Revision as of 01:56, 24 November 2008

Computing Melting Point by Free Eneregy Method

Seunghwa Ryu and Wei Cai

This tutorial describes how to compute melting points from free energy methods. We provide the MD++ script files and describe how to use them in detail. The theoretical background is published in

Comparison of Thermal Properties Predicted by Interatomic Potential Models, Modelling and Simulation in Materials Science and Engineering, 16, 085005 (2008). (PDF).

Download files

First, you need to install MD++ on your computer by following the instructions on MD++ Manuals.

Second, copy files melting_cubic.tcl and melting_noncubic.tcl to your input file directory of MD++. You can do so by

 mkdir -p ~/Codes/MD++/scripts/work/melting
 cd ~/Codes/MD++/scripts/work/melting
 wget http://micro.stanford.edu/mediawiki-1.11.0/images/Melting_cubic.tcl.txt -O melting_cubic.tcl
 wget http://micro.stanford.edu/mediawiki-1.11.0/images/Melting_noncubic.tcl.txt -O melting_noncubic.tcl

Both files contain a big comment section in the beginning that describes in detail the (16) steps to compute the melting point. These steps are fully automated. In this tutorial, we describe how to run these scripts on a parallel cluster (using wcr.stanford.edu as an example) and what kind of results you should expect.

Compile excutable file

For each different potential, MD++ has corresponding excutable files. Stillinger-Weber Silicon - sw Stillinger-Weber Germanium - swge MEAM - meam-lammps, meam-baskes, meam EAM - eam Finnis-Sinclair - fs Tersoff Silicon - tersoff

For example, you can compile sworig by doing

 cd ~/Codes/MD++/
 make sworig build=R SYS=wcr

then you will have 'sworig_wcr' file in the directory '~/Codes/MD++/bin'

For other potentials, refer to the explanations in melting_cubic.tcl or email to shryu@stanford.edu for any question.

Submit jobs

Here are the PBS scripts for submitting the jobs on wcr.stanford.edu.

 cd ~/Codes/MD++/
 mkdir runs/Single_Elem_Tm
 wget http://micro.stanford.edu/mediawiki-1.11.0/images/Melt1.pbs.txt -O Melt1.pbs
 wget http://micro.stanford.edu/mediawiki-1.11.0/images/Melt2.pbs.txt -O Melt2.pbs
 qsub Melt1.pbs
 qsub Melt2.pbs

Then you'll get free energy data in ~/Codes/MD++/runs/Single_Elem_Tm/SW_Si_Solid/ ~/Codes/MD++/runs/Single_Elem_Tm/SW_Si_Liquid/

Analyse data

At the end of the calculation, data files and Matlab files will be automatically generated. Transfer these files to a location where you have Matlab installed. Run the following commands in Matlab and you will get the free energy plot (for solid and liquid phases). The melting point is the temperature at which the two free energy curves cross.

The analysis files are generated in ~/Codes/MD++/runs/Single_Elem_Tm/

Hessian_SW_Si.m Free_Energy_of_SW_Si.m tar_SW_Si

to zip necessary data

 cd ~/Codes/MD++/runs/Single_Elem_Tm
 ./tar_SW_Si

then you'll have inter_SW_Si.tar

copy this to your local computer unzip. then execute Hessian_SW_Si.m Free_Energy_of_SW_Si.m you'll see following output