[Pw_forum] PWneb reads coordinates of images incorrectly
Paolo Giannozzi
p.giannozzi at gmail.com
Thu Jun 30 14:57:04 CEST 2016
The NEB code performs a linear interpolation of the "images" (routine
"initial_guess", module "path_base"). This is the expected behavior if
one provides only the end points. If one provides an already
interpolated path, it has no effect. If however you provide a path
that doesn't fall in either cases, intermediate images will be
modified (actually, overwritten). I am not a big NEB expert so I am
not sure this is the expected or desired behavior. If you do not like
such behavior, the only solution I see is to modify the mentioned
routine in such a way that it doesn't alter the input path if the
number of input images is equal to the number of desired images
Paolo
On Wed, Jun 29, 2016 at 7:45 PM, naseem <naseem91 at gmail.com> wrote:
>
> 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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--
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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