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15043 Commits

Author SHA1 Message Date
Richard Berger 8fccf6b9b4 Use absolute paths for docenv 2018-07-28 23:31:50 -04:00
Richard Berger 99985a1d5b Add profile.d files to set LAMMPS_POTENTIALS environment variable 2018-07-27 20:31:53 -04:00
Richard Berger 06335e77cb Ensure doc is built by default when enabled 2018-07-27 02:56:26 -04:00
Richard Berger 9ffd262039 Add CMake target for html documentation 2018-07-27 02:46:36 -04:00
Richard Berger 819e47b69e Add output dir and verbose option to txt2rst 2018-07-27 02:30:28 -04:00
Richard Berger c8b9a727e4 Add potential files to CMake install target 2018-07-27 00:35:08 -04:00
Steve Plimpton ae0979e1ad
Merge pull request #1017 from lammps/doc-reorg-errors-python 
changes to Errors and Python doc pages
 2018-07-25 16:32:46 -06:00
Richard Berger 532d09bd56 Correct lammps.book 2018-07-25 16:56:49 -04:00
Richard Berger 353ecd2c7a Correct header levels 2018-07-25 16:56:28 -04:00
Richard Berger e6e026433c Fix clean-all in docs Makefile 2018-07-25 16:49:51 -04:00
Steven J. Plimpton 1d9ad55796 changes to Errors and Python doc pages 2018-07-25 14:10:00 -06:00
Steve Plimpton dff8977156
Merge pull request #1016 from lammps/doc-reorg-examples-modify 
doc changes for Examples and Modify sections
 2018-07-25 11:44:54 -06:00
Richard Berger 592804d56f Fix header level of Tools.txt 2018-07-25 11:53:31 -04:00
Richard Berger ee394b0ed1 Fixup header levels 2018-07-25 11:53:17 -04:00
Richard Berger 030f1c0127 Update lammps.book 2018-07-25 11:48:57 -04:00
Steven J. Plimpton 22c9258b8e doc changes for Examples and Modify sections 2018-07-25 09:27:13 -06:00
Steve Plimpton 0fc789bae5
Merge pull request #1015 from akohlmey/allow-commands-after-exception 
Re-allow commands after an exception was caught inside a run.
 2018-07-25 08:43:02 -06:00
Steve Plimpton 8d49d1a8c5
Merge pull request #1010 from lammps/latte-checksum 
new checksum for LATTE download
 2018-07-25 08:42:35 -06:00
Steve Plimpton c31d7c6f45
Merge pull request #1009 from ndtrung81/gpu-maint 
Fixed bugs to the tersoff gpu styles for OpenCL builds and some maintenance
 2018-07-25 08:42:04 -06:00
Steve Plimpton 45532b7106
Merge pull request #996 from marshallmcdonnell/fix_tail_in_gcmc 
Fixes #995: Added tail correction to fix gcmc
 2018-07-25 08:41:37 -06:00
Steve Plimpton bf83e55cfa
Merge pull request #1014 from lammps/doc-reorg2 
Doc Reorganization - Tools Section
 2018-07-25 08:37:38 -06:00
Steven J. Plimpton 80d85841af one more tweak on a link 2018-07-25 08:15:25 -06:00
Richard Berger 7ac3f08eec Fix typo 2018-07-25 09:39:18 -04:00
Richard Berger 678df2498a Updated lammps.book 2018-07-25 09:32:02 -04:00
Axel Kohlmeyer c3661272f1 re-allow commands after an exception was caught inside a run. 
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.
 2018-07-24 19:55:39 -04:00
Steven J. Plimpton 8385f5666b link changes for new Tools.html 2018-07-24 14:43:48 -06:00
Steven J. Plimpton d83d05088f remove replaced file 2018-07-24 14:33:27 -06:00
Steven J. Plimpton da1be29278 2nd try at incremental doc page reorg, Section_tools 2018-07-24 14:31:55 -06:00
Marshall McDonnell eee0df45dd Updated fix gcmc docs for tail correction note 2018-07-24 09:26:06 -04:00
Axel Kohlmeyer 923ae041dc (temporary) workaround for memory leaks with OpenCL and MPI for upcoming stable release 2018-07-23 15:52:42 -04:00
Axel Kohlmeyer 2ac3953e17 update src/Purge.list to cleanly remove obsolete files 2018-07-23 12:37:05 -04:00
Axel Kohlmeyer 35ffa0a214 update MD5SUM entry in CMake build system 2018-07-23 12:36:29 -04:00
Steven J. Plimpton 40dcfa44c9 new checksum for LATTE download 2018-07-23 08:35:40 -06:00
Trung Nguyen 644888d03c 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 2018-07-22 15:12:45 -05:00
Trung Nguyen b612c7ee75 Fixed a copy-paste bug in lal_neighbor.cpp for neigh no 2018-07-22 13:15:01 -05:00
Trung Nguyen d71e037c23 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 2018-07-22 11:27:14 -05:00
Trung Nguyen 94da4be922 Fixed bugs for tersoff gpu styles for OpenCL builds 2018-07-21 13:50:10 -05:00
Trung Nguyen 01c27194d4 Fixes for lal_neighbor.cpp for get_host() and for time_kernel 2018-07-21 00:18:30 -05:00
Trung Nguyen 223de57401 Added set_platform_accelerator() for nvd_device.h for OpenCL compatibility 2018-07-21 00:14:31 -05:00
Steve Plimpton 5c21d2aff9
Merge pull request #962 from ndtrung81/body-dem 
Discrete element models for the BODY package
 2018-07-20 14:37:41 -06:00
Steve Plimpton 884e72a4ba
Merge pull request #1008 from akohlmey/support-platform-select 
OpenCL related fixes and improvements to the GPU package
 2018-07-20 14:32:49 -06:00
Steve Plimpton 2732b8b647
Merge pull request #1007 from rbberger/fix_memleak_in_gpu_package 
Fixes a memory leak when using OpenCL
 2018-07-20 14:27:16 -06:00
Axel Kohlmeyer de8176b4fc various minor OpenCL related fixes and improvements to the GPU package 
- 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
 2018-07-20 14:41:54 -04:00
Steve Plimpton 36081f9ffd
Merge pull request #1005 from timattox/USER-DPD_alpha 
USER-DPD: propagate a minor performance bugfix throughout the DPDE code
 2018-07-19 09:07:21 -06:00
Richard Berger 2eb8d779e8 Fixes a memory leak when using OpenCL 
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
 2018-07-18 18:54:57 -04:00
Axel Kohlmeyer 7d4de932b6
reinstate reference to fix wall/ees in lammps.book 2018-07-18 13:13:57 -04:00
Steven J. Plimpton dfd40c1b70 more doc tweaks 2018-07-18 10:48:29 -06:00
Tim Mattox f9c7fa973b USER-DPD: propagate a minor performance bugfix throughout the DPDE code 
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.
 2018-07-18 10:50:22 -05:00
Steven J. Plimpton 843b96e8dd more changes to new polygon/hedron docs and command names 2018-07-18 08:49:42 -06:00
Trung Nguyen de69e24551 Added replies to Steve's questions 2018-07-17 11:05:32 -05:00