[cig-commits] r5578 - in long/3D/Gale/trunk: . documentation

walter at geodynamics.org walter at geodynamics.org
Sun Dec 10 02:29:27 PST 2006 

Author: walter
Date: 2006-12-10 02:29:26 -0800 (Sun, 10 Dec 2006)
New Revision: 5578

Modified:
   long/3D/Gale/trunk/
   long/3D/Gale/trunk/documentation/gale.lyx
Log:
 r1211 at earth:  boo | 2005-05-05 02:43:28 -0700
 updates to manual



Property changes on: long/3D/Gale/trunk
___________________________________________________________________
Name: svk:merge
   - 3a629746-de10-0410-b17b-fd6ecaaa963e:/cig:1210
   + 3a629746-de10-0410-b17b-fd6ecaaa963e:/cig:1211

Modified: long/3D/Gale/trunk/documentation/gale.lyx
===================================================================
--- long/3D/Gale/trunk/documentation/gale.lyx	2006-12-10 10:29:23 UTC (rev 5577)
+++ long/3D/Gale/trunk/documentation/gale.lyx	2006-12-10 10:29:26 UTC (rev 5578)
@@ -862,10 +862,6 @@
 Gale Usage
 \end_layout
 
-\begin_layout Subsection
-Usage
-\end_layout
-
 \begin_layout Standard
 If you downloaded binaries for your platform, you can run the Gale executable
  directly.
@@ -894,7 +890,8 @@
 output.extension
 \family default
  directory.
- There are also rough examples of shortening and subduction.
+ There are also examples of shortening, subduction, relaxation of a sinusoid,
+ and a fountain.
 \end_layout
 
 \begin_layout Standard
@@ -910,7 +907,7 @@
 \end_layout
 
 \begin_layout Section
-Output Format
+Output
 \end_layout
 
 \begin_layout Standard
@@ -940,166 +937,97 @@
 
 \begin_layout Standard
 Also found in the output directory are a number of .dat and .txt files.
- Most of the .dat files are ASCII and self-explanatory, e.g., 
-\family typewriter
-PressureField.dat
-\family default
- contains pressure field output information.
- Inside each .dat file are found several columns of data:
-\end_layout
+ See Appendix 
+\begin_inset LatexCommand \ref{cha:Output-File-Format}
 
-\begin_layout LyX-Code
+\end_inset
 
-\family typewriter
-0 0.0312539624080715 0.0109361134145122 0 -9.81467103200287
+ for more information.
 \end_layout
 
 \begin_layout LyX-Code
 
-\family typewriter
-1 0.0937630718938361 0.0109356986189374 0 17.7373201951569
 \end_layout
 
-\begin_layout LyX-Code
-
-\family typewriter
-2 0.156270066350344 0.0109368543031399 0 -37.0281780188199
+\begin_layout Section
+Postprocessing
 \end_layout
 
-\begin_layout LyX-Code
-
+\begin_layout Standard
+Included in the 
 \family typewriter
-3 0.218780947570009 0.0109343376815161 0 45.6263762140766
-\end_layout
+tools/
+\family default
+ directory is a short C++ program, 
+\family typewriter
+viz.cxx
+\family default
+, that will convert the yielding.*.txt files into vtk files.
+ These vtk files can be directly visualized in 
+\begin_inset LatexCommand \htmlurl[MayaVi]{mayavi.sourceforge.net}
 
-\begin_layout LyX-Code
+\end_inset
 
-\family typewriter
-4 0.28128858838265 0.010937987088561 0 -65.2132484518426 
-\end_layout
+ or 
+\begin_inset LatexCommand \htmlurl[ParaView]{www.paraview.org}
 
-\begin_layout Standard
-The first column (0,1,2,3, ...) is the node number, and the second, third,
- and fourth columns are the x, y, and z coordinates.
- The last column(s) show the value.
- Note: If performing a 2D run, you will still obtain the z data, but that
- can be ignored.
-\end_layout
+\end_inset
 
-\begin_layout Standard
-The .txt files are the output of 
-\family typewriter
-DumpSwarm
-\family default
-, explained below.
+.
 \end_layout
 
 \begin_layout Section
-Using 
-\family typewriter
-DumpSwarm
-\family default
- for Particle Information
+Gauging Accuracy
 \end_layout
 
 \begin_layout Standard
-All of the particle information is output in the 
+Gale makes a number of approximations when simulating.
+ Before trusting any results we get from Gale, we need to vary a number
+ of parameters to insure that the results are not an artifact of Gale's
+ approximations.
+ Specifically, for every simulation, we need to vary the resolution (
 \family typewriter
-materialSwarm.*.dat
+elementResI
 \family default
- files.
- Unfortunately, they are just a binary dump of the particle structures,
- so their format may vary depending on the machine architecture.
- To get the particle information in a more friendly format, we provide a
- plug-in called 
+, 
 \family typewriter
-DumpSwarm
+elementResJ
 \family default
-.
- The 
+, 
 \family typewriter
-DumpSwarm
+elementResK
 \family default
- plugin is activated by adding the line
-\end_layout
-
-\begin_layout LyX-Code
-    <param>Underworld_DumpSwarm</param> 
-\end_layout
-
-\begin_layout Standard
-to the list of plugins.
- This line is already in the example input files.
- At present, it outputs the files 
+) and the number of particles in each element (
 \family typewriter
-yielding.*.txt
+particlesPerCell
 \family default
-.
- The format of the file is
-\end_layout
-
-\begin_layout LyX-Code
-m x y z
+).
+ In addition, depending on the boundary conditions, we may need to vary
+ the size of the box (
 \family typewriter
- yielded
-\end_layout
-
-\begin_layout Standard
-where 
-\family typewriter
-m
+minX
 \family default
- is the number of the material (in the examples, always 1), and 
+, 
 \family typewriter
-yielded
+minY
 \family default
- is a number between 
+, 
 \family typewriter
-0
+minZ
 \family default
- and 
+, 
 \family typewriter
-1
+maxX
 \family default
- indicating how much a material point has failed.
- If you want to print out some other property of the material, e.g., viscosity,
- you can modify 
+, 
 \family typewriter
-DumpSwarm
+maxY
 \family default
- to provide that information.
- The source for the plugin is found in the directory
-\end_layout
-
-\begin_layout LyX-Code
-src/Underworld/plugins/Output/DumpSwarm/
-\end_layout
-
-\begin_layout Section
-Postprocessing
-\end_layout
-
-\begin_layout Standard
-Included in the 
+, 
 \family typewriter
-tools/
+maxZ
 \family default
- directory is a short C++ program, 
-\family typewriter
-viz.cxx
-\family default
-, that will convert the yielding.*.txt files into vtk files.
- These vtk files can be directly visualized in 
-\begin_inset LatexCommand \htmlurl[MayaVi]{mayavi.sourceforge.net}
-
-\end_inset
-
- or 
-\begin_inset LatexCommand \htmlurl[ParaView]{www.paraview.org}
-
-\end_inset
-
-.
+).
 \end_layout
 
 \begin_layout Chapter
@@ -1116,7 +1044,7 @@
 \end_layout
 
 \begin_layout Standard
-If you wish to change material properties, here is a brief overview of how
+If we wish to change material properties, here is a brief overview of how
  to modify the code.
  The following is currently lacking in many areas, but will be expanded
  and refined in future releases.
@@ -1713,13 +1641,11 @@
 \end_layout
 
 \begin_layout Standard
-This section covers the input parameters of the 
+The 
 \family typewriter
 Underworld_EulerDeform
 \family default
- component.
- This is the component that allows the upper surface to move freely or stay
- rigidly in place.
+ component allows the upper surface to move freely or stay rigidly in place.
  An example 
 \family typewriter
 EulerDeform
@@ -1959,65 +1885,75 @@
  For example, how many time steps, how often to print output, etc.
  We may also declare variables for convenience (e.g., the number of grid points)
  and use it elsewhere, such as in the components.
+ If we are using the basic set of components, then the more important parameters
+ are:
 \end_layout
 
-\begin_layout Standard
-The following are some of the more important variables:
+\begin_layout Description
+maxTimeSteps The number of time steps to take in the simulation.
+ Each time step can cover a different amount of time.
+ Gale determines how big of a step to take by dividing the grid size by
+ the largest velocity during that time step.
+ Unfortunately, there is no way to stop at a maximum time.
 \end_layout
 
 \begin_layout Description
-dim The number of dimensions of the simulation.
- This can be either 2 or 3.
+dumpEvery How often DumpSwarm dumps information to files.
 \end_layout
 
 \begin_layout Description
-maxTimeSteps The number of timesteps to take.
+checkPointEvery How often to dump every variable to files.
 \end_layout
 
 \begin_layout Description
-outputEvery How often to print output to the screen.
+outputPath The directory to put output files in.
 \end_layout
 
 \begin_layout Description
-dumpEvery How often to dump some information to files.
+dim The number of dimensions of the problem (2 or 3).
 \end_layout
 
 \begin_layout Description
-checkpointEvery How often to dump the complete state of the simulation to
- disk.
- This allows us to restart the simulation from the checkpoint.
+minX,minY,minZ,maxX,maxY,maxZ The physical size of the box you are simulating.
+ Note that this may be modified by 
+\family typewriter
+SurfaceAdaptor
+\family default
+ (section 
+\begin_inset LatexCommand \ref{sec:Deformed-Upper-Boundary}
+
+\end_inset
+
+).
 \end_layout
 
 \begin_layout Description
-outputPath What directory to put the output files in.
+elementResI,elementResJ,elementResK The number of elements in each direction.
+ Note that the number of grid points is one larger (e.g.
+ 64 elements -> 65 grid points).
 \end_layout
 
 \begin_layout Description
-seed A random number seed.
- Random numbers are only used in a few optional places, such as when laying
- down an initial set of particles.
+shadowDepth When running in parallel, every parameter only computes quantities
+ over a portion of the grid.
+ To do this, each processor must keep copies of points that belong to other
+ processors.
+ This parameter specifies how wide the region of copied points it.
+ We should never need to change this from 1.
 \end_layout
 
-\begin_layout Standard
-Also, if we use the basic components given in Section 
-\begin_inset LatexCommand \ref{sec:Basic-Components}
+\begin_layout Description
+gaussParticlesX,gaussParticlesY,gaussParticlesZ The number of particles
+ in each direction when putting down particles using a Gaussian distribution.
+ You should never need to change this number.
+\end_layout
 
-\end_inset
-
-, then we will need to specify 
-\family typewriter
-elementResI
-\family default
-, 
-\family typewriter
-elementResJ
-\family default
-, and 
-\family typewriter
-elementResK
-\family default
-.
- 
+\begin_layout Description
+particlesPerCell The ideal number of particles in each element.
+ Gale will attempt to keep the number of particles in each element close
+ to this number.
+ We need to vary this number to gauge how sensitive the results of our simulatio
+n are to this number.
 \end_layout
 
 \begin_layout Section
@@ -2042,1449 +1978,1259 @@
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="geometry">
+<struct name="mesh-constant">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">MeshGeometry</param>
+  <param name="Type">FeMesh</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="mesh">mesh-linear</param>
+  <param name="elementType">constant</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="decomp">decomp-linear</param>
+  <param name="elementMesh">mesh-linear</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeI">elementResI</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeJ">elementResJ</param>
+<struct name="constantMesh-generator">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeK">elementResK</param>
+  <param name="Type">C0Generator</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeShift">+1</param>
+  <param name="mesh">mesh-constant</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="elementTopology">
+<struct name="mesh-linear">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">IJK26Topology</param>
+  <param name="Type">FeMesh</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeI">elementResI</param>
+  <param name="elementType">linear</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeJ">elementResJ</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeK">elementResK</param>
+<struct name="linearMesh-generator">
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Type">CartesianGenerator</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="elementLayout">
+  <param name="mesh">mesh-linear</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">HexaEL</param>
+  <param name="dim">dim</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Topology">elementTopology</param>
+  <param name="shadowDepth">shadowDepth</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Geometry">geometry</param>
+  <list name="size">
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+    <param>elementResI</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="bodyNodeTopology">
+    <param>elementResJ</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">IJK6Topology</param>
+    <param>elementResK</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeI">elementResI</param>
+  </list>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeJ">elementResJ</param>
+  <list name="minCoord">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeK">elementResK</param>
+    <param>minX</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+    <param>minY</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="bodyNodeLayout">
+    <param>minZ</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">BodyNL</param>
+  </list>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ElementLayout">elementLayout</param>
+  <list name="maxCoord">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Topology">bodyNodeTopology</param>
+    <param>maxX</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+    <param>maxY</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="decomp-constant">
+    <param>maxZ</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">HexaMD</param>
+  </list>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ElementLayout">elementLayout</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="NodeLayout">bodyNodeLayout</param>
+<struct name="velocity">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="numPartitionedDims">numPartitionedDims</param>
+  <param name="Type">MeshVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="mesh">mesh-linear</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="meshLayout-constant">
+  <param name="Rank">Vector</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">MeshLayout</param>
+  <param name="DataType">Double</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ElementLayout">elementLayout</param>
+  <param name="VectorComponentCount">dim</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="NodeLayout">bodyNodeLayout</param>
+  <list name="names">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="MeshDecomp">decomp-constant</param>
+    <param>vx</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+    <param>vy</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="mesh-constant">
+    <param>vz</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">FiniteElement_Mesh</param>
+  </list>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="MeshLayout">meshLayout-constant</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ElementSize">8</param>
+<struct name="velocityBCs">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="NodeSize">0</param>
+  <param name="Type">CompositeVC</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Data">mesh-linear</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="cornerNodeTopology">
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">IJK6Topology</param>
+<struct name="velocityICs">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeI">elementResI</param>
+  <param name="Type">CompositeVC</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeJ">elementResJ</param>
+  <param name="Data">mesh-linear</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeK">elementResK</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="sizeShift">1</param>
+<struct name="velocityDofLayout">
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Type">DofLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="cornerNodeLayout">
+  <param name="mesh">mesh-linear</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">CornerNL</param>
+  <param name="BaseVariableCount">dim</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ElementLayout">elementLayout</param>
+  <list name="BaseVariables">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Topology">cornerNodeTopology</param>
+    <param>vx</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+    <param>vy</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="decomp-linear">
+    <param>vz</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">HexaMD</param>
+  </list>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ElementLayout">elementLayout</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="NodeLayout">cornerNodeLayout</param>
+<struct name="VelocityField">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="numPartitionedDims">numPartitionedDims</param>
+  <param name="Type">FeVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="FEMesh">mesh-linear</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="meshLayout-linear">
+  <param name="DofLayout">velocityDofLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">MeshLayout</param>
+  <param name="BC">velocityBCs</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ElementLayout">elementLayout</param>
+  <param name="IC">velocityICs</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="NodeLayout">cornerNodeLayout</param>
+  <param name="LinkedDofInfo">velocityLinkedDofs</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="MeshDecomp">decomp-linear</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+<struct name="VelocityMagnitudeField">
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="mesh-linear">
+  <param name="Type">OperatorFeVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">FiniteElement_Mesh</param>
+  <param name="Operator">Magnitude</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="MeshLayout">meshLayout-linear</param>
+  <param name="FeVariable">VelocityField</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ElementSize">8</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="NodeSize">0</param>
+<struct name="VelocityGradientsField">
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Type">OperatorFeVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="velocity">
+  <param name="Operator">Gradient</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">Variable</param>
+  <param name="FeVariable">VelocityField</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Rank">Vector</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Dependency">decomp-linear</param>
+<struct name="VelocityGradientsInvariantField">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="DataType">Double</param>
+  <param name="Type">OperatorFeVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Count">decomp-linear-nodeDomainCount</param>
+  <param name="Operator">TensorInvariant</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="VectorComponentCount">dim</param>
+  <param name="FeVariable">VelocityGradientsField</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <list name="names">
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-        <param>vx</param>
+<struct name="VelocityXXField">
 \end_layout
 
 \begin_layout LyX-Code
-        <param>vy</param>
+  <param name="Type">OperatorFeVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-        <param>vz</param>
+  <param name="Operator">TakeFirstComponent</param>
 \end_layout
 
 \begin_layout LyX-Code
-      </list>
+  <param name="FeVariable">VelocityField</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="velocityBCs">
+<struct name="VelocityYYField">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">CompositeVC</param>
+  <param name="Type">OperatorFeVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Data">mesh-linear</param>
+  <param name="Operator">TakeSecondComponent</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="FeVariable">VelocityField</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="velocityICs">
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">CompositeVC</param>
+<struct name="StrainRateField">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Data">mesh-linear</param>
+  <param name="Type">OperatorFeVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Operator">TensorSymmetricPart</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="velocityDofLayout">
+  <param name="FeVariable">VelocityGradientsField</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">DofLayout</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Count">decomp-linear-nodeDomainCount</param>
+<struct name="VorticityField">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="BaseVariableCount">dim</param>
+  <param name="Type">OperatorFeVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <list name="BaseVariables">
+  <param name="Operator">TensorAntisymmetricPart</param>
 \end_layout
 
 \begin_layout LyX-Code
-        <param>vx</param>
+  <param name="FeVariable">VelocityGradientsField</param>
 \end_layout
 
 \begin_layout LyX-Code
-        <param>vy</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-        <param>vz</param>
+<struct name="StrainRateInvariantField">
 \end_layout
 
 \begin_layout LyX-Code
-      </list>
+  <param name="Type">OperatorFeVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Operator">SymmetricTensor_Invariant</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="VelocityField">
+  <param name="FeVariable">StrainRateField</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">FeVariable</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FEMesh">mesh-linear</param>
+<struct name="StrainRateXXField">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="DofLayout">velocityDofLayout</param>
+  <param name="Type">OperatorFeVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="BC">velocityBCs</param>
+  <param name="Operator">TakeFirstComponent</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="IC">velocityICs</param>
+  <param name="FeVariable">StrainRateField</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="LinkedDofInfo">velocityLinkedDofs</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+<struct name="StrainRateYYField">
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="VelocityMagnitudeField">
+  <param name="Type">OperatorFeVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">OperatorFeVariable</param>
+  <param name="Operator">TakeSecondComponent</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Operator">Magnitude</param>
+  <param name="FeVariable">StrainRateField</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FeVariable">VelocityField</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+<struct name="pressure">
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="VelocityGradientsField">
+  <param name="Type">MeshVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">OperatorFeVariable</param>
+  <param name="mesh">mesh-constant</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Operator">Gradient</param>
+  <param name="Rank">Scalar</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FeVariable">VelocityField</param>
+  <param name="DataType">Double</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="VelocityXXField">
+<struct name="pressureDofLayout">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">OperatorFeVariable</param>
+  <param name="Type">DofLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Operator">TakeFirstComponent</param>
+  <param name="mesh">mesh-constant</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FeVariable">VelocityField</param>
+  <list name="BaseVariables">
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+    <param>pressure</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="VelocityYYField">
+  </list>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">OperatorFeVariable</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Operator">TakeSecondComponent</param>
+<struct name="PressureField">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FeVariable">VelocityField</param>
+  <param name="Type">FeVariable</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="FEMesh">mesh-constant</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="StrainRateField">
+  <param name="DofLayout">pressureDofLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">OperatorFeVariable</param>
+  <param name="LinkedDofInfo">pressureLinkedDofs</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Operator">TensorSymmetricPart</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FeVariable">VelocityGradientsField</param>
+<struct name="cellLayout">
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Type">SingleCellLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="VorticityField">
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">OperatorFeVariable</param>
+<struct name="particleLayout">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Operator">TensorAntisymmetricPart</param>
+  <param name="Type">GaussParticleLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FeVariable">VelocityGradientsField</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+<struct name="gaussSwarm">
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="StrainRateInvariantField">
+  <param name="Type">IntegrationPointsSwarm</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">OperatorFeVariable</param>
+  <param name="CellLayout">cellLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Operator">SymmetricTensor_Invariant</param>
+  <param name="ParticleLayout">particleLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FeVariable">StrainRateField</param>
+  <param name="FeMesh">mesh-linear</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="TimeIntegrator">timeIntegrator</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="StrainRateXXField">
+  <param name="IntegrationPointMapper">gaussMapper</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">OperatorFeVariable</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Operator">TakeFirstComponent</param>
+<struct name="gaussMapper">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FeVariable">StrainRateField</param>
+  <param name="Type">GaussMapper</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="IntegrationPointsSwarm">gaussSwarm</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="StrainRateYYField">
+  <param name="MaterialPointsSwarm">gaussMaterialSwarm</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">OperatorFeVariable</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Operator">TakeSecondComponent</param>
+<struct name="backgroundLayout">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FeVariable">StrainRateField</param>
+  <param name="Type">BackgroundParticleLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="pressure">
+<struct name="gaussMaterialSwarm">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">Variable</param>
+  <param name="Type">MaterialPointsSwarm</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Rank">Scalar</param>
+  <param name="CellLayout">cellLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Dependency">decomp-constant</param>
+  <param name="ParticleLayout">backgroundLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="DataType">Double</param>
+  <param name="FeMesh">mesh-linear</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Count">decomp-constant-nodeDomainCount</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+<struct name="timeIntegrator">
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="pressureDofLayout">
+  <param name="Type">TimeIntegrator</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">DofLayout</param>
+  <param name="order">1</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Count">decomp-constant-nodeDomainCount</param>
+  <param name="simultaneous">t</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <list name="BaseVariables">
+  <param name="Context">context</param>
 \end_layout
 
 \begin_layout LyX-Code
-        <param>pressure</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      </list>
+<struct name="elementCellLayout">
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Type">ElementCellLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="PressureField">
+  <param name="Mesh">mesh-linear</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">FeVariable</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FEMesh">mesh-constant</param>
+<struct name="discreteVoronoi">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="GeometryMesh">mesh-linear</param>
+  <param name="Type">CellularAutomataVoronoi</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="DofLayout">pressureDofLayout</param>
+  <param name="resolution">10</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="LinkedDofInfo">pressureLinkedDofs</param>
+  <param name="diagonalNeighbours">true</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="cellLayout">
+<struct name="weights">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">SingleCellLayout</param>
+  <param name="Type">DiscreteVoronoiWeights</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="DiscreteVoronoi">discreteVoronoi</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="particleLayout">
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">GaussParticleLayout</param>
+<struct name="localLayout">
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Type">MappedParticleLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="gaussSwarm">
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">IntegrationPointsSwarm</param>
+<struct name="picIntegrationPoints">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="CellLayout">cellLayout</param>
+  <param name="Type">IntegrationPointsSwarm</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ParticleLayout">particleLayout</param>
+  <param name="CellLayout">elementCellLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FiniteElement_Mesh">mesh-linear</param>
+  <param name="ParticleLayout">localLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="TimeIntegrator">timeIntegrator</param>
+  <param name="FeMesh">mesh-linear</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="IntegrationPointMapper">gaussMapper</param>
+  <param name="WeightsCalculator">weights</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="TimeIntegrator">timeIntegrator</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="gaussMapper">
+  <param name="IntegrationPointMapper">mapper</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">GaussMapper</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="IntegrationPointsSwarm">gaussSwarm</param>
+<struct name="mapper">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="MaterialPointsSwarm">gaussMaterialSwarm</param>
+  <param name="Type">CoincidentMapper</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="IntegrationPointsSwarm">picIntegrationPoints</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="backgroundLayout">
+  <param name="MaterialPointsSwarm">materialSwarm</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">BackgroundParticleLayout</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+<struct name="materialSwarmParticleLayout">
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="gaussMaterialSwarm">
+  <param name="Type">SpaceFillerParticleLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">MaterialPointsSwarm</param>
+  <param name="averageInitialParticlesPerCell">particlesPerCell</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="CellLayout">cellLayout</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ParticleLayout">backgroundLayout</param>
+<struct name="materialSwarm">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FiniteElement_Mesh">mesh-linear</param>
+  <param name="Type">MaterialPointsSwarm</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="CellLayout">elementCellLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="timeIntegrator">
+  <param name="ParticleLayout">materialSwarmParticleLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">TimeIntegrator</param>
+  <param name="FeMesh">mesh-linear</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="order">1</param>
+  <param name="SplittingRoutine">splittingRoutine</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="simultaneous">t</param>
+  <param name="RemovalRoutine">removalRoutine</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Context">context</param>
+  <param name="EscapedRoutine">escapedRoutine</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="elementCellLayout">
+<struct name="materialSwarmAdvector">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">ElementCellLayout</param>
+  <param name="Type">SwarmAdvector</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Mesh">mesh-linear</param>
+  <param name="Swarm">materialSwarm</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="TimeIntegrator">timeIntegrator</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="discreteVoronoi">
+  <param name="VelocityField">VelocityField</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">CellularAutomataVoronoi</param>
+  <param name="PeriodicBCsManager">periodicBCsManager</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="resolution">10</param>
+  <param name="allowFallbackToFirstOrder">True</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="diagonalNeighbours">true</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+<struct name="removalRoutine">
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="weights">
+  <param name="Type">DiscreteVoronoiRemove</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">DiscreteVoronoiWeights</param>
+  <param name="idealParticleCount">particlesPerCell</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="DiscreteVoronoi">discreteVoronoi</param>
+  <param name="DiscreteVoronoi">discreteVoronoi</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="localLayout">
+<struct name="splittingRoutine">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">MappedParticleLayout</param>
+  <param name="Type">ReseedSplitting</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="idealParticleCount">particlesPerCell</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="picIntegrationPoints">
+  <param name="DiscreteVoronoi">discreteVoronoi</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">IntegrationPointsSwarm</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="CellLayout">elementCellLayout</param>
+<struct name="solutionVelocity">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ParticleLayout">localLayout</param>
+  <param name="Type">SolutionVector</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FiniteElement_Mesh">mesh-linear</param>
+  <param name="FeVariable">VelocityField</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="WeightsCalculator">weights</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="TimeIntegrator">timeIntegrator</param>
+<struct name="solutionPressure">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="IntegrationPointMapper">mapper</param>
+  <param name="Type">SolutionVector</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="FeVariable">PressureField</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="mapper">
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">CoincidentMapper</param>
+<struct name="mom_force">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="IntegrationPointsSwarm">picIntegrationPoints</param>
+  <param name="Type">ForceVector</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="MaterialPointsSwarm">materialSwarm</param>
+  <param name="FeVariable">VelocityField</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="ExtraInfo">context</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="materialSwarmParticleLayout">
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">MeshParticleLayout</param>
+<struct name="cont_force">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="mesh">mesh-linear</param>
+  <param name="Type">ForceVector</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="cellParticleCount">particlesPerCell</param>
+  <param name="FeVariable">PressureField</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="ExtraInfo">context</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="materialSwarm">
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">MaterialPointsSwarm</param>
+<struct name="k_matrix">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="CellLayout">elementCellLayout</param>
+  <param name="Type">StiffnessMatrix</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ParticleLayout">materialSwarmParticleLayout</param>
+  <param name="RowVariable">VelocityField</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FiniteElement_Mesh">mesh-linear</param>
+  <param name="ColumnVariable">VelocityField</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="SplittingRoutine">splittingRoutine</param>
+  <param name="RHS">mom_force</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="RemovalRoutine">removalRoutine</param>
+  <param name="allowZeroElementContributions">False</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="EscapedRoutine">escapedRoutine</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+<struct name="constitutiveMatrix">
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="materialSwarmAdvector">
+  <param name="Type">ConstitutiveMatrixCartesian</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">SwarmAdvector</param>
+  <param name="Swarm">picIntegrationPoints</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Swarm">materialSwarm</param>
+  <param name="StiffnessMatrix">k_matrix</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="TimeIntegrator">timeIntegrator</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="VelocityField">VelocityField</param>
+<struct name="g_matrix">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="PeriodicBCsManager">periodicBCsManager</param>
+  <param name="Type">StiffnessMatrix</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="allowFallbackToFirstOrder">True</param>
+  <param name="RowVariable">VelocityField</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="ColumnVariable">PressureField</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="removalRoutine">
+  <param name="RHS">cont_force</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">DiscreteVoronoiRemove</param>
+  <param name="allowZeroElementContributions">False</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="idealParticleCount">particlesPerCell</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="DiscreteVoronoi">discreteVoronoi</param>
+<struct name="gradientStiffnessMatrixTerm">
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Type">GradientStiffnessMatrixTerm</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="splittingRoutine">
+  <param name="Swarm">gaussSwarm</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">ReseedSplitting</param>
+  <param name="StiffnessMatrix">g_matrix</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="idealParticleCount">particlesPerCell</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="DiscreteVoronoi">discreteVoronoi</param>
+<struct name="preconditioner">
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Type">StiffnessMatrix</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="solutionVelocity">
+  <param name="RowVariable">PressureField</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">SolutionVector</param>
+  <param name="ColumnVariable">PressureField</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FeVariable">VelocityField</param>
+  <param name="RHS">cont_force</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="allowZeroElementContributions">True</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="solutionPressure">
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">SolutionVector</param>
+<struct name="preconditionerTerm">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FeVariable">PressureField</param>
+  <param name="Type">UzawaPreconditionerTerm</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Swarm">picIntegrationPoints</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="mom_force">
+  <param name="StiffnessMatrix">preconditioner</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">ForceVector</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FeVariable">VelocityField</param>
+<struct name="uzawa">
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ExtraInfo">context</param>
+  <param name="Type">Stokes_SLE_UzawaSolver</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Preconditioner">preconditioner</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="cont_force">
+  <param name="tolerance">1.0e-5</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">ForceVector</param>
+  <param name="maxIterations">5000</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="FeVariable">PressureField</param>
+</struct>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ExtraInfo">context</param>
+<struct name="stokesEqn">
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="Type">Stokes_SLE</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="k_matrix">
+  <param name="SLE_Solver">uzawa</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">StiffnessMatrix</param>
+  <param name="Context">context</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="RowVariable">VelocityField</param>
+  <param name="StressTensorMatrix">k_matrix</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="ColumnVariable">VelocityField</param>
+  <param name="GradientMatrix">g_matrix</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="RHS">mom_force</param>
+  <param name="DivergenceMatrix"></param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="allowZeroElementContributions">False</param>
+  <param name="CompressibilityMatrix">c_matrix</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="VelocityVector">solutionVelocity</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="constitutiveMatrix">
+  <param name="PressureVector">solutionPressure</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">ConstitutiveMatrixCartesian</param>
+  <param name="ForceVector">mom_force</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Swarm">picIntegrationPoints</param>
+  <param name="ContinuityForceVector">cont_force</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="StiffnessMatrix">k_matrix</param>
+  <param name="killNonConvergent">false</param>
 \end_layout
 
 \begin_layout LyX-Code
-    </struct>
+  <param name="nonLinearMaxIterations">nonLinearMaxIterations</param>
 \end_layout
 
 \begin_layout LyX-Code
-    <struct name="g_matrix">
+  <param name="nonLinearTolerance">nonLinearTolerance</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="Type">StiffnessMatrix</param>
+  <param name="makeConvergenceFile">false</param>
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="RowVariable">VelocityField</param>
+</struct>
 \end_layout
 
-\begin_layout LyX-Code
-      <param name="ColumnVariable">PressureField</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="RHS">cont_force</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="allowZeroElementContributions">False</param>
-\end_layout
-
-\begin_layout LyX-Code
-    </struct>
-\end_layout
-
-\begin_layout LyX-Code
-    <struct name="gradientStiffnessMatrixTerm">
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="Type">GradientStiffnessMatrixTerm</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="Swarm">gaussSwarm</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="StiffnessMatrix">g_matrix</param>
-\end_layout
-
-\begin_layout LyX-Code
-    </struct>
-\end_layout
-
-\begin_layout LyX-Code
-    <struct name="preconditioner">
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="Type">StiffnessMatrix</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="RowVariable">PressureField</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="ColumnVariable">PressureField</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="RHS">cont_force</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="allowZeroElementContributions">True</param>
-\end_layout
-
-\begin_layout LyX-Code
-    </struct>
-\end_layout
-
-\begin_layout LyX-Code
-    <struct name="preconditionerTerm">
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="Type">UzawaPreconditionerTerm</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="Swarm">picIntegrationPoints</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="StiffnessMatrix">preconditioner</param>
-\end_layout
-
-\begin_layout LyX-Code
-    </struct>
-\end_layout
-
-\begin_layout LyX-Code
-    <struct name="uzawa">
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="Type">Stokes_SLE_UzawaSolver</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="Preconditioner">preconditioner</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="tolerance">1.0e-5</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="maxIterations">5000</param>
-\end_layout
-
-\begin_layout LyX-Code
-    </struct>
-\end_layout
-
-\begin_layout LyX-Code
-    <struct name="stokesEqn">
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="Type">Stokes_SLE</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="SLE_Solver">uzawa</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="Context">context</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="StressTensorMatrix">k_matrix</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="GradientMatrix">g_matrix</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="DivergenceMatrix"></param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="CompressibilityMatrix">c_matrix</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="VelocityVector">solutionVelocity</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="PressureVector">solutionPressure</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="ForceVector">mom_force</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="ContinuityForceVector">cont_force</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="killNonConvergent">false</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="nonLinearMaxIterations">nonLinearMaxIterations</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="nonLinearTolerance">nonLinearTolerance</param>
-\end_layout
-
-\begin_layout LyX-Code
-      <param name="makeConvergenceFile">false</param>
-\end_layout
-
-\begin_layout LyX-Code
-    </struct>
-\end_layout
-
 \begin_layout Standard
-These components will be more or less unchanged between input files.
- We will need to change some associated variables specifying the resolution:
- 
-\family typewriter
-elementResI
-\family default
-, 
-\family typewriter
-elementResJ
-\family default
-, and 
-\family typewriter
-elementResK
-\family default
-.
+For almost all simulations, we will not need to change these components.
 \end_layout
 
 \begin_layout Section
@@ -5494,15 +5240,14 @@
 
 \begin_layout Description
 initialDamageFactor The maximum initial random strain for a particle is
- 
+\newline
+
 \family typewriter
 initialDamageFactor
 \family default
 *
 \family typewriter
-softening
-\newline
-Strain
+softeningStrain
 \family default
 .
  
@@ -5510,7 +5255,7 @@
 
 \begin_layout Description
 randomSeed A random number seed used when computing which particles are
- initially yielded.
+ initially strained.
 \end_layout
 
 \begin_layout Description
@@ -7010,6 +6755,11 @@
 
 \begin_layout Section
 Deformed Upper Boundary
+\begin_inset LatexCommand \label{sec:Deformed-Upper-Boundary}
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Standard
@@ -7604,13 +7354,220 @@
 \end_layout
 
 \begin_layout Section
-Parallel Options
+Verbosity Options
 \end_layout
 
+\begin_layout Standard
+By default, Gale prints out very little when running.
+ To get more information, we can insert
+\end_layout
+
+\begin_layout LyX-Code
+<param name="journal.info">True</param>
+\end_layout
+
+\begin_layout LyX-Code
+<param name="journal.debug">True</param>
+\end_layout
+
+\begin_layout LyX-Code
+<param name="journal-level.info">2</param>
+\end_layout
+
+\begin_layout LyX-Code
+<param name="journal-level.debug">2</param>
+\end_layout
+
+\begin_layout Standard
+into the variables section (see section 
+\begin_inset LatexCommand \ref{sub:Variables}
+
+\end_inset
+
+).
+ This will print out more information than we need about the components,
+ the solvers, the number of iterations.
+ In addition, we can get even more information about the solvers from PETSc
+ by appending the 
+\begin_inset Quotes sld
+\end_inset
+
+
+\family typewriter
+-ksp_monitor
+\family default
+
+\begin_inset Quotes srd
+\end_inset
+
+ to the command line.
+\end_layout
+
 \begin_layout Chapter
 Output File Format
+\begin_inset LatexCommand \label{cha:Output-File-Format}
+
+\end_inset
+
+
 \end_layout
 
+\begin_layout Standard
+Gale outputs three types of files.
+ 
+\end_layout
+
+\begin_layout Section
+.dat ASCII files
+\end_layout
+
+\begin_layout Standard
+The first type are ASCII files with 
+\family typewriter
+.dat
+\family default
+ extensions.
+ They are mostly self explanatory (e.g., 
+\family typewriter
+PressureField.dat
+\family default
+ contains pressure field output).
+ Inside each 
+\family typewriter
+.dat
+\family default
+ file are several columns of data:
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+0 0.0312539624080715 0.0109361134145122 0 -9.81467103200287
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+1 0.0937630718938361 0.0109356986189374 0 17.7373201951569
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+2 0.156270066350344 0.0109368543031399 0 -37.0281780188199
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+3 0.218780947570009 0.0109343376815161 0 45.6263762140766
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+4 0.28128858838265 0.010937987088561 0 -65.2132484518426 
+\end_layout
+
+\begin_layout Standard
+The first column (0,1,2,3, ...) is the node number, and the second, third,
+ and fourth columns are the x, y, and z coordinates.
+ The last column(s) show the value.
+ Note: If performing a 2D run, there will still be z data, but it can be
+ ignored.
+\end_layout
+
+\begin_layout Standard
+The .txt files are the output of 
+\family typewriter
+DumpSwarm
+\family default
+, explained below.
+\end_layout
+
+\begin_layout Section
+.dat binary files (particle information)
+\end_layout
+
+\begin_layout Standard
+These are the 
+\family typewriter
+materialSwarm.*.dat
+\family default
+ files.
+ They are only useful for checkpointing and have a machine dependent format.
+\end_layout
+
+\begin_layout Section
+.txt files (particle information)
+\end_layout
+
+\begin_layout Standard
+These files are output by the 
+\family typewriter
+Underworld_DumpSwarm
+\family default
+ plugin.
+ These provide particle information in a more friendly format.
+ The 
+\family typewriter
+Underworld_DumpSwarm
+\family default
+ plugin is activated by adding the line
+\end_layout
+
+\begin_layout LyX-Code
+    <param>Underworld_DumpSwarm</param> 
+\end_layout
+
+\begin_layout Standard
+to the list of plugins.
+ This line is already in the example input files.
+ At present, it outputs the files 
+\family typewriter
+yielding.*.txt
+\family default
+.
+ The format of the file is
+\end_layout
+
+\begin_layout LyX-Code
+m x y z
+\family typewriter
+ yielded
+\end_layout
+
+\begin_layout Standard
+where 
+\family typewriter
+m
+\family default
+ is the number of the material (in the examples, always 1), and 
+\family typewriter
+yielded
+\family default
+ is a number between 
+\family typewriter
+0
+\family default
+ and 
+\family typewriter
+1
+\family default
+ indicating how much a material point has failed.
+ If you want to print out some other property of the material, e.g., viscosity,
+ you can modify 
+\family typewriter
+DumpSwarm
+\family default
+ to provide that information.
+ The source for the plugin is found in the directory
+\end_layout
+
+\begin_layout LyX-Code
+src/Underworld/plugins/Output/DumpSwarm/
+\end_layout
+
 \begin_layout Chapter
 Benchmarks
 \end_layout

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