descriptor for crystal about dscribe HOT 10 CLOSED

Hi @StevenAlice93,

Sure, there are several options. I would encourage you to read our Open Access article: https://doi.org/10.1016/j.cpc.2019.106949

In short: MBTR, sine matrix, Ewald sum matrix work natively for crystals, ACSF and SOAP also work with a few tricks.

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Well done! Thank you! I want to know how to use it to transform the POSCAR into descriptors, and I don't find the API to do that.

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You can use ASE for reading structures from POSCAR files. The resulting Atoms object can then be used directly by dscribe.

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Dear lauri-codes,

Oh, thank you! I got it.

I have a another question: if I have two moleculars CH4 and H20, and I use the ACSF Class to get descriptors for them, I will get a numpy array with shape (3, 36) for H20 and a numpy array with shape (5,36) for CH4. For many machine learning models, they only accept these samples with the same length descriptors, so how do I input these descriptors input a machine learning model?

Thank you for your reply!

Best wishes!

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Hi @StevenAlice93,

I have just added a basic tutorial that should cover your questions.

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Closing for now.

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Hi @zhanzghang,

The contents of formation_energy.extxyz come from OQMD 1.1. I created those files by using the SQL database that can be downloaded from http://oqmd.org.

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Dear Lauri,

when I used the Coulomb Matrix and Sine matrix to create the descriptor, it appeared 'ValueError: index can't contain negative values'. And I used the atoms to create the structure, included the Cartesian coordinates I have used in the 'position' for atoms, that really had some negative values. That's the reason for 'ValueError: index can't contain negative values'?

Thanks much for your time!

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Hi, @zhanzghang

The positions can certainly include negative values. The problem must be somewhere else. Could you include a minimal non-working example as a code snippet?

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