[Pw_forum] PWneb reads coordinates of images incorrectly
Tone Kokalj
tone.kokalj at ijs.si
Mon Jul 4 11:29:52 CEST 2016
On Wed, 2016-06-29 at 13:45 -0400, naseem wrote:
> 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.
Note that in NEB only the first and last images are used verbatim,
whereas intermediate images are used only for "steering". This is how
they are used:
first all the images are connected linearly and then the linearized
"path" length is calculated. For N images, the path is then divided
into N-1 equidistant segments and the intermediate images are the
"points" on this equidistant segmented linearized path, which implies
that the so generated images will not coincide with the input specified
images, unless you precisely calculated your intermediate input images
using this algorithm.
Best regards, Tone Kokalj
PS: As an illustration a simple example can be done on the sheet of paper, i.e., draw several points and connect them with line segments (start at the first and finish at the last point); then calculate the linearized "path" length. For N points divide the path into N-1 segments and you have found the your intermediate points.
--
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax: +386-1-251-9385)
> 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
> > >
> >
> >
>
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