[CPMD-list] isolated molecule translation during dynamics
Yong Zhang
zhangymall11 at gmail.com
Mon Jan 22 16:07:00 CET 2007
I gave an initial temperature of 300K.
I first run a traj with "tempcontrol" in order to equilibrate the system
somehow, then run NVE md restart from the last point.
"tempcontrol" input:
##############
&INFO
isolated NMA
RESTART WAVEFUNCTION COORDINATES VELOCITIES ACCUMULATORS LATEST
&END
&CPMD
MOLECULAR DYNAMICS BO
RESTART WAVEFUNCTION COORDINATES LATEST
CONVERGENCE ORBITALS
1.0e-7
REAL SPACE WFN KEEP SIZE
256
EXTRAPOLATE WFN
3
TEMPCONTROL IONS
300.0 30.0
TIMESTEP
20.0
MAXSTEP
1000
TRAJECTORY XYZ SAMPLE
10
&END
&SYSTEM
ANGSTROM
SYMMETRY
1
CELL
12.00 1.0 1.0 0 0 0
CUTOFF
90.0
&END
&DFT
NEWCODE
FUNCTIONAL PBE
GC-CUTOFF
5.0e-6
&END
&ATOMS
ISOTOPE
1.0
2.0
12.0
14.0
16.0
*H_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=S
6
1.69080 .05583 .88430
3.28199 -.14332 .06344
2.16794 -1.45255 .00207
-1.58359 .17630 -2.35128
-.19701 .20889 -3.48962
-.49100 1.60271 -2.37391
*H_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=S
1
-.22859 -.88824 -.93883
*C_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=P
3
2.18368 -.34882 .01350
1.56123 .24388 -1.15711
-.53752 .48601 -2.44731
*N_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=P
1
.32592 -.14815 -1.44467
*O_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=P
1
2.16429 1.09559 -1.77796
&END
##################
follwoing NVE runs
##################
&INFO
isolated NMA
&END
&CPMD
MOLECULAR DYNAMICS BO
RESTART WAVEFUNCTION COORDINATES VELOCITIES ACCUMULATORS LATEST
CONVERGENCE ORBITALS
1.0e-7
REAL SPACE WFN KEEP SIZE
256
EXTRAPOLATE WFN
3
TEMPERATURE
300.0
TIMESTEP
20.0
MAXSTEP
1000
TRAJECTORY XYZ SAMPLE FORCES DCD
2
DIPOLE DYNAMICS SAMPLE WANNIER
2
WANNIER REFERENCE
0.0 0.0 0.0
WANNIER SERIAL
&END
&SYSTEM
ANGSTROM
SYMMETRY
1
CELL
12.00 1.0 1.0 0 0 0
CUTOFF
90.0
&END
&DFT
NEWCODE
FUNCTIONAL PBE
GC-CUTOFF
5.0e-6
&END
&ATOMS
ISOTOPE
1.0
2.0
12.0
14.0
16.0
*H_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=S
6
1.69080 .05583 .88430
3.28199 -.14332 .06344
2.16794 -1.45255 .00207
-1.58359 .17630 -2.35128
-.19701 .20889 -3.48962
-.49100 1.60271 -2.37391
*H_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=S
1
-.22859 -.88824 -.93883
*C_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=P
3
2.18368 -.34882 .01350
1.56123 .24388 -1.15711
-.53752 .48601 -2.44731
*N_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=P
1
.32592 -.14815 -1.44467
*O_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=P
1
2.16429 1.09559 -1.77796
&END
#####################
On 1/22/07, Ari P Seitsonen <ari.p.seitsonen at iki.fi> wrote:
>
>
> Dear Yong,
>
> How did you assign the initial velocities, by hand or by giving an
> initial temperature? Could you please also provide your input file, it
> seems very strange that the molecule would translate that much.
>
> Greetings from Trieste,
>
> apsi
>
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
> Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
> IMPMC, CNRS & Université Pierre et Marie Curie
> Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820
>
> On Mon, 22 Jan 2007, Yong Zhang wrote:
>
> > Thanks for all these suggestions. I am testing the SUBTRACT keyword now.
> >
> > For the symmetry=0 or 1, the manual says, "for many systems using a
> large
> > enough cell and pbc is also an option. ...except in difficult cases such
> as
> > charged molecules..." and "the pbc calculation is always cheaper for a
> box
> > of the same size". Because I have a neutral molecule, I expect similar
> > results by using either symmetry=0 or 1. But, to be honest, I do not
> have
> > special reason to perfer one over the other. And actually, I do not
> really
> > know the advange or disadvantage of one over the other one, especially
> for
> > my system. I appreciate if you or anyone can put more comments on this.
> >
> > Thanks.
> > Yong
> >
> >
> > On 1/22/07, Nisanth Nair <nisanth.nair at theochem.ruhr-uni-bochum.de>
> wrote:
> >>
> >> Hi
> >> One more thing; use also SYMMETRY 0 for isolated molecule. See more
> >> details in
> >> the manual.
> >> cheers,
> >> Nisanth
> >>
> >> On Sunday 21 January 2007 14:12, Juerg Hutter wrote:
> >> > Hi
> >> >
> >> > check the manual for the keywords
> >> >
> >> > SUBTRACT COMVEL
> >> > SUBTRACT ROTVEL
> >> >
> >> > regards
> >> >
> >> > Juerg Hutter
> >> >
> >> > ----------------------------------------------------------
> >> > Juerg Hutter Phone : ++41 44 635 4491
> >> > Physical Chemistry Institute FAX : ++41 44 635 6838
> >> > University of Zurich E-mail: hutter at pci.unizh.ch
> >> > Winterthurerstrasse 190
> >> > CH-8057 Zurich, Switzerland
> >> > ----------------------------------------------------------
> >> >
> >> > On Sat, 20 Jan 2007, Yong Zhang wrote:
> >> > > Hi,
> >> > >
> >> > > I am running BOMD on a isolated, neutral, small molecule (with
> >> dimension
> >> > > < 5A). I used symmetry=1 with a "large enough cell" of 12A. No"
> NOSE"
> >> was
> >> > > used. I found the molecule translated a lot during the MD: the
> >> molecule
> >> > > was at the center of the box (0,0,0) in the beginning, but the
> >> > > coordinates changed to something like (-80, 95, -130) after a
> while,
> >> > > which is much larger than the box dimension. I checked the molecule
> >> > > structure, it seems ok. But will this cause any problem? Is there a
> >> way
> >> > > to remove this translation?
> >> > > Thanks
> >> > >
> >> > > Yong
> >> >
> >> > _______________________________________________
> >> > CPMD-list mailing list
> >> > CPMD-list at cpmd.org
> >> > http://cpmd.org/mailman/listinfo/cpmd-list
> >>
> >> --
> >>
> >>
> ===========================================================================
> >> Nisanth N. Nair
> >> Lehrstuhl fuer Theoretische Chemie Tel: ++49 (0)234 32 22121
> >> Ruhr-Universitaet Bochum Fax: ++49 (0)234 32 14045
> >> Universitaetstrasse 150
> >> D-44801 Bochum, Germany
> >> Email: nisanth.nair at theochem.ruhr-uni-bochum.de
> >> Web : http://www.theochem.ruhr-uni-bochum.de
> >>
> >>
> ===========================================================================
> >>
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://cpmd.org/pipermail/cpmd-list/attachments/20070122/0ef29bab/attachment.html
More information about the CPMD-list
mailing list