Comprehensive Nuclear Materials MD Case Studies

Comprehensive Nuclear Materials - Modelling Section (R. Stoller, Editor)

Case Studies for Chapter 128 Molecular Dynamics

Wei Cai, Ju Li and Sidney Yip

This tutorial describes how to reproduce the case studies on crystals and dislocations described in Comprehensive Nuclear Materials, Chapter 128 Molecular Dynamics. We provide the MD++ script files and describe how to use them in detail.

---

Download files

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

Second, copy files ta_perfect_crystal.tcl and ta_edge_dislocation.tcl to your input file directory of MD++. You can do so by the following commands (assuming you have installed MD++ in ~/Codes/MD++).

 export MDPP=~/Codes/MD++
 mkdir -p ${MDPP}/scripts/work/cnm_chapter
 cd ${MDPP}/scripts/work/cnm_chapter
 wget http://micro.stanford.edu/mediawiki/images/0/08/Ta_perfect_crystal.tcl.txt -O ta_perfect_crystal.tcl
 wget http://micro.stanford.edu/mediawiki/images/4/4a/Ta_edge_dislocation.tcl.txt -O ta_edge_dislocation.tcl

Both files contain a comment section in the beginning that describes in detail the various options to reproduce various steps of the case studies. In this tutorial, we describe how to run these scripts and what kind of results you should expect.

Compile executable file

Different executables in MD++ contains different interatomic potentials, for example,

sw                  - Stillinger-Weber Silicon (modified by Balamane et al.)
sworig              - Original version of SW Silicon
swge                - Stillinger-Weber Germanium
tersoff             - Tersoff potential for Silicon
meam-lammps         - MEAM (taken from lammps)
meam-baskes         - MEAM (taken from Baskes's code dynamo)
meam                - MEAM (directly implemented in MD++)
eam                 - Embedded Atom Method 
fs                  - Finnis-Sinclair

In this tutorial, we compile eam by typing

 cd ${MDPP}
 make eam build=R SYS=gpp

If compilation is successful, this will create binary file eam_gpp file in your ${MDPP}/bin directory. If you would like to use the intel compiler, you should use SYS=intel in the make command. To compile MD++ on a Mac, use SYS=mac.