Add new TT3-Mixed-Model for transmurality example

example_configs/introduction_to_monoalg3d/EX05_transmurality_modeling.ini → example_configs/introduction_to_monoalg3d/EX05_transmurality_modeling_torord_land.ini

@@ -17,7 +17,7 @@
 #       x  |      |  x
 #          |______|
 # -----------------------------------------------------------------------------------------------
-# Execute:> ./bin/MonoAlg3D -c example_configs/intro_to_monoalg3d/EX05_transmurality_modeling.ini
+# Execute:> ./bin/MonoAlg3D -c example_configs/intro_to_monoalg3d/EX05_transmurality_modeling_torord_land.ini
 # Visualize:> ./bin/MonoAlg3D_visualizer ./outputs/EX05_IntroMonoAlg_plain_mesh_healthy_transmurality_200um
 #   - The simulation can be open on Paraview as well! 
 # ===============================================================================================

example_configs/introduction_to_monoalg3d/EX06_transmurality_modeling_tt3.ini

@@ -0,0 +1,94 @@
+# Version: 12/01/2024
+# ===============================================================================================
+# Author: Lucas Berg (@bergolho)
+# Last update: 12/01/2024
+# Description: Plain wave simulation using a slab (5,5cm x 5,5cm) using a
+#              space discretization of 200um. Here, we model transmurality across
+#	       the domain using three types of cells (ENDO/MCELL/EPI).
+# 	Stimulus: 
+#		- Two pulses with a Basic Cycle Length (BCL) equal to 1000ms
+#	Cellular model:
+#		- Ten & Tusscher 3
+#	ECG:
+#		- Two electrodes positioned on each side of the slab.
+#
+#           ______          x = electrodes
+#          |      |
+#       x  |      |  x
+#          |______|
+# -----------------------------------------------------------------------------------------------
+# Execute:> ./bin/MonoAlg3D -c example_configs/intro_to_monoalg3d/EX06_transmurality_modeling_tt3.ini
+# Visualize:> ./bin/MonoAlg3D_visualizer ./outputs/EX06_transmurality_modeling_tt3
+#   - The simulation can be open on Paraview as well! 
+# ===============================================================================================
+[main]
+num_threads=6
+dt_pde=0.02
+simulation_time=500.0
+abort_on_no_activity=false
+use_adaptivity=false
+
+[update_monodomain]
+main_function=update_monodomain_default
+
+[save_result]
+print_rate=200
+output_dir=./outputs/EX06_transmurality_modeling_tt3
+add_timestamp=false
+binary=true
+save_ode_state_variables=false
+main_function=save_as_ensight
+
+; Anisotropic
+[assembly_matrix]
+init_function=set_initial_conditions_fvm
+sigma_x=0.0001334
+sigma_y=0.0000176
+sigma_z=0.0000176
+main_function=homogeneous_sigma_assembly_matrix
+
+[linear_system_solver]
+tolerance=1e-16
+use_preconditioner=no
+max_iterations=500
+library_file=shared_libs/libdefault_linear_system_solver.so
+use_gpu=yes
+main_function=conjugate_gradient
+init_function=init_conjugate_gradient
+end_function=end_conjugate_gradient
+
+[domain]
+name=Plain Mesh Transmurality
+num_layers=1
+start_dx=200.0
+start_dy=200.0
+start_dz=200.0
+side_length=55000
+main_function=initialize_grid_with_square_mesh
+
+[ode_solver]
+dt=0.02
+use_gpu=yes
+gpu_id=0
+library_file=shared_libs/libten_tusscher_tt3_mixed_endo_mid_epi.so
+
+[extra_data]
+main_function=set_extra_data_mixed_tt3
+
+[stim_plain_s1]
+start = 0.0
+duration = 2.0
+current = -38.0
+x_limit = 500.0
+main_function=stim_if_x_less_than
+
+[calc_ecg]
+main_function=pseudo_bidomain
+init_function=init_pseudo_bidomain
+end_function=end_pseudo_bidomain
+calc_rate=10
+lead1=-5000,27500,50  
+lead2=60000,27500,50
+sigma_b=20
+use_gpu=true
+filename=./outputs/EX06_transmurality_modeling_tt3/ecg.txt

src/extra_data_library/extra_data.c

@@ -429,38 +429,46 @@ SET_EXTRA_DATA (set_mixed_model_purkinje_and_tissue)
     return (void*)mapping;
 }
 
-// 'libten_tusscher_2004_mixed_endo_mid_epi.so' transmurality
+// 'libten_tusscher_tt3_mixed_endo_mid_epi.so' with transmurality and fibrosis (all cells healthy)
 SET_EXTRA_DATA (set_extra_data_mixed_tt3) {
     uint32_t num_active_cells = the_grid->num_active_cells;
     real side_length = the_grid->mesh_side_length.x;
     struct cell_node ** ac = the_grid->active_cells;
 
+    //
+    struct extra_data_for_tt3 *extra_data = NULL;
+    extra_data = set_common_tt3_data(config, num_active_cells);
+
     // Divide the domain in three sections (ENDO/MID/EPI)
     // The percentages were taken from the ToRORd paper (Transmural experiment)
     real side_length_endo = side_length*0.45;
     real side_length_mid = side_length_endo + side_length*0.25;
     real side_length_epi = side_length_mid + side_length*0.3;
 
-    *extra_data_size = sizeof(uint32_t)*(num_active_cells);
-    uint32_t *mapping = (uint32_t*)malloc(*extra_data_size);
-
 	int i;
 
+    // Transmurality and fibrosis tags
 	OMP(parallel for)
-	for (i = 0; i < num_active_cells; i++) {
+    for (int i = 0; i < num_active_cells; i++) {
 
         real center_x = ac[i]->center.x;
 
-        // Cellular model tags: ENDO = 0; MCELL = 1; EPI = 2
+        // Tag the model transmurality
+        // ENDO=0, MID=1, EPI=2
         if (center_x < side_length_endo)
-            mapping[i] = 0.0;
+            extra_data->transmurality[i] = 0.0;
         else if (center_x >= side_length_endo && center_x < side_length_mid)
-            mapping[i] = 1.0;
+            extra_data->transmurality[i] = 1.0;
         else
-            mapping[i] = 2.0;    
+            extra_data->transmurality[i] = 2.0;
+
+        // Tag the fibrosis region
+        extra_data->fibrosis[i] = 1.0;
     }
 
-	return (void*)mapping;
+    SET_EXTRA_DATA_SIZE(sizeof(struct extra_data_for_tt3));
+
+    return (void*)extra_data;
 }
 
 // Initial condition - 'libToRORd_fkatp_mixed_endo_mid_epi.so' + transmurality + current modifiers (plain and cuboid)

src/extra_data_library/helper_functions.c

@@ -48,6 +48,48 @@ struct extra_data_for_fibrosis* set_common_schemia_data(struct config *config, u
     return extra_data;
 }
 
+struct extra_data_for_tt3* set_common_tt3_data (struct config *config, uint32_t num_cells) {
+
+    struct extra_data_for_tt3 *extra_data = MALLOC_ONE_TYPE(struct extra_data_for_tt3);
+
+    real atpi = 6.8;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real, atpi, config, "atpi");
+
+    real Ko = 5.4;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real, Ko, config, "Ko");
+
+    real Ki = 138.3;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real, Ki, config, "Ki");
+
+    real GNa_multiplicator = 1.0f;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real, GNa_multiplicator, config, "GNa_multiplicator");
+
+    real GCaL_multiplicator = 1.0f;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real, GCaL_multiplicator, config, "GCaL_multiplicator");
+
+    real INaCa_multiplicator = 1.0f;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real, INaCa_multiplicator, config, "INaCa_multiplicator");
+
+    real Vm_modifier = 0.0f;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real, Vm_modifier, config, "Vm_modifier");
+
+    real Ikatp_multiplicator = 1.0f;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real, Ikatp_multiplicator, config, "Ikatp_multiplicator");
+
+    extra_data->atpi = atpi;
+    extra_data->Ko = Ko;
+    extra_data->Ki = Ki;
+    extra_data->GNa_multiplicator = GNa_multiplicator;
+    extra_data->GCaL_multiplicator = GCaL_multiplicator;
+    extra_data->INaCa_multiplicator = INaCa_multiplicator;
+    extra_data->Ikatp_multiplicator = Ikatp_multiplicator;
+    extra_data->Vm_modifier = Vm_modifier;
+    extra_data->fibrosis = MALLOC_ARRAY_OF_TYPE(real, num_cells);
+    extra_data->transmurality = MALLOC_ARRAY_OF_TYPE(real, num_cells);
+
+    return extra_data;
+}
+
 struct extra_data_for_torord * set_common_torord_data (struct config *config, uint32_t num_cells) {
     struct extra_data_for_torord *extra_data = MALLOC_ONE_TYPE(struct extra_data_for_torord);
 

src/extra_data_library/helper_functions.h

@@ -23,6 +23,19 @@ struct extra_data_for_fibrosis {
     real *fibrosis;
 };
 
+struct extra_data_for_tt3 {
+    real atpi;
+    real Ko;
+    real Ki;
+    real GNa_multiplicator;
+    real GCaL_multiplicator;
+    real INaCa_multiplicator;
+    real Ikatp_multiplicator;
+    real Vm_modifier;
+    real *fibrosis;
+    real *transmurality;
+};
+
 struct extra_data_for_torord {
     real INa_Multiplier; 
     real ICaL_Multiplier;
@@ -108,6 +121,7 @@ struct extra_data_for_trovato {
 };
 
 struct extra_data_for_fibrosis * set_common_schemia_data(struct config *config, uint32_t num_cells);
+struct extra_data_for_tt3 * set_common_tt3_data (struct config *config, uint32_t num_cells);
 struct extra_data_for_torord * set_common_torord_data (struct config *config, uint32_t num_cells);
 struct extra_data_for_torord * set_common_torord_dyncl_data (struct config *config, uint32_t num_cells);
 struct extra_data_for_torord_land * set_common_torord_Land_data (struct config *config, uint32_t num_cells);