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 <[email protected]> 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
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E-mail: <[email protected]>
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