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Removing unused ToRORd model
1 parent 829226b commit 973afe0

11 files changed

+25
-3249
lines changed

.gitignore

+2
Original file line numberDiff line numberDiff line change
@@ -186,6 +186,7 @@ sync_local.sh
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sync_outputs.sh
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private_configs/
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private_parameter_sets/
189+
private_src/
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/src/domains_library/custom_mesh_info_data.h
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retired_code/
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*.gcno
@@ -199,3 +200,4 @@ VV_49900.dat
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*.build_type*
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/ecg.txt
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__pycache__/
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backup/

ToDo

+1-10
Original file line numberDiff line numberDiff line change
@@ -18,13 +18,4 @@
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#KNOW ISSUES:
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The logger symbols are only exported to an executable if an static library linked to a shared library uses then. For now this is ok. But I think it will be a pain in future releases.
2020
The GPU linear system solver is not working for purkinje-only simulations
21-
When the minimum number of PMJs is not reached the solver will be in an infinite loop
22-
23-
Lucas ToDo list:
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25-
0) Revise all the examples inside the example_configs/ folder.
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27-
1) Purkinje coupling:
28-
- Find a better way to write the PMJ delay into a file for the propagation block cases.
29-
30-
21+
When the minimum number of PMJs is not reached the solver will be in an infinite loop

networks/simple_his_bundle_pmj_location.vtk

-10
This file was deleted.

src/domains_library/domain.c

+14-1
Original file line numberDiff line numberDiff line change
@@ -127,6 +127,10 @@ SET_SPATIAL_DOMAIN(initialize_grid_with_rabbit_mesh) {
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return num_loaded > 0;
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}
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130+
/**
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* Sets the current domain as a domain described in the N-version benchmark
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* (http://rsta.royalsocietypublishing.org/content/369/1954/4331)
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*/
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SET_SPATIAL_DOMAIN(initialize_grid_with_benchmark_mesh) {
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132136
real_cpu side_length;
@@ -137,6 +141,15 @@ SET_SPATIAL_DOMAIN(initialize_grid_with_benchmark_mesh) {
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real_cpu max_h = start_h;
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GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real_cpu, max_h, config, "maximum_discretization");
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144+
real_cpu side_length_x = 20000.0;
145+
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, side_length_x, config, "side_length_x");
146+
147+
real_cpu side_length_y = 7000.0;
148+
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, side_length_y, config, "side_length_y");
149+
150+
real_cpu side_length_z = 3000.0;
151+
GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, side_length_z, config, "side_length_z");
152+
140153
log_info("Loading N-Version benchmark mesh using dx %lf um, dy %lf um, dz %lf um\n", start_h, start_h, start_h);
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side_length = start_h;
@@ -150,7 +163,7 @@ SET_SPATIAL_DOMAIN(initialize_grid_with_benchmark_mesh) {
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int num_steps = get_num_refinement_steps_to_discretization(side_length, start_h);
151164

152165
refine_grid(the_grid, num_steps);
153-
set_benchmark_domain(the_grid);
166+
set_benchmark_domain(the_grid, side_length_x, side_length_y, side_length_z);
154167

155168
log_info("Cleaning grid\n");
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int i;

src/domains_library/domain_helpers.c

+5-5
Original file line numberDiff line numberDiff line change
@@ -445,13 +445,13 @@ int calculate_cuboid_side_lengths(real_cpu start_dx, real_cpu start_dy, real_cpu
445445
* (http://rsta.royalsocietypublishing.org/content/369/1954/4331)
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*
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*/
448-
void set_benchmark_domain(struct grid *the_grid) {
448+
void set_benchmark_domain(struct grid *the_grid, real_cpu sx, real_cpu sy, real_cpu sz) {
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struct cell_node *grid_cell = the_grid->first_cell;
450450

451-
real_cpu sx, sy, sz;
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sx = 20000;
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sy = 7000;
454-
sz = 3000;
451+
//real_cpu sx, sy, sz;
452+
//sx = 20000;
453+
//sy = 7000;
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//sz = 3000;
455455

456456
while(grid_cell != 0) {
457457
grid_cell->active = (grid_cell->center.x < sx) && (grid_cell->center.y < sy) && (grid_cell->center.z < sz);

src/domains_library/domain_helpers.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ int set_cuboid_domain_mesh(struct grid *the_grid, real_cpu start_dx, real_cpu st
1717
real_cpu side_length_z);
1818
int set_square_mesh(struct config *config, struct grid *the_grid);
1919

20-
void set_benchmark_domain(struct grid *the_grid);
20+
void set_benchmark_domain(struct grid *the_grid, real_cpu sx, real_cpu sy, real_cpu sz);
2121
void set_cuboid_domain(struct grid *the_grid, real_cpu sizeX, real_cpu sizeY, real_cpu sizeZ);
2222

2323
void set_custom_mesh(struct grid *the_grid, const char *file_name, size_t size, char *read_format);
@@ -58,7 +58,7 @@ void set_cube_sphere_fibrosis(struct grid *the_grid, real_cpu phi, real_cpu sphe
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5959
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,
6060
unsigned fib_seed, real_cpu cone_slope);
61-
61+
6262
int calc_num_refs(real_cpu start_h, real_cpu desired_h);
6363

64-
#endif // MONOALG3D_DOMAIN_HELPERS_H
64+
#endif // MONOALG3D_DOMAIN_HELPERS_H

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