[cig-commits] r8135 - doc/CitcomS/manual
sue at geodynamics.org
sue at geodynamics.org
Wed Oct 17 16:09:50 PDT 2007
Author: sue
Date: 2007-10-17 16:09:43 -0700 (Wed, 17 Oct 2007)
New Revision: 8135
Modified:
doc/CitcomS/manual/citcoms.lyx
doc/CitcomS/manual/citcoms.pdf
Log:
various fixes and edits
Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx 2007-10-17 22:49:22 UTC (rev 8134)
+++ doc/CitcomS/manual/citcoms.lyx 2007-10-17 23:09:43 UTC (rev 8135)
@@ -61,6 +61,8 @@
status open
\begin_layout Standard
+\noindent
+\align center
\begin_inset Graphics
filename graphics/citcoms_cover.pdf
display color
@@ -416,7 +418,7 @@
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
+ 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
@@ -437,7 +439,7 @@
\end_layout
\begin_layout Standard
-CitCom (for
+Citcom (for
\series bold
C
\series default
@@ -472,7 +474,7 @@
\begin_layout Standard
In the mid-1990s Moresi wrote versions of the code that solved the equations
within three-dimensional Cartesian domains.
- Then Shijie Zhong successfully parallelized CitCom using message passing
+ 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
@@ -481,7 +483,7 @@
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
+ A plethora of different versions of Citcom exist both on computers at the
California Institute of Technology and around the world.
\end_layout
@@ -548,7 +550,7 @@
was released under a GPL license and made available from
\begin_inset LatexCommand htmlurl
name "CIG"
-target "www.geodynamics.org"
+target "geodynamics.org"
\end_inset
@@ -625,7 +627,7 @@
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;
+s; (3) multi-component chemical convection; (4) a fixed non-Newtonian solver;
(5) a rheology option for pseudo-plasiticity by Thorsten Becker; (6) compositio
n dependent viscosity and heat generation by Thorsten Becker; (7) compressed
ASCII output by Thorsten Becker; (8) an easier way for mesh refinement
@@ -633,8 +635,8 @@
for solver coupling; (10) removing the rigid body rotation component from
the velocity by Shijie Zhong; and (11) an option to disable monitoring
of maximum temperature.
- Additional backward incompatible changes include: (1) the viscosity field
- at element level is not smoothed (this might slow down the convergence
+ Additional changes that are backward incompatible include: (1) the viscosity
+ field at element level is not smoothed (this might slow down the convergence
but will represent the viscosity field more accurately); (2) the Lenardic
filter on temperature is disabled by default; (3) the type of input parameter
@@ -731,8 +733,7 @@
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.
- Future versions of this documentation will cover coupled simulations generated
- via an ``exchanger'' module.
+
\end_layout
\begin_layout Standard
@@ -1036,7 +1037,7 @@
\begin_inset Formula $\pi$
\end_inset
-is the reduced pressure,
+ is the reduced pressure,
\begin_inset Formula $d_{ph}$
\end_inset
@@ -1221,7 +1222,7 @@
\begin_layout Standard
\noindent
This is not the usual definition of the Raleigh number that is based on
- layer thickness, not
+ layer thickness; it is
\begin_inset Formula $R_{0}.$
\end_inset
@@ -1362,7 +1363,7 @@
\begin_inset Formula $\mathbf{C}$
\end_inset
- is the second term in equation
+ is the second term in Equation
\begin_inset LatexCommand ref
reference "eq:non-dimensional continuity eqn"
@@ -1393,7 +1394,7 @@
\emph on
f
\emph default
- are obtained using a standard finite element formulation, see
+ are obtained using a standard finite element formulation; see
\begin_inset LatexCommand cite
key "Zhong et al The role of temperature"
@@ -1419,7 +1420,7 @@
\begin_inset Formula $\mathrm{\mathbf{B}^{\mathit{T}}\mathit{\mathbf{A}^{\mathbf{\mathit{-1}}}}}$
\end_inset
- and using equation
+ and using Equation
\begin_inset LatexCommand ref
reference "eq:discrete continuite eqn"
@@ -1459,14 +1460,14 @@
\end_layout
\begin_layout Standard
-In the compressible case, there are two different strategies to solve Equation
+In the compressible case, there are two different strategies to solve Equations
\begin_inset LatexCommand ref
reference "eq:discrete continuite eqn"
\end_inset
-and
+ and
\begin_inset LatexCommand ref
reference "eq:discrete momentum eqn"
@@ -1606,7 +1607,7 @@
placement H
wide false
sideways false
-status collapsed
+status open
\begin_layout Description
\begin_inset Graphics
@@ -1677,6 +1678,7 @@
\noindent
\align center
\begin_inset Float figure
+placement H
wide false
sideways false
status collapsed
@@ -1718,7 +1720,7 @@
\begin_layout Standard
The caps are approximately square in map view so that the edges of the square
- are orientated diagonally with respect to latitude and longitude.
+ are oriented diagonally with respect to latitude and longitude.
The four corners of the domain are connected by great circles (Figure
\begin_inset LatexCommand ref
reference "fig:Orthographic-projection-of"
@@ -1804,8 +1806,8 @@
\end_layout
\begin_layout Standard
-To install CitcomS.py, you follow the procedure that is commonly used with
- other open source software packages.
+To install CitcomS.py, 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
tar
@@ -1813,14 +1815,14 @@
file) available at the
\begin_inset LatexCommand htmlurl
name "Geodynamics Software Packages web page"
-target "www.geodynamics.org/cig/software/packages"
+target "geodynamics.org/cig/software/packages"
\end_inset
.
After unpacking the source, you run a prepackaged shell script to configure
CitcomS for your system.
- Finally, you use the
+ Finally, use the
\family typewriter
make
\family default
@@ -1862,7 +1864,7 @@
\begin_inset LatexCommand htmlurl
name "Geodynamics Mail Lists web page"
-target "www.geodynamics.org/cig/lists"
+target "geodynamics.org/cig/lists"
\end_inset
@@ -1924,16 +1926,15 @@
\begin_layout Standard
If you are going to use solver coupling, you will also need a decent C++
- compiler (e.g., g++ 3.2 or newer) and the Exchanger package.
- See Section
+ compiler (e.g., g++ 3.2 or newer) and the Exchanger package; see Section
\begin_inset LatexCommand ref
reference "sec:Exchanger-Configuration-(Optional)"
\end_inset
.
- Optionally, CitcomS can be configured to use a parallel HDF5 library.
- See Section
+ Optionally, CitcomS can be configured to use a parallel HDF5 library; see
+ Section
\begin_inset LatexCommand vref
reference "sec:HDF5-Configuration"
@@ -2074,7 +2075,7 @@
$ fink install lammpi lammpi-dev
\end_layout
-\begin_layout Subsubsection*
+\begin_layout Subsubsection
MPI C Compiler Command
\end_layout
@@ -2097,7 +2098,11 @@
\begin_layout Standard
Your system may already have a suitable Python interpreter installed.
- To check, type the 'python' command:
+ To check, type the
+\family typewriter
+python
+\family default
+ command:
\end_layout
\begin_layout LyX-Code
@@ -2237,7 +2242,7 @@
Download CitcomS.py from the
\begin_inset LatexCommand htmlurl
name "Geodynamics website"
-target "www.geodynamics.org"
+target "geodynamics.org"
\end_inset
@@ -2566,7 +2571,7 @@
configure
\family default
performed.
- Most importantly, it includes the error output (if any) from your compiler.
+ More importantly, it includes the error output (if any) from your compiler.
When seeking help for
\family typewriter
configure
@@ -3378,7 +3383,7 @@
\begin_inset LatexCommand htmlurl
name "Pythia page"
-target "www.geodynamics.org/cig/software/packages/cs/pythia"
+target "geodynamics.org/cig/software/packages/cs/pythia"
\end_inset
@@ -3450,7 +3455,7 @@
The CitcomS source code is available via a Subversion server at the
\begin_inset LatexCommand htmlurl
name "Geodynamics website"
-target "www.geodynamics.org"
+target "geodynamics.org"
\end_inset
@@ -3837,7 +3842,7 @@
\begin_layout Standard
On input, CitcomS.py needs numerous parameters to be specified (see Appendix
-\begin_inset LatexCommand vref
+\begin_inset LatexCommand ref
reference "cha:Appendix-A:-Input"
\end_inset
@@ -3856,7 +3861,7 @@
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
+\begin_inset LatexCommand ref
reference "cha:Appendix-A:-Input"
\end_inset
@@ -4155,8 +4160,8 @@
CitcomS
\family default
installation directory).
- In this directory, you will find a configuration file equivalent the previous
- example:
+ In this directory, you will find a configuration file equivalent to the
+ previous example:
\family typewriter
example0.cfg
\family default
@@ -4743,7 +4748,7 @@
\family typewriter
mpirun
\family default
- requires several command line options to launch a parallel job.
+ 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
@@ -5163,7 +5168,7 @@
See
\begin_inset LatexCommand htmlurl
name "CIG Community Area Software on the TeraGrid"
-target "www.geodynamics.org/cig/software/csa/"
+target "geodynamics.org/cig/software/csa/"
\end_inset
@@ -5223,7 +5228,7 @@
\end_layout
\begin_layout Standard
-HDF5 files are organized in a hierarchical structure, similar to a UNIX
+HDF5 files are organized in a hierarchical structure, similar to a Unix
file system.
Two types of primary objects, groups and datasets, are stored in this structure.
A group contains instances of zero or more groups or datasets, while a
@@ -6209,7 +6214,7 @@
\begin_layout Standard
You can convert the HDF5 files to the ASCII combined capfiles described
- in
+ in Appendix
\begin_inset LatexCommand ref
reference "sec:ASCII-Output"
@@ -6223,13 +6228,14 @@
\end_layout
\begin_layout Standard
-You can also convert the HDF5 files to the velo files described in
+You can also convert the HDF5 files to the velo files described in Appendix
+
\begin_inset LatexCommand vref
reference "sub:Velocity-and-Temperature"
\end_inset
- for restart purpose by using the command included in CitcomS:
+ for restart purposes by using the command included in CitcomS:
\end_layout
\begin_layout LyX-Code
@@ -6245,7 +6251,7 @@
\family typewriter
h5tocap.py
\family default
- provides a good example for using the PyTables extension module to access
+ provides a good example of using the PyTables extension module to access
the data contained in the CitcomS HDF5 files.
In PyTables, datasets can be retrieved from disk as NumPy arrays.
The retrieval avoids unnecessary copying of data by using hyperslabs, which
@@ -6419,7 +6425,7 @@
on your parallel file system).
You now have to retrieve and combine the data for the time step (or age)
of interest.
- To visualize your results, it is recommended that you use the open source
+ To visualize your results, it is recommended that you use the open-source
Open Visualization Data Explorer, better known as OpenDX.
The software is available from the
\begin_inset LatexCommand htmlurl
@@ -6665,8 +6671,8 @@
\family typewriter
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:
+ has run, you will have 2 files (or 24 files for the full spherical version
+ of CitcomS.py) formatted as follows:
\end_layout
\begin_layout LyX-Code
@@ -6680,7 +6686,7 @@
\begin_layout Standard
The former file is the data file containing simulation results and is referred
to as the ``capfile''; its format can be found in Appendix
-\begin_inset LatexCommand vref
+\begin_inset LatexCommand ref
reference "cha:Appendix-C:-CitComS,"
\end_inset
@@ -6706,8 +6712,7 @@
\family typewriter
pressure
\family default
-).
- These fields will be combined in separated files, with filenames:
+), these fields will be combined in separated files, with filenames:
\end_layout
\begin_layout LyX-Code
@@ -6875,8 +6880,8 @@
\begin_layout Enumerate
In the pull-down menu, select
\family sans
-Execute\SpecialChar \menuseparator
-Execute on Change
+Execute \SpecialChar \menuseparator
+ Execute on Change
\family default
.
@@ -6891,8 +6896,8 @@
If you want to zoom, rotate, change projection, and otherwise manipulate
the view of the model, experiment with the menu
\family sans
-Options\SpecialChar \menuseparator
-View Control
+Options \SpecialChar \menuseparator
+ View Control
\family default
.
\end_layout
@@ -6904,7 +6909,7 @@
placement H
wide false
sideways false
-status collapsed
+status open
\begin_layout Standard
\align center
@@ -7097,8 +7102,8 @@
\begin_layout Enumerate
In the pull-down menu, select
\family sans
-Execute\SpecialChar \menuseparator
-Execute on Change
+Execute \SpecialChar \menuseparator
+ Execute on Change
\family default
.
@@ -7113,8 +7118,8 @@
If you want to zoom, rotate, change projection, and otherwise manipulate
the view of the model, experiment with the menu
\family sans
-Options\SpecialChar \menuseparator
-View Control
+Options \SpecialChar \menuseparator
+ View Control
\family default
.
\end_layout
@@ -7211,8 +7216,8 @@
\begin_layout Enumerate
In the pull-down menu, select
\family sans
-File\SpecialChar \menuseparator
-Load Macro,
+File \SpecialChar \menuseparator
+ Load Macro,
\family default
and select the file
\family sans
@@ -7413,20 +7418,21 @@
\end_inset
.
- Besides MayaVi2, you will need to install PyTables (see Section
+ Besides MayaVi2, before using the script you will need to install PyTables
+ (see Section
\begin_inset LatexCommand vref
reference "sub:PyTables"
\end_inset
-) and PyVTK (see
+) and PyVTK; see
\begin_inset LatexCommand htmlurl
name "PyVTK website"
target "cens.ioc.ee/projects/pyvtk"
\end_inset
- for instructions) before using the script.
+ for instructions.
\end_layout
\begin_layout Standard
@@ -9216,7 +9222,7 @@
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.py, are coupled.
\end_layout
\begin_layout Standard
Modified: doc/CitcomS/manual/citcoms.pdf
===================================================================
(Binary files differ)
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