[cig-commits] r4756 - mc/3D/CitcomS/trunk/doc/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Mon Oct 9 16:25:06 PDT 2006
Author: tan2
Date: 2006-10-09 16:25:06 -0700 (Mon, 09 Oct 2006)
New Revision: 4756
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
* Added documentaion of .pml file, which comes from DANSE FAQ
* Added section on visualization of full version
* Moved the discussion on .log and .time files from Section 4.2 to Section 3.5.3
* Updated links to equations
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-10-09 23:14:47 UTC (rev 4755)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-10-09 23:25:06 UTC (rev 4756)
@@ -1,4 +1,4 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.2 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -43,7 +43,7 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -594,7 +594,7 @@
placement h
wide false
sideways false
-status open
+status collapsed
\begin_layout Description
\begin_inset LatexCommand \label{Pyre-Architecture}
@@ -908,7 +908,7 @@
\begin_layout Standard
If there is a phase change,
-\begin_inset LatexCommand \ref{eq:14}
+\begin_inset LatexCommand \ref{eq:Ra, a Rayleigh number}
\end_inset
@@ -980,10 +980,6 @@
is the density jump across a phase change.
\end_layout
-\begin_layout Standard
-
-\end_layout
-
\begin_layout Section
Numerical Methods
\end_layout
@@ -1019,7 +1015,7 @@
.
The discrete form of equations
-\begin_inset LatexCommand \ref{eq:conservation of mass}
+\begin_inset LatexCommand \ref{eq:12}
\end_inset
@@ -2503,7 +2499,8 @@
\begin_layout Standard
There are several methods to set the input parameters for CitComS.py, which
will be discussed in this section.
-
+ The command line input will override the input from the .cfg file, which
+ will in turn override the input from the .pml file.
\end_layout
\begin_layout Subsection
@@ -2564,23 +2561,67 @@
\end_layout
\begin_layout Subsection
-System or Personal Default Parameters in a .pml File
+In a CitcomS.pml File
\end_layout
\begin_layout Standard
-(TODO: where is the system-wide pml file, where is the personal file, and
- the syntax of it?)
+A .pml file is an XML file that assigns values to properties, components,
+ and facilities in an application, allowing a user to override the default
+ values assigned in the respective inventories.
+ The file is composed of nested sections.
+ Each section is like:
\end_layout
-\begin_layout Subsection
-Precedences
+\begin_layout LyX-Code
+<component name='component1'>
+\newline
+ <component name='component2'>
+\newline
+ <property
+ name='property1'>value1</property>
+\newline
+ <property name='property2'>value2</pr
+operty>
+\newline
+ </component>
+\newline
+</component>
\end_layout
\begin_layout Standard
-The command line input will override the input from the .cfg file, which
- will in turn override the input from the .pml file.
+The name of the .pml file must be CitcomS.pml.
+ There are several places to put the CitcomS.pml files, depending on the
+ scope you'd like them to have.
\end_layout
+\begin_layout Enumerate
+In
+\family typewriter
+PREFIX/etc/CitcomS
+\family default
+ directory, meant to override variables system-wide.
+\end_layout
+
+\begin_layout Enumerate
+In
+\family typewriter
+~username/.pyre/CitcomS
+\family default
+ directory, meant to override variables for just one user.
+\end_layout
+
+\begin_layout Enumerate
+In the current directory, meant to be local overrides.
+
+\end_layout
+
+\begin_layout Standard
+You can have multiple CitcomS.pml in different directories.
+ The CitcomS.pml in 3 beats the others, 2 beats 1, and 1 beats whatever the
+ default is.
+
+\end_layout
+
\begin_layout Section
Coordinate System and Mesh
\end_layout
@@ -2622,7 +2663,7 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Description
\begin_inset Graphics
@@ -2898,7 +2939,7 @@
placement h
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -3117,6 +3158,8 @@
launcher
\family default
component.
+ Many properties of the launcher component are pertinent to the cluster
+ you are on, and is best customized in the system-wide CitcomS.pml file.
\end_layout
\begin_layout Subsubsection
@@ -3200,11 +3243,23 @@
Usually, the stderr is directed to your terminal so that you can monitor
the progress.
On some system, the stderr is redirected to a file.
- In any case, the progress is always saved in a log file by the rank-0 processor.
- You should check the log file for any error messages.
- You may also want to login to one of the machine to check that the data
- appears to have been properly generated.
- Following your successful run, you will want to retrieve the output files
+ In any case, the progress is always saved in a log file.
+ The log file contains the convergence progress of the computation and,
+ if an error happened, debugging output.
+ The time file contains the elapsed model time (in non-dimensional unit)
+ and CPU time (in seconds) of every time step.
+ The format of the time file can be found in Appendix
+\begin_inset LatexCommand \vref{cha:Appendix-C:-CitComS,}
+
+\end_inset
+
+.
+ The log and time files are output by the rank-0 processor only.
+
+\end_layout
+
+\begin_layout Standard
+Following your successful run, you will want to retrieve the output files
from all the nodes and process them so they can be visualized with the
visualization program OpenDX and proceed to the chapter
\begin_inset LatexCommand \vref{cha:Postprocessing-and-Graphics}
@@ -3349,27 +3404,17 @@
\end_layout
\begin_layout Standard
-To choose an age to export for postprocessing, you have to find out which
- time step corresponds to the age that interests you.
- This is done by looking at the log or time file, for example,
+If your run used the time-dependent velocity boundary conditions (
\family typewriter
-test-case.log
+solver.param.file_vbcs=on
\family default
-.
- The log file contains data that describes the details of the computation.
- It also has a
+), the log file will also have a
\family typewriter
current age
\family default
field that lists the time step numbers and their corresponding times.
- The time step value you selected is what will be exported for postprocessing.
- The time file contains the non-dimensional model time.
- The format of the time file can be found in Appendix
-\begin_inset LatexCommand \vref{cha:Appendix-C:-CitComS,}
-
-\end_inset
-
-.
+ To choose an age to export for postprocessing, you have to find out which
+ time step corresponds to the age that interests you.
\end_layout
\begin_layout Standard
@@ -3389,11 +3434,12 @@
\family typewriter
pidfile
\family default
- in the chapter.
+ in this chapter.
\end_layout
\begin_layout Standard
-These output files need to be postprocessed before you can do the visualization.
+The output files of CitComS.py need to be postprocessed before you can do
+ the visualization.
There is a script that can postprocess (retrieve and combine) CitComS.py
output:
\family typewriter
@@ -3436,10 +3482,8 @@
\begin_layout LyX-Code
$ autocombine.py [machinefile] [pidfile]
\backslash
-
-\end_layout
-\begin_layout LyX-Code
+\newline
[step1] [step2 or more ...]
\end_layout
@@ -3475,19 +3519,20 @@
\begin_layout LyX-Code
\family typewriter
-test-case.cap0.10.general
+test-case.cap00.10
+\newline
+test-case.cap00.10.general
\end_layout
-\begin_layout LyX-Code
+\begin_layout Standard
+The former file is the data file containing simulation results; its format
+ can be found in Appendix
+\begin_inset LatexCommand \ref{cha:Appendix-C:-CitComS,}
-\family typewriter
-test-case.cap0.10
-\end_layout
+\end_inset
-\begin_layout Standard
-The latter file is the data file containing simulation results; its format
- can be found in Appendix C.
- The former file is the OpenDX header for the data.
+.
+ The later file is the OpenDX header for the data.
\end_layout
\begin_layout Section
@@ -3495,17 +3540,13 @@
\end_layout
\begin_layout Standard
-If you have run CitComS in a non-cluster environment or all of your data
+If you have run CitComS.py in a non-cluster environment or all of your data
resides in a single directory, you can still use
\family typewriter
autocombine.py
\family default
- or
-\family typewriter
-batchcombine.py
-\family default
to combine the data.
- The
+ In this case, the
\family typewriter
machinefile
\family default
@@ -3517,17 +3558,15 @@
\end_layout
\begin_layout LyX-Code
-$ autocombine.py localhost [input_param]
+$ autocombine.py localhost [pidfile]
\backslash
-
-\end_layout
-\begin_layout LyX-Code
+\newline
[step1] [step2 or more ...]
\end_layout
\begin_layout Section
-Using OpenDX for Regional Visualization
+Using OpenDX for Regional Sphere Visualization
\end_layout
\begin_layout Standard
@@ -3536,21 +3575,12 @@
\family typewriter
PREFIX/share/CitcomS/visual
\family default
-, where PREFIX is the directory under which you installed CitcomS.py (default
+, where PREFIX is the directory under which you installed CitComS.py (default
\family typewriter
/usr/local
\family default
).
- You will need both the
-\family typewriter
-.net
-\family default
- and
-\family typewriter
-.cfg
-\family default
- files.
\end_layout
@@ -3560,12 +3590,7 @@
visRegional.net
\family default
to visualize the result of regional CitComS.py.
- (You will use
-\family typewriter
-visFull.net
-\family default
- to visualize the result of full CitComS.py.) You should launch OpenDX by
- typing:
+ You should launch OpenDX by typing:
\end_layout
\begin_layout LyX-Code
@@ -3607,44 +3632,23 @@
window.
In the
\family sans
-CitcomSImport
+CitcomSImport filename
\family default
- filename input box, select your postprocessed data file, e.g.,
+ input box, select the header file of your postprocessed data, e.g.,
\end_layout
\begin_layout LyX-Code
\family typewriter
-test-case.cap0.10.general
+regtest.cap00.100.general
\end_layout
\begin_layout Standard
-(For the global model, double-click on the
-\family sans
-FileSelector
-\family default
- block, select one of the 12 processed data files in
-\family sans
-CitcomsFullImport format_string
-\family default
- field.
- Then, edit the filename with the cap number replaced by
+In the pull-down menu, select
\family typewriter
-%02d
-\family default
-, e.g.,
-\family typewriter
- test-case.cap%02d.10.general
-\family default
-.) In the pulldown menu, select
-\family typewriter
\family sans
Execute\SpecialChar \menuseparator
-Execute Once
-\family default
- or
-\family sans
Execute on Change
\family default
.
@@ -3663,7 +3667,7 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -3694,7 +3698,7 @@
\family sans
CitcomSImport reduced
\family default
-, can increase or reduce the resolution.
+, can increase or reduce the resolution of the velocity vectors and grids.
\end_layout
@@ -3718,7 +3722,7 @@
\end_layout
\begin_layout Itemize
-
+
\family sans
Slab cut dimension
\family default
@@ -3727,7 +3731,7 @@
\end_layout
\begin_layout Itemize
-
+
\family sans
Slab cut position
\family default
@@ -3736,19 +3740,151 @@
\end_layout
\begin_layout Standard
-After changing any of these parameters, you must select
-\family sans
-Execute\SpecialChar \menuseparator
-Execute Once
-\family default
- to redraw the model.
- You can change any of the parameters, visualization, or set-up by going
+You can change any of the parameters, visualization, or set-up by going
back to the main window and clicking on each tab.
If you click on each block, you will be able to change the settings for
that function.
\end_layout
+\begin_layout Section
+Using OpenDX for Full Sphere Visualization
+\end_layout
+
+\begin_layout Standard
+After launched OpenDX, You will see an OpenDX
+\family sans
+Data Explorer
+\family default
+ window.
+ Click
+\family sans
+Edit Visual Programs
+\family default
+ and select
+\family typewriter
+visFull.net
+\family default
+ from the file selector.
+ You will see a
+\family sans
+Visual Program Editor
+\family default
+ window.
+ Then select the
+\family sans
+import
+\family default
+ tab in the main window and double-click on the
+\family sans
+FileSelector
+\family default
+ block, which will open a
+\family sans
+Control Panel
+\family default
+ window.
+ In the
+\family sans
+Format String of CitcomSFullImport
+\family default
+ input box, select one of the 12 header files of your postprocessed data,
+ e.g.,
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+fulltest.cap00.100.general
+\end_layout
+
+\begin_layout Standard
+The results of a full spherical CitComS.py consist of 12 cap files.
+ In order to import the 12 cap files at the same time, edit the filename
+ with the cap number replaced by printf-styled format string
+\family typewriter
+%02d
+\family default
+, e.g.,
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+fulltest.cap%02d.100.general
+\end_layout
+
+\begin_layout Standard
+In the pull-down menu, select
+\family typewriter
+
+\family sans
+Execute\SpecialChar \menuseparator
+Execute on Change
+\family default
+.
+ A new window will appear with the image of the model.
+ If you want to zoom, rotate, change projection, and otherwise manipulate
+ the view of the model, experiment with the menu
+\family sans
+Options\SpecialChar \menuseparator
+View Control
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+Additional options in the control panel window for the regional model include:
+\end_layout
+
+\begin_layout Itemize
+
+\family sans
+CitcomSFullImport reduced
+\family default
+, can increase or reduce the resolution of the velocity vectors and grids.
+
+\end_layout
+
+\begin_layout Itemize
+
+\family sans
+Core radius
+\family default
+ is the size of the orange sphere which represents the core-mantle boundary.
+\end_layout
+
+\begin_layout Itemize
+
+\family sans
+Isosurface value
+\family default
+ is the temperature isosurfaces.
+ You can change the values of the isosurfaces, including adding additional
+ isosurfaces or deleting existing ones.
+
+\end_layout
+
+\begin_layout Itemize
+
+\family sans
+Latitude of normal axis
+\family default
+ and
+\family sans
+Longitude of normal axis
+\family default
+ are the directions of the normal axis to the cross-section plane.
+\end_layout
+
+\begin_layout Section
+Using OpenDX for HDF5 Visualization
+\end_layout
+
+\begin_layout Standard
+(TODO)
+\end_layout
+
\begin_layout Chapter
Cookbooks
\end_layout
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