[cig-commits] r6271 - in long/3D/Gale/trunk/documentation: . images
sue at geodynamics.org
sue at geodynamics.org
Fri Mar 16 11:45:04 PDT 2007
Author: sue
Date: 2007-03-16 11:45:02 -0700 (Fri, 16 Mar 2007)
New Revision: 6271
Modified:
long/3D/Gale/trunk/documentation/gale.lyx
long/3D/Gale/trunk/documentation/gale.pdf
long/3D/Gale/trunk/documentation/images/Paraview_grey_eye.png
Log:
changes requested by gurnis; questions answered or deferred to TODO's inset into the text; new pdf generated]]
Modified: long/3D/Gale/trunk/documentation/gale.lyx
===================================================================
--- long/3D/Gale/trunk/documentation/gale.lyx 2007-03-16 04:19:50 UTC (rev 6270)
+++ long/3D/Gale/trunk/documentation/gale.lyx 2007-03-16 18:45:02 UTC (rev 6271)
@@ -1053,9 +1053,8 @@
\end_layout
\begin_layout Standard
-If you do not specify an input file, you will get a cryptic error (TODO:
- need better description.
- If cryptic, why not fix it?)
+If you do not specify an input file, you will get the following (slightly
+ cryptic) error:
\end_layout
\begin_layout LyX-Code
@@ -1073,15 +1072,7 @@
\end_layout
\begin_layout Standard
-If Gale cannot find the file, you will get a better error (TODO:
-\begin_inset Quotes sld
-\end_inset
-
-better
-\begin_inset Quotes srd
-\end_inset
-
- error awkward, need some other description)
+If Gale cannot find the file, you will get a more descriptive error:
\end_layout
\begin_layout LyX-Code
@@ -1134,7 +1125,7 @@
\family typewriter
mpiexec
\family default
-.
+ (depending on your local implementation of MPI).
The
\family typewriter
extension.xml
@@ -1145,28 +1136,44 @@
output.extension
\family default
directory.
- There [TODO:
-\begin_inset Quotes sld
-\end_inset
+ There you will find examples of shortening, subduction, and relaxation
+ of a sinusoid.
+\end_layout
-you will find
-\begin_inset Quotes srd
-\end_inset
+\begin_layout Standard
+Since Gale uses PETSc for solving the equations, you can easily change which
+ solver to use.
+ The default solver is preconditioned conjugate gradient.
+ There are an enormous number of PETSc options that the expert user may
+ want to explore.
+ But as a simple example, on serial machines, a direct solve can be much
+ faster than the default iterative solver.
+ So to use a direct LU solve, you only need to append arguments to the command
+ line
+\end_layout
- instead of
-\begin_inset Quotes sld
-\end_inset
+\begin_layout LyX-Code
+./Gale-1_1_1 extension.xml -pc_type lu -ksp_type preonly
+\end_layout
-are also
-\begin_inset Quotes srd
-\end_inset
+\begin_layout Standard
+You can also change the default values of extension.xml without modifying
+ that file by appending arguments.
+ For example, to just change the number of time steps from default value
+ 500 to 10, use the following command
+\end_layout
-?] are also examples of shortening, subduction, and relaxation of a sinusoid.
+\begin_layout LyX-Code
+./Gale-1_1_1 extension.xml --maxtimesteps=10
\end_layout
\begin_layout Standard
-Since Gale uses PETSc for solving the equations, you can easily change which
- solver to use.
+You can append any number of modified parameters in one unbroken line
+\end_layout
+
+\begin_layout LyX-Code
+./Gale-1_1_1 extension.xml --maxtimesteps=10 --dim=3 Since Gale uses PETSc
+ for solving the equations, you can easily change which solver to use.
The default solver is preconditioned conjugate gradient.
There are an enormous number of PETSc options that the expert user may
want to explore.
@@ -1180,6 +1187,26 @@
./Gale-1_1_1 extension.xml -pc_type lu -ksp_type preonly
\end_layout
+\begin_layout Standard
+You can also change the default values of extension.xml without modifying
+ that file by appending arguments.
+ For example, to just change the number of time steps from default value
+ 500 to 10, use the following command
+\end_layout
+
+\begin_layout LyX-Code
+./Gale-1_1_1 extension.xml --maxtimesteps=10
+\end_layout
+
+\begin_layout Standard
+You can append any number of modified parameters in one unbroken line
+\end_layout
+
+\begin_layout LyX-Code
+./Gale-1_1_1 extension.xml --maxtimesteps=10 --dim=3 --elementResI=64 --elementRe
+sJ=64 --elementResK=64 --particlesPerCell=60 --dumpEvery=10
+\end_layout
+
\begin_layout Section
Output and Visualization
\end_layout
@@ -1261,7 +1288,7 @@
\end_layout
\begin_layout Standard
-(TODO: example of what changing dumpEvery will look like.)
+(TODO: Need example of what changing dumpEvery will look like.)
\end_layout
\begin_layout Standard
@@ -1279,7 +1306,7 @@
\end_inset
- (recommended),
+,
\begin_inset LatexCommand \htmlurl[MayaVI]{mayavi.sf.net}
\end_inset
@@ -1290,6 +1317,8 @@
\end_inset
.
+ ParaView is recommended as it is easy to get working, easy to use, and
+ scales to large data sets.
\end_layout
\begin_layout Standard
@@ -1377,7 +1406,7 @@
Navigate to the output directory and select
\family typewriter
\color none
-pressure.00010.vtk
+pressure.0.00010.vtk
\family default
.
Paraview will display a pseudocolor plot of the pressure.
@@ -1414,7 +1443,7 @@
You can also look at the velocities and strains by opening
\family typewriter
\color none
-fields.00010.vtk
+fields.0.00010.vtk
\family default
(with
\family sans
@@ -1468,7 +1497,7 @@
next to
\family typewriter
\color none
-fields.00010.vtk
+fields.0.00010.vtk
\family default
, graying it out.
\newline
@@ -1535,7 +1564,7 @@
eye next to
\family typewriter
\color none
-fields.00010.vtk
+fields.0.00010.vtk
\family default
, and then click on the ``Display'' tab.
\end_layout
@@ -1604,7 +1633,7 @@
Starting over, open
\family typewriter
\color none
-particles.00010.vtk
+particles.0.00010.vtk
\family default
and click on the ``Glyph'' button.
Change Glyph to Sphere0, Scale Mode to ``Data Scaling Off,'' the Scale
@@ -2061,8 +2090,9 @@
You should be able to use the template file as a basis for most of your
own input files.
There are two things in the template file, however, that might need modificatio
-n: the force of gravity, which by default is set to 1, and the normal velocities
- on all boundaries except the top, which are set to zero.
+n: the force of gravity, which by default is set to 1 (if you are using
+ cgs, for example, the force of gravity must be changed to 980), and the
+ normal velocities on all boundaries except the top, which are set to zero.
Beyond that, you only need to add where different materials are placed
initially.
\end_layout
@@ -2072,7 +2102,8 @@
\end_layout
\begin_layout Standard
-Unless otherwise specified, when you are instructed to add something
+Unless otherwise specified, when you are instructed to add sections to the
+ input file
\begin_inset Foot
status collapsed
@@ -2140,6 +2171,8 @@
\begin_layout Standard
This example simply fills up the computational domain with a single viscous
material.
+ It is a valid input file, but will not run as nothing is moving.
+ This file mainly serves as the basis for subsequent examples.
\end_layout
\begin_layout Enumerate
@@ -2198,6 +2231,26 @@
</struct>
\end_layout
+\begin_layout Standard
+Note: Default parameters for the box (e.g.,
+\family typewriter
+minX
+\family default
+,
+\family typewriter
+maxX
+\family default
+,
+\family typewriter
+minY
+\family default
+, etc.) are already defined in
+\family typewriter
+template.xml
+\family default
+.
+\end_layout
+
\end_deeper
\begin_layout Enumerate
Then set the material's viscosity
@@ -2222,7 +2275,7 @@
\begin_layout Standard
Remember that Gale has no internal knowledge of units, so if you think of
- everything in cgs, then this gives a viscosity of
+ everything in cgs, then this implies a viscosity of
\begin_inset Formula $1\frac{g}{cm^{2}\, s}$
\end_inset
@@ -2251,6 +2304,16 @@
</struct>
\end_layout
+\begin_layout Standard
+In a particle-based approach,
+\family typewriter
+materialswarm
+\family default
+ is a collection of particles.
+ You are creating a new component that stores the viscosity for all of these
+ components.
+\end_layout
+
\end_deeper
\begin_layout Enumerate
Finally, you create the material, using the components just created.
@@ -2295,7 +2358,7 @@
\end_deeper
\begin_layout Enumerate
-Save this file, as it will be the basis for many other examples that follow.
+Save this file, as it will be the basis for other examples that follow.
\end_layout
@@ -2321,9 +2384,9 @@
\end_inset
- 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
+ is valid, but nothing moves, so Gale will output errors if you try to run
+ it.
+ In this next 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 extensions.
@@ -2422,9 +2485,12 @@
bottom
\family default
.
- Only modify
+ Here we have only modified the
\family typewriter
-right.
+right
+\family default
+\color default
+ side.
\end_layout
\end_deeper
@@ -2516,6 +2582,32 @@
of particles per cell.
\end_layout
+\begin_layout Standard
+[TODO: Gurnis asks: Maybe a scale is needed? Landry: Color bar scale? Maybe.
+ More work, and it would make it more difficult to display the same image
+ output for some.
+
+\end_layout
+
+\begin_layout Standard
+Gurnis asks: If there are only small variations in and if the
+\begin_inset Quotes sld
+\end_inset
+
+banding
+\begin_inset Quotes srd
+\end_inset
+
+ is an artifact, mabe we need to visualizze a different quantity.
+ Landry: It's important that people see it so they see what happens when
+ particle numbers are increased.
+\end_layout
+
+\begin_layout Standard
+Gurnis asks: Does any topography get generated in this problem? Landry:
+ no.]
+\end_layout
+
\begin_layout Section
Viscous Material with Complex Boundaries
\end_layout
@@ -2714,12 +2806,16 @@
\end_inset
-) is shown in Figure
+) shown in Figure
\begin_inset LatexCommand \ref{fig:Strain-complex}
\end_inset
-.
+ shows that strain rate is concentrated around the step function in the
+ bottom velocity boundary.
+ Notice the development of a basin above the discontinuity.
+ The ability to track the development of topography on the free surfaces
+ is one of the strengths of Gale.
\end_layout
\begin_layout Standard
@@ -2765,7 +2861,9 @@
\end_inset
.
-
+ This example is not intended to be geologically realistic in any sense,
+ but is meant to illustrate the enormous flexibility we have in the development
+ of complex boundary conditions.
\end_layout
\begin_layout Standard
@@ -3327,13 +3425,16 @@
\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.
+ However, Gale can also start with the top initially deformed, such as if
+ we had a mountain range with substantial topography.
This example will make it sinusoidal as in Figure
\begin_inset LatexCommand \ref{fig:Sinusoidal-Top}
\end_inset
.
+ This example has no moving boundaries, so the material will simply relax.
+
\end_layout
\begin_layout Standard
@@ -3435,11 +3536,6 @@
\end_deeper
\begin_layout Standard
-This example has no moving boundaries, so the material will simply relax.
-
-\end_layout
-
-\begin_layout Standard
A worked example is in
\family typewriter
input/cookbook/viscous_sinusoid.xml
@@ -3490,6 +3586,15 @@
\end_layout
+\begin_layout Standard
+[TODO: These show substantial asymmetries, maybe if we use a topography
+ such that
+\begin_inset Formula $\frac{\delta topo}{ox}=o$
+\end_inset
+
+ at the left and right?]
+\end_layout
+
\begin_layout Section
Multiple Viscous Materials
\end_layout
@@ -3583,6 +3688,11 @@
</struct>
\end_layout
+\begin_layout Standard
+Note: If run in 3D, this is a sphere.
+ The example shown here is run in 2D, so in fact the result is a circle.
+\end_layout
+
\end_deeper
\begin_layout Enumerate
Then add the new material.
@@ -4145,6 +4255,12 @@
\end_layout
+\begin_layout Standard
+[TODO: Gurnis asks: Shouldn't the first localization example be for a homogeneou
+s material? Can this be run for a longer period of time? Landry: Yes, but
+ maybe this should be done in Benchmarks.]
+\end_layout
+
\begin_layout Chapter
Modifying Gale
\begin_inset LatexCommand \label{cha:Modifying-Gale}
@@ -4569,7 +4685,7 @@
structure is where the bulk of the file will be.
It specifies things like what the mesh will be like, which material goes
where, what the material properties are, what kind of solver to use, etc.
- Most of the ideas you need to specify will go into the components.
+ Most of the ideas you need to specify your problem will go into the components.
When adding a new component, it is important to remember to put the new
component inside the components structure.
Otherwise Gale will (silently) not use that component.
Modified: long/3D/Gale/trunk/documentation/gale.pdf
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Paraview_grey_eye.png
===================================================================
(Binary files differ)
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