计算材料学-上海交通大学

分子动力学实验SJTU.CMS.April20121.空位形成能2.表面、界面能3.层错能4.晶格常数与体弹模量5.熔化You and Your Computer你手机的计算能力，已经超越了NASA1969年拥有的计算能力的总和。NASA用那些计算能力发射人上了月球，而你用更强的计算能力发射愤怒的小鸟去砸猪。Linux分子动力学五要素1. 粒子间相互作用势2. 初始条件3. 边界条件4. 求解牛顿运动方程5. 粒子运动轨迹LAMMPSMolecularDynamicsSimulatorAtomEye:atomisticconfigurationviewerpwdpwdprintnameofworkingdirectorymkdirmkdir□hahamakedirectorycdcd□hahachangedirectorycd□..upperdirectorycdbackhomegeditgedit□aeditafilecatcat□aconcatenatefileslslslistcpcp□a□bcopyfileatofilebcp□–r□A□Bcopyafilefolderrmrm□bremove[Tab]*BasicLinuxCommandsNAMESYNOPSISDESCRIPTION1.空位形成能PointDefects:VacancyModelsystem:Cu,fcc,a0=3.61ÅTasks:1.generateapointdefectwithinanequilibriumlattice2.calculatetheformationenergyModelsystemCuInitialconditionsfcclatticedefect-freestate,vacancySupercellN,PBCsInteratomicpotentialsEAM(Cu)EnsemblesMinimize(1)Copythefilefoldertohomeandthengetintoit.$cp□-r□share/md□.$cd□md$cd□1_vacancy$ls(2)Whatisthesetupininputfile$gedit□in.vacancy(3)RunLAMMPS$lmp□-in□in.vacancy(4)Afterrunning,viewtheconfiguration$A.i686□a0.cfg(5)Viewtheresultdata$cat□dataTab键切换视角k,Alt+H,Alt++/-改变颜色Delete/Insert下一帧/上一帧PgUp/PgDn原子变大/变小滚轮放大/缩小↑↓←→方向键旋转q关闭Atomeye命令unitsmetalboundarypppatom_styleatomiclatticefcc3.61regionboxblock060606create_box1boxcreate_atoms1boxpair_styleeam/alloypair_coeff**jin_copper_lammps.setflCutimestep0.005variableEequalpevariableNequalatomscomputepeallpe/atomdump1allcfg1a*.cfgidtypexsyszsc_perun0fixextraallprint1pefectlattice,0K:atoms=$N,energy=$E“regioncenterpointblock33.0533.0511.05delete_atomsregioncenterpointrun0fixextraallprint1^anatomdeleted,0K:atoms=$N,energy=$E周期边界条件指定fcc晶体box大小Cu的EAM势删除一个原子Vacancyformationenergy：1pefectlattice,0K:atoms=864,energy=-3015.3715122anatomdeleted,0K:atoms=863,energy=-3010.5854693afterminimization:atoms=863,energy=-3010.6240332.表面、界面能PlanarDefects:SurfaceandGrainBoundaryModelsystem:Cu,fcc,a0=3.610ÅTasks:1.Surfaceenergiesof(111)and(100);2.GrainboundaryenergiesModelsystemCuInitialconditionsT,P…SupercellN,PBCs…InteratomicpotentialsEAM(Cu)EnsemblesMinimizeSurfaceenergy:Methodperfectregionvacuum2surfacesN0atoms,E0Natoms,EγS=(E–E0*N/N0)/(2*A)h1h3h2(111)Surface:h1=a0/2[11-2]*L1;h2=a0/2[-110]*L2;h3=a0[111]*L3(100)Surface:h1=a0[100]*L1;h2=a0[010]*L2;h3=a0[001]*L3Surfaceenergy:Calculationsperfect:N0=123772,E0=–431965.9291eV(111):NS1=124722,ES1=–434642.1217eV,AS1=39.792*104.659Å2(100):NS2=123772,ES2=–431275.1878eV,AS2=39.71*104.69Å2γS1=(ES1–E0*NS1/N0)*16020/(2*AS1)=1230mJ/m2γS2=(ES2–E0*NS2/N0)*16020/(2*AS2)=1331mJ/m2GrainboundaryenergyS1:(111)γGB=(E–E0*N/N0)/A–γS1–γS2h3region2vacuumh1h2region1S2:(100)GBGB+S1+S2:N=248494,E=–866449.3465eV,A=39.755*104.677Å2γGB=(E–E0*N/N0)*16020/A–γS1–γS2=512mJ/m2a1a2a3a1a2a3region1:a1=a0/2[11-2];a2=a0/2[-110];a3=a0[111]region2:a1=a0[100];a2=a0[010];a3=a0[001](1)Changeintothe2nddirectory$cd□../2_surface_boundary$ls(2)Whatisthecommandsinbashfile$cat□run.sh(3)Runbashfile$./run.sh(4)Afterrunning,viewtheconfiguration$A.i686□a0.cfg#!/bin/bashlmp in.100 ‐log log.100lmp in.111 ‐log log.111lmp in.GB ‐log log.GBecho %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%echo  echo ‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐(100) ‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐grep^^ log.100echo  echo ‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐(111) ‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐grep^^ log.111echo  echo ‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐GB  ‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐grep^^ log.GBecho  echo %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%run.sh%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐(100) ‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐^‐‐‐Number of Particles = 11520, Energy  = ‐40204.95349^‐‐‐Number of Particles = 8640, Energy  = ‐30075.76547^‐‐‐Size of (100):            A = 469.1556‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐(111) ‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐^‐‐‐Number of Particles = 46080, Energy  = ‐160819.814^‐‐‐Number of Particles = 34560, Energy  = ‐120448.5379^‐‐‐Size of (111):            A = 1083.468448‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐GB  ‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐^‐‐‐Number of Particles = 248494, Energy  = ‐866449.3465^‐‐‐Size of GB x*y:           A = 4161.446533%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%γS=(E–E0*N/N0)/(2*A)Surfaceenergy：(111)surface(100)surfaceTab键切换视角k,Alt+H,Alt++/-改变颜色Delete/Insert下一帧/上一帧PgUp/PgDn原子变大/变小滚轮放大/缩小↑↓←→方向键旋转q关闭Atomeye命令h1h2h3region1region2vacuum56units56unitsbox150units4Grainboundary4.1Modela1a2a3Unitcellregion1:a1=a0/2[11-2];a2=a0/2[-110];a3=a0[111]h1=9*a1;h2=41*a2;h3=56*a3region2:a1=a0[100];a2=a0[010];a3=a0[001]h1=11*a1;h2=29*a2;h3=97*a3S1S2GBGrainboundary3.层错能2High Tensile Strength and Ductility of Cu with Nano‐Sized TwinsLuetal.,Science287(2000)1463;304(2004)422.dislocationfluxtwininexperimentstwinboundary89×118×77Å56,400atomstwininCuTwinfaultsintrinsicstackingfaultExtrinsicstackingfaultISFESFTSFplanarfaultinFCCfreesurfaceESFExtrinsicstackingfault(ESF)freesurfacePlanarDefects:StackingFaultEnergyModelsystem:Cu,Al,fccTasks:(1)clarifythreetypesofplanarfaultsinfccmetals(2)calculatestackingfaultenergies(3)compare:AlandCuModelsystemCu,AlInitialconditionsT,P…SupercellN,PBCs…InteratomicpotentialsEAMEnsemblesMinimizeunitsmetalboundarypppatom_styleatomicread_dataisf-Cu#读取其他文件中的构型pair_styleeam/alloypair_coeff**jin_copper_lammps.setflCutimestep0.0