[cig-commits] r5440 - mc/3D/CitcomS/trunk/doc/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Mon Dec 4 14:19:15 PST 2006
Author: tan2
Date: 2006-12-04 14:19:15 -0800 (Mon, 04 Dec 2006)
New Revision: 5440
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
Revised Chapter 5 and Appendix A
* Minor revision of post-processing
* Update OpenDX section for new HDF5 layout
* Briefly mentioned GMT scripts (unfinished)
* Described new viscosity laws
* Using Greek letter eta in the viscosity equations
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-12-04 21:31:03 UTC (rev 5439)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-12-04 22:19:15 UTC (rev 5440)
@@ -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
@@ -2505,8 +2505,7 @@
\begin_layout Standard
While the following software is not necessary for the normal operation of
- CitComS, you may find it useful for accessing CitComS data stored in HDF5
- files.
+ CitComS, you may find it useful for accessing CitComS data in HDF5 files.
\end_layout
\begin_layout Subsubsection
@@ -5560,6 +5559,9 @@
\end_inset
.
+ Scripts using GMT commands to plot 2-D cross sections of temperature field
+ are also provided.
+
\end_layout
\begin_layout Section
@@ -5594,6 +5596,30 @@
test-case
\family default
.
+
+\end_layout
+
+\begin_layout Standard
+If you select HDF5 for the output format, the output files will have a
+\family typewriter
+.h5
+\family default
+ suffix.
+ You don't need to postprocess the
+\family typewriter
+.h5
+\family default
+ files and can visualize the results using OpenDX.
+ See Section
+\begin_inset LatexCommand \vref{sec:Using-OpenDX-for-HDF5}
+
+\end_inset
+
+for more details.
+\end_layout
+
+\begin_layout Standard
+If you select ASCII for the output format, you will have many output files.
An example of a filename for the velocity output is
\family typewriter
test-case.velo.2.10
@@ -5714,21 +5740,6 @@
\end_layout
\begin_layout Standard
-If all of your data resides in one directory (e.g.,
-\family typewriter
-/scratch/username
-\family default
-) on a parallel file system, postprocess your output files by following
- the instructions in Section
-\begin_inset LatexCommand \ref{sec:Postprocessing-in-a}
-
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Standard
Once
\family typewriter
autocombine.py
@@ -5757,16 +5768,12 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Postprocessing-in-a}
-
-\end_inset
-
Postprocessing in a Non-Cluster Environment
\end_layout
\begin_layout Standard
-If you run CitComS.py in a non-cluster environment or all of your data resides
- in a single directory, you can still use
+If you run CitComS.py in a non-cluster environment or all of your data can
+ be accessed from the local machine, you can still use
\family typewriter
autocombine.py
\family default
@@ -5874,7 +5881,7 @@
\begin_layout LyX-Code
\family typewriter
-regtest.cap00.100.general
+samples/regtest.cap00.100.general
\end_layout
\begin_layout Standard
@@ -6050,7 +6057,7 @@
\begin_layout LyX-Code
\family typewriter
-fulltest.cap00.100.general
+samples/fulltest.cap00.100.general
\end_layout
\begin_layout Standard
@@ -6066,7 +6073,7 @@
\begin_layout LyX-Code
\family typewriter
-fulltest.cap%02d.100.general
+samples/fulltest.cap%02d.100.general
\end_layout
\begin_layout Standard
@@ -6143,6 +6150,10 @@
\end_layout
\begin_layout Section
+\begin_inset LatexCommand \label{sec:Using-OpenDX-for-HDF5}
+
+\end_inset
+
Using OpenDX for HDF5 Visualization
\end_layout
@@ -6168,15 +6179,36 @@
visFull.net
\family default
in OpenDX.
- In the Tools panel of the main window, select the
+ In the pull-down menu, select
+\family typewriter
+
\family sans
+File\SpecialChar \menuseparator
+Load Macro,
+\family default
+ and select the file
+\family sans
+CitcomSImportHDF5.net
+\family default
+ to load it.
+ In the
+\family sans
+Tools
+\family default
+ panel of the main window, select the
+\family sans
CitcomSImportHDF5
\family default
module in the
\family sans
Macros
\family default
- category.
+ category (highlighted in Figure
+\begin_inset LatexCommand \ref{fig:Import-CitComS.py-HDF5}
+
+\end_inset
+
+).
Place the module in the work space and rewire the network as shown in Figure
\begin_inset LatexCommand \ref{fig:Import-CitComS.py-HDF5}
@@ -6184,6 +6216,7 @@
\end_inset
.
+
\end_layout
\begin_layout Standard
@@ -6191,7 +6224,7 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\noindent
@@ -6231,29 +6264,72 @@
CitcomSImportHDF5
\family default
module.
- The first tab (connected to the
+ The first tab (connected to the left
\family sans
FileSelector
\family default
- module) specifies the HDF5 filename.
- The second tab (connected to the
+ module) specifies the HDF5 file containing time-independent information
+ (e.g.,
+\family typewriter
+samples/cookbook1.h5
+\family default
+).
+ The second tab (connected to the right
\family sans
+ FileSelector
+\family default
+ module) specifies the HDF5 file containing time-dependent information (e.g.,
+
+\family sans
+samples
+\family typewriter
+/cookbook1.100.h5
+\family default
+).
+ The third tab (connected to the
+\family sans
Integer
\family default
- module) specifies the resultion reduction factor.
- The third tab (unconnected, default to 0) specifies which time frame to
- import.
+ 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
+ the value of this tab to
+\family typewriter
+{0,1,2,3,4,5,6,7,8,9,10,11}
+\family default
+.
\end_layout
\begin_layout Standard
+After the data are imported, the visualization can be manipulated as described
+ in previous sections.
+\end_layout
-\series bold
-TODO: GMT Scripts
+\begin_layout Section
+Using GMT Commands for Visualization
\end_layout
\begin_layout Standard
+The Generic Mapping Tools (GMT) is a collection of command-line tools for
+ manipulating geographic and Cartesian data and producing Encapsulated PostScrip
+t File (EPS) illustrations.
+ GMT is widely used in the geophysics community.
+ Two scripts
+\family typewriter
+plot_layer.py
+\family default
+ and
+\family typewriter
+plot_annulus.py
+\family default
+, which can plot the temperature field in horizontal and radial cross sections,
+ respectively, are provided.
+ These scripts use GMT commands to generate EPS images.
+\end_layout
+\begin_layout Standard
+
\series bold
TODO: MayaVi Scripts
\end_layout
@@ -9387,7 +9463,11 @@
\begin_inset Text
\begin_layout Standard
-The pre-exponent factor of layered viscosity structure.
+The pre-exponent factor of layered viscosity structure (
+\begin_inset Formula $\eta_{0}$
+\end_inset
+
+in the equations below).
There must be as many entries as
\family typewriter
num_mat
@@ -9437,13 +9517,53 @@
\family typewriter
rheol
\family default
+=1, temperature-dependent viscosity is computed by:
+\family typewriter
+\size footnotesize
+
+\newline
+
+\begin_inset Formula $\eta=\eta_{0}\times\exp(\eta_{E}(\eta_{T}-T))$
+\end_inset
+
+
+\newline
+
+\newline
+
+\family default
+\size default
+When
+\family typewriter
+rheol
+\family default
+=2, temperature-dependent viscosity is computed by:
+\family typewriter
+\size footnotesize
+
+\newline
+
+\begin_inset Formula $\eta=\eta_{0}\times\exp(-\frac{T}{\eta_{T}})$
+\end_inset
+
+
+\newline
+
+\newline
+
+\family default
+\size default
+When
+\family typewriter
+rheol
+\family default
=3, temperature-dependent viscosity is computed by:
\family typewriter
\size footnotesize
\newline
-\begin_inset Formula $v=v_{0}\times\exp^{\frac{v_{E}}{T+v_{T}}-\frac{v_{E}}{1+v_{T}}}$
+\begin_inset Formula $\eta=\eta_{0}\times\exp(\frac{\eta_{E}}{T+\eta_{T}}-\frac{\eta_{E}}{1+\eta_{T}})$
\end_inset
@@ -9463,7 +9583,7 @@
\newline
-\begin_inset Formula $v=v_{0}\times\exp^{\frac{v_{E}+v_{Z}(1-z)}{T+v_{T}}-\frac{v_{E}+v_{Z}(1-z)}{1+v_{T}}}$
+\begin_inset Formula $\eta=\eta_{0}\times\exp(\frac{\eta_{E}+\eta_{Z}(1-z)}{T+\eta_{T}}-\frac{\eta_{E}+\eta_{Z}(1-z)}{1+\eta_{T}})$
\end_inset
@@ -9490,8 +9610,19 @@
\begin_inset Text
\begin_layout Standard
-Parameters defining viscosity law.
- See the equations above.
+Parameters defining viscosity law (
+\begin_inset Formula $\eta_{E}$
+\end_inset
+
+,
+\begin_inset Formula $\eta_{T}$
+\end_inset
+
+, and
+\begin_inset Formula $\eta_{Z}$
+\end_inset
+
+in the equations above, respectively).
There must be as many entries as
\family typewriter
num_mat
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