Crystal structures on the web Caspar Fall January 2000

Warning: This information is provided primarily for users at the University of Exeter!

Three-dimensional crystal structures can easily be displayed on the web using Livegraphics3D, a free Java applet. This avoids using any painful plug-ins and is the most convenient procedure for the viewer:

x2h:

• Convert your XYZ file into an HTML document using x2h:


~fall/bin/x2h [options] crystal.xyz > crystal.html

The options are:

-h    this help message
-i#   work with iteration # from the input file
-e    turn on atom types (on each atom)
-n    turn on numbers (on each atom)
-m    turn on animation (warning: this can be slow for big files)
-a    turn off little axes
-d    turn on numerical axes
-b    turn on bounding box
-l#   change the camera distance factor to #
-p#   change the support directory to #
-s#   change the atom size factor
-c#   index of the last atom to draw fully (then stumps)
-u#   set length of stumpy bonds to #
-w#   change the bond width factor
-y    turn off plotting of hydrogen atoms

x2h also reads any defaults set in .Xresources in the format:
xmol*supportDir : /u3/fall/.XMOL

• Copy the compiled Livegraphics3D Java applet into the same directory as the html file you have just created:


cp ~fall/www/live3d/live.jar .
 

• View the result with your favourite Java-enabled browser, such as Netscape or HotJava:


netscape crystal.html

Examples:

• Mg substitutional atom in GaN

• C6H12 molecule:

Visit number

Caspar Fall              email: C.J.Fall@exeter.ac.uk
University of Exeter     phone: +44 (1392) 264198
Exeter EX4 4QL, UK       fax  : +44 (1392) 264111

28th January 2000