Add integration testing (#19)

.gitattributes

@@ -0,0 +1,2 @@
+*.vtu filter=lfs diff=lfs merge=lfs -text
+*.vtp filter=lfs diff=lfs merge=lfs -text

.github/workflows/test.yml

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+name: Integration
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, ubuntu-22.04, macos-12]
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install Ubuntu dependencies
+        if: startsWith(matrix.os, 'ubuntu')
+        run: |
+          sudo apt update
+          sudo apt install -y build-essential cmake qtbase5-dev libblas-dev liblapack-dev 
+          sudo apt install -y libopenblas-dev mesa-common-dev libgl1-mesa-dev libglu1-mesa-dev
+          sudo apt install -y libvtk7-dev
+      - name: Install MacOS dependencies
+        if: startsWith(matrix.os, 'macos')
+        run: | 
+          brew install cmake vtk openblas lapack mesa open-mpi qt5
+          brew link --force qt5
+          sudo ln -s /usr/local/Cellar/qt@5/5.15.8_2/mkspecs /usr/local/mkspecs
+          sudo ln -s /usr/local/Cellar/qt@5/5.15.8_2/plugins /usr/local/plugins
+      - name: Build svFSIplus
+        run: |
+          mkdir build
+          cd build
+          cmake ..
+          make -j2
+      - name: Install test dependencies
+        run: |
+          conda create -n svfsiplus python=3.9
+          conda run -n svfsiplus pip install pytest pytest-cov pytest-mock numpy meshio
+      - name: Run integration tests
+        run: |
+          git lfs pull
+          cd tests
+          conda run -n svfsiplus pytest -v

.gitignore

@@ -3,3 +3,11 @@ build
 # System files osx 
 **/.DS_Store
 
+# svFSIplus output
+*-procs
+
+# Python files
+__pycache__
+
+# pytest
+.pytest_cache

tests/cases/stokes_manufactured_solution/P1P1/N004/svFSI.inp

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+#----------------------------------------------------------------
+# General simulation parameters
+
+Continue previous simulation: 0
+Number of spatial dimensions: 2
+Number of time steps: 250
+Time step size: 0.002
+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: 250
+Start saving after time step: 1
+
+Increment in saving restart files: 250
+Convert BIN to VTK format: 0
+
+Verbose: 1
+Warning: 0
+Debug: 0
+
+#----------------------------------------------------------------
+# Mesh data
+Add mesh: msh {
+   Mesh file path:    ../mesh/N004/mesh-complete.mesh.vtu
+   Add face: bottom {
+      Face file path: ../mesh/N004/mesh-surfaces/bottom.vtp
+   }
+   Add face: top {
+      Face file path: ../mesh/N004/mesh-surfaces/top.vtp
+   }
+   Add face: left {
+      Face file path: ../mesh/N004/mesh-surfaces/left.vtp
+   }
+   Add face: right {
+      Face file path: ../mesh/N004/mesh-surfaces/right.vtp
+   }
+}
+
+#----------------------------------------------------------------
+# Equations
+Add equation: stokes {
+   Coupled: 1
+   Min iterations: 1
+   Max iterations: 2
+   Tolerance: 1e-9
+   Use Taylor-Hood type basis: f
+
+   Viscosity: Constant {Value: 1.0}
+   Momentum stabilization coefficient: 10.0
+
+   LS type: GMRES
+   {
+      Preconditioner:      svfsi
+      Tolerance:           1D-9
+      Max iterations:      100
+      Krylov space dimension: 50
+   }
+
+   Add BF: msh {
+      Type: vol
+      Time dependence: general
+      Temporal and spatial values file path: ../bforce/N004/bforce.dat
+   }
+
+   Add BC: left {
+      Type: Dir
+      Time dependence: General
+      Temporal and spatial values file path: ../bforce/N004/left_vbc.dat
+   }
+
+   Add BC: right {
+      Type: Dir
+      Time dependence: General
+      Temporal and spatial values file path: ../bforce/N004/right_vbc.dat
+   }
+
+   Add BC: top {
+      Type: Dir
+      Time dependence: General
+      Temporal and spatial values file path: ../bforce/N004/top_vbc.dat
+   }
+}
+

tests/cases/stokes_manufactured_solution/P1P1/N004/svFSI.xml

@@ -0,0 +1,96 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<svFSIFile version="0.1">
+
+<GeneralSimulationParameters>
+  <Continue_previous_simulation> 0 </Continue_previous_simulation>
+  <Number_of_spatial_dimensions> 2 </Number_of_spatial_dimensions> 
+  <Number_of_time_steps> 250 </Number_of_time_steps>
+  <Time_step_size> 0.002 </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> 250 </Increment_in_saving_VTK_files>
+  <Start_saving_after_time_step> 1 </Start_saving_after_time_step> 
+  <Increment_in_saving_restart_files> 200 </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/N004/mesh-complete.mesh.vtu </Mesh_file_path>
+
+  <Add_face name="bottom">
+      <Face_file_path> ../mesh/N004/mesh-surfaces/bottom.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="top">
+      <Face_file_path> ../mesh/N004/mesh-surfaces/top.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="left">
+      <Face_file_path> ../mesh/N004/mesh-surfaces/left.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="right">
+      <Face_file_path> ../mesh/N004/mesh-surfaces/right.vtp </Face_file_path>
+  </Add_face>
+
+</Add_mesh>
+
+<Add_equation type="stokes" > 
+   <Coupled> true </Coupled>
+   <Min_iterations> 1 </Min_iterations>  
+   <Max_iterations> 2 </Max_iterations> 
+   <Tolerance> 1e-9 </Tolerance> 
+   <Use_taylor_hood_type_basis> false </Use_taylor_hood_type_basis> 
+
+   <Viscosity model="Constant" >
+     <Value> 1.0 </Value>
+   </Viscosity>
+
+   <Momentum_stabilization_coefficient> 10.0 </Momentum_stabilization_coefficient> 
+
+   <LS type="GMRES" >
+      <Preconditioner> svfsi </Preconditioner> 
+      <Tolerance> 1e-9 </Tolerance>
+      <Max_iterations> 100 </Max_iterations> 
+      <Krylov_space_dimension> 50 </Krylov_space_dimension>
+   </LS>
+
+   <Output type="Spatial" >
+     <Velocity> true </Velocity>
+     <Pressure> true </Pressure>
+     <Traction> true </Traction>
+     <WSS> true </WSS>
+   </Output>
+
+   <Add_BF mesh="msh" >
+      <Type> volumetric </Type>
+      <Time_dependence> general </Time_dependence> 
+      <Temporal_and_spatial_values_file_path> ../bforce/N004/bforce.dat </Temporal_and_spatial_values_file_path> 
+   </Add_BF> 
+
+   <Add_BC name="left" > 
+      <Type> Dir </Type> 
+      <Time_dependence> General </Time_dependence> 
+      <Temporal_and_spatial_values_file_path> ../bforce/N004/left_vbc.dat </Temporal_and_spatial_values_file_path> 
+   </Add_BC> 
+
+   <Add_BC name="right" > 
+      <Type> Dir </Type> 
+      <Time_dependence> General </Time_dependence> 
+      <Temporal_and_spatial_values_file_path> ../bforce/N004/right_vbc.dat </Temporal_and_spatial_values_file_path> 
+   </Add_BC> 
+
+   <Add_BC name="top" > 
+      <Type> Dir </Type> 
+      <Time_dependence> General </Time_dependence> 
+      <Temporal_and_spatial_values_file_path> ../bforce/N004/top_vbc.dat </Temporal_and_spatial_values_file_path> 
+   </Add_BC> 
+
+</Add_equation>
+
+</svFSIFile>

tests/cases/stokes_manufactured_solution/P1P1/N008/svFSI.inp

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+#----------------------------------------------------------------
+# General simulation parameters
+
+Continue previous simulation: 0
+Number of spatial dimensions: 2
+Number of time steps: 250
+Time step size: 0.002
+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: 250
+Start saving after time step: 1
+
+Increment in saving restart files: 250
+Convert BIN to VTK format: 0
+
+Verbose: 1
+Warning: 0
+Debug: 0
+
+#----------------------------------------------------------------
+# Mesh data
+Add mesh: msh {
+   Mesh file path:    ../mesh/N008/mesh-complete.mesh.vtu
+   Add face: bottom {
+      Face file path: ../mesh/N008/mesh-surfaces/bottom.vtp
+   }
+   Add face: top {
+      Face file path: ../mesh/N008/mesh-surfaces/top.vtp
+   }
+   Add face: left {
+      Face file path: ../mesh/N008/mesh-surfaces/left.vtp
+   }
+   Add face: right {
+      Face file path: ../mesh/N008/mesh-surfaces/right.vtp
+   }
+}
+
+#----------------------------------------------------------------
+# Equations
+Add equation: stokes {
+   Coupled: 1
+   Min iterations: 1
+   Max iterations: 2
+   Tolerance: 1e-9
+   Use Taylor-Hood type basis: f
+
+   Viscosity: Constant {Value: 1.0}
+   Momentum stabilization coefficient: 10.0
+
+   LS type: GMRES
+   {
+      Preconditioner:      svfsi
+      Tolerance:           1D-9
+      Max iterations:      100
+      Krylov space dimension: 50
+   }
+
+   Add BF: msh {
+      Type: vol
+      Time dependence: general
+      Temporal and spatial values file path: ../bforce/N008/bforce.dat
+   }
+
+   Add BC: left {
+      Type: Dir
+      Time dependence: General
+      Temporal and spatial values file path: ../bforce/N008/left_vbc.dat
+   }
+
+   Add BC: right {
+      Type: Dir
+      Time dependence: General
+      Temporal and spatial values file path: ../bforce/N008/right_vbc.dat
+   }
+
+   Add BC: top {
+      Type: Dir
+      Time dependence: General
+      Temporal and spatial values file path: ../bforce/N008/top_vbc.dat
+   }
+}
+