Liquid Si - Freezing: Difference between revisions

Revision as of 07:05, 3 May 2017

Overview > fcc Si > fcc Si DOS > fcc Si bandstructure > cd Si > cd Si volume relaxation > cd Si relaxation > beta-tin Si > fcc Ni > graphite TS binding energy > graphite MBD binding energy > graphite interlayer distance > List of tutorials

Description:

Task

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

Script for INCAR

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

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).

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 following script:

 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).

Download

Si_liquid.tgz

To the list of examples or to the main page

@@ Line 1: / Line 1: @@
 {{Template:Bulk_systems}}
-Description: <tt>script</tt> 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).
+Description:
 ----
-*script
- for i in 2000 1900 1800 1700 1600 1500 1400 1300 1200 1100 1000 900 800
- do
- cat >INCAR <<!
- {{TAGBL|SYSTEM}} =  Si
- # electronic degrees
- {{TAGBL|LREAL}} = A                      # real space projection
- {{TAGBL|PREC}}  = Normal                 # chose Low only after tests
- {{TAGBL|EDIFF}} = 1E-5                   # do not use default (too large drift)
- {{TAGBL|ISMEAR}} = -1 ; SIGMA = 0.130    # Fermi smearing: 1500 K 0.086 10-3
- {{TAGBL|ALGO}} = Very Fast               # recommended for MD (fall back ALGO = Fast)
- {{TAGBL|MAXMIX}} = 40                    # reuse mixer from one MD step to next
- {{TAGBL|ISYM}} = 0                       # no symmetry
- {{TAGBL|NELMIN}} = 4                     # minimum 4 steps per time step, avoid breaking after 2 steps
- # MD (do little writing to save disc space)
- {{TAGBL|IBRION}} = 0 ; {{TAGBL|NSW}} = 400 ; {{TAGBL|NWRITE}} = 0 ; {{TAGBL|LCHARG}} = .FALSE. ; {{TAGBL|LWAVE}} = .FALSE.
- {{TAGBL|TEBEG}} = $i ; {{TAGBL|TEEND}} = $i
- # canonic (Nose) MD with {{TAGBL|XDATCAR}} updated every 10 steps
- {{TAGBL|SMASS}} = 3 ;  {{TAGBL|NBLOCK}} = 10 ; {{TAGBL|POTIM}} = 3
- !
- mpirun -np 2 /path/to/your/vasp/executable
- cp XDATCAR XDATCAR.$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: <tt>mpirun -np 2</tt>).
+== Task ==
-*{{TAG|KPOINTS}}
+== Input ==
-<pre>
-test
-0 0
-monk
-1 1
-0 0
-</pre>
-*{{TAG|POSCAR}}
+=== {{TAG|POSCAR}} ===
   Si
 .12409564534287297131
@@ Line 103: / Line 66: @@
 .6686412136025504  0.7848666926903073  0.5681234351534038
-to analyse the diffusion behaviour at a certain temperature T, the data read from {{FILE|XDATCAR.[T]}} can be processed
+=== Script for {{TAG|INCAR}} ===
+ for i in 2000 1900 1800 1700 1600 1500 1400 1300 1200 1100 1000 900 800
+ do
+ cat >INCAR <<!
+ {{TAGBL|SYSTEM}} =  Si
+ # electronic degrees
+ {{TAGBL|LREAL}} = A                      # real space projection
+ {{TAGBL|PREC}}  = Normal                 # chose Low only after tests
+ {{TAGBL|EDIFF}} = 1E-5                   # do not use default (too large drift)
+ {{TAGBL|ISMEAR}} = -1 ; SIGMA = 0.130    # Fermi smearing: 1500 K 0.086 10-3
+ {{TAGBL|ALGO}} = Very Fast               # recommended for MD (fall back ALGO = Fast)
+ {{TAGBL|MAXMIX}} = 40                    # reuse mixer from one MD step to next
+ {{TAGBL|ISYM}} = 0                       # no symmetry
+ {{TAGBL|NELMIN}} = 4                     # minimum 4 steps per time step, avoid breaking after 2 steps
+ # MD (do little writing to save disc space)
+ {{TAGBL|IBRION}} = 0 ; {{TAGBL|NSW}} = 400 ; {{TAGBL|NWRITE}} = 0 ; {{TAGBL|LCHARG}} = .FALSE. ; {{TAGBL|LWAVE}} = .FALSE.
+ {{TAGBL|TEBEG}} = $i ; {{TAGBL|TEEND}} = $i
+ # canonic (Nose) MD with {{TAGBL|XDATCAR}} updated every 10 steps
+ {{TAGBL|SMASS}} = 3 ;  {{TAGBL|NBLOCK}} = 10 ; {{TAGBL|POTIM}} = 3
+ !
+ mpirun -np 2 /path/to/your/vasp/executable
+ cp XDATCAR XDATCAR.$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
+<tt>script</tt> 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).
+=== {{TAG|KPOINTS}} ===
+<pre>
+test
+0 0
+monk
+1 1
+0 0
+</pre>
+== Calculation ==
+*To analyse the diffusion behaviour at a certain temperature T, the data read from {{FILE|XDATCAR.[T]}} can be processed
 using the following script:
-*diffusion
 <pre>
@@ Line 193: / Line 199: @@
   '
 </pre>
+'''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: <tt>mpirun -np 2</tt>).
 == Download ==