Add test cases for CEP (1Dcable_TTP, 2Dsquare_BO, 2Dspiral_BO, purkin…

…je) (#102)

.gitattributes

@@ -1,2 +1,3 @@
 *.vtu filter=lfs diff=lfs merge=lfs -text
 *.vtp filter=lfs diff=lfs merge=lfs -text
+*.dat filter=lfs diff=lfs merge=lfs -text

tests/cases/1Dcable_TTP/README.md

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+
+# **Problem Description**
+
+Solve electrophysiology inside a 1D cable. The ten-Tusscher-Panfilov model is used to describe the cell activation.
+For more information regarding the model, please refer to the following publications:
+
+> K. H. W. J. ten Tusscher, D. Noble, P. J. Noble, and A. V. Panfilov. A model for hu-
+> man 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.
+
+The input file `svFSI.inp` follows the master input file [`svFSI_master.inp`](./svFSI_master.inp) as a template.

tests/cases/1Dcable_TTP/mesh/.gitattributes

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+domain_info_h0.40.dat filter=lfs diff=lfs merge=lfs -text

tests/cases/1Dcable_TTP/svFSI.xml

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+<?xml version="1.0" encoding="UTF-8" ?>
+<svFSIFile 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="msh" > 
+  <Set_mesh_as_fibers> true </Set_mesh_as_fibers> 
+  <Mesh_file_path> mesh/bar_h0.40.vtu  </Mesh_file_path>
+  <Domain_file_path> mesh/domain_info_h0.40.dat </Domain_file_path> 
+</Add_mesh>
+
+<Add_equation type="CEP" > 
+   <Coupled> true </Coupled>
+   <Min_iterations> 1 </Min_iterations>  
+   <Max_iterations> 5 </Max_iterations> 
+   <Tolerance> 1e-6 </Tolerance> 
+
+   <Domain id="1" >
+     <Electrophysiology_model> TTP </Electrophysiology_model> 
+     <Isotropic_conductivity> 0.15432 </Isotropic_conductivity> 
+     <ODE_solver> RK </ODE_solver> 
+   </Domain>
+
+   <Domain id="2" >
+      <Electrophysiology_model> TTP </Electrophysiology_model> 
+      <Isotropic_conductivity> 0.15432 </Isotropic_conductivity> 
+      <ODE_solver> RK </ODE_solver> 
+      <Stimulus type="Istim" >
+         <Amplitude> -52.0 </Amplitude> 
+         <Start_time> 0.0 </Start_time> 
+         <Duration> 1.0 </Duration> 
+         <Cycle_length> 10000.0 </Cycle_length> 
+      </Stimulus>
+   </Domain>
+
+   <Output type="Spatial" >
+      <Action_potential> true </Action_potential>
+   </Output>
+
+   <LS type="GMRES" >
+      <Max_iterations> 100 </Max_iterations> 
+      <Tolerance> 1e-6 </Tolerance>
+      <Krylov_space_dimension> 50 </Krylov_space_dimension>
+   </LS>
+
+</Add_equation>
+
+</svFSIFile>
+
+

tests/cases/2Dspiral_BO/README.md

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+
+# **Problem Description**
+
+Simulate spiral wave in a plate. 
+
+<p align="center">
+   <img src="./BO_S1S2_spiral_Ts470.0300.png" width="600">
+</p>
+
+The Bueno-Orovio-Cherry-Fenton model is used to describe the cell activation. For details of the model, please refer to the following publications:
+
+> Bueno-Orovio, Alfonso, Elizabeth M. Cherry, and Flavio H. Fenton. "Minimal model for human ventricular action potentials in tissue." *Journal of theoretical biology* 253, no. 3 (2008): 544-560.
+
+The input file `svFSI.inp` follows the master input file [`svFSI_master.inp`](./svFSI_master.inp) as a template.

tests/cases/2Dspiral_BO/svFSI.xml

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+<?xml version="1.0" encoding="UTF-8" ?>
+<svFSIFile version="0.1">
+
+<GeneralSimulationParameters>
+  <Continue_previous_simulation> false </Continue_previous_simulation>
+  <Number_of_spatial_dimensions> 2 </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="msh" > 
+
+  <Mesh_file_path> mesh/mesh-complete.mesh.vtu   </Mesh_file_path>
+
+  <Add_face name="X0">
+      <Face_file_path> mesh/mesh-surfaces/X0.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="X1">
+      <Face_file_path> mesh/mesh-surfaces/X1.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="Y0">
+      <Face_file_path> mesh/mesh-surfaces/Y0.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="Y1">
+      <Face_file_path> mesh/mesh-surfaces/Y1.vtp </Face_file_path>
+  </Add_face>
+
+  <Domain_file_path> mesh/spiral_domain_info.dat </Domain_file_path>
+
+</Add_mesh>
+
+<Add_equation type="CEP" > 
+   <Coupled> true </Coupled>
+   <Min_iterations> 1 </Min_iterations>  
+   <Max_iterations> 5 </Max_iterations> 
+   <Tolerance> 1e-4 </Tolerance> 
+
+  <Domain id="1" >
+     <Electrophysiology_model> BO </Electrophysiology_model>
+     <Isotropic_conductivity> 0.1171 </Isotropic_conductivity>
+     <ODE_solver> RK </ODE_solver>
+   </Domain>
+
+   <Domain id="2" >
+      <Electrophysiology_model> BO </Electrophysiology_model>
+      <Isotropic_conductivity> 0.1171 </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> 100000.0 </Cycle_length>
+      </Stimulus>
+   </Domain>
+
+   <Domain id="3" >
+      <Electrophysiology_model> BO </Electrophysiology_model>
+      <Isotropic_conductivity> 0.1171 </Isotropic_conductivity>
+      <ODE_solver> RK </ODE_solver>
+      <Stimulus type="Istim" >
+         <Amplitude> -52.0 </Amplitude>
+         <Start_time> 440.0 </Start_time>
+         <Duration> 5.0 </Duration>
+         <Cycle_length> 100000.0 </Cycle_length>
+      </Stimulus>
+   </Domain>
+
+   <Output type="Spatial" >
+      <Action_potential> true </Action_potential>
+   </Output>
+
+   <LS type="CG" >
+      <Preconditioner> rcs </Preconditioner> 
+      <Tolerance> 1e-6 </Tolerance>
+   </LS>
+
+</Add_equation>
+
+</svFSIFile>
+

tests/cases/2Dsquare_AP/README.md

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+
+# **Problem Description**
+
+Solve electrophysiology inside a 2D plane. The Aliev-Panfilov model is used to describe the cell activation. For more information regarding the model please refer to the following publication:
+
+> S. Göktepe and E. Kuhl. Computational modeling of cardiac electrophysiology: A novel finite
+> element approach. International Journal for Numerical Methods in Engineering, 79(2):156–
+> 178, jul 2009.
+
+The input file `svFSI.inp` follows the master input file [`svFSI_master.inp`](./svFSI_master.inp) as a template. Some specific input options are discussed below:
+
+## Pacemaker and Non-Pacemaker Cells
+
+The Aliev-Panfilov model is developed to model the non-pacemaker myocytes, which need to receive stimulus from neighboring cells to start the depolarization. In this example, instead of using a different electrophysiological model for the pacemaker cells, we add external stimulus to the Aliev-Panfilov model in a small group of cells so that they can behave like pacemaker cells and initiate the wave propagation. This is achieved through `Domain` object. 
+
+```
+   Domain file path: mesh/h0.25/domain_info.dat
+```
+
+Here, a list of integers is provided for each element to serve as its domain ID. Elements with ID 1 are non-pacemaker cells and those with ID 2 will act as pacemaker cells.
+
+```
+   Domain: 1 {
+      Electrophysiology model: AP
+      Conductivity (iso): 1.0
+      ODE solver: Euler
+   }
+
+   Domain: 2 {
+      Electrophysiology model: AP
+      Conductivity (iso): 1.0
+      Stimulus: Istim {
+         Amplitude: 10.0
+         Start time: 0.0
+         Duration: 10.0
+      }
+      ODE solver: Euler
+   }
+```
+
+To define an external stimulus, users need to provide amplitude, start time and duration. The signal is essentially a square wave.
+