[cig-commits] r11406 - long/3D/Gale/trunk/documentation
sue at geodynamics.org
sue at geodynamics.org
Tue Mar 11 14:00:34 PDT 2008
Author: sue
Date: 2008-03-11 14:00:33 -0700 (Tue, 11 Mar 2008)
New Revision: 11406
Modified:
long/3D/Gale/trunk/documentation/gale.lyx
long/3D/Gale/trunk/documentation/gale.pdf
Log:
fixed typos, formatting probs, bib, and other minor edits
Modified: long/3D/Gale/trunk/documentation/gale.lyx
===================================================================
--- long/3D/Gale/trunk/documentation/gale.lyx 2008-03-11 19:04:02 UTC (rev 11405)
+++ long/3D/Gale/trunk/documentation/gale.lyx 2008-03-11 21:00:33 UTC (rev 11406)
@@ -1,4 +1,4 @@
-#LyX 1.5.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -99,7 +99,7 @@
Walter Landry and Luke Hodkinson
\newline
Version
- 1.2.1
+ 1.2.2
\end_layout
\begin_layout Date
@@ -1275,8 +1275,7 @@
If you have a problem with strong viscosity gradients, the default solver
(GMRES) may converge very slowly.
Strong viscosity gradients occur when you start with materials with different
- viscosities (e.g.
- Appendix
+ viscosities (e.g., Appendix
\begin_inset LatexCommand ref
reference "sec:Circular-Inclusion"
@@ -1294,8 +1293,7 @@
\end_inset
-), or when materials yield (e.g.
- Appendix
+), or when materials yield (e.g., Appendix
\begin_inset LatexCommand ref
reference "sec:Geomod-2004"
@@ -1306,7 +1304,7 @@
\begin_layout Standard
One solution is to use a direct solver instead of GMRES.
- PETSc has a facility where you can use command line arguments to change
+ PETSc has a facility where you can use command-line arguments to change
the solver.
For example, on a single machine, to use a direct LU solve, you only need
to append arguments to the command line
@@ -1319,9 +1317,9 @@
\begin_layout Standard
In parallel, the analogous approach would be to use Mumps, a parallel direct
solver.
- You first need to make sure that your version of Petsc was installed with
+ You first need to make sure that your version of PETSc was installed with
Mumps.
- If you built Petsc yourself, you need to the add the option
+ If you built PETSc yourself, you need to add the option
\begin_inset Quotes sld
\end_inset
@@ -1334,7 +1332,7 @@
\end_inset
when configuring.
- The Petsc installation on TACC Lonestar has been installed with Mumps.
+ The PETSc installation on TACC Lonestar has been installed with Mumps.
\end_layout
\begin_layout Standard
@@ -1348,14 +1346,14 @@
\end_layout
\begin_layout Subsection
-Command line parameters
+Command-Line Parameters
\end_layout
\begin_layout Standard
You can also change the default values of the input file without modifying
that file by appending arguments.
- For example, to just change the number of time steps from the default value
- 10 to 20, use the following command
+ For example, to only change the number of time steps from the default value
+ 10 to value 20, use the following command
\end_layout
\begin_layout LyX-Code
@@ -1363,14 +1361,17 @@
\end_layout
\begin_layout Standard
-You can append any number of modified parameters in one unbroken line
+You can append any number of modified parameters in one unbroken line (here
+ shown wrapped around)
\end_layout
\begin_layout LyX-Code
\size small
./Gale-1_2_2 input/cookbook/yielding.xml --maxTimeSteps=20 --dim=3 --elementResI=
-64 --elementResJ=64 --elementResK=64 --particlesPerCell=60 --dumpEvery=10
+64
+\newline
+--elementResJ=64 --elementResK=64 --particlesPerCell=60 --dumpEvery=10
\end_layout
\begin_layout Subsection
@@ -1401,7 +1402,7 @@
\family default
files are single files that have information from every processor.
Gale uses file locking to ensure this cooperation.
- But on some parallel file systems, this can be problematic.
+ However, on some parallel file systems, this can be problematic.
The only known solution at this point is to turn off checkpointing by setting
the
\family typewriter
@@ -1457,7 +1458,7 @@
.dat
\family default
files will only be created every 25 time steps.
- You can change the value to any number you want.
+ You can change the value to any number you choose.
On the other hand, to change the frequency for creating
\family typewriter
.txt
@@ -1548,8 +1549,7 @@
The last option is to use a spreadsheet program such as Excel.
This is very limited, as you only see the location of the particles.
You cannot visualize the viscosity or degree of yielding of the particles,
- nor can you visualize the fields (e.g.
- strain rate, pressure, etc.).
+ nor can you visualize the fields (e.g., strain rate, pressure, etc.).
\end_layout
\begin_layout Subsection
@@ -1566,7 +1566,7 @@
\color none
These instructions are for Paraview version 3.2.1.
- To visualize step #10 of
+ To visualize step 10 of
\family typewriter
input/cookbook/yielding.xml
\family default
@@ -1591,11 +1591,13 @@
\begin_deeper
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
@@ -1631,11 +1633,13 @@
\begin_deeper
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
@@ -1680,13 +1684,14 @@
\begin_deeper
\begin_layout Standard
+\align center
\color none
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
@@ -1716,11 +1721,15 @@
\color none
fields.00010.pvts
\family default
-, graying it out.
-\newline
+, which will cause the ``eye'' to dim.
+\end_layout
-\newline
+\begin_deeper
+\begin_layout Standard
+\noindent
+\align center
+\color none
\begin_inset Graphics
filename images/Paraview_grey_eye.png
@@ -1729,6 +1738,7 @@
\end_layout
+\end_deeper
\begin_layout Enumerate
Now you can plot the velocity as arrows on top of the pressure: Click on
the ``Glyph'' symbol
@@ -1751,11 +1761,13 @@
\begin_deeper
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -1777,7 +1789,7 @@
\end_deeper
\begin_layout Enumerate
-You can also visualize the magnitude of the velocity: Click on the grayed-out
+You can also visualize the magnitude of the velocity: Click on the dimmed-out
eye next to
\family typewriter
\color none
@@ -1788,11 +1800,13 @@
\begin_deeper
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
@@ -1814,17 +1828,19 @@
\end_deeper
\begin_layout Enumerate
-Finish by clicking on the drop down list to the right of ``Color by'' and
+Finish by clicking on the drop-down list to the right of ``Color by'' and
selecting ``VelocityMagnitudeField.''
\end_layout
\begin_deeper
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -1857,13 +1873,15 @@
\begin_deeper
\begin_layout Standard
+\noindent
+\align center
\color none
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
@@ -1903,11 +1921,13 @@
\begin_deeper
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -1998,6 +2018,8 @@
\begin_deeper
\begin_layout Standard
+\noindent
+\align center
\begin_inset Graphics
filename images/Octave_fig1.png
lyxscale 75
@@ -2006,9 +2028,10 @@
\end_inset
-\end_layout
+\begin_inset VSpace defskip
+\end_inset
-\begin_layout Standard
+
\begin_inset Graphics
filename images/Octave_fig2.png
lyxscale 75
@@ -2017,9 +2040,15 @@
\end_inset
+\begin_inset VSpace defskip
+\end_inset
+
+
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Graphics
filename images/Octave_fig3.png
lyxscale 75
@@ -2039,6 +2068,8 @@
\begin_deeper
\begin_layout Standard
+\noindent
+\align center
\begin_inset Graphics
filename images/Matlab_fig111.png
scale 75
@@ -2046,9 +2077,15 @@
\end_inset
+\begin_inset VSpace defskip
+\end_inset
+
+
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Graphics
filename images/Matlab_fig112.png
width 75col%
@@ -2099,13 +2136,15 @@
\begin_deeper
\begin_layout Standard
+\noindent
+\align center
\color none
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
@@ -2132,11 +2171,13 @@
\begin_deeper
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
@@ -2165,11 +2206,13 @@
\begin_deeper
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -2197,11 +2240,13 @@
\begin_deeper
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -2924,11 +2969,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
-placement h
+placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\align center
@@ -3544,11 +3591,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\align center
@@ -3608,11 +3657,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\align center
@@ -3800,11 +3851,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\align center
@@ -4069,8 +4122,7 @@
\begin_layout Enumerate
When you deleted the bottom boundary condition, the vertical velocity became
unspecified.
- Recall that the momentum equation (eq.
-
+ Recall that the momentum equation (Equation
\begin_inset LatexCommand ref
reference "eq:simple momentum conservation"
@@ -4200,11 +4252,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -4265,11 +4319,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement h
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\align center
@@ -4394,11 +4450,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -4456,11 +4514,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement h
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\align center
@@ -4703,11 +4763,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -4753,11 +4815,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -5030,11 +5094,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -5070,6 +5136,7 @@
\end_layout
\begin_layout Standard
+\noindent
A visualization of the viscosity of the particles is shown in Figure
\begin_inset LatexCommand ref
reference "fig:Viscosity-of-yielding"
@@ -5080,11 +5147,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -5120,6 +5189,7 @@
\end_layout
\begin_layout Standard
+\noindent
and a visualization of the yielding of the particles is shown in Figure
\begin_inset LatexCommand ref
@@ -5131,11 +5201,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -5681,7 +5753,7 @@
\end_deeper
\begin_layout Enumerate
-Tell the buoyancy force term about the temperature field by adding after
+Modify the buoyancy force term by adding the temperature field after
\end_layout
\begin_deeper
@@ -5698,7 +5770,7 @@
\end_layout
\begin_layout Standard
-the line
+with the line
\end_layout
\begin_layout LyX-Code
@@ -5769,11 +5841,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -5814,17 +5888,16 @@
\begin_layout Standard
The previous chapter gave examples on how to make simple problems with simple
- parameters (e.g.
- length=1, viscosity=1).
- Scaling these input parameters to realistic values (e.g.
- length=1000km, viscosity=
+ parameters (e.g., length=1, viscosity=1).
+ Scaling these input parameters to realistic values (e.g., length=1000km,
+ viscosity=
\begin_inset Formula $10^{26}$
\end_inset
) should be as easy as changing the various parameters to the right number.
In practice, it can be difficult to get right, because you may have to
change many different parameters at once to ensure stability.
- To make that transition easier, there is are sample input files in
+ To make that transition easier, use the sample input files in
\family typewriter
input/examples/tibet.xml
\family default
@@ -5834,7 +5907,7 @@
\family default
.
These are the input files used to create the cover images.
- The first file simulates a tibetan scale plateau under extension in 2D.
+ The first file simulates a Tibetan scale plateau under extension in 2D.
A schematic of the simulation is shown in Figure
\begin_inset LatexCommand ref
reference "fig:Schematic-of-extension"
@@ -5845,16 +5918,15 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
+placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
\align center
\begin_inset Graphics
filename images/tibet_setup.eps
@@ -5888,7 +5960,9 @@
then imports a realistic topography from a data file.
At the moment, this location is hard coded in
\family typewriter
-src/StGermain/Discretisation/Mesh/src/SurfaceAdaptor.c
+src/StGermain/Discretisation/Mesh/src/
+\newline
+SurfaceAdaptor.c
\family default
.
It needs a data file
@@ -5897,9 +5971,9 @@
\family default
.
This file is very large, so it is not distributed with Gale.
- You may download it from
-\begin_inset LatexCommand url
-target "http://geodynamics.org/~walter/ascii_topo"
+ You may download it at
+\begin_inset LatexCommand htmlurl
+target "geodynamics.org/~walter/ascii_topo"
\end_inset
@@ -5955,8 +6029,14 @@
\end_layout
\begin_layout Standard
-StGermain provides an infrastructure that can be used to create reusable,
- collaborative computational development environments.
+\begin_inset LatexCommand htmlurl
+name "StGermain"
+target "csd.vpac.org/twiki/bin/view/Stgermain/WebHome"
+
+\end_inset
+
+ provides an infrastructure that can be used to create reusable, collaborative
+ computational development environments.
It aims to provide the efficiency and style of coding near that of traditional
HPC as well as new techniques and methods in scientific computing.
Effectively, it is the application of contemporary software engineering
@@ -5975,13 +6055,6 @@
In turn, intellectual property, skills and adaptability of the recipients
develop over time.
-\begin_inset LatexCommand htmlurl
-name "StGermain Web Site"
-target "csd.vpac.org/twiki/bin/view/Stgermain/WebHome"
-
-\end_inset
-
-
\end_layout
\begin_layout Subsection
@@ -5989,19 +6062,18 @@
\end_layout
\begin_layout Standard
-PETSc, the Portable, Extensible Toolkit for Scientific Computation, is a
- suite of data structures and routines for the uni- and parallel-processor
- solution of large-scale scientific application problems modeled by partial
- differential equations.
- It employs the MPI standard for all message-passing communication.
-
\begin_inset LatexCommand htmlurl
-name "PETSc Web Site"
+name "PETSc"
target "www-unix.mcs.anl.gov/petsc/petsc-as/"
\end_inset
-
+, the Portable, Extensible Toolkit for Scientific Computation, is a suite
+ of data structures and routines for the uni- and parallel-processor solution
+ of large-scale scientific application problems modeled by partial differential
+ equations.
+ It employs the MPI standard for all message-passing communication.
+
\end_layout
\begin_layout Standard
@@ -6057,8 +6129,14 @@
\end_layout
\begin_layout Standard
-StgFEM uses the StGermain philosophy of reusability and collaborative developmen
-t to create a finite element problem composer in terms of both the linear
+\begin_inset LatexCommand htmlurl
+name "StgFEM"
+target "csd.vpac.org/twiki/bin/view/Stgfem/WebHome"
+
+\end_inset
+
+ uses the StGermain philosophy of reusability and collaborative development
+ to create a finite element problem composer in terms of both the linear
system to be solved and the finite element discretization of the problem
domain.
The composition can be described in XML and could be represented in a network
@@ -6066,13 +6144,6 @@
StgFEM describes finite element systems for various formulations in a manner
that can allow the underlying numerics to be interchanged.
-\begin_inset LatexCommand htmlurl
-name "StgFEM Web Site"
-target "csd.vpac.org/twiki/bin/view/Stgfem/WebHome"
-
-\end_inset
-
-
\end_layout
\begin_layout Subsection
@@ -6080,22 +6151,21 @@
\end_layout
\begin_layout Standard
-PICellerator (Particle In Cellerator), a Lagrangian Integration Point Finite
- Element framework, is implemented as an integration scheme substitute for
- the default Gaussian scheme implemented in StgFEM.
+\begin_inset LatexCommand htmlurl
+name "PICellerator"
+target "csd.vpac.org/twiki/bin/view/PICellerator/WebHome"
+
+\end_inset
+
+ (Particle In Cellerator), a Lagrangian Integration Point Finite Element
+ framework, is implemented as an integration scheme substitute for the default
+ Gaussian scheme implemented in StgFEM.
The PICellerator concept has since grown to become a general Lagrangian
integration scheme framework and a Lagrangian constitutive rule framework.
The PIC scheme is provided and other Arbitrary Lagrangian Eulerian schemes
are in development.
Constitutive rules are reusable across these schemes.
-\begin_inset LatexCommand htmlurl
-name "PICellerator Web Site"
-target "csd.vpac.org/twiki/bin/view/PICellerator/WebHome"
-
-\end_inset
-
-
\end_layout
\begin_layout Subsection
@@ -6103,9 +6173,15 @@
\end_layout
\begin_layout Standard
-UnderWorld is a StGermain parallel modeling framework Geoscience research
- code which utilizes a Lagrangian particle-in-cell finite element scheme
- (the prototype of which is the Ellipsis code), visualised using gLucifer.
+\begin_inset LatexCommand htmlurl
+name "UnderWorld"
+target "wasabi.maths.monash.edu.au/twiki/view/Software/Underworld"
+
+\end_inset
+
+ is a StGermain parallel modeling framework Geoscience research code which
+ utilizes a Lagrangian particle-in-cell finite element scheme (the prototype
+ of which is the Ellipsis code), visualized using gLucifer.
UnderWorld (Monash University), StGermain (Victorian Partnership for Advanced
Computing or VPAC) and gLucifer (Monash University) are under development
as part of the Australian Computational Earth Systems Simulator (ACcESS),
@@ -6113,13 +6189,6 @@
located at the Australian Crustal Research Centre (ACRC) at Monash University
(Clayton Campus).
-\begin_inset LatexCommand htmlurl
-name "UnderWorld Web Site"
-target "wasabi.maths.monash.edu.au/twiki/view/Software/Underworld"
-
-\end_inset
-
-
\end_layout
\begin_layout Section
@@ -6165,7 +6234,7 @@
\begin_layout Standard
So, where does the actual physics take place? The answer is in the Rheology
- class, but first look at the PIC (particle in cell) scheme.
+ class, but first look at the PIC (particle-in-cell) scheme.
There are a number of benefits to using a PIC scheme, but the main use
is to store material properties on each particle.
These properties can then be used to drive our constitutive laws, in turn
@@ -6298,7 +6367,7 @@
\begin_layout Standard
The input files are XML files.
- This leverages a well known format to specify concepts like hierarchies,
+ This leverages a well-known format to specify concepts like hierarchies,
lists, parameters, and arbitrary structures.
The entire document is placed withing a
\family typewriter
@@ -6409,7 +6478,7 @@
\end_layout
\begin_layout Standard
-will not.
+will not, and no error message will alert you of the problem.
\end_layout
\begin_layout Subsection
@@ -6437,7 +6506,7 @@
\family typewriter
EulerDeform
\family default
-,and
+, and
\family typewriter
VTKOutput
\family default
@@ -6659,7 +6728,7 @@
\end_layout
\begin_layout Standard
-This tells Gale to remesh both the pressure and velocity field.
+This commands Gale to remesh both the pressure and velocity field.
The components
\family typewriter
\size small
@@ -6708,7 +6777,7 @@
\end_layout
\begin_layout Standard
-that tells Gale to make the top surface conform to the simulation.
+that makes the top surface conform to the simulation.
Other options (
\family typewriter
wrapBottom
@@ -6848,8 +6917,11 @@
\begin_layout Description
elementResI,elementResJ,elementResK The number of elements in each direction.
- Note that the number of grid points is one larger (e.g., 64 elements -> 65
- grid points).
+ Note that the number of grid points is one larger (e.g., 64 elements
+\begin_inset Formula $\Rightarrow$
+\end_inset
+
+ 65 grid points).
\end_layout
\begin_layout Description
@@ -8282,8 +8354,8 @@
\end_layout
\begin_layout Standard
-To have Gale use and evolve the temperature, you need to add the following
- components
+To configure Gale to use and evolve the temperature, you need to add the
+ following components
\end_layout
\begin_layout LyX-Code
@@ -8659,6 +8731,12 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
+\begin_inset VSpace defskip
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
<features>
@@ -8956,7 +9034,7 @@
\end_inset
- So when Gale is trying to figure out whether a coordinate
+ So when Gale attempts to figure out whether a coordinate
\begin_inset Formula $(x,y,z)$
\end_inset
@@ -8982,7 +9060,7 @@
\end_layout
\begin_layout Standard
-Finally, you may tell Gale to invert the shape with the
+Finally, you can command Gale to invert the shape with the
\family typewriter
invert
\family default
@@ -8990,6 +9068,12 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
+\begin_inset VSpace defskip
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="8" columns="2">
<features>
@@ -9176,6 +9260,12 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
+\begin_inset VSpace defskip
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
<features>
@@ -9286,9 +9376,12 @@
\end_inset
-\newline
+\end_layout
-\newline
+\begin_layout Standard
+\begin_inset VSpace defskip
+\end_inset
+
See also the notes for BelowPlane.
\end_layout
@@ -9331,11 +9424,15 @@
\end_inset
, which are only used when computing the volume of this shape.
-\newline
-
\end_layout
\begin_layout Standard
+\noindent
+\align center
+\begin_inset VSpace defskip
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="8" columns="2">
<features>
@@ -9541,11 +9638,15 @@
).
If both are specified for one coordinate, Gale will use start and end.
-\newline
-
\end_layout
\begin_layout Standard
+\noindent
+\align center
+\begin_inset VSpace defskip
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="2">
<features>
@@ -9728,6 +9829,8 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Formula \[
\begin{array}{c}
radius^{2}>x^{2}+y^{2}\\
@@ -9737,6 +9840,10 @@
\end_inset
+
+\begin_inset VSpace defskip
+\end_inset
+
\begin_inset Tabular
<lyxtabular version="3" rows="8" columns="2">
@@ -9949,7 +10056,7 @@
\begin_inset Formula $\pm2\pi$
\end_inset
-, depending on the direction you specify vertices.
+, depending on which direction you specify the vertices.
If the point is outside the polygon, then the angles sum to 0.
A simple example is a triangle
\end_layout
@@ -10009,11 +10116,15 @@
\begin_layout Standard
You can extrude this shape into three dimensions by specifying startZ and
endZ.
-\newline
-
\end_layout
\begin_layout Standard
+\noindent
+\align center
+\begin_inset VSpace defskip
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="2">
<features>
@@ -10100,6 +10211,12 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
+\begin_inset VSpace defskip
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
<features>
@@ -10170,17 +10287,18 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Formula \[
\left(\left(\frac{x}{radiusX}\right)^{2/epsilon2}+\left(\frac{y}{radiusY}\right)^{2/epsilon2}\right)^{epsilon2/epsilon1}+\left(\frac{z}{radiusZ}\right)^{2/epsilon1}<1.\]
\end_inset
-\newline
+\begin_inset VSpace defskip
+\end_inset
-\end_layout
-\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="6" columns="2">
<features>
@@ -10653,6 +10771,15 @@
\end_layout
\begin_layout Standard
+\begin_inset VSpace defskip
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
\begin_inset Tabular
<lyxtabular version="3" rows="6" columns="2">
<features>
@@ -10814,6 +10941,15 @@
\end_layout
\begin_layout Standard
+\begin_inset VSpace defskip
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
<features>
@@ -10881,11 +11017,14 @@
eta0
\family default
.
-\newline
-
\end_layout
\begin_layout Standard
+\align center
+\begin_inset VSpace defskip
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
<features>
@@ -10953,6 +11092,12 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
+\begin_inset VSpace defskip
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="2">
<features>
@@ -11070,8 +11215,8 @@
\end_layout
\begin_layout Description
-MaterialPointsSwarm This is the swarm of particles that this rheology will
- tie itself to.
+MaterialPointsSwarm This is the swarm of particles associated with this
+ rheology.
Given the standard components in Section
\begin_inset LatexCommand ref
reference "sec:Basic-Components"
@@ -11183,6 +11328,8 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Tabular
<lyxtabular version="3" rows="10" columns="2">
<features>
@@ -11471,11 +11618,19 @@
\end_inset
which essentially sets the stress of the particle to the yield stress.
-\newline
+\end_layout
+\end_deeper
+\begin_layout Standard
+\begin_inset VSpace defskip
+\end_inset
+
+
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
<features>
@@ -11588,7 +11743,6 @@
\end_layout
-\end_deeper
\begin_layout Subsubsection
DruckerPrager
\end_layout
@@ -11616,11 +11770,18 @@
is the pressure.
-\newline
+\end_layout
+\begin_layout Standard
+\begin_inset VSpace defskip
+\end_inset
+
+
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="2">
<features>
@@ -11691,18 +11852,16 @@
\end_inset
-\newline
-
\end_layout
\begin_layout Standard
-(See also
+See also Section
\begin_inset LatexCommand ref
reference "sub:VonMises"
\end_inset
-.)
+.
\end_layout
\begin_layout Subsubsection
@@ -11729,11 +11888,18 @@
effective cohesion.
This is because there tends to be numerical problems when using a very
small minimum yield stress under tension.
-\newline
+\end_layout
+\begin_layout Standard
+\begin_inset VSpace defskip
+\end_inset
+
+
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Tabular
<lyxtabular version="3" rows="6" columns="2">
<features>
@@ -11946,11 +12112,18 @@
This tells Gale whether it should check to see whether material will weaken
further in the current direction, or if it should try every direction equally
each time step.
-\newline
+\end_layout
+\begin_layout Standard
+\begin_inset VSpace defskip
+\end_inset
+
+
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Tabular
<lyxtabular version="3" rows="7" columns="2">
<features>
@@ -12735,8 +12908,7 @@
\family typewriter
temperatureBCs
\family default
- and the velocity variable (e.g.
-
+ and the velocity variable (e.g.,
\family typewriter
vx
\family default
@@ -12999,6 +13171,15 @@
\end_layout
\begin_layout Standard
+\begin_inset VSpace defskip
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
\begin_inset Tabular
<lyxtabular version="3" rows="6" columns="2">
<features>
@@ -13199,6 +13380,15 @@
\end_layout
\begin_layout Standard
+\begin_inset VSpace defskip
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
\begin_inset Tabular
<lyxtabular version="3" rows="6" columns="2">
<features>
@@ -13429,7 +13619,7 @@
wedge
\family default
.
-
+ Function
\family typewriter
sine
\family default
@@ -13438,7 +13628,7 @@
cosine
\family default
example above.
-
+ Function
\family typewriter
wedge
\family default
@@ -13526,7 +13716,7 @@
\family typewriter
SolidBodyRotationY
\family default
-, ), out to a radius
+), out to a radius
\family typewriter
RadiusCylinder
\family default
@@ -13543,11 +13733,29 @@
\end_inset
- otherwise return 0.
+ otherwise returns 0.
\end_layout
\begin_layout Description
-Velocity_PartialRotationX Returns the x component of Velocity_SolidBodyRotation.
+Velocity_PartialRotationX Returns the
+\family roman
+\series medium
+\shape up
+\size normal
+\emph off
+\bar no
+\noun off
+\color none
+x
+\family default
+\series default
+\shape default
+\size default
+\emph default
+\bar default
+\noun default
+\color inherit
+ component of Velocity_SolidBodyRotation.
\end_layout
\begin_layout Description
@@ -13555,16 +13763,16 @@
\end_layout
\begin_layout Description
-TaperedRotationX if
+TaperedRotationX If
\begin_inset Formula $r<RadiusCylinder$
\end_inset
-, return Velocity_PartialRotationX.
+, returns Velocity_PartialRotationX.
If
\begin_inset Formula $RadiusCylinder<r<TaperedRadius$
\end_inset
-, return
+, returns
\begin_inset Formula \[
VelocityPartialRotationX\left(\frac{TaperedRadius-r}{TaperedRadius-RadiusCylinder}\right).\]
@@ -13574,7 +13782,7 @@
\begin_inset Formula $r>TaperedRadius$
\end_inset
-, return 0.
+, returns 0.
\end_layout
\begin_layout Description
@@ -13634,7 +13842,7 @@
\end_layout
\begin_layout Description
-Velocity_Lid_CornerOnly Return 1 if the coordinate is on the right boundary.
+Velocity_Lid_CornerOnly Returns 1 if the coordinate is on the right boundary.
\end_layout
\begin_layout Description
@@ -13771,7 +13979,7 @@
\end_inset
- The result then is
+ The result is
\begin_inset Formula \[
f(x,y,z)=\left\{ \begin{array}{cc}
0 & g<0\\
@@ -13829,7 +14037,7 @@
\end_inset
-then if
+ if
\begin_inset Formula $StepFunctionLessThan$
\end_inset
@@ -13999,13 +14207,51 @@
Underworld_VTKOutput
\family default
plugin.
- The .vts and .pvts files contain information about quantities on the grid,
- and the .vtu and .pvtu contain information about quantities on the particles.
- Every processor outputs its own .vts and .vtu file, and the .pvts and .pvtu
+ 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 .pvts and .pvtu files.
+ 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, sich as
+ programs, such as
\begin_inset LatexCommand htmlurl
name "ParaView"
target "paraview.org"
@@ -14027,7 +14273,23 @@
\end_inset
- can understand the raw .vts and .vtu files, but not the .pvtu and .pvts files.
+ 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
@@ -14118,7 +14380,7 @@
and fourth columns are the x, y, and z coordinates (2D runs still have
z data that can be ignored).
The last column(s) show the value.
- The five different types of variables and the order of components is
+ The five different types of variables and the order of components are
\end_layout
\begin_layout Description
@@ -14187,8 +14449,8 @@
\end_layout
\begin_layout Standard
-There will also be a timeInfo file, which records the start time and dt
- for that time step.
+There will also be a timeInfo file, which records the start time and step
+ size 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
@@ -14340,15 +14602,15 @@
stress
\family default
is the components of the stress at that material point.
- If the material does not yield (e.g.
- is purely viscous), then yielded is always zero.
+ If the material does not yield (e.g., is purely viscous), then yielded is
+ always zero.
\end_layout
\begin_layout Standard
You can also output in csv format for easily reading the data into a spreadsheet
like Excel.
- To do this, just set the variable
+ To do this, set the variable
\family typewriter
outputFormat
\family default
@@ -14916,7 +15178,7 @@
Two benchmarks were set up to validate numerical codes against analogue
sandbox experiments
\begin_inset LatexCommand cite
-key "Geomod 2004"
+key "Schreurs et al Analogue Benchmarks"
\end_inset
@@ -15722,7 +15984,7 @@
\shape italic
32(10)
\shape default
-, 1769-1779
+, 1769-1779.
\end_layout
\begin_layout Bibliography
@@ -15745,7 +16007,7 @@
\shape italic
105
\shape default
-, 11, 063-11, 082
+, 11,063-11,082.
\end_layout
\begin_layout Bibliography
@@ -15755,9 +16017,7 @@
\end_inset
-Schmid, D.
- W., and Y.
- Y.
+Schmid, D.W., and Y.Y.
Podladchikov (2003), Analytical solutions for deformable elliptical inclusions
in general shear,
\shape italic
@@ -15769,7 +16029,7 @@
\shape italic
155
\shape default
-, 269-288
+, 269-288.
\end_layout
\begin_layout Bibliography
@@ -15780,8 +16040,11 @@
\end_inset
Batchelor, G.
- K (1967), An Introduction to Fluid Dynamics, Cambridge University Press,
- p236
+ K (1967),
+\emph on
+An Introduction to Fluid Dynamics
+\emph default
+, Cambridge University Press, 236.
\end_layout
\begin_layout Bibliography
@@ -15791,10 +16054,12 @@
\end_inset
- Landau, L.
- D, and E.
- M.
- Lifshitz (1987), Fluid Mechanics, Pergamon Press, p61-62
+ Landau, L.D., and E.M.
+ Lifshitz (1987),
+\emph on
+Fluid Mechanics
+\emph default
+, Pergamon Press, 61-62.
\end_layout
\begin_layout Bibliography
@@ -15804,36 +16069,58 @@
\end_inset
- Johnson, A.
- M., and R.
- C.
- Fletcher, Folding of Viscous Layers (1994), Columbia University Press,
- p19
+ Johnson, A.M., and R.C.
+ Fletcher (1994),
+\emph on
+Folding of Viscous Layers
+\emph default
+, Columbia University Press, 19.
\end_layout
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
label "12"
-key "Geomod 2004"
+key "Schreurs et al Analogue Benchmarks"
\end_inset
-Analogue and Numerical Modelling of Crustal-Scale Processes , Buiter, S.J.H.
- and Schreurs, G.
- (eds), Geological Society, London, Special Publications, 253 : Schreurs,
- G., Buiter, S.J.H., Boutelier, D., Corti, G., Costa, E., Cruden, A., Daniel, J.-M.,
- Hoth, S., Koyi, H., Kukowski, N., Lohrmann, J., Ravaglia, A., Schlische, R.W.,
- Withjack, M.O., Yamada, Y., Cavozzi, C., DelVentisette, C., Elder Brady, J.,
- Hoffmann-Rothe, A., Mengus, J.-M., Montanari, D., and Nilforoushan, F., 2006,
- Analogue benchmarks of shortening and extension experiments, p.
- 1-27 * Susanne J.H.
- Buiter, Andrey Yu.
+ Schreurs, G., Buiter, S.J.H., Boutelier, D., Corti, G., Costa, E., Cruden, A.,
+ Daniel, J.-M., Hoth, S., Koyi, H., Kukowski, N., Lohrmann, J., Ravaglia, A., Schlische
+, R.W., Withjack, M.O., Yamada, Y., Cavozzi, C., DelVentisette, C., Elder Brady,
+ J., Hoffmann-Rothe, A., Mengus, J.-M., Montanari, D., and Nilforoushan, F.
+ (2006), Analogue benchmarks of shortening and extension experiments, in
+
+\emph on
+Analogue and Numerical Modelling of Crustal-Scale Processes
+\emph default
+, vol.
+ 253, edited by S.J.H Buiter and G.
+ Schreurs, pp.
+ 1-27, Geological Society, London, Special Publications, doi: 10.1144/GSL.SP.2006.25
+3.01.01.
+\end_layout
+
+\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "13"
+key "Buiter et al Numerical Sandbox"
+
+\end_inset
+
+Buiter, Susanne J.H., and Andrey Yu.
Babeyko, Susan Ellis, Taras V.
Gerya, Boris J.P.
- Kaus, Antje Kellner, Guido Schreurs, and Yasuhiro Yamada, 2006, The numerical
+ Kaus, Antje Kellner, Guido Schreurs, and Yasuhiro Yamada (2006), The numerical
sandbox: comparison of model results for a shortening and an extension
- experiment, p.
- 29-64
+ experiment, in
+\emph on
+Analogue and Numerical Modelling of Crustal-Scale Processes
+\emph default
+, vol.
+ 253, edited by S.J.H Buiter and G.
+ Schreurs, pp.
+ 29-64, Geological Society, London, Special Publications, doi: 10.1144/GSL.SP.2006.2
+53.01.02.
\end_layout
\end_body
Modified: long/3D/Gale/trunk/documentation/gale.pdf
===================================================================
(Binary files differ)
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