Added 3d pipe flow; test, mesh, write-up (#579)

reg_tests/CTestList.cmake

@@ -181,4 +181,5 @@ if(ENABLE_LABORATORY_TESTS)
   add_test_l(2d_quad4_channel 2)
   add_test_l(2d_quad9_couette 4)
   add_test_l(3d_hex8_open_jet 8)
+  add_test_l(3d_tet4_pipe 8)
 endif(ENABLE_LABORATORY_TESTS)

reg_tests/test_files/laboratory/2d_quad4_channel/write_up/2d_quad4_channel_laboratory.tex

@@ -53,7 +53,7 @@ \section{Theory}
 \end{align}
 %
 In the above equation, $\rho$ is the fluid density and $u_j$ is the fluid velocity. 
-The Cauchy stress is provided by
+The stress tensor is provided by
 \begin{align}
 \sigma_{ij}  = 2 \mu S^*_{ij} - P \delta_{ij},
 \end{align}
@@ -99,7 +99,7 @@ \subsection{Analytical Velocity Profile}
 
 \section{Results}
 Let us test a simulation in which the Reynolds number based on wall friction
-velocity, $u^\tau$, and half-channel height $H/2$, is ten: $Re^\tau = 10$.
+velocity, $u^\tau$, and half-channel height $H/2$, is ten: $Re^\tau$ = 10.
 By constraining the Reynolds number, wall friction velocity, and density, 
 the consistent viscosity is obtained via,
 
@@ -160,7 +160,7 @@ \section{Discussion Points}
           does this finding hold? Why is this?
         \item Probe all degree-of-freedom results, i.e., velocity and pressure. What is of interest?
         \item When the simulation is run and wall shear stress is provided in the output file,
-          what is the value? What are the findings?
+          what is the value? What are your findings?
 \end{itemize}
 
 \end{document}

reg_tests/test_files/laboratory/2d_quad4_channel/write_up/Makefile

@@ -1,6 +1,8 @@
 
 all:
 	pdflatex 2d_quad4_channel_laboratory 
+	pdflatex 2d_quad4_channel_laboratory 
+	pdflatex 2d_quad4_channel_laboratory 
 
 clean:
 	-rm -f *.aux *.log *.dvi *.bbl *.blg *~

reg_tests/test_files/laboratory/2d_quad9_couette/write_up/2d_quad9_couette_laboratory.tex

@@ -53,7 +53,7 @@ \section{Theory}
 \end{align}
 %
 In the above equation, $\rho$ is the fluid density and $u_j$ is the fluid velocity. 
-The Cauchy stress is provided by
+The stress tensor is provided by
 \begin{align}
 \sigma_{ij}  = 2 \mu S^*_{ij} - P \delta_{ij},
 \end{align}
@@ -95,8 +95,8 @@ \section{Results}
 
 
 Let us test a simulation in which a the Reynolds number based on height of the domain,
-assuming the properties of water ($\rho = 1000 kg/m^3$ and $\mu = 8.9e-4 Pa-s$)
-at a bulk top velocity of $u_b = 1e-3 m/s$, is approximately 1236.
+assuming the properties of water ($\rho = $1000 $kg/m^3$ and $\mu = $8.9e-4 $Pa-s$)
+at a bulk top velocity of $u_b = $1e-3 $m/s$, is approximately 1236.
 
 \begin{align}
   Re = \frac{\rho u^b H}{\mu}.

reg_tests/test_files/laboratory/2d_quad9_couette/write_up/Makefile

@@ -1,6 +1,8 @@
 
 all:
 	pdflatex 2d_quad9_couette_laboratory 
+	pdflatex 2d_quad9_couette_laboratory 
+	pdflatex 2d_quad9_couette_laboratory 
 
 clean:
 	-rm -f *.aux *.log *.dvi *.bbl *.blg *~

reg_tests/test_files/laboratory/3d_hex8_open_jet/write_up/3d_hex8_open_jet_laboratory.tex

@@ -23,7 +23,7 @@ \section{Theory}
 The three-dimensional geometry for this tutorial is captured in 
 Figure~\ref{fig:geom}. Here, the cylindrical domain is defined by the 
 vertical height, $H$, the outer diameter, $D_o$, and inlet pipe diameter $d_o$ and 
-specified to be 50 cm, 15 cm, and 0.01 cm, respectively. 
+specified to be 50 cm, 15 cm, and 1.0 cm, respectively. 
 
 The bottom plane contains an inflow and bottom wall while the side and top are represented
 as an open boundary condition where static pressure is specified.
@@ -52,7 +52,7 @@ \section{Theory}
 \end{align}
 %
 In the above equation, $\rho$ is the fluid density and $u_j$ is the fluid velocity. 
-The Cauchy stress is provided by
+The stress tensor is provided by
 \begin{align}
 \sigma_{ij}  = 2 \mu S^*_{ij} - P \delta_{ij},
 \end{align}
@@ -93,7 +93,9 @@ \section{Results}
   u_{inlet} = \frac{\mu Re}{\rho d_o}.
 \label{eq:muForm}
 \end{align}
-
+%
+Values for density, viscosity, and inflow velocity are 1.0e-3 $g/cm^3$, 2.0e-4 $dyne-s/cm^3$, 
+20 $cm/s$, respectively.
 \subsection{Simulation Specification and Results}
 
 For the $Re = 100$ configuration, the simulation is run using a Hex8 (linear hexahedral)
@@ -104,31 +106,31 @@ \subsection{Simulation Specification and Results}
  \subfloat[]
   \centering
   {
-   \includegraphics[height=2.0in]{images/3d_hex8_open_jet_mix_frac.png}
+   \includegraphics[height=3.0in]{images/3d_hex8_open_jet_mix_frac.png}
   }
   \subfloat[]
   \centering
   {
-   \includegraphics[height=2.0in]{images/3d_hex8_open_jet_umag.png}
+   \includegraphics[height=3.0in]{images/3d_hex8_open_jet_umag.png}
   }
   \caption{Planar mixture fraction (a) and velocity magnitude (b) shadings for the $Re = 100$ jet case.}
   \label{fig:results}
 \end{figure}
 
 In Figure~\ref{fig:centerline}, the centerline normalized mixture fraction and vertical velocity
 are presented.
-
+%
 \begin{figure}[!htbp]
   \centering
   {
    \includegraphics[height=2.0in]{images/CenterlineData-crop.pdf}
   }
   \caption{Normalized velocity and normalized-mixture fraction centerline plot for the $Re = 100$ jet case.}
-  \label{fig:results}
+  \label{fig:centerline}
 \end{figure}
-
+%
 Finally, to illustrate the self-similar radial profiles for the downstream locations ($\frac{z}{d_o}$ of 5, 10,
-and 20), see Figure~\cite{fig:simular}. For this procedure, the maximum velocity that occurs on the centerline
+and 20), see Figure~\ref{fig:similar}. For this procedure, the maximum velocity that occurs on the centerline
 is captured at each downstream location. The radial half length, $r_h$, is defined as the radial position where the
 velocity is one-half the peak value on the centerline. The self-similar jet profile is strongly correlated past 
 $\frac{z}{d_o}$ of five - well beyond the core collapse of the jet.
@@ -140,7 +142,7 @@ \subsection{Simulation Specification and Results}
   }
   \caption{Normalized vertical velocity as a function of normalized radial distance (by radial half distance, 
 $r_h$) for the $Re = 100$ jet case.}
-  \label{fig:results}
+  \label{fig:similar}
 \end{figure}
 
 \section{Discussion Points}

reg_tests/test_files/laboratory/3d_hex8_open_jet/write_up/Makefile

@@ -1,6 +1,8 @@
 
 all:
 	pdflatex 3d_hex8_open_jet_laboratory 
+	pdflatex 3d_hex8_open_jet_laboratory 
+	pdflatex 3d_hex8_open_jet_laboratory 
 
 clean:
 	-rm -f *.aux *.log *.dvi *.bbl *.blg *~

reg_tests/test_files/laboratory/3d_tet4_pipe/3d_tet4_pipe.i

@@ -0,0 +1,143 @@
+Simulations:
+  - name: sim1
+
+linear_solvers:
+
+  - name: solve_scalar
+    type: tpetra
+    method: gmres
+    preconditioner: sgs
+    tolerance: 1e-5
+    max_iterations: 50
+    kspace: 50
+    output_level: 0
+
+  - name: solve_cont
+    type: tpetra
+    method: gmres 
+    preconditioner: muelu
+    tolerance: 1e-5
+    max_iterations: 100
+    kspace: 100
+    output_level: 0
+    recompute_preconditioner: no
+    muelu_xml_file_name: ../../../xml/milestone.xml
+
+realms:
+
+  - name: fluidRealm
+    mesh: mesh/3d_tet4_pipe.exo 
+    use_edges: no
+    automatic_decomposition_type: rcb
+
+    time_step_control:
+     target_courant: 2.0
+     time_step_change_factor: 1.2
+
+    equation_systems:
+      name: theEqSys
+      max_iterations: 1
+   
+      solver_system_specification:
+        velocity: solve_scalar
+        pressure: solve_cont
+
+      systems:
+
+        - LowMachEOM:
+            name: myLowMach
+            max_iterations: 1
+            convergence_tolerance: 1e-8
+
+    initial_conditions:
+
+      - constant: ic_1
+        target_name: block_1
+        value:
+          pressure: 0.0
+          velocity: [0.0,0.0,0.0]
+       
+    material_properties:
+
+      target_name: block_1
+
+      specifications:
+ 
+        - name: density
+          type: constant
+          value: 1.0
+
+        - name: viscosity
+          type: constant
+          value: 1.0e-3
+
+    boundary_conditions:
+
+    - open_boundary_condition: bc_left
+      target_name: surface_2
+      open_user_data:
+        pressure: 40.0
+        velocity: [0.0,0.0,0.0]
+
+    - open_boundary_condition: bc_right
+      target_name: surface_1
+      open_user_data:
+        pressure: 0.0
+        velocity: [0.0,0.0,0.0]
+
+    - wall_boundary_condition: bc_wall
+      target_name: surface_3
+      wall_user_data:
+        velocity: [0.0,0.0,0.0]
+
+    solution_options:
+      name: myOptions
+      turbulence_model: laminar
+  
+
+      use_consolidated_solver_algorithm: yes
+      use_consolidated_face_elem_bc_algorithm: yes
+
+      options:
+      
+        - element_source_terms:
+            momentum: [lumped_momentum_time_derivative, advection_diffusion]
+            continuity: advection
+
+        - projected_nodal_gradient:
+            pressure: element
+            velocity: element
+
+    post_processing:
+    
+    - type: surface
+      physics: surface_force_and_moment
+      output_file_name: 3d_tet4_pipe.dat
+      frequency: 1
+      parameters: [0.0,0.0,0.0]
+      target_name: [surface_3]
+
+    output:
+      output_data_base_name: output/3d_tet4_pipe.e
+      output_frequency: 10
+      output_node_set: no 
+      output_variables:
+       - velocity
+       - pressure
+       - dpdx
+       - viscosity
+       - density
+       - tau_wall
+
+Time_Integrators:
+  - StandardTimeIntegrator:
+      name: ti_1
+      start_time: 0
+      termination_step_count: 20
+      time_step: 0.0001
+      time_stepping_type: adaptive
+      time_step_count: 0
+      second_order_accuracy: no
+
+      realms:
+        - fluidRealm

reg_tests/test_files/laboratory/3d_tet4_pipe/3d_tet4_pipe.norm.gold

@@ -0,0 +1,20 @@
+0.007073272807121407 1 0.00012
+0.0008570044281100752 2 0.000264
+0.0002776054675452662 3 0.0004368
+0.0001436606782954027 4 0.00064416
+7.805589617375884e-05 5 0.000892992
+3.859668091837489e-05 6 0.00119159
+2.134345852413653e-05 7 0.00154991
+1.3361438657162e-05 8 0.00197989
+8.438163091291819e-06 9 0.00249587
+5.269030565843482e-06 10 0.00311504
+3.395504180506686e-06 11 0.00385805
+2.459417221016597e-06 12 0.00474966
+2.140824817798169e-06 13 0.00581959
+2.108411955455556e-06 14 0.00710351
+2.124969201267307e-06 15 0.00864421
+2.004313167995332e-06 16 0.0100067
+1.800562092311465e-06 17 0.0112068
+1.504720490455237e-06 18 0.0122982
+1.235142042677227e-06 19 0.0133104
+1.015023029557289e-06 20 0.0142615