Adding test for EP coupling 1D to 3D mesh

tests/cases/cep/cylinder_purkinje_1d3d/README.md

@@ -0,0 +1,19 @@
+
+# **Problem Description**
+
+Simulate the propagation of an electric signal in a cylinder coupled with a network of Purkinje fibers using the ten-Tusscher-Panfilov cell activation model.
+
+Note: Conductivities in the myocardium were selected so that the propagation occurs in the myocardium (if too slow, due to the coarseness of the mesh, the action potential does not propagate beyond the coupled nodes).
+
+<p align="center">
+   <img src="./activation_10fps.gif" width="600">
+</p>
+
+## References
+K. H. W. J. ten Tusscher, D. Noble, P. J. Noble, and A. V. Panfilov. A model for human ventricular tissue. American Journal of Physiology-Heart and Circulatory Physiology,
+286(4):H1573–H1589, apr 2004.
+
+K. H. W. J. ten Tusscher and A. V. Panfilov. Alternans and spiral breakup in a human
+ventricular tissue model. American Journal of Physiology-Heart and Circulatory Physiology,
+291(3):H1088–H1100, sep 2006.
+

tests/cases/cep/cylinder_purkinje_1d3d/mesh/cyl-tree_endnodes.txt

@@ -0,0 +1,81 @@
+1
+16
+54
+62
+66
+74
+84
+85
+91
+99
+101
+122
+123
+124
+128
+129
+137
+141
+149
+151
+164
+167
+175
+178
+203
+227
+231
+239
+252
+268
+283
+285
+287
+291
+294
+298
+302
+307
+323
+326
+327
+328
+329
+333
+334
+338
+342
+346
+350
+351
+355
+363
+364
+368
+369
+373
+376
+378
+379
+380
+381
+384
+392
+396
+400
+402
+409
+411
+414
+415
+419
+426
+430
+432
+436
+438
+441
+442
+443
+445
+446

tests/cases/cep/cylinder_purkinje_1d3d/solver.xml

@@ -0,0 +1,107 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<svMultiPhysicsFile version="0.1">
+
+<GeneralSimulationParameters>
+  <Continue_previous_simulation> false </Continue_previous_simulation>
+  <Number_of_spatial_dimensions> 3 </Number_of_spatial_dimensions> 
+  <Number_of_time_steps> 1 </Number_of_time_steps> 
+  <Time_step_size> 0.1 </Time_step_size> 
+  <Spectral_radius_of_infinite_time_step> 0.50 </Spectral_radius_of_infinite_time_step> 
+  <Searched_file_name_to_trigger_stop> STOP_SIM </Searched_file_name_to_trigger_stop> 
+
+  <Save_results_to_VTK_format> true </Save_results_to_VTK_format> 
+  <Name_prefix_of_saved_VTK_files> result </Name_prefix_of_saved_VTK_files> 
+  <Increment_in_saving_VTK_files> 1 </Increment_in_saving_VTK_files> 
+  <Start_saving_after_time_step> 1 </Start_saving_after_time_step> 
+
+  <Increment_in_saving_restart_files> 1 </Increment_in_saving_restart_files> 
+  <Convert_BIN_to_VTK_format> 0 </Convert_BIN_to_VTK_format> 
+
+  <Verbose> 1 </Verbose> 
+  <Warning> 0 </Warning> 
+  <Debug> 0 </Debug> 
+</GeneralSimulationParameters>
+
+<Add_mesh name="efib" > 
+  <Set_mesh_as_fibers> true </Set_mesh_as_fibers> 
+  <Mesh_file_path> ./mesh/cyl-tree.vtu  </Mesh_file_path>
+  <Add_face name = "fc_efib">
+      <End_nodes_face_file_path> ./mesh/cyl-tree_endnodes.txt </End_nodes_face_file_path>
+  </Add_face>
+  <Domain_file_path> ./mesh/cyl-tree_domain.dat </Domain_file_path>
+  <Mesh_scale_factor> 10 </Mesh_scale_factor> 
+</Add_mesh>
+
+<Add_mesh name="msh" > 
+
+  <Mesh_file_path> ./mesh/cylinder.vtu   </Mesh_file_path>
+
+  <Add_face name="endo">
+      <Face_file_path> ./mesh/mesh-surfaces/cylinder_inner.vtp </Face_file_path>
+  </Add_face>
+
+  <Domain_file_path> ./mesh/cylinder_domain.dat </Domain_file_path>
+
+   <Fiber_direction_file_path> ./mesh/cylinder_fiber.vtu </Fiber_direction_file_path>
+   <Mesh_scale_factor> 10 </Mesh_scale_factor>
+
+</Add_mesh>
+
+<Add_projection name = "fc_efib">
+   <Project_from_face> endo </Project_from_face>
+   <Projection_tolerance> -1.0 </Projection_tolerance>  <!-- a negative value means using the nearest neighbor, no matter how far it is -->
+</Add_projection>
+
+
+<Add_equation type="CEP" > 
+   <Coupled> true </Coupled>
+   <Min_iterations> 1 </Min_iterations>  
+   <Max_iterations> 3 </Max_iterations> 
+   <Tolerance> 1e-12 </Tolerance> 
+
+   <Domain id="1" >
+      <Electrophysiology_model> TTP </Electrophysiology_model>
+      <Myocardial_zone> myocardium </Myocardial_zone> 
+      <Isotropic_conductivity> 0.05 </Isotropic_conductivity>
+      <Anisotropic_conductivity> 0.05 </Anisotropic_conductivity>
+      <ODE_solver> RK </ODE_solver>
+   </Domain>
+
+   <Domain id="2" >
+      <Electrophysiology_model> TTP </Electrophysiology_model>
+      <Myocardial_zone> pfib </Myocardial_zone> 
+      <Isotropic_conductivity> 1.1 </Isotropic_conductivity>
+      <ODE_solver> RK </ODE_solver>
+   </Domain> 
+
+   <Domain id="3" >
+      <Electrophysiology_model> TTP </Electrophysiology_model>
+      <Myocardial_zone> pfib </Myocardial_zone> 
+      <Isotropic_conductivity> 1.1 </Isotropic_conductivity>
+      <ODE_solver> RK </ODE_solver>
+      <Stimulus type="Istim" >
+         <Amplitude> -52.0 </Amplitude>
+         <Start_time> 0.0 </Start_time>
+         <Duration> 2.0 </Duration>
+         <Cycle_length> 1000.0 </Cycle_length>
+      </Stimulus>
+   </Domain>
+
+   <Output type="Spatial" >
+      <Action_potential> true </Action_potential>
+   </Output>
+
+   <LS type="GMRES" >
+      <Linear_algebra type="fsils" >
+         <Preconditioner> fsils </Preconditioner>
+      </Linear_algebra>
+      <Max_iterations> 100 </Max_iterations>
+      <Tolerance> 1e-12 </Tolerance>
+      <Krylov_space_dimension> 50 </Krylov_space_dimension>
+   </LS>
+
+</Add_equation>
+
+</svMultiPhysicsFile>
+
+

tests/test_cep.py

@@ -32,6 +32,10 @@ def test_purkinje(n_proc):
     run_with_reference(base_folder, test_folder, fields, n_proc)
 
 
+def test_cylinder_purkinje_1d3d(n_proc):
+    test_folder = "cylinder_purkinje_1d3d"
+    run_with_reference(base_folder, test_folder, fields, n_proc)
+
 @pytest.mark.parametrize(
     "confs_ecgs",
     [