Add shell test cases plate and valve (#174)

* Add shell test cases plate and valve * Crank up tolerances to the max
SimVascular · Feb 23, 2024 · 69a87f2 · 69a87f2
1 parent 2fd02ed
commit 69a87f2
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diff --git a/.gitattributes b/.gitattributes
@@ -6,3 +6,4 @@
 *.msi filter=lfs diff=lfs merge=lfs -text
 *.bin filter=lfs diff=lfs merge=lfs -text
 *.stl filter=lfs diff=lfs merge=lfs -text
+*.avi filter=lfs diff=lfs merge=lfs -text
diff --git a/tests/cases/shell/plate/mesh/2Dsqr_NURBS_C1.msh b/tests/cases/shell/plate/mesh/2Dsqr_NURBS_C1.msh
@@ -0,0 +1,25 @@
+#knotV 6
+0
+0
+0
+1
+1
+1
+#knotV 6
+0
+0
+0
+1
+1
+1
+#ctrlPts 9
+0.0   0.0   0.0  1.0
+0.0   10.0  0.0  1.0
+0.0   20.0  0.0  1.0
+10.0  0.0   0.0  1.0
+10.0  10.0  0.0  1.0
+10.0  20.0  0.0  1.0
+20.0  0.0   0.0  1.0
+20.0  10.0  0.0  1.0
+20.0  20.0  0.0  1.0
+
diff --git a/tests/cases/shell/plate/mesh/tri3/mesh-complete.mesh.vtu b/tests/cases/shell/plate/mesh/tri3/mesh-complete.mesh.vtu
diff --git a/tests/cases/shell/plate/mesh/tri3/mesh-surfaces/x0.vtp b/tests/cases/shell/plate/mesh/tri3/mesh-surfaces/x0.vtp
diff --git a/tests/cases/shell/plate/mesh/tri3/mesh-surfaces/x1.vtp b/tests/cases/shell/plate/mesh/tri3/mesh-surfaces/x1.vtp
diff --git a/tests/cases/shell/plate/mesh/tri3/mesh-surfaces/y0.vtp b/tests/cases/shell/plate/mesh/tri3/mesh-surfaces/y0.vtp
diff --git a/tests/cases/shell/plate/mesh/tri3/mesh-surfaces/y1.vtp b/tests/cases/shell/plate/mesh/tri3/mesh-surfaces/y1.vtp
diff --git a/tests/cases/shell/plate/result_010.vtu b/tests/cases/shell/plate/result_010.vtu
diff --git a/tests/cases/shell/plate/svFSI.xml b/tests/cases/shell/plate/svFSI.xml
@@ -0,0 +1,110 @@
+<?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> 10 </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> 10 </Increment_in_saving_VTK_files> 
+  <Start_saving_after_time_step> 1 </Start_saving_after_time_step> 
+
+  <Increment_in_saving_restart_files> 10 </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_shell> true </Set_mesh_as_shell> 
+
+  <Mesh_file_path> ./mesh/tri3/mesh-complete.mesh.vtu </Mesh_file_path>
+
+  <Add_face name="left">
+      <Face_file_path> ./mesh/tri3/mesh-surfaces/x0.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="right">
+      <Face_file_path> mesh/tri3/mesh-surfaces/x1.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="bottom">
+      <Face_file_path> mesh/tri3/mesh-surfaces/y0.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="top">
+      <Face_file_path> mesh/tri3/mesh-surfaces/y1.vtp </Face_file_path>
+  </Add_face>
+
+</Add_mesh>
+
+<Add_equation type="shell" > 
+   <Coupled> true </Coupled>
+   <!--Min_iterations> 1 </Min_iterations!-->  
+   <!--Max_iterations> 1 </Max_iterations!--> 
+   <Min_iterations> 3 </Min_iterations>  
+   <Max_iterations> 14 </Max_iterations> 
+   <Tolerance> 1e-11 </Tolerance> 
+
+   <Density> 0.0 </Density> 
+   <Mass_damping> 1.0 </Mass_damping> 
+   <Elasticity_modulus> 12.0 </Elasticity_modulus> 
+   <Poisson_ratio> 0.0 </Poisson_ratio> 
+   <Shell_thickness> 1.0 </Shell_thickness> 
+
+   <Output type="Spatial" >
+     <Displacement> true </Displacement>
+     <Velocity> true </Velocity>
+     <Stress> true </Stress>
+     <Strain> true </Strain>
+   </Output>
+
+   <LS type="GMRES" >
+      <Tolerance> 1e-12 </Tolerance>
+      <Max_iterations> 100 </Max_iterations> 
+      <Krylov_space_dimension> 50 </Krylov_space_dimension>
+   </LS>
+
+   <Add_BF mesh="msh" > 
+      <Type> Neu </Type> 
+      <Value> 0.04 </Value> 
+   </Add_BF> 
+
+   <Add_BC name="left" > 
+      <Type> Dir </Type> 
+      <CST_shell_bc_type> Fixed </CST_shell_bc_type> 
+      <Value> 0.0 </Value> 
+   </Add_BC> 
+
+   <Add_BC name="right" > 
+      <Type> Dir </Type> 
+      <CST_shell_bc_type> Fixed </CST_shell_bc_type> 
+      <Value> 0.0 </Value> 
+   </Add_BC> 
+
+   <Add_BC name="bottom" >
+      <Type> Dir </Type>
+      <CST_shell_bc_type> Fixed </CST_shell_bc_type>
+      <Value> 0.0 </Value>
+   </Add_BC>
+
+   <Add_BC name="top" >
+      <Type> Dir </Type>
+      <CST_shell_bc_type> Fixed </CST_shell_bc_type>
+      <Value> 0.0 </Value>
+   </Add_BC>
+
+</Add_equation>
+
+</svFSIFile>
+
+
diff --git a/tests/cases/shell/valve/leaflet_deform_20fps.avi b/tests/cases/shell/valve/leaflet_deform_20fps.avi
diff --git a/tests/cases/shell/valve/mesh/PAT003_07_LCC.vtu b/tests/cases/shell/valve/mesh/PAT003_07_LCC.vtu
diff --git a/tests/cases/shell/valve/mesh/PAT003_07_NCC.vtu b/tests/cases/shell/valve/mesh/PAT003_07_NCC.vtu
diff --git a/tests/cases/shell/valve/mesh/PAT003_07_RCC.vtu b/tests/cases/shell/valve/mesh/PAT003_07_RCC.vtu
diff --git a/tests/cases/shell/valve/mesh/mesh-surfaces/PAT003_07_LCC_edge1.vtp b/tests/cases/shell/valve/mesh/mesh-surfaces/PAT003_07_LCC_edge1.vtp
diff --git a/tests/cases/shell/valve/mesh/mesh-surfaces/PAT003_07_LCC_edge2.vtp b/tests/cases/shell/valve/mesh/mesh-surfaces/PAT003_07_LCC_edge2.vtp
diff --git a/tests/cases/shell/valve/mesh/mesh-surfaces/PAT003_07_NCC_edge1.vtp b/tests/cases/shell/valve/mesh/mesh-surfaces/PAT003_07_NCC_edge1.vtp
diff --git a/tests/cases/shell/valve/mesh/mesh-surfaces/PAT003_07_NCC_edge2.vtp b/tests/cases/shell/valve/mesh/mesh-surfaces/PAT003_07_NCC_edge2.vtp
diff --git a/tests/cases/shell/valve/mesh/mesh-surfaces/PAT003_07_RCC_edge1.vtp b/tests/cases/shell/valve/mesh/mesh-surfaces/PAT003_07_RCC_edge1.vtp
diff --git a/tests/cases/shell/valve/mesh/mesh-surfaces/PAT003_07_RCC_edge2.vtp b/tests/cases/shell/valve/mesh/mesh-surfaces/PAT003_07_RCC_edge2.vtp
diff --git a/tests/cases/shell/valve/pbc.dat b/tests/cases/shell/valve/pbc.dat
diff --git a/tests/cases/shell/valve/pbc_t.png b/tests/cases/shell/valve/pbc_t.png
diff --git a/tests/cases/shell/valve/result_001.vtu b/tests/cases/shell/valve/result_001.vtu
diff --git a/tests/cases/shell/valve/svFSI.xml b/tests/cases/shell/valve/svFSI.xml
@@ -0,0 +1,181 @@
+<?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> 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="LCC" > 
+
+  <Set_mesh_as_shell> true </Set_mesh_as_shell> 
+
+  <Mesh_file_path> mesh/PAT003_07_LCC.vtu </Mesh_file_path>
+
+  <Add_face name="LCC_fixed_edge">
+      <Face_file_path> mesh/mesh-surfaces/PAT003_07_LCC_edge1.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="LCC_free_edge">
+      <Face_file_path> mesh/mesh-surfaces/PAT003_07_LCC_edge2.vtp </Face_file_path>
+  </Add_face>
+
+  <Mesh_scale_factor> 10.0 </Mesh_scale_factor> 
+
+</Add_mesh>
+
+<!-- ============================================== -->
+
+<Add_mesh name="NCC"> 
+
+  <Set_mesh_as_shell> true </Set_mesh_as_shell>
+
+  <Mesh_file_path> mesh/PAT003_07_NCC.vtu </Mesh_file_path>
+
+  <Add_face name="NCC_fixed_edge">
+      <Face_file_path> mesh/mesh-surfaces/PAT003_07_NCC_edge1.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="NCC_free_edge">
+      <Face_file_path> mesh/mesh-surfaces/PAT003_07_NCC_edge2.vtp </Face_file_path>
+  </Add_face>
+
+  <Mesh_scale_factor> 10.0 </Mesh_scale_factor> 
+
+</Add_mesh>
+
+<!-- ============================================== -->
+
+<Add_mesh name="RCC" > 
+
+  <Set_mesh_as_shell> true </Set_mesh_as_shell>
+
+  <Mesh_file_path> mesh/PAT003_07_RCC.vtu </Mesh_file_path>
+
+  <Add_face name="RCC_fixed_edge">
+      <Face_file_path> mesh/mesh-surfaces/PAT003_07_RCC_edge1.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="RCC_free_edge">
+      <Face_file_path> mesh/mesh-surfaces/PAT003_07_RCC_edge2.vtp </Face_file_path>
+  </Add_face>
+
+  <Mesh_scale_factor> 10.0 </Mesh_scale_factor>
+
+</Add_mesh>
+
+
+<Contact model="penalty" > 
+   <Penalty_constant> 1.0e5 </Penalty_constant>
+   <Desired_separation> 0.05 </Desired_separation> 
+   <Closest_gap_to_activate_penalty> 1.0 </Closest_gap_to_activate_penalty> 
+   <Min_norm_of_face_normals> 0.7 </Min_norm_of_face_normals> 
+</Contact>
+
+
+<Add_equation type="shell" > 
+   <Coupled> true </Coupled>
+   <!--Min_iterations> 1 </Min_iterations-->  
+   <!--Max_iterations> 1 </Max_iterations--> 
+   <Min_iterations> 3 </Min_iterations>  
+   <Max_iterations> 66 </Max_iterations> 
+   <Tolerance> 1e-11 </Tolerance> 
+
+   <Density> 1e-3 </Density> 
+   <Mass_damping> 2.0 </Mass_damping> 
+   <Elasticity_modulus> 1.0e6 </Elasticity_modulus> 
+   <Poisson_ratio> 0.45 </Poisson_ratio> 
+   <Shell_thickness> 0.4 </Shell_thickness> 
+
+   <Output type="Spatial" >
+     <Displacement> true </Displacement>
+     <Velocity> true </Velocity>
+     <Stress> true </Stress>
+     <Strain> true </Strain>
+   </Output>
+
+   <LS type="GMRES" >
+      <Tolerance> 1e-12 </Tolerance>
+      <Max_iterations> 100 </Max_iterations> 
+      <Krylov_space_dimension> 50 </Krylov_space_dimension>
+   </LS>
+
+   <!-- Apply trans-valvular pressure gradient -->
+
+   <Add_BF mesh="LCC" > 
+      <Type> Neu </Type> 
+      <Time_dependence> Unsteady </Time_dependence> 
+      <Temporal_values_file_path> pbc.dat </Temporal_values_file_path>
+   </Add_BF> 
+
+   <Add_BF mesh="NCC" > 
+      <Type> Neu </Type> 
+      <Time_dependence> Unsteady </Time_dependence> 
+      <Temporal_values_file_path> pbc.dat </Temporal_values_file_path>
+   </Add_BF> 
+
+   <Add_BF mesh="RCC" > 
+      <Type> Neu </Type> 
+      <Time_dependence> Unsteady </Time_dependence> 
+      <Temporal_values_file_path> pbc.dat </Temporal_values_file_path>
+   </Add_BF> 
+
+   <!--  Apply leaflet boundary conditions -->
+
+   <Add_BC name="LCC_fixed_edge" > 
+      <Type> Dir </Type> 
+      <Value> 0.0 </Value> 
+      <CST_shell_bc_type> Fixed </CST_shell_bc_type> 
+   </Add_BC> 
+
+   <Add_BC name="NCC_fixed_edge" >
+      <Type> Dir </Type>
+      <Value> 0.0 </Value>
+      <CST_shell_bc_type> Fixed </CST_shell_bc_type>
+   </Add_BC>
+
+   <Add_BC name="RCC_fixed_edge" >
+      <Type> Dir </Type>
+      <Value> 0.0 </Value>
+      <CST_shell_bc_type> Fixed </CST_shell_bc_type>
+   </Add_BC>
+
+   <Add_BC name="LCC_free_edge" >
+      <Type> Neu </Type>
+      <Value> 0.0 </Value>
+      <CST_shell_bc_type> Free </CST_shell_bc_type>
+   </Add_BC>
+
+   <Add_BC name="NCC_free_edge" >
+      <Type> Neu </Type>
+      <Value> 0.0 </Value>
+      <CST_shell_bc_type> Free </CST_shell_bc_type>
+   </Add_BC>
+
+   <Add_BC name="RCC_free_edge" >
+      <Type> Neu </Type>
+      <Value> 0.0 </Value>
+      <CST_shell_bc_type> Free </CST_shell_bc_type>
+   </Add_BC>
+
+</Add_equation>
+
+</svFSIFile>
+
+