RDF with special bonds

LAMMPS LAMMPS Development
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1

Hi. I am using LAMMPS to evaluate the energy of a system using the MOF-FF package. I am also wanting to compute the RDF many times over (and hence would like to avoid writing a dump file and then processing) for all pairs of atoms.

A summary of the pair styles used:

pair_style buck6d/coul/gauss/dsf     0.9000    12.0000
bond_style hybrid class2 morse harmonic
angle_style hybrid class2/p6 cosine/buck6d
dihedral_style opls
improper_style inversion/harmonic

special_bonds lj 0.00 0.00 1.00 coul 1.00 1.00 1.00

As suggested in the compute rdf command documentation, I tried setting the zero special_bonds values to a very small, non-zero value (1.0e-50), however setting the 1-3 weights to non-zero is incompatible with the angle style:

Exception: ERROR: Angle style requires special_bonds lj = x,0,x; otherwise buck6d 1-3 interaction are counted.

Is there any way around this? Thanks.

2

Not without modifying the source code. You could, for example, comment out or modify the check that is producing the error.

1 Like
3

A workaround is to dump the trajectory and use the rerun command to compute the RDFs. It’s pretty straightforward, and of course you don’t need to specify any pair style.

4

Thanks for the suggestion :slight_smile: I was hoping to avoid IO operations because I am carrying it out during the simulation, and modifying the “error” code worked quite well for this