Refactor the neighbor list for training#274
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chrisiacovella wants to merge 5 commits intochoderalab:train-on-dipol-momentfrom
Closed
Refactor the neighbor list for training#274chrisiacovella wants to merge 5 commits intochoderalab:train-on-dipol-momentfrom
chrisiacovella wants to merge 5 commits intochoderalab:train-on-dipol-momentfrom
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chrisiacovella
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wiederm
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Oct 10, 2024
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That's great! I think this makes the code much more readable!
| Whether to regenerate the cache. | ||
| """ | ||
| from modelforge.potential.models import Pairlist | ||
| from modelforge.potential.neighbors import Pairlist |
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its useful to split this off in a neighbors module!
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| # class PairlistData(NamedTuple): | ||
| # """ | ||
| # A namedtuple to store the outputs of the Pairlist and Neighborlist forward methods. | ||
| # | ||
| # Attributes | ||
| # ---------- | ||
| # pair_indices : torch.Tensor | ||
| # A tensor of shape (2, n_pairs) containing the indices of the interacting atom pairs. | ||
| # d_ij : torch.Tensor |
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I belive the commented out code can be removed
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| # class ComputeInteractingAtomPairs(torch.nn.Module): | ||
| # | ||
| # def __init__(self, cutoff: float, only_unique_pairs: bool = False): | ||
| # """ | ||
| # Initialize the ComputeInteractingAtomPairs module. | ||
| # | ||
| # Parameters | ||
| # ---------- | ||
| # cutoff : float | ||
| # The cutoff distance for neighbor list calculations. | ||
| # only_unique_pairs : bool, optional | ||
| # If True, only unique pairs are returned (default is False). | ||
| # """ | ||
| # |
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| # if ( | ||
| # "neighborlist.calculate_distances_and_pairlist.cutoff" | ||
| # in filtered_state_dict | ||
| # ): | ||
| # filtered_state_dict["neighborlist.cutoff"] = filtered_state_dict.pop( | ||
| # "neighborlist.calculate_distances_and_pairlist.cutoff" | ||
| # ) |
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| # Note if the indices are not numbered from 0 to n_molecules - 1, this will not work | ||
| # E.g., bincount on [3,3,3, 4,4,4, 5,5,5] will return [0,0,0,3,3,3,3,3,3] |
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there are a few linebreaks here, can we reformat this?
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Pull Request Summary
This relates to some of the changes suggested in Issue #269. Specifically, this streamlines the Neighborlist for training. The code has changed quite a bit since these initial classes had been sketched out, and this should hopefully make things clearer and make the code easier to read. This also will reduce the need to massage the config dict inputs related to the neighbor list cutoff that currently needs to be done.
Key changes
Notable points that this PR has either accomplished or will accomplish.
NeighborListclass is merged in theCalculateInteractingPairsclass.Neighborlistclass has been removed.CalculateInteractingPairsis renamedNeighborListForTrainingand moved to the neighbors.py filePairListclass has been moved to the neighbors.py fileAssociated Issue(s)
Pull Request Checklist