VASP的电荷密度计算及图像处理


使用的软件:VASP, VESTA, EidtPlus,SshClient


一 电荷密度计算

在能带计算完成基础下,拷贝 band 文件夹为 charge

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cp -rf band charge

编辑 charge 下文件

INCAR

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SYSTEM=x # x 为注释名
#ISTART=1 # 修改
#ICHARG=1 # 修改
#LORBIT=11 # 修改
ENCUT=350
EDIFF=1E-5
IBRION=2
#POTIM=0.25 # 修改
NSW=0
EDIFFG=-1E-2
ISMEAR=0
SIGMA=0.05
PREC=ACCURATE
ISIF=2
NPAR=4
LWAVE=FALSE
#LCHARG=FALSE
LREAL=Auto
#IALGO=48
ISYM=0
LPARD=.TRUE. # 增加,注意打点
IBAND=xxx yyy # 价带顶和导带底所在行数
#KPUSE=1 2 3 4 # 增加
LSEPB=.TRUE. # 增加
LSEPK=.FALSE. # 增加

提交作业,作业完成后,得 PARCHG.0xxx.ALLK 和 PARCHG.0yyy.ALLK 文件,使用软件 SshClient 将文件导出至计算机。

二 图像处理

  1. 将 PARCHG.0xxx.ALLK 和 PARCHG.0yyy.ALLK 文件重命名为 得 PARCHG.0xxx.ALLK.vasp 和 PARCHG.0yyy.ALLK.vasp,在软件 VESTA 中打开。
  2. 简单编辑:Edit - Bonds - New - search molecules 和 Do not search atoms… - Max.length=3 - OK
  3. 取消勾选 Volumetic date 下的 Show sections.
  4. File - Export Raster Image
  5. PS 处理。
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VASP的能带计算与绘图


使用的软件:VASP, Origin, EidtPlus
辅助分析计算的小程序:gk.x, pbnf.x


一 能带计算

1 结构优化

建立opt文件夹,编辑以下文件:

INCAR

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SYSTEM=x # x为注释名
ISTART=0
ENCUT=350
EDIFF=1E-5
IBRION=2
POTIM=0.25
NSW=100
EDIFFG=-1E-2
ISMEAR=0
SIGMA=0.05
PREC=ACCURATE
ISIF=2
NPAR=4
LWAVE=FALSE
LCHARG=FALSE
LREAL=Auto
IALGO=48
ISYM=0

KPOINTS

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auto
0
Monkhorst
x y z # x y z 为K点选取
0 0 0

POSCAR

导入在 Materials Studio 中转换的坐标信息

POTCAR

导入赝势库中的原子信息,例:GeS

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cat ~/xxx/PBE/Ge/POTCAR > POTCAR # ~/xxx 为赝势库存放路径
cat ~/xxx/PBE/S/POTCAR >> POTCAR # 原子赝势导入顺序以POSCAR中为准

如果是集群,还需提交作业的脚本 vasp.job 如下

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#!/bin/bash
#PBS -N vasp
#PBS -o job.log
#PBS -e job.err
#PBS -q batch
#PBS -l walltime=100:00:00
#PBS -l nodes=1:ppn=8
source ~/.bashrc
cd ~/xxx # ~/xxx 为文件路径
mpirun -np 8 vasp > out </dev/null

提交作业

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qsub vasp.job

计算结束后,cat out 查看体系是否收敛,如收敛则进入下一步计算。

2 静态自洽计算

在 opt 文件夹下建立 scf 文件夹,编辑以下文件

INCAR

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SYSTEM=x
ISTART=0
ENCUT=350
EDIFF=1E-5
IBRION=2
POTIM=0.25
NSW=0 # 修改
EDIFFG=-1E-2
ISMEAR=0
SIGMA=0.05
PREC=ACCURATE
ISIF=2
NPAR=4
#LWAVE=FALSE # 修改
#LCHARG=FALSE # 修改
LREAL=Auto
#IALGO=48 # 修改
ISYM=0

KPOINTS

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auto
0
Monkhorst
x y z # 较opt选取,k值增大
0 0 0

POSCAR和POTCAT

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cp ../CONTCAR POSCAR
cp ../POTCAR .

提交作业,产生WAVECAR进行下一步计算

3 能带计算

在 opt 文件夹下拷贝建立 band 文件夹

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cp -rf scf band

编辑 band 下文件

INCAR

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SYSTEM=x
ISTART=1 # 修改
ICHARG=11 # 从CHGCAR中读入电荷分布,并且在计算中保持不变
LORBIT=10 # 增加
ENCUT=350
EDIFF=1E-5
IBRION=2
POTIM=0.25
NSW=0
EDIFFG=-1E-2
ISMEAR=0
SIGMA=0.05
PREC=ACCURATE
ISIF=2
NPAR=4
LWAVE=FALSE # 修改
#LCHARG=FALSE
LREAL=Auto
#IALGO=48
ISYM=0

KPOINTS

1. 设置环境变量

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vi ~/.bashrc
alias gk="~/software/ktool/gk.x"
alias pb="~/software/ktool/pbnf.x"
alias f="grep E-fermi OUTCAR"
alias lv="grep -A3 'lattice vectors' OUTCAR"
source ~/.bashrc

2. 编辑syml文件,例:

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5 # 高对称点数目
20 20 20 20 # 高对称点间隔取点数目
G 0.0 0.0 0.0
M 0.5 0.0 0.0
K 0.5 0.0 0.5
Z 0.0 0.0 0.5
G 0.0 0.0 0.0 # 高对称点选取
12.840000153 0.000000000 0.000000000 0.077881619 0.000000000 0.000000000
0.000000000 10.406299591 0.000000000 0.000000000 0.096095638 0.000000000
0.000000000 0.000000000 39.669998169 0.000000000 0.000000000 0.025207967 # 实坐标与虚坐标
-20.0 20.0 # 取值范围
-0.0460 # 费米能级

实坐标与虚坐标通过命令lv得到,费米能级通过命令f得到,高对称点可查阅参考文献选取。

4 KPOINTS的获取与编辑

输入命令gk获取KOINTS文件,若文件后有多行零,则删去,且第二行数据减去相应删去行数。

提交作业,计算结束后生成 EIGENVAL 文件,输入命令pb得到能带数据文件 bnd.dat 和 highk.dat,将数据导入Origin绘图。

二 能带绘图

将能带数据文件 bnd.dat 和 highk.dat 导入Origin, 前两列为 bnd.dat 数据,后两列为 highk.dat 数据,格式如图,可使用 EditPlus 进行数据编辑。

参考资料

  1. VASP 软件包的使用入门指南
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《论读书》笔记整理【2】

Topic Sentence

  • … serve for …, for …, and for …

    Sentence Pattern 2

  • Their chief use for …, is in … and …;
    for …, is in …;
    and for …, is in …, and …

    Application

  • Digital products serve for delight, for convenience, and for communication. Their chief use for delight, is in leisure and entertainment; for convenience, is in the free resources and information; for communication, is in the long-distance contact, and instant information exchange.

3. For expert men can excute, and perhaps judge of particulars, one by one; but the general counsels and the plots and marshalling of affairs, come best, from those that are learned.

练达之士虽能分别处理细事或一一判别枝节,然纵观统筹、全局策划,则舍好学深思者莫属。

  • Particular=trifle 琐事
  • Marshal

Sentence Pattern 3

  • For …, but …, come best, from those that …

Application

  • 普通的朋友可能陪伴你,但是坚定的支持和衷心的慰藉往往来自于那些真正关心你的朋友。
  • For ordinary friend can accompany with you, but the firm support and heartfelt comfort, come best, from those truly care about you.

4. They perfect nature, and are perfected by experience: for natural plants, that need pruning, by study.

读书补天然之不足,经验又补读书之不足,盖天生之才干犹如花草树木,读书然后知如何修剪移接。

  • Pruning

  • Perfect

  • Flawless
    ex. the flawless skin 无暇的皮肤
  • Stainless
    ex. her stainless past 无污点的过去
    • Unblemished
      ex. unblemished reputation
    • Impeccable
      ex. an impeccable of characer 无可挑剔的性格

  • Perfection is not just about control. It’s also about letting go.
  • The only person standing in your way is you. It’s time to let it go. Lose yourself.
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《论读书》笔记整理【1】

  • Knowledge is power.
  • The founder of English materialist philosophy and modern science.
  • Main Works
  • Advancement of Learnng
  • New instrument
  • Essays
  • New instrument
  • Inductive Mothed of Reasoning
  • First, collect and study facts of this great world, than base your reasoning and conclusion on those facts.

If the imaginative powers of literary creation of English Renaissance found their expression in the poetry of Spenser and the drama of Shakespeare, the intellectual energy of this age showed itself in the achievement of Fancis Bacon.

1. Studies serve for delight, for ornament, and for ability.

读书足以怡情,足以傅彩,足以长才。

  • Serve
  • Serve the devil
  • Serve two masters
  • Serve as a foil to sb. 作某人的陪衬

    三人行,必有我师
    When I work along with two others, they may serve as my techers, I will select their good qualities and follow them, their bad qualities and avoid them.
    理雅各

  • The master said, “In a party of three there must be one whom I can learn from, I will pick his merits to emulate (imitate) them, and find his demerits to amend mine.
  • Ornament
  • —— is like a glass ornament, once it is broken it can rarely be put back together exactly the same way.

2. Their chief use for delight, is in privateness and retiring; for ornament, is in discourse; and for ability, is in judgment, and disposition of business.

其怡情也,最见于独处幽居之时;
其傅彩也,最见于高谈阔论之中;
其长才也,最见于处世判事之际。

  • Business
  • business 正经事
    incident 小事
    accident 祸事
    affair 风流韵事
    trifle 琐事

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