# [Pw_forum] PWneb reads coordinates of images incorrectly

naseem naseem91 at gmail.com
Mon Jul 4 20:50:23 CEST 2016

```Thank you Tone  for your help.

Naseem

Naseem Ud Din
University of Central Florida
Orlando USA
Cell # +1-407-683-3016

On Mon, Jul 4, 2016 at 5:29 AM, Tone Kokalj <tone.kokalj at ijs.si> wrote:

> 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
>
> --
>
> 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
> > 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
> > >
> > >
> > >
> > > Naseem
> > >
> > > Naseem Ud Din
> > > 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
> > > > _______________________________________________
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> > > >
> > >
> > >
> >
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