Remapping across boundaries

Dear Lammps Users,

I have constructed a minimal working example (MWE) to illustrate the difficulty that I have towards comprehending these boundaries.

To describe the problem:

  1. I have a simulation box that is a cube of dimension 30 (LJ units). I create a random set of 28 atoms in the lower half of the cube (the dimensions of the lower half 0 ,30, 0, 30, 0, 15).

  2. The boundary conditions are of the form p p s. It is shrink wrapped on the z axis, periodic along x, y.

  3. I move the atoms with a constant x velocity of 1.0 (LJ units)

  4. Timestep is 0.0005 and I step through 20000 timesteps

When I focus on atom at (14.7725,1.4443,2.3487) this atom’s:

  1. x coordinate moves from X=14.77 to X= 22.37 and shifts to X = 10.0 and increases

  2. y coordinate jumps from Y=1.44 to Y=22.89 when this shift occurs and otherwise remains constant

  3. z coordinate jumps from Z=2.349 to Z = 8.971 when this shift occurs and otherwise remains constant

When I focus on atom at ( 7.3471,2.6826,13.2146) its x component uniformly increases till 17.347 and its other coordinates remain constant.

This behavior is quite confusing as I was always under the impression that if the atom moves along the x axis that needs to hit the edge before it gets remapped and the y/z coordinate never changes. Can anyone please point me to the right direction? I have pasted the input file of MWE (my zipped attachment did not get through to the list I suspect).

Best
Meenakshi

Input file

Initialization

clear

Choice of units - relative units

units lj

3 dimensional problem

dimension 3

We are simulating the interface

so it is periodic on two sides and not on the third side

boundary p p s

Type of atoms involved

atom_style charge

Mapping style

atom_modify map array

Create regions

region sim block 0.000 30.000 0.000 30.000 0.000 30.000
region lower block 0.000 30.000 0.000 30.000 0.000 15.000

create simulation box

create_box 1 sim

Fill up atoms

create_atoms 1 random 28 10231 lower

Atom prop

mass 1 1.0

Neighbor set up

neigh_modify delay 1 check yes

Time Step

reset_timestep 0
timestep 0.0005000

Force Fields

pair_style lj/cut 2.250
pair_coeff 1 1 1 1

velocity

fix 1 all move linear 1.0 0.0 0.0
dump 101 all custom 1 config.dat id x y z
run 20000
undump 101
unfix 1

Dear Lammps Users,

I have constructed a minimal working example (MWE) to illustrate the
difficulty that I have towards comprehending these boundaries.

To describe the problem:
1. I have a simulation box that is a cube of dimension 30 (LJ units). I
create a random set of 28 atoms in the lower half of the cube (the
dimensions of the lower half 0 ,30, 0, 30, 0, 15).
2. The boundary conditions are of the form p p s. It is shrink wrapped on
the z axis, periodic along x, y.
3. I move the atoms with a constant x velocity of 1.0 (LJ units)
4. Timestep is 0.0005 and I step through 20000 timesteps

When I focus on atom at (14.7725,1.4443,2.3487) this atom's:
1. x coordinate moves from X=14.77 to X= 22.37 and shifts to X = 10.0 and
increases
2. y coordinate jumps from Y=1.44 to Y=22.89 when this shift occurs and
otherwise remains constant
3. z coordinate jumps from Z=2.349 to Z = 8.971 when this shift occurs and
otherwise remains constant

i don't see this. neither in the visualization nor in the trajectory file.
atoms are created in randomized places and move uniformly in x-direction.

which version of LAMMPS do you have?
how do you exactly analyse/visualize the file?

[[email protected] mms] grep ^11 config\.dat | head \-10 11 14\.7725 1\.44432 2\.34867 11 14\.773 1\.44432 2\.34867 11 14\.7735 1\.44432 2\.34867 11 14\.774 1\.44432 2\.34867 11 14\.7745 1\.44432 2\.34867 11 14\.775 1\.44432 2\.34867 11 14\.7755 1\.44432 2\.34867 11 14\.776 1\.44432 2\.34867 11 14\.7765 1\.44432 2\.34867 11 14\.777 1\.44432 2\.34867 \[[email protected]\.\.\.1220\.\.\. mms\] grep ^11 config.dat | tail -10
11 24.768 1.44432 2.34867
11 24.7685 1.44432 2.34867
11 24.769 1.44432 2.34867
11 24.7695 1.44432 2.34867
11 24.77 1.44432 2.34867
11 24.7705 1.44432 2.34867
11 24.771 1.44432 2.34867
11 24.7715 1.44432 2.34867
11 24.772 1.44432 2.34867
11 24.7725 1.44432 2.34867

axel.

Hi Axel,

Thanks for pointing this out. I found that my data parsing was incorrect.

Thanks
Meenakshi