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hackingmaterials / robocrystallographer

Automatic generation of crystal structure descriptions.
https://hackingmaterials.github.io/robocrystallographer/
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"Hg is Magnesium structured" #16

Open computron opened 5 years ago

computron commented 5 years ago

(py37) computron-7:~ ajain$ robocrys mp-975272 Adding oxidation states... Hg is Magnesium structured and crystallizes in the orthorhombic Cmcm space group. The structure is one-dimensional and consists of one Hg ribbon oriented in the (0, 0, 1) direction. Hg(1) is bonded in a distorted bent 120 degrees geometry to two equivalent Hg(1) atoms. Both Hg(1)–Hg(1) bond lengths are 3.40 Å.

I think crystallographers will have issue with simultaneously calling something "Mg-structured" and "orthorhombic"

mkhorton commented 5 years ago

I think in this case the mineral name is too general too -- part of this could be fixed by adding a hyperlink to e.g. the specific prototype.

I'll note that when I parsed the AFLOW prototype library, I parsed them based on the CIF files they provided, and that's where the mineral tag "Magnesium" comes from -- however if you go on their website, their title for this prototype is actually "Hexagonal Close Packed (A3)" which is probably better. I think some manual curation of prototype names would be useful, and the Strukturbericht names might be a good idea in some cases, since I imagine most crystallographers have some familiarity with a lot of the common ones.

As for why this is coming up as orthorhombic, is the mineral matching using different symmetry tolerances to the crystal system detection? This could be very confusing.

computron commented 5 years ago

Note: the thing about Mg --> HCP is discussed more in #14