I am trying to use the following to obtain the pairwise distance of particles in a simulation:
compute cPP chrom property/local patom1 patom2 compute cP chrom pair/local dist eng dump 98 all local 10000 HiCp.dump index c_cPP[1] c_cPP[2] c_cP[1] c_cP[2]
Where ‘chrom’ is defined as
group chrom type 1 2 3
And the relevant pair styles and coeffficents and cutoffs are given by:
pair_style hybrid/overlay zero 7 lj/cut 1.12246 pair_coeff * * lj/cut 1.0 1.0 1.12246 pair_coeff 1 2 zero pair_coeff 1 3 zero pair_coeff 2 3 zero
The goal being to use the cutoff from the zero force of 7 as the cutoff for the property/local and pair/local computes. However, when I look at the pairwise distances recorded, they asymptotically approach the cutoff of 1.12246 (for the LJ pair interaction). I’ve tried switching the order for the hybrid pair style:
pair_style hybrid/overlay lj/cut 1.12246 zero 7
And switched the listing of the pair_coeff:
pair_coeff 1 2 zero pair_coeff 1 3 zero pair_coeff 2 3 zero pair_coeff * * lj/cut 1.0 1.0 1.12246
These seemed kinda silly to check, but thought just in case might as well. Same results with them.
How should I configure to use the pair cutoff for the zero force for my property/local and pair/local computes?
Sorry, but I cannot reproduce this. Please find below a simple test based on the melt example.
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 4 0 4 0 4
create_box 5 box
create_atoms 1 box
set type 1 type/fraction 2 (1.0/5.0) 6523
set type 1 type/fraction 3 (1.0/4.0) 12624
set type 1 type/fraction 4 (1.0/3.0) 846234
set type 1 type/fraction 5 (1.0/2.0) 745723
mass * 1.0
velocity all create 3.0 87287 loop geom
pair_style hybrid/overlay lj/cut 1.2 zero 5.0
pair_coeff * * lj/cut 1.0 1.0 1.2
pair_coeff * * zero
neighbor 0.2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
group chrom type 1 2 3
compute cPP chrom property/local patom1 patom2
compute cP chrom pair/local dist eng
dump 98 all local 50 HiCp.dump index c_cPP[1] c_cPP[2] c_cP[1] c_cP[2]
thermo 50
run 250
and that creates the expected output, i.e. pairs of atoms with a distance of up to 5sigma and energies only for atoms with 1.2 sigma or less.
Thank you! I’m honestly not sure what I did, but I deleted all of the comments in my original in file, and made the cutoff a float, not integer (so it was zero 7.0 rather than zero 7). Very weird, but I just looked at the results and they are correct.