Dear Lammps users,
I am doing a poiseille flow of polymers in a rectangular channel.
While equilibrating the initial configuration I have observed some of
the fluid atoms moving out of the walls. The walls atoms are created on a ‘fcc’ lattice.
Since I use the ‘p s s’ boundary condition the fluid atoms are shrink wrapped back into the box.
I have tried to use ‘p f f’ command, but it gives an error ‘Did not assign all atoms correctly’,
the LAMMPS documentation says that this is due to some of the atoms being
out side the non-periodic dimensions. However, the initial coordinates are
well within the box dimensions.
Any comments would be greatly appreciated.
Srikanth Dhondi
You need to figure out why your moving atoms are passing thru
the walls.
If it says some atoms were not assigned correctly, it's likely
a problem with your input data file. You need to figure
out what atom(s) are not being assigned.
Steve
Hi Steve,
I have looked through my initial configuration, none of the atomic positions
are out side the dimensions of the simulation box. With ‘p f f’ boundary
condition I get this error
LAMMPS (5 Oct 2007)
Scanning data file …
1 = max bonds/atom
Reading data file …
orthogonal box = (-26 -5 -5) to (26 5 5)
16 by 2 by 4 processor grid
4703 atoms
ERROR: Did not assign all atoms correctly
I am attaching the input files.
Regards
Srikanth
data.chain (433 KB)
equil.in (2.01 KB)
Your simulation runs if you change the data file to this:
-26.000000 26.000001 xlo xhi
-5.000000 5.000001 ylo yhi
-5.000000 5.000001 zlo zhi
This section of the doc/read_data.html page is relevant:
If the system is non-periodic (in a dimension), then all atoms in the
data file should have coordinates (in that dimension) between the lo
and hi values. Furthermore, if running in parallel, the lo/hi values
should be just a bit smaller/larger than the min/max extent of atoms.
For example, if your atoms extend from 0 to 50, you should not specify
the box bounds as -10000 and 10000. Since LAMMPS uses the specified
box size to layout the 3d grid of processors, this will be sub-optimal
and may cause a parallel simulation to lose atoms when LAMMPS
shrink-wraps the box to the atoms.
What it says about parallel is true in serial as well. It really only
matters on the high
end of the box, due to how LAMMPS decides which proc owns an atom. I'll update
this paragraph to be more clear.
Steve