Relatively new user here. I have two input files here which I thought should give me the same result but do not. Both input files are exactly the same except for the harmonic potentials.
One contains the harmonic keyword that specifies the cut-off as 6.5. The other, uses the keywords ‘harmonic bond’ potential and explicitly connects the atoms. I think I am connecting all the atoms that are specified within the original cut-off so these should be equivalent. The confusing part is that the modes outputted have different frequencies so I must be missing something…
The important thing here is to note the warning in your output:
**** Warning - inter/intra/both directive given on potential line ****
**** but the molecule directive is currently inactive ****
If you don’t specify one of the molecule keywords then the connect/bond won’t do anything. If you’re going to specify connect then you also need “noauto” to stop GULP from choosing the bonds automatically.
NB: 6.5 Ang is a very long distance for bonds & so you’ll pick up multiple shells of atoms in most systems with this.
NNB: I’ve noted that the warning doesn’t specifically mention “bond” (which is a form of “intra”) and so I’ll make this explicit in future versions.