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averages.tex
defunits.tex
fancy.sty
files.tex
forcefield.tex
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gromacs.tex
here.sty
hfill.ist
implement.tex
index.gmx
install.tex
intro.tex
macros.tex
mkfiles
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monster.bib
picins.sty
programs.tex
proteins.bst
special.tex
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README

So, you want to build the manual?

It used to be a bit inconvenient. It still is, but CMake can take care
of more of the LaTeX and file-copying monkey work, using the
UseLaTeX.cmake package. Documentation and source updates for it
can be found here http://www.itk.org/Wiki/CMakeUserUseLATEX

The UseLaTeX.cmake package requires an "out of source" build, so make
a new directory somewhere, and from it run "ccmake ${this_directory}".
This directory can be inside the manual directory, or outside. You
will need to provide values for two CMake cached variables, which
are the location of installed GROMACS binaries, and the location of
a GROMACS source distribution. Obviously, these should correspond to
what you want to build the manual from. This will take care of building
all of the parts of the manual that are made directly from the source,
and the parts that are made from the executables themselves.

Having told cmake about those locations, it will check that you're
not obviously wrong. With ccmake, keep using 'c' for configure
until ccmake will let you use 'g' for generate. Now "make pdf" will
make the PDF manual.

Alternatively, you can run commands like

mkdir build_manual
cd build_manual
cmake .. -DGMXSRC=/home/me/GROMACS/git/release-4-5-patches -DGMXBIN=/home/me/programs/gmx-git/bin

to do it from the command line.

Various files from old-style manual builds can break the CMake
dependency generation. If you run "make clean" from the manual directory,
it will get rid of g_options.tex, proglist.tex, progman.tex and mdp_opt.tex,
as well as the progman directory and old LaTeX output files.

The binaries directory should contain only one version of the GROMACS
binaries - not multiple versions with _mpi, _d suffixes, etc.

Old README contents follow - this are partly out of date.
--------------

It's not terribly difficult, but before you just run 'make' and let
LaTeX do the job, we need to create a couple of files from the Gromacs 
source. 

Over the years we have learnt that the only way we will keep documentation
up to date is if most of it is generated automatically from the same source.

Before you start you need both the Gromacs source and a set of working
executables.

These are the items that need to be generated:

1. A LaTeX version of all the options in the mdp file.
   This is generated from the HTML version in the Gromacs source.
   Run the script mkmdp in this directory, with the HTML directory as
   the first argument, e.g.:

   ./mkmdp /home/lindahl/gromacs-3.2.1/share/html

   NOTE: We do a pretty complicated parsing of the mdp_opt.html file, so even
   if the file displays correctly in a browser it is quite possible that minor
   errors will screw up the TeX parsing completely. If you get inexplicable
   warnings/errors, this file is the first place to look...


2. The help information and command line options for all Gromacs executables.
   This is generated from the compiled executables. Run the script mkman with
   the binary directory as the first argument, e.g.:

   ./mkman /usr/local/gromacs/powerpc-apple-darwin7.2.0/bin/


3. Generate the list of programs, proglist.tex.
   This is done in two steps. First, copy the list of programs from the
   admin directory in the gromacs source, .e.g:

   cp /home/lindahl/gromacs-3.2.1/admin/programs.txt .

   And then generate proglist.tex:

   ./mk_proglist


4. Generate the list of standard options. 
   This is done by compiling the program 'options' in the src/contrib directory
   of Gromacs. Go there and type 'make options', and copy the executable to this
   directory. Then create options.tex in this directory with

   make options.tex


That should be it. Now try 'make pdf' if you have pdflatex installed, or
just 'make' to create a postscript file with classical latex and dvips.


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