[cig-commits] commit: Some manual updates, including the new cover converted to Gimp
Mercurial
hg at geodynamics.org
Wed May 26 15:48:57 PDT 2010
changeset: 287:2b4194568af1
user: Walter Landry <wlandry at caltech.edu>
date: Wed May 26 15:46:16 2010 -0700
files: doc/gale.lyx doc/gale_cover.pdf doc/gale_cover.png doc/gale_cover.psd doc/gale_cover.xcf doc/images/Paraview_display.png doc/images/Paraview_nodal_pressure.png doc/images/Paraview_open_data.png doc/images/Paraview_particles_viscosity.png doc/images/Paraview_particles_yielding.png doc/images/Paraview_pressure_velocity.png doc/images/Paraview_pressure_velocityII.png doc/images/Paraview_pressure_velocity_display.png doc/images/Paraview_strainrate.png doc/images/Paraview_v.png doc/images/Paraview_vmag.png
description:
Some manual updates, including the new cover converted to Gimp
diff -r 64ad85f62182 -r 2b4194568af1 doc/gale.lyx
--- a/doc/gale.lyx Wed May 26 13:46:56 2010 -0700
+++ b/doc/gale.lyx Wed May 26 15:46:16 2010 -0700
@@ -1862,7 +1862,7 @@ MPI
\end_layout
\begin_layout Itemize
-PETSc 2.3.2 (not 2.3.3!)
+PETSc 3.0 (not 3.1!)
\end_layout
\begin_layout Itemize
@@ -1912,41 +1912,173 @@ Advanced users and software developers m
Advanced users and software developers may be interested in downloading
the latest Gale source code directly from the CIG source code repository,
instead of using the prepared source package.
- To check whether you have a subversion client installed on your machine,
+ To check whether you have a Mercurial client installed on your machine,
type:
\end_layout
\begin_layout LyX-Code
-svn
-\end_layout
-
-\begin_layout Standard
-You should get a response that looks something like this:
-\end_layout
-
-\begin_layout LyX-Code
-Type `svn help' for usage.
-\end_layout
-
-\begin_layout Standard
-Otherwise, you will need to download and install a Subversion client, available
- at the Subversion Website
+hg
+\end_layout
+
+\begin_layout Standard
+You should get a help message that starts with:
+\end_layout
+
+\begin_layout LyX-Code
+Mercurial Distributed SCM
+\end_layout
+
+\begin_layout LyX-Code
+...
+\end_layout
+
+\begin_layout Standard
+Otherwise, you will need to download and install a Mercurial client, available
+ at the Mercurial Website
\begin_inset Flex URL
-status collapsed
-
-\begin_layout Plain Layout
-
-subversion.tigris.org/project_packages.html
-\end_layout
-
-\end_inset
-
-.
- Then the code can be checked out with the following command:
-\end_layout
-
-\begin_layout LyX-Code
-svn checkout http://geodynamics.org/svn/cig/long/3D/Gale/trunk Gale
+status open
+
+\begin_layout Plain Layout
+
+mercurial.selenic.com
+\end_layout
+
+\end_inset
+
+.
+ Then the code can be checked out with the following commands:
+\end_layout
+
+\begin_layout LyX-Code
+hg clone http://geodynamics.org/hg/long/3D/gale gale
+\end_layout
+
+\begin_layout LyX-Code
+hg clone http://geodynamics.org/hg/long/3D/gale/PICellerator gale/PICellerator
+\end_layout
+
+\begin_layout LyX-Code
+hg clone http://geodynamics.org/hg/long/3D/gale/StGermain gale/StGermain
+\end_layout
+
+\begin_layout LyX-Code
+hg clone http://geodynamics.org/hg/long/3D/gale/StgDomain gale/StgDomain
+\end_layout
+
+\begin_layout LyX-Code
+hg clone http://geodynamics.org/hg/long/3D/gale/StgFEM gale/StgFEM
+\end_layout
+
+\begin_layout LyX-Code
+hg clone http://geodynamics.org/hg/long/3D/gale/Underworld gale/Underworld
+\end_layout
+
+\begin_layout LyX-Code
+hg clone http://geodynamics.org/hg/long/3D/gale/config gale/config
+\end_layout
+
+\begin_layout LyX-Code
+hg clone http://geodynamics.org/hg/long/3D/gale/gLucifer gale/gLucifer
+\end_layout
+
+\begin_layout Standard
+You can then update your checkout with the commands
+\end_layout
+
+\begin_layout LyX-Code
+cd gale
+\end_layout
+
+\begin_layout LyX-Code
+hg pull
+\end_layout
+
+\begin_layout LyX-Code
+hg up
+\end_layout
+
+\begin_layout LyX-Code
+cd PICellerator
+\end_layout
+
+\begin_layout LyX-Code
+hg pull
+\end_layout
+
+\begin_layout LyX-Code
+hg up
+\end_layout
+
+\begin_layout LyX-Code
+cd ../StGermain
+\end_layout
+
+\begin_layout LyX-Code
+hg pull
+\end_layout
+
+\begin_layout LyX-Code
+hg up
+\end_layout
+
+\begin_layout LyX-Code
+cd ../StgDomain
+\end_layout
+
+\begin_layout LyX-Code
+hg pull
+\end_layout
+
+\begin_layout LyX-Code
+hg up
+\end_layout
+
+\begin_layout LyX-Code
+cd ../StgFEM
+\end_layout
+
+\begin_layout LyX-Code
+hg pull
+\end_layout
+
+\begin_layout LyX-Code
+hg up
+\end_layout
+
+\begin_layout LyX-Code
+cd ../Underworld
+\end_layout
+
+\begin_layout LyX-Code
+hg pull
+\end_layout
+
+\begin_layout LyX-Code
+hg up
+\end_layout
+
+\begin_layout LyX-Code
+cd ../config
+\end_layout
+
+\begin_layout LyX-Code
+hg pull
+\end_layout
+
+\begin_layout LyX-Code
+hg up
+\end_layout
+
+\begin_layout LyX-Code
+cd ../gLucifer
+\end_layout
+
+\begin_layout LyX-Code
+hg pull
+\end_layout
+
+\begin_layout LyX-Code
+hg up
\end_layout
\begin_layout LyX-Code
@@ -2027,7 +2159,7 @@ If you downloaded binaries for your plat
\end_layout
\begin_layout LyX-Code
-./Gale_1_4_1 input/cookbook/yielding.xml
+./Gale_1_5_0 input/cookbook/yielding.xml
\end_layout
\begin_layout Standard
@@ -2051,27 +2183,27 @@ TimeStep = 3, Time = 0.0321333
\end_layout
\begin_layout LyX-Code
-TimeStep = 4, Time = 0.0427394
-\end_layout
-
-\begin_layout LyX-Code
-TimeStep = 5, Time = 0.0532924
-\end_layout
-
-\begin_layout LyX-Code
-TimeStep = 6, Time = 0.0637926
-\end_layout
-
-\begin_layout LyX-Code
-TimeStep = 7, Time = 0.0742401
-\end_layout
-
-\begin_layout LyX-Code
-TimeStep = 8, Time = 0.0846354
-\end_layout
-
-\begin_layout LyX-Code
-TimeStep = 9, Time = 0.0949795
+TimeStep = 4, Time = 0.0427393
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 5, Time = 0.0532923
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 6, Time = 0.0637925
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 7, Time = 0.0742399
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 8, Time = 0.0846353
+\end_layout
+
+\begin_layout LyX-Code
+TimeStep = 9, Time = 0.0949793
\end_layout
\begin_layout Standard
@@ -2083,70 +2215,21 @@ output
\end_layout
\begin_layout Standard
-If you do not specify an input file, you will get an error like
+If you do not specify an input file, you will get no output.
+ If Gale cannot find the file, you will get an error:
\end_layout
\begin_layout LyX-Code
\size small
-Error in _AbstractContext_New: The dictionary is empty, meaning no input
- parameters have been fed
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-into your program.
- Perhaps you have forgotten to pass any input files ( or command-line arguments
- ) in.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-Gale: build/StGermain/Base/IO/src/Journal.c:603: Journal_Firewall: Assertion
- `expression' failed.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-p0_27845: p4_error: interrupt SIGx: 6
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout Standard
-If Gale cannot find the file, you will get a different error:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-Error: File input/cookbook/yielding.xml doesn't exist, not readable, or not
- valid.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-Gale: build/StGermain/Base/IO/src/Journal.c:603: Journal_Firewall: Assertion
- `expression' failed.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-p0_16810: p4_error: interrupt SIGx: 6
+Error: File input/cookbook/foo.xml doesn't exist, not readable, or not valid.
\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_4_1 /home/juser/gale/input/cookbook/yielding.xml
+./Gale_1_5_0 /home/juser/gale/input/cookbook/yielding.xml
\family default
).
\end_layout
@@ -2240,7 +2323,7 @@ One solution is to use a direct solver i
\end_layout
\begin_layout LyX-Code
-./Gale_1_4_1 input/cookbook/yielding.xml -pc_type lu -ksp_type preonly
+./Gale_1_5_0 input/cookbook/yielding.xml -pc_type lu -ksp_type preonly
\end_layout
\begin_layout Standard
@@ -2270,8 +2353,35 @@ Once that is done, enabling it is again
\end_layout
\begin_layout LyX-Code
-./Gale_1_4_1 input/cookbook/yielding.xml -mat_type aijmumps -ksp_type pre
- only -pc_type lu
+./Gale_1_5_0 input/cookbook/yielding.xml -pc_factor_mat_solver_package mumps
+
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+-ksp_type preonly -pc_type lu -mat_mumps_icntl_14 100
+\end_layout
+
+\begin_layout Standard
+Note that this is different from previous versions of Gale.
+ Petsc changed the syntax for calling Mumps solvers.
+ Also, Mumps changed the default amount of memory it allocates.
+ This is not an issue for small simulations, but larger simulations can
+ easily run out of memory.
+ The option
+\begin_inset Quotes sld
+\end_inset
+
+
+\family typewriter
+-mat_mumps_icntl_14 100
+\family default
+
+\begin_inset Quotes sld
+\end_inset
+
+ tells Mumps to allocate more memory.
\end_layout
\begin_layout Subsection
@@ -2286,7 +2396,7 @@ You can also change the default values o
\end_layout
\begin_layout LyX-Code
-./Gale_1_4_1 input/cookbook/yielding.xml --maxTimeSteps=20
+./Gale_1_5_0 input/cookbook/yielding.xml --maxTimeSteps=20
\end_layout
\begin_layout Standard
@@ -2297,7 +2407,7 @@ You can append any number of modified pa
\begin_layout LyX-Code
\size small
-./Gale_1_4_1 input/cookbook/yielding.xml --maxTimeSteps=20 --dim=3 --elementResI=
+./Gale_1_5_0 input/cookbook/yielding.xml --maxTimeSteps=20 --dim=3 --elementResI=
64
\begin_inset Newline newline
\end_inset
@@ -2469,6 +2579,13 @@ tools/
material.
\end_layout
+\begin_layout Standard
+\begin_inset Newpage pagebreak
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Visualization with ParaView
\begin_inset CommandInset label
@@ -2494,7 +2611,7 @@ input/cookbook/yielding.xml
\begin_layout Enumerate
\color none
-Start Paraview and open new data:
+Start Paraview and open a new data file:
\family sans
File
\family default
@@ -2881,7 +2998,7 @@ Now you can look at the particles.
Starting over, open
\family typewriter
\color none
-particles.00009.pvtu
+picIntegrationPoints.00009.pvtu
\family default
and click on the green ``Apply'' button.
\end_layout
@@ -2947,6 +3064,182 @@ status open
\align center
\begin_inset Graphics
filename images/Paraview_particles_yielding.png
+ lyxscale 50
+ scale 50
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_deeper
+\begin_layout Enumerate
+Now we will visualize a 3D simulation.
+ Run Gale with the input file
+\family typewriter
+input/cookbook/viscous_extension3D.xml
+\family default
+ and open
+\family typewriter
+fields.00009.ptvs
+\family default
+.
+ Paraview will display an outline of the 3D volume.
+\end_layout
+
+\begin_deeper
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\noindent
+\align center
+\begin_inset Graphics
+ filename images/Paraview_3D_outline.png
+ lyxscale 50
+ scale 50
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_deeper
+\begin_layout Enumerate
+Click on the button near the top center labeled
+\begin_inset Quotes sld
+\end_inset
+
+Outline
+\begin_inset Quotes srd
+\end_inset
+
+ and change it to
+\begin_inset Quotes sld
+\end_inset
+
+Surface
+\begin_inset Quotes srd
+\end_inset
+
+.
+\end_layout
+
+\begin_deeper
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\noindent
+\align center
+\begin_inset Graphics
+ filename images/Paraview_3D_surface_button.png
+ lyxscale 50
+ scale 50
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_deeper
+\begin_layout Enumerate
+Next click on the button near the top left labeled
+\begin_inset Quotes sld
+\end_inset
+
+Solid Color
+\begin_inset Quotes srd
+\end_inset
+
+ and change it to
+\begin_inset Quotes sld
+\end_inset
+
+StrainRateInvariantField
+\begin_inset Quotes srd
+\end_inset
+
+
+\end_layout
+
+\begin_deeper
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\noindent
+\align center
+\begin_inset Graphics
+ filename images/Paraview_3D_color_button.png
+ lyxscale 50
+ scale 50
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_deeper
+\begin_layout Enumerate
+You can now rotate it by clicking and holding with button 1 on your mouse.
+ You can zoom in and out by clicking and holding button 2, and translate
+ by clicking and holding button 3.
+\end_layout
+
+\begin_deeper
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\noindent
+\align center
+\begin_inset Graphics
+ filename images/Paraview_3D_rotate.png
lyxscale 50
scale 50
diff -r 64ad85f62182 -r 2b4194568af1 doc/gale_cover.pdf
Binary file doc/gale_cover.pdf has changed
diff -r 64ad85f62182 -r 2b4194568af1 doc/gale_cover.png
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diff -r 64ad85f62182 -r 2b4194568af1 doc/gale_cover.psd
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diff -r 64ad85f62182 -r 2b4194568af1 doc/gale_cover.xcf
Binary file doc/gale_cover.xcf has changed
diff -r 64ad85f62182 -r 2b4194568af1 doc/images/Paraview_display.png
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diff -r 64ad85f62182 -r 2b4194568af1 doc/images/Paraview_nodal_pressure.png
Binary file doc/images/Paraview_nodal_pressure.png has changed
diff -r 64ad85f62182 -r 2b4194568af1 doc/images/Paraview_open_data.png
Binary file doc/images/Paraview_open_data.png has changed
diff -r 64ad85f62182 -r 2b4194568af1 doc/images/Paraview_particles_viscosity.png
Binary file doc/images/Paraview_particles_viscosity.png has changed
diff -r 64ad85f62182 -r 2b4194568af1 doc/images/Paraview_particles_yielding.png
Binary file doc/images/Paraview_particles_yielding.png has changed
diff -r 64ad85f62182 -r 2b4194568af1 doc/images/Paraview_pressure_velocity.png
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diff -r 64ad85f62182 -r 2b4194568af1 doc/images/Paraview_pressure_velocityII.png
Binary file doc/images/Paraview_pressure_velocityII.png has changed
diff -r 64ad85f62182 -r 2b4194568af1 doc/images/Paraview_pressure_velocity_display.png
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diff -r 64ad85f62182 -r 2b4194568af1 doc/images/Paraview_strainrate.png
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diff -r 64ad85f62182 -r 2b4194568af1 doc/images/Paraview_v.png
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diff -r 64ad85f62182 -r 2b4194568af1 doc/images/Paraview_vmag.png
Binary file doc/images/Paraview_vmag.png has changed
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