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15007 Commits

Author SHA1 Message Date
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
Trung Nguyen d23788831c Updated to the doc pages of body rounded/polygon and rounded/polyhedra and the pair style: 
+ added examples for special cases with disks and rods for 2d, and spheres and rods for 3d,
+ corrected the definition of the cutoff distance in pair style command
 2018-07-17 10:54:05 -05:00
Steven J. Plimpton fa73fab5df patch 16Jul18 2018-07-16 18:12:15 -06:00
Steve Plimpton a3b6f38a42
Merge pull request #1003 from akohlmey/restart_extra_flags 
include support for 'extra/XXX/per/atom' info in restart files
 2018-07-16 15:07:43 -06:00
Steven J. Plimpton 5abbea3606 doc file changes/Qs added for body DEM particles 2018-07-16 14:52:18 -06:00
Axel Kohlmeyer 783839e985 add support for restarting extra/XXX/per/atom settings in binary restarts 2018-07-16 15:21:52 -04:00
Trung Nguyen cfa6e8717d Updated doc pages for pair body rounded/polygon and rounded/polyhedron with equations 2018-07-16 12:45:23 -05:00
Trung Nguyen 27dc7f3205 Added a tex file for the equations of pair rounded/polygon and rounded/polyhedron 2018-07-16 11:44:45 -05:00
Steve Plimpton c589029219
Merge pull request #1002 from rbberger/set_velocity_command 
Allow 'set' command to change atom velocities
 2018-07-16 08:50:15 -06:00
Steve Plimpton 140767be16
Merge pull request #1001 from stanmoore1/kk_bugfix 
Fix rare crash in Kokkos ReaxFF on GPUs
 2018-07-16 08:49:30 -06:00
Steve Plimpton 1c007ce7a1
Merge pull request #1000 from HaoZeke/fixDocs 
docs: Fix sneaky unicode character
 2018-07-16 08:49:13 -06:00
Steve Plimpton 6f1b6e7abd
Merge pull request #999 from junghans/cmake_doc 
cmake/README.md: fix GPU_ARCH options
 2018-07-16 08:48:48 -06:00
Steve Plimpton 5fc4aaef06
Merge pull request #940 from Pakketeretet2/port-enforce2d-kokkos 
Port enforce2d kokkos
 2018-07-16 08:48:21 -06:00
Trung Nguyen f7d551eb54 Added a figure illustrating pair body rounded/polygon and rounded/polyhedron 2018-07-15 08:27:55 -05:00
Richard Berger aa3d3213c9 Update set command documentation 2018-07-13 23:06:42 -04:00
Richard Berger d00eaef070 Allow 'set' command to change atom velocities 2018-07-13 23:05:44 -04:00
Trung Nguyen 8447d8dd91 Updated doc pages for pair body rounded/polygon and rounded/polyhedra 2018-07-13 14:34:50 -05:00
Stan Moore d4f8940ff2 Update command doc page for Kokkos enforce2d 2018-07-13 07:40:06 -06:00
Stan Moore 16381a52b1 Fix crash in ReaxFF on GPUs 2018-07-12 20:22:38 -06:00
HaoZeke 85511a4db8
docs: Fix sneaky unicode character 
Fixes the `pdf` target of the `Makefile`.
 2018-07-13 00:44:04 +05:30
Trung Nguyen 21f749243a Required newton on for pair styles body rounded/polygon and rounded/polyhedron 2018-07-12 10:21:06 -05:00
Christoph Junghans 4ac47ba037 cmake/README.md: fix GPU_ARCH options 2018-07-12 07:27:11 -06:00
Steve Plimpton 6dfb74f23e
Merge pull request #997 from lammps/balance-bug-fix 
2 small bug fixes to load balancing
 2018-07-11 16:13:22 -06:00
Steven J. Plimpton b31f0245d0 2 small bug fixes to load balancing 2018-07-11 15:55:16 -06:00
Steve Plimpton f288331874
Merge pull request #993 from lammps/doc-plus-makefile 
better rRESPA doc page, also a new Makefile.theta
 2018-07-11 12:53:31 -06:00
Stan Moore 71f6991233 Small tweaks to fix_enforce2d_kokkos 2018-07-11 12:39:04 -06:00
Stan Moore 5d13321425 Standardize suffix paragraph in fix_enforce2d.txt 2018-07-11 12:15:50 -06:00
Steven J. Plimpton acdc240cdd better rRESPA doc page, also a new Makefile.theta 2018-07-11 08:42:28 -06:00
Steve Plimpton 69baaaec16
Merge pull request #991 from akohlmey/collected-small-updates 
Collected small updates for the next patch release
 2018-07-11 07:50:31 -06:00
Axel Kohlmeyer 1f1447c3ac need to update exclusions with the new atom IDs in case of molecular systems 2018-07-11 07:22:47 -04:00
Trung Nguyen c3a32dde12 Updated doc/body.txt for body rounded/polygon and rounded/polyhedron 2018-07-11 00:21:49 -05:00
Trung Nguyen 5124c9e993 Fixed bugs in body rounded/polydedra for correct size_border 2018-07-10 16:53:26 -05:00
Axel Kohlmeyer 1ed25d195b convert c-style includes for c-library calls to c++-style 2018-07-10 09:48:49 -04:00
Axel Kohlmeyer 792b182cb0 whitespace cleanup 2018-07-10 09:46:08 -04:00
julient31 ade9b7bfc3 Commit2 JT 070918 
- modified the citeme reference (replaced by the JCP one)
- same modification in doc and src/SPIN
 2018-07-10 09:44:14 -04:00
julient31 9d5dc561ca Commit1 JT 070918 
- created README in examples/SPIN
- modified doc/src/set.txt to define 'spin' and 'spin/random' keywords
 2018-07-10 09:44:14 -04:00