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

[John Kitchin]

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

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
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