Description of work
Trajectory arrays such as positions, velocities and charges are now split into fixed-size chunks within a single time step.
closes #596
Note: the changes in this PR will break the scripts in MDANSE-Examples. The scripts should be updated around the time of the next release.
Fixes
Changed chunking in TrajectoryWriter. The arrays are padded to ensure that their size is a multiple of the chunk size.
Added chunk size as a parameter to OutputTrajectoryConfigurator.
Added chunk size to OutputTrajectoryWidget.
Replaced test trajectories in unit tests with chunked ones.
Updated test inputs to inlcude the new parameter.
To test
Convert a trajectory using the protos branch. Run Dynamic Coherent/Incoherent Structure Factor analysis on this trajectory and time both runs.
Repeat the same steps using this branch. Compare the results and the timing.
Expected results: DCSF will slow down by ca. 5%, DISF will speed up by ca. 25%, the results should not change.
Description of work Trajectory arrays such as positions, velocities and charges are now split into fixed-size chunks within a single time step.
closes #596
Note: the changes in this PR will break the scripts in MDANSE-Examples. The scripts should be updated around the time of the next release.
Fixes
To test Convert a trajectory using the protos branch. Run Dynamic Coherent/Incoherent Structure Factor analysis on this trajectory and time both runs. Repeat the same steps using this branch. Compare the results and the timing. Expected results: DCSF will slow down by ca. 5%, DISF will speed up by ca. 25%, the results should not change.