Fluid and ustruct test cases (#115)

Co-authored-by: Elena Martinez <elenasm@stanford.edu>

tests/cases/LV_Guccione_passive/svFSI.xml

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+<?xml version="1.0" encoding="UTF-8" ?>
+<svFSIFile version="0.1">
+
+<GeneralSimulationParameters>
+  <Continue_previous_simulation> 0 </Continue_previous_simulation>
+  <Number_of_spatial_dimensions> 3 </Number_of_spatial_dimensions> 
+  <Number_of_time_steps> 1 </Number_of_time_steps> 
+  <Time_step_size> 0.001 </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> 1 </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> 100 </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="endo">
+      <Face_file_path> mesh/mesh-surfaces/endo.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="epi">
+      <Face_file_path> mesh/mesh-surfaces/epi.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="base">
+      <Face_file_path> mesh/mesh-surfaces/base.vtp </Face_file_path>
+  </Add_face>
+
+  <Fiber_direction> (1.0, 0.0, 0.0)  </Fiber_direction>
+  <Fiber_direction> (0.0, 1.0, 0.0)  </Fiber_direction>
+
+</Add_mesh>
+
+
+<Add_equation type="struct" > 
+
+   <Coupled> true </Coupled>
+   <Min_iterations> 1 </Min_iterations>  
+   <Max_iterations> 100 </Max_iterations> 
+   <Tolerance> 1e-9 </Tolerance> 
+
+   <Constitutive_model type="Gucci"> 
+     <c> 880 </c>
+     <bf> 8 </bf>
+     <bt> 6 </bt>
+     <bfs> 12 </bfs>
+   </Constitutive_model>
+
+   <Density> 1e-3 </Density> 
+   <Elasticity_modulus> 1.0 </Elasticity_modulus>
+   <Poisson_ratio> 0.5 </Poisson_ratio>
+
+   <Dilational_penalty_model> ST91 </Dilational_penalty_model>
+   <Penalty_parameter> 1.0e6 </Penalty_parameter> 
+
+   <Output type="Spatial" >
+     <Displacement> true </Displacement>
+     <Velocity> true </Velocity>
+     <Jacobian> true </Jacobian>
+   </Output>
+
+   <LS type="BICG" >
+      <Preconditioner> FSILS </Preconditioner> 
+      <Tolerance> 1e-9 </Tolerance>
+      <Max_iterations> 400 </Max_iterations> 
+   </LS>
+
+   <Add_BC name="base" > 
+      <Type> Dir </Type> 
+      <Value> 0.0 </Value> 
+   </Add_BC> 
+
+   <Add_BC name="endo" > 
+      <Type> Neu </Type> 
+      <Time_dependence> Unsteady </Time_dependence> 
+      <Temporal_values_file_path> load.dat </Temporal_values_file_path> 
+      <Ramp_function> true </Ramp_function> 
+      <Follower_pressure_load> true </Follower_pressure_load> 
+   </Add_BC> 
+
+</Add_equation>
+
+</svFSIFile>

tests/cases/block_compression/README.md

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+
+# **Problem Description**
+
+Solve block compression problem using displacement-based solid equation. The problem set-up is as follows [1]:
+
+<p align="center">
+   <img src="./configuration.png" width="600">
+</p>
+
+The final displacement is plotted below.
+
+<p align="center">
+   <img src="./displacement.png" width="600">
+</p>
+
+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:
+
+## Directional Dirichlet BC
+
+The problem configuration requires enforcing Dirichlet BC along a specific direction. For example, mesh points on the patch should have zero displacement along x and y directions. 
+
+```
+   Add BC: patch {
+      Type: Dir
+      Value: 0.0
+      Effective direction: (1, 1, 0)
+   }
+```
+
+This is achieved through `Effective direction` command. Currently, the software only supports specify Dirichlet BC along Cartesian directions. For example, `(1,0,0)` or `(1,0)` sets Dirichlet BC along x-axis in 3D or 2D.
+
+
+
+## Reference
+1. Liu, Ju, and Alison L. Marsden.  A Unified Continuum and Variational Multiscale Formulation for Fluids, Solids, and Fluid Structure Interaction.  *Computer Methods in Applied Mechanics and Engineering* 337 (August 2018): 549 97. https://doi.org/10.1016/j.cma.2018.03.045.

tests/cases/block_compression/svFSI.xml

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+<?xml version="1.0" encoding="UTF-8" ?>
+<svFSIFile version="0.1">
+
+<GeneralSimulationParameters>
+  <Continue_previous_simulation> 0 </Continue_previous_simulation>
+  <Number_of_spatial_dimensions> 3 </Number_of_spatial_dimensions> 
+  <Number_of_time_steps> 1  </Number_of_time_steps> 
+  <Time_step_size> .0001 </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> 1 </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> 100 </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/P1/mesh-complete.mesh.vtu </Mesh_file_path>
+
+  <Add_face name="X0">
+      <Face_file_path> mesh/P1/mesh-surfaces/X0.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="X1">
+      <Face_file_path> mesh/P1/mesh-surfaces/X1.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="Y0">
+      <Face_file_path> mesh/P1/mesh-surfaces/Y0.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="Y1">
+      <Face_file_path> mesh/P1/mesh-surfaces/Y1.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="Z0">
+      <Face_file_path> mesh/P1/mesh-surfaces/Z0.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="Z1">
+      <Face_file_path> mesh/P1/mesh-surfaces/Z1.vtp </Face_file_path>
+  </Add_face>
+
+  <Mesh_scale_factor> 0.001 </Mesh_scale_factor> 
+
+</Add_mesh>
+
+
+<Add_equation type="struct" > 
+
+   <Coupled> true </Coupled>
+   <Min_iterations> 1</Min_iterations>  
+   <Max_iterations> 10 </Max_iterations> 
+   <Tolerance> 1e-10 </Tolerance> 
+
+   <Constitutive_model type="nHK"> </Constitutive_model>
+   <Density> 1000.0 </Density> 
+   <Elasticity_modulus> 240.56596E6 </Elasticity_modulus>
+   <Poisson_ratio> 0.5 </Poisson_ratio>
+
+   <Dilational_penalty_model> ST91 </Dilational_penalty_model>
+   <Penalty_parameter> 4.0E9 </Penalty_parameter> 
+
+   <Output type="Spatial" >
+     <Displacement> true </Displacement>
+     <Velocity> true </Velocity>
+     <Jacobian> true </Jacobian>
+     <Stress> true </Stress>
+     <Strain> true </Strain>
+     <Cauchy_stress> true </Cauchy_stress>
+     <Def_grad> true </Def_grad>
+     <VonMises_stress> true </VonMises_stress>
+   </Output>
+
+   <LS type="BICG" >
+      <Preconditioner> FSILS </Preconditioner> 
+      <Tolerance> 1e-11 </Tolerance>
+      <Max_iterations> 600 </Max_iterations> 
+   </LS>
+
+   <Add_BC name="X0" > 
+      <Type> Dir </Type> 
+      <Value> 0.0 </Value> 
+      <Effective_direction> (1, 0, 0) </Effective_direction> 
+   </Add_BC> 
+
+   <Add_BC name="Y0" > 
+      <Type> Dir </Type> 
+      <Value> 0.0 </Value> 
+      <Effective_direction> (0, 1, 0) </Effective_direction> 
+   </Add_BC> 
+
+   <Add_BC name="Z0" > 
+      <Type> Dir </Type> 
+      <Value> 0.0 </Value> 
+      <Effective_direction> (0, 0, 1) </Effective_direction> 
+   </Add_BC> 
+
+   <Add_BC name="Z1" > 
+      <Type> Neu </Type>  
+      <Time_dependence> Unsteady </Time_dependence> 
+      <Temporal_values_file_path> load.dat </Temporal_values_file_path> 
+      <Ramp_function> true </Ramp_function> 
+      <Follower_pressure_load> true </Follower_pressure_load> 
+   </Add_BC> 
+
+</Add_equation>   
+
+</svFSIFile>
+
+