Dear all,
I am setting an initial configuration analogue to the attached picture of Mingyong Zhou and Can Weng paper.
I have successfully generated the PMMA layer by means of Packmol -> .pdb file -> Topotools via VMD for obtaining the LAMMPS input file.
However, I do not know how could I define the “Mold insert layer”. Maybe I should use the create_atoms command?
Thanks for your support.
Dear all,
I am setting an initial configuration analogue to the attached picture of Mingyong Zhou and Can Weng paper.
I have successfully generated the PMMA layer by means of Packmol -> .pdb file -> Topotools via VMD for obtaining the LAMMPS input file.
However, I do not know how could I define the “Mold insert layer”. Maybe I should use the create_atoms command?
possibly. depends on the kind of material and the force field that you
want to use. make sure that you edit the data file to leave room for
the additional atom type(s) required.
it may be even easier to first use create_atoms to do the entire layer
and then delete_atoms to create the cavity.
you can also build the region to be filled with atoms using the
union/intersection of multiple regions.
axel.
Dear Axel,
should I read first the data file and then use the create atoms for setting the mold insert layer? Or otherwise?
Thanks!
Dear Axel,
should I read first the data file and then use the create atoms for setting
the mold insert layer? Or otherwise?
you are a researcher, right? this is a perfect question for a little
experimentation. both should work and produce identical results, if
done correctly.
axel.
Dear all,
in order to help the next readers, I’ve solved it with the following code where I first load the polymer data and next to it I generate the mould and its hole:
units real
boundary p p p
atom_style molecular
special_bonds lj/coul 0.0 0.0 1.0 dihedral yes
dielectric 1.0
pair_style lj/cut 12.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data data161118v2.mysystem
thermo 50
#Define polymer group
region polymer block 0 51 0 51 0 51 units box
group polymer_group region polymer
#Fill with atoms whats not polymer. zhi=-1 in order to avoid deleting polymer atoms when making the nanometric hole
lattice bcc 3.499
region niquel block 0 50 0 50 -50 -1 units box
create_atoms 3 region niquel
group 4 region niquel
#Make nanometric hole
region 4 block 10 40 10 40 -30 -1 units box
delete_atoms region 4
region mould block 0 50 0 50 -50 -1 units box
group mould_group region mould
I hope it will be useful for someone in the future 