VASP经典学习教程-有用

1、VASP学习教程XX理工大学量子化学课题组2012/5/25第一章Linux命令11.1 常用命令11.1.1 浏览目录11.1.2 浏览文件11.1.3 目录操作11.1.4 文件操作11.1.5 系统信息1第二章SSH软件使用22.1 软件界面22.2 SSHtransfer的应用32.2.1 文件传输32.2.2 简单应用3第三章VASP的四个输入文件33.1 INCAR33.2 KPOINTS53.3 POSCAR53.4 POTCAR7第四章实例74.1 模型的构建74.2 VASP计算104.2.1 参数测试114.2.2 晶胞优化（Cu）184.2.3 Cu（100外表的能量19

2、4.2.4 吸附分子CO、H、CHO的构造优化214.2.5 CO吸附于Cu100外表H位244.2.6 H吸附于Cu100外表H位264.2.7 CHO吸附于Cu100外表B位284.2.8 CO和H共吸附于Cu100外表294.2.9 过渡态计算31第一章Linux命令1.1 常用命令1.1.1 浏览目录cd:进入某个目录。如：cd/home/songluzhi/vasp/CH4cd.上一层目录；cd/根目录；ls:显示目录下的文件。注：输入目录名时，可只输入前3个字母，按Tab键补全。1.1.2 浏览文件cat:显示文件内容。如：catINCAR如果文件较大，可用：catINCAR|mo

3、re（可以按上下键查看）合并文件：catAB>C（A和B的内容合并，A在前，B在后）1.1.3 目录操作mkdir：建立目录；rmdir：删除目录。如：mkdirT-CH3-Rh1111.1.4 文件操作rm：删除文件；vi:编辑文件；cp：拷贝文件mv:移动文件；pwd:显示当前路径。如：rmINCARrma*（删除以a开头的所有文件）rm-rfabc（强制删除文件abc）tar：解压缩文件。压缩文件？rardf:分区占用大小。如：df-hdu:各级目录的大小。top：运行的任务。psax查看详细任务。kill:杀死任务。如：kill12058杀死PID为12058的任务注：PID为t

4、op命令的第一列数字。第二章SSH软件使用2.1软件界面SSH界面SSHtransfer2.2SSHtransfe的应用1.1 .1文件传输从本地文件中，把所需的计算文件直接拖到效劳器中。一般就是VASP计算的四个文件INCAR,KPOINTS,POSCAR,POTCAR。1.2 .2简单应用在右侧文件夹中可以直接构建文件夹，删除文件，修改文件。从SSH要cd到某个文件夹下时，可先从SSHtransfer®入，直接复制路径栏，可快速进入。第三章VASP的四个输入文件3.1INCARSYSTEM=nameENCUT = 400PREC = MediumEDIFF = 5E-4EDIFF

5、G = -0.1GGA = 91VOSKWN = 1ISYM = 0LREAL = .FALSE.ISPIN = 2ISTART = 0ICHARG = 2ISMEAR = 2SIGMA = 0.1IBRION = 2ISIF = 2NSW = 200POTIM = 0.05NELMIN = 4NELM = 200LWAVE = .FALSE.!磁性计算!对称0无1有!倒空间!2磁性计算1不进展!0初次计算，1再次计算!2构造原子密度!-5半导体；DOS静态计算0;原胞较大，k点小于4，单个原子，小分子；12金属体系。!1DIIS,2CG,5频率，3过渡态!2构造优化，3晶胞优化!离子运动步数

6、!步长!最小迭代次数!最多迭代次数!不输出波函数LCHARG=.FALSE.!不输出密度函数1.3 KPOINTS对于外表surface0M551000对于分子和原子atomormolcular1Rec00011.4 POSCARCH4在Co10O表Top位的吸附！（名称）1.05.01200008390.00000000000.00000000000.00000000005.01200008390.00000000000.00000000000.000000000015.3159999847CoHC164SDirect0.0000000000.0000000000.108070001TTT0

7、.0000000000.0000000000.333149999TTT0.2500000000.2500000000.000000000FFF0.2500100140.2500000000.225119993TTT0.5000000000.0000000000.108060002TTT0.5000000000.0000000000.333149999TTT0.7500000000.2500000000.000000000FFF0.7499899860.2500000000.225119993TTT0.0000000000.5000000000.108070001TTT0.0000000000.

8、5000000000.333139986TTT0.2500000000.7500000000.000000000FFF0.2500100140.7500000000.225130007TTT0.5000000000.5000000000.108070001TTT0.5000000000.5000000000.333149999TTT0.7500000000.7500000000.000000000FFF0.7499899860.7500000000.225119993TTT0.5000799890.5014299750.451510012TTT0.2928200070.5022199750.5

9、46630025TTT0.6018900280.6809200050.546850026TTT0.6020900010.3238700030.547209978TTT0.4992400110.5021299720.523060024TTT1.5 POTCAR从鹰势库中找到所需元素的鹰势文件，命名规那么为：POTCAR-C(元素)。把这几个文件放到一个文件夹下，按照前面POSCAR中的元素顺序合并在一起。命令为：catPOTCAR-CoPOTCAR-HPOTCAR-C>POTCAR第四章实例CO+HCHOCu(100)4.1 模型的构建过程：首先通过MS构建好所需模型，导出为*.cif格式

10、；导入到Vesta程序中，输出为*vaspo根据前面所讲的POSCAR格式修改，得到所需文件。图解：1 .创立MS文件：2.导入Cu晶胞3 ： import Demil me nt回同 «tp Cu强找南国CD.最后近可丽应点面害能W 二 mEi trcjl.msi j算匚r,mi 国NmH20LD/P/22 872010/9/22 8072010/5/2.2 8i72010/22 8l27.E£lIt si2010/*/：2Sl：72O1D/S/2287WQLQ倒葭8邛7?0L0/t/j;R：272010/5/22627Ld.msi2O1O/Q/2287剧|i文件名四：&

11、#39;|打开里京"小型Ct)|c01mg第Mnmiirtic1FM写作f诂：素art.取者军茹西|口eurwrt;7Mt*hrpomd*0米垢丁也用卬口叩仍旧3 .导出为Cif格式翻开File-export,保存类型为*.cif,保存在指定位置4 .通过Vesta导出为*.vasp直接把Cu.cif拖至Uvest刑序中，翻开File-ExportData.,保存类型为*vasp,保存在指定位置。"ExportData爵i，苣机(D：j卜.5.用写字板翻开Cu.vasp根据所需要求修改Cu.vasp这里不需要修改。在吸附外表时那么需要固定,见33CIFfile1.03.61

12、470007900.00000000000.0000000000Cu4Direct0.0000000000.0000000000.5000000000.5000000000.00000000003.61470007900.00000000000.00000000000.00000000003.61470007904.2VASP计算0.0000000000.5000000000.0000000000.5000000000.0000000000.5000000000.5000000000.0000000004.2.1参数测试VASP参数设置这里给出了鹰势、ENCUF、K点、SIMGA一共四个参数。

13、是都要验证吗？还是只要验证其中一些？一、检验赝势的好坏：赝势的好坏这里是特意举例铜原子的吧？还是算铜的晶胞时只用算一下一个铜原子的就行?一方法：对单个原子进展计算；二要求：1、对称性和自旋极化均采用默认值；2、 ENCUT要足够大；3、 原胞的大小要足够大，一般设置为15?足矣，对某些元素还可以取得更小一些。三以计算单个Cu原子为例：1、INCAR文件：SYSTEM=CuatomENCUT=450.00eVNELMDL=5ISMEAR=0SIGMA=0.12、POSCAR文件：atom10.001.000.000.000.001.000.000.000.001.00Cu1Direct0.50.

14、50.53、 KPOINTS文件：Automatic0Gamma1110004、 POTCAR文件：略四计算任务执行方法：输入：mpirun-np4vasp>log&五势好的判断标准：计算得到的OUTCAR文件中的“energywithoutentropy"能量值在-0.001-0.01eV之间。命令：grep'energywithoutentropy'OUTCAR|tail-1计算结果为：root249FP#grep'energywithoutentropy*OUICARItall-1energywithoutentropy三-0.0045S6

15、4Senergy(sigma->0)=-0.02042430rootncd«249EPt|二、筛选适宜的ENCUT大小：一输入文件：1、用脚本程序optencut.sh代替INCAR文件：rmWAVECARforiin300350400450500docat>INCAR<<!SYSTEM=CuENCUT=$iGGA=91ISTART=0;ICHARG=2ISMEAR=-5PREC=Accurate!echo"ENCUT=$ieV"timempirun-np2vasp>log&E=$(grep"TOTEN"O

16、UTCAR|tail-1|awk'printf"%12.6fn",$5')echo$i$E>>mentdone注：每个任务2核，5个截断能，共要1眼。2、POSCAR文件:Cucell1.03.61470007900.00000000000.00000000000.00000000000.0000000000Cu4Direct0.0000000000.0000000000.5000000000.5000000003.61470007900.00000000000.00000000003.61470007900.0000000000.5000000

17、000.0000000000.5000000000.0000000000.5000000000.5000000000.0000000003KPOINTS文件：0M8880.00.00.04POTCAR文件：略二计算任务执行方法：输入：dos2unixoptencut.shbashoptencut.sh三判别标准：计算完成后得到ment文件，它列出了在每个ENCUT时计算得到的相应的总能，只要总能变化在0.001eV左右就足够三、选择适宜的k点数目:一输入文件:1、INCAR文件：SYSTEM=CuENCUT=450.00eVISTART=0;ICHARG=2ISMEAR=-5PREC=Accu

18、rate2、POSCAR文件：Cu1.00.00000000003.61470007900.00000000000.00000000000.00000000003.61470007903.61470007900.00000000000.0000000000Cu4Direct0.0000000000.0000000000.0000000000.5000000000.5000000000.5000000000.0000000000.5000000000.0000000000.5000000000.5000000000.0000000003、用脚本程序optkpoints.sh代替KPOINTS文件

19、:rmWAVECARforiin678910docat>KPOINTS<<!Automaticgeneration0Monkhorst-pack$i$i$i0.00.00.0echo"kmesh=$ix$ix$i"timempirun-np8vasp>log&E=$(grep"TOTEN"OUTCAR|tail-1|awk'printf"%12.6fn",$5')KP=$(grep"irreducible"OUTCAR|tail-1|awk'printf&qu

20、ot;%5in",$2')echo$i$KP$E>>mentdone4、 POTCAR文件：略二计算任务执行方法：输入：dos2unixoptkpoints.shbashoptkpoints.sh三判别标准：计算完成后得到ment文件，它列出了在k点数目与总能的对应值，只要总能变化在0.001eV左右就非常足够了。四、优化选择适宜的SIGMA值展宽值：一为什么要优化SIGMA值？假设展宽6太小，那么计算难以收敛；假设展宽6太大，那么会产生多余的嫡(entropy),因此必须选择适宜的o值。(Toolargesmearing-parametersmightresul

21、tinawrongtotalenergy,smallsmearingparametersrequirealargek-pointmesh.)二ISMEAR和SIGMA：1、 ISMEAR和SIGMA这两个关键词要联合起来使用，前者用来指定smearing的方法，后者用来指定smearing展宽o值。2、 ISMEAR和SIGMA的默认值分别为1和0.2。3、 ISMEAR可能的取值为-5，-4，-3，-2，-1，0，N(N表示正整数)：ISMEAR=-5,表示采用Blochl修正的四面体方法；ISMEAR=-4,表示采用四面体方法，但是没有Blochl修正；ISMEAR=-1,表示采用Ferm

22、i-Diracsmearing法；ISMEAR=0,表示采用Gaussiansmearing?法；ISMEAR=N,表示采用Methfessel-Paxtonsmearing法，其中N是表示此方法中的阶数，一般情况下N取1或2,但是InmostcasesIand:-:_:;.leadstoverysimilarresults。4、(T值一般在0.10.3eVX围内。5、ISMEAR取值的一些经历：1一般说来，无论是对何种体系，进展何种性质的计算，采用ISMEAR=0并选择一个适宜的SIGMA值，都能得到合理的结果。2在进展静态计算能量单点计算，norelaxationinmetals或态密度计

23、算且k点数目大于4时，取ISMEAR=-5。3当原胞较大而k点数目较小小于4个时，取ISMEAR=0,并选择一个适宜的SIGMA值。(Ifthecellistoolarge(orifyouuseonlyasingleortwok-points)useISMEAR=0inbinationwithasmallSIGMA=0.05)4对半导体或绝缘体，不管是静态还是构造优化计算，都取ISMEAR=-5。(Mind:AvoidtouseISMEAR>0forsemiconductorsandinsulators,sinceitmightcauseproblems.Forinsulatorsuse

24、ISMEAR=0orISMEAR=-5.)5对金属体系(forrelaxationsinmetal$,取ISMEAR=1或2,并选择一个适宜的SIGMA值。三当采用ISMEAR=0或N时，如何优化选择适宜的SIGMA值？1、用脚本程序optsigma.shrf弋替INCAR文件：rmWAVECARforiin0.100.120.140.160.180.200.220.240.260.280.30docat>INCAR<<!SYSTEM=bccFeENCUT=450GGA=91ISTART=0;ICHARG=2ISMEAR=0;SIGMA=$iPREC=Accurateecho

25、"SIGMA=$ieV"timevaspTS=$(grep"EENTRO"OUTCAR|tail-1|awk'printf"%12.6fn",$5')echo$i$TS>>mentdone2、POSCAR文件:Cu1.03.61470007900.00000000000.0000000000Cu0.00000000003.61470007900.00000000000.00000000000.00000000003.61470007904Direct0.0000000000.0000000000.00000

26、00000.0000000000.5000000000.5000000000.5000000000.0000000000.5000000000.5000000000.5000000000.0000000003KPOINTS文件：M9990.00.00.04POTCAR文件：略四计算任务执行方法：输入：dos2unixoptsigma.shbashoptsigma.sh五判断标准：嫡（entropy）越小越好，选择entropyT*SEENTRO值中最小的那个所对应的SIGMAo(SIGMAshouldbeaslargeaspossiblekeepingthedifferencebetweent

27、hefreeenergyandthetotalenergy(i.e.theterm'entropyT*S')intheOUTCARfilenegligible(1meV/atom).)五注意：1、当k点的数目发生变化后，要重新优化选择SIGMA值。4.2.2晶胞优化(Cu)INCARSYSTEM=nameENCUT=400PREC=MediumEDIFF=5E-6EDIFFG=-0.01GGA=91ISYM=1LREAL=.FALSE.POSCARCu1.0ISTART=0ICHARG=2INIWAV=1ISMEAR=2SIGMA=0.1IBRION=2ISIF=3NSW=20

28、0POTIM=0.5NELMIN=4NELM=200NELMDL=-5ALGO=FLWAVE=.FALSE.LCHARG=.FALSE.3.61470007900.00000000000.00000000000.00000000003.61470007900.00000000000.00000000000.00000000003.6147000790CuDirect0.0000000000.0000000000.5000000000.5000000000.0000000000.5000000000.0000000000.5000000000.0000000000.5000000000.5000

29、000000.000000000KPOINTSCucell0M888000POTCAR略命令：mpirun-np8vasp>log&计算结果：查看CONTCAR,获取晶胞参数a=b=c=3.629误差=0.4%注：优化后的构造为CONTCAR,导出保存为*.vasp,通过Vesta翻开输出为.cif格式的文件，可用MS翻开。4.2.3 Cu(10g卜表的能量从MS构建模型，直到获得POSCAR。INCARSYSTEM = Cu100ENCUT = 400PREC = MediumEDIFF = 5E-6EDIFFG = -0.01GGA = 91LREAL = .FALSE.旧R

30、ION = 2NELM= 200ISTART = 0ICHARG = 2ISMEAR = 2SIGMA = 0.1POSCARISIF = 2NSW = 200POTIM = 0.5NELMIN = 4LWAVE = .FALSE.LCHARG = .FALSE.CIFfile1.05.11199998860.00000000000.0000000000Cu16SDirect0.0000000000.0000000000.2500000000.2500000000.5000000000.5000000000.7500000000.00000000005.11199998860.00000000

31、000.00000000000.000000000015.42210006710.0000000000.0000000000.2500000000.2500000000.0000000000.0000000000.2500000000.117190003 T T T0.351579994 T T T0.000000000 F F F0.234390005 T T T0.117190003 T T T0.351579994 T T T0.000000000F F F0.7500000000.2500000000.234390005TTT0.0000000000.5000000000.117190

32、003TTT0.0000000000.5000000000.351579994TTT0.2500000000.7500000000.000000000FFF0.2500000000.7500000000.234390005TTT0.5000000000.5000000000.117190003TTT0.5000000000.5000000000.351579994TTT0.7500000000.7500000000.000000000FFF0.7500000000.7500000000.234390005TTTKPOINTS（略）5x5x2POTCAR（略）命令：mpirun-np8vasp&

33、gt;log&grep'energywithoutentropy'OUTCAR|tail-1计算结果：ECu100=-54.891221eV4.2.4 吸附分子CO、H、CHO的构造优化ISTART= 0ICHARG= 2ISMEAR = 0SIGMA= 0.1CO的构造优化：INACARSYSTEM=nameENCUT=400PREC=MediumEDIFF=5E-6EDIFFG=-0.01GGA=91ISYM=0LREAL=.FALSE.ISIF=2NSW=200KPOINTSCO1R0001POSCARCIFfile1.010.00000000000.000000

34、00000.0000000000CO11Direct0.5147899990.514889956POTCAR略NELMIN=4NELM=200LCHARG=.FALSE.0.000000000010.00000000000.00000000000.00000000000.000000000010.00000000000.5577999950.4073899980.4678100050.481169999命令：mpirun-np8vasp>log&grep'energywithoutentropy'OUTCAR|tail-1CHO的优化：POSCARCHO1.010

35、.00.00.00.010.00.00.00.010.0COH111Direct0.4427099820.4480299950.5285999770.4182699920.5970399980.5284299850.5493600370.4077599940.528409958其他同上，POTCAR顺序C-O-H。命令：mpirun-np8vasp>log&grep'energywithoutentropy'OUTCAR|tail-1计算结果：Echo=-16.718H的能量:POSCARCIFfile1.00.000000000010.00000000000.0

36、0000000000.00000000000.000000000010.0000000000Direct0.4765400290.5278699990.510450006命令：mpirun-np8vasp>log&grepTOTENOUTCAR|tail-1注：单原子能量。计算结果：Eh=-0.056eV4.2.5 CO吸附于Cu100外表H位INCARSYSTEM = nameENCUT= 400PREC= MediumEDIFF= 5E-6EDIFFG = -0.01GGA= 91ISYM= 0KPOINTS 5 5 2POSCARLREAL= .FALSE.ISTART=

37、0ICHARG = 2ISMEAR = 2SIGMA= 0.1IBRION = 2ISIF= 2NSW= 200POTIM= 0.5NELMIN = 4NELM= 200LWAVE= .FALSE.LCHARG= .FALSE.CO-H-Cu1005.11199998860.00000000000.00000000000.00000000005.11199998860.00000000000.00000000000.000000000015.4221000671CuCO1611SDirect0.0000000000.0000000000.351579994TTT0.2500000000.250

38、0000000.000000000FFF0.2500000000.2500000000.234390005TTT0.5000000000.0000000000.117190003TTT0.5000000000.0000000000.351579994TTT0.7500000000.2500000000.000000000FFF0.7500000000.2500000000.234390005TTT0.0000000000.5000000000.117190003TTT0.0000000000.5000000000.351579994TTT0.2500000000.7500000000.0000

39、00000FFF0.2500000000.7500000000.234390005TTT0.5000000000.5000000000.117190003TTT0.5000000000.5000000000.351579994TTT0.0000000000.0000000000.117190003TTT0.7500000000.2496500020.2494499980.7500000000.7553900480.7589099410.234390005 T T T0.439150006 T T T0.513199985 T T TPOTCAR按照Cu-C-O的顺序合并。命令：mpirun-n

40、p8vasp>log&grep'energywithoutentropy'OUTCAR|tail-1计算结果：E总=-70.528eVEads=0.808eV426H吸附于Cu100外表H位INCAR(同4.2.5)KPOINTS(552)POSCARH-H-Cu1000.00000000005.11199998860.00000000000.00000000000.000000000015.42210006711.05.11199998860.00000000000.0000000000CuH161SDirect0.0000000000.0000000000.0

41、000000000.351579994TTT0.2500000000.2500000000.000000000FFF0.2500000000.2500000000.234390005TTT0.5000000000.0000000000.117190003TTT0.5000000000.0000000000.351579994TTT0.7500000000.2500000000.000000000FFF0.7500000000.2500000000.234390005TTT0.0000000000.5000000000.117190003TTT0.0000000000.5000000000.35

42、1579994TTT0.2500000000.7500000000.000000000FFF0.2500000000.7500000000.234390005TTT0.5000000000.5000000000.117190003TTT0.5000000000.5000000000.351579994TTT0.7500000000.7500000000.000000000FFF0.7500000000.7500000000.234390005TTT0.7470200060.7502299550.370979995TTT0.0000000000.117190003TTTPOTCAR按照Cu-H的

43、顺序合并。命令：mpirun-np8vasp>log&grep'energywithoutentropy'OUTCAR|tail-1计算结果：E总=-58.425eVEad53.48eV=335.6kJ/molINCAR(同4.2.5)KPOINTS(552)POSCARCHO-B-Cu1001.05.11199998860.00000000000.00000000000.00000000005.11199998860.00000000000.00000000000.000000000015.4221000671CuCOH16111SDirect0.0000000

44、000.0000000000.117190003TTT0.0000000000.0000000000.351579994TTT0.2500000000.2500000000.000000000FFF0.2500000000.2500000000.234390005TTT0.5000000000.0000000000.117190003TTT0.5000000000.0000000000.351579994TTT0.7500000000.2500000000.000000000FFF0.7500000000.2500000000.234390005TTT0.0000000000.50000000

45、00.117190003TTT0.0000000000.5000000000.351579994TTT0.2500000000.7500000000.000000000FFF0.2500000000.7500000000.234390005TTT0.5000000000.5000000000.117190003TTT0.5000000000.5000000000.351579994TTT0.7500000000.7500000000.000000000FFF0.7500000000.7500000000.234390005TTT0.5038599970.7500000000.473500013

46、TTT0.5034500360.9536999460.510500014TTT0.5026600360.5535999540.508180022TTTPOTCAR按照Cu-C-H-O的顺序合并。命令：mpirun-np8vasp>log&grep'energywithoutentropy'OUTCAR|tail-1计算结果：E总=-73.522eVEad51.913eV4.2.8CO和H共吸附于Cu100外表INCAR(同4.2.5)KPOINTS(552)POSCARCO&HH-HCu1001.00.00000000000.000000000015.42

47、21000671CuCOH16111SDirect0.0000000000.0000000000.117190003TTT0.0000000000.0000000000.351579994TTT0.2500000000.2500000000.000000000FFF0.2500000000.2500000000.234390005TTT0.5000000000.0000000000.117190003TTT0.5000000000.0000000000.351579994TTT0.7500000000.2500000000.000000000FFF0.7500000000.2500000000

48、.234390005TTT0.0000000000.5000000000.117190003TTT0.0000000000.5000000000.351579994TTT0.2500000000.7500000000.000000000FFF0.2500000000.7500000000.234390005TTT0.5000000000.5000000000.117190003TTT0.5000000000.5000000000.351579994TTT0.7500000000.7500000000.000000000FFF0.7500000000.7500000000.234390005TTT0.509580016 T T T0.368779987 T T T0.2516799870.7461700440.7487900260.750480056命令：mpirun-np8vasp>log&grep'energywithoutentropy'OUT