compute property/local

Hi,
I’m using the Stillinger-Weber potential with two atom types (corresponding to two groups), and I compute the distances between atoms in the second group with the “compute pair/local” command. I would like also to compute atom IDs included in each pair, so I know which pair of atoms goes with each distance computed. I tried to do this using the “compute property/local” command, and output the distances and atom IDs together with a “dump local” command, though I get the following error message : “Pair style does not support compute property/local”. How can I get the program to dump atom IDs along with the distances ? Should I use the “rerun” command, along with any pair style supporting the property/local command ? Here’s how i first tried to do this :

compute DISTANCE group2 pair/local dist
compute IDs group2 property/local patom1 patom2
dump DISTANCE group2 local 100000 dump.si_group2_dist index c_IDs[1] c_IDs[2] c_DISTANCE

Thank you,
Paule

Hi,
I'm using the Stillinger-Weber potential with two atom types (corresponding
to two groups), and I compute the distances between atoms in the second
group with the "compute pair/local" command. I would like also to compute
atom IDs included in each pair, so I know which pair of atoms goes with each
distance computed. I tried to do this using the "compute property/local"
command, and output the distances and atom IDs together with a "dump local"
command, though I get the following error message : "Pair style does not
support compute property/local". How can I get the program to dump atom IDs

compute property/local only works for pairwise additive potentials.
SW is not, so it cannot work.

along with the distances ? Should I use the "rerun" command, along with any
pair style supporting the property/local command ? Here's how i first tried

you can try, but first see below, please.

to do this :

compute DISTANCE group2 pair/local dist
compute IDs group2 property/local patom1 patom2
dump DISTANCE group2 local 100000 dump.si_group2_dist index c_IDs[1]
c_IDs[2] c_DISTANCE

what do you want to do with those distances?
it is probably much easier to do what you want
though some postprocessing. dumping all pairs
to a text file will create a significant amount of output
writing/formatting and reading/parsing that can
take a significant amount of time. it is likely to be
faster to just recompute pairs as needed.
i typically do these kind of things through scripts
in VMD where through atom selections, one can
very flexibly identify atoms with specific properties
or conforming to specific conditions.

cheers,
    axel.

Axel is correct that you can't use pair SW with compute pair/local
since it is a manybody potential. But you should be able to
use the rerun command as you suggest, and define a pair lj/cut
with a cutoff (so it will form a pairwise neighbor list), and then
use your compute property/local commands to dump out pairwise
distances. That is a good use of the rerun command.

Steve

Thank you for your answer,
the rerun command has indeed worked to compute ID’s of atoms in pairs and distance between them. Now I would like to add each atom’s type in this file. Is it a possible attribute that can be computed and dumped with a “dump local” command ? Otherwise, how can I use a simple “dump” command to output the local informations (ID’s for each pair and distance between atoms for each pair) and associate each atom’s ID with its type ? Cheers,
Paule

Just added new keywords for atom types to the compute property/local command.
See the 15 Aug patch.

Steve