[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
Graduate Student
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
> 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
> > > > _______________________________________________
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> > > > Pw_forum at pwscf.org
> > > > http://pwscf.org/mailman/listinfo/pw_forum
> > > >
> > >
> > >
> >
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