cleaned history

README.md

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+# Time Domain Group
+
+in order to compile the code on a KAUST workstation you need to initialize mpi
+e.g. run mpiInit.sh

SOFI3D_org/AUTHORS

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+Thomas Bohlen
+Denise De Nil
+Simone Dunkl
+Lisa Groos
+Sven Heider
+Olaf Hellwig
+Stefan Jetschny
+Daniel Koehn
+Andre Kurzmann
+Martin Schaefer
+Florian Wittkamp

SOFI3D_org/GETTING_STARTET.txt

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+To compile the program do:
+cd sofi3D/src
+then
+"make sofi3D"  to compile the standard staggered grid version (SSG)
+(you probably need to change the compiler options in sofi3D/src/Makefile)
+
+To run the program on 8 CPUs do
+cd sofi3D/par
+
+mpirun -np 8 ../bin/sofi3D ./in_and_out/sofi3D.json > ./in_and_out/sofi3D.jout
+
+you may also use the shell script startSOFI3D.sh
+
+The file sofi3D/par/in_and_out/sofi3D.jout shows the obtained screen output.
+
+The modelling parameters are specified in sofi3D.json. I hope that the
+parameters are more or less self-explanatory. The synthetic seismograms 
+and snapshots are written to the files specified in :
+sofi3D/par/in_and_out/sofi3D.json.
+
+In the current distribution the model is generated on the fly by the 
+function sofi3D/src/hh_elastic.c . This function generates a homogeneous
+medium with Vp=3500 m/s, Vs=2000 m/s, and rho=2000 kg/(m*m*m). The function 
+readmod.c can be used to read model info from external grid files. 
+See readmod.c for the format of the external files. You can change the 
+function which generates the model grid at the beginning of sofi3D/src/Makefile.
+
+
+For more information, have a look at the SOFI3D manual which you can compile in ./sofi3D/doc/guide_sofi3D.
+Additional you can find the manual at https://git.scc.kit.edu/GPIAG-Software/SOFI3D/wikis/home

SOFI3D_org/README.md

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+# What is SOFI3D?
+
+SOFI3D stands for Seismic mOdeling with FInite differences and denotes our 3-D viscoelastic time domain massive parallel modeling code.    
+The manual and a reference paper is included in the download archive or can be downloaded  [here](https://git.scc.kit.edu/GPIAG-Software/SOFI3D/wikis/home)
+
+# Download and Newsletter
+
+You can Download the [latest stable Release](https://git.scc.kit.edu/GPIAG-Software/SOFI3D/tree/Release) or the current [beta-version](https://git.scc.kit.edu/GPIAG-Software/SOFI3D/tree/master).  
+Also a SOFI3D branch with additional benchmarks is available: [overnightbuilt](https://git.scc.kit.edu/GPIAG-Software/SOFI3D/tree/overnightbuilt)
+
+To receive news and updates please [register](https://www.gpi.kit.edu/Software-WS.php) on the email list sofi@lists.kit.edu.  
+Please use this list also to ask questions on using the software or to report problems or bugs.

SOFI3D_org/doc/guide_sofi3D/README

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+README - Documentation
+
+To create the manual pdf please use the script:
+
+compile_LaTeX_manual.sh
+
+If problems with the compilation occur or Latex isn't installed on your PC,
+please visit https://git.scc.kit.edu/GPIAG-Software/SOFI3D/wikis/home.
+The manual of the latest Release is placed on this page.

SOFI3D_org/doc/guide_sofi3D/compile_LaTeX_manual.sh

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+#!/bin/sh
+cd tex
+
+/bin/rm -rf *.dvi >  /dev/null
+/bin/rm -rf *.log >  /dev/null
+/bin/rm -rf *.out >  /dev/null
+/bin/rm -rf *.aux >  /dev/null
+/bin/rm -rf *.toc >  /dev/null
+/bin/rm -rf *.blg >  /dev/null
+/bin/rm -rf *.bbl >  /dev/null
+/bin/rm -rf *.lof >  /dev/null
+/bin/rm -rf *.lot >  /dev/null
+/bin/rm -rf *.plt >  /dev/null
+/bin/rm -rf *.fff >  /dev/null
+/bin/rm -rf *.ttt >  /dev/null
+/bin/rm -rf *.tit >  /dev/null
+/bin/rm -rf *.spl >  /dev/null
+/bin/rm -rf *.idx >  /dev/null
+/bin/rm -rf *.ilg >  /dev/null
+/bin/rm -rf *.ind >  /dev/null
+
+	pdflatex guide_sofi3D
+	bibtex guide_sofi3D
+	pdflatex guide_sofi3D
+	pdflatex guide_sofi3D
+	pdflatex guide_sofi3D
+	pdflatex guide_sofi3D
+
+/bin/rm -rf *.dvi >  /dev/null
+/bin/rm -rf *.log >  /dev/null
+/bin/rm -rf *.out >  /dev/null
+/bin/rm -rf *.aux >  /dev/null
+/bin/rm -rf *.toc >  /dev/null
+/bin/rm -rf *.blg >  /dev/null
+/bin/rm -rf *.bbl >  /dev/null
+/bin/rm -rf *.lof >  /dev/null
+/bin/rm -rf *.lot >  /dev/null
+/bin/rm -rf *.plt >  /dev/null
+/bin/rm -rf *.fff >  /dev/null
+/bin/rm -rf *.ttt >  /dev/null
+/bin/rm -rf *.tit >  /dev/null
+/bin/rm -rf *.spl >  /dev/null
+/bin/rm -rf *.idx >  /dev/null
+/bin/rm -rf *.ilg >  /dev/null
+/bin/rm -rf *.ind >  /dev/null
+mv guide_sofi3D.pdf ../
+
+cd ..

SOFI3D_org/doc/guide_sofi3D/tex/authda14.sty

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+%  This LaTeX style-option file, authordate1-4.sty, is intended for documents 
+%  that use the author-date citation system.  When used in conjunction with
+%  authordate1.bst, ... , authordate4.bst, it allows citations of the
+%  form \shortcite{bloggs-60} as well as the usual \cite{bloggs-60}.
+%  When
+%       ... \cite{bloggs-60} ... \shortcite{bloggs-60} ...
+%  appears in the input file,
+%       ... (Bloggs, 1960) ... (1960) ...
+%  appears in the final document.
+%
+%  Note that:
+%  - a command \bibtitle is defined, to generate the bibliography title
+%  - a command \bibheadtitle is defined, to generate the text to be used
+%    by \pagestyle{headings}
+%  - \bibtitle and \bibheadtitle are set to generate "References" and
+%    "REFERENCES" respectively.
+%  - an \addcontentsline{toc}{...}{\bibtitle} is issued.
+%  Thus:
+%  - the default bibliography title is "References", but can be changed by
+%    having \renewcommand{\bibtitle}{...} before \begin{thebibliography}
+%    or \bibliography
+%  - the default page header text is "REFERENCES", but can be changed by
+%    \renewcommand{\bibheadtitle}{...}                  
+%  - \tableofcontents will give a table of contents that mentions the
+%    bibliography.
+%
+%                                                     David Rhead
+%                                                     Cripps Computing Centre
+%                                                     February 1990
+
+%  Code taken from apalike.sty.
+%
+\def\@cite#1#2{(#1\if@tempswa , #2\fi)}
+\def\@biblabel#1{}
+
+% Set length of hanging indentation for bibliography entries
+%
+\newlength{\bibhang}
+\setlength{\bibhang}{2em}
+
+%  Define default title and page-head text.
+%
+\def\bibtitle{References}
+\def\bibheadtitle{REFERENCES}
+
+\@ifundefined{chapter}{\def\thebibliography#1{\section*{\bibtitle\@mkboth
+  {\bibheadtitle}{\bibheadtitle}}
+  \addcontentsline{toc}{section}{\bibtitle}\list            %  For styles in
+  {\relax}{\setlength{\labelsep}{0em}                       %  which \chapter
+        \setlength{\itemindent}{-\bibhang}                  %  is undefined.
+        \setlength{\leftmargin}{\bibhang}}
+    \def\newblock{\hskip .11em plus .33em minus .07em}
+    \sloppy\clubpenalty4000\widowpenalty4000
+    \sfcode`\.=1000\relax}}%
+{\def\thebibliography#1{\chapter*{\bibtitle\@mkboth           %  For styles in
+  {\bibheadtitle}{\bibheadtitle}}                             %  which \chapter
+  \addcontentsline{toc}{chapter}{\bibtitle}\list              %  is defined.
+  {\relax}{\setlength{\labelsep}{0em}
+        \setlength{\itemindent}{-\bibhang}
+        \setlength{\leftmargin}{\bibhang}}
+    \def\newblock{\hskip .11em plus .33em minus .07em}
+    \sloppy\clubpenalty4000\widowpenalty4000
+    \sfcode`\.=1000\relax}}
+%
+%  Code taken from aaai.sty.
+%
+% don't box citations, add space between multiple citations, separate with ;
+\def\@citex[#1]#2{\if@filesw\immediate\write\@auxout{\string\citation{#2}}\fi
+  \def\@citea{}\@cite{\@for\@citeb:=#2\do
+    {\@citea\def\@citea{; }\@ifundefined
+       {b@\@citeb}{{\bf ?}\@warning
+       {Citation `\@citeb' on page \thepage \space undefined}}%
+{\csname b@\@citeb\endcsname}}}{#1}}
+% Allow short (name-less) citations, when used in
+% conjunction with a bibliography style that creates labels like
+%       \citename{<names>, }<year>
+\let\@internalcite\cite
+\def\cite{\def\citename##1{##1}\@internalcite}
+\def\shortcite{\def\citename##1{}\@internalcite}