Displacing only few atoms

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1

Hi all,

I am trying to provide strain to only few atoms in the Graphene sheet as shown in figure. I have marked the atoms to which I am applying strain. I created a group which consists of those atoms and then use the fix -move -linear command but it did not move the atoms. Same was the case with displace_atoms command. My boundary conditions are fixed in x -direction and periodic in y direction. I want to know is there any other method which i can use. Previously I had used only box deformation techniques, this is my first attempt to provide strain to few atoms.

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Thank you,
Deepak Behera

2

Hi all,

I am trying to provide strain to only few atoms in the Graphene sheet as shown in figure. I have marked the atoms to which I am applying strain. I created a group which consists of those atoms and then use the fix -move -linear command but it did not move the atoms. Same was the case with displace_atoms command. My boundary conditions are fixed in x -direction and periodic in y direction. I want to know is there any other method which i can use. Previously I had used only box deformation techniques, this is my first attempt to provide strain to few atoms.

there is not enough information here to tell whether you used fix move correctly. many people make the mistake to time integrate that atoms that are moved by fix move with a time integration fix as well and thus leading to incorrect trajectories. LAMMPS will warn about this.

axel.

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3

Hi Axel,

Thank you for your reply. Below are the commands that I have used

reset_timestep 0
timestep 0.0002

fix 2 2 move linear 0.0 -0.01 0.0 units box

dump 200 all cfg 1 dump.nvt_*.cfg mass type xs ys zs

run 1000

Yes I too did a time integration. Any suggestions for correct way to do it.

Thank you,
Deepak Behera

image.jpeg.png

4

this doesn’t help at all.

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5

This is the complete script that I have used.

------------------------ INITIALIZATION ----------------------------

units metal
dimension 3
boundary f p p
atom_style atomic
newton on

----------------------- ATOM DEFINITION ----------------------------

read_data data.graphene

mass 1 12 # carbon
mass 2 12 # The carbon atoms to apply strain

------------------------ FORCE FIELDS ------------------------------

pair_style airebo 3.0
pair_coeff * * CH.airebo C C

------------------------- SETTINGS ---------------------------------

image.jpeg.png

6

When you are using fix move, you do not do time integration for all other atoms. Thus only the atoms in the group 2 are moving, but all others remain in place.

Axel.

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