[cig-commits] r6039 - in long/3D/Gale/trunk: . documentation
walter at geodynamics.org
walter at geodynamics.org
Fri Feb 16 07:05:46 PST 2007
Author: walter
Date: 2007-02-16 07:05:04 -0800 (Fri, 16 Feb 2007)
New Revision: 6039
Modified:
long/3D/Gale/trunk/
long/3D/Gale/trunk/documentation/gale.lyx
long/3D/Gale/trunk/documentation/gale.pdf
Log:
r1578 at earth: boo | 2007-02-16 01:27:02 -0800
Lots of fixes to the manual
Property changes on: long/3D/Gale/trunk
___________________________________________________________________
Name: svk:merge
- 3a629746-de10-0410-b17b-fd6ecaaa963e:/cig:1577
+ 3a629746-de10-0410-b17b-fd6ecaaa963e:/cig:1578
Modified: long/3D/Gale/trunk/documentation/gale.lyx
===================================================================
--- long/3D/Gale/trunk/documentation/gale.lyx 2007-02-16 15:04:49 UTC (rev 6038)
+++ long/3D/Gale/trunk/documentation/gale.lyx 2007-02-16 15:05:04 UTC (rev 6039)
@@ -354,7 +354,7 @@
\end_inset
is the velocity.
- Use the convention that repeated indices (e.g.,
+ We use the convention that repeated indices (e.g.,
\begin_inset Formula $v_{i,i}$
\end_inset
@@ -392,7 +392,7 @@
\end_layout
\begin_layout Standard
-To solve eqs.
+Eqs.
\begin_inset LatexCommand \ref{eq:simple momentum conservation}
@@ -403,12 +403,12 @@
\end_inset
-, assume a simple Newtonian fluid.
- This allows us to write
+ are solved by assuming a simple Newtonian fluid.
+ Then
\begin_inset Formula $\tau$
\end_inset
- in terms of the rate of strain tensor
+ can be written in terms of the rate of strain tensor
\begin_inset Formula $D$
\end_inset
@@ -498,7 +498,7 @@
\end_inset
-You can then eliminate velocity by premultiplying by
+Velocity is eliminated by premultiplying by
\begin_inset Formula $G^{T}K^{-1}$
\end_inset
@@ -1021,7 +1021,7 @@
\end_layout
\begin_layout LyX-Code
-./Gale-1_1_1 extension.xml
+./Gale-1_1_1 input/extension.xml
\end_layout
\begin_layout Standard
@@ -1053,6 +1053,69 @@
\end_layout
\begin_layout Standard
+If you do not specify an input file, you will get a cryptic error
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+\color none
+Gale: build/Gale/src/main.c:154: main: Assertion `componentDict' failed.
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+\color none
+p0_16686: p4_error: interrupt SIGx: 6
+\end_layout
+
+\begin_layout Standard
+If Gale can not find the file, you will get a better error
+\end_layout
+
+\begin_layout LyX-Code
+Error: File input/extension.xml doesn't exist, not readable, or not valid.
+\end_layout
+
+\begin_layout LyX-Code
+Gale: build/StGermain/Base/IO/src/Journal.c:603: Journal_Firewall: Assertion
+ `expression' failed.
+\end_layout
+
+\begin_layout LyX-Code
+p0_16810: p4_error: interrupt SIGx: 6
+\end_layout
+
+\begin_layout Standard
+Due to quirks in some implementations of MPI, you may have to specify the
+ complete path to the input file (e.g.
+
+\family typewriter
+./Gale-1_1_1 /home/juser/gale/input/extension.xml
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+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}
+
+\end_inset
+
+.
+ For a complete description of the input file format, see Appendix
+\begin_inset LatexCommand \ref{cha:Input-File-Format}
+
+\end_inset
+
+.
+
+\end_layout
+
+\begin_layout Standard
If you compiled Gale yourself, then you can run it from where you installed
it.
If running in parallel, then just prepend
@@ -1096,18 +1159,60 @@
\begin_layout Standard
The sample input files will produce a directory in which you will find a
- number of different output files.
- The default setting is to print once for every time step.
- You can change the frequency of that setting, e.g., have it print less frequently
-, by modifying
+ number of
\family typewriter
-extension.xml
+.dat
\family default
- so the parameter
+,
\family typewriter
+.txt
+\family default
+, and
+\family typewriter
+\color none
+.vtk
+\family default
+ files
+\color default
+.
+
+\color none
+The formats of the
+\family typewriter
+\color default
+.dat
+\family default
+\color none
+ and
+\family typewriter
+\color default
+.txt
+\family default
+\color none
+ files are described fully in Appendix
+\begin_inset LatexCommand \ref{cha:Output-File-Format}
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Standard
+The default setting is to create files for every time step.
+ To change the frequency of creating the
+\family typewriter
+.dat
+\family default
+ files, you need to change the parameter
+\family typewriter
checkpointEvery
\family default
- has a different value, e.g.:
+.
+ For example, if you modify the line with
+\family typewriter
+checkpointEvery
+\family default
+ to
\end_layout
\begin_layout LyX-Code
@@ -1115,50 +1220,40 @@
\end_layout
\begin_layout Standard
-You can change the value to any number you want.
-
-\end_layout
-
-\begin_layout Standard
-Gale will output a number of
+then the
\family typewriter
.dat
\family default
-,
+ files will only be created every 25 time steps.
+ You can change the value to any number you want.
+ On the other hand, to change the frequency for creating
\family typewriter
.txt
\family default
-, and
+ and
\family typewriter
-\color none
.vtk
\family default
- files in the output directory.
- Their format is described fully in Appendix
-\begin_inset LatexCommand \ref{cha:Output-File-Format}
-
-\end_inset
-
+ files, you need to change the parameter
+\family typewriter
+dumpEvery
+\family default
.
\end_layout
-\begin_layout Subsection
-Visualization with ParaView
-\begin_inset LatexCommand \label{sub:Visualization-with-ParaView}
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Standard
\color none
-The
+There are a number of different options for visualizing the data.
+ The easiest way is to use the
\family typewriter
+\color default
.vtk
\family default
- files contain all of the information and can be visualized with either
+\color none
+ 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}
@@ -1169,16 +1264,45 @@
\end_inset
-, or
+, and
\begin_inset LatexCommand \htmlurl[Visit]{www.llnl.gov/visit}
\end_inset
-.
- For example, to visualize step #10 of
+).
+\end_layout
+
+\begin_layout Standard
+Another option is to use the Matlab scripts in the
\family typewriter
-extension.xml
+tools/
\family default
+ directory.
+ These scripts only work in 2D and only when running simulations with yielding
+ material.
+\end_layout
+
+\begin_layout Standard
+The last option is to use a spreadsheet program such as Excel.
+ This is very limited.
+\end_layout
+
+\begin_layout Subsection
+Visualization with ParaView
+\begin_inset LatexCommand \label{sub:Visualization-with-ParaView}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+
+\color none
+To visualize step #10 of
+\family typewriter
+input/extension.xml
+\family default
,
\end_layout
@@ -1187,17 +1311,14 @@
\color none
Start Paraview and open new data:
\family sans
-\color default
File
\family default
-\color none
\begin_inset Formula $\triangleright$
\end_inset
\family sans
-\color default
Open Data
\end_layout
@@ -1231,12 +1352,14 @@
\end_deeper
\begin_layout Enumerate
-Select
+A file dialog screen will appear.
+ Navigate to the output directory and select
\family typewriter
\color none
pressure.00010.vtk
\family default
-, and a pseudocolor plot of the pressure will appear
+.
+ Paraview will display a pseudocolor plot of the pressure.
\end_layout
\begin_deeper
@@ -1272,8 +1395,20 @@
\color none
fields.00010.vtk
\family default
-.
- By default, this will obscure the pressure with the velocity magnitude.
+ (with
+\family sans
+File
+\family default
+
+\begin_inset Formula $\triangleright$
+\end_inset
+
+
+\family sans
+Open Data
+\family default
+).
+ By default, Paraview will obscure the pressure with the velocity magnitude.
\end_layout
\begin_deeper
@@ -1308,8 +1443,14 @@
\end_deeper
\begin_layout Enumerate
-You can remove the velocity magnitude by clicking on the ``eye'' symbol,
- graying it out.
+You can remove the velocity magnitude by clicking on the ``eye'' symbol
+ next to
+\family typewriter
+\color none
+fields.00010.vtk
+\family default
+\color default
+, graying it out.
\newline
\newline
@@ -1406,8 +1547,8 @@
\end_deeper
\begin_layout Enumerate
-You finish by clicking on the box to the right of ``Color by'' and selecting
- ``Point StrainRateInvariantField.''
+You finish by clicking on the drop down list to the right of ``Color by''
+ and selecting ``Point StrainRateInvariantField.''
\end_layout
\begin_deeper
@@ -1582,15 +1723,14 @@
\end_layout
\end_deeper
-\begin_layout Enumerate
-Visualizing the 10th step of
+\begin_layout Standard
+Using Octave to visualize the 10th step of
\family typewriter
-extension.xml
+input/extension.xml
\family default
- in Octave results in
+ results in
\end_layout
-\begin_deeper
\begin_layout Standard
\begin_inset Graphics
filename images/Octave_fig1.png
@@ -1626,12 +1766,10 @@
\end_layout
-\end_deeper
-\begin_layout Enumerate
-In Matlab, you obtain these results:
+\begin_layout Standard
+Using Matlab results in
\end_layout
-\begin_deeper
\begin_layout Standard
\begin_inset Graphics
filename images/Matlab_fig111.png
@@ -1654,7 +1792,6 @@
\end_layout
-\end_deeper
\begin_layout Subsection
Visualization with Excel
\end_layout
@@ -1675,9 +1812,9 @@
such as Excel.
For example, for the
\family typewriter
-extension.xml
+input/extension.xml
\family default
- imput file,
+ input file,
\end_layout
\begin_layout Enumerate
@@ -1736,7 +1873,7 @@
\color none
\begin_inset Graphics
- filename images/Gnumeric_two_columns.png
+ filename images/Gnumeric_new_chart.png
lyxscale 50
scale 50
@@ -1760,6 +1897,7 @@
\begin_deeper
\begin_layout Standard
\begin_inset Float figure
+placement H
wide false
sideways false
status open
@@ -1791,6 +1929,7 @@
\begin_deeper
\begin_layout Standard
\begin_inset Float figure
+placement H
wide false
sideways false
status open
@@ -1877,15 +2016,30 @@
\begin_layout Chapter
Cookbooks
+\begin_inset LatexCommand \label{cha:Cookbooks}
+
+\end_inset
+
+
\end_layout
\begin_layout Standard
-In this section, you will edit a template file (
+In this chapter, you will edit a template file (
\family typewriter
input/cookbook/template.xml
\family default
) to create customized input files.
- Unless otherwise specified, when you are instructed to add something,
+ You should be able to use the template file as a basis for most of your
+ own input files.
+ The two things that might need modification are that the force of gravity
+ is set to 1, and the normal velocities on all boundaries except the top
+ are set to zero.
+ Beyond that, you only need to add where different materials are placed
+ initially.
+\end_layout
+
+\begin_layout Standard
+Unless otherwise specified, when you are instructed to add something
\begin_inset Foot
status collapsed
@@ -1896,7 +2050,7 @@
\end_inset
- that text should be added after the line
+, that text should be added after the line
\end_layout
\begin_layout LyX-Code
@@ -1946,6 +2100,11 @@
Viscous Material
\end_layout
+\begin_layout Standard
+This example just fills up the computational domain with a single viscous
+ material.
+\end_layout
+
\begin_layout Enumerate
First, copy
\family typewriter
@@ -2120,28 +2279,17 @@
\end_layout
\begin_layout Standard
-The basis for many problems of current interest involving lithospheric and
- crustal extension involves pulling (with velocity boundary conditions)
- a 2D viscous domain.
- This example helps to set up such a problem.
-\end_layout
-
-\begin_layout Standard
-
-\color red
-TODO: need to alter the next sentence so that the intro paragraph logically
- leads you to the next set of instructions.
- I tried to fix but needs more
-\end_layout
-
-\begin_layout Standard
The input file you created in Section
\begin_inset LatexCommand \ref{sec:Viscous-Material}
\end_inset
- is valid, but Gale will output errors if you try to run it at this point,
- because nothing is moving.
+ is valid, but uninteresting.
+ Nothing is moving, and Gale will output errors if you try to run it.
+ In this example, you will make the material extend by having the right
+ boundary move.
+ This simple model is the basis for many problems of current interest involving
+ lithospheric and crustal extension.
\end_layout
\begin_layout Enumerate
@@ -2287,7 +2435,12 @@
\end_inset
-) results in
+) is shown in Figure
+\begin_inset LatexCommand \ref{fig:Strain-viscous-extension}
+
+\end_inset
+
+.
\end_layout
\begin_layout Standard
@@ -2309,7 +2462,11 @@
\end_layout
\begin_layout Caption
-Visualization of viscous material in simple extension.
+\begin_inset LatexCommand \label{fig:Strain-viscous-extension}
+
+\end_inset
+
+Strain rate invariant and velocities of viscous material in extension.
\end_layout
\end_inset
@@ -2317,6 +2474,11 @@
\end_layout
+\begin_layout Standard
+The banding is a numerical artifact that arises from having a finite number
+ of particles per cell.
+\end_layout
+
\begin_layout Section
Viscous Material with Complex Boundaries
\end_layout
@@ -2324,7 +2486,7 @@
\begin_layout Standard
Another exercise is to make the bottom boundary move differently, and not
just have the material slide along.
- In particular, you want to simulate a box like in Figure
+ In particular, this example will simulate a box like in Figure
\begin_inset LatexCommand \ref{fig:Split-Boundary}
\end_inset
@@ -2515,7 +2677,12 @@
\end_inset
-) results in
+) is shown in Figure
+\begin_inset LatexCommand \ref{fig:Strain-complex}
+
+\end_inset
+
+.
\end_layout
\begin_layout Standard
@@ -2537,7 +2704,11 @@
\end_layout
\begin_layout Caption
-Visualization of viscous material with complex boundaries
+\begin_inset LatexCommand \label{fig:Strain-complex}
+
+\end_inset
+
+Strain rate invariant and velocities with complex boundaries
\end_layout
\end_inset
@@ -2550,8 +2721,8 @@
\end_layout
\begin_layout Standard
-A different kind of boundary condition is to have material flow in one side
- and out another as in Figure
+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}
\end_inset
@@ -2597,7 +2768,7 @@
myviscous.xml
\family default
that you created in Section
-\begin_inset LatexCommand \ref{sub:Viscous-Material}
+\begin_inset LatexCommand \ref{sec:Viscous-Material}
\end_inset
@@ -2890,7 +3061,12 @@
\end_inset
-) results in
+) is shown in Figure
+\begin_inset LatexCommand \ref{fig:Strain-inflow}
+
+\end_inset
+
+.
\end_layout
\begin_layout Standard
@@ -2912,7 +3088,11 @@
\end_layout
\begin_layout Caption
-Visualization of viscous material with inflow/outflow boundaries.
+\begin_inset LatexCommand \label{fig:Strain-inflow}
+
+\end_inset
+
+Strain rate invariant and velocities with inflow/outflow boundaries.
\end_layout
\end_inset
@@ -2925,14 +3105,16 @@
\end_layout
\begin_layout Standard
-Gale also supports stress boundary conditions.
- This lets you simulate a box like Figure
+This example demonstrates yet another boundary condition, where only the
+ stress is specified at the boundary.
+ In particular, this example describes a box like Figure
\begin_inset LatexCommand \ref{fig:Stress-Boundaries}
\end_inset
-, where there is a tangential stress at the bottom causing a circulation,
- but otherwise the bottom is stress-free.
+.
+ There is a tangential stress at the bottom causing a circulation, but otherwise
+ the bottom is stress-free.
\end_layout
\begin_layout Standard
@@ -2972,7 +3154,7 @@
myviscous.xml
\family default
that you created in Section
-\begin_inset LatexCommand \ref{sub:Viscous-Material}
+\begin_inset LatexCommand \ref{sec:Viscous-Material}
\end_inset
@@ -3058,7 +3240,12 @@
\end_inset
-) results in
+) is shown in Figure
+\begin_inset LatexCommand \ref{fig:Strain-stress}
+
+\end_inset
+
+.
\end_layout
\begin_layout Standard
@@ -3080,7 +3267,11 @@
\end_layout
\begin_layout Caption
-Visualization of viscous material with stress boundaries.
+\begin_inset LatexCommand \label{fig:Strain-stress}
+
+\end_inset
+
+Strain rate invariant and velocities with stress boundaries
\end_layout
\end_inset
@@ -3099,7 +3290,7 @@
\begin_layout Standard
All of the previous examples are set up as a regular rectangular box.
However, Gale can also start with the top initially deformed.
- A simple example is to make it sinusoidal as in Figure
+ This example will make it sinusoidal as in Figure
\begin_inset LatexCommand \ref{fig:Sinusoidal-Top}
\end_inset
@@ -3222,7 +3413,12 @@
\end_inset
-) results in
+) is shown in
+\begin_inset LatexCommand \ref{fig:Strain-initial-deformed}
+
+\end_inset
+
+
\end_layout
\begin_layout Standard
@@ -3244,7 +3440,11 @@
\end_layout
\begin_layout Caption
-Visualization of viscous material with initially deformed upper boundary
+\begin_inset LatexCommand \label{fig:Strain-initial-deformed}
+
+\end_inset
+
+Strain rate invariant and velocities with initially deformed upper boundary
\end_layout
\end_inset
@@ -3258,7 +3458,8 @@
\begin_layout Standard
All of the previous examples have only one type of viscous material.
- Gale can also handle multiple viscous materials such as in Figure
+ This example will create a simulation where there are multiple viscous
+ materials such as in Figure
\begin_inset LatexCommand \ref{fig:Multiple-Viscous-Materials}
\end_inset
@@ -3303,7 +3504,7 @@
myviscous_extension.xml
\family default
(see Section
-\begin_inset LatexCommand \ref{sub:Viscous-Extension}
+\begin_inset LatexCommand \ref{sec:Viscous-Material-in}
\end_inset
@@ -3484,7 +3685,12 @@
\end_inset
-) results in
+) is shown in Figure
+\begin_inset LatexCommand \ref{fig:Strain-multiple}
+
+\end_inset
+
+,
\end_layout
\begin_layout Standard
@@ -3506,7 +3712,11 @@
\end_layout
\begin_layout Caption
-Visualization of multiple viscous materials.
+\begin_inset LatexCommand \label{fig:Strain-multiple}
+
+\end_inset
+
+Strain rate invariant and velocities with multiple viscous materials.
\end_layout
\end_inset
@@ -3515,7 +3725,12 @@
\end_layout
\begin_layout Standard
-and the viscosity of the particles results in
+and the viscosity of the particles is shown in Figure
+\begin_inset LatexCommand \ref{fig:Viscosities-with-multiple}
+
+\end_inset
+
+.
\end_layout
\begin_layout Standard
@@ -3537,7 +3752,11 @@
\end_layout
\begin_layout Caption
-Visualization of multiple viscous materials - viscosity of the particles.
+\begin_inset LatexCommand \label{fig:Viscosities-with-multiple}
+
+\end_inset
+
+Viscosities with multiple viscous materials
\end_layout
\end_inset
@@ -3550,9 +3769,8 @@
\end_layout
\begin_layout Standard
-You can make the previous example more interesting by replacing the background
- viscous material with a yielding material.
-
+This example replaces the background viscous material with a yielding material.
+ This will produce localizations as some material fails.
\end_layout
\begin_layout Enumerate
@@ -3769,7 +3987,12 @@
\end_inset
-) results in
+) is shown in Figure
+\begin_inset LatexCommand \ref{fig:strain-yield}
+
+\end_inset
+
+.
\end_layout
\begin_layout Standard
@@ -3791,7 +4014,11 @@
\end_layout
\begin_layout Caption
-Visualization of yielding material in simple extension.
+\begin_inset LatexCommand \label{fig:strain-yield}
+
+\end_inset
+
+Strain rate invariant and velocities of yielding material in extension.
\end_layout
\end_inset
@@ -3800,7 +4027,12 @@
\end_layout
\begin_layout Standard
-A visualization of the viscosity of the particles results in
+A visualization of the viscosity of the particles is shown in Figure
+\begin_inset LatexCommand \ref{fig:Viscosity-of-yielding}
+
+\end_inset
+
+,
\end_layout
\begin_layout Standard
@@ -3822,8 +4054,11 @@
\end_layout
\begin_layout Caption
-Visualization of yielding material in simple extension - viscosity of the
- particles.
+\begin_inset LatexCommand \label{fig:Viscosity-of-yielding}
+
+\end_inset
+
+Viscosity of yielding material in extension
\end_layout
\end_inset
@@ -3832,7 +4067,13 @@
\end_layout
\begin_layout Standard
-and a visualization of the yielding of the particles results in
+and a visualization of the yielding of the particles is shown in Figure
+
+\begin_inset LatexCommand \ref{fig:Degree-of-yielding}
+
+\end_inset
+
+.
\end_layout
\begin_layout Standard
@@ -3854,17 +4095,16 @@
\end_layout
\begin_layout Caption
-Visualization of yielding material in simple extension - yielding of the
- particles.
-\end_layout
+\begin_inset LatexCommand \label{fig:Degree-of-yielding}
\end_inset
-
+Degree of yielding of yielding material in extension
\end_layout
-\begin_layout Standard
+\end_inset
+
\end_layout
\begin_layout Chapter
@@ -4224,6 +4464,11 @@
\begin_layout Chapter
\start_of_appendix
Input File Format
+\begin_inset LatexCommand \label{cha:Input-File-Format}
+
+\end_inset
+
+
\end_layout
\begin_layout Section
Modified: long/3D/Gale/trunk/documentation/gale.pdf
===================================================================
(Binary files differ)
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