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Enabling of parallelization of analysis.atomicdistances.AtomicDistances #4822

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Update atomicdistances.py
talagayev Dec 5, 2024
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5 changes: 4 additions & 1 deletion package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,8 @@ The rules for this file:


-------------------------------------------------------------------------------
??/??/?? IAlibay, ChiahsinChu, RMeli
??/??/?? IAlibay, ChiahsinChu, RMeli, talagayev


* 2.9.0

Expand All @@ -23,6 +24,8 @@ Fixes
Enhancements
* Add check and warning for empty (all zero) coordinates in RDKit converter (PR #4824)
* Added `precision` for XYZWriter (Issue #4775, PR #4771)
* Incorporation of `Results` into `analysis.atomicdistances.AtomicDistances`
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@orbeckst orbeckst Dec 12, 2024

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This is a Breaking Change as it breaks code. If we put it in 2.9.0 then it has to go under Fix, though.

For right now, please put under Fixes and state clearly how it breaks existing code.

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@orbeckst orbeckst Dec 12, 2024

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... assuming a breaking change.

If this PR is done without breaking changes (ie keeping self.results as array at the end) then do not reference the issue (which says that we need to have self.results.distances)

(Issue #4819)

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20 changes: 16 additions & 4 deletions package/MDAnalysis/analysis/atomicdistances.py
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Expand Up @@ -114,6 +114,7 @@

import logging
from .base import AnalysisBase
from .results import Results

logger = logging.getLogger("MDAnalysis.analysis.atomicdistances")

Expand Down Expand Up @@ -145,6 +146,10 @@ class AtomicDistances(AnalysisBase):


.. versionadded:: 2.5.0

.. versionchanged:: 2.9.0
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@orbeckst orbeckst Dec 12, 2024

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Update the docs above!!!!

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@orbeckst orbeckst Dec 12, 2024

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... assuming a breaking change.

Implementation of `Results` into the class
for application in parallelization.
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@orbeckst orbeckst Dec 12, 2024

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Need to be clearer about what was done:

Suggested change
Implementation of `Results` into the class
for application in parallelization.
Changed storage of results from :attr:`results` to
:attr:`results.distances`. This fix **breaks old
code** that expects to find the data array in
:attr:`results`.

... assuming a breaking change.

"""

def __init__(self, ag1, ag2, pbc=True, **kwargs):
Expand All @@ -163,14 +168,21 @@ def __init__(self, ag1, ag2, pbc=True, **kwargs):
self._ag1 = ag1
self._ag2 = ag2
self._pbc = pbc
self.results = Results()

def _prepare(self):
# initialize NumPy array of frames x distances for results
self.results = np.zeros((self.n_frames, self._ag1.atoms.n_atoms))
self.results.distances = np.zeros((
self.n_frames, self._ag1.atoms.n_atoms
))

def _single_frame(self):
# if PBCs considered, get box size
box = self._ag1.dimensions if self._pbc else None
self.results[self._frame_index] = calc_bonds(self._ag1.positions,
self._ag2.positions,
box)
self.results.distances[self._frame_index] = calc_bonds(
self._ag1.positions, self._ag2.positions, box
)

def _conclude(self):
# adjust self.results to self.results.distances
self.results = self.results.distances
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@tylerjereddy tylerjereddy Dec 5, 2024

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Maybe I'm just confused but it looks to me like the tests haven't actually changed yet (just formatting changes as far as I can tell?) and this just restored the original behavior of self.results storing a NumPy array again?

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@talagayev talagayev Dec 5, 2024

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yes, first I modified it to have the output would be self.results.distances, but then I thought that for the convenience to not modify the docs, where it uses my_dists.results to my_dists.results.distances I could define self.results as self.results.distances to not have to change the docs and still be able to implement the parallelization of the class.

As for the pytest changes, first I had the self.results.distances output and thus the tests needed to have also the .distances. The Idea to have self.results came after creating the PR 🙈, but yes I will then remove the mention of the pytest modification, was quite late when I finished up the PR, so didn't think about that :)

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@orbeckst orbeckst Dec 12, 2024

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That's a hack!

If this the way we want to go then you have to write more commentary to say what you're doing and why, with references to issue and a note that this needs to be changed for 3.0.

7 changes: 4 additions & 3 deletions testsuite/MDAnalysisTests/analysis/test_atomicdistances.py
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Expand Up @@ -118,8 +118,9 @@ def test_ad_pairwise_dist(self, ad_ag1, ad_ag2,
expected_dist):
'''Ensure that pairwise distances between atoms are
correctly calculated without PBCs.'''
pairwise_no_pbc = (ad.AtomicDistances(ad_ag1, ad_ag2,
pbc=False).run())
pairwise_no_pbc = ad.AtomicDistances(
ad_ag1, ad_ag2, pbc=False
).run()
actual = pairwise_no_pbc.results

# compare with expected values from dist()
Expand All @@ -129,7 +130,7 @@ def test_ad_pairwise_dist_pbc(self, ad_ag1, ad_ag2,
expected_pbc_dist):
'''Ensure that pairwise distances between atoms are
correctly calculated with PBCs.'''
pairwise_pbc = (ad.AtomicDistances(ad_ag1, ad_ag2).run())
pairwise_pbc = ad.AtomicDistances(ad_ag1, ad_ag2).run()
actual = pairwise_pbc.results

# compare with expected values from dist()
Expand Down
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