{"action":"created","issue":{"url":"https://api.github.com/repos/openpathsampling/openpathsampling/issues/521","repository_url":"https://api.github.com/repos/openpathsampling/openpathsampling","labels_url":"https://api.github.com/repos/openpathsampling/openpathsampling/issues/521/labels{/name}","comments_url":"https://api.github.com/repos/openpathsampling/openpathsampling/issues/521/comments","events_url":"https://api.github.com/repos/openpathsampling/openpathsampling/issues/521/events","html_url":"https://github.com/openpathsampling/openpathsampling/pull/521","id":165871432,"number":521,"title":"Update Alanine MSTIS 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that should be solved before first public release.","creator":{"login":"dwhswenson","id":8178546,"avatar_url":"https://avatars.githubusercontent.com/u/8178546?v=3","gravatar_id":"","url":"https://api.github.com/users/dwhswenson","html_url":"https://github.com/dwhswenson","followers_url":"https://api.github.com/users/dwhswenson/followers","following_url":"https://api.github.com/users/dwhswenson/following{/other_user}","gists_url":"https://api.github.com/users/dwhswenson/gists{/gist_id}","starred_url":"https://api.github.com/users/dwhswenson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dwhswenson/subscriptions","organizations_url":"https://api.github.com/users/dwhswenson/orgs","repos_url":"https://api.github.com/users/dwhswenson/repos","events_url":"https://api.github.com/users/dwhswenson/events{/privacy}","received_events_url":"https://api.github.com/users/dwhswenson/received_events","type":"User","site_admin":false},"open_issues":11,"closed_issues":89,"state":"open","created_at":"2014-11-27T17:27:40Z","updated_at":"2016-08-09T13:35:06Z","due_on":null,"closed_at":null},"comments":19,"created_at":"2016-07-15T20:30:18Z","updated_at":"2016-08-15T15:22:00Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/openpathsampling/openpathsampling/pulls/521","html_url":"https://github.com/openpathsampling/openpathsampling/pull/521","diff_url":"https://github.com/openpathsampling/openpathsampling/pull/521.diff","patch_url":"https://github.com/openpathsampling/openpathsampling/pull/521.patch"},"body":"This updates the Alanine MSTIS example for the paper. I made the following changes.\r\n\r\n- Remove `alpha` and `beta`. This only uses the 6 states `A`-`F`\r\n- Added some parameters to `initial_conditions_from_trajectories`, see below\r\n- New `Ensemble.split` now uses an iterator instead of `n_results`. This makes it easier to keep looking for subtrajectories while doing analysis on the subtrajectories.\r\n- New `DynamicsEngine.extend_forward(trajectory, ensemble)` and `DynamicsEngine.extend_backward(trajectory, ensemble)` which will simply extending an existing trajectory into a new ensemble.\r\n- moved the alanine plots into separate class in `alatools.py`\r\n- New `MSTISNetwork.generate_inter_state_samples(snapshot, engine)` that will create samples that bounce between states until all states are hit. The set of samples will be returned as a list of samples.\r\n- `PathSampling` will not duplicate the initial sampleset when initialized. This would prevent a restart because the connection to the old simulation is broken.\r\n- Alanine bootstrapping does not use bootstrapping anymore. It uses `MSTISNetwork.generate_inter_state_samples` with the mstis network and then runs `SampleSet.generate_from_samples` on the `mstis.all_ensemble` with the high temperature engine. This will fill all ensembles and return the initial sampleset. \r\n- added a generator to generate snapshots, `engine.iter_generate` that will yield the current trajectory in regular intervals. Useful if you generate a long trajectory and want to keep track of progress.\r\n\r\nThe example already runs using UUIDs. Question is how many samples we want to generate. I think starting with 5000? 1000 are about 1GB."},"comment":{"url":"https://api.github.com/repos/openpathsampling/openpathsampling/issues/comments/239830996","html_url":"https://github.com/openpathsampling/openpathsampling/pull/521#issuecomment-239830996","issue_url":"https://api.github.com/repos/openpathsampling/openpathsampling/issues/521","id":239830996,"user":{"login":"dwhswenson","id":8178546,"avatar_url":"https://avatars.githubusercontent.com/u/8178546?v=3","gravatar_id":"","url":"https://api.github.com/users/dwhswenson","html_url":"https://github.com/dwhswenson","followers_url":"https://api.github.com/users/dwhswenson/followers","following_url":"https://api.github.com/users/dwhswenson/following{/other_user}","gists_url":"https://api.github.com/users/dwhswenson/gists{/gist_id}","starred_url":"https://api.github.com/users/dwhswenson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dwhswenson/subscriptions","organizations_url":"https://api.github.com/users/dwhswenson/orgs","repos_url":"https://api.github.com/users/dwhswenson/repos","events_url":"https://api.github.com/users/dwhswenson/events{/privacy}","received_events_url":"https://api.github.com/users/dwhswenson/received_events","type":"User","site_admin":false},"created_at":"2016-08-15T15:22:00Z","updated_at":"2016-08-15T15:22:00Z","body":"Yeah, my intent is that the user may have given the trajectories in a specific order. This allows you to very easily fill new initial conditions (with equivalent but non-identical ensembles) using an old sample set. This is also why it was extremely important to have the ensembles in a canonical order."}}
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