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ADicksonLab
Weighted Ensemble simulation framework in Python
For weighted ensemble analyses it is common to require access to all of the weights at once. Currently, this takes tens of minutes to read the weights from reasonably-sized HDF5...
Currently you can just report on one progress value, you should be able to do multiple of them. By default this is everything in `PROGRESS_RECORD_FIELDS` for a BC.
The `BoundaryCondition` mechanism is pretty good at covering per-walker progress but sometimes you want to track the progress of the entire ensemble. The `BCDashboardSection` already automatically summarizes the min, max,...
Currently this is only introduced in the `WarpBC` base class, but it is required for things like the `BCDashboardSection` so this should have a good default set at the root...
Currently the mechanisms for wrapping and retrieving dynamically available fields in the OpenMMState and how it wraps the OpenMM.State is very flaky and causes problems for the tail of attributes...
In some cases dynamics segments (with OpenMM) can return NaNs which then propagate throughout the other code until something hits it that can't handle NaNs which may be far down...
As seen in the traceback of #112 if the HDF5Reporter is not initialized properly in a context manager you get a confusing AttributeError if there is no `closed` attribute. This...
Hi @salotz and @alexrd, We (I and Ceren) are having this weird issue with WepyHDF5, where in the middle of a wepy simulation (say after 100 or 200 cycles), all...
Either I didn't notice it before or it is new, there is a data type called `IntegratorParameters` that we should support in the OpenMMState etc.
When originally written I didn't know how (or wasn't possible) to cleanly handle errors from OpenMM when retrieving state information that wasn't available for the state, e.g. velocities, forces, etc....
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Weighted Ensemble simulation framework in Python