src/cats/cats.c
+++ b/src/cats/cats.c
@@ -163,6 +163,13 @@ void load_modules(struct cats_configuration *conf)
}
+
+ printf("%s: %d\n", __func__, j);
+ if (p->module_data[j].load_species_param_function) {
+ p->module_data[j].load_species_param_function(conf, conf->ini, p->species_config_section, p);
+ }
+
+
}
}
@@ -177,6 +184,7 @@ struct cats_configuration *load_main_configuration(const struct program_options
setup_directories(conf);
post_process_configuration(conf);
//print_config_summary(conf);
+ register_default_action_functions(conf);
load_modules(conf);
diff --git a/src/cats/configuration/load_configuration_species_params.c b/src/cats/configuration/load_configuration_species_params.c
index 4ec6390101780148741cfb181e2b67b371f6b6f4..6480603f9cefefe6791eb551c4d7a3e0fb1ab827 100644
--- a/src/cats/configuration/load_configuration_species_params.c
+++ b/src/cats/configuration/load_configuration_species_params.c
@@ -101,7 +101,9 @@ void load_conf_vital_rate(struct cats_vital_rate *vr, struct cats_configuration
char *vr_name = vr->name;
char *vital_rate_maximum = compound_string(vr_name, "maximum", " ");
- bool req = vr->preset.have_maximum;
+ bool req = !vr->preset.have_maximum;
+ printf("%s: %s required %d\n", __func__, vr->name, req);
+ if (vr == &p->carrying_capacity) req = true;
bool have_max = load_conf_value(req, ini, species_section, vital_rate_maximum, &vr->max_rate);
if (vr->is_integer_quantity) {
vr->max_rate = roundl(vr->max_rate);
@@ -278,6 +280,7 @@ void load_config_species_parameter(struct cats_configuration *conf, struct cats_
for (int32_t i = 0; i < conf->modules.count; i++) {
+ printf("%s: %d\n", __func__, i);
if (p->module_data[i].load_species_param_function) {
p->module_data[i].load_species_param_function(conf, ini, species_section, p);
}
diff --git a/src/cats/grids/cats_grid.c b/src/cats/grids/cats_grid.c
index 413161ac37dff339df7d018c042c39bc4f15cc2e..292eb16619080c0cdcd840443ca6812e89544f81 100644
--- a/src/cats/grids/cats_grid.c
+++ b/src/cats/grids/cats_grid.c
@@ -251,17 +251,27 @@ void cleanup_grid_seeds_and_juveniles(struct cats_grid *grid)
free_grid(&grid->seeds_produced, grid->dimension.rows);
free_grid(&grid->dispersed_seeds, grid->dimension.rows);
+ if (grid->seed_bank) {
+ for (cats_dt_coord row = 0; row < grid->dimension.rows; row++) {
+ for (cats_dt_coord col = 0; col < grid->dimension.cols; col++) {
+ destroy_seed_structure(grid, row, col);
+ }
- for (cats_dt_coord row = 0; row < grid->dimension.rows; row++) {
- for (cats_dt_coord col = 0; col < grid->dimension.cols; col++) {
- destroy_seed_structure(grid, row, col);
- destroy_juveniles(grid, row, col);
+ free(grid->juveniles[row]);
}
+ }
+
+ if (grid->seed_bank) {
+ for (cats_dt_coord row = 0; row < grid->dimension.rows; row++) {
+ for (cats_dt_coord col = 0; col < grid->dimension.cols; col++) {
+ destroy_juveniles(grid, row, col);
+ }
- free(grid->seed_bank[row]);
- free(grid->juveniles[row]);
+ free(grid->juveniles[row]);
+ }
}
+
free(grid->seed_bank);
free(grid->juveniles);
free(grid->seeds_produced);
diff --git a/src/cats/modules/load_module.c b/src/cats/modules/load_module.c
index 65bc4cb7090b25ce7edeb1c7b6746e37b49235ac..ad1f8c20dd602e18cb9dead2bf6f0e59a9994e77 100644
--- a/src/cats/modules/load_module.c
+++ b/src/cats/modules/load_module.c
@@ -164,7 +164,7 @@ void register_module_vital_rate(struct cats_configuration *conf, struct cats_vit
m->vital_rate_required = realloc_or_die(m->vital_rate_required, sizeof(bool) * (vr_count + 1));
m->vr[vr_count] = vr;
m->vital_rate_name[vr_count] = strdup(name);
-
+ vr->is_carrying_capacity = false;
strncpy(vr->name, name, MAX_VITAL_NAME_LEN + 1);
diff --git a/src/cats/stats/write_stats.c b/src/cats/stats/write_stats.c
index 11844db7fe9eae9c3d75961b9e67eebf48e823c7..b4e440dad9041af9531419b56420ff0d82a75fd9 100644
--- a/src/cats/stats/write_stats.c
+++ b/src/cats/stats/write_stats.c
@@ -189,6 +189,7 @@ void write_grid_stats(struct cats_configuration *conf, struct cats_grid *grid, b
for (int32_t module_id = 0; module_id < conf->modules.count; module_id++) {
struct string_array *module_stats = add_module_stats(conf, grid, header, module_id);
+ if (module_stats == NULL) continue;
write_to_file(file, module_stats, ",");
if (conf->modules.module[module_id].stats_header == NULL) {
conf->modules.module[module_id].stats_header = copy_string_array(module_stats);
diff --git a/src/cats/vital_rates/default_vital_rates.c b/src/cats/vital_rates/default_vital_rates.c
index 83b6de11b4edd9e6675e033dcd0599243e94021f..270c657e830de8e4000e8b49bb7d3070900d603b 100644
--- a/src/cats/vital_rates/default_vital_rates.c
+++ b/src/cats/vital_rates/default_vital_rates.c
@@ -285,12 +285,15 @@ void postprocess_vital_rates(struct cats_configuration *conf)
post_process_vital_rate(conf, ¶m->carrying_capacity, set, param);
- for (enum cats_vital_rate_id vr_idx = VR_MIN + 1; vr_idx < VR_MAX; vr_idx++) {
- struct cats_vital_rate *vr = ¶m->vital_rates[vr_idx];
- vr->default_rate_id = vr_idx;
- post_process_vital_rate(conf, vr, set, param);
+ if (param->demographic_module == NULL) {
+ for (enum cats_vital_rate_id vr_idx = VR_MIN + 1; vr_idx < VR_MAX; vr_idx++) {
+ struct cats_vital_rate *vr = ¶m->vital_rates[vr_idx];
+ vr->default_rate_id = vr_idx;
+ post_process_vital_rate(conf, vr, set, param);
+ }
}
+
for (int32_t i = 0; i < conf->modules.count; i++) {
for (int32_t j = 0; j < param->module_data[i].vital_rate_count; j++) {
post_process_vital_rate(conf, param->module_data[i].vr[j], set, param);
diff --git a/src/cats/vital_rates/setup_rates.c b/src/cats/vital_rates/setup_rates.c
index 9bdace81841818765b64b25bd4a417263bb5ee6e..2f167f5fda18e9eef694a1763e7ba8962f917acd 100644
--- a/src/cats/vital_rates/setup_rates.c
+++ b/src/cats/vital_rates/setup_rates.c
@@ -113,7 +113,7 @@ void set_vital_density(struct cats_vital_rate *vital, enum cats_density_dependen
{
assert(vital != NULL);
if (vital->is_carrying_capacity && density != NO_DENSITY_DEP) {
- log_message(LOG_ERROR, "%s: carrying capacity may never depend on population density", __func__);
+ log_message(LOG_ERROR, "%s (%s): carrying capacity may never depend on population density", __func__, vital->name);
exit_cats(EXIT_FAILURE);
}
vital->density = density;
diff --git a/src/cats/vital_rates/setup_rates.h b/src/cats/vital_rates/setup_rates.h
index f48091952685e1e37672d039c0322442127b4688..f700b88f70d11d30e091675888ada24763859c03 100644
--- a/src/cats/vital_rates/setup_rates.h
+++ b/src/cats/vital_rates/setup_rates.h
@@ -33,10 +33,6 @@ void set_vital_rate_suitability_cutoff_hint(struct cats_vital_rate *vital,
void set_vital_density_ts(struct cats_vital_rate *vital, cats_dt_rates ts);
-void set_vital_rate(struct cats_vital_rate *vital, const char *name, cats_dt_rates max_rate, cats_dt_rates cutoff,
- struct cats_environment *set, enum cats_density_dependence density,
- const struct cats_species_param *param);
-
void set_vital_rate_name(struct cats_vital_rate *vital, const char *name);
int32_t setup_default_links(struct cats_vital_rate_hybrid_function *vital_dependency_registry);
diff --git a/src/cats/vital_rates/vital_rates.h b/src/cats/vital_rates/vital_rates.h
index 21d9cc011687cebd30fb786b66f7408f868f4f85..aa9690935d07061b6bcc13b1c84f1d2c7fecf9d0 100644
--- a/src/cats/vital_rates/vital_rates.h
+++ b/src/cats/vital_rates/vital_rates.h
@@ -26,6 +26,7 @@
#define CATS_VITAL_RATES_H
#include "data/cats_datatypes.h"
+#include "defaults.h"
struct cats_species_param;
struct cats_grid;