[cig-commits] r5481 - mc/3D/CitcomS/trunk/doc/manual
sue at geodynamics.org
sue at geodynamics.org
Wed Dec 6 10:59:57 PST 2006
Author: sue
Date: 2006-12-06 10:59:56 -0800 (Wed, 06 Dec 2006)
New Revision: 5481
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
gurnis corrections and some other fixes
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-12-06 08:52:50 UTC (rev 5480)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-12-06 18:59:56 UTC (rev 5481)
@@ -1,4 +1,4 @@
-#LyX 1.4.1 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -89,7 +89,7 @@
\end_layout
\begin_layout Author
-California Institute of Technology
+© California Institute of Technology
\newline
Version 2.1.0
\end_layout
@@ -319,7 +319,13 @@
\begin_layout Standard
CitComS is a finite element code designed to solve thermal convection problems
- relevant to earth's mantle.
+ relevant to earth's mantle released under the GNU General Public License
+ (see Appendix
+\begin_inset LatexCommand \ref{cha:License}
+
+\end_inset
+
+).
Written in C, the code runs on a variety of parallel processing computers,
including shared and distributed memory platforms.
In an effort to increase the functionality of CitComS to include greater
@@ -448,7 +454,7 @@
Consequently, by 2002, there were so many different versions of the code
that some rationalization was in order.
The software was migrated into a version control system and Eh Tan and
- Eun-seo Choi created a version of the CitComS that generates either a fully
+ Eun-seo Choi created a version of CitComS that generates either a fully
spherical or regional model,
\family typewriter
CitcomSFull
@@ -475,7 +481,7 @@
\begin_layout Standard
CitComS is one component of a larger collection of software encompassed
- by the GeoFramework, a collaborative project between the
+ by the former GeoFramework project, a collaboration between the
\begin_inset LatexCommand \htmlurl[Center for Advanced Computing Research (CACR)]{www.cacr.caltech.edu}
\end_inset
@@ -491,8 +497,8 @@
\end_inset
in Australia.
- The GeoFramework project has been developing a suite of tools to model
- multi-scale deformation for Earth science problems.
+ The GeoFramework project developed a suite of tools to model multi-scale
+ deformation for Earth science problems.
This effort was motivated by the need to understand interactions between
the long-term evolution of plate tectonics and shorter term processes such
as the evolution of faults during and between earthquakes.
@@ -520,7 +526,7 @@
the most important being the use of HDF5 (a parallel version of the Hierarchica
l Data Format).
The HDF5 format allows you to deal with the massive data output created
- for production runs (see Chapter
+ for production runs (see Chapter
\begin_inset LatexCommand \ref{cha:Working-with-HDF5}
\end_inset
@@ -1206,8 +1212,8 @@
There are two forms of meshes and geometries for CitComS.
By default CitComS will produce a mesh within a regional geometry that
is bound by lines of constant latitude and longitude.
- For regional mesh there is an option for mesh refinement in which the mesh
- is refined as a function of latitude, longitude, or radius.
+ For a regional mesh there is an option for mesh refinement in which the
+ mesh is refined as a function of latitude, longitude, or radius.
Such refinement is suitable for higher resolutions near boundary layers
or within the center of the map domain, but is incapable of increasing
the resolution near a curvilinear feature, as a plate boundary, unless
@@ -4394,9 +4400,9 @@
\end_layout
\begin_layout Standard
-The TeraGrid is an open scientific discovery infrastructure combining leadership
- class resources at eight partner sites to create an integrated, persistent
- computational resource.
+The TeraGrid is a set of parallel supercomputer facilities at eight partner
+ sites in the U.S.
+ which creates an integrated, persistent computational resource.
The TeraGrid takes its name from two concepts from high-end computing:
``Tera'' is the metric prefix for ``trillions'' as in teraflops (trillions
of calculations per second) and terabytes (trillions of bytes) and reflects
@@ -4417,7 +4423,9 @@
\begin_layout Standard
Although the TeraGrid is a high-end resource, it was developed to be accessible
to the general community of scientists and engineers as a production facility.
- TeraGrid accounts for small allocations are available directly from CIG.
+ TeraGrid accounts for small allocations are available directly from CIG
+ for investigators in the U.S.
+
\end_layout
\begin_layout Standard
@@ -4429,7 +4437,12 @@
$TG_COMMUNITY/CIG/CitcomS/TG_README
\family default
.
-
+ See
+\begin_inset LatexCommand \htmlurl[CIG Community Area Software on the TeraGrid]{www.geodynamics.org/cig/software/csa/}
+
+\end_inset
+
+ for additional information on access and to apply for allocation time.
\end_layout
\begin_layout Chapter
@@ -4454,8 +4467,9 @@
\end_inset
).
- The CitComS.py 2.1 release solves this problem for parallel file systems
- by assembling a binary HDF5 file in parallel I/O mode.
+ The CitComS.py 2.1 release solves this problem when running the software
+ on computers that have parallel file systems by assembling a binary HDF5
+ file in parallel I/O mode.
\end_layout
@@ -4599,7 +4613,7 @@
a variety of parallel file systems such as GPFS, PVFS, IBRIX FusionFS,
etc., you can specify the following parameters in the CitComS input file.
You may use these parameters to tune the performance of the parallel I/O
- on your system, although in future versions of CitComS this step will become
+ on your system, although in future versions of CitComS this step may become
unnecessary for supported file systems.
\end_layout
@@ -5696,8 +5710,9 @@
current age
\family default
field that lists the time step numbers and their corresponding times.
- To choose an age to export for postprocessing, you have to find out which
- time step corresponds to the age that interests you.
+ To choose an age to export for postprocessing, you have to determine which
+ time step corresponds to the age that interests you by looking at the log
+ file.
\end_layout
\begin_layout Standard
@@ -5721,7 +5736,7 @@
\end_layout
\begin_layout Standard
-The output files of CitComS.py need to be postprocessed before you can do
+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:
@@ -6371,8 +6386,8 @@
\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.
+ manipulating geographic and Cartesian data that produces PostScript (PS)
+ or Encapsulated PostScript File (EPS) illustrations.
GMT is widely used in the geophysics community.
Two scripts
\family typewriter
@@ -6522,8 +6537,8 @@
\align center
\begin_inset Graphics
filename graphics/fulltest.xsect.100.jpg
- lyxscale 40
- scale 40
+ lyxscale 60
+ scale 60
\end_inset
@@ -8561,14 +8576,7 @@
\family typewriter
\size small
-datafile="regtest
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
+datafile="regtest"
\end_layout
\end_inset
@@ -9059,15 +9067,7 @@
\family typewriter
\size small
-datadir_old=
-\begin_inset Quotes srd
-\end_inset
-
-.
-\begin_inset Quotes srd
-\end_inset
-
-
+datadir_old="."
\newline
datafile_old="regtest"
\newline
@@ -14150,24 +14150,7 @@
\family typewriter
\size small
-output_format=
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
-\family typewriter
-\size small
-ascii-local
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
+output_format="ascii-local"
\end_layout
\end_inset
@@ -14190,24 +14173,7 @@
\family typewriter
\size small
-output_optional=
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
-\family typewriter
-\size small
-surf,botm
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
+output_optional="surf,botm"
\end_layout
\end_inset
@@ -14487,24 +14453,7 @@
\family typewriter
\size small
-vel_bound_file=
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
-\family typewriter
-\size small
-bvel.dat
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
+vel_bound_file="bvel.dat"
\end_layout
\end_inset
@@ -14550,24 +14499,7 @@
\family typewriter
\size small
-mat_file=
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
-\family typewriter
-\size small
-mat.dat
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
+mat_file="mat.dat"
\end_layout
\end_inset
@@ -14613,24 +14545,7 @@
\family typewriter
\size small
-lith_age_file=
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
-\family typewriter
-\size small
-age.dat
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
+lith_age_file="age.dat"
\end_layout
\end_inset
@@ -15109,24 +15024,7 @@
\family typewriter
\size small
-tracer_file=
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
-\family typewriter
-\size small
-tracer.dat
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
+tracer_file="tracer.dat"
\end_layout
\end_inset
@@ -15170,24 +15068,7 @@
\family typewriter
\size small
-Viscosity=
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
-\family typewriter
-\size small
-system
-\family default
-\size default
-
-\begin_inset Quotes srd
-\end_inset
-
-
+Viscosity="system"
\end_layout
\end_inset
@@ -16642,6 +16523,10 @@
\end_layout
\begin_layout Chapter
+\begin_inset LatexCommand \label{cha:License}
+
+\end_inset
+
License
\end_layout
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