SNAP bik flag #3142
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SNAP bik flag #3142
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athomps
requested changes
Feb 19, 2022
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This looks nice and clean. The only problem is that the treatment of the last column (reference potential) is not clearly defined in the code or in the documentation. I suggest making a clear choice e.g. 1) snap all[irow][lastcol] = 0; for all b_ik rows 2) same, but with reference energy in first b_ik row 3) Put per-atom reference energy in every b_ik row. Whatever choice is made should be explicitly documented.
athomps
approved these changes
Feb 21, 2022
doc/src/compute_sna_atom.rst
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| descriptors :math:`B_{i,k}` summed over all atoms *i* to produce | ||
| :math:`B_k`, becomes bispectrum rows equal to the number of atoms. Thus, | ||
| the resulting bispectrum rows are :math:`B_{i,k}` instead of just | ||
| :math:`B_k`. |
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Add "In this case, the entries in the final column for these rows are set to zero."
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@athomps @charlessievers as a reminder. If you both consider this to be reading for merging, you need to assign the PR to me.
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Summary
Added in flag for snap compute to provide per atom bispectrum descriptors instead of summed bispectrum descriptors.
Author(s)
Charlie Sievers - Sandia National Labs - charliesievers@cox.net
Licensing
By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
Implementation Notes
Tested file examples/snap/in.snap.compute and produced the same output.
Post Submission Checklist