dear all,
I’m simulating a amorphous bulk system of a polymer with PCFF and atom_style full. My system contains very long chain with 200 repeat units of monomer. Now I want to introduce some voids in the specified region of the domain. For this I was trying with delete_atoms, but this shows the error i.e. the bonded atoms are missing. i included the “mol” keyword also to overcome this. But as far the doc is concerned, the associated atoms are also being deleted which are not essentially in the specified group and as a whole the entire chain also being deleted as all the atoms are bonded for a chain. So, is there any tricks to overcome this ?
dear all,
I'm simulating a amorphous bulk system of a polymer with PCFF and
atom_style full. My system contains very long chain with 200 repeat units
of monomer. Now I want to introduce some voids in the specified region of
the domain. For this I was trying with delete_atoms, but this shows the
error i.e. the bonded atoms are missing. i included the "mol" keyword also
to overcome this. But as far the doc is concerned, the associated atoms are
also being deleted which are not essentially in the specified group and as
a whole the entire chain also being deleted as all the atoms are bonded for
a chain. So, is there any tricks to overcome this ?
have you updated to at least the 11 May 2014 version of LAMMPS?
axel
I’m using 1feb14 stable version. Is this can be solved with the most recent version.
I'm using 1feb14 stable version. Is this can be solved with the most
recent version.
please see: http://lammps.sandia.gov/bug.html
for what has changed since 1 Feb 2014.
Hi Axel,
I was trying that thing with 2May14 patch to create a void inside a bulk polymer, with delete_atom along with mol keyword. But the problem was that almost all the chains were deleted as because of that every atoms are essentially the part of a entire molecule, here a chain in case of a polymer.
The way the “mol” keyword works is by using the
molecule ID. If you have a long chain with all atoms
using the same molecule ID, and you delete one of
the atoms (e.g. in a region), then the entire molecule
will be deleted. I suppose an option could be
added to delete atoms, then also delete any bonded
interactions that include a deleted atom, but no
one has done that (or requested it).
Steve
If I apply delete_bonds with “remove” for a particular region and then “delete_atom”, would that be a solution ?
If I apply delete_bonds with "remove" for a particular region and then
"delete_atom", would that be a solution ?
almost. i think you also have to assign a new molecule id to the part of
the molecule that you want to delete.
axel
Can I “set” a mol ID for a particular group by “set” command along with “mol” keyword with a value that will be the assigned “molecule ID” ?