Merge pull request #62 from bergolho/master

New examples for MonoAlg3D introductory course

.gitignore

@@ -170,6 +170,8 @@ src/*/custom_functions.c
 src/*/custom_functions_BACKUP.c
 src/*/custom_functions.h
 
+bsbash/find_functions_with_mpi.sh
+
 .cache/
 .ccls-cache/
 

example_configs/introduction_to_monoalg3d/EX01_plain_wave.ini

@@ -0,0 +1,90 @@
+# 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.
+# 	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/EX01_plain_wave.ini
+# Visualize:> ./bin/MonoAlg3D_visualizer ./outputs/EX01_IntroMonoAlg_plain_mesh_healthy_200um
+#   - The simulation can be open on Paraview as well! 
+# ===============================================================================================
+
+[main]
+num_threads=6
+dt_pde=0.02                     ; miliseconds
+simulation_time=2000.0          ; miliseconds
+abort_on_no_activity=false
+use_adaptivity=false
+
+[update_monodomain]
+main_function=update_monodomain_default
+
+[save_result]
+print_rate=200
+output_dir=./outputs/EX01_IntroMonoAlg_plain_mesh_healthy_200um
+add_timestamp=false
+binary=true
+main_function=save_as_ensight
+remove_older_simulation=true
+
+[assembly_matrix]
+init_function=set_initial_conditions_fvm
+sigma_x=0.00005336	; mS/um { ~44 cm/s }
+sigma_y=0.00005336	; mS/um { ~44 cm/s }
+sigma_z=0.00005336	; mS/um { ~44 cm/s }
+main_function=homogeneous_sigma_assembly_matrix
+
+[linear_system_solver]
+tolerance=1e-16
+use_preconditioner=no
+max_iterations=200
+use_gpu=true
+init_function=init_conjugate_gradient
+end_function=end_conjugate_gradient
+main_function=conjugate_gradient
+
+[domain]
+name=Plain Mesh
+num_layers=1
+start_dx=200.0          ; micrometers
+start_dy=200.0          ; micrometers
+start_dz=200.0          ; micrometers
+side_length=55000.0     ; micrometers
+main_function=initialize_grid_with_square_mesh
+
+[ode_solver]
+dt=0.02                 ; miliseconds
+use_gpu=yes
+gpu_id=0
+library_file=shared_libs/libten_tusscher_3_endo.so
+
+[stim_plain]
+start = 0.0
+duration = 2.0          ; miliseconds
+period = 1000.0         ; miliseconds
+current = -38.0
+x_limit = 500.0         ; micrometers
+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    ; micrometers 
+lead2=60000,27500,50    ; micrometers
+sigma_b=20
+use_gpu=true
+filename=./outputs/EX01_IntroMonoAlg_plain_mesh_healthy_200um/ecg.txt

example_configs/introduction_to_monoalg3d/EX02_S1S2_protocol.ini

@@ -0,0 +1,103 @@
+# Version: 12/01/2024
+# ===============================================================================================
+# Author: Lucas Berg (@bergolho)
+# Last update: 12/01/2024
+# Description: Simulation using a slab (5,5cm x 5,5cm) considering the S1S2 protocol with a
+#              space discretization of 200um.
+# 	Stimulus: 
+#		- First stimulus (S1=0ms) in the left border of the slab.
+#       - Second stimulus (S2=360ms) in the square [0,27500]x[0,27500] of the slab. 
+#	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/EX02_S1S2_protocol.ini
+# Visualize:> ./bin/MonoAlg3D_visualizer ./outputs/EX02_IntroMonoAlg_plain_mesh_S1S2_protocol_200um
+#   - The simulation can be open on Paraview as well! 
+# ===============================================================================================
+
+[main]
+num_threads=6
+dt_pde=0.02
+simulation_time=2000.0
+abort_on_no_activity=true
+use_adaptivity=false
+
+[update_monodomain]
+main_function=update_monodomain_default
+
+[save_result]
+print_rate=200
+output_dir=./outputs/EX02_IntroMonoAlg_plain_mesh_S1S2_protocol_200um
+add_timestamp=false
+binary=true
+main_function=save_as_ensight
+remove_older_simulation=true
+
+[assembly_matrix]
+init_function=set_initial_conditions_fvm
+sigma_x=0.00005336
+sigma_y=0.00005336
+sigma_z=0.00005336
+main_function=homogeneous_sigma_assembly_matrix
+
+[linear_system_solver]
+tolerance=1e-16
+use_preconditioner=no
+max_iterations=200
+use_gpu=true
+init_function=init_conjugate_gradient
+end_function=end_conjugate_gradient
+main_function=conjugate_gradient
+
+[domain]
+name=Plain Mesh S1S2 Protocol
+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_3_endo.so
+
+; First stimulus S1
+[stim_plain_s1]
+start = 0.0
+duration = 2.0
+current = -38.0
+x_limit = 500.0
+main_function=stim_if_x_less_than
+
+; Second stimulus S2
+[stim_plain_s2]
+start = 360.0
+duration = 2.0
+current = -38.0
+min_x = 0.0
+min_y = 0.0
+max_x = 27550.0
+max_y = 27550.0
+main_function=stim_x_y_limits
+
+[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/EX02_IntroMonoAlg_plain_mesh_S1S2_protocol_200um/ecg.txt
+

example_configs/introduction_to_monoalg3d/EX03_ischemia_modeling.ini

@@ -0,0 +1,123 @@
+# Version: 12/01/2024
+# ===============================================================================================
+# Author: Lucas Berg (@bergolho)
+# Last update: 12/01/2024
+# Description: Simulation using a slab (5,5cm x 5,5cm) considering ischemia remodeling around a 
+#              circle centered at (2.75, 2.75) with a radius equal to 1.5cm and a border zone
+#              size of 0.75cm. Space discretization equal to 200um.
+# 	Stimulus: 
+#		    - First stimulus (S1=0ms) on the left border of the slab.
+#           - Second stimulus (S2=375ms) on the left border of the slab.
+#	Cellular model:
+#		- Ten & Tusscher 3
+#   Ischemia:
+#       - Change the action potential behaviour of the TT3 model inside the ischemic zone using the 
+#         parameters:
+#           - Hyperkelemia = [Ko]
+#           - Hypoxia = [Ikatp_mod]
+#           - Acidosis = [INa_mod, ICaL_mod] 
+#	ECG:
+#		- Two electrodes positioned on each side of the slab.
+#
+#           ______          x = electrodes
+#          |      |
+#       x  |      |  x
+#          |______|
+# -----------------------------------------------------------------------------------------------
+# Execute:> ./bin/MonoAlg3D -c example_configs/intro_to_monoalg3d/EX03_IntroMonoAlg_plain_mesh_ischemia_modeling_200um
+# Visualize:> ./bin/MonoAlg3D_visualizer ./outputs/EX03_IntroMonoAlg_plain_mesh_ischemia_modeling_200um
+#   - The simulation can be open on Paraview as well! 
+# ===============================================================================================
+
+[main]
+num_threads=6
+dt_pde=0.02
+simulation_time=2000.0
+abort_on_no_activity=true
+use_adaptivity=false
+
+[update_monodomain]
+main_function=update_monodomain_default
+
+[save_result]
+print_rate=100
+output_dir=./outputs/EX03_IntroMonoAlg_plain_mesh_ischemia_modeling_200um
+add_timestamp=false
+binary=true
+main_function=save_as_ensight
+remove_older_simulation=true
+
+[assembly_matrix]
+init_function=set_initial_conditions_fvm
+sigma_x=0.00005336
+sigma_y=0.00005336
+sigma_z=0.00005336
+main_function=homogeneous_sigma_assembly_matrix
+
+[linear_system_solver]
+tolerance=1e-16
+use_preconditioner=no
+max_iterations=200
+use_gpu=true
+init_function=init_conjugate_gradient
+end_function=end_conjugate_gradient
+main_function=conjugate_gradient
+
+[domain]
+name=Plain Mesh with fibrosis and circle
+start_dx=200.0
+start_dy=200.0
+start_dz=200.0
+num_layers=1
+side_length=55000
+seed=1508201274
+phi=0.0
+plain_center=27550.0
+sphere_radius=15000.0
+border_zone_radius=22500.0
+border_zone_size=7500.0
+main_function=initialize_grid_with_plain_and_sphere_fibrotic_mesh
+
+[ode_solver]
+dt=0.02
+use_gpu=yes
+gpu_id=0
+library_file=shared_libs/libten_tusscher_3_endo.so
+
+[stim_plain_s1]
+start = 0.0
+duration = 2.0
+current = -38.0
+x_limit = 2500.0
+main_function=stim_if_x_less_than
+
+[stim_plain_s2]
+start = 375.0
+duration = 2.0
+current = -38.0
+x_limit = 2500.0
+main_function=stim_if_x_less_than
+
+; Ischemia parameters
+; Only the cells inside the ischemic region will change!
+[extra_data]
+Ko=9.0                          ; Hyperkelemia
+GNa_multiplicator=0.75          ; Ischemia
+GCaL_multiplicator=0.75         ; Ischemia
+Ikatp_multiplicator=0.01        ; Hypoxia
+plain_center=27550.0
+sphere_radius=15000.0
+border_zone_radius=22500.0
+border_zone_size=7500.0
+main_function=set_extra_data_for_fibrosis_sphere
+
+[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/EX03_IntroMonoAlg_plain_mesh_ischemia_modeling_200um/ecg.txt