{"push_id":645274367,"size":127,"distinct_size":2,"ref":"refs/heads/fit-to-template-rmsd","head":"4d480ba84e8c3d02d6e8dd3d326474d0ed0070a0","before":"5c3f801d861ee363a9bf306b6fc9535f45291524","commits":[{"sha":"df9945f86968eb8641ca6e2a26cca05caf129b22","author":{"email":"d5533d069daf363ec147cf93c6ba0b9ffb4df870@gmail.com","name":"Gareth Tribello"},"message":"Made normalising of eignevectors optional in PCAVars","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/df9945f86968eb8641ca6e2a26cca05caf129b22"},{"sha":"ad0ec62cbcd9624d3a4c336e184d18034a708a85","author":{"email":"d5533d069daf363ec147cf93c6ba0b9ffb4df870@gmail.com","name":"Gareth Tribello"},"message":"Fixed bug in PCAVars::apply","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/ad0ec62cbcd9624d3a4c336e184d18034a708a85"},{"sha":"b46d0793da18d4984faeb49b023c3376eea907ff","author":{"email":"2620b0a465ef47c79ad8385c3e50809eab938bc2@gmail.com","name":"Giovanni Bussi"},"message":"PBC slightly faster on orthorombic cells\n\nTaken from the fccubic branch of @ceriottm\n\nThe \"while\" implementation for orthorombic cells is slighlty faster,\nso I decided to enable it by default.\n\nThe \"while\" implementation for Tools::pbc is either slower\nor equivalent, so I did not include it.\n\nI think the reason is that in the first case one can avoid a couple\nof multiplications, whereas in the second this is more difficult\nsince images are implemented in scaled coordinates and require\nanyway two matrix*vector multiplications.","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/b46d0793da18d4984faeb49b023c3376eea907ff"},{"sha":"13ce3619f5e03f8ab39ddeaae66088439e7186eb","author":{"email":"2620b0a465ef47c79ad8385c3e50809eab938bc2@gmail.com","name":"Giovanni Bussi"},"message":"Revert \"PBC slightly faster on orthorombic cells\"\n\nThis reverts commit b46d0793da18d4984faeb49b023c3376eea907ff.\n\nThis commit break several regtests. Most of the problems are harmless\nnumerical derivatives. However, the regtests on pbc hangs forever.\nI have to further inspect this.","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/13ce3619f5e03f8ab39ddeaae66088439e7186eb"},{"sha":"f4ca4c5d8a53efb12e98eec5118c44fde8d503b2","author":{"email":"2620b0a465ef47c79ad8385c3e50809eab938bc2@gmail.com","name":"Giovanni Bussi"},"message":"Added --natoms and cell check to driver\n\nThis allow amber formats to be properly read","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/f4ca4c5d8a53efb12e98eec5118c44fde8d503b2"},{"sha":"ba1b1bba6ac8a62c9341d363abf79f856bb8f9fc","author":{"email":"2620b0a465ef47c79ad8385c3e50809eab938bc2@gmail.com","name":"Giovanni Bussi"},"message":"Added possibility to inquire for external molfile","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/ba1b1bba6ac8a62c9341d363abf79f856bb8f9fc"},{"sha":"84fc4dd4817645c4519ae49eacc502089562155f","author":{"email":"2620b0a465ef47c79ad8385c3e50809eab938bc2@gmail.com","name":"Giovanni Bussi"},"message":"Added regtests for amber molfile\n\nNotice that these tests will not run on travis-ci\nsince VMD plugins are not available there","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/84fc4dd4817645c4519ae49eacc502089562155f"},{"sha":"a4ab7ed5a29e01323d74e4137ae4c4686bea08f9","author":{"email":"2620b0a465ef47c79ad8385c3e50809eab938bc2@gmail.com","name":"Giovanni Bussi"},"message":"Changelog\n\n[makedoc]","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/a4ab7ed5a29e01323d74e4137ae4c4686bea08f9"},{"sha":"36de97698f36032512ccd95b074a33131ca2985b","author":{"email":"2620b0a465ef47c79ad8385c3e50809eab938bc2@gmail.com","name":"Giovanni Bussi"},"message":"typo and doc\n\n[makedoc]","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/36de97698f36032512ccd95b074a33131ca2985b"},{"sha":"205619db6807ad1bafc5a2e9ba51396e47d7b3d2","author":{"email":"2620b0a465ef47c79ad8385c3e50809eab938bc2@gmail.com","name":"Giovanni Bussi"},"message":"Merge branch 'v2.1'\n\n[makedoc]","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/205619db6807ad1bafc5a2e9ba51396e47d7b3d2"},{"sha":"8b18cc7f94b4be507a9b51293c237f3c206ce693","author":{"email":"38a5c9d36aac7403c337f49bc51e0cc777db9989@sissa.it","name":"alejogiley"},"message":"MOLINFO to nucleic acids and PUCKERING\n\nin MOLINFO added 2 new MOLTYPE for nucleic acids: “rna” and “dna”\ncomponents are: “@epsion-#”, “@gamma-#“, “@beta-#“, “@alpha-#“,\n“@zeta-#“, “@chi-#”, “@v{0..4}-#“, “@base-#”, “@sugar-“ and “@back-#”\n\nin PUCKERING the components are: “.phs”, “.amp”,“.Zx”,”.Zy”\nderivatives are calculate only for “.Zx” and “.Zy”\n(cherry picked from commit 58bf3be6341db37ab032c58e2767c55848a75492)\n\nConflicts:\n\tuser-doc/bibliography.bib","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/8b18cc7f94b4be507a9b51293c237f3c206ce693"},{"sha":"e49f3d4274a0f2938e3f3ce673afe05df1a9df4a","author":{"email":"38a5c9d36aac7403c337f49bc51e0cc777db9989@sissa.it","name":"alejogiley"},"message":"Added derivatives of phs and amp\n(cherry picked from commit ac88fd3ce3e8ff55e69f7bac94cf3e46fdebcc03)","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/e49f3d4274a0f2938e3f3ce673afe05df1a9df4a"},{"sha":"a7c47087f18e4780389fb44fb0ec0f4b4d874658","author":{"email":"38a5c9d36aac7403c337f49bc51e0cc777db9989@sissa.it","name":"alejogiley"},"message":"updated MOLINFO\n(cherry picked from commit 3d165c2ec8dd2e21f55ea1d2d6d94e2e4c9c6b67)","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/a7c47087f18e4780389fb44fb0ec0f4b4d874658"},{"sha":"4f6583e032c3efd4375ecbc2be020762774b56cb","author":{"email":"38a5c9d36aac7403c337f49bc51e0cc777db9989@sissa.it","name":"alejogiley"},"message":"updated MOLINFO\n(cherry picked from commit 0037c97559b3e86d5cfbd062ddc420654e6d9575)","distinct":false,"url":"https://api.github.com/repos/plumed/plumed2/commits/4f6583e032c3efd4375ecbc2be020762774b56cb"},{"sha":"0a334055cfa355f3734642f2997e64d18ed10f60","author":{"email":"2620b0a465ef47c79ad8385c3e50809eab938bc2@gmail.com","name":"Giovanni Bussi"},"message":"Cleanup\n\nThis squeezes several commits. 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