Carrying out molecular Dynamics simulations is a relevant way for understanding growth phenomena at the atomic scale. Initial conditions are defined for reproducing deposition conditions of plasma sputtering experiments. Two case studies are developed for highlighting the implementation of molecular dynamics simulations in the context of plasma sputtering deposition: ZrxCu1-x metallic glass and AlCoCrCuFeNi high entropy alloy thin films deposited onto silicon. Effects of depositing atom kinetic energies and atomic composition are studied in order to predict evolution of morphologies and atomic structure of MD grown thin films. Experimental and simulated X-ray diffraction patterns are compared

Hi Emmanuel,

The method I used when I needed to do something similar to you was the following:

- define the atoms that you want to keep immobile as a group

- set the initial velocities of the atoms in that group to zero

- then set the forces acting on the atoms in that group to zero

With the initial velocities being set to zero and no forces acting on them, the atoms in that group won't move.

The line I used to set the forces to zero was

fix freezebottom bottomlayer setforce 0.0 0.0 0.0

Peter Klaver thanks for your response, I'm trying to follow that procedure but the line I'm using to select the bottom 20a x 2.5a x 20a is only selecting 85 atoms (out of a total of 13600 atoms for the whole box) which I think is a slice. I'm wondering how I can select all atoms from the bottom to that particular slice. Please find attached the kind of box and atoms I'm trying to create

The line I wrote is:

region box block 0 20 0 17 0 20 ## define box sizes along x, y, z (in the unit of a_0)

region R1region block 0 20 0 2.5 0 20 units box

create_box 2 box ## create the simulation box, allowing a max of one specie

create_atoms 1 box ## create type-1 metal atoms in the box

mass * 183.84

group R1 region R1region

fix 4 R1 setforce 0.0 0.0 0.0 ## impose zero force

velocity R1 set 0.0 0.0 0.0 ## impose zero speed

Thanks to everyone who replied, I got it right with the script below (might help someone):

# ---------- Define Groups --------------------------

region box block 0 20 0 17 0 20 ## define box sizes along x, y, z (in the unit of a_0)

create_box 2 box ## create the simulation box, allowing a max of one specie

create_atoms 1 box ## create type-1 metal atoms in the box

region 2 block INF INF INF INF INF 2.5 units box ##create the region of the box to be immobile

group lower_atoms region 2

set group lower_atoms type 2

# define the mass of all atoms of W (*)

mass * 183.84

fix 4 lower_atoms setforce 0.0 0.0 0.0 ## impose zero force

velocity lower_atoms set 0.0 0.0 0.0 ## impose zero speed

You can also, crate group of atoms that you want to be mobile

and then just integrate that group with the time integration scheme

Dear Nitin,

Can you share the script where some of the atoms in a slice (group) can be made mobile. This is specifically an interdiffusion of two materials I.e. setting up bonding/Welding etc. Exact problem is to make one body thermostat and another body to heat up say via NVT.