Hello all,
I’ve been trying to figure out how to invoke a compute command and then identify a group based on the results of the compute.
My specific problem is after reading in my Polycrystalline configuration file, I wan’t to compute the coordination and assign all
miss coordinated atoms (i.e. grain boundary atoms) to a group. Then work with this group to perform other compute commands.
I’m unable to think of away to do this.
Thanks,
Stefan
The dump_modify thresh command can do something
like this for choosing what atoms to dump out.
Similar logic could be added to the group command
to let you select atoms based on a threshhold value,
but it would have to be coded up.
Steve
The dump_modify thresh command can do something
like this for choosing what atoms to dump out.Similar logic could be added to the group command
to let you select atoms based on a threshhold value,
but it would have to be coded up.
hmm... perhaps this can be done with external scripting.
e.g.
1) write a restart file
2) convert with restart2data to a data file
3) write out a custom lammps dump
4) load the data file and the dump into VMD (or Pizza.py?)
and change atom types according to the property of interest.
5) write out a new data file
6) assign groups based on atoms types, but now you
have multiple atom types where you had just one before
and thus pair_coeff would need to be adjusted.
cheers,
axel.
Atom-style variables already have this threshholding option
via their Boolean operators, so I added a "variable" option
to the group command. So you can now add atoms to
a group based on evaluating the per-atom variable.
Try out the 28Aug patch. The group doc page has
an example for using it per-atom potential energies,
e.g. near a GB they would be different than in bulk.
Steve
GREAT!
This is just what I needed.
Thank you Steve and Axel, your help is always much appreciated.
Regards,
Stefan