[Pw_forum] NEB in QE 4.3: NaN values of some of the initially generated images

[Torstein Fjermestad]

 Dear Layla,

 thanks for your suggestion.

 Unfortunately setting nstep_path=1 did not solve the problem. Image 3 
 and 4 of the .path file contained the NaN values just as before.

 In the output file of the calculation it says nearly at the top:

      initial path length           =     NaN bohr
      initial inter-image distance  =     NaN bohr

 To me this result seems fairly obvious. Because two of the initial 
 images contain NaN values, there is no way in which the program can 
 calculate the initial path length.
 

 Some lines further down it says:

        ------------------------------ iteration   1 
 ------------------------------

      tcpu =      3.0    self-consistency for image   1
      tcpu =    129.3    self-consistency for image   2

  
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      from coset : error #         1
      nsym == 0
  
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

      stopping ...


 The way I interpret this information is that the program manages to 
 finish the SCF cycle for image 1 and 2, but when it comes to image 3 it 
 fails because that structure consists only of NaN values.

 The origin of the problem seems to lay in the generation of the initial 
 images.
 Does anyone have further suggestions on how to solve this problem?

 Thank you very much in advance.

 Yours sincerely

 Torstein Fjermestad

 


 On Tue, 17 Jan 2012 15:18:25 +0100, Layla Martin-Samos 
 <lmartinsamos at gmail.com> wrote:
> Dear Torstein, nstep_path=0 produces a "strange behavior" as NEB
> starts counting at 1. So if you just set nstep_path=1 it should work.
>
> bests
>
> Layla
>
> 2012/1/16 Torstein Fjermestad
>  Dear all,
>
>  I have recently made several attempts to submit a NEB calculation
> using Quantum Espresso version 4.3.
>  Unfortunately, every attempt fails with the program printing NaN
> values instead of the Cartesian coordinates for some of the initial
> images. For instance, in the .path file corresponding to the attached
> input file, image 3 and 4 (num_of_images=5) consists entirely of NaN
> values instead of real Cartesian coordinates. Of cause, if some of 
> the
> initial images consist only of NaN values the calculation has no
> chance of continuing.
>
>  There have been significant changes in the way to submit a NEB
> calculation between version 4.2.1 and version 4.3, and to test 
> whether
> the same behavior would occur in version 4.2.1, I submitted a NEB
> calculation with QE version 4.2.1 with exactly the same input
> structures. In that case the program had no problem in generating the
> initial images. Because of this I think we can exclude the 
> possibility
> of the error being caused by the input coordinates themselves.
>
>  In the script I used to submit the calculation, the line to run the
> neb.x executable is the following:
>
>  mpirun -np 16 -npernode 8 neb.x -inp neb_11.inp > neb_11.out
>
>  Have any of you come across a similar problem before?
>  Does anyone have suggestions on how to prevent the NaN values from
> appearing?
>
>  Thanks in advance.
>
>  Yours sincerely
>
>  Torstein Fjermestad
>  University of Oslo,
>  Norway.
>
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