[cig-commits] commit: change doc.

[Mercurial]

changeset:   63:28045e62d08b
parent:      56:9f19993f3e84
user:        Sylvain Barbot <sbarbot at caltech.edu>
date:        Thu Dec 29 13:03:55 2011 -0800
files:       latex/documentation.pdf latex/documentation.tex
description:
change doc.


diff -r 9f19993f3e84 -r 28045e62d08b latex/documentation.pdf
Binary file latex/documentation.pdf has changed
diff -r 9f19993f3e84 -r 28045e62d08b latex/documentation.tex
--- a/latex/documentation.tex	Wed Dec 28 16:19:07 2011 -0800
+++ b/latex/documentation.tex	Thu Dec 29 13:03:55 2011 -0800
@@ -40,7 +40,7 @@
 \title{\bf Relax: Nonlinear Postseismic Relaxation\\in the Fourier Domain}
 
 \author
-{User Manual\\
+{User's Manual\\
 \\
 \normalsize{Sylvain Barbot (sbarbot at caltech.edu)}\\
 \normalsize{Division of Geological and Planetary Sciences, Caltech}\\
@@ -203,8 +203,7 @@ Both the post-processing and the storage
 
 The output of the simulation can be projected on the fly to geographic coordinates, which is convenient to communicate results to others in a global coordinate system. In RELAX, this is performed with the proj4 library. It is recommended to install these libraries on your system.
 
-\subsection{Installation}
-\subsubsection{Installation from the source files}
+\subsection{Installation from the source files}
 
 The compilation procedure, written by Walter Landry, uses Waf, a Python-based framework for configuring, compiling and installing applications. To obtain more information about this installation script, type
 \begin{alltt}
@@ -244,7 +243,7 @@ in the code source directory.
 
 
 
-\subsubsection{Running the program}
+\subsection{Running your compiled program}
 
 When using external libraries, it is required to add to the environment variables \verb'LD_LIBRARY_PATH' the location of the dynamic libraries. For example, on a Mac OS X platform, with libraries installed by Fink, the \verb'LD_LIBRARY_PATH' variable should contain
 \begin{alltt}
@@ -279,15 +278,33 @@ The Relax software is ready to be used. 
 > ./run2.sh}
 \end{alltt}
 
-On Windows Vista and Windows 7, uncompress the .zip file to a local directory of your choice. Then, execute the setup file (\verb`setup.bat`). To run an example, go to the 'examples' directory and execute the \verb`run1.bat` script.
+On Windows Vista and Windows 7, uncompress the .zip file to a local directory of your choice. Then, execute the setup file (\verb`setup.bat`). To run an example, go to the \verb'examples' directory and execute the \verb`run1.bat` script.
 
-On a linux platform, download the compressed tar package to the directory of your choice (dir), then Open a terminal or X11 window and type the following
+On a linux platform, download the compressed tar package to the directory of your choice (dir), then Open a terminal or X11 window and type the following for sh and ksh shells:
 \begin{alltt}
 {\color{orange}> cd dir
 > tar -xzvf package.tgz
-> source setup.sh
-}
+> source setup.sh}
 \end{alltt}
+If you are running the \verb`csh` shell, precede the above lines by a call to 
+\begin{alltt}
+{\color{orange}> bash}
+\end{alltt}
+The Relax software is ready to be used. For example, in the same terminal window, type
+\begin{alltt}
+{\color{orange}> cd examples
+> ./run2.sh}
+\end{alltt}
+If no output messages appear for a long time, you may want to remove the redirection to \verb`in.param` by changing the following line
+\begin{alltt}
+{\color{orange}> OMP_NUM_THREADS=2 time ../relax --no-proj-output \$* <<EOF | 
+    tee \$WDIR/in.param}
+\end{alltt}
+to
+\begin{alltt}
+{\color{orange}> OMP_NUM_THREADS=2 time ../relax --no-proj-output \$* <<EOF }
+\end{alltt}
+The \verb`tee` program may wait until a complete stop of the program before printing on the standard output, preventing you from seeing the results in real time.
 
 \section{Creating stand-alone executable files}
 
@@ -666,11 +683,11 @@ The observation points are given a four-
 The observation points are given a four-character name \verb'name' and the time series of displacement and stress is listed in the output file \verb'name.txt'. Using the above example, we obtain
 \begin{alltt}
 > more output_directory/GPS1.txt
-#         t         u1         u2         u3        s11        s12        s13
-  0.000E+00 -1.736E-05  1.726E-01 -2.343E-08  1.034E-03 -2.199E+03  4.950E-01
-  1.000E-01 -1.738E-05  1.726E-01 -2.356E-08  1.035E-03 -2.198E+03  4.950E-01
-  2.000E-01 -1.739E-05  1.727E-01 -2.368E-08  1.036E-03 -2.197E+03  4.951E-01
-  3.000E-01 -1.741E-05  1.728E-01 -2.376E-08  1.035E-03 -2.197E+03  4.951E-01
+#         t         u1        u2         u3       s11        s12       s13
+  0.000E+00 -1.736E-05 1.726E-01 -2.343E-08 1.034E-03 -2.199E+03 4.950E-01
+  1.000E-01 -1.738E-05 1.726E-01 -2.356E-08 1.035E-03 -2.198E+03 4.950E-01
+  2.000E-01 -1.739E-05 1.727E-01 -2.368E-08 1.036E-03 -2.197E+03 4.951E-01
+  3.000E-01 -1.741E-05 1.728E-01 -2.376E-08 1.035E-03 -2.197E+03 4.951E-01
 ...
 \end{alltt}
 where we have discarded the last three component of the stress tensor in the interest of space. The observation points list the cumulative displacement and stress, including the initial perturbation from an earthquake and the contribution due to the viscoelastic relaxation.
@@ -786,11 +803,12 @@ All VTK output files for visualization i
 \verb'vel-0014.vtk' & subsampled volume of velocity vector\\
 \verb'sigma-0014.vtk' & subsampled volume of stress tensor\\
 \verb'power-0014.vtk' & subsampled volume of power tensor\\
+\verb'disp-relax-0014.vtk' & subsampled volume of the relaxation part of the displacement vector (no coseismic)\\
 \end{tabular}\\
 \\
-The export to files in the VTK binary format \verb'.vtk' can be cancelled for the interest of space with the \verb'--no-vtk-output' option.
+The output \verb'disp-relax-????.vtk' are only available with the \verb`--with-vtk-relax-output` option. The export to files in the VTK binary format \verb'.vtk' can be cancelled for the interest of space with the \verb'--no-vtk-output' option.
 
-Some other files only contain geometrical information, such as geometry of fault patches, grid dimension, position of observation points, and so on\\
+Some other files only contain geometrical information, such as geometry of fault patches, grid dimension, position of observation points:\\
 \\
 \begin{tabular}{ll}
 \verb'opts.dat' & list of observation points (coordinates and names)\\