Adding test cases for reading of fourier coefficient file

Code/Source/solver/read_files.cpp

@@ -1935,10 +1935,9 @@ void read_fourier_coeff_values_file(const std::string& file_name, bcType& lBc)
       values.push_back(value);
     }
 
-    int num_vals = values.size();
-    for (int i = 0; i < values.size(); i++) {
-      lBc.gt.r(i,j) = values[i]; 
-      lBc.gt.i(i,j) = values[i+num_vals];
+    for (int i = 0; i < lBc.gt.d; i++) { 
+      lBc.gt.r(i,j) = values[i];
+      lBc.gt.i(i,j) = values[i + lBc.gt.d];
     }
 
     j += 1;
@@ -2004,10 +2003,9 @@ void read_fourier_coeff_values_file(const std::string& file_name, bfType& lBf)
       values.push_back(value);
     }
 
-    int num_vals = values.size();
-    for (int i = 0; i < values.size(); i++) {
-      lBf.bt.r(i,j) = values[i]; 
-      lBf.bt.i(i,j) = values[i+num_vals];
+    for (int i = 0; i < lBf.bt.d; i++) { 
+      lBf.bt.r(i,j) = values[i];
+      lBf.bt.i(i,j) = values[i + lBf.bt.d];
     }
 
     j += 1;

tests/cases/fluid/pipe_RCR_3d_fourier_coeff/README.md

@@ -0,0 +1,19 @@
+
+# **Problem Description**
+
+Simulate unsteady fluid flow in a pipe. This case is identical to <a href="https://github.com/SimVascular/svFSIplus/tree/main/tests/cases/fluid/pipe_RCR_3d"> Fluid RCR 3D Pipe </a>, except that fourier coefficients are read by the solver (instead of the usual temporal values file). For additional validation, the **results_002.vtu** output file used in this case is the same as the `pipe_RCR_3d` case. 
+
+# Inlet flow boundary condition
+
+Interpolated Fourier coefficients are provided for the **lumen_inlet** boundary condition. These coefficients are specified in the **lumen_inlet.fcs** file, which is an alternative to the flow data that is provided in the **lumen_inlet.flow**. Providing the fourier coefficient file skips the fourier interpolation function (**fft.cpp**) in svMultiphysics. Documentation on the file format can be accessed [here](https://simvascular.github.io/documentation/multi_physics.html#data_file_formats_boundary_condition_fourier) and the `lumen_inlet` boundary condition block is provided in the [solver.xml](./solver.xml). 
+
+The **lumen_inlet.fcs** file can be generated using the **fft_temporal_values.py** which is available in the `utilities` directory ([here](../../../../utilities/fourier_coefficients/)). This script takes the lumen_inlet.flow file, computes the Fourier coefficients using an identical fft python function, and returns the **.fcs** file ready for simulation. It also provides a visualization of the fourier interpolation, which is shown below:
+
+<p align="center">
+   <img src="./fft_reconstruction.png" width="600">
+</p>
+
+
+# Outlet RCR boundary condition
+
+An RCR boundary condition is defined for the **lumen_outlet** outlet face.

tests/cases/fluid/pipe_RCR_3d_fourier_coeff/lumen_inlet.fcs

@@ -0,0 +1,19 @@
+0.0 1.0
+0.0 0.0
+16
+-6.2831852968750006e+01    0.0000000000000000e+00
+6.2630248089319764e+01    -1.8689837176965406e-07
+-1.8510278462895881e-07    1.2598780427743684e-15
+-3.2931465665672273e-07    1.8214078224321383e-07
+2.9676287399904954e-07    -2.2497822192399436e-16
+-7.1346109986563247e-07    -1.7291577648812070e-07
+-1.6679265373961399e-07    4.9995160427554296e-16
+-1.9207332282283037e-06    1.5978005149412804e-07
+5.0660591524529525e-08    -2.5872495521259351e-16
+9.3646292551129305e-07    -1.4351166349130110e-07
+-1.3449131704204189e-07    3.5996515507839091e-18
+-9.4105400926950758e-07    1.2504770956829968e-07
+1.9218453262995655e-07    8.7491530748220019e-18
+9.5400603135350799e-07    -1.0541065198628774e-07
+-9.5475796377833937e-08    -1.1065255404833191e-16
+1.0167834071836435e-06    8.5630083711416610e-08

tests/cases/fluid/pipe_RCR_3d_fourier_coeff/lumen_inlet.flow

@@ -0,0 +1,34 @@
+33    16
+0.000000    0.000000
+0.031250    -1.207301
+0.062500    -4.782786
+0.093750    -10.589077
+0.125000    -18.403023
+0.156250    -27.924348
+0.187500    -38.787146
+0.218750    -50.573962
+0.250000    -62.83185
+0.281250    -75.089744
+0.312500    -86.876560
+0.343750    -97.739358
+0.375000    -107.260684
+0.406250    -115.074629
+0.437500    -120.880920
+0.468750    -124.456405
+0.500000    -125.663706
+0.531250    -124.456405
+0.562500    -120.880920
+0.593750    -115.074629
+0.625000    -107.260684
+0.656250    -97.739358
+0.687500    -86.876560
+0.718750    -75.089744
+0.750000    -62.831853
+0.781250    -50.573962
+0.812500    -38.787146
+0.843750    -27.924348
+0.875000    -18.403023
+0.906250    -10.589077
+0.937500    -4.782786
+0.968750    -1.207301
+1.000000    0.000000

tests/cases/fluid/pipe_RCR_3d_fourier_coeff/solver.xml

@@ -0,0 +1,119 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<svMultiPhysicsFile version="0.1">
+
+<GeneralSimulationParameters>
+
+  <Continue_previous_simulation> false </Continue_previous_simulation>
+  <Number_of_spatial_dimensions> 3 </Number_of_spatial_dimensions> 
+  <Number_of_time_steps> 2 </Number_of_time_steps> 
+  <Time_step_size> 0.005 </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> 2 </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="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="fluid" > 
+   <Coupled> true </Coupled>
+   <Min_iterations> 3 </Min_iterations>  
+   <Max_iterations> 5</Max_iterations> 
+   <Tolerance> 1e-11 </Tolerance> 
+   <Backflow_stabilization_coefficient> 0.2 </Backflow_stabilization_coefficient> 
+
+   <Density> 1.06 </Density> 
+   <Viscosity model="Constant" >
+     <Value> 0.04 </Value>
+   </Viscosity>
+
+   <Output type="Spatial" >
+      <Velocity> true </Velocity>
+      <Pressure> true </Pressure>
+      <Traction> true </Traction>
+      <Vorticity> true</Vorticity>
+      <Divergence> true</Divergence>
+      <WSS> true </WSS>
+   </Output>
+
+   <Output type="B_INT" >
+     <Pressure> true </Pressure>
+     <Velocity> true </Velocity>
+   </Output>
+
+   <Output type="V_INT" >
+     <Pressure> true </Pressure>
+   </Output>
+
+   <LS type="NS" >
+      <Linear_algebra type="fsils" >
+         <Preconditioner> fsils </Preconditioner>
+      </Linear_algebra>
+      <Max_iterations> 15 </Max_iterations>
+      <NS_GM_max_iterations> 10 </NS_GM_max_iterations>
+      <NS_CG_max_iterations> 300 </NS_CG_max_iterations>
+      <Tolerance> 1e-3 </Tolerance>
+      <NS_GM_tolerance> 1e-3 </NS_GM_tolerance>
+      <NS_CG_tolerance> 1e-3 </NS_CG_tolerance>
+      <Absolute_tolerance> 1e-17 </Absolute_tolerance>
+      <Krylov_space_dimension> 250 </Krylov_space_dimension>
+   </LS>
+
+   <Add_BC name="lumen_inlet" > 
+      <Type> Dir </Type> 
+      <Time_dependence> Unsteady </Time_dependence> 
+      <Fourier_coefficients_file_path> lumen_inlet.fcs </Fourier_coefficients_file_path> 
+      <Profile> Parabolic </Profile> 
+      <Impose_flux> true </Impose_flux> 
+   </Add_BC> 
+
+   <Add_BC name="lumen_outlet" > 
+      <Type> Neu </Type> 
+      <Time_dependence> RCR </Time_dependence> 
+      <RCR_values> 
+        <Capacitance> 1.5e-5 </Capacitance> 
+        <Distal_resistance> 1212 </Distal_resistance> 
+        <Proximal_resistance> 121 </Proximal_resistance> 
+        <Distal_pressure> 0 </Distal_pressure> 
+        <Initial_pressure> 0 </Initial_pressure> 
+      </RCR_values> 
+   </Add_BC> 
+
+   <Add_BC name="lumen_wall" > 
+      <Type> Dir </Type> 
+      <Time_dependence> Steady </Time_dependence> 
+      <Value> 0.0 </Value> 
+   </Add_BC> 
+
+</Add_equation>
+
+</svMultiPhysicsFile>
+
+

tests/test_fluid.py

@@ -14,6 +14,11 @@ def test_pipe_RCR_3d(n_proc):
     t_max = 2
     run_with_reference(base_folder, test_folder, fields, n_proc, t_max)
 
+def test_pipe_RCR_3d_fourier_coeff(n_proc):
+    test_folder = "pipe_RCR_3d_fourier_coeff"
+    t_max = 2
+    run_with_reference(base_folder, test_folder, fields, n_proc, t_max)
+
 def test_pipe_RCR_3d_petsc(n_proc):
     test_folder = "pipe_RCR_3d_petsc"
     t_max = 2