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..

explaine how the script works, Temperature, meaning of important lines

The script takes four arguments, the first one ranges from 1-7. the second is the number of repetitions. The third one is the label for the chemical element: 'Au1', 'Si4', etc. which are all found inside the script. The fourth argument is a division factor, 1701/2.70 equals 629 . Hence, the range of temperatures will be from 1701 to 629 K.

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...

Free Energy

Simultaneously one can also calculate the free energy of Si-DC crystal with a gold impurity as:

meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Si4 1701 2.70

After the two scripts finish four MATLAB scripts are produced in the Binary_AuSi_3 folder:

AuSi binary alloy

This tcl scripts, wcr_AuSi_Liquid.tcl, calculates the data needed for the binary system mixture:

meam-lammps_intel scripts/work/si_au/wcr_AuSi_Liquid.tcl 1 1 0 1701 2.704

where the third argument from the left represents the silicon fraction in the mixture, in this example 0%. The other arguments have similar meaning as above.

Plot binary phase diagram

Finally, place in the same folder all the *.dat files from the previous simulations, Au with Si impurity, Si with Au impurity and the AuSi files for for the binary alloy with the range of compositions. you'll also need these three scripts: plot_liquid_free_energy.m, comtan.m and polyfunc.m create

Launch MATLAB and run plot_liquid_free_energy.m and you should get the binary phase diagram.

Step3

results1
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to highlitght sth