gamgi - general atomistic modelling graphic interface

Author

       Written  by  CarlosPereira <jcgp07@gmail.com>, helped by SteffenMoeller <moeller@debian.org> and DanielLeidert <daniel.leidert@wgdd.de>, from the Debian project.

0.14.3                                          November 30 2009                                        GAMGI(1)

Description

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

Environment

GAMGI_HELP
              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;exportGAMGI_HELPGAMGI_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 ~/.bashrc:

              GAMGI_TEXT=~/gamgi/gamgi/src/io/fonts;exportGAMGI_TEXTBROWSER
              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;exportBROWSER

Examples

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

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.

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.

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.

Name

       gamgi - general atomistic modelling graphic interface

Options

file_n.xml is a fullname such as:

           ../dat/molecule/flavors/garlic.xml
           ~/gamgi/dat/molecule/flavors/garlic.xmlhttp://www.gamgi.org/dat/molecule/flavors/garlic.xmlftp://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:

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