Update benchmark Purkinje coupling simulation

.gitignore

@@ -92,9 +92,11 @@ tags
 scripts/output
 scripts/animations/convert_png_to_mp4.sh
 scripts/animations/frames
-scripts/animations/video
+scripts/animations/drop_zone
+scripts/animations/videos
 scripts/animations/videos/*.mp4
 scripts/apd_error/*.png
+scripts/mesh-converter
 scripts/traces/*
 scripts/plot_comparison_potential.py
 scripts/trace_plot.py

example_configs/benchmark_aniso_purkinje_coupling.ini

@@ -9,19 +9,34 @@ use_adaptivity=false
 [update_monodomain]
 main_function=update_monodomain_default
 
+# Ensight
 [save_result]
 print_rate=100
-output_dir=./outputs/9versions_benchmark_aniso_purkinje_coupling
-save_pvd=true
-file_prefix=V_Tissue
-file_prefix_purkinje=V_Purkinje
+# -------------------------------------
+output_dir=./outputs/9versions_benchmark_aniso_purkinje_coupling_ensight_linsystem_CPU
+;output_dir=./outputs/9versions_benchmark_aniso_purkinje_coupling_ensight_linsystem_GPU
+# -------------------------------------
+add_timestamp=false
 binary=false
-compress=false
-remove_older_simulation=true
-library_file=shared_libs/libdefault_save_mesh_purkinje.so
-init_function=init_save_tissue_as_vtk_or_vtu_purkinje_as_vtp
-end_function=end_save_tissue_as_vtk_or_vtu_purkinje_as_vtp
-main_function=save_tissue_as_vtu_purkinje_as_vtp
+main_function=save_as_ensight
+
+# VTK
+;[save_result]
+;print_rate=100
+;# -------------------------------------
+;output_dir=./outputs/9versions_benchmark_aniso_purkinje_coupling_VTK_linsystem_CPU
+;output_dir=./outputs/9versions_benchmark_aniso_purkinje_coupling_VTK_linsystem_GPU
+;# -------------------------------------
+;save_pvd=true
+;file_prefix=V_Tissue
+;file_prefix_purkinje=V_Purkinje
+;binary=false
+;compress=false
+;remove_older_simulation=true
+;library_file=shared_libs/libdefault_save_mesh_purkinje.so
+;init_function=init_save_tissue_as_vtk_or_vtu_purkinje_as_vtp
+;end_function=end_save_tissue_as_vtk_or_vtu_purkinje_as_vtp
+;main_function=save_tissue_as_vtu_purkinje_as_vtp
 
 [assembly_matrix]
 init_function=set_initial_conditions_coupling_fvm
@@ -36,7 +51,7 @@ main_function=purkinje_coupling_with_anisotropic_sigma_assembly_matrix
 [linear_system_solver]
 tolerance=1e-16
 use_preconditioner=no
-use_gpu=yes
+use_gpu=no
 max_iterations=200
 library_file=shared_libs/libdefault_linear_system_solver.so
 main_function=conjugate_gradient
@@ -46,7 +61,7 @@ end_function=end_conjugate_gradient
 [purkinje_linear_system_solver]
 tolerance=1e-16
 use_preconditioner=no
-use_gpu=yes
+use_gpu=no
 max_iterations=200
 init_function=init_conjugate_gradient
 end_function=end_conjugate_gradient
@@ -59,11 +74,10 @@ gpu_id=0
 library_file=shared_libs/libten_tusscher_2006.so
 
 [purkinje_ode_solver]
-adaptive=true
-dt = 0.00001
-use_gpu=no
+dt=0.01
+use_gpu=true
 gpu_id=0
-library_file=shared_libs/libtrovato_2019.so
+library_file=shared_libs/libtrovato_2020.so
 
 [domain]
 name=N-Version Benchmark
@@ -74,11 +88,11 @@ main_function=initialize_grid_with_benchmark_mesh
 [purkinje]
 name=Benchmark Anisotropic Purkinje
 dx=100.0
-rpmj=5.0
+rpmj=50000.0
 asymm_ratio=1.0 
-pmj_scale=1000.0 
-nmin_pmj=20
-nmax_pmj=25
+pmj_scale=1.0 
+nmin_pmj=700
+nmax_pmj=750
 retro_propagation=true
 network_file=networks/benchmark_coupling_aniso_network.vtk
 pmj_location_file=networks/benchmark_coupling_aniso_pmjs.vtk
@@ -89,8 +103,7 @@ main_function=initialize_purkinje_coupling_with_custom_mesh
 start = 0.0
 duration = 2.0
 current = -40.0
-period=500.0
-id_limit = 10
+id_limit = 25
 main_function=stim_if_id_less_than
 
 [extra_data]

networks/benchmark_coupling_aniso_pmjs.vtk

@@ -1,10 +1,10 @@
-# vtk DataFile Version 3.0
+# vtk DataFile Version 4.2
 Purkinje
 ASCII
 DATASET POLYDATA
 POINTS 2 float
-10000	1500	3000
-10000	5500	3000
+10000 1500 3000
+10000 5500 3000
 VERTICES 2 4
-0 1
-0 2
+1 0
+1 1

scripts/compress_custom_and_local_files.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+tar -zcf custom_files.tgz ../src/domains_library/custom_* ../src/extra_data_library/custom_* ../src/matrix_assembly_library/custom_*
+#tar -zcf local_files.tgz ../local_meshes ../local_networks ../private_configs ../private_models

src/domains_library/domain.c

@@ -344,3 +344,29 @@ SET_SPATIAL_DOMAIN(initialize_grid_with_custom_mesh) {
     return ret;
 
 }
+
+SET_SPATIAL_DOMAIN(initialize_grid_with_benchmark_purkinje_coupling_mesh) {
+
+    real_cpu start_dx = 100.0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, start_dx, config, "start_dx");
+
+    real_cpu start_dy = 100.0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, start_dy, config, "start_dy");
+
+    real_cpu start_dz = 100.0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, start_dz, config, "start_dz");
+
+    real_cpu side_length_x = 10000.0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, side_length_x, config, "side_length_x");
+
+    real_cpu side_length_y = 5000.0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, side_length_y, config, "side_length_y");
+
+    real_cpu side_length_z = 5000.0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, side_length_z, config, "side_length_z");
+
+    // Reference: "Influence of the Purkinje-muscle junction on transmural repolarization heterogeneity", Walton, R.D. et al. (2014)
+    log_info("Loading Purkinje coupling benchmark mesh using dx %lf um, dy %lf um, dz %lf um\n", start_dx, start_dy, start_dz);
+
+    return set_cuboid_domain_mesh(the_grid, start_dx, start_dy, start_dz, side_length_x, side_length_y, side_length_z);
+}