{"action":"created","issue":{"url":"https://api.github.com/repos/hackingmaterials/atomate/issues/75","repository_url":"https://api.github.com/repos/hackingmaterials/atomate","labels_url":"https://api.github.com/repos/hackingmaterials/atomate/issues/75/labels{/name}","comments_url":"https://api.github.com/repos/hackingmaterials/atomate/issues/75/comments","events_url":"https://api.github.com/repos/hackingmaterials/atomate/issues/75/events","html_url":"https://github.com/hackingmaterials/atomate/pull/75","id":207238662,"number":75,"title":"Gibbs: phonon workflow test, results to database, improved defaults","user":{"login":"bocklund","id":7681751,"avatar_url":"https://avatars.githubusercontent.com/u/7681751?v=3","gravatar_id":"","url":"https://api.github.com/users/bocklund","html_url":"https://github.com/bocklund","followers_url":"https://api.github.com/users/bocklund/followers","following_url":"https://api.github.com/users/bocklund/following{/other_user}","gists_url":"https://api.github.com/users/bocklund/gists{/gist_id}","starred_url":"https://api.github.com/users/bocklund/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bocklund/subscriptions","organizations_url":"https://api.github.com/users/bocklund/orgs","repos_url":"https://api.github.com/users/bocklund/repos","events_url":"https://api.github.com/users/bocklund/events{/privacy}","received_events_url":"https://api.github.com/users/bocklund/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2017-02-13T14:48:41Z","updated_at":"2017-02-13T15:19:05Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/hackingmaterials/atomate/pulls/75","html_url":"https://github.com/hackingmaterials/atomate/pull/75","diff_url":"https://github.com/hackingmaterials/atomate/pull/75.diff","patch_url":"https://github.com/hackingmaterials/atomate/pull/75.patch"},"body":"# **Do not merge yet!**\r\n\r\nI need some help in the Gibbs phonon unit test. I modeled it similarly to the existing elastic workflow unit test. In isolation, it works well, passes, and tests what I think it should test. But I get several errors when I try to test the whole atomate test suite. \r\n\r\nI've done a git bisect and determined that the whole test suite works up until commit 83b525d, where I add in the phonon workflow test. None of the errors are in the phonon workflow, but are elsewhere. See the comments below for more details on these. \r\n\r\nOnce this is fixed, we can merge.\r\n\r\n## Summary\r\n\r\nA unit test was written for the Gibbs workflow with Phonopy. Debye mode files are included, workflow unit test coming soon. \r\n\r\nThe results from the Gibbs workflows (information about the structure, the free energies, temperatures, and meta data) are written to a \"gibbs\" collection. (With this, a rename of GibbsFreeEnergyTask to GibbsFree\r\n\r\nThe following defaults for the Gibbs workflows were changed or updated\r\n\r\n* `natoms` in `gibbs_summary_dict` changed to `nsites` to better conform with the style elsewhere\r\n* Gibbs deformations changes\r\n  - Default number of deformations to 11, which should be plenty for an average user of the Debye method and the most anyone using Phonopy should need. See http://dx.doi.org/10.1016/j.commatsci.2009.12.006 for more\r\n  - The deformation matrix was changed so that the value passed from `np.linspace` represents the actual volume change. E.g. `np.linspace(-0.10, 0.10, 11)` makes 11 deformations from -10% volume to +10% volume.\r\n* Fix phonopy `t_max` by adding several steps to the maximum temperature given to `PhonopyQHA` because it truncates several values in the fitting. Now the final `t_max` matches the input from the user.\r\n* Use higher accuracy force INCAR settings by default (`LREAL=False`, `ADDGRID=True`)\r\n\r\nMore details for several of these can be found in the commits. \r\n\r\n## TODO (if any)\r\n\r\n* Write a workflow unit test for the \"debye_model\" mode for the Gibbs free energy preset.\r\n\r\n@matk86 should take a look at the changes in the Gibbs preset. "},"comment":{"url":"https://api.github.com/repos/hackingmaterials/atomate/issues/comments/279421324","html_url":"https://github.com/hackingmaterials/atomate/pull/75#issuecomment-279421324","issue_url":"https://api.github.com/repos/hackingmaterials/atomate/issues/75","id":279421324,"user":{"login":"bocklund","id":7681751,"avatar_url":"https://avatars.githubusercontent.com/u/7681751?v=3","gravatar_id":"","url":"https://api.github.com/users/bocklund","html_url":"https://github.com/bocklund","followers_url":"https://api.github.com/users/bocklund/followers","following_url":"https://api.github.com/users/bocklund/following{/other_user}","gists_url":"https://api.github.com/users/bocklund/gists{/gist_id}","starred_url":"https://api.github.com/users/bocklund/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bocklund/subscriptions","organizations_url":"https://api.github.com/users/bocklund/orgs","repos_url":"https://api.github.com/users/bocklund/repos","events_url":"https://api.github.com/users/bocklund/events{/privacy}","received_events_url":"https://api.github.com/users/bocklund/received_events","type":"User","site_admin":false},"created_at":"2017-02-13T15:19:05Z","updated_at":"2017-02-13T15:19:05Z","body":"I just verified that with the both the `test_gibb_workflow.py` and the tests above work in isolation (testing each file separately), but not together. Any insight would be appreciated. "}}
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