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Merge pull request #68 from bergolho/master
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New conic domain function and more general format for the benchmark domain function
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@rsachetto
rsachetto authored Apr 24, 2024
2 parents 4e33523 + 2691a9c commit f461dee
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Showing 3 changed files with 123 additions and 29 deletions.
62 changes: 61 additions & 1 deletion src/domains_library/domain.c
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,10 @@ 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;
Expand All @@ -137,6 +141,15 @@ 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;
Expand All @@ -150,7 +163,7 @@ 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);
set_benchmark_domain(the_grid, side_length_x, side_length_y, side_length_z);

log_info("Cleaning grid\n");
int i;
Expand Down Expand Up @@ -401,5 +414,52 @@ SET_SPATIAL_DOMAIN(initialize_grid_with_square_mesh_and_source_sink_fibrotic_reg

set_plain_fibrosis_source_sink_region(the_grid, phi, seed, min_x, max_x, min_y, max_y, min_z, max_z, source_sink_min_x, source_sink_max_x, side_length);

return 1;
}

SET_SPATIAL_DOMAIN(initialize_grid_with_cuboid_and_sphere_fibrotic_mesh_with_conic_path){
real_cpu side_length_x = 0.0;
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, side_length_x, config, "side_length_x");

real_cpu side_length_y = 0.0;
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, side_length_y, config, "side_length_y");

real_cpu side_length_z = 0.0;
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, side_length_z, config, "side_length_z");

real_cpu start_dx = 0.0;
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, start_dx, config, "start_dx");

real_cpu start_dy = 0.0;
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, start_dy, config, "start_dy");

real_cpu start_dz = 0.0;
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, start_dz, config, "start_dz");

real_cpu phi = 0.0;
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, phi, config, "phi");

real_cpu plain_center = 0.0;
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, plain_center, config, "plain_center");

real_cpu sphere_radius = 0.0;
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, sphere_radius, config, "sphere_radius");

real_cpu border_zone_size = 0.0;
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, border_zone_size, config, "border_zone_size");

real_cpu border_zone_radius = 0.0;
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, border_zone_radius, config, "border_zone_radius");

real_cpu conic_slope = 0.0;
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, conic_slope, config, "conic_slope");

unsigned seed = 0;
GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(unsigned, seed, config, "seed");

//set_square_mesh(config, the_grid);
set_cuboid_domain_mesh(the_grid, start_dx, start_dy, start_dz, side_length_x, side_length_y, side_length_z);
set_cuboid_sphere_fibrosis_with_conic_path(the_grid, phi, plain_center, sphere_radius, border_zone_size, border_zone_radius, seed, conic_slope);

return 1;
}
85 changes: 58 additions & 27 deletions src/domains_library/domain_helpers.c
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Original file line number Diff line number Diff line change
Expand Up @@ -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) {
void set_benchmark_domain(struct grid *the_grid, real_cpu sx, real_cpu sy, real_cpu sz) {
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);
Expand Down Expand Up @@ -1010,12 +1010,10 @@ int calc_num_refs(real_cpu start_h, real_cpu desired_h) {
return num_refs;
}

void set_plain_fibrosis_source_sink_region (struct grid *the_grid, real_cpu phi, unsigned fib_seed, const double min_x, const double max_x, const double min_y,
const double max_y, const double min_z, const double max_z,
real_cpu source_sink_min_x, real_cpu source_sink_max_x, real_cpu side_length) {
log_info("Making %.2lf %% of cells inside the region inactive\n", phi * 100.0);
void set_cuboid_sphere_fibrosis_with_conic_path(struct grid *the_grid, real_cpu phi, real_cpu plain_center, real_cpu sphere_radius, real_cpu bz_size, real_cpu bz_radius,
unsigned fib_seed, real_cpu cone_slope) {

struct cell_node *grid_cell;
log_info("Making %.2lf %% of cells inactive\n", phi * 100.0f);

if(fib_seed == 0)
fib_seed = (unsigned)time(NULL) + getpid();
Expand All @@ -1024,30 +1022,63 @@ void set_plain_fibrosis_source_sink_region (struct grid *the_grid, real_cpu phi,

log_info("Using %u as seed\n", fib_seed);

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;
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;

grid_cell = the_grid->first_cell;
while(grid_cell != 0) {
real center_x = grid_cell->center.x;
real center_y = grid_cell->center.y;
real center_z = grid_cell->center.z;
//Calcula distância da célula para o centro da malha
real_cpu distance = pow(grid_cell->center.x - plain_center, 2.0) + pow(grid_cell->center.y - plain_center, 2.0);
real_cpu h_distance = abs(grid_cell->center.x - plain_center);

if(grid_cell->active) {

if(center_x >= min_x && center_x <= max_x && center_y >= min_y && center_y <= max_y && center_z >= min_z && center_z <= max_z
&& (center_y > a1*center_x + b1 || center_y > a2*center_x + b2)) {
if(grid_cell->active) {
real_cpu p = (real_cpu)(rand()) / (RAND_MAX);
if(p < phi) {
grid_cell->active = false;
}
INITIALIZE_FIBROTIC_INFO(grid_cell);

INITIALIZE_FIBROTIC_INFO(grid_cell);
FIBROTIC(grid_cell) = true;
if(distance <= bz_radius_2) {
//Dentro da border zone
if(distance <= sphere_radius_2) {
//dentro da "esfera"
if(h_distance < cone_slope*grid_cell->center.y*plain_center) //abs(cone_slope*grid_cell->center.y)
{
FIBROTIC(grid_cell) = true;

//Dentro do cone
}
else{
grid_cell->active = false;
grid_cell->can_change = false;
FIBROTIC(grid_cell) = true;
}
} else {
BORDER_ZONE(grid_cell) = true;
}
}
}
grid_cell = grid_cell->next;
}

grid_cell = the_grid->first_cell;

while(grid_cell != 0) {
if(grid_cell->active) {
if(FIBROTIC(grid_cell)) {
real_cpu p = (real_cpu)(rand()) / (RAND_MAX);
if(p < phi)
grid_cell->active = false;
grid_cell->can_change = false;
} else if(BORDER_ZONE(grid_cell)) {
real_cpu distance_from_center = sqrt((grid_cell->center.x - plain_center) * (grid_cell->center.x - plain_center) +
(grid_cell->center.y - plain_center) * (grid_cell->center.y - plain_center));
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)
grid_cell->active = false;
grid_cell->can_change = false;
}
}
grid_cell = grid_cell->next;
}
}
}
5 changes: 4 additions & 1 deletion src/domains_library/domain_helpers.h
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
void set_benchmark_domain(struct grid *the_grid, real_cpu sx, real_cpu sy, real_cpu sz);
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);
Expand Down Expand Up @@ -56,6 +56,9 @@ uint32_t set_custom_mesh_from_file(struct grid *the_grid, const char *mesh_file,

void set_cube_sphere_fibrosis(struct grid *the_grid, real_cpu phi, real_cpu sphere_center[3], real_cpu sphere_radius, unsigned fib_seed);

void set_cuboid_sphere_fibrosis_with_conic_path (struct grid *the_grid, real_cpu phi, real_cpu plain_center, real_cpu sphere_radius, real_cpu bz_size, real_cpu bz_radius,
unsigned fib_seed, real_cpu cone_slope);

int calc_num_refs(real_cpu start_h, real_cpu desired_h);

#endif // MONOALG3D_DOMAIN_HELPERS_H

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