[cig-commits] r8277 - long/3D/Gale/trunk/documentation
sue at geodynamics.org
sue at geodynamics.org
Mon Nov 12 13:30:56 PST 2007
Author: sue
Date: 2007-11-12 13:30:48 -0800 (Mon, 12 Nov 2007)
New Revision: 8277
Modified:
long/3D/Gale/trunk/documentation/gale.lyx
long/3D/Gale/trunk/documentation/gale_cover.psd
Log:
fixed typos
Modified: long/3D/Gale/trunk/documentation/gale.lyx
===================================================================
--- long/3D/Gale/trunk/documentation/gale.lyx 2007-11-12 18:20:49 UTC (rev 8276)
+++ long/3D/Gale/trunk/documentation/gale.lyx 2007-11-12 21:30:48 UTC (rev 8277)
@@ -1,5 +1,5 @@
-#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
-\lyxformat 245
+#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+\lyxformat 276
\begin_document
\begin_header
\textclass book
@@ -11,13 +11,21 @@
\end_preamble
\language english
\inputencoding auto
-\fontscheme default
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
\graphics default
\paperfontsize default
\spacing single
\papersize default
\use_geometry true
\use_amsmath 1
+\use_esint 0
\cite_engine basic
\use_bibtopic false
\paperorientation portrait
@@ -34,7 +42,8 @@
\papersides 2
\paperpagestyle headings
\tracking_changes false
-\output_changes true
+\output_changes false
+\author ""
\end_header
\begin_body
@@ -84,7 +93,7 @@
\end_layout
\begin_layout Author
-© California Institute of Technology
+© California Institute of Technology
\newline
Walter Landry and Luke Hodkinson
\newline
@@ -109,7 +118,7 @@
\end_layout
\begin_layout Standard
-\begin_inset LatexCommand \tableofcontents{}
+\begin_inset LatexCommand tableofcontents
\end_inset
@@ -188,7 +197,7 @@
\begin_layout Itemize
Moresi, L.N., F.
Dufour, and H.-B.
- Mühlhaus (2003), A Lagrangian integration point finite element method for
+ Mühlhaus (2003), A Lagrangian integration point finite element method for
large deformation modeling of viscoelastic geomaterials,
\emph on
J.
@@ -212,17 +221,23 @@
The Gale team requests that in your oral presentations and in your papers
that you indicate your use of this code and acknowledge the authors of
the code,
-\begin_inset LatexCommand \htmlurl[CIG]{www.geodynamics.org}
+\begin_inset LatexCommand htmlurl
+name "CIG"
+target "www.geodynamics.org"
\end_inset
,
-\begin_inset LatexCommand \htmlurl[Victoria Partnership for Advanced Computing]{www.vpac.org}
+\begin_inset LatexCommand htmlurl
+name "Victoria Partnership for Advanced Computing"
+target "www.vpac.org"
\end_inset
, and
-\begin_inset LatexCommand \htmlurl[Monash University]{www.monash.edu}
+\begin_inset LatexCommand htmlurl
+name "Monash University"
+target "www.monash.edu"
\end_inset
@@ -374,7 +389,8 @@
\begin_layout Standard
Note that there is no explicit time dependency in the momentum equation
-\begin_inset LatexCommand \ref{eq:simple momentum conservation}
+\begin_inset LatexCommand ref
+reference "eq:simple momentum conservation"
\end_inset
@@ -394,12 +410,14 @@
\begin_layout Standard
Eqs.
-\begin_inset LatexCommand \ref{eq:simple momentum conservation}
+\begin_inset LatexCommand ref
+reference "eq:simple momentum conservation"
\end_inset
and
-\begin_inset LatexCommand \ref{eq:continuity}
+\begin_inset LatexCommand ref
+reference "eq:continuity"
\end_inset
@@ -432,12 +450,14 @@
\begin_layout Standard
Using standard finite-element techniques, eqs.
-\begin_inset LatexCommand \ref{eq:simple momentum conservation}
+\begin_inset LatexCommand ref
+reference "eq:simple momentum conservation"
\end_inset
and
-\begin_inset LatexCommand \ref{eq:continuity}
+\begin_inset LatexCommand ref
+reference "eq:continuity"
\end_inset
@@ -471,7 +491,8 @@
\begin_layout Standard
At this point, it is common in many codes to introduce a penalty function
to make the right hand side of the continuity equation
-\begin_inset LatexCommand \ref{eq:continuity}
+\begin_inset LatexCommand ref
+reference "eq:continuity"
\end_inset
@@ -516,7 +537,8 @@
\end_inset
This equation is solved using the Uzawa algorithm
-\begin_inset LatexCommand \cite{Uzawa}
+\begin_inset LatexCommand cite
+key "Uzawa"
\end_inset
@@ -541,7 +563,8 @@
\begin_layout Standard
Gravity is accounted for by adding a body force term to eq.
-\begin_inset LatexCommand \ref{eq:simple momentum conservation}
+\begin_inset LatexCommand ref
+reference "eq:simple momentum conservation"
\end_inset
@@ -568,7 +591,8 @@
This modifies eq.
-\begin_inset LatexCommand \ref{eq:matrix form}
+\begin_inset LatexCommand ref
+reference "eq:matrix form"
\end_inset
@@ -624,7 +648,8 @@
is the rate of energy production (e.g., from radiogenic sources).
Note that eq.
-\begin_inset LatexCommand \ref{eq:energy}
+\begin_inset LatexCommand ref
+reference "eq:energy"
\end_inset
@@ -639,13 +664,15 @@
Gale incorporates a number of different rheologies and allows you to create
your own.
For details on the existing rheologies, see Section
-\begin_inset LatexCommand \ref{sec:Materials}
+\begin_inset LatexCommand ref
+reference "sec:Materials"
\end_inset
.
To create your own rheology, see Chapter
-\begin_inset LatexCommand \ref{cha:Modifying-Gale}
+\begin_inset LatexCommand ref
+reference "cha:Modifying-Gale"
\end_inset
@@ -659,7 +686,9 @@
\begin_layout Standard
Gale arose from discussions at an NSF-sponsored workshop on Tectonic Modeling
held in Breckenridge, Colorado, in June 2005; see
-\begin_inset LatexCommand \htmlurl[Geodynamic Modeling of Tectonics Processes 2005 workshop report]{www.geodynamics.org/cig/workinggroups/long/workshops/2005/issues}
+\begin_inset LatexCommand htmlurl
+name "Geodynamic Modeling of Tectonics Processes 2005 workshop report"
+target "www.geodynamics.org/cig/workinggroups/long/workshops/2005/issues"
\end_inset
@@ -677,7 +706,8 @@
problems.
Gale is an open-source code that we hope will be at least as useful as
SOPALE and MicroFEM
-\begin_inset LatexCommand \cite{Fullsack}
+\begin_inset LatexCommand cite
+key "Fullsack"
\end_inset
@@ -687,7 +717,8 @@
In the future, Gale will run benchmarks such as extension and shortening,
as well as the traditional subduction model as shown in Fig.
-\begin_inset LatexCommand \ref{fig:General-subduction-model}
+\begin_inset LatexCommand ref
+reference "fig:General-subduction-model"
\end_inset
@@ -697,19 +728,22 @@
\begin_layout Standard
The development of Gale was jump-started by building on top of Underworld
-\begin_inset LatexCommand \cite{Underworld}
+\begin_inset LatexCommand cite
+key "Underworld"
\end_inset
, a mantle convection code developed by Louis Moresi's group at Monash and
the Victorian Partnership for Advanced Computing (VPAC).
Underworld was created as a parallel version of Ellipsis3D
-\begin_inset LatexCommand \cite{Ellipsis}
+\begin_inset LatexCommand cite
+key "Ellipsis"
\end_inset
, a mantle convection code which grew out of CitCom
-\begin_inset LatexCommand \cite{Citcom}
+\begin_inset LatexCommand cite
+key "Citcom"
\end_inset
@@ -729,13 +763,18 @@
sideways false
status open
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:General-subduction-model}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:General-subduction-model"
+
\end_inset
General subduction model from
-\begin_inset LatexCommand \cite{Fullsack}
+\begin_inset LatexCommand cite
+key "Fullsack"
\end_inset
@@ -775,6 +814,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
\noindent
\align center
@@ -817,7 +861,9 @@
\begin_layout Standard
If you do not need to run on parallel machines, the easiest way to install
Gale is to download binaries for your platform from the
-\begin_inset LatexCommand \htmlurl[Gale website]{geodynamics.org/cig/software/packages/long/gale/}
+\begin_inset LatexCommand htmlurl
+name "Gale website"
+target "geodynamics.org/cig/software/packages/long/gale/"
\end_inset
@@ -903,7 +949,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand \label{sec:Downloading-the-Code}
+\begin_inset LatexCommand label
+name "sec:Downloading-the-Code"
\end_inset
@@ -912,7 +959,9 @@
\begin_layout Standard
You can get the source for the latest release from the
-\begin_inset LatexCommand \htmlurl[Gale website]{geodynamics.org/cig/software/packages/long/gale/}
+\begin_inset LatexCommand htmlurl
+name "Gale website"
+target "geodynamics.org/cig/software/packages/long/gale/"
\end_inset
@@ -949,7 +998,9 @@
\begin_layout Standard
Otherwise, you will need to download and install a Subversion client, available
at the
-\begin_inset LatexCommand \htmlurl[Subversion Website]{subversion.tigris.org/project_packages.html}
+\begin_inset LatexCommand htmlurl
+name "Subversion Website"
+target "subversion.tigris.org/project_packages.html"
\end_inset
@@ -971,7 +1022,9 @@
\begin_layout Standard
The primary point of support for Gale is the
-\begin_inset LatexCommand \url[CIG Long-Term Crustal Dynamics Mailing List]{cig-long at geodynamics.org}
+\begin_inset LatexCommand url
+name "CIG Long-Term Crustal Dynamics Mailing List"
+target "cig-long at geodynamics.org"
\end_inset
@@ -982,7 +1035,9 @@
\end_layout
\begin_layout LyX-Code
-\begin_inset LatexCommand \htmlurl[cig-long Archives]{geodynamics.org/pipermail/cig-long/}
+\begin_inset LatexCommand htmlurl
+name "cig-long Archives"
+target "geodynamics.org/pipermail/cig-long/"
\end_inset
@@ -994,7 +1049,9 @@
\end_layout
\begin_layout LyX-Code
-\begin_inset LatexCommand \htmlurl[Roundup]{geodynamics.org/roundup}
+\begin_inset LatexCommand htmlurl
+name "Roundup"
+target "geodynamics.org/roundup"
\end_inset
@@ -1123,13 +1180,15 @@
In general, Gale does not have many defaults, so almost everything must
be specified in the input file.
For examples of how to create your own input files, see Chapter
-\begin_inset LatexCommand \ref{cha:Cookbooks}
+\begin_inset LatexCommand ref
+reference "cha:Cookbooks"
\end_inset
.
For a complete description of the input file format, see Appendix
-\begin_inset LatexCommand \ref{cha:Input-File-Format}
+\begin_inset LatexCommand ref
+reference "cha:Input-File-Format"
\end_inset
@@ -1247,7 +1306,8 @@
.txt
\family default
files are described fully in Appendix
-\begin_inset LatexCommand \ref{cha:Output-File-Format}
+\begin_inset LatexCommand ref
+reference "cha:Output-File-Format"
\end_inset
@@ -1316,12 +1376,14 @@
StoreStress
\family default
structs to your rheology as in Section
-\begin_inset LatexCommand \ref{sec:Viscous-Material}
+\begin_inset LatexCommand ref
+reference "sec:Viscous-Material"
\end_inset
(see also Section
-\begin_inset LatexCommand \ref{sub:StoreViscosity}
+\begin_inset LatexCommand ref
+reference "sub:StoreViscosity"
\end_inset
@@ -1340,17 +1402,23 @@
files.
These files are in a standard, self-describing file format that can be
easily visualized with several different visualization programs, e.g.,
-\begin_inset LatexCommand \htmlurl[ParaView]{paraview.org}
+\begin_inset LatexCommand htmlurl
+name "ParaView"
+target "paraview.org"
\end_inset
,
-\begin_inset LatexCommand \htmlurl[MayaVI]{mayavi.sf.net}
+\begin_inset LatexCommand htmlurl
+name "MayaVI"
+target "mayavi.sf.net"
\end_inset
, and
-\begin_inset LatexCommand \htmlurl[Visit]{www.llnl.gov/visit}
+\begin_inset LatexCommand htmlurl
+name "Visit"
+target "www.llnl.gov/visit"
\end_inset
@@ -1379,7 +1447,8 @@
\begin_layout Subsection
Visualization with ParaView
-\begin_inset LatexCommand \label{sub:Visualization-with-ParaView}
+\begin_inset LatexCommand label
+name "sub:Visualization-with-ParaView"
\end_inset
@@ -1893,7 +1962,8 @@
\color none
You can set the DumpSwarm plugin (see Section
-\begin_inset LatexCommand \ref{sec:.txt-Files-(Particle}
+\begin_inset LatexCommand ref
+reference "sec:.txt-Files-(Particle"
\end_inset
@@ -2123,12 +2193,14 @@
\family default
).
For problems with inflow boundaries (see Sections
-\begin_inset LatexCommand \ref{sec:Viscous-In-Outflow}
+\begin_inset LatexCommand ref
+reference "sec:Viscous-In-Outflow"
\end_inset
and
-\begin_inset LatexCommand \ref{sub:Flux-Boundary-Conditions}
+\begin_inset LatexCommand ref
+reference "sub:Flux-Boundary-Conditions"
\end_inset
@@ -2178,7 +2250,8 @@
\begin_layout Chapter
Cookbooks
-\begin_inset LatexCommand \label{cha:Cookbooks}
+\begin_inset LatexCommand label
+name "cha:Cookbooks"
\end_inset
@@ -2269,7 +2342,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Viscous-Material}
+\begin_inset LatexCommand label
+name "sec:Viscous-Material"
\end_inset
@@ -2394,7 +2468,8 @@
\begin_layout Enumerate
In order for Gale to include the viscosity and stress in the output, you
have to store them in separate fields (see Section
-\begin_inset LatexCommand \ref{sub:StoreViscosity}
+\begin_inset LatexCommand ref
+reference "sub:StoreViscosity"
\end_inset
@@ -2503,7 +2578,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Viscous-Material-in}
+\begin_inset LatexCommand label
+name "sec:Viscous-Material-in"
\end_inset
@@ -2512,7 +2588,8 @@
\begin_layout Standard
The input file you created in Section
-\begin_inset LatexCommand \ref{sec:Viscous-Material}
+\begin_inset LatexCommand ref
+reference "sec:Viscous-Material"
\end_inset
@@ -2663,12 +2740,14 @@
.
A visualization of the strain rate invariant and velocity (see Section
-\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+\begin_inset LatexCommand ref
+reference "sub:Visualization-with-ParaView"
\end_inset
) is shown in Figure
-\begin_inset LatexCommand \ref{fig:Strain-viscous-extension}
+\begin_inset LatexCommand ref
+reference "fig:Strain-viscous-extension"
\end_inset
@@ -2693,9 +2772,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Strain-viscous-extension}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Strain-viscous-extension"
+
\end_inset
Strain rate invariant and velocities of viscous material in extension
@@ -2706,6 +2789,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
The banding is a numerical artifact that arises from having a finite number
of particles per cell.
@@ -2720,7 +2808,8 @@
Another exercise is to make the bottom boundary move differently, and not
just have the material slide along.
In particular, this example will simulate a box like in Figure
-\begin_inset LatexCommand \ref{fig:Split-Boundary}
+\begin_inset LatexCommand ref
+reference "fig:Split-Boundary"
\end_inset
@@ -2746,9 +2835,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Split-Boundary}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Split-Boundary"
+
\end_inset
Split Boundary
@@ -2759,6 +2852,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Enumerate
First, copy
\family typewriter
@@ -2887,10 +2985,10 @@
\series bold
\color red
-Warning:
+Warning:
\series default
\color none
-Do not add them in the list named
+ Do not add them in the list named
\family typewriter
``variables
\family default
@@ -2906,12 +3004,14 @@
.
A visualization of the strain rate invariant and velocity (see Section
-\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+\begin_inset LatexCommand ref
+reference "sub:Visualization-with-ParaView"
\end_inset
) shown in Figure
-\begin_inset LatexCommand \ref{fig:Strain-complex}
+\begin_inset LatexCommand ref
+reference "fig:Strain-complex"
\end_inset
@@ -2940,9 +3040,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Strain-complex}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Strain-complex"
+
\end_inset
Strain rate invariant and velocities with complex boundaries
@@ -2953,8 +3057,14 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Viscous-In-Outflow}
+\begin_inset LatexCommand label
+name "sec:Viscous-In-Outflow"
\end_inset
@@ -2964,7 +3074,8 @@
\begin_layout Standard
This example implements a different kind of boundary condition, where material
flows in one side and out another as in Figure
-\begin_inset LatexCommand \ref{fig:Inflow/Outflow-Boundary}
+\begin_inset LatexCommand ref
+reference "fig:Inflow/Outflow-Boundary"
\end_inset
@@ -2998,9 +3109,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Inflow/Outflow-Boundary}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Inflow/Outflow-Boundary"
+
\end_inset
Inflow/Outflow Boundary
@@ -3011,13 +3126,19 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Enumerate
Copy the file
\family typewriter
myviscous.xml
\family default
that you created in Section
-\begin_inset LatexCommand \ref{sec:Viscous-Material}
+\begin_inset LatexCommand ref
+reference "sec:Viscous-Material"
\end_inset
@@ -3302,12 +3423,14 @@
.
A visualization of the strain rate invariant and velocity (see Section
-\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+\begin_inset LatexCommand ref
+reference "sub:Visualization-with-ParaView"
\end_inset
) is shown in Figure
-\begin_inset LatexCommand \ref{fig:Strain-inflow}
+\begin_inset LatexCommand ref
+reference "fig:Strain-inflow"
\end_inset
@@ -3332,9 +3455,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Strain-inflow}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Strain-inflow"
+
\end_inset
Strain rate invariant and velocities with inflow/outflow boundaries
@@ -3345,13 +3472,19 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
Viscous Material in Extension with Normal Stress Boundaries
\end_layout
\begin_layout Standard
This example modifies the extension example in Section
-\begin_inset LatexCommand \ref{sec:Viscous-Material-in}
+\begin_inset LatexCommand ref
+reference "sec:Viscous-Material-in"
\end_inset
@@ -3578,7 +3711,8 @@
unspecified.
Recall that the momentum equation (eq.
-\begin_inset LatexCommand \ref{eq:simple momentum conservation}
+\begin_inset LatexCommand ref
+reference "eq:simple momentum conservation"
\end_inset
@@ -3690,12 +3824,14 @@
.
A visualization of the strain rate invariant and velocity (see Section
-\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+\begin_inset LatexCommand ref
+reference "sub:Visualization-with-ParaView"
\end_inset
) is shown in Figure
-\begin_inset LatexCommand \ref{fig:Strain-viscous-normal-stress}
+\begin_inset LatexCommand ref
+reference "fig:Strain-viscous-normal-stress"
\end_inset
@@ -3721,9 +3857,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Strain-viscous-normal-stress}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Strain-viscous-normal-stress"
+
\end_inset
Strain rate invariant and velocities of viscous material in extension with
@@ -3735,8 +3875,14 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Viscous-Material-with}
+\begin_inset LatexCommand label
+name "sec:Viscous-Material-with"
\end_inset
@@ -3748,7 +3894,8 @@
However, Gale can also start with the top initially deformed, such as if
we had a mountain range with substantial topography.
This example will make it sinusoidal as in Figure
-\begin_inset LatexCommand \ref{fig:Sinusoidal-Top}
+\begin_inset LatexCommand ref
+reference "fig:Sinusoidal-Top"
\end_inset
@@ -3775,9 +3922,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Sinusoidal-Top}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Sinusoidal-Top"
+
\end_inset
Sinusoidal Top
@@ -3788,6 +3939,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Enumerate
Copy
\family typewriter
@@ -3863,12 +4019,14 @@
.
A visualization of the strain rate invariant and velocity (see Section
-\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+\begin_inset LatexCommand ref
+reference "sub:Visualization-with-ParaView"
\end_inset
) is shown in
-\begin_inset LatexCommand \ref{fig:Strain-initial-deformed}
+\begin_inset LatexCommand ref
+reference "fig:Strain-initial-deformed"
\end_inset
@@ -3893,9 +4051,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Strain-initial-deformed}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Strain-initial-deformed"
+
\end_inset
Strain rate invariant and velocities with initially deformed upper boundary
@@ -3906,9 +4068,15 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
Multiple Viscous Materials
-\begin_inset LatexCommand \label{sec:Multiple-Viscous-Materials}
+\begin_inset LatexCommand label
+name "sec:Multiple-Viscous-Materials"
\end_inset
@@ -3919,7 +4087,8 @@
All of the previous examples have only one type of viscous material.
This example will create a simulation where there are multiple viscous
materials such as in Figure
-\begin_inset LatexCommand \ref{fig:Multiple-Viscous-Materials}
+\begin_inset LatexCommand ref
+reference "fig:Multiple-Viscous-Materials"
\end_inset
@@ -3944,9 +4113,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Multiple-Viscous-Materials}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Multiple-Viscous-Materials"
+
\end_inset
Multiple Viscous Materials
@@ -3957,13 +4130,19 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Enumerate
Copy
\family typewriter
myviscous_extension.xml
\family default
(see Section
-\begin_inset LatexCommand \ref{sec:Viscous-Material-in}
+\begin_inset LatexCommand ref
+reference "sec:Viscous-Material-in"
\end_inset
@@ -4149,12 +4328,14 @@
.
A visualization of the strain rate invariant and velocity (see Section
-\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+\begin_inset LatexCommand ref
+reference "sub:Visualization-with-ParaView"
\end_inset
) is shown in Figure
-\begin_inset LatexCommand \ref{fig:Strain-multiple}
+\begin_inset LatexCommand ref
+reference "fig:Strain-multiple"
\end_inset
@@ -4179,9 +4360,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Strain-multiple}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Strain-multiple"
+
\end_inset
Strain rate invariant and velocities with multiple viscous materials
@@ -4192,9 +4377,15 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
and the viscosity of the particles is shown in Figure
-\begin_inset LatexCommand \ref{fig:Viscosities-with-multiple}
+\begin_inset LatexCommand ref
+reference "fig:Viscosities-with-multiple"
\end_inset
@@ -4219,9 +4410,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Viscosities-with-multiple}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Viscosities-with-multiple"
+
\end_inset
Viscosities with multiple viscous materials
@@ -4232,6 +4427,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
Yielding Material in Simple Extension
\end_layout
@@ -4459,12 +4659,14 @@
.
A visualization of the strain rate invariant and velocity (see Section
-\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+\begin_inset LatexCommand ref
+reference "sub:Visualization-with-ParaView"
\end_inset
) is shown in Figure
-\begin_inset LatexCommand \ref{fig:strain-yield}
+\begin_inset LatexCommand ref
+reference "fig:strain-yield"
\end_inset
@@ -4489,9 +4691,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:strain-yield}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:strain-yield"
+
\end_inset
Strain rate invariant and velocities of yielding material in extension
@@ -4502,9 +4708,15 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
A visualization of the viscosity of the particles is shown in Figure
-\begin_inset LatexCommand \ref{fig:Viscosity-of-yielding}
+\begin_inset LatexCommand ref
+reference "fig:Viscosity-of-yielding"
\end_inset
@@ -4529,9 +4741,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Viscosity-of-yielding}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Viscosity-of-yielding"
+
\end_inset
Viscosity of yielding material in extension
@@ -4542,10 +4758,16 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
and a visualization of the yielding of the particles is shown in Figure
-\begin_inset LatexCommand \ref{fig:Degree-of-yielding}
+\begin_inset LatexCommand ref
+reference "fig:Degree-of-yielding"
\end_inset
@@ -4570,9 +4792,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Degree-of-yielding}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Degree-of-yielding"
+
\end_inset
Degree of yielding of yielding material in extension
@@ -4583,6 +4809,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
Thermal Convection
\end_layout
@@ -4590,7 +4821,8 @@
\begin_layout Standard
Temperature can play a decisive role in geophyisical processes.
This example takes the multiple viscous material example from Section
-\begin_inset LatexCommand \ref{sec:Multiple-Viscous-Materials}
+\begin_inset LatexCommand ref
+reference "sec:Multiple-Viscous-Materials"
\end_inset
@@ -4609,7 +4841,8 @@
\begin_layout Enumerate
Add in the thermal components from Section
-\begin_inset LatexCommand \ref{sec:Temperature-components}
+\begin_inset LatexCommand ref
+reference "sec:Temperature-components"
\end_inset
@@ -5171,7 +5404,8 @@
\family default
.
A visualization of the temperature and velocity is shown in Figure
-\begin_inset LatexCommand \ref{fig:Temperature-and-velocity}
+\begin_inset LatexCommand ref
+reference "fig:Temperature-and-velocity"
\end_inset
@@ -5196,9 +5430,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Temperature-and-velocity}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Temperature-and-velocity"
+
\end_inset
Temperature and velocities for thermal convection example
@@ -5209,9 +5447,15 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Chapter
Modifying Gale
-\begin_inset LatexCommand \label{cha:Modifying-Gale}
+\begin_inset LatexCommand label
+name "cha:Modifying-Gale"
\end_inset
@@ -5240,7 +5484,8 @@
These are proven, capable, open-source finite element method libraries
written by the Victorian Partnership for Advanced Computing (VPAC) and
Louis Moresi's group at Monash University (see Fig
-\begin_inset LatexCommand \ref{fig:Mapping-between-MicroFEM}
+\begin_inset LatexCommand ref
+reference "fig:Mapping-between-MicroFEM"
\end_inset
@@ -5276,7 +5521,9 @@
In turn, intellectual property, skills and adaptability of the recipients
develop over time.
-\begin_inset LatexCommand \htmlurl[StGermain Web Site]{csd.vpac.org/twiki/bin/view/Stgermain/WebHome}
+\begin_inset LatexCommand htmlurl
+name "StGermain Web Site"
+target "csd.vpac.org/twiki/bin/view/Stgermain/WebHome"
\end_inset
@@ -5294,7 +5541,9 @@
differential equations.
It employs the MPI standard for all message-passing communication.
-\begin_inset LatexCommand \htmlurl[PETSc Web Site]{www-unix.mcs.anl.gov/petsc/petsc-as/}
+\begin_inset LatexCommand htmlurl
+name "PETSc Web Site"
+target "www-unix.mcs.anl.gov/petsc/petsc-as/"
\end_inset
@@ -5310,14 +5559,23 @@
sideways false
status open
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Mapping-between-MicroFEM}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Mapping-between-MicroFEM"
+
\end_inset
Mapping between MicroFEM and Gale
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout LyX-Code
\end_layout
@@ -5354,7 +5612,9 @@
StgFEM describes finite element systems for various formulations in a manner
that can allow the underlying numerics to be interchanged.
-\begin_inset LatexCommand \htmlurl[StgFEM Web Site]{csd.vpac.org/twiki/bin/view/Stgfem/WebHome}
+\begin_inset LatexCommand htmlurl
+name "StgFEM Web Site"
+target "csd.vpac.org/twiki/bin/view/Stgfem/WebHome"
\end_inset
@@ -5375,7 +5635,9 @@
are in development.
Constitutive rules are reusable across these schemes.
-\begin_inset LatexCommand \htmlurl[PICellerator Web Site]{csd.vpac.org/twiki/bin/view/PICellerator/WebHome}
+\begin_inset LatexCommand htmlurl
+name "PICellerator Web Site"
+target "csd.vpac.org/twiki/bin/view/PICellerator/WebHome"
\end_inset
@@ -5397,7 +5659,9 @@
located at the Australian Crustal Research Centre (ACRC) at Monash University
(Clayton Campus).
-\begin_inset LatexCommand \htmlurl[UnderWorld Web Site]{wasabi.maths.monash.edu.au/twiki/view/Software/Underworld}
+\begin_inset LatexCommand htmlurl
+name "UnderWorld Web Site"
+target "wasabi.maths.monash.edu.au/twiki/view/Software/Underworld"
\end_inset
@@ -5566,7 +5830,8 @@
\begin_layout Chapter
\start_of_appendix
Input File Format
-\begin_inset LatexCommand \label{cha:Input-File-Format}
+\begin_inset LatexCommand label
+name "cha:Input-File-Format"
\end_inset
@@ -5612,7 +5877,8 @@
\begin_layout Subsection
Components
-\begin_inset LatexCommand \label{sub:Components}
+\begin_inset LatexCommand label
+name "sub:Components"
\end_inset
@@ -5694,7 +5960,8 @@
\begin_layout Subsection
Plugins
-\begin_inset LatexCommand \label{sub:Plugins}
+\begin_inset LatexCommand label
+name "sub:Plugins"
\end_inset
@@ -5801,14 +6068,15 @@
\family default
option when compiling) and set your
\family typewriter
-LD_LIBRARY_PATH
+LD_LIBRARY_PATH
\family default
-environment variable appropriately.
+ environment variable appropriately.
\end_layout
\begin_layout Subsection
EulerDeform
-\begin_inset LatexCommand \label{sub:EulerDeform}
+\begin_inset LatexCommand label
+name "sub:EulerDeform"
\end_inset
@@ -5968,7 +6236,8 @@
\family default
\size default
all must be defined earlier (see Section
-\begin_inset LatexCommand \ref{sub:Components}
+\begin_inset LatexCommand ref
+reference "sub:Components"
\end_inset
@@ -6029,7 +6298,8 @@
Underworld_EulerDeform
\family default
in the list of plugins (see Section
-\begin_inset LatexCommand \ref{sub:Plugins}
+\begin_inset LatexCommand ref
+reference "sub:Plugins"
\end_inset
@@ -6044,17 +6314,20 @@
These sections specify the boundary conditions on the velocity, and the
initial and boundary conditions for the temperature.
See Sections
-\begin_inset LatexCommand \ref{sub:Velocity-Boundary-Conditions}
+\begin_inset LatexCommand ref
+reference "sub:Velocity-Boundary-Conditions"
\end_inset
,
-\begin_inset LatexCommand \ref{sub:Temperature-Boundary-Conditions}
+\begin_inset LatexCommand ref
+reference "sub:Temperature-Boundary-Conditions"
\end_inset
, and
-\begin_inset LatexCommand \ref{sec:Temperature-Initial-Conditions}
+\begin_inset LatexCommand ref
+reference "sec:Temperature-Initial-Conditions"
\end_inset
@@ -6063,7 +6336,8 @@
\begin_layout Subsection
Variables
-\begin_inset LatexCommand \label{sub:Variables}
+\begin_inset LatexCommand label
+name "sub:Variables"
\end_inset
@@ -6110,7 +6384,8 @@
SurfaceAdaptor
\family default
(Section
-\begin_inset LatexCommand \ref{sec:Deformed-Upper-Boundary}
+\begin_inset LatexCommand ref
+reference "sec:Deformed-Upper-Boundary"
\end_inset
@@ -6167,7 +6442,8 @@
\begin_layout Section
Basic Components
-\begin_inset LatexCommand \label{sec:Basic-Components}
+\begin_inset LatexCommand label
+name "sec:Basic-Components"
\end_inset
@@ -7531,7 +7807,8 @@
\begin_layout Section
Temperature components
-\begin_inset LatexCommand \label{sec:Temperature-components}
+\begin_inset LatexCommand label
+name "sec:Temperature-components"
\end_inset
@@ -7876,7 +8153,8 @@
\begin_layout Standard
to the list of variables.
You can also override this default for each material (see Section
-\begin_inset LatexCommand \ref{sec:Materials}
+\begin_inset LatexCommand ref
+reference "sec:Materials"
\end_inset
@@ -7886,24 +8164,28 @@
\begin_layout Standard
You will also need to add in initial and boundary conditions (see Sections
-\begin_inset LatexCommand \ref{sub:Temperature-Boundary-Conditions}
+\begin_inset LatexCommand ref
+reference "sub:Temperature-Boundary-Conditions"
\end_inset
and
-\begin_inset LatexCommand \ref{sec:Temperature-Initial-Conditions}
+\begin_inset LatexCommand ref
+reference "sec:Temperature-Initial-Conditions"
\end_inset
).
Finally, you may want to set material properties for the buoyancy forces
(see Section
-\begin_inset LatexCommand \ref{sec:Buoyancy-Forces}
+\begin_inset LatexCommand ref
+reference "sec:Buoyancy-Forces"
\end_inset
) and radiogenic heating (see Section
-\begin_inset LatexCommand \ref{sec:Materials}
+\begin_inset LatexCommand ref
+reference "sec:Materials"
\end_inset
@@ -7965,7 +8247,8 @@
\begin_layout Section
Shapes
-\begin_inset LatexCommand \label{sec:Shapes}
+\begin_inset LatexCommand label
+name "sec:Shapes"
\end_inset
@@ -9566,7 +9849,8 @@
\begin_layout Section
Materials
-\begin_inset LatexCommand \label{sec:Materials}
+\begin_inset LatexCommand label
+name "sec:Materials"
\end_inset
@@ -9668,7 +9952,8 @@
materialShape
\family default
(see Section
-\begin_inset LatexCommand \ref{sec:Shapes}
+\begin_inset LatexCommand ref
+reference "sec:Shapes"
\end_inset
@@ -9811,13 +10096,15 @@
BuoyancyForceTerm
\family default
component (see Section
-\begin_inset LatexCommand \ref{sub:BouyancyForceTerm}
+\begin_inset LatexCommand ref
+reference "sub:BouyancyForceTerm"
\end_inset
) to create buoyancy forces.
The diffusivity is used by the temperature solver (see Section
-\begin_inset LatexCommand \ref{sec:Temperature-components}
+\begin_inset LatexCommand ref
+reference "sec:Temperature-components"
\end_inset
@@ -10034,7 +10321,8 @@
\begin_layout Subsection
StoreVisc and StoreStress
-\begin_inset LatexCommand \label{sub:StoreViscosity}
+\begin_inset LatexCommand label
+name "sub:StoreViscosity"
\end_inset
@@ -10303,7 +10591,8 @@
TimeIntegrator This is the component used for time integration to accumulate
strain.
Given the standard components in Section
-\begin_inset LatexCommand \ref{sec:Basic-Components}
+\begin_inset LatexCommand ref
+reference "sec:Basic-Components"
\end_inset
@@ -10318,7 +10607,8 @@
MaterialPointsSwarm This is the swarm of particles that this rheology will
tie itself to.
Given the standard components in Section
-\begin_inset LatexCommand \ref{sec:Basic-Components}
+\begin_inset LatexCommand ref
+reference "sec:Basic-Components"
\end_inset
@@ -10643,7 +10933,8 @@
\end_layout
\begin_layout Subsubsection
-\begin_inset LatexCommand \label{sub:VonMises}
+\begin_inset LatexCommand label
+name "sub:VonMises"
\end_inset
@@ -10940,7 +11231,8 @@
\begin_layout Standard
(See also
-\begin_inset LatexCommand \ref{sub:VonMises}
+\begin_inset LatexCommand ref
+reference "sub:VonMises"
\end_inset
@@ -11105,8 +11397,9 @@
\begin_layout Standard
This is a fairly complicated non-isotropic rheology.
- The full details can be found in Moresi and Mülhaus (2006)
-\begin_inset LatexCommand \cite{Moresi faulting}
+ The full details can be found in Moresi and Mülhaus (2006)
+\begin_inset LatexCommand cite
+key "Moresi faulting"
\end_inset
@@ -11117,7 +11410,8 @@
\family default
.
For the standard components given in Section
-\begin_inset LatexCommand \ref{sec:Basic-Components}
+\begin_inset LatexCommand ref
+reference "sec:Basic-Components"
\end_inset
@@ -11336,7 +11630,8 @@
\begin_layout Section
Boundary Conditions
-\begin_inset LatexCommand \label{sec:Boundary-Conditions}
+\begin_inset LatexCommand label
+name "sec:Boundary-Conditions"
\end_inset
@@ -11402,7 +11697,8 @@
\begin_layout Subsection
Velocity Boundary Conditions
-\begin_inset LatexCommand \label{sub:Velocity-Boundary-Conditions}
+\begin_inset LatexCommand label
+name "sub:Velocity-Boundary-Conditions"
\end_inset
@@ -11495,7 +11791,8 @@
If you want the sides to remain fixed, then you probably want flux boundaries,
in which case you will also have to specify a few more things (see Section
-\begin_inset LatexCommand \ref{sub:Flux-Boundary-Conditions}
+\begin_inset LatexCommand ref
+reference "sub:Flux-Boundary-Conditions"
\end_inset
@@ -11618,14 +11915,16 @@
\begin_layout Standard
Note that the parameters are separated out into the variables section (see
Section
-\begin_inset LatexCommand \ref{sub:Variables}
+\begin_inset LatexCommand ref
+reference "sub:Variables"
\end_inset
).
In general, you can use any of the Standard Condition Functions (see Section
-\begin_inset LatexCommand \ref{sec:Standard-Condition-Functions}
+\begin_inset LatexCommand ref
+reference "sec:Standard-Condition-Functions"
\end_inset
@@ -11634,7 +11933,8 @@
\begin_layout Subsection
Flux Boundary Conditions
-\begin_inset LatexCommand \label{sub:Flux-Boundary-Conditions}
+\begin_inset LatexCommand label
+name "sub:Flux-Boundary-Conditions"
\end_inset
@@ -11645,7 +11945,8 @@
Sometimes, you may wish to have material flow across the boundary instead
of having the boundary move.
A simple example would be like Figure
-\begin_inset LatexCommand \ref{fig:General-subduction-model}
+\begin_inset LatexCommand ref
+reference "fig:General-subduction-model"
\end_inset
@@ -11657,9 +11958,9 @@
\series bold
The boundaries do not move.
-
+
\series default
-For the slab subduction model, you need to ensure that neither the bottom
+ For the slab subduction model, you need to ensure that neither the bottom
nor left boundaries move.
Do this by specifying
\end_layout
@@ -11675,7 +11976,8 @@
\begin_layout Standard
in EulerDeform (see Section
-\begin_inset LatexCommand \ref{sub:EulerDeform}
+\begin_inset LatexCommand ref
+reference "sub:EulerDeform"
\end_inset
@@ -11692,7 +11994,8 @@
Again, for slab subduction this involves inflow conditions on the left
boundary and outflow conditions on bottom.
See Section
-\begin_inset LatexCommand \ref{sub:Velocity-Boundary-Conditions}
+\begin_inset LatexCommand ref
+reference "sub:Velocity-Boundary-Conditions"
\end_inset
@@ -11737,7 +12040,8 @@
\end_deeper
\begin_layout Subsection
Stress Boundary Conditions
-\begin_inset LatexCommand \label{sub:Stress-Boundary-Conditions}
+\begin_inset LatexCommand label
+name "sub:Stress-Boundary-Conditions"
\end_inset
@@ -11764,7 +12068,8 @@
\begin_layout Standard
StressBC is a component, so it must be inside the list of components (see
Section
-\begin_inset LatexCommand \ref{sub:Components}
+\begin_inset LatexCommand ref
+reference "sub:Components"
\end_inset
@@ -11811,7 +12116,8 @@
\begin_layout Standard
You can also use the Standard Condition Functions (see Section
-\begin_inset LatexCommand \ref{sec:Standard-Condition-Functions}
+\begin_inset LatexCommand ref
+reference "sec:Standard-Condition-Functions"
\end_inset
@@ -11899,7 +12205,8 @@
\begin_layout Standard
And then in the list of variables (see Section
-\begin_inset LatexCommand \ref{sub:Variables}
+\begin_inset LatexCommand ref
+reference "sub:Variables"
\end_inset
@@ -11928,7 +12235,8 @@
\begin_layout Subsection
Temperature Boundary Conditions
-\begin_inset LatexCommand \label{sub:Temperature-Boundary-Conditions}
+\begin_inset LatexCommand label
+name "sub:Temperature-Boundary-Conditions"
\end_inset
@@ -11938,7 +12246,8 @@
\begin_layout Standard
Setting the boundary conditions on the temperature works almost exactly
the same as velocity boundary conditions (see Section
-\begin_inset LatexCommand \ref{sub:Velocity-Boundary-Conditions}
+\begin_inset LatexCommand ref
+reference "sub:Velocity-Boundary-Conditions"
\end_inset
@@ -12030,7 +12339,8 @@
\begin_layout Section
Temperature Initial Conditions
-\begin_inset LatexCommand \label{sec:Temperature-Initial-Conditions}
+\begin_inset LatexCommand label
+name "sec:Temperature-Initial-Conditions"
\end_inset
@@ -12122,7 +12432,8 @@
\begin_layout Section
Buoyancy Forces
-\begin_inset LatexCommand \label{sec:Buoyancy-Forces}
+\begin_inset LatexCommand label
+name "sec:Buoyancy-Forces"
\end_inset
@@ -12142,7 +12453,8 @@
\begin_layout Subsection
BouyancyForceTerm
-\begin_inset LatexCommand \label{sub:BouyancyForceTerm}
+\begin_inset LatexCommand label
+name "sub:BouyancyForceTerm"
\end_inset
@@ -12181,7 +12493,8 @@
\end_inset
) are taken from the material properties (see Section
-\begin_inset LatexCommand \ref{sec:Materials}
+\begin_inset LatexCommand ref
+reference "sec:Materials"
\end_inset
@@ -12345,7 +12658,8 @@
\begin_layout Subsection
BuoyancyForceTermThermoChem
-\begin_inset LatexCommand \label{sub:BuoyancyForceTermThermoChem}
+\begin_inset LatexCommand label
+name "sub:BuoyancyForceTermThermoChem"
\end_inset
@@ -12544,7 +12858,8 @@
\begin_layout Section
Deformed Upper Boundary
-\begin_inset LatexCommand \label{sec:Deformed-Upper-Boundary}
+\begin_inset LatexCommand label
+name "sec:Deformed-Upper-Boundary"
\end_inset
@@ -12682,7 +12997,8 @@
\begin_layout Section
Standard Condition Functions
-\begin_inset LatexCommand \label{sec:Standard-Condition-Functions}
+\begin_inset LatexCommand label
+name "sec:Standard-Condition-Functions"
\end_inset
@@ -13145,7 +13461,8 @@
\begin_layout Standard
into the variables section (see Section
-\begin_inset LatexCommand \ref{sub:Variables}
+\begin_inset LatexCommand ref
+reference "sub:Variables"
\end_inset
@@ -13170,7 +13487,8 @@
\begin_layout Chapter
Output File Format
-\begin_inset LatexCommand \label{cha:Output-File-Format}
+\begin_inset LatexCommand label
+name "cha:Output-File-Format"
\end_inset
@@ -13284,7 +13602,8 @@
\begin_layout Standard
The complete list of output files per time step with the default components
(see Section
-\begin_inset LatexCommand \ref{sec:Basic-Components}
+\begin_inset LatexCommand ref
+reference "sec:Basic-Components"
\end_inset
@@ -13319,7 +13638,8 @@
for that time step.
So to get the time at the end of the step, you need to add the two numbers.
The materialSwarm files are described in Section
-\begin_inset LatexCommand \ref{sec:.dat-Binary-Files}
+\begin_inset LatexCommand ref
+reference "sec:.dat-Binary-Files"
\end_inset
@@ -13333,7 +13653,8 @@
DumpSwarm
\family default
, explained below in Section
-\begin_inset LatexCommand \ref{sec:.txt-Files-(Particle}
+\begin_inset LatexCommand ref
+reference "sec:.txt-Files-(Particle"
\end_inset
@@ -13343,10 +13664,11 @@
\begin_layout Section
\family typewriter
-.dat
+.dat
\family default
-Binary Files (Particle Information)
-\begin_inset LatexCommand \label{sec:.dat-Binary-Files}
+ Binary Files (Particle Information)
+\begin_inset LatexCommand label
+name "sec:.dat-Binary-Files"
\end_inset
@@ -13368,7 +13690,8 @@
.txt
\family default
Files (Particle Information)
-\begin_inset LatexCommand \label{sec:.txt-Files-(Particle}
+\begin_inset LatexCommand label
+name "sec:.txt-Files-(Particle"
\end_inset
@@ -13502,7 +13825,8 @@
.vtk
\family default
Files (Visualization)
-\begin_inset LatexCommand \label{sec:.vtk-Files-(Visualization)}
+\begin_inset LatexCommand label
+name "sec:.vtk-Files-(Visualization)"
\end_inset
@@ -13517,17 +13841,23 @@
plugin.
These files are in a format understood by a wide variety of visualization
programs, sich as
-\begin_inset LatexCommand \htmlurl[ParaView]{paraview.org}
+\begin_inset LatexCommand htmlurl
+name "ParaView"
+target "paraview.org"
\end_inset
(recommended),
-\begin_inset LatexCommand \htmlurl[MayaVi]{mayavi.sf.net}
+\begin_inset LatexCommand htmlurl
+name "MayaVi"
+target "mayavi.sf.net"
\end_inset
, or
-\begin_inset LatexCommand \htmlurl[Visit]{www.llnl.gov/visit}
+\begin_inset LatexCommand htmlurl
+name "Visit"
+target "www.llnl.gov/visit"
\end_inset
@@ -13563,8 +13893,8 @@
\end_layout
\begin_layout Standard
-To check the results yoursel, run the accompanying input file with 3 different
- resolutions
+To check the results yourself, run the accompanying input file with 3 different
+ resolutions:
\end_layout
\begin_layout LyX-Code
@@ -13573,18 +13903,22 @@
\begin_layout LyX-Code
Gale spherical_inclusion.xml --elementResI=128 --elementResJ=128 --outputPath=128
- -pc_type lu -ksp_type preonly
+
+\newline
+-pc_type lu -ksp_type preonly
\end_layout
\begin_layout LyX-Code
Gale spherical_inclusion.xml --elementResI=256 --elementResJ=256 --outputPath=256
- -pc_type lu -ksp_type preonly
+
+\newline
+-pc_type lu -ksp_type preonly
\end_layout
\begin_layout Standard
-The last run will require about 800M of memory and take about 30 minutes
- on a reasonable machine.
- Then run paraview and load in the state file
+The last run will require about 800MB of memory and take about 30 minutes
+ on a recent-era machine.
+ Then run ParaView and load in the state file
\end_layout
\begin_layout LyX-Code
@@ -13593,7 +13927,8 @@
\begin_layout Standard
That will give you a picture like Figure
-\begin_inset LatexCommand \ref{fig:Circular Inclusion error}
+\begin_inset LatexCommand ref
+reference "fig:Circular Inclusion error"
\end_inset
@@ -13604,6 +13939,7 @@
\begin_layout Standard
\begin_inset Float figure
+placement H
wide false
sideways false
status open
@@ -13620,15 +13956,30 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Circular Inclusion error}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Circular Inclusion error"
+
\end_inset
Numerical error for the circular inclusion benchmark around the interface
between the low and high viscosity regision.
- Blue is high resolution (256x256), green is medium resolution (128x128),
- and red is low resolution (64x64).
+ Blue is high resolution (256
+\begin_inset Formula $\times$
+\end_inset
+
+ 256), green is medium resolution (128
+\begin_inset Formula $\times$
+\end_inset
+
+ 128), and red is low resolution (64
+\begin_inset Formula $\times$
+\end_inset
+
+ 64).
\end_layout
\end_inset
@@ -13636,11 +13987,15 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
-Far away from the hole, the error becomes dominated by factors besides finite
- resolution (e.g.
- finite distance to the boundary and non-zero tolerance when solving the
- stokes flow).
+Far away from the hole, the error becomes dominated by factors other than
+ finite resolution (e.g., finite distance to the boundary and non-zero tolerance
+ when solving the Stokes flow).
\end_layout
\begin_layout Chapter
@@ -14177,7 +14532,7 @@
One line to give the program's name and a brief idea of what it does.
Copyright
\size footnotesize
-© (
+© (
\size default
year) (name of author)
\end_layout
@@ -14215,7 +14570,7 @@
\end_layout
\begin_layout Quote
-Gnomovision version 69, Copyright © year name of author Gnomovision comes
+Gnomovision version 69, Copyright © year name of author Gnomovision comes
with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it under certain
conditions; type `show c' for details.
@@ -14261,8 +14616,11 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "Fullsack"
-\bibitem {Fullsack}
+\end_inset
+
Fullsack, Phillipe (1995).
An arbitrary Lagrangian-Eulerian formulation for creeping flows and its
application in tectonic models,
@@ -14275,8 +14633,11 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "VPAC"
-\bibitem {VPAC}
+\end_inset
+
Quenette, S., B.
Appelbe, M.
Gurnis, L.
@@ -14295,11 +14656,14 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "Underworld"
-\bibitem {Underworld}
+\end_inset
+
Moresi, L.N., F.
Dufour, and H.-B.
- Mühlhaus (2003), A Lagrangian integration point finite element method for
+ Mühlhaus (2003), A Lagrangian integration point finite element method for
large deformation modeling of viscoelastic geomaterials,
\emph on
J.
@@ -14313,10 +14677,13 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "Moresi faulting"
-\bibitem {Moresi faulting}
+\end_inset
+
Moresi, L.N., and H.-B.
- Mühlhaus (2006), Anisotropic viscous models of large-deformation MohrCoulomb
+ Mühlhaus (2006), Anisotropic viscous models of large-deformation MohrCoulomb
failure,
\emph on
Philosophical Magazine, 86,
@@ -14325,8 +14692,11 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "Uzawa"
-\bibitem {Uzawa}
+\end_inset
+
Moresi, L.N., and V.S.
Solomatov (1995), Numerical investigation of 2D convection with extremely
large viscosity variations,
@@ -14342,9 +14712,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "Ellipsis"
-\bibitem {Ellipsis}
-O'Neill, C., Moresi, L., Müller, D., Albert, R., Dufour, F.
+\end_inset
+
+O'Neill, C., Moresi, L., Müller, D., Albert, R., Dufour, F.
(2006), Ellipsis 3D: a particle-in-cell finite element hybrid code for
modelling mantle convection and lithospheric deformation,
\shape italic
@@ -14358,8 +14731,11 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "Citcom"
-\bibitem {Citcom}
+\end_inset
+
Zhong, S., M.T.
Zuber, L.N.
Moresi, and M.
Modified: long/3D/Gale/trunk/documentation/gale_cover.psd
===================================================================
(Binary files differ)
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