Known issues¶
Feel free to drop them as issues here. In decreasing order of relevance we are aware of the following technical issues with pynxtools-apm and its use in NOMAD OASIS.
Eventually slow charge state analysis¶
When the ranging definitions have molecular ions which are composed from many atoms and elements with many isotopes it is possible that the interpretation of the ranging definitions can take long. The situation is case dependent. The reason is that a combinatorial algorithm is used for identifying the charge state(s) from the ranging definitions. The computation time of this algorithm depends on the number of isotopic combinations.
Warnings about non-finite values in NOMAD's parsing log¶
NOMAD by definition does not index non-finite values in its elasticsearch software component. The charge state analysis typically though sets the half-life of each candidate to be infinite. This non-finite real value is picked up by NOMAD during the parsing stage and causes these warnings but does not cause the parsing to fail.
Limits on the complexity of molecular ions¶
pynxtools-apm currently supports to define molecular ions with up to 32 atoms. This covers for almost all cases of molecular ions typically studied with atom probe. Note that in mass spectrometry fragments with a considerable larger number of atoms are observed but telling them apart in atom probe would in practice be even more complicated than it is in mass spectrometry. Users who seriously wish to have this limit raised should file an issue here.
Too many ranging definitions when working with paraprobe-toolbox in a NOMAD Remote Tools Hub.¶
The post-processing software paraprobe-toolbox currently supports working with up to 255 ranging definitions. In all cases where we have seen range files from groups across the world where more ranging definitions have been made, these were typically duplicated definitions. The NeXus/HDF5 representation and NXapm allow to have more than 255 ranging definitions. However, entries with numbers above this limited may cause issues during post-processing with NORTH as not all analysis tools are able to deal with more than 255 ranging definitions.
Ranging definitions occasionally triggering a NOMAD parsing failure¶
We observed two cases so far where parsing ranging definitions with both more than approximately thousand molecular ions did not parse successfully, likely because of running limitations as a consequence of conservative default settings in a default NOMAD installation related to elasticsearch.
A more detailed overview for resolving molecular ions in atom probe is available in the literature.
Slow verification of instance data against cardinality and existence constraints for outdated versions of pynxtools-apm¶
Version of pynxtools-apm which used pynxtools<=0.2.1 are known to face the issue that the verification of the instantiated schema can be slow. With pynxtools>=0.3.1 this issues has been fixed thanks to a refactored verification algorithm.