[cig-commits] r14572 - doc/CitcomS/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Thu Apr 2 13:47:11 PDT 2009
Author: tan2
Date: 2009-04-02 13:47:11 -0700 (Thu, 02 Apr 2009)
New Revision: 14572
Modified:
doc/CitcomS/manual/citcoms.lyx
Log:
Replace CitcomS.py -> CitcomS. Slightly modified Section 1.1-1.4.
Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx 2009-04-02 19:38:45 UTC (rev 14571)
+++ doc/CitcomS/manual/citcoms.lyx 2009-04-02 20:47:11 UTC (rev 14572)
@@ -1,4 +1,4 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.5 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -156,7 +156,7 @@
Part I consists of traditional book front matter, including this preface.
Part II begins with an introduction to Pyre and the Pyre-compatible version
of CitcomS and their capabilities and proceeds to the details of implementation
-, including a ``cookbook'' of short tutorials.
+, including several ``cookbooks'' of short tutorials.
Part III provides appendices and references.
\end_layout
@@ -216,11 +216,12 @@
\end_layout
\begin_layout Standard
-The manual was written for the usage of CitcomS.py on a variety of different
+The manual was written for the usage of CitcomS on a variety of different
platforms.
- CitcomS.py has run on shared memory computers (Sun, Hewlett-Packard, SGI,
+ CitcomS has run on shared memory computers (Sun, Hewlett-Packard, SGI,
and IBM), commercial distributed memory machines (Intel and Cray/SGI),
- and clusters (including machines on the NSF TeraGrid).
+ clusters (including machines on the NSF TeraGrid), Linux PCs and Mac OS
+ X desktops.
\end_layout
@@ -235,7 +236,7 @@
The underlying C code for the finite element package and the Python bindings
for the framework were donated to CIG in July of 2005.
A number of individuals have contributed a significant portion of their
- careers toward the development of CitcomS.py and Pyre.
+ careers toward the development of CitcomS and Pyre.
It is essential that you recognize these individuals in the normal scientific
practice by citing the appropriate peer reviewed papers and making appropriate
acknowledgements.
@@ -329,7 +330,7 @@
\end_inset
Information Technology Research (ITR) program (grant #0205653).
- Continued support of CitcomS.py is based upon work supported by the National
+ Continued support of CitcomS is based upon work supported by the National
Science Foundation under Grant No.
EAR-0406751.
Any opinions, findings, and conclusions or recommendations expressed in
@@ -342,10 +343,8 @@
\end_layout
\begin_layout Standard
-Throughout this documentation CitcomS.py refers to the Pyre-compatible version
- of CitcomS unless specifically stated otherwise.
- Any mention of ``username'' is meant to indicate the user, meaning you
- should substitute your account name in its place.
+Throughout this documentation, any mention of ``username'' is meant to indicate
+ the user, meaning you should substitute your account name in its place.
\end_layout
\begin_layout Part
@@ -383,24 +382,17 @@
\end_layout
\begin_layout Standard
-CitcomS is a finite element code written in C that solves for thermal convection
- within a spherical shell.
- It has two variants,
-\family typewriter
-CitcomSFull
-\family default
- and
-\family typewriter
-CitcomSRegional
-\family default
-; the first solves for problems within a full spherical domain, and the
- second, for a restricted domain of a full sphere.
+CitcomS is a finite element code written in C that solves for thermo-chemical
+ convection within a spherical shell.
+ It can solves for problems within either a full, or a restricted, spherical
+ domain.
Although the code is capable of solving many different kinds of convection
problems using the flexibility of finite elements, there are aspects of
CitcomS which make it well-suited for solving problems in which the plate
tectonic history is incorporated.
- CitcomS.py allows easy use of either one of these two geometries by simply
- changing command line options.
+ Variable viscosity, including temperature-, pressure-, position-, composition-,
+ and stress-dependent viscosity are all possible.
+
\end_layout
\begin_layout Standard
@@ -408,23 +400,18 @@
n problem is the sequential solution of an equation of motion and an energy
equation.
Convection problems are initially valued with boundary conditions, including
- all of the problems which are solved with CitcomS.py.
+ all of the problems which are solved with CitcomS.
The normal sequence of steps for the solution of convection problems starts
with an initial temperature field.
First, the momentum equation is solved.
The solution of this equation gives us the velocity from which we then
solve the advection-diffusion equation, giving us a new temperature.
- CitcomS.py uses this interleaved strategy.
+ CitcomS uses this interleaved strategy.
It is possible to run convection backward in time so as to guess an initial
condition for a normal forward running initial and boundary value problem.
However, users should be aware that even specialists in mantle convection
modeling are just now starting to explore methods in this area and, as
such, this is an emerging area of research.
- There are versions of Citcom which solve for these classes of forward and
- backward problems.
- Variable viscosity, including temperature-, pressure-, position-, composition-,
- and stress-dependent viscosity are all possible, although they may not
- be fully implemented in the current version.
\end_layout
@@ -481,10 +468,10 @@
Zhong then created a spherical version of the code which he named CitcomS.
Lijie Han then created a regional version of CitcomS as well as an alternate
version of message passing for an arbitrarily large number of processors.
- Clint Conrad created the first Beowulf implementations of the code, then
- Conrad and Eh Tan re-coded the message passing of the fully spherical version
- so that problems run on arbitrarily large numbers of processors could also
- be solved.
+ Clint Conrad created the first Beowulf implementations of the code using
+ the MPI library, then Conrad and Eh Tan re-coded the message passing of
+ the fully spherical version so that problems run on arbitrarily large numbers
+ of processors could also be solved.
A plethora of different versions of Citcom exist both on computers at the
California Institute of Technology and around the world.
@@ -495,15 +482,7 @@
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 CitcomS that generates either a fully
- spherical or regional model,
-\family typewriter
-CitcomSFull
-\family default
- and
-\family typewriter
-CitcomSRegional
-\family default
- respectively.
+ spherical or regional model.
CitcomS was released to the community through the former GeoFramework project
as version 1.0 and 1.1.
@@ -513,10 +492,10 @@
By 2004, in order to increase the functionality of CitcomS, the developers
began to reengineer the code into an object-oriented environment specifically
so it could work with a Python-based modeling framework called Pyre.
- This release of the software, now named CitcomS.py, is essentially the product
- of those reengineering efforts.
- Eh Tan was the principal developer of CitcomS.py, with considerable help
- from Eun-seo Choi, Puru Thoutireddy, and Michael Aivazis.
+ This release of the software is essentially the product of those reengineering
+ efforts.
+ Eh Tan was the principal developer of CitcomS, with considerable help from
+ Eun-seo Choi, Puru Thoutireddy, and Michael Aivazis.
\end_layout
\begin_layout Standard
@@ -570,9 +549,9 @@
\end_layout
\begin_layout Standard
-The third major release of CitcomS (2.1) incorporated new features and functional
-ity, the most important being the use of HDF5 (a parallel version of the
- Hierarchical Data Format).
+The release of CitcomS 2.1 incorporated new features and functionality, the
+ most important being the use of HDF5 (a parallel version of the Hierarchical
+ Data Format).
The HDF5 format allows you to deal with the massive data output created
for production runs (see Chapter
\begin_inset LatexCommand vref
@@ -615,8 +594,8 @@
\end_layout
\begin_layout Standard
-The fourth major release of CitcomS (2.2) incorporated the ability of tracing
- particles in the flow.
+The release of CitcomS 2.2 incorporated the ability of tracing particles
+ in the flow.
The tracer code was developed by Allen McNamara and Shijie Zhong in 2004
and donated to CIG in early 2007.
The tracer code has a wide range of applications in the mantle convection.
@@ -626,13 +605,13 @@
\end_layout
\begin_layout Standard
-This release of CitcomS (3.0) contains many new features, including two implement
-ations of compressible convection, one by Wei Leng and Shijie Zhong and
- the other by Eh Tan; the ability to resume computation from previous checkpoint
-s; multi-component chemical convection; a fixed non-Newtonian solver; an
- exchanger package for solver coupling; removing the rigid body rotation
- component from the velocity by Shijie Zhong; and an option to disable monitorin
-g of maximum temperature.
+The release of CitcomS 3.0 contains many new features, including two implementati
+ons of compressible convection, one by Wei Leng and Shijie Zhong and the
+ other by Eh Tan; the ability to resume computation from previous checkpoints;
+ multi-component chemical convection; a fixed non-Newtonian solver; an exchanger
+ package for solver coupling; removing the rigid body rotation component
+ from the velocity by Shijie Zhong; and an option to disable monitoring
+ of maximum temperature.
In addition, a rheology option for pseudo-plasiticity, composition dependent
viscosity and heat generation, compressed ASCII output, and an easier way
for mesh refinement for the radial coordinate were added by Thorsten Becker.
@@ -669,6 +648,10 @@
the results.
\end_layout
+\begin_layout Standard
+This release of CitcomS 3.1 contains TODO...
+\end_layout
+
\begin_layout Section
About Pyre
\end_layout
@@ -730,24 +713,12 @@
\end_layout
-\begin_layout Section
-Pyre and CitcomS.py
-\end_layout
-
\begin_layout Standard
-Pyre provides a simulation framework that includes solver integration and
- coupling, uniform access to facilities, and integrated visualization.
- The framework offers a way to add new solvers to CitcomS.py and to fine-tune
- CitcomS.py simulations.
-
-\end_layout
-
-\begin_layout Standard
\begin_inset Float figure
placement H
wide false
sideways false
-status collapsed
+status open
\begin_layout Description
\begin_inset LatexCommand label
@@ -789,22 +760,34 @@
\end_layout
+\begin_layout Section
+Pyre and CitcomS
+\end_layout
+
\begin_layout Standard
-Developers have created Pyre classes for CitcomS.py to facilitate simulation
+Pyre provides a simulation framework that includes solver integration and
+ coupling, uniform access to facilities, and integrated visualization.
+ The framework offers a way to add new solvers to CitcomS and to fine-tune
+ CitcomS simulations.
+
+\end_layout
+
+\begin_layout Standard
+Developers have created Pyre classes for CitcomS to facilitate simulation
setup.
However, they are not independent classes in a strict sense.
They still share the same underlying data structure and their functionality
is not divided clearly.
- CitcomS.py was not designed to be object-oriented and to make it so would
+ CitcomS was not designed to be object-oriented and to make it so would
require significant investment of effort with little return.
However, the lack of object-oriented features does not hinder the coupling
- of CitcomS.py with other solvers.
+ of CitcomS with other solvers.
\end_layout
\begin_layout Standard
-This version of CitcomS.py ``attaches'' to Pyre via the use of bindings.
- They are included with CitcomS.py, eliminating the need for users to write
+This version of CitcomS ``attaches'' to Pyre via the use of bindings.
+ They are included with CitcomS, eliminating the need for users to write
or alter them.
\end_layout
@@ -1918,7 +1901,7 @@
\end_layout
\begin_layout Standard
-To install CitcomS.py, follow the procedure that is commonly used with other
+To install CitcomS, follow the procedure that is commonly used with other
open-source software packages.
First, download the source package (in the form of a compressed
\family typewriter
@@ -1955,7 +1938,7 @@
\end_layout
\begin_layout Standard
-CitcomS.py has been tested on Linux, Mac OS X, and several NSF TeraGrid platforms.
+CitcomS has been tested on Linux, Mac OS X, and several NSF TeraGrid platforms.
\end_layout
@@ -1988,7 +1971,7 @@
\end_layout
\begin_layout Standard
-Installation of CitcomS.py requires the following:
+Installation of CitcomS requires the following:
\end_layout
\begin_layout Itemize
@@ -2351,7 +2334,7 @@
\end_layout
\begin_layout Standard
-Download CitcomS.py from the
+Download CitcomS from the
\begin_inset LatexCommand htmlurl
name "Geodynamics website"
target "geodynamics.org"
@@ -2759,7 +2742,7 @@
\emph default
.
These are Python packages which are required (either directly or indirectly)
- by CitcomS.py.
+ by CitcomS.
\end_layout
\begin_layout Subsection
@@ -3862,7 +3845,7 @@
\end_layout
\begin_layout Chapter
-Running CitcomS.py
+Running CitcomS
\end_layout
\begin_layout Section
@@ -3920,7 +3903,7 @@
\end_layout
\begin_layout Standard
-If you build CitcomS.py with the Pyre framework, an additional executable,
+If you build CitcomS with the Pyre framework, an additional executable,
\family typewriter
citcoms
@@ -3952,7 +3935,7 @@
\end_layout
\begin_layout Standard
-On input, CitcomS.py needs numerous parameters to be specified (see Appendix
+On input, CitcomS needs numerous parameters to be specified (see Appendix
\begin_inset LatexCommand ref
reference "cha:Appendix-A:-Input"
@@ -3961,18 +3944,18 @@
for a full list).
All parameters have sensible default values.
- Since you will likely want to specify the parameters of your CitcomS.py
- runs, you will need to alter both computational details (such as the number
- of time steps) and controlling parameters specific to your problem (such
- as the Rayleigh number).
+ Since you will likely want to specify the parameters of your CitcomS runs,
+ you will need to alter both computational details (such as the number of
+ time steps) and controlling parameters specific to your problem (such as
+ the Rayleigh number).
These input parameters, or properties in the Pyre terminology, are grouped
under several Pyre components.
\end_layout
\begin_layout Standard
-Most of the properties you will set using CitcomS.py have names which are
- identical to the parameters for the old CitcomS, which are described in
- Appendix
+Most of the properties you will set using CitcomS have names which are identical
+ to the parameters for the old CitcomS, which are described in Appendix
+
\begin_inset LatexCommand ref
reference "cha:Appendix-A:-Input"
@@ -3986,8 +3969,8 @@
\end_layout
\begin_layout Standard
-There are several methods to set the input parameters for CitcomS.py: via
- the command line, or by using a configuration file in
+There are several methods to set the input parameters for CitcomS: via the
+ command line, or by using a configuration file in
\family typewriter
.cfg
\family default
@@ -4251,7 +4234,7 @@
.cfg
\family default
file.
- The CitcomS.py source package contains an
+ The CitcomS source package contains an
\family typewriter
examples
\family default
@@ -4344,9 +4327,9 @@
examples
\family default
directory.
- CitcomS.py has been extensively used on both environments, using up to several
+ CitcomS has been extensively used on both environments, using up to several
hundred processors.
- How to run a multiprocessor CitcomS.py model depends on your hardware and
+ How to run a multiprocessor CitcomS model depends on your hardware and
software settings, e.g., whether a batch system is used, what the names of
the computers in a cluster are, and how the file system is organized.
This section will lead you through the different settings of a parallel
@@ -4522,10 +4505,10 @@
\end_layout
\begin_layout Standard
-CitcomS.py potentially generates a large number of ASCII files.
+CitcomS potentially generates a large number of ASCII files.
This means that you will have to organize your directories carefully when
- running CitcomS.py so that you can manage these files as well as use a post-proc
-essing program contained in this distribution.
+ running CitcomS so that you can manage these files as well as use a post-proces
+sing program contained in this distribution.
\end_layout
@@ -4544,7 +4527,7 @@
\end_layout
\begin_layout Standard
-If you want CitcomS.py to write its output to the local hard disks, you need
+If you want CitcomS to write its output to the local hard disks, you need
to have a common directory structure on all of the local hard disks.
For example, if the directory
\family typewriter
@@ -4637,8 +4620,8 @@
\end_layout
\begin_layout Standard
-If you want CitcomS.py to write its output to a parallel file system, you
- have several choices.
+If you want CitcomS to write its output to a parallel file system, you have
+ several choices.
You can run the example script as follows (substitute
\family typewriter
\emph on
@@ -4757,7 +4740,7 @@
\begin_layout Standard
The ASCII output can potentially take a lot of disk space.
- CitcomS.py can write
+ CitcomS can write
\family typewriter
gzip
\family default
@@ -4788,11 +4771,11 @@
\begin_layout Standard
The last choice is the most powerful one.
- Instead of writing many ASCII files, CitcomS.py can write its results into
+ Instead of writing many ASCII files, CitcomS can write its results into
a single HDF5 (Hierarchical Data Format) file per time step.
These HDF5 files take less disk space than all the ASCII files combined
and don't require additional post-processing to be visualized in OpenDX.
- In order to use this feature, you must compile CitcomS.py with the parallel
+ In order to use this feature, you must compile CitcomS with the parallel
HDF5 library if you haven't done so already (see Section
\begin_inset LatexCommand vref
reference "sec:HDF5-Configuration"
@@ -4863,8 +4846,7 @@
requires several command-line options to launch a parallel job.
Or if you have used one of the batch systems, you will know that the batch
system requires you to write a script to launch a job.
- Fortunately, launching a parallel CitcomS.py job is simplified by Pyre's
-
+ Fortunately, launching a parallel CitcomS job is simplified by Pyre's
\family typewriter
launcher
\family default
@@ -5127,7 +5109,7 @@
mpirun.nodes
\family default
is generated.
- It will contain a list of the nodes where CitcomS.py has run.
+ It will contain a list of the nodes where CitcomS has run.
Save the machine file as it will be useful in the postprocessing step.
\end_layout
@@ -5202,7 +5184,7 @@
\end_layout
\begin_layout Standard
-Once launched, CitcomS.py will print the progress of the model to the standard
+Once launched, CitcomS will print the progress of the model to the standard
error stream (stderr).
Usually, the stderr is directed to your terminal so that you can monitor
the progress.
@@ -5236,7 +5218,7 @@
\end_layout
\begin_layout Section
-Using CitcomS.py on the TeraGrid
+Using CitcomS on the TeraGrid
\end_layout
\begin_layout Standard
@@ -5269,9 +5251,9 @@
\end_layout
\begin_layout Standard
-CitcomS.py has already been installed and tested on several NSF TeraGrid
- platforms, includes NCSA, SDSC and TACC.
- To use CitcomS.py on these machines, please log in to your TeraGrid account
+CitcomS has already been installed and tested on several NSF TeraGrid platforms,
+ includes NCSA, SDSC and TACC.
+ To use CitcomS on these machines, please log in to your TeraGrid account
and read the instructions at
\family typewriter
$TG_COMMUNITY/CIG/CitcomS/TG_README
@@ -5311,7 +5293,7 @@
\end_inset
).
- Since the v2.1 release, CitcomS.py solves this problem when running the software
+ Since the v2.1 release, CitcomS 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.
@@ -6532,8 +6514,8 @@
\end_layout
\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 in a set of directories
+Once you have run CitcomS, you should have a series of output files (potentially
+ 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.
@@ -6588,7 +6570,7 @@
\end_layout
\begin_layout Standard
-Generally, the results from your CitcomS.py run will be distributed on disks
+Generally, the results from your CitcomS run will be distributed on disks
attached to individual nodes of your Beowulf cluster.
The output files are written in each node under the directory that you
specified as the
@@ -6697,8 +6679,8 @@
\end_layout
\begin_layout Standard
-When you execute a CitcomS.py run, your input parameters will be saved in
- a file
+When you execute a CitcomS run, your input parameters will be saved in a
+ file
\family typewriter
pidxxxxx.cfg
\family default
@@ -6713,14 +6695,14 @@
\end_layout
\begin_layout Standard
-The ASCII output files of CitcomS.py need to be postprocessed before you
- can perform the visualization.
+The ASCII output files of CitcomS need to be postprocessed before you can
+ perform the visualization.
The script
\family typewriter
autocombine.py
\family default
- 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
+ can postprocess (retrieve and combine) CitcomS output; it will retrieve
+ CitcomS data to the current directory and combine the output into a few
files.
\end_layout
@@ -6741,7 +6723,7 @@
\family typewriter
mpirun.nodes
\family default
-) and the CitcomS.py pidfile (
+) and the CitcomS pidfile (
\family typewriter
pid12345.cfg
\family default
@@ -6784,7 +6766,7 @@
autocombine.py
\family default
has run, you will have 2 files (or 24 files for the full spherical version
- of CitcomS.py) formatted as follows:
+ of CitcomS) formatted as follows:
\end_layout
\begin_layout LyX-Code
@@ -6847,7 +6829,7 @@
\end_layout
\begin_layout Standard
-If you run CitcomS.py in a non-cluster environment or all of your data can
+If you run CitcomS 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
@@ -6877,7 +6859,7 @@
\end_layout
\begin_layout Standard
-OpenDX modules designed for CitcomS.py can be found in the source directory
+OpenDX modules designed for CitcomS can be found in the source directory
called
\family typewriter
visual
@@ -6907,7 +6889,7 @@
\family typewriter
visRegional.net
\family default
- to visualize the results of regional CitcomS.py.
+ to visualize the results of regional CitcomS.
\end_layout
@@ -7194,7 +7176,7 @@
\end_deeper
\begin_layout Enumerate
-The results of a full spherical CitcomS.py consist of 12 cap files.
+The results of a full spherical CitcomS 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
@@ -7401,7 +7383,7 @@
\end_inset
- How to import CitcomS.py HDF5 data.
+ How to import CitcomS HDF5 data.
The
\family sans
CitcomSImportHDF5
@@ -7899,7 +7881,7 @@
\begin_layout Standard
These cookbook examples are meant to serve as a guide to some of the types
- of problems CitcomS.py can solve.
+ of problems CitcomS can solve.
Cookbook examples range from regional to full spherical shell problems
that address traditional mantle convection problems.
These cookbook examples are distributed with the package under the
@@ -7933,11 +7915,11 @@
\begin_layout Standard
This example solves for thermal convection within a full spherical shell
domain.
- The full spherical version of CitcomS.py is designed to run on a cluster
- that decomposes the spherical shell into 12 equal ``caps'' and then distributes
+ The full spherical version of CitcomS is designed to run on a cluster that
+ decomposes the spherical shell into 12 equal ``caps'' and then distributes
the calculation for caps onto separate processors.
- To run CitcomS.py with the full solver parameter set, it is recommended
- that you have a minimum of 12 processors available on your cluster.
+ To run CitcomS with the full solver parameter set, it is recommended that
+ you have a minimum of 12 processors available on your cluster.
\end_layout
@@ -7963,7 +7945,7 @@
\begin_layout Standard
Global Model ``Caps.'' Left (A): Three-dimensional perspective image showing
- seven of the 12 spherical caps used in a full CitcomS.py run.
+ seven of the 12 spherical caps used in a full CitcomS run.
Right (B): The temperature field at 1081 km depth from a Cookbook 1 run.
\end_layout
@@ -8148,7 +8130,7 @@
\end_layout
\begin_layout Standard
-You have generated a simple example of the full CitcomS.py model, with minimal
+You have generated a simple example of the full CitcomS model, with minimal
parameter alterations.
With a default Rayleigh number of
\begin_inset Formula $10^{5}$
@@ -8198,7 +8180,7 @@
\begin_layout Standard
This example solves for thermal convection with velocity boundary conditions
imposed on the top surface within a given region of a sphere.
- This requires using the regional version of CitcomS.py.
+ This requires using the regional version of CitcomS.
\end_layout
@@ -9328,7 +9310,7 @@
to short wavelength topography is of interest or the lithosphere has a
very high effective viscosity.
Another situation where free-surface formulation is desired is when two
- Pyre solvers, Snac and Citcom.py, are coupled.
+ Pyre solvers, Snac and Citcom, are coupled.
\end_layout
\begin_layout Standard
@@ -9369,7 +9351,7 @@
\end_layout
\begin_layout Standard
-To verify that the above algorithm works, you will run two different CitcomS.py
+To verify that the above algorithm works, you will run two different CitcomS
models with each boundary condition (BC) (free-slip and pseudo-free-surface)
and compare the topography computed accordingly.
The scripts in
@@ -11670,7 +11652,7 @@
\end_inset
-Input Parameters for CitcomS.py
+Input Parameters for CitcomS
\end_layout
\begin_layout Section
@@ -11678,7 +11660,7 @@
\end_layout
\begin_layout Standard
-This section explains the meaning of the input parameters for CitcomS.py.
+This section explains the meaning of the input parameters for CitcomS.
These parameters are grouped by their functionality.
Parameters are given with their default values.
\end_layout
@@ -12279,9 +12261,9 @@
\begin_layout Standard
Controls the interval between output files.
- CitcomS.py dynamically determines the size of the time step; this means
- that you might not get an output at the exact time required, but you can
- always get close depending on how small this number is.
+ CitcomS dynamically determines the size of the time step; this means that
+ you might not get an output at the exact time required, but you can always
+ get close depending on how small this number is.
Do not make this number too small since outputs slow the code down and
you may end up with an unmanageable number of output files.
@@ -12590,7 +12572,7 @@
fi_max
\family default
are the longitudes measured from the prime meridian eastward in radians.
- Only in regional CitcomS.py.
+ Only in regional CitcomS.
\end_layout
\end_inset
@@ -15925,7 +15907,7 @@
\begin_inset Text
\begin_layout Standard
-For this version of CitcomS.py, all of these parameters must be set as indicated.
+For this version of CitcomS, all of these parameters must be set as indicated.
\end_layout
\end_inset
@@ -15939,14 +15921,14 @@
\end_layout
\begin_layout Section
-CitcomS.py Facilities and Properties
+CitcomS Facilities and Properties
\end_layout
\begin_layout Standard
This section lists the facilities and properties in the Pyre version of
- CitcomS.py.
+ CitcomS.
Most of the properties have names which are identical to the parameters
- used in the non-Pyre version of CitcomS.py and are explained in the section
+ used in the non-Pyre version of CitcomS and are explained in the section
above.
This section highlights those which have changed and those which are entirely
new.
@@ -16141,7 +16123,7 @@
\end_layout
\begin_layout Standard
-The launcher facility controls how CitcomS.py, an MPI application, is executed
+The launcher facility controls how CitcomS, an MPI application, is executed
on multiple processors.
It is the equivalent to
\family typewriter
@@ -16257,7 +16239,7 @@
\end_layout
\begin_layout Standard
-The scheduler facility controls how CitcomS.py submits jobs to a batch scheduler.
+The scheduler facility controls how CitcomS submits jobs to a batch scheduler.
\end_layout
\begin_layout Standard
@@ -21728,7 +21710,7 @@
\end_layout
\begin_layout Chapter
-CitcomS.py Input File Format
+CitcomS Input File Format
\end_layout
\begin_layout Section
@@ -21736,7 +21718,7 @@
\end_layout
\begin_layout Standard
-CitcomS.py expects Unix-styled ASCII files (i.e., no carriage character following
+CitcomS expects Unix-styled ASCII files (i.e., no carriage character following
new line character) for all input files.
This can be a nuisance in DOS/Windows systems.
You may want to find a text editor that can write Unix-style ASCII files.
@@ -21767,7 +21749,7 @@
\end_layout
\begin_layout Standard
-For regional version of CitcomS.py, the mesh must be regular, but the mesh
+For regional version of CitcomS, the mesh must be regular, but the mesh
spacing may be unequal.
The
\family typewriter
@@ -21872,7 +21854,7 @@
\end_layout
\begin_layout Standard
-For the full spherical version of CitcomS.py, the mesh of each cap must be
+For the full spherical version of CitcomS, the mesh of each cap must be
regular and equidistant in the horizontal dimension.
Only the vertical dimension is specified by
\family typewriter
@@ -22057,8 +22039,8 @@
\end_layout
\begin_layout Standard
-In this version of CitcomS.py, the implementation of material support is
- not working.
+In this version of CitcomS, the implementation of material support is not
+ working.
The material output has been disabled and is documented here for completion.
If
\family typewriter
@@ -22268,7 +22250,7 @@
\end_inset
-CitcomS.py Output File Format
+CitcomS Output File Format
\end_layout
\begin_layout Section
@@ -22276,7 +22258,7 @@
\end_layout
\begin_layout Standard
-The format of the output files of CitcomS.py is described here.
+The format of the output files of CitcomS is described here.
In the following sections, the model prefix is assumed as
\family typewriter
test-case
@@ -22300,8 +22282,8 @@
\family typewriter
autocombine.py
\family default
- produces 1 cap file for regional CitcomS.py and 12 cap files for the full
- CitcomS.py.
+ produces 1 cap file for regional CitcomS and 12 cap files for the full
+ CitcomS.
The first line of the cap file is a comment describing the node geometry
(
\family typewriter
@@ -22359,8 +22341,8 @@
\family typewriter
autocombine.py
\family default
- produces 1 opt file for regional CitcomS.py and 12 opt files for the full
- CitcomS.py.
+ produces 1 opt file for regional CitcomS and 12 opt files for the full
+ CitcomS.
The first line of the opt file is a comment describing the node geometry
(
\family typewriter
@@ -22564,8 +22546,8 @@
\end_layout
\begin_layout Standard
-In this version of CitcomS.py, the implementation of material support is
- not working.
+In this version of CitcomS, the implementation of material support is not
+ working.
The material output has been disabled and is documented here for completion.
This file is only outputted at the 0th time step.
There is no header.
More information about the CIG-COMMITS
mailing list