Adrianos at 11:40, 1 December 2016

2016-12-01T11:40:24Z

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	(MD++,LAMMPS,MATLAB</STRONG></font></P>		(MD++,LAMMPS,MATLAB</STRONG></font></P>
	<DIV>		<DIV>
	<P ALIGN="CENTER"><STRONG>~~Yanming Wang,~~ Adriano Santana ~~and Wei Cai~~</STRONG></P>		<P ALIGN="CENTER"><STRONG>Adriano Santana</STRONG></P>
	</DIV>		</DIV>
	<P ALIGN="CENTER"> Created ~~Nov~~, ~~2015~~</P>		<P ALIGN="CENTER"> Created Dec, 2016</P>
	<P>		<P>

			This tutorial discusses the procedure of creating, running and analyzing the data for semiconductor nanowire (NW) simulations, SiAu, GeAu etc. Here we will employ MD++ to create
	This tutorial discusses how to perform a series of simulations that generate free energy data of pure solid, solid with impurity and binary liquid alloy with different mixing ratio. Based on these data, the binary phase diagram can be obtained from common tangent construction using the free energy curves. As an example this tutorial explains how to produce the binary phase diagram for the Au-Si system.
			the structures (solid plus liquid droplet), LAMMPS to run classical MD on a cluster and MATLAB to analyze (plot) histograms, velocity growth, growth etc.

	===Pure element with impurities===		===Pure element with impurities===

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Tutorial for MD simulations of semiconductor NW (MD++,LAMMPS,MATLAB

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Tutorial for MD simulations of semiconductor NW
(MD++,LAMMPS,MATLAB
<DIV>
Yanming Wang, Adriano Santana and Wei Cai
</DIV>
 Created Nov, 2015


This tutorial discusses how to perform a series of simulations that generate free energy data of pure solid, solid with impurity and binary liquid alloy with different mixing ratio. Based on these data, the binary phase diagram can be obtained from common tangent construction using the free energy curves. As an example this tutorial explains how to produce the binary phase diagram for the Au-Si system.

===Pure element with impurities===

The first script, wcrAuSi_Solid_imp.tcl, run MC simulations and produces the free energy raw data for Au FCC lattice with Si impurities and Si DC with gold impurities. First calculate the free energy of Au-fcc crystal with a Si impurity:

<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Au1 1701 2.70
</pre>

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.

Simultaneously one can also calculate the free energy of Si-DC crystal with a gold impurity as:
<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Si4 1701 2.70
</pre>

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:

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

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'''

<pre>
results1
results2
</pre>

 '''to highlitght sth'''