[cig-commits] r15402 - doc/CitcomS/manual
sue at geodynamics.org
sue at geodynamics.org
Tue Jun 30 15:06:07 PDT 2009
Author: sue
Date: 2009-06-30 15:06:06 -0700 (Tue, 30 Jun 2009)
New Revision: 15402
Modified:
doc/CitcomS/manual/citcoms.lyx
doc/CitcomS/manual/citcoms.pdf
Log:
fixed images not appearing; fixed problems causing trouble with pdf; other typos caught
Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx 2009-06-30 22:05:38 UTC (rev 15401)
+++ doc/CitcomS/manual/citcoms.lyx 2009-06-30 22:06:06 UTC (rev 15402)
@@ -1,5 +1,5 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
@@ -11,6 +11,7 @@
\raggedbottom
\end_preamble
+\use_default_options false
\language english
\inputencoding auto
\font_roman default
@@ -21,9 +22,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 0
@@ -60,12 +63,11 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
filename graphics/citcoms_cover.pdf
- display color
width 75page%
\end_inset
@@ -84,7 +86,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
\backslash
@@ -102,7 +104,9 @@
\begin_layout Author
© California Institute of Technology
-\newline
+\begin_inset Newline newline
+\end_inset
+
Version 3.1.0
\end_layout
@@ -111,7 +115,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
\backslash
@@ -124,7 +128,8 @@
\end_layout
\begin_layout Standard
-\begin_inset LatexCommand tableofcontents
+\begin_inset CommandInset toc
+LatexCommand tableofcontents
\end_inset
@@ -161,26 +166,40 @@
\end_layout
\begin_layout Standard
-The style of this publication is based on the
-\begin_inset LatexCommand htmlurl
-name "Apple Publications Style Guide"
-target "developer.apple.com/documentation/UserExperience/Conceptual/APStyleGuide/AppleStyleGuide2003.pdf"
+The style of this publication is based on the Apple Publications Style Guide
+
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+developer.apple.com/documentation/UserExperience/Conceptual/APStyleGuide/AppleStyl
+eGuide2003.pdf
+\end_layout
+
\end_inset
-, as recommended by
-\begin_inset LatexCommand htmlurl
-name "Python.org"
-target "www.python.org"
+, as recommended by Python.org
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.python.org
+\end_layout
+
\end_inset
.
- The documentation was produced using
-\begin_inset LatexCommand htmlurl
-name "LyX"
-target "www.lyx.org"
+ The documentation was produced using LyX
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.lyx.org
+\end_layout
+
\end_inset
to facilitate the transformation of files from one format to another.
@@ -190,11 +209,16 @@
\end_layout
\begin_layout Standard
-Errors and bug fixes in this manual should be directed to the
-\begin_inset LatexCommand htmlurl
-name "CIG Mantle Convection Mailing List"
-target "cig-mc at geodynamics.org"
+Errors and bug fixes in this manual should be directed to the CIG Mantle
+ Convection Mailing List
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+cig-mc at geodynamics.org
+\end_layout
+
\end_inset
.
@@ -300,11 +324,15 @@
\begin_layout Standard
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
-name "CIG"
-target "geodynamics.org"
+ of the code, and CIG
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org
+\end_layout
+
\end_inset
.
@@ -315,18 +343,28 @@
\end_layout
\begin_layout Standard
-Pyre development is funded by the
-\begin_inset LatexCommand htmlurl
-name "U.S. Dept. of Energy's Advanced Simulation and Computing program"
-target "www.sandia.gov/NNSA/ASC"
+Pyre development is funded by the U.S.
+ Dept.
+ of Energy's Advanced Simulation and Computing program
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.sandia.gov/NNSA/ASC
+\end_layout
+
\end_inset
- and the
-\begin_inset LatexCommand htmlurl
-name "National Science Foundation's"
-target "www.nsf.gov"
+ and the National Science Foundation's
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.nsf.gov
+\end_layout
+
\end_inset
Information Technology Research (ITR) program (grant #0205653).
@@ -359,7 +397,8 @@
CitcomS is a finite element code designed to solve thermal convection problems
relevant to earth's mantle released under the GNU General Public License
(see Appendix
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "cha:License"
\end_inset
@@ -500,25 +539,39 @@
\begin_layout Standard
CitcomS is one component of a larger collection of software encompassed
- by the former GeoFramework project, a collaboration between the
-\begin_inset LatexCommand htmlurl
-name "Center for Advanced Computing Research (CACR)"
-target "www.cacr.caltech.edu"
+ by the former GeoFramework project, a collaboration between the Center
+ for Advanced Computing Research (CACR)
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.cacr.caltech.edu
+\end_layout
+
\end_inset
- and the
-\begin_inset LatexCommand htmlurl
-name "Seismological Laboratory"
-target "www.gps.caltech.edu/seismo"
+ and the Seismological Laboratory
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.gps.caltech.edu/seismo
+\end_layout
+
\end_inset
-, both at Caltech, and the
-\begin_inset LatexCommand htmlurl
-name "Victorian Partnership for Advanced Computing"
-target "www.vpac.org"
+, both at Caltech, and the Victorian Partnership for Advanced Computing
+
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.vpac.org
+\end_layout
+
\end_inset
in Australia.
@@ -528,11 +581,15 @@
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 released under a GPL license and made available from
-\begin_inset LatexCommand htmlurl
-name "CIG"
-target "geodynamics.org"
+ was released under a GPL license and made available from CIG
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org
+\end_layout
+
\end_inset
.
@@ -554,7 +611,8 @@
Data Format).
The HDF5 format allows you to deal with the massive data output created
for production runs (see Chapter
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "cha:Working-with-HDF5"
\end_inset
@@ -567,25 +625,37 @@
files on input, which are easier to create and read.
Other improvements included the incorporation of geoid calculations that
had been left out of earlier releases, as well as new scripts to allow
- results to be visualized with
-\begin_inset LatexCommand htmlurl
-name "MayaVi2"
-target "svn.enthought.com/enthought/wiki/MayaVi"
+ results to be visualized with MayaVi2
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+svn.enthought.com/enthought/wiki/MayaVi
+\end_layout
+
\end_inset
- in addition to
-\begin_inset LatexCommand htmlurl
-name "Generic Mapping Tools (GMT)"
-target "gmt.soest.hawaii.edu"
+ in addition to Generic Mapping Tools (GMT)
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+gmt.soest.hawaii.edu
+\end_layout
+
\end_inset
- and
-\begin_inset LatexCommand htmlurl
-name "OpenDX"
-target "www.opendx.org"
+ and OpenDX
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.opendx.org
+\end_layout
+
\end_inset
.
@@ -651,12 +721,12 @@
\begin_layout Standard
This release of CitcomS 3.1 adds the ability to convert temperature and compositi
on to seismic velocities.
- The seismic velocities output can be uploaded to CIG seismic portal for
- SPECFEM3D simulation to generate synthetic seismograms.
+ The seismic velocities output can be uploaded to CIG Seismology Web Portal
+ for SPECFEM3D simulation to generate synthetic seismograms.
Other enhancements includes: Allowing tracers in global model with nproc
> 2 by changing the mesh slightly; The convergence of Stokes solver is
- controlled by parameter "accuracy" in [CitcomS.solver.vsolver].
- "tole_compressibility" is not used anymore.
+ controlled by parameter ``accuracy'' in [CitcomS.solver.vsolver].
+ ``tole_compressibility'' is not used anymore.
Also, the norms of div(u), u, and p are no longer dependent on the grid
size; Adding self-gravitational effect on geoid and adding Consistent-Boundary-
Flux (CBF) method to compute dynamic topography, contributed by Shijie Zhong;
@@ -667,21 +737,21 @@
by Mike Gurnis; Allowing multi-component chemical viscosity; Optimizing
the speed.
Cookbook 8 becomes 13% faster than v3.0; Better convergence for the coupled
- solver case; Moving input parameter "mantle_temp" from [CitcomS.solver.param]
+ solver case; Moving input parameter ``mantle_temp'' from [CitcomS.solver.param]
to [CitcomS.solver.ic] section.
Several bugs are fixed.
Important bug fixes include: A memory bug in visual/project_geoid.c, fixed
- by Thorsten Becker; Initial temperature "tic_method=0" for regional model
+ by Thorsten Becker; Initial temperature ``tic_method=0'' for regional model
applied sinusoidal perturbations to 0th processor only; Initial temperature
- "tic_method=1" for regional model generated a top thermal boundary layer
- 25x older than specfied by "half_space_age"; Compiling with both HDF5 and
- Exchanger support will crash Cookbook 9 (Issue 528); Insufficient error
+ ``tic_method=1'' for regional model generated a top thermal boundary layer
+ 25x older than specfied by ``half_space_age''; Compiling with both HDF5
+ and Exchanger support will crash Cookbook 9 (Issue 528); Insufficient error
checking when reading input files (Issue 265, reported by Clint Conrad);
Installation bug: Python.h and system header not properly checked by configure
script (Isse 45, reported by Vlad Manea and Ricardo Arevalo); Manual fixes:
description of rheol=4 (Isse 152, reported by James Robert), energy equation
- (Issue 162 & 164, reported by Dan Bower), documented all "tic_method" and
- "rheol" options.
+ (Issue 162 & 164, reported by Dan Bower), documented all ``tic_method''
+ and ``rheol'' options.
\end_layout
\begin_layout Section
@@ -737,7 +807,8 @@
\begin_layout Section
Governing Equations
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Governing-Equations"
\end_inset
@@ -1301,7 +1372,8 @@
\begin_layout Standard
The governing equations are solved with the finite element method
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Hughes The Finite Element Method"
\end_inset
@@ -1309,7 +1381,8 @@
.
CitcomS employs an Uzawa algorithm to solve the momentum equation coupled
with the incompressibility constraints
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Moresi/Gurnis Contraints,Ramage/Wathen Iterative solution"
\end_inset
@@ -1317,7 +1390,8 @@
.
The energy equation is solved with a Steamline-Upwind Petrov-Galerkin method
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Brooks A.N."
\end_inset
@@ -1328,26 +1402,30 @@
The use of brick elements in 3D (or rectangular elements in 2D) is important
for accurately determining the pressure, which controls the dynamic topography,
in incompressible Stokes flow
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Hughes The Finite Element Method"
\end_inset
.
The discrete form of Equations
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:non-dimensional continuity eqn"
\end_inset
and
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:non-dimensional momentum eqn"
\end_inset
may be written in the following matrix form
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Zhong et al The role of temperature"
\end_inset
@@ -1394,7 +1472,8 @@
\end_inset
is the second term in Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:non-dimensional continuity eqn"
\end_inset
@@ -1425,7 +1504,8 @@
f
\emph default
are obtained using a standard finite element formulation; see
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Zhong et al The role of temperature"
\end_inset
@@ -1441,7 +1521,8 @@
is zero.
Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:discrete momentum eqn"
\end_inset
@@ -1451,7 +1532,8 @@
\end_inset
and using Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:discrete continuite eqn"
\end_inset
@@ -1473,14 +1555,16 @@
\noindent
This equation is solved using the Uzawa algorithm, an established method
for solving the minimization of a dual function
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Cahouet/Chabard Some fast 3D"
\end_inset
, which simultaneously yields the velocity field.
A conjugate gradient scheme
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Ramage/Wathen Iterative solution,Atanga/Silvester Iterative methods"
\end_inset
@@ -1492,13 +1576,15 @@
\begin_layout Standard
In the compressible case, there are two different strategies to solve Equations
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:discrete continuite eqn"
\end_inset
and
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:discrete momentum eqn"
\end_inset
@@ -1506,7 +1592,8 @@
.
The first strategy is to add another layer of iterations when solving Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:cg"
\end_inset
@@ -1530,7 +1617,8 @@
\begin_layout Standard
\noindent
The second strategy is to transform Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:discrete momentum eqn"
\end_inset
@@ -1540,7 +1628,8 @@
\end_inset
and using Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:discrete continuite eqn"
\end_inset
@@ -1608,7 +1697,8 @@
\emph default
are in units of radians.
Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Global-Node-Numbering."
\end_inset
@@ -1650,11 +1740,12 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Global-Node-Numbering."
\end_inset
@@ -1695,7 +1786,8 @@
area.
In the full spherical mode, CitcomS has 12 caps numbered 0 to 11 (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Topological-connectivity-of"
\end_inset
@@ -1711,24 +1803,25 @@
placement H
wide false
sideways false
-status collapsed
+status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
- filename graphics/cap_order.eps
+ filename graphics/cap_order.pdf
\end_inset
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Topological-connectivity-of"
\end_inset
@@ -1752,7 +1845,8 @@
The caps are approximately square in map view so that the edges of the square
are oriented diagonally with respect to latitude and longitude.
The four corners of the domain are connected by great circles (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Orthographic-projection-of"
\end_inset
@@ -1762,7 +1856,8 @@
However, CitcomS can further decompose the domain such that additional
processors are used to divide caps uniformly along the two edges of the
caps (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Orthographic-projection-of"
\end_inset
@@ -1780,7 +1875,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -1792,11 +1887,12 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Orthographic-projection-of"
\end_inset
@@ -1848,7 +1944,8 @@
Advanced users and software developers may be interested in downloading
the latest CitcomS source code directly from the CIG source code repository,
instead of using the prepared source package; see Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Software-Repository"
\end_inset
@@ -1861,20 +1958,28 @@
\end_layout
\begin_layout Standard
-For help, send e-mail to the
-\begin_inset LatexCommand htmlurl
-name "CIG Mantle Convection Mailing List"
-target "cig-mc at geodynamics.org"
+For help, send e-mail to the CIG Mantle Convection Mailing List
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+cig-mc at geodynamics.org
+\end_layout
+
\end_inset
.
You can subscribe to the Mailing List and view archived discussion at the
-
-\begin_inset LatexCommand htmlurl
-name "Geodynamics Mail Lists web page"
-target "geodynamics.org/cig/lists"
+ Geodynamics Mail Lists web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/lists
+\end_layout
+
\end_inset
.
@@ -1914,7 +2019,9 @@
$ apt-get install build-essential python-dev
\backslash
-\newline
+\begin_inset Newline newline
+\end_inset
+
openmpi-dev openmpi-bin
\end_layout
@@ -1931,7 +2038,9 @@
$ yum install make automake gcc gcc-c++ kernel-devel
\backslash
-\newline
+\begin_inset Newline newline
+\end_inset
+
python python-devel openmpi openmpi-libs openmpi-devel
\end_layout
@@ -1964,7 +2073,8 @@
, and forgo use of Python and the Pyre framework.
This process requires only a C compiler and an MPI library.
For more information, see Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Installing-without-Pyre"
\end_inset
@@ -1975,7 +2085,8 @@
\begin_layout Standard
If you are going to use solver coupling, you will also need a decent C++
compiler (e.g., g++ 3.2 or newer) and the Exchanger package; see Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Exchanger-Configuration-(Optional)"
\end_inset
@@ -1983,7 +2094,8 @@
.
Optionally, CitcomS can be configured to use a parallel HDF5 library; see
Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:HDF5-Configuration"
\end_inset
@@ -2029,11 +2141,16 @@
\begin_layout Standard
The Mac OS X version of GCC is included in a software development suite
called Xcode.
- Xcode is available as a free download at the
-\begin_inset LatexCommand htmlurl
-name "Apple Developer Connection"
-target "developer.apple.com"
+ Xcode is available as a free download at the Apple Developer Connection
+
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+developer.apple.com
+\end_layout
+
\end_inset
.
@@ -2083,26 +2200,38 @@
\end_layout
\begin_layout Standard
-A popular choice is
-\begin_inset LatexCommand htmlurl
-name "MPICH"
-target "www-unix.mcs.anl.gov/mpi/mpich"
+A popular choice is MPICH
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www-unix.mcs.anl.gov/mpi/mpich
+\end_layout
+
\end_inset
.
- Other choices include
-\begin_inset LatexCommand htmlurl
-name "LAM/MPI"
-target "www.lam-mpi.org"
+ Other choices include LAM/MPI
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.lam-mpi.org
+\end_layout
+
\end_inset
- and
-\begin_inset LatexCommand htmlurl
-name "Open MPI"
-target "www.open-mpi.org"
+ and Open MPI
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.open-mpi.org
+\end_layout
+
\end_inset
.
@@ -2120,18 +2249,27 @@
\begin_layout Standard
Linux users may have a prebuilt MPI package available for their distribution.
- On Mac OS X, the Fink package manager offers a prepackaged version of
-\begin_inset LatexCommand htmlurl
-name "LAM/MPI"
-target "www.lam-mpi.org"
+ On Mac OS X, the Fink package manager offers a prepackaged version of LAM/MPI
+
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.lam-mpi.org
+\end_layout
+
\end_inset
-; so if you have
-\begin_inset LatexCommand htmlurl
-name "Fink"
-target "fink.sourceforge.net"
+; so if you have Fink
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+fink.sourceforge.net
+\end_layout
+
\end_inset
installed, simply enter the following command from a Terminal window to
@@ -2183,11 +2321,15 @@
\begin_layout Standard
Mac OS X 10.3 and later ships with a suitable version of Python preinstalled.
If you're using an older version of Mac OS X, or for more information in
- general, see
-\begin_inset LatexCommand htmlurl
-name "Python on the Mac"
-target "www.python.org/download/mac"
+ general, see Python on the Mac
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.python.org/download/mac
+\end_layout
+
\end_inset
at the Python web site.
@@ -2294,11 +2436,15 @@
\begin_layout Standard
If absolutely necessary, one can easily build Python from source using a
C compiler.
- You can download Python from the
-\begin_inset LatexCommand htmlurl
-name "Python website"
-target "www.python.org"
+ You can download Python from the Python website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.python.org
+\end_layout
+
\end_inset
.
@@ -2310,11 +2456,15 @@
\end_layout
\begin_layout Standard
-To obtain CitcomS, go to the
-\begin_inset LatexCommand htmlurl
-name "Geodynamics Software Packages web page"
-target "geodynamics.org/cig/software/packages/mc/citcoms"
+To obtain CitcomS, go to the Geodynamics Software Packages web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/mc/citcoms
+\end_layout
+
\end_inset
, download the source archive and unpack it using the
@@ -2352,9 +2502,13 @@
) to the directory containing the CitcomS source
\family typewriter
.
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ cd CitcomS-3.1.0
\end_layout
@@ -2366,9 +2520,13 @@
to configure the package for your system
\family typewriter
.
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ ./configure
\end_layout
@@ -2380,9 +2538,13 @@
to build the package.
\family typewriter
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ make
\end_layout
@@ -2419,7 +2581,8 @@
configure
\family default
, see Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Configuration"
\end_inset
@@ -2508,7 +2671,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Configuration"
\end_inset
@@ -2581,11 +2745,15 @@
\family typewriter
configure
\family default
- failures on the
-\begin_inset LatexCommand htmlurl
-name "CIG Mantle Convection Mailing List"
-target "cig-mc at geodynamics.org"
+ failures on the CIG Mantle Convection Mailing List
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+cig-mc at geodynamics.org
+\end_layout
+
\end_inset
, please send
@@ -2683,19 +2851,19 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="7" columns="2">
<features>
-<column alignment="center" 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">
+<column alignment="center" valignment="top" width="1in">
+<column alignment="left" valignment="top" width="3.5in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Variable
@@ -2703,10 +2871,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Description
@@ -2715,11 +2883,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
PYTHON
\end_layout
@@ -2728,37 +2896,59 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Python interpreter.
This is useful if you have Python installed in a non-standard location,
e.g.,
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
-\InsetSpace ~
-\InsetSpace ~
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
./configure
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
PYTHON=/opt/python2.5/bin/python
\family default
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
By default,
\family typewriter
configure
@@ -2773,11 +2963,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
CC
\end_layout
@@ -2786,36 +2976,59 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
C compiler command.
This is usually set to the name of an MPI wrapper command, e.g.,
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
-\InsetSpace ~
-\InsetSpace ~
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
./configure
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
CC=/opt/mpich-1.2.6/bin/mpicc
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
See Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:MPI-Configuration"
\end_inset
@@ -2826,20 +3039,20 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
CFLAGS
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
C compiler flags.
This can be set for optimization flags.
\end_layout
@@ -2847,20 +3060,20 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
CPPFLAGS
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
C preprocessor flags; e.g.,
\family typewriter
-I<dir>
@@ -2871,20 +3084,20 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
LDFLAGS
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Linker flags; e.g.,
\family typewriter
-L<dir>
@@ -2895,20 +3108,20 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
LIBS
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Library flags; e.g., -l<lib> if additional library is needed
\end_layout
@@ -2928,7 +3141,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:MPI-Configuration"
\end_inset
@@ -3115,7 +3329,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Exchanger-Configuration-(Optional)"
\end_inset
@@ -3127,18 +3342,23 @@
This version of CitcomS is capable of solver coupling.
Two or more instances of CitcomS solvers can be coupled together to solve
a problem with different length and time scales
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Tan et al GeoFramework Part I"
\end_inset
.
An external Exchanger package is needed for solver coupling.
- You can download Exchanger at
-\begin_inset LatexCommand htmlurl
-name "CIG's Exchanger web page"
-target "geodynamics.org/cig/software/packages/cs/exchanger"
+ You can download Exchanger at CIG's Exchanger web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/cs/exchanger
+\end_layout
+
\end_inset
.
@@ -3182,7 +3402,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:HDF5-Configuration"
\end_inset
@@ -3225,7 +3446,8 @@
NOTE:
\series default
Most post-processing and visualization scripts discussed in Chapter
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Postprocessing-and-Graphics"
\end_inset
@@ -3266,11 +3488,15 @@
\begin_layout Standard
NumPy is an extension to Python which adds support for multi-dimensional
arrays for use in scientific computing.
- You may download NumPy from the
-\begin_inset LatexCommand htmlurl
-name "NumPy home page"
-target "numpy.scipy.org"
+ You may download NumPy from the NumPy home page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+numpy.scipy.org
+\end_layout
+
\end_inset
.
@@ -3300,7 +3526,8 @@
\end_layout
\begin_layout Subsubsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sub:PyTables"
\end_inset
@@ -3311,11 +3538,15 @@
\begin_layout Standard
PyTables is an extension to Python and can expose HDF5 array datasets as
Python NumPy arrays.
- It is available at
-\begin_inset LatexCommand htmlurl
-name "PyTables"
-target "www.pytables.org"
+ It is available at PyTables
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.pytables.org
+\end_layout
+
\end_inset
.
@@ -3353,18 +3584,23 @@
\begin_layout Standard
HDFView is a visual tool written in Java for browsing and editing HDF5 files.
- You may download it from the
-\begin_inset LatexCommand htmlurl
-name "HDFView home page"
-target "hdf.ncsa.uiuc.edu/hdf-java-html/hdfview"
+ You may download it from the HDFView home page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+hdf.ncsa.uiuc.edu/hdf-java-html/hdfview
+\end_layout
+
\end_inset
.
\end_layout
\begin_layout Subsubsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sub:OpenDXutils"
\end_inset
@@ -3375,11 +3611,15 @@
\begin_layout Standard
In order to import HDF5 files into OpenDX, you need the OpenDXutils package
from the Cactus project.
- Go to the
-\begin_inset LatexCommand url
-name "OpenDXutils package website"
-target "www.cactuscode.org/Visualization/openDX"
+ Go to the OpenDXutils package website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.cactuscode.org/Visualization/openDX
+\end_layout
+
\end_inset
and follow the instructions to download and install the package.
@@ -3412,11 +3652,15 @@
\begin_layout Standard
The GRD file support can be enabled at configuration time.
- It requires the installation of
-\begin_inset LatexCommand htmlurl
-name "HC package"
-target "geodynamics.org/cig/software/packages/mc/hc"
+ It requires the installation of HC package
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/mc/hc
+\end_layout
+
\end_inset
, a 1D global mantle circulation solver which can compute velocities, tractions,
@@ -3457,7 +3701,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Batch-System-Configuration"
\end_inset
@@ -3487,11 +3732,16 @@
\family default
is invoked directly from the batch script.
On others, a special wrapper is used instead.
- If you need help to configure Pyre for your cluster, you can contact
-\begin_inset LatexCommand htmlurl
-name "CIG Mantle Convection Mailing List"
-target "cig-mc at geodynamics.org"
+ If you need help to configure Pyre for your cluster, you can contact CIG
+ Mantle Convection Mailing List
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+cig-mc at geodynamics.org
+\end_layout
+
\end_inset
for assistance.
@@ -3510,17 +3760,22 @@
\begin_layout Standard
For more information on configuring Pyre for your batch system, see CIG's
-
-\begin_inset LatexCommand htmlurl
-name "Pythia page"
-target "geodynamics.org/cig/software/packages/cs/pythia/docs/batch"
+ Pythia page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/cs/pythia/docs/batch
+\end_layout
+
\end_inset
.
For more information on batch system configuration as it pertains to running
CitcomS, see Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sub:Launchers-and-Schedulers"
\end_inset
@@ -3529,7 +3784,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Installing-without-Pyre"
\end_inset
@@ -3572,7 +3828,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Software-Repository"
\end_inset
@@ -3581,11 +3838,16 @@
\end_layout
\begin_layout Standard
-The CitcomS source code is available via a Subversion server at the
-\begin_inset LatexCommand htmlurl
-name "Geodynamics website"
-target "geodynamics.org"
+The CitcomS source code is available via a Subversion server at the Geodynamics
+ website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org
+\end_layout
+
\end_inset
.
@@ -3630,11 +3892,15 @@
\end_layout
\begin_layout Standard
-For more information on Subversion, visit the
-\begin_inset LatexCommand htmlurl
-name "Subversion website"
-target "subversion.tigris.org"
+For more information on Subversion, visit the Subversion website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+subversion.tigris.org
+\end_layout
+
\end_inset
.
@@ -3658,11 +3924,15 @@
\end_layout
\begin_layout Standard
-For more information about these GNU tools, see the
-\begin_inset LatexCommand htmlurl
-name "GNU website"
-target "www.gnu.org/software"
+For more information about these GNU tools, see the GNU website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.gnu.org/software
+\end_layout
+
\end_inset
.
@@ -3908,9 +4178,10 @@
\begin_layout LyX-Code
$ mpirun [mpi_options] CitcomSRegional inputfile
-\newline
-$ mpirun [mpi_options] CitcomSFu
-ll inputfile
+\begin_inset Newline newline
+\end_inset
+
+$ mpirun [mpi_options] CitcomSFull inputfile
\end_layout
\begin_layout Standard
@@ -3925,7 +4196,8 @@
\family default
directories, respectively.
The meaning of the input parameters is described in Appendix
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "cha:Appendix-A:-Input"
\end_inset
@@ -3939,7 +4211,8 @@
and in launching parallel jobs.
Users are encouraged to use the Pyre version if possible.
In the following sections and Chapter
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Cookbooks"
\end_inset
@@ -3975,7 +4248,8 @@
will run a regional model with default parameters.
It can also run a full spherical model if the correct parameters are set
(see Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:Cookbook-1:-Global"
\end_inset
@@ -3986,7 +4260,8 @@
\begin_layout Standard
On input, CitcomS needs numerous parameters to be specified (see Appendix
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Appendix-A:-Input"
\end_inset
@@ -4005,7 +4280,8 @@
Most of the properties you will set using CitcomS have names which are identical
to the parameters for CitcomS in pure C version, which are described in
Appendix
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Appendix-A:-Input"
\end_inset
@@ -4079,13 +4355,18 @@
\begin_layout LyX-Code
[CitcomS.component1.component2]
-\newline
+\begin_inset Newline newline
+\end_inset
+
# this is a comment
-\newline
+\begin_inset Newline newline
+\end_inset
+
property1 = value1
-\newline
-property2
- = value2 ; this is another comment
+\begin_inset Newline newline
+\end_inset
+
+property2 = value2 ; this is another comment
\end_layout
\begin_layout Standard
@@ -4136,17 +4417,25 @@
\begin_layout LyX-Code
<component name='component1'>
-\newline
+\begin_inset Newline newline
+\end_inset
+
<component name='component2'>
-\newline
- <property
- name='property1'>value1</property>
-\newline
- <property name='property2'>value2</pr
-operty>
-\newline
+\begin_inset Newline newline
+\end_inset
+
+ <property name='property1'>value1</property>
+\begin_inset Newline newline
+\end_inset
+
+ <property name='property2'>value2</property>
+\begin_inset Newline newline
+\end_inset
+
</component>
-\newline
+\begin_inset Newline newline
+\end_inset
+
</component>
\end_layout
@@ -4231,7 +4520,9 @@
$ citcoms --steps=10 --controller.monitoringFrequency=5
\backslash
-\newline
+\begin_inset Newline newline
+\end_inset
+
--solver.datafile=example0 --solver.mesher.nodex=17 --solver.mesher.nodey=17
\end_layout
@@ -4310,33 +4601,55 @@
\begin_layout LyX-Code
[CitcomS]
-\newline
+\begin_inset Newline newline
+\end_inset
+
steps = 5
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.controller]
-\newline
+\begin_inset Newline newline
+\end_inset
+
monitoringFrequency = 1
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver]
-\newline
-dataf
-ile = example0
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+datafile = example0
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.mesher]
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodex = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodey = 17
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Multiprocessor-Example"
\end_inset
@@ -4370,37 +4683,63 @@
\begin_layout LyX-Code
[CitcomS]
-\newline
+\begin_inset Newline newline
+\end_inset
+
steps = 70
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.controller]
-\newline
+\begin_inset Newline newline
+\end_inset
+
monitoringFrequency = 10
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver]
-\newline
-dat
-afile = example1
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+datafile = example1
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.mesher]
-\newline
+\begin_inset Newline newline
+\end_inset
+
nprocx = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
nprocy = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodex = 17
-\newline
-nodey
- = 17
-\newline
-nodez = 9
-
+\begin_inset Newline newline
+\end_inset
+
+nodey = 17
+\begin_inset Newline newline
+\end_inset
+
+nodez = 9
+
\end_layout
\begin_layout Standard
@@ -4447,9 +4786,13 @@
\begin_layout LyX-Code
nodex = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodey = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodez = 9
\end_layout
@@ -4483,7 +4826,9 @@
\begin_layout LyX-Code
nprocx = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
nprocy = 2
\end_layout
@@ -4492,24 +4837,23 @@
placement H
wide false
sideways false
-status collapsed
+status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
- filename graphics/cookbook2.eps
+ filename graphics/cookbook2.pdf
width 50page%
- keepAspectRatio
\end_inset
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Computational Domain.
Map view on the configuration of the top layer of the computational nodes
and the processors.
@@ -4789,7 +5133,9 @@
\backslash
-\newline
+\begin_inset Newline newline
+\end_inset
+
--solver.output.output_format=ascii-gz
\end_layout
@@ -4806,7 +5152,8 @@
and don't require additional post-processing to be visualized in OpenDX.
In order to use this feature, you must compile CitcomS with the parallel
HDF5 library if you haven't done so already (see Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:HDF5-Configuration"
\end_inset
@@ -4827,7 +5174,9 @@
\backslash
-\newline
+\begin_inset Newline newline
+\end_inset
+
--solver.output.output_format=hdf5
\end_layout
@@ -4850,7 +5199,8 @@
\family default
.
See Chapter
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "cha:Working-with-HDF5"
\end_inset
@@ -4859,7 +5209,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sub:Launchers-and-Schedulers"
\end_inset
@@ -5157,33 +5508,46 @@
\begin_layout LyX-Code
scheduler = lsf ; the type of the installed batch system
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.lsf]
\end_layout
\begin_layout LyX-Code
bsub-options = [-a mpich_gm] ; special options for 'bsub'
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.launcher]
\end_layout
\begin_layout LyX-Code
command = mpirun.lsf ; 'mpirun' command to use on our cluster
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.job]
\end_layout
\begin_layout LyX-Code
queue = normal ; default queue for jobs
-\newline
-walltime = 5*minute
- ; run time limit of the job
+\begin_inset Newline newline
+\end_inset
+
+walltime = 5*minute ; run time limit of the job
\end_layout
\begin_layout Standard
@@ -5235,7 +5599,8 @@
) contains the elapsed model time (in non-dimensional units) and CPU time
(in seconds) of every time step.
The format of the time file can be found in Appendix
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "cha:Appendix-C:-CitComS,"
\end_inset
@@ -5249,7 +5614,8 @@
Following your successful run, you will want to retrieve the output files
from all the nodes and process them so they can be visualized with the
visualization program OpenDX (see Chapter
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "cha:Postprocessing-and-Graphics"
\end_inset
@@ -5285,18 +5651,23 @@
$TG_COMMUNITY/CIG/CitcomS/TG_README
\family default
.
- See
-\begin_inset LatexCommand htmlurl
-name "CIG Community Area Software on the TeraGrid"
-target "geodynamics.org/cig/software/csa/"
+ See CIG Community Area Software on the TeraGrid
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/csa/
+\end_layout
+
\end_inset
for additional information on access and to apply for allocation time.
\end_layout
\begin_layout Chapter
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "cha:Working-with-HDF5"
\end_inset
@@ -5313,7 +5684,8 @@
files.
This situation is inefficient since it requires an extra post-processing
step for assembling the results from each processor (see Chapter
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "cha:Postprocessing-and-Graphics"
\end_inset
@@ -5331,11 +5703,15 @@
\begin_layout Standard
The Hierarchical Data Format (HDF) is a portable file format developed at
- the
-\begin_inset LatexCommand htmlurl
-name "National Center for Supercomputing Applications (NCSA)"
-target "hdf.ncsa.uiuc.edu/HDF5"
+ the National Center for Supercomputing Applications (NCSA)
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+hdf.ncsa.uiuc.edu/HDF5
+\end_layout
+
\end_inset
.
@@ -5575,8 +5951,10 @@
\family default
\size default
: Size of raw data chunk cache in bytes.
-\newline
+\begin_inset Newline newline
+\end_inset
+
\end_layout
\end_deeper
@@ -5587,10 +5965,15 @@
\begin_layout Itemize
\series bold
-\begin_inset LatexCommand htmlurl
-name "MPI-2: Extensions to the Message-Passing Interface, section 9.2.8"
-target "www-unix.mcs.anl.gov/mpi/mpi-standard/mpi-report-2.0/node182.htm"
+MPI-2: Extensions to the Message-Passing Interface, section 9.2.8
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www-unix.mcs.anl.gov/mpi/mpi-standard/mpi-report-2.0/node182.htm
+\end_layout
+
\end_inset
@@ -5602,10 +5985,15 @@
\begin_layout Itemize
\series bold
-\begin_inset LatexCommand htmlurl
-name "HDF5 documentation"
-target "hdf.ncsa.uiuc.edu/HDF5/doc/UG/08_TheFile.html"
+HDF5 documentation
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+hdf.ncsa.uiuc.edu/HDF5/doc/UG/08_TheFile.html
+\end_layout
+
\end_inset
@@ -5616,10 +6004,15 @@
\begin_layout Itemize
\series bold
-\begin_inset LatexCommand htmlurl
-name "HDF5 User's Guide: Data Caching"
-target "hdf.ncsa.uiuc.edu/HDF5/doc/Caching.html"
+HDF5 User's Guide: Data Caching
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+hdf.ncsa.uiuc.edu/HDF5/doc/Caching.html
+\end_layout
+
\end_inset
@@ -5648,25 +6041,35 @@
\begin_layout LyX-Code
cb_block_size = 1048576 # 1 MiB
-\newline
-cb_buffer_size = 4194304
- # 4 MiB
-\newline
+\begin_inset Newline newline
+\end_inset
+
+cb_buffer_size = 4194304 # 4 MiB
+\begin_inset Newline newline
+\end_inset
+
sieve_buf_size = 1048576 # 1 MiB
-\newline
-output_alignment
- = 262144 # 256 KiB
-\newline
-output_alignment_threshold = 524288 # 512
- KiB
-\newline
+\begin_inset Newline newline
+\end_inset
+
+output_alignment = 262144 # 256 KiB
+\begin_inset Newline newline
+\end_inset
+
+output_alignment_threshold = 524288 # 512 KiB
+\begin_inset Newline newline
+\end_inset
+
cache_rdcc_nelmts = 521
-\newline
+\begin_inset Newline newline
+\end_inset
+
cache_rdcc_nbytes = 1048576
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Data-Layout"
\end_inset
@@ -5740,21 +6143,21 @@
placement H
wide false
sideways false
-status collapsed
+status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="0">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="0">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="0">
+<column alignment="left" valignment="top" width="0">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Dataset
@@ -5762,10 +6165,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Shape
@@ -5774,11 +6177,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/input
@@ -5789,7 +6192,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
N/A
@@ -5798,11 +6201,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/coord
@@ -5813,7 +6216,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodex, nodey, nodez, 3)
@@ -5822,11 +6225,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/connectivity
@@ -5834,10 +6237,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(cap_elements, 8)
@@ -5853,10 +6256,10 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Layout of the time-independent data file
\end_layout
@@ -5877,21 +6280,21 @@
placement H
wide false
sideways false
-status collapsed
+status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="16" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="0">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="0">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="0">
+<column alignment="left" valignment="top" width="0">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Dataset
@@ -5899,10 +6302,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Shape
@@ -5911,11 +6314,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/velocity
@@ -5926,7 +6329,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodex, nodey, nodez, 3)
@@ -5935,11 +6338,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/temperature
@@ -5947,10 +6350,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodex, nodey, nodez)
@@ -5959,11 +6362,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/viscosity
@@ -5971,10 +6374,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodex, nodey, nodez)
@@ -5983,11 +6386,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/pressure
@@ -5995,10 +6398,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodex, nodey, nodez)
@@ -6007,11 +6410,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/stress
@@ -6019,10 +6422,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodex, nodey, nodez, 6)
@@ -6031,11 +6434,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/geoid
@@ -6043,16 +6446,17 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(8)
\family default
See Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sub:Geoid-Output-(test-case.geoid.10)"
\end_inset
@@ -6063,11 +6467,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/surf/velocity
@@ -6075,10 +6479,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodex, nodey, 2)
@@ -6087,11 +6491,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/surf/heatflux
@@ -6099,10 +6503,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodex, nodey)
@@ -6111,11 +6515,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/surf/topography
@@ -6123,10 +6527,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodex, nodey)
@@ -6135,11 +6539,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/botm/velocity
@@ -6147,10 +6551,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodex, nodey, 2)
@@ -6159,11 +6563,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/botm/heatflux
@@ -6171,10 +6575,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodex, nodey)
@@ -6183,11 +6587,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/botm/topography
@@ -6198,7 +6602,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodex, nodey)
@@ -6207,11 +6611,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/horiz_avg/temperature
@@ -6219,10 +6623,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodez)
@@ -6231,11 +6635,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/horiz_avg/velocity_xy
@@ -6243,10 +6647,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodez)
@@ -6255,11 +6659,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
/horiz_avg/velocity_z
@@ -6267,10 +6671,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
(caps, nodez)
@@ -6286,10 +6690,10 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Layout of the time-dependent data file
\end_layout
@@ -6342,7 +6746,8 @@
\begin_layout Standard
You can convert the HDF5 files to the ASCII combined capfiles described
in Appendix
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:ASCII-Output"
\end_inset
@@ -6357,7 +6762,8 @@
\begin_layout Standard
You can also convert the HDF5 files to the velo files described in Appendix
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sub:Velocity-and-Temperature"
\end_inset
@@ -6393,19 +6799,26 @@
\begin_layout LyX-Code
import tables
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
h5file = tables.openFile('samples/cookbook1.h5', 'r')
\end_layout
\begin_layout LyX-Code
surface_coords = h5file.root.coord[0:12,:,:,-1,:]
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-data100 = tables.openFile('samples
-/cookbook1.100.h5', 'r')
+
+\begin_inset Newline newline
+\end_inset
+
+data100 = tables.openFile('samples/cookbook1.100.h5', 'r')
\end_layout
\begin_layout LyX-Code
@@ -6441,18 +6854,26 @@
\end_layout
\begin_layout Standard
-For more details, refer to the documentation for
-\begin_inset LatexCommand htmlurl
-name "PyTables"
-target "www.pytables.org"
+For more details, refer to the documentation for PyTables
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.pytables.org
+\end_layout
+
\end_inset
- and
-\begin_inset LatexCommand htmlurl
-name "NumPy"
-target "numpy.scipy.org"
+ and NumPy
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+numpy.scipy.org
+\end_layout
+
\end_inset
.
@@ -6471,13 +6892,15 @@
with navigation arrow buttons that enable you to range over the entire
extent of a third dimension.
An example of using HDFView is found in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:A-screenshot-of"
\end_inset
which uses data from Cookbook 1 in Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:Cookbook-1:-Global"
\end_inset
@@ -6492,9 +6915,9 @@
placement H
wide false
sideways false
-status collapsed
+status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -6507,11 +6930,12 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:A-screenshot-of"
\end_inset
@@ -6534,7 +6958,8 @@
\end_layout
\begin_layout Chapter
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "cha:Postprocessing-and-Graphics"
\end_inset
@@ -6554,11 +6979,15 @@
of interest.
To visualize your results, it is recommended that you use the open-source
Open Visualization Data Explorer, better known as OpenDX.
- The software is available from the
-\begin_inset LatexCommand htmlurl
-name "OpenDX website"
-target "www.opendx.org"
+ The software is available from the OpenDX website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.opendx.org
+\end_layout
+
\end_inset
.
@@ -6571,17 +7000,22 @@
opendx
\family default
in your distribution.
- If you are using Mac OS X, OpenDX is available via
-\begin_inset LatexCommand htmlurl
-name "Fink"
-target "fink.sourceforge.net"
+ If you are using Mac OS X, OpenDX is available via Fink
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+fink.sourceforge.net
+\end_layout
+
\end_inset
.
We provide experimental scripts for a 3D visualization program called MayaVi2;
see Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:Using-MayaVi-for"
\end_inset
@@ -6589,7 +7023,8 @@
.
Scripts using GMT commands to plot 2D cross sections of temperature field
are also provided; see Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:Using-GMT-Commands"
\end_inset
@@ -6651,7 +7086,8 @@
\family default
files; you can visualize the results using OpenDX.
See Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:Using-OpenDX-for-HDF5"
\end_inset
@@ -6772,7 +7208,9 @@
$ autocombine.py [machinefile] [pidfile]
\backslash
-\newline
+\begin_inset Newline newline
+\end_inset
+
[step1] [step2 or more ...]
\end_layout
@@ -6806,14 +7244,17 @@
\family typewriter
test-case.cap00.10
-\newline
+\begin_inset Newline newline
+\end_inset
+
test-case.cap00.10.general
\end_layout
\begin_layout Standard
The former file is the data file containing simulation results and is referred
to as the ``capfile''; its format can be found in Appendix
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Appendix-C:-CitComS,"
\end_inset
@@ -6846,7 +7287,9 @@
\family typewriter
test-case.opt00.10
-\newline
+\begin_inset Newline newline
+\end_inset
+
test-case.opt00.10.general
\end_layout
@@ -6883,7 +7326,9 @@
$ autocombine.py localhost [pidfile]
\backslash
-\newline
+\begin_inset Newline newline
+\end_inset
+
[step1] [step2 or more ...]
\end_layout
@@ -7036,22 +7481,22 @@
placement H
wide false
sideways false
-status collapsed
+status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
- filename graphics/c_fig5.eps
+ filename graphics/c_fig5.pdf
\end_inset
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Regional Model Visualized with OpenDX.
A snapshot of an upwelling (blue isosurface) with a slice of the temperature
field (bisecting plane).
@@ -7312,7 +7757,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Using-OpenDX-for-HDF5"
\end_inset
@@ -7328,7 +7774,8 @@
), you can directly visualize the data without postprocessing.
First, you need to install and set up the OpenDXutils package (see Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sub:OpenDXutils"
\end_inset
@@ -7374,7 +7821,8 @@
Macros
\family default
category (highlighted in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Import-CitComS.py-HDF5"
\end_inset
@@ -7386,7 +7834,8 @@
\begin_layout Enumerate
Place the module in the work space and rewire the network as shown in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Import-CitComS.py-HDF5"
\end_inset
@@ -7399,7 +7848,7 @@
sideways false
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -7413,11 +7862,12 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Import-CitComS.py-HDF5"
\end_inset
@@ -7521,7 +7971,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Using-MayaVi-for"
\end_inset
@@ -7536,33 +7987,47 @@
It is an interactive program allowing elaborate plots of scientific data.
MayaVi2 relies on the Visualization Toolkit (VTK) and allows easy scripting
in Python.
- To install MayaVi2, you should follow the instructions on the
-\begin_inset LatexCommand htmlurl
-name "MayaVi2 website"
-target "https://svn.enthought.com/enthought/wiki/GrabbingAndBuilding"
+ To install MayaVi2, you should follow the instructions on the MayaVi2 website
+
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+https://svn.enthought.com/enthought/wiki/GrabbingAndBuilding
+\end_layout
+
\end_inset
- and on the
-\begin_inset LatexCommand htmlurl
-name "SciPy website"
-target "www.scipy.org/Cookbook/MayaVi/Installation"
+ and on the SciPy website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.scipy.org/Cookbook/MayaVi/Installation
+\end_layout
+
\end_inset
.
Besides MayaVi2, before using the script you will need to install PyTables
(see Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sub:PyTables"
\end_inset
-) and PyVTK; see
-\begin_inset LatexCommand htmlurl
-name "PyVTK website"
-target "cens.ioc.ee/projects/pyvtk"
+) and PyVTK; see PyVTK website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+cens.ioc.ee/projects/pyvtk
+\end_layout
+
\end_inset
for instructions.
@@ -7610,7 +8075,8 @@
\family default
.
An example of using this script is found in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Example-MayaVi2-visualization"
\end_inset
@@ -7622,11 +8088,15 @@
\shape italic
The Visualization Toolkit User's Guide
\shape default
- (ISBN 1-930934-13-0) or see the
-\begin_inset LatexCommand htmlurl
-name "VTK website"
-target "www.vtk.org"
+ (ISBN 1-930934-13-0) or see the VTK website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.vtk.org
+\end_layout
+
\end_inset
.
@@ -7639,9 +8109,9 @@
placement H
wide false
sideways false
-status collapsed
+status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -7654,11 +8124,12 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Example-MayaVi2-visualization"
\end_inset
@@ -7686,7 +8157,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Using-GMT-Commands"
\end_inset
@@ -7774,7 +8246,7 @@
sideways false
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -7787,10 +8259,10 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Temperature field generated by
\family typewriter
plot_layer.py
@@ -7852,7 +8324,7 @@
sideways false
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -7865,10 +8337,10 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Temperature fields generated by
\family typewriter
plot_annulus.py
@@ -7912,7 +8384,8 @@
\begin_layout Chapter
Cookbooks
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "cha:Cookbooks"
\end_inset
@@ -7936,7 +8409,8 @@
directory.
However, you might need to edit these example scripts slightly to launch
the job on your cluster (see Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:Multiprocessor-Example"
\end_inset
@@ -7958,14 +8432,17 @@
Cookbook 9 introduces embedding one CitcomS domain within another CitcomS
domain, and further tuning of the advection solver.
Cookbook 10 introduces how to convert the convection field to seismic velocitie
-s and how to generate synthetic seismograms using SPECFEM3D_GLOBE at CIG
- seismic portal.
-\newpage
+s and how to generate synthetic seismograms using SPECFEM3D_GLOBE at the
+ CIG Seismology Web Portal.
+\begin_inset Newpage newpage
+\end_inset
+
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Cookbook-1:-Global"
\end_inset
@@ -7995,20 +8472,20 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
- filename graphics/cookbook1.eps
+ filename graphics/cookbook1.pdf
\end_inset
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Global Model ``Caps.'' Left (A): Three-dimensional perspective image showing
seven of the 12 spherical caps used in a full CitcomS run.
Right (B): The temperature field at 1081 km depth from a Cookbook 1 run.
@@ -8051,9 +8528,13 @@
\begin_layout LyX-Code
steps = 100
-\newline
+\begin_inset Newline newline
+\end_inset
+
monitoringFrequency = 25
-\newline
+\begin_inset Newline newline
+\end_inset
+
datafile = cookbook1
\end_layout
@@ -8078,15 +8559,22 @@
\begin_layout LyX-Code
num_perturbations = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbl = 3
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbm = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturblayer = 5
-\newline
-perturbmag
- = 0.05
+\begin_inset Newline newline
+\end_inset
+
+perturbmag = 0.05
\end_layout
\begin_layout Standard
@@ -8105,40 +8593,66 @@
\begin_layout LyX-Code
[CitcomS]
-\newline
+\begin_inset Newline newline
+\end_inset
+
solver = full
-\newline
+\begin_inset Newline newline
+\end_inset
+
steps = 100 ; number of time steps
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[CitcomS.
-controller]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.controller]
+\begin_inset Newline newline
+\end_inset
+
monitoringFrequency = 25 ; how often outputs are created
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[CitcomS.so
-lver]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.solver]
+\begin_inset Newline newline
+\end_inset
+
datafile = cookbook1 ; prefix of output filenames
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.ic]
-\newline
-nu
-m_perturbations = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
+num_perturbations = 1
+\begin_inset Newline newline
+\end_inset
+
perturbl = 3
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbm = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturblayer = 5
-\newline
-perturbmag =
- 0.05
+\begin_inset Newline newline
+\end_inset
+
+perturbmag = 0.05
\end_layout
\begin_layout Standard
@@ -8159,7 +8673,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename graphics/cookbook1.2.jpg
@@ -8171,10 +8685,10 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Cookbook 1: Global Model.
This image, created by OpenDX, depicts a slice through a spherical model
of convection, with warmer colors indicating upwelling and the cooler colors
@@ -8222,7 +8736,9 @@
$ citcoms cookbook1.cfg --launcher.nodegen="n%03d"
\backslash
-\newline
+\begin_inset Newline newline
+\end_inset
+
--launcher.nodelist=[1,1,1,1,1,1,1,1,1,1,1,1]
\end_layout
@@ -8232,8 +8748,9 @@
\end_layout
\begin_layout Standard
+\begin_inset Newpage newpage
+\end_inset
-\newpage
\end_layout
@@ -8272,9 +8789,13 @@
\begin_layout LyX-Code
steps = 60
-\newline
+\begin_inset Newline newline
+\end_inset
+
monitoringFrequency = 30
-\newline
+\begin_inset Newline newline
+\end_inset
+
datafile = cookbook2
\end_layout
@@ -8339,28 +8860,49 @@
\begin_layout LyX-Code
nprocx = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
nprocy = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodex = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodey = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodez = 9
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
theta_min = 0.7854
-\newline
-theta_ma
-x = 1.5708
-\newline
+\begin_inset Newline newline
+\end_inset
+
+theta_max = 1.5708
+\begin_inset Newline newline
+\end_inset
+
fi_min = 0.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
fi_max = 0.7854
-\newline
+\begin_inset Newline newline
+\end_inset
+
radius_inner = 0.55
-\newline
+\begin_inset Newline newline
+\end_inset
+
radius_outer = 1.0
\end_layout
@@ -8372,7 +8914,8 @@
facility allows you to impose a uniform velocity across the top surface.
You have a velocity which is purely in the colatitude direction with a
non-dimensional velocity of 100 (see Equation
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "eq:u dim"
\end_inset
@@ -8382,9 +8925,13 @@
\begin_layout LyX-Code
topvbc = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
topvbxval = 100
-\newline
+\begin_inset Newline newline
+\end_inset
+
topvbyval = 0
\end_layout
@@ -8401,7 +8948,9 @@
\begin_layout LyX-Code
num_perturbations = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbmag = 0.0
\end_layout
@@ -8413,79 +8962,137 @@
\begin_layout LyX-Code
[CitcomS]
-\newline
+\begin_inset Newline newline
+\end_inset
+
steps = 60 ; number of time steps
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.controller]
-\newline
-mo
-nitoringFrequency = 30 ; how often outputs are created
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+monitoringFrequency = 30 ; how often outputs are created
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver]
-\newline
-datafile
- = cookbook2 ; prefix of output filenames
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-# Modify the layout of the
- mesh.
-\newline
+datafile = cookbook2 ; prefix of output filenames
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+# Modify the layout of the mesh.
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.mesher]
-\newline
+\begin_inset Newline newline
+\end_inset
+
nprocx = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
nprocy = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodex = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodey = 17
-\newline
-nodez
- = 9
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+nodez = 9
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
theta_min = 0.7854
-\newline
+\begin_inset Newline newline
+\end_inset
+
theta_max = 1.5708
-\newline
+\begin_inset Newline newline
+\end_inset
+
fi_min = 0.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
fi_max = 0.7854
-\newline
-radius_inner
- = 0.55
-\newline
+\begin_inset Newline newline
+\end_inset
+
+radius_inner = 0.55
+\begin_inset Newline newline
+\end_inset
+
radius_outer = 1.0
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
# Impose a uniform velocity across the top surface.
-\newline
-[Citcom
-S.solver.bc]
-\newline
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.solver.bc]
+\begin_inset Newline newline
+\end_inset
+
topvbc = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
topvbxval = 100
-\newline
+\begin_inset Newline newline
+\end_inset
+
topvbyval = 0
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-# In addition, set
- the initial temperature perturbation to zero.
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+# In addition, set the initial temperature perturbation to zero.
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.ic]
-\newline
-num_perturbations
- = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
+num_perturbations = 1
+\begin_inset Newline newline
+\end_inset
+
perturbmag = 0.0
\end_layout
@@ -8495,7 +9102,8 @@
\begin_layout Standard
Using OpenDX to visualize the results (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Cookbook-2:-Velocity"
\end_inset
@@ -8516,21 +9124,22 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
- filename graphics/cookbook2.2.eps
+ filename graphics/cookbook2.2.pdf
\end_inset
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Cookbook-2:-Velocity"
\end_inset
@@ -8552,8 +9161,9 @@
\end_layout
\begin_layout Standard
+\begin_inset Newpage newpage
+\end_inset
-\newpage
\end_layout
@@ -8595,11 +9205,17 @@
\begin_layout LyX-Code
steps = 200
-\newline
+\begin_inset Newline newline
+\end_inset
+
monitoringFrequency = 25
-\newline
+\begin_inset Newline newline
+\end_inset
+
datafile = cookbook3
-\newline
+\begin_inset Newline newline
+\end_inset
+
rayleigh = 1e6
\end_layout
@@ -8636,30 +9252,50 @@
\begin_layout LyX-Code
VISC_UPDATE = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
num_mat = 4
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc0 = 1,1,1,1
-\newline
+\begin_inset Newline newline
+\end_inset
+
TDEPV = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
rheol = 4
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscE = 0.2,0.2,0.2,0.2
-\newline
+\begin_inset Newline newline
+\end_inset
viscT = 0,0,0,0
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscZ = 0,0,0,0
-\newline
+\begin_inset Newline newline
+\end_inset
+
VMIN = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc_min = 1.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
VMAX = on
-\newline
-visc_max =
- 100.0
+\begin_inset Newline newline
+\end_inset
+
+visc_max = 100.0
\end_layout
\begin_layout Standard
@@ -8691,7 +9327,8 @@
\family default
parameter.
All available viscosity laws can be found in Appendix
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sub:Viscosity-input"
\end_inset
@@ -8732,7 +9369,8 @@
.
Comparing Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:non-dim visc law"
\end_inset
@@ -8762,7 +9400,8 @@
is the universal gas constant, and other symbols are as defined in Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Governing-Equations"
\end_inset
@@ -8796,74 +9435,129 @@
\begin_layout LyX-Code
[CitcomS]
-\newline
+\begin_inset Newline newline
+\end_inset
+
steps = 200 ; number of time steps
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.controller]
-\newline
-mo
-nitoringFrequency = 25 ; how often outputs are created
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+monitoringFrequency = 25 ; how often outputs are created
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver]
-\newline
-datafile
- = cookbook3 ; prefix of output filenames
-\newline
-rayleigh = 1e6
- ; Rayleigh number
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+datafile = cookbook3 ; prefix of output filenames
+\begin_inset Newline newline
+\end_inset
+
+rayleigh = 1e6 ; Rayleigh number
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
# Modify the layout of the mesh.
-\newline
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.mesher]
-\newline
-nprocx
- = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
+nprocx = 2
+\begin_inset Newline newline
+\end_inset
+
nprocy = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodex = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodey = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodez = 9
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
# Assign the viscosities.
-\newline
-[Citcom
-S.solver.visc]
-\newline
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.solver.visc]
+\begin_inset Newline newline
+\end_inset
+
VISC_UPDATE = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
num_mat = 4
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc0 = 1,1,1,1
-\newline
+\begin_inset Newline newline
+\end_inset
+
TDEPV = on
-\newline
-rheol =
- 4
-\newline
+\begin_inset Newline newline
+\end_inset
+
+rheol = 4
+\begin_inset Newline newline
+\end_inset
+
viscE = 0.2,0.2,0.2,0.2
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscT = 0,0,0,0
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscZ = 0,0,0,0
-\newline
+\begin_inset Newline newline
+\end_inset
+
VMIN = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc_min = 1.0
-\newline
-VMAX
- = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
+VMAX = on
+\begin_inset Newline newline
+\end_inset
+
visc_max = 100.0
\end_layout
@@ -8874,20 +9568,20 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
- filename graphics/cookbook3.eps
+ filename graphics/cookbook3.pdf
\end_inset
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Cookbook 3: Temperature-Dependent Viscosity.
This model, visualized with OpenDX, highlights a region that features both
the heated upwelling (warm colors) and the even distribution of the velocities
@@ -8905,8 +9599,9 @@
\end_layout
\begin_layout Standard
+\begin_inset Newpage newpage
+\end_inset
-\newpage
\end_layout
@@ -8954,7 +9649,8 @@
\family default
).
The format of the coordinate input file is described in Appendix
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:Coordinate-files"
\end_inset
@@ -8964,7 +9660,9 @@
\begin_layout LyX-Code
coor = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
coor_file = coor.dat
\end_layout
@@ -8986,102 +9684,181 @@
\begin_layout LyX-Code
[CitcomS]
-\newline
+\begin_inset Newline newline
+\end_inset
+
steps = 250 ; number of time steps
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.controller]
-\newline
-mo
-nitoringFrequency = 10 ; how often outputs are created
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+monitoringFrequency = 10 ; how often outputs are created
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver]
-\newline
-rayleigh
- = 1e6 ; Rayleigh number
-\newline
-datafile = cookbook4 ; prefix
- of output filenames
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+rayleigh = 1e6 ; Rayleigh number
+\begin_inset Newline newline
+\end_inset
+
+datafile = cookbook4 ; prefix of output filenames
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.ic]
-\newline
+\begin_inset Newline newline
+\end_inset
+
num_perturbations = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbmag = 0.05
-\newline
-pertur
-blayer = 10
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+perturblayer = 10
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
# Perturb the initial temperature gradient in the longitudinal
-\newline
-#
- direction.
-\newline
+\begin_inset Newline newline
+\end_inset
+
+# direction.
+\begin_inset Newline newline
+\end_inset
+
perturbl = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbm = 0
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.mesher]
-\newline
-# Read uneven mesh
- point coordinates from 'coor.dat'.
-\newline
+\begin_inset Newline newline
+\end_inset
+
+# Read uneven mesh point coordinates from 'coor.dat'.
+\begin_inset Newline newline
+\end_inset
+
coor = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
coor_file = coor.dat
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
nprocx = 2
-\newline
-nprocy
- = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
+nprocy = 1
+\begin_inset Newline newline
+\end_inset
+
nprocz = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodex = 33
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodey = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodez = 17
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.visc]
-\newline
-VISC_UPDATE
- = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
+VISC_UPDATE = on
+\begin_inset Newline newline
+\end_inset
+
num_mat = 4
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc0 = 1,1,1,1
-\newline
+\begin_inset Newline newline
+\end_inset
+
TDEPV = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
rheol = 4
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscE = 0.2,0.2,0.2,0.2
-\newline
-viscT
- = 0,0,0,0
-\newline
+\begin_inset Newline newline
+\end_inset
+
+viscT = 0,0,0,0
+\begin_inset Newline newline
+\end_inset
+
viscZ = 0,0,0,0
-\newline
+\begin_inset Newline newline
+\end_inset
+
VMIN = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc_min = 1.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
VMAX = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc_max = 100.0
\end_layout
@@ -9092,20 +9869,20 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
- filename graphics/cookbook4.eps
+ filename graphics/cookbook4.pdf
\end_inset
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Cookbook 4: Regionally Refined Mesher.
This model shows the temperature (upwelling -- warm colors, downwelling
-- cool colors) and the uneven distribution of the velocities (yellow arrows).
@@ -9147,8 +9924,9 @@
\end_layout
\begin_layout Standard
+\begin_inset Newpage newpage
+\end_inset
-\newpage
\end_layout
@@ -9179,7 +9957,8 @@
The following scenario is proposed for this cookbook: there are two plates
centered along the equator, with two different Euler poles (see Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Cookbook-5:-Left"
\end_inset
@@ -9200,13 +9979,21 @@
\begin_layout LyX-Code
[CitcomS.solver.bc]
-\newline
+\begin_inset Newline newline
+\end_inset
+
topvbc = 1
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.param]
-\newline
+\begin_inset Newline newline
+\end_inset
+
file_vbcs = on
\end_layout
@@ -9217,7 +10004,9 @@
\begin_layout LyX-Code
start_age = 55
-\newline
+\begin_inset Newline newline
+\end_inset
+
vel_bound_file = ./velocity/bvel.dat
\end_layout
@@ -9233,7 +10022,8 @@
\family default
).
The format of the velocity file is described in Appendix
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:Velocity-boundary-condition"
\end_inset
@@ -9250,7 +10040,8 @@
is set, the initial temperature field is read from setup files.
The files have the same naming scheme and format as the CitcomS velo output,
as described in Appendix
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sub:Velocity-and-Temperature"
\end_inset
@@ -9280,18 +10071,29 @@
\begin_layout LyX-Code
[CitcomS.solver]
-\newline
+\begin_inset Newline newline
+\end_inset
+
datadir_old = ./ic
-\newline
+\begin_inset Newline newline
+\end_inset
+
datafile_old = cookbook5
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.ic]
-\newline
-tic_met
-hod = -1
-\newline
+\begin_inset Newline newline
+\end_inset
+
+tic_method = -1
+\begin_inset Newline newline
+\end_inset
+
solution_cycles_init = 0
\end_layout
@@ -9307,9 +10109,13 @@
\begin_layout LyX-Code
[CitcomS.solver.tsolver]
-\newline
+\begin_inset Newline newline
+\end_inset
+
finetunedt = 0.75
-\newline
+\begin_inset Newline newline
+\end_inset
+
monitor_max_T = on
\end_layout
@@ -9320,10 +10126,10 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
- filename graphics/cookbook5.eps
+ filename graphics/cookbook5.pdf
lyxscale 65
scale 65
@@ -9332,11 +10138,12 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Cookbook-5:-Left"
\end_inset
@@ -9367,141 +10174,232 @@
\begin_layout LyX-Code
[CitcomS]
-\newline
+\begin_inset Newline newline
+\end_inset
+
steps = 1100 ; number of time steps
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.controller]
-\newline
-mo
-nitoringFrequency = 100 ; how often outputs are created
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+monitoringFrequency = 100 ; how often outputs are created
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver]
-\newline
-datafile
- = cookbook5
-\newline
+\begin_inset Newline newline
+\end_inset
+
+datafile = cookbook5
+\begin_inset Newline newline
+\end_inset
+
datadir_old = ./ic
-\newline
+\begin_inset Newline newline
+\end_inset
+
datafile_old = cookbook5
-\newline
+\begin_inset Newline newline
+\end_inset
+
rayleigh = 4.07e+08
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[CitcomS.s
-olver.bc]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.solver.bc]
+\begin_inset Newline newline
+\end_inset
+
topvbc = 1
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.param]
-\newline
+\begin_inset Newline newline
+\end_inset
+
file_vbcs = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
start_age = 55
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-# Since
- the starting age is set to 55 Ma, there will be 57 velocity
-\newline
-# files, one
- for each Ma (bvel.dat0, bvel.dat1, ...
+
+\begin_inset Newline newline
+\end_inset
+
+# Since the starting age is set to 55 Ma, there will be 57 velocity
+\begin_inset Newline newline
+\end_inset
+
+# files, one for each Ma (bvel.dat0, bvel.dat1, ...
bvel.dat56).
-\newline
+\begin_inset Newline newline
+\end_inset
+
vel_bound_file = ./velocity/bvel.dat
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.ic]
-\newline
-tic_method
- = -1
-\newline
+\begin_inset Newline newline
+\end_inset
+
+tic_method = -1
+\begin_inset Newline newline
+\end_inset
+
solution_cycles_init = 0
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.mesher]
-\newline
+\begin_inset Newline newline
+\end_inset
+
coor = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
coor_file = ./coor.dat
-\newline
-np
-rocx = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
+nprocx = 1
+\begin_inset Newline newline
+\end_inset
+
nprocy = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
nprocz = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodex = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodey = 65
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodez = 33
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.tsolver]
-\newline
+\begin_inset Newline newline
+\end_inset
finetunedt = 0.75
-\newline
+\begin_inset Newline newline
+\end_inset
+
monitor_max_T = on
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.visc]
-\newline
+\begin_inset Newline newline
+\end_inset
+
num_mat = 4
-\newline
-visc0 =
- 100,0.003,1,2
-\newline
+\begin_inset Newline newline
+\end_inset
+
+visc0 = 100,0.003,1,2
+\begin_inset Newline newline
+\end_inset
+
TDEPV = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscE = 24,24,24,24
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscT = 0.182,0.182,0.182,0.182
-\newline
-VMIN
- = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
+VMIN = on
+\begin_inset Newline newline
+\end_inset
+
visc_min = 0.01
-\newline
+\begin_inset Newline newline
+\end_inset
+
VMAX = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc_max = 100.0
\end_layout
\begin_layout Standard
\begin_inset Float figure
-placement h
+placement H
wide false
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
- filename graphics/cookbook5.2.eps
+ filename graphics/cookbook5.2.pdf
\end_inset
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Cookbook-5:-the"
\end_inset
@@ -9527,7 +10425,8 @@
\begin_layout Standard
The results for this problem are presented in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Cookbook-5:-the"
\end_inset
@@ -9543,8 +10442,9 @@
\end_layout
\begin_layout Standard
+\begin_inset Newpage newpage
+\end_inset
-\newpage
\end_layout
@@ -9571,7 +10471,8 @@
\begin_layout Standard
The basic algorithm
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Zhong et al Free-surface formulation,Zhong et al Three-dimensional"
\end_inset
@@ -9590,7 +10491,8 @@
Calculate the normal traction on the top surface based on the accumulated
topography up to the current time step, and add it to the forcing term
in Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:discrete momentum eqn"
\end_inset
@@ -9682,9 +10584,13 @@
\begin_layout LyX-Code
[CitcomS.solver.bc]
-\newline
+\begin_inset Newline newline
+\end_inset
+
topvbc = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
pseudo_free_surf = on
\end_layout
@@ -9698,7 +10604,9 @@
\begin_layout LyX-Code
[CitcomS.solver.tsolver]
-\newline
+\begin_inset Newline newline
+\end_inset
+
fixed_timestep = 7.77e-10
\end_layout
@@ -9709,14 +10617,16 @@
\begin_layout Standard
The plots of the topography profile are consistent with results described
in
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Zhong et al Free-surface formulation"
\end_inset
.
In the graphs in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Cookbook-6.-Graphs"
\end_inset
@@ -9734,7 +10644,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -9747,11 +10657,12 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Cookbook-6.-Graphs"
\end_inset
@@ -9771,8 +10682,9 @@
\end_layout
\begin_layout Standard
+\begin_inset Newpage newpage
+\end_inset
-\newpage
\end_layout
@@ -9908,9 +10820,13 @@
\begin_layout LyX-Code
tracer_ic_method = 0
-\newline
+\begin_inset Newline newline
+\end_inset
+
tracers_per_element = 20
-\newline
+\begin_inset Newline newline
+\end_inset
+
tracer_file = tracer.dat
\end_layout
@@ -9944,9 +10860,13 @@
\begin_layout LyX-Code
tracer_flavors = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
ic_method_for_flavors = 0
-\newline
+\begin_inset Newline newline
+\end_inset
+
z_interface = 0.7
\end_layout
@@ -9964,7 +10884,8 @@
buoy_type=1
\family default
)
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Tackely King tracer ratio method"
\end_inset
@@ -9981,7 +10902,9 @@
\begin_layout LyX-Code
buoy_type = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
buoyancy_ratio = 0.5
\end_layout
@@ -10002,7 +10925,8 @@
\begin_layout Standard
The regular grid is an auxiliary grid that helps locate the tracers
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "McNamara Zhong Thermochemical"
\end_inset
@@ -10021,7 +10945,9 @@
\begin_layout LyX-Code
regular_grid_deltheta = 1.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
regular_grid_delphi = 1.0
\end_layout
@@ -10091,11 +11017,17 @@
\begin_layout LyX-Code
Solver = cgrad
-\newline
+\begin_inset Newline newline
+\end_inset
+
accuracy = 1e-03
-\newline
+\begin_inset Newline newline
+\end_inset
+
vlowstep = 1000
-\newline
+\begin_inset Newline newline
+\end_inset
+
piterations = 1000
\end_layout
@@ -10107,133 +11039,237 @@
\begin_layout LyX-Code
[CitcomS]
-\newline
+\begin_inset Newline newline
+\end_inset
+
solver = full
-\newline
+\begin_inset Newline newline
+\end_inset
+
steps = 15 ; number of time steps
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[CitcomS.c
-ontroller]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.controller]
+\begin_inset Newline newline
+\end_inset
+
monitoringFrequency = 5 ; how often outputs are created
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[CitcomS.solv
-er]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.solver]
+\begin_inset Newline newline
+\end_inset
+
datadir = output ; path to output directory
-\newline
-datafile = cookbook7
- ; prefix of output filenames
-\newline
+\begin_inset Newline newline
+\end_inset
+
+datafile = cookbook7 ; prefix of output filenames
+\begin_inset Newline newline
+\end_inset
+
rayleigh = 1e7
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.ic]
-\newline
-num_perturbati
-ons = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
+num_perturbations = 1
+\begin_inset Newline newline
+\end_inset
+
perturbl = 3
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbm = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturblayer = 5
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbmag = 0.05
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[CitcomS.solver.out
-put]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.solver.output]
+\begin_inset Newline newline
+\end_inset
+
output_optional = tracer,comp_nd
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.tracer]
-\newline
+\begin_inset Newline newline
+\end_inset
+
tracer = on
-\newline
-tracer_ic_me
-thod = 0
-\newline
+\begin_inset Newline newline
+\end_inset
+
+tracer_ic_method = 0
+\begin_inset Newline newline
+\end_inset
+
tracers_per_element = 20
-\newline
+\begin_inset Newline newline
+\end_inset
+
tracer_file = tracer.dat
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-tracer_flavors =
- 2
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+tracer_flavors = 2
+\begin_inset Newline newline
+\end_inset
+
ic_method_for_flavors = 0
-\newline
+\begin_inset Newline newline
+\end_inset
+
z_interface = 0.7
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
chemical_buoyancy = 1
-\newline
-buoy_type
- = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
+buoy_type = 1
+\begin_inset Newline newline
+\end_inset
+
buoyancy_ratio = 0.5
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
regular_grid_deltheta = 1.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
regular_grid_delphi = 1.0
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[Citcom
-S.solver.vsolver]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.solver.vsolver]
+\begin_inset Newline newline
+\end_inset
+
Solver = cgrad
-\newline
+\begin_inset Newline newline
+\end_inset
+
accuracy = 1e-04
-\newline
+\begin_inset Newline newline
+\end_inset
+
vlowstep = 1000
-\newline
-piterations
- = 1000
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+piterations = 1000
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
# Assign the viscosities.
-\newline
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.visc]
-\newline
+\begin_inset Newline newline
+\end_inset
+
VISC_UPDATE = on
-\newline
-num_mat
- = 4
-\newline
+\begin_inset Newline newline
+\end_inset
+
+num_mat = 4
+\begin_inset Newline newline
+\end_inset
+
visc0 = 1,1,1,1
-\newline
+\begin_inset Newline newline
+\end_inset
+
TDEPV = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
rheol = 4
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscE = 0.2,0.2,0.2,0.2
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscT = 0,0,0,0
-\newline
-viscZ
- = 0,0,0,0
-\newline
+\begin_inset Newline newline
+\end_inset
+
+viscZ = 0,0,0,0
+\begin_inset Newline newline
+\end_inset
+
VMIN = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc_min = 1.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
VMAX = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc_max = 100.0
\end_layout
@@ -10246,7 +11282,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -10259,11 +11295,12 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Cookbook-7:-The"
\end_inset
@@ -10304,29 +11341,41 @@
\begin_layout LyX-Code
nz radius depth rho layer
-\newline
- 1 0.550000
- 0.450000 1.000000e+00 4
-\newline
- 2 0.606250 0.393750 1.000000e+00
- 4
-\newline
+\begin_inset Newline newline
+\end_inset
+
+ 1 0.550000 0.450000 1.000000e+00 4
+\begin_inset Newline newline
+\end_inset
+
+ 2 0.606250 0.393750 1.000000e+00 4
+\begin_inset Newline newline
+\end_inset
+
3 0.662500 0.337500 1.000000e+00 4
-\newline
- 4 0.718750
- 0.281250 1.000000e+00 4
-\newline
- 5 0.775000 0.225000 1.000000e+00
- 4
-\newline
+\begin_inset Newline newline
+\end_inset
+
+ 4 0.718750 0.281250 1.000000e+00 4
+\begin_inset Newline newline
+\end_inset
+
+ 5 0.775000 0.225000 1.000000e+00 4
+\begin_inset Newline newline
+\end_inset
+
6 0.831250 0.168750 1.000000e+00 4
-\newline
- 7 0.887500
- 0.112500 1.000000e+00 4
-\newline
- 8 0.943750 0.056250 1.000000e+00
- 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
+ 7 0.887500 0.112500 1.000000e+00 4
+\begin_inset Newline newline
+\end_inset
+
+ 8 0.943750 0.056250 1.000000e+00 2
+\begin_inset Newline newline
+\end_inset
+
9 1.000000 0.000000 1.000000e+00 1
\end_layout
@@ -10341,7 +11390,8 @@
\begin_layout Standard
This line gives the magnitude the right-hand side vector in Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:discrete momentum eqn"
\end_inset
@@ -10397,18 +11447,24 @@
\begin_layout LyX-Code
(000) 7.0 s v=1.470010e+02 p=0.000000e+00 div/v=5.37e+00 dv/v=1.00e+00 dp/p=1.00e+00
step 0
-\newline
+\begin_inset Newline newline
+\end_inset
+
\begin_inset Formula $\vdots$
\end_inset
-\newline
+\begin_inset Newline newline
+\end_inset
+
(090) 151.3 s v=1.012752e+02 p=1.304499e+04 div/v=5.54e-04 dv/v=1.84e-05 dp/p=9.20e-05
step 0
-\newline
-(091) 151.8 s v=1.012752e+02 p=1.304512e+04 div/v=5.66e-04 dv/v=2.07e-05
- dp/p=7.45e-05 step 0
+\begin_inset Newline newline
+\end_inset
+
+(091) 151.8 s v=1.012752e+02 p=1.304512e+04 div/v=5.66e-04 dv/v=2.07e-05 dp/p=7.45e-05
+ step 0
\end_layout
\begin_layout Standard
@@ -10426,7 +11482,9 @@
\begin_layout LyX-Code
surface heat flux= 2.227892
-\newline
+\begin_inset Newline newline
+\end_inset
+
bottom heat flux= 2.216542
\end_layout
@@ -10461,7 +11519,8 @@
\begin_layout Standard
The results for this problem are presented in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Cookbook-7:-The"
\end_inset
@@ -10476,8 +11535,9 @@
\end_layout
\begin_layout Standard
+\begin_inset Newpage newpage
+\end_inset
-\newpage
\end_layout
@@ -10523,11 +11583,15 @@
\family typewriter
CitcomS-cookbook8- restart.tar.gz
\family default
-) is provided at CIG's
-\begin_inset LatexCommand htmlurl
-name "CitcomS web page"
-target "geodynamics.org/cig/software/packages/mc/citcoms"
+) is provided at CIG's CitcomS web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/mc/citcoms
+\end_layout
+
\end_inset
.
@@ -10542,9 +11606,13 @@
\begin_layout LyX-Code
[CitcomS.solver.ic]
-\newline
+\begin_inset Newline newline
+\end_inset
+
restart = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
solution_cycles_init = 9000
\end_layout
@@ -10571,7 +11639,8 @@
, and the non-dimensionalized absolute surface temperature, which are defined
in Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Governing-Equations"
\end_inset
@@ -10599,11 +11668,17 @@
\begin_layout LyX-Code
rayleigh = 7.68175583e4
-\newline
+\begin_inset Newline newline
+\end_inset
+
dissipation_number = 0.5
-\newline
+\begin_inset Newline newline
+\end_inset
+
gruneisen = 1.25
-\newline
+\begin_inset Newline newline
+\end_inset
+
surfaceT = 0.1
\end_layout
@@ -10614,11 +11689,17 @@
\begin_layout LyX-Code
nodex = 33
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodey = 33
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodez = 33
-\newline
+\begin_inset Newline newline
+\end_inset
+
levels = 5
\end_layout
@@ -10666,7 +11747,8 @@
\family default
.
See Appendix
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Appendix-A:-Input"
\end_inset
@@ -10676,7 +11758,9 @@
\begin_layout LyX-Code
reference_state = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
refstate_file = ref.dat
\end_layout
@@ -10694,7 +11778,9 @@
\begin_layout LyX-Code
output_optional = geoid,surf,botm
-\newline
+\begin_inset Newline newline
+\end_inset
+
output_ll_max = 20
\end_layout
@@ -10712,16 +11798,25 @@
\begin_layout LyX-Code
tic_method = 3
-\newline
+\begin_inset Newline newline
+\end_inset
+
num_perturbations = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbl = 3
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbm = 2
-\newline
-perturblayer
- = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
+perturblayer = 17
+\begin_inset Newline newline
+\end_inset
+
perturbmag = 0.01
\end_layout
@@ -10734,13 +11829,18 @@
\begin_layout LyX-Code
output_optional = geoid,surf,botm
-\newline
+\begin_inset Newline newline
+\end_inset
+
use_cbf_topo = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
self_gravitation = on
-\newline
-output_ll
-_max = 20
+\begin_inset Newline newline
+\end_inset
+
+output_ll_max = 20
\end_layout
\begin_layout Standard
@@ -10813,18 +11913,29 @@
\begin_layout LyX-Code
Solver = multigrid
-\newline
+\begin_inset Newline newline
+\end_inset
+
mg_cycle = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
down_heavy = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
up_heavy = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
vlowstep = 20
-\newline
-vhighstep
- = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
+vhighstep = 2
+\begin_inset Newline newline
+\end_inset
+
max_mg_cycles = 50
\end_layout
@@ -10840,7 +11951,8 @@
\begin_layout Standard
The stiffness matrix uses augmented Lagrangian formulation to improve the
convergence for large viscosity variations
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Moresi/Zhong/Gurnis The accuracy"
\end_inset
@@ -10852,19 +11964,23 @@
\begin_layout LyX-Code
aug_lagr = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
aug_number = 2.0e3
\end_layout
\begin_layout Standard
The discrete Stokes equations
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:discrete continuite eqn"
\end_inset
and
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:discrete momentum eqn"
\end_inset
@@ -10879,7 +11995,8 @@
\family default
common to the three variations, specifies the maximum number of iterations
and the desired residual level for the continuity equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:discrete continuite eqn"
\end_inset
@@ -10904,7 +12021,8 @@
uzawa=cg
\family default
, the algorithm described in Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:iter-cg"
\end_inset
@@ -10917,7 +12035,9 @@
\begin_layout LyX-Code
uzawa = cg
-\newline
+\begin_inset Newline newline
+\end_inset
+
compress_iter_maxstep = 100
\end_layout
@@ -10927,7 +12047,8 @@
uzawa=bicg
\family default
, the algorithm described in Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:bicg"
\end_inset
@@ -10938,13 +12059,15 @@
\begin_layout Standard
The overall accuracy of the velocity solver is controlled by a single parameter.
The solver is converged if the residuals of Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:discrete continuite eqn"
\end_inset
and
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:discrete momentum eqn"
\end_inset
@@ -10980,7 +12103,9 @@
\begin_layout LyX-Code
remove_rigid_rotation = off
-\newline
+\begin_inset Newline newline
+\end_inset
+
remove_angular_momentum = on
\end_layout
@@ -11003,199 +12128,361 @@
\begin_layout LyX-Code
# Cookbook 8: Compressible Model and Checkpointing
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS]
-\newline
+\begin_inset Newline newline
+\end_inset
+
solver = full
-\newline
-steps
- = 10000
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+steps = 10000
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.controller]
-\newline
+\begin_inset Newline newline
+\end_inset
+
monitoringFrequency = 1000
-\newline
-checkpointFrequency
- = 1000
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+checkpointFrequency = 1000
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver]
-\newline
+\begin_inset Newline newline
+\end_inset
+
datadir = output
-\newline
+\begin_inset Newline newline
+\end_inset
+
datafile = cookbook8
-\newline
-datadir_old =
- restart
-\newline
+\begin_inset Newline newline
+\end_inset
+
+datadir_old = restart
+\begin_inset Newline newline
+\end_inset
+
datafile_old = cookbook8
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
rayleigh = 7.68175583e4
-\newline
-dissipation_number
- = 0.5
-\newline
+\begin_inset Newline newline
+\end_inset
+
+dissipation_number = 0.5
+\begin_inset Newline newline
+\end_inset
+
gruneisen = 1.25
-\newline
+\begin_inset Newline newline
+\end_inset
+
surfaceT = 0.1
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.mesher]
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodex = 33
-\newline
-nodey =
- 33
-\newline
+\begin_inset Newline newline
+\end_inset
+
+nodey = 33
+\begin_inset Newline newline
+\end_inset
+
nodez = 33
-\newline
+\begin_inset Newline newline
+\end_inset
+
levels = 5
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
coor = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
coor_file = coord.dat
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.param]
-\newline
-reference
-_state = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
+reference_state = 1
+\begin_inset Newline newline
+\end_inset
+
refstate_file = ref.dat
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.output]
-\newline
-output_optional = geoid,sur
-f,botm
-\newline
+\begin_inset Newline newline
+\end_inset
+
+output_optional = geoid,surf,botm
+\begin_inset Newline newline
+\end_inset
+
use_cbf_topo = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
self_gravitation = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
output_ll_max = 20
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.ic]
-\newline
-t
-ic_method = 3
-\newline
+\begin_inset Newline newline
+\end_inset
+
+tic_method = 3
+\begin_inset Newline newline
+\end_inset
+
num_perturbations = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbl = 3
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbm = 2
-\newline
-perturblayer =
- 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
+perturblayer = 17
+\begin_inset Newline newline
+\end_inset
+
perturbmag = 0.01
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
restart = off
-\newline
+\begin_inset Newline newline
+\end_inset
+
solution_cycles_init = 9000
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.visc]
-\newline
-VI
-SC_UPDATE = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
+VISC_UPDATE = on
+\begin_inset Newline newline
+\end_inset
+
visc_smooth_method = 1
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
TDEPV = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
rheol = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
num_mat = 4
-\newline
-viscE
- = 2.99573,2.99573,2.99573,2.99573
-\newline
+\begin_inset Newline newline
+\end_inset
+
+viscE = 2.99573,2.99573,2.99573,2.99573
+\begin_inset Newline newline
+\end_inset
+
viscT = 0.5,0.5,0.5,0.5
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc0 = 1,1,1,1
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
VMIN = on
-\newline
-visc_mi
-n = 0.001
-\newline
+\begin_inset Newline newline
+\end_inset
+
+visc_min = 0.001
+\begin_inset Newline newline
+\end_inset
+
VMAX = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc_max = 1e+06
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.tsolver]
-\newline
+\begin_inset Newline newline
+\end_inset
+
finetunedt = 0.75
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[CitcomS.s
-olver.vsolver]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.solver.vsolver]
+\begin_inset Newline newline
+\end_inset
+
uzawa = cg
-\newline
+\begin_inset Newline newline
+\end_inset
+
Solver = multigrid
-\newline
+\begin_inset Newline newline
+\end_inset
+
mg_cycle = 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
down_heavy = 2
-\newline
-up_heavy
- = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
+up_heavy = 2
+\begin_inset Newline newline
+\end_inset
+
vlowstep = 20
-\newline
+\begin_inset Newline newline
+\end_inset
+
vhighstep = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
max_mg_cycles = 50
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
aug_lagr = on
-\newline
-aug_number
- = 2.0e3
-\newline
+\begin_inset Newline newline
+\end_inset
+
+aug_number = 2.0e3
+\begin_inset Newline newline
+\end_inset
+
precond = on
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
piterations = 375
-\newline
+\begin_inset Newline newline
+\end_inset
+
accuracy = 0.001
-\newline
-compress_iter_maxstep
- = 100
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+compress_iter_maxstep = 100
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
remove_rigid_rotation = off
-\newline
+\begin_inset Newline newline
+\end_inset
+
remove_angular_momentum = on
\end_layout
@@ -11205,7 +12492,8 @@
\begin_layout Standard
The results for this problem are presented in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Cookbook-8"
\end_inset
@@ -11227,7 +12515,8 @@
) is -0.38%.
The Nussult number, converted from the surface heat flux by Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:Nusselt number"
\end_inset
@@ -11269,7 +12558,8 @@
\end_inset
in Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:T dim"
\end_inset
@@ -11279,24 +12569,41 @@
\begin_layout LyX-Code
[CitcomS.solver.const]
-\newline
+\begin_inset Newline newline
+\end_inset
+
radius=6.371e+06
-\newline
+\begin_inset Newline newline
+\end_inset
+
density=3340
-\newline
+\begin_inset Newline newline
+\end_inset
+
thermdiff=1e-06
-\newline
+\begin_inset Newline newline
+\end_inset
+
gravacc=9.81
-\newline
-thermex
-p=3e-05
-\newline
+\begin_inset Newline newline
+\end_inset
+
+thermexp=3e-05
+\begin_inset Newline newline
+\end_inset
+
refvisc=1e+21
-\newline
+\begin_inset Newline newline
+\end_inset
+
cp=1200
-\newline
+\begin_inset Newline newline
+\end_inset
+
density_above=1030
-\newline
+\begin_inset Newline newline
+\end_inset
+
density_below=6600
\end_layout
@@ -11307,7 +12614,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename graphics/cookbook8.png
@@ -11318,11 +12625,12 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Cookbook-8"
\end_inset
@@ -11344,8 +12652,9 @@
\end_layout
\begin_layout Standard
+\begin_inset Newpage newpage
+\end_inset
-\newpage
\end_layout
@@ -11356,7 +12665,8 @@
\begin_layout Standard
To run this cookbook, you need to install the Exchanger package.
See Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:Exchanger-Configuration-(Optional)"
\end_inset
@@ -11411,9 +12721,10 @@
\begin_layout LyX-Code
csolver = regional ; containing solver
-\newline
-esolver = regional ; embedded
- solver
+\begin_inset Newline newline
+\end_inset
+
+esolver = regional ; embedded solver
\end_layout
\begin_layout Standard
@@ -11425,15 +12736,20 @@
\begin_layout LyX-Code
[CitcomS.layout]
-\newline
+\begin_inset Newline newline
+\end_inset
+
containing_group = [0-1]
-\newline
+\begin_inset Newline newline
+\end_inset
+
embedded_group = [2-3]
\end_layout
\begin_layout Standard
The procedure for the nested solver coupling is described elsewhere
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Tan et al GeoFramework Part I"
\end_inset
@@ -11528,20 +12844,33 @@
\begin_layout LyX-Code
[CitcomS]
-\newline
+\begin_inset Newline newline
+\end_inset
+
steps = 200
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.ccontroller]
-\newline
+\begin_inset Newline newline
+\end_inset
+
monitoringFrequency = 2
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[CitcomS.econtroll
-er]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.econtroller]
+\begin_inset Newline newline
+\end_inset
+
monitoringFrequency = 10
\end_layout
@@ -11592,14 +12921,17 @@
\begin_layout LyX-Code
exclude_top = off
-\newline
+\begin_inset Newline newline
+\end_inset
+
exclude_bottom = off
\end_layout
\begin_layout Standard
The next parameter deserves a little more explanation.
The continuity equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:conservation of mass"
\end_inset
@@ -11620,7 +12952,8 @@
outflow, which could cause a convergence problem in the embedded solver.
One can amend the received normal velocity slightly to satisfy Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:gauss div"
\end_inset
@@ -11642,7 +12975,9 @@
\begin_layout LyX-Code
[CitcomS.esolver.bc]
-\newline
+\begin_inset Newline newline
+\end_inset
+
side_sbcs = on
\end_layout
@@ -11663,18 +12998,29 @@
\begin_layout LyX-Code
[CitcomS.csolver.bc]
-\newline
+\begin_inset Newline newline
+\end_inset
+
topvbc = 1
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.csolver.param]
-\newline
+\begin_inset Newline newline
+\end_inset
+
file_vbcs = on
-\newline
-vel_bound_file
- = velocity/bvel.dat
-\newline
+\begin_inset Newline newline
+\end_inset
+
+vel_bound_file = velocity/bvel.dat
+\begin_inset Newline newline
+\end_inset
+
start_age = 0
\end_layout
@@ -11719,57 +13065,101 @@
\begin_layout LyX-Code
[CitcomS.csolver.mesher]
-\newline
+\begin_inset Newline newline
+\end_inset
+
nprocz = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodex = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodey = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodez = 25
-\newline
-radius_outer
- = 1.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
+radius_outer = 1.0
+\begin_inset Newline newline
+\end_inset
+
radius_inner = 0.55
-\newline
+\begin_inset Newline newline
+\end_inset
+
theta_min = 1.171
-\newline
+\begin_inset Newline newline
+\end_inset
+
theta_max = 1.971
-\newline
+\begin_inset Newline newline
+\end_inset
+
fi_min = 0
-\newline
-fi_max
- = 0.8
-\newline
+\begin_inset Newline newline
+\end_inset
+
+fi_max = 0.8
+\begin_inset Newline newline
+\end_inset
+
coor = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
coor_refine = 0.1,0.15,0.1,0.2
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.esolver.mesher]
-\newline
+\begin_inset Newline newline
+\end_inset
+
nprocz = 2
-\newline
-nodex
- = 21
-\newline
+\begin_inset Newline newline
+\end_inset
+
+nodex = 21
+\begin_inset Newline newline
+\end_inset
+
nodey = 21
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodez = 49
-\newline
+\begin_inset Newline newline
+\end_inset
+
radius_outer = 0.999
-\newline
+\begin_inset Newline newline
+\end_inset
+
radius_inner = 0.551
-\newline
-theta_min
- = 1.421
-\newline
+\begin_inset Newline newline
+\end_inset
+
+theta_min = 1.421
+\begin_inset Newline newline
+\end_inset
+
theta_max = 1.721
-\newline
+\begin_inset Newline newline
+\end_inset
+
fi_min = 0.25
-\newline
+\begin_inset Newline newline
+\end_inset
+
fi_max = 0.55
\end_layout
@@ -11822,18 +13212,29 @@
\begin_layout LyX-Code
ADV = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
filter_temp = off
-\newline
+\begin_inset Newline newline
+\end_inset
+
monitor_max_T = off
-\newline
+\begin_inset Newline newline
+\end_inset
+
finetunedt = 0.9
-\newline
-fixed_timestep
- = 0
-\newline
+\begin_inset Newline newline
+\end_inset
+
+fixed_timestep = 0
+\begin_inset Newline newline
+\end_inset
+
adv_gamma = 0.5
-\newline
+\begin_inset Newline newline
+\end_inset
+
adv_sub_iterations = 2
\end_layout
@@ -11846,17 +13247,26 @@
\begin_layout LyX-Code
[CitcomS.csolver.vsolver]
-\newline
+\begin_inset Newline newline
+\end_inset
+
accuracy = 2e-2
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.esolver.vsolver]
-\newline
-accuracy =
- 1e-3
-\newline
+\begin_inset Newline newline
+\end_inset
+accuracy = 1e-3
+\begin_inset Newline newline
+\end_inset
+
+
\end_layout
\begin_layout Subsubsection
@@ -11865,309 +13275,558 @@
\begin_layout LyX-Code
# Cookbook 9: Nested Solver Coupling for Ridge-Plume Interaction
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS]
-\newline
-steps
- = 200
-\newline
+\begin_inset Newline newline
+\end_inset
+
+steps = 200
+\begin_inset Newline newline
+\end_inset
+
csolver = regional ; containing solver
-\newline
-esolver = regional
- ; embedded solver
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+esolver = regional ; embedded solver
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.ccoupler]
-\newline
+\begin_inset Newline newline
+\end_inset
+
two_way_communication = on
-\newline
-exchange_initial_t
-emperature = off
-\newline
+\begin_inset Newline newline
+\end_inset
+
+exchange_initial_temperature = off
+\begin_inset Newline newline
+\end_inset
+
exchange_pressure = on
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.ecoupler]
-\newline
-two_way_communication
- = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
+two_way_communication = on
+\begin_inset Newline newline
+\end_inset
+
exchange_initial_temperature = off
-\newline
+\begin_inset Newline newline
+\end_inset
+
exchange_pressure = on
-\newline
-amending_outflow
- = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
+amending_outflow = on
+\begin_inset Newline newline
+\end_inset
+
exclude_top = off
-\newline
+\begin_inset Newline newline
+\end_inset
+
exclude_bottom = off
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-# assigning processors to csolver
- and esolver
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+# assigning processors to csolver and esolver
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.layout]
-\newline
+\begin_inset Newline newline
+\end_inset
+
containing_group = [0-1]
-\newline
+\begin_inset Newline newline
+\end_inset
+
embedded_group = [2-3]
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[Citcom
-S.ccontroller]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.ccontroller]
+\begin_inset Newline newline
+\end_inset
+
monitoringFrequency = 2
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.econtroller]
-\newline
-monitoringFrequency
- = 10
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+monitoringFrequency = 10
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.csolver]
-\newline
+\begin_inset Newline newline
+\end_inset
+
datadir_old = ic
-\newline
+\begin_inset Newline newline
+\end_inset
+
datafile_old = cntn
-\newline
+\begin_inset Newline newline
+\end_inset
+
datadir = output
-\newline
-datafile
- = cntn
-\newline
+\begin_inset Newline newline
+\end_inset
+
+datafile = cntn
+\begin_inset Newline newline
+\end_inset
+
rayleigh = 1e8
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.csolver.mesher]
-\newline
+\begin_inset Newline newline
+\end_inset
+
nprocz = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodex = 17
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodey = 17
-\newline
-nodez
- = 25
-\newline
+\begin_inset Newline newline
+\end_inset
+
+nodez = 25
+\begin_inset Newline newline
+\end_inset
+
radius_outer = 1.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
radius_inner = 0.55
-\newline
+\begin_inset Newline newline
+\end_inset
+
theta_min = 1.171
-\newline
+\begin_inset Newline newline
+\end_inset
+
theta_max = 1.971
-\newline
-fi_min
- = 0
-\newline
+\begin_inset Newline newline
+\end_inset
+
+fi_min = 0
+\begin_inset Newline newline
+\end_inset
+
fi_max = 0.8
-\newline
+\begin_inset Newline newline
+\end_inset
+
coor = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
coor_refine = 0.1,0.15,0.1,0.2
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.csolver.bc]
-\newline
-topvbc
- = 1
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+topvbc = 1
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.csolver.param]
-\newline
+\begin_inset Newline newline
+\end_inset
+
file_vbcs = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
vel_bound_file = velocity/bvel.dat
-\newline
-start_ag
-e = 0
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+start_age = 0
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.csolver.ic]
-\newline
+\begin_inset Newline newline
+\end_inset
+
tic_method = -1
-\newline
+\begin_inset Newline newline
+\end_inset
+
solution_cycles_init = 0
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[CitcomS.csolver.tso
-lver]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.csolver.tsolver]
+\begin_inset Newline newline
+\end_inset
+
ADV = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
filter_temp = off
-\newline
+\begin_inset Newline newline
+\end_inset
+
monitor_max_T = off
-\newline
+\begin_inset Newline newline
+\end_inset
+
finetunedt = 0.9
-\newline
-fixed_timestep
- = 0
-\newline
+\begin_inset Newline newline
+\end_inset
+
+fixed_timestep = 0
+\begin_inset Newline newline
+\end_inset
+
adv_gamma = 0.5
-\newline
+\begin_inset Newline newline
+\end_inset
+
adv_sub_iterations = 2
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.csolver.vsolver]
-\newline
-accuracy
- = 2e-2
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+accuracy = 2e-2
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.csolver.visc]
-\newline
+\begin_inset Newline newline
+\end_inset
+
VISC_UPDATE = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
num_mat = 4
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc0 = 1,1,1,1
-\newline
-TDEPV
- = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
+TDEPV = on
+\begin_inset Newline newline
+\end_inset
+
viscE = 1.6,1.6,1.6,1.6
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscT = 0,0,0,0
-\newline
+\begin_inset Newline newline
+\end_inset
+
VMIN = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc_min = 1.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
VMAX = on
-\newline
-visc_max
- = 100.0
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+visc_max = 100.0
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
###############################################
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.esolver]
-\newline
-datadir_ol
-d = ic
-\newline
+\begin_inset Newline newline
+\end_inset
+
+datadir_old = ic
+\begin_inset Newline newline
+\end_inset
+
datafile_old = embd
-\newline
+\begin_inset Newline newline
+\end_inset
+
datadir = output
-\newline
+\begin_inset Newline newline
+\end_inset
+
datafile = embd
-\newline
+\begin_inset Newline newline
+\end_inset
+
rayleigh = 1e8
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[CitcomS.es
-olver.mesher]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.esolver.mesher]
+\begin_inset Newline newline
+\end_inset
+
nprocz = 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodex = 21
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodey = 21
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodez = 49
-\newline
+\begin_inset Newline newline
+\end_inset
+
radius_outer = 0.999
-\newline
-radius_in
-ner = 0.551
-\newline
+\begin_inset Newline newline
+\end_inset
+
+radius_inner = 0.551
+\begin_inset Newline newline
+\end_inset
+
theta_min = 1.421
-\newline
+\begin_inset Newline newline
+\end_inset
+
theta_max = 1.721
-\newline
+\begin_inset Newline newline
+\end_inset
+
fi_min = 0.25
-\newline
+\begin_inset Newline newline
+\end_inset
+
fi_max = 0.55
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[CitcomS.esolve
-r.ic]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.esolver.ic]
+\begin_inset Newline newline
+\end_inset
+
tic_method = -1
-\newline
+\begin_inset Newline newline
+\end_inset
+
solution_cycles_init = 0
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.esolver.vsolver]
-\newline
-accuracy
- = 1e-3
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+accuracy = 1e-3
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.esolver.tsolver]
-\newline
+\begin_inset Newline newline
+\end_inset
+
ADV = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
filter_temp = off
-\newline
+\begin_inset Newline newline
+\end_inset
+
monitor_max_T = off
-\newline
-finetu
-nedt = 0.9
-\newline
+\begin_inset Newline newline
+\end_inset
+
+finetunedt = 0.9
+\begin_inset Newline newline
+\end_inset
+
fixed_timestep = 0
-\newline
+\begin_inset Newline newline
+\end_inset
+
adv_gamma = 0.5
-\newline
+\begin_inset Newline newline
+\end_inset
+
adv_sub_iterations = 2
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-[CitcomS.esolver.vi
-sc]
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+[CitcomS.esolver.visc]
+\begin_inset Newline newline
+\end_inset
+
VISC_UPDATE = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
num_mat = 4
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc0 = 1,1,1,1
-\newline
+\begin_inset Newline newline
+\end_inset
+
TDEPV = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscE = 1.6,1.6,1.6,1.6
-\newline
-viscT
- = 0,0,0,0
-\newline
+\begin_inset Newline newline
+\end_inset
+
+viscT = 0,0,0,0
+\begin_inset Newline newline
+\end_inset
+
VMIN = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc_min = 1.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
VMAX = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc_max = 100.0
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.esolver.bc]
-\newline
-side_s
-bcs = on
+\begin_inset Newline newline
+\end_inset
+
+side_sbcs = on
\end_layout
\begin_layout Subsection
@@ -12176,7 +13835,8 @@
\begin_layout Standard
The solution of this problem is presented in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Cookbook-9"
\end_inset
@@ -12197,7 +13857,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename graphics/cookbook9.png
@@ -12208,11 +13868,12 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Cookbook-9"
\end_inset
@@ -12235,8 +13896,9 @@
\end_layout
\begin_layout Standard
+\begin_inset Newpage newpage
+\end_inset
-\newpage
\end_layout
@@ -12250,7 +13912,8 @@
\begin_layout Standard
This example is a step-up of Cookbook
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Cookbook-7:-The"
\end_inset
@@ -12273,19 +13936,28 @@
This cookbook uses CitcomS and SPECFEM3D_GLOBE.
SPECFEM3D_GLOBE is a spectral element code to simulate seismic wave propogation
in the global scale.
- To use SPECFEM3D_GLOBE, you can either download the code from this
-\begin_inset LatexCommand htmlurl
-name "link"
-target "geodynamics.org/cig/software/packages/seismo/specfem3d-globe/"
+ To use SPECFEM3D_GLOBE, you can either download the code from this link
+
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/seismo/specfem3d-globe/
+\end_layout
+
\end_inset
and install it on your machine, which requires a Fortran 90 compiler and
- a cluster, or you can go to
-\begin_inset LatexCommand htmlurl
-name "CIG Seismology Web Portal"
-target "https://crust.geodynamics.org/portals/seismo/"
+ a cluster, or you can go to CIG Seismology Web Portal
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+https://crust.geodynamics.org/portals/seismo/
+\end_layout
+
\end_inset
to launch a job, which only requires a browser.
@@ -12298,7 +13970,8 @@
\begin_layout Standard
Most of the parameters are copied from Cookbook
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Cookbook-7:-The"
\end_inset
@@ -12331,7 +14004,8 @@
Trampert, Vacher, and Vlaar
\shape default
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Trampert mineral physics model 2001"
\end_inset
@@ -12368,7 +14042,8 @@
\family default
files) that SPECFEM3D_GLOBE will read.
The formats of these binary files are provided in Appendix
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Misc.-Binary-Output"
\end_inset
@@ -12398,17 +14073,25 @@
\begin_layout LyX-Code
steps = 15
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.controller]
\end_layout
\begin_layout LyX-Code
monitoringFrequency = 5
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver]
\end_layout
@@ -12422,17 +14105,25 @@
\begin_layout LyX-Code
rayleigh = 1e9
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.mesher]
\end_layout
\begin_layout LyX-Code
radius_inner = 0.546
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.ic]
\end_layout
@@ -12454,25 +14145,37 @@
\begin_layout LyX-Code
perturbmag = 0.05
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.output]
\end_layout
\begin_layout LyX-Code
output_optional = tracer,comp_nd,seismic
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.param]
\end_layout
\begin_layout LyX-Code
mineral_physics_model = 3
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.tracer]
\end_layout
@@ -12490,9 +14193,13 @@
\begin_layout LyX-Code
tracer_file = tracer.dat
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
tracer_flavors = 2
\end_layout
@@ -12502,9 +14209,13 @@
\begin_layout LyX-Code
z_interface = 0.7
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
chemical_buoyancy = 1
\end_layout
@@ -12514,17 +14225,25 @@
\begin_layout LyX-Code
buoyancy_ratio = 0.5
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
regular_grid_deltheta = 1.0
\end_layout
\begin_layout LyX-Code
regular_grid_delphi = 1.0
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
[CitcomS.solver.vsolver]
\end_layout
@@ -12542,9 +14261,13 @@
\begin_layout LyX-Code
piterations = 1000
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
# Assign the viscosities.
\end_layout
@@ -12601,15 +14324,19 @@
\end_layout
\begin_layout Subsubsection
-Running SPECFEM3D_GLOBE from CIG Seismic Portal
+Running SPECFEM3D_GLOBE from CIG Seismology Web Portal
\end_layout
\begin_layout Standard
-Using your favorite browser, go to the
-\begin_inset LatexCommand htmlurl
-name "CIG Seismology Web Portal"
-target "https://crust.geodynamics.org/portals/seismo/"
+Using your favorite browser, go to the CIG Seismology Web Portal
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+https://crust.geodynamics.org/portals/seismo/
+\end_layout
+
\end_inset
.
@@ -13123,7 +14850,8 @@
\end_layout
\begin_layout Standard
-When your simulation is finished, the portal will send you an email notification.
+When your simulation is finished, the portal will send you an e-mail notificatio
+n.
Log in to the portal, click on the
\family typewriter
Runs
@@ -13163,7 +14891,8 @@
\begin_layout Standard
The dimensional value of total temperature contrast across the mantle is
derived from the Rayleigh number in Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:Ra, Rayleigh number"
\end_inset
@@ -13186,19 +14915,20 @@
\begin_layout Standard
The event and stations are all on the equatorial plane.
Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:cookbook10"
\end_inset
shows the temperature field of the equatorial slice.
- A large warm upwelling is benearth
+ A large warm upwelling is beneath
\begin_inset Formula $60^{\circ}$
\end_inset
E.
We should be able to observe its effect on delaying teleseismic waves in
-
+ the
\begin_inset Formula $70^{\circ}$
\end_inset
@@ -13213,11 +14943,12 @@
\noindent
\align center
\begin_inset Float figure
+placement H
wide false
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename graphics/cookbook10.png
@@ -13229,11 +14960,12 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:cookbook10"
\end_inset
@@ -13285,7 +15017,8 @@
\begin_layout Chapter
\start_of_appendix
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "cha:Appendix-A:-Input"
\end_inset
@@ -13311,18 +15044,20 @@
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
reference_state=1
-\newline
+\begin_inset Newline newline
+\end_inset
+
refstate_file="refstate.dat"
\end_layout
@@ -13331,7 +15066,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
\size small
@@ -13375,11 +15110,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -13388,26 +15123,28 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Using which mineral physics model to convert the seismic velocities.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
file_vbcs=off
-\newline
+\begin_inset Newline newline
+\end_inset
+
vel_bound_file="bvel.dat"
\end_layout
@@ -13416,7 +15153,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
\size small
@@ -13459,11 +15196,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true" newpage="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row newpage="true">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -13471,8 +15208,10 @@
\family default
\size default
-\newline
+\begin_inset Newline newline
+\end_inset
+
\family typewriter
\size small
mat_file="mat.dat"
@@ -13480,10 +15219,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
\size small
@@ -13512,11 +15251,11 @@
\end_inset
</cell>
</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -13524,16 +15263,20 @@
\family default
\size default
-\newline
+\begin_inset Newline newline
+\end_inset
+
\family typewriter
\size small
lith_age_file="age.dat"
\family default
\size default
-\newline
+\begin_inset Newline newline
+\end_inset
+
\family typewriter
\size small
lith_age_time=off
@@ -13541,10 +15284,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
\size small
@@ -13600,13 +15343,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="9" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -13618,7 +15361,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Choose the format and layout of the output files.
Can be either
\family typewriter
@@ -13652,16 +15395,18 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
output_optional="surf,
-\newline
+\begin_inset Newline newline
+\end_inset
+
botm,tracer"
\end_layout
@@ -13670,7 +15415,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Choose additional output, including
\family typewriter
surf
@@ -13713,11 +15458,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -13729,7 +15474,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Controls the location of output files.
\end_layout
@@ -13737,11 +15482,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -13753,7 +15498,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Controls the prefix of output file names such as
\family typewriter
regtest.xxx
@@ -13773,11 +15518,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -13785,28 +15530,36 @@
\family default
\size default
-\newline
+\begin_inset Newline newline
+\end_inset
+
(in non-Pyre version)
-\newline
+\begin_inset Newline newline
+\end_inset
+
or
-\newline
+\begin_inset Newline newline
+\end_inset
+
\family typewriter
\size small
monitoringFrequency=100
\family default
\size default
-\newline
+\begin_inset Newline newline
+\end_inset
+
(in Pyre version)
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Controls the interval between output files.
CitcomS dynamically determines the size of the time step; this means that
you might not get an output at the exact time required, but you can always
@@ -13819,11 +15572,11 @@
\end_inset
</cell>
</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -13832,10 +15585,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The time-step interval between checkpoint output, which can be used later
to resume the computation.
\end_layout
@@ -13843,11 +15596,11 @@
\end_inset
</cell>
</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -13856,10 +15609,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
This parameter controls the maximum degree of spherical harmonics coefficients
for geoid output.
\end_layout
@@ -13867,11 +15620,11 @@
\end_inset
</cell>
</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
self_gravitation=off
@@ -13879,21 +15632,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Considering the effect the self gravitation on the geoid or not.
\end_layout
\end_inset
</cell>
</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
use_cbf_topo=off
@@ -13901,10 +15654,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Using the Consistent Boundary Flux (CBF) method to compute the dynamic topograph
y or not.
\end_layout
@@ -13928,13 +15681,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -13946,7 +15699,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
This specifies the number of spherical caps of the mesh; must be
\family typewriter
\size small
@@ -13965,18 +15718,22 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
nprocx=1
-\newline
+\begin_inset Newline newline
+\end_inset
+
nprocy=1
-\newline
+\begin_inset Newline newline
+\end_inset
+
nprocz=1
\end_layout
@@ -13985,12 +15742,15 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
These specify the number of processors in each spherical cap.
-\newline
+\end_layout
-\newline
+\begin_layout Plain Layout
+\begin_inset VSpace defskip
+\end_inset
+
For a full spherical model,
\family typewriter
nprocx
@@ -14003,18 +15763,22 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
nodex=9
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodey=9
-\newline
+\begin_inset Newline newline
+\end_inset
+
nodez=9
\end_layout
@@ -14023,14 +15787,16 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
These specify the number of FEM nodes in each spherical cap.
These parameters are not used in the C version if multigrid solver is used.
-\newline
+\end_layout
-\newline
-For
- a full spherical model,
+\begin_layout Plain Layout
+\begin_inset VSpace defskip
+\end_inset
+
+For a full spherical model,
\family typewriter
nodex
\family default
@@ -14042,45 +15808,54 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
mgunitx=8
-\newline
+\begin_inset Newline newline
+\end_inset
+
mgunity=8
-\newline
+\begin_inset Newline newline
+\end_inset
+
mgunitz=8
-\newline
+\begin_inset Newline newline
+\end_inset
+
levels=1
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
These specify the nested level of multigrid units.
Used by multigrid solver only.
These parameters are not completely independent to each other.
The constraint of Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:mgunit"
\end_inset
must be satisfied.
These parameters are not used in the C version if conjgrad solver is used.
-\newline
+\end_layout
-\newline
-For
- a full spherical model,
+\begin_layout Plain Layout
+\begin_inset VSpace defskip
+\end_inset
+
+For a full spherical model,
\family typewriter
mgunitx
\family default
@@ -14109,22 +15884,28 @@
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
theta_min=1.0708
-\newline
+\begin_inset Newline newline
+\end_inset
+
theta_max=2.0708
-\newline
+\begin_inset Newline newline
+\end_inset
+
fi_min=0
-\newline
+\begin_inset Newline newline
+\end_inset
+
fi_max=1
\end_layout
@@ -14133,7 +15914,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
These parameters specify the horizontal extent of the computational domain.
\family typewriter
@@ -14159,25 +15940,27 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
radius_inner=0.55
-\newline
+\begin_inset Newline newline
+\end_inset
+
radius_outer=1.0
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
These parameters specify the radial extent of the computational domain.
\family typewriter
@@ -14199,35 +15982,37 @@
\end_inset
</cell>
</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
coor
\size small
=0
-\newline
+\end_layout
-\family default
-\size default
+\begin_layout Plain Layout
+\begin_inset VSpace defskip
+\end_inset
-\newline
\family typewriter
coor_file="coor.dat"
-\newline
+\begin_inset Newline newline
+\end_inset
+
coor_refine=0.1,0.15,0.1,0.2
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
coor=0
@@ -14235,7 +16020,9 @@
, there will be uniform mesh in the latitudinal, longitudinal, and radial
directions.
-\newline
+\end_layout
+
+\begin_layout Plain Layout
If
\family typewriter
coor=1
@@ -14246,7 +16033,9 @@
\family default
.
This is used to have a regular but uneven spacing between elements.
-\newline
+\end_layout
+
+\begin_layout Plain Layout
If
\family typewriter
coor=
@@ -14286,13 +16075,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -14304,7 +16093,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
restart
@@ -14321,11 +16110,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -14337,7 +16126,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Similar to
\family typewriter
restart
@@ -14349,27 +16138,31 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
datadir_old="."
-\newline
+\begin_inset Newline newline
+\end_inset
+
datafile_old="regtest"
-\newline
+\begin_inset Newline newline
+\end_inset
+
solution_cycles_init=0
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
restart
@@ -14408,39 +16201,49 @@
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
minstep=1
-\newline
+\begin_inset Newline newline
+\end_inset
+
maxtotstep=1000000
-\newline
+\begin_inset Newline newline
+\end_inset
+
\family default
\size default
(only in pure C version)
\family typewriter
\size small
-\newline
+\begin_inset Newline newline
+\end_inset
+
\family default
\size default
or
\family typewriter
\size small
-\newline
+\begin_inset Newline newline
+\end_inset
+
steps=1
-\newline
+\begin_inset Newline newline
+\end_inset
+
\family default
\size default
(only in Pyre version)
@@ -14451,7 +16254,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The maximum and minimum number of time steps for the model, including the
0th time step.
\end_layout
@@ -14459,28 +16262,39 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
cpu_limits_in_seconds=
-\newline
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
360000000
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Controls the termination of the code based on total wall clock time used.
Available only in pure C version.
\end_layout
@@ -14503,14 +16317,14 @@
\align left
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="2">
-<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<features islongtable="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -14519,39 +16333,45 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Which method to use to generate the initial temperature field.
\end_layout
\end_inset
</cell>
</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
datadir_old="."
-\newline
+\begin_inset Newline newline
+\end_inset
+
datafile_old="regtest"
-\newline
+\begin_inset Newline newline
+\end_inset
+
solution_cycles_init=0
-\newline
+\begin_inset Newline newline
+\end_inset
+
zero_elapsed_time=on
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
\size small
@@ -14674,46 +16494,67 @@
\end_inset
</cell>
</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
num_perturbations=1
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbmag=0.05
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbl=1
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturbm=1
-\newline
+\begin_inset Newline newline
+\end_inset
+
perturblayer=5
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-half_space_ag
-e=40
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
+half_space_age=40
+\begin_inset Newline newline
+\end_inset
+
mantle_temp=1.0
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
blob_center=[-999,-999,-999]
-\newline
+\begin_inset Newline newline
+\end_inset
+
blob_radius=0.063
-\newline
+\begin_inset Newline newline
+\end_inset
+
blob_dT=0.18
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
tic_method
@@ -14751,7 +16592,9 @@
\end_inset
for the regional sphere.
-\newline
+\begin_inset Newline newline
+\end_inset
+
If
\family typewriter
tic_method
@@ -14772,7 +16615,9 @@
\size default
(in million of years, Myrs).
-\newline
+\begin_inset Newline newline
+\end_inset
+
If
\family typewriter
tic_method
@@ -14815,7 +16660,9 @@
\noun default
\color inherit
-\newline
+\begin_inset Newline newline
+\end_inset
+
If
\family typewriter
tic_method
@@ -14838,7 +16685,9 @@
\end_inset
for the regional sphere.
-\newline
+\begin_inset Newline newline
+\end_inset
+
If
\family typewriter
tic_method
@@ -14847,7 +16696,9 @@
\family default
\size default
4, the initial temperature is read from grd files.
-\newline
+\begin_inset Newline newline
+\end_inset
+
If
\family typewriter
tic_method
@@ -14867,7 +16718,9 @@
tic_method=3
\family default
.
-\newline
+\begin_inset Newline newline
+\end_inset
+
If
\family typewriter
tic_method
@@ -14887,7 +16740,9 @@
tic_method=3
\family default
.
-\newline
+\begin_inset Newline newline
+\end_inset
+
If
\family typewriter
tic_method
@@ -14909,7 +16764,7 @@
.
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
tic_method
@@ -14945,20 +16800,24 @@
\begin_inset Tabular
<lyxtabular version="3" rows="7" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
topvbc=0
-\newline
+\begin_inset Newline newline
+\end_inset
+
topvbxval=0.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
topvbyval=0.0
\end_layout
@@ -14967,7 +16826,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Surface velocity boundary condition parameters.
If
\family typewriter
@@ -15001,18 +16860,22 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
botvbc=0
-\newline
+\begin_inset Newline newline
+\end_inset
+
botvbxval=0.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
botvbyval=0.0
\end_layout
@@ -15021,18 +16884,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
As above, but for bottom velocity boundary conditions.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15041,10 +16904,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Enable traction boundary condition for the sidewalls or not.
Must be
\family typewriter
@@ -15058,11 +16921,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15071,26 +16934,28 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Enable pseudo free surface or not.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
t
\family typewriter
\size small
optbc=1
-\newline
+\begin_inset Newline newline
+\end_inset
+
toptbcval=0.0
\end_layout
@@ -15099,7 +16964,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Surface temperature boundary conditions.
If
\family typewriter
@@ -15125,16 +16990,18 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
bottbc=1
-\newline
+\begin_inset Newline newline
+\end_inset
+
bottbcval=1.0
\end_layout
@@ -15143,7 +17010,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
As above, but for bottom temperature boundary conditions.
\end_layout
@@ -15151,30 +17018,35 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
temperature_bound_adj=off
-\newline
+\begin_inset Newline newline
+\end_inset
+
depth_bound_adj=0.157
-\newline
+\begin_inset Newline newline
+\end_inset
+
width_bound_adj=0.08727
-\newline
-lith_age_dept
-h=0.0314
+\begin_inset Newline newline
+\end_inset
+
+lith_age_depth=0.0314
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Additional parameters for temperature boundary conditions when
\family typewriter
lith_age
@@ -15207,13 +17079,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15225,7 +17097,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
This specifies the Rayleigh number, which is one of the most important parameter
s you may want to change.
\end_layout
@@ -15233,11 +17105,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15249,18 +17121,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The dissipation number.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15272,7 +17144,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The Gruneisen parameter.
When this parameter is 0, the code treats it as infinity (i.e., incompressible
case).
@@ -15282,11 +17154,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15298,18 +17170,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The non-dimensional value of surface temperature.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15318,10 +17190,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
This specifies the internal heating number.
\end_layout
@@ -15344,31 +17216,37 @@
\begin_inset Tabular
<lyxtabular version="3" rows="1" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
z_lith=0.014
-\newline
+\begin_inset Newline newline
+\end_inset
+
z_410=0.06435
-\newline
+\begin_inset Newline newline
+\end_inset
+
z_lmantle=0.105
-\newline
+\begin_inset Newline newline
+\end_inset
+
z_cmb=0.439
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
These specify the non-dimensional depth of the Moho, 410km discontinuity,
660km discontinuity and D".
These parameters are used to determine the depth of viscosity layers and
@@ -15393,7 +17271,8 @@
\begin_layout Subsection
Viscosity
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sub:Viscosity-input"
\end_inset
@@ -15405,13 +17284,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="20" columns="2">
<features islongtable="true">
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15423,18 +17302,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
This parameter must be set as indicated.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15446,7 +17325,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
This specifies which method to use to smooth viscosity projection for the
multigrid solver.
@@ -15455,11 +17334,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15471,7 +17350,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
VISC_UPDATE
@@ -15489,11 +17368,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15505,7 +17384,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
This specifies the number of material layers.
Material 1 is at depth between 0 and
\family typewriter
@@ -15544,11 +17423,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15560,7 +17439,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The pre-exponent factor of layered viscosity structure (
\begin_inset Formula $\eta_{0}$
\end_inset
@@ -15577,11 +17456,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15593,18 +17472,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Enable temperature dependence or not.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15616,7 +17495,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
When
\family typewriter
rheol
@@ -15629,8 +17508,10 @@
\end_inset
-\newline
+\begin_inset Newline newline
+\end_inset
+
\family default
\size default
When
@@ -15645,8 +17526,10 @@
\end_inset
-\newline
+\begin_inset Newline newline
+\end_inset
+
\family default
\size default
When
@@ -15671,8 +17554,10 @@
\family typewriter
\size footnotesize
-\newline
+\begin_inset Newline newline
+\end_inset
+
\family default
\size default
When
@@ -15687,8 +17572,10 @@
\end_inset
-\newline
+\begin_inset Newline newline
+\end_inset
+
\family default
\size default
When
@@ -15704,7 +17591,9 @@
mat_control
\family default
.
-\newline
+\begin_inset Newline newline
+\end_inset
+
When
\family typewriter
rheol
@@ -15717,8 +17606,10 @@
\end_inset
-\newline
+\begin_inset Newline newline
+\end_inset
+
\family default
\size default
When
@@ -15740,7 +17631,9 @@
\end_inset
is the inner radius of the mesh.
-\newline
+\begin_inset Newline newline
+\end_inset
+
When
\family typewriter
rheol
@@ -15751,7 +17644,9 @@
\family default
=3, except viscosity reduction is applied when the temperature exceeds the
solidus.
-\newline
+\begin_inset Newline newline
+\end_inset
+
When
\family typewriter
rheol
@@ -15769,7 +17664,9 @@
\end_inset
-\newline
+\begin_inset Newline newline
+\end_inset
+
When
\family typewriter
rheol
@@ -15792,18 +17689,22 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
viscE=1,1,1,1
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscT=1,1,1,1
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscZ=1,1,1,1
\end_layout
@@ -15812,7 +17713,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Parameters defining viscosity law (
\begin_inset Formula $E_{\eta}$
\end_inset
@@ -15837,11 +17738,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15850,26 +17751,28 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Enable stress dependence (non-Newtonian) or not.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
sdepv_expt=1,1,1,1
-\newline
+\begin_inset Newline newline
+\end_inset
+
sdepv_misfit=0.001
\end_layout
@@ -15878,7 +17781,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
\size small
@@ -15899,11 +17802,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -15912,10 +17815,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Pseudo-plastic rheology, implemented by adding a plastic viscosity
\begin_inset Formula $\eta_{p}=\frac{\sigma_{y}}{\left(2\epsilon_{II}+10^{-7}\right)+\eta_{p}^{0}}$
\end_inset
@@ -15964,27 +17867,31 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
pdepv_a=1e20,1e20,1e20,1e20
-\newline
+\begin_inset Newline newline
+\end_inset
+
pdepv_b=0,0,0,0
-\newline
+\begin_inset Newline newline
+\end_inset
+
pdepv_y=1e20,1e20,1e20,1e20
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Parameters for
\begin_inset Formula $\sigma_{y}$
\end_inset
@@ -15995,11 +17902,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16008,21 +17915,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Effective or minimum viscosity ``plasticity'' (see above).
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16031,10 +17938,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Offset for plastic viscosity
\begin_inset Formula $\eta_{p}^{0}$
\end_inset
@@ -16045,11 +17952,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16058,10 +17965,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Compositionally dependent viscosity pre-factor (only for
\family typewriter
\size small
@@ -16089,11 +17996,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16102,10 +18009,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Flavor-wise viscosity pre-factors for
\begin_inset Formula $\mathrm{C}=0$
\end_inset
@@ -16120,25 +18027,27 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
low_visc_channel=off
-\newline
+\begin_inset Newline newline
+\end_inset
+
low_visc_wedge=off
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Used in conjunction with tracers.
The tracers define the upper boundary of the subducted slab.
@@ -16147,35 +18056,41 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
lv_min_radius=0.9764
-\newline
+\begin_inset Newline newline
+\end_inset
+
lv_max_radius=0.9921
\family default
\size default
-\newline
+\begin_inset Newline newline
+\end_inset
+
\family typewriter
\size small
lv_channel_thickness=0.0047
-\newline
+\begin_inset Newline newline
+\end_inset
+
lv_reduction=0.5
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
\size small
@@ -16196,25 +18111,27 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
VMIN=off
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc_min=0.001
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
VMIN
@@ -16230,25 +18147,27 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
VMAX=off
-\newline
+\begin_inset Newline newline
+\end_inset
+
visc_max=1000
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
VMAX
@@ -16279,22 +18198,28 @@
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
Ra_410=0.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
clapeyron410=0.0235
-\newline
+\begin_inset Newline newline
+\end_inset
+
transT410=0.78
-\newline
+\begin_inset Newline newline
+\end_inset
+
width410=0.0058
\end_layout
@@ -16303,7 +18228,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
These specify the phase change parameters (phase change Rayleigh number,
Clapeyron slope, ambient temperature, and phase change width, respectively).
The depth of this phase change is specified by
@@ -16316,20 +18241,26 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
Ra_670=0.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
clapeyron670=-0.0235
-\newline
+\begin_inset Newline newline
+\end_inset
+
transT670=0.875
-\newline
+\begin_inset Newline newline
+\end_inset
+
width670=0.0058
\end_layout
@@ -16338,7 +18269,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
As above.
The depth of this phase change is specified by
\family typewriter
@@ -16350,29 +18281,35 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
Ra_cmb=0.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
clapeyroncmb=-0.0235
-\newline
+\begin_inset Newline newline
+\end_inset
+
transTcmb=0.875
-\newline
+\begin_inset Newline newline
+\end_inset
+
widthcmb=0.0058
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
As above.
The depth of this phase change is specified by
\family typewriter
@@ -16399,13 +18336,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="10" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16417,7 +18354,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If you wish only to solve for the velocity once (e.g., Stokes flow) then change
this parameter to
\family typewriter
@@ -16438,16 +18375,18 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
remove_rigid_rotation=on
-\newline
+\begin_inset Newline newline
+\end_inset
+
remove_angular_momentum=on
\end_layout
@@ -16456,7 +18395,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether to remove rigid body rotation component or net angular momentum
from the velocity solution.
Only effective for global models.
@@ -16465,11 +18404,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16481,7 +18420,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Can be either
\family typewriter
\size small
@@ -16500,11 +18439,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16516,31 +18455,41 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether to assemble stiffness matrix at the node level or not.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
mg_cycle=1
-\newline
+\begin_inset Newline newline
+\end_inset
+
down_heavy=3
-\newline
+\begin_inset Newline newline
+\end_inset
+
up_heavy=3
-\newline
+\begin_inset Newline newline
+\end_inset
+
vlowstep=1000
-\newline
+\begin_inset Newline newline
+\end_inset
+
vhighstep=3
-\newline
+\begin_inset Newline newline
+\end_inset
+
max_mg_cycles=50
\end_layout
@@ -16549,7 +18498,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Parameters for
\family typewriter
\size small
@@ -16608,7 +18557,9 @@
is the maximum number of multigrid cycles used per solve; all these parameters
should be small integers.
-\newline
+\begin_inset Newline newline
+\end_inset
+
For
\family typewriter
\size small
@@ -16629,11 +18580,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16645,18 +18596,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Maximum iterations of the outer loop for the momentum solver.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16668,7 +18619,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Convergence criterion for the momentum solver.
\end_layout
@@ -16676,16 +18627,18 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
uzawa=cg
-\newline
+\begin_inset Newline newline
+\end_inset
+
compress_iter_maxstep=100
\end_layout
@@ -16694,7 +18647,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Can be either
\family typewriter
\size small
@@ -16720,11 +18673,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16736,32 +18689,34 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether to use the preconditioner.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
aug_lagr=on
-\newline
+\begin_inset Newline newline
+\end_inset
+
aug_number=2.0e3
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether to use augmented stiff matrix and the weight of the augmented stiff
matrix.
\end_layout
@@ -16784,13 +18739,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="7" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16802,18 +18757,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If on, solves the energy equation.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16825,7 +18780,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If it is equal to 0, the size of the time step is variable and is determined
dynamically.
Otherwise, the size of the time step is fixed at the specified value.
@@ -16834,11 +18789,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16850,7 +18805,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Set the size of the time step to the specified fraction of a maximum stable
advection time step.
Must be between 0 and 1.
@@ -16859,16 +18814,18 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
adv_sub_iterations=2
-\newline
+\begin_inset Newline newline
+\end_inset
+
adv_gamma=0.5
\end_layout
@@ -16877,7 +18834,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The number of iterations and the weight of each iteration for the energy
predictor-corrector solver.
\end_layout
@@ -16885,11 +18842,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16901,7 +18858,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Using a Lenardic filter to remove the overshoots and undershoots of the
temperature field or not.
The filter conserves the total energy.
@@ -16910,11 +18867,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16923,10 +18880,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If on, the maximum value of the current and previous temperature fields
are compared.
If the maximum temperature increases more than 5%, the energy equation
@@ -16937,11 +18894,11 @@
\end_inset
</cell>
</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16950,10 +18907,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Currently, don't change this parameter.
It is used only in problems which are integrated backward in time.
\end_layout
@@ -16976,13 +18933,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -16994,7 +18951,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Set initial age (in Myrs).
This age determines which files of various time-dependent input to read
in.
@@ -17004,11 +18961,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17017,10 +18974,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
\size small
@@ -17064,20 +19021,24 @@
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
DESCRIBE=off
-\newline
+\begin_inset Newline newline
+\end_inset
+
BEGINNER=off
-\newline
+\begin_inset Newline newline
+\end_inset
+
VERBOSE=off
\end_layout
@@ -17086,7 +19047,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
These parameters affect the echo behavior of the CitcomS parser.
Only in non-Pyre version.
\end_layout
@@ -17094,11 +19055,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17110,7 +19071,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
This is used for debugging.
If verbose is
\family typewriter
@@ -17131,11 +19092,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17144,10 +19105,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
\size small
@@ -17176,18 +19137,20 @@
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
cb_block_size=1048576
-\newline
+\begin_inset Newline newline
+\end_inset
+
cb_buffer_size=4194304
\end_layout
@@ -17196,18 +19159,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Size for collective buffer in MPI-IO.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17216,31 +19179,44 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Size of data sieve buffer.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
output_alignment=262144
-\newline
+\begin_inset Newline newline
+\end_inset
+
output_alignment_threshold=
-\newline
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
524288
\end_layout
@@ -17249,34 +19225,38 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Memory alignment.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
cache_mdc_nelmts=10330
-\newline
+\begin_inset Newline newline
+\end_inset
+
cache_rdcc_nelmts=521
-\newline
+\begin_inset Newline newline
+\end_inset
+
cache_rdcc_nbytes=1048576
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Cache size for chunked dataset.
\end_layout
@@ -17298,13 +19278,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="10" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17316,7 +19296,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If on, enables the tracers.
\end_layout
@@ -17324,18 +19304,22 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
tracer_ic_method=0
-\newline
+\begin_inset Newline newline
+\end_inset
+
tracers_per_element=10
-\newline
+\begin_inset Newline newline
+\end_inset
+
tracer_file="tracer.dat"
\end_layout
@@ -17344,7 +19328,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Specify the initial location of the tracers.
If
\family typewriter
@@ -17392,11 +19376,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17408,7 +19392,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The number of flavors among the tracers.
If set to 0, flavor counting is turned off.
\end_layout
@@ -17416,16 +19400,18 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
ic_method_for_flavors=0
-\newline
+\begin_inset Newline newline
+\end_inset
+
z_interface=0.7
\end_layout
@@ -17434,7 +19420,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Specify the initial flavors of the tracers.
Used only when
\family typewriter
@@ -17477,16 +19463,18 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
regular_grid_deltheta=1.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
regular_grid_delphi=1.0
\end_layout
@@ -17495,7 +19483,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The grid spacing of the regular grid.
The regular grid is an auxiliary grid to help locate the tracers.
\end_layout
@@ -17503,11 +19491,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17519,18 +19507,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If on, enables thermo-chemical convection.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17542,7 +19530,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
\size small
@@ -17550,7 +19538,8 @@
\family default
\size default
, the composition field is determined by the ratio method
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Tackely King tracer ratio method"
\end_inset
@@ -17562,11 +19551,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17578,7 +19567,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The ratio of chemical density anomaly to the reference density, must be
a comma-separated list with
\family typewriter
@@ -17592,11 +19581,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17608,32 +19597,34 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The warning level of the tracer module.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
tracer_enriched=off
-\newline
+\begin_inset Newline newline
+\end_inset
+
Q0_enriched=0.0
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether the composition anomaly is associated with radioactive heating anomaly.
If
\family typewriter
@@ -17662,42 +19653,57 @@
\begin_inset Tabular
<lyxtabular version="3" rows="1" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
r
\family typewriter
\size small
adius=6371e3
-\newline
+\begin_inset Newline newline
+\end_inset
+
density=3340.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
thermdiff=1.0e-6
-\newline
+\begin_inset Newline newline
+\end_inset
+
gravacc=9.81
-\newline
+\begin_inset Newline newline
+\end_inset
+
thermexp=3.0e-5
-\newline
+\begin_inset Newline newline
+\end_inset
+
refvisc=1.0e+21
-\newline
-c
-p=1200
-\newline
+\begin_inset Newline newline
+\end_inset
+
+cp=1200
+\begin_inset Newline newline
+\end_inset
+
density_above=1030.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
density_below=6600.0
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Various dimensional information in SI units.
\end_layout
@@ -17719,27 +19725,29 @@
\begin_inset Tabular
<lyxtabular version="3" rows="1" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
Problem=convection
-\newline
+\begin_inset Newline newline
+\end_inset
+
Geometry=sphere
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
For this version of CitcomS, all of these parameters must be set as indicated.
\end_layout
@@ -17778,13 +19786,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17796,18 +19804,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
How many time steps to run.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17819,7 +19827,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility specifying which launcher to use.
Choices include
\family typewriter
@@ -17839,11 +19847,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17852,10 +19860,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility specifying which scheduler to use.
Choices are
\family typewriter
@@ -17881,11 +19889,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17897,7 +19905,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility.
User cannot change it.
\end_layout
@@ -17905,11 +19913,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17918,10 +19926,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility specifying which solver to use.
Must be either
\family typewriter
@@ -17971,13 +19979,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -17989,7 +19997,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If on, prints the
\family typewriter
mpirun
@@ -18000,11 +20008,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18016,7 +20024,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A printf-styled format string, used in conjunction with
\family typewriter
nodelist
@@ -18031,11 +20039,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18044,10 +20052,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A comma-separated list of machine names in square brackets.
Example:
\family typewriter
@@ -18057,11 +20065,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18070,10 +20078,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
The command used to launch the job.
@@ -18120,11 +20128,15 @@
customized for the Ranger cluster at Texas Advanced Computing Center).
Only the command options for these schedulers are listed below.
For more information on configuring Pyre for your batch system, see CIG's
-
-\begin_inset LatexCommand htmlurl
-name "Pythia page"
-target "geodynamics.org/cig/software/packages/cs/pythia/docs/batch"
+ Pythia page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/cs/pythia/docs/batch
+\end_layout
+
\end_inset
.
@@ -18135,13 +20147,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18153,7 +20165,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
\size small
@@ -18166,11 +20178,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18179,10 +20191,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
If
\family typewriter
\size small
@@ -18224,13 +20236,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="6" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18242,18 +20254,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The name of the job.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18265,18 +20277,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The name of the queue to which the job is scheduled.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18288,7 +20300,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Time limit for the job, specified using units, e.g.,
\family typewriter
5*minute
@@ -18303,11 +20315,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18319,18 +20331,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
File to read as the input stream.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18342,18 +20354,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
File to write for the output stream.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18362,10 +20374,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
File to write for the error stream.
\end_layout
@@ -18390,13 +20402,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18408,7 +20420,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The time-step interval between disk output.
It replaces the
\family typewriter
@@ -18420,11 +20432,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18433,10 +20445,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The time-step interval between checkpoint output, which can be used later
to resume the computation.
\end_layout
@@ -18462,13 +20474,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="23" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18480,7 +20492,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility.
Must be either
\family typewriter
@@ -18507,11 +20519,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18523,7 +20535,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility for the temperature solver using Petrov-Galerkin time integration.
\end_layout
@@ -18531,11 +20543,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18547,7 +20559,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility for the velocity solver using Boussinesq approximation and the
Uzawa algorithm.
@@ -18556,11 +20568,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18572,18 +20584,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility of boundary conditions.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18595,18 +20607,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility for dimensional constants.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18618,18 +20630,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility for initial conditions.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18641,18 +20653,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility for output options.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18664,18 +20676,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility for some additional input parameter files.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18687,18 +20699,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility for phase change parameters.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18707,21 +20719,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility for tracer parameters.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18733,18 +20745,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
A facility for viscosity parameters.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18756,18 +20768,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18779,18 +20791,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18802,18 +20814,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18825,18 +20837,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18848,18 +20860,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18871,18 +20883,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18894,18 +20906,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18917,18 +20929,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18940,18 +20952,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18963,18 +20975,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -18986,18 +20998,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19006,10 +21018,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
@@ -19035,13 +21047,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="16" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19053,18 +21065,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19076,18 +21088,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19099,18 +21111,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19122,18 +21134,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19145,18 +21157,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19168,18 +21180,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19191,18 +21203,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19214,18 +21226,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19237,18 +21249,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19260,18 +21272,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19283,18 +21295,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19306,18 +21318,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19329,18 +21341,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19352,18 +21364,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19375,18 +21387,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19395,10 +21407,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
@@ -19424,13 +21436,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="8" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19442,18 +21454,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19465,18 +21477,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19488,18 +21500,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19511,18 +21523,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19534,18 +21546,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19557,18 +21569,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19580,18 +21592,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19600,10 +21612,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
@@ -19629,13 +21641,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="17" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19647,18 +21659,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19670,18 +21682,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19693,18 +21705,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19716,18 +21728,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19739,18 +21751,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19762,18 +21774,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19785,18 +21797,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19808,18 +21820,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19831,18 +21843,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19854,18 +21866,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19877,18 +21889,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19900,18 +21912,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19923,18 +21935,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19946,18 +21958,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19969,18 +21981,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -19989,21 +22001,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20012,10 +22024,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
@@ -20041,13 +22053,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="15" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20059,18 +22071,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20079,21 +22091,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20105,18 +22117,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20128,18 +22140,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20151,18 +22163,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20174,18 +22186,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20197,18 +22209,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20220,18 +22232,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20243,18 +22255,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20266,18 +22278,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20289,18 +22301,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20312,18 +22324,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20335,18 +22347,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20358,18 +22370,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20378,10 +22390,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
@@ -20407,13 +22419,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="13" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="1.85in">
-<column alignment="left" valignment="top" rightline="true" width="4.25in">
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20422,21 +22434,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20445,21 +22457,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20468,21 +22480,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20491,21 +22503,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20514,21 +22526,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20537,21 +22549,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20560,21 +22572,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20583,21 +22595,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20606,21 +22618,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20629,21 +22641,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20652,21 +22664,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20675,21 +22687,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20698,10 +22710,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
@@ -20727,13 +22739,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="15" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20745,18 +22757,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20768,18 +22780,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20791,18 +22803,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20814,18 +22826,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20834,21 +22846,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20860,18 +22872,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20883,18 +22895,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20906,18 +22918,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20929,18 +22941,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20952,18 +22964,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20975,18 +22987,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -20995,21 +23007,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21021,18 +23033,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21044,18 +23056,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21064,10 +23076,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
@@ -21092,13 +23104,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="13" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21110,43 +23122,45 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
output_optional="surf,botm,
-\newline
+\begin_inset Newline newline
+\end_inset
+
tracer"
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21155,21 +23169,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
self_gravitation=off
@@ -21177,21 +23191,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
use_cbf_topo=off
@@ -21199,21 +23213,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21222,21 +23236,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21245,21 +23259,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21268,21 +23282,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21291,50 +23305,64 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
output_alignment_threshold=
-\newline
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
524288
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21343,21 +23371,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21369,18 +23397,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21389,10 +23417,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
@@ -21418,13 +23446,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="13" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21436,18 +23464,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21459,18 +23487,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21479,21 +23507,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21505,18 +23533,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21528,18 +23556,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21551,18 +23579,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21574,18 +23602,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21597,18 +23625,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21620,18 +23648,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21643,18 +23671,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21666,18 +23694,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21689,18 +23717,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21709,10 +23737,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
@@ -21738,13 +23766,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="12" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21756,18 +23784,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21779,18 +23807,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21802,18 +23830,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21825,18 +23853,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21848,18 +23876,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21871,18 +23899,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21894,18 +23922,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21917,18 +23945,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21940,18 +23968,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21963,18 +23991,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -21986,18 +24014,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22006,10 +24034,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
@@ -22035,13 +24063,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="15" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="1.85in">
-<column alignment="left" valignment="top" rightline="true" width="4.25in">
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22050,21 +24078,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22073,21 +24101,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22096,21 +24124,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22119,21 +24147,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22142,21 +24170,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22165,21 +24193,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22188,21 +24216,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22211,21 +24239,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22234,21 +24262,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22257,21 +24285,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22280,21 +24308,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22303,21 +24331,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22326,21 +24354,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22349,21 +24377,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22372,10 +24400,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
@@ -22401,13 +24429,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="31" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.85in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
-<row topline="true">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22419,18 +24447,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -22442,18 +24470,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
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@@ -22465,18 +24493,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22488,18 +24516,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22511,18 +24539,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
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@@ -22534,18 +24562,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22557,18 +24585,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22580,18 +24608,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22603,18 +24631,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22626,18 +24654,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22649,18 +24677,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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</row>
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22695,18 +24723,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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</row>
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22718,18 +24746,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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</row>
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22741,18 +24769,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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</row>
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22764,18 +24792,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22810,18 +24838,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22833,18 +24861,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
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<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22899,21 +24927,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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\size small
@@ -22922,21 +24950,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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@@ -22945,21 +24973,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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\size small
@@ -22968,21 +24996,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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\size small
@@ -22991,21 +25019,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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\size small
@@ -23014,21 +25042,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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\end_inset
</cell>
</row>
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-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
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\begin_inset Text
-\begin_layout Standard
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@@ -23106,10 +25134,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
@@ -23134,20 +25162,24 @@
\begin_layout Standard
The following facilities are only used in the coupled CitcomS solver.
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+\begin_inset Newline newline
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="1.85in">
-<column alignment="left" valignment="top" rightline="true" width="4.25in">
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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\family typewriter
\size small
@@ -23156,21 +25188,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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The processors to be assigned to the csolver.
\end_layout
\end_inset
</cell>
</row>
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-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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\family typewriter
\size small
@@ -23179,10 +25211,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
The processors to be assigned to the esolver.
\end_layout
@@ -23208,13 +25240,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="1.85in">
-<column alignment="left" valignment="top" rightline="true" width="4.25in">
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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\family typewriter
\size small
@@ -23223,21 +25255,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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Whether to exchange information in SI units.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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\family typewriter
\size small
@@ -23246,21 +25278,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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Whether to exchange information in Cartesian coordinate.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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\family typewriter
\size small
@@ -23269,46 +25301,48 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether to transfer information from esolver to csolver.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
exchange_initial_temperature
-\newline
+\begin_inset Newline newline
+\end_inset
+
=on
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether to ensure consistent initial temperature between csolver or esolver.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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\size small
@@ -23317,10 +25351,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether to send the pressure solution to esolver.
\end_layout
@@ -23346,13 +25380,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="8" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="1.85in">
-<column alignment="left" valignment="top" rightline="true" width="4.25in">
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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\family typewriter
\size small
@@ -23361,21 +25395,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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Whether to exchange information in SI units.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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\family typewriter
\size small
@@ -23384,21 +25418,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
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Whether to exchange information in Cartesian coordinate.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -23407,21 +25441,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether to transfer information from esolver to csolver.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -23430,21 +25464,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether to ensure consistent initial temperature between csolver or esolver.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -23453,21 +25487,21 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether to receive the initial guess of pressure from csolver.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -23476,10 +25510,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether to exclude the top boundary when receiving boundary conditions from
the csolver.
If the esolver has imposed plate velocity and constant temperature at the
@@ -23489,11 +25523,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -23502,10 +25536,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether to exclude the bottom boundary when receiving boundary conditions
from the csolver.
\end_layout
@@ -23513,11 +25547,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -23526,10 +25560,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Whether to amend the velocity boundary conditions to satisfy the continuity
equation.
\end_layout
@@ -23563,20 +25597,24 @@
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 Newline newline
+\end_inset
-\newline
+\begin_inset Newline newline
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="1.85in">
-<column alignment="left" valignment="top" rightline="true" width="4.25in">
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="1.85in">
+<column alignment="left" valignment="top" width="4.25in">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -23585,10 +25623,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Debugging information.
Default off.
\end_layout
@@ -23596,11 +25634,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -23609,10 +25647,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Unrecoverable runtime error.
Default on.
@@ -23621,11 +25659,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -23634,10 +25672,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Fatal programming error.
Default on.
@@ -23646,11 +25684,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -23659,10 +25697,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Descriptive information.
Default off.
\end_layout
@@ -23670,11 +25708,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
\size small
@@ -23683,10 +25721,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Recoverable runtime error.
Default off.
\end_layout
@@ -23699,9 +25737,13 @@
\end_inset
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
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.
@@ -23727,9 +25769,13 @@
\family typewriter
[CitcomS.journal.debug]
-\newline
+\begin_inset Newline newline
+\end_inset
+
Exchanger = on
-\newline
+\begin_inset Newline newline
+\end_inset
+
CitcomS-Exchanger = on
\end_layout
@@ -23764,7 +25810,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Coordinate-files"
\end_inset
@@ -23784,7 +25831,9 @@
\begin_layout LyX-Code
nsd= 1
-\newline
+\begin_inset Newline newline
+\end_inset
+
1
\series bold
@@ -23793,7 +25842,9 @@
\series default
\emph default
-\newline
+\begin_inset Newline newline
+\end_inset
+
2
\series bold
@@ -23802,21 +25853,29 @@
\series default
\emph default
-\newline
+\begin_inset Newline newline
+\end_inset
+
...
...
\series bold
-\newline
+\begin_inset Newline newline
+\end_inset
+
\emph on
nodex theta_nodex
\series default
\emph default
-\newline
+\begin_inset Newline newline
+\end_inset
+
nsd= 2
-\newline
+\begin_inset Newline newline
+\end_inset
+
1
\series bold
@@ -23825,7 +25884,9 @@
\series default
\emph default
-\newline
+\begin_inset Newline newline
+\end_inset
+
2
\series bold
@@ -23834,21 +25895,29 @@
\series default
\emph default
-\newline
+\begin_inset Newline newline
+\end_inset
+
...
...
\series bold
-\newline
+\begin_inset Newline newline
+\end_inset
+
\emph on
nodey phi_nodey
\series default
\emph default
-\newline
+\begin_inset Newline newline
+\end_inset
+
nsd= 3
-\newline
+\begin_inset Newline newline
+\end_inset
+
1
\series bold
@@ -23857,7 +25926,9 @@
\series default
\emph default
-\newline
+\begin_inset Newline newline
+\end_inset
+
2
\series bold
@@ -23866,13 +25937,17 @@
\series default
\emph default
-\newline
+\begin_inset Newline newline
+\end_inset
+
...
...
\series bold
-\newline
+\begin_inset Newline newline
+\end_inset
+
\emph on
nodez r_nodez
\end_layout
@@ -23894,7 +25969,9 @@
\begin_layout LyX-Code
nsd= 3
-\newline
+\begin_inset Newline newline
+\end_inset
+
1
\series bold
@@ -23903,7 +25980,9 @@
\series default
\emph default
-\newline
+\begin_inset Newline newline
+\end_inset
+
2
\series bold
@@ -23912,19 +25991,24 @@
\series default
\emph default
-\newline
+\begin_inset Newline newline
+\end_inset
+
...
...
\series bold
-\newline
+\begin_inset Newline newline
+\end_inset
+
\emph on
nodez r_nodez
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Velocity-boundary-condition"
\end_inset
@@ -23955,13 +26039,21 @@
\begin_layout LyX-Code
bvel.dat84
-\newline
+\begin_inset Newline newline
+\end_inset
+
bvel.dat83
-\newline
+\begin_inset Newline newline
+\end_inset
+
bvel.dat82
-\newline
+\begin_inset Newline newline
+\end_inset
+
...
-\newline
+\begin_inset Newline newline
+\end_inset
+
bvel.dat0
\end_layout
@@ -24025,13 +26117,21 @@
\begin_layout LyX-Code
bvel.dat82.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
bvel.dat82.1
-\newline
+\begin_inset Newline newline
+\end_inset
+
bvel.dat82.2
-\newline
+\begin_inset Newline newline
+\end_inset
+
...
-\newline
+\begin_inset Newline newline
+\end_inset
+
bvel.dat82.11
\end_layout
@@ -24090,13 +26190,21 @@
\begin_layout LyX-Code
mat.dat84
-\newline
+\begin_inset Newline newline
+\end_inset
+
mat.dat83
-\newline
+\begin_inset Newline newline
+\end_inset
+
mat.dat82
-\newline
+\begin_inset Newline newline
+\end_inset
+
...
-\newline
+\begin_inset Newline newline
+\end_inset
+
mat.dat0
\end_layout
@@ -24106,7 +26214,8 @@
vel_bound_file
\family default
(see Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Velocity-boundary-condition"
\end_inset
@@ -24153,13 +26262,21 @@
\begin_layout LyX-Code
lith.dat84
-\newline
+\begin_inset Newline newline
+\end_inset
+
lith.dat83
-\newline
+\begin_inset Newline newline
+\end_inset
+
lith.dat82
-\newline
+\begin_inset Newline newline
+\end_inset
+
...
-\newline
+\begin_inset Newline newline
+\end_inset
+
lith.dat0
\end_layout
@@ -24169,7 +26286,8 @@
vel_bound_file
\family default
(see Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Velocity-boundary-condition"
\end_inset
@@ -24183,13 +26301,21 @@
\begin_layout LyX-Code
lith.dat82.0
-\newline
+\begin_inset Newline newline
+\end_inset
+
lith.dat82.1
-\newline
+\begin_inset Newline newline
+\end_inset
+
lith.dat82.2
-\newline
+\begin_inset Newline newline
+\end_inset
+
...
-\newline
+\begin_inset Newline newline
+\end_inset
+
lith.dat82.11
\end_layout
@@ -24225,7 +26351,9 @@
\series bold
\emph on
num_tracers num_columns
-\newline
+\begin_inset Newline newline
+\end_inset
+
theta phi radius [flavor]
\end_layout
@@ -24269,7 +26397,8 @@
\end_layout
\begin_layout Chapter
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "cha:Appendix-C:-CitComS,"
\end_inset
@@ -24409,7 +26538,9 @@
\family typewriter
field = composition, pressure, stress
-\newline
+\begin_inset Newline newline
+\end_inset
+
structure = scalar, scalar, 6-vector
\end_layout
@@ -24485,7 +26616,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:ASCII-Output"
\end_inset
@@ -24515,7 +26647,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sub:Velocity-and-Temperature"
\end_inset
@@ -24708,7 +26841,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sub:Geoid-Output-(test-case.geoid.10)"
\end_inset
@@ -24740,19 +26874,19 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="8" columns="2">
<features>
-<column alignment="center" valignment="top" leftline="true" width="0">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="0">
-<row topline="true">
+<column alignment="center" valignment="top" width="0">
+<column alignment="left" valignment="top" width="0">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
col 1
\end_layout
@@ -24761,7 +26895,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
spherical harmonic degrees (
\family typewriter
l
@@ -24772,11 +26906,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
col 2
\end_layout
@@ -24785,18 +26919,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
spherical harmonic orders (m)
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
col 3
\end_layout
@@ -24805,7 +26939,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
sine coefficients of total geoid (S
\begin_inset Formula $_{\mathrm{lm}}$
\end_inset
@@ -24816,11 +26950,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
col 4
\end_layout
@@ -24829,7 +26963,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
cosine coefficients of total geoid (C
\begin_inset Formula $_{\mathrm{lm}}$
\end_inset
@@ -24840,11 +26974,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
col 5
\end_layout
@@ -24853,18 +26987,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
sine coefficients of the geoid due to internal density variation
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
col 6
\end_layout
@@ -24873,18 +27007,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
cosine coefficents of the geoid due to internal density variation
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
col 7
\end_layout
@@ -24893,27 +27027,27 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
sine coefficients of the geoid due to surface topography
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
col 8
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
cosine coefficients of the geoid due to surface topography
\end_layout
@@ -25052,7 +27186,8 @@
\begin_layout Standard
The format and layout of HDF5 output is described in Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:Data-Layout"
\end_inset
@@ -25063,7 +27198,8 @@
\begin_layout Section
Misc.
Binary Output
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Misc.-Binary-Output"
\end_inset
@@ -25213,7 +27349,8 @@
\end_layout
\begin_layout Chapter
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "cha:License"
\end_inset
@@ -25229,8 +27366,10 @@
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
\series default
-\newline
+\begin_inset Newline newline
+\end_inset
+
\series medium
Everyone is permitted to copy and distribute verbatim copies of this license
document, but changing it is not allowed.
@@ -25320,7 +27459,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
\backslash
@@ -25336,7 +27475,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
\backslash
@@ -25355,12 +27494,15 @@
into another language.
(Hereinafter, translation is included without limitation in the term ``modifica
tion.'') Each licensee is addressed as ``you.''
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-Activities other than copying,
- distribution and modification are not covered by this License; they are
- outside its scope.
+
+\begin_inset Newline newline
+\end_inset
+
+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).
@@ -25372,7 +27514,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
\backslash
@@ -25647,7 +27789,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
\backslash
@@ -25663,7 +27805,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
\backslash
@@ -25689,7 +27831,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
\backslash
@@ -25713,7 +27855,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
\backslash
@@ -25821,9 +27963,13 @@
\begin_layout Quote
(signature of Ty Coon)
-\newline
+\begin_inset Newline newline
+\end_inset
+
1 April 1989
-\newline
+\begin_inset Newline newline
+\end_inset
+
Ty Coon, President of Vice
\end_layout
@@ -25837,7 +27983,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "1"
key "Moresi et al Plate tectonics"
@@ -25856,7 +28003,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "2"
key "Moresi/Solomatov Numerical"
@@ -25877,7 +28025,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "3"
key "Moresi/Zhong/Gurnis The accuracy"
@@ -25895,7 +28044,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "4"
key "Moresi/Gurnis Contraints"
@@ -25917,7 +28067,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "5"
key "Zhong/Moresi The role of faults"
@@ -25940,7 +28091,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "6"
key "Zhong et al The role of temperature"
@@ -25960,7 +28112,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "7"
key "Tan et al Slabs in the lower"
@@ -25983,7 +28136,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "8"
key "Conrad/Gurnis Seismic tomography"
@@ -26005,7 +28159,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "9"
key "Hughes The Finite Element Method"
@@ -26022,7 +28177,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "10"
key "Ramage/Wathen Iterative solution"
@@ -26046,7 +28202,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "11"
key "Brooks A.N."
@@ -26063,7 +28220,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "12"
key "Cahouet/Chabard Some fast 3D"
@@ -26087,7 +28245,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "13"
key "Atanga/Silvester Iterative methods"
@@ -26111,7 +28270,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "14"
key "Hager/OConnell A simple global"
@@ -26133,7 +28293,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "15"
key "Tan et al GeoFramework Part I"
@@ -26154,7 +28315,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "16"
key "Zhong et al Free-surface formulation"
@@ -26177,7 +28339,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "17"
key "Zhong et al Three-dimensional"
@@ -26200,7 +28363,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "18"
key "McNamara Zhong Thermochemical"
@@ -26222,7 +28386,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "19"
key "Tackely King tracer ratio method"
@@ -26240,7 +28405,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "20"
key "Trampert mineral physics model 2001"
Modified: doc/CitcomS/manual/citcoms.pdf
===================================================================
(Binary files differ)
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