.TH GAMGI 1 "June 4, 2008" 0.13.6 "GAMGI Manual Page"

.SH NAME
gamgi \- general atomistic modelling graphic interface

.SH SYNOPSIS
gamgi [file_1.xml] ... [file_n.xml]

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

.SH OPTIONS
file_n.xml is a fullname such as:

 ../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

Object and config data can be mixed, so file_1.xml might be a preferences 
file, loaded before the other object files. To automate the procedure, 
just add a line as this to .bashrc:

alias gamgi='gamgi ~/gamgi/my_defaults.xml'

.SH ENVIRONMENT
Set the variable GAMGI_HELP, to let Gamgi know where are the Help 
documentation files. For example, add a line as this to ~/.bashrc:

GAMGI_HELP=~/gamgi/gamgi/doc; export GAMGI_HELP

Set the variable GAMGI_TEXT, to let Gamgi know where are the .ttf Bitstream 
Vera files, to render solid fonts. For example, add a line as this to ~/.bashrc:

GAMGI_TEXT=~/gamgi/gamgi/src/io/fonts; export GAMGI_TEXT

Set the variable BROWSER, to let GAMGI know which browser to launch, in case 
this is chosen to read Help. For example, add a line as this to ~/.bashrc:

BROWSER=firefox; export BROWSER

.SH HELP
Read introductory information with Help->Start. Browse the documentation
at http://www.gamgi.org/ or its local copy at gamgi/doc/. Use the help mechanisms
reunited under the Help button. Subscribe the mailling list <gamgi-users@gamgi.org>.
Contact the author at <jcgp07@gmail.com>.
  
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).

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.
  
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.
  
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.
  
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.

To see detailed explanations of Gamgi interfaces, consult the reference manual at 
http://www.gamgi.org/interfaces/reference.html, doc/interfaces/reference.html or 
Help->Topic->Interfaces.

.SH FORMATS
Gamgi can import files in .xyz and .xml native format, selected automatically by the 
file extension. Gamgi can export files in .ps, .ppm, .jp[e]g, .png, .tif[f], .x3d and 
native .xml formats, selected automatically by the file extension.

In Gamgi native XML format, a water molecule can be described as:

<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>

To see detailed explanations of Gamgi formats, consult the reference manual at 
http://www.gamgi.org/formats/reference.html, doc/formats/reference.html 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
http://www.gamgi.org/

.SH AUTHOR
Written by Carlos Pereira <jcgp07@gmail.com>, helped by Steffen Moeller 
<moeller@debian.org>, from the Debian project.
