Visualisation

Brief notes on the three visualisation programs which the author finds useful are given below.

Jmol

Perhaps the most intuitive visualisation program is jmol, available from http://jmol.sf.net. As this is Java based, it will run on any platform provided the appropriate run-time environment is installed. Jmol will read xmol files as written by MDTEP without modification.

Jmol allows specification of lattice vectors and hence replication of the CASTEP super-cell over space. It will also animate the atomic trajectory. Functionality is available to measure inter-atomic distances, bond angles and dihedrals. Jmol is not however able to animate cell vectors.

Figure 5.1: Jmol showing a snapshot from the 8 atom silicon example simulation discussed in section 4.2.

GopenMol

Gopenmol is an OpenGL based visualisation package, available from http://www.csc.fi/gopenmol/. Like jmol it will read and animate xmol files. Features include the ability to output a time series of bond lengths and angles, and the ability to superimpose an isosurface of a scalar field such as charge or spin density.

It is available as source-code, or as binaries for Intel-Linux, IBM-AIX, and SG-IRIX.

Figure 5.2: Gopenmol showing a snapshot from the constrained n-pentane simulation discussed in section 4.3.

XCrysDen

XCrysDen can be obtained from http://www.xcrysden.org. Although it can read xmol files, the axsf files written by MDTEP are the native format. This format includes information about variable cell vectors, making XCrysDen very useful for visualisation of variable cell MD calculations.

XCrysDen includes many of the features of Jmol, with the capability to visualise scalar fields at single points in time. It is available as source code or as binaries for Intel-Linux.

Figure 5.3: XCrysDen showing a snapshot from the 8 atom silicon example simulation discussed in section 4.2.