Use Au-Si MEAM Potential in LAMMPS: Difference between revisions

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=== Preparing for compiling MEAM potential ===
=== Preparing for compiling MEAM potential ===


Au-Si MEAM potential is a potential developed by Dr. Seunghwa Ryu and Prof. Wei Cai<ref>[http://iopscience.iop.org/0953-8984/22/5/055401]</ref><ref>http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8368065
Au-Si MEAM potential is a potential developed by Dr. Seunghwa Ryu and Prof. Wei Cai<ref>
[http://iopscience.iop.org/0953-8984/22/5/055401 Seunghwa Ryu and Wei Cai, "Molecular Dynamics Simulations of Gold-Catalyzed Growth of Silicon Bulk Crystals and Nanowires", Journal of Materials Research, 26, 2199 (2011).]</ref><ref>[http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8368065 Seunghwa Ryu and Wei Cai, "A Gold-Silicon Potential Fitted to the Binary Phase Diagram", Journal of Physics Condensed Matter, 22, 055401 (2010).]
</ref>for gold-silicon binary system. To compile this potential in LAMMPS, you need to open the Makefile file under the '''LAMMPS.svn''' directory, finding the following line
</ref>for gold-silicon binary system. To compile this potential in LAMMPS, you need to open the Makefile file under the '''LAMMPS.svn''' directory, finding the following line

Revision as of 07:53, 21 June 2012

Use Au-Si MEAM Potential in LAMMPS

Yanming wang, Seunghwa Ryu and Wei Cai

June, 2012

This tutorial explains how to use Au-Si MEAM potential in LAMMPS on a cluster like mc2. It starts with the installation of LAMMPS on mc2, then talks about the compiling of the Au-Si MEAM potential. This tutorial also includes a test case to make sure the result from LAMMPS with this MEAM potential is consistent with that from MD++.

Installing LAMMPS on mc2

LAMMPS is a classical molecular dynamics code for large-scale atomic/molecular massively parallel simulation. On mc2, you can get LAMMPS from our SVN server using the following commands. 

mkdir Codes
cd Codes
mkdir LAMMPS.svn
cd LAMMPS.svn
svn co https://micro.stanford.edu/svn/LAMMPS/ ./

Typing the following SVN command from within the "LAMMPS.svn" directory, you can update your LAMMPS package. 

svn update

Compiling MEAM potential in LAMMPS

Preparing for parallel run

First, you need to download the fftw.tar.gz and upload this archive file to your account on mc2. In your home directory, make a new folder named usr, then type the following command to unzip the fftw library in your usr folder. 

cd ~usr/
tar -zxvf fftw.tar.gz

ALso add the following lines at the end of your ~/.bash_profile file to clarify the compiler. 

module load intel/intel-11
module load mvapich/1.2rc1-intel-11-dell-gen2

Preparing for compiling MEAM potential

Au-Si MEAM potential is a potential developed by Dr. Seunghwa Ryu and Prof. Wei Cai[1][2]for gold-silicon binary system. To compile this potential in LAMMPS, you need to open the Makefile file under the LAMMPS.svn directory, finding the following line 

cd lib/meam;  make -f Makefile.$(libFC.$(SYS)) F90FLAGS="-O -D_EROSE_FUNCTION=1"

and replace it with 

cd lib/meam;  make -f Makefile.$(libFC.$(SYS)) F90FLAGS="-O -D_EROSE_FUNCTION=3"

Next, in the ~/.bash_profile file, add the following line to specify the system you are using. 

export TARGET=mc2

Finally, go to LAMMPS.svn directory and type 

make

This will make lmp_mc2 in LAMMPS.svn/src/ directory.

  1. ↑ Seunghwa Ryu and Wei Cai, "Molecular Dynamics Simulations of Gold-Catalyzed Growth of Silicon Bulk Crystals and Nanowires", Journal of Materials Research, 26, 2199 (2011).
  2. ↑ Seunghwa Ryu and Wei Cai, "A Gold-Silicon Potential Fitted to the Binary Phase Diagram", Journal of Physics Condensed Matter, 22, 055401 (2010).
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