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H2O molecular dynamics

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Task

Molecular dynamics calculation for a molecule.

Input

POSCAR

H2O _2
0.52918   ! scaling parameter
 12 0 0
 0 12 0
 0 0 12
1 2
select
cart
     0.00     0.00     0.00 T T F
     1.10    -1.43     0.00 T T F
     1.10     1.43     0.00 T T F

To save time the box size is reduced to 12 a.u.

INCAR

PREC = Normal    ! standard precision 
ENMAX = 400      ! cutoff should be set manually
ISMEAR = 0 ; SIGMA = 0.1
ISYM = 0         ! strongly recommended for MD
IBRION = 0       ! molecular dynamics
NSW = 100        ! 100 steps
POTIM = 1.0      ! timestep 1 fs
SMASS = -3       ! Nose Hoover thermostat
TEBEG =  2000 ; TEEND = 2000 ! temperature


KPOINTS

Gamma-point only
 0
Monkhorst Pack
 1 1 1
 0 0 0

Calculation

  • An example OSZICAR file (with 1000 steps and a step size of 0.5 fs) looks like this:
1 T=  2134. E= -.13655511E+02 F= -.14207209E+02 E0=.. EK= 0.55170E+00 SP= 0.00E+00 SK= 0.00E+00
2 T=  1971. E= -.13643254E+02 F= -.14152912E+02 E0=.. EK= 0.50966E+00 SP= 0.00E+00 SK= 0.00E+00
3 T=  1336. E= -.13629241E+02 Fd, which just encloses the cutoff sphere corresponding to the plane wave cutoff, is used. This accelerates the calculations by roughly a factor two to three, but causes slight changes in the tot= -.13974630E+02 E0=.. EK= 0.34539E+00 SP= 0.00E+00 SK= 0.00E+00
4 T=  1011. E= -.13624149E+02 F= -.13885486E+02 E0=.. EK= 0.26134E+00 SP= 0.00E+00 SK= 0.00E+00
5 T=  1307. E= -.13629772E+02 F= -.13967549E+02 E0=.. EK= 0.33778E+00 SP= 0.00E+00 SK= 0.00E+00

Fig H2O 1.png

  • The pair correlation function can be visualized using e.g. the following script:
  • plot_PCDAT
awk <PCDAT >PCDAT.dat '
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
}
'
cat >plotfile<<!
# set term postscript enhanced colour lw 2 "Helvetica" 20
# set output "pair_correlation.eps"
set title "pair-correlation of H2O at 2000 K"
set xlabel "r [Angstrom]"
set ylabel "g(r)"
plot [0:15] "PCDAT.dat"  w lines
!
gnuplot -persist plotfile

Download

H2Omd.tgz

d, which just encloses the cutoff sphere corresponding to the plane wave cutoff, is used. This accelerates the calculations by roughly a factor two to three, but causes slight changes in the tot Back to the main page.