Lammps error ; create_atoms lattice size overflow

LAMMPS LAMMPS Beginners
1

Respected Lammps users, I am getting error of create_atoms lattice size overflow on one or more procs during running lammps script on version March, 2021. Here is my script
‘’‘’‘’
units metal
dimension 3
boundary p p p
atom_style atomic

neighbor 0.3 bin

neigh_modify every 20 delay 0 check no

region simbox block -8100 11700 -100 29900 -8900 19500 units box

lattice fcc 3.567

region substratediamond block -7900 11500 100 4100 -8000 19000 side in units box

lattice fcc 4.09

region outer2 sphere 1900 7963 5441 3663 side in units box

create_box 2 simbox

mass 1 12

mass 2* 107.8

create_atoms 1 region substratediamond

create_atoms 2 region outer2

group slab region substratediamond

group water region outer2

set group slab type 1

set group water type 2

pair_style hybrid eam lj/cut 12
pair_coeff 1 1 none
pair_coeff 22 22 eam Ag_u3.eam

pair_coeff 1 2 lj/cut 0.043 3.5

thermo 1
thermo_style custom step lx ly lz press pxx pyy pzz pe temp
thermo_modify norm yes
thermo_modify lost ignore flush yes

#minimize 1.0e-21 1.0e-21 10000 10000

timestep 0.001

velocity water create 1500 12345 mom no rot no
run 0
velocity water scale 1500

fix 1 water nvt temp 1500 1500 0.1
fix 5 slab setforce 0 0 0
#fix 3 slab move linear 0 0 0

dump movie all atom 100 m.1part
run 1100000 ‘’‘’‘’
How to solve this error?

Thanks for cooperation

2

You are doing too many things in one pass.
a) start by setting up only one part of the system, e.g. the “diamondsubstrate” part
b) your boxes are HUUUGE and thus requiring a lot of memory and thus likely requiring to run on a very big supercomputer in parallel. Thus start with a smaller system, figure out how large this is and how this fits with your available resources and whether it can give you the answers you are looking for. Then increase the size, if needed.

There are lots of things that don’t make sense, e.g. the multiple lattice commands. the second will wipe out the first before it had any effect on anything. Also, I see references to “water”, but nothing that looks like any reasonable representation of water.

Again, the advice is to start small and build up to the final system in stages and do simple setups first.

3

Respected Sir, If the second lattice command wipe out the first then how to use both of these in one simulation box, then how to define two different lattice interaction.

4

Sir, How to disintegrate the system in two parts. Which command help to do it in parts and then how to get combined effects?

5

If you don’t understand how to do that, you need more help that an online forum can provide. Please find yourself a tutor that can show you basic steps of doing scientific work. What I am suggesting is not using some special commands, but rather just common sense and best practices when learning a new skill. You are trying to do your production calculation without sufficient understanding and practice in the individual steps and the functionality and limitations of the tools you are using. Some of this can be learned by following online tutorials and following them step by step and re-reading documentation and thinking through every step. That takes time.

6

How the lattice command works and what it does and what not is explained in the documentation.

You seem to see the input file as if you give it to another human being that you can reason with. That is not the case here. You are effectively writing a compute program and what happens is exactly what LAMMPS has been programmed to do. Nothing more, nothing less. It does not reason and cannot know your intentions. It is your job to structure your input script exactly so that it does what you expect it to do. That requires understanding of each step and that in turn requires familiarity with the documentation and also some experimenting with commands and what effects they have.