[cig-commits] r8055 - doc/CitcomS/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Fri Sep 28 12:13:25 PDT 2007
Author: tan2
Date: 2007-09-28 12:13:24 -0700 (Fri, 28 Sep 2007)
New Revision: 8055
Modified:
doc/CitcomS/manual/citcoms.lyx
Log:
Convert to Lyx 1.5
Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx 2007-09-28 19:03:02 UTC (rev 8054)
+++ doc/CitcomS/manual/citcoms.lyx 2007-09-28 19:13:24 UTC (rev 8055)
@@ -1,5 +1,5 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
-\lyxformat 245
+#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+\lyxformat 276
\begin_document
\begin_header
\textclass book
@@ -13,13 +13,21 @@
\end_preamble
\language english
\inputencoding auto
-\fontscheme default
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
\graphics default
\paperfontsize default
\spacing single
\papersize default
\use_geometry true
\use_amsmath 0
+\use_esint 0
\cite_engine basic
\use_bibtopic false
\paperorientation portrait
@@ -36,7 +44,8 @@
\papersides 2
\paperpagestyle headings
\tracking_changes false
-\output_changes true
+\output_changes false
+\author ""
\end_header
\begin_body
@@ -89,7 +98,7 @@
\end_layout
\begin_layout Author
-© California Institute of Technology
+© California Institute of Technology
\newline
Version 3.0.0
\end_layout
@@ -112,7 +121,7 @@
\end_layout
\begin_layout Standard
-\begin_inset LatexCommand \tableofcontents{}
+\begin_inset LatexCommand tableofcontents
\end_inset
@@ -150,18 +159,24 @@
\begin_layout Standard
The style of this publication is based on the
-\begin_inset LatexCommand \htmlurl[Apple Publications Style Guide]{developer.apple.com/documentation/UserExperience/Conceptual/APStyleGuide/AppleStyleGuide2003.pdf}
+\begin_inset LatexCommand htmlurl
+name "Apple Publications Style Guide"
+target "developer.apple.com/documentation/UserExperience/Conceptual/APStyleGuide/AppleStyleGuide2003.pdf"
\end_inset
, as recommended by
-\begin_inset LatexCommand \htmlurl[Python.org]{www.python.org}
+\begin_inset LatexCommand htmlurl
+name "Python.org"
+target "www.python.org"
\end_inset
.
The documentation was produced using
-\begin_inset LatexCommand \htmlurl[LyX]{www.lyx.org}
+\begin_inset LatexCommand htmlurl
+name "LyX"
+target "www.lyx.org"
\end_inset
@@ -173,7 +188,9 @@
\begin_layout Standard
Errors and bug fixes in this manual should be directed to the
-\begin_inset LatexCommand \htmlurl[CIG Mantle Convection Mailing List]{cig-mc at geodynamics.org}
+\begin_inset LatexCommand htmlurl
+name "CIG Mantle Convection Mailing List"
+target "cig-mc at geodynamics.org"
\end_inset
@@ -237,17 +254,15 @@
J.
Geophys.
Res.,
-\series bold
\emph default
-\series default
\emph on
105
\series bold
-,
+,
\series default
\emph default
-11,063-11,082
+ 11,063-11,082
\end_layout
\begin_layout Itemize
@@ -260,11 +275,8 @@
\emph on
Geochem., Geophys., Geosyst.
7,
-\series bold
-
-\series default
\emph default
-Q06001, doi:10.1029/2005GC001155.
+ Q06001, doi:10.1029/2005GC001155.
\end_layout
@@ -288,7 +300,9 @@
The developers also request that in your oral presentations and in your
paper acknowledgements that you indicate your use of this code, the authors
of the code, and
-\begin_inset LatexCommand \htmlurl[CIG]{www.geodynamics.org}
+\begin_inset LatexCommand htmlurl
+name "CIG"
+target "www.geodynamics.org"
\end_inset
@@ -301,12 +315,16 @@
\begin_layout Standard
Pyre development is funded by the
-\begin_inset LatexCommand \htmlurl[U.S. Dept. of Energy's Advanced Simulation and Computing program]{www.sandia.gov/NNSA/ASC}
+\begin_inset LatexCommand htmlurl
+name "U.S. Dept. of Energy's Advanced Simulation and Computing program"
+target "www.sandia.gov/NNSA/ASC"
\end_inset
and the
-\begin_inset LatexCommand \htmlurl[National Science Foundation's]{www.nsf.gov}
+\begin_inset LatexCommand htmlurl
+name "National Science Foundation's"
+target "www.nsf.gov"
\end_inset
@@ -337,7 +355,8 @@
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{cha:License}
+\begin_inset LatexCommand vref
+reference "cha:License"
\end_inset
@@ -498,17 +517,23 @@
\begin_layout Standard
CitComS is one component of a larger collection of software encompassed
by the former GeoFramework project, a collaboration between the
-\begin_inset LatexCommand \htmlurl[Center for Advanced Computing Research (CACR)]{www.cacr.caltech.edu}
+\begin_inset LatexCommand htmlurl
+name "Center for Advanced Computing Research (CACR)"
+target "www.cacr.caltech.edu"
\end_inset
and the
-\begin_inset LatexCommand \htmlurl[Seismological Laboratory]{www.gps.caltech.edu/seismo}
+\begin_inset LatexCommand htmlurl
+name "Seismological Laboratory"
+target "www.gps.caltech.edu/seismo"
\end_inset
, both at Caltech, and the
-\begin_inset LatexCommand \htmlurl[Victorian Partnership for Advanced Computing]{www.vpac.org}
+\begin_inset LatexCommand htmlurl
+name "Victorian Partnership for Advanced Computing"
+target "www.vpac.org"
\end_inset
@@ -520,7 +545,9 @@
as the evolution of faults during and between earthquakes.
During 2005 and 2006 much of the remaining software developed by GeoFramework
was released under a GPL license and made available from
-\begin_inset LatexCommand \htmlurl[CIG]{www.geodynamics.org}
+\begin_inset LatexCommand htmlurl
+name "CIG"
+target "www.geodynamics.org"
\end_inset
@@ -543,7 +570,8 @@
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{cha:Working-with-HDF5}
+\begin_inset LatexCommand vref
+reference "cha:Working-with-HDF5"
\end_inset
@@ -556,17 +584,23 @@
Other improvements included the incorporation of geoid calculations that
had been left out of earlier releases, as well as new scripts to allow
results to be visualized with
-\begin_inset LatexCommand \htmlurl[MayaVi2]{svn.enthought.com/enthought/wiki/MayaVi}
+\begin_inset LatexCommand htmlurl
+name "MayaVi2"
+target "svn.enthought.com/enthought/wiki/MayaVi"
\end_inset
in addition to
-\begin_inset LatexCommand \htmlurl[Generic Mapping Tools (GMT)]{gmt.soest.hawaii.edu}
+\begin_inset LatexCommand htmlurl
+name "Generic Mapping Tools (GMT)"
+target "gmt.soest.hawaii.edu"
\end_inset
and
-\begin_inset LatexCommand \htmlurl[OpenDX]{www.opendx.org}
+\begin_inset LatexCommand htmlurl
+name "OpenDX"
+target "www.opendx.org"
\end_inset
@@ -686,7 +720,8 @@
status collapsed
\begin_layout Description
-\begin_inset LatexCommand \label{Pyre-Architecture}
+\begin_inset LatexCommand label
+name "Pyre-Architecture"
\end_inset
@@ -706,7 +741,10 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Pyre Architecture.
The integration framework is a set of cooperating abstract services.
\end_layout
@@ -716,6 +754,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
Developers have created Pyre classes for CitComS.py to facilitate simulation
setup.
@@ -785,13 +828,19 @@
\end_inset
+\emph default
+
\shape italic
- is the density,
+\emph on
+is the density,
\shape default
- u
\emph default
-is the velocity,
+
\emph on
+u
+\emph default
+ is the velocity,
+\emph on
P
\emph default
is the dynamic pressure,
@@ -822,11 +871,7 @@
\begin_inset Formula $c_{P}$
\end_inset
- is the heat capacity,
-\shape italic
-
-\shape default
-
+ is the heat capacity,
\begin_inset Formula $\kappa$
\end_inset
@@ -895,24 +940,18 @@
\end_inset
+\emph default
+
\shape italic
- is the radial profile of density,
+\emph on
+is the radial profile of density,
\shape default
-
\emph default
-
+
\begin_inset Formula $\bar{T_{a}}$
\end_inset
- is the radial profile
-\emph on
-
-\emph default
-of adiabatic temperature,
-\emph on
-
-\emph default
-
+ is the radial profile of adiabatic temperature,
\begin_inset Formula $\delta\rho_{ph}$
\end_inset
@@ -926,10 +965,16 @@
\begin_inset Formula $\Gamma$
\end_inset
+
+\emph default
\shape italic
-is the phase function, and
+\emph on
+is the phase function, and
\shape default
+\emph default
+
+\emph on
C
\emph default
is the composition.
@@ -956,9 +1001,9 @@
\begin_inset Formula $T_{ph}$
\end_inset
- are the ambient depth and temperature of a phase change,
+ are the ambient depth and temperature of a phase change,
\emph on
- s
+s
\emph default
is the Clapeyron slope of a phase change, and
\begin_inset Formula $w_{ph}$
@@ -1169,20 +1214,23 @@
\begin_layout Standard
The governing equations are solved with the finite element method
-\begin_inset LatexCommand \cite{Hughes The Finite Element Method}
+\begin_inset LatexCommand cite
+key "Hughes The Finite Element Method"
\end_inset
.
CitComS employs an Uzawa algorithm to solve the momentum equation coupled
with the incompressibility constraints
-\begin_inset LatexCommand \cite{Moresi/Gurnis Contraints,Ramage/Wathen Iterative solution}
+\begin_inset LatexCommand cite
+key "Moresi/Gurnis Contraints,Ramage/Wathen Iterative solution"
\end_inset
.
The energy equation is solved with a Petrov-Galerkin method
-\begin_inset LatexCommand \cite{Brooks A.N.}
+\begin_inset LatexCommand cite
+key "Brooks A.N."
\end_inset
@@ -1192,23 +1240,27 @@
The use of brick elements in 3D (or rectangular elements in 2D) is important
for accurately determining the pressure, such as dynamic topography, in
incompressible Stokes flow
-\begin_inset LatexCommand \cite{Hughes The Finite Element Method}
+\begin_inset LatexCommand cite
+key "Hughes The Finite Element Method"
\end_inset
.
The discrete form of Equations
-\begin_inset LatexCommand \ref{eq:non-dimensional continuity eqn}
+\begin_inset LatexCommand ref
+reference "eq:non-dimensional continuity eqn"
\end_inset
and
-\begin_inset LatexCommand \ref{eq:non-dimensional momentum eqn}
+\begin_inset LatexCommand ref
+reference "eq:non-dimensional momentum eqn"
\end_inset
may be written in the following matrix form
-\begin_inset LatexCommand \cite{Zhong et al The role of temperature}
+\begin_inset LatexCommand cite
+key "Zhong et al The role of temperature"
\end_inset
@@ -1254,7 +1306,8 @@
\end_inset
is the second term in equation
-\begin_inset LatexCommand \ref{eq:non-dimensional continuity eqn}
+\begin_inset LatexCommand ref
+reference "eq:non-dimensional continuity eqn"
\end_inset
@@ -1264,9 +1317,9 @@
\emph default
is a vector of unknown pressures, and
\emph on
-f
+f
\emph default
-is a vector composed of the body and boundary forces acting on the fluid.
+ is a vector composed of the body and boundary forces acting on the fluid.
The individual entries of
\begin_inset Formula $\mathbf{A}$
\end_inset
@@ -1284,7 +1337,8 @@
f
\emph default
are obtained using a standard finite element formulation, see
-\begin_inset LatexCommand \cite{Zhong et al The role of temperature}
+\begin_inset LatexCommand cite
+key "Zhong et al The role of temperature"
\end_inset
@@ -1299,7 +1353,8 @@
is zero.
Equation
-\begin_inset LatexCommand \ref{eq:discrete momentum eqn}
+\begin_inset LatexCommand ref
+reference "eq:discrete momentum eqn"
\end_inset
@@ -1308,7 +1363,8 @@
\end_inset
and using equation
-\begin_inset LatexCommand \ref{eq:discrete continuite eqn}
+\begin_inset LatexCommand ref
+reference "eq:discrete continuite eqn"
\end_inset
@@ -1329,13 +1385,15 @@
\noindent
This equation is solved using the Uzawa algorithm, an established method
for solving the minimization of a dual function
-\begin_inset LatexCommand \cite{Cahouet/Chabard Some fast 3D}
+\begin_inset LatexCommand cite
+key "Cahouet/Chabard Some fast 3D"
\end_inset
, which simultaneously yields the velocity field.
A conjugate gradient scheme
-\begin_inset LatexCommand \cite{Ramage/Wathen Iterative solution,Atanga/Silvester Iterative methods}
+\begin_inset LatexCommand cite
+key "Ramage/Wathen Iterative solution,Atanga/Silvester Iterative methods"
\end_inset
@@ -1346,19 +1404,22 @@
\begin_layout Standard
In the compressible case, there are two different strategies to solve Equation
-\begin_inset LatexCommand \ref{eq:discrete continuite eqn}
+\begin_inset LatexCommand ref
+reference "eq:discrete continuite eqn"
\end_inset
and
-\begin_inset LatexCommand \ref{eq:discrete momentum eqn}
+\begin_inset LatexCommand ref
+reference "eq:discrete momentum eqn"
\end_inset
.
The first strategy is to add another layer of iterations when solving Equation
-\begin_inset LatexCommand \ref{eq:cg}
+\begin_inset LatexCommand ref
+reference "eq:cg"
\end_inset
@@ -1381,7 +1442,8 @@
This equation can be solved using the same conjugate gradient scheme as
the incompressible case.
The second strategy is to transform Equation
-\begin_inset LatexCommand \ref{eq:discrete momentum eqn}
+\begin_inset LatexCommand ref
+reference "eq:discrete momentum eqn"
\end_inset
@@ -1390,7 +1452,8 @@
\end_inset
and using Equation
-\begin_inset LatexCommand \ref{eq:discrete continuite eqn}
+\begin_inset LatexCommand ref
+reference "eq:discrete continuite eqn"
\end_inset
@@ -1457,7 +1520,8 @@
\emph default
are in units of radians.
Figure
-\begin_inset LatexCommand \ref{fig:Global-Node-Numbering.}
+\begin_inset LatexCommand ref
+reference "fig:Global-Node-Numbering."
\end_inset
@@ -1498,9 +1562,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Global-Node-Numbering.}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Global-Node-Numbering."
+
\end_inset
Global Node Numbering.
@@ -1528,13 +1596,19 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
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
-\begin_inset LatexCommand \ref{fig:Topological-connectivity-of}
+\begin_inset LatexCommand ref
+reference "fig:Topological-connectivity-of"
\end_inset
@@ -1561,9 +1635,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Topological-connectivity-of}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Topological-connectivity-of"
+
\end_inset
Topological connectivity of the 12 caps.
@@ -1576,11 +1654,17 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\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.
The four corners of the domain are connected by great circles (Figure
-\begin_inset LatexCommand \ref{fig:Orthographic-projection-of}
+\begin_inset LatexCommand ref
+reference "fig:Orthographic-projection-of"
\end_inset
@@ -1589,7 +1673,8 @@
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{fig:Orthographic-projection-of}
+\begin_inset LatexCommand ref
+reference "fig:Orthographic-projection-of"
\end_inset
@@ -1618,9 +1703,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Orthographic-projection-of}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Orthographic-projection-of"
+
\end_inset
Orthographic projection of processors from a full CitComS mesh in which
@@ -1644,6 +1733,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Chapter
Installation and Getting Help
\end_layout
@@ -1660,7 +1754,9 @@
tar
\family default
file) available at the
-\begin_inset LatexCommand \htmlurl[Geodynamics Software Packages web page]{www.geodynamics.org/cig/software/packages}
+\begin_inset LatexCommand htmlurl
+name "Geodynamics Software Packages web page"
+target "www.geodynamics.org/cig/software/packages"
\end_inset
@@ -1679,7 +1775,8 @@
Advanced users and software developers may be interested in downloading
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{sec:Software-Repository}
+\begin_inset LatexCommand ref
+reference "sec:Software-Repository"
\end_inset
@@ -1697,14 +1794,18 @@
\begin_layout Standard
For help, send e-mail to the
-\begin_inset LatexCommand \htmlurl[CIG Mantle Convection Mailing List]{cig-mc at geodynamics.org}
+\begin_inset LatexCommand htmlurl
+name "CIG Mantle Convection Mailing List"
+target "cig-mc at geodynamics.org"
\end_inset
.
You can subscribe to the Mailing List and view archived discussion at the
-\begin_inset LatexCommand \htmlurl[Geodynamics Mail Lists web page]{www.geodynamics.org/cig/lists}
+\begin_inset LatexCommand htmlurl
+name "Geodynamics Mail Lists web page"
+target "www.geodynamics.org/cig/lists"
\end_inset
@@ -1756,7 +1857,8 @@
, and forgo use of Python and the Pyre framework.
This process requires only a C compiler and an MPI library.
For more information, see Section
-\begin_inset LatexCommand \ref{sec:Installing-without-Pyre}
+\begin_inset LatexCommand ref
+reference "sec:Installing-without-Pyre"
\end_inset
@@ -1767,14 +1869,16 @@
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
-\begin_inset LatexCommand \ref{sec:Exchanger-Configuration-(Optional)}
+\begin_inset LatexCommand ref
+reference "sec:Exchanger-Configuration-(Optional)"
\end_inset
.
Optionally, CitComS can be configured to use a parallel HDF5 library.
See Section
-\begin_inset LatexCommand \vref{sec:HDF5-Configuration}
+\begin_inset LatexCommand vref
+reference "sec:HDF5-Configuration"
\end_inset
@@ -1820,7 +1924,9 @@
The Mac OS X version of GCC is included in a software development suite
called Xcode.
Xcode is available as a free download at the
-\begin_inset LatexCommand \htmlurl[Apple Developer Connection]{developer.apple.com}
+\begin_inset LatexCommand htmlurl
+name "Apple Developer Connection"
+target "developer.apple.com"
\end_inset
@@ -1831,19 +1937,33 @@
\color red
Warning:
+\color none
+
\color black
- If you are using an Intel compiler on an Itanium CPU, do not use the
+If you are using an Intel compiler on an Itanium CPU, do not use the
+\color none
+
\family typewriter
+\color black
-O3
\family default
- optimization flag as reports indicate that this optimization level will
+\color none
+
+\color black
+optimization flag as reports indicate that this optimization level will
generate incorrect codes.
For any compiler, you should always be careful about the correctness of
- the compiled codes when using an
+ the compiled codes when using an
+\color none
+
\family typewriter
+\color black
-O3
\family default
- or higher optimization level.
+\color none
+
+\color black
+or higher optimization level.
\end_layout
\begin_layout Subsection
@@ -1858,7 +1978,9 @@
\begin_layout Standard
A popular choice is
-\begin_inset LatexCommand \htmlurl[MPICH]{www-unix.mcs.anl.gov/mpi/mpich}
+\begin_inset LatexCommand htmlurl
+name "MPICH"
+target "www-unix.mcs.anl.gov/mpi/mpich"
\end_inset
@@ -1874,12 +1996,16 @@
\begin_layout Standard
Linux users may have a prebuilt MPI package available for their distribution.
On Mac OS X, the Fink package manager offers a prepackaged version of
-\begin_inset LatexCommand \htmlurl[LAM/MPI]{www.lam-mpi.org}
+\begin_inset LatexCommand htmlurl
+name "LAM/MPI"
+target "www.lam-mpi.org"
\end_inset
; so if you have
-\begin_inset LatexCommand \htmlurl[Fink]{fink.sourceforge.net}
+\begin_inset LatexCommand htmlurl
+name "Fink"
+target "fink.sourceforge.net"
\end_inset
@@ -1929,7 +2055,9 @@
Mac OS X 10.3 and later ships with a suitable version of Python preinstalled.
If you're using an older version of Mac OS X, or for more information in
general, see
-\begin_inset LatexCommand \htmlurl[Python on the Mac]{www.python.org/download/mac}
+\begin_inset LatexCommand htmlurl
+name "Python on the Mac"
+target "www.python.org/download/mac"
\end_inset
@@ -2034,7 +2162,9 @@
If absolutely necessary, one can easily build Python from source using a
C compiler.
You can download Python from the
-\begin_inset LatexCommand \htmlurl[Python website]{www.python.org}
+\begin_inset LatexCommand htmlurl
+name "Python website"
+target "www.python.org"
\end_inset
@@ -2048,7 +2178,9 @@
\begin_layout Standard
Download CitComS.py from the
-\begin_inset LatexCommand \htmlurl[Geodynamics website]{www.geodynamics.org}
+\begin_inset LatexCommand htmlurl
+name "Geodynamics website"
+target "www.geodynamics.org"
\end_inset
@@ -2170,7 +2302,8 @@
configure
\family default
, see Section
-\begin_inset LatexCommand \ref{sec:Configuration}
+\begin_inset LatexCommand ref
+reference "sec:Configuration"
\end_inset
@@ -2308,7 +2441,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Configuration}
+\begin_inset LatexCommand label
+name "sec:Configuration"
\end_inset
@@ -2381,7 +2515,9 @@
configure
\family default
failures on the
-\begin_inset LatexCommand \htmlurl[CIG Mantle Convection Mailing List]{cig-mc at geodynamics.org}
+\begin_inset LatexCommand htmlurl
+name "CIG Mantle Convection Mailing List"
+target "cig-mc at geodynamics.org"
\end_inset
@@ -2614,7 +2750,8 @@
C compiler command.
This is usually set to the name of an MPI wrapper command.
See Section
-\begin_inset LatexCommand \vref{sec:MPI-Configuration}
+\begin_inset LatexCommand vref
+reference "sec:MPI-Configuration"
\end_inset
@@ -2685,7 +2822,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand \label{sec:MPI-Configuration}
+\begin_inset LatexCommand label
+name "sec:MPI-Configuration"
\end_inset
@@ -2702,9 +2840,9 @@
PATH
\family default
environment variable.
- It prefers MPI wrapper commands (such as
+ It prefers MPI wrapper commands (such as
\family typewriter
- mpicc
+mpicc
\family default
) to ordinary compiler commands (such as
\family typewriter
@@ -2871,7 +3009,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Exchanger-Configuration-(Optional)}
+\begin_inset LatexCommand label
+name "sec:Exchanger-Configuration-(Optional)"
\end_inset
@@ -2882,14 +3021,17 @@
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{Tan et al GeoFramework Part I}
+\begin_inset LatexCommand cite
+key "Tan et al GeoFramework Part I"
\end_inset
.
An external Exchanger package is needed for solver coupling.
You can download Exchanger at
-\begin_inset LatexCommand \htmlurl[CIG's Exchanger web page]{geodynamics.org/cig/software/packages/cs/exchanger}
+\begin_inset LatexCommand htmlurl
+name "CIG's Exchanger web page"
+target "geodynamics.org/cig/software/packages/cs/exchanger"
\end_inset
@@ -2935,7 +3077,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:HDF5-Configuration}
+\begin_inset LatexCommand label
+name "sec:HDF5-Configuration"
\end_inset
@@ -3003,7 +3146,9 @@
NumPy is an extension to Python which adds support for multi-dimensional
arrays for use in scientific computing.
You may download NumPy from the
-\begin_inset LatexCommand \htmlurl[NumPy home page]{numpy.scipy.org}
+\begin_inset LatexCommand htmlurl
+name "NumPy home page"
+target "numpy.scipy.org"
\end_inset
@@ -3034,7 +3179,8 @@
\end_layout
\begin_layout Subsubsection
-\begin_inset LatexCommand \label{sub:PyTables}
+\begin_inset LatexCommand label
+name "sub:PyTables"
\end_inset
@@ -3045,7 +3191,9 @@
PyTables is an extension to Python and can expose HDF5 array datasets as
Python NumPy arrays.
It is available at
-\begin_inset LatexCommand \htmlurl[PyTables]{www.pytables.org}
+\begin_inset LatexCommand htmlurl
+name "PyTables"
+target "www.pytables.org"
\end_inset
@@ -3085,7 +3233,9 @@
\begin_layout Standard
HDFView is a visual tool written in Java for browsing and editing HDF5 files.
You may download it from the
-\begin_inset LatexCommand \htmlurl[HDFView home page]{hdf.ncsa.uiuc.edu/hdf-java-html/hdfview}
+\begin_inset LatexCommand htmlurl
+name "HDFView home page"
+target "hdf.ncsa.uiuc.edu/hdf-java-html/hdfview"
\end_inset
@@ -3093,7 +3243,8 @@
\end_layout
\begin_layout Subsubsection
-\begin_inset LatexCommand \label{sub:OpenDXutils}
+\begin_inset LatexCommand label
+name "sub:OpenDXutils"
\end_inset
@@ -3104,7 +3255,9 @@
In order to import HDF5 files into OpenDX, you need the OpenDXutils package
from the Cactus project.
Go to the
-\begin_inset LatexCommand \url[OpenDXutils package website]{www.cactuscode.org/Visualization/openDX}
+\begin_inset LatexCommand url
+name "OpenDXutils package website"
+target "www.cactuscode.org/Visualization/openDX"
\end_inset
@@ -3121,7 +3274,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Batch-System-Configuration}
+\begin_inset LatexCommand label
+name "sec:Batch-System-Configuration"
\end_inset
@@ -3166,14 +3320,17 @@
\begin_layout Standard
For more information on configuring Pyre for your batch system, see CIG's
-\begin_inset LatexCommand \htmlurl[Pythia page]{www.geodynamics.org/cig/software/packages/cs/pythia}
+\begin_inset LatexCommand htmlurl
+name "Pythia page"
+target "www.geodynamics.org/cig/software/packages/cs/pythia"
\end_inset
.
For more information on batch system configuration as it pertains to running
CitComS, see Section
-\begin_inset LatexCommand \vref{sub:Launchers-and-Schedulers}
+\begin_inset LatexCommand vref
+reference "sub:Launchers-and-Schedulers"
\end_inset
@@ -3181,7 +3338,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Installing-without-Pyre}
+\begin_inset LatexCommand label
+name "sec:Installing-without-Pyre"
\end_inset
@@ -3210,9 +3368,9 @@
a C compiler.
The
\family typewriter
-make
+make
\family default
-command will build two command-line tools,
+ command will build two command-line tools,
\family typewriter
CitcomSFull
\family default
@@ -3224,7 +3382,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Software-Repository}
+\begin_inset LatexCommand label
+name "sec:Software-Repository"
\end_inset
@@ -3233,7 +3392,9 @@
\begin_layout Standard
The CitComS source code is available via a Subversion server at the
-\begin_inset LatexCommand \htmlurl[Geodynamics website]{www.geodynamics.org}
+\begin_inset LatexCommand htmlurl
+name "Geodynamics website"
+target "www.geodynamics.org"
\end_inset
@@ -3245,9 +3406,10 @@
\begin_layout Quote
\series bold
-NOTE:
+NOTE:
\series default
-If you are content with the prepared source package, you may skip this section.
+ If you are content with the prepared source package, you may skip this
+ section.
\end_layout
\begin_layout Subsection
@@ -3279,7 +3441,9 @@
\begin_layout Standard
For more information on Subversion, visit the
-\begin_inset LatexCommand \htmlurl[Subversion website]{subversion.tigris.org}
+\begin_inset LatexCommand htmlurl
+name "Subversion website"
+target "subversion.tigris.org"
\end_inset
@@ -3305,7 +3469,9 @@
\begin_layout Standard
For more information about these GNU tools, see the
-\begin_inset LatexCommand \htmlurl[GNU website]{www.gnu.org/software}
+\begin_inset LatexCommand htmlurl
+name "GNU website"
+target "www.gnu.org/software"
\end_inset
@@ -3568,7 +3734,8 @@
\family default
directories, respectively.
The meaning of the input parameters is described in Appendix
-\begin_inset LatexCommand \vref{cha:Appendix-A:-Input}
+\begin_inset LatexCommand vref
+reference "cha:Appendix-A:-Input"
\end_inset
@@ -3603,7 +3770,8 @@
will run a regional model with default parameters.
It can also run a full spherical model if the correct parameters are set
(see Section
-\begin_inset LatexCommand \vref{sec:Cookbook-1:-Global}
+\begin_inset LatexCommand vref
+reference "sec:Cookbook-1:-Global"
\end_inset
@@ -3613,7 +3781,8 @@
\begin_layout Standard
On input, CitComS.py needs numerous parameters to be specified (see Appendix
-\begin_inset LatexCommand \vref{cha:Appendix-A:-Input}
+\begin_inset LatexCommand vref
+reference "cha:Appendix-A:-Input"
\end_inset
@@ -3631,7 +3800,8 @@
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{cha:Appendix-A:-Input}
+\begin_inset LatexCommand vref
+reference "cha:Appendix-A:-Input"
\end_inset
@@ -3985,7 +4155,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Multiprocessor-Example}
+\begin_inset LatexCommand label
+name "sec:Multiprocessor-Example"
\end_inset
@@ -4154,7 +4325,10 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Computational Domain.
Map view on the configuration of the top layer of the computational nodes
and the processors.
@@ -4165,6 +4339,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Output Directories and Output Formats
\end_layout
@@ -4442,7 +4621,8 @@
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
HDF5 library if you haven't done so already (see Section
-\begin_inset LatexCommand \vref{sec:HDF5-Configuration}
+\begin_inset LatexCommand vref
+reference "sec:HDF5-Configuration"
\end_inset
@@ -4473,19 +4653,20 @@
\emph on
username
\emph default
-/
+/
\family default
-with a filename prefix
+ with a filename prefix
\family typewriter
-example1
+example1
\family default
-and a filename suffix
+ and a filename suffix
\family typewriter
h5
\family default
.
See Chapter
-\begin_inset LatexCommand \vref{cha:Working-with-HDF5}
+\begin_inset LatexCommand vref
+reference "cha:Working-with-HDF5"
\end_inset
@@ -4493,7 +4674,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand \label{sub:Launchers-and-Schedulers}
+\begin_inset LatexCommand label
+name "sub:Launchers-and-Schedulers"
\end_inset
@@ -4761,9 +4943,9 @@
\begin_layout Quote
\color red
-Warning:
+Warning:
\color none
-This assumes your machine list has enough nodes for the simulation in question.
+ This assumes your machine list has enough nodes for the simulation in question.
\end_layout
\begin_layout Standard
@@ -4858,7 +5040,8 @@
The time file contains the elapsed model time (in non-dimensional units)
and CPU time (in seconds) of every time step.
The format of the time file can be found in Appendix
-\begin_inset LatexCommand \vref{cha:Appendix-C:-CitComS,}
+\begin_inset LatexCommand vref
+reference "cha:Appendix-C:-CitComS,"
\end_inset
@@ -4871,7 +5054,8 @@
Following your successful run, you will want to retrieve the output files
from all the nodes and process them so they can be visualized with the
visualization program OpenDX (see Chapter
-\begin_inset LatexCommand \vref{cha:Postprocessing-and-Graphics}
+\begin_inset LatexCommand vref
+reference "cha:Postprocessing-and-Graphics"
\end_inset
@@ -4921,7 +5105,9 @@
\family default
.
See
-\begin_inset LatexCommand \htmlurl[CIG Community Area Software on the TeraGrid]{www.geodynamics.org/cig/software/csa/}
+\begin_inset LatexCommand htmlurl
+name "CIG Community Area Software on the TeraGrid"
+target "www.geodynamics.org/cig/software/csa/"
\end_inset
@@ -4929,7 +5115,8 @@
\end_layout
\begin_layout Chapter
-\begin_inset LatexCommand \label{cha:Working-with-HDF5}
+\begin_inset LatexCommand label
+name "cha:Working-with-HDF5"
\end_inset
@@ -4945,7 +5132,8 @@
files.
This situation is inefficient since it requires an extra post-processing
step for assembling the results from each processor (see Chapter
-\begin_inset LatexCommand \vref{cha:Postprocessing-and-Graphics}
+\begin_inset LatexCommand vref
+reference "cha:Postprocessing-and-Graphics"
\end_inset
@@ -4963,7 +5151,9 @@
\begin_layout Standard
The Hierarchical Data Format (HDF) is a portable file format developed at
the
-\begin_inset LatexCommand \htmlurl[National Center for Supercomputing Applications (NCSA)]{hdf.ncsa.uiuc.edu/HDF5}
+\begin_inset LatexCommand htmlurl
+name "National Center for Supercomputing Applications (NCSA)"
+target "hdf.ncsa.uiuc.edu/HDF5"
\end_inset
@@ -5209,7 +5399,9 @@
\begin_layout Itemize
\series bold
-\begin_inset LatexCommand \htmlurl[MPI-2: Extensions to the Message-Passing Interface, section 9.2.8]{www-unix.mcs.anl.gov/mpi/mpi-standard/mpi-report-2.0/node182.htm}
+\begin_inset LatexCommand htmlurl
+name "MPI-2: Extensions to the Message-Passing Interface, section 9.2.8"
+target "www-unix.mcs.anl.gov/mpi/mpi-standard/mpi-report-2.0/node182.htm"
\end_inset
@@ -5222,7 +5414,9 @@
\begin_layout Itemize
\series bold
-\begin_inset LatexCommand \htmlurl[HDF5 documentation]{hdf.ncsa.uiuc.edu/HDF5/doc/UG/08_TheFile.html}
+\begin_inset LatexCommand htmlurl
+name "HDF5 documentation"
+target "hdf.ncsa.uiuc.edu/HDF5/doc/UG/08_TheFile.html"
\end_inset
@@ -5234,7 +5428,9 @@
\begin_layout Itemize
\series bold
-\begin_inset LatexCommand \htmlurl[HDF5 User's Guide: Data Caching]{hdf.ncsa.uiuc.edu/HDF5/doc/Caching.html}
+\begin_inset LatexCommand htmlurl
+name "HDF5 User's Guide: Data Caching"
+target "hdf.ncsa.uiuc.edu/HDF5/doc/Caching.html"
\end_inset
@@ -5282,7 +5478,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Data-Layout}
+\begin_inset LatexCommand label
+name "sec:Data-Layout"
\end_inset
@@ -5468,7 +5665,10 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Layout of the time-independent data file
\end_layout
@@ -5477,6 +5677,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
\noindent
\align center
@@ -5659,7 +5864,8 @@
(8)
\family default
See Section
-\begin_inset LatexCommand \vref{sub:Geoid-Output-(test-case.geoid.10)}
+\begin_inset LatexCommand vref
+reference "sub:Geoid-Output-(test-case.geoid.10)"
\end_inset
@@ -5892,7 +6098,10 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Layout of the time-dependent data file
\end_layout
@@ -5901,6 +6110,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
Accessing Data
\end_layout
@@ -5940,7 +6154,8 @@
\begin_layout Standard
You can convert the HDF5 files to the ASCII combined capfiles described
in
-\begin_inset LatexCommand \ref{sec:ASCII-Output}
+\begin_inset LatexCommand ref
+reference "sec:ASCII-Output"
\end_inset
@@ -5953,7 +6168,8 @@
\begin_layout Standard
You can also convert the HDF5 files to the velo files described in
-\begin_inset LatexCommand \vref{sub:Velocity-and-Temperature}
+\begin_inset LatexCommand vref
+reference "sub:Velocity-and-Temperature"
\end_inset
@@ -6040,12 +6256,16 @@
\begin_layout Standard
For more details, refer to the documentation for
-\begin_inset LatexCommand \htmlurl[PyTables]{www.pytables.org}
+\begin_inset LatexCommand htmlurl
+name "PyTables"
+target "www.pytables.org"
\end_inset
and
-\begin_inset LatexCommand \htmlurl[NumPy]{numpy.scipy.org}
+\begin_inset LatexCommand htmlurl
+name "NumPy"
+target "numpy.scipy.org"
\end_inset
@@ -6065,12 +6285,14 @@
with navigation arrow buttons that enable you to range over the entire
extent of a third dimension.
An example of using HDFView is found in Figure
-\begin_inset LatexCommand \ref{fig:A-screenshot-of}
+\begin_inset LatexCommand ref
+reference "fig:A-screenshot-of"
\end_inset
which uses data from Cookbook 1 in Section
-\begin_inset LatexCommand \vref{sec:Cookbook-1:-Global}
+\begin_inset LatexCommand vref
+reference "sec:Cookbook-1:-Global"
\end_inset
@@ -6099,9 +6321,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:A-screenshot-of}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:A-screenshot-of"
+
\end_inset
A screenshot of HDFView.
@@ -6116,8 +6342,14 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Chapter
-\begin_inset LatexCommand \label{cha:Postprocessing-and-Graphics}
+\begin_inset LatexCommand label
+name "cha:Postprocessing-and-Graphics"
\end_inset
@@ -6137,7 +6369,9 @@
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[OpenDX website]{www.opendx.org}
+\begin_inset LatexCommand htmlurl
+name "OpenDX website"
+target "www.opendx.org"
\end_inset
@@ -6152,21 +6386,25 @@
\family default
in your distribution.
If you are using Mac OS X, OpenDX is available via
-\begin_inset LatexCommand \htmlurl[Fink]{fink.sourceforge.net}
+\begin_inset LatexCommand htmlurl
+name "Fink"
+target "fink.sourceforge.net"
\end_inset
.
We provide experimental scripts for a 3D visualization program called MayaVi2;
see Section
-\begin_inset LatexCommand \vref{sec:Using-MayaVi-for}
+\begin_inset LatexCommand vref
+reference "sec:Using-MayaVi-for"
\end_inset
.
Scripts using GMT commands to plot 2D cross sections of temperature field
are also provided; see Section
-\begin_inset LatexCommand \vref{sec:Using-GMT-Commands}
+\begin_inset LatexCommand vref
+reference "sec:Using-GMT-Commands"
\end_inset
@@ -6227,7 +6465,8 @@
\family default
files; you can visualize the results using OpenDX.
See Section
-\begin_inset LatexCommand \vref{sec:Using-OpenDX-for-HDF5}
+\begin_inset LatexCommand vref
+reference "sec:Using-OpenDX-for-HDF5"
\end_inset
@@ -6388,7 +6627,8 @@
\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{cha:Appendix-C:-CitComS,}
+\begin_inset LatexCommand vref
+reference "cha:Appendix-C:-CitComS,"
\end_inset
@@ -6489,11 +6729,8 @@
\end_deeper
\begin_layout Enumerate
-Click
-\series bold
-
+Click
\family sans
-\series default
Edit Visual Programs
\family default
and select
@@ -6551,9 +6788,7 @@
\end_deeper
\begin_layout Enumerate
-In the pull-down menu, select
-\family typewriter
-
+In the pull-down menu, select
\family sans
Execute\SpecialChar \menuseparator
Execute on Change
@@ -6596,7 +6831,10 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Regional Model Visualized with OpenDX.
A snapshot of an upwelling (blue isosurface) with a slice of the temperature
field (bisecting plane).
@@ -6607,6 +6845,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
Additional options in the control panel window for the regional model include:
\end_layout
@@ -6706,11 +6949,8 @@
\family sans
Visual Program Editor
\family default
-\series bold
+ window.
-\series default
-window.
-
\end_layout
\begin_layout Enumerate
@@ -6729,11 +6969,8 @@
block, which will open a
\family sans
Control Panel
-\series bold
-
\family default
-\series default
-window.
+ window.
\end_layout
@@ -6773,9 +7010,7 @@
\end_deeper
\begin_layout Enumerate
-In the pull-down menu, select
-\family typewriter
-
+In the pull-down menu, select
\family sans
Execute\SpecialChar \menuseparator
Execute on Change
@@ -6854,7 +7089,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Using-OpenDX-for-HDF5}
+\begin_inset LatexCommand label
+name "sec:Using-OpenDX-for-HDF5"
\end_inset
@@ -6869,7 +7105,8 @@
), you can directly visualize the data without postprocessing.
First, you need to install and set up the OpenDXutils package (see Section
-\begin_inset LatexCommand \vref{sub:OpenDXutils}
+\begin_inset LatexCommand vref
+reference "sub:OpenDXutils"
\end_inset
@@ -6887,9 +7124,7 @@
\end_layout
\begin_layout Enumerate
-In the pull-down menu, select
-\family typewriter
-
+In the pull-down menu, select
\family sans
File\SpecialChar \menuseparator
Load Macro,
@@ -6916,7 +7151,8 @@
Macros
\family default
category (highlighted in Figure
-\begin_inset LatexCommand \ref{fig:Import-CitComS.py-HDF5}
+\begin_inset LatexCommand ref
+reference "fig:Import-CitComS.py-HDF5"
\end_inset
@@ -6927,7 +7163,8 @@
\begin_layout Enumerate
Place the module in the work space and rewire the network as shown in Figure
-\begin_inset LatexCommand \ref{fig:Import-CitComS.py-HDF5}
+\begin_inset LatexCommand ref
+reference "fig:Import-CitComS.py-HDF5"
\end_inset
@@ -6953,9 +7190,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Import-CitComS.py-HDF5}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Import-CitComS.py-HDF5"
+
\end_inset
How to import CitComS.py HDF5 data.
@@ -6971,6 +7212,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Enumerate
There are four input tabs in the
\family sans
@@ -6996,9 +7242,9 @@
\end_layout
\begin_layout Enumerate
-The second tab (connected to the right
+The second tab (connected to the right
\family sans
- FileSelector
+FileSelector
\family default
module) specifies the HDF5 file containing time-dependent information (e.g.,
@@ -7052,7 +7298,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Using-MayaVi-for}
+\begin_inset LatexCommand label
+name "sec:Using-MayaVi-for"
\end_inset
@@ -7067,23 +7314,30 @@
MayaVi2 relies on the Visualization Toolkit (VTK) and allows easy scripting
in Python.
To install MayaVi2, you should follow the instructions on the
-\begin_inset LatexCommand \htmlurl[MayaVi2 website]{https://svn.enthought.com/enthought/wiki/GrabbingAndBuilding}
+\begin_inset LatexCommand htmlurl
+name "MayaVi2 website"
+target "https://svn.enthought.com/enthought/wiki/GrabbingAndBuilding"
\end_inset
and on the
-\begin_inset LatexCommand \htmlurl[SciPy website]{www.scipy.org/Cookbook/MayaVi/Installation}
+\begin_inset LatexCommand htmlurl
+name "SciPy website"
+target "www.scipy.org/Cookbook/MayaVi/Installation"
\end_inset
.
Besides MayaVi2, you will need to install PyTables (see Section
-\begin_inset LatexCommand \vref{sub:PyTables}
+\begin_inset LatexCommand vref
+reference "sub:PyTables"
\end_inset
) and PyVTK (see
-\begin_inset LatexCommand \htmlurl[PyVTK website]{cens.ioc.ee/projects/pyvtk}
+\begin_inset LatexCommand htmlurl
+name "PyVTK website"
+target "cens.ioc.ee/projects/pyvtk"
\end_inset
@@ -7132,7 +7386,8 @@
\family default
.
An example of using this script is found in Figure
-\begin_inset LatexCommand \ref{fig:Example-MayaVi2-visualization}
+\begin_inset LatexCommand ref
+reference "fig:Example-MayaVi2-visualization"
\end_inset
@@ -7144,7 +7399,9 @@
The Visualization Toolkit User's Guide
\shape default
(ISBN 1-930934-13-0) or see the
-\begin_inset LatexCommand \htmlurl[VTK website]{www.vtk.org}
+\begin_inset LatexCommand htmlurl
+name "VTK website"
+target "www.vtk.org"
\end_inset
@@ -7173,9 +7430,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Example-MayaVi2-visualization}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Example-MayaVi2-visualization"
+
\end_inset
Example MayaVi2 visualization of
@@ -7195,8 +7456,14 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Using-GMT-Commands}
+\begin_inset LatexCommand label
+name "sec:Using-GMT-Commands"
\end_inset
@@ -7296,7 +7563,10 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Temperature field generated by
\family typewriter
plot_layer.py
@@ -7323,6 +7593,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
The usage of
\family typewriter
@@ -7366,7 +7641,10 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Temperature fields generated by
\family typewriter
plot_annulus.py
@@ -7403,6 +7681,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Chapter
Cookbooks
\end_layout
@@ -7423,7 +7706,8 @@
directory.
However, you might need to edit these example scripts slightly to launch
the job on your cluster (see Section
-\begin_inset LatexCommand \vref{sec:Multiprocessor-Example}
+\begin_inset LatexCommand vref
+reference "sec:Multiprocessor-Example"
\end_inset
@@ -7431,7 +7715,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Cookbook-1:-Global}
+\begin_inset LatexCommand label
+name "sec:Cookbook-1:-Global"
\end_inset
@@ -7470,7 +7755,10 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\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.
Right (B): The temperature field at 1081 km depth from a Cookbook 1 run.
@@ -7481,6 +7769,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Solution
\end_layout
@@ -7627,7 +7920,10 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Cookbook 1: Global Model.
This image, created by OpenDX, depicts a slice through a spherical model
of convection, with warmer colors indicating upwelling and the cooler colors
@@ -7639,6 +7935,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Discussion
\end_layout
@@ -7757,7 +8058,8 @@
facility allows you to impose a uniform velocity across the top surface.
You have a velocity which is purely in the colatitude direction with a
non-dimensional velocity of 100 (see Equation
-\begin_inset LatexCommand \vref{eq:u dim}
+\begin_inset LatexCommand vref
+reference "eq:u dim"
\end_inset
@@ -7891,7 +8193,8 @@
\begin_layout Standard
Using OpenDX to visualize the results (Figure
-\begin_inset LatexCommand \ref{fig:Cookbook-2:-Velocity}
+\begin_inset LatexCommand ref
+reference "fig:Cookbook-2:-Velocity"
\end_inset
@@ -7922,9 +8225,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Cookbook-2:-Velocity}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Cookbook-2:-Velocity"
+
\end_inset
Cookbook 2: Velocity Boundary Conditions.
@@ -7938,6 +8245,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
Cookbook 3: Temperature-Dependent Viscosity
\end_layout
@@ -8159,7 +8471,10 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Cookbook 3: Temperature-Dependent Viscosity.
This model, visualized with OpenDX, highlights a region that features both
the heated upwelling (warm colors) and the even distribution of the velocities
@@ -8171,6 +8486,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
Cookbook 4: Regionally Refined Meshes
\end_layout
@@ -8215,7 +8535,8 @@
\family default
).
The format of the coordinate input file is described in Appendix
-\begin_inset LatexCommand \vref{sec:Coordinate-files}
+\begin_inset LatexCommand vref
+reference "sec:Coordinate-files"
\end_inset
@@ -8381,7 +8702,10 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Cookbook 4: Regionally Refined Mesher.
This model shows the temperature (upwelling -- warm colors, downwelling
-- cool colors) and the uneven distribution of the velocities (yellow arrows).
@@ -8393,6 +8717,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Discussion
\end_layout
@@ -8444,7 +8773,8 @@
The following scenario is proposed for this cookbook: there are two plates
centered along the equator, with two different Euler poles (see Figure
-\begin_inset LatexCommand \ref{fig:Cookbook-5:-Left}
+\begin_inset LatexCommand ref
+reference "fig:Cookbook-5:-Left"
\end_inset
@@ -8491,7 +8821,8 @@
\family default
).
The format of the velocity file is described in Appendix
-\begin_inset LatexCommand \vref{sec:Velocity-boundary-condition}
+\begin_inset LatexCommand vref
+reference "sec:Velocity-boundary-condition"
\end_inset
@@ -8507,7 +8838,8 @@
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,
as described in Appendix
-\begin_inset LatexCommand \vref{sub:Velocity-and-Temperature}
+\begin_inset LatexCommand vref
+reference "sub:Velocity-and-Temperature"
\end_inset
@@ -8564,9 +8896,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Cookbook-5:-Left}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Cookbook-5:-Left"
+
\end_inset
Cookbook 5: Left (A): Initially, both plates have Euler poles (magenta and
@@ -8582,6 +8918,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsubsection
Example: Subduction Models with Trench Rollback,
\family typewriter
@@ -8722,9 +9063,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Cookbook-5:-the}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Cookbook-5:-the"
+
\end_inset
Cookbook 5: The pole jump after 30 Ma produced a flat slab on one side (fore
@@ -8737,13 +9082,19 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Discussion
\end_layout
\begin_layout Standard
The results for this problem are presented in Figure
-\begin_inset LatexCommand \ref{fig:Cookbook-5:-the}
+\begin_inset LatexCommand ref
+reference "fig:Cookbook-5:-the"
\end_inset
@@ -8780,7 +9131,8 @@
\begin_layout Standard
The basic algorithm
-\begin_inset LatexCommand \cite{Zhong et al Free-surface formulation,Zhong et al Three-dimensional}
+\begin_inset LatexCommand cite
+key "Zhong et al Free-surface formulation,Zhong et al Three-dimensional"
\end_inset
@@ -8899,13 +9251,15 @@
\begin_layout Standard
The plots of the topography profile are consistent with results described
in
-\begin_inset LatexCommand \cite{Zhong et al Free-surface formulation}
+\begin_inset LatexCommand cite
+key "Zhong et al Free-surface formulation"
\end_inset
.
In the graphs in Figure
-\begin_inset LatexCommand \ref{fig:Cookbook-6.-Graphs}
+\begin_inset LatexCommand ref
+reference "fig:Cookbook-6.-Graphs"
\end_inset
@@ -8935,9 +9289,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Cookbook-6.-Graphs}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Cookbook-6.-Graphs"
+
\end_inset
Cookbook 6: Graphs of topography profiles.
@@ -8949,6 +9307,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
Cookbook 7: Thermo-Chemical Convection
\end_layout
@@ -9145,7 +9508,8 @@
buoy_type=1
\family default
)
-\begin_inset LatexCommand \cite{Tackely King tracer ratio method}
+\begin_inset LatexCommand cite
+key "Tackely King tracer ratio method"
\end_inset
@@ -9190,7 +9554,8 @@
\begin_layout Standard
The regular grid is an auxiliary grid that helps locate the tracers
-\begin_inset LatexCommand \cite{McNamara Zhong Thermochemical}
+\begin_inset LatexCommand cite
+key "McNamara Zhong Thermochemical"
\end_inset
@@ -9385,9 +9750,13 @@
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Cookbook-7:-The}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Cookbook-7:-The"
+
\end_inset
Cookbook 7: The composition and velocity field at the 20th step.
@@ -9400,13 +9769,19 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Discussion
\end_layout
\begin_layout Standard
The results for this problem are presented in Figure
-\begin_inset LatexCommand \ref{fig:Cookbook-7:-The}
+\begin_inset LatexCommand ref
+reference "fig:Cookbook-7:-The"
\end_inset
@@ -9425,7 +9800,8 @@
\begin_layout Chapter
\start_of_appendix
-\begin_inset LatexCommand \label{cha:Appendix-A:-Input}
+\begin_inset LatexCommand label
+name "cha:Appendix-A:-Input"
\end_inset
@@ -11840,8 +12216,9 @@
If
\family typewriter
\size small
-low_visc_channel
+low_visc_channel
\family default
+
\size default
or
\family typewriter
@@ -13054,7 +13431,8 @@
\family default
\size default
, the composition field is determined by the ratio method
-\begin_inset LatexCommand \cite{Tackely King tracer ratio method}
+\begin_inset LatexCommand cite
+key "Tackely King tracer ratio method"
\end_inset
@@ -18041,7 +18419,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Coordinate-files}
+\begin_inset LatexCommand label
+name "sec:Coordinate-files"
\end_inset
@@ -18166,7 +18545,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Velocity-boundary-condition}
+\begin_inset LatexCommand label
+name "sec:Velocity-boundary-condition"
\end_inset
@@ -18346,7 +18726,8 @@
vel_bound_file
\family default
(see Section
-\begin_inset LatexCommand \ref{sec:Velocity-boundary-condition}
+\begin_inset LatexCommand ref
+reference "sec:Velocity-boundary-condition"
\end_inset
@@ -18407,7 +18788,8 @@
vel_bound_file
\family default
(see Section
-\begin_inset LatexCommand \ref{sec:Velocity-boundary-condition}
+\begin_inset LatexCommand ref
+reference "sec:Velocity-boundary-condition"
\end_inset
@@ -18465,7 +18847,8 @@
\end_layout
\begin_layout Chapter
-\begin_inset LatexCommand \label{cha:Appendix-C:-CitComS,}
+\begin_inset LatexCommand label
+name "cha:Appendix-C:-CitComS,"
\end_inset
@@ -18552,7 +18935,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:ASCII-Output}
+\begin_inset LatexCommand label
+name "sec:ASCII-Output"
\end_inset
@@ -18581,7 +18965,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand \label{sub:Velocity-and-Temperature}
+\begin_inset LatexCommand label
+name "sub:Velocity-and-Temperature"
\end_inset
@@ -18773,7 +19158,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand \label{sub:Geoid-Output-(test-case.geoid.10)}
+\begin_inset LatexCommand label
+name "sub:Geoid-Output-(test-case.geoid.10)"
\end_inset
@@ -19114,7 +19500,8 @@
\begin_layout Standard
The format and layout of HDF5 output is described in Section
-\begin_inset LatexCommand \vref{sec:Data-Layout}
+\begin_inset LatexCommand vref
+reference "sec:Data-Layout"
\end_inset
@@ -19122,7 +19509,8 @@
\end_layout
\begin_layout Chapter
-\begin_inset LatexCommand \label{cha:License}
+\begin_inset LatexCommand label
+name "cha:License"
\end_inset
@@ -19660,7 +20048,7 @@
One line to give the program's name and a brief idea of what it does.
Copyright
\size footnotesize
-© (
+© (
\size default
year) (name of author)
\end_layout
@@ -19698,7 +20086,7 @@
\end_layout
\begin_layout Quote
-Gnomovision version 69, Copyright © year name of author Gnomovision comes
+Gnomovision version 69, Copyright © year name of author Gnomovision comes
with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it under certain
conditions; type `show c' for details.
@@ -19745,8 +20133,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "1"
+key "Moresi et al Plate tectonics"
-\bibitem [1]{Moresi et al Plate tectonics}
+\end_inset
+
Moresi, L., M.
Gurnis, and S.
Zhong (2000), Plate tectonics and convection in the Earth's mantle: Toward
@@ -19760,8 +20152,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "2"
+key "Moresi/Solomatov Numerical"
-\bibitem [2]{Moresi/Solomatov Numerical}
+\end_inset
+
Moresi, L.N., and V.S.
Solomatov (1995), Numerical investigation of 2D convection with extremely
large viscosity variations,
@@ -19777,8 +20173,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "3"
+key "Moresi/Gurnis Contraints"
-\bibitem [3]{Moresi/Gurnis Contraints}
+\end_inset
+
Moresi, L.N., and M.
Gurnis (1996), Constraints on the lateral strength of slabs from three-dimensio
nal dynamic flow models,
@@ -19795,8 +20195,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "4"
+key "Zhong/Moresi The role of faults"
-\bibitem [4]{Zhong/Moresi The role of faults}
+\end_inset
+
Zhong, S., M.
Gurnis, and L.
Moresi (1998), The role of faults, nonlinear rheology, and viscosity structure
@@ -19814,8 +20218,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "5"
+key "Zhong et al The role of temperature"
-\bibitem [5]{Zhong et al The role of temperature}
+\end_inset
+
Zhong, S., M.T.
Zuber, L.N.
Moresi, and M.
@@ -19830,8 +20238,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "6"
+key "Tan et al Slabs in the lower"
-\bibitem [6]{Tan et al Slabs in the lower}
+\end_inset
+
Tan, E., M.
Gurnis, and L.
Han (2002), Slabs in the lower mantle and their modulation of plume formation,
@@ -19849,8 +20261,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "7"
+key "Conrad/Gurnis Seismic tomography"
-\bibitem [7]{Conrad/Gurnis Seismic tomography}
+\end_inset
+
Conrad, C.P., and M.
Gurnis (2003), Seismic tomography, surface uplift, and the breakup of Gondwanal
and: Integrating mantle convection backwards in time,
@@ -19867,8 +20283,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "8"
+key "Hughes The Finite Element Method"
-\bibitem [8]{Hughes The Finite Element Method}
+\end_inset
+
Hughes, T.J.R.
\emph on
@@ -19880,8 +20300,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "9"
+key "Ramage/Wathen Iterative solution"
-\bibitem [9]{Ramage/Wathen Iterative solution}
+\end_inset
+
Ramage, A., and A.J.
Wathen (1994), Iterative solution techniques for the Stokes and Navier-Stokes
equations,
@@ -19900,12 +20324,16 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "10"
+key "Brooks A.N."
-\bibitem [10]{Brooks A.N.}
+\end_inset
+
Brooks, A.N.
-
+
\emph on
- A Petrov-Galerkin Finite Element Formulation for Convecton Dominated Flows.
+A Petrov-Galerkin Finite Element Formulation for Convecton Dominated Flows.
\emph default
Unpublished doctoral thesis, California Institute of Technology, Pasadena,
@@ -19913,8 +20341,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "11"
+key "Cahouet/Chabard Some fast 3D"
-\bibitem [11]{Cahouet/Chabard Some fast 3D}
+\end_inset
+
Cahouet, J., and J.-P.
Chabard (1988), Some fast 3D finite element solvers for the generalized
Stokes problem
@@ -19933,8 +20365,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "12"
+key "Atanga/Silvester Iterative methods"
-\bibitem [12]{Atanga/Silvester Iterative methods}
+\end_inset
+
Atanga, J., and D.
Silvester (1992), Iterative methods for stabilized mixed velocity-pressure
finite elements,
@@ -19953,8 +20389,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "13"
+key "Hager/OConnell A simple global"
-\bibitem [13]{Hager/OConnell A simple global}
+\end_inset
+
Hager, B.H., and R.J.
O'Connell (1981), A simple global model of plate dynamics and mantle convection
,
@@ -19971,8 +20411,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "14"
+key "Tan et al GeoFramework Part I"
-\bibitem [14]{Tan et al GeoFramework Part I}
+\end_inset
+
Tan, E., E.
Choi, P.
Thoutireddy, M.
@@ -19982,17 +20426,18 @@
\emph on
Geochem., Geophys., Geosyst.
7,
-\series bold
-
-\series default
\emph default
-Q06001, doi:10.1029/2005GC001155.
+ Q06001, doi:10.1029/2005GC001155.
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "15"
+key "Zhong et al Free-surface formulation"
-\bibitem [15]{Zhong et al Free-surface formulation}
+\end_inset
+
Zhong, S., M.
Gurnis, and L.
Moresi (1996), Free-surface formulation of mantle convection--I.
@@ -20010,8 +20455,12 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "16"
+key "Zhong et al Three-dimensional"
-\bibitem [16]{Zhong et al Three-dimensional}
+\end_inset
+
Zhong, S., A.
Paulson, and J.
Wahr (2003), Three-dimensional finite-element modeling of Earth's viscoelastic
@@ -20029,13 +20478,17 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "17"
+key "McNamara Zhong Thermochemical"
-\bibitem [17]{McNamara Zhong Thermochemical}
+\end_inset
+
McNamara, A.K., and S.
Zhong (2004), Thermochemical structures within a spherical mantle: Superplumes
- or Piles?
+ or Piles?
\emph on
- J.
+J.
Geophys.
Res.
\emph default
@@ -20043,17 +20496,21 @@
\end_layout
\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "18"
+key "Tackely King tracer ratio method"
-\bibitem [18]{Tackely King tracer ratio method}
+\end_inset
+
Tackley, P.J., and S.D.
King (2003), Testing the tracer ratio method for modeling active compositional
fields in mantle convection simulations,
\emph on
Geochem.
Geophys.
- Geosyst., 4,
+ Geosyst., 4,
\emph default
-8302, doi:10.1029/2001GC000214.
+ 8302, doi:10.1029/2001GC000214.
\end_layout
\end_body
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