Diffusion lammps 05847a0e8713

Merge branch 'master' into user-intel-update
05847a0e8713
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Oct 6 2017, 16:18.

Description

Merge branch 'master' into user-intel-update

Details

Committed

GitHub <noreply@github.com>

Oct 6 2017, 16:18

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPS439c2fd980f8: Merge pull request #677 from stanmoore1/kk_update
rLAMMPS9dc42fd4db71: intel_simd.h is currently also needed by dihedral/charmm, not just sw.

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Event Timeline

GitHub <noreply@github.com> committed rLAMMPS05847a0e8713: Merge branch 'master' into user-intel-update (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Oct 6 2017, 16:18

Merged Changes

Commit	Author	Details	Committed
439c2fd980f8	Steve Plimpton/GitHub	Merge pull request #677 from stanmoore1/kk_update	Oct 6 2017
15853a0e38dc	Steve Plimpton/GitHub	Merge pull request #676 from stanmoore1/kokkos_reverse_comm	Oct 6 2017
bd17ee5df74a	Steve Plimpton/GitHub	Merge pull request #675 from wesbarnett/master	Oct 6 2017
a9b7ff1154d3	Steve Plimpton/GitHub	Merge pull request #679 from stanmoore1/kk_reax_comm	Oct 6 2017
0dd7ba26c080	Steve Plimpton/GitHub	Merge pull request #672 from akohlmey/phana-w-tricubic	Oct 6 2017
7a90eef527ed	Steve Plimpton/GitHub	Merge pull request #668 from ovilab/modify_deallocation_fix	Oct 6 2017
5d0626e50e30	Steve Plimpton/GitHub	Merge pull request #665 from akohlmey/collected-small-fixes	Oct 6 2017
4b7ca0383aac	Steve Plimpton/GitHub	Merge pull request #664 from timattox/kokkos_atom2bin	Oct 6 2017
0ed987dc6186	Steve Plimpton/GitHub	Merge pull request #663 from jdevemy/master	Oct 6 2017
55a3fdca8065	Steve Plimpton/GitHub	Merge pull request #660 from junghans/latte_fix	Oct 6 2017
e0efdd50fab3	Stan Moore	Switch to classic comm if ghost_velocity. The check_forward and check_reverse…	Oct 5 2017
44d2e8ff74d5	Stan Moore	Add pre_reverse to verlet_kokkos and comment out timer	Oct 5 2017
6bf2c60c07ed	Stan Moore	Fix issues in Kokkos comm	Oct 5 2017
eecd2fbaee77	Stan Moore	Remove hardcoded value in fix_qeq_reax	Oct 5 2017
2b0bfcb10f90	Stan Moore	Fix memory leak in pair_reaxc_kokkos	Oct 5 2017
3653f4012013	Stan Moore	Reduce unnecessary communication in fix_qeq_reax	Oct 4 2017
bda0ee3aa1eb	Stan Moore	Destroy unneeded fix in pair_reaxc_kokkos	Oct 4 2017
c522b1b7a974	Axel Kohlmeyer	add call to fftw_cleanup() before exiting to avoid bogus leak reports when…	Oct 4 2017
a55adf4a6848	Stan Moore	Update to Kokkos r2.04.04 and add workaround for performance regression	Oct 3 2017
2876baafd07d	James Barnett	Use -restrict whenever Intel is used, no matter the package	Oct 3 2017
ca032f21fbfa	Stan Moore	Add Kokkos threaded reverse comm option	Oct 3 2017
197f08278442	James Barnett	cmake: Add -restrict for Intel compilers for some packages	Oct 3 2017
8d384b9149c7	Axel Kohlmeyer	whitespace cleanup	Oct 2 2017
529eeb603923	Stan Moore	Reduce GPU data transfer	Oct 2 2017
091d0580904a	Richard Berger	Fix typo	Sep 30 2017
4c71beb02409	Axel Kohlmeyer	cleanup/simplification of compilation for fix phonon analysis tool "phana"	Sep 30 2017
a86572f4fcb4	Stan Moore	Reduce memory churn in Kokkos package	Sep 30 2017
9f2740b7f18f	Stan Moore	Partially revert 01d0a5c, avoid atomics, safe because of the while loop. Worst…	Sep 29 2017
d7aac2fed53c	Stan Moore	Add sync/modify to nbin_kokkos	Sep 29 2017
d898afaafb7a	Axel Kohlmeyer	use <> for system includes not ""	Sep 29 2017
23e283f13551	Anders Hafreager	Fixed proper deletion of fixes if fix is NULL	Sep 27 2017
de45fa6e7107	Axel Kohlmeyer	correct bogus links in LATTE docs	Sep 27 2017
bfdc4acb8bbe	Axel Kohlmeyer	add missing entry for pdf version of manual	Sep 26 2017
fd3ecd048120	Axel Kohlmeyer	fix typo in formatting	Sep 26 2017
8bba6d3e8c63	Axel Kohlmeyer	correct formatting and broken/colliding link issues with LATTE package related…	Sep 26 2017
53e4ee4f2dc9	Axel Kohlmeyer	need to re-init timers after initial setup	Sep 26 2017
b60cff7e7773	Axel Kohlmeyer	USER-OMP package depends on USER-DRUDE	Sep 26 2017
38530415c8f0	Axel Kohlmeyer	-ltbbmalloc is required	Sep 26 2017
0573aaa6da3a	Axel Kohlmeyer	update src/.gitignore for LATTE package	Sep 26 2017
e6969002ce55	Axel Kohlmeyer	having plain filelink instead of filelink.o confuses KOKKOS linking with nvcc	Sep 26 2017
836a6d292c10	Axel Kohlmeyer	whitespace fixes, silence compiler warning about too few format specifiers	Sep 25 2017
32e0de7a67a1	Tim Mattox	first pass at implementing atom2bin for KOKKOS neighbor lists	Sep 25 2017
789812ec3dce	Tim Mattox	KOKKOS: minor typo fix	Sep 25 2017
78a486c0fdfe	Julien Devemy	Authorize hybrid/overlay for fix srp	Sep 25 2017
d6316c40d94e	Christoph Junghans	cmake: fix build with system latte	Sep 22 2017

Changes (86)

				Path
	M			cmake/CMakeLists.txt
	M			doc/src/Section_packages.txt
	M			doc/src/fix_latte.txt
	M			doc/src/fix_neb.txt
	M			doc/src/fixes.txt
	M			doc/src/lammps.book
	M			doc/src/package.txt
	M			doc/src/pair_eam.txt
	M			lib/kokkos/CHANGELOG.md
	M			lib/kokkos/Makefile.kokkos
	M			lib/kokkos/algorithms/src/Kokkos_Random.hpp
	M			lib/kokkos/algorithms/unit_tests/Makefile
	A			lib/kokkos/algorithms/unit_tests/TestROCm.cpp
	M			lib/kokkos/bin/hpcbind
	D			lib/kokkos/bin/kokkos-bind
	M			lib/kokkos/bin/nvcc_wrapper
	M			lib/kokkos/config/master_history.txt
	M			lib/kokkos/config/trilinos-integration/checkin-test
	M			lib/kokkos/containers/src/Kokkos_StaticCrsGraph.hpp
	M			lib/kokkos/core/src/Cuda/KokkosExp_Cuda_IterateTile_Refactor.hpp
	M			lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp
	M			lib/kokkos/core/src/Kokkos_Complex.hpp
	M			lib/kokkos/core/src/Kokkos_Crs.hpp
	M			lib/kokkos/core/src/Kokkos_HBWSpace.hpp
	M			lib/kokkos/core/src/Kokkos_NumericTraits.hpp
	M			lib/kokkos/core/src/Kokkos_ROCm.hpp
	M			lib/kokkos/core/src/Makefile
	M			lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Exec.hpp
	M			lib/kokkos/core/src/ROCm/Kokkos_ROCm_Reduce.hpp
	M			lib/kokkos/core/src/ROCm/Kokkos_ROCm_Scan.hpp
	M			lib/kokkos/core/src/impl/Kokkos_BitOps.hpp
	M			lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp
	M			lib/kokkos/core/unit_test/TestComplex.hpp
	M			lib/kokkos/core/unit_test/TestMDRange.hpp
	M			lib/latte/Install.py
	M			lib/latte/Makefile.lammps.gfortran
	M			lib/latte/Makefile.lammps.ifort
	M			src/.gitignore
	M			src/Depend.sh
	M			src/KOKKOS/atom_vec_atomic_kokkos.cpp
	M			src/KOKKOS/atom_vec_atomic_kokkos.h
	M			src/KOKKOS/atom_vec_bond_kokkos.cpp
	M			src/KOKKOS/atom_vec_bond_kokkos.h
	M			src/KOKKOS/atom_vec_charge_kokkos.cpp
	M			src/KOKKOS/atom_vec_charge_kokkos.h
	M			src/KOKKOS/atom_vec_dpd_kokkos.h
	M			src/KOKKOS/atom_vec_full_kokkos.cpp
	M			src/KOKKOS/atom_vec_full_kokkos.h
	M			src/KOKKOS/atom_vec_kokkos.cpp
	M			src/KOKKOS/atom_vec_kokkos.h
	M			src/KOKKOS/comm_kokkos.cpp
	M			src/KOKKOS/comm_kokkos.h
	M			src/KOKKOS/fix_qeq_reax_kokkos.cpp
	M			src/KOKKOS/kokkos.cpp
	M			src/KOKKOS/kokkos.h
	M			src/KOKKOS/nbin_kokkos.cpp
	M			src/KOKKOS/nbin_kokkos.h
	M			src/KOKKOS/neighbor_kokkos.cpp
	M			src/KOKKOS/npair_kokkos.cpp
	M			src/KOKKOS/npair_kokkos.h
	M			src/KOKKOS/pair_reaxc_kokkos.cpp
	M			src/KOKKOS/verlet_kokkos.cpp
	M			src/MAKE/OPTIONS/Makefile.intel_cpu_mpich
	M			src/REPLICA/prd.cpp
	M			src/REPLICA/tad.cpp
	M			src/USER-MANIFOLD/manifold_gaussian_bump.cpp
	M			src/USER-MISC/fix_srp.cpp
	M			src/USER-OMP/fix_qeq_reax_omp.cpp
	M			src/USER-REAXC/fix_qeq_reax.cpp
	M			src/comm_brick.cpp
	M			src/dump.cpp
	M			src/finish.cpp
	M			src/input.cpp
	M			src/main.cpp
	M			src/modify.cpp
	M			src/modify.h
	M			tools/phonon/Makefile
	M			tools/phonon/README
	M			tools/phonon/disp.cpp
	M			tools/phonon/dynmat.cpp
	M			tools/phonon/dynmat.h
	M			tools/phonon/green.cpp
	M			tools/phonon/interpolate.cpp
	M			tools/phonon/interpolate.h
	M			tools/phonon/phonon.cpp
	M			tools/phonon/version.h