replace atoms.coordinates() with atoms.positions in benchmarks

[orbeckst]

Expected behavior

Benchmarks run with latest release.

Actual behavior

Some benchmarks use outdated and removed AtomGroup.coordinates() instead of AtomGroup.positions.

Code to reproduce the behavior

Output from git grep 'coordinates() for the benchmarks:

benchmarks/benchmarks/analysis/rms.py:        # ag.coordinates()
benchmarks/benchmarks/analysis/rms.py:            self.A = self.u.atoms.coordinates().copy()[:num_atoms]
benchmarks/benchmarks/analysis/rms.py:            self.B = self.u.atoms.coordinates().copy()[:num_atoms]

(Follow-up from #3467 )

Current version of MDAnalysis

• Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)") develop 2.2.0

[orbeckst]

See https://github.com/MDAnalysis/benchmarks for the benchmark repo with the README giving an introduction on how to run ASV locally.

The benchmarks wiki also has some notes.

[aditi2906]

@orbeckst I want to work on this issue.. However, the readme of benchmarks repo
does not give a good headstart on how to run asv locally. Can you help me with it.
Thankyou

[orbeckst]

Please see https://github.com/MDAnalysis/mdanalysis/blob/develop/benchmarks/README.rst