[cig-commits] commit: Update manual

Mercurial hg at geodynamics.org
Sat Oct 8 04:04:23 PDT 2011 

changeset:   380:e8416a557e74
tag:         tip
user:        Walter Landry <wlandry at caltech.edu>
date:        Sat Oct 08 04:01:54 2011 -0700
files:       doc/gale.lyx doc/gale_cover.png doc/gale_cover.xcf doc/images/Paraview_bottom.png doc/images/Paraview_deformed_bottom.png doc/images/Paraview_multi_material.png doc/images/Paraview_multi_viscosity.png doc/images/Paraview_non_newtonian.png doc/images/Paraview_normal_stress.png doc/images/Paraview_thermal.png doc/images/Paraview_thermal_file.png doc/images/Paraview_viscous_extension.png doc/images/Paraview_viscous_inflow.png doc/images/Paraview_viscous_sinusoid.png doc/images/Paraview_viscous_split.png doc/images/Paraview_yielding.png doc/images/Paraview_yielding_viscosity.png doc/images/Paraview_yielding_yielding.png
description:
Update manual


diff -r e8d08f6a076f -r e8416a557e74 doc/gale.lyx
--- a/doc/gale.lyx	Sat Oct 08 04:00:11 2011 -0700
+++ b/doc/gale.lyx	Sat Oct 08 04:01:54 2011 -0700
@@ -124,7 +124,7 @@ Walter Landry and Luke Hodkinson
 \begin_inset Newline newline
 \end_inset
 
-Version 1.6.2
+Version 2.0.0
 \end_layout
 
 \begin_layout Date
@@ -884,187 +884,69 @@ Numerical Solution
 \end_layout
 
 \begin_layout Subsubsection
-\begin_inset CommandInset label
-LatexCommand label
-name "sub:Artificial-Compressibility"
-
-\end_inset
-
-Artificial Compressibility
-\end_layout
-
-\begin_layout Standard
-In Gale, the velocity and pressure are represented by linear (Q1) finite
- elements (formally, this is called a Q1-Q1 scheme).
- Normally, this formulation is unstable.
- To stabilize it, we follow Dohrmann & Bochev 
-\begin_inset CommandInset citation
-LatexCommand cite
-key "Stable Stokes"
-
-\end_inset
-
- 
-\begin_inset CommandInset citation
-LatexCommand cite
-key "Fast Solvers"
-
-\end_inset
-
- and add a compressibility term to the divergence equation
-\end_layout
-
-\begin_layout Standard
-\begin_inset Formula 
-\begin{equation}
-v_{i,i}+Cp=d,\label{eq:stabilized}
-\end{equation}
-
-\end_inset
-
- where
-\end_layout
-
-\begin_layout Standard
-\begin_inset Formula 
-\[
-\begin{array}{ccc}
-C & \equiv & \frac{1}{\nu}\left(M-D\right)\\
-M & \equiv & \int_{\Omega_{e}}\psi(x)\psi^{T}(x)d\Omega_{e}\\
-D & \equiv & \int_{\Omega_{e}}d\Omega_{e}
-\end{array},
-\]
-
-\end_inset
-
- 
-\begin_inset Formula $\Omega_{e}$
-\end_inset
-
- is the finite element, and 
-\begin_inset Formula $\psi(x)$
-\end_inset
-
- is its basis function.
- That is, we add a compressibility that is scaled by the viscosity and proportio
-nal to the mass matrix and the area.
- So as we increase resolution, both of these terms scale as the area of
- the element and go to zero.
-\end_layout
-
-\begin_layout Standard
-Prior versions of Gale used constant elements for the pressure (a Q1-P0
- scheme).
- That scheme admits solutions that have an arbitrarily sized checkerboard
- pressure term.
- For simple viscous problems, the pressure is not used any further than
- getting the velocity solution, which the checkerboard term does not affect.
- However, with a yielding rheology, pressure plays a critical role in determinin
-g when materials yield.
- We can moderate this checkerboard instability by averaging the pressure
- at the nodes of the elements.
- In practice, this does not solve all of the problems.
- Figure 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "fig:Q1-P0"
-
-\end_inset
-
- shows a simple subduction model with the old Q1-P0 scheme and averaged
- pressures.
- Figure 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "fig:Q1-Q1"
-
-\end_inset
-
- shows the new Q1-Q1 scheme.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Plain Layout
-\align center
-\begin_inset Graphics
-	filename images/Q1P0.png
-	width 100col%
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Plain Layout
-\begin_inset Caption
-
-\begin_layout Plain Layout
-\begin_inset CommandInset label
-LatexCommand label
-name "fig:Q1-P0"
-
-\end_inset
-
-Pressure for a subduction model using Q1-P0 elements and averaged pressures.
- Notice that, even when averaging the pressure, there is an even-odd artifact
- centered on the bottom.
- 
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Plain Layout
-\align center
-\begin_inset Graphics
-	filename images/Q1Q1.png
-	width 100col%
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Plain Layout
-\begin_inset Caption
-
-\begin_layout Plain Layout
-\begin_inset CommandInset label
-LatexCommand label
-name "fig:Q1-Q1"
-
-\end_inset
-
-Strain rate invariant for a subduction model using Q1-Q1 elements 
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-These instabilities in the old Q1-P0 scheme also slowed down convergence,
- while the new Q1-Q1 scheme is dramatically faster.
+Finite Elements
+\end_layout
+
+\begin_layout Standard
+Gale can use a few different types of finite elements to represent the solution.
+ The recommended elements are quadratic (
+\begin_inset Formula $Q_{2}$
+\end_inset
+
+) elements for the velocity and discontinuous linear (
+\begin_inset Formula $P_{-1}$
+\end_inset
+
+) elements for the pressure.
+ These elements are mathematically well behaved and have been used in other
+ computational codes with success.
+\end_layout
+
+\begin_layout Standard
+If, for some reason, you wish use a different element type, Gale also supports
+ continuous linear (
+\begin_inset Formula $Q_{1}$
+\end_inset
+
+) element and piecewise constant (
+\begin_inset Formula $P_{0}$
+\end_inset
+
+) elements.
+ One formulation common in many solid earth modelling codes is to use 
+\begin_inset Formula $Q_{1}$
+\end_inset
+
+ elements for the velocity and 
+\begin_inset Formula $P_{0}$
+\end_inset
+
+ elements for the pressure.
+ This formulation gives rise to a checkerboard instability.
+ While this instability is not always fatal, dealing with it can be difficult
+ and error prone.
+\end_layout
+
+\begin_layout Standard
+Previous versions of Gale did not support 
+\begin_inset Formula $Q_{2}$
+\end_inset
+
+ or 
+\begin_inset Formula $P_{-1}$
+\end_inset
+
+ elements, so the recommendation was to use 
+\begin_inset Formula $Q_{1}$
+\end_inset
+
+ elements for both the velocity and pressure.
+ This formulation has its own instability that is fixed by adding an artificial
+ compressibility.
+ In principle, this artificial compressibility should be small and get smaller
+ as resolution increases.
+ In practice, for realistic geologic problems, the artificial compressibility
+ would be far too large and dramatically alter the dynamics.
 \end_layout
 
 \begin_layout Subsubsection
@@ -1078,28 +960,25 @@ Scaling
 \end_layout
 
 \begin_layout Standard
-The new scheme is not without its downsides.
- First of all, the new code does not scale the physical quantities as well
- as the old code.
- In particular, note that the units for Equations 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "eq:body force"
-
-\end_inset
-
- and 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "eq:stabilized"
-
-\end_inset
-
- are different.
+One thing to note is that Equations 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "eq:simple momentum conservation"
+
+\end_inset
+
+ and 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "eq:continuity"
+
+\end_inset
+
+ have different units.
  Equation 
 \begin_inset CommandInset ref
 LatexCommand ref
-reference "eq:stabilized"
+reference "eq:continuity"
 
 \end_inset
 
@@ -1199,155 +1078,6 @@ A
 \end_inset
 
 .
-\end_layout
-
-\begin_layout Subsubsection
-\begin_inset CommandInset label
-LatexCommand label
-name "sub:Hydrostatic-Pressure"
-
-\end_inset
-
-Hydrostatic Pressure
-\end_layout
-
-\begin_layout Standard
-Ideally, the compressibility term should be applied to the dynamic pressure,
- not the hydrostatic pressure.
- This is not a problem in simple sandbox simulations, where the dynamic
- pressure is about the same size as the hydrostatic pressure.
- However, in geological models, the hydrostatic pressure is much, much larger
- than the dynamic pressure.
- This means that the compressibility term is far too large, leading to excessive
- compressibility.
- As Figure 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "fig:Collapsing_compressible"
-
-\end_inset
-
- shows, this can completely alter the dynamics.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Plain Layout
-\align center
-\begin_inset Graphics
-	filename images/collapsing_compressible.png
-	lyxscale 50
-	width 100col%
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Plain Layout
-\begin_inset Caption
-
-\begin_layout Plain Layout
-\begin_inset CommandInset label
-LatexCommand label
-name "fig:Collapsing_compressible"
-
-\end_inset
-
-Strain rate invariant and velocity arrows for a geologic model without hydrostat
-ic correction.
- The compressibility is so large on the bottom that the whole region falls
- down, dominating the dynamics.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-To fix this, you can subtract out the hydrostatic term.
- You can write Equation 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "eq:body force"
-
-\end_inset
-
- as
-\end_layout
-
-\begin_layout Standard
-\begin_inset Formula 
-\begin{equation}
-\tau_{ij,j}-p_{0,i}-\delta p_{,i}=f_{0i}+\delta f_{i},\label{eq:hydrostatic}
-\end{equation}
-
-\end_inset
-
- where 
-\begin_inset Formula $p_{0}$
-\end_inset
-
- is the hydrostatic pressure, and 
-\begin_inset Formula $f_{0}$
-\end_inset
-
- is the background buoyancy force that leads to a hydrostatic pressure.
- Since 
-\begin_inset Formula $p_{0}$
-\end_inset
-
- and 
-\begin_inset Formula $f_{0}$
-\end_inset
-
- are constructed to be hydrostatic, they cancel each other.
- You can then rewrite Equations 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "eq:body force"
-
-\end_inset
-
- and 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "eq:divergence"
-
-\end_inset
-
- as
-\end_layout
-
-\begin_layout Standard
-\begin_inset Formula 
-\begin{equation}
-\begin{array}{ccc}
-\tau_{ij,j}-\delta p_{,i} & = & \delta f_{i}\\
-v_{i,i}+C\delta p & = & d
-\end{array}.\label{eq:complete numerical stokes}
-\end{equation}
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Note that if you are simulating a simple viscous problem in a box, you never
- even use the complete pressure.
- In the general case such as with a yielding rheology, the viscosity may
- depend on the overall pressure.
 \end_layout
 
 \begin_layout Subsubsection
@@ -1960,7 +1690,7 @@ Gale works on a variety of computational
 \end_layout
 
 \begin_layout Itemize
-Mac OS X 10.4.6 and 10.6.0
+Mac OS X 10.4.6, 10.6.0, and 10.7.0
 \end_layout
 
 \begin_layout Itemize
@@ -1968,7 +1698,7 @@ Windows Vista (32 and 64 bit)
 \end_layout
 
 \begin_layout Itemize
-Debian stable (AMD64)
+Debian testing (AMD64)
 \end_layout
 
 \begin_layout Itemize
@@ -1979,10 +1709,6 @@ RedHat Enterprise Linux 3 (EM64T)
 RedHat Enterprise Linux 3 (EM64T)
 \end_layout
 
-\begin_layout Itemize
-Rocks 4.1 (Opteron)
-\end_layout
-
 \begin_layout Subsection
 Dependencies
 \end_layout
@@ -2002,6 +1728,10 @@ PETSc 3.0 (not 3.1!)
 
 \begin_layout Itemize
 libxml2
+\end_layout
+
+\begin_layout Itemize
+HDF5
 \end_layout
 
 \begin_layout Standard
@@ -2013,7 +1743,8 @@ You must also have python 2.2.1 or great
 \end_layout
 
 \begin_layout Standard
-For checkpointing, you will also need HDF5.
+HDF5 is not strictly required, but checkpointing and visualization will
+ not work without it.
 \end_layout
 
 \begin_layout Subsection
@@ -2299,7 +2030,7 @@ If you downloaded binaries for your plat
 \end_layout
 
 \begin_layout LyX-Code
-./Gale-1_6_2 input/cookbook/yielding.xml
+./Gale-2_0_0 input/cookbook/yielding.xml
 \end_layout
 
 \begin_layout Standard
@@ -2311,39 +2042,43 @@ TimeStep = 0, Time = 0
 \end_layout
 
 \begin_layout LyX-Code
-TimeStep = 1, Time = 0.010764
-\end_layout
-
-\begin_layout LyX-Code
-TimeStep = 2, Time = 0.0214745
-\end_layout
-
-\begin_layout LyX-Code
-TimeStep = 3, Time = 0.0321333
-\end_layout
-
-\begin_layout LyX-Code
-TimeStep = 4, Time = 0.0427393
-\end_layout
-
-\begin_layout LyX-Code
-TimeStep = 5, Time = 0.0532923
-\end_layout
-
-\begin_layout LyX-Code
-TimeStep = 6, Time = 0.0637925
-\end_layout
-
-\begin_layout LyX-Code
-TimeStep = 7, Time = 0.0742399
-\end_layout
-
-\begin_layout LyX-Code
-TimeStep = 8, Time = 0.0846353
-\end_layout
-
-\begin_layout LyX-Code
-TimeStep = 9, Time = 0.0949793
+TimeStep = 1, Time = 0.0107467
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 2, Time = 0.021442
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 3, Time = 0.0320895
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 4, Time = 0.0426866
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 5, Time = 0.0532321
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 6, Time = 0.0637259
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 7, Time = 0.0741676
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 8, Time = 0.0845553
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 9, Time = 0.0948918
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 10, Time = 0.105179
 \end_layout
 
 \begin_layout Standard
@@ -2369,7 +2104,7 @@ Due to quirks in some implementations of
 Due to quirks in some implementations of MPI, you may have to specify the
  complete path to the input file (e.g., 
 \family typewriter
-./Gale-1_6_2 /home/juser/gale/input/cookbook/yielding.xml
+./Gale-2_0_0 /home/juser/gale/input/cookbook/yielding.xml
 \family default
 ).
 \end_layout
@@ -2653,7 +2388,7 @@ One solution is to use a direct solver i
 \end_layout
 
 \begin_layout LyX-Code
-./Gale-1_6_2  input/cookbook/yielding.xml -pc_type lu -ksp_type preonly
+./Gale-2_0_0  input/cookbook/yielding.xml -pc_type lu -ksp_type preonly
 \end_layout
 
 \begin_layout Standard
@@ -2682,7 +2417,7 @@ Once that is done, enabling it is again 
 \end_layout
 
 \begin_layout LyX-Code
-./Gale-1_6_2  input/cookbook/yielding.xml -pc_factor_mat_solver_package mumps
+./Gale-2_0_0  input/cookbook/yielding.xml -pc_factor_mat_solver_package mumps
  
 \backslash
 
@@ -2829,7 +2564,7 @@ You can also change the default values o
 \end_layout
 
 \begin_layout LyX-Code
-./Gale-1_6_2  input/cookbook/yielding.xml --maxTimeSteps=20
+./Gale-2_0_0  input/cookbook/yielding.xml --maxTimeSteps=20
 \end_layout
 
 \begin_layout Standard
@@ -2840,7 +2575,7 @@ You can append any number of modified pa
 \begin_layout LyX-Code
 
 \size small
-./Gale-1_6_2  input/cookbook/yielding.xml --maxTimeSteps=20 --dim=3 --elementResI=
+./Gale-2_0_0  input/cookbook/yielding.xml --maxTimeSteps=20 --dim=3 --elementResI=
 64 
 \begin_inset Newline newline
 \end_inset
@@ -2960,28 +2695,9 @@ reference "cha:Output-File-Format"
 \end_layout
 
 \begin_layout Standard
-The default setting is to create VTK files every 10 time steps.
- To change the frequency for creating VTK files, you need to change the
- parameter 
-\family typewriter
-dumpEvery
-\family default
-.
- For example, if you modify the line with 
-\family typewriter
-dumpEvery
-\family default
- to
-\end_layout
-
-\begin_layout LyX-Code
-<param name="dumpEvery">25</param>
-\end_layout
-
-\begin_layout Standard
-then the VTK files will only be created every 25 time steps.
- Similarly, to change the frequency of checkpoints, you need to change the
- parameter 
+XDMF visualization files are created at the same time as checkpoints.
+ So to change the frequency at which Gale outputs XDMF files, you can change
+ the parameter 
 \family typewriter
 checkpointEvery
 \family default
@@ -2993,7 +2709,7 @@ checkpointEvery
 
 \color none
 There are a number of different options for visualizing the data.
- The easiest way is to use the VTK files.
+ The easiest way is to use the XDMF files.
  These files are in a standard, self-describing file format that can be
  easily visualized with several different visualization programs, e.g., ParaView
  
@@ -3007,18 +2723,7 @@ paraview.org
 
 \end_inset
 
-, MayaVI 
-\begin_inset Flex URL
-status collapsed
-
-\begin_layout Plain Layout
-
-mayavi.sf.net
-\end_layout
-
-\end_inset
-
-, and Visit 
+ and Visit 
 \begin_inset Flex URL
 status collapsed
 
@@ -3039,7 +2744,7 @@ Another option is to use the scripts in 
 \family typewriter
 tools/
 \family default
- directory to convert the VTK files into CSV format.
+ directory to convert the XDMF files into CSV format.
  Then the data can be easily manipulated with standard tools like Python
  or Matlab.
 \end_layout
@@ -3125,7 +2830,7 @@ A file dialog screen will appear.
  Navigate to the output directory and select 
 \family typewriter
 \color none
-fields.00009.pvts
+fields.00010.pvts
 \family default
 .
  Then click the green ``Apply
@@ -3304,7 +3009,7 @@ eye
 
  next to 
 \family typewriter
-fields.00009.pvts
+fields.00010.pvts
 \family default
 .
 \end_layout
@@ -3350,7 +3055,7 @@ click the ``eye
  again, then click on the text 
 \family typewriter
 \color inherit
-fields.00009.pvts
+fields.00010.pvts
 \family default
 \color none
 .
@@ -3463,7 +3168,7 @@ Now you can look at the particles.
  Starting over, open 
 \family typewriter
 \color none
-picIntegrationPoints.00009.pvtu
+picIntegrationPoints.00010.pvtu
 \family default
  and click on the green ``Apply'' button.
 \end_layout
@@ -3551,7 +3256,7 @@ input/cookbook/viscous_extension3D.xml
 \family default
  and open 
 \family typewriter
-fields.00009.ptvs
+fields.00010.ptvs
 \family default
 .
  Paraview will display an outline of the 3D volume.
@@ -3719,119 +3424,6 @@ status open
 \end_layout
 
 \end_deeper
-\begin_layout Subsection
-Visualizing Movies with Paraview
-\end_layout
-
-\begin_layout Standard
-To create a movie, with Paraview, you need to create a special 
-\family typewriter
-pvd
-\family default
- file that stitches all of the individual frames together.
- You can do this with the utility 
-\family typewriter
-tools/generate_pvd
-\family default
-.
- You generally invoke it as
-\end_layout
-
-\begin_layout LyX-Code
-generate_pvd NAME TYPE START END STEP
-\end_layout
-
-\begin_layout Standard
-where 
-\family typewriter
-NAME
-\family default
- is usually either 
-\begin_inset Quotes sld
-\end_inset
-
-fields
-\begin_inset Quotes srd
-\end_inset
-
- or 
-\begin_inset Quotes sld
-\end_inset
-
-picIntegrationPoints
-\begin_inset Quotes srd
-\end_inset
-
-, depending on whether you want to animate the fields or the particles.
- If you create your own swarm of particles, then they will have their own
- VTK files, and you would use that name with 
-\family typewriter
-generate_pvd
-\family default
-.
- 
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-TYPE
-\family default
- is either '
-\family typewriter
-u
-\family default
-' for unstructured (particles), or '
-\family typewriter
-s
-\family default
-' for unstructured (fields).
- START is the time of the first time step, END is the last step, and STEP
- is the step size between successive frames.
- So the command
-\end_layout
-
-\begin_layout LyX-Code
-generate_pvd picIntegrationPoints u 0 100 10
-\end_layout
-
-\begin_layout Standard
-will generate 
-\family typewriter
-picIntegrationPoints.pvd
-\family default
-.
- That file starts at t=0 and includes every 10'th step up to and including
- 100.
- So to animate the post yielding strain in 
-\family typewriter
-input/viscous_extension3D.xml
-\family default
-, you would run, from the top directory,
-\end_layout
-
-\begin_layout LyX-Code
-generate_pvd fields s 0 9
-\end_layout
-
-\begin_layout Standard
-Loading up 
-\family typewriter
-fields.pvd
-\family default
- in Paraview gives you access to the movie buttons
-\end_layout
-
-\begin_layout Standard
-\align center
-\begin_inset Graphics
-	filename images/Paraview_movie_controls.png
-
-\end_inset
-
-
-\end_layout
-
 \begin_layout Subsection
 Generating CSV files
 \end_layout
@@ -4376,31 +3968,9 @@ output
 output
 \family default
 .
- If you want to run in 3D, you only need to change the line after
-\end_layout
-
-\begin_deeper
-\begin_layout LyX-Code
-<param name="outputPath">./output.template</param> 
-\end_layout
-
-\begin_layout Standard
-from
-\end_layout
-
-\begin_layout LyX-Code
-<param name="dim">2</param>
-\end_layout
-
-\begin_layout Standard
-to
-\end_layout
-
-\begin_layout LyX-Code
-<param name="dim">3</param>
-\end_layout
-
-\end_deeper
+ 
+\end_layout
+
 \begin_layout Standard
 You can compare your result with the worked example in the file 
 \family typewriter
@@ -4603,29 +4173,7 @@ Strain rate invariant and velocity of vi
 \end_layout
 
 \begin_layout Standard
-The structure in the strain rate invariant arises from the artificial compressib
-ility (see Section 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "sub:Artificial-Compressibility"
-
-\end_inset
-
-).
- The magnitude of this structure is small, so you can ignore it for now.
- Later, in Section 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "sec:Hydrostatic-Term"
-
-\end_inset
-
-, you will remove it by adding a 
-\family typewriter
-HydrostaticTerm
-\family default
-.
- 
+
 \end_layout
 
 \begin_layout Section
@@ -4781,7 +4329,7 @@ Specify the x-velocity equation by addin
 
 \begin_deeper
 \begin_layout LyX-Code
-<param name="Equation1">step(0.5-x)</param>
+<param name="Equation1">step(x-1)
 \end_layout
 
 \begin_layout Standard
@@ -4989,7 +4537,7 @@ Specify the particulars of the file by a
 
 \begin_deeper
 \begin_layout LyX-Code
-<param name="File1_Name">velocities</param>
+<param name="File1_Name">input/cookbook/velocities</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -5298,15 +4846,15 @@ after the lines
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="resolutionX">10</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="resolutionY">10</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="resolutionZ">10</param>
+  <param name="resolutionX">20</param>
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="resolutionY">20</param>
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="resolutionZ">20</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -5591,15 +5139,15 @@ after the lines
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="resolutionX">10</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="resolutionY">10</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="resolutionZ">10</param>
+  <param name="resolutionX">20</param>
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="resolutionY">20</param>
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="resolutionZ">20</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -5984,11 +5532,11 @@ SurfaceAdaptor
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="mesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="sourceGenerator">linearMesh-generator</param>
+  <param name="mesh">mesh-Q2</param>
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="sourceGenerator">Q2Mesh-generator</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -6017,6 +5565,100 @@ SurfaceAdaptor
 
 \begin_layout LyX-Code
 </struct>
+\end_layout
+
+\end_deeper
+\begin_layout Enumerate
+Replace the current 
+\family typewriter
+boxShape
+\family default
+ 
+\end_layout
+
+\begin_deeper
+\begin_layout LyX-Code
+<struct name="boxShape">
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="Type">Box</param>
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="startX">minX</param>
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="endX">maxX</param>
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="startY">minY</param>
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="endY">maxY</param>
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="startZ">minZ</param>
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="endZ">maxZ</param>
+\end_layout
+
+\begin_layout LyX-Code
+</struct>
+\end_layout
+
+\begin_layout Standard
+with a 
+\family typewriter
+backgroundShape
+\family default
+.
+\end_layout
+
+\begin_layout LyX-Code
+<struct name="backgroundShape">
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="Type">Everywhere</param>
+\end_layout
+
+\begin_layout LyX-Code
+</struct>
+\end_layout
+
+\begin_layout Standard
+Also, in the 
+\family typewriter
+viscous
+\family default
+ component, change 
+\family typewriter
+boxShape
+\family default
+ to 
+\family typewriter
+backgroundShape
+\family default
+.
+ This is needed because the deformed top will go beyond the boundary of
+ the original 
+\family typewriter
+boxShape
+\family default
+.
+ An 
+\family typewriter
+Everywhere
+\family default
+ shape covers everywhere.
+ 
 \end_layout
 
 \end_deeper
@@ -6175,11 +5817,11 @@ SurfaceAdaptor
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="mesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="sourceGenerator">linearMesh-generator</param>
+  <param name="mesh">mesh-Q2</param>
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="sourceGenerator">Q2Mesh-generator</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -6237,19 +5879,30 @@ with
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="Equation1">r=hypot(x,y+3); step(r-3.15)*step(3.35-r)*(y+3)/r</param
->
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Equation2">r=hypot(x,y+3); step(r-3.15)*step(3.35-r)*x/r</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Equation3">Equation1</param>
-\end_layout
-
-\end_deeper
+  <param name="Equation1">r=hypot(x,y+3), step(3.35-r)*(y+3)</param>
+\end_layout
+
+\begin_layout LyX-Code
+  <param name="Equation2">r=hypot(x,y+3), -step(3.35-r)*x</param>
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\end_deeper
+\begin_layout Enumerate
+In the boundary conditions, replace the one occurrence of 
+\family typewriter
+Equation3
+\family default
+ with 
+\family typewriter
+Equation1
+\family default
+.
+\end_layout
+
 \begin_layout Enumerate
 Add parameters for the bottom surface shape
 \end_layout
@@ -6273,6 +5926,60 @@ Add parameters for the bottom surface sh
 
 \begin_layout LyX-Code
   <param name="CylinderMaxX">0.960468635615</param>
+\end_layout
+
+\end_deeper
+\begin_layout Enumerate
+Ensure that the height of the incoming material remains fixed by adding
+\end_layout
+
+\begin_deeper
+\begin_layout LyX-Code
+  <param name="staticLeftTop">True</param>
+\end_layout
+
+\begin_layout Standard
+in the 
+\family typewriter
+EulerDeform
+\family default
+ struct, right after
+\end_layout
+
+\begin_layout LyX-Code
+<struct name="EulerDeform">
+\end_layout
+
+\begin_layout LyX-Code
+  <list name="systems">
+\end_layout
+
+\begin_layout LyX-Code
+    <struct>
+\end_layout
+
+\begin_layout LyX-Code
+      <param name="mesh">mesh-Q2</param>
+\end_layout
+
+\begin_layout LyX-Code
+      <param name="innerMesh">mesh-Pm1</param>
+\end_layout
+
+\begin_layout LyX-Code
+      <param name="remesher">velocityRemesher</param>
+\end_layout
+
+\begin_layout LyX-Code
+      <param name="velocityField">VelocityField</param>
+\end_layout
+
+\begin_layout LyX-Code
+      <param name="wrapTop">True</param>
+\end_layout
+
+\begin_layout LyX-Code
+      <param name="staticLeft">True</param>
 \end_layout
 
 \end_deeper
@@ -6467,7 +6174,7 @@ Add the components
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="CellLayout">elementCellLayout</param>
+  <param name="CellLayout">cellLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -6475,11 +6182,7 @@ Add the components
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="FiniteElement_Mesh">linearMesh</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeMesh">mesh-linear</param>
+  <param name="FeMesh">mesh-Q2</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -6495,6 +6198,10 @@ Add the components
 \end_layout
 
 \begin_layout LyX-Code
+ <param name="EscapedRoutine">escapedRoutine</param>
+\end_layout
+
+\begin_layout LyX-Code
 </struct>
 \end_layout
 
@@ -6535,10 +6242,6 @@ Add the components
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="PressureField">PressureField</param>
-\end_layout
-
-\begin_layout LyX-Code
   <list name="Fields">
 \end_layout
 
@@ -6556,6 +6259,10 @@ Add the components
 
 \begin_layout LyX-Code
 </struct>
+\end_layout
+
+\begin_layout LyX-Code
+
 \end_layout
 
 \end_deeper
@@ -6610,10 +6317,6 @@ status open
 status open
 
 \begin_layout Plain Layout
-
-\end_layout
-
-\begin_layout Plain Layout
 \align center
 \begin_inset Graphics
 	filename images/tracers.eps
@@ -6636,10 +6339,6 @@ Particle tracks of tracers
 
 \end_inset
 
-
-\end_layout
-
-\begin_layout Plain Layout
 
 \end_layout
 
@@ -7932,10 +7631,18 @@ This makes the sphere more expansive, co
 
 \end_deeper
 \begin_layout Enumerate
-Modify the buoyancy force term by adding the temperature field after
-\end_layout
-
-\begin_deeper
+Modify the buoyancy force term by adding the temperature field
+\end_layout
+
+\begin_deeper
+\begin_layout LyX-Code
+<param name="TemperatureField">TemperatureField</param>
+\end_layout
+
+\begin_layout Standard
+after the lines
+\end_layout
+
 \begin_layout LyX-Code
 <struct name="buoyancyForceTerm">
 \end_layout
@@ -7946,10 +7653,6 @@ Modify the buoyancy force term by adding
 
 \begin_layout LyX-Code
   <param name="ForceVector">mom_force</param>
-\end_layout
-
-\begin_layout Standard
-the line
 \end_layout
 
 \begin_layout LyX-Code
@@ -9221,15 +8924,11 @@ components
 components
 \family default
  structure.
- For example, the following lines will enable the 
+ For example, the following line will enable the 
 \family typewriter
 EulerDeform
 \family default
- and 
-\family typewriter
-VTKOutput
-\family default
- plugins
+ plugin
 \end_layout
 
 \begin_layout LyX-Code
@@ -9238,10 +8937,6 @@ VTKOutput
 
 \begin_layout LyX-Code
   <param>Underworld_EulerDeform</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param>Underworld_VTKOutput</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -9294,7 +8989,11 @@ EulerDeform
 \end_layout
 
 \begin_layout LyX-Code
-      <param name="mesh">mesh-linear</param>
+      <param name="mesh">mesh-Q2</param>
+\end_layout
+
+\begin_layout LyX-Code
+      <param name="innerMesh">mesh-Pm1</param> 
 \end_layout
 
 \begin_layout LyX-Code
@@ -9310,46 +9009,6 @@ EulerDeform
 \end_layout
 
 \begin_layout LyX-Code
-      <list name="fields">
-\end_layout
-
-\begin_layout LyX-Code
-        <struct>
-\end_layout
-
-\begin_layout LyX-Code
-          <param name="field">VelocityField</param>
-\end_layout
-
-\begin_layout LyX-Code
-          <param name="variable">velocity</param>
-\end_layout
-
-\begin_layout LyX-Code
-        </struct>
-\end_layout
-
-\begin_layout LyX-Code
-        <struct> 
-\end_layout
-
-\begin_layout LyX-Code
-          <param name="field">PressureField</param>
-\end_layout
-
-\begin_layout LyX-Code
-          <param name="variable">pressure</param>
-\end_layout
-
-\begin_layout LyX-Code
-        </struct>
-\end_layout
-
-\begin_layout LyX-Code
-      </list>
-\end_layout
-
-\begin_layout LyX-Code
     </struct>
 \end_layout
 
@@ -9359,28 +9018,6 @@ EulerDeform
 
 \begin_layout LyX-Code
 </struct>
-\end_layout
-
-\begin_layout Standard
-This commands Gale to interpolate both the pressure and velocity field onto
- the new mesh.
- This interpolation can sometimes go awry.
- Often, this is because something else is going wrong.
- For example, if your velocity solution is bad and you get large velocities,
- then the mesh can turn itself inside out.
- This, in turn, will cause 
-\family typewriter
-EulerDeform
-\family default
- to fail.
- If you are getting spurious problems with interpolation, then you can turn
- off this interpolation by removing these two fields from 
-\family typewriter
-EulerDeform
-\family default
-.
- It may slightly affect the speed of your solution, since Gale uses those
- pressure and velocity fields as a starting guess for the next time step.
 \end_layout
 
 \begin_layout Standard
@@ -10267,17 +9904,6 @@ maxTimeSteps The number of time steps to
  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
-dumpEvery How often to write VTK output (see Section 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "sec:.vtk-Files-(Visualization)"
-
-\end_inset
-
-).
 \end_layout
 
 \begin_layout Description
@@ -10442,1395 +10068,12 @@ Gale is built on top of StGermain, which
  For example, you must tell StGermain that you want to set up a regular
  mesh and solve a finite element problem on it.
  This means you have to include a number of components in every input file.
- These components are
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="mesh-linear">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">FeMesh</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="elementType">linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="linearMesh-generator">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">CartesianGenerator</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="mesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="dim">dim</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="shadowDepth">shadowDepth</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <list name="size">
-\end_layout
-
-\begin_layout LyX-Code
-    <param>elementResI</param>
-\end_layout
-
-\begin_layout LyX-Code
-    <param>elementResJ</param>
-\end_layout
-
-\begin_layout LyX-Code
-    <param>elementResK</param>
-\end_layout
-
-\begin_layout LyX-Code
-  </list>
-\end_layout
-
-\begin_layout LyX-Code
-  <list name="minCoord">
-\end_layout
-
-\begin_layout LyX-Code
-    <param>minX</param>
-\end_layout
-
-\begin_layout LyX-Code
-    <param>minY</param>
-\end_layout
-
-\begin_layout LyX-Code
-    <param>minZ</param>
-\end_layout
-
-\begin_layout LyX-Code
-  </list>
-\end_layout
-
-\begin_layout LyX-Code
-  <list name="maxCoord">
-\end_layout
-
-\begin_layout LyX-Code
-    <param>maxX</param>
-\end_layout
-
-\begin_layout LyX-Code
-    <param>maxY</param>
-\end_layout
-
-\begin_layout LyX-Code
-    <param>maxZ</param>
-\end_layout
-
-\begin_layout LyX-Code
-  </list>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="velocity">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">MeshVariable</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="mesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Rank">Vector</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="DataType">Double</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="VectorComponentCount">dim</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <list name="names">
-\end_layout
-
-\begin_layout LyX-Code
-    <param>vx</param>
-\end_layout
-
-\begin_layout LyX-Code
-    <param>vy</param>
-\end_layout
-
-\begin_layout LyX-Code
-    <param>vz</param>
-\end_layout
-
-\begin_layout LyX-Code
-  </list>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="velocityBCs">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">CompositeVC</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Data">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="velocityICs">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">CompositeVC</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Data">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="velocityDofLayout">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">DofLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="mesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="BaseVariableCount">dim</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <list name="BaseVariables">
-\end_layout
-
-\begin_layout LyX-Code
-    <param>vx</param>
-\end_layout
-
-\begin_layout LyX-Code
-    <param>vy</param>
-\end_layout
-
-\begin_layout LyX-Code
-    <param>vz</param>
-\end_layout
-
-\begin_layout LyX-Code
-  </list>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="VelocityField">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">FeVariable</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FEMesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="DofLayout">velocityDofLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="BC">velocityBCs</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="IC">velocityICs</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="LinkedDofInfo">velocityLinkedDofs</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="VelocityMagnitudeField">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">OperatorFeVariable</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Operator">Magnitude</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeVariable">VelocityField</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="VelocityGradientsField">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">OperatorFeVariable</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Operator">Gradient</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeVariable">VelocityField</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="VelocityGradientsInvariantField">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">OperatorFeVariable</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Operator">TensorInvariant</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeVariable">VelocityGradientsField</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="VelocityXXField">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">OperatorFeVariable</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Operator">TakeFirstComponent</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeVariable">VelocityField</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="VelocityYYField">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">OperatorFeVariable</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Operator">TakeSecondComponent</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeVariable">VelocityField</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="StrainRateField">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">OperatorFeVariable</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Operator">TensorSymmetricPart</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeVariable">VelocityGradientsField</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="VorticityField">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">OperatorFeVariable</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Operator">TensorAntisymmetricPart</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeVariable">VelocityGradientsField</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="StrainRateInvariantField">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">OperatorFeVariable</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Operator">SymmetricTensor_Invariant</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeVariable">StrainRateField</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="pressure">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">MeshVariable</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="mesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Rank">Scalar</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="DataType">Double</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="pressureDofLayout">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">DofLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="mesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <list name="BaseVariables">
-\end_layout
-
-\begin_layout LyX-Code
-    <param>pressure</param>
-\end_layout
-
-\begin_layout LyX-Code
-  </list>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="PressureField">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">FeVariable</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FEMesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="DofLayout">pressureDofLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="LinkedDofInfo">pressureLinkedDofs</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="StressField">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">StressField</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="StrainRateField">StrainRateField</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Context">context</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="ConstitutiveMatrix">constitutiveMatrix</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Swarm">picIntegrationPoints</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Mesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="IC">stressICs</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct> 
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="ViscosityField">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">ViscosityField</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Context">context</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Swarm">picIntegrationPoints</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Mesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="ConstitutiveMatrix">constitutiveMatrix</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct> 
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="cellLayout">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">SingleCellLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="particleLayout">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">GaussParticleLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="gaussSwarm">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">IntegrationPointsSwarm</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="CellLayout">cellLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="ParticleLayout">particleLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeMesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="TimeIntegrator">timeIntegrator</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="IntegrationPointMapper">gaussMapper</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="gaussMapper">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">GaussMapper</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="IntegrationPointsSwarm">gaussSwarm</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="MaterialPointsSwarm">gaussMaterialSwarm</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="backgroundLayout">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">BackgroundParticleLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="gaussMaterialSwarm">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">MaterialPointsSwarm</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="CellLayout">cellLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="ParticleLayout">backgroundLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeMesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="timeIntegrator">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">TimeIntegrator</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="order">1</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="simultaneous">t</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Context">context</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="elementCellLayout">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">ElementCellLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Mesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="weights">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">PCDVC</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="resolutionX">10</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="resolutionY">10</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="resolutionZ">10</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="lowerT">0.6</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="upperT">25</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="maxDeletions">3</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="maxSplits">3</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="MaterialPointsSwarm">materialSwarm</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="localLayout">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">MappedParticleLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="picIntegrationPoints">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">IntegrationPointsSwarm</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="CellLayout">elementCellLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="ParticleLayout">localLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeMesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="WeightsCalculator">weights</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="TimeIntegrator">timeIntegrator</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="IntegrationPointMapper">mapper</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="mapper">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">CoincidentMapper</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="IntegrationPointsSwarm">picIntegrationPoints</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="MaterialPointsSwarm">materialSwarm</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="materialSwarmParticleLayout">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">MeshParticleLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="mesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="cellParticleCount">particlesPerCell</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="materialSwarm">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">MaterialPointsSwarm</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="CellLayout">elementCellLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="ParticleLayout">materialSwarmParticleLayout</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeMesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="SplittingRoutine">splittingRoutine</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="RemovalRoutine">removalRoutine</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="EscapedRoutine">escapedRoutine</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="materialSwarmAdvector">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">SwarmAdvector</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Swarm">materialSwarm</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="TimeIntegrator">timeIntegrator</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="VelocityField">VelocityField</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="PeriodicBCsManager">periodicBCsManager</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="allowFallbackToFirstOrder">True</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="splittingRoutine">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">ReseedSplitting</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="idealParticleCount">particlesPerCell</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="solutionVelocity">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">SolutionVector</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeVariable">VelocityField</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="solutionPressure">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">SolutionVector</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeVariable">PressureField</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="mom_force">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">ForceVector</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeVariable">VelocityField</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="ExtraInfo">context</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="cont_force">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">ForceVector</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeVariable">PressureField</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="ExtraInfo">context</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="k_matrix">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">StiffnessMatrix</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="RowVariable">VelocityField</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="ColumnVariable">VelocityField</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="RHS">mom_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="constitutiveMatrix">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">ConstitutiveMatrixCartesian</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Swarm">picIntegrationPoints</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="StiffnessMatrix">k_matrix</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="g_matrix">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">StiffnessMatrix</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="RowVariable">VelocityField</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">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 LyX-Code
-<struct name="c_matrix">
-\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="mixedStabiliser">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">MixedStabiliserTerm</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Swarm">gaussSwarm</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="picSwarm">picIntegrationPoints</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="storeVisc">storeViscosity</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="StiffnessMatrix">c_matrix</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="background">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">Everywhere</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="escapedRoutine">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">EscapedRoutine</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="idealParticleCount">0</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="velocityRemesher">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">StripRemesher</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="mesh">mesh-linear</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="meshType">regular</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <list name="dim">
-\end_layout
-
-\begin_layout LyX-Code
-    <param>true</param>
-\end_layout
-
-\begin_layout LyX-Code
-    <param>true</param>
-\end_layout
-
-\begin_layout LyX-Code
-    <param>true</param>
-\end_layout
-
-\begin_layout LyX-Code
-  </list>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="storeViscosity">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">StoreVisc</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="MaterialPointsSwarm">materialSwarm</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="storeStress">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">StoreStress</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="MaterialPointsSwarm">materialSwarm</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout Standard
-For almost all simulations, you will not need to change these components.
+ These components are listed in the sample input file 
+\family typewriter
+input/cookbook/template.xml
+\family default
+.
+ For almost all simulations, you will not need to change these components.
 \end_layout
 
 \begin_layout Section
@@ -11874,7 +10117,7 @@ To configure Gale to use and evolve the 
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="mesh">mesh-linear</param>
+  <param name="mesh">mesh-Q2</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -11890,7 +10133,7 @@ To configure Gale to use and evolve the 
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="Data">mesh-linear</param>
+  <param name="Data">mesh-Q2</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -11906,7 +10149,7 @@ To configure Gale to use and evolve the 
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="Data">mesh-linear</param>
+  <param name="Data">mesh-Q2</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -11922,7 +10165,7 @@ To configure Gale to use and evolve the 
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="mesh">mesh-linear</param>
+  <param name="mesh">mesh-Q2</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -11950,7 +10193,7 @@ To configure Gale to use and evolve the 
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="FEMesh">mesh-linear</param>
+  <param name="FEMesh">mesh-Q2</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -12180,6 +10423,10 @@ after the lines
 
 \begin_layout LyX-Code
 <list name="FieldVariablesToCheckpoint">
+\end_layout
+
+\begin_layout LyX-Code
+  <param>StrainRateInvariant</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -16032,18 +14279,6 @@ frictionCoefficient
 
 \begin_layout Standard
 Finally, DruckerPrager requires a pressure.
- If you are using 
-\family typewriter
-HydrostaticTerm
-\family default
- (see Section 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "sec:HydrostaticTerm"
-
-\end_inset
-
-), you have to remember to give it that as well.
 \end_layout
 
 \begin_layout Standard
@@ -16057,7 +14292,7 @@ reference "sec:HydrostaticTerm"
 \noindent
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="18" columns="2">
+<lyxtabular version="3" rows="17" columns="2">
 <features tabularvalignment="middle">
 <column alignment="center" valignment="top" width="0">
 <column alignment="center" valignment="top" width="0">
@@ -16087,26 +14322,6 @@ Defaults
 
 \begin_layout Plain Layout
 PressureField
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-none
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-HydrostaticTerm
 \end_layout
 
 \end_inset
@@ -17306,122 +15521,6 @@ Gaussian
 \end_layout
 
 \begin_layout Standard
-The type can also be 
-\family typewriter
-HydrostaticTerm
-\family default
-.
- If you are using a 
-\family typewriter
-HydrostaticTerm
-\family default
- component (see Section 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "sec:HydrostaticTerm"
-
-\end_inset
-
-), then you need a 
-\family typewriter
-StressBC
-\family default
- component on the top to act as a restoring force when the surface of the
- material dips below equilibrium.
- So it would be something like
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="stressBCTop">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">StressBC</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="ForceVector">mom_force</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Swarm">picIntegrationPoints</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="wall">top</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="y_type">HydrostaticTerm</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="y_value">hydrostaticTerm</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout Standard
-If the bottom boundary can move (that is, you have not set 
-\family typewriter
-StaticBottom
-\family default
- in 
-\family typewriter
-EulerDeform
-\family default
- and 
-\begin_inset Formula $v_{y}\neq0$
-\end_inset
-
-), and the material outside the simulation is different from inside, then
- you must also set a StressBC on the bottom.
- For this, you must also set 
-\family typewriter
-bottomDensity
-\family default
-, giving something like
-\end_layout
-
-\begin_layout LyX-Code
-<struct name="stressBCTop">
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">StressBC</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="ForceVector">mom_force</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Swarm">picIntegrationPoints</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="wall">bottom</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="y_type">HydrostaticTerm</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="y_value">hydrostaticTerm</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="bottomDensity">3000</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout Standard
 Note that you must not have a separate 
 \family typewriter
 StressBC
@@ -17572,7 +15671,7 @@ SurfaceAdaptor
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="mesh">mesh-linear</param>
+  <param name="mesh">mesh-Q2</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -17661,7 +15760,7 @@ bottom
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="mesh">mesh-linear</param>
+  <param name="mesh">mesh-Q2</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -18996,181 +17095,6 @@ AllNodesVC
 \end_layout
 
 \begin_layout Section
-\begin_inset CommandInset label
-LatexCommand label
-name "sec:HydrostaticTerm"
-
-\end_inset
-
-HydrostaticTerm
-\end_layout
-
-\begin_layout Standard
-This term subtracts out the hydrostatic part of the pressure as described
- in Section 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "sub:Hydrostatic-Pressure"
-
-\end_inset
-
-.
- You give it the equations for the density and pressure.
- Section 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "sec:Standard-Condition-Functions"
-
-\end_inset
-
- has complete details on how to enter those equations.
- As an example, consider the case where the material has a density of 5,
- going from the bottom to a height of 13, with a gravity of 10.
- The 
-\family typewriter
-densityEquation
-\family default
- would then be
-\end_layout
-
-\begin_layout LyX-Code
-step(13-y)*5
-\end_layout
-
-\begin_layout Standard
-and the 
-\family typewriter
-pressureEquation
-\family default
- would be the integral of that, multiplied by the gravity
-\end_layout
-
-\begin_layout LyX-Code
-step(13-y)*5*step(13-y)*10
-\end_layout
-
-\begin_layout Standard
-If you have temperature and thermal expansity in your problem, remember
- to put those effects in.
- So if the temperature is a linear gradient from 0 at the top to 1 at the
- bottom, and your thermal expansity is 
-\begin_inset Formula $10^{-5}$
-\end_inset
-
-, then the 
-\family typewriter
-densityEquation
-\family default
- would be
-\end_layout
-
-\begin_layout LyX-Code
-step(13-y)*5*(1-(10^(-5))*(13-y)/13)
-\end_layout
-
-\begin_layout Standard
-and the 
-\family typewriter
-pressureEquation
-\family default
- would be the integral of this multiplied by gravity, with the boundary
- condition that the pressure is 0 at the surface
-\end_layout
-
-\begin_layout LyX-Code
-step(13-y)*5*((13-y) - (10^(-5))*((13-y)^2)/26)*10
-\end_layout
-
-\begin_layout Standard
-The integral for the pressure, in particular, may become very tricky.
- If your setup defies simple analytic treatments, it may be ok to use simpler,
- approximate density and temperature.
- However, it is 
-\series bold
-\color red
-critical
-\series default
-\color inherit
- that the pressure is always the integral of the density.
- Otherwise, you will get wrong results.
- 
-\end_layout
-
-\begin_layout Standard
-\align center
-\begin_inset Tabular
-<lyxtabular version="3" rows="3" columns="2">
-<features tabularvalignment="middle">
-<column alignment="center" valignment="top" width="0">
-<column alignment="center" valignment="top" width="0">
-<row>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-Defaults
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-densityEquation
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-pressureEquation
-\end_layout
-
-\end_inset
-</cell>
-<cell multicolumn="1" alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-
-\end_layout
-
-\end_inset
-</cell>
-</row>
-</lyxtabular>
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Section
 Buoyancy Forces
 \begin_inset CommandInset label
 LatexCommand label
@@ -19271,18 +17195,6 @@ picIntegrationPoints
 \end_layout
 
 \begin_layout Standard
-If you have defined a 
-\family typewriter
-HydrostaticTerm
-\family default
- (Section ), then you need to pass it in to the 
-\family typewriter
-BuoyancyForceTerm
-\family default
- for it to take effect.
-\end_layout
-
-\begin_layout Standard
 \begin_inset VSpace defskip
 \end_inset
 
@@ -19293,7 +17205,7 @@ BuoyancyForceTerm
 \noindent
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="7" columns="2">
+<lyxtabular version="3" rows="6" columns="2">
 <features tabularvalignment="middle">
 <column alignment="center" valignment="top" width="0">
 <column alignment="center" valignment="top" width="0">
@@ -19403,26 +17315,6 @@ none
 
 \begin_layout Plain Layout
 Swarm
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-none
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-HydrostaticTerm
 \end_layout
 
 \end_inset
@@ -19512,18 +17404,6 @@ Swarm
  is always 
 \family typewriter
 picIntegrationPoints
-\family default
-.
-\end_layout
-
-\begin_layout Standard
-Note that this component does not take a 
-\family typewriter
-HydrostaticTerm
-\family default
-, so you can not use this component if you are using 
-\family typewriter
-HydrostaticTerm
 \family default
 .
 \end_layout
@@ -19703,7 +17583,7 @@ Swarm picIntegrationPoints
 \end_layout
 
 \begin_layout Description
-GeometryMesh mesh-linear
+GeometryMesh mesh-Q2
 \end_layout
 
 \begin_layout Standard
@@ -21233,7 +19113,7 @@ Then add some components to set up the m
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="Type"> ParticleMovementHandler </param>
+  <param name="Type">ParticleMovementHandler</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -21249,7 +19129,7 @@ Then add some components to set up the m
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="CellLayout">elementCellLayout</param>
+  <param name="CellLayout">cellLayout</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -21257,11 +19137,7 @@ Then add some components to set up the m
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="FiniteElement_Mesh">linearMesh</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="FeMesh">mesh-linear</param>
+  <param name="FeMesh">mesh-Q2</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -21323,15 +19199,11 @@ Finally, add a swarmOutput component to 
 \end_layout
 
 \begin_layout LyX-Code
-  <param name="PressureField">PressureField</param>
-\end_layout
-
-\begin_layout LyX-Code
   <list name="Fields">
 \end_layout
 
 \begin_layout LyX-Code
-    <param>VelocityMagnitudeField</param>
+    <param>PressureField</param>
 \end_layout
 
 \begin_layout LyX-Code
@@ -21347,13 +19219,7 @@ Finally, add a swarmOutput component to 
 \end_layout
 
 \begin_layout Standard
-Note that to output the pressure correctly with hydrostatic corrections,
- you must use the 
-\family typewriter
-PressureField
-\family default
- variable slot.
- All other fields are output by adding them to the 
+All fields are output by adding them to the 
 \family typewriter
 Fields
 \family default
@@ -21435,75 +19301,10 @@ name "cha:Output-File-Format"
 \end_layout
 
 \begin_layout Standard
-Gale outputs two types of files: VTK files for data analysis and visualization,
- and checkpointing files for restarting a run.
-\end_layout
-
-\begin_layout Section
-\begin_inset CommandInset label
-LatexCommand label
-name "sec:.vtk-Files-(Visualization)"
-
-\end_inset
-
-VTK Files: 
-\family typewriter
-.vts, .pvts, .vtu, and .pvtu
-\family default
- (Visualization)
-\end_layout
-
-\begin_layout Standard
-These files are output by the 
-\family typewriter
-Underworld_VTKOutput
-\family default
- plugin.
- The 
-\family typewriter
-.vts
-\family default
- and 
-\family typewriter
-.pvts
-\family default
- files contain information about quantities on the grid, and the 
-\family typewriter
-.vtu
-\family default
- and 
-\family typewriter
-.pvtu
-\family default
- contain information about quantities on the particles.
- Every processor outputs its own 
-\family typewriter
-.vts
-\family default
- and 
-\family typewriter
-.vtu 
-\family default
-file, and the 
-\family typewriter
-.pvts
-\family default
- and 
-\family typewriter
-.pvtu
-\family default
- are small files that have information on how to stitch them all together.
- Ordinarily, you would only open the 
-\family typewriter
-.pvts
-\family default
- and 
-\family typewriter
-.pvtu
-\family default
- files.
- These files are in a format understood by a wide variety of visualization
- programs, such as ParaView 
+Gale outputs two types of files: HDF5 checkpointing files for restarting
+ a run, and XDMF files which use those checkpoint files for visualization.
+ XDMF files are understood by a wide variety of visualization programs,
+ such as ParaView 
 \begin_inset Flex URL
 status collapsed
 
@@ -21514,161 +19315,18 @@ paraview.org
 
 \end_inset
 
- (recommended) or MayaVi 
+ or VisIt 
 \begin_inset Flex URL
 status collapsed
 
 \begin_layout Plain Layout
 
-mayavi.sf.net
-\end_layout
-
-\end_inset
-
-.
- VisIt 
-\begin_inset Flex URL
-status collapsed
-
-\begin_layout Plain Layout
-
 www.llnl.gov/visit
 \end_layout
 
 \end_inset
 
- can understand the raw 
-\family typewriter
-.vts
-\family default
- and 
-\family typewriter
-.vtu
-\family default
- files, but not the 
-\family typewriter
-.pvtu
-\family default
- and 
-\family typewriter
-.pvts
-\family default
- files.
- So VisIt is mostly useful for visualizing serial runs.
-\end_layout
-
-\begin_layout Standard
-The 
-\family typewriter
-Underworld_VTKOutput
-\family default
- plugin is activated by adding the lines
-\end_layout
-
-\begin_layout LyX-Code
-<struct>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Type">Underworld_VTKOutput</param>
-\end_layout
-
-\begin_layout LyX-Code
-  <param name="Context">context</param>
-\end_layout
-
-\begin_layout LyX-Code
-</struct>
-\end_layout
-
-\begin_layout Standard
-to the list of plugins.
- This line is already in the example input files.
-\end_layout
-
-\begin_layout Standard
-The particle files can get quite large.
- Many times, you do not need to see every single particle.
- You can configure Gale to only output every Nth particle by setting 
-\family typewriter
-particleStepping
-\family default
- to N.
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Tabular
-<lyxtabular version="3" rows="2" columns="2">
-<features tabularvalignment="middle">
-<column alignment="center" valignment="top" width="0">
-<column alignment="center" valignment="top" width="0">
-<row>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-Defaults
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-particleStepping
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-1
-\end_layout
-
-\end_inset
-</cell>
-</row>
-</lyxtabular>
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Section
-\begin_inset CommandInset label
-LatexCommand label
-name "sec:Checkpoint Files"
-
-\end_inset
-
-
-\family typewriter
-Checkpoint
-\family default
- Files: .h5, .dat and .xmf
-\end_layout
-
-\begin_layout Standard
-These files are mostly useful for checkpointing.
- They are in a machine dependent format and have the bare minimum needed
- to restart the run.
+.
 \end_layout
 
 \begin_layout Chapter
diff -r e8d08f6a076f -r e8416a557e74 doc/gale_cover.png
Binary file doc/gale_cover.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/gale_cover.xcf
Binary file doc/gale_cover.xcf has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_bottom.png
Binary file doc/images/Paraview_bottom.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_deformed_bottom.png
Binary file doc/images/Paraview_deformed_bottom.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_multi_material.png
Binary file doc/images/Paraview_multi_material.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_multi_viscosity.png
Binary file doc/images/Paraview_multi_viscosity.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_non_newtonian.png
Binary file doc/images/Paraview_non_newtonian.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_normal_stress.png
Binary file doc/images/Paraview_normal_stress.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_thermal.png
Binary file doc/images/Paraview_thermal.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_thermal_file.png
Binary file doc/images/Paraview_thermal_file.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_viscous_extension.png
Binary file doc/images/Paraview_viscous_extension.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_viscous_inflow.png
Binary file doc/images/Paraview_viscous_inflow.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_viscous_sinusoid.png
Binary file doc/images/Paraview_viscous_sinusoid.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_viscous_split.png
Binary file doc/images/Paraview_viscous_split.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_yielding.png
Binary file doc/images/Paraview_yielding.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_yielding_viscosity.png
Binary file doc/images/Paraview_yielding_viscosity.png has changed
diff -r e8d08f6a076f -r e8416a557e74 doc/images/Paraview_yielding_yielding.png
Binary file doc/images/Paraview_yielding_yielding.png has changed

More information about the CIG-COMMITS mailing list