{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":9942565,"defaultBranch":"master","name":"plumed2","ownerLogin":"plumed","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2013-05-08T17:59:40.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/4379652?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1721812646.0","currentOid":""},"activityList":{"items":[{"before":"7e0f4358bc9d0af35140945287ada43a16f9e345","after":"e0f560683c13abda72691f172d81f0dae1fa82b7","ref":"refs/heads/derivatives-from-backpropegation","pushedAt":"2024-07-25T08:17:57.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Reduced the size of the forces array that is manipulated in matrix vector multiplication","shortMessageHtmlLink":"Reduced the size of the forces array that is manipulated in matrix ve…"}},{"before":"3e1bc056a3d858d2e980f8b4259f4fabe1d52c5a","after":"9a807021ae6c252178676efa9341880a353f6d4d","ref":"refs/heads/master","pushedAt":"2024-07-24T21:28:43.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"GiovanniBussi","name":"Giovanni","path":"/GiovanniBussi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4378974?s=80&v=4"},"commit":{"message":"Merge pull request #1101 from Iximiel/benchmark-fix-help\n\nminimal change in the benchmark help text","shortMessageHtmlLink":"Merge pull request #1101 from Iximiel/benchmark-fix-help"}},{"before":"7401ac896e6326ac153e16972fe44272bd5a7de6","after":"3e1bc056a3d858d2e980f8b4259f4fabe1d52c5a","ref":"refs/heads/master","pushedAt":"2024-07-24T21:27:35.000Z","pushType":"pr_merge","commitsCount":7,"pusher":{"login":"GiovanniBussi","name":"Giovanni","path":"/GiovanniBussi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4378974?s=80&v=4"},"commit":{"message":"Merge pull request #1090 from Iximiel/plumed_hCasts\n\nRemoved old-style-cast from Plumed.h","shortMessageHtmlLink":"Merge pull request #1090 from Iximiel/plumed_hCasts"}},{"before":"95e959f551e99de024fed8174ed457c96a250fe3","after":"7401ac896e6326ac153e16972fe44272bd5a7de6","ref":"refs/heads/master","pushedAt":"2024-07-24T21:26:53.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"GiovanniBussi","name":"Giovanni","path":"/GiovanniBussi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4378974?s=80&v=4"},"commit":{"message":"Merge pull request #1095 from Iximiel/benchmark-signals\n\nAdded sigterm to the signal handler for Benchmark","shortMessageHtmlLink":"Merge pull request #1095 from Iximiel/benchmark-signals"}},{"before":"a24a72afe5c83c145faae1dfcac5fb4d5542d340","after":"95e959f551e99de024fed8174ed457c96a250fe3","ref":"refs/heads/master","pushedAt":"2024-07-24T21:24:22.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"GiovanniBussi","name":"Giovanni","path":"/GiovanniBussi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4378974?s=80&v=4"},"commit":{"message":"Merge branch 'v2.9'","shortMessageHtmlLink":"Merge branch 'v2.9'"}},{"before":"cfbbc3d5283fd239038317b100e47b3d9f93ffa1","after":"fe18eee22011d20850c062fb2a6f12d41126c257","ref":"refs/heads/v2.9","pushedAt":"2024-07-24T21:22:35.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"GiovanniBussi","name":"Giovanni","path":"/GiovanniBussi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4378974?s=80&v=4"},"commit":{"message":"Merge pull request #1096 from Iximiel/CoordinationStride\n\nSmall optimization in CoordinationBase","shortMessageHtmlLink":"Merge pull request #1096 from Iximiel/CoordinationStride"}},{"before":"e284c706c85d24c78498c3ffd38d7c15d2d21f88","after":"900a1f18ff44c72e3d0d4717d28a859502ede533","ref":"refs/heads/fix-link-cells-nopbc","pushedAt":"2024-07-24T09:31:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Added code to test link cell stuff with nopbc","shortMessageHtmlLink":"Added code to test link cell stuff with nopbc"}},{"before":null,"after":"e284c706c85d24c78498c3ffd38d7c15d2d21f88","ref":"refs/heads/fix-link-cells-nopbc","pushedAt":"2024-07-24T09:17:26.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Made implementation of link cells that should work even if you don't have PBC","shortMessageHtmlLink":"Made implementation of link cells that should work even if you don't …"}},{"before":"21155289a184500ffd6591c0c23b3260509b5d97","after":"7e0f4358bc9d0af35140945287ada43a16f9e345","ref":"refs/heads/derivatives-from-backpropegation","pushedAt":"2024-07-19T17:20:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Optimised adding of forces in AdjacencyMatrixBase by using the fact that we already worked out that some of the elements of the matrix are zero and that the forces on these elements are zero","shortMessageHtmlLink":"Optimised adding of forces in AdjacencyMatrixBase by using the fact t…"}},{"before":"033d957c0ff576a0d32dfe37bc0304457b80abfb","after":"21155289a184500ffd6591c0c23b3260509b5d97","ref":"refs/heads/derivatives-from-backpropegation","pushedAt":"2024-07-19T15:16:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Optimisations of derivatives by back propegation","shortMessageHtmlLink":"Optimisations of derivatives by back propegation"}},{"before":"94d33a9d2406273e94554936c208a98c25172fed","after":"033d957c0ff576a0d32dfe37bc0304457b80abfb","ref":"refs/heads/derivatives-from-backpropegation","pushedAt":"2024-07-19T10:51:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Added optimisation for matrix times vector to avoid allocating large arrays.","shortMessageHtmlLink":"Added optimisation for matrix times vector to avoid allocating large …"}},{"before":"cd6f553b7cb536b70130922cbef4d22a9536eaf5","after":"94d33a9d2406273e94554936c208a98c25172fed","ref":"refs/heads/derivatives-from-backpropegation","pushedAt":"2024-07-18T15:09:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Added some optimisations in AdjacencyMatrixBase","shortMessageHtmlLink":"Added some optimisations in AdjacencyMatrixBase"}},{"before":"10da9a4d66551369aeccd110ca4339558153ab61","after":"cd6f553b7cb536b70130922cbef4d22a9536eaf5","ref":"refs/heads/derivatives-from-backpropegation","pushedAt":"2024-07-16T13:51:33.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Added faster version of matrix vector multiply that is used when not employing the chain","shortMessageHtmlLink":"Added faster version of matrix vector multiply that is used when not …"}},{"before":"2a1e7d3dfa43f41680aaac6e9b7f1cb98e06f483","after":"a24a72afe5c83c145faae1dfcac5fb4d5542d340","ref":"refs/heads/master","pushedAt":"2024-07-16T11:04:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Optimisation of MatrixVectorProduct to improve performance when multiplying matrix by vector of ones\n\nIf you are multiplying the matrix by a vector of ones you don't need to do any multiplication. You can just sum each row of the matrix.\nThis is now used to calculate this type of matrix-vector product. The change speeds up the code slightly in an operation that is done reasonably often.\nChanges to regtests are due to the derivatives on the constant vector of ones no longer being stored or used.","shortMessageHtmlLink":"Optimisation of MatrixVectorProduct to improve performance when multi…"}},{"before":"d15c12f00d2b98f103e6bb43bc0035de43795095","after":"10da9a4d66551369aeccd110ca4339558153ab61","ref":"refs/heads/derivatives-from-backpropegation","pushedAt":"2024-07-16T10:07:11.000Z","pushType":"push","commitsCount":7,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Merge branch 'master' into derivatives-from-backpropegation","shortMessageHtmlLink":"Merge branch 'master' into derivatives-from-backpropegation"}},{"before":"ce48b26a2a5f455f2f3a89d97ba06fc8af0d5b9c","after":"2a1e7d3dfa43f41680aaac6e9b7f1cb98e06f483","ref":"refs/heads/master","pushedAt":"2024-07-16T09:15:03.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Ensuring derivatives are not added in ContactMap when they are not required","shortMessageHtmlLink":"Ensuring derivatives are not added in ContactMap when they are not re…"}},{"before":null,"after":"767169b3a1de91c4849435ffd95b3382812fa912","ref":"refs/heads/faster-matrix","pushedAt":"2024-07-15T17:05:04.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Changes to speed up multiplication of sparse matrices by vectors","shortMessageHtmlLink":"Changes to speed up multiplication of sparse matrices by vectors"}},{"before":"6ceb747e0e8bd9533a9fc0b9c3c8cb245c1a951c","after":"ce48b26a2a5f455f2f3a89d97ba06fc8af0d5b9c","ref":"refs/heads/master","pushedAt":"2024-07-12T20:49:30.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"GiovanniBussi","name":"Giovanni","path":"/GiovanniBussi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4378974?s=80&v=4"},"commit":{"message":"Merge pull request #1097 from Iximiel/benchmark-header\n\nAdding a small header to the benchmark utility","shortMessageHtmlLink":"Merge pull request #1097 from Iximiel/benchmark-header"}},{"before":"639e810472d15943e53f5cabf8b75b9c1208b712","after":"6ceb747e0e8bd9533a9fc0b9c3c8cb245c1a951c","ref":"refs/heads/master","pushedAt":"2024-07-11T15:01:00.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Small speedup when calculating matrices without using derivatives\n\nDerivatives do not need to be cleared in these cases so we avoid clearing them now.","shortMessageHtmlLink":"Small speedup when calculating matrices without using derivatives"}},{"before":"b9b8969c9abb7476ab4f5ec375b887197bb32438","after":"d15c12f00d2b98f103e6bb43bc0035de43795095","ref":"refs/heads/derivatives-from-backpropegation","pushedAt":"2024-07-10T09:44:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Optimisations in adjacency matrix calculator","shortMessageHtmlLink":"Optimisations in adjacency matrix calculator"}},{"before":null,"after":"b9b8969c9abb7476ab4f5ec375b887197bb32438","ref":"refs/heads/derivatives-from-backpropegation","pushedAt":"2024-07-04T15:31:21.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Now turning off derivatives on forward pass through task loop when storing values as they are only needed on the backward pass to calculate forces","shortMessageHtmlLink":"Now turning off derivatives on forward pass through task loop when st…"}},{"before":"639e810472d15943e53f5cabf8b75b9c1208b712","after":null,"ref":"refs/heads/fix-sparse-matrix-store","pushedAt":"2024-07-04T11:24:40.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"}},{"before":"120447eecb9c4d2e33417335c54c5c1f4c93000e","after":"639e810472d15943e53f5cabf8b75b9c1208b712","ref":"refs/heads/master","pushedAt":"2024-07-04T11:24:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Fixed derivatives for matrix vector multiplication when matrix is sparse and stored\n\nThis commit fixes a bug with the derivatives for matrix-vector multiplication that occurs when you store the derivatives\nand compute the forces in the back-propegation (apply) step instead of calculating the derivatives in the forward (calculate) loop by using\nthe chain. The problems occur when the matrix that is being used is sparse.\n\nThe feature that is fixed here is not currently used as in all the cases it could be used the derivatives are calculated during the calculate step.\nI think it is better to fix it here, however, as it may be used in the future.\n\nNotice that chnages were required to KDE because this does apply forces to a sparse matrix. In the old version of the code when applying forces in KDE\nthe matrix was assumed to be full even if it was sparse. The changes to KDE are thus using the sparsity more effectively when doing the back propegation\nfor the forces.","shortMessageHtmlLink":"Fixed derivatives for matrix vector multiplication when matrix is spa…"}},{"before":null,"after":"639e810472d15943e53f5cabf8b75b9c1208b712","ref":"refs/heads/fix-sparse-matrix-store","pushedAt":"2024-07-04T10:03:39.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Fixed derivatives for matrix vector multiplication when matrix is sparse and stored\n\nThis commit fixes a bug with the derivatives for matrix-vector multiplication that occurs when you store the derivatives\nand compute the forces in the back-propegation (apply) step instead of calculating the derivatives in the forward (calculate) loop by using\nthe chain. The problems occur when the matrix that is being used is sparse.\n\nThe feature that is fixed here is not currently used as in all the cases it could be used the derivatives are calculated during the calculate step.\nI think it is better to fix it here, however, as it may be used in the future.\n\nNotice that chnages were required to KDE because this does apply forces to a sparse matrix. In the old version of the code when applying forces in KDE\nthe matrix was assumed to be full even if it was sparse. The changes to KDE are thus using the sparsity more effectively when doing the back propegation\nfor the forces.","shortMessageHtmlLink":"Fixed derivatives for matrix vector multiplication when matrix is spa…"}},{"before":"531abd871efb9c452bdb8cc52e416f8d3a318fd0","after":"120447eecb9c4d2e33417335c54c5c1f4c93000e","ref":"refs/heads/master","pushedAt":"2024-06-27T14:34:01.000Z","pushType":"pr_merge","commitsCount":33,"pusher":{"login":"GiovanniBussi","name":"Giovanni","path":"/GiovanniBussi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4378974?s=80&v=4"},"commit":{"message":"Merge pull request #1082 from lab-cosmo/action-metatensor\n\nInterface to metatensor to use arbitrary machine learning models as collective variables","shortMessageHtmlLink":"Merge pull request #1082 from lab-cosmo/action-metatensor"}},{"before":"2e07dd1ebd5ac717b16f86a9eb5a481a384a9f20","after":"531abd871efb9c452bdb8cc52e416f8d3a318fd0","ref":"refs/heads/master","pushedAt":"2024-06-14T19:15:52.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"carlocamilloni","name":"Carlo Camilloni","path":"/carlocamilloni","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4580854?s=80&v=4"},"commit":{"message":"Merge branch 'v2.9'","shortMessageHtmlLink":"Merge branch 'v2.9'"}},{"before":"5273edf90b543b1bce4977daf43561019f1b43d1","after":"cfbbc3d5283fd239038317b100e47b3d9f93ffa1","ref":"refs/heads/v2.9","pushedAt":"2024-06-14T19:15:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"carlocamilloni","name":"Carlo Camilloni","path":"/carlocamilloni","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4580854?s=80&v=4"},"commit":{"message":"gmx2024 remove unneeded files","shortMessageHtmlLink":"gmx2024 remove unneeded files"}},{"before":"24fe95a37e736e774d3033bf7ea18e68b0fd2e4e","after":"9398658637833a0bd658fd0c430b066c68d3022b","ref":"refs/heads/read-mass-charge-action","pushedAt":"2024-06-14T13:43:29.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Added functionality to READMASSCHARGE so that you can read masses and charges from an mcfile or a pdb file. This is the same as driver","shortMessageHtmlLink":"Added functionality to READMASSCHARGE so that you can read masses and…"}},{"before":"b300e575ab60e7083edf32f20e3aedcbc0e1e8d3","after":"24fe95a37e736e774d3033bf7ea18e68b0fd2e4e","ref":"refs/heads/read-mass-charge-action","pushedAt":"2024-06-13T19:46:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Fixed manual for MassChangeInput action","shortMessageHtmlLink":"Fixed manual for MassChangeInput action"}},{"before":null,"after":"b300e575ab60e7083edf32f20e3aedcbc0e1e8d3","ref":"refs/heads/read-mass-charge-action","pushedAt":"2024-06-13T16:53:11.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"gtribello","name":"Gareth Tribello","path":"/gtribello","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4581364?s=80&v=4"},"commit":{"message":"Added action that allows you to set the masses and charges from a PDB file in the plumed.dat input file\n\nThis is useful for i-Pi as with this code it is not straightforward to pass the masses and charges to PLUMED.","shortMessageHtmlLink":"Added action that allows you to set the masses and charges from a PDB…"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEiMGykwA","startCursor":null,"endCursor":null}},"title":"Activity · plumed/plumed2"}