Classical Simulation of GeAu droplet on Ge substrate

Molecular Dynamics simulations of Semiconductor Nanowires

Adriano Santana

Created Dec, 2016

Under Construction!!! This tutorial discusses the simulation procedure to study semiconductor nanowire or surface growth of a liquid binary alloy on top a solid substrate. As a step-by-step process the structures are created with MD++, classically simulated with molecular dynamics (LAMMPS) and the dump files from the simulation are further studied with different MATLAB scripts in order to plot velocity growth, histogram growth at the interface, 3D movie creation, etc. As an example, we will explain this procedure to simulate AuGe liquid droplet deposition on crystalline Ge substrate for different temperatures and initial molar fraction of Ge in the liquid.

Create 3D structures

The first step is to create the structures (LAMMPS input file) that will be employed for the molecular dynamics. This can be easily achieved with MD++ providing a suitable potential is available. In this case we would need to have the an Au-Ge MEAM potential and the following TCL script: si_au.md.tcl

This script is lengthy and can be used for multiple purposes. Here briefly we discuss relevant parts. The section proc readmeam-lammps sets the description of where to find the relevant MEAM files needed for the meam-lammps potential. For example, if you install MD++ on your local computer inside a folder called "/Codes" you need to set the path to "meamfile" and "meafile". 'AuBt' 'Si4' are the label names for Au and Si which refer to a line in "meamf" and "AuSi2nn.meam" files. If you wanted to run Au/Ge instead of Au/Si simulation then you could use 'Ge5' instead of 'Si4' and also change the file AuSi2nn.meam for AuGe2nn.meam and the path to meafile accordingly.

#------------------------------------------------------------
proc readmeam-lammps {} {
 MD++ {
  meamfile = "~/Codes/MD++/potentials/MEAMDATA/meamf"
  meafile  = "~/Codes/MD++/potentials/MEAMDATA/AuSi2nn.meam"
  nspecies=2 element0="AuBt" element1="Si4" rcut = 4.5 readMEAM
  NNM=3000
    }
}
#end of proc readmeam-lammps
>/pre>

<pre>
talk about temperature, meaning of important lines

Run molecular dynamics simulations

Once MD++ has completed there will be a file in the /runs folder. It will look something like this:

file1.lammps.gz

which is the compressed form of the input file for LAMMPS (only cartesian coordinates)

We will place this file in a new folder with these files for the potential: meamf, library.meam and the LAMMPS file run.in which has important parameters and refers to the file1.lammps file.

We explain the content run.in here and how to run it...

Data analysis

After LAMMPS has finished the simulation there will be a certain (usually large) amount of dump files with the form (dump*.md). Each of these files has the Cartesian coordinates of the system for each time step throughout the whole run. Typically you will have about 1000 files to analyze although the output of dump files can be regulated.

With this raw data several observables can be calculated; surface growth versus simulation time, histogram through the z axis even 3D movies of the surface growth. We explain how to calculate them with the help of the following MATLAB scripts:

Plot data

to highlitght sth