Diffusion lammps d47c6b276105

Merge branch 'master' into USER-DPD_kokkos
d47c6b276105
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Authored by Stan Moore <stanmoore1@gmail.com> on Dec 14 2016, 19:25.

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Merge branch 'master' into USER-DPD_kokkos

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Committed

Stan Moore <stanmoore1@gmail.com>

Dec 14 2016, 19:25

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPSf93c62d3e203: Reverting accidental change
rLAMMPSf509f133afd9: patch 13Dec16: neighbor refactor, Stan pppm/disp bug fix, M Brown INTEL package…

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Stan Moore <stanmoore1@gmail.com> committed rLAMMPSd47c6b276105: Merge branch 'master' into USER-DPD_kokkos (authored by Stan Moore <stanmoore1@gmail.com>).Dec 14 2016, 19:25

Merged Changes

Commit	Author	Details	Committed
f509f133afd9	Steve Plimpton	patch 13Dec16: neighbor refactor, Stan pppm/disp bug fix, M Brown INTEL package…	Dec 14 2016
624c57e9dacb	sjplimp/GitHub	Merge pull request #185 from akohlmey/new-neighbor	Dec 14 2016
f3b355bcbea7	sjplimp/GitHub	Merge pull request #298 from akohlmey/collected-small-fixes	Dec 14 2016
ae5764beac4e	Steve Plimpton	added functionity to lib interface	Dec 14 2016
fda43c00fd99	Axel Kohlmeyer	add deleted file in package to purge list	Dec 12 2016
b34be30be6f5	Axel Kohlmeyer/GitHub	Merge pull request #53 from stanmoore1/new-neighbor	Dec 12 2016
13b6196b8235	Stan Moore	Fixing Kokkos compile error	Dec 12 2016
baf55c90f472	Stan Moore	Whitespace change	Dec 12 2016
770f5d0bf736	Stan Moore	Whitespace change	Dec 12 2016
a31b00965a81	Stan Moore	Updating to master	Dec 12 2016
a5e46e3e6ad9	Stan Moore	Merging	Dec 10 2016
31be0da59008	Stan Moore	Merging pull request	Dec 10 2016
0f3b2544a13c	stanmoore1/GitHub	Merge pull request #1 from timattox/new-neighbor	Dec 10 2016
586514e05c51	stanmoore1/GitHub	Merge branch 'new-neighbor' into new-neighbor	Dec 10 2016
43c459ba5694	Stan Moore	More changes for Kokkos neighbor	Dec 9 2016
b5c3d2f66c25	Axel Kohlmeyer/GitHub	Merge pull request #52 from timattox/new-neighbor	Dec 9 2016
5187cb97e5f1	Tim Mattox	USER-DPD: Make fix_shardlow request its own SSA-specific neighbor list, instead…	Dec 9 2016
eff503e56c1f	Tim Mattox	Prevent neighbor list copies between SSA and non-SSA neighbor list requests.	Dec 9 2016
cdcebab3bd63	Axel Kohlmeyer	make the output of the %CPU/OpenMP threads line consistent with compiling in…	Dec 9 2016
ddf678da5161	Axel Kohlmeyer	make fix gcmc command overview consistent	Dec 9 2016
435421301b0b	Stan Moore	Small tweaks to Kokkos neighbor	Dec 9 2016
9b48c49f8348	Stan Moore	Removing used Kokkos file	Dec 8 2016
d3d5ac17bf67	Efrem Braun	Fixed small typos in doc	Dec 8 2016
8318c6781697	Stan Moore	Kokkos neighbor refactor	Dec 7 2016
7c61dbf5e209	Axel Kohlmeyer	Merge branch 'new-neighbor' of github.com:akohlmey/lammps into new-neighbor	Dec 7 2016
39a12b15d7ea	Axel Kohlmeyer	Merge branch 'master' into new-neighbor	Dec 7 2016
114926a4886b	Axel Kohlmeyer	Merge branch 'master' into new-neighbor	Oct 2 2016
5eb9dd0c5d9c	Axel Kohlmeyer	Merge branch 'master' into new-neighbor	Sep 30 2016
ebabc8f0bc3b	Axel Kohlmeyer	Merge remote-tracking branch 'lammps-rw/integration' into update-neighbor	Sep 9 2016
232abf853468	Axel Kohlmeyer	restore locale and enforce grep option squashing	Sep 9 2016
d22caf26580e	Axel Kohlmeyer/GitHub	Merge pull request #29 from timattox/new-neighbor	Sep 9 2016
3842aa609531	Axel Kohlmeyer	forward skip lists /omp neighbor list builds to non-omp implementations	Sep 9 2016
32c240978aa3	Tim Mattox	USER-DPD: remove several files from src that came from src/USER-DPD/ These were…	Sep 9 2016
212c2617f6e4	Axel Kohlmeyer	delete a couple more files, that don't belong into src/	Sep 9 2016
40f85c93ba4e	Axel Kohlmeyer	corrected mismatched free() vs. delete[]	Sep 9 2016
2f02d9846976	Axel Kohlmeyer	remove USER-DPD files that should not be where they are	Sep 9 2016
4553881fc28f	Axel Kohlmeyer/GitHub	Merge pull request #28 from timattox/new-neighbor	Sep 9 2016
81fcbcd99cd0	Tim Mattox	USER-DPD: move nstencil_ssa out of core LAMMPS into USER-DPD	Sep 9 2016
82c6eb467539	Tim Mattox	USER-DPD: Set missing NP_HALF flag in npair_half_bin_newton_ssa.h	Sep 9 2016
8ed3f4226e5b	Tim Mattox	USER-DPD: move custom binning stuff to a NBinSSA child class. Removes most SSA…	Sep 9 2016
9b7a0d7e1c1a	Tim Mattox	Update gitignore for the new USER-DPD source files.	Sep 9 2016
c9c2ae6c6134	Steve Plimpton	new neighbor list changes	Sep 7 2016

Changes (362)
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				Path
	M			doc/src/Manual.txt
	M			doc/src/Section_howto.txt
	M			doc/src/compute_bond_local.txt
	M			doc/src/fix_gcmc.txt
	M			src/.gitignore
	M			src/KOKKOS/Install.sh
	M			src/KOKKOS/fix_qeq_reax_kokkos.cpp
	M			src/KOKKOS/kokkos.cpp
	M			src/KOKKOS/kokkos.h
	A			src/KOKKOS/nbin_kokkos.cpp
	A			src/KOKKOS/nbin_kokkos.h
	V			src/KOKKOS/{neigh_full_kokkos.h → npair_kokkos.cpp}
	M			src/KOKKOS/neigh_list_kokkos.cpp
	M			src/KOKKOS/neigh_list_kokkos.h
	M			src/KOKKOS/neighbor_kokkos.cpp
	P			src/KOKKOS/neighbor_kokkos.h Copied to src/KOKKOS/npair_kokkos.h
	A			src/KOKKOS/npair_copy_kokkos.cpp
	P			src/KOKKOS/npair_copy_kokkos.h Copied from src/neigh_derive.h
	V			src/KOKKOS/{npair_kokkos.cpp ← neigh_full_kokkos.h}
	P			src/KOKKOS/npair_kokkos.h Copied from src/KOKKOS/neighbor_kokkos.h
	M			src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
	M			src/KOKKOS/pair_buck_coul_long_kokkos.cpp
	M			src/KOKKOS/pair_buck_kokkos.cpp
	M			src/KOKKOS/pair_buck_kokkos.h
	M			src/KOKKOS/pair_coul_cut_kokkos.cpp
	M			src/KOKKOS/pair_coul_debye_kokkos.cpp
	M			src/KOKKOS/pair_coul_dsf_kokkos.cpp
	M			src/KOKKOS/pair_coul_long_kokkos.cpp
	M			src/KOKKOS/pair_coul_wolf_kokkos.cpp
	M			src/KOKKOS/pair_eam_alloy_kokkos.cpp
	M			src/KOKKOS/pair_eam_fs_kokkos.cpp
	M			src/KOKKOS/pair_eam_kokkos.cpp
	M			src/KOKKOS/pair_kokkos.h
	M			src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
	M			src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
	M			src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
	M			src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
	M			src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
	M			src/KOKKOS/pair_lj_class2_kokkos.cpp
	M			src/KOKKOS/pair_lj_class2_kokkos.h
	M			src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
	M			src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
	M			src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
	M			src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
	M			src/KOKKOS/pair_lj_cut_kokkos.cpp
	M			src/KOKKOS/pair_lj_cut_kokkos.h
	M			src/KOKKOS/pair_lj_expand_kokkos.cpp
	M			src/KOKKOS/pair_lj_expand_kokkos.h
	M			src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
	M			src/KOKKOS/pair_lj_gromacs_kokkos.cpp
	M			src/KOKKOS/pair_lj_sdk_kokkos.cpp
	M			src/KOKKOS/pair_lj_sdk_kokkos.h
	M			src/KOKKOS/pair_reax_c_kokkos.cpp
	M			src/KOKKOS/pair_sw_kokkos.cpp
	M			src/KOKKOS/pair_table_kokkos.cpp
	M			src/KOKKOS/pair_table_kokkos.h
	M			src/KOKKOS/pair_tersoff_kokkos.cpp
	M			src/KOKKOS/pair_tersoff_mod_kokkos.cpp
	M			src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
	M			src/KSPACE/ewald_disp.cpp
	A			src/MAKE/MACHINES/Makefile.cori2
	A			src/MAKE/OPTIONS/Makefile.intel_cpu
	A			src/MAKE/OPTIONS/Makefile.intel_knl_coprocessor
	M			src/Make.sh
	M			src/Purge.list
	M			src/REPLICA/prd.cpp
	M			src/RIGID/compute_rigid_local.cpp
	M			src/RIGID/compute_rigid_local.h
	M			src/USER-DPD/fix_shardlow.cpp
	M			src/USER-DPD/fix_shardlow.h
	A			src/USER-DPD/nbin_ssa.cpp
	A			src/USER-DPD/nbin_ssa.h
	A			src/USER-DPD/npair_half_bin_newton_ssa.cpp
	P			src/USER-DPD/npair_half_bin_newton_ssa.h Copied from src/neigh_full.h
	A			src/USER-DPD/npair_halffull_newton_ssa.cpp
	P			src/USER-DPD/npair_halffull_newton_ssa.h Copied from src/neigh_full.h
	A			src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp
	P			src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h Copied from src/neigh_full.h
	A			src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp
	P			src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h Copied from src/neigh_full.h
	V			src/{USER-DPD/nstencil_ssa.h ← neigh_half_bin.h}
	M			src/USER-DPD/pair_dpd_fdt.cpp
	M			src/USER-DPD/pair_dpd_fdt_energy.cpp
	M			src/USER-INTEL/Install.sh
	M			src/USER-INTEL/fix_intel.cpp
	M			src/USER-INTEL/intel_buffers.cpp
	M			src/USER-INTEL/intel_buffers.h
	M			src/USER-INTEL/intel_intrinsics.h
	M			src/USER-INTEL/intel_preprocess.h
	A			src/USER-INTEL/nbin_intel.cpp
	A			src/USER-INTEL/nbin_intel.h
	D			src/USER-INTEL/neigh_half_bin_intel.cpp
	A			src/USER-INTEL/npair_full_bin_intel.cpp
	A			src/USER-INTEL/npair_full_bin_intel.h
	A			src/USER-INTEL/npair_half_bin_newtoff_intel.cpp
	A			src/USER-INTEL/npair_half_bin_newtoff_intel.h
	A			src/USER-INTEL/npair_half_bin_newton_intel.cpp
	A			src/USER-INTEL/npair_half_bin_newton_intel.h
	A			src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp
	A			src/USER-INTEL/npair_half_bin_newton_tri_intel.h
	A			src/USER-INTEL/npair_intel.cpp
	A			src/USER-INTEL/npair_intel.h
	M			src/USER-INTEL/verlet_lrt_intel.cpp
	M			src/USER-INTEL/verlet_lrt_intel.h
	P			src/USER-OMP/neigh_derive_omp.cpp Deleted after being copied to multiple locations: src/USER-OMP/npair_halffull_newtoff_omp.cpp src/USER-OMP/npair_halffull_newton_omp.cpp src/npair_halffull_newton.cpp
	D			src/USER-OMP/neigh_full_omp.cpp
	D			src/USER-OMP/neigh_gran_omp.cpp
	D			src/USER-OMP/neigh_half_bin_omp.cpp
	D			src/USER-OMP/neigh_half_multi_omp.cpp
	D			src/USER-OMP/neigh_half_nsq_omp.cpp
	D			src/USER-OMP/neigh_respa_omp.cpp
	V			src/USER-OMP/{neighbor_omp.h → npair_omp.h}
	A			src/USER-OMP/npair_full_bin_ghost_omp.cpp
	P			src/USER-OMP/npair_full_bin_ghost_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_full_bin_omp.cpp
	P			src/USER-OMP/npair_full_bin_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_full_multi_omp.cpp
	P			src/USER-OMP/npair_full_multi_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_full_nsq_ghost_omp.cpp
	P			src/USER-OMP/npair_full_nsq_ghost_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_full_nsq_omp.cpp
	P			src/USER-OMP/npair_full_nsq_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp
	P			src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_bin_newtoff_omp.cpp
	P			src/USER-OMP/npair_half_bin_newtoff_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_bin_newton_omp.cpp
	P			src/USER-OMP/npair_half_bin_newton_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_bin_newton_tri_omp.cpp
	P			src/USER-OMP/npair_half_bin_newton_tri_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_multi_newtoff_omp.cpp
	P			src/USER-OMP/npair_half_multi_newtoff_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_multi_newton_omp.cpp
	P			src/USER-OMP/npair_half_multi_newton_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_multi_newton_tri_omp.cpp
	P			src/USER-OMP/npair_half_multi_newton_tri_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp
	P			src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_nsq_newtoff_omp.cpp
	P			src/USER-OMP/npair_half_nsq_newtoff_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_nsq_newton_omp.cpp
	P			src/USER-OMP/npair_half_nsq_newton_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp
	P			src/USER-OMP/npair_half_respa_bin_newtoff_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_respa_bin_newton_omp.cpp
	P			src/USER-OMP/npair_half_respa_bin_newton_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp
	P			src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp
	P			src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp
	P			src/USER-OMP/npair_half_respa_nsq_newton_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
	P			src/USER-OMP/npair_half_size_bin_newtoff_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_size_bin_newton_omp.cpp
	P			src/USER-OMP/npair_half_size_bin_newton_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
	P			src/USER-OMP/npair_half_size_bin_newton_tri_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
	P			src/USER-OMP/npair_half_size_nsq_newtoff_omp.h Copied from src/neigh_full.h
	A			src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
	P			src/USER-OMP/npair_half_size_nsq_newton_omp.h Copied from src/neigh_full.h
	P			src/USER-OMP/npair_halffull_newtoff_omp.cpp Copied from src/USER-OMP/neigh_derive_omp.cpp
	P			src/USER-OMP/npair_halffull_newtoff_omp.h Copied from src/neigh_full.h
	P			src/USER-OMP/npair_halffull_newton_omp.cpp Copied from src/USER-OMP/neigh_derive_omp.cpp
	P			src/USER-OMP/npair_halffull_newton_omp.h Copied from src/neigh_full.h
	V			src/USER-OMP/{npair_omp.h ← neighbor_omp.h}
	A			src/USER-OMP/npair_skip_omp.h
	D			src/accelerator_intel.h
	M			src/compute.cpp
	M			src/compute_angle_local.cpp
	M			src/compute_angle_local.h
	M			src/compute_bond_local.cpp
	M			src/compute_bond_local.h
	M			src/compute_dihedral_local.cpp
	M			src/compute_dihedral_local.h
	M			src/compute_gyration_chunk.cpp
	M			src/compute_improper_local.cpp
	M			src/compute_improper_local.h
	M			src/compute_pair_local.cpp
	M			src/compute_pair_local.h
	M			src/compute_property_atom.cpp
	M			src/compute_property_local.cpp
	M			src/compute_property_local.h
	M			src/compute_slice.cpp
	M			src/domain.cpp
	M			src/domain.h
	M			src/finish.cpp
	M			src/fix_langevin.cpp
	M			src/force.cpp
	M			src/integrate.cpp
	M			src/library.cpp
	M			src/library.h
	M			src/memory.cpp
	M			src/modify.cpp
	A			src/nbin.cpp
	A			src/nbin.h
	A			src/nbin_standard.cpp
	P			src/nbin_standard.h Copied from src/neigh_full.h
	D			src/neigh_bond.cpp
	D			src/neigh_bond.h
	D			src/neigh_derive.cpp
	P			src/neigh_derive.h Deleted after being copied to multiple locations: src/KOKKOS/npair_copy_kokkos.h src/ntopo_bond_all.h
	D			src/neigh_full.cpp
	P			src/neigh_full.h Deleted after being copied to multiple locations: src/USER-DPD/npair_half_bin_newton_ssa.h src/USER-DPD/npair_halffull_newton_ssa.h src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h src/USER-OMP/npair_full_bin_ghost_omp.h src/USER-OMP/npair_full_bin_omp.h src/USER-OMP/npair_full_multi_omp.h src/USER-OMP/npair_full_nsq_ghost_omp.h src/USER-OMP/npair_full_nsq_omp.h src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h src/USER-OMP/npair_half_bin_newtoff_omp.h src/USER-OMP/npair_half_bin_newton_omp.h src/USER-OMP/npair_half_bin_newton_tri_omp.h src/USER-OMP/npair_half_multi_newtoff_omp.h src/USER-OMP/npair_half_multi_newton_omp.h src/USER-OMP/npair_half_multi_newton_tri_omp.h src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h src/USER-OMP/npair_half_nsq_newtoff_omp.h src/USER-OMP/npair_half_nsq_newton_omp.h src/USER-OMP/npair_half_respa_bin_newtoff_omp.h src/USER-OMP/npair_half_respa_bin_newton_omp.h src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h src/USER-OMP/npair_half_respa_nsq_newton_omp.h src/USER-OMP/npair_half_size_bin_newtoff_omp.h src/USER-OMP/npair_half_size_bin_newton_omp.h src/USER-OMP/npair_half_size_bin_newton_tri_omp.h src/USER-OMP/npair_half_size_nsq_newtoff_omp.h src/USER-OMP/npair_half_size_nsq_newton_omp.h src/USER-OMP/npair_halffull_newtoff_omp.h src/USER-OMP/npair_halffull_newton_omp.h src/nbin_standard.h src/npair_full_bin.h src/npair_full_bin_ghost.h src/npair_full_multi.h src/npair_full_nsq.h src/npair_full_nsq_ghost.h src/npair_half_bin_newtoff.h src/npair_half_bin_newtoff_ghost.h src/npair_half_bin_newton.h src/npair_half_bin_newton_tri.h src/npair_half_multi_newtoff.h src/npair_half_multi_newton.h src/npair_half_multi_newton_tri.h src/npair_half_nsq_newtoff.h src/npair_half_nsq_newtoff_ghost.h src/npair_half_nsq_newton.h src/npair_half_respa_bin_newtoff.h src/npair_half_respa_bin_newton.h src/npair_half_respa_bin_newton_tri.h src/npair_half_respa_nsq_newtoff.h src/npair_half_respa_nsq_newton.h src/npair_half_size_bin_newtoff.h src/npair_half_size_bin_newton.h src/npair_half_size_bin_newton_tri.h src/npair_half_size_nsq_newtoff.h src/npair_half_size_nsq_newton.h src/npair_halffull_newtoff.h src/npair_halffull_newton.h src/npair_skip.h src/npair_skip_respa.h src/npair_skip_size.h src/npair_skip_size_off2on.h src/npair_skip_size_off2on_oneside.h src/nstencil_full_bin_2d.h src/nstencil_full_bin_3d.h src/nstencil_full_ghost_bin_2d.h src/nstencil_full_ghost_bin_3d.h src/nstencil_full_multi_2d.h src/nstencil_full_multi_3d.h src/nstencil_half_bin_2d_newtoff.h src/nstencil_half_bin_2d_newton.h src/nstencil_half_bin_2d_newton_tri.h src/nstencil_half_bin_3d_newtoff.h src/nstencil_half_bin_3d_newton.h src/nstencil_half_bin_3d_newton_tri.h src/nstencil_half_ghost_bin_2d_newtoff.h src/nstencil_half_ghost_bin_3d_newtoff.h src/nstencil_half_multi_2d_newtoff.h src/nstencil_half_multi_2d_newton.h src/nstencil_half_multi_2d_newton_tri.h src/nstencil_half_multi_3d_newtoff.h src/nstencil_half_multi_3d_newton.h src/nstencil_half_multi_3d_newton_tri.h src/ntopo_angle_all.h src/ntopo_angle_partial.h src/ntopo_angle_template.h src/ntopo_bond_partial.h src/ntopo_bond_template.h src/ntopo_dihedral_all.h src/ntopo_dihedral_partial.h src/ntopo_dihedral_template.h src/ntopo_improper_all.h src/ntopo_improper_partial.h src/ntopo_improper_template.h
	D			src/neigh_gran.cpp
	V			src/{neigh_gran.h → npair_copy.h}
	D			src/neigh_half_bin.cpp
	V			src/{neigh_half_bin.h → USER-DPD/nstencil_ssa.h}
	D			src/neigh_half_multi.cpp
	D			src/neigh_half_multi.h
	D			src/neigh_half_nsq.cpp
	D			src/neigh_half_nsq.h
	M			src/neigh_list.cpp
	M			src/neigh_list.h
	M			src/neigh_request.cpp
	M			src/neigh_request.h
	D			src/neigh_respa.cpp
	D			src/neigh_respa.h
	D			src/neigh_shardlow.cpp
	D			src/neigh_shardlow.h
	D			src/neigh_stencil.cpp
	M			src/neighbor.cpp
	M			src/neighbor.h
	A			src/npair.cpp
	A			src/npair.h
	A			src/npair_copy.cpp
	V			src/{npair_copy.h ← neigh_gran.h}
	A			src/npair_full_bin.cpp
	P			src/npair_full_bin.h Copied from src/neigh_full.h
	A			src/npair_full_bin_ghost.cpp
	P			src/npair_full_bin_ghost.h Copied from src/neigh_full.h
	A			src/npair_full_multi.cpp
	P			src/npair_full_multi.h Copied from src/neigh_full.h
	A			src/npair_full_nsq.cpp
	P			src/npair_full_nsq.h Copied from src/neigh_full.h
	A			src/npair_full_nsq_ghost.cpp
	P			src/npair_full_nsq_ghost.h Copied from src/neigh_full.h
	A			src/npair_half_bin_newtoff.cpp
	P			src/npair_half_bin_newtoff.h Copied from src/neigh_full.h
	A			src/npair_half_bin_newtoff_ghost.cpp
	P			src/npair_half_bin_newtoff_ghost.h Copied from src/neigh_full.h
	A			src/npair_half_bin_newton.cpp
	P			src/npair_half_bin_newton.h Copied from src/neigh_full.h
	A			src/npair_half_bin_newton_tri.cpp
	P			src/npair_half_bin_newton_tri.h Copied from src/neigh_full.h
	A			src/npair_half_multi_newtoff.cpp
	P			src/npair_half_multi_newtoff.h Copied from src/neigh_full.h
	A			src/npair_half_multi_newton.cpp
	P			src/npair_half_multi_newton.h Copied from src/neigh_full.h
	A			src/npair_half_multi_newton_tri.cpp
	P			src/npair_half_multi_newton_tri.h Copied from src/neigh_full.h
	A			src/npair_half_nsq_newtoff.cpp
	P			src/npair_half_nsq_newtoff.h Copied from src/neigh_full.h
	A			src/npair_half_nsq_newtoff_ghost.cpp
	P			src/npair_half_nsq_newtoff_ghost.h Copied from src/neigh_full.h
	A			src/npair_half_nsq_newton.cpp
	P			src/npair_half_nsq_newton.h Copied from src/neigh_full.h
	A			src/npair_half_respa_bin_newtoff.cpp
	P			src/npair_half_respa_bin_newtoff.h Copied from src/neigh_full.h
	A			src/npair_half_respa_bin_newton.cpp
	P			src/npair_half_respa_bin_newton.h Copied from src/neigh_full.h
	A			src/npair_half_respa_bin_newton_tri.cpp
	P			src/npair_half_respa_bin_newton_tri.h Copied from src/neigh_full.h
	A			src/npair_half_respa_nsq_newtoff.cpp
	P			src/npair_half_respa_nsq_newtoff.h Copied from src/neigh_full.h
	A			src/npair_half_respa_nsq_newton.cpp
	P			src/npair_half_respa_nsq_newton.h Copied from src/neigh_full.h
	A			src/npair_half_size_bin_newtoff.cpp
	P			src/npair_half_size_bin_newtoff.h Copied from src/neigh_full.h
	A			src/npair_half_size_bin_newton.cpp
	P			src/npair_half_size_bin_newton.h Copied from src/neigh_full.h
	A			src/npair_half_size_bin_newton_tri.cpp
	P			src/npair_half_size_bin_newton_tri.h Copied from src/neigh_full.h
	A			src/npair_half_size_nsq_newtoff.cpp
	P			src/npair_half_size_nsq_newtoff.h Copied from src/neigh_full.h
	A			src/npair_half_size_nsq_newton.cpp
	P			src/npair_half_size_nsq_newton.h Copied from src/neigh_full.h
	A			src/npair_halffull_newtoff.cpp
	P			src/npair_halffull_newtoff.h Copied from src/neigh_full.h
	V			src/{npair_halffull_newton.cpp ← USER-OMP/neigh_derive_omp.cpp}
	P			src/npair_halffull_newton.h Copied from src/neigh_full.h
	A			src/npair_skip.cpp
	P			src/npair_skip.h Copied from src/neigh_full.h
	A			src/npair_skip_respa.cpp
	P			src/npair_skip_respa.h Copied from src/neigh_full.h
	A			src/npair_skip_size.cpp
	P			src/npair_skip_size.h Copied from src/neigh_full.h
	A			src/npair_skip_size_off2on.cpp
	P			src/npair_skip_size_off2on.h Copied from src/neigh_full.h
	A			src/npair_skip_size_off2on_oneside.cpp
	P			src/npair_skip_size_off2on_oneside.h Copied from src/neigh_full.h
	A			src/nstencil.cpp
	A			src/nstencil.h
	A			src/nstencil_full_bin_2d.cpp
	P			src/nstencil_full_bin_2d.h Copied from src/neigh_full.h
	A			src/nstencil_full_bin_3d.cpp
	P			src/nstencil_full_bin_3d.h Copied from src/neigh_full.h
	A			src/nstencil_full_ghost_bin_2d.cpp
	P			src/nstencil_full_ghost_bin_2d.h Copied from src/neigh_full.h
	A			src/nstencil_full_ghost_bin_3d.cpp
	P			src/nstencil_full_ghost_bin_3d.h Copied from src/neigh_full.h
	A			src/nstencil_full_multi_2d.cpp
	P			src/nstencil_full_multi_2d.h Copied from src/neigh_full.h
	A			src/nstencil_full_multi_3d.cpp
	P			src/nstencil_full_multi_3d.h Copied from src/neigh_full.h
	A			src/nstencil_half_bin_2d_newtoff.cpp
	P			src/nstencil_half_bin_2d_newtoff.h Copied from src/neigh_full.h
	A			src/nstencil_half_bin_2d_newton.cpp
	P			src/nstencil_half_bin_2d_newton.h Copied from src/neigh_full.h
	A			src/nstencil_half_bin_2d_newton_tri.cpp
	P			src/nstencil_half_bin_2d_newton_tri.h Copied from src/neigh_full.h
	A			src/nstencil_half_bin_3d_newtoff.cpp
	P			src/nstencil_half_bin_3d_newtoff.h Copied from src/neigh_full.h
	A			src/nstencil_half_bin_3d_newton.cpp
	P			src/nstencil_half_bin_3d_newton.h Copied from src/neigh_full.h
	A			src/nstencil_half_bin_3d_newton_tri.cpp
	P			src/nstencil_half_bin_3d_newton_tri.h Copied from src/neigh_full.h
	A			src/nstencil_half_ghost_bin_2d_newtoff.cpp
	P			src/nstencil_half_ghost_bin_2d_newtoff.h Copied from src/neigh_full.h
	A			src/nstencil_half_ghost_bin_3d_newtoff.cpp
	P			src/nstencil_half_ghost_bin_3d_newtoff.h Copied from src/neigh_full.h
	A			src/nstencil_half_multi_2d_newtoff.cpp
	P			src/nstencil_half_multi_2d_newtoff.h Copied from src/neigh_full.h
	A			src/nstencil_half_multi_2d_newton.cpp
	P			src/nstencil_half_multi_2d_newton.h Copied from src/neigh_full.h
	A			src/nstencil_half_multi_2d_newton_tri.cpp
	P			src/nstencil_half_multi_2d_newton_tri.h Copied from src/neigh_full.h
	A			src/nstencil_half_multi_3d_newtoff.cpp
	P			src/nstencil_half_multi_3d_newtoff.h Copied from src/neigh_full.h
	A			src/nstencil_half_multi_3d_newton.cpp
	P			src/nstencil_half_multi_3d_newton.h Copied from src/neigh_full.h
	A			src/nstencil_half_multi_3d_newton_tri.cpp
	P			src/nstencil_half_multi_3d_newton_tri.h Copied from src/neigh_full.h
	A			src/ntopo.cpp
	A			src/ntopo.h
	A			src/ntopo_angle_all.cpp
	P			src/ntopo_angle_all.h Copied from src/neigh_full.h
	A			src/ntopo_angle_partial.cpp
	P			src/ntopo_angle_partial.h Copied from src/neigh_full.h
	A			src/ntopo_angle_template.cpp
	P			src/ntopo_angle_template.h Copied from src/neigh_full.h
	A			src/ntopo_bond_all.cpp
	V			src/{ntopo_bond_all.h ← neigh_derive.h}
	A			src/ntopo_bond_partial.cpp
	P			src/ntopo_bond_partial.h Copied from src/neigh_full.h
	A			src/ntopo_bond_template.cpp
	P			src/ntopo_bond_template.h Copied from src/neigh_full.h
	A			src/ntopo_dihedral_all.cpp
	P			src/ntopo_dihedral_all.h Copied from src/neigh_full.h
	A			src/ntopo_dihedral_partial.cpp
	P			src/ntopo_dihedral_partial.h Copied from src/neigh_full.h
	A			src/ntopo_dihedral_template.cpp
	P			src/ntopo_dihedral_template.h Copied from src/neigh_full.h
	A			src/ntopo_improper_all.cpp
	P			src/ntopo_improper_all.h Copied from src/neigh_full.h
	A			src/ntopo_improper_partial.cpp
	P			src/ntopo_improper_partial.h Copied from src/neigh_full.h
	A			src/ntopo_improper_template.cpp
	V			src/{ntopo_improper_template.h ← neigh_full.h}
	M			src/variable.h
	M			src/version.h