[lammps-users] deleteing molecules using region/group

A question for anyone out there:

I have a box of water (read in from datafile) and would like to make a
spherical cavity in it. I can assign a sphere region, group the atoms inside
and delete them....however some of the molecules are cut in half. I'd like to
get rid of those leftovers. The only way I know to do this is:
1. Run LAMMPS and let it complain about missing bond atoms and note the atom
ID numbers
2. Goto the data file and track down offending molecule
3. Delete the molecule ID in the input script
4. Repeat 1-3 for every "partial" molecule.

This is really slow. Does anyone know a good way to do this in LAMMPS, or is
it something I should preprocess in the datafile?
As usual, thanks for any suggestions.
Tim Sirk

I can't think of any clever way to do this automatically in LAMMPS.
I think just pre-processing your data file to remove waters would
be your best bet.

Steve

Hi Tim,

I wrote a fix that would slowly grow a spherical (and cylindrical) cavity
using a harmonic potential on the surface to push the atoms out (I the
used the . I can send it to you if you want (although you would have to
integrate into your lammps source distribution).

Naveen

Oops, sorry the last message was garbled.

Hi Tim,

I wrote a fix that would slowly grow a spherical (and cylindrical) cavity
using a harmonic potential on the surface to push the atoms out (I used
fix indent as inspiration). I can send it to you if you want (although you
would have to integrate into your lammps source distribution).

Naveen