[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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