[cig-commits] r4492 - geodyn/3D/MAG/trunk/doc

[sue at geodynamics.org]

Author: sue
Date: 2006-09-07 15:21:49 -0700 (Thu, 07 Sep 2006)
New Revision: 4492

Added:
   geodyn/3D/MAG/trunk/doc/mag_book.lyx
Log:
started inputting mag data into lyx format using citcoms as model

Added: geodyn/3D/MAG/trunk/doc/mag_book.lyx
===================================================================
--- geodyn/3D/MAG/trunk/doc/mag_book.lyx	2006-09-07 21:07:38 UTC (rev 4491)
+++ geodyn/3D/MAG/trunk/doc/mag_book.lyx	2006-09-07 22:21:49 UTC (rev 4492)
@@ -0,0 +1,10307 @@
+#LyX 1.4.1 created this file. For more info see http://www.lyx.org/
+\lyxformat 245
+\begin_document
+\begin_header
+\textclass book
+\begin_preamble
+\usepackage{hyperref}
+\end_preamble
+\language english
+\inputencoding auto
+\fontscheme default
+\graphics default
+\paperfontsize default
+\spacing single
+\papersize default
+\use_geometry true
+\use_amsmath 0
+\cite_engine basic
+\use_bibtopic false
+\paperorientation portrait
+\leftmargin 1in
+\topmargin 1in
+\rightmargin 1in
+\bottommargin 1in
+\secnumdepth 2
+\tocdepth 5
+\paragraph_separation indent
+\defskip medskip
+\quotes_language swedish
+\papercolumns 1
+\papersides 2
+\paperpagestyle headings
+\tracking_changes false
+\output_changes true
+\end_header
+
+\begin_body
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status collapsed
+
+\begin_layout Standard
+\begin_inset Graphics
+	filename CitcomS/manual/citcoms_cover.pdf
+	display color
+	width 75page%
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+thispagestyle{empty}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Title
+MAG Manual
+\end_layout
+
+\begin_layout Author
+California Institute of Technology
+\newline
+Version ?.0.?
+\end_layout
+
+\begin_layout Date
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+today
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset LatexCommand \tableofcontents{}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset FloatList figure
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Part
+Preface
+\end_layout
+
+\begin_layout Chapter*
+Preface
+\end_layout
+
+\begin_layout Section*
+About This Document
+\end_layout
+
+\begin_layout Standard
+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 ?????? and their capabilities and proceeds to the details of implementation,
+ including a "cookbook" of short tutorials.
+ Part III provides appendices and references.
+\end_layout
+
+\begin_layout Standard
+The style of this publication is based on the 
+\begin_inset LatexCommand \htmlurl[Apple Publications Style Guide]{http://developer.apple.com/documentation/UserExperience/Conceptual/APStyleGuide/AppleStyleGuide2003.pdf}
+
+\end_inset
+
+, as recommended by 
+\begin_inset LatexCommand \htmlurl[Python.org]{http://www.python.org/}
+
+\end_inset
+
+.
+ The documentation was produced using 
+\begin_inset LatexCommand \htmlurl[LyX]{http://www.lyx.org/}
+
+\end_inset
+
+ to facilitate the transformation of files from one format to another.
+ LyX is a document processor that encourages an approach to writing based
+ on the structure of your documents, not their appearance.
+ It is released under a Free Software/Open Source license.
+\end_layout
+
+\begin_layout Standard
+Errors and bug fixes in this manual should be directed to 
+\begin_inset LatexCommand \url[CIG Geodynamo Mailing List]{<cig-mc at geodynamics.org>}
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Section*
+Who Will Use This Document
+\end_layout
+
+\begin_layout Standard
+This documentation is aimed at scientists who prefer to use prepackaged
+ and specialized analysis tools.
+ Users are likely to be experienced computational Earth scientists and have
+ familiarity with basic scripting, software installation, and programming;
+ but are not likely to be professional programmers.
+ Of those, there are likely to be two classes of users: those who just run
+ models and those who modify the source code.
+ 
+\end_layout
+
+\begin_layout Standard
+The manual was written for the usage of Mag on a variety of different platforms.
+ ??? MAG has run on shared memory computers (Sun, Hewlett-Packard, SGI,
+ and IBM), commercial distributed memory machines (Intel and Cray/SGI),
+ and Beowulf implementations (including Beowulfs at the California Institute
+ of Technology's Center for Advanced Computing Research and Seismological
+ Laboratory, Sydney University, and the Geological Survey of Norway).
+ ????
+\end_layout
+
+\begin_layout Section*
+Citation
+\end_layout
+
+\begin_layout Standard
+Computational Infrastructure for Geodynamics (CIG) is making this source
+ code available to you in the hope that the software will enhance your research
+ in geophysics.
+ 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 MAG 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.
+ 
+\end_layout
+
+\begin_layout Standard
+The MAG development team asks that you cite both of the following:
+\end_layout
+
+\begin_layout Itemize
+Olson, P., G.A.
+ Glatzmaier (1995), TITLE.
+ 
+\emph on
+Geophys.
+ Astrophys.
+ Fluid Dyn.,
+\series bold
+\emph default
+ 
+\series default
+\emph on
+92
+\series bold
+, 
+\series default
+\emph default
+109
+\end_layout
+
+\begin_layout Itemize
+Olson, P., G.A.
+ Glatzmaier (1996), TITLE.
+ 
+\emph on
+Phil.
+ Trans.
+ R.
+ Soc.
+ Lond., A354,
+\emph default
+ 1413
+\end_layout
+
+\begin_layout Itemize
+Olson, P., U.
+ Christensen, G.A.
+ Glatzmaier (1999), TITLE.
+ 
+\emph on
+J.
+ Geophys.
+ Res., 104
+\emph default
+, 10,383
+\end_layout
+
+\begin_layout Itemize
+Christensen, U., P.
+ Olson, G.A.
+ Glatzmaier (1999), TITLE.
+ 
+\emph on
+Geophys.
+ J.
+ Int., 138
+\emph default
+, 393
+\end_layout
+
+\begin_layout Itemize
+Christensen, et al.
+ (2001), TITLE.
+
+\emph on
+ Phys.
+ Earth Planet Int., 128
+\emph default
+, 25 (benchmark cases)
+\end_layout
+
+\begin_layout Standard
+[Note: there are more recent papers by the same authors.] 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]{http://www.geodynamics.org/}
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Section*
+Support
+\end_layout
+
+\begin_layout Standard
+??? Mag development is funded by the 
+\begin_inset LatexCommand \htmlurl[U.S. Dept. of Energy's Advanced Simulation and Computing program]{http://www.sandia.gov/NNSA/ASC/}
+
+\end_inset
+
+ and the 
+\begin_inset LatexCommand \htmlurl[National Science Foundation's]{http://www.nsf.gov/}
+
+\end_inset
+
+ Information Technology Research (ITR) program (grant #0205653).
+ Continued support of Mag is made possible under NSF EAR-0406751.
+\end_layout
+
+\begin_layout Section*
+Conventions
+\end_layout
+
+\begin_layout Standard
+Any mention of "username" is meant to indicate the user, meaning you should
+ substitute your account name in its place.
+\end_layout
+
+\begin_layout Part
+Chapters
+\end_layout
+
+\begin_layout Chapter
+Introduction
+\end_layout
+
+\begin_layout Standard
+Mag is a serial version of Gary Glatzmaier's rotating spherical convection/magne
+toconvection/dynamo code, modified by Uli Christensen and Peter Olson.
+ 
+\end_layout
+
+\begin_layout Section
+About CitComS
+\end_layout
+
+\begin_layout Standard
+The code solves the nondimensional Boussinesq equations for time-dependent
+ thermal convection in a rotating spherical shell filled with an electrically
+ conducting fluid.
+ The equations of motion are: the Navier-Stokes equation including Coriolis,
+ Lorentz, Buoyancy, pressure, viscous, and inertial terms; the heat equation
+ including advection, diffusion, and uniform-density heat sources; the continuit
+y equation for velocity and Gauss' law for magnetic field, and the induction
+ equation for the magnetic field.
+\end_layout
+
+\begin_layout Standard
+All variables are nondimensional; time scale is viscous diffusion, length
+ scale is shell thickness, temperature scale is boundary temperature difference,
+ magnetic field and electric currents use Elsasser number scaling.
+ 
+\end_layout
+
+\begin_layout Standard
+A variety of boundary and initial conditions are selected as options.
+\end_layout
+
+\begin_layout Standard
+Mag uses toroidal-poloidal decomposition for velocity and magnetic field
+ with explicit timesteps.
+ Linear terms are evaluated spectrally (spherical harmonics plus Chebycheff
+ polynomials in radius) and nonlinear terms are evaluated on a spherical
+ grid.
+\end_layout
+
+\begin_layout Section
+History
+\end_layout
+
+\begin_layout Standard
+CitCom (for 
+\series bold
+C
+\series default
+alifornia 
+\series bold
+I
+\series default
+nstitute of 
+\series bold
+T
+\series default
+echnology 
+\series bold
+Co
+\series default
+nvection in the 
+\series bold
+M
+\series default
+antle) was originally written in the early 1990's by Louis Moresi.
+ Although the code for three-dimensional problems was incorporated from
+ its inception, early versions of the software only solved for time-dependent
+ convection problems within two-dimensional Cartesian domains.
+ Moresi's original code turned out to be incredibly modular and easily extensibl
+e.
+ Consequently, the fundamental finite element infrastructure which Louis
+ wrote is still in place and forms the basis for much of the code contained
+ in the present release.
+ 
+\end_layout
+
+\begin_layout Standard
+In the mid-1990's Moresi wrote versions of the code that solved the equations
+ 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
+ version of message passing for an arbitrarily large number of processors.
+ Clint Conrad created the first Beowulf implementations of the code, then
+ Conrad and Eh Tan re-coded the message passing of the fully spherical version
+ so that problems run on arbitrarily large numbers of processors could also
+ be solved.
+ A plethora of different versions of CitCom exist both on computers at the
+ California Institute of Technology and around the world.
+ 
+\end_layout
+
+\begin_layout Standard
+Consequently, by 2002, there were so many different versions of the code
+ that some rationalization was in order.
+ The software was migrated into a version control system and Eh Tan and
+ Eun-seo Choi created a version of the CitComS that generates either a fully
+ spherical or regional model, 
+\family typewriter
+CitcomSFull
+\family default
+ and 
+\family typewriter
+CitcomSRegional
+\family default
+ respectively.
+ CitComS was released to the community through the GeoFramework website
+ as version 1.0 and 1.1, and is currently available from 
+\begin_inset LatexCommand \htmlurl[CIG]{http://www.geodynamics.org/}
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Standard
+By 2004, in order to increase the functionality of CitComS, the developers
+ began to reengineer the code into an object-oriented environment specifically
+ so it could work with a Python-based modeling framework called Pyre.
+ This release of the software, now named CitComS.py, is essentially the product
+ of those reengineering efforts.
+ Eh Tan was the principal developer of CitComS.py, with considerable help
+ from Eun-seo Choi, Puru Thoutireddy, and Michael Aivazis.
+\end_layout
+
+\begin_layout Standard
+CitComS is one component of a larger collection of software encompassed
+ by the GeoFramework, a collaborative project between the 
+\begin_inset LatexCommand \htmlurl[Center for Advanced Computing Research (CACR)]{http://www.cacr.caltech.edu/}
+
+\end_inset
+
+ and the 
+\begin_inset LatexCommand \htmlurl[Seismological Laboratory]{http://www.gps.caltech.edu/seismo/}
+
+\end_inset
+
+, both at Caltech, and the 
+\begin_inset LatexCommand \htmlurl[Victorian Partnership for Advanced Computing]{http://www.vpac.org/}
+
+\end_inset
+
+ in Australia.
+ The GeoFramework project has been developing a suite of tools to model
+ multi-scale deformation for Earth science problems.
+ This effort was motivated by the need to understand interactions between
+ the long-term evolution of plate tectonics and shorter term processes such
+ as the evolution of faults during and between earthquakes.
+ During 2005 and 2006 much of the remaining software developed by GeoFramework
+ was donated to CIG.
+\end_layout
+
+\begin_layout Standard
+The second major release of CitComS (2.0) incorporates the software framework
+ Pyre, free surface modeling methods, and stress boundary conditions around
+ the top and bottom surfaces.
+ In the summer of 2005, as part of the 2.0.1 release, the CIG replaced the
+ old build procedure with the GNU Build System.
+ A subsequent release, version 2.0.2, could compile and run on 64-bit systems.
+\end_layout
+
+\begin_layout Section
+About Pyre
+\end_layout
+
+\begin_layout Standard
+Pyre is an object-oriented environment capable of specifying and launching
+ numerical simulations on multiple platforms, including Beowulf class parallel
+ computers and grid computing systems.
+ Pyre allows the binding of multiple components such as solid and fluid
+ models used in Earth science simulations, and different meshers.
+ The Pyre framework enables the elegant setup, modification and launching
+ of massively parallel three-dimensional solver applications.
+ 
+\end_layout
+
+\begin_layout Standard
+Pyre is a framework, a combination of software and design philosophy that
+ promotes the reuse of code.
+ In their canonical software design book, 
+\emph on
+Design Patterns
+\emph default
+, Erich Gamma 
+\emph on
+et al
+\emph default
+ condense the concept of a framework concept down to, "When you use a framework,
+ you reuse the main body and write the code it calls." In the context of
+ frameworks and object-oriented programming, Pyre can be thought of as a
+ collection of classes and the way their instances interact.
+ Programming applications based on Pyre will look similar to those written
+ in any other object-oriented language.
+ The Pyre framework contains a subset of parts that make up the overall
+ framework.
+ Each of those parts is designed to solve a specific problem.
+ 
+\end_layout
+
+\begin_layout Standard
+The framework approach to computation offers many advantages.
+ It permits the exchange of codes and promotes the reuse of standardized
+ software while preserving efficiency.
+ Frameworks are also an efficient way to handle changes in computer architecture.
+ They present programmers and scientists with a unified and well-defined
+ task and allow for shared costs of the housekeeping aspects of software
+ development.
+ They provide greater institutional continuity to model development than
+ piecemeal approaches.
+\end_layout
+
+\begin_layout Standard
+The Pyre framework incorporates features aimed at enabling the scientific
+ non-expert to perform tasks easily without hindering the expert.
+ Target features for end users allow complete and intuitive simulation specifica
+tion, reasonable defaults, consistency checks of input, good diagnostics,
+ easy access to remote facilities, and status monitoring.
+ Target features for developers include easy access to user input, a shorter
+ development cycle, and good debugging support.
+ 
+\end_layout
+
+\begin_layout Section
+Governing Equations
+\end_layout
+
+\begin_layout Standard
+With CitComS, the mantle is treated as an incompressible viscous spherical
+ shell.
+ With these assumptions, thermal convection is governed by the equations
+ for conservation of mass, momentum, and energy:
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+u_{i,i}=0\label{eq:conservation of mass}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula $ $
+\end_inset
+
+
+\begin_inset Formula \begin{equation}
+-P_{,i}+(\eta u_{i,j}+\eta u_{j,i})_{,j}+\delta\rho g\delta_{ir}=0\label{eq:conservation of momentum}\end{equation}
+
+\end_inset
+
+ 
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+T_{,t}+u_{i}T_{,i}=\kappa T_{,ii}+H\label{eq:conservation of energy}\end{equation}
+
+\end_inset
+
+ 
+\end_layout
+
+\begin_layout Standard
+\noindent
+where 
+\emph on
+u 
+\emph default
+is the velocity, 
+\emph on
+P
+\emph default
+ is the dynamic pressure, 
+\begin_inset Formula $\delta\rho$
+\end_inset
+
+ is the density anomaly, 
+\emph on
+g
+\emph default
+ is the gravitational acceleration, 
+\begin_inset Formula $\eta$
+\end_inset
+
+ is the viscosity, 
+\emph on
+T
+\emph default
+ is the temperature, 
+\begin_inset Formula $\kappa$
+\end_inset
+
+ is the thermal diffusivity, and 
+\emph on
+H
+\emph default
+ is the heat production rate.
+ 
+\begin_inset Formula $X_{,y}$
+\end_inset
+
+ represents the derivative of 
+\emph on
+X
+\emph default
+ with respect to 
+\emph on
+y
+\emph default
+, 
+\emph on
+i
+\emph default
+ and 
+\emph on
+j
+\emph default
+ are spatial indices, 
+\emph on
+r
+\emph default
+ is the radial direction, and 
+\emph on
+t
+\emph default
+ is time.
+ Without phase transitions, the density anomalies are:
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+\delta\rho=-\alpha\rho_{0}(T-T_{0})\label{eq:density anomalies}\end{equation}
+
+\end_inset
+
+ 
+\end_layout
+
+\begin_layout Standard
+These equations lead to the following normalization in which primed quantities
+ are nondimensional:
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+x_{i}=R_{0}x_{i}^{'}\label{eq:5}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Formula \begin{equation}
+u_{i}=\frac{\kappa}{R_{0}}u_{i}^{'}\label{eq:6}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+T=\Delta TT'+T_{0}\label{eq:7}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+t=\frac{R_{0}^{2}}{\kappa}t^{'}\label{eq:8}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+\gamma=\frac{HR_{0}^{2}}{\kappa\Delta T}\label{eq:9}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+\eta=\eta_{0}\eta^{'}\label{eq:10}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+P=\frac{\eta_{0}\kappa}{R_{0}^{2}}P^{'}\label{eq:11}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\noindent
+where 
+\begin_inset Formula $R_{0}$
+\end_inset
+
+ is the radius of the earth, 
+\begin_inset Formula $\eta_{0}$
+\end_inset
+
+ is a reference viscosity, 
+\begin_inset Formula $\Delta T$
+\end_inset
+
+ is the superadiabatic temperature drop from the core-mantle boundary (CMB)
+ to the surface.
+ Dropping the primes, the equations become:
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+u_{i,i}=0\label{eq:conservation of mass}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Formula \begin{equation}
+-P_{,i}+(\eta u_{i,j}+\eta u_{j,i})_{,j}+RaT\delta_{ir}=0\label{eq:13}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+T_{,t}+u_{i}T_{,i}=T_{,ii}+\gamma\label{eq:14}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\noindent
+where 
+\emph on
+Ra
+\emph default
+, a Rayleigh number, is defined as:
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+Ra=\frac{\rho g\alpha\Delta TR_{0}^{3}}{\eta_{0}\kappa}\label{eq:Ra, a Rayleigh number}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+If there is a phase change, 
+\begin_inset LatexCommand \ref{eq:13}
+
+\end_inset
+
+ is modified to:
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+-P_{,i}+(\eta u_{i,j}+\eta u_{j,i})_{,j}+(RaT+R_{b}\Gamma)\delta_{ir}=0\label{eq:16}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+\Gamma=\frac{1}{2}\left(1+\tanh\left(\frac{1-r-d_{ph}-s(T-T_{ph})}{w_{ph}}\right)\right)\label{eq:17}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\noindent
+where 
+\begin_inset Formula $d_{ph}$
+\end_inset
+
+ and 
+\begin_inset Formula $T_{ph}$
+\end_inset
+
+ are the ambient depth and temperature of a phase change,
+\emph on
+ s
+\emph default
+ is the Clapeyron slope of a phase change, and 
+\begin_inset Formula $w_{ph}$
+\end_inset
+
+ is the width of a phase transition.
+ The phase-change Rayleigh number, 
+\begin_inset Formula $R_{b}$
+\end_inset
+
+, is defined as:
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+R_{b}=\frac{\Delta\rho_{ph}gR_{0}^{3}}{\eta_{0}\kappa}\label{eq:Rb, the phase-change Rayleigh number}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\noindent
+where 
+\begin_inset Formula $\Delta\rho_{ph}$
+\end_inset
+
+ is the density jump across a phase change.
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Section
+Numerical Methods
+\end_layout
+
+\begin_layout Standard
+The governing equations are solved with the finite element method, see 
+\begin_inset LatexCommand \cite{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}
+
+\end_inset
+
+.
+ The energy equation is solved with a Petrov-Galerkin method 
+\begin_inset LatexCommand \cite{Brooks A.N.}
+
+\end_inset
+
+.
+ Brick elements are used, such as eight velocity nodes with trilinear shape
+ functions and one constant pressure node for each element.
+ 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}
+
+\end_inset
+
+.
+ The discrete form of equations 
+\begin_inset LatexCommand \ref{eq:conservation of mass}
+
+\end_inset
+
+ and 
+\begin_inset LatexCommand \ref{eq:13}
+
+\end_inset
+
+ may be written in the following matrix form 
+\begin_inset LatexCommand \cite{Zhong et al The role of temperature}
+
+\end_inset
+
+:
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+\mathrm{\mathbf{B}^{\mathit{T}}\mathit{u=0}}\label{eq:19}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+\mathbf{A\mathit{u+}}\mathbf{B\mathit{p=f}}\label{eq:20}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\noindent
+where 
+\begin_inset Formula $\mathbf{A}$
+\end_inset
+
+ is the "stiffness" matrix, 
+\emph on
+u
+\emph default
+ is a vector of unknown velocities; 
+\begin_inset Formula $\mathbf{B}$
+\end_inset
+
+ is the discrete gradient operator, 
+\emph on
+p
+\emph default
+ is a vector of unknown pressures, and 
+\emph on
+f 
+\emph default
+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
+
+, 
+\begin_inset Formula $\mathbf{B}$
+\end_inset
+
+, and 
+\emph on
+f
+\emph default
+ are obtained using a standard finite element formulation, see 
+\begin_inset LatexCommand \cite{Zhong et al The role of temperature}
+
+\end_inset
+
+ for the explicit entries.
+ Equation 
+\begin_inset LatexCommand \ref{eq:20}
+
+\end_inset
+
+ can be transformed by premultiplying by 
+\begin_inset Formula $\mathrm{\mathbf{B}^{\mathit{T}}\mathit{\mathbf{A}^{\mathbf{\mathit{-1}}}}}$
+\end_inset
+
+ and using equation 
+\begin_inset LatexCommand \ref{eq:19}
+
+\end_inset
+
+ to eliminate the velocity unknowns:
+\end_layout
+
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+\mathbf{B}^{\mathit{T}}\mathit{\mathbf{A}^{\mathbf{\mathit{-1}}}\mathbf{B}\mathit{p=\mathbf{B^{\mathit{T}}A^{\mathit{-1}}\mathit{f}}}}\label{eq:21}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+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}
+
+\end_inset
+
+, which simultaneously yields the velocity field.
+ A conjugate gradient scheme for this iteration is described by 
+\begin_inset LatexCommand \cite{Ramage/Wathen Iterative solution,Atanga/Silvester Iterative methods}
+
+\end_inset
+
+, and forms the basis for the technique used in CitComS.
+\end_layout
+
+\begin_layout Chapter
+Installation and Getting Help
+\end_layout
+
+\begin_layout Section
+Introduction
+\end_layout
+
+\begin_layout Standard
+To test run Mag, you will download the source package (in the form of a
+ compressed 
+\family typewriter
+tar
+\family default
+ file) from the 
+\begin_inset LatexCommand \htmlurl[Geodynamics Software Packages web page]{http://www.geodynamics.org/cig/software/packages/}
+
+\end_inset
+
+.
+ After unpacking the source, ???you will run a prepackaged shell script
+ to configure Mag for your system.??? Then you will use the 
+\family typewriter
+make
+\family default
+ utility to build Mag from source, and background execute the bench input
+ file.
+ 
+\end_layout
+
+\begin_layout Standard
+Advanced users and software developers may be interested in downloading
+ the latest Mag source code directly from the CIG source code repository,
+ instead of using the prepared source package.
+ See the 
+\begin_inset LatexCommand \ref{sec:Software-Repository}
+
+\end_inset
+
+ section later in this chapter.
+ ??? Mag has been tested on Linux, Mac OS X, and several NSF TeraGrid platforms.
+ ????
+\end_layout
+
+\begin_layout Section
+Getting Help
+\end_layout
+
+\begin_layout Standard
+For help, send e-mail to the 
+\begin_inset LatexCommand \url[CIG Geodynamo Mailing List]{<cig-geodyn at geodynamics.org>}
+
+\end_inset
+
+.
+ You can subscribe to the Mailing List and view archived discussion at 
+\begin_inset LatexCommand \htmlurl[Geodynamics Mail Lists]{http://www.geodynamics.org/cig/lists/}
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Section
+System Requirements
+\end_layout
+
+\begin_layout Standard
+Mag requires the following:
+\end_layout
+
+\begin_layout Itemize
+Python 2.3 or greater
+\end_layout
+
+\begin_layout Itemize
+An MPI library which implements version 1 of the MPI standard (If you are
+ using MPICH, MPICH version 1.2.3 or later is required.)
+\end_layout
+
+\begin_layout Itemize
+A modern C++ compiler
+\end_layout
+
+\begin_layout Itemize
+A C compiler
+\end_layout
+
+\begin_layout Standard
+
+\series bold
+Note:
+\series default
+ Users familiar with older versions of CitComS may prefer to install only
+ the legacy CitComS tools, CitcomSFull and CitcomSRegional, and forgo use
+ of the Pyre framework.
+ Installing the legacy tools requires simply:
+\end_layout
+
+\begin_layout Itemize
+An MPI library
+\end_layout
+
+\begin_layout Itemize
+A C compiler
+\end_layout
+
+\begin_layout Standard
+For more information, see the subsection 
+\begin_inset LatexCommand \ref{sec:Installing-without-Pyre}
+
+\end_inset
+
+ on page 
+\begin_inset LatexCommand \pageref{sec:Installing-without-Pyre}
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Standard
+You can download Python from the 
+\begin_inset LatexCommand \htmlurl[Python website]{http://www.python.org/}
+
+\end_inset
+
+.
+ If your system is running a recent release of Linux or Mac OS X, chances
+ are you already have a suitable Python interpreter installed.
+ To check, type the 'python' command:
+\end_layout
+
+\begin_layout LyX-Code
+$ python -V
+\end_layout
+
+\begin_layout LyX-Code
+Python 2.3.4
+\end_layout
+
+\begin_layout Standard
+MPICH is a freely available, portable implementation of MPI.
+ For more information, visit the 
+\begin_inset LatexCommand \htmlurl[MPICH home page]{http://www-unix.mcs.anl.gov/mpi/mpich/}
+
+\end_inset
+
+.
+ 
+\end_layout
+
+\begin_layout Quote
+
+\series bold
+Note for Mac OS X Users
+\series default
+: You will need Xcode, which is freely available from 
+\begin_inset LatexCommand \htmlurl[Apple]{http://developer.apple.com/}
+
+\end_inset
+
+.
+ Instead of using MPICH, you will probably want to use 
+\begin_inset LatexCommand \htmlurl[LAM/MPI]{http://www.lam-mpi.org/}
+
+\end_inset
+
+.
+ LAM/MPI is available as a Fink package; if you have 
+\begin_inset LatexCommand \htmlurl[Fink]{http://fink.sourceforge.net/}
+
+\end_inset
+
+ installed, simply enter the following command from a Terminal window to
+ install LAM/MPI:
+\end_layout
+
+\begin_layout LyX-Code
+$ fink install lammpi lammpi-dev
+\end_layout
+
+\begin_layout Section
+Downloading and Unpacking Source
+\end_layout
+
+\begin_layout Standard
+Download Mag from the 
+\begin_inset LatexCommand \htmlurl[Geodynamics website]{http://www.geodynamics.org/}
+
+\end_inset
+
+.
+ Click the "software" tab at the top of the page.
+ Then click "Software Packages." Once you click the Mag link, downloaded
+ the source archive and unpack it using the 
+\family typewriter
+tar
+\family default
+ command:
+\end_layout
+
+\begin_layout LyX-Code
+$ tar xzf CitcomS-2.0.2.tar.gz
+\end_layout
+
+\begin_layout Standard
+If you don't have GNU Tar, try the following command instead: 
+\end_layout
+
+\begin_layout LyX-Code
+$ gunzip -c CitcomS-2.0.2.tar.gz | tar xf -
+\end_layout
+
+\begin_layout Section
+Installation Procedure
+\end_layout
+
+\begin_layout Standard
+After unpacking the source, use the following procedure to install CitComS:
+\end_layout
+
+\begin_layout Enumerate
+Navigate (i.e., 
+\family typewriter
+cd
+\family default
+) to the directory containing the CitComS source and type .
+\family typewriter
+/configure
+\family default
+ to configure the package for your system
+\newline
+
+\newline
+
+\family typewriter
+$ cd CitcomS-2.0.2
+\family default
+
+\newline
+
+\family typewriter
+$ ./configure
+\end_layout
+
+\begin_layout Enumerate
+Type '
+\family typewriter
+make
+\family default
+' to build the package.
+\family typewriter
+
+\newline
+
+\newline
+$ make
+\end_layout
+
+\begin_layout Enumerate
+Become 
+\family typewriter
+root
+\family default
+ and type 
+\family typewriter
+make install
+\family default
+ to install CitcomS.
+\newline
+
+\newline
+
+\family typewriter
+$ su
+\newline
+Password:
+\newline
+# make install
+\end_layout
+
+\begin_layout Standard
+To install as an ordinary user instead of 
+\family typewriter
+root
+\family default
+, give 
+\family typewriter
+configure
+\family default
+ the 
+\family typewriter
+--prefix
+\family default
+ option, specifying a directory to which you have write access:
+\end_layout
+
+\begin_layout LyX-Code
+$ cd CitcomS-2.0.2
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure --prefix=$HOME/cig
+\end_layout
+
+\begin_layout LyX-Code
+$ make
+\end_layout
+
+\begin_layout LyX-Code
+$ make install
+\end_layout
+
+\begin_layout Standard
+For more details about 
+\family typewriter
+configure
+\family default
+, see the Configuration section below.
+\end_layout
+
+\begin_layout Quote
+
+\series bold
+NOTE:
+\series default
+ If you install as an ordinary user using 
+\family typewriter
+--prefix=PREFIX
+\family default
+ be mindful of the fact that you may have to set various environment variables
+ in order for CitComS to function properly under the given 
+\family typewriter
+PREFIX
+\family default
+.
+ First, you will want to add 
+\family typewriter
+PREFIX/bin
+\family default
+ to your 
+\family typewriter
+PATH.
+
+\family default
+ You may need or want to add 
+\family typewriter
+PREFIX/lib/python2.3/site-packages
+\family default
+ to your 
+\family typewriter
+PYTHONPATH
+\family default
+.
+ Finally, on some obscure Unix systems, you may need to add 
+\family typewriter
+PREFIX/lib
+\family default
+ to your 
+\family typewriter
+LD_LIBRARY_PATH
+\family default
+ (or equivalent).
+ 
+\end_layout
+
+\begin_layout Section
+Configuration
+\end_layout
+
+\begin_layout Standard
+The 
+\family typewriter
+configure
+\family default
+ script checks for various system features.
+ As it runs, it prints messages informing you of which features it is checking
+ for.
+ Upon successful completion, it generates a 
+\family typewriter
+Makefile
+\family default
+ in each source directory of the package.
+ It also generates one or more 
+\family typewriter
+portinfo
+\family default
+ header files, which contain system-dependent definitions (
+\family typewriter
+portinfo
+\family default
+ is equivalent to 
+\family typewriter
+config.h
+\family default
+ in other open-source software packages).
+ 
+\end_layout
+
+\begin_layout Standard
+The 
+\family typewriter
+configure
+\family default
+ script will attempt to guess the correct values of various installation
+ parameters.
+ In the event that the default values used by 
+\family typewriter
+configure
+\family default
+ are incorrect for your system, or 
+\family typewriter
+configure
+\family default
+ is unable to guess the value a certain parameter, you may have to specify
+ the correct value by hand.
+ 
+\end_layout
+
+\begin_layout Section
+Configure Usage
+\end_layout
+
+\begin_layout Standard
+For a detailed list of 
+\family typewriter
+configure
+\family default
+ variables and options, give 
+\family typewriter
+configure
+\family default
+ the 
+\family typewriter
+--help
+\family default
+ option:
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure --help
+\end_layout
+
+\begin_layout Standard
+The following is a summary of the variables and options that are important
+ when installing CitComS.
+ 
+\end_layout
+
+\begin_layout Section
+Environment Variables
+\end_layout
+
+\begin_layout Standard
+Environment variables may be specified as arguments to 
+\family typewriter
+configure
+\family default
+, e.g.,
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure CXX=icpc # compile C++ using the Intel compiler
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="5" columns="2">
+<features>
+<column alignment="left" valignment="top" leftline="true" width="1in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Variable
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Description
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+PYTHON
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Python interpreter.
+ This is useful if you have Python installed in a non-standard location,
+ e.g.,
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\InsetSpace ~
+\InsetSpace ~
+./configure 
+\backslash
+
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\InsetSpace ~
+\InsetSpace ~
+\InsetSpace ~
+\InsetSpace ~
+\InsetSpace ~
+\InsetSpace ~
+PYTHON=/opt/python2.3/bin/python
+\family default
+ 
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+By default, 
+\family typewriter
+configure
+\family default
+ will search for a suitable Python interpreter using your 
+\family typewriter
+PATH
+\family default
+ environment variable.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+CC
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+C compiler command
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+CXX
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+C++ compiler command
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+MPICC
+\end_layout
+
+\begin_layout Standard
+MPICXX
+\end_layout
+
+\begin_layout Standard
+MPIINCLUDES
+\end_layout
+
+\begin_layout Standard
+MPILIBS
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+These variables collectively specify how to build MPI programs.
+ The variables MPICC and MPICXX specify compiler commands; MPIINCLUDES specifies
+ preprocessor flags, and MPILIBS specifies linker flags.
+ See 
+\begin_inset LatexCommand \ref{sec:MPI-Configuration}
+
+\end_inset
+
+ for details and examples.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section
+\begin_inset LatexCommand \label{sec:MPI-Configuration}
+
+\end_inset
+
+MPI Configuration
+\end_layout
+
+\begin_layout Standard
+By default, 
+\family typewriter
+configure
+\family default
+ will search for MPI wrappers (such as
+\family typewriter
+ mpicxx/mpic++
+\family default
+ and 
+\family typewriter
+mpicc
+\family default
+) using your PATH environment variable.
+ You may specify MPI wrappers manually using the variables MPICC and MPICXX.
+ If found, the wrappers will be used to compile MPI-related source, and
+ CC and CXX will default to underlying C/C++ compiler commands (e.g., CC will
+ default to the result of 
+\family typewriter
+mpicc -compile_info
+\family default
+ if you are using MPICH).
+ You may also set CC and CXX manually.
+ The commands specified by CXX and CC are used to compile ordinary C/C++
+ source, and for linking shared libraries.
+\end_layout
+
+\begin_layout Subsection
+Manually specifying MPI wrappers
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+MPICC=/opt/mpich-1.2.6/bin/mpicc 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+MPICXX=/opt/mpich-1.2.6/bin/mpicxx
+\end_layout
+
+\begin_layout Standard
+If MPI wrappers are not found, 
+\family typewriter
+configure
+\family default
+ will set MPICC and MPICXX to CC and CXX, respectively (i.e., the same commands
+ used to build ordinary C/C++ source).
+ Then, configure will attempt to find 
+\family typewriter
+mpi.h
+\family default
+ and an MPI library in the standard locations (e.g., 
+\family typewriter
+/usr/include
+\family default
+ and 
+\family typewriter
+/usr/lib
+\family default
+) using the ordinary compiler.
+ In this scenario, if your MPI header files and libraries are installed
+ in a non-standard location, you must specify MPIINCLUDES and MPILIBS, so
+ that the compiler can find the MPI header files and libraries.
+\end_layout
+
+\begin_layout Subsection
+Manually specifying MPI 
+\family typewriter
+include
+\family default
+ and 
+\family typewriter
+lib
+\family default
+ directories
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+MPIINCLUDES="-I/opt/mpich-1.2.6/include" 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+MPILIBS="-L/opt/mpich-1.2.6/lib -lmpich"
+\end_layout
+
+\begin_layout Subsection
+Manually specifying MPI 
+\family typewriter
+include
+\family default
+ and 
+\family typewriter
+lib
+\family default
+ directories, and an alternative compiler
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+CC=icc 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+CXX=icpc 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+MPIINCLUDES="-I/opt/mpich-1.2.6/include" 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+MPILIBS="-L/opt/mpich-1.2.6/lib -lmpich"
+\end_layout
+
+\begin_layout Standard
+Some words of caution when specifying the MPI configuration:
+\end_layout
+
+\begin_layout Itemize
+Specifying MPI commands and flags in general-purpose 
+\family typewriter
+configure
+\family default
+ variables (such as CC, CXX, CPPFLAGS, and LDFLAGS) may work on some systems,
+ but is not recommended unless you happen to have a shared version of the
+ MPI library installed on your system (
+\family typewriter
+libmpich.so
+\family default
+ or 
+\family typewriter
+libmpi.so
+\family default
+).
+ 
+\end_layout
+
+\begin_layout Itemize
+If you explicitly specify both MPICXX and CXX, CXX will be used to compile
+ all C++ source; MPICXX is invoked merely to determine the correct values
+ for MPIINCLUDES and MPILIBS (if necessary).
+ Likewise, if you explicitly specify both MPICC and CC, CC will be used
+ to compile all C source; MPICC will only be used to determine the MPI flags.
+\end_layout
+
+\begin_layout Itemize
+Configuring CitComS with a different C++ compiler than was used to configure
+ your MPI library may cause link errors.
+ However, the 
+\family typewriter
+configure
+\family default
+ script attempts to detect this scenario and automatically work around the
+ problem for you.
+\end_layout
+
+\begin_layout Section
+Batch System Configuration
+\end_layout
+
+\begin_layout Standard
+If you are installing CitComS on a cluster with a batch system, you can
+ configure CitComS such that the Pyre-based commands 
+\family typewriter
+citcomsregional.sh
+\family default
+ and 
+\family typewriter
+citcomsfull.sh
+\family default
+ automatically submit jobs to the batch queue.
+ CitComS contains support for the LSF, PBS, and Globus batch systems.
+\end_layout
+
+\begin_layout Standard
+The 
+\family typewriter
+configure
+\family default
+ script searches for the 
+\family typewriter
+bsub
+\family default
+, 
+\family typewriter
+qsub
+\family default
+, and 
+\family typewriter
+globusrun
+\family default
+ batch commands.
+ If one of these is found, CitComS is configured to use the corresponding
+ batch system (LSF, PBS, and Globus, respectively) instead of launching
+ MPI jobs directly using 
+\family typewriter
+mpirun
+\family default
+.
+ Run 
+\family typewriter
+./configure --help
+\family default
+ for information on how to configure the batch system parameters manually.
+\end_layout
+
+\begin_layout Standard
+The proper commands to use in a batch script varies from one cluster to
+ the next.
+ On some systems, 
+\family typewriter
+mpirun
+\family default
+ is invoked directly from the batch script.
+ On others, a special wrapper is used instead.
+ Therefore, after successfully installing CitComS, you must edit the following
+ XML configuration file: 
+\end_layout
+
+\begin_layout LyX-Code
+PREFIX/etc/CitcomS/CitcomS.pml
+\end_layout
+
+\begin_layout Standard
+where PREFIX is the directory under which you installed CitcomS (default
+ 
+\family typewriter
+/usr/local
+\family default
+).
+ Edit the defaults as appropriate for your system.
+ For example, if you are using LSF, first verify that CitComS is configured
+ to use LSF: 
+\end_layout
+
+\begin_layout LyX-Code
+<property name="launcher">lsf</property>
+\end_layout
+
+\begin_layout Standard
+Next, edit the LSF section: 
+\end_layout
+
+\begin_layout LyX-Code
+<component name="lsf"> 
+\end_layout
+
+\begin_layout LyX-Code
+      <property name="command">mpijob mpirun</property>
+\end_layout
+
+\begin_layout LyX-Code
+      <property name="batch-command">bsub</property> 
+\end_layout
+
+\begin_layout LyX-Code
+</component>
+\end_layout
+
+\begin_layout Standard
+In particular, set the 
+\family typewriter
+command
+\family default
+ property to the correct command for launching MPI jobs from a batch script
+ on your system.
+ For example:
+\end_layout
+
+\begin_layout LyX-Code
+<property name="command">pam -g 1 gmmpirun_wrapper</property>
+\end_layout
+
+\begin_layout Standard
+You may find the 
+\family typewriter
+--launcher.dry
+\family default
+ option useful while debugging the batch system configuration: 
+\end_layout
+
+\begin_layout LyX-Code
+citcomsregional.sh --launcher.dry
+\end_layout
+
+\begin_layout Standard
+This option will cause CitcomS to perform a "dry run," dumping the batch
+ script to the console, instead of actually submitting it for execution.
+\end_layout
+
+\begin_layout Section
+\begin_inset LatexCommand \label{sec:Installing-without-Pyre}
+
+\end_inset
+
+Installing without Pyre
+\end_layout
+
+\begin_layout Standard
+To build just the CitComS tools (or "drivers") from the legacy C code, give
+ 
+\family typewriter
+configure
+\family default
+ the 
+\family typewriter
+--without-pyre
+\family default
+ option:
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure --without-pyre
+\end_layout
+
+\begin_layout Standard
+The only system requirements for this configuration are an MPI library and
+ a decent C compiler.
+ The final 
+\family typewriter
+make install
+\family default
+ step will install two command-line tools: 
+\family typewriter
+CitcomSFull
+\family default
+ and 
+\family typewriter
+CitcomSRegional
+\family default
+.
+\end_layout
+
+\begin_layout Section
+\begin_inset LatexCommand \label{sec:Software-Repository}
+
+\end_inset
+
+Installing from the Software Repository
+\end_layout
+
+\begin_layout Standard
+The CitcomS source code is available via a Subversion server at the 
+\begin_inset LatexCommand \htmlurl[Geodynamics website]{http://www.geodynamics.org/}
+
+\end_inset
+
+.
+ This allows users to view the revision history of the code, and check out
+ the most recent development version of the software.
+\end_layout
+
+\begin_layout Quote
+
+\series bold
+NOTE: 
+\series default
+If you are content with the prepared source package, feel free to skip this
+ section.
+\end_layout
+
+\begin_layout Subsection
+Tools You Will Need
+\end_layout
+
+\begin_layout Standard
+In addition to the usual system requirements, you will need a handful of
+ additional development tools installed in order to work with the source
+ from the CIG software repository.
+\end_layout
+
+\begin_layout Standard
+First you must have a Subversion client installed.
+ To check, type 
+\family typewriter
+svn
+\family default
+; it should return a usage message.
+ For more information on Subversion, visit the 
+\begin_inset LatexCommand \htmlurl[Subversion website]{http://subversion.tigris.org/}
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout LyX-Code
+$ svn
+\end_layout
+
+\begin_layout LyX-Code
+Type 'svn help' for usage.
+\end_layout
+
+\begin_layout Standard
+Second, you must have the GNU tools Autoconf, Automake, and Libtool installed.
+ To check, enter the following commands:
+\end_layout
+
+\begin_layout LyX-Code
+$ autoconf --version
+\end_layout
+
+\begin_layout LyX-Code
+$ automake --version
+\end_layout
+
+\begin_layout LyX-Code
+$ libtoolize --version
+\end_layout
+
+\begin_layout Standard
+For more information about these GNU tools, see the 
+\begin_inset LatexCommand \htmlurl[GNU website]{http://www.gnu.org/software/}
+
+\end_inset
+
+.
+ The CitComS v2.0.2 source package was created with Autoconf 2.59, Automake
+ 1.9.2, and Libtool 1.5.6.
+\end_layout
+
+\begin_layout Subsection
+Download Source from Subversion
+\end_layout
+
+\begin_layout Standard
+To check out the latest version of the software, use the 
+\family typewriter
+svn checkout
+\family default
+ command:
+\end_layout
+
+\begin_layout LyX-Code
+$ svn checkout svn://geodynamics.org/cig/mc/3D/CitcomS/trunk CitcomS
+\end_layout
+
+\begin_layout Standard
+Like the release version, the development version depends upon Pythia v0.8.
+ In addition, the development version also depends upon a package called
+ Exchanger.
+ Unless you plan to build only the legacy CitComS tools (see 
+\begin_inset LatexCommand \ref{sec:Installing-without-Pyre}
+
+\end_inset
+
+ earlier in this chapter), you will need to check out the Pythia and Exchanger
+ packages as well.
+ Like CitComS, Exchanger is available from the geodynamics.org server.
+ For convenience, Pythia is also available from geodynamics.org.
+ To check out Pythia and Exchanger, use the following commands:
+\end_layout
+
+\begin_layout LyX-Code
+$ svn checkout svn://geodynamics.org/cig/vendor/pythia/v0.8 pythia-0.8 
+\end_layout
+
+\begin_layout LyX-Code
+$ svn checkout svn://geodynamics.org/cig/cs/Exchanger/trunk Exchanger
+\end_layout
+
+\begin_layout Subsection
+Generating the GNU Build System
+\end_layout
+
+\begin_layout Standard
+Your working directory should now contain three subdirectories:
+\end_layout
+
+\begin_layout LyX-Code
+$ ls
+\end_layout
+
+\begin_layout LyX-Code
+CitcomS Exchanger pythia-0.8
+\end_layout
+
+\begin_layout Standard
+Each of the three packages must be configured and built separately, in the
+ following order:
+\end_layout
+
+\begin_layout Enumerate
+pythia-0.8
+\end_layout
+
+\begin_layout Enumerate
+Exchanger
+\end_layout
+
+\begin_layout Enumerate
+CitcomS
+\end_layout
+
+\begin_layout Standard
+But before you can run 
+\family typewriter
+configure
+\family default
+ or 
+\family typewriter
+make
+\family default
+, you must generate the necessary files using the GNU tools.
+ The easiest way to do this is to run 
+\family typewriter
+autoreconf -i 
+\family default
+:
+\end_layout
+
+\begin_layout LyX-Code
+$ cd pythia-0.8
+\end_layout
+
+\begin_layout LyX-Code
+$ autoreconf -i
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure --prefix=$HOME/cig
+\end_layout
+
+\begin_layout LyX-Code
+$ make
+\end_layout
+
+\begin_layout LyX-Code
+$ make install
+\end_layout
+
+\begin_layout Standard
+Then, repeat this process for Exchanger and CitcomS:
+\end_layout
+
+\begin_layout LyX-Code
+$ cd ../Exchanger
+\end_layout
+
+\begin_layout LyX-Code
+$ autoreconf -i
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure --prefix=$HOME/cig
+\end_layout
+
+\begin_layout LyX-Code
+$ make
+\end_layout
+
+\begin_layout LyX-Code
+$ make install
+\end_layout
+
+\begin_layout LyX-Code
+$ # set PYTHONPATH  
+\family roman
+[so that CitComS can find the newly installed Exchanger]
+\end_layout
+
+\begin_layout LyX-Code
+$ export PYTHONPATH=$HOME/cig/lib/python2.4/site-packages:$PYTHONPATH
+\end_layout
+
+\begin_layout LyX-Code
+$ cd ../CitcomS
+\end_layout
+
+\begin_layout LyX-Code
+$ autoreconf -i
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure --prefix=$HOME/cig
+\end_layout
+
+\begin_layout LyX-Code
+$ make
+\end_layout
+
+\begin_layout LyX-Code
+$ make install
+\end_layout
+
+\begin_layout Standard
+The 
+\family typewriter
+autoreconf
+\family default
+ tool runs Autoconf to generate the 
+\family typewriter
+configure
+\family default
+ script from 
+\family typewriter
+configure.ac
+\family default
+.
+ It also runs Automake to generate 
+\family typewriter
+Makefile.in
+\family default
+ from 
+\family typewriter
+Makefile.am
+\family default
+ in each source directory.
+\end_layout
+
+\begin_layout Chapter
+Running CitComS.py
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Section
+Using CitComS.py
+\end_layout
+
+\begin_layout Standard
+CitComS.py usage is similar to that of previous versions of CitComS.
+ Installed under the 
+\family typewriter
+bin
+\family default
+ directory (default 
+\family typewriter
+/usr/local/bin
+\family default
+), 
+\family typewriter
+citcomsregional.sh
+\family default
+ is used for regional models and 
+\family typewriter
+citcomsfull.sh
+\family default
+ for full spherical models.
+ The program
+\family typewriter
+ citcomsregional.sh
+\family default
+ can be executed without any command line options and will run with default
+ parameters; 
+\family typewriter
+citcomsfull.sh
+\family default
+ requires at least 12 processors to run.
+ To do so, you must specify the 
+\family typewriter
+launcher
+\family default
+ parameters, which are called "facilities."
+\end_layout
+
+\begin_layout Standard
+Since you will likely want to specify the parameters of your CitComS runs,
+ you will need to alter both computational details (such as the number of
+ time steps) and controlling parameters specific to your problem (such as
+ the Rayleigh number).
+ Most of the properties you will set using CitComS.py have identical names
+ as the parameters for the old CitComS.
+ 
+\end_layout
+
+\begin_layout Section
+Changing Parameters
+\end_layout
+
+\begin_layout Standard
+Pyre has the following syntax to change parameters from their default values.
+ To change the value of a property of a component, use:
+\end_layout
+
+\begin_layout LyX-Code
+--[component].[property]=[value]
+\end_layout
+
+\begin_layout Standard
+Each component is attached to a facility, so the option above can also be
+ written as: 
+\end_layout
+
+\begin_layout LyX-Code
+--[facility].[property]=[value]
+\end_layout
+
+\begin_layout Standard
+A different component can be attached to a facility by:
+\end_layout
+
+\begin_layout LyX-Code
+--[facility]=[new_component] 
+\end_layout
+
+\begin_layout Section
+Coordinate System and Mesh
+\end_layout
+
+\begin_layout Standard
+In general, CitComS uses meshes that are regular, although considerable
+ flexibility exists for grid refinement in the regional models.
+ In regional meshes, 
+\emph on
+theta
+\emph default
+ is the colatitude measured from the north pole, 
+\emph on
+fi
+\emph default
+ is the east longitude, and z is the radius.
+ 
+\emph on
+theta
+\emph default
+ and 
+\emph on
+fi
+\emph default
+ are in units of radians.
+ Figure 3.1 shows the organization of the mesh in a regional problem.
+ 
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status collapsed
+
+\begin_layout Description
+\begin_inset Graphics
+	filename CitcomS/manual/graphics/c_fig3.jpg
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Global\InsetSpace ~
+Node\InsetSpace ~
+Numbering.
+ Left: Global node numbering starts at the base of arrow A (theta
+\size scriptsize
+min
+\size default
+, fi
+\size scriptsize
+min
+\size default
+, r
+\size scriptsize
+min
+\size default
+), and advances from 1 at the base to 
+\emph on
+nz
+\emph default
+ at the tip.
+ Upon reaching the tip, numbering continues from the base of arrow B (
+\emph on
+nz
+\emph default
++1) to its tip (2 
+\emph on
+nz
+\emph default
+), and so on for all nodes on the plane fi = fi
+\size scriptsize
+min
+\size default
+.
+ Right: After completing each theta radius plane, the fi index is incremented
+ and numbering commences from (theta
+\size scriptsize
+min
+\size default
+, r
+\size scriptsize
+min
+\size default
+) as on the left.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section
+A Simple CitComS Test
+\end_layout
+
+\begin_layout Standard
+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.
+ Instructions for using the full version can be found at 
+\begin_inset LatexCommand \vref{sec:Cookbook-1:-Global}
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Standard
+Execute the following on the command line:
+\end_layout
+
+\begin_layout Paragraph
+\begin_inset LatexCommand \label{sub:Uniprocessor-CitComS-from}
+
+\end_inset
+
+Example: Uniprocessor CitComS from the Command Line
+\end_layout
+
+\begin_layout LyX-Code
+citcomsregional.sh --steps=10 
+\end_layout
+
+\begin_layout LyX-Code
+--controller.monitoringFrequency=5 --solver.datafile=example 
+\end_layout
+
+\begin_layout LyX-Code
+--solver.mesher.nodex=17 --solver.mesher.nodey=17
+\end_layout
+
+\begin_layout Standard
+This runs a default convection problem in a regional domain for 10 time
+ steps and with a mesh of 17 
+\begin_inset Formula $\times$
+\end_inset
+
+ 17 
+\begin_inset Formula $\times$
+\end_inset
+
+ 9 nodal points.
+ See Chapter 
+\begin_inset LatexCommand \vref{cha:Postprocessing-and-Graphics}
+
+\end_inset
+
+ for instructions to immediately visualize your results with OpenDX.
+\end_layout
+
+\begin_layout Section
+Multiprocessor Example
+\end_layout
+
+\begin_layout Standard
+On input, CitComS needs numerous parameters specified (see Appendix A for
+ full list).
+ Most parameters have sensible default values.
+ Depending on those input parameters, CitComS could also require numerous
+ input files, such as velocity boundary conditions which could be used for
+ time dependent, plate tectonic problems.
+ Finally, CitComS will potentially output a large number of files which
+ will be spread throughout the file systems contained in the individual
+ nodes of your Beowulf.
+ This means that you will have to organize your directories carefully when
+ running CitComS so that you can find your way through these files as well
+ as use a post-processing program contained with this distribution.
+ (In the example that follows, these output files would be placed in 
+\family typewriter
+/scratch/username
+\family default
+ with a filename prefix 
+\family typewriter
+example1
+\family default
+ on each individual node.)
+\end_layout
+
+\begin_layout Standard
+It is possible to input the parameters relevant to your test run from the
+ command line:
+\end_layout
+
+\begin_layout Paragraph
+Example: Multiprocessor CitComS from the Command Line
+\end_layout
+
+\begin_layout LyX-Code
+$ citcomsregional.sh --launcher.nodes=4 
+\end_layout
+
+\begin_layout LyX-Code
+--launcher.nodegen="n%03d" --launcher.nodelist=[101-102] 
+\end_layout
+
+\begin_layout LyX-Code
+--solver.mesher.nprocx=2 --solver.mesher.nprocy=2 
+\end_layout
+
+\begin_layout LyX-Code
+--solver.datafile="/scratch/username/example1"
+\end_layout
+
+\begin_layout Standard
+However, entering all those parameters via the command line involves the
+ risk of typographical errors, which can lead to undesired results.
+ So, you may find it easier to write a brief shell script that contains
+ the parameters.
+ The file should have the suffix 
+\family typewriter
+.sh
+\family default
+.
+ When you downloaded the CitComS source, this included an 
+\family typewriter
+examples
+\family default
+ directory.
+ In this directory, you will find a script called 
+\family typewriter
+example1.sh
+\family default
+.
+ 
+\end_layout
+
+\begin_layout Paragraph
+Example: Simple Regional CitComS Shell Script, example1.sh 
+\end_layout
+
+\begin_layout LyX-Code
+#!/bin/sh
+\newline
+
+\end_layout
+
+\begin_layout LyX-Code
+citcomsregional.sh 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--steps=71 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--controller.monitoringFrequency=10 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--launcher.nodes=4 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--launcher.nodegen="n%03d" 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--launching.nodelist=[101-102,101-102] 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--solver.datafile=/scratch/username/example1 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--solver.mesher.nprocx=2 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--solver.mesher.nprocy=2 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--solver.mesher.nodex=17 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--solver.mesher.nodey=17 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--solver.mesher.nodez=9 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+# End of file
+\end_layout
+
+\begin_layout Standard
+This is a basic problem with 2 processors in colatitude (x-coordinate),
+ 2 in longitude (y-direction), and 1 in the radial (z-direction).
+ In addition, there will be 17 nodes in x, 17 nodes in y, and 9 nodes in
+ z.
+\end_layout
+
+\begin_layout Standard
+It is important to realize that within the code (and in finite element analysis)
+ the term "node" refers to the mesh points defining the corners of the elements.
+ Unfortunately, "nodes" also refers to the individual computers which make
+ up the Beowulf PC cluster.
+ In 
+\family typewriter
+example1.sh
+\family default
+, this is indicated with:
+\end_layout
+
+\begin_layout LyX-Code
+--solver.mesher.nprocx=2 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--solver.mesher.nprocy=2 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--solver.mesher.nodex=17 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--solver.mesher.nodey=17 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--solver.mesher.nodez=9 
+\backslash
+ 
+\end_layout
+
+\begin_layout Standard
+These quantities refer to the total number of FEM nodes in a given direction
+ for the complete problem and for the example it works out that within a
+ given processor there will be 9 x 9 x 9 nodes.
+ Note that in the x-direction (or y) that for the entire problem there are
+ 17 nodes and there is one node shared between two processors.
+ This shared node is duplicated in two adjacent processors.
+ The global numbering of FEM nodes is z-direction first, then x-direction,
+ then y-direction.
+ This numbering convention is used for the input and output data.
+\end_layout
+
+\begin_layout Standard
+In order to run this example you should be on your front end and be in the
+ directory in which the input file is located, in this case, the 
+\family typewriter
+examples
+\family default
+ directory.
+ To run the test example, invoke the following:
+\end_layout
+
+\begin_layout LyX-Code
+$ ./example1.sh
+\end_layout
+
+\begin_layout Standard
+Once you have completed your run, you will notice that it generates a file
+ called 
+\family typewriter
+mpirun.nodes
+\family default
+.
+ It will contain a list of the nodes where CitComS has run.
+ You may want to login to one of the nodes to check that the data appears
+ to have been properly generated.
+ You should also check the log file for any error messages.
+ 
+\end_layout
+
+\begin_layout Standard
+If you receive a message such as 
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+bash: --solver.mesher.nodez=9: command not found
+\end_layout
+
+\begin_layout Standard
+chances are your script is missing a line continuation or has an extra space.
+ However, most of the time CitComS will just run using the default values
+ -- even if it finds a typographical error such as "nnode" instead of "node."
+ So, along with double-checking your parameters as you type them in, you
+ should check your results to be sure they make sense.
+ 
+\end_layout
+
+\begin_layout Standard
+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 and proceed to the next chapter.
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Chapter
+\begin_inset LatexCommand \label{cha:Postprocessing-and-Graphics}
+
+\end_inset
+
+Postprocessing and Graphics
+\end_layout
+
+\begin_layout Section
+Introduction
+\end_layout
+
+\begin_layout Standard
+Once you have run CitComS, you should have a series of output files (potentially
+ spread throughout the file systems of your Beowulf).
+ You will have to retrieve and combine the data for the time-step (age)
+ of interest.
+\end_layout
+
+\begin_layout Standard
+To visualize your results, it is recommended that you use the open source
+ Open Visualization Data Explorer, better known as OpenDX.
+ Both the software and tutorials are available from the 
+\begin_inset LatexCommand \htmlurl[OpenDX website]{http://www.opendx.org/}
+
+\end_inset
+
+.
+ If you are using Mac OS X, a free version OpenDX is available via 
+\begin_inset LatexCommand \htmlurl[Fink]{http://fink.sourceforge.net/}
+
+\end_inset
+
+.
+ However, if the installation proves to be difficult, a binary version is
+ available (for a fee) from 
+\begin_inset LatexCommand \htmlurl[VIS Inc.]{http://www.vizsolutions.com/macdx.html}
+
+\end_inset
+
+.
+ 
+\end_layout
+
+\begin_layout Section
+Processing on a Beowulf Cluster
+\end_layout
+
+\begin_layout Standard
+Generally, the results from your CitComS run will be distributed on disks
+ attached to individual nodes of your Beowulf cluster.
+ The output files are written in each node under the directory that you
+ specified as your datafile in the input file.
+ To examine those files, login to a node and change directories to the one
+ you specified with a prefix.
+ For example, if you selected your datafile to be called 
+\family typewriter
+datafile="/scratch/username/test-case"
+\family default
+, then your output file will be written to 
+\family typewriter
+/scratch/username
+\family default
+ and will have the prefix 
+\family typewriter
+test-case
+\family default
+.
+ An example of a filename for the velocity output is 
+\family typewriter
+test-case.velo.2.10
+\family default
+ where 
+\family typewriter
+test-case
+\family default
+ is the model prefix, 
+\family typewriter
+velo
+\family default
+ means that this is a velocity data file, 
+\family typewriter
+2
+\family default
+ corresponds to the processor number (so it is output by the 2nd processor)
+ , and 
+\family typewriter
+10
+\family default
+ corresponds to the time-step.
+ 
+\end_layout
+
+\begin_layout Standard
+To choose an age to export for postprocessing, you have to find out which
+ time step corresponds to the age that interests you.
+ This is done by looking at the log or time file, for example, 
+\family typewriter
+test-case.log
+\family default
+.
+ The log file contains data that describes the details of the computation.
+ It also has a 
+\family typewriter
+current age
+\family default
+ field that lists the time step numbers and their corresponding times.
+ The time step value you selected is what will be exported for postprocessing.
+ The time file contains the non-dimensional model time.
+ The format of the time file can be found in Appendix C.
+ 
+\end_layout
+
+\begin_layout Standard
+These output files need to be post-processed before you can do the visualization.
+ There are two scripts and both can post-process (retrieve and combine)
+ CitComS output: 
+\family typewriter
+autocombine.py
+\family default
+ and 
+\family typewriter
+batchcombine.py
+\family default
+.
+ It is recommened to use 
+\family typewriter
+autocombine.py
+\family default
+ over 
+\family typewriter
+batchcombine.py
+\family default
+, as the former is easier to use.
+ 
+\end_layout
+
+\begin_layout Standard
+To use 
+\family typewriter
+autocombine.py
+\family default
+, you have to run CitComS.py in a slightly different way.
+ CitComS.py prints out the input parameters to the screen.
+ That printout can be redirected to a file, which can be used later to retrieve
+ input parameters.
+ This is done with: 
+\end_layout
+
+\begin_layout LyX-Code
+$ my_citcoms.py_script > input_param 
+\end_layout
+
+\begin_layout Standard
+Then, you can retrieve and combine data of step 10 by using: 
+\end_layout
+
+\begin_layout LyX-Code
+$ autocombine.py mpirun.nodes input_param 10 
+\end_layout
+
+\begin_layout Standard
+This reads the MPI machinefile (
+\family typewriter
+mpirun.nodes
+\family default
+) and CitComS.py input parameters (
+\family typewriter
+input_param
+\family default
+), then calls 
+\family typewriter
+batchcombine.py
+\family default
+ to do the actual job.
+ The general usage for 
+\family typewriter
+autocombine.py
+\family default
+ is: 
+\end_layout
+
+\begin_layout LyX-Code
+$ autocombine.py [machinefile] [input_param] 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+[step1] [step2 or more ...] 
+\end_layout
+
+\begin_layout Standard
+If you do not have the input parameters saved to a file, you have to use
+ 
+\family typewriter
+batchcombine.py
+\family default
+ to retrieve and combine the data.
+ The general usage for 
+\family typewriter
+batchcombine.py
+\family default
+ is: 
+\end_layout
+
+\begin_layout LyX-Code
+$ batchcombine.py [machinefile] [modeldir] [modelname] 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+[timestep] [nodex] [nodey] [nodez] [n-surf-cap] 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+[nprocx] [nprocy] [nprocz] 
+\end_layout
+
+\begin_layout Standard
+where 
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+machinefile
+\family default
+ is the file with a list of all the machines you are using, which under
+ normal circumstances are the same as the launching nodes.
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+modeldir
+\family default
+ is the scratch directory where all your files are located.
+ This should correspond to the first part of the 
+\family typewriter
+datafile
+\family default
+ entry, e.g., 
+\family typewriter
+/scratch/username
+\family default
+.
+ 
+\family typewriter
+modelname
+\family default
+ is the model prefix for example 
+\family typewriter
+test_case
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+timestep
+\family default
+ is the time step you want to export.
+ This corresponds to the last term in the filename of the velocity file.
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+nodex
+\family default
+, 
+\family typewriter
+nodey
+\family default
+, 
+\family typewriter
+nodez
+\family default
+ are the same values as those used in the input file.
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+n-surf-cap
+\family default
+ is equal to 1 for regional CitComS and 12 for full CitComS.
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+nprocx
+\family default
+, 
+\family typewriter
+nprocy
+\family default
+, 
+\family typewriter
+nprocz
+\family default
+ are the same values as those used in the input file.
+\end_layout
+
+\begin_layout Standard
+If your Beowulf cluster uses ssh (rather than rsh) to access the computation
+ nodes, you have to manually edit 
+\family typewriter
+bin/batchpaste.sh
+\family default
+ and replace 'rsh' to 'ssh' in the file.
+ If your cluster forbids access to the computation nodes, you can still
+ post-process your output files (if they all reside in one directory) by
+ following the instructions in the next section.
+ 
+\end_layout
+
+\begin_layout Standard
+Once 
+\family typewriter
+autocombine.py
+\family default
+ or 
+\family typewriter
+batchcombine.py
+\family default
+ has been run, you should end up with 2 files (or 24 files for full CitComS)
+ that resemble these: 
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+test-case.cap0.10.general
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+test-case.cap0.10
+\end_layout
+
+\begin_layout Standard
+The latter file is the data file containing simulation results; its format
+ can be found in Appendix C.
+ The former file is the OpenDX header for the data.
+\end_layout
+
+\begin_layout Section
+Postprocessing in a Non-Cluster Environment
+\end_layout
+
+\begin_layout Standard
+If you have run CitComS in a non-cluster environment or all of your data
+ resides in a single directory, you can still use 
+\family typewriter
+autocombine.py
+\family default
+ or 
+\family typewriter
+batchcombine.py
+\family default
+ to combine the data.
+ The 
+\family typewriter
+machinefile
+\family default
+ is not needed and can be replaced by 
+\family typewriter
+localhost
+\family default
+, such as: 
+\end_layout
+
+\begin_layout LyX-Code
+$ autocombine.py localhost [input_param] 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+[step1] [step2 or more ...] 
+\end_layout
+
+\begin_layout Standard
+or 
+\end_layout
+
+\begin_layout LyX-Code
+$ batchcombine.py localhost [modeldir] [modelname] [timestep] 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+[nodex] [nodey] [nodez] [n-surf-cap] 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+[nprocx] [nprocy] [nprocz] 
+\end_layout
+
+\begin_layout Section
+Using OpenDX for Regional Visualization
+\end_layout
+
+\begin_layout Standard
+OpenDX modules designed for CitComS can be found in the directory called
+ 
+\family typewriter
+PREFIX/share/CitcomS/visual
+\family default
+, where PREFIX is the directory under which you installed CitcomS (default
+ 
+\family typewriter
+/usr/local
+\family default
+).
+ You will need both the 
+\family typewriter
+.net
+\family default
+ and 
+\family typewriter
+.cfg
+\family default
+ files.
+ 
+\end_layout
+
+\begin_layout Standard
+In this example, you will use 
+\family typewriter
+visRegional.net
+\family default
+ to visualize the result of regional CitComS.py.
+ (You will use 
+\family typewriter
+visFull.net
+\family default
+ to visualize the result of full CitComS.py.) You should launch OpenDX by
+ typing: 
+\end_layout
+
+\begin_layout LyX-Code
+$ dx 
+\end_layout
+
+\begin_layout Standard
+You will see an OpenDX 
+\family sans
+Data Explorer
+\family default
+ window.
+ Click 
+\family sans
+Edit Visual Programs
+\family default
+ and select 
+\family typewriter
+visRegional.net
+\family default
+ from the file selector.
+ You will see a 
+\family sans
+Visual Program Editor
+\family default
+ window.
+ Then select the 
+\family sans
+import
+\family default
+ tab in the main window and double-click on the 
+\family sans
+FileSelector
+\family default
+ block, which will open a 
+\family sans
+Control Panel
+\family default
+ window.
+ In the 
+\family sans
+CitcomSImport
+\family default
+ filename input box, select your postprocessed data file, e.g.,
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+test-case.cap0.10.general
+\end_layout
+
+\begin_layout Standard
+(For the global model,  double-click on the 
+\family sans
+FileSelector
+\family default
+ block, select one of the 12 processed data files in 
+\family sans
+CitcomsFullImport format_string
+\family default
+ field.
+ Then, edit the filename with the cap number replaced by 
+\family typewriter
+%d
+\family default
+, e.g.,
+\family typewriter
+ test-case.cap%d.10.general
+\family default
+.) In the pulldown menu, select
+\family typewriter
+ 
+\family sans
+Execute\SpecialChar \menuseparator
+Execute Once
+\family default
+ or 
+\family sans
+Execute on Change
+\family default
+.
+ A new window will appear with the image of the model.
+ 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
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\begin_inset Graphics
+	filename CitcomS/manual/graphics/c_fig5.eps
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Regional Model Visualized with OpenDX.
+ A snapshot of an upwelling (blue isosurface) with a slice of the temperature
+ field (bisecting plane).
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+Additional options in the control panel window for the regional model include:
+\end_layout
+
+\begin_layout Itemize
+
+\family sans
+CitcomSImport reduced
+\family default
+, can increase or reduce the resolution.
+ 
+\end_layout
+
+\begin_layout Itemize
+
+\family sans
+Core radius
+\family default
+ is the size of the orange sphere which represents the core-mantle boundary.
+\end_layout
+
+\begin_layout Itemize
+
+\family sans
+Isosurface value
+\family default
+ is the temperature isosurfaces.
+ You can change the values of the isosurfaces, including adding additional
+ isosurfaces or deleting existing ones.
+ 
+\end_layout
+
+\begin_layout Itemize
+ 
+\family sans
+Slab cut dimension
+\family default
+ is the direction of the slab (an OpenDX term of cross-section).
+ 
+\end_layout
+
+\begin_layout Itemize
+ 
+\family sans
+Slab cut position
+\family default
+ is the position of the slab.
+  
+\end_layout
+
+\begin_layout Standard
+After changing any of these parameters, you must select 
+\family sans
+Execute\SpecialChar \menuseparator
+Execute Once
+\family default
+ to redraw the model.
+ You can change any of the parameters, visualization, or set-up by going
+ back to the main window and clicking on each tab.
+ If you click on each block, you will be able to change the settings for
+ that function.
+ 
+\end_layout
+
+\begin_layout Chapter
+Cookbooks
+\end_layout
+
+\begin_layout Section
+Introduction
+\end_layout
+
+\begin_layout Standard
+These cookbook examples are meant to serve as a guide to some of the types
+ of problems CitComS.py can solve.
+ Cookbook examples range from regional to full spherical shell problems
+ that address traditional convection problems.
+\end_layout
+
+\begin_layout Section
+\begin_inset LatexCommand \label{sec:Cookbook-1:-Global}
+
+\end_inset
+
+Cookbook 1: Global Model Using 
+\family sans
+fullcitcoms
+\end_layout
+
+\begin_layout Subsection
+Problem
+\end_layout
+
+\begin_layout Standard
+You would like to solve for thermal convection within a full spherical shell
+ domain.
+ One of the versions of CitComS.py is designed to run on a cluster that decompose
+s the shell into 12 equal "caps" and then distributes the calculation for
+ caps onto separate processors.
+ To run CitComS.py with the full solver parameter set, it is recommended
+ that you have a minimum of 12 processors available on your cluster.
+ 
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement h
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\begin_inset Graphics
+	filename CitcomS/manual/graphics/cookbook1.eps
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+\begin_inset LatexCommand \label{fig:Global-Model-"Caps":}
+
+\end_inset
+
+Global\InsetSpace ~
+Model\InsetSpace ~
+"Caps": Left (A): Three-dimensional perspective image showing
+ 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
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Solution
+\end_layout
+
+\begin_layout Standard
+You will be running 
+\family sans
+cookbook1.sh
+\family default
+ which calls the script 
+\family sans
+citcomsfull.sh
+\family default
+.
+ The first set of parameters specifies the number of nodes (12) and their
+ names on your cluster through Pyre's 
+\family sans
+launcher
+\family default
+ facility.
+\end_layout
+
+\begin_layout LyX-Code
+--launcher.nodes=12 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--launcher.nodegen="n%03d" 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--launcher.nodelist=[101-106,101-106] 
+\backslash
+  
+\end_layout
+
+\begin_layout Standard
+The second set of parameters specifies the number of time steps (101), and
+ how often the computation should be monitored (25).
+\end_layout
+
+\begin_layout LyX-Code
+--steps=101 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--controller.monitoringFrequency=25 
+\backslash
+ 
+\end_layout
+
+\begin_layout Standard
+The last set of parameters includes 
+\end_layout
+
+\begin_layout Itemize
+the location of the output, e.g.,
+\family typewriter
+ /scratch/username/cookbook1
+\end_layout
+
+\begin_layout Itemize
+the number of perturbations (1)
+\end_layout
+
+\begin_layout Itemize
+the number of nodal lines in the longitudinal direction (4), e.g., spherical
+ harmonic in terms of time-step order or 
+\family typewriter
+perturbm=2
+\family default
+,
+\end_layout
+
+\begin_layout Itemize
+the number of nodal lines in the latitudinal direction, e.g., spherical harmonic
+ degree 
+\family typewriter
+perturbl=3
+\end_layout
+
+\begin_layout Quote
+Note that although the number of perturbations is assigned here as 
+\family typewriter
+solver.ic.num_perturbations=1
+\family default
+, that is actually the default value.
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout LyX-Code
+--solver.datafile="/scratch/username/cookbook1" 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--solver.ic.num_perturbations=1 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--solver.ic.perturbl=3 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--solver.ic.perturbm=2 
+\end_layout
+
+\begin_layout Standard
+Assuming your script is named 
+\family typewriter
+cookbook1.sh
+\family default
+, it is run by typing 
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout LyX-Code
+$ ./cookbook1.sh
+\end_layout
+
+\begin_layout Subsection
+Cookbook 1: Global Model
+\end_layout
+
+\begin_layout LyX-Code
+#!/bin/sh
+\newline
+
+\newline
+../../tests/citcomsfull.sh 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--launcher.nodes=12 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--launcher.nodegen="n%03d" 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--launcher.nodelist=[141-146,141-146] 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--steps=101 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--controller.monitoringFrequency=25 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--solver.datafile="/scratch/username/Test/cookbook1" 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--solver.ic.num_perturbations=1 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--solver.ic.perturbl=3 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--solver.ic.perturbm=2 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--solver.rayleigh=5.0e+4
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+# End of file
+\end_layout
+
+\begin_layout Standard
+Once you have run the model, you can visualize it using OpenDX, described
+ in the previous chapter.
+ When you invoke "Edit Visual Program," you will need to select 
+\family typewriter
+visFull.net
+\family default
+.
+ 
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\begin_inset Graphics
+	filename CitcomS/manual/graphics/cookbook1.2.jpg
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Cookbook 1: Global Model.
+ This image depicts a slice through a spherical model of convection, with
+ warmer colors indicating upwelling and the cooler colors showing downwelling.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Discussion
+\end_layout
+
+\begin_layout Standard
+You have generated a simple example of the full CitComS model, with minimal
+ parameter alterations.
+ With a default Rayleigh number of 
+\begin_inset Formula $10^{5}$
+\end_inset
+
+ and perturbation on the initial temperature field which has a degree-3
+ and an order-2 pattern, after 100 time steps, the convection pattern remains
+ relatively steady.
+\end_layout
+
+\begin_layout Standard
+As a note, it is not required that 12 processors, with one spherical cap
+ per processor, be used.
+ As an end-member possibility, 12 different jobs could be run on a single
+ computer by invoking:
+\end_layout
+
+\begin_layout LyX-Code
+--launcher.node=12 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+--launcher.node="n%03d" 
+\backslash
+ 
+\end_layout
+
+\begin_layout LyX-Code
+--launcher.nodelist=[101,101,101,101,101,101,101,101,101,101,101,101]
+\backslash
+
+\end_layout
+
+\begin_layout Standard
+This is not particularly efficient, but it does illustrate the flexibility
+ of both 
+\family typewriter
+mpi
+\family default
+ and Pyre.
+\end_layout
+
+\begin_layout Part
+Appendices
+\end_layout
+
+\begin_layout Chapter
+\start_of_appendix
+\begin_inset LatexCommand \label{cha:Appendix-A:-Facilities,}
+
+\end_inset
+
+Facilities, Properties, and Parameters
+\end_layout
+
+\begin_layout Section*
+Introduction
+\end_layout
+
+\begin_layout Standard
+Most of the properties have identical names for the parameters as those
+ used in the regular version of CitComS.
+ This section highlights those which have changed and those which are entirely
+ new.
+ All the parameters which can be set are included in an appendix at the
+ end of this documentation.
+ Parameters are given with their default values.
+ 
+\end_layout
+
+\begin_layout Section*
+Parameters that Control Input Files
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="8" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+datafile=""
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+datafile
+\family default
+ controls the location of output files and the prefix of their names.
+ In this case the directory /scratch/ must be created a priori.
+ Files such as test.xxx, e.g., 
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size small
+datafile="/scratch/test"
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+file_vbcs=0 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If 
+\family typewriter
+file_vbcs
+\family default
+ is true (it is set=1) then the top surface velocity boundary conditions
+ are read in from files which have location and name specified by 
+\family typewriter
+vel_bound_file.
+
+\family default
+ The conditions on the top surface must be correctly set, as indicated below.
+ If you wish to have a uniform top surface velocity boundary condition or
+ some simple geometric pattern, then 
+\family typewriter
+file_vbcs
+\family default
+ should be set to zero.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+vel_bound_file=""
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+See explanation for 
+\family typewriter
+file_vbcs
+\family default
+, above.
+ Velocity boundary conditions are read by setting the pathway to the boundary
+ conditions file, e.g., 
+\family typewriter
+\size footnotesize
+vel_bound_file="/username/Models/New_Tonga/Vel/bvel.dat" 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+coor=off
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If you wish to have a regular, but uneven, spacing between elements then
+ 
+\family typewriter
+coor
+\family default
+ should be set to on.
+ If 
+\family typewriter
+coor
+\family default
+ is set to off, then there will be uniform mesh in the latitudinal, longitudinal
+, and radial directions, e.g.,  
+\family typewriter
+\size small
+coor_file="/username/Models/New_Tonga/Case2/coor.dat"
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+coor_file=""
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+See 
+\family typewriter
+coor
+\family default
+, above, e.g., 
+\family typewriter
+\size small
+coor_file="/username/Models/New_Tonga/Case2/coor.dat"
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" newpage="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+mat_control=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+\size small
+mat_file="/home/clint/back/ra8/mat.dat"
+\family default
+\size default
+ If mat_control is true (it is set=1) then the time- and positional-dependent
+ viscosity factor is defined by file having location and name specified
+ bymat_file.
+ These parameters allow you to define the material group of each element
+ (such as a moving weak zone).
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+lith_age=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+\size footnotesize
+lith_age_file="/username/Models/New_Tonga/Case6/age.dat"
+\family default
+\size default
+ If lith_age is true (it is set=1) then the lith_age_file is read.
+ These parameters control the thermal age of the top thermal boundary condition.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+tracer=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+\size small
+tracer_file=""
+\family default
+\size default
+ This controls the tracer particles which are advected passively by the
+ flow.
+ This part of the code has not been made parallel and must be used with
+ caution with the present implementation.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Mesh Set-up and Processors
+\end_layout
+
+\begin_layout Standard
+Parameters control the logical set-up of the mesh as well as the number
+ of processors in the three coordinate directions.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="5" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nproc_surf=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+This specifies the number of spherical caps of the mesh, must be 1 for CitComS.py
+ and 12 for fullCitComS.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nprocx=2
+\newline
+nprocy=2
+\newline
+nprocz=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+These specify the number of processors in each spherical cap.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nodex=17
+\newline
+nodey=17
+\newline
+nodez=9
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+These specify the number of FEM nodes in each spherical cap.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+mgunitx=8
+\newline
+mgunity=8
+\newline
+mgunitz=8
+\newline
+levels=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+These specify the nested level of multigrid unit.
+ Used by multigrid solver only.
+ These parameters are not completely independent to each other.
+ Some constraints must be satisfied:
+\newline
+
+\newline
+nodex = 1 + nprocx * mgunitx * 2 **
+ (levels-1)
+\newline
+nodey = 1 + nprocy * mgunity * 2 ** (levels-1)
+\newline
+nodez = 1 + nprocz
+ * mgunitz * 2 ** (levels-1)
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nprocx=nprocy; 
+\newline
+nodex=nodey;
+\newline
+mgunitx=mgunity
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+For fullCitComS only
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+\noindent
+Domain Size
+\end_layout
+
+\begin_layout Standard
+\noindent
+Parameters which control the actual physical size of the domain (a cut out
+ of a sphere).
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="2" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+theta_min=1.0780
+\newline
+theta_max=2.0708
+\newline
+fi_min=0
+\newline
+fi_max=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+theta_min and theta_max are the colatitude measured in radians from the
+ north pole.
+ fi_min and fi_max are the longitudes measured from the prime meridian eastward
+ in radians.
+ Only in CitComS.py.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+radius_inner=0.55
+\newline
+radius_outer=1.0 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+radius_inner and radius_outer are the inner and outer radius in non-dimensional
+ units.
+ It is probably most convenient to normalize lengths by the radius of the
+ Earth.
+ If you do this, then the Rayleigh number, given below, must be calculated
+ with the radius of the Earth, not the thickness of the mantle.
+ The core mantle boundary is close to having a non-dimensional radius of
+ 0.55.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Restarting the Code
+\end_layout
+
+\begin_layout Standard
+Parameters which control the restarting of the code.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="2" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+restart=0
+\newline
+post_p=0
+\newline
+datafile_old=""
+\newline
+solution_cycles_init=100
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If restart is true, for example, processor #5 will read its initial temperature
+ field formfile 
+\family typewriter
+/scratch/test.velo.5.100
+\family default
+ in this case.
+ If post_p is true, e.g., processor #5 will read its initial temperature field
+ form file
+\family typewriter
+ /scratch/test.velo.5.100
+\family default
+ in this case, just like when restart is true.
+ But the program will run for 1 time step only.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+zero_elapsed_time=1 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If zero_elapsed_time is true, the initial time is set to zero.
+ If it is false and restart or post_p is true, the initial time is read
+ in from previous output files.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Run Length, Output Interval
+\end_layout
+
+\begin_layout Standard
+Parameters which control the length of the run and the interval between
+ writing output files.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="1" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+minstep=1
+\newline
+run=8001
+\newline
+maxtotstep=8001
+\newline
+monitoringFrequency=10
+\newline
+cpu_limits_in_seconds=
+  \InsetSpace ~
+\InsetSpace ~
+\InsetSpace ~
+360000000
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+The maximum number of time steps is set with run and maxtotstep.
+ It is recommended that these be set to the same value.
+ Add one to the total number of steps; in this example, the total steps
+ is 8000.
+ The minimum number of time steps is set with minstep; monitoringFrequency
+ controls the interval between output files.
+ CitComS dynamically determines the non-dimensional time step (such as _t);
+ this means that you might not get an output at the exact time required,
+ but you can always get close depending on how small monitoringFrequency
+ is.
+ Do not make this number too small since outputs slow the code down and
+ you may end up with an unmanageable number of output files.
+ You can also control the termination of the code based on total wall clock
+ time using cpu_limits_in_seconds.
+ If you are just learning to use the code, you might want to give this a
+ small value so that it doesn't burn up valuable computer time.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Initial Conditions
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Tabular
+<lyxtabular version="3" rows="1" columns="2">
+<features>
+<column alignment="center" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+\align left
+num_perturbations=1
+\newline
+perturbmag=0.05
+\newline
+perturbl=1 
+\newline
+perturbm=1  
+\newline
+perturblayer=5
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+The initial temperature is a linear temperature gradient with some perturbations
+, and num_perturbations specifies the number of perturbations.
+ The amplitude of the perturbations is specified in the list of real numbers
+ by perturbmag.
+ In fullCitComS, perturbl and perturbm specify the shape of the perturbations
+ in spherical harmonic degree and order; perturblayer specifies the layers
+ to be perturbed.
+ In regitcoms, perturbl and preturbm specify the number of nodal lines in
+ longitudinal and latitudinal directions; perturblayer is not used, although
+ the pertublayer represents the number of the mesh node in radiad direction.
+ There must be as many entries in a comma-separated list as in num_perturbations.
+ No spaces are allowed in the list.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Boundary Conditions
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="5" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+topvbc=0
+\newline
+topvbxval=0.0
+\newline
+topvbyval=0.0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Surface velocity boundary condition parameters.
+ If topvbc is 0, the topvbxval and topvbyval specify the tangential surface
+ stress (forced BC).
+ If topvbc is 1, topvbxval and topvbyval specify the tangential surface
+ velocity (fixed BC).
+ The surface normal velocity is zero in these two cases (impermeable BC).
+ If topvbc is 2, the surface normal and tangential stress are zero (permeable
+ BC).
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+botvbc=0
+\newline
+botvbxval=0.0
+\newline
+botvbyval=0.0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+As above, but for bottom velocity boundary conditions.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+toptbc=1
+\newline
+toptbcval=0.0 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Surface temperature boundary conditions.
+ If toptbc is 0, the toptbcval specifies the surface heatflux.
+ If toptbc is 1, the toptbcval specifies the surface temperature.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+bottbc=1
+\newline
+bottbcval=1.0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+As above, but for bottom temperature boundary conditions.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+lith_age_time=0  lith_age_depth=0.031400  mantle_temp=1.000000  temperature_bound_
+adj=0  depth_bound_adj=0.157000  width_bound_adj=0.087270 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Boundary condition when lith_age is true.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Miscellaneous
+\end_layout
+
+\begin_layout Standard
+The following are some miscellaneous parameters.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="2" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+stokes_flow_only=0 inputdiffusivity= 0.001000
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+stokes_flow_only is a parameter which can lead to confusion.
+ If you wish only to solve for the velocity once (e.g., Stokes flow) then
+ make this parameter true (i.e.
+ ,1 or on).
+ However, if you want to do a convection problem then this should be false,
+ as indicated in the example.
+ At this point, don't change the parameter inputdiffusivity -- this may
+ play a role in problems which are integrated backward in time.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+rayleigh=1.357e+08 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+This specifies the Rayleigh number, which is one of the most important parameter
+s you may want to change.
+ It is defined as Q0=0.0 This specifies the internal heating number.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Required Information
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="1" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Problem=convection
+\newline
+Geometry=sphere
+\newline
+Spacing=regular 
+\newline
+Solver=cgrad 
+\newline
+node_assemble=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+For the version of CitComS you received in your distribution, all of these
+ parameters must be set as indicated.
+ You need other versions of CitComS if you wish these parameters to take
+ on different geometries, problems, or mesh spacing, or use different solvers.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Depth Information
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="1" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+z_lith=0.014
+\newline
+z_410=0.06435
+\newline
+z_lmantle=0.105
+\newline
+z_cmb=0.439
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Specify the non-dimensional depth of Moho, 410km discontinuity, 660km discontinu
+ity and D".
+ These parameters are used to determine the depth of material interfaces
+ and phase changes (see next two sections).
+ The names are only suggestive.
+ You are free to refer z_lith to an arbitrary depth, for example.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Viscosity
+\end_layout
+
+\begin_layout Standard
+Parameters which control the viscosity.
+ 
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="7" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Viscosity=system
+\newline
+rheol=3 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+For the version of CitComS you received in your distribution, all of these
+ parameters must be set as indicated.
+ When rheol=3, temperature dependent viscosity is computed by: 
+\family typewriter
+\size footnotesize
+viscosity = visc0 * exp( viscE/(T+viscT) - viscE/(1+viscT) )
+\family default
+\size default
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+visc_smooth_method=3 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+This specifies which method to smooth viscosity projection for multigrid
+ solver.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+VISC_UPDATE=on 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If visc_update is true (i.e., 1 or on), viscosity is updated every time step
+ by the following parameters.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+num_mat=4
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+This specifies the number of material layers.
+ Material 1 is at depth between 0 and z_lith, material 2 is between z_lith
+ and z_410, material 3 is between z_410 and z_lmantle, and material 4 is
+ between z_lmantle and (radius_outer - radius_inner).
+ If mat_control is true, then a multiplicative factor is applied to the
+ viscosity, as defined below.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+TDEPV=on  viscE=0.1,0.1,1.0,1.0  viscT=-1.02126,-1.01853, -1.32722,-1.32722
+\newline
+visc0=1.0e2,2.e
+-3, 2.e0,2.e1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If TDEPV is true (i.e., 1 or on), viscE, viscT, and visc0 are parameters defining
+ viscosity law.
+ See the equation above.
+ There must be as many entries in a comma-separated list as num_mat.
+ No space is allowed in the list.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+SDEPV=off  sdepv_expt=1,1,1,1,1,1,1,1 sdepv_misfit=0.020
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If SDEPV is true (i.e., 1 or on), these specify the exponent in the viscosity
+ law and the criterion of convergence test.
+ There must be as many entries in a comma-separated list as num_mat.
+ No space is allowed in the list.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+VMIN=on visc_min=1.e-4 VMAX=on visc_max=1.e3
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If VMIN is true (i.e., 1 or on), minimum viscosity is cut off at visc_min.
+ VMAX and visc_max are for the maximum viscosity cutoff.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Phase Change Information
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="3" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Ra_410=0.0
+\newline
+clapeyron410=0.0235
+\newline
+transT410=0.78
+\newline
+width410=0.0058 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+These specify the phase change parameters (density change, Clapeyron slope,
+ ambient temperature, and phase change width, respectively).
+ The depth of this phase change is specified by z_410.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Ra_670=0.0
+\newline
+clapeyron670=-0.0235
+\newline
+transT670=0.875
+\newline
+width670=0.0058
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+As above.
+ The depth of this phase change is specified by z_lmantle.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Ra_cmb=0.0
+\newline
+clapeyroncmb=-0.0235
+\newline
+transTcmb=0.875
+\newline
+widthcmb=0.0058
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+As above.
+ The depth of this phase change is specified by z_cmb.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Dimensional Information
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="1" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+layerd=6371e3
+\newline
+density=3500.0
+\newline
+thermdiff=1.0e-6
+\newline
+gravacc=10.0
+\newline
+thermexp=3.0e-5
+\newline
+refvisc=1e21
+\newline
+cp
+=1250
+\newline
+wdensity=0.0 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Various dimensional information.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Data input and program debugging
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="3" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+DESCRIBE=off  BEGINNER=off 
+\newline
+VERBOSE=off
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+These parameters affect the echo behavior of the CitComS parser.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+verbose=off 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+This is used for debugging.
+ If verbose is true, additional information is output to a .info file.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+see_convergence=1 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If see_convergence is true, the velocity residual will be output on the
+ screen for every iteration.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Solver Related Parameters
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="10" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+mg_cycle=1
+\newline
+down_heavy=3
+\newline
+up_heavy=3
+\newline
+vlowstep=2000
+\newline
+vhighstep=3
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Multigrid parameters.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+piterations=375
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Maximum iterations for momentum solver.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+accuracy=1.0e-6  tole_compressibility=1.0e-7
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Convergence criterion for momentum solver.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+ADV=on
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If true, solve energy equation.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+fixed_timestep=0.0 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Set fixed time step.
+ If it is 0, the size of time step is variable and is determined dynamically.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+finetunedt=0.7
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Set fraction of maximum advection time step.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+adv_sub_iterations=2
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Set the number of iterations for energy solver.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+maxadvtime=10
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Maximum elapsed non-dimensional advection time.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+precond=on
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Pre-conditioning flag.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+aug_lagr=on aug_number=2.0e3
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Augmented stiff matrix flag and value.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Age Information
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="2" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+start_age=40.0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Set initial age (in Myrs).
+ This age determines which vel_bound_file and mat_file to read in.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+reset_startage=0 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If reset_startage is true, the initial age is set to start_age.
+ If it is false and restart or post_p is true, the initial age is read in
+ from previous output.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+Spherical Harmonics Information
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="1" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+ll_max=20
+\newline
+output_ll_max=20
+\newline
+nlong=361
+\newline
+nlati=181 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+These parameters control the resolution of spherical harmonics.
+ Currently not used.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+launcher
+\end_layout
+
+\begin_layout Standard
+The Pyre facility 
+\family typewriter
+\size footnotesize
+launcher
+\family default
+\size default
+ controls how CitComS.py, an MPI application, is executed on multiple processors.
+ It is the equivalent to mpirun in MPICH.
+ 
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="5" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+dry
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If on, print command line and exit.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nodegen
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+A printf-style format string, used in conjunction with nodelist to generate
+ list of machine names.
+ Example: 
+\family typewriter
+n%
+\begin_inset Formula $\textrm{\O}$
+\end_inset
+
+3d
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nodelist 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+A comma-separated list of machine names in square brackets.
+ Example: 
+\family typewriter
+ [101-103,105,107] 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nodes
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Number of machine nodes.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+machinefile
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Filename of machine file.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+journal 
+\end_layout
+
+\begin_layout Standard
+The Pyre facility 
+\family typewriter
+\size footnotesize
+journal
+\family default
+\size default
+ provides five types of debugging output for conceptually different types
+ of information.
+ The journal output stream can be instantiated as separated channels multiple
+ times, and each channel can be individually activated or deactivated, and
+ sent to different locations (the terminal, sockets, files, devices, etc.).
+ The streams and their default states of the journal streams are: 
+\newline
+
+\begin_inset Tabular
+<lyxtabular version="3" rows="5" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="1.75in">
+<column alignment="left" valignment="top" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+debug
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Filename of machine file.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+error
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Unrecoverable runtime error.
+ Default on.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+firewall
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Fatal programming error.
+ Default on.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+info
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Descriptive information.
+ Default off.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+warning
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Recoverable runtime error.
+ Default off.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+The journal facility is not used in the uncoupled 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.
+ The most important ones are  
+\family typewriter
+journal.debug.Exchanger
+\family default
+  and 
+\family typewriter
+journal.debug.CitComSExchanger
+\family default
+.
+  Try running the scripts with
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+--journal.debug.Exchanger=on --journal.debug.CitComSExchanger=on 
+\end_layout
+
+\begin_layout Section*
+controller
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="1" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+monitoringFrequency=100
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+The time step interval between disk output.
+ It replaces the storage_spacing parameter in the (old) CitComS input file.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+solver 
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="16" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+mesher 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Can be either full-sphere or regional-sphere.
+ It is set by the solver facility automatically.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+tsolver 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+A temperature solver using Petrov-Galerkin time integration.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+vsolver 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+A velocity solver using Boussinesq approximation and Uzawa algorithm.
+ 
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+bc 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Boundary conditions.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+const
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Dimensional constants.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+ic
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Initial conditions.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+param
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Some additional input parameter files.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+phase 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Phase change.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+visc
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Viscosity.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+datafile
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+default="regtest"
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+datafile_old
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+default="regtest"
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+rayleigh
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+default=1e+08
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Q0 =0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+stokes_flow_only =0 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+verbos =0 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+see_convergence =1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+solver.mesher
+\end_layout
+
+\begin_layout Standard
+Available properties and default values include:
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="20" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nproc_surf=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nprocx=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nprocy=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nprocz=1 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+coor=0 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+coor_file="coor.dat"
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nodex=9
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nodey=9
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nodez=9
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+levels=1 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+radius_outer=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+radius_inner=0.55
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+theta_min=1.5
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+theta_max=1.8
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+fi_min=0 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+fi_max=0.4
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+ll_max=20 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nlong=361
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+nlati=181
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+output_ll_max=20
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+solver.tsolver
+\end_layout
+
+\begin_layout Standard
+Available properties and default values include: 
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="8" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+inputdiffusivity=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+ADV=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
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+
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+\begin_inset Text
+
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+
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+
+\end_inset
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+</row>
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+
+\begin_layout Standard
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+
+\end_inset
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+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
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+
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+
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+
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+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
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+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+aug_lagr=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
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+
+\end_layout
+
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+
+\begin_layout Standard
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+\end_layout
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+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+solver.vsolver
+\end_layout
+
+\begin_layout Standard
+Available properties and default values include:
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="10" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
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+\begin_inset Text
+
+\begin_layout Standard
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+\end_layout
+
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+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
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+<row topline="true">
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+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
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+
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+
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+
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+
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+\begin_layout Standard
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+
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+
+\begin_layout Standard
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+\end_inset
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+
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+<row topline="true">
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+
+\begin_layout Standard
+
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+
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+<row topline="true">
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+
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+\begin_inset Text
+
+\begin_layout Standard
+
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+
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+</row>
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+
+\begin_layout Standard
+vhighstep=3
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+
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+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
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+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+solver.bc 
+\end_layout
+
+\begin_layout Standard
+Available properties and default values are 0, 1, or 2 (open top).
+ You cannot use "yes" or "no" for these values.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="14" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
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+
+\begin_layout Standard
+side_sbcs=0 
+\end_layout
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+\begin_inset Text
+
+\begin_layout Standard
+
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+
+\end_inset
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+\end_inset
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+
+\begin_layout Standard
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+\begin_layout Standard
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+
+\begin_layout Standard
+
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+\end_inset
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+
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+
+\begin_layout Standard
+
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+
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+</cell>
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+\begin_inset Text
+
+\begin_layout Standard
+
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+
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+
+\begin_layout Standard
+toptbcval=0
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+
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+\begin_inset Text
+
+\begin_layout Standard
+
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+
+\end_inset
+</cell>
+</row>
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+
+\begin_layout Standard
+bottbc=1
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+
+\end_inset
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+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
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+\begin_inset Text
+
+\begin_layout Standard
+bottbcval=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+temperature_bound_adj=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
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+<row topline="true">
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+
+\begin_layout Standard
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+\end_layout
+
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+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
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+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+solver.const 
+\end_layout
+
+\begin_layout Standard
+Available properties and default values include:
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="13" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="1.75in">
+<column alignment="left" valignment="top" rightline="true" width="3.5in">
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+\begin_inset Text
+
+\begin_layout Standard
+layerd=6.371e+06
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+density=3500
+\end_layout
+
+\end_inset
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+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
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+
+\begin_layout Standard
+thermdiff=1e-06
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+
+\end_inset
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+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
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+
+\begin_layout Standard
+
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+
+\begin_layout Standard
+gravacc=10
+\end_layout
+
+\end_inset
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+
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+\begin_layout Standard
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+
+\begin_layout Standard
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+\end_layout
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+
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+
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+\begin_layout Standard
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+\end_inset
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+
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+
+\begin_layout Standard
+
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+
+\end_inset
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+\begin_layout Standard
+depth_660=660000
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+
+\end_inset
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+\end_inset
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+\begin_layout Standard
+depth_cmb=2.691e+06
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+
+\begin_layout Standard
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+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+solver.ic 
+\end_layout
+
+\begin_layout Standard
+Available properties and default values include:
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="9" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+restart=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+post_p=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+solution_cycles_init=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+zero_elapsed_time=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+num_perturbations=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+perturbl=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+perturbm=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+perturblayer=5 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+perturbmag=0.05
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+solver.param
+\end_layout
+
+\begin_layout Standard
+Available properties and default values include:
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="13" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+file_vbcs=0 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+vel_bound_file="bvel.dat"
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+mat_control=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+mat_file="mat.dat"
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+lith_age=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+lith_age_file="age.dat"
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+lith_age_time=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+lith_age_depth=0.0314
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+mantle_temp=1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+tracer=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+tracer_file="tracer.dat"
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+start_age=40 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+reset_startage=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+solver.phase
+\end_layout
+
+\begin_layout Standard
+Available properties and default values include:
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="12" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Ra_410=0 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+clapeyron410=0.0235
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+transT410=0.78 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+width410=0.0058
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Ra_670=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+clapeyron670=-0.0235
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+transT670=0.78
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+width670=0.0058
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Ra_cmb=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+clapeyroncmb=-0.0235
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+transTcmb=0.875
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+widthcmb=0.0058
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section*
+solver.visc
+\end_layout
+
+\begin_layout Standard
+Available properties and default values include:
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="16" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Viscosity="system"
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+rheol=3 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+visc_smooth_method=3
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+VISC_UPDATE=on
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+num_mat=4
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+visc0=1,1,1,1,
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+TDEPV=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+viscE=1,1,1,1,
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+viscT=1,1,1,1, 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+SDEPV=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+sdepv_misfit=0.02
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+sdepv_expt=1,1,1,1,
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+VMIN=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+visc_min=0.001
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+VMAX=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+visc_max=1000
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+ 
+\end_layout
+
+\begin_layout Chapter
+CitComS Input File Format
+\end_layout
+
+\begin_layout Section*
+Introduction
+\end_layout
+
+\begin_layout Standard
+CitComS expects Unix-styled ASCII files (i.e., no carriage character following
+ new line character) for all input files.
+ This can be a nuisance in DOS/Windows systems.
+ You may want to find a text editor that can write Unix-style ASCII files.
+ In the following, words in normal 
+\family typewriter
+courier
+\family default
+ must be input exactly as shown, while 
+\series bold
+bold
+\series default
+ words should be substituted by your values.
+ All parameters are in non-dimensional units unless specified.
+ 
+\end_layout
+
+\begin_layout Section*
+\begin_inset LatexCommand \label{sec:Coordinate-files}
+
+\end_inset
+
+Coordinate files
+\end_layout
+
+\begin_layout Standard
+For 
+\family typewriter
+regCitComS
+\family default
+, the mesh must be regular, but the mesh spacing may be unequal.
+ The 
+\family typewriter
+coor_file
+\family default
+ has the format: 
+\end_layout
+
+\begin_layout LyX-Code
+nsd=1 
+\end_layout
+
+\begin_layout LyX-Code
+1 
+\series bold
+    theta1
+\series default
+ 
+\end_layout
+
+\begin_layout LyX-Code
+2 
+\series bold
+    theta2
+\end_layout
+
+\begin_layout LyX-Code
+...
+   ...
+ 
+\end_layout
+
+\begin_layout LyX-Code
+
+\series bold
+nodex theta_nodex
+\series default
+ 
+\end_layout
+
+\begin_layout LyX-Code
+nsd=2 
+\end_layout
+
+\begin_layout LyX-Code
+1 
+\series bold
+    phi1
+\series default
+ 
+\end_layout
+
+\begin_layout LyX-Code
+2 
+\series bold
+    phi2
+\series default
+ 
+\end_layout
+
+\begin_layout LyX-Code
+...
+   ...
+ 
+\end_layout
+
+\begin_layout LyX-Code
+
+\series bold
+nodey phi_nodey
+\series default
+ 
+\end_layout
+
+\begin_layout LyX-Code
+nsd=3 
+\end_layout
+
+\begin_layout LyX-Code
+1 
+\series bold
+    r1
+\series default
+ 
+\end_layout
+
+\begin_layout LyX-Code
+2 
+\series bold
+    r2
+\series default
+ 
+\end_layout
+
+\begin_layout LyX-Code
+...
+   ...
+ 
+\end_layout
+
+\begin_layout LyX-Code
+
+\series bold
+nodez r_nodez
+\end_layout
+
+\begin_layout Standard
+For 
+\family typewriter
+fullCitComS
+\family default
+, the mesh must be regular and equidistant in the horizontal dimension.
+ Only vertical dimension is specified by 
+\family typewriter
+coor_file
+\family default
+.
+ The 
+\family typewriter
+coor_file
+\family default
+ has the format:
+\end_layout
+
+\begin_layout LyX-Code
+nsd=3 
+\end_layout
+
+\begin_layout LyX-Code
+1 
+\series bold
+    r1
+\series default
+ 
+\end_layout
+
+\begin_layout LyX-Code
+2 
+\series bold
+    r2
+\series default
+ 
+\end_layout
+
+\begin_layout LyX-Code
+...
+   ...
+ 
+\end_layout
+
+\begin_layout LyX-Code
+
+\series bold
+nodez r_nodez
+\end_layout
+
+\begin_layout Section*
+Velocity boundary condition files
+\end_layout
+
+\begin_layout Standard
+If 
+\family typewriter
+vel_bound_file
+\family default
+ is set to 
+\family typewriter
+bvel.dat
+\family default
+, then it is necessary to have one 
+\family typewriter
+bvel.dat
+\family default
+ file for each million year interval.
+ For example, if 
+\family typewriter
+start_age=83
+\family default
+, then the following files are needed:  
+\end_layout
+
+\begin_layout LyX-Code
+bvel.dat84 
+\end_layout
+
+\begin_layout LyX-Code
+bvel.dat83 
+\end_layout
+
+\begin_layout LyX-Code
+bvel.dat82 
+\end_layout
+
+\begin_layout LyX-Code
+...
+ 
+\end_layout
+
+\begin_layout LyX-Code
+bvel.dat0
+\end_layout
+
+\begin_layout Quote
+
+\series bold
+TIP:
+\series default
+ Even though the model starts at 83 million years before present, by default
+ it will attempt to read in both a file for 84 and a file for 83 million
+ years ago.
+ To deal with this, just create a duplicate copy of 
+\family typewriter
+bvel.dat83
+\family default
+ and call it 
+\family typewriter
+bvel.d
+\family default
+ 
+\end_layout
+
+\begin_layout LyX-Code
+
+\series bold
+Vx Vy
+\end_layout
+
+\begin_layout Section*
+Material files
+\end_layout
+
+\begin_layout Standard
+If 
+\family typewriter
+mat_file
+\family default
+ is set to 
+\family typewriter
+mat.dat
+\family default
+, then it is necessary to have one mat.dat file for each million year interval.
+ For example, if 
+\family typewriter
+start_age=83
+\family default
+, then the following files are needed: 
+\end_layout
+
+\begin_layout LyX-Code
+mat.dat84 
+\end_layout
+
+\begin_layout LyX-Code
+mat.dat83 
+\end_layout
+
+\begin_layout LyX-Code
+mat.dat82 
+\end_layout
+
+\begin_layout LyX-Code
+...
+ 
+\end_layout
+
+\begin_layout LyX-Code
+mat.dat0
+\end_layout
+
+\begin_layout Standard
+The same note about 
+\family typewriter
+vel_bound_file
+\family default
+ (see above) applies.
+ The format of 
+\family typewriter
+mat_file
+\family default
+ is: 
+\end_layout
+
+\begin_layout LyX-Code
+
+\series bold
+n viscosity_factor
+\end_layout
+
+\begin_layout Section*
+Lithosphere Age Files
+\end_layout
+
+\begin_layout Standard
+If 
+\family typewriter
+lith_age_file
+\family default
+ is set to 
+\family typewriter
+lith.dat
+\family default
+, then it is necessary to have one 
+\family typewriter
+bvel.dat
+\family default
+ file for each million year interval.
+ For example, if 
+\family typewriter
+start_age=83
+\family default
+, then the following files are needed: 
+\end_layout
+
+\begin_layout LyX-Code
+lith.dat84
+\end_layout
+
+\begin_layout LyX-Code
+lith.dat83 
+\end_layout
+
+\begin_layout LyX-Code
+lith.dat82 
+\end_layout
+
+\begin_layout LyX-Code
+...
+ 
+\end_layout
+
+\begin_layout LyX-Code
+lith.dat0
+\end_layout
+
+\begin_layout Standard
+The same note about 
+\family typewriter
+vel_bound_file
+\family default
+ (see above) still applies.
+ The input age is in millions of years.
+ The format of 
+\family typewriter
+lith_age_file
+\family default
+ is: 
+\end_layout
+
+\begin_layout LyX-Code
+
+\series bold
+n age
+\end_layout
+
+\begin_layout Section*
+Tracer Files
+\end_layout
+
+\begin_layout Standard
+In this version of CitComS, the implementation of tracer is neither parallelized
+, nor has it been tested.
+ We strongly advise you not to use this feature.
+ The format of 
+\family typewriter
+tracer_file
+\family default
+ is described here for completion: 
+\end_layout
+
+\begin_layout LyX-Code
+num_tracers 
+\end_layout
+
+\begin_layout LyX-Code
+type x y z
+\end_layout
+
+\begin_layout Chapter
+\begin_inset LatexCommand \label{cha:Appendix-C:-CitComS,}
+
+\end_inset
+
+CitComS Output File Format
+\end_layout
+
+\begin_layout Section*
+Introduction
+\end_layout
+
+\begin_layout Standard
+All outputs are in non-dimensional units unless specified.
+\end_layout
+
+\begin_layout Section*
+Postprocessed Cap Output
+\end_layout
+
+\begin_layout Standard
+The commands 
+\family typewriter
+autocombine.py
+\family default
+ and 
+\family typewriter
+batchcombine.py
+\family default
+ produce 1 cap file for regional CitComS and 12 cap files for full CitComS,
+ e.g., 
+\family typewriter
+test-case.cap0.10
+\family default
+.
+ The first line of the cap file is a comment describing the node geometry
+ (
+\family typewriter
+nodex
+\family default
+ 
+\begin_inset Formula $\times$
+\end_inset
+
+ 
+\family typewriter
+nodey
+\family default
+ 
+\begin_inset Formula $\times$
+\end_inset
+
+ 
+\family typewriter
+nodez
+\family default
+).
+ The rest of the file is column-based, where the meaning of each column
+ is: 
+\end_layout
+
+\begin_layout LyX-Code
+colatitude longitude radius vel_colat vel_lon vel_r temperature viscosity
+\end_layout
+
+\begin_layout Section*
+CitComS Output
+\end_layout
+
+\begin_layout Standard
+The format of the raw output of CitComS.py is described here.
+ In the following sections, the model prefix is assumed as 
+\family typewriter
+test-case
+\family default
+, the processor number as 0, and the time step as 10.
+ 
+\end_layout
+
+\begin_layout Subsection*
+Time Output (test-case.time)
+\end_layout
+
+\begin_layout Standard
+It reports non-dimensional elapsed model time and spent CPU time (in seconds).
+ Only outputted on computer node 0.
+ The meaning of each column is: 
+\end_layout
+
+\begin_layout LyX-Code
+step total_t delta_t total_cpu_time step_cpu_time 
+\end_layout
+
+\begin_layout Subsection*
+Coordinate Output (test-case.coord.0)
+\end_layout
+
+\begin_layout Standard
+Only outputted at 0th time step.
+ The first line is a header.
+ The rest of the file is column-based, where the meaning of each column
+ is: 
+\end_layout
+
+\begin_layout LyX-Code
+colatitude longitude radius
+\end_layout
+
+\begin_layout Subsection*
+Velocity and Temperature Output (test-case.velo.0.10)
+\end_layout
+
+\begin_layout Standard
+The two lines are headers.
+ The rest of the file is column-based, where the meaning of each column
+ is: 
+\end_layout
+
+\begin_layout LyX-Code
+vel_colat vel_lon vel_r temperature
+\end_layout
+
+\begin_layout Subsection*
+Viscosity Output (test-case.visc.0.10)
+\end_layout
+
+\begin_layout Standard
+The first line is a header.
+ The rest of the file is column-based, where the meaning of each column
+ is: 
+\end_layout
+
+\begin_layout LyX-Code
+viscosity
+\end_layout
+
+\begin_layout Subsection*
+Material Output (test-case.mat.0)
+\end_layout
+
+\begin_layout Standard
+Only output at 0th time step.
+ There is no header.
+ The meaning of each column is: 
+\end_layout
+
+\begin_layout LyX-Code
+element_number layer material
+\end_layout
+
+\begin_layout Subsection*
+Surface Variables Output (test-case.surf.0.10 and 
+\newline
+test-case.botm.0.10)
+\end_layout
+
+\begin_layout Standard
+The first line is a header.
+ The rest of the file is column-based, where the meaning of each column
+ is: 
+\end_layout
+
+\begin_layout LyX-Code
+topography heatflux vel_colat vel_lon
+\end_layout
+
+\begin_layout Chapter
+License 
+\end_layout
+
+\begin_layout Standard
+
+\series bold
+GNU GENERAL PUBLIC LICENSE Version 2, June 1991.
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+ 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+\series default
+ 
+\newline
+
+\series medium
+Everyone is permitted to copy and distribute verbatim copies of this license
+ document, but changing it is not allowed.
+\end_layout
+
+\begin_layout Section*
+Preamble
+\end_layout
+
+\begin_layout Standard
+The licenses for most software are designed to take away your freedom to
+ share and change it.
+ By contrast, the GNU General Public License is intended to guarantee your
+ freedom to share and change free software -- to make sure the software
+ is free for all its users.
+ This General Public License applies to most of the Free Software Foundation's
+ software and to any other program whose authors commit to using it.
+ (Some other Free Software Foundation software is covered by the GNU Library
+ General Public License instead.) You can apply it to your programs, too.
+\end_layout
+
+\begin_layout Standard
+When we speak of free software, we are referring to freedom, not price.
+ Our General Public Licenses are designed to make sure that you have the
+ freedom to distribute copies of free software (and charge for this service
+ if you wish), that you receive source code or can get it if you want it,
+ that you can change the software or use pieces of it in new free programs;
+ and that you know you can do these things.
+\end_layout
+
+\begin_layout Standard
+To protect your rights, we need to make restrictions that forbid anyone
+ to deny you these rights or to ask you to surrender the rights.
+ These restrictions translate to certain responsibilities for you if you
+ distribute copies of the software, or if you modify it.
+\end_layout
+
+\begin_layout Standard
+For example, if you distribute copies of such a program, whether gratis
+ or for a fee, you must give the recipients all the rights that you have.
+ You must make sure that they, too, receive or can get the source code.
+ And you must show them these terms so they know their rights.
+\end_layout
+
+\begin_layout Standard
+We protect your rights with two steps:
+\end_layout
+
+\begin_layout Enumerate
+Copyright the software, and 
+\end_layout
+
+\begin_layout Enumerate
+Offer you this license which gives you legal permission to copy, distribute
+ and/or modify the software.
+\end_layout
+
+\begin_layout Standard
+Also, for each author's protection and ours, we want to make certain that
+ everyone understands that there is no warranty for this free software.
+ If the software is modified by someone else and passed on, we want its
+ recipients to know that what they have is not the original, so that any
+ problems introduced by others will not reflect on the original authors'
+ reputations.
+\end_layout
+
+\begin_layout Standard
+Finally, any free program is threatened constantly by software patents.
+ We wish to avoid the danger that redistributors of a free program will
+ individually obtain patent licenses, in effect making the program proprietary.
+ To prevent this, we have made it clear that any patent must be licensed
+ for everyone's free use or not licensed at all.
+ 
+\end_layout
+
+\begin_layout Standard
+The precise terms and conditions for copying, distribution and modification
+ follow.
+\end_layout
+
+\begin_layout Section*
+GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION
+ AND MODIFICATION 
+\end_layout
+
+\begin_layout Standard
+0.
+ This License applies to any program or other work which contains a notice
+ placed by the copyright holder saying it may be distributed under the terms
+ of this General Public License.
+ The "Program,",below, refers to any such program or work, and a "work based
+ on the Program" means either the Program or any derivative work under copyright
+ law: that is to say, a work containing the Program or a portion of it,
+ either verbatim or with modifications and/or translated into another language.
+ (Hereinafter, translation is included without limitation in the term "modificat
+ion.") Each licensee is addressed as "you."
+\end_layout
+
+\begin_layout Standard
+Activities other than copying, distribution and modification are not covered
+ by this License; they are outside its scope.
+ The act of running the Program is not restricted, and the output from the
+ Program is covered only if its contents constitute a work based on the
+ Program (independent of having been made by running the Program).
+ Whether that is true depends on what the Program does.
+ 
+\end_layout
+
+\begin_layout Standard
+1.
+ You may copy and distribute verbatim copies of the Program's source code
+ as you receive it, in any medium, provided that you conspicuously and appropria
+tely publish on each copy an appropriate copyright notice and disclaimer
+ of warranty; keep intact all the notices that refer to this License and
+ to the absence of any warranty; and give any other recipients of the Program
+ a copy of this License along with the Program.
+ 
+\end_layout
+
+\begin_layout Standard
+You may charge a fee for the physical act of transferring a copy, and you
+ may at your option offer warranty protection in exchange for a fee.
+ 
+\end_layout
+
+\begin_layout Standard
+2.
+ You may modify your copy or copies of the Program or any portion of it,
+ thus forming a work based on the Program, and copy and distribute such
+ modifications or work under the terms of Section 1 above, provided that
+ you also meet all of these conditions: 
+\end_layout
+
+\begin_layout Standard
+a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+ 
+\end_layout
+
+\begin_layout Standard
+b) You must cause any work that you distribute or publish, that in whole
+ or in part contains or is derived from the Program or any part thereof,
+ to be licensed as a whole at no charge to all third parties under the terms
+ of this License.
+ 
+\end_layout
+
+\begin_layout Standard
+c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an appropriate
+ copyright notice and a notice that there is no warranty (or else, saying
+ that you provide a warranty) and that users may redistribute the program
+ under these conditions, and telling the user how to view a copy of this
+ License.
+ (Exception: if the Program itself is interactive but does not normally
+ print such an announcement, your work based on the Program is not required
+ to print an announcement.) 
+\end_layout
+
+\begin_layout Standard
+These requirements apply to the modified work as a whole.
+ If identifiable sections of that work are not derived from the Program,
+ and can be reasonably considered independent and separate works in themselves,
+ then this License, and its terms, do not apply to those sections when you
+ distribute them as separate works.
+ But when you distribute the same sections as part of a whole which is a
+ work based on the Program, the distribution of the whole must be on the
+ terms of this License, whose permissions for other licensees extend to
+ the entire whole, and thus to each and every part regardless of who wrote
+ it.
+ 
+\end_layout
+
+\begin_layout Standard
+Thus, it is not the intent of this section to claim rights or contest your
+ rights to work written entirely by you; rather, the intent is to exercise
+ the right to control the distribution of derivative or collective works
+ based on the Program.
+ 
+\end_layout
+
+\begin_layout Standard
+In addition, mere aggregation of another work not based on the Program with
+ the Program (or with a work based on the Program) on a volume of a storage
+ or distribution medium does not bring the other work under the scope of
+ this License.
+ 
+\end_layout
+
+\begin_layout Standard
+3.
+ You may copy and distribute the Program (or a work based on it, under Section
+ 2) in object code or executable form under the terms of Sections 1 and
+ 2 above provided that you also do one of the following: 
+\end_layout
+
+\begin_layout Standard
+a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or, 
+\end_layout
+
+\begin_layout Standard
+b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections
+ 1 and 2 above on a medium customarily used for software interchange; or,
+ 
+\end_layout
+
+\begin_layout Standard
+c) Accompany it with the information you received as to the offer to distribute
+ corresponding source code.
+ (This alternative is allowed only for noncommercial distribution and only
+ if you received the program in object code or executable form with such
+ an offer, in accord with Subsection b above.) 
+\end_layout
+
+\begin_layout Standard
+The source code for a work means the preferred form of the work for making
+ modifications to it.
+ For an executable work, complete source code means all the source code
+ for all modules it contains, plus any associated interface definition files,
+ plus the scripts used to control compilation and installation of the executable.
+ However, as a special exception, the source code distributed need not include
+ anything that is normally distributed (in either source or binary form)
+ with the major components (compiler, kernel, and so on) of the operating
+ system on which the executable runs, unless that component itself accompanies
+ the executable.
+\end_layout
+
+\begin_layout Standard
+If distribution of executable or object code is made by offering access
+ to copy from a designated place, then offering equivalent access to copy
+ the source code from the same place counts as distribution of the source
+ code, even though third parties are not compelled to copy the source along
+ with the object code.
+ 
+\end_layout
+
+\begin_layout Standard
+4.
+ You may not copy, modify, sublicense, or distribute the Program except
+ as expressly provided under this License.
+ Any attempt otherwise to copy, modify, sublicense or distribute the Program
+ is void, and will automatically terminate your rights under this License.
+ However, parties who have received copies, or rights, from you under this
+ License will not have their licenses terminated so long as such parties
+ remain in full compliance.
+ 
+\end_layout
+
+\begin_layout Standard
+5.
+ You are not required to accept this License, since you have not signed
+ it.
+ However, nothing else grants you permission to modify or distribute the
+ Program or its derivative works.
+ These actions are prohibited by law if you do not accept this License.
+ Therefore, by modifying or distributing the Program (or any work based
+ on the Program), you indicate your acceptance of this License to do so,
+ and all its terms and conditions for copying, distributing or modifying
+ the Program or works based on it.
+ 
+\end_layout
+
+\begin_layout Standard
+6.
+ Each time you redistribute the Program (or any work based on the Program),
+ the recipient automatically receives a license from the original licensor
+ to copy, distribute or modify the Program subject to these terms and conditions.
+ You may not impose any further restrictions on the recipients' exercise
+ of the rights granted herein.
+ You are not responsible for enforcing compliance by third parties to this
+ License.
+ 
+\end_layout
+
+\begin_layout Standard
+7.
+ If, as a consequence of a court judgment or allegation of patent infringement
+ or for any other reason (not limited to patent issues), conditions are
+ imposed on you (whether by court order, agreement or otherwise) that contradict
+ the conditions of this License, they do not excuse you from the conditions
+ of this License.
+ If you cannot distribute so as to satisfy simultaneously your obligations
+ under this License and any other pertinent obligations, then as a consequence
+ you may not distribute the Program at all.
+ For example, if a patent license would not permit royalty-free redistribution
+ of the Program by all those who receive copies directly or indirectly through
+ you, then the only way you could satisfy both it and this License would
+ be to refrain entirely from distribution of the Program.
+\end_layout
+
+\begin_layout Standard
+If any portion of this section is held invalid or unenforceable under any
+ particular circumstance, the balance of the section is intended to apply
+ and the section as a whole is intended to apply in other circumstances.
+\end_layout
+
+\begin_layout Standard
+It is not the purpose of this section to induce you to infringe any patents
+ or other property right claims or to contest validity of any such claims;
+ this section has the sole purpose of protecting the integrity of the free
+ software distribution system, which is implemented by public license practices.
+ Many people have made generous contributions to the wide range of software
+ distributed through that system in reliance on consistent application of
+ that system; it is up to the author/donor to decide if he or she is willing
+ to distribute software through any other system and a licensee cannot impose
+ that choice.
+ 
+\end_layout
+
+\begin_layout Standard
+This section is intended to make thoroughly clear what is believed to be
+ a consequence of the rest of this License.
+ 
+\end_layout
+
+\begin_layout Standard
+8.
+ If the distribution and/or use of the Program is restricted in certain
+ countries either by patents or by copyrighted interfaces, the original
+ copyright holder who places the Program under this License may add an explicit
+ geographical distribution limitation excluding those countries, so that
+ distribution is permitted only in or among countries not thus excluded.
+ In such case, this License incorporates the limitation as if written in
+ the body of this License.
+ 
+\end_layout
+
+\begin_layout Standard
+9.
+ The Free Software Foundation may publish revised and/or new versions of
+ the General Public License from time to time.
+ Such new versions will be similar in spirit to the present version, but
+ may differ in detail to address new problems or concerns.
+ 
+\end_layout
+
+\begin_layout Standard
+Each version is given a distinguishing version number.
+ If the Program specifies a version number of this License which applies
+ to it and "any later version," you have the option of following the terms
+ and conditions either of that version or of any later version published
+ by the Free Software Foundation.
+ If the Program does not specify a version number of this License, you may
+ choose any version ever published by the Free Software Foundation.
+\end_layout
+
+\begin_layout Standard
+10.
+ If you wish to incorporate parts of the Program into other free programs
+ whose distribution conditions are different, write to the author to ask
+ for permission.
+ For software which is copyrighted by the Free Software Foundation, write
+ to the Free Software Foundation; we sometimes make exceptions for this.
+ Our decision will be guided by the two goals of preserving the free status
+ of all derivatives of our free software and of promoting the sharing and
+ reuse of software generally.
+ 
+\end_layout
+
+\begin_layout Subsection*
+NO WARRANTY 
+\end_layout
+
+\begin_layout Standard
+11.
+ BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+ THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
+ EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER
+ PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER
+ EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH
+ YOU.
+ SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY
+ SERVICING, REPAIR OR CORRECTION.
+ 
+\end_layout
+
+\begin_layout Standard
+12.
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE
+ THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING
+ ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF
+ THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS
+ OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR
+ THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+ EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY
+ OF SUCH DAMAGES.
+\end_layout
+
+\begin_layout Section*
+END OF TERMS AND CONDITIONS 
+\end_layout
+
+\begin_layout Subsection*
+How to Apply These Terms to Your New Programs
+\end_layout
+
+\begin_layout Standard
+If you develop a new program, and you want it to be of the greatest possible
+ use to the public, the best way to achieve this is to make it free software
+ which everyone can redistribute and change under these terms.
+ 
+\end_layout
+
+\begin_layout Standard
+To do so, attach the following notices to the program.
+ It is safest to attach them to the start of each source file to most effectivel
+y convey the exclusion of warranty; and each file should have at least the
+ "copyright" line and a pointer to where the full notice is found.
+ For example:
+\end_layout
+
+\begin_layout Quote
+one line to give the program's name and a brief idea of what it does.
+ Copyright (C) (year) (name of author) 
+\end_layout
+
+\begin_layout Quote
+This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+ 
+\end_layout
+
+\begin_layout Quote
+This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ FOR A PARTICULAR PURPOSE.
+ See the GNU General Public License for more details.
+ 
+\end_layout
+
+\begin_layout Quote
+You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA 
+\end_layout
+
+\begin_layout Standard
+Also add information on how to contact you by electronic and paper mail.
+ 
+\end_layout
+
+\begin_layout Standard
+If the program is interactive, make it output a short notice like this when
+ it starts in an interactive mode: 
+\end_layout
+
+\begin_layout Quote
+Gnomovision version 69, Copyright (C) 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.
+ 
+\end_layout
+
+\begin_layout Standard
+The hypothetical commands `show w' and `show c' should show the appropriate
+ parts of the General Public License.
+ Of course, the commands you use may be called something other than `show
+ w' and `show c'; they could even be mouse-clicks or menu items -- whatever
+ suits your program.
+ 
+\end_layout
+
+\begin_layout Standard
+You should also get your employer (if you work as a programmer) or your
+ school, if any, to sign a "copyright disclaimer" for the program, if necessary.
+ Here is a sample; alter the names: 
+\end_layout
+
+\begin_layout Quote
+Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovisi
+on' (which makes passes at compilers) written by James Hacker.
+ 
+\end_layout
+
+\begin_layout Quote
+(signature of Ty Coon)
+\newline
+1 April 1989 
+\newline
+Ty Coon, President of Vice 
+\end_layout
+
+\begin_layout Standard
+This General Public License does not permit incorporating your program into
+ proprietary programs.
+ If your program is a subroutine library, you may consider it more useful
+ to permit linking proprietary applications with the library.
+ If this is what you want to do, use the GNU Library General Public License
+ instead of this License.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [1]{Moresi et al Plate tectonics}
+Moresi, L., M.
+ Gurnis, and S.
+ Zhong (2000), Plate tectonics and convection in the Earth's mantle: Toward
+ a numerical simulation, 
+\emph on
+Comp.
+ Sci.
+ Engin., 
+\emph default
+2, 22-33.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [2]{Moresi/Solomatov Numerical}
+Moresi, L.
+ N., and V.
+ S.
+ Solomatov (1995), Numerical investigation of 2D convection with extremely
+ large viscosity variations, 
+\emph on
+Phys.
+ Fluid,
+\emph default
+ 7, 2,154-2,162.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [3]{Moresi/Gurnis Contraints}
+Moresi, L.
+ N., and M.
+ Gurnis (1996), Constraints on the lateral strength of slabs from three-dimensio
+nal dynamic flow models, 
+\emph on
+Earth Planet.
+ Sci.
+ Lett.,
+\emph default
+ 138, 15-28.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [4]{Zhong/Moresi The role of faults}
+Zhong, S., M.
+ Gurnis, and L.
+ Moresi (1998), The role of faults, nonlinear rheology, and viscosity structure
+ in generating plates from instantaneous mantle flow models, 
+\emph on
+J.
+ Geophys.
+ Res.,
+\emph default
+ 103, 15,255-15,268.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [5]{Zhong et al The role of temperature}
+Zhong, S., M.
+ T.
+ Zuber, L.
+ N.
+ Moresi, and M.
+ Gurnis (2000), The role of temperature-dependent viscosity and surface
+ plates in spherical shell models of mantle convection, 
+\emph on
+J.
+ Geophys.
+ Res., 
+\emph default
+105, 11,063-11,082.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [6]{Tan et al Slabs in the lower}
+Tan, E., M.
+ Gurnis, and L.
+ Han (2002), Slabs in the lower mantle and their modulation of plume formation,
+ 
+\emph on
+Geochem.
+ Geophys.
+ Geosys.,
+\emph default
+ 3, 1067.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [7]{Conrad/Gurnis Seismic tomography}
+Conrad, C.
+ P., and M.
+ Gurnis (2003), Seismic tomography, surface uplift, and the breakup of Gondwanal
+and: Integrating mantle convection backwards in time, 
+\emph on
+Geochem.
+ Geophys.
+ Geosys.,
+\emph default
+ 4(3), 1031, doi:10.1029/2001GC000299.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [8]{Hughes The Finite Element Method}
+Hughes, T.
+ J.
+ R.
+ 
+\emph on
+The Finite Element Method: Linear Static and Dynamic Finite Element Analysis.
+
+\emph default
+ Englewood Cliffs, New Jersey: Prentice-Hall, Inc.; 1987.
+ 672 p.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [9]{Ramage/Wathen Iterative solution}
+Ramage, A., and A.
+ J.
+ Wathen (1994), Iterative solution techniques for the Stokes and Navier-Stokes
+ equations, 
+\emph on
+Int.
+ J.
+ Numer.
+ Methods.
+ Fluids,
+\emph default
+ 19, 67-83.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [10]{Brooks A.N.}
+Brooks, A.
+ N.
+
+\emph on
+ A Petrov-Galerkin Finite Element Formulation for Convecton Dominated Flows.
+
+\emph default
+ Unpublished doctoral thesis, California Institute of Technology, Pasadena,
+ CA, 1981.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [11]{Cahouet/Chabard Some fast 3D}
+Cahouet, J., and J.-P.
+ Chabard (1988), Some fast 3D finite element solvers for the generalized
+ Stokes problem
+\emph on
+, Int.
+ J.
+ Numer.
+ Methods.
+ Fluids,
+\emph default
+ 8, 869-895.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [12]{Atanga/Silvester Iterative methods}
+Atanga, J., and D.
+ Silvester (1992), Iterative methods for stabilized mixed velocity-pressure
+ finite elements, 
+\emph on
+Int.
+ J.
+ Numer.
+ Methods.
+ Fluids,
+\emph default
+ 14, 71-81.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [13]{Hager/OConnell A simple global}
+Hager, B.
+ H., and R.
+ J.
+ O'Connell (1981), A simple global model of plate dynamics and mantle convection
+, 
+\emph on
+J.
+ Geophys.
+ Res.,
+\emph default
+ 86, 4,843-4,867.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [14]{Tan et al GeoFramework Part I}
+Tan, E., E.
+ Choi, P.
+ Thoutireddy, M.
+ Gurnis, and M.
+ Aivazis (2006), GeoFramework: Coupling multiple models of mantle convection
+ within a computational framework,  
+\emph on
+Geochem., Geophys., Geosyst.
+ 7,
+\series bold
+ 
+\series default
+\emph default
+Q06001, doi:10.1029/2005GC001155.
+ 
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [15]{Zhong et al Free-surface formulation}
+Zhong, S., M.
+ Gurnis, and L.
+ Moresi (1996), Free-surface formulation of mantle convection--I.
+ Basic theory and appication to plumes
+\emph on
+, Geophys.
+ J.
+ Int.
+\emph default
+, 127, 708-718.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [16]{Zhong et al Three-dimensional}
+Zhong, S., A.
+ Paulson, and J.
+ Wahr (2003), Three-dimensional finite-element modeling of Earth's viscoelastic
+ deformation: effects of lateral variations in lithospheric thickness, 
+\emph on
+Geophys.
+ J.
+ Int.,
+\emph default
+ 155, 679-695.
+ 
+\end_layout
+
+\end_body
+\end_document