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Published by Philip Finlay-Bryan
It is said great opportunities seldom come twice. Google (hallowed be its name) changed one of its "o" s into a Bucky Ball which I seized or Plucked or Carped (Carpe Diem) see http://ecollegecourses.net
It is said great opportunities seldom come twice. Google (hallowed be its name) changed one of its "o" s into a Bucky Ball which I seized or Plucked or Carped (Carpe Diem) see http://ecollegecourses.net

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Categories:Types, Research
Published by: Philip Finlay-Bryan on Sep 05, 2010
Copyright:Attribution Non-commercial


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Please seehttp://eCollegeCourses.netfor animationsBlog Post Info :
Flat Fact : Carpe diem is a phrase from a Latin poem by Horace. It is popularlytranslated as "seize the day". Carpe means "pick, pluck, pluck off, gather", but Horace usedthe word to mean "enjoy, make use of".."
Enjoy, Make Use Of, Gather
For me, when I see something cool I enjoy it and then I MAKE USE OF IT! I Seize it. MyPA had logged off my account and logged in to hers. When I was back in front of mycomputer I started Google.WTF? Wow thats cool! What is it? I looked at the source of the page and it wasdescribed as a buckyball. Hmm, new to me. I did some searching and REsearching. Wowthats interesting. I should know this...did a bit more researching ....hmmm Fullerene... Great alittle vid explaining it. Right I'll seize that, so i turned it into an animation BECAUSE IKNOW HOW TO DO STUFF!! Here is the result >>>
ullerenes are a group of molecules made with only carbon atoms.These molecules exhibit veryspecial properties. The reason why scientists are interested inunderstanding the behavior of fullerenesis because they have extra ordinary properties in superconductivity,electricity and elasticity. Theycould have numerous applications to improve many of our existing productsand develop new products. There
are lots of unexplained answers regarding the behavior of fullerenes. Itis believed that makingsimulations of these molecules is the most safe and efficient approach.
Manual 01 for MD++
Introduction to MD++
Keonwook Kang and Wei CaiJanuary 10, 2007
1 Overview
MD++ is a molecular dynamics simulation package written in C++. It isoriginally developed by Wei Cai when he was a graduate student at MIT andstill being updated to include more features. MD++ is supposed to run ina Unix/Linux environment. However, if you have cygwin
, a linux-like envi-ronment installed in your Windows machine, you can also enjoy MD++ there.Currently, this code is designed mainly for studying the atomic behavior in solidcrystal materials. It can also be extended to study other systems, such as °uids,polymers and bio-molecules. This document is the ¯rst of a series of manualswritten for those new to MD simulations. These manuals explain how to useMD++ with simple examples.
2 Installation
The latest version of MD++ code can be downloaded from the web site [1],http://micro.stanford.edu/. Here we assume that the reader is familiar withbasic Unix/Linux shell commands.
Before you download MD++ code, we rec-ommend that that you make a sub-directory Codes in your home directory,$ mkdir Codes$ cd CodesSave the MD++ package in this directory (
 /Codes). Suppose the downloaded¯le is named md++-2007-01-07.tar.gz, then we can extract it by,$ tar -zxvf md++-2007-01-07.tar.gz
For download and installation, visit http://www.cygwin.com/. You must download andinstall the full package of cygwin. See http://micro.stanford.edu/ 
caiwei/Forum/2004-12-12-MD++/cygwin.html for installation instructions.
For those who are not familiar with the 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 ¯nd several good web sites that list all the shell commands.
1This command creates the MD++ sub-directory and extracts all the ¯les intoit. Go to the MD++ directory and make a runs directory if it does not exist.$ cd MD++$ mkdir runsTo compile the codes in Release mode
in a Linux system, type$ make all build=RIn a di®erent system (such as Windows), you can specify the SYS variable in theabove command line, such as,$ make all build=R SYS=cygwinprovided that cygwin is installed. You can also compile MD++ code in anApple/Machintosh computer, using$ make all SYS=mac build=RBy default SYS=gpp, which corresponds to the GNU c++ compiler. Use SYS=intelto activate the intel c/c++ compiler icc, which produces a faster executablethan gpp.After compilation, you have executable ¯les such as fs gpp, eam gpp, and sw gppin the bin directory.
If you just want to compile one executable ¯le, such asfs gpp, use$ make fs build=R
The name of each execution ¯le stands for the potential model used in the MDsimulation. For example, fs stands for the Finnis-Sinclair (FS)potential[2], ljfor the Lennard-Jones (LJ) pair potential[3], eam for the embedded-atom method(EAM) potential[4], and sw for the Stillinger-Weber (SW) potential[5, 6]. Eachpotential model is applicable to a set of atomic species. For example, the FSpotential was designed for body-centered-cubic (BCC) metals such as Mo, Ta,and W. The SW potential was designed for diamond-cubic semiconductors suchas Si and Ge. The executable md gpp does not contain any potential model.Hence it cannot be used to compute any material properties but it can still beused to display atomic structures.If you modify the source code (in the src directory), you need to recompile
If build=R, MD++ is compiled with the -O3 option. By default build=D, corresponding tothe debug mode, in which MD++ is compiled with the -g option. If build=R the executable¯les run faster but the compilation time is slightly longer than if build=D.
If SYS=cygwin, the executable ¯les would be fs cygwin.exe, eam cygwin.exe, etc.
2MD++. We recommend you to clean up the previous executables and rebuildby,$ make clean; make all build=RTo see more help on make, type$ make helpTo check if the installation and compilation is successful, try to run a scriptin the Examples directory, e.g.$ bin/fs gpp scripts/Examples/example01-mo.scriptIf you want to stop an MD++ run, press Ctrl-c or close the visualizationwindow.
3 MD++ Directories
After installation, the MD++ directory will contain the following sub-directories.$ lsbin Doc makefile potentials scripts ToolsCSD-book Examples matlab README srcThe contents in each directory is described below.src source codesbin Binary executable ¯les generated by makeDoc Manualsscripts Input script ¯les for running MD++runs Where the simulation outputs are storedpotentials Data ¯les to specify various potential modelsExamples Some example input script ¯lesTools External tools such as atomeye for visualizationmatlab Matlab codes for postprocessing
4 Script File
To execute a molecular simuation, the MD++ code reads a script ¯le whichcontains a series of commands and variable assignments for the simulation. Tocreate or modify a script ¯le in a Unix/Linux environment, you can use
, or
editor, or any of your favorite editors. For example,$ vi scripts/example01-mo.script3or$ emacs scripts/example01-mo.script &or$ nedit scripts/example01-mo.script &You can see how a script ¯le looks like by opening example script ¯le. Allscript ¯les have a common head region,# -*-shell-script-*-setnolog # No log file savedsetoverwrite # Overwrite a log filedirname = runs/mo-example # Specify output directoryThe ¯rst line tells the
editor to use the shell-script mode to displaythe ¯le. In a script ¯le, you can comment out a line or part of the line by

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