Diffusion lammps 99791ce01c09

Merge pull request #632 from timattox/USER-DPD_kokkos_merge
99791ce01c09
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Authored by Steve Plimpton <sjplimp@sandia.gov> on Sep 6 2017, 16:50.

Description

Merge pull request #632 from timattox/USER-DPD_kokkos_merge

Add Kokkos version of the USER-DPD package

Details

Committed

GitHub <noreply@github.com>

Sep 6 2017, 16:50

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPS0248a7b98e9e: remove duplicate listing of deleted USER-DPD files from Purge.list
rLAMMPSb1706060529b: Merge pull request #620 from amilumas/master

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GitHub <noreply@github.com> committed rLAMMPS99791ce01c09: Merge pull request #632 from timattox/USER-DPD_kokkos_merge (authored by Steve Plimpton <sjplimp@sandia.gov>).Sep 6 2017, 16:50

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.

Commit	Author	Details	Committed
0248a7b98e9e	Tim Mattox	remove duplicate listing of deleted USER-DPD files from Purge.list	Sep 6 2017
4c5d901e2b04	Axel Kohlmeyer	fix stupid typo (too much compiling of fortran codes...)	Sep 5 2017
c8f92c1a617a	Axel Kohlmeyer	add a couple deleted files from USER-DPD to Purge.list	Sep 5 2017
d95a5f219e69	Stan Moore	Remove all thread fences except one in verlet_kokkos	Aug 31 2017
3e6cdd140011	Tim Mattox	USER-DPD: finish renaming #ifdef DEBUG_PAIR_CT to DEBUG_SSA_PAIR_CT	Aug 30 2017
dc7f1281b832	Tim Mattox	USER-DPD: Kokkos version of Const Temperature DPD isn't implemented yet	Aug 30 2017
2dd202cc761d	Tim Mattox	USER-DPD: remove some out-of-date FIXME comments in fix_shardlow_kokkos.cpp	Aug 30 2017
f2d8c37f27b1	Tim Mattox	Rename SSA specific debug #ifdef to DEBUG_SSA_PAIR_CT	Aug 30 2017
a4a45f1d9cfb	Stan Moore	Remove unnecessary check in npair_kokkos	Aug 30 2017
736e063971bc	Tim Mattox	Merge branch 'master' (21893539cb Aug 25) into USER-DPD_kokkos_merge	Aug 28 2017
e52a28f8afaf	Stan Moore	Update docs for Kokkos version of USER-DPD package	Aug 26 2017
01dd0e173e51	Stan Moore	Merge branch 'master' into USER-DPD_kokkos_merge	Aug 26 2017
1f8c4f2c62df	Stan Moore	Remove hardcoded map variables and debug output	Aug 25 2017
b73999ef215c	Stan Moore	Revert change to read_data.cpp	Aug 25 2017
1e16fed9ab94	Stan Moore	Error out if using pair hybrid with Kokkos, but not pair hybrid/overlay	Aug 25 2017
a062944de95e	Stan Moore	Fix execution space issues	Aug 25 2017
a641289d5ba3	Stan Moore	Must use atomics for GPUs in pair_exp6_rx_kokkos	Aug 25 2017
e55fa9d320d3	Stan Moore	Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks	Aug 23 2017
cbf3646806f9	Stan Moore	Merge branch 'master' into USER-DPD_kokkos	Aug 23 2017
f5a99dece766	Stan Moore	Remove unnecessary thread fences	Aug 23 2017
4784506ba907	Stan Moore	Remove unused function in rand_pool_wrap_kokkos	Aug 23 2017
270abff2a2a1	Stan Moore	Fix compile error for CUDA in pair_exp6_rx_kokkos	Aug 23 2017
5c985946d58f	Stan Moore	Merge branch 'master' into USER-DPD_kokkos	Aug 22 2017
13b804eeeba5	Tim Mattox	Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks as of patch 10Aug17	Aug 11 2017
4041db8d1a74	Tim Mattox	Merge branch 'master' into USER-DPD_kokkos as of patch 10Aug17	Aug 11 2017
378989e06529	Tim Mattox/GitHub	Merge pull request #27 from timattox/USER-DPD_kokkos_update	Aug 10 2017
e86b139817fc	Tim Mattox/GitHub	Merge pull request #25 from timattox/USER-DPD_GBhacks_cudafix	Aug 9 2017
9695aa60925d	Stan Moore	Merge branch 'master' into USER-DPD_kokkos_testing	Jul 27 2017
bc446bb8b01b	Stan Moore	Merge branch 'master' into USER-DPD_kokkos_testing	Jul 25 2017
ea4d11fc5eff	Stan Moore	Merge branch 'master' into USER-DPD_kokkos_testing	Jun 26 2017
67a0183b3332	Stan Moore	Removing atom2bin change since ssa neighlists aren't be used for occasional…	Jun 19 2017
b96b6b9cd775	Stan Moore	Fixing error checks	Jun 19 2017
da0dcbe0bb2a	Stan Moore	Updating to master	Jun 19 2017
3c8e75ad590a	Stan Moore	Add missing sync/modify to fix_shardlow_kokkos	Jun 9 2017
c51cadcc6c38	Stan Moore	Fixing CUDA runtime issues in fix_shardlow_kokkos	Jun 9 2017
86497949f20a	Stan Moore	Fixing CUDA runtime issues in fix_shardlow_kokkos	Jun 8 2017
b4b731088438	Stan Moore	Fixing CUDA runtime issues in pair_exp6_rx_kokkos	Jun 8 2017
046900cd51d3	Stan Moore/GitHub	Merge pull request #26 from timattox/USER-DPD_GBhacks_optimize	Jun 8 2017
43cfa10ea48d	Stan Moore	Reduce memory churn in pair_multi_lucy_rx_kokkos	Jun 8 2017
6f24c58c1a31	Stan Moore	Reduce memory churn in fix_rx_kokkos	Jun 8 2017
611bb6f13035	Stan Moore	Reduce memory churn in pair_table_rx_kokkos	Jun 8 2017
520ab26bd966	Stan Moore	Fixing more CUDA runtime issues	Jun 7 2017
efe60bf991c6	Stan Moore	Fixing more CUDA runtime issues	Jun 6 2017
36cbe439780d	Stan Moore	Fixing some CUDA runtime issues in npair_ssa_kokkos	Jun 6 2017
2cf83d9fca6e	Stan Moore	Updating from master to 19May17	May 25 2017
ca4619e22791	Stan Moore	Fix format issue in pair_exp6_rx_kokkos	Apr 11 2017
6c0b6918821a	Stan Moore	Removing more memory churn in pair_exp6_rx_kokkos	Apr 11 2017
035d0a80d7bc	Stan Moore	Reducing memory churn in pair_exp6_rx_kokkos	Apr 11 2017
178af2ec9e72	Tim Mattox	USER-DPD Kokkos: use a parallel_for() to build the ghosts workplan for SSA	Apr 6 2017
9e272cb393fd	Tim Mattox	USER-DPD Kokkos: use a parallel_for() to build the locals workplan for SSA	Apr 6 2017

Changes (111)
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This commit is very large. Load each file individually.

				Path
	M			doc/src/fix_dpd_energy.txt
	M			doc/src/fix_eos_table_rx.txt
	M			doc/src/fix_rx.txt
	M			doc/src/fix_shardlow.txt
	M			doc/src/fix_wall.txt
	M			doc/src/pair_dpd_fdt.txt
	M			doc/src/pair_exp6_rx.txt
	M			doc/src/pair_hybrid.txt
	M			doc/src/pair_multi_lucy_rx.txt
	M			doc/src/pair_table_rx.txt
	M			lib/kokkos/algorithms/src/Kokkos_Random.hpp
	M			src/Depend.sh
	M			src/KOKKOS/Install.sh
	M			src/KOKKOS/atom_kokkos.cpp
	M			src/KOKKOS/atom_kokkos.h
	M			src/KOKKOS/atom_vec_angle_kokkos.cpp
	P			src/KOKKOS/atom_vec_atomic_kokkos.cpp Copied to src/KOKKOS/atom_vec_dpd_kokkos.cpp
	M			src/KOKKOS/atom_vec_bond_kokkos.cpp
	M			src/KOKKOS/atom_vec_charge_kokkos.cpp
	P			src/KOKKOS/atom_vec_dpd_kokkos.cpp Copied from src/KOKKOS/atom_vec_atomic_kokkos.cpp
	A			src/KOKKOS/atom_vec_dpd_kokkos.h
	M			src/KOKKOS/atom_vec_full_kokkos.cpp
	A			src/KOKKOS/atom_vec_hybrid_kokkos.cpp
	A			src/KOKKOS/atom_vec_hybrid_kokkos.h
	M			src/KOKKOS/atom_vec_molecular_kokkos.cpp
	M			src/KOKKOS/comm_kokkos.cpp
	M			src/KOKKOS/domain_kokkos.cpp
	A			src/KOKKOS/fix_dpd_energy_kokkos.cpp
	A			src/KOKKOS/fix_dpd_energy_kokkos.h
	A			src/KOKKOS/fix_eos_table_rx_kokkos.cpp
	A			src/KOKKOS/fix_eos_table_rx_kokkos.h
	A			src/KOKKOS/fix_property_atom_kokkos.cpp
	P			src/KOKKOS/fix_property_atom_kokkos.h Copied from src/fix_property_atom.h
	A			src/KOKKOS/fix_rx_kokkos.cpp
	A			src/KOKKOS/fix_rx_kokkos.h
	A			src/KOKKOS/fix_shardlow_kokkos.cpp
	A			src/KOKKOS/fix_shardlow_kokkos.h
	A			src/KOKKOS/fix_wall_lj93_kokkos.cpp
	A			src/KOKKOS/fix_wall_lj93_kokkos.h
	M			src/KOKKOS/kokkos.cpp
	M			src/KOKKOS/nbin_kokkos.cpp
	A			src/KOKKOS/nbin_ssa_kokkos.cpp
	A			src/KOKKOS/nbin_ssa_kokkos.h
	M			src/KOKKOS/neigh_bond_kokkos.cpp
	M			src/KOKKOS/neigh_list_kokkos.h
	M			src/KOKKOS/neighbor_kokkos.cpp
	M			src/KOKKOS/npair_kokkos.cpp
	M			src/KOKKOS/npair_kokkos.h
	A			src/KOKKOS/npair_ssa_kokkos.cpp
	A			src/KOKKOS/npair_ssa_kokkos.h
	A			src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp
	A			src/KOKKOS/pair_dpd_fdt_energy_kokkos.h
	A			src/KOKKOS/pair_exp6_rx_kokkos.cpp
	A			src/KOKKOS/pair_exp6_rx_kokkos.h
	A			src/KOKKOS/pair_hybrid_kokkos.cpp
	P			src/KOKKOS/pair_hybrid_kokkos.h Copied from src/pair_hybrid.h
	A			src/KOKKOS/pair_hybrid_overlay_kokkos.cpp
	V			src/{KOKKOS/pair_hybrid_overlay_kokkos.h ← USER-DPD/npair_halffull_newton_ssa.h}
	A			src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp
	A			src/KOKKOS/pair_multi_lucy_rx_kokkos.h
	A			src/KOKKOS/pair_table_rx_kokkos.cpp
	A			src/KOKKOS/pair_table_rx_kokkos.h
	A			src/KOKKOS/rand_pool_wrap_kokkos.cpp
	A			src/KOKKOS/rand_pool_wrap_kokkos.h
	M			src/KOKKOS/region_block_kokkos.cpp
	A			src/MAKE/MACHINES/Makefile.icex
	M			src/MPIIO/dump_custom_mpiio.cpp
	M			src/Purge.list
	M			src/USER-DPD/fix_dpd_energy.cpp
	M			src/USER-DPD/fix_eos_table_rx.cpp
	M			src/USER-DPD/fix_rx.cpp
	M			src/USER-DPD/fix_rx.h
	M			src/USER-DPD/fix_shardlow.cpp
	M			src/USER-DPD/fix_shardlow.h
	M			src/USER-DPD/nbin_ssa.cpp
	M			src/USER-DPD/nbin_ssa.h
	M			src/USER-DPD/npair_half_bin_newton_ssa.cpp
	M			src/USER-DPD/npair_half_bin_newton_ssa.h
	D			src/USER-DPD/npair_halffull_newton_ssa.cpp
	V			src/{USER-DPD/npair_halffull_newton_ssa.h → KOKKOS/pair_hybrid_overlay_kokkos.h}
	M			src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp
	M			src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h
	M			src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp
	M			src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h
	M			src/USER-DPD/nstencil_ssa.h
	M			src/USER-DPD/pair_dpd_fdt.cpp
	M			src/USER-DPD/pair_dpd_fdt_energy.cpp
	M			src/USER-DPD/pair_dpd_fdt_energy.h
	M			src/USER-DPD/pair_exp6_rx.cpp
	M			src/USER-DPD/pair_exp6_rx.h
	M			src/USER-DPD/pair_multi_lucy_rx.cpp
	M			src/USER-DPD/pair_multi_lucy_rx.h
	M			src/USER-DPD/pair_table_rx.cpp
	M			src/USER-DPD/pair_table_rx.h
	M			src/atom.cpp
	M			src/atom.h
	M			src/atom_masks.h
	M			src/fix_property_atom.cpp
	P			src/fix_property_atom.h Copied to src/KOKKOS/fix_property_atom_kokkos.h
	M			src/fix_wall.cpp
	M			src/fix_wall_lj93.h
	M			src/neigh_list.cpp
	M			src/neigh_list.h
	M			src/neighbor.cpp
	M			src/nstencil.h
	M			src/pair.h
	M			src/pair_hybrid.cpp
	P			src/pair_hybrid.h Copied to src/KOKKOS/pair_hybrid_kokkos.h
	M			src/pair_hybrid_overlay.h
	M			src/pair_table.h
	M			src/read_restart.cpp