adding test case for precomputed velocity solutions to the heatf equa…

…tion, removing commented lines for testing in heatf.cpp, fixing spelling mistakes in ComMod.h (SimVascular#202)

Code/Source/svFSI/ComMod.h

@@ -1453,7 +1453,7 @@ class ComMod {
     /// @brief Time step size
     double dt = 0.0;
 
-    /// @breif Time step size of the precomputed state-variables
+    /// @brief Time step size of the precomputed state-variables
     double precompDt = 0.0;
 
     /// @brief Time
@@ -1477,7 +1477,7 @@ class ComMod {
     /// @brief Precomputed state-variable file name
     std::string precompFileName;
 
-    /// @breif Precomputed state-variable field name
+    /// @brief Precomputed state-variable field name
     std::string precompFieldName;
     // ALLOCATABLE DATA
 

Code/Source/svFSI/heatf.cpp

@@ -323,9 +323,7 @@ void heatf_3d(ComMod& com_mod, const int eNoN, const double w, const Vector<doub
       u(2) = u(2) - N(a)*yl(6,a);
     }
   }
-  //if (u(2) > 0.0) {
-  //    std::cout << "u: " << u(0) << " " << u(1) << " " << u(2) << std::endl;
-  //}
+
   double kU = u(0)*u(0)*ksix(0,0) + u(1)*u(0)*ksix(1,0) + u(2)*u(0)*ksix(2,0) + u(0)*u(1)*ksix(0,1) + 
               u(1)*u(1)*ksix(1,1) + u(2)*u(1)*ksix(2,1) + u(0)*u(2)*ksix(0,2) + u(1)*u(2)*ksix(1,2) + 
               u(2)*u(2)*ksix(2,2);

tests/cases/fluid/precomputed_dye_AD/README.md

@@ -0,0 +1,40 @@
+
+# **Problem Description**
+
+Solve dye transportation with fluid flow in a cylindrical tube with zero neumann boundary condition at the outlet and steady flow at the inlet. The dye is passively transported by the flow through advection and diffusion.
+
+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:
+
+## Scalar transport equation
+Unlike the test case in `04-fluid/02-dye_AD`, the advection-diffusion equation that governs the dye transportation is added to the input file without a proceeding fluid equation. 
+Here we assume that we already have a velocity field that has been precomputed by some prior physics simulation (denoted `precomputed_velocity.vtu`). The specified velocity field solution
+is then taken to advect a scalar field. 
+This equation is built on top of the heat transfer equation, so some of the terminology in the input file follows those in the heat equation, e.g. "Conductivity", "Temperature".
+
+Some noticeable setting in the input file are:
+
+```
+   <Use_precomputed_solution> true </Use_precomputed_solution>
+   <Precomputed_solution_file_path> precomputed_velocity.vtu </Precomputed_solution_file_path>
+   <Precomputed_solution_field_name> Velocity </Precomputed_solution_field_name>
+```
+
+This tell the solver that this is a one-way coupling study, and the dye is passively transported by the flow.
+
+```
+   <Output type="Alias" >
+     <Temperature> Concentration </Temperature>
+   </Output>
+```
+
+This renames  "Temperature" to "Concentration" for ease of interpretation.
+
+```
+   <Add_BC name="lumen_inlet" >
+      <Type> Dirichlet </Type>
+      <Time_dependence> Steady </Time_dependence>
+      <Value> 1.0 </Value>
+   </Add_BC>
+```
+
+The dye is constantly released at the inlet.

tests/cases/fluid/precomputed_dye_AD/svFSI.xml

@@ -0,0 +1,87 @@
+<?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> 0.01 </Time_step_size> 
+  <Use_precomputed_solution> true </Use_precomputed_solution>
+  <Precomputed_solution_file_path> precomputed_velocity.vtu </Precomputed_solution_file_path>
+  <Precomputed_solution_field_name> Velocity </Precomputed_solution_field_name>
+  <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> 0 </Start_saving_after_time_step> 
+
+  <Increment_in_saving_restart_files> 5 </Increment_in_saving_restart_files> 
+  <Convert_BIN_to_VTK_format> 0 </Convert_BIN_to_VTK_format> 
+
+  <Verbose> 1 </Verbose> 
+  <Warning> 0 </Warning> 
+  <Debug> 1 </Debug> 
+</GeneralSimulationParameters>
+
+<Add_mesh name="msh" > 
+
+  <Mesh_file_path> mesh/mesh-complete.mesh.vtu </Mesh_file_path>
+
+  <Add_face name="lumen_inlet">
+      <Face_file_path> mesh/mesh-surfaces/lumen_inlet.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="lumen_outlet">
+      <Face_file_path> mesh/mesh-surfaces/lumen_outlet.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="lumen_wall">
+      <Face_file_path> mesh/mesh-surfaces/lumen_wall.vtp </Face_file_path>
+  </Add_face>
+
+</Add_mesh>
+
+
+<Add_equation type="scalarTransport" >
+   <Coupled> false </Coupled>
+   <Min_iterations> 2 </Min_iterations>
+   <Max_iterations> 5 </Max_iterations>
+   <Tolerance> 1e-6 </Tolerance>
+
+   <Conductivity> 1e-8 </Conductivity>
+   <Source_term> 0.0  </Source_term>
+
+   <Output type="Spatial">
+     <Velocity> true </Velocity>
+     <Temperature> true </Temperature>
+   </Output>
+
+   <Output type="Volume_integral" >
+     <Temperature> true </Temperature>
+   </Output>
+
+   <Output type="Alias" >
+     <Temperature> Concentration </Temperature>
+   </Output>
+
+   <LS type="GMRES" >
+      <Preconditioner> FSILS </Preconditioner> 
+      <Tolerance> 1e-6 </Tolerance>
+      <Max_iterations> 100 </Max_iterations>
+      <Krylov_space_dimension> 50 </Krylov_space_dimension>
+   </LS>
+
+   <Add_BC name="lumen_inlet" >
+      <Type> Dirichlet </Type>
+      <Time_dependence> Steady </Time_dependence>
+      <Value> 1.0 </Value>
+   </Add_BC>
+
+</Add_equation>
+
+
+</svFSIFile>
+
+

tests/conftest.py

@@ -13,6 +13,7 @@
 RTOL = {
     "Action_potential": 1.0e-10,
     "Cauchy_stress": 1.0e-4,
+    "Concentration": 1.0e-10,
     "Def_grad": 1.0e-10,
     "Divergence": 1.0e-9,
     "Displacement": 1.0e-10,

tests/test_fluid.py

@@ -23,6 +23,9 @@ def test_dye_AD(n_proc):
     test_folder = "dye_AD"
     run_with_reference(base_folder, test_folder, fields, n_proc)
 
+def test_precomputed_dye_AD(n_proc):
+    test_folder = "precomputed_dye_AD"
+    run_with_reference(base_folder, test_folder, ['Velocity', 'Concentration'], n_proc)
 
 def test_newtonian(n_proc):
     test_folder = "newtonian"