Particle doesn't move

LAMMPS LAMMPS Beginners
1

Hello,
I am new in LAMMMPS.
Trying to do LEBC in lammmps but stuck with this error:

I was able to run simulation but particles doesn’t move when I visualize colloid file in oveto.
My script is:

# move one atom in LE (Lees-Edwards) like boundary conditions

# log to the screen and to the log.lammps file
echo     both
variable        pmass index 1.0
units           si
#atom_modify     map array sort 0.0 0.0
atom_modify     map yes

#region		box block 0 10 0 10 0 10 units box
region		box prism 0 10 0 10 0 10 0 0 0 units box

create_box	1 box
mass            1 ${pmass}

create_atoms 1 single 5 9 5 units box
group        fst id == 1
velocity     fst set 0.0 10.0 0.0 units box

variable xpos equal x[1]
variable ypos equal y[1]
variable xvel equal vx[1]

timestep 0.01

# N = perform box deformation every this many timesteps 
variable     N equal 1
# {erate} value = R
#   R = engineering strain rate (1/time units)
variable     R equal 1.0
fix	     idfdef all deform ${N} xy erate ${R} remap v
fix	     1 all nve
neigh_modify    delay 0 every 1

fix extra all print 1 "${xpos} ${ypos}" file le.coord

dump		1 all image 10 le.*.jpg type type adiam 1.0
dump_modify	1 pad 5
dump		1 all atom 1000 dump.colloid
dump		1 all vtk 100 post/dump*.myforce.vtk id type vx fx
run 100
print "x(t=1) = ${xpos}"
print "y(t=1) = ${ypos}"
print "vx(t=1) = ${xvel}"

How can I fixed it?

I have few more questions? Can anyone help me please…

  1. I am trying to do LEBC in LAMMMPS. Is there any example? I couldn’t find out.
  2. How can i dump files for paraview viewer?
  3. How can I insert more than 1000 particles ?

Thank you. Hoping for help.

2

Your input is not properly quoted and thus not readable. Please edit to use triple back quotes “```” at the beginning and end of the quoted text so it looks like this:

# this is quoted text

print "$(step)"
3

I edited it.

4
  1. MD of a single atom interacting with nothing is a very pointless exercise
  2. There is no fix doing time integration which is required to move atoms
  3. There is no command requesting time stepping and thus triggering time integration

Conclusion: You need to work through some tutorials on MD in general and LAMMPS in particular and get a better understanding what it means to do an MD simulation.

LAMMPS does not support Lees-Edwards boundary conditions directly but something equivalent. There should be discussions about that in the mailing list archives. Remember “Google is your friend” :wink:

Use the dump vtk command — LAMMPS documentation

This is a superfluous question. Please study some LAMMPS tutorials and examples and the documentation, e.g.:

5

Check also the examples provided with Moltemplate. It is a scripting language designed to handle complex geometrical operations on single molecules or groups of atoms/molecules.
Another useful feature of Moltemplate is to read PDB and XYZ files for the creation of the data file, allowing you to use a graphical molecular modelling program (my favourite, GDIS) to build a system, and then let Moltemplate use the coordinates and create the topological information (bonds, angles, etc).

6

I did not notice that the quoted text block also scrolls vertically in addition to horizontally.
The time integration fix ane run command were thusly hidden. Apologies.

It looks like you ran for 100 steps but set the dump output to be performed only every 1000 steps. Therefore there should be only one frame stored in it.

7

Thank you so much, Let me go through few tutorials.
I might come back for the LEBC condition.
Anyways thank you so much.