Liquid Si - Freezing
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Task
In this example the goal is to simulate the freezing of liquid Si.
Input
POSCAR
Si
15.12409564534287297131
0.5000000000000000 0.5000000000000000 0.0000000000000000
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
48
Direct
0.8550657259653851 0.3204575801875221 0.6180363868822553
0.6045454476433229 0.0546379652195404 0.1629680405553871
0.4803889256776521 0.2999635319377835 0.0131251454718051
0.8413504226620471 0.7598095803296524 0.1917781560970181
0.9754163118144437 0.6134171268457649 0.7421364242876367
0.2668229391055025 0.0066502741664650 0.0031140604380929
0.8935777664000575 0.3324172908647429 0.9535738516718881
0.0527608886321274 0.5249316429131962 0.5293744880144071
0.4396089233132741 0.7564833235979471 0.5665855438788387
0.5907859878830199 0.5198033580597228 0.3581725847640679
0.2120832721474721 0.4042899613004446 0.7921535013319151
0.0225803885096466 0.8414911198321031 0.1209255489569852
0.0992500701525566 0.3917384466892963 0.3612433325214984
0.9673794138223195 0.5206425706394114 0.1719623236201897
0.2774602656926126 0.8480860088162007 0.2673309412777037
0.0196991774214161 0.8282178425383616 0.6986213756952502
0.3570927152895376 0.2951488295546784 0.2651851032568589
0.1663829731894614 0.9766237917413699 0.6051764245375237
0.4931841331696695 0.8689890620771937 0.2612357008392290
0.8006473407426477 0.1033419073227807 0.4706563716777467
0.0161340851939779 0.9953827418297991 0.8853439845676159
0.7827740166661069 0.1821830067208054 0.9399555168314748
0.0720651739141343 0.2539424963694544 0.6857919074323433
0.4443385370769313 0.0486404637002326 0.4180706114402839
0.7055263679666055 0.6802623819082319 0.7983614866719116
0.2237125282521105 0.4055474352416297 0.0077044950891134
0.2963682069847125 0.5771265542042112 0.2019757061665083
0.2782449529809642 0.0451513130915826 0.7644934848784113
0.9312079203181675 0.9090938018377080 0.3429249881187518
0.6341882597200124 0.2969253226419481 0.3227590981305088
0.3587691103780569 0.1061057273904179 0.0931868777500710
0.8710437838676732 0.6541301230631744 0.4261617089364881
0.6784300588817769 0.3263889355408940 0.5560491395978739
0.5597052314845080 0.0174390112509929 0.6129003207931863
0.0595962318875451 0.1019295953521402 0.3340999072062676
0.7689671766774326 0.1768870209149794 0.1604177484299765
0.9603661624482890 0.3311649224573259 0.1439224909303592
0.3792868784787023 0.2806150985211180 0.4921541531665999
0.8079860889823454 0.9194188799048340 0.9131036494263627
0.3002081239026374 0.7834053620019006 0.8650323716139056
0.4704528574512951 0.7221628305989689 0.9746107190983403
0.2886552568292480 0.5927625600330780 0.4239421203107919
0.4116743942942291 0.2198943758058664 0.7072597030225044
0.2104494234814825 0.6457654201409418 0.8275863924787099
0.6784628197745537 0.7205455185203838 0.1093053357228383
0.6344130299021448 0.1650970001101275 0.8037018707797643
0.3965793440603315 0.5364088146415013 0.6064549771969059
0.6686412136025504 0.7848666926903073 0.5681234351534038
INCAR
Since several calculations at different temperatures are required in this calculation, the INCAR is created with a script for each temperature:
for i in 2000 1900 1800 1700 1600 1500 1400 1300 1200 1100 1000 900 800 do cat >INCAR <<! SYSTEM = Si # electronic degrees LREAL = A # real space projection PREC = Normal # chose Low only after tests EDIFF = 1E-5 # do not use default (too large drift) ISMEAR = -1 ; SIGMA = 0.130 # Fermi smearing: 1500 K 0.086 10-3 ALGO = Very Fast # recommended for MD (fall back ALGO = Fast) MAXMIX = 40 # reuse mixer from one MD step to next ISYM = 0 # no symmetry NELMIN = 4 # minimum 4 steps per time step, avoid breaking after 2 steps # MD (do little writing to save disc space) IBRION = 0 ; NSW = 400 ; NWRITE = 0 ; LCHARG = .FALSE. ; LWAVE = .FALSE. TEBEG = $i ; TEEND = $i # canonic (Nose) MD with XDATCAR updated every 10 steps SMASS = 3 ; NBLOCK = 10 ; POTIM = 3 ! mpirun -np 2 /path/to/your/vasp/executable cp XDATCAR XDATCAR.$i cp OUTCAR OUTCAR.$i cp PCDAT PCDAT.$i cp CONTCAR CONTCAR.$i cp POSCAR POSCAR.$i cp OSZICAR OSZICAR.$i cp CONTCAR POSCAR done
The script performs molecular dynamics runs on liquid Si at decreasing temperatures, starting at 2000 K and ending at 800 K. This should contain the transition from liquid Si to crystalline Si (amorphous).
KPOINTS
test 0 0 0 monk 1 1 1 0 0 0
Calculation
- To analyse the diffusion behaviour at a certain temperature T, the data read from XDATCAR.T can be processed
using the script diffusion (caution - this script is written for VASP version 4.x output):
awk <XDATCAR >diffusion.xy '
#
# simple module function
#
function mod(x,y) { return x-int(x/y)*y }
function minim(x) { return mod(x+2.5,1.0)-0.5 }
#
# calculate mean square displacement
#
function diff() {
d=0
for (ion=1; ion<=ions; ion++) {
dx=minim(xn[ion]-x[ion])
dy=minim(yn[ion]-y[ion])
dz=minim(zn[ion]-z[ion])
xn[ion]=x[ion]+dx
yn[ion]=y[ion]+dy
zn[ion]=z[ion]+dz
d=d+(xn[ion]-x0[ion])*(xn[ion]-x0[ion])*a1*a1
d=d+(yn[ion]-y0[ion])*(yn[ion]-y0[ion])*a2*a2
d=d+(zn[ion]-z0[ion])*(zn[ion]-z0[ion])*a3*a3
}
# d=d/(set*t)/6
d=d/6
print set*t,d
}
#
# set the number of ions
#
NR==1 { ions = $1 }
NR==2 { a1=$2*10^10 ; a2=$3*10^10 ; a3=$4*10^10 ; t=$5*10^12 }
#
# at this point a complete set of ionic positions has been found
#
mod(NR-6,ions+1)==0 {
if (set>=2) diff()
if (set==1) {
for (ion=1; ion<=ions; ion++) {
x0[ion]=xn[ion]
y0[ion]=yn[ion]
z0[ion]=zn[ion]
}
}
for (ion=1; ion<=ions; ion++) {
x[ion]=xn[ion]
y[ion]=yn[ion]
z[ion]=zn[ion]
}
head=headn
headn=$0
set=set+1
}
# store coordinates
mod(NR-6,ions+1)>0 {
ion=mod(NR-6,ions+1)
xn[ion]=$1
yn[ion]=$2
zn[ion]=$3
}
'
- The pair-correlation function written on [[PCDAT.[T]]] should be processed using the script PCDATtoPCDATxy:
awk <PCDAT >PCDAT.xy '
NR==8 { pcskal=$1}
NR==9 { pcfein=$1}
NR>=13 {
line=line+1
if (line==257) {
print " "
line=0
}
else
print (line-0.5)*pcfein/pcskal,$1
}
'
Mind: You will have to set the correct path to your VASP executable and invoke VASP with the correct command (e.g., in the above: mpirun -np 2).