[Pw_forum] PWneb reads coordinates of images incorrectly
naseem
naseem91 at gmail.com
Mon Jul 4 20:49:53 CEST 2016
Thank you for your help.
Naseem
Naseem Ud Din
Graduate Student
University of Central Florida
Orlando USA
Cell # +1-407-683-3016
On Thu, Jun 30, 2016 at 8:57 AM, Paolo Giannozzi <p.giannozzi at gmail.com>
wrote:
> The NEB code performs a linear interpolation of the "images" (routine
> "initial_guess", module "path_base"). This is the expected behavior if
> one provides only the end points. If one provides an already
> interpolated path, it has no effect. If however you provide a path
> that doesn't fall in either cases, intermediate images will be
> modified (actually, overwritten). I am not a big NEB expert so I am
> not sure this is the expected or desired behavior. If you do not like
> such behavior, the only solution I see is to modify the mentioned
> routine in such a way that it doesn't alter the input path if the
> number of input images is equal to the number of desired images
>
> Paolo
>
> On Wed, Jun 29, 2016 at 7:45 PM, naseem <naseem91 at gmail.com> wrote:
> >
> > Dear Paolo Giannozzi
> >
> > Thanks for your help.
> > Here is the example, where the program reads input for first and last
> image
> > correctly,
> > while for intermediate images the program reads the atomic coordinates
> > incorrectly.
> > In this example I have the input files for 4 images and their outputs.
> >
> > Thank you so much
> >
> > Naseem
> >
> >
> >
> >
> >
> > Naseem Ud Din
> > Graduate Student
> > University of Central Florida
> > Orlando USA
> > Cell # +1-407-683-3016
> >
> > On Tue, Jun 28, 2016 at 2:19 PM, naseem <naseem91 at gmail.com> wrote:
> >>
> >> Dear Paolo Giannozzi
> >>
> >> The input file, I have shown here only last few coordinates for
> >> comparison.
> >>
> >> &CONTROL
> >> ! .control.settings.
> >> prefix = 'pwneb',
> >> pseudo_dir = '/home/ndin/PP',
> >>
> >> ! .control.io.
> >> verbosity = 'low',
> >> disk_io = 'low',
> >> wf_collect = .false.,
> >> outdir = './tmp/',
> >>
> >> ! .control.ion_relax.
> >> etot_conv_thr = 0.0001,
> >> forc_conv_thr = 0.001,
> >> nstep = 200,
> >> tprnfor = .true.,
> >> tstress = .false.,
> >> /
> >>
> >> &SYSTEM
> >> ! .system.structure.
> >> a = 1.0,
> >> ibrav = 0,
> >> nat = 56,
> >> ntyp = 5,
> >>
> >> ! .system.ecut.
> >> ecutwfc = 50,
> >> ecutrho = 300,
> >>
> >> ! .system.occupations.
> >> degauss = 0.007,
> >> smearing = 'fd',
> >> occupations = 'smearing',
> >>
> >> ! .system.spin_pol.
> >> nspin = 2,
> >> ! .system.starting_magnetization.
> >> starting_magnetization(1) = 0.0 ,
> >> starting_magnetization(2) = 0.0 ,
> >> starting_magnetization(3) = 0.0 ,
> >> starting_magnetization(4) = 0.5 ,
> >> starting_magnetization(5) = 0.0 ,
> >> /
> >>
> >> &ELECTRONS
> >> ! .electrons.
> >> diagonalization = 'david',
> >> mixing_mode = 'plain',
> >> electron_maxstep = 300,
> >> mixing_beta = 0.7,
> >> conv_thr = 1e-06,
> >> /
> >>
> >> &IONS
> >> ! .ions.
> >> pot_extrapolation = 'atomic',
> >> wfc_extrapolation = 'none',
> >> ion_dynamics = 'bfgs',
> >> /
> >>
> >> ATOMIC_SPECIES
> >> C 12.0110 C.pbe-n-kjpaw_psl.1.0.0.UPF
> >> H 1.0079 H.pbe-kjpaw_psl.1.0.0.UPF
> >> N 14.0070 N.pbe-n-kjpaw_psl.1.0.0.UPF
> >> Mo 95.9500 Mo.pbe-spn-rrkjus_psl.1.0.0.UPF
> >> O 15.9990 O.pbe-n-kjpaw_psl.1.0.0.UPF
> >>
> >> ATOMIC_POSITIONS crystal
> >> N 0.95485020750000 0.56357849666667 0.49624390333334 1
> 1
> >> 1
> >> N 0.20503544416667 0.60630526600000 0.50618120133333 1
> 1
> >> 1
> >> N 0.79510299916667 0.39320398866667 0.49454676300000 1
> 1
> >> 1
> >> N 0.90059305466666 0.50404797983333 0.49540709750000 1
> 1
> >> 1
> >> Mo 0.25000197816666 0.50000281250000 0.50385069500000 1
> 1
> >> 1
> >> Mo 0.75000097116666 0.49999966450000 0.49496505900000 1
> 1
> >> 1
> >> O 0.27857126900000 0.52379958000000 0.78735826900000 1
> 1
> >> 1
> >> O 0.21917709500000 0.47518250400000 0.78830996200000 1
> 1
> >> 1
> >> CELL_PARAMETERS
> >> 13.96747600000000 0.00000000000000 0.00000000000000
> >> 0.00000000000000 19.29957382133830 0.00000000000000
> >> 0.00000000000000 0.00000000000000 15.00000000000000
> >>
> >> K_POINTS automatic
> >> 3 1 1 0 0 0
> >>
> >>
> >> The out put reads like this
> >>
> >>
> >> coordinates at iteration 0
> >>
> >>
> >> ATOMIC_POSITIONS (crystal)
> >> N 0.957544089 0.564108314 0.491040077
> >> N 0.206819548 0.605649544 0.515574286
> >> N 0.796628928 0.393825710 0.491616776
> >> N 0.902045066 0.504897968 0.488557042
> >> Mo 0.249999821 0.500000792 0.503850698
> >> Mo 0.749998615 0.499998178 0.494965059
> >> O 0.278571269 0.523799580 0.690302740
> >> O 0.219177095 0.475182504 0.690540490
> >>
> >>
> >>
> >> Info: using nr1, nr2, nr3 values from input
> >>
> >> Info: using nr1s, nr2s, nr3s values from input
> >>
> >> Parallelization info
> >> --------------------
> >> sticks: dense smooth PW G-vecs: dense smooth
> PW
> >> Min 89 59 15 9347 5072
> 655
> >> Max 90 60 16 9360 5110
> 662
> >> Sum 22973 15343 3923 2394473 1303361
> 168491
> >>
> >>
> >> Thank you in advance for your help.
> >>
> >> Naseem
> >>
> >> Naseem Ud Din
> >> Graduate Student
> >> University of Central Florida
> >> Orlando USA
> >> Cell # +1-407-683-3016
> >>
> >> On Mon, Jun 27, 2016 at 1:34 PM, Paolo Giannozzi <p.giannozzi at gmail.com
> >
> >> wrote:
> >>>
> >>> Please support your claim with some data, such as e.g. input and output
> >>> files
> >>>
> >>> Paolo
> >>>
> >>> On Mon, Jun 27, 2016 at 6:32 PM, naseem <naseem91 at gmail.com> wrote:
> >>> > Dear All
> >>> >
> >>> > I am trying to calculate reaction barrier using neb. The program
> >>> > doesn't
> >>> > read the coordinates correctly for intermediate image. It reads
> >>> > correctly
> >>> > the coordinates of initial and final image.
> >>> >
> >>> > Any help is really appreciated.
> >>> >
> >>> > thanks
> >>> >
> >>> > Naseem Ud Din
> >>> > Graduate Student
> >>> > University of Central Florida
> >>> > Orlando USA
> >>> > Cell # +1-407-683-3016
> >>> >
> >>> > _______________________________________________
> >>> > Pw_forum mailing list
> >>> > Pw_forum at pwscf.org
> >>> > http://pwscf.org/mailman/listinfo/pw_forum
> >>>
> >>>
> >>>
> >>> --
> >>> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> >>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> >>> Phone +39-0432-558216, fax +39-0432-558222
> >>> _______________________________________________
> >>> Pw_forum mailing list
> >>> Pw_forum at pwscf.org
> >>> http://pwscf.org/mailman/listinfo/pw_forum
> >>
> >>
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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