Comments (2)
Hi @lundnguy!
Adding a new species simply means that the length and order of the output changes. I don't see the existing non-zero values changing in your examples, just zero elements being added to the end (Si has bigger atomic number than C or O) or to the beginning (H has smaller atomic number than C or O). If you can point of that some non-zero element in the vector has not simply changed location, but its value has changed, then that would be a big problem. But I can't now see this in your example output.
Essentially by specifying species
you select a subspace where you start mapping your individual structures into. You should stick to one set of species
during your analysis since vectors produced with different species
are not compatible anymore.
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Thank you, @lauri-codes.
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Related Issues (20)
- Descriptor that recognizes each atom of the same species differently HOT 1
- The example in README.md is not correct HOT 1
- [Bug] Error in SOAP derivatives when using weighting. HOT 2
- API compatibility is broken since 0696656 HOT 1
- ACSF.create cannot accept cartesian positions as "centers" parameter HOT 2
- Numpy operations on sparsed derivatives HOT 5
- Similarity based on Average kernel obtain deferent value between each atom and its replica atoms. HOT 1
- Similarity value is different between equivalent atoms HOT 5
- Segmentation fault in SOAP for l_max > 9 HOT 2
- Analytic Integral of SH expansion coefficients HOT 2
- SOAP polynomial RBF error HOT 3
- MBTR HOT 3
- ACSF G5 values HOT 2
- Segmentation fault in creation of SOAP descriptor HOT 4
- SOAP_sparse=True HOT 2
- Molecular representations for bio-molecules HOT 1
- Can not Flatten CoulombMatrix HOT 3
- Inconsistency of Numerical SOAP Derivative with Finite-Difference Test HOT 2
- MBTR k2, k3
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