Dear all,
My intention is to create a spherical pore region inside a bulk polymer. Now I’m defining that region as a group and after setting mol ID of that group, “delete_atoms” was used. As expected, after deleting the random atoms, the error is throwing that “bond atom missing”. So, can you please share any idea regarding this issue ? Is it possible within Lammps framework ?
Thanks in advance.
The delete_atoms command has a “mol yes” option
to also delete entire molecules (if any atom in the
molecule is deleted).
If instead you want LAMMPS to truncate your molecules
and remove the dangling bonds, then there is no
current option for that.
Steve
The delete_atoms command has a "mol yes" option
to also delete entire molecules (if any atom in the
molecule is deleted).If instead you want LAMMPS to truncate your molecules
and remove the dangling bonds, then there is no
current option for that.
removing atoms such a way is best done with an external software and
then the bond topology would need to be recreated.
another possible option to create a void in a molecular system is to
"grow" large soft core particles using fix adapt and then remove them
after proper equilibration time. of course, the resulting pore will
have a different morphology than one with truncated bonds, but
depending on the nature of the pore that should be modeled, it may or
may not matter or may even be closer to comparable experiments (pores
created by template leeching).
axel.
Just added a “bond yes” option to the delete_atoms command,
to also delete any bonded interactions that include a deleted atom.
In a 6Jan15 patch.
However, as Axel said, you have to be careful if you’re going
to delete such bonds (angles, etc), as they may lead to
an odd model, particularly at surfaces.
Steve