Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

New conic domain function and more general format for the benchmark domain function #68

Merged
merged 4 commits into from
Apr 24, 2024
Merged

New conic domain function and more general format for the benchmark domain function #68

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
f4fc428
Add new conic path domain function to model fibrotic isthmus/Changed …
bergolho Feb 28, 2024
a746cb7
Merge branch 'rsachetto-master'
bergolho Mar 8, 2024
73fca83
Merge branch 'rsachetto-master'
bergolho Mar 21, 2024
2691a9c
Merge branch 'rsachetto-master'
bergolho Apr 22, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
62 changes: 61 additions & 1 deletion src/domains_library/domain.c
View file
Open in desktop
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
View file
Open in desktop
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
View file
Open in desktop
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
Loading