[ase-users] atomic symbols in netcdf file get lost

[Jakob Schiotz]

On Thursday 22 January 2009, John Kitchin wrote:
> was there ever any resolution to what caused the problem at:
>
> https://listserv.fysik.dtu.dk/pipermail/campos/2007-June/002261.html
>
> the issue is related to the final error:
>     Z = numbers[symbol]
> KeyError: '\x00\x00'
> which is caused because in the netcdf file the atomic symbols are replaced
> by '\x00\x00'
> I have seen this problem intermittently over the years, and am seeing it
> again intermittently lately, especially with parallel NEB calculations.
>
> I am suspicious that somehow this is a problem with the netcdf library
> because the text in the key error above looks alot like

I cannot really help you, I have not seen the problem myself.  But a few 
thoughts:  The \x00\x00 characters are two 0-bytes, so it is most likely 
caused by uninitialized data.  Does ncdump show something useful for the 
atomic symbols?  Could it be that the writing script crashed before the 
NetCDF files was properly closed?

/Jakob


>
> NC_CHAR      = '\x00\x00\x00\x02'  (from the pupynere documentation at). I
> am not using pupynere here, but the character strings look similar. it
> almost looks like the netcdf library is reading from the wrong place in the
> file. I can't explain why the rest of the ncfile looks fine though.
> I also suspect the timing of when dacapo fortran does something to the
> netcdf file and when python does something, but as I mentioned, the problem
> is intermittent.
>
> any ideas? or solutions from the past?
>
> thanks,
>
> j
>
> -----------------------------------
> John Kitchin
> Assistant Professor
> NETL-IAES Resident Institute Fellow
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> http://kitchingroup.cheme.cmu.edu



-- 
Jakob Schiotz, Ph.D., Associate professor (lektor)
CINF, Department of Physics
Technical University of Denmark
DK-2800 Kongens Lyngby, Denmark
http://www.cinf.dtu.dk/~schiotz/