Hi,
So I'm trying to model a polymer interacting with a rough wall, so I
set the atom_style to hybrid sphere bond.
In the data section, I found I didn't / couldn't use Masses since the
masses are all individually defined for each atom so I never
explicitly define and attributes for an atom type. I get an error when
I use the command in the data file
Atom
1 1 1 x y z diameter density
...
since I never defined atom type 1 to be anything, when I try leaving
it blank I get an error that the atom section is improperly formatted.
What is the proper workaround to define a spherical atom if all of the
attributes given to an atom type are the default value?
~Nickhil Rokkam
Not sure why you need atom_style sphere to model a polymer.
Most of the wall potentials use a sigma for the monomers for
their effective diameter, which is compatible with just atom_style
atomic or bond.
But if you want atom_style hybrid sphere bond, then you
need to read the read_data doc page carefully. The bond style
defines a molecule ID which you do not list below, at least in
the correct location.
Steve
So my advisor suggested I freeze the wall so we don't unnecessarily
compute trajectories, but in LAMMPS to freeze something it had to have
torque (according to the error i got), since i also needed the atoms
to have bonds I thought I needed to make a hybrid type. Is there a
class that will let me have torque and create bonds?
~Nickhil Rokkam
So my advisor suggested I freeze the wall so we don't unnecessarily
compute trajectories, but in LAMMPS to freeze something it had to have
forces are computed regardless. you can play tricks with the exclusion
list, but that doesn't help very much if you are running in parallel.
if you don't want to generate as large trajectory files, use the dump
command only on a group of atoms that interest you.
torque (according to the error i got), since i also needed the atoms
to have bonds I thought I needed to make a hybrid type. Is there a
didn't i tell you before, that you don't want to use fix freeze?
simply skip the atoms that you don't want to get moved.from
the time integration fix or set there velocities to 0 and then
use fix setforce. 0.0 0.0 0.0
its been discussed on this list several hundred times.
axel.
You don't want atoms with torque or fix freeze. That
is for granular systems with finite-size particles that
can rotate. As Axel said, just use fix setforce. It is
like fix freeze for point particles.
Steve