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

[Laurent Pizzagalli]

Dear Pietro,

thank you for your help. I think that your description of what happened 
is probably accurate, because the displacement of the 'fixed' atoms is a 
bit unexpected (actually, these atoms are fixed so as to maintain a 
stress on a defect, and the stress field is changing as a function of 
the defect moving. Therefore if the 'fixed' atoms were completely free, 
the stress field would completely relax, which is not the case here.). 
The displacements are compatible with those associated to the spring 
forces only.

I will try to use the trick that you suggested. I am reasonably 
confident it could address my issue.

Thank you again,

Best regards

Laurent




On 24/10/2019 18:41, Pietro Delugas wrote:
>
> 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
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