[lammps-users] FAO Axel - Topotools

[Michael Doig <m.doig@sms.ed.ac.uk>]

I have been using Topotools to generate my LAMMPS data file from an xyz 
coordinate file but am having some problems.

When it writes the LAMMPS data file, all bond types are defined as type 
1, regardless of which atoms are actually bonded together. However, when 
it outputs the angles and dihedrals data, after I have used the 
guessangles/dihedrals command, the angle/dihedral type are all numbered 
uniquely, based on the which atoms form the angle/dihedral.

Is there anything I can do to get the bond type numbered correctly, so 
different atom types which are bonded together are regarded as a 
different type of bond.

Thanks,

Michael Doig
---
PhD Student
School of Chemistry
University of Edinburgh


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