lammps:ddd8533d819ff2aba8cc537e115b384ca935795a commits - 南方科技大学 https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commits/ddd8533d819ff2aba8cc537e115b384ca935795a 2018-08-10T16:33:20+02:00 https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/ddd8533d819ff2aba8cc537e115b384ca935795a make -DLAMMPS_MEMALIGN optional in CMake by checking of 0 alignment. also som... 2018-08-10T16:33:20+02:00 Axel Kohlmeyer akohlmey@gmail.com this changes the CMake configuration file. also, the special case of Windows not supporting posix_memalign() is documented. some more explanations for FFTs and memory alignment are added https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/bc8939a08b9fba2b45f6b59ec2a42f250e80b718 more corrections/rewrites/additions for OpenMP, QM/MM and USER-QUIP 2018-08-10T15:55:32+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/f67b198c24a02ee785f87dc222288601aee58112 discourage the use of MEAM and REAX, which have been supersede by USER-MEAMC ... 2018-08-10T13:04:31+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/13d1f26a0fa5a5e6167c68bd45bea41e3692b12c provide additional information about building QM/MM with QE 2018-08-10T12:15:49+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/8318b96c118348ecc9b6112ad3164b2a959b0d55 update OpenMP support info in build basics 2018-08-10T11:54:51+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/0b523cb48e2fcb884a273b3d76474d2c19ae5c33 some rewording and updates for the traditional and cmake documentation 2018-08-10T11:38:59+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/76289cd955d1bd6fc5397fa150a66cbdd0845b3b Add LAMMPS shared library instructions for CMake 2018-08-09T17:50:55-04:00 Richard Berger richard.berger@temple.edu https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/edb535d36fad7ca1d2dd144f6659db7f77a534cf Fix some of the missing TODOs in cmake docs 2018-08-09T17:21:00-04:00 Richard Berger richard.berger@temple.edu https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/4db08f53510af9ad53da09185ce20cbd45af820a Some tweaks and corrections 2018-08-09T16:02:54-04:00 Richard Berger richard.berger@temple.edu https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/630a46ad6764638dda8cd06f1bc88c929bc5e81b Move Manual_version to Intro 2018-08-09T14:53:40-04:00 Richard Berger richard.berger@temple.edu It should not be its own chapter. The intro seems to be the right place for it. https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/aca9416c7f21ccbb02fd585e500014a910d78265 Merge branch 'master' into doc-reorg-start and resolve merge conflicts with m... 2018-08-09T20:18:12+02:00 Axel Kohlmeyer akohlmey@gmail.com Conflicts: doc/src/Speed_kokkos.txt doc/src/package.txt https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/f7164e593e3ea08e42f5df16e235b880b7a88e38 fix a few more broken or non-unique links 2018-08-09T20:09:11+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/a5170e93ece28c35af98ce72adb38dc5b14d32f0 fix a bunch more broken, duplicate links and misformatted text 2018-08-09T19:46:25+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/108f2d0ed7f9ddddf45b0d5490d77ad0237918eb Merge branch 'collected-small-changes' into doc-reorg-start 2018-08-09T18:48:11+02:00 Axel Kohlmeyer akohlmey@gmail.com Resolved Conflicts: doc/src/Packages_details.txt doc/src/Python_shlib.txt doc/src/fix_manifoldforce.txt https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/6663fbeb113177be706564416776f1cef43d3ebb Merge pull request #928 from akohlmey/fix-rcb-balance-issue 2018-08-09T10:24:38-06:00 Steve Plimpton sjplimp@sandia.gov Fix rcb balance issue https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/cfc1b3a82399f636197d3271deeaaf522519f681 more changes induced by removing Section_start.txt 2018-08-09T10:20:02-06:00 Steven J. Plimpton sjplimp@singsing.sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/c97e6537c805abcae1a6e8fd466b07f070b8d2c7 changes to replace Section_start.txt 2018-08-09T10:19:10-06:00 Steven J. Plimpton sjplimp@singsing.sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/9dde50a4f2c6c51f8dc31cc2f5e51ae8d16e59fb Merge pull request #1042 from akohlmey/kokkos-vs-gpu-direct 2018-08-09T09:25:24-06:00 Steve Plimpton sjplimp@sandia.gov Kokkos vs gpu direct https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/08636889ca05db7658728b4dd0e2a7cb2bd37f01 Merge pull request #1043 from lammps/compute-cluster-atom 2018-08-09T09:15:09-06:00 Steve Plimpton sjplimp@sandia.gov bug fix for compute cluster/atom when computing values used to update… https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/bb25e5d98a8933ecbfb8b762e45759a2bdc4b0b4 adjust header levels for Tools section 2018-08-09T17:13:07+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/8e9ea1e4fadeb57268fcc378e3622a378b16cb35 formatting tweak for Build the manual page 2018-08-09T17:13:07+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/f4ea28cd322399cced20b9bb30cbbf5de1e3da36 update src/lammps.book file with missing entries 2018-08-09T17:13:07+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/1604f011d223b686ea493392568d629fa282d4dc fix a couple more broken links 2018-08-09T17:13:07+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/a06514372388ad7e7d003259aa51990cda621518 create missing "Build_manual.txt" file from 'doc/README' 2018-08-09T17:13:07+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/df20fbbca499b9a86f65b16d7719929940f8c296 fix a bunch of broken linke or make links unique across files 2018-08-09T17:13:07+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/a97ad15d22699e22adb269df95aa9fc33ee85081 update .gitignore 2018-08-09T17:13:06+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/d5594350c4f57dae239ba5c3c00b1f831f3456e2 change zero-size shrink box to original box 2018-08-09T08:50:11-06:00 Steven J. Plimpton sjplimp@singsing.sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/9521814441246f55c3d26087bc2e09b597c22978 rename Kokkos::gpu_direct to Kokkos::gpu_direct_flag 2018-08-09T04:52:58-04:00 Axel Kohlmeyer akohlmey@gmail.com This is for consistency with other parts of LAMMPS where such variables have "flag" in their name. Also reduces confusion with have_gpu_direct() function. When we can safely detect, that GPU-direct is not available, change the default setting of Kokkos::gpu_direct_flag from 1 to 0 https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/dd9fed11dc047ab3b1acd512e58666c51f0cdade use '-pk kokkos gpu/direct on/off' consistently in comments and docs 2018-08-09T04:16:22-04:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/01b81347468fede39abc6e90845827572f116a1c Small tweak to GPU direct not available warning 2018-08-09T09:35:11+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/32658c20d48340afa4fca9813c44a4a95b50c625 Fix typo in gridcomm_kokkos 2018-08-08T17:07:12-06:00 Stan Moore stamoor@sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/1c550d8f39ce3db88050333860395923f406726f Change defaults for GPU-direct to use comm host 2018-08-08T16:46:36-06:00 Stan Moore stamoor@sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/d8aa6d534b8025a16c9aec0f7499742ff5e04975 Remove hardcoded GPU-direct in KOKKOS package 2018-08-08T16:09:41-06:00 Stan Moore stamoor@sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/9202896e75330db552759ddfa84cb2ffe97f0d8b bug fix for compute cluster/atom when computing values used to update a dynam... 2018-08-08T09:31:16-06:00 Steven J. Plimpton sjplimp@singsing.sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/985318203d12b041c6f4ae5057dfe5afa1a362e9 Merge pull request #1038 from stanmoore1/issue-1037 2018-08-08T08:42:21-06:00 Steve Plimpton sjplimp@sandia.gov KOKKOS Package bugfix: Workaround for issue #1037 https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/ff87cdb8f477a8d7ef2b2baec66283de1d7bc3fc Merge pull request #1041 from rbberger/fix_gpu_segfault 2018-08-08T08:41:32-06:00 Steve Plimpton sjplimp@sandia.gov Add extra check for OpenCL timers https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/a3fad229ab0c2718908f8be1703d11674353fdda Merge pull request #1040 from lammps/natom 2018-08-08T08:41:15-06:00 Steve Plimpton sjplimp@sandia.gov enable more correct natoms computation when atoms are lost https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/fac5e29f485eb90979e5c0b8683c8112984a115a Merge pull request #994 from danicholson/user-uef-image-flags 2018-08-08T08:40:56-06:00 Steve Plimpton sjplimp@sandia.gov USER-UEF support for image flags https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/64e152bced4dfb792e2c71f5d83f87b85704e354 add some notes about GPU-direct support requirements to the manual 2018-08-08T14:25:49+02:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/5d87e0c6515f52c68180194496f9b21a8a66e6a4 add wrapper for MPI implementation specific GPU-direct detection 2018-08-08T13:57:41+02:00 Axel Kohlmeyer akohlmey@gmail.com this adds a local wrapper function have_gpu_direct(), that informs about the support for GPU-direct, if possible and add a warning message in case it cannot be detected or is not available and using more than 1 MPI rank.