Commit Graph

8540 Commits

Author SHA1 Message Date
b7d64e0374 patch 16Aug18 2018-08-16 11:55:57 -06:00
ccacf0d4bb Merge pull request #1048 from lammps/doc-reorg-start
Documentation Refactoring: Section Start
2018-08-15 15:25:17 -06:00
6069d392a3 favor qsort over mergesort for stable release 2018-08-15 16:44:31 -04:00
c9131cf1de drop FFTW2 support, and change doc pages 2018-08-15 13:54:37 -06:00
7ec52784cb more changes to doc pages and CMakeLists.txt 2018-08-14 15:44:25 -06:00
aca9416c7f Merge branch 'master' into doc-reorg-start and resolve merge conflicts with master
Conflicts:
	doc/src/Speed_kokkos.txt
	doc/src/package.txt
2018-08-09 20:18:12 +02:00
6663fbeb11 Merge pull request #928 from akohlmey/fix-rcb-balance-issue
Fix rcb balance issue
2018-08-09 10:24:38 -06:00
9dde50a4f2 Merge pull request #1042 from akohlmey/kokkos-vs-gpu-direct
Kokkos vs gpu direct
2018-08-09 09:25:24 -06:00
a97ad15d22 update .gitignore 2018-08-09 17:13:06 +02:00
d5594350c4 change zero-size shrink box to original box 2018-08-09 08:50:11 -06:00
9521814441 rename Kokkos::gpu_direct to Kokkos::gpu_direct_flag
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
2018-08-09 04:52:58 -04:00
dd9fed11dc use '-pk kokkos gpu/direct on/off' consistently in comments and docs 2018-08-09 04:16:22 -04:00
01b8134746 Small tweak to GPU direct not available warning 2018-08-09 09:35:11 +02:00
32658c20d4 Fix typo in gridcomm_kokkos 2018-08-08 17:07:12 -06:00
1c550d8f39 Change defaults for GPU-direct to use comm host 2018-08-08 16:46:36 -06:00
d8aa6d534b Remove hardcoded GPU-direct in KOKKOS package 2018-08-08 16:09:41 -06:00
9202896e75 bug fix for compute cluster/atom when computing values used to update a dynamic group 2018-08-08 09:31:16 -06:00
a3fad229ab Merge pull request #1040 from lammps/natom
enable more correct natoms computation when atoms are lost
2018-08-08 08:41:15 -06:00
fac5e29f48 Merge pull request #994 from danicholson/user-uef-image-flags
USER-UEF support for image flags
2018-08-08 08:40:56 -06:00
5d87e0c651 add wrapper for MPI implementation specific GPU-direct detection
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.
2018-08-08 13:57:41 +02:00
3d537850fd make communication settings consistent, in case the package command is used multiple times. 2018-08-08 10:20:24 +02:00
b6c458192c reword misleading message about GPU usage 2018-08-08 10:19:48 +02:00
d27215b7e1 enable more correct natoms computation when atoms are lost 2018-08-07 15:05:07 -06:00
5789ef9128 bug-fix for slope() function in variable 2018-08-03 10:08:02 -06:00
1b0a8fdc9b Merge pull request #942 from tootea/nhfixes
Fix discrepancies between fix_nh and papers
2018-08-02 11:16:54 -06:00
fb03924e83 patch 2Aug18 2018-08-02 11:12:57 -06:00
d598e7c60e rename preprocessor guard to prevent multiple inclusion to be consistent with file name 2018-08-01 15:54:46 +02:00
77e5445bfe Need to purge old pair_cdeam.* files 2018-07-31 14:16:54 -04:00
eb967a8a6c Merge pull request #1027 from akohlmey/move-cdeam
Move pair style eam/cd from USER-MISC to MANYBODY
2018-07-31 10:39:18 -06:00
c6186bf00d whitespace and formatting update 2018-07-31 17:36:49 +02:00
e9d40d3c6d rename class from PairCDEAM to PairEAMCD 2018-07-31 17:16:18 +02:00
67e70316de rename pair_cdeam.* to pair_eam_cd.* 2018-07-31 16:58:44 +02:00
f3615e83e8 move pair style eam/cd from USER-MISC to MANYBODY and update docs accordingly 2018-07-31 09:18:37 +02:00
2bb11ef47a Merge pull request #1021 from akohlmey/spin-package-fixes
SPIN package fixes, especially for DMI
2018-07-30 10:39:35 -06:00
28993d9823 Commit JT 072618
- improvements documentation (dmi and exchange)
- correction error cross product in pair_spin_dmi.cpp
- implementation mech. part in pair_spin_dmi.cpp
- correction in all pairs: init_one for [j][i] couples
- correction in atom_vec_spin.cpp: index error in read_data
- some improvements in pair_spin_dmi.cpp and pair_spin_magelec.cpp
2018-07-27 12:00:15 +02:00
2af88dcc26 avoid uninitialized variables 2018-07-27 10:39:01 +02:00
8075b98fc5 initialize rsqinv 2018-07-27 10:24:38 +02:00
f63e2b6eaf simplify code and guarantee that "mode" is initialized 2018-07-27 10:24:15 +02:00
1d9ad55796 changes to Errors and Python doc pages 2018-07-25 14:10:00 -06:00
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
8d49d1a8c5 Merge pull request #1010 from lammps/latte-checksum
new checksum for LATTE download
2018-07-25 08:42:35 -06:00
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
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
e37ee02eed port nh fixes to USER-BOCS package 2018-07-24 11:19:00 -04:00
57ad197b7d port nh fixes to KOKKOS 2018-07-24 10:48:06 -04:00
2ac3953e17 update src/Purge.list to cleanly remove obsolete files 2018-07-23 12:37:05 -04:00
5c21d2aff9 Merge pull request #962 from ndtrung81/body-dem
Discrete element models for the BODY package
2018-07-20 14:37:41 -06:00
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
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
843b96e8dd more changes to new polygon/hedron docs and command names 2018-07-18 08:49:42 -06:00