[cig-commits] r5486 - mc/3D/CitcomS/trunk/doc/manual
sue at geodynamics.org
sue at geodynamics.org
Wed Dec 6 15:31:58 PST 2006
Author: sue
Date: 2006-12-06 15:31:57 -0800 (Wed, 06 Dec 2006)
New Revision: 5486
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
enumerating several sections of the instructions in chap 5 for clarity, and a few minor text fixes
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-12-06 21:25:42 UTC (rev 5485)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-12-06 23:31:57 UTC (rev 5486)
@@ -5593,7 +5593,7 @@
\begin_layout Standard
Once you have run CitComS.py, you should have a series of output files (potential
-ly spread throughout the file systems of your Beowulf or on a set of directories
+ly spread throughout the file systems of your Beowulf or in a set of directories
on your parallel file system).
You now have to retrieve and combine the data for the time step (or age)
of interest.
@@ -5642,20 +5642,26 @@
datadir
\family default
property in the input file.
- To examine those files, login to a node and change directories to the one
- you specified with a prefix.
+ To examine those files, log in to a node and change directories to the
+ one you specified with a prefix.
For example, if you set
\family typewriter
-datadir=/scratch/username
+datadir=/scratch/
+\emph on
+username
\family default
+\emph default
and
\family typewriter
datafile=test-case
\family default
in your input file, then your output files will be written to
\family typewriter
-/scratch/username
+/scratch/
+\emph on
+username
\family default
+\emph default
and will have the prefix
\family typewriter
test-case
@@ -5674,13 +5680,13 @@
\family typewriter
.h5
\family default
- files, and you can visualize the results using OpenDX.
+ files; you can visualize the results using OpenDX.
See Section
\begin_inset LatexCommand \vref{sec:Using-OpenDX-for-HDF5}
\end_inset
-for more details.
+ for more details.
\end_layout
\begin_layout Standard
@@ -5701,7 +5707,7 @@
\family typewriter
2
\family default
- corresponds to the processor number (so it is output by the 2nd processor),
+ corresponds to the processor number (i.e., it is output by the 2nd processor),
and
\family typewriter
10
@@ -5736,26 +5742,21 @@
xxxxx
\family default
is usually a five-digit number for the process ID.
- This file contains most of the input parameters, which can be useful for
- archiving and postprocessing.
- This file will be referred to as the
-\family typewriter
-pidfile
-\family default
- in this chapter.
+ This pidfile contains most of the input parameters, which can be useful
+ for archiving and postprocessing.
+
\end_layout
\begin_layout Standard
-The output files of CitComS.py need to be postprocessed before you can perform
- the visualization.
- There is a script that can postprocess (retrieve and combine) CitComS.py
- output:
+The ASCII output files of CitComS.py need to be postprocessed before you
+ can perform the visualization.
+ The script
\family typewriter
autocombine.py
\family default
-.
- The script will retrieve CitComS.py data to the current directory and combine
- the output into a few files.
+ can postprocess (retrieve and combine) CitComS.py output; it will retrieve
+ CitComS.py data to the current directory and combine the output into a few
+ files.
\end_layout
\begin_layout Standard
@@ -5808,7 +5809,7 @@
\family typewriter
batchpaste.sh
\family default
- and replace 'rsh' with 'ssh' in the script.
+ and replace `rsh' with `ssh' in the script.
\end_layout
@@ -5905,10 +5906,15 @@
\family typewriter
visRegional.net
\family default
- to visualize the result of regional CitComS.py.
- Launch OpenDX by typing:
+ to visualize the results of regional CitComS.py.
+
\end_layout
+\begin_layout Enumerate
+Launch OpenDX by typing:
+\end_layout
+
+\begin_deeper
\begin_layout LyX-Code
$ dx
\end_layout
@@ -5919,7 +5925,12 @@
Data Explorer
\family default
window.
- Click
+
+\end_layout
+
+\end_deeper
+\begin_layout Enumerate
+Click
\series bold
\family sans
@@ -5931,12 +5942,29 @@
visRegional.net
\family default
from the file selector.
- You will see a
+
+\end_layout
+
+\begin_layout Enumerate
+You will see a
\family sans
Visual Program Editor
\family default
- window and double-click on the
+ window.
+
+\end_layout
+
+\begin_layout Enumerate
+Select the
\family sans
+import
+\family default
+ tab in the
+\family sans
+Visual Program Editor
+\family default
+'s main window and double-click on the
+\family sans
FileSelector
\family default
block, which will open a
@@ -5944,20 +5972,26 @@
Control Panel
\family default
window.
- In the
+
+\end_layout
+
+\begin_layout Enumerate
+In the
\family sans
CitcomSImport filename
\family default
input box, select the header file of your postprocessed data, e.g.,
\end_layout
+\begin_deeper
\begin_layout LyX-Code
\family typewriter
samples/regtest.cap00.100.general
\end_layout
-\begin_layout Standard
+\end_deeper
+\begin_layout Enumerate
In the pull-down menu, select
\family typewriter
@@ -5966,8 +6000,16 @@
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
+
+\end_layout
+
+\begin_layout Enumerate
+A new window will appear with the image of the model.
+
+\end_layout
+
+\begin_layout Enumerate
+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
@@ -5977,6 +6019,8 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
@@ -6076,13 +6120,17 @@
Using OpenDX for Full Sphere Visualization
\end_layout
-\begin_layout Standard
+\begin_layout Enumerate
After launching OpenDX, you will see an OpenDX
\family sans
Data Explorer
\family default
window.
- Click
+
+\end_layout
+
+\begin_layout Enumerate
+Click
\family sans
Edit Visual Programs
\family default
@@ -6091,7 +6139,11 @@
visFull.net
\family default
from the file selector.
- You will see a
+
+\end_layout
+
+\begin_layout Enumerate
+You will see a
\family sans
Visual Program Editor
\family default
@@ -6099,7 +6151,11 @@
\series default
window.
- Select the
+
+\end_layout
+
+\begin_layout Enumerate
+Select the
\family sans
import
\family default
@@ -6119,7 +6175,11 @@
\family default
\series default
window.
- In the
+
+\end_layout
+
+\begin_layout Enumerate
+In the
\family sans
Format String of CitcomSFullImport
\family default
@@ -6127,13 +6187,15 @@
e.g.,
\end_layout
+\begin_deeper
\begin_layout LyX-Code
\family typewriter
samples/fulltest.cap00.100.general
\end_layout
-\begin_layout Standard
+\end_deeper
+\begin_layout Enumerate
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
@@ -6143,13 +6205,15 @@
, e.g.,
\end_layout
+\begin_deeper
\begin_layout LyX-Code
\family typewriter
samples/fulltest.cap%02d.100.general
\end_layout
-\begin_layout Standard
+\end_deeper
+\begin_layout Enumerate
In the pull-down menu, select
\family typewriter
@@ -6158,8 +6222,16 @@
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
+
+\end_layout
+
+\begin_layout Enumerate
+A new window will appear with the image of the model.
+
+\end_layout
+
+\begin_layout Enumerate
+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
@@ -6252,7 +6324,11 @@
visFull.net
\family default
in OpenDX.
- In the pull-down menu, select
+
+\end_layout
+
+\begin_layout Enumerate
+In the pull-down menu, select
\family typewriter
\family sans
@@ -6264,7 +6340,11 @@
CitcomSImportHDF5.net
\family default
to load it.
- In the
+
+\end_layout
+
+\begin_layout Enumerate
+In the
\family sans
Tools
\family default
@@ -6282,19 +6362,20 @@
\end_inset
).
- Place the module in the work space and rewire the network as shown in Figure
+\end_layout
+
+\begin_layout Enumerate
+Place the module in the work space and rewire the network as shown in Figure
+
\begin_inset LatexCommand \ref{fig:Import-CitComS.py-HDF5}
\end_inset
.
-\end_layout
-
-\begin_layout Standard
\begin_inset Float figure
-placement H
+placement t
wide false
sideways false
status collapsed
@@ -6331,13 +6412,18 @@
\end_layout
-\begin_layout Standard
+\begin_layout Enumerate
There are four input tabs in the
\family sans
CitcomSImportHDF5
\family default
module.
- The first tab (connected to the left
+
+\end_layout
+
+\begin_deeper
+\begin_layout Enumerate
+The first tab (connected to the left
\family sans
FileSelector
\family default
@@ -6347,7 +6433,11 @@
samples/cookbook1.h5
\family default
).
- The second tab (connected to the right
+
+\end_layout
+
+\begin_layout Enumerate
+The second tab (connected to the right
\family sans
FileSelector
\family default
@@ -6359,23 +6449,45 @@
/cookbook1.100.h5
\family default
).
- The third tab (connected to the
+\end_layout
+
+\begin_layout Enumerate
+The third tab (connected to the
\family sans
Integer
\family default
module) specifies the resolution reduction factor.
- The fourth tab (unconnected, default to 0) specifies which cap(s) to import.
- To visualize a regional model, leave this tab unchanged.
- To visualize a full spherical model, double-click this module and change
+
+\end_layout
+
+\begin_layout Enumerate
+The fourth tab (unconnected, default to 0) specifies which cap(s) to import.
+
+\end_layout
+
+\begin_deeper
+\begin_layout Enumerate
+To visualize a regional model, leave this tab unchanged.
+
+\end_layout
+
+\begin_layout Enumerate
+To visualize a full spherical model, double-click this module and change
the value of this tab to
\family typewriter
{0,1,2,3,4,5,6,7,8,9,10,11}
\family default
.
- You can also specify a subset of caps to visualize.
+
\end_layout
-\begin_layout Standard
+\begin_layout Enumerate
+You can also specify a subset of caps to visualize.
+\end_layout
+
+\end_deeper
+\end_deeper
+\begin_layout Enumerate
After the data are imported, the visualization can be manipulated as described
in previous sections.
\end_layout
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