Liquid Si - Freezing: Difference between revisions
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== Calculation == | == Calculation == | ||
=== Diffusion === | |||
To analyse the diffusion behaviour at a certain temperature T, the data read from {{TAG|XDATCAR}}.T can be processed | |||
using the script diffusion ('''caution - this script is written for VASP version 4.x output'''): | using the script diffusion ('''caution - this script is written for VASP version 4.x output'''): | ||
| Line 178: | Line 180: | ||
</pre> | </pre> | ||
=== Pair correlation function === | |||
The pair-correlation function provides information about the probability of finding two atoms at a given distance <math> r </math>. | |||
The pair-correlation function written on {{FILE|PCDAT}}.T should be processed using the script PCDATtoPCDATxy: | |||
<pre> | <pre> | ||
Revision as of 14:36, 7 June 2019
Overview >Liquid Si - Standard MD > Liquid Si - Freezing > Nucleophile Substitution CH3Cl - Standard MD > Nuclephile Substitution CH3Cl - mMD1 > Nuclephile Substitution CH3Cl - mMD2 > Nuclephile Substitution CH3Cl - mMD3 > Nuclephile Substitution CH3Cl - SG > Nuclephile Substitution CH3Cl - BM > List of tutorials
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
Diffusion
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
}
'
Pair correlation function
The pair-correlation function provides information about the probability of finding two atoms at a given distance . 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).