{"action":"created","issue":{"url":"https://api.github.com/repos/MITgcm/MITgcm/issues/96","repository_url":"https://api.github.com/repos/MITgcm/MITgcm","labels_url":"https://api.github.com/repos/MITgcm/MITgcm/issues/96/labels{/name}","comments_url":"https://api.github.com/repos/MITgcm/MITgcm/issues/96/comments","events_url":"https://api.github.com/repos/MITgcm/MITgcm/issues/96/events","html_url":"https://github.com/MITgcm/MITgcm/pull/96","id":320043115,"node_id":"MDExOlB1bGxSZXF1ZXN0MTg1ODA5Njk1","number":96,"title":"Implementing QG Leith","user":{"login":"edoddridge","id":6049169,"node_id":"MDQ6VXNlcjYwNDkxNjk=","avatar_url":"https://avatars3.githubusercontent.com/u/6049169?v=4","gravatar_id":"","url":"https://api.github.com/users/edoddridge","html_url":"https://github.com/edoddridge","followers_url":"https://api.github.com/users/edoddridge/followers","following_url":"https://api.github.com/users/edoddridge/following{/other_user}","gists_url":"https://api.github.com/users/edoddridge/gists{/gist_id}","starred_url":"https://api.github.com/users/edoddridge/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/edoddridge/subscriptions","organizations_url":"https://api.github.com/users/edoddridge/orgs","repos_url":"https://api.github.com/users/edoddridge/repos","events_url":"https://api.github.com/users/edoddridge/events{/privacy}","received_events_url":"https://api.github.com/users/edoddridge/received_events","type":"User","site_admin":false},"labels":[{"id":822941118,"node_id":"MDU6TGFiZWw4MjI5NDExMTg=","url":"https://api.github.com/repos/MITgcm/MITgcm/labels/enhancement","name":"enhancement","color":"a2eeef","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":21,"created_at":"2018-05-03T19:07:13Z","updated_at":"2018-07-26T21:11:15Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/MITgcm/MITgcm/pulls/96","html_url":"https://github.com/MITgcm/MITgcm/pull/96","diff_url":"https://github.com/MITgcm/MITgcm/pull/96.diff","patch_url":"https://github.com/MITgcm/MITgcm/pull/96.patch"},"body":"## What changes does this PR introduce?\r\nImplementation of QG Leith subgrid model as described in [Bachman et al. (2017)](https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016JC012265) and [Pearson et al. (2017)](http://dx.doi.org/10.1016/j.ocemod.2017.05.007).\r\n\r\n## Other information:\r\n~~**This branch is not ready to be merged.** It is intended to provide a space for collaboration as we work on the code.~~\r\n\r\nThe initial code dump has been placed within the `verification` folder as a subtle reminder that we will need a test for this new functionality before it can be merged.\r\n\r\n## To do\r\nThis list constitutes an initial pass - there is more to do than listed here. Some additional issues are described in 'QG_LEITH_README'\r\n- [x] remove extraneous files\r\n- [x] remove CSV headers\r\n- [x] move subroutines to their correct homes within the source code\r\n- [x] Remove the dynamic computation of the Leith coefficient? Bachman et al. (2017) shows that it isn't particularly useful\r\n- [x] fix the boundary condition issue in `calc_germanoK.F` lines 328-335\r\n- [x] include a verification experiment that tests the new code\r\n- [x] new subroutine `MOM_CALC_QG_STRETCHING` is only called from `mom_fluxform.F` not `mom_vecinv.F`\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/MITgcm/MITgcm/issues/comments/408236476","html_url":"https://github.com/MITgcm/MITgcm/pull/96#issuecomment-408236476","issue_url":"https://api.github.com/repos/MITgcm/MITgcm/issues/96","id":408236476,"node_id":"MDEyOklzc3VlQ29tbWVudDQwODIzNjQ3Ng==","user":{"login":"jm-c","id":5165946,"node_id":"MDQ6VXNlcjUxNjU5NDY=","avatar_url":"https://avatars0.githubusercontent.com/u/5165946?v=4","gravatar_id":"","url":"https://api.github.com/users/jm-c","html_url":"https://github.com/jm-c","followers_url":"https://api.github.com/users/jm-c/followers","following_url":"https://api.github.com/users/jm-c/following{/other_user}","gists_url":"https://api.github.com/users/jm-c/gists{/gist_id}","starred_url":"https://api.github.com/users/jm-c/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jm-c/subscriptions","organizations_url":"https://api.github.com/users/jm-c/orgs","repos_url":"https://api.github.com/users/jm-c/repos","events_url":"https://api.github.com/users/jm-c/events{/privacy}","received_events_url":"https://api.github.com/users/jm-c/received_events","type":"User","site_admin":false},"created_at":"2018-07-26T21:11:15Z","updated_at":"2018-07-26T21:11:15Z","author_association":"CONTRIBUTOR","body":"Good news: I checked that the MLAdjust examples pass test 2+2 ; also checked that results \n  don't change when I #define DYNAMICS_GUGV_EXCH_CHECK in dynamics.F, tested on CS-grid \n  with dry corners.\nRegarding code changes:\n1) currently, serious problems with Adjoint (I only tried TAF, none of verif exp can\n  even compile); We need a specific CPP option to protect this code (and 2 new calls \n  in mom_fluxform.F and mom_vecinv.F) from being always seen by TAF. \n2) option ALLOW_GM_LEITH_QG  is set in 2 places and it's confusing. Since it's only \n  used in pkg/gmredi it should stay there and should be removed from MOM_COMMON_OPTIONS.h\n3) what happens if I try: viscC2LeithQG=1 and useLeithQG=F ? \n  seems that results are different from full QG-Leith (=1,=T) but also different\n  from no QG-Leith at all (=0,=F).\n  Seems that in some part of the code it tests for viscC2LeithQG > 0 and in other places \n  it tests for useLeithQG, but would be better to to clarify this.\n4) few \"#include \"MOM_VISC.h\" have been added in pkg/gmredi but I am not convinced\n  that all are necessary. Also the 3 added *.F files could have shorter name, currently\n  mom_visc_qgleith_calc_stretching.F is the longest of any pkg, and all in lower-case\n  (except suffix .F) is preferable.\n\nOn Thu, Jul 12, 2018 at 02:16:09PM -0700, Ed Doddridge wrote:\n> Apart from updating `tag-index` I think this is done. I'll leave that until it's been reviewed to avoid potential conflicts.\n> \n> - the floating point exception that @jm-c pointed out before has been fixed: `testreport` passes with the `-devel` option\n> - the new functionality has been documented, including the runtime and compile time options, as well as a recommended value for the non-dimensional viscosity parameter\n> - both locations in which the QGLeith viscosity is calculated (`pkg/gmredi` and `pkg/mom_common`) can output the array through `pkg/diagnostics` (and the values are extremely similar)\n> - the GM functionality is now controlled by both compile time and runtime parameters, so it can be switched on and off at will\n> \n> \n> -- \n> You are receiving this because you were mentioned.\n> Reply to this email directly or view it on GitHub:\n> https://github.com/MITgcm/MITgcm/pull/96#issuecomment-404653335\n"}}
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