[QE-users] NEB calculation issue with 'fixed' atoms

[Laurent Pizzagalli]

Dear Giuseppe,

you are certainly right, according to the generated output files. It was 
not explicitely mentioned in the documentation (or I did not find it), 
and I (wrongly) supposed that it could work.

Thank you for your help.

Best regards

Laurent


On 24/10/2019 20:16, Giuseppe Mattioli wrote:
>
> Dear Laurent
> AFAIK, in NEB you can only fix atoms once, in the initial image, and 
> keep them fixed across the whole reaction coordinate (no need to add 0 
> 0 0 in images 2...final).
> HTH
> Giuseppe
>
> Pietro Delugas <pdelugas at sissa.it> ha scritto:
>
>> Dear Laurent
>>
>> It might be that the  fixed-position acts only at the "engine" level 
>> inside pw, the forces are then are sent to the path level and there 
>> the longitudinal component  is changed accordingly to the neb 
>> algorithm you are using,  if the neb part of the program is unaware 
>> of the fixed positions then these atoms could be moved.  When fixed 
>> positions are equal for all the images this is not an issue as 
>> distances on that coordinate are all zero and the longitudinal 
>> reaction will also be 0.
>>
>> I am just guessing though. I should look in the code to see if this 
>> is   what's actually  happening.
>>
>> In the meantime you could try  set
>>
>> use_masses =  .true.  in the &path namelist and then specify 
>> fictitious masses,  something like 1 for atoms which are free to move 
>> and 10000 for the fixed ones.
>>
>> hope it helps
>>
>> regards - Pietro
>>
>> On 21/10/19 10:08, Laurent Pizzagalli wrote:
>>> Dear all,
>>>
>>> I encountered a weird and unexpected behavior when running a NEB 
>>> calculation with QE. In this calculation, several (boundary) atoms 
>>> are fixed. All initial images were provided in the input file, with 
>>> the required flags "1 1 1" for mobile and "0 0 0" for fixed atoms. 
>>> However, during NEB iterations, the positions of the fixed atoms are 
>>> updated with new values, which is obviously something I'd like to 
>>> avoid. It appears in all images, except in the first one.
>>> I do not understand the issue, because in the 'PW.out' output files 
>>> contained in the subdirectories associated to each image, one can 
>>> clearly see that the '0 0 0' flags are correctly set for the fixed 
>>> atoms, for all images, and are conserved throughout the 
>>> calculations. Still, the coordinates of these atoms are evolving. 
>>> Moreover, in the .crd ouput file in the main directory, which 
>>> includes the updated coordinates for all images during the NEB 
>>> calculations, only the fixed atoms of the first image have the '0 0 
>>> 0' flags.
>>>
>>> One specificity of my calculation is that the (x,y,z) positions of 
>>> the fixed atoms change from one image to the other (but the ordering 
>>> of the atoms in each image is the same). This is not common, and I 
>>> was wondering whether this could be the cause of my issue? If not, I 
>>> do not have a clue why I got this weird behavior.
>>>
>>> Any help or suggestions are welcome,
>>>
>>> Best regards
>>>
>>> L. Pizzagalli
>>> _______________________________________________
>>> Quantum ESPRESSO is supported by MaX 
>>> (www.max-centre.eu/quantum-espresso)
>>> users mailing list users at lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
>
> GIUSEPPE MATTIOLI
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> Via Salaria Km 29,300 - C.P. 10
> I-00015 - Monterotondo Scalo (RM)
> Mob (*preferred*) +39 373 7305625
> Tel + 39 06 90672342 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
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<Laurent.Pizzagalli at univ-poitiers.fr>
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