{"action":"created","issue":{"url":"https://api.github.com/repos/Amber-MD/cpptraj/issues/245","repository_url":"https://api.github.com/repos/Amber-MD/cpptraj","labels_url":"https://api.github.com/repos/Amber-MD/cpptraj/issues/245/labels{/name}","comments_url":"https://api.github.com/repos/Amber-MD/cpptraj/issues/245/comments","events_url":"https://api.github.com/repos/Amber-MD/cpptraj/issues/245/events","html_url":"https://github.com/Amber-MD/cpptraj/pull/245","id":131505681,"number":245,"title":"Numerous fixes and enhancements","user":{"login":"drroe","id":10144183,"avatar_url":"https://avatars.githubusercontent.com/u/10144183?v=3","gravatar_id":"","url":"https://api.github.com/users/drroe","html_url":"https://github.com/drroe","followers_url":"https://api.github.com/users/drroe/followers","following_url":"https://api.github.com/users/drroe/following{/other_user}","gists_url":"https://api.github.com/users/drroe/gists{/gist_id}","starred_url":"https://api.github.com/users/drroe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drroe/subscriptions","organizations_url":"https://api.github.com/users/drroe/orgs","repos_url":"https://api.github.com/users/drroe/repos","events_url":"https://api.github.com/users/drroe/events{/privacy}","received_events_url":"https://api.github.com/users/drroe/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-02-04T23:30:22Z","updated_at":"2016-02-05T16:51:55Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/Amber-MD/cpptraj/pulls/245","html_url":"https://github.com/Amber-MD/cpptraj/pull/245","diff_url":"https://github.com/Amber-MD/cpptraj/pull/245.diff","patch_url":"https://github.com/Amber-MD/cpptraj/pull/245.patch"},"body":"This PR covers a lot of ground.\r\n\r\n- Address #96 for IRED output labels.\r\n- Address #100; add `name` keyword for `parm` and `reference` commands which can be used in place of tags.\r\n- Correctly handle file name wildcards on the command line for `-p`, `-y` etc ( #109 ). \r\n- Add `-d` and `-w` command line flags for reading and writing data sets from/to files (which also enables command-line conversion of data files).\r\n- Add dihedral co-variance matrix tests ( #243 ), as well as tests for `curvefit`, `multicurve`, `avg`, and `vectormath`.\r\n- Add data set scalar math functionality for 2D and 3D data sets (min, max, avg, etc).\r\n- Add `allframes` keyword to `nastruct` to allow finding of base pairs every frame (not parallel-enabled yet).\r\n- Fix issue where in `nastruct` step parameters were being calculated even if base pair parameters were not - now correctly set to 0.0 when this is the case.\r\n- Add `calcnohb` keyword to calculate parameters even if base pairing not detected (no hbonds).\r\n- nastruct: Add BP to base pair output, which is 1 if base pair is present (number hbonds > 0) and 0 otherwise. Also add Zp to base pair step output.\r\n- Fix `nastruct` in parallel when base pairing changes in a run.\r\n- Attempt to get tests working with MPI in Travis ( #145 ).\r\n- `avg` analysis now uses data set/data file framework.\r\n- Allow either vector to be of size 1 in `vectormath`, which allows vec OP vec(n) math.\r\n- Add `nomod` keyword to `rms` command to prevent modification of coordinates during calculation of RMSD and adds a test for it."},"comment":{"url":"https://api.github.com/repos/Amber-MD/cpptraj/issues/comments/180436758","html_url":"https://github.com/Amber-MD/cpptraj/pull/245#issuecomment-180436758","issue_url":"https://api.github.com/repos/Amber-MD/cpptraj/issues/245","id":180436758,"user":{"login":"drroe","id":10144183,"avatar_url":"https://avatars.githubusercontent.com/u/10144183?v=3","gravatar_id":"","url":"https://api.github.com/users/drroe","html_url":"https://github.com/drroe","followers_url":"https://api.github.com/users/drroe/followers","following_url":"https://api.github.com/users/drroe/following{/other_user}","gists_url":"https://api.github.com/users/drroe/gists{/gist_id}","starred_url":"https://api.github.com/users/drroe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drroe/subscriptions","organizations_url":"https://api.github.com/users/drroe/orgs","repos_url":"https://api.github.com/users/drroe/repos","events_url":"https://api.github.com/users/drroe/events{/privacy}","received_events_url":"https://api.github.com/users/drroe/received_events","type":"User","site_admin":false},"created_at":"2016-02-05T16:51:55Z","updated_at":"2016-02-05T16:51:55Z","body":"OK, I think I have fixed the OpenMPI issues. Turns out OpenMPI gets cranky if MPI_Reduce() is called with a null pointer, even if the count is 0 (this isn't an issue with mpich/mvapich). Should be fixed now (I hope)."}}