.TH GAMGI 1 "November 30 2009" "0.14.3" "GAMGI Manual Page"

.SH NAME
gamgi \- general atomistic modelling graphic interface

.SH SYNOPSIS
.B gamgi
.BI [ file_1.xml ]
.I ...
.BI [ file_n.xml ]

.SH DESCRIPTION
.B gamgi
is a computer package to construct, view and analyse atomic structures.

.SH OPTIONS
\fIfile_n.xml\fP is a fullname such as:
.PP
.nf
    \%../dat/molecule/flavors/garlic.xml
    \%~/gamgi/dat/molecule/flavors/garlic.xml
    \%http://www.gamgi.org/dat/molecule/flavors/garlic.xml
    \%ftp://ftp.gamgi.org/gamgi/dat/molecule/flavors/garlic.xml
.fi
.PP
Object and config data can be mixed, so \fIfile_1.xml\fP might be a preferences
file, loaded before the other object files. To automate the procedure, 
just add a line as this to \fI~/.bashrc\fP:
.IP
.B alias gamgi='gamgi ~/gamgi/my_defaults.xml'

.SH ENVIRONMENT
.TP
.B GAMGI_HELP
Set this variable to let GAMGI know where the Help documentation files are.
For example, add a line as this to \fI~/.bashrc \fP:
.IP
.B GAMGI_HELP=~/gamgi/gamgi/doc; export GAMGI_HELP
.TP
.B GAMGI_TEXT
Set this variable to let GAMGI know where are the .ttf DejaVu files, to render
solid fonts. For example, add a line as this to \fI~/.bashrc\fP:
.IP
.B GAMGI_TEXT=~/gamgi/gamgi/src/io/fonts; export GAMGI_TEXT
.TP
.B BROWSER
Set this variable to let GAMGI know which browser to launch, in case this is
chosen to read Help. For example, add a line as this to \fI~/.bashrc\fP:
.IP
.B BROWSER=firefox; export BROWSER

.SH HELP
Read introductory information with \%Help->Start. Browse the documentation at
\fI\%http://www.gamgi.org/\fP or its local copy at \fIgamgi/doc/\fP. Use the
help mechanisms reunited under the Help button. Subscribe the mailling list
<\&gamgi-users@gamgi.org\&>.
.PP
Contact the author at <\&jcgp07@gmail.com\&>.
.PP
Throughout all interfaces and formats, lengths are in angstrom, angles 
in degrees and decimal numbers are represented with dots. Every parameter
that can be defined in an interface can be also defined in a file
and vice-versa.

.SH INTERFACES
Rotate, move, scale the selected object pressing the left, middle, right mouse
button. Export the selected object choosing \%File->Export. The statusbar
shows the selected object (left) and layer (right).
.PP
To select an object, choose \%Object->Select and press over the object. Or
choose the object class on the menu above, with the middle button, before
pressing on the object. Or press twice Layer, Window or GAMGI on the menu
above. When the object has no visual representation, press the mouse over the
graphic area, to pop up a menu.
.PP
To select a layer, choose \%Layer->Select and press the mouse over the graphic
area, to pop up a menu. Or choose the layer class on the menu above, with the
middle button, before pressing the mouse over the graphic area, to pop up a
menu.
.PP
Solid objects usually require lights with diffuse and specular components to
be properly represented in 3D space, otherwise they look flat. Wired objects
do not have a 3D representation, so diffuse and specular lights are not
reflected, becoming poorly visible when using lights, unless a significant
ambient component is used. Often it is worth to draw solid and wired objects
in different layers, with and without lights.
.PP
When a task dialog is open, to learn how it works, just select \%Help->Current
and another dialog will pop up, explaining the meaning of all the parameters
in the task dialog.
.PP
To see detailed explanations of GAMGI interfaces, consult the reference manual
at \fI\%http://www.gamgi.org/interfaces/reference.html\fP,
\fI\%doc/interfaces/reference.html\fP or 
\%Help->Topic->Interfaces.

.SH FORMATS
GAMGI can import files in \fI.xyz\fP and \fI.xml\fP native format, selected
automatically by the file extension. GAMGI can export files in
.IR .ps ,
.IR .ppm ,
.IR .jp[e]g ,
.IR .png ,
.IR .tif[f] ,
.I .x3d
and native
.I .xml
formats, selected automatically by the file extension.
.PP
In GAMGI native XML format, a water molecule can be described as:
.PP
.nf
<gml>
  <molecule>
    <atom element="O"  x="0.000" y="0.000" z="0.000" id="O1"/>
    <atom element="H"  x="0.776" y="0.540" z="0.000" id="H1"/>
    <atom element="H" x="-0.776" y="0.540" z="0.000" id="H2"/>

    <bond parent1="O1" parent2="H1"/>
    <bond parent1="O1" parent2="H2"/>
  </molecule>
</gml>
.fi
.PP
To see detailed explanations of GAMGI formats, consult the reference manual at 
\fI\%http://www.gamgi.org/formats/reference.html\fP,
\fI\%doc/formats/reference.html\fP or 
\%Help->Topic->Formats.

.SH EXAMPLES
Choose \%Help->Tutorials to get a list of fully described procedures, 
exemplifying most aspects of the work with GAMGI.

.SH "SEE ALSO"
.I \%http://www.gamgi.org/

.SH AUTHOR
Written by \fBCarlos Pereira\fP <\&jcgp07@gmail.com\&>, helped by
\fBSteffen Moeller\fP <\&moeller@debian.org\&> and \fBDaniel Leidert\fP
<\&daniel.leidert@wgdd.de\&>, from the Debian project.
