Visualisation of atomic configurations - tool possibilities

Here are some ideas for visualisation, mostly as per earlier discussions

A visualisation tool as a workbench, with incorporation of the following codes (mostly Fortran)

1. CRUSH for rigid unit modes
   
2. Group theory analysis (GROUP code)
   
3. pair (radial) distribution function

Analysis of many configurations or structures

1. Read many files at once (Apple's "open *.tag" command does this at the shell level)
   
2. Read many configurations from one file (eg molecular dynamics history or trajectory file)
3. Constant scale and range for all files
4. One action affects all (eg change view, scale, orientation)
5. Change size of window for each (ideally perhaps have an automatic window size that matches the view of the configuration)
6. Compute some averages across all configurations (eg accumulated pair distribution function)
7. Easy creating of animations from molecular dynamics trajectory files

Input file formats

1. XML (particularly CML) files
   
2. Input from some standard codes (eg DLPOLY) that don't have outputs in standard formats

Tools for configurations

1. Move origin on a mouse (only for P1) as per atomeye
2. (From before) Analysis include pair distribution function, average bond length, average coordination number

martin, 17-Aug-2007 08:25 (GMT)