GitHub PushEvent at 2014-02-22 13:53:41
Repository: gromacs
Actor: gromacs-upload
Payload: {"shas":[["a08d3d6adf7c5ec7959f1c13aa7f0df0a304ef8f","f6594cfb7aad94cc0a4edad303fb5f7264f88ed9@votca.org","cmake eats slashes\n\nChange-Id: I5ea157c4a5e9df2212643b49ba9b270ffd9a6978","Christoph Junghans",false],["a4c5fb33614c0a8e0d6b739bbd41a45a3900003b","c77fa36e024582f895b7890956168d58ecb78926@gmail.com","Issue fatal errors rather than use broken shell code\n\nRefs #1429\n\nChange-Id: I18a17f1e232a86a13f4e3b591bd992702af3017b","Mark Abraham",false],["dd2f13a0570ba46b9126ae14a7088ffb7da6990e","00d605d9d58a482d971ebfe38384e160756a7a61@gwdg.de","Added safety check for fitting group in anaeig.\n\nPreviously, g_anaeig would not check the number of atoms in the selected\nfit group against the number of atoms in the reference structure if this\nwas read from the eigenvector file (g_covar adds the reference structure\nto the eigenvector file if fit and analysis group are identitcal). As a\nresult, anaeig would run out of bounds when selecting the atoms for\nfitting, reading random values from memory.\n\nThis simple check should prevent this behaviour by terminating anaeig\nwith a fatal error similar to the one that is invoked if the group\nselected for analysis has an incorrect number of atoms.\n\nChange-Id: I63a1e1629144e539808d95d867e0ad0673480fdf","Jan Henning Peters",false],["5241daea0fb588d5153b716792bc182e17e1eabc","7753713cfb86fa7e935b6e533a6cafa3d90f8cbd@gmail.com","Added information about how to cite the TNG paper.\n\nChange-Id: I698582f296603f741842f99437bcf872a42682d7","Magnus Lundborg",false],["e5e37f2c62c3ec8bf75b2e90774b3f603c6ce098","c195b508e6f0c57aeafdb5e96947e2b79e6a4b40@kth.se","First part of commit for redesigned SIMD module - namechanges.\n\nThis patch contains the bulk part of trivial name changes\nin preparation for the new SIMD module.\n- Add the gmx_simd_ prefix, and _r suffix for real simd data.\n  This makes the module more generic, and we separate the\n  gromacs SIMD layer from x86 implementation better.\n- epi32 (intel name to indicate 64-bit var extended to 128 bits)\n  has been changed to int32 in types and defines.\n- Negated-fused-multiply-add nomenclature has been changed\n  so \"-a*b+c\" is fnmsub. This is the standard on both Intel\n  and AMD, where most people have SIMD coding experience.\n  My apologies for first recommending Berk to use the opposite.\n- GMX_CPU_ACCELERATION_ strings have been changed to GMX_SIMD_,\n  both in the code and in CMake.\n- Defines like GMX_X86_SSE2 that indicate instruction set\n  availability have received the _OR_HIGHER suffix to clarify\n  that those are cumulative in contrast to the SIMD setting,\n  which only indicates the highest level. These will be moved\n  away from config.h to the simd headers in the next patch.\n- GMX_SIMD_WITDH_HERE has been changed to GMX_SIMD_REAL_WIDTH.\n\nChange-Id: I7a2567f7ddaf8ecd95a4f3b1162bbf03342b2b63","Erik Lindahl",false],["9a31310e7030099c40cc6d7e1533bb4c76cd60f8","c77fa36e024582f895b7890956168d58ecb78926@gmail.com","Update stuff for old BlueGene\n\nBlueGene/L is likely completely dead. We have no ability to\nsupport SIMD on BlueGene/P (technically we can do 2-wide SIMD,\nbut there's probably issues and this platform is almost dead).\n\nChange-Id: Ib607fd11f0b575bcddf4085351ceb2989529247d","Mark Abraham",false],["b9a814f8b39edd4206f22a28d7e0e8505d23e0ef","88d699931980bb01562e478a862e866ce8c20d4a@xray.bmc.uu.se","Fixed another vmdio issue.\n\nAn include that was missed previsouly in trxio.h.\n\nChange-Id: Id7f491e402dec0ee6783d933e98692abb6ce9f1a","David van der Spoel",false],["fda91536f4ce962c6b62e647edb4cd58f9b2e2f6","c77fa36e024582f895b7890956168d58ecb78926@gmail.com","Split genbox into 'solvate' and 'insert-molecules'\n\nAll working old functionality is retained in new 'solvate' and\n'insert-molecules' programs. Registered genbox as obsolete, so someone\nusing gmx genbox gets a hint, which is also triggered by the old\nsymlink. No new symlinks, of course. Updated all mentions of genbox in\nthe whole repo.\n\nFor gmx solvate:\n* Cleaned up unused functions\n* Cleaned up unused headers\n* Cleaned up useless command-line options\n* Updated documentation\n* Checked that its behaviour for writing velocities is OK (but there's\n  no good way to test that)\n\nFor gmx insert-molecules:\n* Cleaned up unused functions\n* Cleaned up unused headers\n* Cleaned up useless command-line options\n* Updated documentation\n* Added tests, worked out that -vdwd and spc216.gro were not required\n  for a decent test and updated accordingly\n* Renamed -cs to -f for consistency with other tools. It would be nice\n  to have a hidden fallback so that -cs does the right thing, but the\n  machinery does not exist.\n* Added helpful check now that -ci is required (generic file I/O error\n  previously)\n* Fixed bug with gmx insert-molecules -ci and velocities. Old version\n  would dereference v pointer because the insertion function does not\n  return velocities for the inserted molecules.\n\nSplit the respective test cases into separate compilation\nunits. Consolidated functions called by both new tools into\nread-conformation.[ch]. The naming and use of those functions are\nhorrendous, and will be fixed in the next patch.\n\ngenbox-addconf.[ch] is no longer specific to any tool, so renamed it\nback to addconf.[ch].\n\nChange-Id: I7781c3db189f5d95d5731e4e86cc0585f7d677c7","Mark Abraham",false],["8fa45f0b685bfe8b2faeaf40c3f70293a1d4673d","c77fa36e024582f895b7890956168d58ecb78926@gmail.com","Re-fix compiler warnings with scanner.cpp\n\nThe existing check for -Wno-deprecated-register worked with a pre-3.4\nclang SVN release, but the release 3.4 compiler only has\n-Wno-deprecated. Not sure if any compiler does or will support\n-Wno-deprecated-register but even if it's wasted, it's not doing any\nharm.\n\nChange-Id: I274255415b66b889dc155472c5f81b6073cdce3e","Mark Abraham",false],["c7a1e248090ccd3f7e1501bec4a687bac30232fb","c77fa36e024582f895b7890956168d58ecb78926@gmail.com","Refactored 'solvate' and 'insert-molecules'\n\nThe use of \"VDW radii\" in these tools was misleading in both\ndocumentation and code. VDW radii are used if they are found, but they\nused to be scaled down via a hidden option, and the user had to\nmagically know what kind of number to give to -vdwd. Documented what\nis going on here.\n\nMade that hidden option public, and renamed -vdwd to -radius. Renamed\nvariables named r to be more reflective of their use as additive\ninter-atomic exclusion half-distances. This clarified what \"mk_vdw\"\nwas really doing, and that a call to it should not be living at the\nend of a function that reads in a conformation from a file. Renamed\nlots of things and documented more behaviour. Freed some memory\nthat should have been freed all along.\n\nThis exposed some horrible use of t_atoms. Fixed the code to always\nallocate on the heap, call the initializer and call the destructor.\n\nChange-Id: I3f8bbbed07442ccc6cd8e563168f5a68736c6b40","Mark Abraham",false],["7b8b0fc840cc4b8bcb9f730b4136b69d4dcfd5a1","7753713cfb86fa7e935b6e533a6cafa3d90f8cbd@gmail.com","Bumped TNG to latest version.\n\nChange-Id: Iefbb35ce46f0c545a23b8bea6b90ad5e11caeffc","Magnus Lundborg",false],["08e18ffa1adfff93ef0a4d75a13a7ee1f98a0d8f","7753713cfb86fa7e935b6e533a6cafa3d90f8cbd@gmail.com","Enable TNG builds on Windows by default.\n\nWith the latest version of TNG the problems encountered on\nWindows should be fixed.\n\nChange-Id: I52d7fd609d086ba4abe4eb8cd95337a58ee35641","Magnus Lundborg",false],["38504456937f7b28b8546da6f13de7549d637187","7753713cfb86fa7e935b6e533a6cafa3d90f8cbd@gmail.com","Removed option to use OpenMP with the TNG library.\n\nOpenMP was only used for compiling a few of the examples. With\nthe latest version of the TNG library the detection is done when\ncompiling those examples and skipping them if OpenMP is not\navailable.\n\nFixes #1432\n\nChange-Id: I76df67b10067f2fbc57a4cf0b1825875239e435d","Magnus Lundborg",false],["a26a0a6fe7e13129696cef23555465df9d958bd8","7753713cfb86fa7e935b6e533a6cafa3d90f8cbd@gmail.com","One more bump of the TNG version.\n\nThis is just to include the improved warning flag settings.\n\nChange-Id: Idc1e0b43b963e8431cd943214c424012d09b6a4c","Magnus Lundborg",false],["0285c365da71173492da24b9c6d848c37fe9b484","01183f156a2a6162e583011cd4263f86ff57a409@gmail.com","Fix some broken links in HTML pages\n\nLinks to programs need to be prefixed with the relative path, as well as\n\"gmx-\".  Also added the \"gmx \" prefix to the displayed names.\n\nChange-Id: I60bd0a58761a725804aa4c5b02619c3031ae7d26","Teemu Murtola",false],["64fd20de16e5ea975b1064ba0cc8b9b252eea1e8","01183f156a2a6162e583011cd4263f86ff57a409@gmail.com","Fix default enum values in help output\n\nnenum() does not return an enum value, but an index into the underlying\narray, which means that the first element is 1 and not zero like the\ncode assumed.  The help output was off-by-one, and could error out if\nsome environment variable was set that was affecting the help output.\n\nFixes #1438.\n\nChange-Id: Iec2f05c9ced55868902069ce59bc4979a6879f86","Teemu Murtola",false],["5ac574b96419900d504156ecc07fc1fb6e99f213","01183f156a2a6162e583011cd4263f86ff57a409@gmail.com","Improve man page formatting slightly\n\n- Don't add extra space whenever [TT]/[BB]/[II] is specified.  This may\n  have been necessary 15 years ago, or has always been broken, but\n  currently it adds a lot of forced double spaces and leading spaces\n  onto man pages.  The text is much more readable without it.\n- Merge all command line options into a single OPTIONS section. Divide\n  it into groups using extra paragraphs in between.  Could possibly be\n  formatted nicer, but that would require extra nroff trickery that we\n  might rather get rid of.\n\nRelated to #1437.\n\nChange-Id: I4b27b79604a1830914cd5d14d6581918f33bb107","Teemu Murtola",false],["423b5001540ff9e4a8695b1bd1496e58e8824ee2","6bd758daef6350b75dea4e7011cdf6bb2f39c608@gwdg.de","Small enhancement of computational electrophysiology manual section.\n\nAdded a note about what can be done if large membrane undulations turn out\nto be a problem in a Computational Electrophysiology setup.\n\nChange-Id: I5f50b4026ea1a8b88368b10c39d2207070c4740c","Carsten Kutzner",false],["8cc7218b0154e77fc3f02b7b65de6f7778e2271a","c77fa36e024582f895b7890956168d58ecb78926@gmail.com","Remove support for .g87 and .xyz I/O formats\n\nAspects of support for these have been broken since before GROMACS\n4.5. That support is sometimes interactive, and thus a poor fit for\nthe way GROMACS supports other trajectory and coordinate formats.\nOther file-format conversion options exist; GROMACS does not have to\nbe a Swiss-army knife.\n\nRemoved undocumented features of gmx helix that required .g87 support\nfor no particularly good reason.\n\nUncrustified files in this commit\n\nChange-Id: Iad4845fd66ad4c55f9a31965d33ded745656db53","Mark Abraham",false],["6cc55526261b9344ae83b11a9a4411d7a6379e10","c77fa36e024582f895b7890956168d58ecb78926@gmail.com","Fix test reference data accidentally broken\n\nChange-Id: Ib622b126b0331c88acab924aff660211122f9d03","Mark Abraham",false]],"size":42,"ref":"refs/heads/alexandria","head":"0fc7f65a35c119b708ac9e273b2e9f2058832635"}