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Refactoring of MC moves#21

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wiederm merged 47 commits intomultistagechoderalab/chiron:multistagefrom mcchoderalab/chiron:mcCopy head branch name to clipboardFeb 27, 2024

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Commits on Jan 18, 2024

• Fix u_kn shape in test_multistate_run

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• Refactor MCMCMove subclasses and update method names

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Commits on Jan 21, 2024

• Merge branch 'multistage' into mc

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Commits on Jan 22, 2024

• Merge branch 'multistage' into mc

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• Started MC refactor, merging from multistage branch that includes new reporters and random number scheme. This primarily sketches out the new MCMove class (updates to the actual moves is forthcoming).

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• Merge remote-tracking branch 'main_origin/mc' into mc

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Commits on Jan 23, 2024

• Small refactor to Langevin integrator. Small changes: run command now takes variable to allow for velocity initialization. The Langevin ntegrator now returns a sampler state rather tha updating. St…

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• created initialize_velocities funtion in utilities; langevin code now uses this if users request velocities to be regenerated each time. The reaosn to split was to make it easy to define velocities…

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Commits on Jan 25, 2024

• Finished fixing up langevin integrator/move

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• Implemented Metropolis displacement move in new scheme.

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• Added refactored barostat move and ideal gas test case.

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• Abstractmethod for _reporting wrapper (this will make it easier for each move to have custom/appropriate logging for what is being changed).

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Commits on Jan 26, 2024

• Added _reporter to the displacement moves and the ability to only move a subset of atoms: tests need to be updated/implemented still.

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Commits on Jan 29, 2024

• Added in stepsize updater to allow move_parameters to be updated on the fly.

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Commits on Jan 30, 2024

• Continued reworking to ensure expected behavior of loggers and stepsize adjustments.

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• Fixed test_integrator and atom_subsetting in displacement move.

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• Added in flag to initialize velocities the first time langevin is called. This is different than reinitialize which will call reinit every time run is called. The velocity init function was spun of…

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• test_multistate still is failing an assertion, but I think that is fine, since this PR was focused on revamping the MC moves. That can be tackled separately in the multistate PR.

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Commits on Jan 31, 2024

• Modified the routines to ensure that passing the nbr_list fits in more with the functional programming model (passing and return a neighborlist).

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• Added ideal gas test written in the other PR. updated logic in langevin to take into account the iteration not just the current step; reporters now also log the elapsed_step.

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• Added ideal gas test written in the other PR. updated logic in langevin to take into account the iteration not just the current step; reporters now also log the elapsed_step. Updated the examples

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• Added in additional tests for barostat

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Commits on Feb 1, 2024

• Fixed convergence test syntax: these were missed on my part because they were marked to be skipped because they take too long.

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• Fixed convergence test syntax: these were missed on my part because they were marked to be skipped because they take too long. for Harmonic oscillator we do not seem to need to run as long as set i…

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Commits on Feb 2, 2024

• Updated CI.yaml to enabled CI to run for branches commiting to the multistage branch. Thanks Mike Henry!

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• Added in skip to the multistate testing, as this still needs to be worked on in the multistate branch this is being commited to"

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• match/case statements don't exist in python 3.9. I commented this out and just added in if/elif statements.

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• fixture was missing in test_testsystems

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• fixture was missing in test_testsystems

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• weirdly wrong syntax in the test ideal gas test.

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Commits on Feb 9, 2024

• Updating ideal gas example.

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• Update Examples/Idealgas.py with descriptive assert statement

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• Update Examples/Idealgas.py with descriptive assert statement

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• Updating ideal gas example.

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• Updating ideal gas example.

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• removed velocity initialization flag in langevin

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• updated various functions in reponse to marcus' comments.

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• Merge branch 'multistage' into mc

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Commits on Feb 10, 2024

• Merge failed to correctly merge, and broke MCMCSampler; fixed now. multistate reporter giving an error.

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Commits on Feb 12, 2024

• Working through comments from Jchodera.

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Commits on Feb 20, 2024

• Fixed error with multistate systems. Various other updates based on comments.

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• Changed coordinates to positions in neighbor/pairlist routines to be consistent with samplerstate variable name change.

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Commits on Feb 21, 2024

• Changed PairListNsqrd to allow setting the cutoff to None which will use no cutoff (i.e. all pairs interact). Revamped some internal tooling regarding how units are treated internally. Space was re…

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Commits on Feb 22, 2024

• mised an instance where the reporter called space.box_vectors. fixed.

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• name refactoring in MCMC

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Commits on Feb 23, 2024

• further addressing comments.

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Commits on Feb 27, 2024

• Added accumulated for number_of_attemps_made instead of elapsed_steps. (I missed this comment in the PR comments)

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