Hello All,
I am using a pair potential (AI-REBO), and at every timestep I would like to output the number of pairs in the system. This data seems available, since at the end of a run the log outputs the max, min and average number of neighbors.
I know that “compute pair/local” or “compute property/local” can output arrays whose length is the total number of interactions, but I would like to know if there was a way to simply output that number as a scalar.
Any suggestions?
As always, thank you for your help!
-Emil
Hello All,
I am using a pair potential (AI-REBO), and at every timestep I would like to
output the number of pairs in the system. This data seems available, since
at the end of a run the log outputs the max, min and average number of
neighbors.
those are two different properties. how do you define "a pair"?
by the non-bonded force cutoff? the neighbor lists are only "potential pairs".
axel.
Axel- thanks,
I would like to count the number of atoms within the non-bounded force
cutoff throughout the run.
-Emil
You can't do this via pair airebo, or some tallying within it.
Nor via any other pair style. As Axel said, the neighbor list
is different than the force list (i.e. which atoms are within
the cutoff distance). You might look at compute coord/atom.
If you set that cutoff to the force cutoff, then I think you will
get "neighbors" of each atom. If you sum the result via
compute reduce, you will have total # of interacting pairs (if
you divide by 2).
Steve
You can't do this via pair airebo, or some tallying within it.
Nor via any other pair style. As Axel said, the neighbor list
is different than the force list (i.e. which atoms are within
the cutoff distance). You might look at compute coord/atom.
If you set that cutoff to the force cutoff, then I think you will
get "neighbors" of each atom. If you sum the result via
compute reduce, you will have total # of interacting pairs (if
you divide by 2).
an alternative would be compute the radial distribution function
_and__ the number integral. you can easily do that in postprocessing,
e.g. using VMD: http://www.ks.uiuc.edu/Research/vmd/plugins/gofrgui/
the number integral gives you the average number of neighbors
atoms in the first selected group of atoms has from the group of
atoms selected for the second group (those can be the same, of course)
up to the distance r.
cheers,
axel.