0 Tools

本节主要介绍使用VASP计算时，常用的一些工具。

VASPKIT

VASPKIT是一个针对VASP的程序集，通过命令行调用可以方便地生成与修改输入文件和初步处理输出数据，一些常用的命令如下:

Command-预处理 Function
vaspkit -task 102 生成KPOINTS
vaspkit -task 103 生成POTCAR，默认PBE
vaspkit -task 105 从cif文件生成POSCAR
vaspkit -task 303 生成KPOINTS，用于体相能带计算
vaspkit -task 601 给出晶体对称性
vaspkit -task 602 给出原胞的POSCAR
vaspkit -task 603 给出惯用晶胞的POSCAR
vaspkit -task 604 给出对称等价的原子
vaspkit -task 608 给出弛豫结构的对称性
Command-后处理 Function
vaspkit -task 111 提取总的态密度
vaspkit -task 113 提取每种元素的投影态密度
vaspkit -task 211 提取能带
vaspkit -task 213 提取每种元素的投影能带
vaspkit -task 263 FermiSurfer格式的费米面

Python

python用于提取数据与可视化结果。

Vesta

Vesta用于可视化和编辑晶体结构文件。

p4vasp

P4VASP通过读取vasprun.xml文件，便捷地可视化输出文件。

1 Examples Reproduce

1.1 Bulk Systems

1.1.1 fcc Si

任务

找到 fcc Si 的最佳晶格参数。

输入文件

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##POSCAR
fcc Si:
 3.9
 0.5 0.5 0.0
 0.0 0.5 0.5
 0.5 0.0 0.5
   1
   Si
cartesian
0 0 0
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##INCAR
System = fcc Si
ISTART = 0 ; ICHARG = 2
ENCUT = 500
ISMEAR = 0; SIGMA = 0.1

自行准备KPOINTS, POTCAR。

计算

  • 计算不同晶格参数的能量。
  • 拟合某些状态方程获得平衡体积。（可尝试vaspkit）
  • bash脚本loop.sh计算不同晶格常数(3.5-4.3$\mathring{A}$)的fcc Si并提取对应的自由能于SUMMARY.fcc中。
  • 注意-在VASP6.5.1中，ENCUT增加至约500才能使得脚本中的所有晶格参数所对应的计算收敛。
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##loop.sh
rm WAVECAR SUMMARY.fcc
for i in  3.5 3.6 3.7 3.8 3.9 4.0 4.1 4.2 4.3 ; do
cat >POSCAR <<!
fcc:
   $i
 0.5 0.5 0.0
 0.0 0.5 0.5
 0.5 0.0 0.5
   1
cartesian
0 0 0
!
echo "a= $i"
mpirun vasp_std &> vasp.log
E=`awk '/F=/ {print $0}' OSZICAR` ; echo $i $E  >>SUMMARY.fcc
done
cat SUMMARY.fcc
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##SUMMARY.fcc
3.5 1 F= -.44610629E+01 E0= -.44588862E+01 d E =-.435335E-02
3.6 1 F= -.46872871E+01 E0= -.46859153E+01 d E =-.274377E-02
3.7 1 F= -.48211455E+01 E0= -.48190962E+01 d E =-.409845E-02
3.8 1 F= -.48862039E+01 E0= -.48846919E+01 d E =-.302386E-02
3.9 1 F= -.48966342E+01 E0= -.48951129E+01 d E =-.304247E-02
4.0 1 F= -.48652835E+01 E0= -.48646264E+01 d E =-.131428E-02
4.1 1 F= -.47993069E+01 E0= -.47985430E+01 d E =-.152769E-02
4.2 1 F= -.47047953E+01 E0= -.47033649E+01 d E =-.286075E-02
4.3 1 F= -.45911248E+01 E0= -.45891970E+01 d E =-.385564E-02

1.1.2 fcc Si DOS

任务

计算fcc Si的态密度

输入文件

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##POSCAR
fcc Si:
 3.9
 0.5 0.5 0.0
 0.0 0.5 0.5
 0.5 0.0 0.5
   1
   Si
cartesian
0 0 0
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##INCAR
System = fcc Si
ICHARG = 11 # read CHGCAR file
ENCUT = 500
ISMEAR = -5 # tetrahedron方法
LORBIT = 11 # projection

##E-range and density
#Emin = 
#Emax = 
#NEDOS = 
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## CHGCAR
# 从自洽计算文件夹中复制

自行准备KPOINTS, POTCAR。

计算

  • 使用下面的脚本从scf文件夹中复制DOS计算所需文件并提交任务。
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##dos.sh
mkdir dos
cp incar.2.dos dos/INCAR #incar.2.dos is pre-prepared INCAR file for dos calculation
for ii in POSCAR POTCAR KPOINTS CHGCAR;do
cp scf/${ii} dos
done
cd dos
#generate dense kpoints
awk 'NR==4 {$1=$1*2+1;$2=$2*2+1;$3=$3*2+1} 1' KPOINTS > KPOINTS_dense && cp KPOINTS_dense KPOINTS

mpirun vasp_std &> dos.log
  • 对大的体系：
    • 先用较少的k点收敛。
    • 计算DOS时增加k点密度并通过设置ICHARG = 11，使电荷密度与电势能固定。
  • 设置ISMEAR = -5，使用blochl修正的四面体积分方法。
  • 使用p4vasp或python绘制DOS。
  • 使用下面的bash脚本调用awk与gnuplot来绘制dos。
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##dosplot.sh
awk 'BEGIN{i=1} /dos>/,\
                /\/dos>/ \
                 {a[i]=$2 ; b[i]=$3 ; i=i+1} \
     END{for (j=12;j<i-5;j++) print a[j],b[j]}' vasprun.xml > dos.dat

ef=`awk '/efermi/ {print $3}' vasprun.xml`

cat >plotfile<<!
# set term postscript enhanced eps colour lw 2 "Helvetica" 20
# set output "optics.eps"
plot "dos.dat" using (\$1-$ef):(\$2) w lp
! 

gnuplot -persist plotfile

rm dos.dat plotfile

1.1.3 fcc Si bandstructure

任务

计算fcc Si能带。

输入文件

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##POSCAR
fcc Si:
 3.9
 0.5 0.5 0.0
 0.0 0.5 0.5
 0.5 0.0 0.5
   1
   Si
cartesian
0 0 0
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##INCAR
System = fcc Si
ICHARG = 11 # read CHGCAR file
ENCUT = 500
ISMEAR = 0; SIGMA = 0.1 
LORBIT = 10 # 10 for l-decomposed and 11 for lm-decomposed

使用vaspkit自动生成或手动写入高对称k点。

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##KPOINTS
k-points for bandstructure L-G-X-U K-G
 10
liciprocal
  kkaokaokaokaokaokaokaokaokaokaone
reciprocal
  0.50000  0.50000  0.50000    1
  0.00000  0.00000  0.00000    1

  0.00000  0.00000  0.00000    1
  0.00000  0.50000  0.50000    1

  0.00000  0.50000  0.50000    1
  0.25000  0.62500  0.62500    1

  0.37500  0.7500   0.37500    1
  0.00000  0.00000  0.00000    1
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##CHGCAR
# 从自洽计算文件夹中复制

计算

  • 使用下面的脚本从scf中复制BAND计算所需文件。
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##band.sh
mkdir band
cp incar.3.band band/INCAR #incar.2.band is pre-prepared INCAR file for band calculation
for ii in POSCAR POTCAR CHGCAR;do
cp scf/${ii} band
done
cd band
#generate k-path through vaspkit or write it by yourself
vaspkit -task 303
cp KPATH.in KPOINTS

mpirun vasp_std &> band.log
  • 使用p4vasp或python绘制能带。

1.1.4 cd Si relaxation

任务

弛豫cubic diamond Si的内部坐标，体积与单胞形状。

输入文件

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##POSCAR
cubic diamond
   5.5
 0.0    0.5     0.5
 0.5    0.0     0.5
 0.5    0.5     0.0
  Si
  2
Direct
 -0.125 -0.125 -0.125
  0.125  0.125  0.125
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##INCAR
System = diamond Si
ISMEAR = 0; SIGMA = 0.1;
ENMAX  =  500
IBRION = 2; ISIF=3 ; NSW=100
PREC = high #set the FFT grids, the accuracy of the projectors in real space.
EDIFF  = 0.1E-06
#EDIFFG = -0.01 #default is equal to EDIFF * 10

自行准备KPOINTS, POTCAR

计算

1.1.5 fcc Ni

任务

计算自旋极化(ISPIN = 2)的fcc Ni。

输入文件

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##POSCAR
fcc:
 3.53 
 0.5 0.5 0.0
 0.0 0.5 0.5
 0.5 0.0 0.5
   Ni
   1
direct
0 0 0
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##INCAR
  SYSTEM = fcc Ni
  ISTART = 0 ; ICHARG=2
  ENCUT  =    500
  ISMEAR =    1  ; SIGMA = 0.2
  EDIFF = 1E-06
  ISPIN = 2; ISYM = -1
  MAGMOM = 1

自行生成KPOINTS，POTCAR

计算

1.1.6 Graphite TS binding energy

任务

使用Tchatchenko-Scheffler方法确定实验结构石墨的层间结合能。

输入文件

  • 石墨：
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##POSCAR
graphite
1.0
1.22800000 -2.12695839  0.00000000
1.22800000  2.12695839  0.00000000
0.00000000  0.00000000  6.71
4
direct
   0.00000000  0.00000000  0.25000000
   0.00000000  0.00000000  0.75000000
   0.33333333  0.66666667  0.25000000
   0.66666667  0.33333333  0.75000000
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##KPOINTS
K-Spacing Value to Generate K-Mesh: 0.040
0
Gamma
  15  15   4
0.0  0.0  0.0
  • 石墨烯：
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##POSCAR
graphene
1.0
1.22800000 -2.12695839  0.00000000
1.22800000  2.12695839  0.00000000
0.00000000  0.00000000  20.
C
2
direct
   0.00000000  0.00000000  0.25000000
   0.33333333  0.66666667  0.25000000
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##KPOINTS
K-Spacing Value to Generate K-Mesh: 0.040
0
Gamma
  15  15   1
0.0  0.0  0.0
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##INCAR
System = graphite
ISMEAR = 0; SIGMA = 0.01
ENCUT = 500
LWAVE = .FALSE.
LCHARG = .FALSE.
EDIFF = 1e-6
IVDW = 20            
LVDW_EWALD =.TRUE.

计算

分别提交graphite和graphene的计算，使用下面的脚本提取结合能。

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##extract.sh
#!/bin/bash
en2=$(grep "free  ene" graphite/OUTCAR |tail -1|awk '{print $5}')
en1=$(grep "free  ene" graphene/OUTCAR |tail -1|awk '{print $5}')
deltaE=$(echo "$en2/4 - $en1/2" | bc -l)
echo "Binding energy (eV/atom):" $deltaE > results.dat

1.1.7 Graphite MBD binding energy

任务

使用MBD方法计算实验结构石墨的层间结合能。

输入文件

POSCAR和KPOINTS与1.1.6-TS方法中相同。

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##INCAR
System = graphite
ISMEAR = 0; SIGMA = 0.01
ENCUT = 500
LWAVE = .FALSE.
LCHARG = .FALSE.
EDIFF = 1e-6
IVDW = 202            
LVDWEXPANSION = .TRUE.

计算

分别提交graphite和graphene的计算，使用下面的脚本提取结合能。

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##extract.sh
#!/bin/bash
en2=$(grep "free  ene" graphite/OUTCAR |tail -1|awk '{print $5}')
en1=$(grep "free  ene" graphene/OUTCAR |tail -1|awk '{print $5}')
deltaE=$(echo "$en2/4 - $en1/2" | bc -l)
echo "Binding energy (eV/atom):" $deltaE > results.dat

1.2 Calculate $U$ for LSDA+$U$

任务

输入文件

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##POSCAR
AFM  NiO
   4.03500000 
 2.0000000000   1.0000000000   1.0000000000 
 1.0000000000   2.0000000000   1.0000000000 
 1.0000000000   1.0000000000   2.0000000000 
  1 15   16 
Direct
 0.0000000000   0.0000000000   0.0000000000 
 0.2500000000   0.2500000000   0.2500000000 
 0.0000000000   0.0000000000   0.5000000000 
 0.2500000000   0.2500000000   0.7500000000 
 0.0000000000   0.5000000000   0.0000000000 
 0.2500000000   0.7500000000   0.2500000000 
 0.0000000000   0.5000000000   0.5000000000 
 0.2500000000   0.7500000000   0.7500000000 
 0.5000000000   0.0000000000   0.0000000000 
 0.7500000000   0.2500000000   0.2500000000 
 0.5000000000   0.0000000000   0.5000000000 
 0.7500000000   0.2500000000   0.7500000000 
 0.5000000000   0.5000000000   0.0000000000 
 0.7500000000   0.7500000000   0.2500000000 
 0.5000000000   0.5000000000   0.5000000000 
 0.7500000000   0.7500000000   0.7500000000 
 0.1250000000   0.1250000000   0.1250000000 
 0.3750000000   0.3750000000   0.3750000000 
 0.1250000000   0.1250000000   0.6250000000 
 0.3750000000   0.3750000000   0.8750000000 
 0.1250000000   0.6250000000   0.1250000000 
 0.3750000000   0.8750000000   0.3750000000 
 0.1250000000   0.6250000000   0.6250000000 
 0.3750000000   0.8750000000   0.8750000000 
 0.6250000000   0.1250000000   0.1250000000 
 0.8750000000   0.3750000000   0.3750000000 
 0.6250000000   0.1250000000   0.6250000000 
 0.8750000000   0.3750000000   0.8750000000 
 0.6250000000   0.6250000000   0.1250000000 
 0.8750000000   0.8750000000   0.3750000000 
 0.6250000000   0.6250000000   0.6250000000 
 0.8750000000   0.8750000000   0.8750000000
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##KPOINTS
Gamma only
 0
Monkhorst
 1 1 1 
 0 0 0
1
2
##INCAR

计算

1.3 Magnetism

1.2.3 NiO LSDA+$U$

任务

使用DFT+$U$(Dudarev方法)计算反铁磁NiO。

输入文件

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##POSCAR
AFM  NiO
 4.17
 1.0 0.5 0.5
 0.5 1.0 0.5
 0.5 0.5 1.0
 2 2
Cartesian
 0.0 0.0 0.0
 1.0 1.0 1.0
 0.5 0.5 0.5
 1.5 1.5 1.5
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##INCAR
SYSTEM   = NiO
    
ISTART   = 0
    
ISPIN    = 2
MAGMOM   = 2.0 -2.0 2*0
    
ENMAX    = 250.0
EDIFF    = 1E-3
    
ISMEAR   = -5
    
AMIX     = 0.2
BMIX     = 0.00001
AMIX_MAG = 0.8
BMIX_MAG = 0.00001
    
LORBIT   = 11
    
LDAU      = .TRUE.
LDAUTYPE  = 2
LDAUL     = 2 -1
LDAUU     = 8.00 0.00
LDAUJ     = 0.95 0.00
LDAUPRINT = 1
    
LMAXMIX   = 4          ! Important: mix paw occupancies up to L=4
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##KPOINTS
k-points
 0
gamma
 4  4  4 
 0  0  0

计算

1.4 BSE

1.4.1 Dielectric properties of Si using BSE

任务

通过求解GW0上的Bethe-Salpeter方程(BSE)，计算包含激子效应的Si的介电函数。

输入文件

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##POSCAR
Si
 5.4300
0.5 0.5 0.0
0.0 0.5 0.5
0.5 0.0 0.5
Si
2
cart
0.00 0.00 0.00 
0.25 0.25 0.25 
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##KPOINTS
K-Spacing Value to Generate K-Mesh: 0.040
0
Gamma
   6   6   6
0.0  0.0  0.0

自行准备POTCAR文件。

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##incar.1.dft
System  = Si
ENCUT = 500
ISMEAR = 0 ; SIGMA = 0.01
EDIFF = 1.E-8
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##incar.2.diag
System  = Si
PREC = Normal ; ENCUT = 500
ALGO = EXACT ; NELM = 1
ISMEAR = 0 ; SIGMA = 0.01
NBANDS = 128
LOPTICS = .TRUE. ; LPEAD = .TRUE.
OMEGAMAX = 40
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##incar.3.gw0
System  = Si
PREC = Normal ; ENCUT = 500
ALGO = GW0  
ISMEAR = 0 ; SIGMA = 0.01 
ENCUTGW = 150 ; NELM = 1 ;  NOMEGA =  50 ;  OMEGATL = 280
#NBANDSO=4 ; NBANDSV=8 ; LADDER=.TRUE. ; LUSEW=.TRUE.
NBANDS = 128
NBANDSGW = 12
LWAVE = .TRUE.
PRECFOCK = Normal
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##incar.4.none
System  = Si
PREC = Normal ; ENCUT = 500
ALGO = Nothing ; NELM = 1
ISMEAR = 0 ; SIGMA = 0.01
KPAR = 2
NBANDS = 128
LWAVE = .FALSE.
LOPTICS = .TRUE. ; LPEAD = .TRUE.
OMEGAMAX = 40  
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##incar.5.bse
SYSTEM = Si
PREC = Normal ; ENCUT = 500
ALGO = BSE 
ANTIRES = 0
ISMEAR = 0 ; SIGMA = 0.01
ENCUTGW = 150
EDIFF = 1.E-8
NBANDS = 128
NBANDSO = 4
NBANDSV = 8
OMEGAMAX = 20
PRECFOCK = Normal

计算

GW0+BSE计算的工作流程在doall.sh中给出，包含以下连续步骤：

  1. 标准的DFT基态计算
  2. 获取虚能带：需要步骤1中的WAVECAR。
  3. GW0计算：需要步骤2中的WAVECAR和WAVEDER。
  4. 可选步骤：使用LOPTICS=.TRUE.来给出独立粒子近似(IPA)下的介电函数，使用GW0准粒子能量而非DFT能量。
  5. BSE计算：需要步骤3中的WAVECAR和步骤2中的WAVEDER。
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##doall.sh
rm WAVECAR* WAVEDER*
#step 1
cp incar.1.dft INCAR
mpirun vasp_std &> DFT.log

cp OUTCAR OUTCAR.DFT
cp vasprun.xml vasprun.DFT.xml

#step 2
cp incar.2.diag INCAR
mpirun vasp_std &> DIAG.log

cp OUTCAR OUTCAR.DIAG
cp vasprun.xml vasprun.DIAG.xml

./extract_optics.sh
mv optics.dat optics.DFT.dat

# cp WAVECAR WAVECAR.chi
# cp WAVEDER WAVEDER.chi
# cp INCAR.scGW0 INCAR
# $vasp_std
# cp OUTCAR OUTCAR.scGW0
# cp vasprun.xml vasprun.scGW0.xml

#step 3
cp incar.3.gwp INCAR
mpirun vasp_std &> GW0.log

cp OUTCAR OUTCAR.GW0
cp vasprun.xml vasprun.GW0.xml

#step 4
cp incar.4.none INCAR
mpirun vasp_std &> NONE.log

cp OUTCAR OUTCAR.NONE
cp vasprun.xml vasprun.NONE.xml

./extract_optics.sh
mv optics.dat optics.RPA.dat

#step 5
cp incar.5.bse INCAR
mpirun vasp_std &> BSE.log

cp OUTCAR OUTCAR.BSE
cp vasprun.xml vasprun.BSE.xml

./extract_optics.sh
mv optics.dat optics.BSE.dat
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##extract.sh
awk 'BEGIN{i=0} /<dielectricfunction>/,\

                /<\/dielectricfunction>/ \

                 {if ($1=="<r>") {a[i]=$2 ; b[i]=($3+$4+$5)/3 ; c[i]=$4 ; d[i]=$5 ; i=i+1}} \

     END{for (j=0;j<i/2;j++) print a[j],b[j],b[j+i/2]}' vasprun.xml > optics.dat

所有计算完成后，使用脚本plotall.sh绘制IPA和BSE下的吸收系数。

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##plotall.sh
cat >plotfile<<!
# set term postscript enhanced eps colour lw 2 "Helvetica" 20
# set output "optics.eps"

set xrange [0:10]

plot "optics.DFT.dat" using (\$1):(\$2)  w l lt -1 lw 1  lc -1 title "DFT", \
     "optics.RPA.dat" using (\$1):(\$2)  w l lt -1 lw 1  lc  1 title "RPA", \
     "optics.BSE.dat" using (\$1):(\$2)  w l lt -1 lw 1  lc  3 title "BSE"
!

gnuplot -persist plotfile

1.5 Molecular Dynamics

1.5.1 Liquid Si - Standard MD

任务

通过分子动力学熔化晶体结构来生成液态Si。

输入文件

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##poscar111
Si cubic diamond conventional cell
  5.43100000000000
 1.00000000 0.00000000 0.00000000
 0.00000000 1.00000000 0.00000000
 0.00000000 0.00000000 1.00000000
  Si
  8
Direct
  0.00000000 0.00000000 0.00000000
  0.75000000 0.25000000 0.75000000
  0.00000000 0.50000000 0.50000000
  0.75000000 0.75000000 0.25000000
  0.50000000 0.00000000 0.50000000
  0.25000000 0.25000000 0.25000000
  0.50000000 0.50000000 0.00000000
  0.25000000 0.75000000 0.75000000
  • supercell $2\times2\times2$
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##poscar222
Si cubic diamond 2x2x2 super cell of conventional cell
     5.43090000000000
    2.00000000   0.00000000   0.00000000
    0.00000000   2.00000000   0.00000000
    0.00000000   0.00000000   2.00000000
   Si
   64
Direct
   0.00000000   0.00000000   0.00000000
   0.50000000   0.00000000   0.00000000
   0.00000000   0.50000000   0.00000000
   0.50000000   0.50000000   0.00000000
   0.00000000   0.00000000   0.50000000
   0.50000000   0.00000000   0.50000000
   0.00000000   0.50000000   0.50000000
   0.50000000   0.50000000   0.50000000
   0.37500000   0.12500000   0.37500000
   0.87500000   0.12500000   0.37500000
   0.37500000   0.62500000   0.37500000
   0.87500000   0.62500000   0.37500000
   0.37500000   0.12500000   0.87500000
   0.87500000   0.12500000   0.87500000
   0.37500000   0.62500000   0.87500000
   0.87500000   0.62500000   0.87500000
   0.00000000   0.25000000   0.25000000
   0.50000000   0.25000000   0.25000000
   0.00000000   0.75000000   0.25000000
   0.50000000   0.75000000   0.25000000
   0.00000000   0.25000000   0.75000000
   0.50000000   0.25000000   0.75000000
   0.00000000   0.75000000   0.75000000
   0.50000000   0.75000000   0.75000000
   0.37500000   0.37500000   0.12500000
   0.87500000   0.37500000   0.12500000
   0.37500000   0.87500000   0.12500000
   0.87500000   0.87500000   0.12500000
   0.37500000   0.37500000   0.62500000
   0.87500000   0.37500000   0.62500000
   0.37500000   0.87500000   0.62500000
   0.87500000   0.87500000   0.62500000
   0.25000000   0.00000000   0.25000000
   0.75000000   0.00000000   0.25000000
   0.25000000   0.50000000   0.25000000
   0.75000000   0.50000000   0.25000000
   0.25000000   0.00000000   0.75000000
   0.75000000   0.00000000   0.75000000 
   0.25000000   0.50000000   0.75000000
   0.75000000   0.50000000   0.75000000
   0.12500000   0.12500000   0.12500000
   0.62500000   0.12500000   0.12500000
   0.12500000   0.62500000   0.12500000
   0.62500000   0.62500000   0.12500000
   0.12500000   0.12500000   0.62500000
   0.62500000   0.12500000   0.62500000
   0.12500000   0.62500000   0.62500000
   0.62500000   0.62500000   0.62500000
   0.25000000   0.25000000   0.00000000
   0.75000000   0.25000000   0.00000000
   0.25000000   0.75000000   0.00000000
   0.75000000   0.75000000   0.00000000
   0.25000000   0.25000000   0.50000000
   0.75000000   0.25000000   0.50000000
   0.25000000   0.75000000   0.50000000
   0.75000000   0.75000000   0.50000000
   0.12500000   0.37500000   0.37500000
   0.62500000   0.37500000   0.37500000
   0.12500000   0.87500000   0.37500000
   0.62500000   0.87500000   0.37500000
   0.12500000   0.37500000   0.87500000
   0.62500000   0.37500000   0.87500000
   0.12500000   0.87500000   0.87500000
   0.62500000   0.87500000   0.87500000
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##KPOINTS
K-Points
 0
Gamma
 1  1  1
 0  0  0
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##INCAR

计算