{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/perses/issues/307","repository_url":"https://api.github.com/repos/choderalab/perses","labels_url":"https://api.github.com/repos/choderalab/perses/issues/307/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/perses/issues/307/comments","events_url":"https://api.github.com/repos/choderalab/perses/issues/307/events","html_url":"https://github.com/choderalab/perses/pull/307","id":197528429,"number":307,"title":"Ensure acceptance probability is synchronized with LaTeX document","user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-12-26T03:08:35Z","updated_at":"2016-12-26T03:56:42Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/choderalab/perses/pulls/307","html_url":"https://github.com/choderalab/perses/pull/307","diff_url":"https://github.com/choderalab/perses/pull/307.diff","patch_url":"https://github.com/choderalab/perses/pull/307.patch"},"body":"This PR brings the NCMC and ExpandedEnsembleSampler acceptance criteria into complete correspondence with the LaTeX document describing the acceptance probability for hybrid and two-stage schemes. \r\n\r\n* Equation numbers are used throughout to reference which mathematical quantity is beinc computed.\r\n* A copy of the LaTeX document has also been ingested into `notes/` for reference, though we should likely continue to work on the overleaf version collaboratively.\r\n\r\nThis PR includes a number of bugfixes:\r\n* `deepcopy` of `Topology` issues in `relative.py` and the proposal engines\r\n* overhaul of NCMC integrators\r\n* fixes to tests\r\n* don't allow `softening` for relative alchemical factory to be set to anything but 1.0\r\n\r\nOn my `osx` laptop, I'm tracing down a weird bug where simply calling `context.setVelocitiesToTemperature(temperature)` suddenly causes velocities to be insanely large. The temperature and particle masses are all sane, so I wonder if it has to do with the recent `clang`-based rebuild of the `openmm` packages. I've left some debug code in there to help me."},"comment":{"url":"https://api.github.com/repos/choderalab/perses/issues/comments/269157360","html_url":"https://github.com/choderalab/perses/pull/307#issuecomment-269157360","issue_url":"https://api.github.com/repos/choderalab/perses/issues/307","id":269157360,"user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"created_at":"2016-12-26T03:56:42Z","updated_at":"2016-12-26T03:56:42Z","body":"cc: https://github.com/pandegroup/openmm/issues/1699"}}
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