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lsmo-epfl / aiida-zeopp

AiiDA plugin for zeo++
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Raise warning if CIF file shows signs of zeo++ incompatibility #62

Closed ltalirz closed 3 years ago

ltalirz commented 3 years ago

As (re)discovered by @mpougin, the zeo++ CIF parser is very fragile, and CIFs it does not understand can result in weird errors (even "out of memory" in her case).

If some of these issues are easy to detect, the prepare_for_submission function could check for signs of these and raise a warning or even an exception.

@mpougin @danieleongari @pzarabadip
If we could collect examples of "working" and "broken" CIF files here, we could then implement those in the plugin.

mpougin commented 3 years ago

I just recently had problems with the following structure: ZIF-67_opt.cif (auto-created by AiiDA-DDEC plugin) gives "out of memory" error. I manually corrected it (ZIF-67_opt2.cif) that runs without problems ZIF-67_opt.txt ZIF-67_opt2.txt

ltalirz commented 3 years ago

fixed directly in zeo++ by PR https://github.com/lsmo-epfl/zeopp-lsmo/pull/11 ; to be released in zeopp-lsmo v0.4.2

ltalirz commented 3 years ago

I'm closing this for the moment, but feel free to reopen when encountering issues - the zeo++ cif parser is homegrown and will never be perfect.

in case we keep running into issues, it would be very straightforward to add a normalize_cif calcfunction to the zeo++ plugin that calls manage_crystal under the hood and can be used as needed.