[Pw_forum] PWneb reads coordinates of images incorrectly

naseem naseem91 at gmail.com
Wed Jun 29 19:45:48 CEST 2016


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
>>
>
>
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