[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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