gamgi - general atomistic modelling graphic interface
gamgi [file_1.xml] ... [file_n.xml]
gamgi is a computer package to construct, view and analyse atomic
file_n.xml is a fullname such as:
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’
Set this variable to let GAMGI know where the Help documentation
files are. For example, add a line as this to ~/.bashrc :
GAMGI_HELP=~/gamgi/gamgi/doc; export GAMGI_HELP
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
GAMGI_TEXT=~/gamgi/gamgi/src/io/fonts; export GAMGI_TEXT
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 ~/.bashrc:
BROWSER=firefox; export BROWSER
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 <firstname.lastname@example.org>.
Contact the author at <email@example.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.
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
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.
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:
<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"/>
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.
Choose Help->Tutorials to get a list of fully described procedures,
exemplifying most aspects of the work with GAMGI.
Written by Carlos Pereira <firstname.lastname@example.org>, helped by Steffen Moeller
<email@example.com> and Daniel Leidert <firstname.lastname@example.org>, from
the Debian project.