[cig-commits] r11387 - in long/3D/Gale/trunk: . documentation documentation/images
walter at geodynamics.org
walter at geodynamics.org
Mon Mar 10 11:45:17 PDT 2008
Author: walter
Date: 2008-03-10 11:45:17 -0700 (Mon, 10 Mar 2008)
New Revision: 11387
Modified:
long/3D/Gale/trunk/
long/3D/Gale/trunk/documentation/gale.lyx
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_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_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_vmag.png
Log:
r2020 at earth: boo | 2008-03-05 17:47:10 -0800
Update the viz chapter
Property changes on: long/3D/Gale/trunk
___________________________________________________________________
Name: svk:merge
- 3a629746-de10-0410-b17b-fd6ecaaa963e:/cig:2018
+ 3a629746-de10-0410-b17b-fd6ecaaa963e:/cig:2020
Modified: long/3D/Gale/trunk/documentation/gale.lyx
===================================================================
--- long/3D/Gale/trunk/documentation/gale.lyx 2008-03-10 18:13:04 UTC (rev 11386)
+++ long/3D/Gale/trunk/documentation/gale.lyx 2008-03-10 18:45:17 UTC (rev 11387)
@@ -1088,7 +1088,7 @@
\end_layout
\begin_layout LyX-Code
-./Gale-1_2_1 input/extension.xml
+./Gale-1_2_2 input/cookbook/yielding.xml
\end_layout
\begin_layout Standard
@@ -1100,25 +1100,45 @@
\end_layout
\begin_layout LyX-Code
-TimeStep = 2, Start time = 0 + 0.0291667 prev timeStep dt
+TimeStep = 2, Start time = 0 + 0.0107639 prev timeStep dt
\end_layout
\begin_layout LyX-Code
-TimeStep = 3, Start time = 0.0291667 + 0.0283326 prev timeStep dt
+TimeStep = 3, Start time = 0.0107639 + 0.0107105 prev timeStep dt
\end_layout
\begin_layout LyX-Code
-TimeStep = 4, Start time = 0.0574992 + 0.0274655 prev timeStep dt
+TimeStep = 4, Start time = 0.0214744 + 0.0106587 prev timeStep dt
\end_layout
\begin_layout LyX-Code
-TimeStep = 5, Start time = 0.0849647 + 0.0265162 prev timeStep dt
+TimeStep = 5, Start time = 0.0321332 + 0.0106059 prev timeStep dt
\end_layout
\begin_layout LyX-Code
-...
+TimeStep = 6, Start time = 0.0427391 + 0.0105527 prev timeStep dt
\end_layout
+\begin_layout LyX-Code
+TimeStep = 7, Start time = 0.0532918 + 0.0104996 prev timeStep dt
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 8, Start time = 0.0637914 + 0.0104465 prev timeStep dt
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 9, Start time = 0.0742378 + 0.0103941 prev timeStep dt
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 10, Start time = 0.0846319 + 0.0103424 prev timeStep dt
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
\begin_layout Standard
If you do not specify an input file, you will get an error like
\end_layout
@@ -1162,7 +1182,8 @@
\begin_layout LyX-Code
\size small
-Error: File input/extension.xml doesn't exist, not readable, or not valid.
+Error: File input/cookbook/yielding.xml doesn't exist, not readable, or not
+ valid.
\end_layout
\begin_layout LyX-Code
@@ -1182,7 +1203,7 @@
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_2_1 /home/juser/gale/input/extension.xml
+./Gale-1_2_1 /home/juser/gale/input/cookbook/yielding.xml
\family default
).
\end_layout
@@ -1222,7 +1243,7 @@
\end_layout
\begin_layout LyX-Code
-mpirun -np 2 bin/Gale /home/juser/gale/input/extension.xml
+mpirun -np 2 bin/Gale /home/juser/gale/input/cookbook/yielding.xml
\end_layout
\begin_layout Standard
@@ -1232,15 +1253,14 @@
\begin_layout Standard
The
\family typewriter
-extension.xml
+yielding.xml
\family default
- example should run for 100 time steps and generate a great deal of output
+ example should run for 10 time steps and generate a great deal of output
in the
\family typewriter
-output.extension
+output.template
\family default
directory.
- There are also examples of shortening, subduction, and relaxation of topography.
\end_layout
\begin_layout Standard
@@ -1254,21 +1274,21 @@
\end_layout
\begin_layout LyX-Code
-./Gale-1_2_1 input/extension.xml -pc_type lu -ksp_type preonly
+./Gale-1_2_1 input/cookbook/yielding.xml -pc_type lu -ksp_type preonly
\end_layout
\begin_layout Standard
You can also change the default values of
\family typewriter
-extension.xml
+yielding.xml
\family default
without modifying that file by appending arguments.
For example, to just change the number of time steps from the default value
- 100 to 10, use the following command
+ 10 to 20, use the following command
\end_layout
\begin_layout LyX-Code
-./Gale-1_2_1 input/extension.xml --maxTimeSteps=10
+./Gale-1_2_1 input/cookbook/yielding.xml --maxTimeSteps=20
\end_layout
\begin_layout Standard
@@ -1278,45 +1298,20 @@
\begin_layout LyX-Code
\size small
-./Gale-1_2_1 input/extension.xml --maxTimeSteps=10 --dim=3 --elementResI=64
-
+./Gale-1_2_1 input/cookbook/yielding.xml --maxTimeSteps=20 --dim=3 --elementResI=
+64 --elementResJ=64 --elementResK=64 --particlesPerCell=60 --dumpEvery=10
\end_layout
-\begin_layout LyX-Code
-
-\size small
---elementResJ=64 --elementResK=64 --particlesPerCell=60 --dumpEvery=10
-\end_layout
-
\begin_layout Section
Output and Visualization
\end_layout
\begin_layout Standard
The sample input files will produce a directory in which you will find a
- number of
-\family typewriter
-.dat
-\family default
-,
-\family typewriter
-.txt
-\family default
-, and
-\family typewriter
+ number of
\color none
-.vtk
-\family default
files.
- The formats of the
-\family typewriter
-.dat
-\family default
- and
-\family typewriter
-.txt
-\family default
- files are described fully in Appendix
+ The formats of these files are described fully in Appendix
\begin_inset LatexCommand ref
reference "cha:Output-File-Format"
@@ -1358,12 +1353,8 @@
\family typewriter
.txt
\family default
- and
+ and VTK files, you need to change the parameter
\family typewriter
-.vtk
-\family default
- files, you need to change the parameter
-\family typewriter
dumpEvery
\family default
.
@@ -1406,11 +1397,7 @@
\color none
There are a number of different options for visualizing the data.
- The easiest way is to use the
-\family typewriter
-.vtk
-\family default
- files.
+ The easiest way is to use the VTK 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
@@ -1469,9 +1456,10 @@
\begin_layout Standard
\color none
-To visualize step #10 of
+These instructions are for Paraview version 3.2.1.
+ To visualize step #10 of
\family typewriter
-input/extension.xml
+input/cookbook/yielding.xml
\family default
,
\end_layout
@@ -1526,7 +1514,7 @@
Navigate to the output directory and select
\family typewriter
\color none
-pressure.0.00010.vtk
+pressure.00010.pvts
\family default
.
Paraview will display a pseudocolor plot of the pressure.
@@ -1563,7 +1551,7 @@
You can also look at the velocities and strains by opening
\family typewriter
\color none
-fields.0.00010.vtk
+fields.00010.pvts
\family default
(with
\family sans
@@ -1578,7 +1566,7 @@
Open Data
\family default
).
- By default, Paraview will obscure the pressure with the velocity magnitude.
+ By default, Paraview will obscure the pressure with the strain rate invariant.
\end_layout
\begin_deeper
@@ -1595,7 +1583,7 @@
\color none
\begin_inset Graphics
- filename images/Paraview_vmag.png
+ filename images/Paraview_strainrate.png
lyxscale 50
scale 50
@@ -1613,11 +1601,11 @@
\end_deeper
\begin_layout Enumerate
-You can remove the velocity magnitude by clicking on the ``eye'' symbol
+You can remove the strain rate invariant by clicking on the ``eye'' symbol
next to
\family typewriter
\color none
-fields.0.00010.vtk
+fields.00010.pvts
\family default
, graying it out.
\newline
@@ -1648,7 +1636,7 @@
\newline
\newline
-and then press the green ``Accept'' button.
+and then press the green ``Apply'' button.
The result will look like this:
\end_layout
@@ -1680,11 +1668,11 @@
\end_deeper
\begin_layout Enumerate
-You can also visualize the Strain Rate Invariant: Click on the grayed-out
+You can also visualize the magnitude of the velocity: Click on the grayed-out
eye next to
\family typewriter
\color none
-fields.0.00010.vtk
+fields.00010.pvts
\family default
, and then click on the ``Display'' tab.
\end_layout
@@ -1718,7 +1706,7 @@
\end_deeper
\begin_layout Enumerate
Finish by clicking on the drop down list to the right of ``Color by'' and
- selecting ``Point StrainRateInvariantField.''
+ selecting ``VelocityMagnitudeField.''
\end_layout
\begin_deeper
@@ -1731,7 +1719,7 @@
\begin_layout Standard
\begin_inset Graphics
- filename images/Paraview_strainrate.png
+ filename images/Paraview_vmag.png
lyxscale 50
scale 50
@@ -1753,11 +1741,9 @@
Starting over, open
\family typewriter
\color none
-particles.0.00010.vtk
+particles.00010.pvts
\family default
- and click on the ``Glyph'' button.
- Change Glyph to Sphere0, Scale Mode to ``Data Scaling Off,'' the Scale
- Factor to 0.01, and press the Accept button.
+ and click on the green ``Apply'' button.
\end_layout
\begin_deeper
@@ -1803,7 +1789,7 @@
\end_deeper
\begin_layout Enumerate
To see explicitly which material has yielded, click on the ``Display'' tab
- and change the ``Color by'' box to ``Point Yielding_fraction.''
+ and change the ``Color by'' box to ``Yielding_fraction.''
\end_layout
\begin_deeper
@@ -1896,7 +1882,7 @@
\begin_layout Enumerate
Using Octave to visualize the 10th step of
\family typewriter
-input/extension.xml
+input/cookbook/yielding.xml
\family default
results in
\end_layout
@@ -1956,7 +1942,7 @@
\begin_layout Standard
\begin_inset Graphics
filename images/Matlab_fig112.png
- scale 75
+ width 75col%
\end_inset
@@ -1986,7 +1972,7 @@
such as Excel.
For example, for the
\family typewriter
-input/extension.xml
+input/cookbook/yielding.xml
\family default
input file,
\end_layout
@@ -1996,7 +1982,7 @@
\color none
Open the file
\family typewriter
-output.extension/particles.00010.csv
+output.template/particles.00010.csv
\family default
with your spreadsheet program.
Select the second two columns
@@ -13526,6 +13512,79 @@
\begin_layout Section
\family typewriter
+VTK
+\family default
+Files:
+\family typewriter
+.vts, .pvts, .vtu, and .pvtu
+\family default
+ (Visualization)
+\begin_inset LatexCommand label
+name "sec:.vtk-Files-(Visualization)"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+These files are output by the
+\family typewriter
+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
+ are small files that have information on how to stitch them all together.
+ Ordinarily, you would only open the .pvts and .pvtu files.
+ These files are in a format understood by a wide variety of visualization
+ programs, sich as
+\begin_inset LatexCommand htmlurl
+name "ParaView"
+target "paraview.org"
+
+\end_inset
+
+ (recommended) or
+\begin_inset LatexCommand htmlurl
+name "MayaVi"
+target "mayavi.sf.net"
+
+\end_inset
+
+.
+
+\begin_inset LatexCommand htmlurl
+name "Visit"
+target "www.llnl.gov/visit"
+
+\end_inset
+
+ can understand the raw .vts and .vtu files, but not the .pvtu and .pvts files.
+ So Visit is mostly useful for visualizing serial runs.
+\end_layout
+
+\begin_layout Standard
+The
+\family typewriter
+Underworld_VTKOutput
+\family default
+ plugin is activated by adding the line
+\end_layout
+
+\begin_layout LyX-Code
+ <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 Section
+
+\family typewriter
.dat
\family default
ASCII Files
@@ -13689,7 +13748,7 @@
\family typewriter
.dat
\family default
- Binary Files (Particle Information)
+ Binary Files
\begin_inset LatexCommand label
name "sec:.dat-Binary-Files"
@@ -13712,7 +13771,7 @@
\family typewriter
.txt
\family default
- Files (Particle Information)
+ Files
\begin_inset LatexCommand label
name "sec:.txt-Files-(Particle"
@@ -13727,7 +13786,8 @@
Underworld_DumpSwarm
\family default
plugin.
- They provide particle information in a more friendly format.
+ They provide particle information in a more friendly format than the .dat
+ binary files.
The
\family typewriter
Underworld_DumpSwarm
@@ -13842,65 +13902,6 @@
src/Underworld/plugins/Output/DumpSwarm/
\end_layout
-\begin_layout Section
-
-\family typewriter
-.vtk
-\family default
- Files (Visualization)
-\begin_inset LatexCommand label
-name "sec:.vtk-Files-(Visualization)"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-These files are output by the
-\family typewriter
-Underworld_VTKOutput
-\family default
- plugin.
- These files are in a format understood by a wide variety of visualization
- programs, sich as
-\begin_inset LatexCommand htmlurl
-name "ParaView"
-target "paraview.org"
-
-\end_inset
-
- (recommended),
-\begin_inset LatexCommand htmlurl
-name "MayaVi"
-target "mayavi.sf.net"
-
-\end_inset
-
-, or
-\begin_inset LatexCommand htmlurl
-name "Visit"
-target "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
- <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
Modified: long/3D/Gale/trunk/documentation/images/Gnumeric_final.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Gnumeric_new_chart.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Gnumeric_two_columns.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Gnumeric_xy_plot.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Matlab_fig111.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Matlab_fig112.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Octave_fig1.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Octave_fig2.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Octave_fig3.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Paraview_glyph.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Paraview_grey_eye.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Paraview_open_data.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Paraview_particles_viscosity.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Paraview_particles_yielding.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Paraview_pressure.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Paraview_pressure_velocity.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Paraview_strainrate.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Paraview_v_vector.png
===================================================================
(Binary files differ)
Modified: long/3D/Gale/trunk/documentation/images/Paraview_vmag.png
===================================================================
(Binary files differ)
More information about the cig-commits
mailing list