Skip to content

Optimize the calculation speed and logic of InterRDF_s to ensure that the results are consistent with InterRDF #5073

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
wants to merge 4 commits into
base: develop
Choose a base branch
from
Draft

Optimize the calculation speed and logic of InterRDF_s to ensure that the results are consistent with InterRDF #5073

Changes from 1 commit
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
8965375
Refactored bin index calculation in the _single_frame function of Int…
gitzhangch Jun 29, 2025
2760210
Adjust the code to ensure the test passes.
gitzhangch Jul 1, 2025
375ecc9
Fewer revisions
gitzhangch Jul 3, 2025
fa271c2
formt revisions
gitzhangch Jul 3, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 17 additions & 3 deletions package/MDAnalysis/analysis/rdf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -633,6 +633,7 @@ def _prepare(self):
if self.norm == "rdf":
# Cumulative volume for rdf normalization
self.volume_cum = 0
self._minrange = self.rdf_settings["range"][0] if self.rdf_settings["range"][0] > 0 else 0.0
self._maxrange = self.rdf_settings["range"][1]

def _single_frame(self):
Expand All @@ -641,13 +642,24 @@ def _single_frame(self):
ag1.positions,
ag2.positions,
self._maxrange,
self._minrange,
box=self._ts.dimensions,
backend=self.backend,
)

# Different people write code for different purposes. For my needs, the following two lines are sufficient:
# count, _ = np.histogram(dist, **self.rdf_settings)
# self.results.count[i][0, 0, :] += count

# The following is an optimized version based on the old logic.
bins = self.rdf_settings["bins"]
minv, maxv = self._minrange, self._maxrange
# Calculate bin indices for each value in dist, similar to np.histogram's bin assignment.
bin_indices = ((dist - minv) * bins / (maxv - minv)).astype(np.int64)

for j, (idx1, idx2) in enumerate(pairs):
count, _ = np.histogram(dist[j], **self.rdf_settings)
self.results.count[i][idx1, idx2, :] += count
self.results.count[i][idx1, idx2, bin_indices[j]] += 1
self.results.count[i][0, 0, bin_indices[j]] += 1

if self.norm == "rdf":
self.volume_cum += self._ts.volume
Expand All @@ -669,8 +681,10 @@ def _conclude(self):

for i, (ag1, ag2) in enumerate(self.ags):
# Number of each selection
if self.norm == "rdf":
N = len(ag1) * len(ag2)
self.results.indices.append([ag1.indices, ag2.indices])
self.results.rdf.append(self.results.count[i] / norm)
self.results.rdf.append(self.results.count[i] / (norm * N)) # Modify to make it consistent with InterRDF

def get_cdf(self):
r"""Calculate the cumulative counts for all sites.
Expand Down
Loading