Add ALE test case (#93)

* adding ale pipe test

* adapting test to svFSI+ format

* modify test file

* changing reference to orginal svFSI output

* removing non-lfs files

* adding test as lfs compatible

* adding files for 1 timestep check

* modifying test ale for 1 timestep

* modifying test ale for 1 timestep

* make FSI mesh much coarser

* remove fine mesh results

* give more meaningful error message

* run 5 steps

* add int32 coarse meash

* also test pressure and velocity

---------

Co-authored-by: Erica <schwarze@stanford.edu>
Co-authored-by: Erica Leigh Schwarz <schwarze@exp-9-56.expanse.sdsc.edu>

tests/cases/ale_3d_pipe/README.md

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+
+# **Problem Description**
+
+Solve pressure wave propagation in an arterial model using the Arbitrary Lagrangian-Eulerian method [1]. The problem set-up is as follows.
+
+<p align="center">
+   <img src="./configuration.png" width="600">
+</p>
+
+And the results are
+
+<p align="center">
+   <img src="./results.gif" width="600">
+</p>
+
+The input file `svFSI.xml` follows the input file format for svFSIplus. More on ALE-FSI simulations can be found here:
+
+- SimVascular Website: https://simvascular.github.io/docssvFSI-FSI.html
+- Youtube Tutorial: https://www.youtube.com/watch?v=QIpyThIAD7k
+
+## 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/ale_3d_pipe/svFSI.inp

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+#----------------------------------------------------------------
+# General simulation parameters
+
+Continue previous simulation: 0
+Number of spatial dimensions: 3
+Number of time steps: 80
+Time step size: 1e-4
+Spectral radius of infinite time step: 0.50
+Searched file name to trigger stop: STOP_SIM
+
+Save results to VTK format: 1
+Name prefix of saved VTK files: result
+Increment in saving VTK files: 1
+Start saving after time step: 1
+
+Increment in saving restart files: 1
+Convert BIN to VTK format: 0
+
+Verbose: 1
+Warning: 0
+Debug: 0
+
+#----------------------------------------------------------------
+# Mesh data
+Add mesh: lumen {
+   Mesh file path: mesh/fluid/mesh-complete.mesh.vtu
+   Add face: lumen_inlet {
+      Face file path: mesh/fluid/mesh-surfaces/start.vtp
+   }
+   Add face: lumen_outlet {
+      Face file path: mesh/fluid/mesh-surfaces/end.vtp
+   }
+   Add face: lumen_wall {
+      Face file path: mesh/fluid/mesh-surfaces/interface.vtp
+   }
+   Domain: 0
+}
+
+Add mesh: wall {
+   Mesh file path: mesh/solid/mesh-complete.mesh.vtu
+   Add face: wall_inlet {
+      Face file path: mesh/solid/mesh-surfaces/start.vtp
+   }
+   Add face: wall_outlet {
+      Face file path: mesh/solid/mesh-surfaces/end.vtp
+   }
+   Add face: wall_inner {
+      Face file path: mesh/solid/mesh-surfaces/interface.vtp
+   }
+   Add face: wall_outer {
+      Face file path: mesh/solid/mesh-surfaces/outside.vtp
+   }
+   Domain: 1
+}
+
+#----------------------------------------------------------------
+# Projections
+Add projection: wall_inner {
+   Project from face: lumen_wall
+}
+
+#----------------------------------------------------------------
+# Equations
+Add equation: FSI {
+   Coupled: 1
+   Min iterations: 1
+   Max iterations: 10
+   Tolerance: 1e-6
+
+   Domain: 0 {
+      Equation: fluid
+      Density: 1.0
+      Viscosity: Constant {Value: 0.04}
+      Backflow stabilization coefficient: 0.2
+   }
+
+   Domain: 1 {
+      Equation: struct  # (or) ustruct
+      Constitutive model: nHK
+      Dilational penalty model: M94
+      Density: 1.0
+      Elasticity modulus: 1.0e7
+      Poisson ratio: 0.3
+
+      ##### For ustruct eq.
+      ## Momentum stabilization coefficient: 0.001
+      ## Continuity stabilization coefficient: 0.0
+   }
+
+   LS type: GMRES {
+#      Preconditioner: Trilinos-ILUT
+      Tolerance: 1e-6
+      Max iterations: 100
+      Krylov space dimension: 50
+   }
+
+   Output: Spatial {
+      Displacement: t
+      Velocity: t
+      Pressure: t
+   }
+
+   Output: Alias {
+      Displacement: FS_Displacement
+   }
+
+   Add BC: lumen_inlet {
+      Type: Neu
+      Value: 5.0e4
+   }
+
+   Add BC: wall_inlet {
+      Type: Dir
+      Value: 0.0
+      Impose on state variable integral: t
+      Zero out perimeter: f
+      Effective direction: (0, 0, 1)
+   }
+
+   Add BC: wall_outlet {
+      Type: Dir
+      Value: 0.0
+      Impose on state variable integral: t
+      Zero out perimeter: f
+      Effective direction: (0, 0, 1)
+   }
+}
+
+Add equation: mesh {
+   Coupled: 1
+   Min iterations: 1
+   Max iterations: 5
+   Tolerance: 1e-4
+   Poisson ratio: 0.3
+
+   LS type: CG {
+      Preconditioner: FSILS
+      Tolerance: 1e-4
+   }
+
+   Output: Spatial {
+      Displacement: t
+   }
+
+   Add BC: lumen_inlet {
+      Type: Dir
+      Value: 0.0
+   }
+
+   Add BC: lumen_outlet {
+      Type: Dir
+      Value: 0.0
+   }
+}
+

tests/cases/ale_3d_pipe/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> 5 </Number_of_time_steps> 
+  <Time_step_size> 1e-4 </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="lumen" > 
+  <Mesh_file_path> mesh/fluid/mesh-complete.mesh.vtu  </Mesh_file_path>
+  <Add_face name="lumen_inlet">
+      <Face_file_path> mesh/fluid/mesh-surfaces/start.vtp </Face_file_path>
+  </Add_face>
+  <Add_face name="lumen_outlet">
+      <Face_file_path> mesh/fluid/mesh-surfaces/end.vtp </Face_file_path>
+  </Add_face>
+  <Add_face name="lumen_wall">
+      <Face_file_path> mesh/fluid/mesh-surfaces/interface.vtp </Face_file_path>
+  </Add_face>
+  <Domain> 0 </Domain>
+
+</Add_mesh>
+
+<Add_mesh name="wall" >
+  <Mesh_file_path> mesh/solid/mesh-complete.mesh.vtu  </Mesh_file_path>
+  <Add_face name="wall_inlet">
+      <Face_file_path> mesh/solid/mesh-surfaces/start.vtp </Face_file_path>
+  </Add_face>
+  <Add_face name="wall_outlet">
+      <Face_file_path> mesh/solid/mesh-surfaces/end.vtp </Face_file_path>
+  </Add_face>
+  <Add_face name="wall_inner">
+      <Face_file_path> mesh/solid/mesh-surfaces/interface.vtp </Face_file_path>
+  </Add_face>
+  <Add_face name="wall_outer">
+      <Face_file_path> mesh/solid/mesh-surfaces/outside.vtp </Face_file_path>
+  </Add_face>
+  <Domain> 1 </Domain>
+</Add_mesh>
+
+<Add_projection name="wall_inner" >
+   <Project_from_face> lumen_wall </Project_from_face>
+</Add_projection> 
+
+<Add_equation type="FSI" > 
+   <Coupled> true </Coupled>
+   <Min_iterations> 1 </Min_iterations>  
+   <Max_iterations> 10 </Max_iterations> 
+   <Tolerance> 1e-6 </Tolerance> 
+
+   <Domain id="0" >
+      <Equation> fluid </Equation> 
+      <Density> 1.0 </Density> 
+      <Viscosity model="Constant" >
+         <Value> 0.04 </Value>
+      </Viscosity>
+      <Backflow_stabilization_coefficient> 0.2 </Backflow_stabilization_coefficient> 
+   </Domain>
+
+   <Domain id="1" >
+      <Equation> struct </Equation> 
+      <Constitutive_model type="neoHookean"> </Constitutive_model> 
+      <Dilational_penalty_model> M94 </Dilational_penalty_model> 
+      <Density> 1.0 </Density> 
+      <Elasticity_modulus> 1.0e7 </Elasticity_modulus> 
+      <Poisson_ratio> 0.3 </Poisson_ratio> 
+   </Domain>
+
+   <LS type="GMRES" >
+      <Preconditioner> FSILS </Preconditioner>
+      <!--Preconditioner> Trilinos-ILUT </Preconditioner-->
+      <Tolerance> 1e-6 </Tolerance>
+      <Max_iterations> 100 </Max_iterations> 
+      <Krylov_space_dimension> 50 </Krylov_space_dimension>
+   </LS>
+
+   <Output type="Spatial" >
+     <Displacement> true </Displacement>
+     <Velocity> true </Velocity>
+     <Pressure> true </Pressure>
+     <VonMises_stress> true </VonMises_stress>
+   </Output>
+
+   <Output type="Alias" >
+       <Displacement> FS_Displacement </Displacement>
+   </Output>
+
+   <Add_BC name="lumen_inlet" > 
+      <Type> Neu </Type> 
+      <Value> 5.0e4 </Value> 
+   </Add_BC> 
+
+   <Add_BC name="wall_inlet" > 
+      <Type> Dir </Type> 
+      <Value> 0.0 </Value> 
+      <Impose_on_state_variable_integral> true </Impose_on_state_variable_integral> 
+      <Zero_out_perimeter> false </Zero_out_perimeter> 
+      <Effective_direction> (0, 0, 1) </Effective_direction> 
+   </Add_BC> 
+
+   <Add_BC name="wall_outlet" >
+      <Type> Dir </Type> 
+      <Value> 0.0 </Value> 
+      <Impose_on_state_variable_integral> true </Impose_on_state_variable_integral>
+      <Zero_out_perimeter> false </Zero_out_perimeter> 
+      <Effective_direction> (0, 0, 1 ) </Effective_direction> 
+   </Add_BC> 
+
+</Add_equation>
+
+
+<Add_equation type="mesh" >
+   <Coupled> true </Coupled>
+   <Min_iterations> 1 </Min_iterations>
+   <Max_iterations> 5 </Max_iterations>
+   <Tolerance> 1e-4 </Tolerance>
+   <Poisson_ratio> 0.3 </Poisson_ratio> 
+
+   <LS type="CG" >
+      <Preconditioner> FSILS </Preconditioner>
+      <Tolerance> 1e-4 </Tolerance>
+   </LS>
+
+   <Output type="Spatial" >
+     <Displacement> true </Displacement>
+   </Output>
+
+   <Add_BC name="lumen_inlet" > 
+      <Type> Dir </Type> 
+      <Value> 0.0 </Value> 
+   </Add_BC> 
+
+   <Add_BC name="lumen_outlet" > 
+      <Type> Dir </Type> 
+      <Value> 0.0 </Value> 
+   </Add_BC> 
+
+</Add_equation>
+
+</svFSIFile>