Dear All,
I`m working on a polymer cross-linking problem where I do not want new bonds to be created between atoms of the same molecule. In other words, I want to implement the fix, i.e attempt to create new bonds using fix bond/create for an i-j atom pair, if and only if they belong to different molecules.
Is there a way one could implement this in the current build of LAMMPS?
Regards,
Srivastav Ranganathan
IIT Bombay
Dear All,
I`m working on a polymer cross-linking problem where I do not want new bonds
to be created between atoms of the same molecule. In other words, I want to
implement the fix, i.e attempt to create new bonds using fix bond/create for
an i-j atom pair, if and only if they belong to different molecules.Is there a way one could implement this in the current build of LAMMPS?
if the capability you are asking for is not in the documentation, that
it would need to be added.
i would expect that adding a functionality like this would be rather
straightforward to add (just a comparison of the molecule ids and code
to add a flag to control this feature).
however, it may be even more flexible to add an option that would
require bonds only be done for atoms in either the same or in
different chunks. then one could use the many options of compute
chunk/atom to partition the system (including molecule ids) instead.
axel.
A good Q is: if you have long chains, what physical reasoning
prevents a cross-link from forming between 2 monomers on
the same chain. I.e. how would monomers know they are
on the same chain?
If you simply want to prevent a cross-link from forming between
nearby monomers (on the same chain), then you can model
chains that are stiffer (e.g. with an angle term that makes them
more straight), so that monomers close along the same chain
never get geometrically close to each other.
Steve