# [cig-commits] r8122 - in doc/CitcomS/manual: . graphics

sue at geodynamics.org sue at geodynamics.org
Tue Oct 16 16:33:12 PDT 2007

Author: sue
Date: 2007-10-16 16:32:38 -0700 (Tue, 16 Oct 2007)
New Revision: 8122

doc/CitcomS/manual/graphics/citcoms_cover.psd
Modified:
doc/CitcomS/manual/citcoms.lyx
doc/CitcomS/manual/citcoms.pdf
doc/CitcomS/manual/graphics/citcoms_cover.pdf
Log:
small edits, new cover, new pdf, clean up file names

Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx	2007-10-16 21:55:11 UTC (rev 8121)
+++ doc/CitcomS/manual/citcoms.lyx	2007-10-16 23:32:38 UTC (rev 8122)
@@ -95,7 +95,7 @@
\end_layout

\begin_layout Title
-CitComS User Manual
+CitcomS User Manual
\end_layout

\begin_layout Author
@@ -153,7 +153,7 @@
This document is organized into three parts.
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
+ of CitcomS and their capabilities and proceeds to the details of implementation
, including a cookbook'' of short tutorials.
Part III provides appendices and references.
\end_layout
@@ -214,9 +214,9 @@
\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.py on a variety of different
platforms.
- CitComS.py has run on shared memory computers (Sun, Hewlett-Packard, SGI,
+ CitcomS.py 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).

@@ -233,7 +233,7 @@
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.py 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.
@@ -241,7 +241,7 @@
\end_layout

\begin_layout Standard
-The CitComS development team asks that you cite both of the following:
+The CitcomS development team asks that you cite both of the following:
\end_layout

\begin_layout Itemize
@@ -282,7 +282,7 @@
\end_layout

\begin_layout Standard
-Additionally, if you are using tracers in CitComS, please cite the following:
+Additionally, if you are using tracers in CitcomS, please cite the following:
\end_layout

\begin_layout Itemize
@@ -330,7 +330,7 @@
\end_inset

Information Technology Research (ITR) program (grant #0205653).
- Continued support of CitComS.py is made possible under NSF EAR-0406751.
+ Continued support of CitcomS.py is made possible under NSF EAR-0406751.
\end_layout

\begin_layout Section*
@@ -338,8 +338,8 @@
\end_layout

\begin_layout Standard
-Throughout this documentation CitComS.py refers to the Pyre-compatible version
- of CitComS unless specifically stated otherwise.
+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.
\end_layout
@@ -353,7 +353,7 @@
\end_layout

\begin_layout Standard
-CitComS is a finite element code designed to solve thermal convection problems
+CitcomS is a finite element code designed to solve thermal convection problems
relevant to earth's mantle released under the GNU General Public License
(see Appendix
\begin_inset LatexCommand vref
@@ -364,22 +364,22 @@
).
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
+ In an effort to increase the functionality of CitcomS to include greater
control during simulations on large parallel systems, the software has
- been reengineered from previous versions of CitComS to work with a Python-based
+ been reengineered from previous versions of CitcomS to work with a Python-based
modeling framework called Pyre.
- With Pyre, CitComS can be dynamically coupled with other CitComS simulations
+ With Pyre, CitcomS can be dynamically coupled with other CitcomS simulations
or with other codes such as SNAC, which solves crustal and lithospheric
problems.

\end_layout

\begin_layout Section
\end_layout

\begin_layout Standard
-CitComS is a finite element code written in C that solves for thermal convection
+CitcomS is a finite element code written in C that solves for thermal convection
within a spherical shell.
It has two variants,
\family typewriter
@@ -393,9 +393,9 @@
second, for a restricted domain of a full sphere.
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
+ 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
+ CitcomS.py allows easy use of either one of these two geometries by simply
changing command line options.
\end_layout

@@ -404,13 +404,13 @@
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.py.
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.py 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
@@ -474,8 +474,8 @@
within three-dimensional Cartesian domains.
Then Shijie Zhong successfully parallelized CitCom using message passing
routines on a limited release Intel supercomputer.
- 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
+ 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
@@ -490,7 +490,7 @@
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 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
@@ -500,23 +500,23 @@
CitcomSRegional
\family default
respectively.
- CitComS was released to the community through the former GeoFramework project
+ CitcomS was released to the community through the former GeoFramework project
as version 1.0 and 1.1.

\end_layout

\begin_layout Standard
-By 2004, in order to increase the functionality of CitComS, the developers
+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
+ 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
+ Eh Tan was the principal developer of CitcomS.py, with considerable help
from Eun-seo Choi, Puru Thoutireddy, and Michael Aivazis.
\end_layout

\begin_layout Standard
-CitComS is one component of a larger collection of software encompassed
+CitcomS is one component of a larger collection of software encompassed
by the former GeoFramework project, a collaboration between the
\begin_inset LatexCommand htmlurl
name "Center for Advanced Computing Research (CACR)"
@@ -556,7 +556,7 @@
\end_layout

\begin_layout Standard
-The second major release of CitComS (2.0) incorporated the software framework
+The second major release of CitcomS (2.0) incorporated the software framework
Pyre, free surface modeling methods, and stress boundary conditions on
the top and bottom surfaces.
In the summer of 2005, as part of the 2.0.1 release, CIG replaced the old
@@ -566,7 +566,7 @@
\end_layout

\begin_layout Standard
-The third major release of CitComS (2.1) incorporated new features and functional
+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 HDF5 format allows you to deal with the massive data output created
@@ -611,7 +611,7 @@
\end_layout

\begin_layout Standard
-The fourth major release of CitComS (2.2) incorporated the ability of tracing
+The fourth major 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.
@@ -622,7 +622,7 @@
\end_layout

\begin_layout Standard
-This release of CitComS (3.0) contains several new features: (1) two implementati
+This release of CitcomS (3.0) contains several new features: (1) two implementati
ons of compressible convection, one by Wei Leng and Shijie Zhong and the
other by Eh Tan; (2) the ability to resume computation from previous checkpoint
s; (3) multi-component chemical convection; (4) fixed non-Newtonian solver;
@@ -723,14 +723,14 @@
\end_layout

\begin_layout Section
-Pyre and CitComS.py
+Pyre and CitcomS.py
\end_layout

\begin_layout Standard
Pyre provides a simulation framework that includes solver integration and
- The framework offers a way to add new solvers to CitComS.py and to fine-tune
- CitComS.py simulations.
+ The framework offers a way to add new solvers to CitcomS.py and to fine-tune
+ CitcomS.py simulations.
Future versions of this documentation will cover coupled simulations generated
via an exchanger'' module.
\end_layout
@@ -783,21 +783,21 @@
\end_layout

\begin_layout Standard
-Developers have created Pyre classes for CitComS.py to facilitate simulation
+Developers have created Pyre classes for CitcomS.py 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.py 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.py 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.py attaches'' to Pyre via the use of bindings.
+ They are included with CitcomS.py, eliminating the need for users to write
or alter them.
\end_layout

@@ -812,7 +812,7 @@
\end_layout

\begin_layout Standard
-With CitComS, the mantle is treated as an anelastic, compressible, viscous
+With CitcomS, the mantle is treated as an anelastic, compressible, viscous
spherical shell under Truncated Anelastic Liquid Approximation.
With these assumptions, thermal convection is governed by the equations
for conservation of mass, momentum, and energy:
@@ -1277,7 +1277,7 @@
\end_inset

.
- CitComS employs an Uzawa algorithm to solve the momentum equation coupled
+ CitcomS employs an Uzawa algorithm to solve the momentum equation coupled
with the incompressibility constraints
\begin_inset LatexCommand cite
key "Moresi/Gurnis Contraints,Ramage/Wathen Iterative solution"
@@ -1455,7 +1455,7 @@
\end_inset

is used for this iteration and forms the basis for the technique used in
- CitComS.
+ CitcomS.
\end_layout

\begin_layout Standard
@@ -1528,14 +1528,14 @@
\end_layout

\begin_layout Standard
-There are two forms of meshes and geometries for CitComS.
- By default CitComS will produce a mesh within a regional geometry that
+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.
There is an option to generate a global mesh of a spherical shell.
\end_layout

\begin_layout Standard
-For a regional mesh, CitComS uses meshes that are regular, although considerable
+For a regional mesh, CitcomS uses meshes that are regular, although considerable
flexibility exists for grid refinement in the regional models.
There is an option for mesh refinement in which the mesh is refined as
a function of latitude, longitude, or radius.
@@ -1659,10 +1659,10 @@
\end_layout

\begin_layout Standard
-For a global mesh, CitComS is also capable of generating a mesh for an entire
+For a global mesh, CitcomS is also capable of generating a mesh for an entire
spherical shell in which elements in map view are approximately equal in
area.
- In the full spherical mode, CitComS has 12 caps numbered 0 to 11 (Figure
+ In the full spherical mode, CitcomS has 12 caps numbered 0 to 11 (Figure

\begin_inset LatexCommand ref
reference "fig:Topological-connectivity-of"
@@ -1727,7 +1727,7 @@

).
One would normally associate at least one processor with one cap.
- However, CitComS can further automatically generate meshes with domain
+ However, CitcomS can further automatically generate meshes with domain
decomposition such that additional processors are used to divide caps uniformly
along the two edges of the caps (Figure
\begin_inset LatexCommand ref
@@ -1769,9 +1769,9 @@

\end_inset

-Orthographic projection of processors from a full CitComS mesh in which
+Orthographic projection of processors from a full CitcomS mesh in which
there are 16 processors in map view for each cap.
- The CitComS cap is shown as distinct colors while the processor domains
+ The CitcomS cap is shown as distinct colors while the processor domains
within the caps are indicated by the intensity of the color.
This example was produced for a run with 2 processors in radius such that
the total number of processors was 12
@@ -1804,7 +1804,7 @@
\end_layout

\begin_layout Standard
-To install CitComS.py, you follow the procedure that is commonly used with
+To install CitcomS.py, you follow the procedure that is commonly used with
other open source software packages.
\family typewriter
@@ -1819,18 +1819,18 @@

.
After unpacking the source, you run a prepackaged shell script to configure
Finally, you use the
\family typewriter
make
\family default
- utility to build and install CitComS from source.
+ utility to build and install CitcomS from source.

\end_layout

\begin_layout Standard
- the latest CitComS source code directly from the CIG source code repository,
+ the latest CitcomS source code directly from the CIG source code repository,
instead of using the prepared source package; see Section
\begin_inset LatexCommand ref
reference "sec:Software-Repository"
@@ -1841,7 +1841,7 @@
\end_layout

\begin_layout Standard
-CitComS.py has been tested on Linux, Mac OS X, and several NSF TeraGrid platforms.
+CitcomS.py has been tested on Linux, Mac OS X, and several NSF TeraGrid platforms.

\end_layout

@@ -1874,7 +1874,7 @@
\end_layout

\begin_layout Standard
-Installation of CitComS.py requires the following:
+Installation of CitcomS.py requires the following:
\end_layout

\begin_layout Itemize
@@ -1902,8 +1902,8 @@
\series bold
Note:
\series default
- Users familiar with older versions of CitComS may prefer to install only
- the legacy CitComS tools,
+ Users familiar with older versions of CitcomS may prefer to install only
+ the legacy CitcomS tools,
\family typewriter
CitcomSFull
\family default
@@ -1932,7 +1932,7 @@
\end_inset

.
- Optionally, CitComS can be configured to use a parallel HDF5 library.
+ Optionally, CitcomS can be configured to use a parallel HDF5 library.
See Section
\begin_inset LatexCommand vref
reference "sec:HDF5-Configuration"
@@ -2028,7 +2028,7 @@
\end_layout

\begin_layout Standard
-CitComS requires a library which implements the MPI standard (either version
+CitcomS requires a library which implements the MPI standard (either version
1 or 2).
Several free, open-source implementations of MPI are available.
\end_layout
@@ -2083,7 +2083,7 @@
Unfortunately, the name of this command varies from one MPI implementation
to the next.
- The CitComS configuration script searches for the following MPI C command
+ The CitcomS configuration script searches for the following MPI C command
names:
\end_layout

@@ -2131,7 +2131,7 @@
) in addition to the core Python package -- even if you don't plan on doing
any Python software development.
The development package contains the Python include files, which are necessary
- for building CitComS.
+ for building CitcomS.
\end_layout

\begin_layout Standard
@@ -2234,7 +2234,7 @@
\end_layout

\begin_layout Standard
\begin_inset LatexCommand htmlurl
name "Geodynamics website"
target "www.geodynamics.org"
@@ -2256,7 +2256,7 @@
Mantle Convection
\family default
.
it using the
\family typewriter
tar
@@ -2281,7 +2281,7 @@
\end_layout

\begin_layout Standard
-After unpacking the source, use the following procedure to install CitComS:
+After unpacking the source, use the following procedure to install CitcomS:
\end_layout

\begin_layout Enumerate
@@ -2289,7 +2289,7 @@
\family typewriter
cd
\family default
-) to the directory containing the CitComS source
+) to the directory containing the CitcomS source
\family typewriter
.
\newline
@@ -2327,7 +2327,7 @@
\end_layout

\begin_layout Standard
-If you are content to run CitComS from the build directory, then you are
+If you are content to run CitcomS from the build directory, then you are
done.
Upon successful completion, the
\family typewriter
@@ -2341,7 +2341,7 @@
\family typewriter
bin
\family default
- subdirectory; this is the script you will use to run CitComS.
+ subdirectory; this is the script you will use to run CitcomS.
You may wish to add the
\family typewriter
bin
@@ -2372,7 +2372,7 @@
\end_layout

\begin_layout Standard
-Optionally, after building CitComS, you can install it in a secondary location
+Optionally, after building CitcomS, you can install it in a secondary location
using the
\family typewriter
make install
@@ -2385,11 +2385,11 @@
\series bold
Note:
\series default
- The following is not recommended if you plan on modifying the CitComS source.
+ The following is not recommended if you plan on modifying the CitcomS source.
\end_layout

\begin_layout Standard
-By default, CitComS is configured to install under
+By default, CitcomS is configured to install under
\family typewriter
/usr/local
\family default
@@ -2455,7 +2455,7 @@
\end_layout

\begin_layout Standard
-The above commands will install CitComS under
+The above commands will install CitcomS under
\family typewriter
$HOME/cig \family default @@ -2608,7 +2608,7 @@ \end_layout \begin_layout Standard -CitComS 3.0.0 requires Pythia v0.8.1.x, which +CitcomS 3.0.0 requires Pythia v0.8.1.x, which \family typewriter configure \family default @@ -2642,7 +2642,7 @@ \emph default . These are Python packages which are required (either directly or indirectly) - by CitComS.py. + by CitcomS.py. \end_layout \begin_layout Subsection @@ -2671,7 +2671,7 @@ \begin_layout Standard The following is a summary of the variables and options that are important - when installing CitComS. + when installing CitcomS. \end_layout @@ -3075,8 +3075,8 @@ \end_layout \begin_layout Standard -This version of CitComS is capable of solver coupling. - Two or more instances of CitComS solvers can be coupled together to solve +This version of CitcomS is capable of solver coupling. + Two or more instances of CitcomS solvers can be coupled together to solve a problem with different length and time scales \begin_inset LatexCommand cite key "Tan et al GeoFramework Part I" @@ -3114,7 +3114,7 @@ \end_layout \begin_layout Standard -By default, CitComS will attempt to auto-detect your Exchanger installation +By default, CitcomS will attempt to auto-detect your Exchanger installation and will disable Exchanger support if it is not found. You may specify the location of your Exchanger installation by setting the PYTHONPATH environment variable to the appropriate installation prefix. @@ -3142,7 +3142,7 @@ \end_layout \begin_layout Standard -For writing its output in binary format, CitComS requires parallel HDF5 +For writing its output in binary format, CitcomS requires parallel HDF5 (PHDF5). In turn, PHDF5 requires an MPI compiler with MPI-IO support and a parallel file system. @@ -3171,7 +3171,7 @@ \end_layout \begin_layout Standard -By default, CitComS will attempt to auto-detect your PHDF5 installation, +By default, CitcomS will attempt to auto-detect your PHDF5 installation, and will disable HDF5 support if it is not found. You may specify the location of your PHDF5 installation by setting the PHDF5_HOME environment variable to the appropriate installation prefix. @@ -3191,7 +3191,7 @@ \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 in HDF5 files. + CitcomS, you may find it useful for accessing CitcomS data in HDF5 files. \end_layout \begin_layout Subsubsection @@ -3339,7 +3339,7 @@ \end_layout \begin_layout Standard -If you are installing CitComS on a cluster with a batch system, you can +If you are installing CitcomS on a cluster with a batch system, you can configure Pyre such that the \family typewriter citcoms @@ -3384,7 +3384,7 @@ . For more information on batch system configuration as it pertains to running - CitComS, see Section + CitcomS, see Section \begin_inset LatexCommand vref reference "sub:Launchers-and-Schedulers" @@ -3403,7 +3403,7 @@ \end_layout \begin_layout Standard -To build just the CitComS tools (or drivers'') from the legacy C code, +To build just the CitcomS tools (or drivers'') from the legacy C code, give \family typewriter configure @@ -3447,7 +3447,7 @@ \end_layout \begin_layout Standard -The CitComS source code is available via a Subversion server at the +The CitcomS source code is available via a Subversion server at the \begin_inset LatexCommand htmlurl name "Geodynamics website" target "www.geodynamics.org" @@ -3532,7 +3532,7 @@ \end_inset . - The CitComS v3.0.0 source package was created with Autoconf 2.59, Automake + The CitcomS v3.0.0 source package was created with Autoconf 2.59, Automake 1.9.2, and Libtool 1.5.6. \end_layout @@ -3557,7 +3557,7 @@ \family typewriter CitcomS \family default - (if it doesn't already exist) and fill it with the latest CitComS source + (if it doesn't already exist) and fill it with the latest CitcomS source from the CIG software repository. \end_layout @@ -3595,7 +3595,7 @@ \end_layout \begin_layout Standard -Your working directory should now contain a fresh checkout of CitComS: +Your working directory should now contain a fresh checkout of CitcomS: \end_layout \begin_layout LyX-Code @@ -3745,15 +3745,15 @@ \end_layout \begin_layout Chapter -Running CitComS.py +Running CitcomS.py \end_layout \begin_layout Section -Using CitComS without Pyre +Using CitcomS without Pyre \end_layout \begin_layout Standard -When you build CitComS, two binary executables, +When you build CitcomS, two binary executables, \family typewriter CitcomSRegional \family default @@ -3766,7 +3766,7 @@ bin \family default directory. - These programs do not use Python or the Pyre framework (even if CitComS + These programs do not use Python or the Pyre framework (even if CitcomS was configured to use the Pyre framework). Each program has the same usage: \end_layout @@ -3799,11 +3799,11 @@ \end_layout \begin_layout Section -Using CitComS with Pyre +Using CitcomS with Pyre \end_layout \begin_layout Standard -If you build CitComS.py with the Pyre framework, an additional executable, +If you build CitcomS.py with the Pyre framework, an additional executable, \family typewriter citcoms @@ -3835,7 +3835,7 @@ \end_layout \begin_layout Standard -On input, CitComS.py needs numerous parameters to be specified (see Appendix +On input, CitcomS.py needs numerous parameters to be specified (see Appendix \begin_inset LatexCommand vref reference "cha:Appendix-A:-Input" @@ -3844,7 +3844,7 @@ for a full list). All parameters have sensible default values. - Since you will likely want to specify the parameters of your CitComS.py + 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). @@ -3853,8 +3853,8 @@ \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 +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 \begin_inset LatexCommand vref reference "cha:Appendix-A:-Input" @@ -3869,7 +3869,7 @@ \end_layout \begin_layout Standard -There are several methods to set the input parameters for CitComS.py: via +There are several methods to set the input parameters for CitcomS.py: via the command line, or by using a configuration file in \family typewriter .cfg @@ -4002,7 +4002,7 @@ \family typewriter .pml \family default - file format is intended for applications in which CitComS input files are + file format is intended for applications in which CitcomS input files are generated by another program, e.g., a GUI, web application, or a high-level structured editor. This file fomat will not be discussed further here. @@ -4094,7 +4094,7 @@ \end_layout \begin_layout Standard -CitComS runs similarly in full spherical or regional modes. +CitcomS runs similarly in full spherical or regional modes. For the purpose of this example, you will perform a test run of the regional version on a workstation. Execute the following on the command line: @@ -4134,7 +4134,7 @@ .cfg \family default file. - The CitComS.py source package contains an + The CitcomS.py source package contains an \family typewriter examples \family default @@ -4227,9 +4227,9 @@ examples \family default directory. - CitComS.py has been extensively used on both environments, using up to several + CitcomS.py 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.py 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 @@ -4405,9 +4405,9 @@ \end_layout \begin_layout Standard -CitComS.py potentially generates a large number of ASCII files. +CitcomS.py 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 + running CitcomS.py so that you can manage these files as well as use a post-proc essing program contained in this distribution. \end_layout @@ -4427,7 +4427,7 @@ \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.py 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 @@ -4520,7 +4520,7 @@ \end_layout \begin_layout Standard -If you want CitComS.py to write its output to a parallel file system, you +If you want CitcomS.py to write its output to a parallel file system, you have several choices. You can run the example script as follows (substitute \family typewriter @@ -4640,7 +4640,7 @@ \begin_layout Standard The ASCII output can potentially take a lot of disk space. - CitComS.py can write + CitcomS.py can write \family typewriter gzip \family default @@ -4671,11 +4671,11 @@ \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.py 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.py with the parallel HDF5 library if you haven't done so already (see Section \begin_inset LatexCommand vref reference "sec:HDF5-Configuration" @@ -4746,7 +4746,7 @@ 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.py job is simplified by Pyre's \family typewriter launcher @@ -4766,7 +4766,7 @@ \family default are pertinent to the cluster you are on, and are best customized in a configura tion file. - Your personal CitComS configuration file ( + Your personal CitcomS configuration file ( \family typewriter ~/.pyre/CitcomS/CitcomS.cfg \family default @@ -4878,7 +4878,7 @@ \end_layout \begin_layout Standard -This option will cause CitComS to perform a dry run,'' dumping the batch +This option will cause CitcomS to perform a dry run,'' dumping the batch script to the console, instead of actually submitting it for execution (the output is only meaningful if you're using a batch system). Likewise, to debug the launcher configuration, use the @@ -4893,13 +4893,13 @@ \end_layout \begin_layout Standard -This option will cause CitComS to print the +This option will cause CitcomS to print the \family typewriter mpirun \family default command, instead of actually executing it. (If you're using a batch system, a job will be submitted for execution; - when it runs, CitComS will simply print the + when it runs, CitcomS will simply print the \family typewriter mpirun \family default @@ -5010,7 +5010,7 @@ 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.py has run. Save the machine file as it will be useful in the postprocessing step. \end_layout @@ -5085,7 +5085,7 @@ \end_layout \begin_layout Standard -Once launched, CitComS.py will print the progress of the model to the standard +Once launched, CitcomS.py 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. @@ -5119,7 +5119,7 @@ \end_layout \begin_layout Section -Using CitComS.py on the TeraGrid +Using CitcomS.py on the TeraGrid \end_layout \begin_layout Standard @@ -5152,9 +5152,9 @@ \end_layout \begin_layout Standard -CitComS.py has already been installed and tested on several NSF TeraGrid +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 + To use CitcomS.py on these machines, please log in to your TeraGrid account and read the instructions at \family typewriter$TG_COMMUNITY/CIG/CitcomS/TG_README
@@ -5176,7 +5176,7 @@

\end_inset

-Working with CitComS HDF5 Files
+Working with CitcomS HDF5 Files
\end_layout

\begin_layout Section
@@ -5184,7 +5184,7 @@
\end_layout

\begin_layout Standard
-A typical run of CitComS can create thousands if not millions of ASCII output
+A typical run of CitcomS can create thousands if not millions of ASCII output
files.
This situation is inefficient since it requires an extra post-processing
step for assembling the results from each processor (see Chapter
@@ -5194,7 +5194,7 @@
\end_inset

).
- Since the v2.1 release, CitComS.py solves this problem when running the software
+ Since the v2.1 release, CitcomS.py 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.

@@ -5285,7 +5285,7 @@
\end_layout

\begin_layout Standard
-To enable HDF5 output in CitComS, all you need to do is include the following
+To enable HDF5 output in CitcomS, all you need to do is include the following
\family typewriter
.cfg
@@ -5332,7 +5332,7 @@
I/O.
The optimal values for these parameters may vary from file system to file
system.
- Ideally, before compiling CitComS, the build procedure would configure
+ Ideally, before compiling CitcomS, the build procedure would configure
these parameters based on your platform.

\end_layout
@@ -5340,9 +5340,9 @@
\begin_layout Standard
In order to facilitate the process of gathering I/O performance data from
a variety of parallel file systems such as GPFS, PVFS, IBRIX FusionFS,
- etc., you can specify the following parameters in the CitComS input file.
+ 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 may become
+ on your system, although in future versions of CitcomS this step may become
unnecessary for supported file systems.
\end_layout

@@ -5504,7 +5504,7 @@
\begin_layout Standard

\family roman
-Finally, here is an example section that would appear in a typical CitComS
+Finally, here is an example section that would appear in a typical CitcomS
input file:
\end_layout

@@ -5559,9 +5559,9 @@
\family default
\size default
contains data of time step 10).
- Most of the output data from CitComS is specified at the nodes of a logically
+ Most of the output data from CitcomS is specified at the nodes of a logically
cartesian grid and is therefore well represented by multi-dimensional arrays.
- A cap dimension is defined for addressing each of the CitComS caps, followed
+ A cap dimension is defined for addressing each of the CitcomS caps, followed
by three spatial indices
\begin_inset Formula $(i,j,k)$
\end_inset
@@ -6215,7 +6215,7 @@

\end_inset

- for specific time steps by using the command included in CitComS:
+ for specific time steps by using the command included in CitcomS:
\end_layout

\begin_layout LyX-Code
@@ -6229,7 +6229,7 @@

\end_inset

- for restart purpose by using the command included in CitComS:
+ for restart purpose by using the command included in CitcomS:
\end_layout

\begin_layout LyX-Code
@@ -6246,7 +6246,7 @@
h5tocap.py
\family default
provides a good example for using the PyTables extension module to access
- the data contained in the CitComS HDF5 files.
+ the data contained in the CitcomS HDF5 files.
The retrieval avoids unnecessary copying of data by using hyperslabs, which
take advantage of Python's powerful array slice-indexing.
@@ -6414,7 +6414,7 @@
\end_layout

\begin_layout Standard
-Once you have run CitComS.py, you should have a series of output files (potential
+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
You now have to retrieve and combine the data for the time step (or age)
@@ -6470,7 +6470,7 @@
\end_layout

\begin_layout Standard
-Generally, the results from your CitComS.py run will be distributed on disks
+Generally, the results from your CitcomS.py 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
@@ -6579,7 +6579,7 @@
\end_layout

\begin_layout Standard
-When you execute a CitComS.py run, your input parameters will be saved in
+When you execute a CitcomS.py run, your input parameters will be saved in
a file
\family typewriter
pidxxxxx.cfg
@@ -6595,14 +6595,14 @@
\end_layout

\begin_layout Standard
-The ASCII output files of CitComS.py need to be postprocessed before you
+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
- 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.py output; it will retrieve
+ CitcomS.py data to the current directory and combine the output into a few
files.
\end_layout

@@ -6623,7 +6623,7 @@
\family typewriter
mpirun.nodes
\family default
-) and the CitComS.py pidfile (
+) and the CitcomS.py pidfile (
\family typewriter
pid12345.cfg
\family default
@@ -6666,7 +6666,7 @@
autocombine.py
\family default
has run, you will have with 2 files (or 24 files for the full spherical
- version of CitComS.py) formatted as follows:
+ version of CitcomS.py) formatted as follows:
\end_layout

\begin_layout LyX-Code
@@ -6730,7 +6730,7 @@
\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.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
@@ -6760,7 +6760,7 @@
\end_layout

\begin_layout Standard
-OpenDX modules designed for CitComS.py can be found in the source directory
+OpenDX modules designed for CitcomS.py can be found in the source directory
called
\family typewriter
visual
@@ -6790,7 +6790,7 @@
\family typewriter
visRegional.net
\family default
- to visualize the results of regional CitComS.py.
+ to visualize the results of regional CitcomS.py.

\end_layout

@@ -7077,7 +7077,7 @@

\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.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
@@ -7284,7 +7284,7 @@

\end_inset

- How to import CitComS.py HDF5 data.
+ How to import CitcomS.py HDF5 data.
The
\family sans
CitcomSImportHDF5
@@ -7392,7 +7392,7 @@
\end_layout

\begin_layout Standard
-This distribution also comes with scripts for visualizing CitComS using
+This distribution also comes with scripts for visualizing CitcomS using
MayaVi2.
MayaVi2 is the successor of MayaVi for 2D/3D scientific data visualization.
It is an interactive program allowing elaborate plots of scientific data.
@@ -7781,7 +7781,7 @@

\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.py can solve.
Cookbook examples range from regional to full spherical shell problems
These cookbook examples are distributed with the package under the
@@ -7815,10 +7815,10 @@
\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
+ 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 calculation for caps onto separate processors.
- To run CitComS.py with the full solver parameter set, it is recommended
+ 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.

\end_layout
@@ -7845,7 +7845,7 @@

\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.py run.
Right (B): The temperature field at 1081 km depth from a Cookbook 1 run.
\end_layout

@@ -8030,7 +8030,7 @@
\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.py model, with minimal
parameter alterations.
With a default Rayleigh number of
\begin_inset Formula $10^{5}$
@@ -8080,7 +8080,7 @@
\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.py.

\end_layout

@@ -8926,7 +8926,7 @@
tic_method=-1
\family default
is set, the initial temperature field is read from setup files.
- The files have the same naming scheme and format as the CitComS velo output,
+ The files have the same naming scheme and format as the CitcomS velo output,
as described in Appendix
\begin_inset LatexCommand vref
reference "sub:Velocity-and-Temperature"
@@ -9257,7 +9257,7 @@
\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.py
models with each boundary condition (BC) (free-slip and pseudo-free-surface)
and compare the topography computed accordingly.
The scripts in
@@ -9630,7 +9630,7 @@

.
The optimal grid spacing of the regular grid depends on the size of the
- CitComS mesh.
+ CitcomS mesh.
A general rule of thumb is that the grid spacing of the regular grid should
be less than
\begin_inset Formula $18/(nodex\times nprocx)$
@@ -9900,9 +9900,9 @@
the computation from the checkpointed state.
To shorten the computation time, a checkpoint at the 9,000th time step
is provided.
- (Note that the checkpoint files are produced by a x86 machine and may not
- be usable by other types of machines, e.g., PowerPC.) To resume the computation
- from the 9,000th time-step checkpoint, set these parameters:
+ (Note that the checkpoint files are produced by an x86 machine and may
+ not be usable by other types of machines, e.g., PowerPC.) To resume the computatio
+n from the 9,000th time-step checkpoint, set these parameters:
\end_layout

\begin_layout LyX-Code
@@ -9923,7 +9923,7 @@
\end_inset

.
- The Rayleigh number of CitComS is scaled by the radius of the Earth.
+ The Rayleigh number of CitcomS is scaled by the radius of the Earth.
If scaled to the thickness of the mantle, the effective Rayleigh number
is
\begin_inset Formula $7\times10{}^{3}$
@@ -9972,7 +9972,7 @@
\begin_layout Standard
The initial temperature is a conductive profile with a single spherical
harmonic perturbation.
- The perturbation is located at the mid-depth and is defined as:
+ The perturbation is located at mid-depth and is defined as:
\begin_inset Formula $mag\times\sin\left(\frac{(r-r_{in})\pi}{r_{out}-r_{in}}\right)\left(\sin(m\phi)+\cos(m\phi)\right)P_{lm}(\cos\theta)$

@@ -10012,7 +10012,7 @@
The maximum size of each time step is determined dynamically by the Courant
criterion.
To enhance the stability of the energy equation solver, you will only use
- three quarters of the maximum Courant time step size.
+ three quarters of the maximum Courant time-step size.
\end_layout

\begin_layout LyX-Code
@@ -10035,7 +10035,7 @@
\family typewriter
mg_cycle=1
\family default
- for V cycle and 2 for W cycle;
+ for the V cycle and 2 for the W cycle;
\family typewriter
down_heavy
\family default
@@ -10116,7 +10116,7 @@

are solved using a Uzawa algorithm, which iteratively updates the pressure
and velocity solutions.
- Three variations of the Uzawa algorithm are used in CitComS, one for the
+ Three variations of the Uzawa algorithm are used in CitcomS, one for the
incompressible case, and the other two for the compressible case.
Two parameters are common to the three variations.
These parameters specify the maximum number of iterations and the desired
@@ -10146,7 +10146,7 @@
\end_layout

\begin_layout Standard
-For the compressible case, two choices of Uzawa algorithm are available.
+For the compressible case, two choices of the Uzawa algorithm are available.
If
\family typewriter
uzawa=cg
@@ -10183,15 +10183,10 @@

\begin_layout Standard
Finally, the rigid body rotation component of the velocity solution is removed.
- The mode of rigid body rotation is unconstrainted by the Stokes equation,
+ The mode of rigid body rotation is unconstrained by the Stokes equation,
if free-slip boundary conditions are used for the top and bottom boundaries
in a full spherical model.
- However, for models with imposed plate velocity, it is advised to turn
- off
-\family typewriter
-remove_rigid_rotation
-\family default
-.
+
\end_layout

\begin_layout LyX-Code
@@ -10199,8 +10194,8 @@
\end_layout

\begin_layout Standard
-However, for models with imposed plate velocity, it is advised to turn off
-
+However, for models with imposed plate velocity, it is advisable to turn
+ off
\family typewriter
remove_rigid_rotation
\family default
@@ -10435,7 +10430,7 @@
\end_inset

.
- A tetrahedra symmetric pattern is developed for the convection.
+ A tetrahedral symmetric pattern is developed for the convection.
The surface heatflux
\begin_inset Formula $Q_{surf}$
\end_inset
@@ -10445,7 +10440,7 @@
\end_inset

is 12.817.
- The heatflux inbalance (
+ The heatflux imbalance (
\begin_inset Formula $Q_{botm}r_{inner}^{2}/Q_{surf}r_{outer}^{2}-1$
\end_inset

@@ -10480,7 +10475,7 @@
\end_inset

Cookbook 8: The steady state temperature field at the 10,000th time step.
- A tetrahedra symmetric convection pattern is developed.
+ A tetrahedral symmetric convection pattern is developed.
Two temperature isosurfaces of 0.4 and 0.8 are shown.

\end_layout
@@ -10504,16 +10499,16 @@
\end_layout

\begin_layout Standard
-You would like to model the interaction between a segment of mid-ocean ridge
- and a plume.
- A small grid spacing is required to resolve the thin plume conduit and
- the flow near the ridge.
- On the other hand, the plume must be sufficiently away from the sidewalls
+In order to model the interaction between a segment of a mid-ocean ridge
+ and a plume, a small grid spacing is required to resolve the thin plume
+ conduit and the flow near the ridge.
+ In addition, the plume must be placed sufficiently away from the sidewalls
to avoid possible boundary effects.
- Satisfying both requirements in a model will take a long computation time.
+ Satisfying both of these requirements in a model entails a long computation
+ time.
Using solver coupling, a high-resolution model with a smaller domain can
- be nested within a low-resolution model, and the computation time is significan
-tly reduced.
+ be nested within a low-resolution model, and the computation time significantly
+ reduced.

\end_layout

@@ -10524,7 +10519,7 @@
\begin_layout Standard
You will use two solvers in the model.
A special command-line option is required for a coupled model.
- Typing the following command to run this cookbook example:
+ Type the following command to run this cookbook example:
\end_layout

\begin_layout LyX-Code
@@ -10532,10 +10527,10 @@
\end_layout

\begin_layout Standard
-The embeded solver (esolver) is nested within the domain of the containing
+The embedded solver (esolver) is nested within the domain of the containing
solver (csolver).
- Both solvers are instances of a regional CitComS solver.
- The containing solver can be a full CitComS solver.
+ Both solvers are instances of a regional CitcomS solver.
+ The containing solver can be a full CitcomS solver.
\end_layout

\begin_layout LyX-Code
@@ -10548,8 +10543,8 @@
\begin_layout Standard
You will use four processors for this model.
Each solver will use two processors.
- The rank-0 and rank-1 processors will be assigned to the csolver, and rank-2
- and rank-3 processors will be assigned to the esolver.
+ The rank-0 and rank-1 processors will be assigned to the csolver, and the
+ rank-2 and rank-3 processors will be assigned to the esolver.
\end_layout

\begin_layout LyX-Code
@@ -10570,11 +10565,11 @@

\end_inset

- and is only briefly described here:
+ and is only briefly described below:
\end_layout

\begin_layout Enumerate
-The containing solver solves the velocity and computes its time step size
+The containing solver solves the velocity and computes its time-step size

\begin_inset Formula $dt_{c}$
\end_inset
@@ -10630,7 +10625,7 @@
\end_layout

\begin_layout Enumerate
-The containing solver solves the temperature with a time step size
+The containing solver solves the temperature with a time-step size
\begin_inset Formula $dt_{c}$
\end_inset

@@ -10638,7 +10633,7 @@
\end_layout

\begin_layout Enumerate
-The entire process beginning at step 1 is repeated.
+The entire process repeats beginning at step 1.
\end_layout

\begin_layout Standard
@@ -10648,8 +10643,8 @@
with the csolver, and the embedded coupler and controller (ecoupler and
econtroller) with the esolver.
Each of the two solvers will track its own number of time steps.
- The esolver is have a smaller time step size and, hence, a larger number
- of time steps.
+ The esolver has a smaller time-step size and, hence, a larger number of
+ time steps.
The model will finish when either of the solvers reaches the 200th time
step.
The csolver will output for every 2 steps and the esolver for every 10
@@ -10691,7 +10686,8 @@
There is an option to exchange initial temperature, which could ensure that
the initial temperature field of both solvers is consistent.
The initial temperature field is read from velo files, which already contain
- consistent temperture fields, and don't need to exchange again.
+ consistent temperature fields and don't need to exchange that information
+ again.

\end_layout

@@ -10704,7 +10700,7 @@
These parameters specify whether the top and bottom boundary of the esolver
will be imposed with the velocity and temperature from the csolver.
For models with prescribed top or bottom boundary conditions, you can turn
- on these two parameters.
+ on these two parameters:
\end_layout

\begin_layout LyX-Code
@@ -10766,7 +10762,7 @@
The radial dimension of the esolver will shrink slightly with respect to
the csolver so that the domain of the esolver is completely inside the
domain of the csolver.
- The radial coordinate of the csolver is refined near the top and bottom
+ The radial coordinates of the csolver is refined near the top and bottom
boundaries (
\family typewriter
coor=2
@@ -10783,9 +10779,9 @@
coor_refine
\family default
(see below), be careful not to set the first or third value (in example
- below,
+ below,
\family typewriter
- 0.1
+0.1
\family default
) too low, or the second or fourth value (in example below,
\family typewriter
@@ -10891,7 +10887,7 @@
fixed_timestep
\family default
is non-zero.
- The temperature solver uses an explicitly predictor-corrector algorithm.
+ The temperature solver uses an explicit predictor-corrector algorithm.
Using 0.5 for the predictor (
\family typewriter
@@ -10925,7 +10921,7 @@
\end_layout

\begin_layout LyX-Code
-# Cookbook 9: Nested Solver Coupling for Ridge-Plume Interation
+# Cookbook 9: Nested Solver Coupling for Ridge-Plume Interaction
\newline

\newline
@@ -11342,7 +11338,7 @@

\end_inset

-Input Parameters for CitComS.py
+Input Parameters for CitcomS.py
\end_layout

\begin_layout Section
@@ -11350,7 +11346,7 @@
\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.py.
These parameters are grouped by their functionality.
Parameters are given with their default values.
\end_layout
@@ -11951,7 +11947,7 @@

\begin_layout Standard
Controls the interval between output files.
- CitComS.py dynamically determines the size of the time step; this means
+ 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.
Do not make this number too small since outputs slow the code down and
@@ -12262,7 +12258,7 @@
fi_max
\family default
are the longitudes measured from the prime meridian eastward in radians.
- Only in regional CitComS.py.
+ Only in regional CitcomS.py.
\end_layout

\end_inset
@@ -14899,7 +14895,7 @@
\begin_inset Text

\begin_layout Standard
-These parameters affect the echo behavior of the CitComS parser.
+These parameters affect the echo behavior of the CitcomS parser.
Only in non-Pyre version.
\end_layout

@@ -15533,7 +15529,7 @@
\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.py, all of these parameters must be set as indicated.
\end_layout

\end_inset
@@ -15547,14 +15543,14 @@
\end_layout

\begin_layout Section
-CitComS.py Facilities and Properties
+CitcomS.py Facilities and Properties
\end_layout

\begin_layout Standard
This section lists the facilities and properties in the Pyre version of
- CitComS.py.
+ CitcomS.py.
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.py and are explained in the section
above.
This section highlights those which have changed and those which are entirely
new.
@@ -15749,7 +15745,7 @@
\end_layout

\begin_layout Standard
-The launcher facility controls how CitComS.py, an MPI application, is executed
+The launcher facility controls how CitcomS.py, an MPI application, is executed
on multiple processors.
It is the equivalent to
\family typewriter
@@ -15865,7 +15861,7 @@
\end_layout

\begin_layout Standard
-The scheduler facility controls how CitComS.py submits jobs to a batch scheduler.
+The scheduler facility controls how CitcomS.py submits jobs to a batch scheduler.
\end_layout

\begin_layout Standard
@@ -16152,7 +16148,7 @@
\family typewriter
storage_spacing
\family default
- parameter in the (old) CitComS input file.
+ parameter in the (old) CitcomS input file.
\end_layout

\end_inset
@@ -20951,7 +20947,7 @@
\newline

\newline
-The journal facility is only used in the coupled CitComS solver.
+The journal facility is only used in the coupled CitcomS solver.
For coupled solvers, there is a large amount of debugging information that
outputs through the journal facility.
That output can be turned on/off with command line options.
@@ -20980,7 +20976,7 @@
\end_layout

\begin_layout Chapter
-CitComS.py Input File Format
+CitcomS.py Input File Format
\end_layout

\begin_layout Section
@@ -20988,7 +20984,7 @@
\end_layout

\begin_layout Standard
-CitComS.py expects Unix-styled ASCII files (i.e., no carriage character following
+CitcomS.py 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.
@@ -21017,7 +21013,7 @@
\end_layout

\begin_layout Standard
-For regional version of CitComS.py, the mesh must be regular, but the mesh
+For regional version of CitcomS.py, the mesh must be regular, but the mesh
spacing may be unequal.
The
\family typewriter
@@ -21096,7 +21092,7 @@
\end_layout

\begin_layout Standard
-For full spherical version of CitComS.py, the mesh of each cap must be regular
+For full spherical version of CitcomS.py, the mesh of each cap must be regular
and equidistant in the horizontal dimension.
Only the vertical dimension is specified by
\family typewriter
@@ -21272,7 +21268,7 @@
\end_layout

\begin_layout Standard
-In this version of CitComS.py, the implementation of material support is
+In this version of CitcomS.py, the implementation of material support is
not working.
The material output has been disabled and is documented here for completion.
If
@@ -21478,7 +21474,7 @@

\end_inset

-CitComS.py Output File Format
+CitcomS.py Output File Format
\end_layout

\begin_layout Section
@@ -21486,7 +21482,7 @@
\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.py is described here.
In the following sections, the model prefix is assumed as
\family typewriter
test-case
@@ -21504,7 +21500,7 @@
\family typewriter
autocombine.py
\family default
- produces 1 cap file for regional CitComS.py and 12 cap files for full CitComS.py,
+ produces 1 cap file for regional CitcomS.py and 12 cap files for full CitcomS.py,
e.g.,
\family typewriter
test-case.cap00.10
@@ -21646,7 +21642,7 @@
\end_layout

\begin_layout Standard
-In this version of CitComS.py, the implementation of material support is
+In this version of CitcomS.py, 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.

Modified: doc/CitcomS/manual/citcoms.pdf
===================================================================
(Binary files differ)

Modified: doc/CitcomS/manual/graphics/citcoms_cover.pdf
===================================================================
(Binary files differ)