[cig-commits] r8982 - geodyn/3D/MAG/trunk/doc

sue at geodynamics.org sue at geodynamics.org
Thu Jan 3 14:08:39 PST 2008


Author: sue
Date: 2008-01-03 14:08:37 -0800 (Thu, 03 Jan 2008)
New Revision: 8982

Modified:
   geodyn/3D/MAG/trunk/doc/mag_book.lyx
   geodyn/3D/MAG/trunk/doc/mag_book.pdf
Log:
disclaimer required by nsf added

Modified: geodyn/3D/MAG/trunk/doc/mag_book.lyx
===================================================================
--- geodyn/3D/MAG/trunk/doc/mag_book.lyx	2008-01-03 21:49:12 UTC (rev 8981)
+++ geodyn/3D/MAG/trunk/doc/mag_book.lyx	2008-01-03 22:08:37 UTC (rev 8982)
@@ -1,5 +1,5 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
-\lyxformat 245
+#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+\lyxformat 276
 \begin_document
 \begin_header
 \textclass book
@@ -12,13 +12,21 @@
 \end_preamble
 \language english
 \inputencoding auto
-\fontscheme default
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
 \graphics default
 \paperfontsize default
 \spacing single
 \papersize default
 \use_geometry true
 \use_amsmath 0
+\use_esint 0
 \cite_engine basic
 \use_bibtopic false
 \paperorientation portrait
@@ -35,7 +43,8 @@
 \papersides 2
 \paperpagestyle headings
 \tracking_changes false
-\output_changes true
+\output_changes false
+\author "" 
 \end_header
 
 \begin_body
@@ -87,7 +96,7 @@
 \end_layout
 
 \begin_layout Author
-© California Institute of Technology
+© California Institute of Technology
 \newline
 Peter Olson and Wei Mi
 \newline
@@ -112,7 +121,7 @@
 
 \begin_layout Standard
 \noindent
-\begin_inset LatexCommand \tableofcontents{}
+\begin_inset LatexCommand tableofcontents
 
 \end_inset
 
@@ -169,18 +178,24 @@
 
 \begin_layout Standard
 The style of this publication is based on the 
-\begin_inset LatexCommand \htmlurl[Apple Publications Style Guide]{developer.apple.com/documentation/UserExperience/Conceptual/APStyleGuide/AppleStyleGuide2003.pdf}
+\begin_inset LatexCommand htmlurl
+name "Apple Publications Style Guide"
+target "developer.apple.com/documentation/UserExperience/Conceptual/APStyleGuide/AppleStyleGuide2003.pdf"
 
 \end_inset
 
 , as recommended by 
-\begin_inset LatexCommand \htmlurl[Python.org]{www.python.org}
+\begin_inset LatexCommand htmlurl
+name "Python.org"
+target "www.python.org"
 
 \end_inset
 
 .
  The documentation was produced using 
-\begin_inset LatexCommand \htmlurl[LyX]{www.lyx.org}
+\begin_inset LatexCommand htmlurl
+name "LyX"
+target "www.lyx.org"
 
 \end_inset
 
@@ -192,7 +207,9 @@
 
 \begin_layout Standard
 Errors and bug fixes in this manual should be directed to the 
-\begin_inset LatexCommand \url[CIG Geodynamo Mailing List]{cig-geodyn at geodynamics.org}
+\begin_inset LatexCommand url
+name "CIG Geodynamo Mailing List"
+target "cig-geodyn at geodynamics.org"
 
 \end_inset
 
@@ -244,29 +261,27 @@
 Geophys.
  Astrophys.
  Fluid Dyn.,
-\series bold
 \emph default
  
-\series default
 \emph on
 70
 \series bold
-, 
+,
 \series default
 \emph default
-113-136.
+ 113-136.
 \end_layout
 
 \begin_layout Itemize
 Olson, P., G.A.
  Glatzmaier (1995), Magnetoconvection in a rotating spherical shell: structure
  of flow in the outer core.
-
+ 
 \emph on
- Phys.
- Earth Planet Int., 92, 
+Phys.
+ Earth Planet Int., 92,
 \emph default
-109-118.
+ 109-118.
 \end_layout
 
 \begin_layout Itemize
@@ -329,9 +344,9 @@
 \begin_layout Itemize
 Christensen, et al.
  (2001), A numerical dynamo benchmark.
-
+ 
 \emph on
- Phys.
+Phys.
  Earth Planet Int., 128
 \emph default
 , 25-34 (benchmark cases).
@@ -344,7 +359,9 @@
  Glatzmaier, U.
  Christensen, P.
  Olson), and 
-\begin_inset LatexCommand \htmlurl[CIG]{geodynamics.org}
+\begin_inset LatexCommand htmlurl
+name "CIG"
+target "geodynamics.org"
 
 \end_inset
 
@@ -357,7 +374,12 @@
 
 \begin_layout Standard
 MAG development was funded by grants from NASA HPC and NSF Geophysics.
- Continued support of MAG is made possible under NSF EAR-0406751.
+ Continued support of MAG is based upon work supported by the National Science
+ Foundation under Grant No.
+ EAR-0406751.
+ Any opinions, findings, and conclusions or recommendations expressed in
+ this material are those of the authors and do not necessarily reflect the
+ views of the National Science Foundation.
 \end_layout
 
 \begin_layout Part
@@ -406,7 +428,8 @@
 
 \begin_layout Standard
 All variables are non-dimensional (see Appendix 
-\begin_inset LatexCommand \ref{cha:Variables-used-in}
+\begin_inset LatexCommand ref
+reference "cha:Variables-used-in"
 
 \end_inset
 
@@ -426,12 +449,14 @@
 
 \begin_layout Standard
 Additional technical information is found in 
-\begin_inset LatexCommand \cite{key-1}
+\begin_inset LatexCommand cite
+key "key-1"
 
 \end_inset
 
 -
-\begin_inset LatexCommand \cite{key-8}
+\begin_inset LatexCommand cite
+key "key-8"
 
 \end_inset
 
@@ -447,7 +472,8 @@
  equations for dynamo action due to thermal convection of an electrically
  conducting fluid in a rotating spherical shell (e.g., Olson et al.
  1999)
-\begin_inset LatexCommand \cite{key-5}
+\begin_inset LatexCommand cite
+key "key-5"
 
 \end_inset
 
@@ -530,12 +556,14 @@
 
 \begin_layout Standard
 Four basic non-dimensional parameters in 
-\begin_inset LatexCommand \ref{eq:1}
+\begin_inset LatexCommand ref
+reference "eq:1"
 
 \end_inset
 
  - 
-\begin_inset LatexCommand \ref{eq:4}
+\begin_inset LatexCommand ref
+reference "eq:4"
 
 \end_inset
 
@@ -654,7 +682,9 @@
 tar
 \family default
  file) from the 
-\begin_inset LatexCommand \htmlurl[Geodynamics Software Packages web page]{geodynamics.org/cig/software/packages}
+\begin_inset LatexCommand htmlurl
+name "Geodynamics Software Packages web page"
+target "geodynamics.org/cig/software/packages"
 
 \end_inset
 
@@ -673,7 +703,8 @@
  the latest MAG source code directly from the CIG source code repository,
  instead of using the prepared source package.
  See Section 
-\begin_inset LatexCommand \ref{sec:Software-Repository}
+\begin_inset LatexCommand ref
+reference "sec:Software-Repository"
 
 \end_inset
 
@@ -687,13 +718,17 @@
 
 \begin_layout Standard
 For help, send e-mail to the 
-\begin_inset LatexCommand \url[CIG Geodynamo Mailing List]{cig-geodyn at geodynamics.org}
+\begin_inset LatexCommand url
+name "CIG Geodynamo Mailing List"
+target "cig-geodyn at geodynamics.org"
 
 \end_inset
 
 .
  You can subscribe to the Mailing List and view archived discussion at 
-\begin_inset LatexCommand \htmlurl[Geodynamics Mail Lists]{geodynamics.org/cig/lists}
+\begin_inset LatexCommand htmlurl
+name "Geodynamics Mail Lists"
+target "geodynamics.org/cig/lists"
 
 \end_inset
 
@@ -714,7 +749,9 @@
 
 \begin_layout Itemize
 For Windows you need to install 
-\begin_inset LatexCommand \htmlurl[cygwin]{cygwin.com}
+\begin_inset LatexCommand htmlurl
+name "cygwin"
+target "cygwin.com"
 
 \end_inset
 
@@ -731,7 +768,9 @@
 
 \begin_layout Standard
 Download MAG from the 
-\begin_inset LatexCommand \htmlurl[Geodynamics website]{geodynamics.org}
+\begin_inset LatexCommand htmlurl
+name "Geodynamics website"
+target "geodynamics.org"
 
 \end_inset
 
@@ -762,7 +801,8 @@
 \end_layout
 
 \begin_layout Subsection
-\begin_inset LatexCommand \label{sub:MAG-file-structure}
+\begin_inset LatexCommand label
+name "sub:MAG-file-structure"
 
 \end_inset
 
@@ -818,7 +858,8 @@
  conductive temperature perturbation with imposed perturbation with l=4,
  m=4, and running for a short time.
  This is the ``benchmark0'' test case in Christensen et al., 2001
-\begin_inset LatexCommand \cite{benchmark cases}
+\begin_inset LatexCommand cite
+key "benchmark cases"
 
 \end_inset
 
@@ -831,7 +872,8 @@
 \size default
 , the dynamo ``benchmark1'' case in Christensen et al.
  
-\begin_inset LatexCommand \cite{benchmark cases}
+\begin_inset LatexCommand cite
+key "benchmark cases"
 
 \end_inset
 
@@ -878,7 +920,8 @@
 \size default
  obtained with short runs of benchmark0 and benchmark1 on a Linux workstation.
  Explanations of the contents of these files are found in Appendix 
-\begin_inset LatexCommand \ref{cha:MAG-Output-File}
+\begin_inset LatexCommand ref
+reference "cha:MAG-Output-File"
 
 \end_inset
 
@@ -906,7 +949,8 @@
 \end_layout
 
 \begin_layout Subsection
-\begin_inset LatexCommand \label{sub:Prepare-MAG-for}
+\begin_inset LatexCommand label
+name "sub:Prepare-MAG-for"
 
 \end_inset
 
@@ -937,8 +981,9 @@
  in the source directory, which by default uses the existing 
 \family typewriter
 \size small
-param.f 
+param.f
 \family default
+ 
 \size default
 grid and symmetry 
 \end_layout
@@ -990,7 +1035,8 @@
 
 \end_deeper
 \begin_layout Section
-\begin_inset LatexCommand \label{sec:Software-Repository}
+\begin_inset LatexCommand label
+name "sec:Software-Repository"
 
 \end_inset
 
@@ -999,7 +1045,9 @@
 
 \begin_layout Standard
 The MAG source code is available via a Subversion server at the 
-\begin_inset LatexCommand \htmlurl[Geodynamics website]{geodynamics.org}
+\begin_inset LatexCommand htmlurl
+name "Geodynamics website"
+target "geodynamics.org"
 
 \end_inset
 
@@ -1011,9 +1059,10 @@
 \begin_layout Quote
 
 \series bold
-NOTE: 
+NOTE:
 \series default
-If you are content with the prepared source package, you may skip this section.
+ If you are content with the prepared source package, you may skip this
+ section.
 \end_layout
 
 \begin_layout Subsection
@@ -1039,7 +1088,9 @@
 \begin_layout Standard
 It should return a usage message.
  For more information on Subversion, visit the 
-\begin_inset LatexCommand \htmlurl[Subversion website]{subversion.tigris.org}
+\begin_inset LatexCommand htmlurl
+name "Subversion website"
+target "subversion.tigris.org"
 
 \end_inset
 
@@ -1076,7 +1127,8 @@
 \end_inset
 
  is the directory created with the file structure mentioned in 
-\begin_inset LatexCommand \ref{sub:MAG-file-structure}
+\begin_inset LatexCommand ref
+reference "sub:MAG-file-structure"
 
 \end_inset
 
@@ -1097,7 +1149,8 @@
 
 \begin_layout Enumerate
 Uncompress all files, and create a path (see 
-\begin_inset LatexCommand \ref{sub:Prepare-MAG-for}
+\begin_inset LatexCommand ref
+reference "sub:Prepare-MAG-for"
 
 \end_inset
 
@@ -1133,8 +1186,9 @@
  Examples of 
 \family typewriter
 \size small
-param.f 
+param.f
 \family default
+ 
 \size default
 are 
 \family typewriter
@@ -1258,15 +1312,16 @@
  
 \family typewriter
 \size default
-ls.bench0, g[i].bench0 
+ls.bench0, g[i].bench0
 \family default
-and 
+ and 
 \family typewriter
 d[i].bench0
 \family default
 , where i=0,1,2...9.
  See Appendix 
-\begin_inset LatexCommand \ref{cha:MAG-Output-File}
+\begin_inset LatexCommand ref
+reference "cha:MAG-Output-File"
 
 \end_inset
 
@@ -1315,7 +1370,8 @@
 \end_layout
 
 \begin_layout Chapter
-\begin_inset LatexCommand \label{cha:Postprocessing-and-Graphics}
+\begin_inset LatexCommand label
+name "cha:Postprocessing-and-Graphics"
 
 \end_inset
 
@@ -1339,13 +1395,17 @@
 \family default
  is the directory under which you installed MAG.
  We should mention here that IDL is a commercial visualization tool by 
-\begin_inset LatexCommand \htmlurl[ITT Visual Information Solutions]{www.ittvis.com/idl}
+\begin_inset LatexCommand htmlurl
+name "ITT Visual Information Solutions"
+target "www.ittvis.com/idl"
 
 \end_inset
 
 .
  A free IDL compatible program called 
-\begin_inset LatexCommand \htmlurl[GDL]{gnudatalanguage.sourceforge.net}
+\begin_inset LatexCommand htmlurl
+name "GDL"
+target "gnudatalanguage.sourceforge.net"
 
 \end_inset
 
@@ -1379,7 +1439,8 @@
  statistics.
  This version reads an l-file consisting of 17 time series, the first record
  being dimensionless time (see Appendix 
-\begin_inset LatexCommand \ref{cha:MAG-Output-File}
+\begin_inset LatexCommand ref
+reference "cha:MAG-Output-File"
 
 \end_inset
 
@@ -1387,12 +1448,14 @@
  Energies and rms magnetic field and velocity are scaled as in MAG; tilt
  is dipole vector colatitude; pole longitude is dipole vector longitude.
  Figures 
-\begin_inset LatexCommand \ref{fig:Time-series-plot}
+\begin_inset LatexCommand ref
+reference "fig:Time-series-plot"
 
 \end_inset
 
  and 
-\begin_inset LatexCommand \ref{fig:Spectra-plot-of}
+\begin_inset LatexCommand ref
+reference "fig:Spectra-plot-of"
 
 \end_inset
 
@@ -1423,9 +1486,13 @@
 
 \end_layout
 
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Time-series-plot}
+\begin_layout Standard
+\begin_inset Caption
 
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Time-series-plot"
+
 \end_inset
 
 Time series plot of energy
@@ -1436,6 +1503,11 @@
 
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Standard
 \noindent
 \align center
@@ -1457,9 +1529,13 @@
 
 \end_layout
 
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Spectra-plot-of}
+\begin_layout Standard
+\begin_inset Caption
 
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Spectra-plot-of"
+
 \end_inset
 
 Spectra plot of a time depentant dynamo
@@ -1470,6 +1546,11 @@
 
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Section
 Interactive IDL Procedures 
 \end_layout
@@ -1502,7 +1583,8 @@
  Producing each plot is straightforward and accomplished by choosing from
  the option menu.
  Figure 
-\begin_inset LatexCommand \ref{fig:IDL-figure-with}
+\begin_inset LatexCommand ref
+reference "fig:IDL-figure-with"
 
 \end_inset
 
@@ -1532,9 +1614,13 @@
 
 \end_layout
 
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:IDL-figure-with}
+\begin_layout Standard
+\begin_inset Caption
 
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:IDL-figure-with"
+
 \end_inset
 
 IDL figure with Map option
@@ -1545,6 +1631,11 @@
 
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Standard
 MAGVOL.pro is another interactive IDL procedure to display volume results
  from rotating convection, magnetoconvection and dynamo calculations (written
@@ -1583,7 +1674,8 @@
  the z-component of vorticity, kinetic and magnetic energy, joule heating,
  work by Lorentz forces and buoyancy forces.
  Figure 
-\begin_inset LatexCommand \ref{fig:Kinetic-energy-(yellow)}
+\begin_inset LatexCommand ref
+reference "fig:Kinetic-energy-(yellow)"
 
 \end_inset
 
@@ -1616,9 +1708,13 @@
 
 \end_layout
 
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Kinetic-energy-(yellow)}
+\begin_layout Standard
+\begin_inset Caption
 
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Kinetic-energy-(yellow)"
+
 \end_inset
 
 Kinetic energy (yellow) and Magnetic energy (blue) plot by the MAGVOL procedure
@@ -1629,6 +1725,11 @@
 
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Chapter
 Examples
 \end_layout
@@ -1647,7 +1748,8 @@
 Historically, these are the cases defined in the benchmark study published
  in the 2001 paper by Christensen et al.
  
-\begin_inset LatexCommand \cite{benchmark cases}
+\begin_inset LatexCommand cite
+key "benchmark cases"
 
 \end_inset
 
@@ -1682,7 +1784,8 @@
 .
  Note that the definition of the Rayleigh number differs from the one in
  the published cases 
-\begin_inset LatexCommand \cite{benchmark cases}
+\begin_inset LatexCommand cite
+key "benchmark cases"
 
 \end_inset
 
@@ -1695,7 +1798,8 @@
 \end_inset
 
 .
-\begin_inset LatexCommand \cite{benchmark cases}
+\begin_inset LatexCommand cite
+key "benchmark cases"
 
 \end_inset
 
@@ -2229,7 +2333,8 @@
 \begin_layout Standard
 This case has run on 32-bit and 64-bit Intel processors.
  Figure 
-\begin_inset LatexCommand \ref{fig:Field-Plot1}
+\begin_inset LatexCommand ref
+reference "fig:Field-Plot1"
 
 \end_inset
 
@@ -2237,14 +2342,16 @@
  dipole and the dipole tilt on the outer boundary.
  It indicated a magnetic field reversal between time steps 25 and 30.
  Figure 
-\begin_inset LatexCommand \ref{fig:Field-Plot2}
+\begin_inset LatexCommand ref
+reference "fig:Field-Plot2"
 
 \end_inset
 
  shows a longer run of MAG, where we see the magnetic field reversed again.
  At this time, the magnetic field had weakened substantially.
  In Figure 
-\begin_inset LatexCommand \ref{fig:The-pole}
+\begin_inset LatexCommand ref
+reference "fig:The-pole"
 
 \end_inset
 
@@ -2275,9 +2382,13 @@
 
 \end_layout
 
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Field-Plot1}
+\begin_layout Standard
+\begin_inset Caption
 
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Field-Plot1"
+
 \end_inset
 
 Field Plot for Reversal Dynamo Case
@@ -2288,6 +2399,11 @@
 
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Standard
 \noindent
 \align center
@@ -2310,9 +2426,13 @@
 
 \end_layout
 
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Field-Plot2}
+\begin_layout Standard
+\begin_inset Caption
 
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Field-Plot2"
+
 \end_inset
 
  Field Plot for Reversal Dynamo Case (longer run)
@@ -2323,6 +2443,11 @@
 
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Standard
 \noindent
 \align center
@@ -2359,9 +2484,13 @@
 
 \end_layout
 
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:The-pole}
+\begin_layout Standard
+\begin_inset Caption
 
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:The-pole"
+
 \end_inset
 
 Magnetic Field Pole Plot.
@@ -2374,6 +2503,11 @@
 
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Subsection
 Creating a Reversal Dynamo Movie
 \end_layout
@@ -2410,7 +2544,8 @@
  For our reversal dynamo case we examine the field plot and decide to record
  the first field reversal.
  As shown the figure 
-\begin_inset LatexCommand \ref{fig:Interval-to-record}
+\begin_inset LatexCommand ref
+reference "fig:Interval-to-record"
 
 \end_inset
 
@@ -2462,7 +2597,8 @@
  and displays the magnetic field at the outer surface.
  This procedure can also create JPG files of the movie-frame images.
  Figure 
-\begin_inset LatexCommand \ref{fig:a:-first-frame}
+\begin_inset LatexCommand ref
+reference "fig:a:-first-frame"
 
 \end_inset
 
@@ -2492,9 +2628,13 @@
 
 \end_layout
 
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Interval-to-record}
+\begin_layout Standard
+\begin_inset Caption
 
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:Interval-to-record"
+
 \end_inset
 
 Interval to record movie
@@ -2505,6 +2645,11 @@
 
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Standard
 \noindent
 \align center
@@ -2537,9 +2682,13 @@
 
 \end_layout
 
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:a:-first-frame}
+\begin_layout Standard
+\begin_inset Caption
 
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:a:-first-frame"
+
 \end_inset
 
  Reversal Dynamo Movie.
@@ -2551,6 +2700,11 @@
 
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Subsubsection
 Creating MPEGs with IDL
 \end_layout
@@ -2559,7 +2713,9 @@
 IDL provides an IDLgrMPEG class that allows the user to save an array of
  image frames as an MPEG movie.
  See the 
-\begin_inset LatexCommand \htmlurl[IDL Reference Guide]{www.rsinc.com/idl/pdfs/refguide.pdf}
+\begin_inset LatexCommand htmlurl
+name "IDL Reference Guide"
+target "www.rsinc.com/idl/pdfs/refguide.pdf"
 
 \end_inset
 
@@ -2775,7 +2931,8 @@
  In contrast, the geomagnetism scientific community uses real-valued Schmidt-typ
 e spherical harmonics for representing the main field, with dimensional
  coefficients called the Gauss coefficients (see 
-\begin_inset LatexCommand \cite{key-8,key-9}
+\begin_inset LatexCommand cite
+key "key-8,key-9"
 
 \end_inset
 
@@ -2818,7 +2975,8 @@
 
 \begin_layout Chapter
 \start_of_appendix
-\begin_inset LatexCommand \label{cha:Variables-used-in}
+\begin_inset LatexCommand label
+name "cha:Variables-used-in"
 
 \end_inset
 
@@ -4315,7 +4473,8 @@
 \end_layout
 
 \begin_layout Chapter
-\begin_inset LatexCommand \label{cha:MAG-Input-File}
+\begin_inset LatexCommand label
+name "cha:MAG-Input-File"
 
 \end_inset
 
@@ -4722,7 +4881,8 @@
 \end_layout
 
 \begin_layout Chapter
-\begin_inset LatexCommand \label{cha:MAG-Output-File}
+\begin_inset LatexCommand label
+name "cha:MAG-Output-File"
 
 \end_inset
 
@@ -4805,9 +4965,9 @@
 \begin_layout Quote
 
 \series bold
-Note: 
+Note:
 \series default
-If one of the above files already exists, the program will not run.
+ If one of the above files already exists, the program will not run.
 \end_layout
 
 \begin_layout Standard
@@ -5719,8 +5879,12 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "1"
+key "key-1"
 
-\bibitem [1]{key-1}
+\end_inset
+
 Olson, P., G.A.
  Glatzmaier (1995), Highly supercritical thermal convection in a rotating
  spherical shell: centrifugal vs.
@@ -5730,36 +5894,42 @@
 Geophys.
  Astrophys.
  Fluid Dyn.,
-\series bold
 \emph default
  
-\series default
 \emph on
 70
 \series bold
-, 
+,
 \series default
 \emph default
-113-136
+ 113-136
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "2"
+key "key-2"
 
-\bibitem [2]{key-2}
+\end_inset
+
 Olson, P., G.A.
  Glatzmaier (1995), Magnetoconvection in a rotating spherical shell: structure
  of flow in the outer core.
-
+ 
 \emph on
- Phys.
- Earth Planet Int., 92, 
+Phys.
+ Earth Planet Int., 92,
 \emph default
-109-118
+ 109-118
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "3"
+key "key-3"
 
-\bibitem [3]{key-3}
+\end_inset
+
 Olson, P., G.A.
  Glatzmaier (1996), Magnetoconvection and Thermal Coupling of the Earth's
  Core and Mantle.
@@ -5775,8 +5945,12 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "4"
+key "key-4"
 
-\bibitem [4]{key-4}
+\end_inset
+
 Olson, P., U.
  Christensen, G.A.
  Glatzmaier (1999), Numerical Modeling of the Geodynamo: Mechanisms of Field
@@ -5791,8 +5965,12 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "5"
+key "key-5"
 
-\bibitem [5]{key-5}
+\end_inset
+
 Christensen, U., P.
  Olson, G.A.
  Glatzmaier (1999), Numerical modelling of the geodynamo: a systematic parameter
@@ -5807,21 +5985,29 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "6"
+key "benchmark cases"
 
-\bibitem [6]{benchmark cases}
+\end_inset
+
 Christensen, et al.
  (2001), A numerical dynamo benchmark.
-
+ 
 \emph on
- Phys.
+Phys.
  Earth Planet Int., 128
 \emph default
 , 25-34 (benchmark cases)
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "7"
+key "key-7"
 
-\bibitem [7]{key-7}
+\end_inset
+
 Olson, P., G.A.
  Glatzmaier (2005), Probing the geodynamo.
  
@@ -5830,14 +6016,18 @@
 \emph default
 (2)
 \emph on
-, 
+,
 \emph default
-29-35
+ 29-35
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "8"
+key "key-8"
 
-\bibitem [8]{key-8}
+\end_inset
+
 Christensen, U.R., J.
  Aubert (2006), Scaling properties of convection-driven dynamos in rotating
  spherical shells and application to planetary magnetic fields.
@@ -5852,8 +6042,11 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "key-9"
 
-\bibitem {key-9}
+\end_inset
+
  Backus, G., Parker, R., Constable, C.
  
 \emph on
@@ -5863,11 +6056,14 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "key-10"
 
-\bibitem {key-10}
- Merrill, R.T., McElhinny, M.W., McFadden, P.L.,
+\end_inset
+
+ Merrill, R.T., McElhinny, M.W., McFadden, P.L., 
 \emph on
- The Magnetic Field of the Earth, Paleomagnetism, the Core, and the Deep
+The Magnetic Field of the Earth, Paleomagnetism, the Core, and the Deep
  Mantle
 \emph default
 , Academic Press, 1998 

Modified: geodyn/3D/MAG/trunk/doc/mag_book.pdf
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