{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/openmmtools/issues/389","repository_url":"https://api.github.com/repos/choderalab/openmmtools","labels_url":"https://api.github.com/repos/choderalab/openmmtools/issues/389/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/openmmtools/issues/389/comments","events_url":"https://api.github.com/repos/choderalab/openmmtools/issues/389/events","html_url":"https://github.com/choderalab/openmmtools/pull/389","id":391497485,"node_id":"MDExOlB1bGxSZXF1ZXN0MjM4OTg1Mzkw","number":389,"title":"TestSystems for Double Well in WCA Fluid","user":{"login":"dwhswenson","id":8178546,"node_id":"MDQ6VXNlcjgxNzg1NDY=","avatar_url":"https://avatars1.githubusercontent.com/u/8178546?v=4","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},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-12-16T19:31:05Z","updated_at":"2018-12-24T19:05:36Z","closed_at":null,"author_association":"COLLABORATOR","pull_request":{"url":"https://api.github.com/repos/choderalab/openmmtools/pulls/389","html_url":"https://github.com/choderalab/openmmtools/pull/389","diff_url":"https://github.com/choderalab/openmmtools/pull/389.diff","patch_url":"https://github.com/choderalab/openmmtools/pull/389.patch"},"body":"This PR adds (two generalizations of) a test system that has been frequently used in rare events. I'm calling these `DoubleWellDimer_WCAFluid` and `DoubleWellChain_WCAFluid`. In both cases, we start with the existing `WCAFluid` test system, and add bonded interactions of the form $h (1 - ((r - r_0 - w) / w)^2)^2$. This is a symmetric potential with a minimum at $(r_0, 0)$, a maximum at $(r_0+w, h)$, and a second minimum at $(r_0 + 2w, 0)$. The widely-used test system adds this interaction between 2 atoms, so there is one dimer in the WCA fluid.\r\n\r\nFor the `DoubleWellDimer_WCAFluid`, the system will create bonds between pairs of atoms, so the bonds are created between atom 0 and 1, atom 2 and 3, etc., resulting in multiple separated dimers, each dimer connected by the double-well potential. This is similar to what was done in [Swenson and Bolhuis, JCP 2014](http://doi.org/10.1063/1.4890037). The standard example is `ndimers=1`.\r\n\r\nFor the `DoubleWellChain_WCAFluid`, the system will create a chain of bonds of the desired length, so bonds are created between atom 0 and 1, atom 1 and 2, etc. For `nchained=1`, this is just the WCA fluid; for `nchained=2`, this is identical to the `DoubleWellDimer_WCAFluid` with `ndimers=1`, and for `nchained=3` this is the same as the potential used in [Rogal and Bolhuis, JCP 2008](https://doi.org/10.1063/1.3029696).\r\n\r\nThe clever bit in the implementation is to recognize that the same algorithm works for both; the only difference is in which atom pairs are selected to have the custom bond force added to them.\r\n\r\n - [x] Implement feature / fix bug\r\n - [ ] Add [tests](https://github.com/choderalab/openmmtools/tree/master/openmmtools/tests)\r\n - [ ] Update [documentation](https://github.com/choderalab/openmmtools/tree/master/docs) as needed\r\n - [ ] Update [changelog](https://github.com/choderalab/openmmtools/blob/master/docs/releasehistory.rst)"},"comment":{"url":"https://api.github.com/repos/choderalab/openmmtools/issues/comments/449764233","html_url":"https://github.com/choderalab/openmmtools/pull/389#issuecomment-449764233","issue_url":"https://api.github.com/repos/choderalab/openmmtools/issues/389","id":449764233,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0OTc2NDIzMw==","user":{"login":"andrrizzi","id":1682142,"node_id":"MDQ6VXNlcjE2ODIxNDI=","avatar_url":"https://avatars3.githubusercontent.com/u/1682142?v=4","gravatar_id":"","url":"https://api.github.com/users/andrrizzi","html_url":"https://github.com/andrrizzi","followers_url":"https://api.github.com/users/andrrizzi/followers","following_url":"https://api.github.com/users/andrrizzi/following{/other_user}","gists_url":"https://api.github.com/users/andrrizzi/gists{/gist_id}","starred_url":"https://api.github.com/users/andrrizzi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrrizzi/subscriptions","organizations_url":"https://api.github.com/users/andrrizzi/orgs","repos_url":"https://api.github.com/users/andrrizzi/repos","events_url":"https://api.github.com/users/andrrizzi/events{/privacy}","received_events_url":"https://api.github.com/users/andrrizzi/received_events","type":"User","site_admin":false},"created_at":"2018-12-24T19:05:36Z","updated_at":"2018-12-24T19:05:36Z","author_association":"CONTRIBUTOR","body":"> Let me add another commit with docs and changelog update ;-)\r\n\r\nThanks! I appreciate.\r\n\r\n> Any recommended way/location to add these extra tests?\r\n\r\nI think an extra test function(s) in `tests/test_testsystems.py` will be good enough. Unless you think there are reasons to separate them in a different file."}}
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