Liquid Si - Freezing

Description: script performs molecular dynamics runs on liquid Si a decreasing temperatures, starting at 2000 K and ending at 800 K. This should contain the transition from liquid Si to crystalline Si (amorphous).

---

• script

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

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).

• KPOINTS

test
0 0 0
monk
 1 1 1
 0 0 0

• 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

to analyse the diffusion behaviour at a certain temperature T, the data read from [[XDATCAR.[T]]] can be processed using the following script:

• diffusion

 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
 }
 '

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

1. MD (do little writing to save disc space)

IBRION = 0 ; NSW = 400 ; NWRITE = 0 ; LCHARG = .FALSE. ; LWAVE = .FALSE. TEBEG = $i ; TEEND = $i

1. canonic (Nose) MD with XDATCAR updated every 10 steps

SMASS = 3 ; NBLOCK = 10 ; POTIM = 3

Used INCAR Tags

ALGO, EDIFF, IBRION, ISMEAR, ISYM, LCHARG, LREAL, LWAVE, MAXMIX, NBLOCK, NELMIN, NSW, NWRITE, POTIM, PREC, SMASS, TEBEG, TEEND

Download

Si_liquid.tgz

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