{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":433602054,"defaultBranch":"main","name":"libMobility","ownerLogin":"stochasticHydroTools","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2021-11-30T22:11:20.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/12700742?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1726755474.0","currentOid":""},"activityList":{"items":[{"before":"d013acf9bb3abc24a16240791f4c5ebf7e6dc2e7","after":"f07856c7aa2745ab0b4b29d75c99c82abce38c6c","ref":"refs/heads/main","pushedAt":"2024-09-19T14:14:06.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Add torques (#21)\n\n* Add torques to pythonify\r\n\r\n* Add torque to mobility interface\r\n\r\n* Add torques to DPStokes\r\n\r\n* Add torques to NBody\r\n\r\n* Add torques to PSE\r\n\r\n* Add torques to selfMobility\r\n\r\n* Update pythonify\r\n\r\n* Update python example\r\n\r\n* Update cpp example\r\n\r\n* Update test\r\n\r\n* Update test\r\n\r\n* Update test\r\n\r\n* Update test\r\n\r\n* Update test\r\n\r\n* Typo\r\n\r\n* Fix initialize\r\n\r\n* Typo\r\n\r\n* Update pythonify\r\n\r\n* Update pythonify\r\n\r\n* Typo\r\n\r\n* Update sqrtM\r\n\r\n* Update\r\n\r\n* Update\r\n\r\n* Typo\r\n\r\n* Change name\r\n\r\n* Update\r\n\r\n* Always send valid pointers to hydrodynamicVelocities\r\n\r\n* dont complain if receiving angular\r\n\r\n* Typo in tests\r\n\r\n* added torques to selfmobility test\r\n\r\n* angular mobility matrix test setup\r\n\r\n* added torques to selfmobility\r\n\r\n* updated interface so that the linear fluctuation dissipation test is passing. the problem was that a zero vector of angular velocities was always being passed into sqrtMdotW inside pythonify.h so solvers where torques weren't implemented would always throw the error, even though we were only trying to compute with forces.\r\n\r\n* removed unnecessary allocation for when torques aren't being used in sqrtMdotW\r\n\r\n* Squashed commit of the following:\r\n\r\ncommit ac2b4056bb7bb32adde80991b2d44d8335edff7d\r\nAuthor: Ryker Fish \r\nDate: Tue Jul 16 19:41:16 2024 -0600\r\n\r\n regenerated data w new defaults after verifying against old repository\r\n\r\ncommit 07b47942945621861e78c9d01804bdb1afacafc5\r\nAuthor: Ryker Fish \r\nDate: Tue Jul 16 19:05:08 2024 -0600\r\n\r\n added parameter to initialize that sets whether the box size can get altered or not\r\n\r\ncommit 447e54310693efed56def672572ab49e8f739ad9\r\nAuthor: Ryker Fish \r\nDate: Tue Jul 16 18:22:27 2024 -0600\r\n\r\n added mode that preserves L\r\n\r\ncommit 74ec4368d58c540f10189a6c373c568ca79899e1\r\nAuthor: Ryker Fish \r\nDate: Tue Jul 16 17:23:24 2024 -0600\r\n\r\n checkpoint commit- adding functionality to have parameter select that modifies the box size and another version that preserves it\r\n\r\ncommit 1113390bb21839563a281f726f7f0035dc2676c5\r\nAuthor: Ryker Fish \r\nDate: Wed Jul 10 14:59:33 2024 -0600\r\n\r\n the changes to DPStokes parameters seem to made the mobility matrix less symmetric\r\n\r\ncommit 800f63472076bf6277ca7e2a529f76c1b0c009cc\r\nAuthor: Ryker Fish \r\nDate: Wed Jul 10 14:56:08 2024 -0600\r\n\r\n had to change the ref file to use the right positions. nbody test working.\r\n\r\ncommit 830866eeee8c544c08a61588638d2da563741299\r\nAuthor: Ryker Fish \r\nDate: Mon Jul 8 18:46:51 2024 -0600\r\n\r\n the two pair DPStokes tests are passing. currently having issues with the nbody test\r\n\r\ncommit 9b3a4d3c582db82899e28710fce5fd9f32f8926a\r\nAuthor: Ryker Fish \r\nDate: Fri Jun 28 14:19:28 2024 -0600\r\n\r\n self mobility tests done\r\n\r\ncommit c4f266478b9b48b162bbb4e55eb85da4ae73480a\r\nAuthor: Ryker Fish \r\nDate: Wed Jun 12 15:31:55 2024 -0600\r\n\r\n larger safety factor near open boundary for dpstokes\r\n\r\ncommit 5da7450738b5fa73ab785d74789ab2e70a819ccb\r\nAuthor: Ryker Fish \r\nDate: Wed Jun 12 12:15:33 2024 -0600\r\n\r\n modify how N gets rounded in all dimensions to be fft friendly\r\n\r\ncommit 51db36a04ea7cc174a0a968b61427e9b725f82d9\r\nAuthor: Ryker Fish \r\nDate: Wed Jun 12 11:58:39 2024 -0600\r\n\r\n changed selection of grid parameters to not modify h. instead, modify the box size to make L/h an integer\r\n\r\ncommit 5127394e4f5a647791788408c260e63b9fa9b668\r\nAuthor: Ryker Fish \r\nDate: Thu Jun 6 14:07:01 2024 -0600\r\n\r\n changed test pass threshold\r\n\r\ncommit 4fb82bf15db19e0a823bed5c819e77f194097953\r\nAuthor: Ryker Fish \r\nDate: Thu Jun 6 13:42:52 2024 -0600\r\n\r\n regenerated all ref data using libmobility implementations in single precision\r\n\r\ncommit 439290376f4620801b5c4bf7bbd396b90b4119d9\r\nAuthor: Ryker Fish \r\nDate: Thu Jun 6 13:25:04 2024 -0600\r\n\r\n regenerated refs using gpu implementations from dpstokes library. tests are now passing if the same kernel parameters are used as the ref implementation\r\n\r\ncommit 1ce606ad8c03dad67e044b8a0b2af2be0bbed7b7\r\nAuthor: Ryker Fish \r\nDate: Thu May 30 16:06:32 2024 -0600\r\n\r\n fixed bug in nbody wall correction that came from normalizing by a factor of 1/8pi in the original implementation instead of 1/6pi in the Swan paper.\r\n\r\ncommit edf78f5ecacb717d8f0b2bfa1c7c246f4a6c7155\r\nAuthor: Ryker Fish \r\nDate: Thu May 30 16:05:21 2024 -0600\r\n\r\n switched all tests to w=4 kernels, added nbody to pair mobility tests\r\n\r\ncommit c575ef2d9b4cc2dc98d022dd16d3606f28d5aef1\r\nAuthor: Ryker Fish \r\nDate: Wed May 29 15:11:48 2024 -0600\r\n\r\n change dpstokes to use w=4 kernel by default for forces\r\n\r\ncommit 070728b1b0db4ece15a33e8b6a78ecaf9b40e74c\r\nAuthor: Ryker Fish \r\nDate: Tue May 28 16:57:09 2024 -0600\r\n\r\n started pair mobility test\r\n\r\ncommit ca4e1c7c2f6beca2ba2de5f017e830b15aa16c78\r\nAuthor: Ryker Fish \r\nDate: Sat May 18 12:19:26 2024 -0600\r\n\r\n combined self mobility tests into one function\r\n\r\ncommit e90e9e2b72fd796950d6fc6cdfcc4ffc42a9799c\r\nAuthor: Ryker Fish \r\nDate: Fri May 17 20:45:24 2024 -0600\r\n\r\n bug fix in NBody with wall correction- test now passing. the fix uses the correct constants from the Swan correction paper- the previous implementation was using constants based on a self mobility constant of 1/(8*pi*eta*a) instead of 1/(6*pi*eta*a)\r\n\r\ncommit 98e2ae08f1b8c80dec1a7752ebd388d9004e4b08\r\nAuthor: Ryker Fish \r\nDate: Fri May 17 15:37:25 2024 -0600\r\n\r\n changed dpstokes test to compare to dpstokes reference and added a not-working nbody test\r\n\r\ncommit 7aaa0b1d4c50fbaf32bbad7318c4768437cf2376\r\nMerge: 79fe6a7 d6144a5\r\nAuthor: Ryker \r\nDate: Mon May 13 14:25:35 2024 -0600\r\n\r\n Merge pull request #18 from stochasticHydroTools/minor_test_edits\r\n\r\n Minor test edits\r\n\r\ncommit d6144a51a18d597c73b670c0f921dcbc850a248d\r\nAuthor: Ryker Fish \r\nDate: Thu May 9 15:40:00 2024 -0600\r\n\r\n removed test cases for small numbers of particles for the fluctuation dissipation test.\r\n\r\ncommit 0e368d476348ec5fdbd51d109e042547cf255c45\r\nAuthor: Ryker \r\nDate: Thu May 9 14:37:44 2024 -0600\r\n\r\n Edit comment on nbody test\r\n\r\n Comment had the answer for the PSE test. Removed the periodic correction part\r\n\r\ncommit 79fe6a7264aa185f1ab5a7603d116cf95249456a\r\nAuthor: Ryker Fish \r\nDate: Thu May 9 12:47:42 2024 -0600\r\n\r\n now testing if mobility is 0 on the bottom wall\r\n\r\ncommit 3c5002ecd30975546cba329461c292cc2ecd924d\r\nAuthor: Ryker Fish \r\nDate: Wed May 8 19:02:35 2024 -0600\r\n\r\n possible correction to DPStokes code to add a buffer the top instead of the bottom when there is a wall\r\n\r\ncommit c66303c744f216328d4b5dda094de3543beee76f\r\nAuthor: Ryker Fish \r\nDate: Wed May 8 18:27:40 2024 -0600\r\n\r\n selfmobility test working in comparison to refernce results for one and two wall cases\r\n\r\ncommit 70aa3291ce4c9ec8372cb2a522689d787e8d9e59\r\nAuthor: Ryker Fish \r\nDate: Wed May 8 17:12:19 2024 -0600\r\n\r\n mobility doesn't go to zero at the wall unless this section is commented out.\r\n\r\ncommit fe2c964355378f1c5e07918a3bb38e68dc19c9ea\r\nAuthor: Ryker Fish \r\nDate: Wed May 8 16:37:04 2024 -0600\r\n\r\n first pass at computing translational self mobility components for bottom wall scenario\r\n\r\n* modified wall tests to still pass in single precision by using variable tolerance based on machine epsilon\r\n\r\n* modified how symmetric matrix has to be for fluctuation dissipation tests to accomodate dpstokes parameters\r\n\r\n* changed to only allocate angular vec if torques are provided so that PSE and NBody work when torques aren't provided\r\n\r\n* interface test for mdot with torques\r\n\r\n* updated all interfaces to accept torques\r\n\r\n* started implementing NBody torques. naive algorithm works for main diagonal blocks- still need to do off diagonal blocks\r\n\r\n* fast algorithm now working for main diagonal\r\n\r\n* updated angular test to use different torques and forces\r\n\r\n* added off-diagonal blocks for torques and fixed bug in memory allocation for fast algorithm when using torques\r\n\r\n* added torque test for when forces are zero with nonzero torques\r\n\r\n* added test for freespace nbody with torques\r\n\r\n* bug fix in nbody UT component\r\n\r\n* add test for PSE not supporting torques\r\n\r\n* added torque parameters\r\n\r\n* add DPStokes to mob. matrix tests and remove PSE from tests involving torques\r\n\r\n* self mobility tests for DPstokes with torques\r\n\r\n* dpstokes pair wall tests complete\r\n\r\n* rewrite linear wall test to be more like angular test\r\n\r\n* fix bug in NBody bloc kalgorithm\r\n\r\n* added parameterization to test different nbody algorithms to show bug\r\n\r\n* bug fix- thanks Raul!\r\n\r\n* add block algorithm back to nbody tests\r\n\r\n* added torques to nbody block\r\n\r\n* added nbody wall kernels for self mobilities. still need to do pair mobilities\r\n\r\n* checkpoint commit for today, stuff still kinda broken but I think I know why\r\n\r\n* simplified tests since ref files have changed\r\n\r\n* added wall test for particle offset in y direction\r\n\r\n* wall kernels for torques in Nbody now working after bug fixes\r\n\r\n* added some comments on the subtle parts of the NBody wall kernels\r\n\r\n* minor optimization changes (went division hunting) and standardized notation between functions\r\n\r\n* add line to example to indicate to compile in double if necessary\r\n\r\n* change python example function calls to reflect interface\r\n\r\n* Set pybind11 as required\r\n\r\n* Take some code out of the PYTHONIFY macro\r\n\r\n* Format\r\n\r\n* Fix module name\r\n\r\n* Fix typo in docstring\r\n\r\n* Set C++ std to 17\r\n\r\n* Update docstrings\r\n\r\n* Check if torques are being passed when needsTorques=False\r\n\r\n* Fix test not setting needsTorque=True\r\n\r\n* Install test scripts to /share/\r\n\r\n* Add a different test per file\r\n\r\n* Improve mkl detection\r\n\r\n---------\r\n\r\nCo-authored-by: Ryker Fish ","shortMessageHtmlLink":"Add torques (#21)"}},{"before":"46ed238f593a6905bfa8ec2a9e9ce81b48ac42c9","after":"b03e42dbddddb5f6baf6887168b3ec3f3183e604","ref":"refs/heads/add_torques","pushedAt":"2024-09-04T15:50:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Improve mkl detection","shortMessageHtmlLink":"Improve mkl detection"}},{"before":"0c455ce90a1eb0da91bdf4ae66c8ec9050f041d6","after":"46ed238f593a6905bfa8ec2a9e9ce81b48ac42c9","ref":"refs/heads/add_torques","pushedAt":"2024-09-04T14:36:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Add a different test per file","shortMessageHtmlLink":"Add a different test per file"}},{"before":"7aaee328d96a3045d597a97a87e220b8d594102f","after":"0c455ce90a1eb0da91bdf4ae66c8ec9050f041d6","ref":"refs/heads/add_torques","pushedAt":"2024-09-04T14:34:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Install test scripts to /share/","shortMessageHtmlLink":"Install test scripts to /share/"}},{"before":"506fc2da06f7158c88d0fff5313d21c8381d8a3f","after":"7aaee328d96a3045d597a97a87e220b8d594102f","ref":"refs/heads/add_torques","pushedAt":"2024-09-04T13:02:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Fix test not setting needsTorque=True","shortMessageHtmlLink":"Fix test not setting needsTorque=True"}},{"before":"5f37028e24480018773f3848fdc084669dea39f1","after":"506fc2da06f7158c88d0fff5313d21c8381d8a3f","ref":"refs/heads/add_torques","pushedAt":"2024-09-04T12:24:50.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Check if torques are being passed when needsTorques=False","shortMessageHtmlLink":"Check if torques are being passed when needsTorques=False"}},{"before":"f32a428eceb5d60c45609ba57de2eafc010077de","after":"5f37028e24480018773f3848fdc084669dea39f1","ref":"refs/heads/add_torques","pushedAt":"2024-09-04T11:59:42.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Fix typo in docstring","shortMessageHtmlLink":"Fix typo in docstring"}},{"before":"a900a3bf51aac02a1903d4a4cc611e46b0389a14","after":"f32a428eceb5d60c45609ba57de2eafc010077de","ref":"refs/heads/add_torques","pushedAt":"2024-09-04T11:19:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Fix module name","shortMessageHtmlLink":"Fix module name"}},{"before":"cdd59ed92273405277b67ddbfd5e1f9de36ce9ab","after":"a900a3bf51aac02a1903d4a4cc611e46b0389a14","ref":"refs/heads/add_torques","pushedAt":"2024-09-04T10:27:39.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Format","shortMessageHtmlLink":"Format"}},{"before":"797634682bc27f2b022efaaf6fc1e83ecd37d4e2","after":"cdd59ed92273405277b67ddbfd5e1f9de36ce9ab","ref":"refs/heads/add_torques","pushedAt":"2024-09-04T10:26:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Set pybind11 as required","shortMessageHtmlLink":"Set pybind11 as required"}},{"before":"40939a55ed2157085dff7bd90570781b7e725ede","after":"797634682bc27f2b022efaaf6fc1e83ecd37d4e2","ref":"refs/heads/add_torques","pushedAt":"2024-09-03T23:28:16.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"rykerfish","name":"Ryker","path":"/rykerfish","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19866074?s=80&v=4"},"commit":{"message":"change python example function calls to reflect interface","shortMessageHtmlLink":"change python example function calls to reflect interface"}},{"before":"2b92689f3467285374c0a540381cbecc6117825a","after":"40939a55ed2157085dff7bd90570781b7e725ede","ref":"refs/heads/add_torques","pushedAt":"2024-08-29T23:35:50.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"rykerfish","name":"Ryker","path":"/rykerfish","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19866074?s=80&v=4"},"commit":{"message":"minor optimization changes (went division hunting) and standardized notation between functions","shortMessageHtmlLink":"minor optimization changes (went division hunting) and standardized n…"}},{"before":"e237f56a7f29b954e28d023d39ef716af4a79787","after":"2b92689f3467285374c0a540381cbecc6117825a","ref":"refs/heads/add_torques","pushedAt":"2024-08-27T04:35:46.000Z","pushType":"push","commitsCount":13,"pusher":{"login":"rykerfish","name":"Ryker","path":"/rykerfish","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19866074?s=80&v=4"},"commit":{"message":"resolved the awful merge commit from combining wall_tests and add_torques.","shortMessageHtmlLink":"resolved the awful merge commit from combining wall_tests and add_tor…"}},{"before":"86d26dca98ebd5aafdeb0f06efc90abc54b2c8c2","after":"d013acf9bb3abc24a16240791f4c5ebf7e6dc2e7","ref":"refs/heads/main","pushedAt":"2024-08-22T07:54:12.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Conda packages for several cuda versions (#25)\n\n* Export CUDA_VERSION as an env variable\r\n\r\n* Set CUDA_VERSION to 12\r\n\r\n* Set label to dev\r\n\r\n* Relax run requirements\r\n\r\n* Remove comments\r\n\r\n* Typo\r\n\r\n* Turn off fluctuating tests in conda package build\r\n\r\n* Remove run on PR","shortMessageHtmlLink":"Conda packages for several cuda versions (#25)"}},{"before":"182abcdc4f84a651be6884c2619727543da9cf6c","after":"4ea55c1f58b93d0a60be43b1a4849ffc3f17ba49","ref":"refs/heads/conda","pushedAt":"2024-08-22T07:53:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Remove run on PR","shortMessageHtmlLink":"Remove run on PR"}},{"before":"049a2bd72be33e3e39a3eada095aa88b5176ac4e","after":"182abcdc4f84a651be6884c2619727543da9cf6c","ref":"refs/heads/conda","pushedAt":"2024-08-22T07:47:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Turn off fluctuating tests in conda package build","shortMessageHtmlLink":"Turn off fluctuating tests in conda package build"}},{"before":"50f5673dbc0cad5a375246077b032c1947de912c","after":"049a2bd72be33e3e39a3eada095aa88b5176ac4e","ref":"refs/heads/conda","pushedAt":"2024-08-22T07:39:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Typo","shortMessageHtmlLink":"Typo"}},{"before":"33068de8a2da0093820e419c12aade8814e723df","after":"50f5673dbc0cad5a375246077b032c1947de912c","ref":"refs/heads/conda","pushedAt":"2024-08-22T07:34:30.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Remove comments","shortMessageHtmlLink":"Remove comments"}},{"before":"0c4b09f27b9de4c78e1177b65e50fa890e50229f","after":"33068de8a2da0093820e419c12aade8814e723df","ref":"refs/heads/conda","pushedAt":"2024-08-22T07:28:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Set label to dev","shortMessageHtmlLink":"Set label to dev"}},{"before":"602ef859ea2aaabc4c0c7ad5c6d2b43b6935f653","after":"0c4b09f27b9de4c78e1177b65e50fa890e50229f","ref":"refs/heads/conda","pushedAt":"2024-08-22T07:26:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Set CUDA_VERSION to 12","shortMessageHtmlLink":"Set CUDA_VERSION to 12"}},{"before":null,"after":"602ef859ea2aaabc4c0c7ad5c6d2b43b6935f653","ref":"refs/heads/conda","pushedAt":"2024-08-22T07:22:27.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Export CUDA_VERSION as an env variable","shortMessageHtmlLink":"Export CUDA_VERSION as an env variable"}},{"before":"daeaac23eea35f9de06bbd33cfa44dd49492e668","after":"86d26dca98ebd5aafdeb0f06efc90abc54b2c8c2","ref":"refs/heads/main","pushedAt":"2024-08-22T07:17:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Typo","shortMessageHtmlLink":"Typo"}},{"before":"14ebe24c8ee44fa06fef3c2b71f6080be2eec058","after":"daeaac23eea35f9de06bbd33cfa44dd49492e668","ref":"refs/heads/main","pushedAt":"2024-08-22T07:14:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Update conda package action","shortMessageHtmlLink":"Update conda package action"}},{"before":"99a06866950107a00fbb57a224c04e1d713c8f63","after":"14ebe24c8ee44fa06fef3c2b71f6080be2eec058","ref":"refs/heads/main","pushedAt":"2024-08-22T07:10:39.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Wall tests (#17)\n\n* first pass at computing translational self mobility components for bottom wall scenario\r\n\r\n* mobility doesn't go to zero at the wall unless this section is commented out.\r\n\r\n* selfmobility test working in comparison to refernce results for one and two wall cases\r\n\r\n* possible correction to DPStokes code to add a buffer the top instead of the bottom when there is a wall\r\n\r\n* now testing if mobility is 0 on the bottom wall\r\n\r\n* Edit comment on nbody test\r\n\r\nComment had the answer for the PSE test. Removed the periodic correction part\r\n\r\n* removed test cases for small numbers of particles for the fluctuation dissipation test.\r\n\r\n* changed dpstokes test to compare to dpstokes reference and added a not-working nbody test\r\n\r\n* bug fix in NBody with wall correction- test now passing. the fix uses the correct constants from the Swan correction paper- the previous implementation was using constants based on a self mobility constant of 1/(8*pi*eta*a) instead of 1/(6*pi*eta*a)\r\n\r\n* combined self mobility tests into one function\r\n\r\n* started pair mobility test\r\n\r\n* change dpstokes to use w=4 kernel by default for forces\r\n\r\n* switched all tests to w=4 kernels, added nbody to pair mobility tests\r\n\r\n* fixed bug in nbody wall correction that came from normalizing by a factor of 1/8pi in the original implementation instead of 1/6pi in the Swan paper.\r\n\r\n* regenerated refs using gpu implementations from dpstokes library. tests are now passing if the same kernel parameters are used as the ref implementation\r\n\r\n* regenerated all ref data using libmobility implementations in single precision\r\n\r\n* changed test pass threshold\r\n\r\n* changed selection of grid parameters to not modify h. instead, modify the box size to make L/h an integer\r\n\r\n* modify how N gets rounded in all dimensions to be fft friendly\r\n\r\n* larger safety factor near open boundary for dpstokes\r\n\r\n* self mobility tests done\r\n\r\n* the two pair DPStokes tests are passing. currently having issues with the nbody test\r\n\r\n* had to change the ref file to use the right positions. nbody test working.\r\n\r\n* the changes to DPStokes parameters seem to made the mobility matrix less symmetric\r\n\r\n* checkpoint commit- adding functionality to have parameter select that modifies the box size and another version that preserves it\r\n\r\n* added mode that preserves L\r\n\r\n* added parameter to initialize that sets whether the box size can get altered or not\r\n\r\n* regenerated data w new defaults after verifying against old repository\r\n\r\n* minor test edits\r\n\r\n* added header and description in poly_fits.h for the DPStokes kernel polynomials\r\n\r\n* added short comments to DPStokes parameter selection\r\n\r\n* added rtol to mobility matrix test\r\n\r\n* simplified computation of nx, ny, & nz\r\n\r\n* renamed tests\r\n\r\n* simplified wall test comparisons\r\n\r\n* switched from .mat to .npz\r\n\r\n* added error for non-square periodic boxes in dpstokes\r\n\r\n* changed tolerance in fluctuation dissipation test to reflect the tolerance for the test of M being symmetric\r\n\r\n* add precision disclaimer\r\n\r\n* Reintroduce some test cases\r\n\r\n---------\r\n\r\nCo-authored-by: Raul ","shortMessageHtmlLink":"Wall tests (#17)"}},{"before":"5adc595147747954c6cfbb6142e4c0719647a7a9","after":"fb780d4ec224a8aeea038af8c53b2c2d29420935","ref":"refs/heads/wall_tests","pushedAt":"2024-08-22T07:09:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Reintroduce some test cases","shortMessageHtmlLink":"Reintroduce some test cases"}},{"before":"0c02a8f44248994acffd659709532bb845856bcc","after":"5adc595147747954c6cfbb6142e4c0719647a7a9","ref":"refs/heads/wall_tests","pushedAt":"2024-08-22T01:39:33.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"rykerfish","name":"Ryker","path":"/rykerfish","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19866074?s=80&v=4"},"commit":{"message":"add precision disclaimer","shortMessageHtmlLink":"add precision disclaimer"}},{"before":"f63d4b7d46547d512180006503345b6beb3d22ea","after":"0c02a8f44248994acffd659709532bb845856bcc","ref":"refs/heads/wall_tests","pushedAt":"2024-08-21T23:18:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"rykerfish","name":"Ryker","path":"/rykerfish","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19866074?s=80&v=4"},"commit":{"message":"added error for non-square periodic boxes in dpstokes","shortMessageHtmlLink":"added error for non-square periodic boxes in dpstokes"}},{"before":"638a3838eb4ad5775e75e72ef73395876daa0eb1","after":"99a06866950107a00fbb57a224c04e1d713c8f63","ref":"refs/heads/main","pushedAt":"2024-08-12T14:44:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"},"commit":{"message":"Update installation instructions","shortMessageHtmlLink":"Update installation instructions"}},{"before":"0c586d105e8dd6457d16b6e4ce7bf24be5b1a8c2","after":null,"ref":"refs/tags/v0.1.2","pushedAt":"2024-08-12T14:22:25.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"}},{"before":"638a3838eb4ad5775e75e72ef73395876daa0eb1","after":null,"ref":"refs/tags/0.1.2","pushedAt":"2024-08-12T14:22:21.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"RaulPPelaez","name":"Raul","path":"/RaulPPelaez","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13015792?s=80&v=4"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0xOVQxNDoxNDowNi4wMDAwMDBazwAAAAS684es","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOC0xMlQxNDoyMjoyMS4wMDAwMDBazwAAAASYNBfq"}},"title":"Activity · stochasticHydroTools/libMobility"}