From ce26bdaf8dc3658bde3aed663a9d46011dde4666 Mon Sep 17 00:00:00 2001
From: Andreas Gattringer <andreas.gattringer@univie.ac.at>
Date: Thu, 27 Jul 2023 11:34:15 +0200
Subject: [PATCH] cats: no longer directly access seed data structures, use new
getter/setter functions instead
---
.../actions/process_inter_period_survival.c | 6 +-
src/cats/actions/process_seed_dispersal.c | 9 +-
src/cats/dispersal/dispersal.c | 3 +-
src/cats/dispersal/local_dispersal.c | 8 +-
src/cats/grids/cats_grid.c | 2 +-
src/cats/grids/gdal_save.c | 6 +-
src/cats/grids/grid_setup.c | 2 +-
src/cats/inline.h | 109 ++++++++++++++++--
src/cats/misc/debug.c | 6 +-
src/cats/mpi/mpi_save.c | 3 +-
src/cats/mpi/mpi_seeds.c | 5 +-
src/cats/plants/inter_period.c | 41 ++++---
src/cats/plants/long_range_dispersal.c | 2 +-
src/cats/plants/plant_structures.c | 36 +++---
src/cats/plants/seeds.c | 43 +++----
15 files changed, 192 insertions(+), 89 deletions(-)
diff --git a/src/cats/actions/process_inter_period_survival.c b/src/cats/actions/process_inter_period_survival.c
index 479385a..0f6d050 100644
--- a/src/cats/actions/process_inter_period_survival.c
+++ b/src/cats/actions/process_inter_period_survival.c
@@ -57,10 +57,10 @@ void write_stats(struct cats_grid *grid, const struct cats_configuration *conf,
j_sum_weighted,
get_seed_sum(g, 0, 0));
- fprintf(f, ",%f", g->dispersed_seeds[0][0]);
+ fprintf(f, ",%f", get_dispersed_seeds(grid, 0, 0));
for (int32_t i = 0; i < seed_persistence; i++) {
- if (g->seed_bank[0][0]) {
- fprintf(f, ",%f", g->seed_bank[0][0][i]);
+ if (seed_bank_exists(g, 0, 0)) {
+ fprintf(f, ",%f", get_seed_bank_seeds(g, 0, 0, i));
} else {
fprintf(f, ",%f", 0.0);
diff --git a/src/cats/actions/process_seed_dispersal.c b/src/cats/actions/process_seed_dispersal.c
index 8157c95..ab47e31 100644
--- a/src/cats/actions/process_seed_dispersal.c
+++ b/src/cats/actions/process_seed_dispersal.c
@@ -43,6 +43,7 @@
#include "inline_overlays.h"
#include "actions/cats_actions.h"
#include "temporal/years.h"
+#include "inline.h"
void area_post_process_seeds(struct cats_grid *grid, struct cats_thread_info *ts);
@@ -106,7 +107,7 @@ enum action_status process_disperse_seeds(struct cats_grid *grid, struct cats_co
if (conf->command_line_options.lambda_test) {
disperse_seeds(grid, 0, 0, grid->single_thread);
- grid->seeds_produced[0][0] = 0.0f;
+ set_produced_seeds(grid, 0, 0, 0.0f);
cell_post_process_seeds(grid, conf, 0, 0, grid->single_thread);
return ACTION_RUN;
}
@@ -172,7 +173,7 @@ void area_post_process_seeds(struct cats_grid *grid, struct cats_thread_info *ts
mark_cell_done(&debug, row, col);
#endif
if (cell_excluded_by_overlay(conf, row, col)) {
- grid->dispersed_seeds[row][col] = 0;
+ set_dispersed_seeds(grid, row, col, 0.0f);
} else {
cell_post_process_seeds(grid, conf, row, col, ts);
}
@@ -194,8 +195,8 @@ void dispersal_wrapper(struct cats_grid *grid, struct cats_thread_info *ts)
mark_cell_done(&debug, row, col);
#endif
if (cell_excluded_by_overlay(conf, row, col)) { continue; }
- if (grid->seeds_produced[row][col] > 0.0) disperse_seeds(grid, row, col, ts);
- grid->seeds_produced[row][col] = 0.0f;
+ if (get_produced_seeds(grid, row, col) > 0.0) disperse_seeds(grid, row, col, ts);
+ set_produced_seeds(grid, row, col, 0.0f);
}
}
}
diff --git a/src/cats/dispersal/dispersal.c b/src/cats/dispersal/dispersal.c
index 938c362..4f13f4a 100644
--- a/src/cats/dispersal/dispersal.c
+++ b/src/cats/dispersal/dispersal.c
@@ -51,6 +51,7 @@
#include "memory/cats_memory.h"
#include "inline_overlays.h"
+#include "inline.h"
// ANSATZPUNKTE
// 3 verschiedene dispersals:
@@ -153,7 +154,7 @@ void disperse_seeds(const struct cats_grid *restrict grid, cats_dt_coord s_row,
assert(s_col < grid->dimension.cols);
- float seeds = grid->seeds_produced[s_row][s_col];
+ float seeds = get_produced_seeds(grid, s_row, s_col);
assert(seeds >= 0.0);
if (seeds < 1.0) return;
diff --git a/src/cats/dispersal/local_dispersal.c b/src/cats/dispersal/local_dispersal.c
index c91fd54..14c4191 100644
--- a/src/cats/dispersal/local_dispersal.c
+++ b/src/cats/dispersal/local_dispersal.c
@@ -29,6 +29,7 @@
#include "configuration/configuration.h"
#include "data/cats_grid.h"
#include "local_dispersal.h"
+#include "inline.h"
void cell_local_dispersal(struct cats_configuration *conf, struct cats_grid *grid, cats_dt_coord row,
@@ -37,11 +38,12 @@ void cell_local_dispersal(struct cats_configuration *conf, struct cats_grid *gri
const struct cats_dispersal *const dispersal = grid->dispersal;
if (dispersal->local_dispersal <= 0.0) return;
- float seeds = grid->seeds_produced[row][col];
+ float seeds = get_produced_seeds(grid, row, col);
cats_dt_seeds self = (float) (seeds * dispersal->local_dispersal);
self = min_float(seeds, self);
- grid->dispersed_seeds[row][col] += self;
- grid->seeds_produced[row][col] -= self;
+ increase_dispersed_seeds(grid, row, col, self);
+ decrease_produced_seeds(grid, row, col, self);
+
}
\ No newline at end of file
diff --git a/src/cats/grids/cats_grid.c b/src/cats/grids/cats_grid.c
index 8814d97..3ddb38e 100644
--- a/src/cats/grids/cats_grid.c
+++ b/src/cats/grids/cats_grid.c
@@ -255,7 +255,7 @@ void cleanup_grid_seeds_and_juveniles(struct cats_grid *grid)
for (cats_dt_coord col = 0; col < grid->dimension.cols; col++) {
destroy_seed_structure(grid, row, col);
}
- free(grid->seed_bank[row]);
+ free(grid->seed_bank[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 ba02526..89d05a6 100644
--- a/src/cats/grids/gdal_save.c
+++ b/src/cats/grids/gdal_save.c
@@ -173,13 +173,13 @@ void *save_seeds_to_gdal(struct cats_grid *grid, struct cats_configuration *conf
for (cats_dt_coord col = 0; col < cols; col++) {
if (i > 0) {
int year = i - 1;
- if (grid->seed_bank[row][col]) {
- seeds[row][col] = (int32_t) grid->seed_bank[row][col][year];
+ if (seed_bank_exists(grid, row, col)) {
+ seeds[row][col] = (int32_t) get_seed_bank_seeds(grid, row, col, year);
} else {
seeds[row][col] = 0;
}
} else {
- seeds[row][col] = (int32_t) grid->dispersed_seeds[row][col];
+ seeds[row][col] = (int32_t) get_dispersed_seeds(grid, row, col);
}
}
}
diff --git a/src/cats/grids/grid_setup.c b/src/cats/grids/grid_setup.c
index 5c31dcd..899ce48 100644
--- a/src/cats/grids/grid_setup.c
+++ b/src/cats/grids/grid_setup.c
@@ -53,7 +53,7 @@ void setup_grid_seed_structures(const struct cats_configuration *conf, struct ca
grid->seed_bank = calloc_or_die(rows, sizeof(cats_dt_seeds **));
for (cats_dt_coord row = 0; row < rows; row++) {
- grid->seed_bank[row] = calloc_or_die(cols, sizeof(cats_dt_seeds *));
+ grid->seed_bank[row] = calloc_or_die(cols, sizeof(cats_dt_seeds *)); // initialisation [setup_grid_seed_structure]
for (cats_dt_coord col = 0; col < cols; col++) {
grid->seed_bank[row][col] = NULL; // initialisation [setup_grid_seed_structure]
diff --git a/src/cats/inline.h b/src/cats/inline.h
index 5c17dc4..fe3ae80 100644
--- a/src/cats/inline.h
+++ b/src/cats/inline.h
@@ -44,14 +44,15 @@
#include "inline_vital_ages.h"
#include "grids/dimensions.h"
-static inline bool valid_dispersed_seed_grid(const struct cats_grid *grid, cats_dt_coord row)
+static inline bool valid_dispersed_seeds_grid(const struct cats_grid *grid, cats_dt_coord row)
{
if (grid == NULL) return false;
if (grid->dispersed_seeds == NULL) return false;
- if (grid->dispersed_seeds[row] == NULL) return false; // validator [valid_population_grid]
+ if (grid->dispersed_seeds[row] == NULL) return false; // validator [valid_dispersed_seeds_grid]
return true;
}
+
static inline bool valid_produced_seed_grid(const struct cats_grid *grid, cats_dt_coord row)
{
if (grid == NULL) return false;
@@ -75,18 +76,109 @@ static inline cats_dt_seeds
get_dispersed_seeds(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col)
{
assert(valid_coordinates(&grid->dimension, row, col));
- assert(valid_dispersed_seed_grid(grid, row));
- return grid->dispersed_seeds[row][col]; // get [get_dispersed_seeds]
+ assert(valid_dispersed_seeds_grid(grid, row));
+ return grid->dispersed_seeds[row][col]; // getter [get_dispersed_seeds]
+}
+
+static inline void
+set_dispersed_seeds(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, cats_dt_seeds seeds)
+{
+ assert(valid_coordinates(&grid->dimension, row, col));
+ assert(valid_dispersed_seeds_grid(grid, row));
+ assert(seeds >= 0);
+ grid->dispersed_seeds[row][col] = seeds; // setter [set_dispersed_seeds]
+}
+
+static inline void
+increase_dispersed_seeds(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, cats_dt_seeds by)
+{
+ assert(valid_coordinates(&grid->dimension, row, col));
+ assert(valid_dispersed_seeds_grid(grid, row));
+ assert(by >= 0);
+ grid->dispersed_seeds[row][col] += by; // setter [increase_dispersed_seeds]
+}
+
+static inline void
+decrease_dispersed_seeds(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, cats_dt_seeds by)
+{
+ assert(valid_coordinates(&grid->dimension, row, col));
+ assert(valid_dispersed_seeds_grid(grid, row));
+ assert(by >= 0);
+ grid->dispersed_seeds[row][col] -= by; // setter [decrease_dispersed_seeds]
+ assert(grid->dispersed_seeds[row][col] >= 0); // setter [decrease_dispersed_seeds]
}
+
+
static inline cats_dt_seeds
get_produced_seeds(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col)
{
assert(valid_coordinates(&grid->dimension, row, col));
assert(valid_produced_seed_grid(grid, row));
- return grid->seeds_produced[row][col]; // get [get_produced_seeds]
+ return grid->seeds_produced[row][col]; // getter [get_produced_seeds]
+}
+
+static inline bool valid_seed_bank_grid(const struct cats_grid *grid, cats_dt_coord row)
+{
+ if (grid == NULL || grid->seed_bank == NULL || grid->seed_bank[row] == NULL) return false; // validator [valid_seed_bank_grid]
+ return true;
}
+static inline bool seed_bank_exists(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col)
+{
+ assert(valid_coordinates(&grid->dimension, row, col));
+ assert(valid_seed_bank_grid(grid, row));
+ return grid->seed_bank[row][col] != NULL; // validator [seed_bank_exists]
+}
+
+static inline cats_dt_seeds get_seed_bank_seeds(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, int32_t year)
+{
+ assert(seed_bank_exists(grid, row, col));
+ assert(year < get_vital_age(grid, VA_SEED_PERSISTENCE));
+ assert(year >= 0);
+ return grid->seed_bank[row][col][year]; // getter [get_seed_bank_seeds]
+}
+
+static inline void set_seed_bank_seeds(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, int32_t year, cats_dt_seeds seeds)
+{
+ assert(seed_bank_exists(grid, row, col));
+ assert(year < get_vital_age(grid, VA_SEED_PERSISTENCE));
+ assert(seeds >= 0.0f);
+ grid->seed_bank[row][col][year] = seeds; // setter [set_seed_bank_seeds]
+}
+
+
+
+static inline void
+set_produced_seeds(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, cats_dt_seeds seeds)
+{
+ assert(valid_coordinates(&grid->dimension, row, col));
+ assert(valid_produced_seed_grid(grid, row));
+ assert(seeds >= 0);
+ grid->seeds_produced[row][col] = seeds; // setter [set_produced_seeds]
+}
+
+static inline void
+increase_produced_seeds(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, cats_dt_seeds by)
+{
+ assert(valid_coordinates(&grid->dimension, row, col));
+ assert(valid_produced_seed_grid(grid, row));
+ assert(by > 0);
+ grid->seeds_produced[row][col] += by; // setter [increase_produced_seeds]
+}
+
+
+static inline void
+decrease_produced_seeds(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, cats_dt_seeds by)
+{
+ assert(valid_coordinates(&grid->dimension, row, col));
+ assert(valid_produced_seed_grid(grid, row));
+ assert(by > 0);
+ grid->seeds_produced[row][col] -= by; // setter [decrease_produced_seeds]
+ assert(grid->seeds_produced[row][col] >= 0); // setter [decrease_produced_seeds]
+}
+
+
static inline void
set_suitability(struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, cats_dt_environment value)
@@ -213,10 +305,11 @@ static inline double get_seed_sum(const struct cats_grid *grid, cats_dt_coord ro
assert(grid != NULL && grid->juveniles != NULL);
assert(valid_coordinates(&grid->dimension, row, col));
const int32_t max_sp = get_vital_age(grid, VA_SEED_PERSISTENCE); //grid->param.seed_persistence;
- double sum = grid->dispersed_seeds[row][col];
- if (grid->seed_bank[row][col] == NULL) return sum;
+ double sum = get_dispersed_seeds(grid, row, col);
+
+ if (!seed_bank_exists(grid, row, col)) return sum;
for (int32_t i = 0; i < max_sp; i++) {
- sum += grid->seed_bank[row][col][i];
+ sum += get_seed_bank_seeds(grid, row, col, i);
}
return sum;
}
diff --git a/src/cats/misc/debug.c b/src/cats/misc/debug.c
index 4900cc3..9683654 100644
--- a/src/cats/misc/debug.c
+++ b/src/cats/misc/debug.c
@@ -57,11 +57,11 @@ void debug_seeds(struct cats_grid *grid, const struct cats_configuration *conf,
{
if (row == cats_debug.misc_debug_coords.row && col == cats_debug.misc_debug_coords.col) {
fprintf(cats_debug.misc_debug_file, "%d,%d,%s,seeds,%f", grid->id, conf->time.year_current, action,
- grid->dispersed_seeds[row][col]); // debug [debug_seeds]
+ get_dispersed_seeds(grid, row, col));
const int32_t seed_persistence = get_vital_age(grid, VA_SEED_PERSISTENCE);
for (int32_t i = 0; i < seed_persistence; i++) {
- if (grid->seed_bank[row][col]) { // debug [debug_seeds]
- fprintf(cats_debug.misc_debug_file, ",%f", grid->seed_bank[row][col][i]); // debug [debug_seeds]
+ if (seed_bank_exists(grid, row, col)) {
+ fprintf(cats_debug.misc_debug_file, ",%f", get_seed_bank_seeds(grid, row, col, i));
} else {
fprintf(cats_debug.misc_debug_file, ",%d", 0);
}
diff --git a/src/cats/mpi/mpi_save.c b/src/cats/mpi/mpi_save.c
index 3af93da..c667d1e 100644
--- a/src/cats/mpi/mpi_save.c
+++ b/src/cats/mpi/mpi_save.c
@@ -35,6 +35,7 @@
#include "memory/cats_memory.h"
#include "mpi/mpi_grid_helpers.h"
#include "paths/output_paths.h"
+#include "inline.h"
/*
@@ -80,7 +81,7 @@ void *save_seeds0_to_gdal_mpi(struct cats_grid *grid, struct cats_configuration
for (int r = 0; r < grid->dimension.rows; r++) {
for (int c = 0; c < grid->dimension.cols; c++) {
- seeds0[r * grid->dimension.cols + c] = grid->dispersed_seeds[r][c];
+ seeds0[r * grid->dimension.cols + c] = get_dispersed_seeds(grid, r, c);
}
}
diff --git a/src/cats/mpi/mpi_seeds.c b/src/cats/mpi/mpi_seeds.c
index 9b3f153..89bb25d 100644
--- a/src/cats/mpi/mpi_seeds.c
+++ b/src/cats/mpi/mpi_seeds.c
@@ -29,6 +29,7 @@
#include "mpi_grid_helpers.h"
#include "memory/raw_arrays.h"
#include "mpi_seeds.h"
+#include "inline.h"
void send_and_receive_dispersed_seeds_mpi(struct cats_grid *grid, struct cats_configuration *conf)
@@ -143,7 +144,7 @@ void add_seeds0_from_below(const struct cats_configuration *conf, struct cats_gr
for (int r = 0; r < radius; r++) {
for (int c = 0; c < cols; c++) {
- grid->dispersed_seeds[start_row + r][c] += from_below[r * cols + c];
+ increase_dispersed_seeds(grid, start_row + r, c, (cats_dt_seeds) from_below[r * cols + c]);
}
}
}
@@ -159,7 +160,7 @@ void add_seeds0_from_above(const struct cats_configuration *conf, struct cats_gr
for (int r = 0; r < radius; r++) {
for (int c = 0; c < cols; c++) {
- grid->dispersed_seeds[r][c] += from_above[r * cols + c];
+ increase_dispersed_seeds(grid, r, c, (cats_dt_seeds) from_above[r * cols + c]);
}
}
}
\ No newline at end of file
diff --git a/src/cats/plants/inter_period.c b/src/cats/plants/inter_period.c
index 2c6ae48..267c288 100644
--- a/src/cats/plants/inter_period.c
+++ b/src/cats/plants/inter_period.c
@@ -35,46 +35,55 @@ void inter_period_survival_seeds(struct cats_grid *grid, struct cats_configurati
cats_dt_coord col, struct cats_thread_info *ts)
{
// if we have no seeds, we are done
- if (grid->dispersed_seeds[row][col] == 0.0 && grid->seed_bank[row][col] == NULL) return;
+ cats_dt_seeds disp_seeds = get_dispersed_seeds(grid, row, col);
+ if (disp_seeds == 0.0 && seed_bank_exists(grid, row, col) == false) return;
cats_dt_rates seed_survival_rate;
+ bool have_seed_bank = seed_bank_exists(grid, row, col);
const struct cats_vital_rate *rate_link_surv = get_default_vital_rate(grid, VR_SEED_SURVIVAL);
seed_survival_rate = calculate_rate(rate_link_surv, NAN, &grid->param, grid, row, col, NULL);
- if (grid->dispersed_seeds[row][col] > 0) {
- cats_dt_seeds dying_0 = poisson_seeds_capped(ts->rng, grid->dispersed_seeds[row][col] *
+ if (disp_seeds > 0) {
+ cats_dt_seeds dying_0 = poisson_seeds_capped(ts->rng, disp_seeds *
(1.0 - seed_survival_rate),
- grid->dispersed_seeds[row][col]);
+ disp_seeds);
- grid->dispersed_seeds[row][col] = grid->dispersed_seeds[row][col] - dying_0;
+ disp_seeds = disp_seeds - dying_0;
+ set_dispersed_seeds(grid, row, col, disp_seeds);
- if (grid->dispersed_seeds[row][col] > 0.0 && grid->seed_bank[row][col] == NULL) {
+
+ if (disp_seeds > 0.0 && have_seed_bank == false) {
create_seed_structure(grid, row, col);
}
}
- if (grid->dispersed_seeds[row][col] == 0.0 && grid->seed_bank[row][col] == NULL) return;
+
+ if (disp_seeds == 0.0 && have_seed_bank == false) return;
+
+ if (have_seed_bank == false) create_seed_structure(grid, row, col);
const int32_t seed_persistence = get_vital_age(grid, VA_SEED_PERSISTENCE);
- for (int32_t stage = 0; stage < seed_persistence - 0; stage++) { // -1
+ for (int32_t stage = 0; stage < seed_persistence; stage++) {
+ cats_dt_seeds seeds_i = get_seed_bank_seeds(grid, row, col, stage);
cats_dt_seeds dying = poisson_seeds_capped(ts->rng,
- grid->seed_bank[row][col][stage] *
+ seeds_i *
(1.0 - seed_survival_rate),
- grid->seed_bank[row][col][stage]);
- grid->seed_bank[row][col][stage] = grid->seed_bank[row][col][stage] - dying;
+ seeds_i);
+ set_seed_bank_seeds(grid, row, col, stage, seeds_i - dying);
}
- for (int32_t k = seed_persistence - 1; k >= 1; k--) { // -2
- grid->seed_bank[row][col][k] = grid->seed_bank[row][col][k - 1];
+ for (int32_t k = seed_persistence - 1; k >= 1; k--) {
+ cats_dt_seeds s = get_seed_bank_seeds(grid, row, col, k - 1);
+ set_seed_bank_seeds(grid, row, col, k, s);
}
- grid->seed_bank[row][col][0] = grid->dispersed_seeds[row][col];
- assert(grid->seed_bank[row][col][0] >= 0.0);
- grid->dispersed_seeds[row][col] = 0.0f;
+ set_seed_bank_seeds(grid, row, col, 0, get_dispersed_seeds(grid, row, col));
+ assert(get_seed_bank_seeds(grid, row, col, 0) >= 0);
+ set_dispersed_seeds(grid, row, col, 0.0f);
}
diff --git a/src/cats/plants/long_range_dispersal.c b/src/cats/plants/long_range_dispersal.c
index 6168429..eb6d86d 100644
--- a/src/cats/plants/long_range_dispersal.c
+++ b/src/cats/plants/long_range_dispersal.c
@@ -87,7 +87,7 @@ void disperse_long_range(struct cats_grid *grid)
}
// disperse seeds and reduce number of local seeds
- grid->dispersed_seeds[trow][tcol] += (cats_dt_seeds) package;
+ increase_dispersed_seeds(grid, trow, tcol, (cats_dt_seeds) package);
grid->seeds_produced[row][col] -= (cats_dt_seeds) package;
// stop if no more seeds are left to distribute
diff --git a/src/cats/plants/plant_structures.c b/src/cats/plants/plant_structures.c
index 8d1378c..cd36a39 100644
--- a/src/cats/plants/plant_structures.c
+++ b/src/cats/plants/plant_structures.c
@@ -40,50 +40,42 @@ void destroy_plant_cell(struct cats_grid *grid, const cats_dt_coord row, const c
assert(col >= 0 && col < grid->dimension.cols);
destroy_juveniles(grid, row, col);
destroy_seed_structure(grid, row, col);
- grid->dispersed_seeds[row][col] = 0.0f;
- grid->seeds_produced[row][col] = 0.0f;
+ set_dispersed_seeds(grid, row, col, 0.0f);
+ set_produced_seeds(grid, row, col, 0.0f);
set_population_ignore_cc(grid, row, col, 0);
}
void create_seed_structure(const struct cats_grid *grid, const cats_dt_coord row, const cats_dt_coord col)
{
- assert(grid != NULL);
- if (grid->seed_bank[row][col] != NULL) return;
+
+ assert(valid_seed_bank_grid(grid, row));
+ if (seed_bank_exists(grid, row, col) == true) return;
const int32_t seed_persistence = get_vital_age(grid, VA_SEED_PERSISTENCE);
- const int32_t size = seed_persistence - 0; // - 1);
+ const int32_t size = seed_persistence;
if (size <= 0) return; // no seed persistence
- assert(grid->seed_bank != NULL);
- assert(row >= 0 && row < grid->dimension.rows);
- assert(col >= 0 && col < grid->dimension.cols);
- assert(grid->seed_bank[row][col] == NULL);
-
- grid->seed_bank[row][col] = calloc_or_die(size, sizeof(cats_dt_seeds));
-
-
+ grid->seed_bank[row][col] = calloc_or_die(size, sizeof(cats_dt_seeds)); // initialisation [create_seed_structure]
}
void destroy_seed_structure(const struct cats_grid *grid, const cats_dt_coord row, const cats_dt_coord col)
{
assert(grid != NULL);
- assert(grid->seed_bank != NULL);
- assert(row >= 0 && row < grid->dimension.rows);
- assert(col >= 0 && col < grid->dimension.cols);
+
const int32_t seed_persistence = get_vital_age(grid, VA_SEED_PERSISTENCE);
- const int size = (seed_persistence - 0); // -1
+ const int size = (seed_persistence - 0);
// do we actually have seeds in the ground?
- if (size <= 0 || grid->seed_bank[row][col] == NULL) return;
+ if (size <= 0 || seed_bank_exists(grid, row, col) == false) return;
- for (uint32_t i = 0; i < size; i++) {
- grid->seed_bank[row][col][i] = 0.0f;
+ for (int32_t i = 0; i < size; i++) {
+ set_seed_bank_seeds(grid, row, col, i, 0.0f); // clean-up [destroy_seed_structure]
}
- free(grid->seed_bank[row][col]);
- grid->seed_bank[row][col] = NULL;
+ free(grid->seed_bank[row][col]); // clean-up [destroy_seed_structure]
+ grid->seed_bank[row][col] = NULL; // clean-up [destroy_seed_structure]
}
diff --git a/src/cats/plants/seeds.c b/src/cats/plants/seeds.c
index c4cb44d..0cd63b9 100644
--- a/src/cats/plants/seeds.c
+++ b/src/cats/plants/seeds.c
@@ -87,9 +87,8 @@ void cell_seed_production(struct cats_grid *grid, cats_dt_coord row, cats_dt_coo
assert(grid->seeds_produced != NULL);
// ensure that no seeds are left-over in the cell
- assert(grid->seeds_produced[row][col] == 0.0);
-
- grid->seeds_produced[row][col] = 0.0f;
+ assert(get_produced_seeds(grid, row, col) == 0.0f);
+ set_produced_seeds(grid, row, col, 0.0f);
// no population -> no seeds
cats_dt_rates N = get_adult_population(grid, row, col);
@@ -124,10 +123,11 @@ void cell_seed_production(struct cats_grid *grid, cats_dt_coord row, cats_dt_coo
const cats_dt_rates total_seeds = N * flowering_frequency * seed_yield * pollination_rate;
assert(total_seeds >= 0.0);
+ cats_dt_seeds seeds = poisson_seeds(ts->rng, total_seeds); // we don't cap
+ set_produced_seeds(grid, row, col, seeds);
- grid->seeds_produced[row][col] = poisson_seeds(ts->rng, total_seeds); // we don't cap
- if (grid->seeds_produced[row][col] > 0) ts->stats[grid->id].stats[CS_SEEDS_PRODUCED] += 1;
+ if (seeds > 0) ts->stats[grid->id].stats[CS_SEEDS_PRODUCED] += 1;
cats_dt_rates hapaxanth = grid->param.hapaxanthy;
@@ -167,17 +167,19 @@ germinate_seeds_in_ground(struct cats_thread_info *ts, struct cats_grid *grid, c
for (int32_t k = 0; k < max_k; k++) {
- cats_dt_population germinated = poisson(ts->rng, grid->seed_bank[row][col][k] * germination_rate);
+ cats_dt_seeds seeds_k = get_seed_bank_seeds(grid, row, col, k);
+ cats_dt_population germinated = poisson(ts->rng, seeds_k * germination_rate);
if (germinated <= 0) continue;
add_germinated(ts, grid, row, col, germinated, K_class);
- grid->seed_bank[row][col][k] = max_float(grid->seed_bank[row][col][k] - (float) germinated, 0.0f);
-
+ seeds_k = max_float(seeds_k - (float) germinated, 0.0f);
+ set_seed_bank_seeds(grid, row, col, k, seeds_k);
}
}
-
+/*
+// no longer used
static inline void
germinate_seeds0(struct cats_grid *grid, const cats_dt_coord row, const cats_dt_coord col, struct cats_thread_info *ts,
const cats_dt_rates germination_rate)
@@ -197,16 +199,16 @@ germinate_seeds0(struct cats_grid *grid, const cats_dt_coord row, const cats_dt_
grid->dispersed_seeds[row][col] = max_float(grid->dispersed_seeds[row][col] - (float) germinated,
0.0f); // fixme max_seeds
}
-
+*/
inline static bool
have_seeds_in_cell(const struct cats_grid *grid, const struct cats_configuration *conf, cats_dt_coord row,
cats_dt_coord col, const struct cats_thread_info *ts)
{
- assert(grid->dispersed_seeds != NULL);
- assert(grid->dispersed_seeds[row][col] >= 0);
- return (grid->seed_bank[row][col] != NULL || grid->dispersed_seeds[row][col] > 0.5);
+ cats_dt_seeds d_seeds = get_dispersed_seeds(grid, row, col);
+ assert(d_seeds >= 0);
+ return (seed_bank_exists(grid, row, col) || d_seeds > 0.5);
}
@@ -242,21 +244,22 @@ cell_post_process_seeds(struct cats_grid *grid, struct cats_configuration *conf,
struct cats_thread_info *ts)
{
assert(grid != NULL);
- assert(grid->dispersed_seeds != NULL);
- assert(grid->dispersed_seeds[row][col] >= 0);
+ assert(valid_dispersed_seeds_grid(grid, row));
+
+ cats_dt_seeds disp_seeds = get_dispersed_seeds(grid, row, col);
+ assert(disp_seeds >= 0);
+ if (disp_seeds == 0.0f) return;
if (cell_excluded_by_overlay(conf, row, col)) {
- grid->dispersed_seeds[row][col] = 0;
+ set_dispersed_seeds(grid, row, col, 0.0f);
return;
}
- if (grid->dispersed_seeds[row][col] == 0.0) return;
-
const int32_t id = grid->id;
ts->stats[id].stats[CS_SEEDS_BEFORE_POISSON] += 1;
cats_dt_seeds seeds_after_poisson = poisson_seeds(ts->rng,
- grid->dispersed_seeds[row][col]); /* IMPORTANT stochasticity required */
- grid->dispersed_seeds[row][col] = seeds_after_poisson;
+ disp_seeds); /* IMPORTANT stochasticity required */
+ set_dispersed_seeds(grid, row, col, seeds_after_poisson);
if (seeds_after_poisson > 0) ts->stats[id].stats[CS_SEEDS_AFTER_POISSON] += 1;
}
--
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