Frequently Asked Questions about TeX software at SEP
Frequently Asked Questions
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This is a little backward compatibility problem. Previously, you could use something like \activesideplot{plot}{2in}{}{Caption}, where 2in was taken as the plot height. Now you have to say \activesideplot{plot}{height=2in}{Caption} explicitly. You can use either one or both or none of width and height. If you use only one of them, the aspect ratio should be preserved by default. Some other possible keys in the argument to activeplot (supplied by the graphicx package) are:
If you have a file called file.f90, \listing{file.f90} will do. If you want to reference it in a different place, try \progblock{label}{file.f90} and reference it with \ref{prog:label}. For cross-referencing among different chapters in a book there is also \gprogblock{label}{file.f90}. These are referenced with \ref{/prog:label}. You can find more information in the standard documentation on SEP2e.
If you create a dvi file with SEP2e, xtex will not display figures in it. This is also true for non-SEP latex files that don't use xtex macro. If you really want to use xtex, try make xtex. It will creates a dvi file using the old macros. Xtex has been declared obsolete, and we expect it to move slowly out of usage...
By the makerule default, xdvi starts with -nopostscript option. To activate a display of encapsulated postscript figures, press the View PS button on the right menu bar. If you see a file name in a box instead of a figure, check if this figure is listed in your makefile's RESULTSER, RESULTSCR, or RESULTSNR list.
It has never been easier (though it probably should be). The system of book maintenance, described below, has been tested on SEP reports (from SEP-92 to SEP-94), SEPHELP document, Jon's books (from FGDP to TDF), and Biondo's lecture notes.
To build a book, you need to create a directory tree, with each sister directory containing a makefile and a paper.tex file. The requirement for the directory names to start with a small letter is not essential. The requirement for the directories to be in a sister tree will be lifted eventually, but is assumed currently by the system.
One of the directories (traditionally, Adm) is designated for general controls. It should contain Makefile (the capital "M" is important) with the usual include ${SEPINC}/SEP.top and include ${SEPINC}/SEP.bottom. Before include ${SEPINC}/SEP.bottom, put include ${SEPINC}/Doc.rules.book. Somewhere in the Makefile put LATOPTS = option=book for books or LATOPTS = option=report for a reports. LATOPTS (arguments to Latify) can include additional arguments. For example, style=makeidx is needed for Index.This is the bare minimum you need to build a book. Running gmake read in the administration directory will create a dvi file and display it with xdvi, gmake print will print it out, etc. When you are satisfied with the dvi, run gmake install to move it into the Dvi directory. gmake clean will clean the machine-generated files in the adm. directory, gmake distclean will also clean the relevant directories in the tree. Additionally, gmake papername.readit (e.g. gmake sergey10.readit) will display an individual chapter papername (with correct page numbers!), and gmake papername.printit will print it. The chapters will appear in a random order unless you define a sorted list with Makefile's PAPERS variable. This list will also allow you to exclude chapters from the book or to include capital-letter directories.
The top file in the adm. directory (formerly known as all.tex) is called paper.tex to comply with the makerule defaults. It is created by four perl scripts: SEPdocTPG, SEPdocBIO, SEPdocTOC, SEPdocALL (not good names, according to Matt, but they are actually hidden in the make rules).
SEPdocTPG creates a title page (tpg.tex). It accepts a number of arguments, which you can list in Makefile's TPGOPTS variable. For books, the author name and the book title are supplied in the Makefile with AUTHOR = and TITLE=. Use "\n" (C-style syntax) to indicate new lines. For reports, the author information is picked automatically from the included papers. If the automatic picking fails, you can redefine the author information for any paper by including AUTHOR.papername = in the Makefile.
SEPdocBIO creates a list of biographies (bio.tex), which normally appears at the end of a book or a report. The biographies are picked from a simple database. The database currently lives in /usr/local/share/TEX/database. This directory contains files of the form user.bio and user.ps, where user is a login name (e.g. christin), user.bio contains a biography (in the LaTeX format), and user.ps is a postscript picture. The database itself contains pointers "FirstName LastName" -> user (e.g. Matthias Schwab -> matt), where "FirstName LastName" is the author name as it would appear on the title page of a report. Two simple scripts, CreateDB and TestDB, are provided to maintain and expand the database.
SEPdocTOC will do nothing for books, but will create an artificial table of contents (toc.tex) for reports. Again, the author and title information are picked automatically, and if it fails, you can redefine any author or title in the Makefile with AUTHOR.papername = and TITLE.papername =. To divide the table of contents into sections ("3-D seismic","Unimportant computer stuff", etc.), put SECTION.papername =, where papername is the first paper of the section.
Finally, SEPdocALL compiles paper.tex. Additionally to (automatically generated) tpg.tex, bio.tex, and toc.tex, you can have the following two files in the adm. directory: preface.tex for the text that goes between tpg and toc, and intro.tex for the text between toc.tex and the main body of the book (roman pagenumbering.) Reports also include pub.tex with a list of recent publications.
The pstogif script does break sometimes, especially with non-vplot figures. I haven't seen enough examples to notice the pattern, but, for example, none of my Mathematica figures could convert to GIF. I hope we will find a way around it after getting more experience. You may try converting postscript to GIF with xv.
Include files like file1.tex, file2.tex in your paper with \input{file1}, \input{file2}. Additionally, put paper.tex: file1.tex file2.tex ... in your makefile to let make touch paper.tex for you each time one of those files changes.
The old macros still exist on our system. If you really want to use them, put LATOPTS = class=old in your makefile or simply run gmake xtex.
Feel free to do that. The makerules are in $SEPINC, the tex macros are in $TEXMF/tex/latex/sep2e, the tex-related perl scripts are in /usr/local/share/TEX/bin. Please use RCS if you make any changes.
To get the most current version of the tex macros, scripts, and makerules, run ~sergey/tarit and ftp the sep2e.tar.gz file. This file contains everything you need for tex processing. Unpack it from the root directory with tar xvzf sep2e.tar.gz. You may need to run rehash and texconfig rehash to update the system. This distribution doesn't contain yet the scripts and extra programs required by gmake html.
Check your ~/.netscape/preferences file. It should say something like
MIME_TYPES: /usr/local/lib/netscape/mime.types PERSONAL_MIME_TYPES: ~/.mime.types MAILCAP: /usr/local/lib/netscape/mailcap PERSONAL_MAILCAP: ~/.mailcapEither of the files /usr/local/lib/netscape/mime.types or ~/.mime.types should have the lines
application/sepshell sepsh application/sepclean cleanEither of the files /usr/local/lib/netscape/mailcap or ~/.mailcap should have the lines
application/sepshell;xterm -e sepshell %s application/sepclean; sepshell %s
If for some reason you don't want to use make, run Latify paper.tex > paper.ltx to create a valid latex file and latex2dvi paper.ltx to process it with LaTeX. For figures to show up in the DVI file, you need to use \plot (\sideplot) instead of \activeplot (\activesideplot).
To add or update your biography and/or picture in the report, follow the following procedure:
TestDB | grep userThe output should look like FirstName LastName => user. For example,
356 spur> TestDB | grep berryman James Berryman=>berryman 357 spur>FirstName LastName is your name as it will appear on the report title page.
CreateDB user 'FirstName LastName'For example,
359 spur> CreateDB berryman 'James Berryman' CreateDB: added James Berryman 360 spur>
Simply put LATOPTS = class=seg97 into your makefile (or run
gmake LATOPTS=class=seg97 paper.ps). After you create a
postscript file, you need to take it to Adobe Distiller. The result
will be a PDF file, ready for electronic submission.
Several people pointed out to me that the font size in SEG abstracts
turns out smaller than usual. You shouldn't worry about it, because
this size complies precisely with the sample abstract, distributed by
SEG.
The seg97 class is designed to fit the SEP style. That is, it knows
about all the macros we use in our papers and translates them
accordingly. There is a smaller export version, called seg-99.
A simple command for doublespace is
\renewcommand{\baselinestretch}{2.0}
This line has to be in the preamble (before \begin{document}.) If you
use SEP's scripts, put include='\renewcommand{\baselinestretch}{2.0}'
in the arguments of Latify (or put
LATOPTS = include='\renewcommand{\baselinestretch}{2.0}'
in the makefile.)
They are back! In the "old days", we used those buttons with xtex (now obsolete). Now \syscall{comm} will translate into a link to comm.sepsh and allow you to execute virtually any make command from the HTML version of your document. To create the sepshell files automatically, put a list of the buttons in your makefile under SYSCALLS variable. This is mostly useful for TAs, preparing interactive exercises.
Yes! The sep2e class has now a thesis option,
connected with the standard LaTeX2e package for Stanford University
theses.
February 2007, Brad Artman made some updates, to include the latest
suthesis2e.sty
style file. Check out an entire Thesis/Adm directory of files
that will build (in Make) your thesis in 3 formats.
BE CAREFUL!! The book definitions contain a rule to make a paper.tex file in your Adm directory. Get the whole directory to make things go smoothly (/net/sepwww/sepwww/pub/software/softtex/Thesis).
Basically, follow the instructions on book maintainence. with these additional definitions:
\principaladviser{Jon F. Claerbout}
\firstreader{Biondo Biondi}
\secondreader{Norman Sleep}
\thirdreader{Donald Knuth}
%\figurespagefalse
%\tablespagefalse
\beforepreface
\prefacesection{Preface}
blah, blah, blah...
\prefacesection{Acknowledgements}
Thank you, Sergey!
\afterpreface
Use geophysics, a LaTeX2e class. Check out the RSF
SEGtex
website for the latest. \old{} and \new{} commands are
great for sending in marked revisions. Makeing the pdf with and without
the LATOPTS option=revised statement will either include only the
things in \new{}, or both with strike-out and color changes.
Put LATOPTS = class=geophysics in your makefile, run the usual make
commands (make read, make print, etc), and your SEP
report paper will appear in the form ready for submission to
Geophysics.
Also new are form-fillable pdf's that Geophysics wants filled out for your submission.
2 sentance summary.
Address.
Checklist.
Pagecharge.
Use can also use the geophysics class supplimented
with some changes in the
style of bibliography references. Put the following in your makefile:
LATOPTS = class=geophysics include='\bibpunct{(}{)}{;}{a}{}{\,}' bibstyle=eage
The usual make
commands (make read, make print, etc) will prepare your SEP
report paper for submission to
Geophysical Prospecting.
Use the html LaTeX2e package, provided together with LaTeX2HTML.
To do that, put LATOPTS = style=html in your makefile. The
commands to use in your LaTeX file are
\htmladdnormallink{text}{URL}
makes text appear normally in the DVI file, but as a hyperlink in HTML
\htmladdimg{URL}
includes an image (ignored completely by LaTEX)
\htmladdnormallinkfoot{text}{URL}
like htmladdnormallink but makes URL a footnote in the
DVI version. There is a more
complete documentation of these commands.
Look under
$TEXMF/tex/latex/resume/examplesfor several available examples. (You can also submit your own example there.)
Run swish-e -c congiffile on the web server. Here configfile is a configuration file. The configuration file for SEP reports is in
/public/docs/toc_html/docs-config. The configuration file for Jon's books is in
/sepwww/pub/sep/prof/prof-config.
The SEP bibtex databases are located in
$TEXMF/bibtex/bib/sep/. The most useful ones are SEP.bib - SEP reports and theses, SEG.bib - SEG cumulative database, and MISC.bib - miscellaneous items. To use bibtex references in your paper, include something like
\bibliographystyle{sep}
\bibliography{SEP,SEG,paper}
where paper.bib is your own database in the paper directory. To search databases, run
bibindex [keyword] [database] bibindex stolt SEGor use the web search
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Department of Geophysics Stanford University |
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