[cig-commits] r4670 - geodyn/3D/MAG/trunk/doc
wei at geodynamics.org
wei at geodynamics.org
Fri Sep 29 17:40:29 PDT 2006
Author: wei
Date: 2006-09-29 17:40:29 -0700 (Fri, 29 Sep 2006)
New Revision: 4670
Modified:
geodyn/3D/MAG/trunk/doc/mag_book.lyx
Log:
mag manual update
Modified: geodyn/3D/MAG/trunk/doc/mag_book.lyx
===================================================================
--- geodyn/3D/MAG/trunk/doc/mag_book.lyx 2006-09-29 23:42:07 UTC (rev 4669)
+++ geodyn/3D/MAG/trunk/doc/mag_book.lyx 2006-09-30 00:40:29 UTC (rev 4670)
@@ -1,4 +1,4 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.2 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -42,7 +42,7 @@
\noindent
\align left
\begin_inset ERT
-status open
+status collapsed
\begin_layout Standard
@@ -77,10 +77,6 @@
\end_layout
-\begin_layout Title
-MAG User Guide 1.0.0
-\end_layout
-
\begin_layout Standard
\noindent
\begin_inset LatexCommand \tableofcontents{}
@@ -143,7 +139,7 @@
\begin_layout Standard
Errors and bug fixes in this manual should be directed to
-\begin_inset LatexCommand \url[CIG Geodynamo Mailing List]{<cig-mc at geodynamics.org>}
+\begin_inset LatexCommand \url[CIG Geodynamo Mailing List]{<cig-geodyn at geodynamics.org>}
\end_inset
@@ -352,7 +348,7 @@
\begin_layout Standard
MAG is a serial version of Gary Glatzmaier's rotating spherical convection/magne
toconvection/dynamo code, modified by Uli Christensen and Peter Olson.
- The code solves the nondimensional Boussinesq equations for time-dependent
+ The code solves the non-dimensional Boussinesq equations for time-dependent
thermal convection in a rotating spherical shell filled with an electrically
conducting fluid.
The equations of motion are: the Navier-Stokes equation including Coriolis,
@@ -363,12 +359,12 @@
\end_layout
\begin_layout Standard
-All variables are nondimensional
-\begin_inset LatexCommand \ref{cha:Appendix-A:-Parameters}
+All variables are non-dimensional (see Appendix
+\begin_inset LatexCommand \ref{cha:Variables-used-in}
\end_inset
-; time scale is viscous diffusion, length scale is shell thickness, temperature
+); time scale is viscous diffusion, length scale is shell thickness, temperature
scale is boundary temperature difference, magnetic field and electric currents
use Elsasser number scaling.
A variety of boundary and initial conditions are selected as options.
@@ -387,13 +383,45 @@
\end_layout
\begin_layout Standard
-\begin_inset LatexCommand \cite{key-1,key-3,key-5,key-6,key-7}
+\begin_inset LatexCommand \cite{key-1}
\end_inset
\end_layout
+\begin_layout Standard
+\begin_inset LatexCommand \cite{key-3}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset LatexCommand \cite{key-5}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset LatexCommand \cite{key-6}
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset LatexCommand \cite{key-7}
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
Governing Equations
\end_layout
@@ -586,7 +614,7 @@
\end_layout
\begin_layout Standard
-An additional (optional) control parameter is the nondimensional volumetric
+An additional (optional) control parameter is the non-dimensional volumetric
heat source (or heat sink) strength
\begin_inset Formula $\epsilon$
\end_inset
@@ -708,6 +736,10 @@
\end_layout
\begin_layout Subsection
+\begin_inset LatexCommand \label{sub:MAG-file-structure}
+
+\end_inset
+
MAG file structure
\end_layout
@@ -756,13 +788,14 @@
\labelwidthstring 00.00.0000
~/bench-data: Output files "ls.benchX", "l.benchX", "g.benchx", and "d.benchx"
obtained with short runs of benchmark0 and benchmark1 on a Linux workstation.
- Explanations of the contents of these files are found in
-\begin_inset LatexCommand \ref{cha:MAG-Input-File}
+ Explanations of the contents of these files are found in Appendix
+\begin_inset LatexCommand \ref{cha:MAG-Output-File}
\end_inset
.
- These data files can be used for comprison with your local run of the MAG.
+ These data files can be used for comprison with the result obtained by
+ your local run of the MAG.
\end_layout
\begin_layout List
@@ -771,7 +804,11 @@
\end_layout
\begin_layout Subsection
-use the following procedure to prepare MAG for running
+\begin_inset LatexCommand \label{sub:Prepare-MAG-for}
+
+\end_inset
+
+Prepare MAG for running
\end_layout
\begin_layout Itemize
@@ -780,7 +817,7 @@
\end_layout
\begin_layout LyX-Code
-printenv PATH $ PATH=$PATH:/home/dynamo/magCIG $ export PATH
+printenv PATH $ PATH=$PATH:/your_mag_dir_path $ export PATH
\end_layout
\begin_layout Itemize
@@ -871,7 +908,7 @@
\end_layout
\begin_layout LyX-Code
-$ svn checkout svn://geodynamics.org/cig/geodyn/3D/MAG/trunk MAG
+$ svn checkout http://geodynamics.org/svn/cig/geodyn/3D/MAG/trunk MAG
\end_layout
\begin_layout Standard
@@ -883,7 +920,12 @@
\begin_inset Quotes srd
\end_inset
- is the directory created with the file structure mentioned in 2.5.1.
+ is the directory created with the file structure mentioned in
+\begin_inset LatexCommand \ref{sub:MAG-file-structure}
+
+\end_inset
+
+
\end_layout
\begin_layout LyX-Code
@@ -903,7 +945,12 @@
\end_layout
\begin_layout Enumerate
-Uncompress all files, and create a path (see PATHMAKE)
+Uncompress all files, and create a path (see
+\begin_inset LatexCommand \ref{sub:Prepare-MAG-for}
+
+\end_inset
+
+)
\end_layout
\begin_layout Enumerate
@@ -974,23 +1021,13 @@
\end_layout
\begin_layout Section
-Changing Parameter
+Changing Parameters
\end_layout
\begin_layout LyX-Code
\end_layout
-\begin_layout Standard
-Following your successful run, you will want to retrieve the output files
- from all the nodes and process them so they can be visualized with the
- visualization program OpenDX and proceed to the next chapter.
-\end_layout
-
-\begin_layout Standard
-
-\end_layout
-
\begin_layout Chapter
\begin_inset LatexCommand \label{cha:Postprocessing-and-Graphics}
@@ -1004,51 +1041,119 @@
\end_layout
\begin_layout Standard
-Once you have run MAG, you should have a series of output files.
- You will have to retrieve and combine the data for the time-step (age)
- of interest.
+Upon finishing running MAG, you should have a series of output data files.
+ To visualize your results, MAG software package provid a set of IDL routines.
+ IDL routines designed for MAG can be found in the directory called
+\family typewriter
+PREFIX/idl
+\family default
+, where PREFIX is the directory under which you installed MAG.
+
\end_layout
+\begin_layout Section
+Time Series Plot
+\end_layout
+
\begin_layout Standard
-To visualize your results, it is recommended that you use IDL.
+Procedure MAGTS.pro takes data from l-files generated by MAG and creates
+ time series plots and statistics.
+ This version reads an l-file consisting of 17 time series, the frist record
+ being dimensionless time.
+ Engergies and rms magnetic field and velocity are scaled as in MAG; tilt
+ is dipole vector colatitude; pole longitude is dipole vector longitude.
\end_layout
-\begin_layout LyX-Code
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+\begin_layout Standard
+\begin_inset Graphics
+ filename map.jpeg
+ lyxscale 30
+ scale 30
+
+\end_inset
+
+
\end_layout
+\begin_layout Caption
+Time series plot
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Section
-Using IDL for Visualization
+Interactive IDL Procedures
\end_layout
\begin_layout Standard
-IDL routines designed for MAG can be found in the directory called
-\family typewriter
-PREFIX/idl
-\family default
-, where PREFIX is the directory under which you installed MAG.
+MAGSYM.pro is an interactive procedure display results from g-file produced
+ by MAG.
+ This version uses modified IDL color tables and assumes formatted input.
+ It creates either postscript .ps or .gif files.
+ If other output file formats are required, modification of
+\begin_inset Quotes sld
+\end_inset
+
+LABELOUT
+\begin_inset Quotes srd
+\end_inset
+
+ are required.
\end_layout
\begin_layout Standard
-In this example,
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename tmppertub.jpeg
+ lyxscale 30
+ scale 30
+
+\end_inset
+
+
\end_layout
-\begin_layout LyX-Code
+\begin_layout Caption
+IDL figure with Map option
+\end_layout
+\end_inset
+
+
\end_layout
\begin_layout Chapter
Benchmark Cases
\end_layout
+\begin_layout LyX-Code
+
+\end_layout
+
\begin_layout Part
Appendices
\end_layout
\begin_layout Chapter
\start_of_appendix
-\begin_inset LatexCommand \label{cha:Appendix-A:-Parameters}
+\begin_inset LatexCommand \label{cha:Variables-used-in}
\end_inset
@@ -2760,7 +2865,7 @@
\end_layout
\begin_layout Chapter
-\begin_inset LatexCommand \label{cha:Appendix-C:-Output Files}
+\begin_inset LatexCommand \label{cha:MAG-Output-File}
\end_inset
@@ -3131,7 +3236,7 @@
m in the last two records of a block.
\end_layout
-\begin_layout Chapter
+\begin_layout Chapter*
License
\end_layout
@@ -3650,8 +3755,8 @@
\begin_layout Bibliography
-\bibitem [Olson, P., G.A. Glatzmaier (1995), Highly supercritical thermal convection]{key-1}
-Olson, P., G.A.
+\bibitem [1]{key-1}
+1Olson, P., G.A.
Glatzmaier (1995), Highly supercritical thermal convection in a rotating
spherical shell: centrifugal vs.
radial gravity.
@@ -3675,7 +3780,7 @@
\begin_layout Bibliography
-\bibitem [Olson, P., G.A. Glatzmaier (1995), Magnetoconvection in a rotating spherical shell]{key-2}
+\bibitem [2]{key-2}
Olson, P., G.A.
Glatzmaier (1995), Magnetoconvection in a rotating spherical shell: structure
of flow in the outer core.
@@ -3689,7 +3794,7 @@
\begin_layout Bibliography
-\bibitem [Olson, P., G.A. Glatzmaier (1996), Magnetoconvection and Thermal Coupling]{key-3}
+\bibitem [3]{key-3}
Olson, P., G.A.
Glatzmaier (1996), Magnetoconvection and Thermal Coupling of the Earth's
Core and Mantle.
@@ -3706,7 +3811,7 @@
\begin_layout Bibliography
-\bibitem [Olson, P., G.A. Glatzmaier (2005), Probing the Geodynamo]{key-4}
+\bibitem [4]{key-4}
Olson, P., G.A.
Glatzmaier (2005), Probing the Geodynamo.
@@ -3718,7 +3823,7 @@
\begin_layout Bibliography
-\bibitem [Olson, P., U. Christensen, G.A. Glatzmaier (1999), Numerical Modeling of the Geodynamo]{key-5}
+\bibitem [5]{key-5}
Olson, P., U.
Christensen, G.A.
Glatzmaier (1999), Numerical Modeling of the Geodynamo: Mechanisms of Field
@@ -3734,7 +3839,7 @@
\begin_layout Bibliography
-\bibitem [Christensen, U., P. Olson, G.A. Glatzmaier (1999), Numerical modelling of the geodynamo: a systematic parameter study]{key-6}
+\bibitem [6]{key-6}
Christensen, U., P.
Olson, G.A.
Glatzmaier (1999), Numerical modelling of the geodynamo: a systematic parameter
@@ -3750,7 +3855,7 @@
\begin_layout Bibliography
-\bibitem [Christensen, U., P. Olson, G.A. Glatzmaier (1999), Numerical modelling of the geodynamo: a systematic parameter study]{key-7}
+\bibitem [7]{key-7}
Christensen, et al.
(2001), A numerical dynamo benchmark.
More information about the cig-commits
mailing list