Comprehensive Nuclear Materials MD Case Studies

Revision as of 21:55, 13 March 2011

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 the Finnis-Sinclair potential model fs by typing

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

If compilation is successful, this will create binary file fs_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.

The parameters for the fs potential for several BCC metals are specified by the potential files in the ${MDPP}/potentials folder, e.g. ta_pot for Ta.

Perfect Crystal

Zero Temperature Properties

To create a perfect crystal of BCC Ta and compute its equilibrium lattice constant $a 0$ , cohesive energy $E coh$ and bulk modulus $B$ , run the following command.

cd ${MDPP}
bin/fs_gpp scripts/work/cnm_chap/ta_perfect_crystal.tcl 0

If you would like to visualize the crystal during this (short) simulation, uncomment the following lines (i.e. remove the # sign) in ta_perfect_crystal.tcl file.

 #openwindow
 #MD++ sleep

The data files of this simulation are saved in the ${MDPP}/runs/ta-perf directory. To analyze the result, use the following commands.

cd ${MDPP}/runs/ta-perf
wget http://micro.stanford.edu/mediawiki/images/2/26/Fit_a0EB.m.txt -O fit_a0EB.m
octave 
   fit_a0EB('EPOT_a_coarse.dat',1,2)
   fit_a0EB('EPOT_a_fine.dat',  1,2)

Octave should plot the potential energy of the crystal as a function of the lattice constant, and print out the fitted value for $a 0$ , $E coh$ and $B$ . When using the EPOT_a_coarse.dat file, the fitted values are: $a_0 = 3.3058 \AA$ , $E coh = - 8.1000$ eV and $B = 197.19$ GPa. When using the EPOT_a_fine.dat file, the fitted values are: $a_0 = 3.3058 \AA$ , $E coh = - 8.1000$ eV and $B = 196.14$ GPa. (This reproduces Fig.5 of our chapter.)

You can also run fit_a0EB.m in Matlab if it is installed on your computer.

To compute the other (cubic) elastic constants of BCC Ta, run the following command.

cd ${MDPP}
bin/fs_gpp scripts/work/cnm_chap/ta_perfect_crystal.tcl 0

The data are saved in the files C11_C12.dat, C44.dat in the ${MDPP}/runs/ta-perf folder. To analyze the result, use the following commands.

cd ${MDPP}/runs/ta-perf
wget http://micro.stanford.edu/mediawiki/images/1/11/Fit_C11C12C44.m.txt -O fit_C11C12C44.m
octave 
   fit_C11C12C44('C11_C12.dat','C44.dat')

Octave should plot the stress as a function of strain and print out the fitted value of the elastic constants:

Revision as of 21:55, 13 March 2011

Contents

Download files

Compile executable file

Perfect Crystal

Zero Temperature Properties

Finite Temperature Properties

Dislocation

Peierls Stress at Zero Temperature

Mobility at Finite Temperature