Multistatereporter variable pos frequency by ianmkenney · Pull Request #767 · choderalab/openmmtools

ianmkenney · 2025-01-16T18:33:37Z

Continuation of #712. ~~There are multiple avenues to address the current failing tests. I would like to address those concerns here before continuing in that PR.~~

…rent frequency to energies data.

currently no pos test is failing...

ianmkenney · 2025-01-17T18:36:34Z

This PR will take over #712.

Accessing data from netCDF returns a masked array, even if no data is masked. For valid data, extract it and give back just the basic numpy array. For invalid data, give back a nan array with the proper shape.

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ianmkenney · 2025-01-17T19:24:22Z

@ijpulidos @IAlibay @mikemhenry I can't request reviewers, but I think this is ready for review.

ijpulidos

This looks good to me. Thanks a lot! Great work. Just a couple of non-blocking comments.

ijpulidos · 2025-01-17T20:12:10Z

openmmtools/multistate/multistatereporter.py

+                        raise IndexError
+                    # pull the valid data out of masked array
+                    positions = unit.Quantity(x.data, unit.nanometers)
+                except (IndexError, KeyError):


Non-blocking comment. Should we try outputting something here when an error is caught? Maybe something warning users that there's missing data or something similar. What are the reasons for the array to be masked?

On the topic of how MaskedArrays work here. Assuming that a particular coordinate exists in a dimension (e.g. at least some data exists for a given iteration) we always get back a MaskedArray. The MaskedArray will have a data attribute with a numpy array that will be masked by the MaskedArrays mask attribute. If the data was all valid, then we just pull that information out and expose it to the user. If no data exists at that dimension coordinate, then we'll just get an IndexError so we give back a zero array in place of the nonsense data inside the MaskedArray. By doing it this way, a user never has to deal with a MaskedArray.

I think that if the data was masked it's basically the same behavior as if the data didn't exist and we would have expected a zero array anyways. I don't really see much of a reason to give a warning about this since having a giant array of zeros is kind of a warning already. I'd even be careful saying the data is missing since that would imply it should have been there in the first place.

ijpulidos · 2025-01-17T20:14:18Z

openmmtools/multistate/multistatereporter.py

+        information, 0 would prevent information being written
+    velocity_interval : int, default 1
+        the frequency at which to write positions relative to analysis
+        information, 0 would prevent information being written


Non-blocking question. This might be too late now to ask, but why is that we want positions and velocities to be stored at different intervals? Does it make sense to define a state (i.e. with positions and velocities) from different intervals? Just thinking about ways of not having to deal with the "complexity" of having to check for pos and vel intervals independently.

I think this would depend on the intent of the simulation. I could see that someone interested in doing VAC calculations wouldn't care as much about the positions.

So the one case I can think of is that you might not want to store the velocities but you do want to store the positions.

I might be wrong, but as far as I remember the "state" is stored in the checkpoint? So you could recover a simulation from the checkpoint, and just store positions in the simulation file.

IAlibay · 2025-01-17T21:39:18Z

I'll be testing this in a Protocol before I review :)

IAlibay · 2025-01-19T22:35:00Z

openmmtools/multistate/multistatereporter.py

    analysis_particle_indices : tuple of ints, Optional. Default: () (empty tuple)
        If specified, it will serialize positions and velocities for the specified particles, at every iteration, in the
        reporter storage (.nc) file. If empty, no positions or velocities will be stored in this file for any atoms.
+    position_interval : int, default 1


Could we store these values inside of the NetCDF file as additional variables? This would make it a lot easier to know what the spacing is between frames, rather than having to iterate through the positions.

I'm being blind sorry 🙈 - it's below

openmmtools/multistate/multistatereporter.py

IAlibay · 2025-01-19T23:16:57Z

openmmtools/multistate/multistatereporter.py

                if 'box_vectors' in storage.variables:
                    # Restore box vectors.
                    x = storage.variables['box_vectors'][read_iteration, replica_index, :, :].astype(np.float64)
+                    # TODO: Are box vectors also variably saved?


From wwhat I can tell, they seem to be saved at the same rate as positions - worth double checking though!

It is saved at the same rate of positions assuming that the sampler_state's box_vectors is not None (line 1669). I find this line a little odd though since there is ais_periodic property of the reporter (line 204) that follows slightly different logic. I'm not sure which is best to use. @ijpulidos do you have any thoughts on this (I've pinged you directly at the offending line)?

To me it makes sense that these are stored at the same rate of positions, but again, there might be a use case where we want different rates for it? The logic here being that to maintain the thermodynamic states (especially pressure) you need to vary the box size and that's dependent on the positions. I'd argue that having positions without box sizes, or vice versa, is probably something we don't want to deal with.

Try and retrieve values from the netcdf file. If the data is masked, assume it hasn't been written at that iteration and raise an `IndexError`. If the box_vectors variable doesn't exist, then a `KeyError` is raised. Both execptions will bind None to the `box_vectors` variable.

ianmkenney · 2025-01-21T21:15:39Z

openmmtools/multistate/multistatereporter.py

        storage = self._storage_dict[storage_file]
        # Check if the schema must be initialized, do this regardless of the checkpoint_interval for consistency
-        is_periodic = True if (sampler_states[0].box_vectors is not None) else False
+        is_periodic = sampler_states[0].box_vectors is not None


@ijpulidos is there a reason we aren't using the MultiStateReporter.is_periodic property here?

I cannot say for sure. I guess this means that one can have a box_vectors variable in the reporter but not necessarily have box_vectors attribute in the sampler states, and vice versa. I don't know if we ever want those NOT to match. Is there a use case for such scenario?

I suppose I'd be inclined to keep it the same in this PR, it just struck me as strange. Both lines were introduced in the same commit so I'm going to go on the assumption it was deliberate rather than an oversight.

ianmkenney · 2025-01-24T17:16:04Z

@IAlibay @ijpulidos unless there is more to do here, I think this can be merged!

IAlibay

I can't approve on this repo, but lgtm!

richardjgowers and others added 11 commits July 13, 2023 13:48

allow MultiStateReporter to write positions and velocities at a diffe…

4805553

…rent frequency to energies data.

MultiStateReporter use 0 for do not write

59ca4d5

Merge branch 'main' into multistatereporter_variable_pos_frequency

7a3bd40

Merge branch 'main' into multistatereporter_variable_pos_frequency

d8f80b9

WIP of multistatereporter tests

8fba23f

test for variable position saving

e0555c5

more tests for smaller nc files

2d88a33

currently no pos test is failing...

catch IndexError when file had no position/velocity data ever stored

9a24479

Merge branch 'main' into multistatereporter_variable_pos_frequency

981fe1b

Merge branch 'main' into multistatereporter_variable_pos_frequency

542f341

Merge branch 'main' into multistatereporter_variable_pos_frequency

a262c2b

ianmkenney force-pushed the multistatereporter_variable_pos_frequency branch 2 times, most recently from a0e7dbb to a262c2b Compare January 17, 2025 18:25

ianmkenney changed the title ~~Multistatereporter variable pos frequency and masked arrays~~ [DNM/WIP] Multistatereporter variable pos frequency and masked arrays Jan 17, 2025

ianmkenney changed the base branch from multistatereporter_variable_pos_frequency to main January 17, 2025 18:33

ijpulidos mentioned this pull request Jan 17, 2025

MultiStateReporter variable pos/vel save frequency #712

Closed

5 tasks

ianmkenney added 4 commits January 17, 2025 11:44

Improve clarity of boolean logic

7fd7639

Interpret masked data as invalid data

bae275c

Accessing data from netCDF returns a masked array, even if no data is masked. For valid data, extract it and give back just the basic numpy array. For invalid data, give back a nan array with the proper shape.

Give back zero arrays instead of nan arrays

0b770d5

Allow CI to run for all branches

c211252

ianmkenney changed the title ~~[DNM/WIP] Multistatereporter variable pos frequency and masked arrays~~ [DNM/WIP] Multistatereporter variable pos frequency Jan 17, 2025

ianmkenney changed the title ~~[DNM/WIP] Multistatereporter variable pos frequency~~ Multistatereporter variable pos frequency Jan 17, 2025

ijpulidos requested review from ijpulidos and mikemhenry January 17, 2025 19:28

ijpulidos approved these changes Jan 17, 2025

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IAlibay mentioned this pull request Jan 19, 2025

Add support for masked frames (i.e. positions missing at certain frames) OpenFreeEnergy/openfe_analysis#41

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IAlibay reviewed Jan 19, 2025

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openmmtools/multistate/multistatereporter.py Outdated Show resolved Hide resolved

IAlibay reviewed Jan 19, 2025

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IAlibay mentioned this pull request Jan 20, 2025

Add support for variable position/velocity trajectory writing OpenFreeEnergy/openfe#1083

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9 tasks

ianmkenney added 2 commits January 21, 2025 09:54

Clarify that position_interval also determines write of box_vectors

31b8284

ianmkenney commented Jan 21, 2025

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IAlibay reviewed Jan 24, 2025

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ijpulidos merged commit c83cb98 into choderalab:main Jan 27, 2025
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ijpulidos mentioned this pull request Jan 31, 2025

Adding notes for new minor release #769

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ianmkenney mentioned this pull request Mar 5, 2025

Decouple checkpoint_interval and online_analysis_interval #770

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