Manual 01 for MD++
Introduction to MD++
Keonwook Kang and Wei Cai
Contents |
Overview
MD++ is a molecular dynamics simulation package written in C++. It is originally developed by Wei Cai when he was a graduate student at MIT and still being updated to include more features. MD++ is supposed to run in a Unix/Linux environment. However, if you have cygwin,<ref>For download and installation, visit http://www.cygwin.com/. You must download and install the full package of cygwin. See http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/cygwin.html for installation instructions.</ref> a linux-like environment installed in your Windows machine, you can also enjoy MD++ there. Currently, this code is designed mainly for studying the atomic behavior in solid crystal materials. It can also be extended to study other systems, such as fluids, polymers and bio-molecules. This document is the first of a series of manuals written for those new to MD simulations. These manuals explain how to use MD++ with simple examples.
Installation
The latest version of MD++ code can be downloaded from the web site,
http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/.
Here we assume that the reader is familiar with basic Unix/Linux shell
commands.<ref>For those who are not familiar with Unix/Linux
environment, we suggest the book A practical guide to Linux
commands, editors and shell programming by Mark G. Sobell. You can
also easily find several good web sties about the shell
commands.</ref> Before you download MD++ code, we recommend
that you make a sub-directory Codes in your home directory.
$ mkdir Codes $ cd Codes
Save the MD++ package in this directory(~/Codes). Suppose the downloaded file is md++-2007-01-07.tar.gz, then we can extract it by,
$ tar -zxvf md++-2007-01-07.tar.gz
This command creates the MD++ sub-directory and extracts all the files into it. Go to the MD++ directory and make a runs directory if it does not exist.
$ cd MD++; mkdir runs
To compile the codes in release(R) mode <ref>If build=R, MD++ is compiled with the -O3 option. By default(build=D), MD++ compiles as debug mode with the -g option. In release mode, the executabale files run faster but the compilation time is slightly longer than debug mode</ref> in a Linux system, type
$ make all build=R
In order to compile MD++ In a different system (such as Windows), you can specify the SYS variable in the command line, such as
$ make all build=R SYS=cygwin
provided that cygwin is installed. You can also compile MD++ code in an Apple/Machintosh computer, using
$ make all SYS=mac build=R
By default, SYS=gpp which corresponds to the GNU c++ compiler. If you have the intel c/c++ compiler icc in your system, use SYS=intel to activate icc, which produces much faster executables than GNU c++ compiler. For more SYS values, take a look at the file ~/Codes/MD++/src/Makefie.base. You may get an TCL-related error during compilation. You can bypass this error using, e.g.
$make SYS=cygwin TCL=no
by suppressing TCL option. After compilation, you have executable files such as fs_gpp, eam_gpp, and sw_gpp in the bin directory.<ref>If you use SYS=cygwin, the executable files would be fs_cygwin.exe, eam_cygwin.exe, etc.</ref> If you just want to compile one executable file, such as fs_gpp, use
$ make fs build=R
The name of each execution file stands for the potential model that will be used in the atomisitic simulation. For example, fs stands for the Finnis-Sinclair (FS) potential<ref>M. W. Finnis and J. E. Sinclair, Philos. Mag. A. 50 45 (1984)</ref> , lj for the Lennard-Jones (LJ) pair potential,<ref>J. E. Lennard-Jones, "Cohesion" Proceedings of the Physical Society 43 461-482 (1931)</ref> eam for the embedded-atom method (EAM) potential,<ref>M. S. Daw and M. I. Baskes, "Embedded-atom method: Derivation and application to impurities, surfaces, and
other defects in metals", Phys. Rev. B 29 6443 (1984)</ref> and sw
for the Stillinger-Weber (SW) potential.<ref>F. H. Stillinger and T. A. Weber, "Computer simulation of local order in condensed phases of silicon", Phys. Rev. B 31 5262 (1985)</ref><ref>H. Balamane, T. Halicioglu, and W. A. Tiller, "Comparative study of silicon empirical interatomic potentials", Phys. Rev. B 46 2250 (1992)</ref> Each potential model is applicable to a group of atomic species. For example, the FS potential was designed for body-centered-cubic (BCC) metals such as Mo, Ta and W. The SW potential was designed for diamond-cubic semiconductors such as Si and Ge. By the way, the executable md_gpp does not contain any potential model. Hence it cannot be used to compute any material properties but it can still be used to display atomic structures.
If you modify the source code (in the src directory), you need to recompile MD++. we recommend you to clean the previous executables and rebuild by typing,
$ make clean; make all build=R
To see more help on make, type
$ make help
To check if you successfully install and compile MD++, try to run one of example scripts in the Examples directory, e.g.
$ bin/fs_gpp scripts/Examples/example01-mo.script
If you want to stop MD++ running, press ctrl+c or close the visualization window.
MD++ Directories
Script File
Visualization Window Control
Bibliography
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