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user:mgough:gamgi [2010/05/09 16:46]
mgough
user:mgough:gamgi [2010/05/09 16:48] (current)
mgough
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 +====== General Atomic Model Graphic Interface ======
 +
 +The installation,​ configuration,​ and useage of GAMGI - a program that will graphically show you what the atomic structure of your Red Bull looks like.
 +
 +According to the overview at: www.gamgi.org
 +<​code>​
 +Our goal is to provide a free package to construct, view and analyse atomic structures, as powerful and simple to use as possible.
 +
 +GAMGI aims to be useful for: 
 +1) the scientific community working in atomistic modelling, who needs a graphic interface to build and analyse atomic structures; ​
 +2) the scientific community at large, who needs a graphic interface to study atomic structures and to prepare images for presentations; ​
 +3) teaching the atomic structure of matter in schools and universities,​ even inviting students to run GAMGI at home; 
 +4) science promotion, in exhibitions and science museums. ​
 +</​code>​
 +
 +This could be of great use for chemistry students and professors to understand and display the physical structure and interaction of molecules.  ​
 +
 +==== Installation ====
 +
 +The Gamgi package can be obtained via source at the gamgi.org site, or through aptitude installation.  ​
 +
 +To install via aptitude, follow this procedure.
 +
 +<​code>​
 +~$ aptitude search gamgi
 +p   ​gamgi ​                          - construct, view and analyse atomic structu
 +p   ​gamgi-data ​                     - extra data for the gamgi atomic structure ​
 +p   ​gamgi-doc ​                      - data for the gamgi atomic structure displa
 +</​code>​
 +
 +Note that there are other options, we want all of them, so use the following command line.
 +
 +<​code> ​
 +:~$ sudo aptitude install gamgi gamgi-data gamgi-doc
 +
 +Do you want to continue? [Y/​n/?​] ​
 +</​code>​
 +
 +Of course, select yes. The program will now automatically download and install itself.
 +
 +==== Running GAMGI =====
 +
 +GAMGI can be started from the command line or your menu items, from the command line simply type "​gamgi"​ at the prompt.
 +
 +The program will now open and you are ready to roll
 +
 +==== Using the Tutorials ====
 +
 +The easiest way to get started in GAMGI is by running through the tutorials. ​ You can find the tutorials by selecting "​help->​tutorials"​. ​ This will bring up a list of available demonstrations.  ​
 +
 +This is a copy of the first tuturial - CsCl and gives you a good starting point.
 +
 +''​
 +The CsCl structure is observed in metallic compounds such as CuZn (beta-brass),​ AlNi, AgMg and CuPd, but also in ionic crystals with equal number of cations and anions, when the cation is slightly smaller than the anion: CsCl, Nh4Cl, TlBr, etc. 
 +
 +To build this structure, first we create the cell with the observed lattice parameters, then the Cs, Cl atoms used as models, with the observed ionic radius, and then link the cell with the atoms. ​
 +
 +Press Cell->​Create and set System to c, Lattice to P (Primitive Cubic) and a to 4.018 (so ions will be in contact along <111> directions). Press Ok to create the cell. 
 +
 +
 +Select Atom->​Create and set Style to Solid, Size to 1.0 and Variancy to 1.0. Set Element to Cs, Radius to 1.670 (ionic radius for Cs+) and press the mouse over the graphic area. A Cs atom is created where the mouse was pressed. ​
 +
 +
 +Set Element to Cl, Radius to 1.810 (ionic radius for Cl-) and press the mouse over the graphic area. A Cl atom is created where the mouse was pressed. ​
 +
 +
 +Press Cell->​Link and select the Independent link method. Press the mouse over the cell, and then over the Cs atom, to identify the objects to link. Set the x, y, z coordinates (Position page) to 0.5, 0.5, 0.5 and press Ok. 1 atom of Cs is now visible, in the center, inside the cell. 
 +
 +
 +Repeat the link procedure above, but this time pressing the mouse over the Cl atom, and setting the x, y, z coordinates to 0.0, 0.0, 0.0. 8 atoms of Cl are now visible, in the vertices, corresponding to a total of 1 atom inside the cell. 
 +
 +
 +Select Light->​Create and press Ok, to add a light and give atoms a three dimensional look. 
 +
 +
 +Remove the Cs,Cl atoms used as models during the building process, pressing Atom->​Remove and clicking the mouse over the two atoms. ​
 +
 +
 +Rotate,​move,​scale the CsCl cell with the mouse. Press Atom->​Measure to determine lengths and angles between atoms. ​
 +''​
 +
  
user/mgough/gamgi.txt · Last modified: 2010/05/09 16:48 by mgough