<div dir="ltr">Thank you <span style="font-size:12.8px">Tone for your help.</span><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Naseem</span></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Naseem Ud Din<br>Graduate Student<br>University of Central Florida<br>Orlando USA<br>Cell # +1-407-683-3016</div></div></div>
<br><div class="gmail_quote">On Mon, Jul 4, 2016 at 5:29 AM, Tone Kokalj <span dir="ltr"><<a href="mailto:tone.kokalj@ijs.si" target="_blank">tone.kokalj@ijs.si</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">On Wed, 2016-06-29 at 13:45 -0400, naseem wrote:<br>
> Here is the example, where the program reads input for first and last<br>
> image correctly,<br>
> while for intermediate images the program reads the atomic<br>
> coordinates incorrectly.<br>
<br>
</span>Note that in NEB only the first and last images are used verbatim,<br>
whereas intermediate images are used only for "steering". This is how<br>
they are used:<br>
first all the images are connected linearly and then the linearized<br>
"path" length is calculated. For N images, the path is then divided<br>
into N-1 equidistant segments and the intermediate images are the<br>
"points" on this equidistant segmented linearized path, which implies<br>
that the so generated images will not coincide with the input specified<br>
images, unless you precisely calculated your intermediate input images<br>
using this algorithm. <br>
<br>
<br>
Best regards, Tone Kokalj<br>
<br>
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.<br>
<span class="HOEnZb"><font color="#888888"><br>
--<br>
<br>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia <br>
(tel: <a href="tel:%2B386-1-477-3523" value="+38614773523">+386-1-477-3523</a> // fax: <a href="tel:%2B386-1-251-9385" value="+38612519385">+386-1-251-9385</a>)<br>
</font></span><div class="HOEnZb"><div class="h5">> In this example I have the input files for 4 images and their<br>
> outputs.<br>
><br>
> Thank you so much <br>
><br>
> Naseem <br>
> <br>
><br>
><br>
><br>
><br>
> Naseem Ud Din<br>
> Graduate Student<br>
> University of Central Florida<br>
> Orlando USA<br>
> Cell # <a href="tel:%2B1-407-683-3016" value="+14076833016">+1-407-683-3016</a><br>
><br>
> On Tue, Jun 28, 2016 at 2:19 PM, naseem <<a href="mailto:naseem91@gmail.com">naseem91@gmail.com</a>> wrote:<br>
> > Dear Paolo Giannozzi<br>
> ><br>
> > The input file, I have shown here only last few coordinates for<br>
> > comparison.<br>
> ><br>
> > &CONTROL<br>
> > ! .control.settings.<br>
> > prefix = 'pwneb',<br>
> > pseudo_dir = '/home/ndin/PP',<br>
> ><br>
> > ! .<a href="http://control.io" rel="noreferrer" target="_blank">control.io</a>.<br>
> > verbosity = 'low',<br>
> > disk_io = 'low',<br>
> > wf_collect = .false.,<br>
> > outdir = './tmp/',<br>
> ><br>
> > ! .control.ion_relax.<br>
> > etot_conv_thr = 0.0001,<br>
> > forc_conv_thr = 0.001,<br>
> > nstep = 200,<br>
> > tprnfor = .true.,<br>
> > tstress = .false.,<br>
> > /<br>
> ><br>
> > &SYSTEM<br>
> > ! .system.structure.<br>
> > a = 1.0,<br>
> > ibrav = 0,<br>
> > nat = 56,<br>
> > ntyp = 5,<br>
> ><br>
> > ! .system.ecut.<br>
> > ecutwfc = 50,<br>
> > ecutrho = 300,<br>
> ><br>
> > ! .system.occupations.<br>
> > degauss = 0.007,<br>
> > smearing = 'fd',<br>
> > occupations = 'smearing',<br>
> ><br>
> > ! .system.spin_pol.<br>
> > nspin = 2,<br>
> > ! .system.starting_magnetization.<br>
> > starting_magnetization(1) = 0.0 ,<br>
> > starting_magnetization(2) = 0.0 ,<br>
> > starting_magnetization(3) = 0.0 ,<br>
> > starting_magnetization(4) = 0.5 ,<br>
> > starting_magnetization(5) = 0.0 ,<br>
> > /<br>
> ><br>
> > &ELECTRONS<br>
> > ! .electrons.<br>
> > diagonalization = 'david',<br>
> > mixing_mode = 'plain',<br>
> > electron_maxstep = 300,<br>
> > mixing_beta = 0.7,<br>
> > conv_thr = 1e-06,<br>
> > /<br>
> ><br>
> > &IONS<br>
> > ! .ions.<br>
> > pot_extrapolation = 'atomic',<br>
> > wfc_extrapolation = 'none',<br>
> > ion_dynamics = 'bfgs',<br>
> > /<br>
> ><br>
> > ATOMIC_SPECIES<br>
> > C 12.0110 C.pbe-n-kjpaw_psl.1.0.0.UPF<br>
> > H 1.0079 H.pbe-kjpaw_psl.1.0.0.UPF<br>
> > N 14.0070 N.pbe-n-kjpaw_psl.1.0.0.UPF<br>
> > Mo 95.9500 Mo.pbe-spn-rrkjus_psl.1.0.0.UPF<br>
> > O 15.9990 O.pbe-n-kjpaw_psl.1.0.0.UPF<br>
> ><br>
> > ATOMIC_POSITIONS crystal <br>
> > N 0.95485020750000 0.56357849666667 0.49624390333334<br>
> > 1 1 1<br>
> > N 0.20503544416667 0.60630526600000 0.50618120133333<br>
> > 1 1 1<br>
> > N 0.79510299916667 0.39320398866667 0.49454676300000<br>
> > 1 1 1<br>
> > N 0.90059305466666 0.50404797983333 0.49540709750000<br>
> > 1 1 1<br>
> > Mo 0.25000197816666 0.50000281250000 0.50385069500000<br>
> > 1 1 1<br>
> > Mo 0.75000097116666 0.49999966450000 0.49496505900000<br>
> > 1 1 1<br>
> > O 0.27857126900000 0.52379958000000 0.78735826900000<br>
> > 1 1 1<br>
> > O 0.21917709500000 0.47518250400000 0.78830996200000<br>
> > 1 1 1<br>
> > CELL_PARAMETERS<br>
> > 13.96747600000000 0.00000000000000 0.00000000000000<br>
> > 0.00000000000000 19.29957382133830 0.00000000000000<br>
> > 0.00000000000000 0.00000000000000 15.00000000000000<br>
> ><br>
> > K_POINTS automatic<br>
> > 3 1 1 0 0 0<br>
> ><br>
> ><br>
> > The out put reads like this<br>
> ><br>
> ><br>
> > coordinates at iteration 0<br>
> ><br>
> ><br>
> > ATOMIC_POSITIONS (crystal)<br>
> > N 0.957544089 0.564108314 0.491040077<br>
> > N 0.206819548 0.605649544 0.515574286<br>
> > N 0.796628928 0.393825710 0.491616776<br>
> > N 0.902045066 0.504897968 0.488557042<br>
> > Mo 0.249999821 0.500000792 0.503850698<br>
> > Mo 0.749998615 0.499998178 0.494965059<br>
> > O 0.278571269 0.523799580 0.690302740<br>
> > O 0.219177095 0.475182504 0.690540490<br>
> ><br>
> ><br>
> ><br>
> > Info: using nr1, nr2, nr3 values from input<br>
> ><br>
> > Info: using nr1s, nr2s, nr3s values from input<br>
> > <br>
> > Parallelization info<br>
> > --------------------<br>
> > sticks: dense smooth PW G-vecs: dense smooth <br>
> > PW<br>
> > Min 89 59 15 9347 5072 <br>
> > 655<br>
> > Max 90 60 16 9360 5110 <br>
> > 662<br>
> > Sum 22973 15343 3923 2394473 1303361<br>
> > 168491<br>
> ><br>
> ><br>
> > Thank you in advance for your help.<br>
> ><br>
> > Naseem<br>
> ><br>
> > Naseem Ud Din<br>
> > Graduate Student<br>
> > University of Central Florida<br>
> > Orlando USA<br>
> > Cell # +1-407-683-3016<br>
> ><br>
> > On Mon, Jun 27, 2016 at 1:34 PM, Paolo Giannozzi <p.giannozzi@gmail<br>
> > .com> wrote:<br>
> > > Please support your claim with some data, such as e.g. input and<br>
> > > output files<br>
> > ><br>
> > > Paolo<br>
> > ><br>
> > > On Mon, Jun 27, 2016 at 6:32 PM, naseem <<a href="mailto:naseem91@gmail.com">naseem91@gmail.com</a>><br>
> > > wrote:<br>
> > > > Dear All<br>
> > > ><br>
> > > > I am trying to calculate reaction barrier using neb. The<br>
> > > program doesn't<br>
> > > > read the coordinates correctly for intermediate image. It reads<br>
> > > correctly<br>
> > > > the coordinates of initial and final image.<br>
> > > ><br>
> > > > Any help is really appreciated.<br>
> > > ><br>
> > > > thanks<br>
> > > ><br>
> > > > Naseem Ud Din<br>
> > > > Graduate Student<br>
> > > > University of Central Florida<br>
> > > > Orlando USA<br>
> > > > Cell # <a href="tel:%2B1-407-683-3016" value="+14076833016">+1-407-683-3016</a><br>
> > > ><br>
> > > > _______________________________________________<br>
> > > > Pw_forum mailing list<br>
> > > > <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> > > > <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
> > ><br>
> > ><br>
> > ><br>
> > > --<br>
> > > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
> > > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
> > > Phone <a href="tel:%2B39-0432-558216" value="+390432558216">+39-0432-558216</a>, fax <a href="tel:%2B39-0432-558222" value="+390432558222">+39-0432-558222</a><br>
> > > _______________________________________________<br>
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> > ><br>
> ><br>
> ><br>
><br>
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