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
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.