pmda
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MDAnalysis
Parallel algorithms for MDAnalysis
Follow up from: https://github.com/MDAnalysis/mdanalysis/issues/3036 As our Travis allocation is organisation wide, it might be best to switch over to Github actions where possible.
Hello, To simplify my problem, I want to select atoms based on coordinates through all frames. I tried to do this with pmda but it doesn't work with n_jobs >...
### Expected behaviour reading frames from a trajectory imported by MDAnalysis from a **.nc file** ### Actual behaviour `TypeError: cannot serialize '_io.BufferedReader' object` ### Code to reproduce the behaviour ```...
### Expected behaviour Successfully running `AnalysisFromFunction()` on all available CPUs by setting `n_jobs=-1` even for very small trajectories. ### Actual behaviour A Warning is raised: ``` /srv/home/lponzoni/anaconda3/envs/ifpe/lib/python3.7/site-packages/pmda/parallel.py:360: UserWarning: run() uses...
### Expected behaviour PMDA uses the serializable Universe in MDAnalysis ≥ 2.0.0 (PR https://github.com/MDAnalysis/mdanalysis/pull/2723) ### Actual behaviour Current code uses MDA 1.0.0 workaround
Fixes #133 Changes made in this Pull Request: - refactor each part of pmda (test passed) - [x] parallel.py - [x] custom.py - [x] rmsd - [x] rmsf - [x]...
### Expected behaviour Analysis of a `Universe` with on-the-fly transformation scales good (reasonable). ### Actual behaviour The scaling performance is really bad even with two cores. ### Code ```python import...
Fixes #135 Note the only file changes from #132 is `parallel.py` You can read https://github.com/yuxuanzhuang/pmda/pull/1/files to get the actual changes. Changes made in this Pull Request: - See #135 PR...
### Expected behaviour `cdf` function returns cummulative distribution function between particles A and particles B. ### Actual behaviour `cdf` function returns cummulative number density of particles B in a shell...
