-
Notifications
You must be signed in to change notification settings - Fork 23
Description
Description
When calculating PDF from ICSD .cif
files, there exists ~70k files that would raise ValueError: Unknown atom or ion symbol
.
To Reproduce
Take icsd_000001.cif
as example. First load the file and create a structure
instance using diffpy.structure
, then try calculating the PDF by calling diffpy.srreal.pdfcalculator.PDFCalculator
. It will raise ValueError: Unknown atom or ion symbol 'Te4+'.
.
Traceback
The error is raised in findWKFormula
function in libdiffpy
. With further investigation this error occurs when the ion (atom bare symbol with atom valence) is not in the file f0_WaasKirf.dat
. The file was created in 2002 (the link inside is outdated) but I found the most recent version of it on ESRF Anonymous FTP Server. The new version can't solve the issue though, as there's still no data of ions such as Te4+
.
Guessing
We might need to add new items in the existing file, or write functions to convert missing ion to existing entries.
Also see diffpy/libdiffpy#33