diff --git a/src/cats/actions/process_inter_period_survival.c b/src/cats/actions/process_inter_period_survival.c
index 0f6d0509820d51ede8fadfdb39abad906bb07c44..24c48b3000a25ca838e877d9d10e590efec142e9 100644
--- a/src/cats/actions/process_inter_period_survival.c
+++ b/src/cats/actions/process_inter_period_survival.c
@@ -66,13 +66,9 @@ void write_stats(struct cats_grid *grid, const struct cats_configuration *conf,
}
}
- for (int32_t i = 0; i < max_age_of_maturity + 1; i++) {
- if (g->juveniles[0][0]) {
- fprintf(f, ",%d", g->juveniles[0][0][i]);
- } else {
- fprintf(f, ",%d", 0);
- }
+ for (int32_t i = 0; i < max_age_of_maturity + 1; i++) {
+ fprintf(f, ",%d", get_juveniles(g, 0, 0, i));
}
fprintf(f, "\n");
diff --git a/src/cats/grids/cats_grid.c b/src/cats/grids/cats_grid.c
index 3ddb38ed12b0caf63ebb524979880918086b7279..b3edba612207830d1238ac09480daa84701def54 100644
--- a/src/cats/grids/cats_grid.c
+++ b/src/cats/grids/cats_grid.c
@@ -266,7 +266,7 @@ void cleanup_grid_seeds_and_juveniles(struct cats_grid *grid)
destroy_juveniles(grid, row, col);
}
- free(grid->juveniles[row]);
+ free(grid->juveniles[row]); // clean-up [cleanup_grid_seeds_and_juveniles]
}
}
diff --git a/src/cats/grids/gdal_save.c b/src/cats/grids/gdal_save.c
index 89d05a6e264a0931c115cb3520880ff8d74b51d1..6a2e0a244b11a08f903391cce702a10606134692 100644
--- a/src/cats/grids/gdal_save.c
+++ b/src/cats/grids/gdal_save.c
@@ -221,11 +221,7 @@ void *save_juveniles_to_gdal(struct cats_grid *grid, struct cats_configuration *
sizeof(int32_t));//new_int32t_grid(grid->rows, grid->cols);
for (cats_dt_coord row = 0; row < rows; row++) {
for (cats_dt_coord col = 0; col < cols; col++) {
- if (grid->juveniles[row][col]) {
- juvs[row][col] = grid->juveniles[row][col][i];
- } else {
- juvs[row][col] = 0;
- }
+ juvs[row][col] = get_juveniles(grid, row, col, i);
}
}
struct cats_dimension dim = {.rows = rows, .cols = cols};
diff --git a/src/cats/grids/grid_setup.c b/src/cats/grids/grid_setup.c
index 899ce48177ece06f06e2c4f96b07846440a0e0d3..3f879c20afa42ce1dc704d4a1c2a1870667337f9 100644
--- a/src/cats/grids/grid_setup.c
+++ b/src/cats/grids/grid_setup.c
@@ -98,10 +98,10 @@ void setup_grid_juvenile_structures_opt(struct cats_configuration *conf, struct
grid->juveniles = calloc_or_die(grid->dimension.rows, sizeof(cats_dt_population **));
for (cats_dt_coord row = 0; row < grid->dimension.rows; row++) {
- grid->juveniles[row] = calloc_or_die(grid->dimension.cols, sizeof(cats_dt_population *));
+ grid->juveniles[row] = calloc_or_die(grid->dimension.cols, sizeof(cats_dt_population *)); // initialisation [setup_grid_juvenile_structures_opt]
for (cats_dt_coord col = 0; col < grid->dimension.cols; col++) {
- grid->juveniles[row][col] = NULL;
+ grid->juveniles[row][col] = NULL; // initialisation [setup_grid_juvenile_structures_opt]
}
}
}
diff --git a/src/cats/inline.h b/src/cats/inline.h
index fe3ae806afc01023a11ee094600c41b24e2a5f74..cb0f3b5c0a46255c77760fd78e1753426867c5ce 100644
--- a/src/cats/inline.h
+++ b/src/cats/inline.h
@@ -319,19 +319,16 @@ static inline cats_dt_population_sum
get_juvenile_sum(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col)
{
assert(grid != NULL && grid->juveniles != NULL);
- assert(valid_coordinates(&grid->dimension, row, col));
- assert(grid->juveniles[row] != NULL);
+ if (!juveniles_exist(grid, row, col)) return 0;
- const cats_dt_population *juveniles = grid->juveniles[row][col];
- if (juveniles == NULL) return 0;
+ const cats_dt_population *juveniles = grid->juveniles[row][col]; // getter [get_juvenile_sum]
cats_dt_population_sum juvenile_sum = 0;
- const int32_t max_stage =
- get_vital_age(grid, VA_AGE_OF_MATURITY_MAX) + 1; //grid->param.max_age_of_maturity + 1;
+ const int32_t max_stage = get_vital_age(grid, VA_AGE_OF_MATURITY_MAX) + 1;
+
for (int32_t i = 0; i < max_stage; i++) {
- juvenile_sum += juveniles[i];
+ juvenile_sum += juveniles[i]; // getter [get_juvenile_sum]
}
-
return juvenile_sum;
}
diff --git a/src/cats/inline_overlays.h b/src/cats/inline_overlays.h
index 1de2612958c8c58229d7b91d7716316fa42b0b79..5248ecb2a67bcae8df8a5badcd96b782e0b70df7 100644
--- a/src/cats/inline_overlays.h
+++ b/src/cats/inline_overlays.h
@@ -39,7 +39,6 @@ cell_excluded_by_habitat(const struct cats_configuration *config, cats_dt_coord
return (load_input_2d_array_double(config->overlays.habitat_cc, row, col) == 0.0);
}
-
static inline bool
cell_excluded_by_overlay(const struct cats_configuration *config, cats_dt_coord row, cats_dt_coord col)
{
diff --git a/src/cats/inline_population.h b/src/cats/inline_population.h
index 0a1c7d225d29c00f2760c70337131da90cad1255..f537dad855770c1e3312e9b06cdfee01d33cae7d 100644
--- a/src/cats/inline_population.h
+++ b/src/cats/inline_population.h
@@ -35,13 +35,13 @@
#include "populations/carrying_capacity.h"
#include "populations/plant_juveniles.h"
#include "grids/dimensions.h"
+#include "inline_vital_ages.h"
+
static inline bool valid_population_grid(const struct cats_grid *grid, cats_dt_coord row)
{
- if (grid == NULL) return false;
- if (grid->population == NULL) return false;
- if (grid->population[row] == NULL) return false; // validator [valid_population_grid]
- return true;
+ if (grid && grid->population && grid->population[row]) return true; // validator [valid_population_grid]
+ return false;
}
static inline bool valid_juvenile_grid(const struct cats_grid *grid, cats_dt_coord row)
@@ -53,12 +53,27 @@ static inline bool valid_juvenile_grid(const struct cats_grid *grid, cats_dt_coo
}
-static inline cats_dt_population get_juveniles(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, int year)
+static inline bool juveniles_exist(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col)
{
- assert(valid_juvenile_grid(grid, row));
assert(valid_coordinates(&grid->dimension, row, col));
- if (grid->juveniles[row][col] == NULL) return 0;
- return grid->juveniles[row][col][year];
+ assert(valid_juvenile_grid(grid, row));
+ return grid->juveniles[row][col] != NULL; // validator [juveniles_exist]
+}
+
+static inline cats_dt_population get_juveniles(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, int year)
+{
+ if (juveniles_exist(grid, row, col) == false) return 0;
+ assert(year < get_vital_age(grid, VA_AGE_OF_MATURITY_MAX) + 1);
+ // FIXME check year
+ return grid->juveniles[row][col][year]; // getter [get_juveniles]
+}
+
+static inline void set_juveniles(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, int year, cats_dt_population juv)
+{
+ assert(juveniles_exist(grid, row, col));
+ assert(year < get_vital_age(grid, VA_AGE_OF_MATURITY_MAX) + 1);
+ assert(juv >= 0);
+ grid->juveniles[row][col][year] = juv; // setter [set_juveniles]
}
diff --git a/src/cats/misc/debug.c b/src/cats/misc/debug.c
index 9683654bf17849cf49f9ca4d343c9f941b5ba8b0..487140b58696b6feb281fcfc7984a82e1deeef61 100644
--- a/src/cats/misc/debug.c
+++ b/src/cats/misc/debug.c
@@ -30,8 +30,8 @@
static inline cats_dt_population debug_get_juveniles(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, int year)
{
- if (grid->juveniles[row][col] == NULL) return 0;
- return grid->juveniles[row][col][year];
+ if (grid->juveniles[row][col] == NULL) return 0; // debug [debug_get_juveniles]
+ return grid->juveniles[row][col][year]; // debug [debug_get_juveniles]
}
void
diff --git a/src/cats/plants/inter_period.c b/src/cats/plants/inter_period.c
index 267c2883d9ab49ed161dd4ab318652e9d6325bfc..c8d4eeb68857495ce3e1593b777dd559e075f797 100644
--- a/src/cats/plants/inter_period.c
+++ b/src/cats/plants/inter_period.c
@@ -90,7 +90,8 @@ void inter_period_survival_seeds(struct cats_grid *grid, struct cats_configurati
void inter_period_survival_juveniles(struct cats_grid *grid, struct cats_configuration *conf, cats_dt_coord row,
cats_dt_coord col, struct cats_thread_info *ts)
{
- if (grid->juveniles[row][col] == NULL) return;
+ if (juveniles_exist(grid, row, col) == false) return;
+
const int32_t mat_max = get_vital_age(grid, VA_AGE_OF_MATURITY_MAX);
const int32_t mat_min = get_vital_age(grid, VA_AGE_OF_MATURITY_MIN);
@@ -103,30 +104,34 @@ void inter_period_survival_juveniles(struct cats_grid *grid, struct cats_configu
germination_to_adult_survival, &grid->param);
for (int32_t i = 0; i <= mat_max; i++) {
+
cats_dt_rates modified_juvenile_transition_rate = age_modified_juvenile_survival_rate(
juvenile_transition_rate, i, mat_min, mat_max);
+
cats_dt_rates juvenile_mortality = (1.0 - modified_juvenile_transition_rate);
assert(juvenile_mortality >= 0 && juvenile_mortality <= 1.0);
- assert(grid->juveniles[row][col][i] >= 0);
+ cats_dt_population juveniles_i = get_juveniles(grid, row, col, i);
+ assert(juveniles_i >= 0);
+
cats_dt_population dying = poisson_population_capped(ts->rng,
- (cats_dt_rates) grid->juveniles[row][col][i] *
+ (cats_dt_rates) juveniles_i *
juvenile_mortality,
- grid->juveniles[row][col][i]);
+ juveniles_i);
+ set_juveniles(grid, row, col, i, juveniles_i - dying);
- grid->juveniles[row][col][i] = grid->juveniles[row][col][i] - dying;
- assert(grid->juveniles[row][col][i] >= 0);
+ assert(get_juveniles(grid, row, col, i) >= 0);
}
// advance juvenile stage (after transition rates have been applied)
for (int32_t stage = mat_max; stage > 0; stage--) {
- grid->juveniles[row][col][stage] = grid->juveniles[row][col][stage - 1];
+ cats_dt_population juveniles_younger = get_juveniles(grid, row, col, stage - 1);
+ set_juveniles(grid, row, col, stage, juveniles_younger);
}
// youngest stage now empty
- grid->juveniles[row][col][0] = 0;
-
+ set_juveniles(grid, row, col, 0, 0);
}
diff --git a/src/cats/plants/juveniles.c b/src/cats/plants/juveniles.c
index 010876337f050000f6bd887f89553e0c4cf72d7c..a83e1e6e88cf8b2e243cd0e5fe6014f8ef6bd162 100644
--- a/src/cats/plants/juveniles.c
+++ b/src/cats/plants/juveniles.c
@@ -54,21 +54,23 @@ juvenile_adult_transition(struct cats_grid *g, cats_dt_coord row, cats_dt_coord
// once the cell is full, we stop and juveniles have to wait at least until
// the next year to have a chance to mature
+ // FIXME check max age!
for (int32_t age = mat_max; age >= mat_min; age--) {
- cats_dt_population juveniles = g->juveniles[row][col][age];
+ cats_dt_population juveniles = get_juveniles(g, row, col, age);
if (juveniles == 0) continue;
// the cell_maturation rate depends on the age -- the older the juvenile, the higher the probability to mature
cats_dt_rates maturation_rate = age_specific_maturation_rate(age, juvenile_survival_rate, mat_min,
mat_max);
+
cats_dt_population newly_matured = poisson_population_capped(ts->rng, (cats_dt_rates) juveniles *
maturation_rate,
juveniles);
newly_matured = min_population_t(newly_matured, space_left);
+ set_juveniles(g, row, col, age, juveniles - newly_matured);
- g->juveniles[row][col][age] = juveniles - newly_matured;
- assert(g->juveniles[row][col][age] >= 0);
+ assert(get_juveniles(g, row, col, age) >= 0);
newly_matured_sum += newly_matured;
space_left -= newly_matured;
@@ -100,8 +102,7 @@ cell_maturation(struct cats_grid *grid, struct cats_thread_info *ts, cats_dt_coo
#else
if (__builtin_expect(cell_excluded_by_overlay(conf, row, col), false)) { return 0; }
#endif
-
- if (grid->juveniles[row][col] == NULL) return 0;
+ if (juveniles_exist(grid, row, col) == false) return 0;
const int32_t mat_max = get_vital_age(grid, VA_AGE_OF_MATURITY_MAX);
const int32_t mat_min = get_vital_age(grid, VA_AGE_OF_MATURITY_MIN);
diff --git a/src/cats/plants/plant_structures.c b/src/cats/plants/plant_structures.c
index cd36a398abb9c890df539615c40432c9a368994b..3218cdfcc5cdfe722403939b43b30984601f4316 100644
--- a/src/cats/plants/plant_structures.c
+++ b/src/cats/plants/plant_structures.c
@@ -85,19 +85,18 @@ inline
void
create_juvenile_structure_if_needed(struct cats_grid *grid, const cats_dt_coord row, const cats_dt_coord col)
{
- if (grid->juveniles[row][col]) return;
+ if (juveniles_exist(grid, row, col)) return;
const int32_t max_age_of_maturity = get_vital_age(grid, VA_AGE_OF_MATURITY_MAX);
-
- grid->juveniles[row][col] = create_juvenile_structure(max_age_of_maturity);
+ grid->juveniles[row][col] = create_juvenile_structure(max_age_of_maturity); // initialisation [create_juvenile_structure_if_needed]
}
void destroy_juveniles(const struct cats_grid *grid, const cats_dt_coord row, const cats_dt_coord col)
{
- assert(grid != NULL);
- assert(row >= 0 && row < grid->dimension.rows);
- assert(col >= 0 && col < grid->dimension.cols);
+ assert(grid != NULL); // clean-up [destroy_juveniles]
+ assert(row >= 0 && row < grid->dimension.rows); // clean-up [destroy_juveniles]
+ assert(col >= 0 && col < grid->dimension.cols); // clean-up [destroy_juveniles]
assert(grid->juveniles != NULL);
@@ -106,10 +105,10 @@ void destroy_juveniles(const struct cats_grid *grid, const cats_dt_coord row, co
const int32_t stages = max_age_of_maturity + 1;
assert(stages >= 0);
- if (grid->juveniles[row] && grid->juveniles[row][col]) {
- memset(grid->juveniles[row][col], 0, stages * sizeof(cats_dt_population));
- free(grid->juveniles[row][col]);
- grid->juveniles[row][col] = NULL;
+ if (grid->juveniles[row] && grid->juveniles[row][col]) { // clean-up [destroy_juveniles]
+ memset(grid->juveniles[row][col], 0, stages * sizeof(cats_dt_population)); // clean-up [destroy_juveniles]
+ free(grid->juveniles[row][col]); // clean-up [destroy_juveniles]
+ grid->juveniles[row][col] = NULL; // clean-up [destroy_juveniles]
}
}
diff --git a/src/cats/populations/carrying_capacity.c b/src/cats/populations/carrying_capacity.c
index 1e45bca313bb56519b3dc56638728912bd6cdc70..6d9ef8c8d30d7f7e4c5c38a82ea272a65ddf5dc4 100644
--- a/src/cats/populations/carrying_capacity.c
+++ b/src/cats/populations/carrying_capacity.c
@@ -51,7 +51,7 @@ get_carrying_capacity_all_classes(struct cats_grid **grids, cats_dt_coord row, c
cats_dt_population
get_carrying_capacity(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col)
{
- assert(grid->conf != NULL);
+ assert(grid != NULL && grid->conf != NULL);
const struct cats_configuration *conf = grid->conf;
@@ -63,7 +63,6 @@ get_carrying_capacity(const struct cats_grid *grid, cats_dt_coord row, cats_dt_c
cats_dt_rates cc;
-
const struct cats_vital_rate *link = &grid->param.carrying_capacity;
cc = calculate_rate(link, NAN, &grid->param, grid, row, col, NULL);
@@ -89,7 +88,7 @@ cell_apply_carrying_capacity(struct cats_grid *grid, struct cats_thread_info *ts
if (grid->param.default_demographics) {
cats_dt_population N = get_adult_population(grid, row, col);
- if (N == 0 && grid->juveniles[row][col] == NULL) return;
+ if (N == 0 && juveniles_exist(grid, row, col) == false) return;
if (N > 0) ts->stats[grid_id].stats[CS_POPULATED_BEFORE_CC] += 1;
cats_dt_population K_A = get_adult_carrying_capacity_from_cc(grid, K_tot);
diff --git a/src/cats/populations/plant_juveniles.c b/src/cats/populations/plant_juveniles.c
index e80a9a7c9efadfe6c2e200451d7bdb32ae0f5208..1f41a8532394afe0aa5b3b2d9793a5c2f73ac687 100644
--- a/src/cats/populations/plant_juveniles.c
+++ b/src/cats/populations/plant_juveniles.c
@@ -87,12 +87,12 @@ scale_down_juveniles2(struct cats_grid *grid, cats_dt_coord row, cats_dt_coord c
assert(grid != NULL && grid->juveniles != NULL);
assert(row >= 0 && row < grid->dimension.rows);
assert(col >= 0 && col < grid->dimension.cols);
- assert(grid->juveniles[row] != NULL);
+ assert(juveniles_exist(grid, row, col));
assert(juvenile_cc > 0);
- if (grid->juveniles[row][col] == NULL || weighted_juvenile_sum == 0) return;
+ if (juveniles_exist(grid, row, col) == false || weighted_juvenile_sum == 0) return;
if (weighted_juvenile_sum < juvenile_cc) return;
- const int32_t mat_max = get_vital_age(grid, VA_AGE_OF_MATURITY_MAX); // grid->param.max_age_of_maturity;
+ const int32_t mat_max = get_vital_age(grid, VA_AGE_OF_MATURITY_MAX);
cats_dt_rates factor = 1.0;
for (int32_t i = 0; i < mat_max + 1; i++) {
@@ -121,8 +121,8 @@ scale_down_juveniles2(struct cats_grid *grid, cats_dt_coord row, cats_dt_coord c
log_message(LOG_ERROR, "%s: weighted juvenile sum > juvenile CC", __func__);
log_message(LOG_RAW, "sum: %"PRId64", cc %"PRId64"\n", weighted_juvenile_sum, juvenile_cc);
log_message(LOG_RAW, "factor %f\n", (double) factor);
- for (int32_t i = 0; i < mat_max + 1 - 1; i++) {
- log_message(LOG_RAW, "juvenile stage %d: %d - multiplier %f\n", i,
+ for (int32_t i = 0; i < mat_max + 1; i++) {
+ log_message(LOG_RAW, "juvenile stage %d: %d - multiplier %f\n", i,
grid->juveniles[row][col][i],
(double) juvenile_cc_multiplier(&grid->param, i));
}
@@ -137,7 +137,7 @@ void cell_apply_juvenile_cc(struct cats_grid *g, cats_dt_coord row,
cats_dt_coord col, cats_dt_population K_tot, cats_dt_population N)
{
if (g->juveniles == NULL) return;
- if (g->juveniles[row][col] == NULL) return;
+ if (juveniles_exist(g, row, col) == false) return;
cats_dt_population K_J = K_tot - N;
diff --git a/src/cats/populations/population.c b/src/cats/populations/population.c
index e5143ea6200926e355d00f7725c0ad969b6d75b9..c6509c1443e9b9ae74f228e48b4f8ae68d8843db 100644
--- a/src/cats/populations/population.c
+++ b/src/cats/populations/population.c
@@ -56,14 +56,15 @@ void adjust_juvenile_populations(struct cats_configuration *conf, struct cats_gr
//cats_dt_rates w = juvenile_cc_multiplier(&grid->param, i);
cats_dt_rates w = grid->param.juvenile_cc_weights[i];
cats_dt_rates juv_pop = (cats_dt_rates) N * multi / w;
+
if (juv_pop > CATS_MAX_POPULATION) {
juv_pop = CATS_MAX_POPULATION / 2.0;
}
- grid->juveniles[r][c][i] = round_population_safe(juv_pop);
+
+ set_juveniles(grid, r, c, i, round_population_safe(juv_pop));
}
}
}
-
}
@@ -153,7 +154,8 @@ void prune_initial_population_under_threshold(struct cats_configuration *conf, s
}
}
- log_message(LOG_INFO, "Species '%s': pruned %"PRId64" of %"PRId64" initial populations (suitability < threshold), %"PRId64" remaining",
+ log_message(LOG_INFO,
+ "Species '%s': pruned %"PRId64" of %"PRId64" initial populations (suitability < threshold), %"PRId64" remaining",
grid->param.species_name, destroyed, populated, populated - destroyed);
}