mdanalysis

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Optimize RDF histogram with Cython+OpenMP

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This PR adds an optimized histogram implementation using **Cython and OpenMP** that provides **10-18x speedup** for RDF calculations with large datasets. ## Context This PR supersedes #5103, which used Numba....

rhowardstone

Convert units of trajectory data when constructing a universe

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## Is your feature request related to a problem? ## Reading in trajectory files that combine atomic forces along with positions, the units for forces are automatically converted from kcal/(mol.Ang)...

jkalayan

These include: - namiroues - jpkrowe - schuhmc - gitsirsha - Pradyumn-cloud

IAlibay

topologyattrs._Connection.get_atoms reinitializes the TopologyGroup every time

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## Expected behavior ## One would expect that when a universe is loaded, the `TopologyGroup`s would be initialized once. ## Actual behavior ## Every time `topologyattrs._Connection.get_atoms` is called, it reinitializes...

jaclark5

FIX: LAMMPSDUMP Convert forces from kcal to kJ units

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Fixes #5115 Changes made in this Pull Request: - Add `units` attribute to `DumpReader` class specifying LAMMPS "real" units (time: fs, length: Angstrom, velocity: Angstrom/fs, force: kcal/(mol*Angstrom)) - Implement force...

Rupesh-Singh-Karki

We have to turn it on because the released MDA version isn't compatible with the latest numpy & cython. Next release we should be good, so we should turn it...

IAlibay

Build time tests makes machine to hang

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Hello. This was reported to Debian here: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1108309 When building (the Debian package of) mdanalysis, version 2.9.0, on AWS machines of types `m7a.large` or `r7a.large`, which incidentally have 2 vCPUs,...

sanvila

Inncorrect use of simple method when random frames are selected in run()

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> Thanks for the updates. I only have minor cosmetic changes. > > While reviewing, I also realized that your code can solve a problem that has been inherent in...

gitsirsha

We shouldn't be using `nose` anywhere in our source/testing infrastructure at this point, so the subset of related references that show up via `git grep -E -i "nose"` are likely...

tylerjereddy