[cig-commits] r5857 - long/3D/Gale/trunk/documentation
sue at geodynamics.org
sue at geodynamics.org
Mon Jan 22 14:34:18 PST 2007
Author: sue
Date: 2007-01-22 14:34:16 -0800 (Mon, 22 Jan 2007)
New Revision: 5857
Modified:
long/3D/Gale/trunk/documentation/gale.lyx
long/3D/Gale/trunk/documentation/gale.pdf
Log:
incorporated MG and SK notes, edits, additions; regen. PDF
Modified: long/3D/Gale/trunk/documentation/gale.lyx
===================================================================
--- long/3D/Gale/trunk/documentation/gale.lyx 2007-01-22 22:16:42 UTC (rev 5856)
+++ long/3D/Gale/trunk/documentation/gale.lyx 2007-01-22 22:34:16 UTC (rev 5857)
@@ -153,8 +153,13 @@
\end_layout
\begin_layout Standard
-The main audience for Gale is research scientists interested in tectonic
- modeling.
+The main audience for Gale is research scientists interested in modeling
+ the tectonic processes on long time scales.
+ Examples of problems that can be solved are the development of tectonic
+ structure associated with extension and compression, especially where localizat
+ion is important.
+ One should not have to be an expert in finite element analysis or scientific
+ computing to use this software.
\end_layout
\begin_layout Section
@@ -243,8 +248,8 @@
\begin_layout Standard
Gale is a parallel, two- or three-dimensional, implicit finite element code
- focusing on orogenesis, rifting, and subduction with coupling to surface
- erosion models.
+ that solves problems related to orogenesis, rifting, and subduction with
+ coupling to surface erosion models.
Gale uses a hybrid particle-in-cell scheme which combines a deformable
mesh of computational points and a dense arrangement of mobile material
points.
@@ -272,9 +277,9 @@
\end_layout
\begin_layout Standard
-Gale uses both a regular grid and particles for simulation.
+Gale uses both a regular grid and particles.
The regular grid is used to solve differential equations, and particles
- are used to record material properties (e.g., strain history).
+ are used to track material properties (e.g., strain history).
Note that the regular grid can become distorted, since it may conform to
an uneven upper surface.
\end_layout
@@ -319,7 +324,7 @@
\end_inset
-subject to the continuity equation
+subject to the (incompressible) continuity equation
\end_layout
\begin_layout Standard
@@ -351,7 +356,16 @@
\end_layout
\begin_layout Standard
-Note that there is no explicit time dependency (yet).
+Note that there is no explicit time dependency in the momentum equation
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset LatexCommand \ref{eq:simple momentum conservation}
+
+\end_inset
+
+.
Gale simulates creeping flows, so acceleration terms are neglected and
material motion evolves through a series of equilibria.
If your boundary condition has a time component, then we may infer a time.
@@ -360,8 +374,7 @@
\end_layout
\begin_layout Standard
-So far, these equations are very simple, taking no account of gravity or
- temperature.
+So far, these equations are simple, taking no account of gravity or temperature.
So this is mostly useful when simulating laboratory experiments.
\end_layout
@@ -377,7 +390,7 @@
\end_inset
-, we assume a simple viscous material.
+, we assume a simple Linear viscous material.
This allows us to write
\begin_inset Formula $\tau$
\end_inset
@@ -494,7 +507,23 @@
\end_inset
.
+ It should be noted that CIG's finite element code CitCom used to solve
+ mantle convection problems uses the same approach as in Equations
+\begin_inset LatexCommand \ref{eq:matrix form}
+
+\end_inset
+
+ and
+\begin_inset LatexCommand \ref{eq:final simple elliptic}
+
+\end_inset
+
+\begin_inset LatexCommand \cite{key-4}
+
+\end_inset
+
+.
\end_layout
\begin_layout Subsection
@@ -529,8 +558,7 @@
\end_inset
- This modifies eq.
-
+ This modifies Equation
\begin_inset LatexCommand \ref{eq:matrix form}
\end_inset
@@ -563,12 +591,12 @@
\begin_layout Standard
\begin_inset Formula \begin{equation}
-\frac{dT}{dt}=\kappa\nabla^{2}T+Q,\label{eq:energy}\end{equation}
+\frac{DT}{Dt}=\kappa\nabla^{2}T+Q,\label{eq:energy}\end{equation}
\end_inset
where
-\begin_inset Formula $d/dt$
+\begin_inset Formula $\frac{D}{Dt}$
\end_inset
is the material time derivative (taken at a point moving with respect to
@@ -585,8 +613,7 @@
\end_inset
is the rate of energy production (e.g., from radiogenic sources).
- Note that eq.
-
+ Note that Equation
\begin_inset LatexCommand \ref{eq:energy}
\end_inset
@@ -599,9 +626,9 @@
\end_layout
\begin_layout Standard
-Gale incorporates a number of different rheologies, as well as letting you
- create your own.
- For details on the existing Rheologies, see Section
+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}
\end_inset
@@ -621,19 +648,29 @@
\begin_layout Standard
Gale arose from discussions at an NSF-sponsored workshop on Tectonic Modeling
- held in Breckenridge, Colorado.
+ 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}
+
+\end_inset
+
+).
At that workshop, members of the tectonics community advocated that CIG
develop a new open-source software package based on the Arbitrary Lagrangian
Eulerian (ALE) method for solving tectonic problems.
The ALE method, as it is implemented in the tectonics community, was developed
primarily at Dalhousie University in Canada.
- It solves a Stokes Flow problem on an Eulerian grid and uses a Lagrangian
+ It solves a Stokes flow problem on an Eulerian grid and uses a Lagrangian
grid to track material properties and to integrate strain.
- This method has seen much use in lithosphere deformation problems such
- as orogenesis, rifting, subduction, as well as in coupling to surface erosion
- models and has been employed for deeper mantle dynamics problems.
- Gale is an open-source code that is at least as useful as SOPALE and MicroFEM
- for addressing these research areas, with the addition of 3D capability.
+ This method has seen much use in crustal and lithospheric deformation problems
+ such as orogenesis, rifting, and subduction, as well as in coupling to
+ surface erosion models, and has been employed for deeper mantle dynamics
+ problems.
+ Gale is an open-source code that we hope will be at least as useful as
+ SOPALE and MicroFEM for addressing these research areas
+\color red
+[TODO: References? - MG]
+\color default
+, with the addition of 3D capability.
In the future, Gale will run benchmarks such as extension and shortening,
as well as the traditional subduction model as shown in Fig.
@@ -665,7 +702,12 @@
\end_inset
-General subduction model from Fullsack (1995).
+General subduction model from
+\begin_inset LatexCommand \cite{key-5}
+
+\end_inset
+
+.
The basic subduction model can be modified by introducing isostasy and/or
boundary mass fluxes.
(a) Flexural or local isostasy.
@@ -706,6 +748,8 @@
\align center
\begin_inset Graphics
filename images/GALE_image1.eps
+ lyxscale 75
+ scale 70
\end_inset
@@ -722,12 +766,46 @@
\end_layout
\begin_layout Section
+Introduction
+\end_layout
+
+\begin_layout Standard
+To install Gale, you follow the procedure that is commonly used with other
+ open source software packages.
+ First, download the binaries for your platform or the source package (in
+ the form of a compressed
+\family typewriter
+tar
+\family default
+ file) available at the
+\begin_inset LatexCommand \htmlurl[CIG Software Packages: Long-Term Crustal Dynamics: Gale]{geodynamics.org/cig/software/packages/long/gale/}
+
+\end_inset
+
+.
+ After unpacking the source, you run an .xml script to configure Gale for
+ your system.
+
+\end_layout
+
+\begin_layout Standard
+Advanced users and software developers may be interested in downloading
+ the latest Cale source code directly from the CIG source code repository,
+ instead of using the prepared source package; see Section
+\begin_inset LatexCommand \ref{sec:Downloading-the-Code}
+
+\end_inset
+
+ later in this chapter.
+\end_layout
+
+\begin_layout Section
System Requirements
\end_layout
\begin_layout Standard
-Gale works on a variety of platforms and has been tested on workstations
- running
+Gale works on a variety of computational platforms and has been tested on
+ workstations running
\end_layout
\begin_layout Itemize
@@ -788,12 +866,16 @@
\end_layout
\begin_layout Section
-Getting the Code
+\begin_inset LatexCommand \label{sec:Downloading-the-Code}
+
+\end_inset
+
+Downloading the Code
\end_layout
\begin_layout Standard
Gale can be downloaded at
-\begin_inset LatexCommand \htmlurl[CIG Software Packages: Gale]{www.geodynamics.org/cig/software/packages/long/gale/}
+\begin_inset LatexCommand \htmlurl[CIG Software Packages: Long-Term Crustal Dynamics: Gale]{geodynamics.org/cig/software/packages/long/gale/}
\end_inset
@@ -811,7 +893,7 @@
\end_layout
\begin_layout LyX-Code
-Type 'svn help' for usage.
+Type `svn help' for usage.
\end_layout
\begin_layout Standard
@@ -956,11 +1038,11 @@
\end_layout
\begin_layout Enumerate
-At the command line, cd to the install directory and run
+At the command line, navigate to the install directory and run
\end_layout
\begin_layout LyX-Code
-./Gale extention.xml
+./Gale-Linux-1.1 extension.xml
\end_layout
\begin_layout Subsection
@@ -999,11 +1081,11 @@
\end_layout
\begin_layout Enumerate
-At the command line, cd to the install directory and run
+At the command line, navigate to the install directory and run
\end_layout
\begin_layout LyX-Code
-./Gale extention.xml
+./Gale-Mac_1_1 extension.xml
\end_layout
\begin_layout Subsection
@@ -1030,11 +1112,11 @@
\end_layout
\begin_layout Enumerate
-At the command line, cd to the install directory and run
+At the command line, navigate to the install directory and run
\end_layout
\begin_layout LyX-Code
-./Gale extention.xml
+./Gale-Win32-1_1 extension.xml
\end_layout
\begin_layout Section
@@ -1090,7 +1172,7 @@
\end_layout
\begin_layout LyX-Code
-\begin_inset LatexCommand \htmlurl[cig-long Archives]{www.geodynamics.org/pipermail/cig-long/}
+\begin_inset LatexCommand \htmlurl[cig-long Archives]{geodynamics.org/pipermail/cig-long/}
\end_inset
@@ -1110,7 +1192,7 @@
\end_layout
\begin_layout Standard
-to submit bugs and request features.
+to submit bugs and requests for new features.
\end_layout
\begin_layout Chapter
@@ -1128,7 +1210,7 @@
\end_layout
\begin_layout LyX-Code
-./Gale-Linux.1.0.0 extension.xml
+./Gale-Linux-1.1 extension.xml
\end_layout
\begin_layout Standard
@@ -1136,14 +1218,22 @@
\end_layout
\begin_layout LyX-Code
+
+\size small
Warning - in _WallVC_GetSet: Can't build a back wall VC when mesh has no
elements in the K axis.
- Returning an empty set.
+
+\newline
+Returning an empty set.
\end_layout
\begin_layout LyX-Code
+
+\size small
Warning: () called to allocate a 2D variable length array where the
- total size calculated was 0.
+ total size calculated
+\newline
+was 0.
Returning NULL.
\end_layout
@@ -1177,15 +1267,19 @@
\end_layout
\begin_layout Standard
-Gale uses PETSc for solvers, so you can easily change which solver to use.
+Since Gale uses PETSc for solving the equation, so you can easily change
+ which solver to use.
The default solver is preconditioned conjugate gradient.
- There are too many options of PETSc to go into them here.
+ There are an enormous number of PETSc options that the expert user may
+ want to explore.
But as a simple example, to use a direct LU solve, simply append arguments
- to the command line
+ to the command line
+\color red
+[TODO: sentence awkward, how to fix?]
\end_layout
\begin_layout LyX-Code
-./Gale-Linux.1.0.0 extension.xml -pc_type lu -ksp_type preonly
+./Gale-Linux-1.1 extension.xml -pc_type lu -ksp_type preonly
\end_layout
\begin_layout Section
@@ -1218,7 +1312,27 @@
\end_layout
\begin_layout Standard
-Also found in the output directory are a number of .dat and .txt files.
+In the output directory you will find a number of
+\family typewriter
+.dat
+\family default
+ and
+\family typewriter
+.txt
+\family default
+ files that
+\color red
+[TODO:
+\begin_inset Quotes sld
+\end_inset
+
+Please say at least a few words
+\begin_inset Quotes srd
+\end_inset
+
+ -MG]
+\color default
+.
See Appendix
\begin_inset LatexCommand \ref{cha:Output-File-Format}
@@ -1228,13 +1342,27 @@
\end_layout
\begin_layout Standard
+
+\color red
+[TODO:
+\begin_inset Quotes sld
+\end_inset
+
+Is this a visualization section or visualization chapter?
+\begin_inset Quotes srd
+\end_inset
+
+ -MG]
+\end_layout
+
+\begin_layout Standard
You can visualise the output using the Matlab scripts found in the
\family typewriter
tools/
\family default
directory.
- The scripts also work with Octave.
- Also, you can set the DumpSwarm plugin (see section
+ The scripts also work with Octave and Octave B.
+ Also, you can set the DumpSwarm plugin (see Section
\begin_inset LatexCommand \ref{sec:.txt-Files-(Particle}
\end_inset
@@ -1245,7 +1373,7 @@
\end_inset
- or
+,
\begin_inset LatexCommand \htmlurl[ParaView]{paraview.org}
\end_inset
@@ -1254,6 +1382,20 @@
such as Excel.
\end_layout
+\begin_layout Standard
+
+\color red
+[TODO:
+\begin_inset Quotes sld
+\end_inset
+
+What about default values? Are there any?
+\begin_inset Quotes srd
+\end_inset
+
+ -MG]
+\end_layout
+
\begin_layout Section
Cookbook examples
\end_layout
@@ -1264,26 +1406,18 @@
input/cookbook/template.xml
\family default
) to create customized input files.
- Unless otherwise specified, when we say to add something
+ Unless otherwise specified, when we say to add something,
\begin_inset Foot
status collapsed
\begin_layout Standard
To copy and paste from this PDF with Adobe Acrobat, right click to get the
- context menu and select
-\begin_inset Quotes sld
-\end_inset
-
-Allow Hand Tool to Select Text
-\begin_inset Quotes srd
-\end_inset
-
-.
+ context menu and select ``Allow Hand Tool to Select Text.''
\end_layout
\end_inset
-, that text should be added after the line
+ that text should be added after the line
\end_layout
\begin_layout LyX-Code
@@ -1333,7 +1467,7 @@
Viscous Material
\end_layout
-\begin_layout Standard
+\begin_layout Enumerate
First, copy
\family typewriter
template.xml
@@ -1342,16 +1476,17 @@
\family typewriter
myviscous.xml
\family default
- and edit that.
+ to edit as follows.
\end_layout
-\begin_layout Standard
-The first thing we have to do is add in a material.
+\begin_layout Enumerate
+Add in a material.
The simplest variety is a purely viscous material.
- So we add a box covering the whole domain
+ So we add a box covering the whole domain:
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<struct name="boxShape">
\end_layout
@@ -1389,9 +1524,25 @@
\end_layout
\begin_layout Standard
+
+\color red
+[TODO:
+\begin_inset Quotes sld
+\end_inset
+
+Should the above coordinates be shown in a line diagram?
+\begin_inset Quotes srd
+\end_inset
+
+ -MG]
+\end_layout
+
+\end_deeper
+\begin_layout Enumerate
Then we set the material's viscosity
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<struct name="backgroundViscosity">
\end_layout
@@ -1409,9 +1560,26 @@
\end_layout
\begin_layout Standard
-We tell Gale to store the viscosity on the material points
+
+\color red
+[TODO:
+\begin_inset Quotes sld
+\end_inset
+
+RE: 1.0 immediately above, does Gale work with dimensional or nondimensional
+ variables?
+\begin_inset Quotes srd
+\end_inset
+
+ -MG]
\end_layout
+\end_deeper
+\begin_layout Enumerate
+Next we need Gale to store the viscosity on the material points
+\end_layout
+
+\begin_deeper
\begin_layout LyX-Code
<struct name="storeViscosity">
\end_layout
@@ -1428,10 +1596,12 @@
</struct>
\end_layout
-\begin_layout Standard
-Finally, we create the material, using the components we just created.
+\end_deeper
+\begin_layout Enumerate
+Finally, we create the material, using the components just created.
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<struct name="viscous">
\end_layout
@@ -1468,9 +1638,14 @@
</struct>
\end_layout
+\end_deeper
+\begin_layout Enumerate
+Save this file, as it will be the basis for many other examples that follow.
+
+\end_layout
+
\begin_layout Standard
-Save this file, as it will be the basis for many other examples.
- You can compare your result with the worked example in the file
+You can compare your result with the worked example in the file
\family typewriter
input/cookbook/viscous.xml
\family default
@@ -1486,12 +1661,15 @@
\end_layout
\begin_layout Standard
-This input file is valid, but there are no dynamics.
- Gale will complain if you try to run it.
+The input file you have just created is valid, but Gale will complain if
+ you try to run it because there are no dynamics.
+
+\color red
+[TODO: need more intro here]
\end_layout
-\begin_layout Standard
-First, copy
+\begin_layout Enumerate
+Copy
\family typewriter
myviscous.xml
\family default
@@ -1502,10 +1680,11 @@
.
\end_layout
-\begin_layout Standard
-We make the right boundary move by changing the line after
+\begin_layout Enumerate
+Make the right boundary move by changing the line after this section
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<param name="type">WallVC</param>
\end_layout
@@ -1530,10 +1709,6 @@
<param name="type">double</param>
\end_layout
-\begin_layout LyX-Code
-
-\end_layout
-
\begin_layout Standard
from
\end_layout
@@ -1550,8 +1725,14 @@
<param name="value">1.0</param>
\end_layout
-\begin_layout Standard
-Be careful! There are several
+\begin_layout Quote
+
+\series bold
+\color red
+Warning:
+\series default
+\color default
+ There are several
\family typewriter
WallVC
\family default
@@ -1585,7 +1766,8 @@
right.
\end_layout
-\begin_layout Standard
+\end_deeper
+\begin_layout Enumerate
We can now run this example, and the output will go into the directory
\family typewriter
output.template
@@ -1594,6 +1776,7 @@
If we want to run in 3D, we only need to change the line after
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<param name="outputPath">./output.template</param>
\end_layout
@@ -1614,8 +1797,9 @@
<param name="dims">3</param>
\end_layout
+\end_deeper
\begin_layout Standard
-A worked example is in
+A worked example is at
\family typewriter
input/cookbook/myviscous-example.xml
\family default
@@ -1627,6 +1811,21 @@
\end_layout
\begin_layout Standard
+
+\color red
+[TODO:
+\begin_inset Quotes sld
+\end_inset
+
+All of the following examples seem to be EXCELLENT but all would benefit
+ from more intro discussion, showing results, and then explaining the results
+\begin_inset Quotes srd
+\end_inset
+
+ - MG]
+\end_layout
+
+\begin_layout Standard
Now we want to make the bottom boundary move differently, and not just have
the material slide along.
In particular, we want to simulate a box like in Figure
@@ -1634,7 +1833,8 @@
\end_inset
-, where the bottom right side of the box moves, but the bottom left sticks.
+, where the bottom right side of the box moves, but the viscous material
+ sticks to the bottom left.
\end_layout
\begin_layout Standard
@@ -1669,6 +1869,21 @@
\end_layout
\begin_layout Standard
+
+\color red
+[TODO:
+\begin_inset Quotes sld
+\end_inset
+
+Wouldn't it be better to include all these as cookbook1.xml etc., so that
+ there is no possibility of error?
+\begin_inset Quotes srd
+\end_inset
+
+ - MG]
+\end_layout
+
+\begin_layout Enumerate
First, copy
\family typewriter
myviscous_extension.xml
@@ -1676,10 +1891,13 @@
to
\family typewriter
myviscous_split.xml
-\family default
-, then modify the bottom boundary condition to
\end_layout
+\begin_layout Enumerate
+Modify the bottom boundary condition of WallVC to
+\end_layout
+
+\begin_deeper
\begin_layout LyX-Code
<struct>
\end_layout
@@ -1746,10 +1964,15 @@
\begin_layout Standard
This makes the velocity of the bottom boundary a step function.
- We must also specify the parameters of the step function by adding the
- variables
+
\end_layout
+\end_deeper
+\begin_layout Enumerate
+We must also specify the parameters of the step function by adding the variables
+\end_layout
+
+\begin_deeper
\begin_layout LyX-Code
<param name="StepFunctionLowerOffset">1.0</param>
\end_layout
@@ -1780,24 +2003,44 @@
>
\family default
).
- Do not add it in the list named
+
+\end_layout
+
+\begin_layout Quote
+
+\series bold
+\color red
+Warning:
+\series default
+\color default
+Do not add it in the list named
\family typewriter
+``variables
+\family default
+.''
+\end_layout
+\end_deeper
+\begin_layout Standard
+A worked example is in the file
+\family typewriter
+input/cookbook/viscous_split.xml
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+
+\color red
+[TODO:
\begin_inset Quotes sld
\end_inset
-variables
+Visualization? What do we see? Why? Please explain.
\begin_inset Quotes srd
\end_inset
-
-\family default
-.
- A worked example is in the file
-\family typewriter
-input/cookbook/viscous_split.xml
-\family default
-.
+ - MG]
\end_layout
\begin_layout Subsection
@@ -1846,12 +2089,12 @@
\end_layout
-\begin_layout Standard
-To start, copy the file
+\begin_layout Enumerate
+Copy the file
\family typewriter
myviscous.xml
\family default
- that we created in section
+ that we created in Section
\begin_inset LatexCommand \ref{sub:Viscous-Material}
\end_inset
@@ -1861,10 +2104,15 @@
myviscous_inflow.xml
\family default
.
- Then, we need to tell Gale to keep the left and bottom sides fixed, no
- matter what, by adding the lines
+
\end_layout
+\begin_layout Enumerate
+Then, we need to tell Gale to keep the left and bottom sides fixed, no matter
+ what, by adding the lines
+\end_layout
+
+\begin_deeper
\begin_layout LyX-Code
<param name="staticLeft">True</param>
\end_layout
@@ -1874,14 +2122,15 @@
\end_layout
\begin_layout Standard
-after
+after the
\family typewriter
wrapTop
\family default
-.
+ line.
\end_layout
-\begin_layout Standard
+\end_deeper
+\begin_layout Enumerate
Now we specify the velocities on the boundaries using the
\family typewriter
StepFunctionProduct
@@ -1894,6 +2143,7 @@
to
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<param name="type">WallVC</param>
\end_layout
@@ -1950,7 +2200,8 @@
<param name="StepFunctionProduct3Value">1</param>
\end_layout
-\begin_layout Standard
+\end_deeper
+\begin_layout Enumerate
For the bottom boundary, we modify the the bottom
\family typewriter
WallVC
@@ -1958,6 +2209,7 @@
to
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<param name="type">WallVC</param>
\end_layout
@@ -2046,6 +2298,7 @@
<param name="StepFunctionProduct2Value">-1.0</param>
\end_layout
+\end_deeper
\begin_layout Standard
A worked example is in the file
\family typewriter
@@ -2100,12 +2353,12 @@
\end_layout
-\begin_layout Standard
-Again, copy the file
+\begin_layout Enumerate
+Copy the file
\family typewriter
myviscous.xml
\family default
- that we created in section
+ that we created in Section
\begin_inset LatexCommand \ref{sub:Viscous-Material}
\end_inset
@@ -2115,13 +2368,18 @@
myviscous_stressbc.xml
\family default
.
- We add a
+
+\end_layout
+
+\begin_layout Enumerate
+Add a
\family typewriter
StressBC
\family default
component
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<struct name="stressBC">
\end_layout
@@ -2174,6 +2432,7 @@
<param name="StepFunctionProduct1Value">1.0</param>
\end_layout
+\end_deeper
\begin_layout Standard
A worked example is in the file
\family typewriter
@@ -2232,8 +2491,8 @@
\end_layout
-\begin_layout Standard
-To create this example, copy
+\begin_layout Enumerate
+Copy
\family typewriter
myviscous.xml
\family default
@@ -2242,18 +2501,18 @@
myviscous_sinusoid.xml
\family default
.
- Then add a
+
+\end_layout
+
+\begin_layout Enumerate
+Add a
\family typewriter
SurfaceAdaptor
\family default
- component to the input file from section
-\begin_inset LatexCommand \ref{sub:Viscous-Material}
-
-\end_inset
-
-.
+ component:
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<struct name="surfaceAdaptor">
\end_layout
@@ -2298,19 +2557,20 @@
</struct>
\end_layout
+\end_deeper
\begin_layout Standard
This example has no moving boundaries, so the material will simply relax.
- A worked example is in
+
+\end_layout
+
+\begin_layout Standard
+A worked example is in
\family typewriter
input/cookbook/viscous_sinusoid.xml
\family default
.
\end_layout
-\begin_layout LyX-Code
-
-\end_layout
-
\begin_layout Subsection
Multiple Viscous Materials
\end_layout
@@ -2356,7 +2616,7 @@
\end_layout
-\begin_layout Standard
+\begin_layout Enumerate
Copy
\family typewriter
myviscous_extension.xml
@@ -2374,10 +2634,11 @@
\end_layout
-\begin_layout Standard
-First we create the sphere.
+\begin_layout Enumerate
+Add the sphere.
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<struct name="sphereShape">
\end_layout
@@ -2402,10 +2663,12 @@
</struct>
\end_layout
-\begin_layout Standard
-Then we add the new material.
+\end_deeper
+\begin_layout Enumerate
+Then add the new material.
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<struct name="sphereViscosity">
\end_layout
@@ -2458,12 +2721,13 @@
</struct>
\end_layout
-\begin_layout Standard
-We also need change the shape of the original material so it is not inside
- the sphere.
+\end_deeper
+\begin_layout Enumerate
+Change the shape of the original material so it is not inside the sphere.
We do this by creating a new shape which is the old shape minus the sphere.
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<struct name="nonSphereShape">
\end_layout
@@ -2492,7 +2756,8 @@
</struct>
\end_layout
-\begin_layout Standard
+\end_deeper
+\begin_layout Enumerate
Finally, we modify the original viscous material to use this new
\family typewriter
nonSphereShape
@@ -2501,6 +2766,7 @@
So we change the line after
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<struct name="viscous">
\end_layout
@@ -2525,6 +2791,7 @@
<param name="Shape">nonSphereShape</param>
\end_layout
+\end_deeper
\begin_layout Standard
A worked example is in
\family typewriter
@@ -2540,16 +2807,21 @@
\begin_layout Standard
We can make the previous example more interesting by replacing the background
viscous material with a yielding material.
- First we copy
+
+\end_layout
+
+\begin_layout Enumerate
+Copy
\family typewriter
mymulti_material.xml
\family default
to
\family typewriter
myyielding.xml
-\family default
-.
- Then we create a
+\end_layout
+
+\begin_layout Enumerate
+Add a
\family typewriter
StrainWeakening
\family default
@@ -2560,6 +2832,7 @@
component
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<struct name="strainWeakening">
\end_layout
@@ -2652,12 +2925,14 @@
</struct>
\end_layout
-\begin_layout Standard
-Finally, we remove the existing viscous
+\end_deeper
+\begin_layout Enumerate
+Finally, remove the existing viscous
\family typewriter
RheologyMaterial
\end_layout
+\begin_deeper
\begin_layout LyX-Code
<struct name="viscous">
\end_layout
@@ -2736,6 +3011,7 @@
</struct>
\end_layout
+\end_deeper
\begin_layout Standard
A worked example is in
\family typewriter
@@ -2749,6 +3025,21 @@
\end_layout
\begin_layout Standard
+
+\color red
+[TODO:
+\begin_inset Quotes sld
+\end_inset
+
+This would be a good chapter with specific links to a web site with results
+ shown.
+\begin_inset Quotes srd
+\end_inset
+
+ - MG]
+\end_layout
+
+\begin_layout Standard
Gale makes a number of approximations when simulating.
Before trusting any results we get from Gale, we need to vary a number
of parameters to insure that the results are not an artifact of Gale's
@@ -2837,13 +3128,12 @@
PiCellerator, and UnderWorld.
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
+ Louis Moresi's group at Monash University (see Fig
\begin_inset LatexCommand \ref{fig:Mapping-between-MicroFEM}
\end_inset
-.
+).
Gale also makes use of PETSc, a suite of data structures and routines for
the parallel solution of scientific applications modeled by partial differentia
l equations.
@@ -2914,9 +3204,11 @@
\end_inset
-Mapping between MicroFEM and Gale
-\newline
+Mapping between MicroFEM and Gale
+\end_layout
+\begin_layout LyX-Code
+
\end_layout
\begin_layout Standard
@@ -3006,7 +3298,7 @@
\end_layout
\begin_layout Standard
-Gale uses StG_FEM to formulate implicit finite element systems, with the
+Gale uses StgFEM to formulate implicit finite element systems, with the
bulk of the information placed in a stiffness matrix and a force vector.
Depending on the type of solver used, there may be several matrices and
vectors.
@@ -3037,7 +3329,7 @@
\family typewriter
StiffnessMatrixTerm
\family default
-, providing an interface tailored to implementing material based continuum
+, providing an interface tailored to implementing material-based continuum
physics.
\end_layout
@@ -3253,7 +3545,7 @@
\end_layout
\begin_layout Standard
-will correctly intialize
+will correctly initialize
\family typewriter
StgFEM_StandardConditionFunctions
\family default
@@ -3518,7 +3810,7 @@
\begin_layout Standard
This tells Gale to remesh both the pressure and velocity field.
-
+ The components
\family typewriter
pressureRemesher
\family default
@@ -3542,7 +3834,7 @@
\family typewriter
velocity
\family default
- are all components that must be defined earlier (see Section
+ all must be defined earlier (see Section
\begin_inset LatexCommand \ref{sub:Components}
\end_inset
@@ -3674,7 +3966,7 @@
\family typewriter
SurfaceAdaptor
\family default
- (section
+ (Section
\begin_inset LatexCommand \ref{sec:Deformed-Upper-Boundary}
\end_inset
@@ -5006,7 +5298,7 @@
put where.
For example, we can create a simulation with different materials by creating
different shapes and putting different materials in them.
- As a simple example, we can create 3D box
+ As a simple example, we can create a 3D box
\end_layout
\begin_layout LyX-Code
@@ -6813,7 +7105,7 @@
\end_layout
\begin_layout Standard
-This is a temperature dependent viscosity
+This is a temperature-dependent viscosity
\begin_inset Formula \[
eta=eta0*\exp\left(-theta*T\right).\]
@@ -7267,14 +7559,21 @@
\end_layout
\begin_layout Subsubsection
+\begin_inset LatexCommand \label{sub:VonMises}
+
+\end_inset
+
VonMises
\end_layout
\begin_layout Standard
This is the simplest yielding rheology in Gale.
The yielding stress is simply the effective cohesion, so this rheology
- only has a few input parameters.
-
+ only has a few input parameters:
+\end_layout
+
+\begin_layout Itemize
+
\family typewriter
cohesion
\family default
@@ -7284,13 +7583,17 @@
\family default
have the obvious meanings.
+\end_layout
+
+\begin_layout Itemize
+
\family typewriter
minimumYieldStress
\family default
sets an absolute minimum to the stress required to make the material yield.
\end_layout
-\begin_layout Standard
+\begin_layout Itemize
\family typewriter
StrainRateSoftening
@@ -7319,6 +7622,7 @@
Otherwise the viscosity is set to
\end_layout
+\begin_deeper
\begin_layout Standard
\begin_inset Formula \[
\eta_{effective}=\eta\sigma_{yield}/I_{2},\]
@@ -7443,6 +7747,7 @@
\end_layout
+\end_deeper
\begin_layout Subsubsection
DruckerPrager
\end_layout
@@ -7550,7 +7855,12 @@
\end_layout
\begin_layout Standard
-(See also VonMises)
+(See also
+\begin_inset LatexCommand \ref{sub:VonMises}
+
+\end_inset
+
+.)
\end_layout
\begin_layout Subsubsection
@@ -7777,7 +8087,7 @@
\family default
.
This tells Gale whether it should check to see whether material will weaken
- further in the current direction, or it will try every direction equally
+ further in the current direction, or if it should try every direction equally
each time step.
\newline
@@ -9076,7 +9386,7 @@
\end_layout
\begin_layout Standard
-into the variables section (see section
+into the variables section (see Section
\begin_inset LatexCommand \ref{sub:Variables}
\end_inset
@@ -9115,7 +9425,11 @@
\end_layout
\begin_layout Section
-.dat ASCII Files
+
+\family typewriter
+.dat
+\family default
+ ASCII Files
\end_layout
\begin_layout Standard
@@ -9183,15 +9497,15 @@
\end_layout
\begin_layout Description
-Vector 2D:x y
+Vector 2D: x y
\newline
-3D:x, y, z
+3D: x, y, z
\end_layout
\begin_layout Description
-Tensor 2D:xx, xy, yx, yy
+Tensor 2D: xx, xy, yx, yy
\newline
-3D:xx, xy, xz, yx, yy, yz, zx, zy, zz
+3D: xx, xy, xz, yx, yy, yz, zx, zy, zz
\end_layout
\begin_layout Description
@@ -9206,12 +9520,12 @@
Tensor 2D: xx, xy, yx, yy
\newline
3D: xx, xy, xz, yx, yy, yz, zx, zy,
- zz (note that xx, yy, and zz are identically zero)
+ zz (note that xx, yy, and zz are identical to zero)
\end_layout
\begin_layout Standard
The complete list of output files per time step with the default components
- (see section
+ (see Section
\begin_inset LatexCommand \ref{sec:Basic-Components}
\end_inset
@@ -9244,7 +9558,7 @@
\begin_layout Standard
There will also be a timeInfo file, which records the start time and dt
- for that time step, and materialSwarm which is described in section
+ for that time step, and materialSwarm which is described in Section
\begin_inset LatexCommand \ref{sec:.dat-Binary-Files}
\end_inset
@@ -9258,7 +9572,7 @@
\family typewriter
DumpSwarm
\family default
-, explained below in section
+, explained below in Section
\begin_inset LatexCommand \ref{sec:.txt-Files-(Particle}
\end_inset
@@ -9267,7 +9581,11 @@
\end_layout
\begin_layout Section
-.dat Binary Files (Particle Information)
+
+\family typewriter
+.dat
+\family default
+Binary Files (Particle Information)
\begin_inset LatexCommand \label{sec:.dat-Binary-Files}
\end_inset
@@ -9285,7 +9603,11 @@
\end_layout
\begin_layout Section
-.txt Files (Particle Information)
+
+\family typewriter
+.txt
+\family default
+ Files (Particle Information)
\begin_inset LatexCommand \label{sec:.txt-Files-(Particle}
\end_inset
@@ -10023,6 +10345,20 @@
\begin_layout Bibliography
+\bibitem {key-5}
+Fullsack, Phillipe (1995).
+ An arbitrary Lagrangian-Eulerian formulation for creeping flows and its
+ application in tectonic models,
+\emph on
+Geophys.
+ J.
+ Int., 120
+\emph default
+, 1-23.
+\end_layout
+
+\begin_layout Bibliography
+
\bibitem {key-1}
Quenette, S., B.
Appelbe, M.
Modified: long/3D/Gale/trunk/documentation/gale.pdf
===================================================================
(Binary files differ)
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