Merge pull request #60 from bergolho/master

New "ToRORd_Land" cellular model and minor changes

ToDo

@@ -32,4 +32,7 @@ When the minimum number of PMJs is not reached the solver will be in an infinite
 <t> <sv_1> <sv_2> <sv_3> ... <sv_n>
 .   .       .       .           .
 .   .       .       .           .
-.   .       .       .           .
+.   .       .       .           .
+
+
+Fix the "save_multiple_cell_state_variables". It cannot find the proper cell center.

example_configs/activation_time_and_apd_example.ini

@@ -0,0 +1,64 @@
+[main]
+num_threads=4
+dt_pde=0.01
+simulation_time=5000.0
+abort_on_no_activity=false
+use_adaptivity=false
+
+[update_monodomain]
+main_function=update_monodomain_default
+
+[save_result]
+print_rate=10
+mesh_print_rate=100
+mesh_format=ensight
+output_dir=./outputs/cable_save_activation_time_and_apd_example
+init_function=init_save_with_activation_times
+end_function=end_save_with_activation_times
+main_function=save_with_activation_times
+time_threshold=0.0
+activation_threshold=-50.0
+apd_threshold=-70.0
+save_visible_mask=false
+remove_older_simulation=true
+
+[assembly_matrix]
+init_function=set_initial_conditions_fvm
+sigma_x=0.0000176
+sigma_y=0.0000176
+sigma_z=0.0000176
+library_file=shared_libs/libdefault_matrix_assembly.so
+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=no
+main_function=conjugate_gradient
+init_function=init_conjugate_gradient
+end_function=end_conjugate_gradient
+
+[domain]
+name=Cable Mesh with no fibrosis
+start_dx=100.0
+start_dy=100.0
+start_dz=100.0
+cable_length=10000.0
+main_function=initialize_grid_with_cable_mesh
+
+[ode_solver]
+adaptive=false
+dt=0.01
+use_gpu=false
+gpu_id=0
+library_file= shared_libs/libToRORd_dynCl_mixed_endo_mid_epi.so
+
+[stim_plain]
+start = 0.0
+duration = 2.0
+current = -53.0
+x_limit = 500.0
+period=1000.0
+main_function=stim_if_x_less_than

example_configs/cable_mesh_with_ToRORd_Land_endo_mid_epi.ini

@@ -0,0 +1,79 @@
+# ===========================================================================
+# Author: Lucas Berg
+# Description: Simple simulation to test the ToRORd_Land model in a cable.
+# When no [extra_data] information is provided all cells are 
+# considered to be control ENDO.
+# ============================================================================
+[main]
+num_threads=6
+dt_pde=0.01
+simulation_time=1000.0
+abort_on_no_activity=false
+use_adaptivity=false
+
+[update_monodomain]
+main_function=update_monodomain_default
+
+[save_result]
+print_rate=100
+output_dir=./outputs/cable_ToRORd_Land_endo_baseline_cpu_en
+add_timestamp=false
+binary=true
+main_function=save_as_ensight
+
+;[save_result]
+;print_rate=1
+;output_dir=./outputs/cable_ToRORd_Land_endo_baseline_cpu
+;file_name=./outputs/cable_ToRORd_Land_endo_baseline_cpu/full_trace_first_cell_endo.txt
+;output_dir=./outputs/cable_ToRORd_Land_mid_baseline_cpu
+;file_name=./outputs/cable_ToRORd_Land_mid_baseline_cpu/full_trace_first_cell_mid.txt
+;output_dir=./outputs/cable_ToRORd_Land_epi_baseline_cpu
+;file_name=./outputs/cable_ToRORd_Land_epi_baseline_cpu/full_trace_first_cell_epi.txt
+;main_function=save_one_cell_state_variables
+;init_function=init_save_one_cell_state_variables
+;end_function=end_save_one_cell_state_variables
+;cell_center_x=50
+;cell_center_y=50
+;cell_center_z=50
+;remove_older_simulation=true
+
+[assembly_matrix]
+init_function=set_initial_conditions_fvm
+sigma_x=0.000176
+sigma_y=0.000176
+sigma_z=0.000176
+library_file=shared_libs/libdefault_matrix_assembly.so
+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=Cable Mesh with no fibrosis
+start_dx=100.0
+start_dy=100.0
+start_dz=100.0
+cable_length=20000.0
+main_function=initialize_grid_with_cable_mesh
+
+[ode_solver]
+adaptive=false
+dt=0.01
+use_gpu=no
+gpu_id=0
+library_file= shared_libs/libToRORd_Land_mixed_endo_mid_epi.so
+
+[stim_plain]
+start = 0.0
+duration = 1.0
+;period = 800.0
+current = -53.0
+x_limit = 500.0
+main_function = stim_if_x_less_than

example_configs/cable_mesh_with_ToRORd_fkatp_endo_mid_epi.ini

@@ -1,26 +1,27 @@
-
 # ====================================================================
 # Author: Lucas Berg
-# Description: 
+# Description: Simple simulation to test the ToRORd_fkatp model in a cable.
+# When no [extra_data] information is provided all cells are 
+# considered to be control ENDO.
 # ====================================================================
 [main]
-num_threads=4
-dt_pde=0.02
-simulation_time=600.0
+num_threads=6
+dt_pde=0.01
+simulation_time=500.0
 abort_on_no_activity=false
 use_adaptivity=false
 
 [update_monodomain]
 main_function=update_monodomain_default
 
+; Save using ensight format and store the state variables as CELL_DATA
 [save_result]
-print_rate=50
-output_dir=./outputs/cable_ToRORd_endo_mid_epi_cpu
-main_function=save_as_vtu
-init_function=init_save_as_vtk_or_vtu
-end_function=end_save_as_vtk_or_vtu
-save_pvd=true
-file_prefix=V
+print_rate=100
+output_dir=./outputs/cable_ToRORd_fkatp_endo_baseline_cpu_en
+add_timestamp=false
+binary=true
+save_ode_state_variables=true
+main_function=save_as_ensight
 
 #[save_result]
 #print_rate=1
@@ -44,7 +45,7 @@ main_function=homogeneous_sigma_assembly_matrix
 [linear_system_solver]
 tolerance=1e-16
 use_preconditioner=no
-max_iterations=200
+max_iterations=500
 library_file=shared_libs/libdefault_linear_system_solver.so
 use_gpu=no
 main_function=conjugate_gradient
@@ -60,19 +61,19 @@ cable_length=20000.0
 main_function=initialize_grid_with_cable_mesh
 
 [ode_solver]
-adaptive=true
-dt=0.0001 
+adaptive=false
+dt=0.01 
 use_gpu=no
 gpu_id=0
 library_file= shared_libs/libToRORd_fkatp_mixed_endo_mid_epi.so
 
 [stim_plain]
 start = 0.0
-duration = 2.0
-period = 1000.0
+duration = 1.0
+;period = 1000.0
 current = -53.0
 x_limit = 500.0
 main_function=stim_if_x_less_than
 
 [extra_data]
-main_function=set_extra_data_mixed_model_epi_mid_endo
+main_function=set_extra_data_mixed_torord_fkatp_epi_mid_endo

example_configs/plain_mesh_ToRORd_Land_endo_mid_epi.ini

@@ -0,0 +1,66 @@
+[main]
+num_threads=6
+dt_pde=0.01
+simulation_time=500.0
+abort_on_no_activity=false
+use_adaptivity=false
+
+[update_monodomain]
+main_function=update_monodomain_default
+
+[save_result]
+print_rate=100
+output_dir=./outputs/plain_ToRORd_Land_endo_mid_epi_gpu_en
+add_timestamp=false
+binary=true
+save_ode_state_variables=false
+main_function=save_as_ensight
+
+[assembly_matrix]
+init_function=set_initial_conditions_fvm
+sigma_x=0.000176
+sigma_y=0.000176
+sigma_z=0.000176
+library_file=shared_libs/libdefault_matrix_assembly.so
+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
+num_layers=1
+start_dx=100.0
+start_dy=100.0
+start_dz=100.0
+side_length=20000
+main_function=initialize_grid_with_square_mesh
+
+[ode_solver]
+adaptive=false
+;reltol=1e-10
+;abstol=1e-10
+dt=0.01
+use_gpu=yes
+gpu_id=0
+library_file= shared_libs/libToRORd_Land_mixed_endo_mid_epi.so
+
+[stim_corner]
+start = 0.0
+duration = 1.0
+current = -53.0
+min_x = 0.0
+max_x = 1000.0
+min_y = 0.0
+max_y = 1000.0
+main_function=stim_x_y_limits
+
+[extra_data]
+main_function=set_extra_data_mixed_torord_Land_epi_mid_endo

example_configs/plain_mesh_ToRORd_fkatp_endo_mid_epi.ini

@@ -1,25 +1,16 @@
 [main]
 num_threads=6
-dt_pde=0.02
-simulation_time=600.0
+dt_pde=0.01
+simulation_time=500.0
 abort_on_no_activity=false
 use_adaptivity=false
 
 [update_monodomain]
 main_function=update_monodomain_default
 
-#[save_result]
-#print_rate=50
-#output_dir=./outputs/plain_ToRORd_endo_mid_epi
-#main_function=save_as_vtu
-#init_function=init_save_as_vtk_or_vtu
-#end_function=end_save_as_vtk_or_vtu
-#save_pvd=true
-#file_prefix=V
-
 [save_result]
-print_rate=50
-output_dir=./outputs/plain_ToRORd_endo_mid_epi_ensight
+print_rate=100
+output_dir=./outputs/plain_ToRORd_fkatp_endo_mid_epi_gpu_en
 add_timestamp=false
 binary=true
 save_ode_state_variables=false
@@ -36,7 +27,7 @@ main_function=homogeneous_sigma_assembly_matrix
 [linear_system_solver]
 tolerance=1e-16
 use_preconditioner=no
-max_iterations=200
+max_iterations=500
 library_file=shared_libs/libdefault_linear_system_solver.so
 use_gpu=yes
 main_function=conjugate_gradient
@@ -56,9 +47,6 @@ main_function=initialize_grid_with_square_mesh
 dt=0.01
 use_gpu=yes
 gpu_id=0
-;adaptive=false
-;abstol=1e-12
-;reltol=1e-5
 library_file= shared_libs/libToRORd_fkatp_mixed_endo_mid_epi.so
 
 [stim_corner]