Atomic embeddings for QM9 models about megnet HOT 6 CLOSED

@araquejc for historic reasons, the QM9 models were built by using atom types, so the model will first convert the atomic number to the corresponding type before passing it to the model.

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@araquejc To be precise, our original qm9 models were initially trained on the processed qm9 dataset by Faber et. al. J. Chem. Theory Comput. 2017, 13, 11, 5255–5264, where they have atom types (integer) instead of atomic number. In later model developments, we decided to use the atomic number for graph construction, so we had to make this conversion to be compatible.

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@chc273 Thanks for your quick reply!

Does that mean that in the code above embedding[1] == "H", embedding[2] == "C", embedding[4] == "N", embedding[6] == "O" and embedding[8] == "F"?

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Yes you are right @araquejc

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Thanks again! That was my initial guess, but I wanted to cross check with you. I think it is useful to know this before trying transfer learning for MEGNet models reading pymatgen molecules directly (i.e., using atomic number).

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BTW, you are welcome to close the issue.

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