斯坦福分子模拟教程

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1、ME346–IntroductiontoMolecularSimulations–StanfordUniversity–Winter2007Handout1.AnOverviewofMolecularSimulationWeiCaicAllrightsreservedSeptember26,2005Contents1Examplesofmolecularsimulations12Whatconsistsofamoleculardynamics?23Newton’sequationofmotion24Asimplenumericalintegrator:Verletalgor

2、ithm51ExamplesofmolecularsimulationsPicturesandmoviesofmodernlargescalemolecularsimulationscanbedownloadedfromthecoursewebsitehttp://micro.stanford.edu/∼me346(click“CourseMaterials”).Exam-plesincludeplasticdeformationinmetalscontainingacrack,phasetransformationinducedbyshockwaves,nano-inde

3、ntationofmetalfilm,laserablationonmetalsurface,etc.Ineachoftheseexamples,molecularsimulationsnotonlyproducebeautifulpictures,buttheyalsooffernewunderstandingonthebehaviorofmaterialsatthenano-scale.Manytimessuchunderstandingprovidesnewinsightsonhowthematerialswouldbehaveatthemicro-scaleandnan

4、o-scale.Withuniquecapabilitiestooffer,molecularsimulationhasbecomeawidelyusedtoolforscientificinvestigationthatcomplementsourtraditionalwayofdoingscience:experimentandtheory.Thepurposeofthiscourseistoprovidethefirstintroductiontomolecularlevelsimulations—howdotheywork,whatquestionscantheyansw

5、er,andhowmuchcanwetrusttheirresults—sothatthesimulationtoolsarenolongerblackboxestous.StudentswilldevelopasetofsimulationcodesinMatlabbythemselves.(AsimpleMatlabtutorialwrittenbySigmon[5]mayhelpyourefreshyourmemory.)WewillalsogivetutorialandexerciseproblemsbasedonMD++,amolecularsimulationp

6、ackageusedinmyresearchgroup.MD++willbeusedforillustrationinclassaswellastoolstosolvehomeworkproblems.12Whatconsistsofamoleculardynamics?Inamolecularsimulation,weviewmaterialsasacollectionofdiscreteatoms.TheatomsinteractbyexertingforcesoneachotherandtheyfollowtheNewton’sequationofmotion.Bas

7、edontheinteractionmodel,asimulationcomputetheatoms’trajectoriesnumerically.Thusamolecularsimulationnecessarilycontainsthefollowingingredients.•Themodelthatdescribestheinteractionbetweenatoms.Thisisusuallycalledtheinteratomicpotential:V({ri}),where{ri}represent