lammps:e6e026433c09be429fe2066d7016c0569564519a commits - 南方科技大学 https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commits/e6e026433c09be429fe2066d7016c0569564519a 2018-07-25T16:49:51-04:00 https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/e6e026433c09be429fe2066d7016c0569564519a Fix clean-all in docs Makefile 2018-07-25T16:49:51-04:00 Richard Berger richard.berger@temple.edu https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/1d9ad557967507181f71f34c5dec7d76dda9177c changes to Errors and Python doc pages 2018-07-25T14:10:00-06:00 Steven J. Plimpton sjplimp@singsing.sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/dff89771564980dc62b60eee635d04c8c71ae7e4 Merge pull request #1016 from lammps/doc-reorg-examples-modify 2018-07-25T11:44:54-06:00 Steve Plimpton sjplimp@sandia.gov doc changes for Examples and Modify sections https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/592804d56f43cc5adf9e94b22d46840ed3732063 Fix header level of Tools.txt 2018-07-25T11:53:31-04:00 Richard Berger richard.berger@temple.edu https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/ee394b0ed10e43e054ca3429db40295b9f8ebe37 Fixup header levels 2018-07-25T11:53:17-04:00 Richard Berger richard.berger@temple.edu https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/030f1c0127fe4e8efe3a50006668a9f532645d89 Update lammps.book 2018-07-25T11:48:57-04:00 Richard Berger richard.berger@temple.edu https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/22c9258b8e78f74c50ced55c88307d3ed5d55d0b doc changes for Examples and Modify sections 2018-07-25T09:27:13-06:00 Steven J. Plimpton sjplimp@singsing.sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/0fc789bae5b5f8b6fd2aa3519fdd9e314a0d6a73 Merge pull request #1015 from akohlmey/allow-commands-after-exception 2018-07-25T08:43:02-06:00 Steve Plimpton sjplimp@sandia.gov Re-allow commands after an exception was caught inside a run. https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/8d49d1a8c53eb336ec2b556a7619cf1f7c8d9aa3 Merge pull request #1010 from lammps/latte-checksum 2018-07-25T08:42:35-06:00 Steve Plimpton sjplimp@sandia.gov new checksum for LATTE download https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/c31d7c6f4585ff8243c47b8b0a37d49ca4129703 Merge pull request #1009 from ndtrung81/gpu-maint 2018-07-25T08:42:04-06:00 Steve Plimpton sjplimp@sandia.gov Fixed bugs to the tersoff gpu styles for OpenCL builds and some maintenance https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/45532b7106e0346701a3de88bff9fd8ef7b4f163 Merge pull request #996 from marshallmcdonnell/fix_tail_in_gcmc 2018-07-25T08:41:37-06:00 Steve Plimpton sjplimp@sandia.gov Fixes #995: Added tail correction to fix gcmc https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/bf83e55cfac86132d4f33531fdbd295aa1edf918 Merge pull request #1014 from lammps/doc-reorg2 2018-07-25T08:37:38-06:00 Steve Plimpton sjplimp@sandia.gov Doc Reorganization - Tools Section https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/80d85841af82b105ea2b6bd5afe35b765dee7df3 one more tweak on a link 2018-07-25T08:15:25-06:00 Steven J. Plimpton sjplimp@singsing.sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/7ac3f08eec6c17c5666bbaa0083a0c8f7569e6ab Fix typo 2018-07-25T09:39:18-04:00 Richard Berger richard.berger@temple.edu https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/678df2498acbf439d1eee9a02070f9a2956f49c9 Updated lammps.book 2018-07-25T09:32:02-04:00 Richard Berger richard.berger@temple.edu https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/c3661272f17cbb0b0aed0cfb6bcbe8cb5f365d5c re-allow commands after an exception was caught inside a run. 2018-07-24T19:55:39-04:00 Axel Kohlmeyer akohlmey@gmail.com after an exception "all bets are off", i.e. the user should be allowed to do anything to recover. through setting Update::whichflag to 0, the guard against running commands during a run is removed. https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/8385f5666bef66882a3d5d7aebd41593db0e6900 link changes for new Tools.html 2018-07-24T14:43:48-06:00 Steven J. Plimpton sjplimp@singsing.sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/d83d05088fa284a0608d8cace4f7ac0be6d1482b remove replaced file 2018-07-24T14:33:27-06:00 Steven J. Plimpton sjplimp@singsing.sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/da1be29278a7a9e623fdd76478cd572a789f77f5 2nd try at incremental doc page reorg, Section_tools 2018-07-24T14:31:55-06:00 Steven J. Plimpton sjplimp@singsing.sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/eee0df45dd1307223ddde73ec74b42feb4729e7f Updated fix gcmc docs for tail correction note 2018-07-24T09:26:06-04:00 Marshall McDonnell mcdonnellmt@ornl.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/923ae041dcfe0fdebbb146ec9a9b71fa8eba5a55 (temporary) workaround for memory leaks with OpenCL and MPI for upcoming stab... 2018-07-23T15:52:42-04:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/2ac3953e17b94bb16f402185eaa8904809aeeb01 update src/Purge.list to cleanly remove obsolete files 2018-07-23T12:37:05-04:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/35ffa0a214d25b5a6f6d6bc60563b7e7507b33fe update MD5SUM entry in CMake build system 2018-07-23T12:36:29-04:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/40dcfa44c9a0f545e9e33432bb06e471a5023de7 new checksum for LATTE download 2018-07-23T08:35:40-06:00 Steven J. Plimpton sjplimp@singsing.sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/644888d03c495258655518d9cf40f51e79acb033 Fixed bugs with time_q and time_quat not calling start() and stop() when... 2018-07-22T15:12:45-05:00 Trung Nguyen ndactrung@gmail.com Fixed bugs with time_q and time_quat not calling start() and stop() when _charge and/or _rot in Atom are true for OpenCL builds https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/b612c7ee75662dc3530e0a112063486b0f3d080c Fixed a copy-paste bug in lal_neighbor.cpp for neigh no 2018-07-22T13:15:01-05:00 Trung Nguyen ndactrung@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/d71e037c233fcd5e49bab5d71d472e9db1249e52 Renamed dev_acc to dev_ilist for better description and updated the 3-body... 2018-07-22T11:27:14-05:00 Trung Nguyen ndactrung@gmail.com Renamed dev_acc to dev_ilist for better description and updated the 3-body styles accordingly; also fixed bugs with accessing dev_packed from the three_end kernel of tersoff/mod and tersoff/zbl gpu styles for OpenCL builds https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/94da4be922532f15aa159b3fa60e95e81ac89874 Fixed bugs for tersoff gpu styles for OpenCL builds 2018-07-21T13:50:10-05:00 Trung Nguyen ndactrung@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/01c27194d4de20ab3002091fe20d396495019e66 Fixes for lal_neighbor.cpp for get_host() and for time_kernel 2018-07-21T00:18:30-05:00 Trung Nguyen ndactrung@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/223de57401ff2547715e24b44226eba5599946ed Added set_platform_accelerator() for nvd_device.h for OpenCL compatibility 2018-07-21T00:14:31-05:00 Trung Nguyen ndactrung@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/5c21d2aff9b3b6a17a53e94eff3ecbcf188e3d16 Merge pull request #962 from ndtrung81/body-dem 2018-07-20T14:37:41-06:00 Steve Plimpton sjplimp@sandia.gov Discrete element models for the BODY package https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/884e72a4ba7cbb5beaf9d5f0afa3b1d80f4ed229 Merge pull request #1008 from akohlmey/support-platform-select 2018-07-20T14:32:49-06:00 Steve Plimpton sjplimp@sandia.gov OpenCL related fixes and improvements to the GPU package https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/2732b8b647d070c0b9eee782605f806f58442dac Merge pull request #1007 from rbberger/fix_memleak_in_gpu_package 2018-07-20T14:27:16-06:00 Steve Plimpton sjplimp@sandia.gov Fixes a memory leak when using OpenCL https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/de8176b4fc0556d758d7c49bea43f92c5006f234 various minor OpenCL related fixes and improvements to the GPU package 2018-07-20T14:41:54-04:00 Axel Kohlmeyer akohlmey@gmail.com - document previously undocumented OpenCL tune settings - implement OpenCL platform selection through prefixing the device type with the platform id separated by a colon - allow passing custom tune parameters though postfixing the device type with the 13 tuneable parameters separated by commas - remove an extra clear() that would delete device properties structs an cause LAMMPS to output garbage strings https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/36081f9ffdf1746a5b1cf4fa25b762ee468d3e48 Merge pull request #1005 from timattox/USER-DPD_alpha 2018-07-19T09:07:21-06:00 Steve Plimpton sjplimp@sandia.gov USER-DPD: propagate a minor performance bugfix throughout the DPDE code https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/2eb8d779e8bc657a8767c4cad7ab72f20f65955f Fixes a memory leak when using OpenCL 2018-07-18T18:54:57-04:00 Richard Berger richard.berger@temple.edu The GPU package uses OpenCL events for measuring time. These have to be released to free up memory. I removed the clReleaseEvent() calls in the clear() method because in some cases they don't exist yet and I couldn't find a way to check for a valid event (clRetainEvent didn't work). This at least fixes the massive leak during simulations. See issue #1006 https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/7d4de932b6945045779ae4e2a867b4e99f898d19 reinstate reference to fix wall/ees in lammps.book 2018-07-18T13:13:57-04:00 Axel Kohlmeyer akohlmey@gmail.com https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/dfd40c1b70c04ac3d3a8c24c4a2e0e399aa5168b more doc tweaks 2018-07-18T10:48:29-06:00 Steven J. Plimpton sjplimp@singsing.sandia.gov https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/f9c7fa973b29f17bacc2d5dfd7686f08fd529f8d USER-DPD: propagate a minor performance bugfix throughout the DPDE code 2018-07-18T10:50:22-05:00 Tim Mattox timothy.mattox@engilitycorp.com The fix_shardlow_kokkos.cpp code had already factored out a redundant sqrt() calculation in the innermost loop of ssa_update_dpde(). This changeset propagates an equivilent optimization to: fix_shardlow.cpp pair_dpd_fdt_energy.cpp pair_dpd_fdt_energy_kokkos.cpp The alpha_ij variable was really just an [itype][jtype] lookup parameter, replacing a sqrt() and two multiplies per interacting particle pair by a cached memory read. Even if there isn't much time savings, the code is now consistent across the various versions. https://mirrors.sustech.edu.cn/git/11930499/lammps/-/commit/843b96e8dd579f7c02cac30948b258186664b0a0 more changes to new polygon/hedron docs and command names 2018-07-18T08:49:42-06:00 Steven J. Plimpton sjplimp@singsing.sandia.gov