[cig-commits] r6014 - in long/3D/Gale/trunk: . documentation
documentation/images
walter at geodynamics.org
walter at geodynamics.org
Tue Feb 13 16:18:54 PST 2007
Author: walter
Date: 2007-02-13 16:18:52 -0800 (Tue, 13 Feb 2007)
New Revision: 6014
Added:
long/3D/Gale/trunk/documentation/images/Gnumeric_final.png
long/3D/Gale/trunk/documentation/images/Gnumeric_new_chart.png
long/3D/Gale/trunk/documentation/images/Gnumeric_preview.png
long/3D/Gale/trunk/documentation/images/Gnumeric_two_columns.png
long/3D/Gale/trunk/documentation/images/Gnumeric_xy_plot.png
long/3D/Gale/trunk/documentation/images/Matlab_fig111.png
long/3D/Gale/trunk/documentation/images/Matlab_fig112.png
long/3D/Gale/trunk/documentation/images/Octave_fig1.png
long/3D/Gale/trunk/documentation/images/Octave_fig2.png
long/3D/Gale/trunk/documentation/images/Octave_fig3.png
long/3D/Gale/trunk/documentation/images/Paraview_glyph.png
long/3D/Gale/trunk/documentation/images/Paraview_grey_eye.png
long/3D/Gale/trunk/documentation/images/Paraview_multi_material.png
long/3D/Gale/trunk/documentation/images/Paraview_multi_viscosity.png
long/3D/Gale/trunk/documentation/images/Paraview_open_data.png
long/3D/Gale/trunk/documentation/images/Paraview_particles_viscosity.png
long/3D/Gale/trunk/documentation/images/Paraview_particles_yielding.png
long/3D/Gale/trunk/documentation/images/Paraview_pressure.png
long/3D/Gale/trunk/documentation/images/Paraview_pressure_velocity.png
long/3D/Gale/trunk/documentation/images/Paraview_strainrate.png
long/3D/Gale/trunk/documentation/images/Paraview_v_vector.png
long/3D/Gale/trunk/documentation/images/Paraview_viscous_extension.png
long/3D/Gale/trunk/documentation/images/Paraview_viscous_inflow.png
long/3D/Gale/trunk/documentation/images/Paraview_viscous_sinusoid.png
long/3D/Gale/trunk/documentation/images/Paraview_viscous_split.png
long/3D/Gale/trunk/documentation/images/Paraview_viscous_stressbc.png
long/3D/Gale/trunk/documentation/images/Paraview_vmag.png
long/3D/Gale/trunk/documentation/images/Paraview_yielding.png
long/3D/Gale/trunk/documentation/images/Paraview_yielding_viscosity.png
long/3D/Gale/trunk/documentation/images/Paraview_yielding_yielding.png
long/3D/Gale/trunk/documentation/images/viscous_extension.png
Modified:
long/3D/Gale/trunk/
long/3D/Gale/trunk/documentation/gale.lyx
Log:
r1556 at earth: boo | 2007-02-13 16:16:49 -0800
Add lots of pictures to the manual. Update for the new VTKOutput plugin
Property changes on: long/3D/Gale/trunk
___________________________________________________________________
Name: svk:merge
- 3a629746-de10-0410-b17b-fd6ecaaa963e:/cig:1555
+ 3a629746-de10-0410-b17b-fd6ecaaa963e:/cig:1556
Modified: long/3D/Gale/trunk/documentation/gale.lyx
===================================================================
--- long/3D/Gale/trunk/documentation/gale.lyx 2007-02-14 00:18:49 UTC (rev 6013)
+++ long/3D/Gale/trunk/documentation/gale.lyx 2007-02-14 00:18:52 UTC (rev 6014)
@@ -1076,7 +1076,7 @@
\end_layout
\begin_layout Section
-Output
+Output and Visualization
\end_layout
\begin_layout Standard
@@ -1109,10 +1109,16 @@
\family typewriter
.dat
\family default
- and
+,
\family typewriter
.txt
\family default
+, and
+\family typewriter
+\color none
+.vtk
+\family default
+\color default
files in the output directory
\color none
.
@@ -1122,48 +1128,485 @@
\end_inset
.
- Gale includes a number of Matlab visualization scripts in the
+\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
\family typewriter
-tools/
+.vtk
\family default
- directory.
- The scripts also work with Octave, a free Matlab clone.
- Furthermore, you can set the DumpSwarm plugin (see Section
-\begin_inset LatexCommand \ref{sec:.txt-Files-(Particle}
+ files contain all of the information and can be visualized with either
+
+\begin_inset LatexCommand \htmlurl[ParaView]{paraview.org}
\end_inset
-) to directly output either
+ (recommended),
+\begin_inset LatexCommand \htmlurl[MayaVI]{mayavi.sf.net}
+
+\end_inset
+
+,
+\color default
+or
+\begin_inset LatexCommand \htmlurl[Visit]{www.llnl.gov/visit}
+
+\end_inset
+
+
+\color none
+.
+ For example, to visualize step #10 of
\family typewriter
-.vtk
+extension.xml
\family default
- files or
+\color default
+, start Paraview and open new data
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_open_data.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+Select
\family typewriter
-.csv
+\color none
+pressure.00010.vtk
\family default
- files.
- You can visualize
+\color default
+, and a pseudocolor plot of the pressure will appear
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_pressure.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+We can also look at the velocities and strains by opening
\family typewriter
-.vtk
+\color none
+fields.00010.vtk
\family default
- files with either
-\begin_inset LatexCommand \htmlurl[ParaView]{paraview.org}
+\color default
+.
+ By default, this will obscure the pressure with the velocity magnitude.
+\end_layout
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_vmag.png
+
\end_inset
- (recommended) or
-\begin_inset LatexCommand \htmlurl[MayaVI]{mayavi.sf.net}
+\end_layout
+
+\begin_layout Standard
+You can remove the velocity magnitude by clicking on the
+\begin_inset Quotes sld
\end_inset
+eye
+\begin_inset Quotes srd
+\end_inset
+
+ symbol, graying it out.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_grey_eye.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+Now you can plot the velocity as arrows on top of the pressure by first
+ clicking on the
+\begin_inset Quotes sld
+\end_inset
+
+Glyph
+\begin_inset Quotes srd
+\end_inset
+
+ symbol
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_glyph.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+and then pressing the green
+\begin_inset Quotes sld
+\end_inset
+
+Accept
+\begin_inset Quotes srd
+\end_inset
+
+ button.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_pressure_velocity.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+You can also visualize the Strain Rate Invariant.
+ You start by clicking on the greyed-out eye next to
+\family typewriter
+\color none
+fields.00010.vtk
+\family default
+\color default
+ and then clicking on the
+\begin_inset Quotes sld
+\end_inset
+
+Display
+\begin_inset Quotes srd
+\end_inset
+
+ tab.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_v_vector.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+You finish by clicking on the box next to
+\begin_inset Quotes sld
+\end_inset
+
+Color by
+\begin_inset Quotes srd
+\end_inset
+
+ and selecting
+\begin_inset Quotes sld
+\end_inset
+
+Point StrainRateInvariantField
+\begin_inset Quotes srd
+\end_inset
+
.
- You can visualize
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_strainrate.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+The last thing to look at is the particles.
+ Starting over, open
\family typewriter
+\color none
+particles.00010.vtk
+\family default
+\color default
+ and click on the
+\begin_inset Quotes sld
+\end_inset
+
+Glyph
+\begin_inset Quotes srd
+\end_inset
+
+ button.
+ Change the Glyph to Sphere0, Scale Mode to
+\begin_inset Quotes sld
+\end_inset
+
+Data Scaling Off
+\begin_inset Quotes srd
+\end_inset
+
+, the Scale Factor to 0.01, and hit Accept.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_particles_viscosity.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+This displays the viscosity of the particles.
+ The blue points represent low viscosity material, either the material at
+ the bottom that was originally low viscosity, or the material that has
+ yielded.
+ To see explicitly which material has yielded, click on the
+\begin_inset Quotes sld
+\end_inset
+
+Display
+\begin_inset Quotes srd
+\end_inset
+
+ tab and change the
+\begin_inset Quotes sld
+\end_inset
+
+Color by
+\begin_inset Quotes srd
+\end_inset
+
+ box to
+\begin_inset Quotes sld
+\end_inset
+
+Point Yielding_fraction
+\begin_inset Quotes srd
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_particles_yielding.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Visualization with Matlab or Octave
+\end_layout
+
+\begin_layout Standard
+
+\color none
+Gale includes a number of Matlab visualization scripts in the
+\family typewriter
+tools/
+\family default
+ directory.
+ The scripts also work with Octave, a free Matlab clone.
+ To use these scripts, cd into the
+\family typewriter
+\color default
+tools/
+\family default
+\color none
+ and modify
+\family typewriter
+\color default
+fname
+\family default
+\color none
+ in
+\family typewriter
+\color default
+PlotGaleOutput.m
+\family default
+\color none
+ to point to the output directory, and change
+\family typewriter
+\color default
+step
+\family default
+\color none
+ to the time step.
+ Then start Matlab or Octave and type
+\end_layout
+
+\begin_layout LyX-Code
+PlotGaleOutput
+\end_layout
+
+\begin_layout Standard
+Visualizing the 10th step of
+\family typewriter
+extension.xml
+\family default
+ in Octave gives
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Octave_fig1.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Octave_fig2.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Octave_fig3.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+and in Matlab gives
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Matlab_fig111.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Matlab_fig112.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Visualization with Excel
+\end_layout
+
+\begin_layout Standard
+
+\color none
+You can set the DumpSwarm plugin (see Section
+\begin_inset LatexCommand \ref{sec:.txt-Files-(Particle}
+
+\end_inset
+
+) to directly output
+\family typewriter
.csv
\family default
- files with a spreadsheet program such as Excel.
+ files, which you can use for limited visualization with a spreadsheet program
+ such as Excel.
+ For example, for the
+\family typewriter
+extension.xml
+\family default
+ imput file, open the file
+\family typewriter
+output.extension/particles.00010.csv
+\family default
+ with your spreadsheet program.
+ Select the second two columns
\end_layout
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Gnumeric_two_columns.png
+ scale 80
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+create a chart
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Gnumeric_new_chart.png
+ scale 80
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+select an XY plot and press Insert
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Gnumeric_xy_plot.png
+ scale 80
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+then press anywhere on the spreadsheet, and you will have a plot of the
+ particles.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Gnumeric_final.png
+ scale 80
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
Cookbook examples
\end_layout
@@ -1546,11 +1989,27 @@
\begin_layout Standard
A worked example is at
\family typewriter
-input/cookbook/myviscous-example.xml
+input/cookbook/viscous_extension.xml
\family default
.
+ A visualization of the strain rate invariant and velocity (see Section
+
+\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+
+\end_inset
+
+) gives
\end_layout
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_viscous_extension.png
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Viscous Material with Complex Boundaries
\end_layout
@@ -1742,8 +2201,24 @@
input/cookbook/viscous_split.xml
\family default
.
+ A visualization of the strain rate invariant and velocity (see Section
+
+\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+
+\end_inset
+
+) gives
\end_layout
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_viscous_split.png
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Viscous Material with Inflow/Outflow Boundaries
\end_layout
@@ -2083,8 +2558,24 @@
input/cookbook/viscous_inflow.xml
\family default
.
+ A visualization of the strain rate invariant and velocity (see Section
+
+\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+
+\end_inset
+
+) gives
\end_layout
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_viscous_inflow.png
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Viscous Material with Stress Boundaries
\end_layout
@@ -2217,8 +2708,24 @@
input/cookbook/viscous_stressbc.xml
\family default
.
+ A visualization of the strain rate invariant and velocity (see Section
+
+\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+
+\end_inset
+
+) gives
\end_layout
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_viscous_stressbc.png
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
\begin_inset LatexCommand \label{sub:Viscous-Initially-Deformed}
@@ -2347,8 +2854,24 @@
input/cookbook/viscous_sinusoid.xml
\family default
.
+ A visualization of the strain rate invariant and velocity (see Section
+
+\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+
+\end_inset
+
+) gives
\end_layout
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_viscous_sinusoid.png
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Multiple Viscous Materials
\end_layout
@@ -2430,11 +2953,11 @@
\end_layout
\begin_layout LyX-Code
- <param name="CentreY">1.5</param>
+ <param name="CentreY">0.15</param>
\end_layout
\begin_layout LyX-Code
- <param name="radius">1.0</param>
+ <param name="radius">0.10</param>
\end_layout
\begin_layout LyX-Code
@@ -2456,7 +2979,7 @@
\end_layout
\begin_layout LyX-Code
- <param name="eta0">2.0</param>
+ <param name="eta0">10.0</param>
\end_layout
\begin_layout LyX-Code
@@ -2576,8 +3099,37 @@
input/cookbook/multi_material.xml
\family default
.
+ A visualization of the strain rate invariant and velocity (see Section
+
+\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+
+\end_inset
+
+) gives
\end_layout
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_multi_material.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+and the viscosity of the particles gives
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_multi_viscosity.png
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Yielding Material in Simple Extension
\end_layout
@@ -2680,7 +3232,7 @@
\end_layout
\begin_layout LyX-Code
- <param name="cohesion">10.0</param>
+ <param name="cohesion">1.0</param>
\end_layout
\begin_layout LyX-Code
@@ -2796,8 +3348,50 @@
input/cookbook/yielding.xml
\family default
.
+ A visualization of the strain rate invariant and velocity (see Section
+
+\begin_inset LatexCommand \ref{sub:Visualization-with-ParaView}
+
+\end_inset
+
+) gives
\end_layout
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_yielding.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+A visualization of the viscosity of the particles gives
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_yielding_viscosity.png
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+and a visualization of the yielding of the particles gives
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename images/Paraview_yielding_yielding.png
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
Gauging Accuracy
\end_layout
@@ -3359,10 +3953,14 @@
\family typewriter
DumpSwarm
\family default
- and
+,
\family typewriter
EulerDeform
\family default
+,and
+\family typewriter
+VTKOutput
+\family default
plugins
\end_layout
@@ -3379,6 +3977,10 @@
\end_layout
\begin_layout LyX-Code
+ <param>Underworld_VTKOutput</param>
+\end_layout
+
+\begin_layout LyX-Code
</list>
\end_layout
@@ -3417,6 +4019,10 @@
Underworld_DumpSwarm
\end_layout
+\begin_layout LyX-Code
+Underworld_VTKOutput
+\end_layout
+
\begin_layout Standard
Note that we must still include those plugins in the list of plugins in
order to use them.
@@ -9323,7 +9929,7 @@
\end_layout
\begin_layout Standard
-Gale outputs three types of files.
+Gale outputs four types of files.
\end_layout
@@ -9550,7 +10156,7 @@
\begin_layout LyX-Code
m x y z
\family typewriter
- yielded
+ yielded viscosity
\end_layout
\begin_layout Standard
@@ -9558,7 +10164,7 @@
\family typewriter
m
\family default
- is the number of the material (in the examples, always 1), and
+ is a unique number for the material,
\family typewriter
yielded
\family default
@@ -9570,7 +10176,14 @@
\family typewriter
1
\family default
- indicating how much a material point has failed.
+ indicating how much a material point has failed, and
+\family typewriter
+viscosity
+\family default
+ is material's isotropic viscosity.
+ If the material does not yield (e.g.
+ is purely viscous), then yielded is always zero.
+
\end_layout
\begin_layout Standard
@@ -9588,37 +10201,71 @@
\end_layout
\begin_layout Standard
-We can also set the format to
+If we want to print out some other property of the material, e.g., non-isotropic
+ viscosity, we can modify
\family typewriter
-vtk
+DumpSwarm
\family default
- for viewing the data in
-\begin_inset LatexCommand \htmlurl[MayaVi]{mayavi.sf.net}
+ to provide that information.
+ The source for the plugin is found in the directory
+\end_layout
-\end_inset
+\begin_layout LyX-Code
+src/Underworld/plugins/Output/DumpSwarm/
+\end_layout
- or
-\begin_inset LatexCommand \htmlurl[ParaView]{paraview.org}
+\begin_layout Section
+\family typewriter
+.vtk
+\family default
+ Files (Visualization)
+\begin_inset LatexCommand \label{sec:.vtk-Files-(Visualization)}
+
\end_inset
-.
+
\end_layout
\begin_layout Standard
-If we want to print out some other property of the material, e.g., viscosity,
- we can modify
+These files are output by the
\family typewriter
-DumpSwarm
+Underworld_VTKOutput
\family default
- to provide that information.
- The source for the plugin is found in the directory
+ plugin.
+ These files are in a format understood by a wide variety of visualization
+ programs, sich as
+\begin_inset LatexCommand \htmlurl[ParaView]{paraview.org}
+
+\end_inset
+
+ (recommended),
+\begin_inset LatexCommand \htmlurl[MayaVi]{mayavi.sf.net}
+
+\end_inset
+
+, or
+\begin_inset LatexCommand \htmlurl[Visit]{www.llnl.gov/visit}
+
+\end_inset
+
+.
+ The
+\family typewriter
+Underworld_VTKOutput
+\family default
+ plugin is activated by adding the line
\end_layout
\begin_layout LyX-Code
-src/Underworld/plugins/Output/DumpSwarm/
+ <param>Underworld_VTKOutput</param>
\end_layout
+\begin_layout Standard
+to the list of plugins.
+ This line is already in the example input files.
+\end_layout
+
\begin_layout Chapter
Benchmarks
\end_layout
Added: long/3D/Gale/trunk/documentation/images/Gnumeric_final.png
===================================================================
(Binary files differ)
Property changes on: long/3D/Gale/trunk/documentation/images/Gnumeric_final.png
___________________________________________________________________
Name: svn:mime-type
+ image/x-png
Added: long/3D/Gale/trunk/documentation/images/Gnumeric_new_chart.png
===================================================================
(Binary files differ)
Property changes on: long/3D/Gale/trunk/documentation/images/Gnumeric_new_chart.png
___________________________________________________________________
Name: svn:mime-type
+ image/x-png
Added: long/3D/Gale/trunk/documentation/images/Gnumeric_preview.png
===================================================================
(Binary files differ)
Property changes on: long/3D/Gale/trunk/documentation/images/Gnumeric_preview.png
___________________________________________________________________
Name: svn:mime-type
+ image/x-png
Added: long/3D/Gale/trunk/documentation/images/Gnumeric_two_columns.png
===================================================================
(Binary files differ)
Property changes on: long/3D/Gale/trunk/documentation/images/Gnumeric_two_columns.png
___________________________________________________________________
Name: svn:mime-type
+ image/x-png
Added: long/3D/Gale/trunk/documentation/images/Gnumeric_xy_plot.png
===================================================================
(Binary files differ)
Property changes on: long/3D/Gale/trunk/documentation/images/Gnumeric_xy_plot.png
___________________________________________________________________
Name: svn:mime-type
+ image/x-png
Added: long/3D/Gale/trunk/documentation/images/Matlab_fig111.png
===================================================================
(Binary files differ)
Property changes on: long/3D/Gale/trunk/documentation/images/Matlab_fig111.png
___________________________________________________________________
Name: svn:mime-type
+ image/x-png
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