Liquid Si - Freezing: Difference between revisions

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  {{TAGBL|NSW}} = 400                      # number of MD steps
  {{TAGBL|NSW}} = 400                      # number of MD steps
  {{TAGBL|POTIM}} = 3                      # time step of MD
  {{TAGBL|POTIM}} = 3                      # time step of MD
  {{TAGBL|NWRITE}} = 0                     
  {{TAGBL|NWRITE}} = 0                    # controls output
  {{TAGBL|NBLOCK}} = 10                    #
  {{TAGBL|NBLOCK}} = 10                    # after ten steps pair correlation function is written out
  {{TAGBL|LCHARG}} = .FALSE.
  {{TAGBL|LCHARG}} = .FALSE.               # no charge density written out
  {{TAGBL|LWAVE}} = .FALSE.
  {{TAGBL|LWAVE}} = .FALSE.               # no wave function coefficients written out
  {{TAGBL|TEBEG}} = $i                    # starting temperature for MD
  {{TAGBL|TEBEG}} = $i                    # starting temperature for MD
  {{TAGBL|TEEND}} = $i                    # end temperature for MD
  {{TAGBL|TEEND}} = $i                    # end temperature for MD
Line 87: Line 87:
  {{TAGBL|MDALGO}} = 2                    ä switch to select thermostat
  {{TAGBL|MDALGO}} = 2                    ä switch to select thermostat
  {{TAGBL|SMASS}} =  3                    # Nose mass
  {{TAGBL|SMASS}} =  3                    # Nose mass
{{TAGBL|ISIF}} = 2                      # this tag selects the ensemble in combination with the thermostat
*Most of the tags here are very similar to the tags used in the previous example ({{TAG|Liquid Si - Standard MD}}.
*A stepwise cooling will be applied in this example via a script where $i for {{TAG|TEBEG}} and {{TAG|TEEND}} will be replaced in each calculation (see below).
=== {{TAG|KPOINTS}} ===
<pre>
test
0 0 0
monk
1 1 1
0 0 0
</pre>
*A single k-point is sufficient in this example.




== Calculation ==


Since several calculations at different temperatures are required in this calculation, the {{TAG|INCAR}} is created with a script for each temperature:  
Since several calculations at different temperatures are required in this calculation, the {{TAG|INCAR}} is created with a script for each temperature and run seperately. After each step the important files are save to file.$i, where $i are the temperatures ranging from 2000 to 800 K in steps of 100 K. The script running the calculations looks like the following:  
  for i in 2000 1900 1800 1700 1600 1500 1400 1300 1200 1100 1000 900 800
  for i in 2000 1900 1800 1700 1600 1500 1400 1300 1200 1100 1000 900 800
  do
  do
Line 105: Line 119:
  {{TAGBL|ISYM}} = 0                      # no symmetry                                     
  {{TAGBL|ISYM}} = 0                      # no symmetry                                     
  {{TAGBL|NELMIN}} = 4                    # minimum 4 steps per time step, avoid breaking after 2 steps
  {{TAGBL|NELMIN}} = 4                    # minimum 4 steps per time step, avoid breaking after 2 steps
   
  # MD (do little writing to save disc space)
  # MD (do little writing to save disc space)
  {{TAGBL|IBRION}} = 0 ; {{TAGBL|NSW}} = 400 ; {{TAGBL|NWRITE}} = 0 ; {{TAGBL|LCHARG}} = .FALSE. ; {{TAGBL|LWAVE}} = .FALSE.
  {{TAGBL|IBRION}} = 0                     # main molecular dynamics tag
  {{TAGBL|TEBEG}} = $i ; {{TAGBL|TEEND}} = $i
{{TAGBL|NSW}} = 400                     # number of MD steps
{{TAGBL|POTIM}} = 3                      # time step of MD
{{TAGBL|NWRITE}} = 0                     # controls output
{{TAGBL|NBLOCK}} = 10                    # after ten steps pair correlation function is written out
{{TAGBL|LCHARG}} = .FALSE.               # no charge density written out
{{TAGBL|LWAVE}} = .FALSE.               # no wave function coefficients written out
  {{TAGBL|TEBEG}} = $i                     # starting temperature for MD
{{TAGBL|TEEND}} = $i                     # end temperature for MD
  # canonic (Nose) MD with {{TAGBL|XDATCAR}} updated every 10 steps
  # canonic (Nose) MD with {{TAGBL|XDATCAR}} updated every 10 steps
  {{TAGBL|SMASS}} = 3 ; {{TAGBL|NBLOCK}} = 10 ; {{TAGBL|POTIM}} = 3
  {{TAGBL|MDALGO}} = 2                    ä switch to select thermostat
  {{TAGBL|SMASS}} = 3                    # Nose mass
{{TAGBL|ISIF}} = 2                      # this tag selects the ensemble in combination with the thermostat
  !
  !
  mpirun -np 2 /path/to/your/vasp/executable
  mpirun -np 2 /path/to/your/vasp/executable
Line 124: Line 146:
The <tt>script</tt> 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).
The <tt>script</tt> 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).


=== {{TAG|KPOINTS}} ===
=== Diffusion ===
<pre>
test
0 0 0
monk
1 1 1
0 0 0
</pre>


== Calculation ==
=== Diffusion ===


To analyse the diffusion behaviour at a certain temperature T, the data read from {{TAG|XDATCAR}}.T can be processed
To analyse the diffusion behaviour at a certain temperature T, the data read from {{TAG|XDATCAR}}.T can be processed

Revision as of 13:09, 29 June 2019

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

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                     # main molecular dynamics tag
NSW = 400                      # number of MD steps
POTIM = 3                      # time step of MD
NWRITE = 0                     # controls output
NBLOCK = 10                    # after ten steps pair correlation function is written out
LCHARG = .FALSE.               # no charge density written out
LWAVE = .FALSE.                # no wave function coefficients written out
TEBEG = $i                     # starting temperature for MD
TEEND = $i                     # end temperature for MD
# canonic (Nose) MD with XDATCAR updated every 10 steps
MDALGO = 2                     ä switch to select thermostat
SMASS =  3                     # Nose mass
ISIF = 2                       # this tag selects the ensemble in combination with the thermostat
  • Most of the tags here are very similar to the tags used in the previous example (Liquid Si - Standard MD.
  • A stepwise cooling will be applied in this example via a script where $i for TEBEG and TEEND will be replaced in each calculation (see below).

KPOINTS

test
0 0 0
monk
 1 1 1
 0 0 0
  • A single k-point is sufficient in this example.


Calculation

Since several calculations at different temperatures are required in this calculation, the INCAR is created with a script for each temperature and run seperately. After each step the important files are save to file.$i, where $i are the temperatures ranging from 2000 to 800 K in steps of 100 K. The script running the calculations looks like the following: 

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                     # main molecular dynamics tag
NSW = 400                      # number of MD steps
POTIM = 3                      # time step of MD
NWRITE = 0                     # controls output
NBLOCK = 10                    # after ten steps pair correlation function is written out
LCHARG = .FALSE.               # no charge density written out
LWAVE = .FALSE.                # no wave function coefficients written out
TEBEG = $i                     # starting temperature for MD
TEEND = $i                     # end temperature for MD
# canonic (Nose) MD with XDATCAR updated every 10 steps
MDALGO = 2                     ä switch to select thermostat
SMASS =  3                     # Nose mass
ISIF = 2                       # this tag selects the ensemble in combination with the thermostat
!
mpirun -np 2 /path/to/your/vasp/executable
cp XDATCAR XDATCAR.$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).

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).

Download

Si_liquid.tgz

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