H2O molecular dynamics: Difference between revisions

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*plot_PCDAT
*plot_PCDAT
<pre>
<pre>
awk <PCDAT >PCDAT.xy '
awk <PCDAT >PCDAT.xy '
NR==8 { pcskal=$1}
NR==8 { pcskal=$1}
NR==9 { pcfein=$1}
NR==9 { pcfein=$1}
NR>=13 {
NR>=13 {
  line=line+1
line=line+1
  if (line==257)  {
if (line==257)  {
    print " "
    print " "
    line=0
    line=0
  }
  else
    print (line-0.5)*pcfein/pcskal,$1
  }
  }
  '
  else
cat >plotfile<<!
    print (line-0.5)*pcfein/pcskal,$1
# set term postscript enhanced colour lw 2 "Helvetica" 20
}
# set output "pair_correlation.eps"
'
set title "pair-correlation of H2O at 2000 K"
cat >plotfile<<!
set xlabel "r [Angstrom]"
# set term postscript enhanced colour lw 2 "Helvetica" 20
set ylabel "g(r)"
# set output "pair_correlation.eps"
plot [0:15] "PCDAT.xy"  w lines
set title "pair-correlation of H2O at 2000 K"
!
set xlabel "r [Angstrom]"
gnuplot -persist plotfile
set ylabel "g(r)"
plot [0:15] "PCDAT.xy"  w lines
!
gnuplot -persist plotfile
</pre>
</pre>
== Download ==
== Download ==

Revision as of 11:53, 23 August 2016

  • 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
 1        ! one k-point
rec       ! in units of the reciprocal lattice vector
 0 0 0 1  ! 3 coordinates and weight
  • 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

the pair correlation function can be visualized using e.g. the following script:

  • plot_PCDAT
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
}
'
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.xy"  w lines
!
gnuplot -persist plotfile

Download

1_10_H2Omd.tgz


To the list of examples or to the main page