[CPMD-list] about vibrational analysis

[Yong Zhang]

Hi

Thank Juerg Hutter for the suggestion. I am trying this now.
I have a question about the energy terms in CPMD calculation. I will need
the total potential energy for each C=O length, which I guess should be
(E1+L+N+X). I found in the output file E1=A-S+R. I guess S is the
electron-electron repulsion energy, but what is A and R?

Thanks

On 11/17/06, Juerg Hutter <hutter at pci.unizh.ch> wrote:
>
> Hi
>
> it seems that what you see is an effect of the anharmonicity
> of the C=O bond (and environment). The force field
> is much more harmonic (iposed by its analytic form) then
> DFT. You could do the following test:
> Calculate the C=O mode for H2CO for different C-O
> bond lengths or map out the potential along the C-O
> bond and then calculate what the distribution of
> frequencies would be using your method (instantaneous
> harmonic approximation).
>
> 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 Mon, 13 Nov 2006, Yong Zhang wrote:
>
> > Hi CPMDers,
> >
> > I have a question about vibrational analysis in cpmd.
> > My system is one N-methylacetamide molecule (with N-H deuterated to N-D)
> in
> > vacuum. The situation is like this: I generated a trajectory (10ps)
> > following general procedure (with Nose Hoover thermostat at 300K); then
> 80
> > snapshots were taken from this traj (one every 100fs for the 8ps); for
> each
> > of these snapshots, a wavefunction ompimization was carried out, and
> based
> > on this optimized wavefunction (by "restart wavefunction..."), the freq
> was
> > calculated using FD method; Then I checked the C=O stretching frequency
> (so
> > called amide I mode). Surprisingly, the freq has a distribution over the
> > range as wide as 400cm-1 (1500cm-1 ~ 1900cm-1). The experimental
> observation
> > of this mode in gas phase is 1717cm-1. I did the similar calculation
> using
> > charmm force field, the freq distribution is much narrower (1685+/-15
> cm-1),
> > which is more reasonable under harmonic approximation. So my question
> is,
> > why the freq dirtribution in CPMD calaulation is so wide?
> >
> > If quench the snapshots to a minimized structure and do the freq ana,
> their
> > freq are close to each other, which might indicate a "single" local
> minimum.
> > I also tried LR for freq calculation, the resultant freq is about 10cm-1
> > lower than the corresponding FD one for all cases; I also tried BO
> dynamics,
> > similar results.
> >
> > Any comments or suggestions are appreciated.
> >
> > Best wishes
> > Yong
> >
> >
> > The input file for dynamics run:
> > ==================
> > &CPMD
> > MOLECULAR DYNAMICS CP
> > RESTART WAVEFUNCTION COORDINATES VELOCITIES ACCUMULATORS LATEST
> >
> > TEMPERATURE
> > 300.0
> > NOSE IONS MASSIVE
> > 300.0 1700.0
> > NOSE ELECTRONS
> > 0.002 10000.0
> >
> > TIMESTEP
> > 4.0
> >
> > MAXSTEP
> > 10000
> >
> > EMASS
> > 500.0
> >
> > TRAJECTORY XYZ SAMPLE
> > 5
> >
> > DIPOLE DYNAMICS SAMPLE WANNIER
> > 10
> > WANNIER REFERENCE
> > 0.0 0.0 0.0
> >
> > &END
> >
> > &SYSTEM
> > ANGSTROM
> > SYMMETRY
> > 1
> > CELL
> > 12.14  1.0  1.0  0  0  0
> > CUTOFF
> > 70.0
> > &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
> >
> > ======================
> >
> >
> >
> > input file for vib ana:
> > =====================
> > &CPMD
> > VIBRATIONAL ANALYSIS FD GAUSS SAMPLE
> > 2
> > RESTART WAVEFUNCTION COORDINATES LATEST
> > &END
> >
> > &SYSTEM
> > ANGSTROM
> > SYMMETRY
> > 1
> > CELL
> > 12.14  1.0  1.0  0  0  0
> > CUTOFF
> > 70.0
> > &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
> > ======================
> >
>
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