H2O molecular dynamics: Difference between revisions
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== Task == | == Task == | ||
Molecular dynamics calculation for a <math>\mathrm{H}_{2}\mathrm{O}</math> molecule. | |||
== Input == | == Input == | ||
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1.10 -1.43 0.00 T T F | 1.10 -1.43 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 the the box size is reduced to 12 a.u. | |||
=== {{TAG|INCAR}} === | === {{TAG|INCAR}} === | ||
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{{TAGBL|SMASS}} = -3 ! Nose Hoover thermostat | {{TAGBL|SMASS}} = -3 ! Nose Hoover thermostat | ||
{{TAGBL|TEBEG}} = 2000 ; {{TAGBL|TEEND}} = 2000 ! temperature | {{TAGBL|TEBEG}} = 2000 ; {{TAGBL|TEEND}} = 2000 ! temperature | ||
=== {{TAG|KPOINTS}} === | === {{TAG|KPOINTS}} === | ||
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== Calculation == | == Calculation == | ||
=== {{TAG|OSZICAR}} === | |||
An example {{TAG|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 F= -.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 | |||
(picture missing) | |||
The pair correlation function can be visualized using e.g. the following script: | The pair correlation function can be visualized using e.g. the following script: | ||
Revision as of 10:14, 28 April 2017
Overview > O atom > O atom spinpolarized > O atom spinpolarized low symmetry > O dimer > CO > CO vibration > CO partial DOS > H2O >
H2O vibration > H2O molecular dynamics > Further things to try > List of tutorials
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 the 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
OSZICAR
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 F= -.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
(picture missing)
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
To the list of examples or to the main page