From c9c2ae6c613486bbc2b78a19df4e77691197eb32 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Wed, 7 Sep 2016 13:42:58 -0600
Subject: [PATCH] new neighbor list changes
---
src/Make.sh | 17 +-
src/Purge.list | 33 +
.../#npair_half_bin_newton_ssa.cpp#} | 241 +-
src/USER-DPD/fix_shardlow.cpp | 1 -
src/USER-DPD/npair_half_bin_newton_ssa.cpp | 311 ++
src/USER-DPD/npair_half_bin_newton_ssa.h | 43 +
src/USER-DPD/npair_halffull_newton_ssa.cpp | 132 +
src/USER-DPD/npair_halffull_newton_ssa.h | 44 +
.../nstencil_half_bin_2d_newton_ssa.cpp | 64 +
.../nstencil_half_bin_2d_newton_ssa.h | 43 +
.../nstencil_half_bin_3d_newton_ssa.cpp | 74 +
.../nstencil_half_bin_3d_newton_ssa.h | 43 +
src/USER-INTEL/Install.sh | 16 +-
src/USER-INTEL/fix_intel.cpp | 2 -
src/USER-INTEL/intel_buffers.cpp | 107 +-
src/USER-INTEL/intel_buffers.h | 70 +-
src/USER-INTEL/nbin_intel.cpp | 253 ++
src/USER-INTEL/nbin_intel.h | 69 +
src/USER-INTEL/neigh_half_bin_intel.cpp | 2455 ----------------
src/USER-INTEL/npair_full_bin_intel.cpp | 552 ++++
src/USER-INTEL/npair_full_bin_intel.h | 51 +
.../npair_half_bin_newtoff_intel.cpp | 451 +++
src/USER-INTEL/npair_half_bin_newtoff_intel.h | 52 +
.../npair_half_bin_newton_intel.cpp | 610 ++++
src/USER-INTEL/npair_half_bin_newton_intel.h | 51 +
.../npair_half_bin_newton_tri_intel.cpp | 513 ++++
.../npair_half_bin_newton_tri_intel.h | 51 +
src/USER-INTEL/npair_intel.cpp | 69 +
src/USER-INTEL/npair_intel.h | 117 +
src/USER-OMP/neigh_full_omp.cpp | 621 ----
src/USER-OMP/neigh_gran_omp.cpp | 618 ----
src/USER-OMP/neigh_half_bin_omp.cpp | 559 ----
src/USER-OMP/neigh_half_multi_omp.cpp | 435 ---
src/USER-OMP/neigh_half_nsq_omp.cpp | 376 ---
src/USER-OMP/neigh_respa_omp.cpp | 972 -------
src/USER-OMP/npair_full_bin_ghost_omp.cpp | 166 ++
src/USER-OMP/npair_full_bin_ghost_omp.h | 44 +
src/USER-OMP/npair_full_bin_omp.cpp | 135 +
src/USER-OMP/npair_full_bin_omp.h | 44 +
src/USER-OMP/npair_full_multi_omp.cpp | 143 +
src/USER-OMP/npair_full_multi_omp.h | 44 +
src/USER-OMP/npair_full_nsq_ghost_omp.cpp | 148 +
src/USER-OMP/npair_full_nsq_ghost_omp.h | 44 +
src/USER-OMP/npair_full_nsq_omp.cpp | 134 +
src/USER-OMP/npair_full_nsq_omp.h | 44 +
.../npair_half_bin_newtoff_ghost_omp.cpp | 173 ++
.../npair_half_bin_newtoff_ghost_omp.h | 44 +
src/USER-OMP/npair_half_bin_newtoff_omp.cpp | 138 +
src/USER-OMP/npair_half_bin_newtoff_omp.h | 43 +
src/USER-OMP/npair_half_bin_newton_omp.cpp | 172 ++
src/USER-OMP/npair_half_bin_newton_omp.h | 43 +
.../npair_half_bin_newton_tri_omp.cpp | 144 +
src/USER-OMP/npair_half_bin_newton_tri_omp.h | 43 +
src/USER-OMP/npair_half_multi_newtoff_omp.cpp | 145 +
src/USER-OMP/npair_half_multi_newtoff_omp.h | 43 +
src/USER-OMP/npair_half_multi_newton_omp.cpp | 178 ++
src/USER-OMP/npair_half_multi_newton_omp.h | 43 +
.../npair_half_multi_newton_tri_omp.cpp | 154 +
.../npair_half_multi_newton_tri_omp.h | 43 +
.../npair_half_nsq_newtoff_ghost_omp.cpp | 157 +
.../npair_half_nsq_newtoff_ghost_omp.h | 44 +
src/USER-OMP/npair_half_nsq_newtoff_omp.cpp | 133 +
src/USER-OMP/npair_half_nsq_newtoff_omp.h | 43 +
src/USER-OMP/npair_half_nsq_newton_omp.cpp | 151 +
src/USER-OMP/npair_half_nsq_newton_omp.h | 43 +
.../npair_half_respa_bin_newtoff_omp.cpp | 204 ++
.../npair_half_respa_bin_newtoff_omp.h | 44 +
.../npair_half_respa_bin_newton_omp.cpp | 250 ++
.../npair_half_respa_bin_newton_omp.h | 43 +
.../npair_half_respa_bin_newton_tri_omp.cpp | 211 ++
.../npair_half_respa_bin_newton_tri_omp.h | 43 +
.../npair_half_respa_nsq_newtoff_omp.cpp | 198 ++
.../npair_half_respa_nsq_newtoff_omp.h | 44 +
.../npair_half_respa_nsq_newton_omp.cpp | 217 ++
.../npair_half_respa_nsq_newton_omp.h | 44 +
.../npair_half_size_bin_newtoff_omp.cpp | 179 ++
.../npair_half_size_bin_newtoff_omp.h | 44 +
.../npair_half_size_bin_newton_omp.cpp | 227 ++
src/USER-OMP/npair_half_size_bin_newton_omp.h | 43 +
.../npair_half_size_bin_newton_tri_omp.cpp | 121 +
.../npair_half_size_bin_newton_tri_omp.h | 43 +
.../npair_half_size_nsq_newtoff_omp.cpp | 177 ++
.../npair_half_size_nsq_newtoff_omp.h | 44 +
.../npair_half_size_nsq_newton_omp.cpp | 195 ++
src/USER-OMP/npair_half_size_nsq_newton_omp.h | 44 +
src/USER-OMP/npair_halffull_newtoff_omp.cpp | 91 +
src/USER-OMP/npair_halffull_newtoff_omp.h | 44 +
..._omp.cpp => npair_halffull_newton_omp.cpp} | 77 +-
src/USER-OMP/npair_halffull_newton_omp.h | 44 +
src/USER-OMP/{neighbor_omp.h => npair_omp.h} | 19 +-
src/accelerator_intel.h | 68 -
src/nbin.cpp | 143 +
src/nbin.h | 78 +
src/nbin_standard.cpp | 232 ++
src/nbin_standard.h | 44 +
src/neigh_bond.cpp | 1028 -------
src/neigh_bond.h | 88 -
src/neigh_derive.cpp | 845 ------
src/neigh_full.cpp | 590 ----
src/neigh_gran.cpp | 839 ------
src/neigh_half_bin.cpp | 534 ----
src/neigh_half_multi.cpp | 415 ---
src/neigh_half_multi.h | 22 -
src/neigh_half_nsq.cpp | 360 ---
src/neigh_half_nsq.h | 22 -
src/neigh_list.cpp | 268 +-
src/neigh_list.h | 49 +-
src/neigh_request.cpp | 18 +-
src/neigh_request.h | 26 +-
src/neigh_respa.cpp | 928 ------
src/neigh_respa.h | 22 -
src/neigh_shardlow.h | 22 -
src/neigh_stencil.cpp | 536 ----
src/neighbor.cpp | 2563 ++++++++---------
src/neighbor.h | 400 +--
src/npair.cpp | 258 ++
src/npair.h | 146 +
src/npair_copy.cpp | 46 +
src/{neigh_gran.h => npair_copy.h} | 31 +-
src/npair_full_bin.cpp | 125 +
src/npair_full_bin.h | 43 +
src/npair_full_bin_ghost.cpp | 156 +
src/npair_full_bin_ghost.h | 44 +
src/npair_full_multi.cpp | 132 +
src/npair_full_multi.h | 43 +
src/npair_full_nsq.cpp | 125 +
src/npair_full_nsq.h | 43 +
src/npair_full_nsq_ghost.cpp | 138 +
src/npair_full_nsq_ghost.h | 44 +
src/npair_half_bin_newtoff.cpp | 129 +
src/npair_half_bin_newtoff.h | 43 +
src/npair_half_bin_newtoff_ghost.cpp | 162 ++
src/npair_half_bin_newtoff_ghost.h | 43 +
src/npair_half_bin_newton.cpp | 161 ++
src/npair_half_bin_newton.h | 43 +
src/npair_half_bin_newton_ssa.cpp | 311 ++
src/npair_half_bin_newton_ssa.h | 43 +
src/npair_half_bin_newton_tri.cpp | 134 +
src/npair_half_bin_newton_tri.h | 43 +
src/npair_half_multi_newtoff.cpp | 135 +
src/npair_half_multi_newtoff.h | 43 +
src/npair_half_multi_newton.cpp | 168 ++
src/npair_half_multi_newton.h | 43 +
src/npair_half_multi_newton_tri.cpp | 143 +
src/npair_half_multi_newton_tri.h | 43 +
src/npair_half_nsq_newtoff.cpp | 125 +
src/npair_half_nsq_newtoff.h | 43 +
src/npair_half_nsq_newtoff_ghost.cpp | 150 +
src/npair_half_nsq_newtoff_ghost.h | 43 +
src/npair_half_nsq_newton.cpp | 142 +
src/npair_half_nsq_newton.h | 43 +
src/npair_half_respa_bin_newtoff.cpp | 190 ++
src/npair_half_respa_bin_newtoff.h | 43 +
src/npair_half_respa_bin_newton.cpp | 236 ++
src/npair_half_respa_bin_newton.h | 43 +
src/npair_half_respa_bin_newton_tri.cpp | 198 ++
src/npair_half_respa_bin_newton_tri.h | 43 +
src/npair_half_respa_nsq_newtoff.cpp | 185 ++
src/npair_half_respa_nsq_newtoff.h | 43 +
src/npair_half_respa_nsq_newton.cpp | 205 ++
src/npair_half_respa_nsq_newton.h | 43 +
src/npair_half_size_bin_newtoff.cpp | 171 ++
src/npair_half_size_bin_newtoff.h | 43 +
src/npair_half_size_bin_newton.cpp | 215 ++
src/npair_half_size_bin_newton.h | 43 +
src/npair_half_size_bin_newton_tri.cpp | 180 ++
src/npair_half_size_bin_newton_tri.h | 43 +
src/npair_half_size_nsq_newtoff.cpp | 169 ++
src/npair_half_size_nsq_newtoff.h | 43 +
src/npair_half_size_nsq_newton.cpp | 187 ++
src/npair_half_size_nsq_newton.h | 43 +
src/npair_halffull_newtoff.cpp | 82 +
src/npair_halffull_newtoff.h | 44 +
src/npair_halffull_newton.cpp | 99 +
src/npair_halffull_newton.h | 44 +
src/npair_halffull_newton_ssa.cpp | 132 +
src/npair_halffull_newton_ssa.h | 44 +
src/npair_skip.cpp | 103 +
src/npair_skip.h | 44 +
src/npair_skip_respa.cpp | 169 ++
src/npair_skip_respa.h | 45 +
src/npair_skip_size.cpp | 161 ++
src/npair_skip_size.h | 44 +
src/npair_skip_size_off2on.cpp | 168 ++
src/npair_skip_size_off2on.h | 45 +
src/npair_skip_size_off2on_oneside.cpp | 223 ++
src/npair_skip_size_off2on_oneside.h | 45 +
src/nstencil.cpp | 230 ++
src/nstencil.h | 84 +
src/nstencil_full_bin_2d.cpp | 38 +
src/nstencil_full_bin_2d.h | 44 +
src/nstencil_full_bin_3d.cpp | 39 +
src/nstencil_full_bin_3d.h | 44 +
src/nstencil_full_ghost_bin_2d.cpp | 45 +
src/nstencil_full_ghost_bin_2d.h | 44 +
src/nstencil_full_ghost_bin_3d.cpp | 46 +
src/nstencil_full_ghost_bin_3d.h | 44 +
src/nstencil_full_multi_2d.cpp | 52 +
src/nstencil_full_multi_2d.h | 44 +
src/nstencil_full_multi_3d.cpp | 53 +
src/nstencil_full_multi_3d.h | 44 +
src/nstencil_half_bin_2d_newtoff.cpp | 39 +
src/nstencil_half_bin_2d_newtoff.h | 43 +
src/nstencil_half_bin_2d_newton.cpp | 39 +
src/nstencil_half_bin_2d_newton.h | 43 +
src/nstencil_half_bin_2d_newton_ssa.cpp | 64 +
src/nstencil_half_bin_2d_newton_ssa.h | 43 +
src/nstencil_half_bin_2d_newton_tri.cpp | 39 +
src/nstencil_half_bin_2d_newton_tri.h | 43 +
src/nstencil_half_bin_3d_newtoff.cpp | 40 +
src/nstencil_half_bin_3d_newtoff.h | 43 +
src/nstencil_half_bin_3d_newton.cpp | 40 +
src/nstencil_half_bin_3d_newton.h | 43 +
src/nstencil_half_bin_3d_newton_ssa.cpp | 74 +
src/nstencil_half_bin_3d_newton_ssa.h | 43 +
src/nstencil_half_bin_3d_newton_tri.cpp | 40 +
src/nstencil_half_bin_3d_newton_tri.h | 43 +
src/nstencil_half_ghost_bin_2d_newtoff.cpp | 46 +
src/nstencil_half_ghost_bin_2d_newtoff.h | 44 +
src/nstencil_half_ghost_bin_3d_newtoff.cpp | 47 +
src/nstencil_half_ghost_bin_3d_newtoff.h | 44 +
src/nstencil_half_multi_2d_newtoff.cpp | 53 +
src/nstencil_half_multi_2d_newtoff.h | 43 +
src/nstencil_half_multi_2d_newton.cpp | 54 +
src/nstencil_half_multi_2d_newton.h | 43 +
src/nstencil_half_multi_2d_newton_tri.cpp | 53 +
src/nstencil_half_multi_2d_newton_tri.h | 43 +
src/nstencil_half_multi_3d_newtoff.cpp | 54 +
src/nstencil_half_multi_3d_newtoff.h | 43 +
src/nstencil_half_multi_3d_newton.cpp | 55 +
src/nstencil_half_multi_3d_newton.h | 43 +
src/nstencil_half_multi_3d_newton_tri.cpp | 54 +
src/nstencil_half_multi_3d_newton_tri.h | 43 +
src/ntopo.cpp | 218 ++
src/ntopo.h | 56 +
src/ntopo_angle_all.cpp | 99 +
src/{neigh_full.h => ntopo_angle_all.h} | 29 +-
src/ntopo_angle_partial.cpp | 100 +
src/ntopo_angle_partial.h | 41 +
src/ntopo_angle_template.cpp | 119 +
src/ntopo_angle_template.h | 41 +
src/ntopo_bond_all.cpp | 91 +
src/{neigh_derive.h => ntopo_bond_all.h} | 29 +-
src/ntopo_bond_partial.cpp | 92 +
...{neigh_half_bin.h => ntopo_bond_partial.h} | 29 +-
src/ntopo_bond_template.cpp | 109 +
src/ntopo_bond_template.h | 41 +
src/ntopo_dihedral_all.cpp | 106 +
src/ntopo_dihedral_all.h | 41 +
src/ntopo_dihedral_partial.cpp | 108 +
src/ntopo_dihedral_partial.h | 41 +
src/ntopo_dihedral_template.cpp | 127 +
src/ntopo_dihedral_template.h | 41 +
src/ntopo_improper_all.cpp | 106 +
src/ntopo_improper_all.h | 41 +
src/ntopo_improper_partial.cpp | 108 +
src/ntopo_improper_partial.h | 41 +
src/ntopo_improper_template.cpp | 127 +
src/ntopo_improper_template.h | 41 +
259 files changed, 23057 insertions(+), 14631 deletions(-)
rename src/{neigh_shardlow.cpp => USER-DPD/#npair_half_bin_newton_ssa.cpp#} (60%)
create mode 100644 src/USER-DPD/npair_half_bin_newton_ssa.cpp
create mode 100644 src/USER-DPD/npair_half_bin_newton_ssa.h
create mode 100644 src/USER-DPD/npair_halffull_newton_ssa.cpp
create mode 100644 src/USER-DPD/npair_halffull_newton_ssa.h
create mode 100644 src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp
create mode 100644 src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h
create mode 100644 src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp
create mode 100644 src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h
create mode 100644 src/USER-INTEL/nbin_intel.cpp
create mode 100644 src/USER-INTEL/nbin_intel.h
delete mode 100644 src/USER-INTEL/neigh_half_bin_intel.cpp
create mode 100644 src/USER-INTEL/npair_full_bin_intel.cpp
create mode 100644 src/USER-INTEL/npair_full_bin_intel.h
create mode 100644 src/USER-INTEL/npair_half_bin_newtoff_intel.cpp
create mode 100644 src/USER-INTEL/npair_half_bin_newtoff_intel.h
create mode 100644 src/USER-INTEL/npair_half_bin_newton_intel.cpp
create mode 100644 src/USER-INTEL/npair_half_bin_newton_intel.h
create mode 100644 src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp
create mode 100644 src/USER-INTEL/npair_half_bin_newton_tri_intel.h
create mode 100644 src/USER-INTEL/npair_intel.cpp
create mode 100644 src/USER-INTEL/npair_intel.h
delete mode 100644 src/USER-OMP/neigh_full_omp.cpp
delete mode 100644 src/USER-OMP/neigh_gran_omp.cpp
delete mode 100644 src/USER-OMP/neigh_half_bin_omp.cpp
delete mode 100644 src/USER-OMP/neigh_half_multi_omp.cpp
delete mode 100644 src/USER-OMP/neigh_half_nsq_omp.cpp
delete mode 100644 src/USER-OMP/neigh_respa_omp.cpp
create mode 100644 src/USER-OMP/npair_full_bin_ghost_omp.cpp
create mode 100644 src/USER-OMP/npair_full_bin_ghost_omp.h
create mode 100644 src/USER-OMP/npair_full_bin_omp.cpp
create mode 100644 src/USER-OMP/npair_full_bin_omp.h
create mode 100644 src/USER-OMP/npair_full_multi_omp.cpp
create mode 100644 src/USER-OMP/npair_full_multi_omp.h
create mode 100644 src/USER-OMP/npair_full_nsq_ghost_omp.cpp
create mode 100644 src/USER-OMP/npair_full_nsq_ghost_omp.h
create mode 100644 src/USER-OMP/npair_full_nsq_omp.cpp
create mode 100644 src/USER-OMP/npair_full_nsq_omp.h
create mode 100644 src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp
create mode 100644 src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h
create mode 100644 src/USER-OMP/npair_half_bin_newtoff_omp.cpp
create mode 100644 src/USER-OMP/npair_half_bin_newtoff_omp.h
create mode 100644 src/USER-OMP/npair_half_bin_newton_omp.cpp
create mode 100644 src/USER-OMP/npair_half_bin_newton_omp.h
create mode 100644 src/USER-OMP/npair_half_bin_newton_tri_omp.cpp
create mode 100644 src/USER-OMP/npair_half_bin_newton_tri_omp.h
create mode 100644 src/USER-OMP/npair_half_multi_newtoff_omp.cpp
create mode 100644 src/USER-OMP/npair_half_multi_newtoff_omp.h
create mode 100644 src/USER-OMP/npair_half_multi_newton_omp.cpp
create mode 100644 src/USER-OMP/npair_half_multi_newton_omp.h
create mode 100644 src/USER-OMP/npair_half_multi_newton_tri_omp.cpp
create mode 100644 src/USER-OMP/npair_half_multi_newton_tri_omp.h
create mode 100644 src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp
create mode 100644 src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h
create mode 100644 src/USER-OMP/npair_half_nsq_newtoff_omp.cpp
create mode 100644 src/USER-OMP/npair_half_nsq_newtoff_omp.h
create mode 100644 src/USER-OMP/npair_half_nsq_newton_omp.cpp
create mode 100644 src/USER-OMP/npair_half_nsq_newton_omp.h
create mode 100644 src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp
create mode 100644 src/USER-OMP/npair_half_respa_bin_newtoff_omp.h
create mode 100644 src/USER-OMP/npair_half_respa_bin_newton_omp.cpp
create mode 100644 src/USER-OMP/npair_half_respa_bin_newton_omp.h
create mode 100644 src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp
create mode 100644 src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h
create mode 100644 src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp
create mode 100644 src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h
create mode 100644 src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp
create mode 100644 src/USER-OMP/npair_half_respa_nsq_newton_omp.h
create mode 100644 src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
create mode 100644 src/USER-OMP/npair_half_size_bin_newtoff_omp.h
create mode 100644 src/USER-OMP/npair_half_size_bin_newton_omp.cpp
create mode 100644 src/USER-OMP/npair_half_size_bin_newton_omp.h
create mode 100644 src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
create mode 100644 src/USER-OMP/npair_half_size_bin_newton_tri_omp.h
create mode 100644 src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
create mode 100644 src/USER-OMP/npair_half_size_nsq_newtoff_omp.h
create mode 100644 src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
create mode 100644 src/USER-OMP/npair_half_size_nsq_newton_omp.h
create mode 100644 src/USER-OMP/npair_halffull_newtoff_omp.cpp
create mode 100644 src/USER-OMP/npair_halffull_newtoff_omp.h
rename src/USER-OMP/{neigh_derive_omp.cpp => npair_halffull_newton_omp.cpp} (61%)
create mode 100644 src/USER-OMP/npair_halffull_newton_omp.h
rename src/USER-OMP/{neighbor_omp.h => npair_omp.h} (81%)
delete mode 100644 src/accelerator_intel.h
create mode 100644 src/nbin.cpp
create mode 100644 src/nbin.h
create mode 100644 src/nbin_standard.cpp
create mode 100644 src/nbin_standard.h
delete mode 100644 src/neigh_bond.cpp
delete mode 100644 src/neigh_bond.h
delete mode 100644 src/neigh_derive.cpp
delete mode 100644 src/neigh_full.cpp
delete mode 100644 src/neigh_gran.cpp
delete mode 100644 src/neigh_half_bin.cpp
delete mode 100644 src/neigh_half_multi.cpp
delete mode 100644 src/neigh_half_multi.h
delete mode 100644 src/neigh_half_nsq.cpp
delete mode 100644 src/neigh_half_nsq.h
delete mode 100644 src/neigh_respa.cpp
delete mode 100644 src/neigh_respa.h
delete mode 100644 src/neigh_shardlow.h
delete mode 100644 src/neigh_stencil.cpp
create mode 100644 src/npair.cpp
create mode 100644 src/npair.h
create mode 100644 src/npair_copy.cpp
rename src/{neigh_gran.h => npair_copy.h} (67%)
create mode 100644 src/npair_full_bin.cpp
create mode 100644 src/npair_full_bin.h
create mode 100644 src/npair_full_bin_ghost.cpp
create mode 100644 src/npair_full_bin_ghost.h
create mode 100644 src/npair_full_multi.cpp
create mode 100644 src/npair_full_multi.h
create mode 100644 src/npair_full_nsq.cpp
create mode 100644 src/npair_full_nsq.h
create mode 100644 src/npair_full_nsq_ghost.cpp
create mode 100644 src/npair_full_nsq_ghost.h
create mode 100644 src/npair_half_bin_newtoff.cpp
create mode 100644 src/npair_half_bin_newtoff.h
create mode 100644 src/npair_half_bin_newtoff_ghost.cpp
create mode 100644 src/npair_half_bin_newtoff_ghost.h
create mode 100644 src/npair_half_bin_newton.cpp
create mode 100644 src/npair_half_bin_newton.h
create mode 100644 src/npair_half_bin_newton_ssa.cpp
create mode 100644 src/npair_half_bin_newton_ssa.h
create mode 100644 src/npair_half_bin_newton_tri.cpp
create mode 100644 src/npair_half_bin_newton_tri.h
create mode 100644 src/npair_half_multi_newtoff.cpp
create mode 100644 src/npair_half_multi_newtoff.h
create mode 100644 src/npair_half_multi_newton.cpp
create mode 100644 src/npair_half_multi_newton.h
create mode 100644 src/npair_half_multi_newton_tri.cpp
create mode 100644 src/npair_half_multi_newton_tri.h
create mode 100644 src/npair_half_nsq_newtoff.cpp
create mode 100644 src/npair_half_nsq_newtoff.h
create mode 100644 src/npair_half_nsq_newtoff_ghost.cpp
create mode 100644 src/npair_half_nsq_newtoff_ghost.h
create mode 100644 src/npair_half_nsq_newton.cpp
create mode 100644 src/npair_half_nsq_newton.h
create mode 100644 src/npair_half_respa_bin_newtoff.cpp
create mode 100644 src/npair_half_respa_bin_newtoff.h
create mode 100644 src/npair_half_respa_bin_newton.cpp
create mode 100644 src/npair_half_respa_bin_newton.h
create mode 100644 src/npair_half_respa_bin_newton_tri.cpp
create mode 100644 src/npair_half_respa_bin_newton_tri.h
create mode 100644 src/npair_half_respa_nsq_newtoff.cpp
create mode 100644 src/npair_half_respa_nsq_newtoff.h
create mode 100644 src/npair_half_respa_nsq_newton.cpp
create mode 100644 src/npair_half_respa_nsq_newton.h
create mode 100644 src/npair_half_size_bin_newtoff.cpp
create mode 100644 src/npair_half_size_bin_newtoff.h
create mode 100644 src/npair_half_size_bin_newton.cpp
create mode 100644 src/npair_half_size_bin_newton.h
create mode 100644 src/npair_half_size_bin_newton_tri.cpp
create mode 100644 src/npair_half_size_bin_newton_tri.h
create mode 100644 src/npair_half_size_nsq_newtoff.cpp
create mode 100644 src/npair_half_size_nsq_newtoff.h
create mode 100644 src/npair_half_size_nsq_newton.cpp
create mode 100644 src/npair_half_size_nsq_newton.h
create mode 100644 src/npair_halffull_newtoff.cpp
create mode 100644 src/npair_halffull_newtoff.h
create mode 100644 src/npair_halffull_newton.cpp
create mode 100644 src/npair_halffull_newton.h
create mode 100644 src/npair_halffull_newton_ssa.cpp
create mode 100644 src/npair_halffull_newton_ssa.h
create mode 100644 src/npair_skip.cpp
create mode 100644 src/npair_skip.h
create mode 100644 src/npair_skip_respa.cpp
create mode 100644 src/npair_skip_respa.h
create mode 100644 src/npair_skip_size.cpp
create mode 100644 src/npair_skip_size.h
create mode 100644 src/npair_skip_size_off2on.cpp
create mode 100644 src/npair_skip_size_off2on.h
create mode 100644 src/npair_skip_size_off2on_oneside.cpp
create mode 100644 src/npair_skip_size_off2on_oneside.h
create mode 100644 src/nstencil.cpp
create mode 100644 src/nstencil.h
create mode 100644 src/nstencil_full_bin_2d.cpp
create mode 100644 src/nstencil_full_bin_2d.h
create mode 100644 src/nstencil_full_bin_3d.cpp
create mode 100644 src/nstencil_full_bin_3d.h
create mode 100644 src/nstencil_full_ghost_bin_2d.cpp
create mode 100644 src/nstencil_full_ghost_bin_2d.h
create mode 100644 src/nstencil_full_ghost_bin_3d.cpp
create mode 100644 src/nstencil_full_ghost_bin_3d.h
create mode 100644 src/nstencil_full_multi_2d.cpp
create mode 100644 src/nstencil_full_multi_2d.h
create mode 100644 src/nstencil_full_multi_3d.cpp
create mode 100644 src/nstencil_full_multi_3d.h
create mode 100644 src/nstencil_half_bin_2d_newtoff.cpp
create mode 100644 src/nstencil_half_bin_2d_newtoff.h
create mode 100644 src/nstencil_half_bin_2d_newton.cpp
create mode 100644 src/nstencil_half_bin_2d_newton.h
create mode 100644 src/nstencil_half_bin_2d_newton_ssa.cpp
create mode 100644 src/nstencil_half_bin_2d_newton_ssa.h
create mode 100644 src/nstencil_half_bin_2d_newton_tri.cpp
create mode 100644 src/nstencil_half_bin_2d_newton_tri.h
create mode 100644 src/nstencil_half_bin_3d_newtoff.cpp
create mode 100644 src/nstencil_half_bin_3d_newtoff.h
create mode 100644 src/nstencil_half_bin_3d_newton.cpp
create mode 100644 src/nstencil_half_bin_3d_newton.h
create mode 100644 src/nstencil_half_bin_3d_newton_ssa.cpp
create mode 100644 src/nstencil_half_bin_3d_newton_ssa.h
create mode 100644 src/nstencil_half_bin_3d_newton_tri.cpp
create mode 100644 src/nstencil_half_bin_3d_newton_tri.h
create mode 100644 src/nstencil_half_ghost_bin_2d_newtoff.cpp
create mode 100644 src/nstencil_half_ghost_bin_2d_newtoff.h
create mode 100644 src/nstencil_half_ghost_bin_3d_newtoff.cpp
create mode 100644 src/nstencil_half_ghost_bin_3d_newtoff.h
create mode 100644 src/nstencil_half_multi_2d_newtoff.cpp
create mode 100644 src/nstencil_half_multi_2d_newtoff.h
create mode 100644 src/nstencil_half_multi_2d_newton.cpp
create mode 100644 src/nstencil_half_multi_2d_newton.h
create mode 100644 src/nstencil_half_multi_2d_newton_tri.cpp
create mode 100644 src/nstencil_half_multi_2d_newton_tri.h
create mode 100644 src/nstencil_half_multi_3d_newtoff.cpp
create mode 100644 src/nstencil_half_multi_3d_newtoff.h
create mode 100644 src/nstencil_half_multi_3d_newton.cpp
create mode 100644 src/nstencil_half_multi_3d_newton.h
create mode 100644 src/nstencil_half_multi_3d_newton_tri.cpp
create mode 100644 src/nstencil_half_multi_3d_newton_tri.h
create mode 100644 src/ntopo.cpp
create mode 100644 src/ntopo.h
create mode 100644 src/ntopo_angle_all.cpp
rename src/{neigh_full.h => ntopo_angle_all.h} (68%)
create mode 100644 src/ntopo_angle_partial.cpp
create mode 100644 src/ntopo_angle_partial.h
create mode 100644 src/ntopo_angle_template.cpp
create mode 100644 src/ntopo_angle_template.h
create mode 100644 src/ntopo_bond_all.cpp
rename src/{neigh_derive.h => ntopo_bond_all.h} (68%)
create mode 100644 src/ntopo_bond_partial.cpp
rename src/{neigh_half_bin.h => ntopo_bond_partial.h} (66%)
create mode 100644 src/ntopo_bond_template.cpp
create mode 100644 src/ntopo_bond_template.h
create mode 100644 src/ntopo_dihedral_all.cpp
create mode 100644 src/ntopo_dihedral_all.h
create mode 100644 src/ntopo_dihedral_partial.cpp
create mode 100644 src/ntopo_dihedral_partial.h
create mode 100644 src/ntopo_dihedral_template.cpp
create mode 100644 src/ntopo_dihedral_template.h
create mode 100644 src/ntopo_improper_all.cpp
create mode 100644 src/ntopo_improper_all.h
create mode 100644 src/ntopo_improper_partial.cpp
create mode 100644 src/ntopo_improper_partial.h
create mode 100644 src/ntopo_improper_template.cpp
create mode 100644 src/ntopo_improper_template.h
diff --git a/src/Make.sh b/src/Make.sh
index fbed1a8bcd..a76f7d5ac1 100644
--- a/src/Make.sh
+++ b/src/Make.sh
@@ -5,12 +5,6 @@
# sh Make.sh Makefile.shlib
# sh Make.sh Makefile.list
-# turn off enforced customizations
-GREP_OPTIONS=
-# enforce using portable C locale
-LC_ALL=C
-export LC_ALL GREP_OPTIONS
-
# function to create one style_*.h file
# must whack *.d files that depend on style_*.h file,
# else Make will not recreate them
@@ -59,8 +53,9 @@ style () {
# called by "make machine"
# col 1 = string to search for
# col 2 = search in *.h files starting with this name
-# col 3 = prefix of style file
-# col 4
+# col 3 = name of style file
+# col 4 = file that includes the style file
+# col 5 = optional 2nd file that includes the style file
if (test $1 = "style") then
@@ -69,7 +64,7 @@ if (test $1 = "style") then
style BODY_CLASS body_ body atom_vec_body
style BOND_CLASS bond_ bond force
style COMMAND_CLASS "" command input
- style COMPUTE_CLASS compute_ compute modify modify_cuda
+ style COMPUTE_CLASS compute_ compute modify
style DIHEDRAL_CLASS dihedral_ dihedral force
style DUMP_CLASS dump_ dump output write_dump
style FIX_CLASS fix_ fix modify
@@ -77,6 +72,10 @@ if (test $1 = "style") then
style INTEGRATE_CLASS "" integrate update
style KSPACE_CLASS "" kspace force
style MINIMIZE_CLASS min_ minimize update
+ style NBIN_CLASS nbin_ nbin neighbor
+ style NPAIR_CLASS npair_ npair neighbor
+ style NSTENCIL_CLASS nstencil_ nstencil neighbor
+ style NTOPO_CLASS ntopo_ ntopo neighbor
style PAIR_CLASS pair_ pair force
style READER_CLASS reader_ reader read_dump
style REGION_CLASS region_ region domain
diff --git a/src/Purge.list b/src/Purge.list
index 37d137e838..b6398358de 100644
--- a/src/Purge.list
+++ b/src/Purge.list
@@ -13,6 +13,39 @@ style_kspace.h
style_minimize.h
style_pair.h
style_region.h
+style_neigh_bin.h
+style_neigh_pair.h
+style_neigh_stencil.h
+# deleted on 30 Aug 2016
+accelerator_intel.h
+neigh_bond.cpp
+neigh_bond.h
+neigh_derive.cpp
+neigh_derive.h
+neigh_full.cpp
+neigh_full.h
+neigh_gran.cpp
+neigh_gran.h
+neigh_half_bin.cpp
+neigh_half_bin.h
+neigh_half_multi.cpp
+neigh_half_multi.h
+neigh_half_nsq.cpp
+neigh_half_nsq.h
+neigh_respa.cpp
+neigh_respa.h
+neigh_shardlow.cpp
+neigh_shardlow.h
+neigh_stencil.cpp
+neigh_half_bin_intel.cpp
+neighbor_omp.h
+neigh_derive_omp.cpp
+neigh_full_omp.cpp
+neigh_gran_omp.cpp
+neigh_half_bin_omp.cpp
+neigh_half_multi_omp.cpp
+neigh_half_nsq_omp.cpp
+neigh_respa_omp.cpp
# deleted on 31 May 2016
fix_ave_spatial_sphere.cpp
fix_ave_spatial_sphere.h
diff --git a/src/neigh_shardlow.cpp b/src/USER-DPD/#npair_half_bin_newton_ssa.cpp#
similarity index 60%
rename from src/neigh_shardlow.cpp
rename to src/USER-DPD/#npair_half_bin_newton_ssa.cpp#
index 1b87ab65d7..b529121a0a 100644
--- a/src/neigh_shardlow.cpp
+++ b/src/USER-DPD/#npair_half_bin_newton_ssa.cpp#
@@ -16,195 +16,38 @@
James Larentzos and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */
+#include "npair_half_bin_newton_ssa.h"
#include "neighbor.h"
#include "neigh_list.h"
-#include "neigh_request.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "domain.h"
#include "group.h"
#include "memory.h"
+#include "my_page.h"
#include "error.h"
-#include "update.h"
using namespace LAMMPS_NS;
-/* ----------------------------------------------------------------------
- routines to create a stencil = list of bin offsets
- stencil = bins whose closest corner to central bin is within cutoff
- sx,sy,sz = bin bounds = furthest the stencil could possibly extend
- 3d creates xyz stencil, 2d creates xy stencil
- for half list with newton on:
- stencil is bins to the "upper right" of central bin
- stencil does not include self
-------------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_bin_2d_ssa(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j;
- int *stencil = list->stencil;
- int nstencil = 0;
-
- for (j = 0; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (j > 0 || (j == 0 && i > 0))
- if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil[nstencil++] = j*mbinx + i;
-
- list->nstencil = nstencil;
-
- // Now include additional bins for AIR ghosts only
- for (j = -sy; j <= 0; j++)
- for (i = -sx; i <= sx; i++) {
- if (j == 0 && i > 0) continue;
- if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil[nstencil++] = j*mbinx + i;
- }
-
- while (nstencil < list->maxstencil) {
- stencil[nstencil++] = INT_MAX;
- }
-}
-
-/* ---------------------------------------------------------------------- */
+// allocate space for static class variable
+// prototype for non-class function
-void Neighbor::stencil_half_bin_3d_ssa(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,k;
- int *stencil = list->stencil;
- int nstencil = 0;
-
- for (k = 0; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (k > 0 || j > 0 || (j == 0 && i > 0))
- if (bin_distance(i,j,k) < cutneighmaxsq)
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
-
- list->nstencil = nstencil;
-
- // Now include additional bins for AIR ghosts only
- for (k = -sz; k < 0; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,k) < cutneighmaxsq)
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
- k = 0; // skip already included bins at k == 0
- for (j = -sy; j <= 0; j++)
- for (i = -sx; i <= sx; i++) {
- if (j == 0 && i > 0) continue;
- if (bin_distance(i,j,k) < cutneighmaxsq)
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
- }
-
- while (nstencil < list->maxstencil) {
- stencil[nstencil++] = INT_MAX;
- }
-}
-
-// space for static variable ssaAIRptr so it
-// can be used in qsort's compair function "cmp_ssaAIR()"
static int *ssaAIRptr;
+static int cmp_ssaAIR(const void *, const void *);
-static int cmp_ssaAIR(const void *iptr, const void *jptr)
-{
- int i = *((int *) iptr);
- int j = *((int *) jptr);
- if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
- if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
- return 0;
-}
-
-
-/* ----------------------------------------------------------------------
- build half list from full list for use by Shardlow Spliting Algorithm
- pair stored once if i,j are both owned and i < j
- if j is ghost, only store if j coords are "above and to the right" of i
- works if full list is a skip list
-------------------------------------------------------------------------- */
-
-void Neighbor::half_from_full_newton_ssa(NeighList *list)
-{
- int i,j,ii,jj,n,jnum,joriginal;
- int *neighptr,*jlist;
-
- int nlocal = atom->nlocal;
- int *ssaAIR = atom->ssaAIR;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- int *ilist_full = list->listfull->ilist;
- int *numneigh_full = list->listfull->numneigh;
- int **firstneigh_full = list->listfull->firstneigh;
- int inum_full = list->listfull->inum;
-
- int inum = 0;
- ipage->reset();
-
- // loop over parent full list
-
- for (ii = 0; ii < inum_full; ii++) {
- int AIRct[8] = { 0 };
- n = 0;
- neighptr = ipage->vget();
-
- i = ilist_full[ii];
-
- // loop over full neighbor list
-
- jlist = firstneigh_full[i];
- jnum = numneigh_full[i];
-
- for (jj = 0; jj < jnum; jj++) {
- joriginal = jlist[jj];
- j = joriginal & NEIGHMASK;
- if (j < nlocal) {
- if (i > j) continue;
- ++(AIRct[0]);
- } else {
- if (ssaAIR[j] < 2) continue; // skip ghost atoms not in AIR
- ++(AIRct[ssaAIR[j] - 1]);
- }
- neighptr[n++] = joriginal;
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- // sort the locals+ghosts in the neighbor list by their ssaAIR number
- ssaAIRptr = atom->ssaAIR;
- qsort(&(neighptr[0]), n, sizeof(int), cmp_ssaAIR);
+/* ---------------------------------------------------------------------- */
- // Do a prefix sum on the counts to turn them into indexes.
- list->ndxAIR_ssa[i][0] = AIRct[0];
- for (int ndx = 1; ndx < 8; ++ndx) {
- list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
- }
- }
-
- list->inum = inum;
-}
+NPairHalfBinNewtonSSA::NPairHalfBinNewtonSSA(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
- for Shardlow Spliting Algorithm:
binned neighbor list construction with full Newton's 3rd law
+ for use by Shardlow Spliting Algorithm
each owned atom i checks its own bin and other bins in Newton stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
-void Neighbor::half_bin_newton_ssa(NeighList *list)
+void NPairHalfBinNewtonSSA::build(NeighList *list)
{
int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
tagint tagprev;
@@ -220,6 +63,7 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
+ if (includegroup) nlocal = atom->nfirst;
int *ssaAIR = atom->ssaAIR;
int *molindex = atom->molindex;
@@ -232,18 +76,27 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int maxstencil = list->maxstencil;
- int *stencil = list->stencil;
MyPage<int> *ipage = list->ipage;
int inum = 0;
- if (binatomflag) { /* only false in Neighbor::build_one */
-/* ----------------------------------------------------------------------
- bin owned and ghost atoms for use by Shardlow Splitting Algorithm
- exclude ghost atoms that are not in the Active Interaction Regions (AIR)
-------------------------------------------------------------------------- */
+ // bin owned and ghost atoms for use by Shardlow Splitting Algorithm
+ // exclude ghost atoms that are not in the Active Interaction Regions (AIR)
+
+ // NOTE to Tim: this binatomflag no longer exists
+ // the logic up higher assures that binning has been done
+ // before this build() method is called
+ // maybe this code below needs to be in a new NBinShardlow class?
+ // this class also inherits NPair::nb from its parent
+ // which points to the NBin class that did the binning
+ // there are last_step variables stored there which indicate
+ // the last time binning was done
+ // the basic question is what data is created/stored by SSA binning
+ // and in what class should it live?
+ // if it is created by the binning operation, then I think
+ // it should be in a new NBinShardlow class
+
+ if (true /* binatomflag */) { // only false in Neighbor::build_one
if (mbins > list->maxhead_ssa) {
list->maxhead_ssa = mbins;
@@ -257,8 +110,8 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
list->binhead_ssa[i] = -1;
}
- if (maxbin > list->maxbin_ssa) {
- list->maxbin_ssa = maxbin;
+ if (nall > list->maxbin_ssa) {
+ list->maxbin_ssa = nall;
memory->destroy(list->bins_ssa);
memory->create(list->bins_ssa,list->maxbin_ssa,"bins_ssa");
}
@@ -267,7 +120,8 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
if (includegroup) {
int bitmask = group->bitmask[includegroup];
- for (i = nall-1; i >= nlocal; i--) {
+ int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above
+ for (i = nall-1; i >= nowned; i--) {
if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
if (mask[i] & bitmask) {
ibin = coord2bin(x[i]);
@@ -275,7 +129,6 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
list->gbinhead_ssa[ibin] = i;
}
}
- nlocal = atom->nfirst; // This is important for the code that follows!
} else {
for (i = nall-1; i >= nlocal; i--) {
if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
@@ -289,7 +142,7 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
list->bins_ssa[i] = list->binhead_ssa[ibin];
list->binhead_ssa[ibin] = i;
}
- } /* else reuse previous binning. See Neighbor::build_one comment. */
+ } // else reuse previous binning. See Neighbor::build_one comment
ipage->reset();
@@ -343,8 +196,10 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
ibin = coord2bin(x[i]);
// loop over all local atoms in other bins in "half" stencil
+
for (k = 0; k < nstencil; k++) {
- for (j = list->binhead_ssa[ibin+stencil[k]]; j >= 0; j = list->bins_ssa[j]) {
+ for (j = list->binhead_ssa[ibin+stencil[k]]; j >= 0;
+ j = list->bins_ssa[j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
@@ -377,9 +232,10 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
// Note: the non-AIR ghost atoms have already been filtered out
// That is a significant time savings because of the "full" stencil
// Note2: only non-pure locals can have ghosts as neighbors
- if (ssaAIR[i] == 1) for (k = 0; k < maxstencil; k++) {
- if (stencil[k] > mbins) break; /* Check if ghost stencil bins are exhausted */
- for (j = list->gbinhead_ssa[ibin+stencil[k]]; j >= 0; j = list->bins_ssa[j]) {
+
+ if (ssaAIR[i] == 1) for (k = 0; k < nstencil_ssa; k++) {
+ for (j = list->gbinhead_ssa[ibin+stencil[k]]; j >= 0;
+ j = list->bins_ssa[j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
@@ -424,10 +280,12 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
// sort the ghosts in the neighbor list by their ssaAIR number
+
ssaAIRptr = atom->ssaAIR;
qsort(&(neighptr[AIRct[0]]), n - AIRct[0], sizeof(int), cmp_ssaAIR);
- // Do a prefix sum on the counts to turn them into indexes.
+ // do a prefix sum on the counts to turn them into indexes
+
list->ndxAIR_ssa[i][0] = AIRct[0];
for (int ndx = 1; ndx < 8; ++ndx) {
list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
@@ -436,3 +294,18 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
list->inum = inum;
}
+
+/* ----------------------------------------------------------------------
+ comparison function invoked by qsort()
+ accesses static class member ssaAIRptr, set before call to qsort()
+------------------------------------------------------------------------- */
+
+static int cmp_ssaAIR(const void *iptr, const void *jptr)
+{
+ int i = *((int *) iptr);
+ int j = *((int *) jptr);
+ if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
+ if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
+ return 0;
+}
+
diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp
index fd9f4d7d74..f8fe426c77 100644
--- a/src/USER-DPD/fix_shardlow.cpp
+++ b/src/USER-DPD/fix_shardlow.cpp
@@ -226,7 +226,6 @@ void FixShardlow::ssa_update(
int newton_pair = force->newton_pair;
double randPair;
- int *ssaAIR = atom->ssaAIR;
double *uCond = atom->uCond;
double *uMech = atom->uMech;
double *dpdTheta = atom->dpdTheta;
diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.cpp b/src/USER-DPD/npair_half_bin_newton_ssa.cpp
new file mode 100644
index 0000000000..b529121a0a
--- /dev/null
+++ b/src/USER-DPD/npair_half_bin_newton_ssa.cpp
@@ -0,0 +1,311 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors:
+ James Larentzos and Timothy I. Mattox (Engility Corporation)
+------------------------------------------------------------------------- */
+
+#include "npair_half_bin_newton_ssa.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "group.h"
+#include "memory.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+// allocate space for static class variable
+// prototype for non-class function
+
+static int *ssaAIRptr;
+static int cmp_ssaAIR(const void *, const void *);
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfBinNewtonSSA::NPairHalfBinNewtonSSA(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with full Newton's 3rd law
+ for use by Shardlow Spliting Algorithm
+ each owned atom i checks its own bin and other bins in Newton stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfBinNewtonSSA::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+ if (includegroup) nlocal = atom->nfirst;
+ int *ssaAIR = atom->ssaAIR;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ int molecular = atom->molecular;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+
+ // bin owned and ghost atoms for use by Shardlow Splitting Algorithm
+ // exclude ghost atoms that are not in the Active Interaction Regions (AIR)
+
+ // NOTE to Tim: this binatomflag no longer exists
+ // the logic up higher assures that binning has been done
+ // before this build() method is called
+ // maybe this code below needs to be in a new NBinShardlow class?
+ // this class also inherits NPair::nb from its parent
+ // which points to the NBin class that did the binning
+ // there are last_step variables stored there which indicate
+ // the last time binning was done
+ // the basic question is what data is created/stored by SSA binning
+ // and in what class should it live?
+ // if it is created by the binning operation, then I think
+ // it should be in a new NBinShardlow class
+
+ if (true /* binatomflag */) { // only false in Neighbor::build_one
+
+ if (mbins > list->maxhead_ssa) {
+ list->maxhead_ssa = mbins;
+ memory->destroy(list->gbinhead_ssa);
+ memory->destroy(list->binhead_ssa);
+ memory->create(list->binhead_ssa,list->maxhead_ssa,"binhead_ssa");
+ memory->create(list->gbinhead_ssa,list->maxhead_ssa,"gbinhead_ssa");
+ }
+ for (i = 0; i < mbins; i++) {
+ list->gbinhead_ssa[i] = -1;
+ list->binhead_ssa[i] = -1;
+ }
+
+ if (nall > list->maxbin_ssa) {
+ list->maxbin_ssa = nall;
+ memory->destroy(list->bins_ssa);
+ memory->create(list->bins_ssa,list->maxbin_ssa,"bins_ssa");
+ }
+
+ // bin in reverse order so linked list will be in forward order
+
+ if (includegroup) {
+ int bitmask = group->bitmask[includegroup];
+ int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above
+ for (i = nall-1; i >= nowned; i--) {
+ if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
+ if (mask[i] & bitmask) {
+ ibin = coord2bin(x[i]);
+ list->bins_ssa[i] = list->gbinhead_ssa[ibin];
+ list->gbinhead_ssa[ibin] = i;
+ }
+ }
+ } else {
+ for (i = nall-1; i >= nlocal; i--) {
+ if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
+ ibin = coord2bin(x[i]);
+ list->bins_ssa[i] = list->gbinhead_ssa[ibin];
+ list->gbinhead_ssa[ibin] = i;
+ }
+ }
+ for (i = nlocal-1; i >= 0; i--) {
+ ibin = coord2bin(x[i]);
+ list->bins_ssa[i] = list->binhead_ssa[ibin];
+ list->binhead_ssa[ibin] = i;
+ }
+ } // else reuse previous binning. See Neighbor::build_one comment
+
+ ipage->reset();
+
+ // loop over owned atoms, storing half of the neighbors
+
+ for (i = 0; i < nlocal; i++) {
+ int AIRct[8] = { 0 };
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over rest of local atoms in i's bin
+ // just store them, since j is beyond i in linked list
+
+ for (j = list->bins_ssa[i]; j >= 0; j = list->bins_ssa[j]) {
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ ibin = coord2bin(x[i]);
+
+ // loop over all local atoms in other bins in "half" stencil
+
+ for (k = 0; k < nstencil; k++) {
+ for (j = list->binhead_ssa[ibin+stencil[k]]; j >= 0;
+ j = list->bins_ssa[j]) {
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+ AIRct[0] = n;
+
+ // loop over AIR ghost atoms in all bins in "full" stencil
+ // Note: the non-AIR ghost atoms have already been filtered out
+ // That is a significant time savings because of the "full" stencil
+ // Note2: only non-pure locals can have ghosts as neighbors
+
+ if (ssaAIR[i] == 1) for (k = 0; k < nstencil_ssa; k++) {
+ for (j = list->gbinhead_ssa[ibin+stencil[k]]; j >= 0;
+ j = list->bins_ssa[j]) {
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) {
+ neighptr[n++] = j;
+ ++(AIRct[ssaAIR[j] - 1]);
+ } else if (domain->minimum_image_check(delx,dely,delz)) {
+ neighptr[n++] = j;
+ ++(AIRct[ssaAIR[j] - 1]);
+ } else if (which > 0) {
+ neighptr[n++] = j ^ (which << SBBITS);
+ ++(AIRct[ssaAIR[j] - 1]);
+ }
+ } else {
+ neighptr[n++] = j;
+ ++(AIRct[ssaAIR[j] - 1]);
+ }
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ // sort the ghosts in the neighbor list by their ssaAIR number
+
+ ssaAIRptr = atom->ssaAIR;
+ qsort(&(neighptr[AIRct[0]]), n - AIRct[0], sizeof(int), cmp_ssaAIR);
+
+ // do a prefix sum on the counts to turn them into indexes
+
+ list->ndxAIR_ssa[i][0] = AIRct[0];
+ for (int ndx = 1; ndx < 8; ++ndx) {
+ list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
+ }
+ }
+
+ list->inum = inum;
+}
+
+/* ----------------------------------------------------------------------
+ comparison function invoked by qsort()
+ accesses static class member ssaAIRptr, set before call to qsort()
+------------------------------------------------------------------------- */
+
+static int cmp_ssaAIR(const void *iptr, const void *jptr)
+{
+ int i = *((int *) iptr);
+ int j = *((int *) jptr);
+ if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
+ if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
+ return 0;
+}
+
diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.h b/src/USER-DPD/npair_half_bin_newton_ssa.h
new file mode 100644
index 0000000000..a2e72d772b
--- /dev/null
+++ b/src/USER-DPD/npair_half_bin_newton_ssa.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/bin/newton/ssa,
+ NPairHalfBinNewtonSSA,
+ NP_BIN | NP_NEWTON | NP_ORTHO | NP_SSA)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_BIN_NEWTON_SSA_H
+#define LMP_NPAIR_HALF_BIN_NEWTON_SSA_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfBinNewtonSSA : public NPair {
+ public:
+ NPairHalfBinNewtonSSA(class LAMMPS *);
+ ~NPairHalfBinNewtonSSA() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-DPD/npair_halffull_newton_ssa.cpp b/src/USER-DPD/npair_halffull_newton_ssa.cpp
new file mode 100644
index 0000000000..f09a2c3ae1
--- /dev/null
+++ b/src/USER-DPD/npair_halffull_newton_ssa.cpp
@@ -0,0 +1,132 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors:
+ James Larentzos and Timothy I. Mattox (Engility Corporation)
+------------------------------------------------------------------------- */
+
+#include "npair_halffull_newton_ssa.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+// allocate space for static class variable
+// prototype for non-class function
+
+static int *ssaAIRptr;
+static int cmp_ssaAIR(const void *, const void *);
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalffullNewtonSSA::NPairHalffullNewtonSSA(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ build half list from full list for use by Shardlow Spliting Algorithm
+ pair stored once if i,j are both owned and i < j
+ if j is ghost, only store if j coords are "above and to the right" of i
+ works if full list is a skip list
+------------------------------------------------------------------------- */
+
+void NPairHalffullNewtonSSA::build(NeighList *list)
+{
+ int i,j,ii,jj,n,jnum,joriginal;
+ int *neighptr,*jlist;
+
+ int nlocal = atom->nlocal;
+ int *ssaAIR = atom->ssaAIR;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int *ilist_full = list->listfull->ilist;
+ int *numneigh_full = list->listfull->numneigh;
+ int **firstneigh_full = list->listfull->firstneigh;
+ int inum_full = list->listfull->inum;
+
+ int inum = 0;
+ ipage->reset();
+
+ // loop over parent full list
+
+ for (ii = 0; ii < inum_full; ii++) {
+ int AIRct[8] = { 0 };
+ n = 0;
+ neighptr = ipage->vget();
+
+ i = ilist_full[ii];
+
+ // loop over full neighbor list
+
+ jlist = firstneigh_full[i];
+ jnum = numneigh_full[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (j < nlocal) {
+ if (i > j) continue;
+ ++(AIRct[0]);
+ } else {
+ if (ssaAIR[j] < 2) continue; // skip ghost atoms not in AIR
+ ++(AIRct[ssaAIR[j] - 1]);
+ }
+ neighptr[n++] = joriginal;
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ // sort the locals+ghosts in the neighbor list by their ssaAIR number
+
+ ssaAIRptr = atom->ssaAIR;
+ qsort(&(neighptr[0]), n, sizeof(int), cmp_ssaAIR);
+
+ // do a prefix sum on the counts to turn them into indexes
+
+ list->ndxAIR_ssa[i][0] = AIRct[0];
+ for (int ndx = 1; ndx < 8; ++ndx) {
+ list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
+ }
+ }
+
+ list->inum = inum;
+}
+
+/* ----------------------------------------------------------------------
+ comparison function invoked by qsort()
+ accesses static class member ssaAIRptr, set before call to qsort()
+------------------------------------------------------------------------- */
+
+static int cmp_ssaAIR(const void *iptr, const void *jptr)
+{
+ int i = *((int *) iptr);
+ int j = *((int *) jptr);
+ if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
+ if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
+ return 0;
+}
+
diff --git a/src/USER-DPD/npair_halffull_newton_ssa.h b/src/USER-DPD/npair_halffull_newton_ssa.h
new file mode 100644
index 0000000000..4935349f77
--- /dev/null
+++ b/src/USER-DPD/npair_halffull_newton_ssa.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(halffull/newton/ssa,
+ NPairHalffullNewtonSSA,
+ NP_HALFFULL | NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON |
+ NP_ORTHO | NP_TRI | NP_SSA)
+
+#else
+
+#ifndef LMP_NPAIR_HALFFULL_NEWTON_SSA_H
+#define LMP_NPAIR_HALFFULL_NEWTON_SSA_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalffullNewtonSSA : public NPair {
+ public:
+ NPairHalffullNewtonSSA(class LAMMPS *);
+ ~NPairHalffullNewtonSSA() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp
new file mode 100644
index 0000000000..8c53abfe80
--- /dev/null
+++ b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp
@@ -0,0 +1,64 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors:
+ James Larentzos and Timothy I. Mattox (Engility Corporation)
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_bin_2d_newton_ssa.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) :
+ NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+ stencil = bins whose closest corner to central bin is within cutoff
+ sx,sy,sz = bin bounds = furthest the stencil could possibly extend
+ 3d creates xyz stencil, 2d creates xy stencil
+ for half list with newton on:
+ stencil is bins to the "upper right" of central bin
+ stencil does not include self
+ additionally, includes the bins beyond nstencil that are needed
+ to locate all the Active Interaction Region (AIR) ghosts for SSA
+------------------------------------------------------------------------- */
+
+void NStencilHalfBin2dNewtonSSA::create()
+{
+ int i,j,pos = 0;
+
+ for (j = 0; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (j > 0 || (j == 0 && i > 0))
+ if (bin_distance(i,j,0) < cutneighmaxsq)
+ stencil[pos++] = j*mbinx + i;
+
+ nstencil = pos; // record where normal half stencil ends
+
+ // include additional bins for AIR ghosts only
+
+ for (j = -sy; j <= 0; j++)
+ for (i = -sx; i <= sx; i++) {
+ if (j == 0 && i > 0) continue;
+ if (bin_distance(i,j,0) < cutneighmaxsq)
+ stencil[pos++] = j*mbinx + i;
+ }
+
+ nstencil_ssa = pos; // record where full stencil ends
+}
diff --git a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h
new file mode 100644
index 0000000000..319a8ce670
--- /dev/null
+++ b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/bin/2d/newton/ssa,
+ NStencilHalfBin2dNewtonSSA,
+ NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_SSA | NS_ORTHO)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H
+#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfBin2dNewtonSSA : public NStencil {
+ public:
+ NStencilHalfBin2dNewtonSSA(class LAMMPS *);
+ ~NStencilHalfBin2dNewtonSSA() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp
new file mode 100644
index 0000000000..1ac15fe61e
--- /dev/null
+++ b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp
@@ -0,0 +1,74 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors:
+ James Larentzos and Timothy I. Mattox (Engility Corporation)
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_bin_3d_newton_ssa.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) :
+ NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+ stencil = bins whose closest corner to central bin is within cutoff
+ sx,sy,sz = bin bounds = furthest the stencil could possibly extend
+ 3d creates xyz stencil, 2d creates xy stencil
+ for half list with newton on:
+ stencil is bins to the "upper right" of central bin
+ stencil does not include self
+ additionally, includes the bins beyond nstencil that are needed
+ to locate all the Active Interaction Region (AIR) ghosts for SSA
+------------------------------------------------------------------------- */
+
+void NStencilHalfBin3dNewtonSSA::create()
+{
+ int i,j,k,pos = 0;
+
+ for (k = 0; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (k > 0 || j > 0 || (j == 0 && i > 0))
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;
+
+ nstencil = pos; // record where normal half stencil ends
+
+ // include additional bins for AIR ghosts only
+
+ for (k = -sz; k < 0; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;
+
+ // For k==0, make sure to skip already included bins
+
+ k = 0;
+ for (j = -sy; j <= 0; j++)
+ for (i = -sx; i <= sx; i++) {
+ if (j == 0 && i > 0) continue;
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+
+ nstencil_ssa = pos; // record where full stencil ends
+}
diff --git a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h
new file mode 100644
index 0000000000..8cb130a712
--- /dev/null
+++ b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/bin/3d/newton/ssa,
+ NStencilHalfBin3dNewtonSSA,
+ NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_SSA | NS_ORTHO)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H
+#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfBin3dNewtonSSA : public NStencil {
+ public:
+ NStencilHalfBin3dNewtonSSA(class LAMMPS *);
+ ~NStencilHalfBin3dNewtonSSA() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-INTEL/Install.sh b/src/USER-INTEL/Install.sh
index 79cc1158e9..736059aa06 100644
--- a/src/USER-INTEL/Install.sh
+++ b/src/USER-INTEL/Install.sh
@@ -3,10 +3,6 @@
mode=$1
-# enforce using portable C locale
-LC_ALL=C
-export LC_ALL
-
# arg1 = file, arg2 = file it depends on
action () {
@@ -44,6 +40,10 @@ action intel_preprocess.h
action intel_buffers.h
action intel_buffers.cpp
action math_extra_intel.h
+action nbin_intel.h
+action nbin_intel.cpp
+action npair_intel.h
+action npair_intel.cpp
action intel_simd.h pair_sw_intel.cpp
action intel_intrinsics.h pair_tersoff_intel.cpp
action verlet_lrt_intel.h pppm.cpp
@@ -58,18 +58,10 @@ if (test $mode = 1) then
sed -i -e 's|^PKG_INC =[ \t]*|&-DLMP_USER_INTEL |' ../Makefile.package
fi
- # force rebuild of files with LMP_USER_INTEL switch
-
- touch ../accelerator_intel.h
-
elif (test $mode = 0) then
if (test -e ../Makefile.package) then
sed -i -e 's/[^ \t]*INTEL[^ \t]* //' ../Makefile.package
fi
- # force rebuild of files with LMP_USER_INTEL switch
-
- touch ../accelerator_intel.h
-
fi
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 226396681f..06bd23abcc 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -317,8 +317,6 @@ void FixIntel::init()
error->all(FLERR,
"Currently, cannot use more than one intel style with hybrid.");
- neighbor->fix_intel = (void *)this;
-
check_neighbor_intel();
if (_precision_mode == PREC_MODE_SINGLE)
_single_buffers->zero_ev();
diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp
index 4980cdcac8..c81dffec83 100644
--- a/src/USER-INTEL/intel_buffers.cpp
+++ b/src/USER-INTEL/intel_buffers.cpp
@@ -26,18 +26,17 @@ IntelBuffers<flt_t, acc_t>::IntelBuffers(class LAMMPS *lmp_in) :
_buf_size(0), _buf_local_size(0) {
_list_alloc_atoms = 0;
_ntypes = 0;
- _off_map_maxlocal = 0;
+ _off_map_listlocal = 0;
_ccachex = 0;
- _host_nmax = 0;
#ifdef _LMP_INTEL_OFFLOAD
_separate_buffers = 0;
_off_f = 0;
_off_map_ilist = 0;
_off_map_nmax = 0;
- _off_map_maxhead = 0;
_off_list_alloc = false;
_off_threads = 0;
_off_ccache = 0;
+ _host_nmax = 0;
#endif
}
@@ -173,21 +172,15 @@ void IntelBuffers<flt_t, acc_t>::free_nmax()
const int * tag = _off_map_tag;
const int * special = _off_map_special;
const int * nspecial = _off_map_nspecial;
- const int * bins = _off_map_bins;
- const int * binpacked = _binpacked;
- if (tag != 0 && special != 0 && nspecial !=0 && bins != 0) {
+ if (tag != 0 && special != 0 && nspecial !=0) {
#pragma offload_transfer target(mic:_cop) \
nocopy(tag:alloc_if(0) free_if(1)) \
- nocopy(special,nspecial:alloc_if(0) free_if(1)) \
- nocopy(bins,binpacked:alloc_if(0) free_if(1))
+ nocopy(special,nspecial:alloc_if(0) free_if(1))
}
_off_map_nmax = 0;
- }
- #endif
- if (_host_nmax > 0) {
- lmp->memory->destroy(_binpacked);
_host_nmax = 0;
}
+ #endif
}
/* ---------------------------------------------------------------------- */
@@ -195,12 +188,11 @@ void IntelBuffers<flt_t, acc_t>::free_nmax()
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::_grow_nmax(const int offload_end)
{
+ #ifdef _LMP_INTEL_OFFLOAD
free_nmax();
int size = lmp->atom->nmax;
_host_nmax = size;
- lmp->memory->create(_binpacked, _host_nmax, "_binpacked");
- #ifdef _LMP_INTEL_OFFLOAD
if (!offload_end) return;
int *special, *nspecial;
int tag_length, special_length, nspecial_length;
@@ -220,10 +212,7 @@ void IntelBuffers<flt_t, acc_t>::_grow_nmax(const int offload_end)
else
tag_length = 1;
int *tag = lmp->atom->tag;
- int *bins = lmp->neighbor->bins;
- int * binpacked = _binpacked;
#pragma offload_transfer target(mic:_cop) \
- nocopy(bins,binpacked:length(size) alloc_if(1) free_if(0)) \
nocopy(tag:length(tag_length) alloc_if(1) free_if(0)) \
nocopy(special:length(special_length) alloc_if(1) free_if(0)) \
nocopy(nspecial:length(nspecial_length) alloc_if(1) free_if(0))
@@ -231,18 +220,16 @@ void IntelBuffers<flt_t, acc_t>::_grow_nmax(const int offload_end)
_off_map_special = special;
_off_map_nspecial = nspecial;
_off_map_nmax = size;
- _off_map_bins = bins;
#endif
}
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::free_local()
+void IntelBuffers<flt_t, acc_t>::free_list_local()
{
- if (_off_map_maxlocal > 0) {
+ if (_off_map_listlocal > 0) {
int * cnumneigh = _cnumneigh;
- int * atombin = _atombin;
#ifdef _LMP_INTEL_OFFLOAD
if (_off_map_ilist != NULL) {
const int * ilist = _off_map_ilist;
@@ -250,40 +237,36 @@ void IntelBuffers<flt_t, acc_t>::free_local()
_off_map_ilist = NULL;
if (numneigh != 0 && ilist != 0) {
#pragma offload_transfer target(mic:_cop) \
- nocopy(ilist,numneigh,cnumneigh,atombin:alloc_if(0) free_if(1))
+ nocopy(ilist,numneigh,cnumneigh:alloc_if(0) free_if(1))
}
}
#endif
lmp->memory->destroy(cnumneigh);
- lmp->memory->destroy(atombin);
- _off_map_maxlocal = 0;
+ _off_map_listlocal = 0;
}
}
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::_grow_local(NeighList *list,
- const int offload_end)
+void IntelBuffers<flt_t, acc_t>::_grow_list_local(NeighList *list,
+ const int offload_end)
{
- free_local();
+ free_list_local();
int size = list->get_maxlocal();
lmp->memory->create(_cnumneigh, size, "_cnumneigh");
- lmp->memory->create(_atombin, size, "_atombin");
- _off_map_maxlocal = size;
+ _off_map_listlocal = size;
#ifdef _LMP_INTEL_OFFLOAD
if (offload_end > 0) {
int * numneigh = list->numneigh;
int * ilist = list->ilist;
int * cnumneigh = _cnumneigh;
- int * atombin = _atombin;
- if (cnumneigh != 0 && atombin != 0) {
+ if (cnumneigh != 0) {
#pragma offload_transfer target(mic:_cop) \
nocopy(ilist:length(size) alloc_if(1) free_if(0)) \
nocopy(numneigh:length(size) alloc_if(1) free_if(0)) \
- nocopy(cnumneigh:length(size) alloc_if(1) free_if(0)) \
- nocopy(atombin:length(size) alloc_if(1) free_if(0))
+ nocopy(cnumneigh:length(size) alloc_if(1) free_if(0))
}
_off_map_ilist = ilist;
_off_map_numneigh = numneigh;
@@ -293,39 +276,6 @@ void IntelBuffers<flt_t, acc_t>::_grow_local(NeighList *list,
/* ---------------------------------------------------------------------- */
-template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::free_binhead()
-{
- #ifdef _LMP_INTEL_OFFLOAD
- if (_off_map_maxhead > 0) {
- const int * binhead = _off_map_binhead;
- if (binhead !=0) {
- #pragma offload_transfer target(mic:_cop) \
- nocopy(binhead:alloc_if(0) free_if(1))
- }
- _off_map_maxhead = 0;
- }
- #endif
-}
-
-/* ---------------------------------------------------------------------- */
-
-template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::_grow_binhead()
-{
- #ifdef _LMP_INTEL_OFFLOAD
- free_binhead();
- int * binhead = lmp->neighbor->binhead;
- const int maxhead = lmp->neighbor->maxhead;
- #pragma offload_transfer target(mic:_cop) \
- nocopy(binhead:length(maxhead+1) alloc_if(1) free_if(0))
- _off_map_binhead = binhead;
- _off_map_maxhead = maxhead;
- #endif
-}
-
-/* ---------------------------------------------------------------------- */
-
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::free_nbor_list()
{
@@ -333,11 +283,8 @@ void IntelBuffers<flt_t, acc_t>::free_nbor_list()
#ifdef _LMP_INTEL_OFFLOAD
if (_off_list_alloc) {
int * list_alloc = _list_alloc;
- int * stencil = _off_map_stencil;
- if (list_alloc != 0 && stencil != 0) {
- #pragma offload_transfer target(mic:_cop) \
- nocopy(list_alloc:alloc_if(0) free_if(1))
- }
+ #pragma offload_transfer target(mic:_cop) \
+ nocopy(list_alloc:alloc_if(0) free_if(1))
_off_list_alloc = false;
}
#endif
@@ -364,33 +311,16 @@ void IntelBuffers<flt_t, acc_t>::_grow_nbor_list(NeighList *list,
#ifdef _LMP_INTEL_OFFLOAD
if (offload_end > 0) {
int * list_alloc =_list_alloc;
- int * stencil = list->stencil;
if (list_alloc != NULL) {
#pragma offload_transfer target(mic:_cop) \
- in(stencil:length(list->maxstencil) alloc_if(1) free_if(0)) \
nocopy(list_alloc:length(list_alloc_size) alloc_if(1) free_if(0))
- _off_map_stencil = stencil;
_off_list_alloc = true;
}
}
#endif
}
-template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::_grow_stencil(NeighList *list)
-{
- #ifdef _LMP_INTEL_OFFLOAD
- int * stencil = _off_map_stencil;
- #pragma offload_transfer target(mic:_cop) \
- nocopy(stencil:alloc_if(0) free_if(1))
- stencil = list->stencil;
- #pragma offload_transfer target(mic:_cop) \
- in(stencil:length(list->maxstencil) alloc_if(1) free_if(0))
- _off_map_stencil = stencil;
- #endif
-}
-
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
@@ -544,7 +474,6 @@ double IntelBuffers<flt_t, acc_t>::memory_usage(const int nthreads)
if (_off_f) tmem += fstride*_off_threads * sizeof(vec3_acc_t);
#endif
- tmem += _off_map_maxlocal * sizeof(int) * 2;
tmem += (_list_alloc_atoms + _off_threads) * get_max_nbors() * sizeof(int);
tmem += _ntypes * _ntypes * sizeof(int);
diff --git a/src/USER-INTEL/intel_buffers.h b/src/USER-INTEL/intel_buffers.h
index df72234dbe..3462d013a1 100644
--- a/src/USER-INTEL/intel_buffers.h
+++ b/src/USER-INTEL/intel_buffers.h
@@ -61,50 +61,35 @@ class IntelBuffers {
}
void free_buffers();
-
+ void free_nmax();
+ inline void set_bininfo(int *atombin, int *binpacked)
+ { _atombin = atombin; _binpacked = binpacked; }
inline void grow(const int nall, const int nlocal, const int nthreads,
const int offload_end) {
if (nall >= _buf_size || nlocal >= _buf_local_size)
_grow(nall, nlocal, nthreads, offload_end);
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (lmp->atom->nmax > _host_nmax)
+ _grow_nmax(offload_end);
+ #endif
}
inline void free_all_nbor_buffers() {
free_nbor_list();
free_nmax();
- free_binhead();
- free_local();
+ free_list_local();
}
- inline void grow_nbor(NeighList *list, const int nlocal, const int nthreads,
+ inline void grow_list(NeighList *list, const int nlocal, const int nthreads,
const int offload_end, const int pack_width=1) {
- grow_local(list, offload_end);
- grow_nmax(offload_end);
- if (offload_end)
- grow_binhead();
+ grow_list_local(list, offload_end);
grow_nbor_list(list, nlocal, nthreads, offload_end, pack_width);
}
- void free_nmax();
-
- inline void grow_nmax(const int offload_end) {
- if (lmp->atom->nmax > _host_nmax)
- _grow_nmax(offload_end);
- }
-
- void free_local();
-
- inline void grow_local(NeighList *list, const int offload_end) {
- if (list->get_maxlocal() > _off_map_maxlocal)
- _grow_local(list, offload_end);
- }
-
- void free_binhead();
-
- inline void grow_binhead() {
- #ifdef _LMP_INTEL_OFFLOAD
- if (lmp->neighbor->maxhead > _off_map_maxhead)
- _grow_binhead();
- #endif
+ void free_list_local();
+ inline void grow_list_local(NeighList *list, const int offload_end) {
+ if (list->get_maxlocal() > _off_map_listlocal)
+ _grow_list_local(list, offload_end);
}
void free_ccache();
@@ -134,19 +119,15 @@ class IntelBuffers {
const int pack_width) {
if (nlocal > _list_alloc_atoms)
_grow_nbor_list(list, nlocal, nthreads, offload_end, pack_width);
- #ifdef _LMP_INTEL_OFFLOAD
- else if (offload_end > 0 && _off_map_stencil != list->stencil)
- _grow_stencil(list);
- #endif
}
void set_ntypes(const int ntypes);
inline int * firstneigh(const NeighList *list) { return _list_alloc; }
inline int * cnumneigh(const NeighList *list) { return _cnumneigh; }
-
inline int * get_atombin() { return _atombin; }
inline int * get_binpacked() { return _binpacked; }
+
inline atom_t * get_x(const int offload = 1) {
#ifdef _LMP_INTEL_OFFLOAD
if (_separate_buffers && offload == 0) return _host_x;
@@ -271,13 +252,10 @@ class IntelBuffers {
flt_t *_q;
quat_t *_quat;
vec3_acc_t * _f;
- int _off_threads, _off_map_maxlocal;
+ int _off_threads, _off_map_listlocal;
int _list_alloc_atoms;
- int * _list_alloc;
- int * _cnumneigh;
- int * _atombin;
- int * _binpacked;
+ int *_list_alloc, *_cnumneigh, *_atombin, *_binpacked;
flt_t **_cutneighsq;
int _ntypes;
@@ -296,26 +274,24 @@ class IntelBuffers {
flt_t *_host_q;
quat_t *_host_quat;
vec3_acc_t *_off_f;
- int _off_map_nmax, _off_map_maxhead, _cop, _off_ccache;
+ int _off_map_nmax, _cop, _off_ccache;
int *_off_map_ilist;
- int *_off_map_stencil, *_off_map_special, *_off_map_nspecial, *_off_map_tag;
- int *_off_map_binhead, *_off_map_bins, *_off_map_numneigh;
+ int *_off_map_special, *_off_map_nspecial, *_off_map_tag;
+ int *_off_map_numneigh;
bool _off_list_alloc;
- int _need_tag;
+ int _need_tag, _host_nmax;
#endif
- int _buf_size, _buf_local_size, _host_nmax;
+ int _buf_size, _buf_local_size;
_alignvar(acc_t _ev_global[8],64);
_alignvar(acc_t _ev_global_host[8],64);
void _grow(const int nall, const int nlocal, const int nthreads,
const int offload_end);
void _grow_nmax(const int offload_end);
- void _grow_local(NeighList *list, const int offload_end);
- void _grow_binhead();
+ void _grow_list_local(NeighList *list, const int offload_end);
void _grow_nbor_list(NeighList *list, const int nlocal, const int nthreads,
const int offload_end, const int pack_width);
- void _grow_stencil(NeighList *list);
};
}
diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp
new file mode 100644
index 0000000000..8dceafd3ab
--- /dev/null
+++ b/src/USER-INTEL/nbin_intel.cpp
@@ -0,0 +1,253 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: W. Michael Brown (Intel)
+------------------------------------------------------------------------- */
+
+#include "nbin_intel.h"
+#include "atom.h"
+#include "group.h"
+#include "domain.h"
+#include "comm.h"
+#include "update.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NBinIntel::NBinIntel(LAMMPS *lmp) : NBinStandard(lmp) {
+ int ifix = modify->find_fix("package_intel");
+ if (ifix < 0)
+ error->all(FLERR,
+ "The 'package intel' command is required for /intel styles");
+ _fix = static_cast<FixIntel *>(modify->fix[ifix]);
+ _precision_mode = _fix->precision();
+ _atombin = NULL;
+ _binpacked = NULL;
+ #ifdef _LMP_INTEL_OFFLOAD
+ _cop = _fix->coprocessor_number();
+ _offload_alloc = 0;
+ #endif
+}
+
+/* ---------------------------------------------------------------------- */
+
+NBinIntel::~NBinIntel() {
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (_offload_alloc) {
+ const int * binhead = this->binhead;
+ const int * bins = this->bins;
+ const int * _atombin = this->_atombin;
+ const int * _binpacked = this->_binpacked;
+ #pragma offload_transfer target(mic:_cop) \
+ nocopy(binhead,bins,_atombin,_binpacked:alloc_if(0) free_if(1))
+ }
+ #endif
+}
+
+/* ----------------------------------------------------------------------
+ setup for bin_atoms()
+------------------------------------------------------------------------- */
+
+void NBinIntel::bin_atoms_setup(int nall)
+{
+ // binhead = per-bin vector, mbins in length
+ // add 1 bin for USER-INTEL package
+
+ if (mbins > maxbin) {
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (_offload_alloc) {
+ const int * binhead = this->binhead;
+ #pragma offload_transfer target(mic:_cop) \
+ nocopy(binhead:alloc_if(0) free_if(1))
+ }
+ #endif
+
+ maxbin = mbins;
+ memory->destroy(binhead);
+ memory->create(binhead,maxbin+1,"neigh:binhead");
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (_fix->offload_balance() != 0) {
+ int * binhead = this->binhead;
+ #pragma offload_transfer target(mic:_cop) \
+ nocopy(binhead:length(maxbin+1) alloc_if(1) free_if(0))
+ }
+ #endif
+ last_bin_memory = update->ntimestep;
+ }
+
+ // bins = per-atom vector
+
+ if (nall > maxatom) {
+ maxatom = nall;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (_offload_alloc) {
+ const int * bins = this->bins;
+ const int * _atombin = this->_atombin;
+ const int * _binpacked = this->_binpacked;
+ #pragma offload_transfer target(mic:_cop) \
+ nocopy(bins,_atombin,_binpacked:alloc_if(0) free_if(1))
+ }
+ #endif
+ memory->destroy(bins);
+ memory->destroy(_atombin);
+ memory->destroy(_binpacked);
+
+ memory->create(bins,maxatom,"neigh:bins");
+ memory->create(_atombin,maxatom,"neigh:bins");
+ memory->create(_binpacked,maxatom,"neigh:bins");
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (_fix->offload_balance() != 0) {
+ const int * bins = this->bins;
+ const int * _atombin = this->_atombin;
+ const int * _binpacked = this->_binpacked;
+ #pragma offload_transfer target(mic:_cop) \
+ nocopy(bins,_atombin,_binpacked:length(maxatom) alloc_if(1) free_if(0))
+ _offload_alloc=1;
+ }
+ #endif
+
+ if (_precision_mode == FixIntel::PREC_MODE_MIXED)
+ _fix->get_mixed_buffers()->set_bininfo(_atombin,_binpacked);
+ else if (_precision_mode == FixIntel::PREC_MODE_SINGLE)
+ _fix->get_single_buffers()->set_bininfo(_atombin,_binpacked);
+ else
+ _fix->get_double_buffers()->set_bininfo(_atombin,_binpacked);
+
+ last_bin_memory = update->ntimestep;
+ }
+
+ last_bin = update->ntimestep;
+}
+
+/* ----------------------------------------------------------------------
+ bin owned and ghost atoms
+------------------------------------------------------------------------- */
+
+void NBinIntel::bin_atoms()
+{
+ if (_precision_mode == FixIntel::PREC_MODE_MIXED)
+ bin_atoms(_fix->get_mixed_buffers());
+ else if (_precision_mode == FixIntel::PREC_MODE_SINGLE)
+ bin_atoms(_fix->get_single_buffers());
+ else
+ bin_atoms(_fix->get_double_buffers());
+}
+
+template <class flt_t, class acc_t>
+void NBinIntel::bin_atoms(IntelBuffers<flt_t,acc_t> * buffers) {
+ const int nlocal = atom->nlocal;
+ const int nall = nlocal + atom->nghost;
+ const int aend = _fix->offload_end_neighbor();
+
+
+ // ---------- Sanity check for padding --------------
+ {
+ const flt_t dx = (INTEL_BIGP - bboxhi[0]);
+ const flt_t dy = (INTEL_BIGP - bboxhi[1]);
+ const flt_t dz = (INTEL_BIGP - bboxhi[2]);
+ if (dx * dx + dy * dy + dz * dz <
+ static_cast<flt_t>(neighbor->cutneighmaxsq))
+ error->one(FLERR,
+ "Intel package expects no atoms within cutoff of {1e15,1e15,1e15}.");
+ }
+
+ // ---------- Grow and cast/pack buffers -------------
+ _fix->start_watch(TIME_PACK);
+ buffers->grow(nall, atom->nlocal, comm->nthreads, aend);
+
+ ATOM_T biga;
+ biga.x = INTEL_BIGP;
+ biga.y = INTEL_BIGP;
+ biga.z = INTEL_BIGP;
+ biga.w = 1;
+ buffers->get_x()[nall] = biga;
+
+ const int nthreads = comm->nthreads;
+ #if defined(_OPENMP)
+ #pragma omp parallel default(none) shared(buffers)
+ #endif
+ {
+ int ifrom, ito, tid;
+ IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
+ sizeof(ATOM_T));
+ buffers->thr_pack(ifrom, ito, 0);
+ }
+ _fix->stop_watch(TIME_PACK);
+
+
+ // ---------- Bin Atoms -------------
+ _fix->start_watch(TIME_HOST_NEIGHBOR);
+ const ATOM_T * _noalias const x = buffers->get_x();
+ int * _noalias const atombin = this->_atombin;
+ int * _noalias const binpacked = this->_binpacked;
+
+
+ const double sboxlo0 = bboxlo[0] + mbinxlo/bininvx;
+ const double sboxlo1 = bboxlo[1] + mbinylo/bininvy;
+ const double sboxlo2 = bboxlo[2] + mbinzlo/bininvz;
+
+ int i, ibin;
+
+ for (i = 0; i < mbins; i++) binhead[i] = -1;
+
+ int *mask = atom->mask;
+
+ if (includegroup) {
+ int bitmask = group->bitmask[includegroup];
+ for (i = nall-1; i >= nlocal; i--) {
+ if (mask[i] & bitmask) {
+ ibin = coord2bin(atom->x[i]);
+ bins[i] = binhead[ibin];
+ binhead[ibin] = i;
+ }
+ }
+ for (i = atom->nfirst-1; i >= 0; i--) {
+ ibin = coord2bin(atom->x[i]);
+ atombin[i] = ibin;
+ bins[i] = binhead[ibin];
+ binhead[ibin] = i;
+ }
+ } else {
+ for (i = nall-1; i >= nlocal; i--) {
+ ibin = coord2bin(atom->x[i]);
+ bins[i] = binhead[ibin];
+ binhead[ibin] = i;
+ }
+ for (i = nlocal-1; i >= 0; i--) {
+ ibin = coord2bin(atom->x[i]);
+ atombin[i]=ibin;
+ bins[i] = binhead[ibin];
+ binhead[ibin] = i;
+ }
+ }
+ int newhead = 0;
+ for (i = 0; i < mbins; i++) {
+ int j = binhead[i];
+ binhead[i] = newhead;
+ for ( ; j >= 0; j = bins[j])
+ binpacked[newhead++] = j;
+ }
+ binhead[mbins] = newhead;
+}
+
+/* ---------------------------------------------------------------------- */
+
+bigint NBinIntel::memory_usage()
+{
+ return NBinStandard::memory_usage() + maxatom*2*sizeof(int);
+}
diff --git a/src/USER-INTEL/nbin_intel.h b/src/USER-INTEL/nbin_intel.h
new file mode 100644
index 0000000000..d96f31885e
--- /dev/null
+++ b/src/USER-INTEL/nbin_intel.h
@@ -0,0 +1,69 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NBIN_CLASS
+
+NBinStyle(intel,
+ NBinIntel,
+ NB_INTEL)
+
+#else
+
+#ifndef LMP_NBIN_INTEL_H
+#define LMP_NBIN_INTEL_H
+
+#include "nbin_standard.h"
+#include "fix_intel.h"
+#include "memory.h"
+
+namespace LAMMPS_NS {
+
+class NBinIntel : public NBinStandard {
+ public:
+ NBinIntel(class LAMMPS *);
+ ~NBinIntel();
+ void bin_atoms_setup(int);
+ void bin_atoms();
+ int * get_binpacked() { return _binpacked; }
+
+ private:
+ FixIntel *_fix;
+ int *_atombin, *_binpacked;
+ int _precision_mode;
+ bigint memory_usage();
+
+ template <class flt_t, class acc_t>
+ void bin_atoms(IntelBuffers<flt_t,acc_t> *);
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ int _cop, _offload_alloc;
+ #endif
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: The 'package intel' command is required for /intel styles
+
+Self-explanatory.
+
+E: Intel package expects no atoms within cutoff of {1e15,1e15,1e15}.
+
+The Intel package can make use of dummy atoms for padding with a large position
+that should not be within the cutoff.
+
+*/
diff --git a/src/USER-INTEL/neigh_half_bin_intel.cpp b/src/USER-INTEL/neigh_half_bin_intel.cpp
deleted file mode 100644
index c8d4657818..0000000000
--- a/src/USER-INTEL/neigh_half_bin_intel.cpp
+++ /dev/null
@@ -1,2455 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing author: W. Michael Brown (Intel)
-------------------------------------------------------------------------- */
-
-//#define OUTER_CHUNK 1
-
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "comm.h"
-#include "group.h"
-#include "fix_intel.h"
-
-#if defined(_OPENMP)
-#include <omp.h>
-#endif
-
-#ifdef LMP_USE_AVXCD
-#include "intel_simd.h"
-#endif
-
-#ifdef OUTER_CHUNK
-#include "intel_simd.h"
-#endif
-
-using namespace LAMMPS_NS;
-
-#ifdef _LMP_INTEL_OFFLOAD
-#pragma offload_attribute(push,target(mic))
-#endif
-
-#define ofind_special(which, special, nspecial, i, tag) \
-{ \
- which = 0; \
- const int n1 = nspecial[i * 3]; \
- const int n2 = nspecial[i * 3 + 1]; \
- const int n3 = nspecial[i * 3 + 2]; \
- const tagint *sptr = special + i * maxspecial; \
- for (int s = 0; s < n3; s++) { \
- if (sptr[s] == tag) { \
- if (s < n1) { \
- which = 1; \
- } else if (s < n2) { \
- which = 2; \
- } else { \
- which = 3; \
- } \
- } \
- } \
-}
-
-#define ominimum_image_check(answer, dx, dy, dz) \
-{ \
- answer = 0; \
- if (xperiodic && fabs(dx) > xprd_half) answer = 1; \
- if (yperiodic && fabs(dy) > yprd_half) answer = 1; \
- if (zperiodic && fabs(dz) > zprd_half) answer = 1; \
-}
-
-#define dminimum_image_check(answer, dx, dy, dz) \
-{ \
- answer = 0; \
- if (domain->xperiodic && fabs(dx) > domain->xprd_half) answer = 1; \
- if (domain->yperiodic && fabs(dy) > domain->yprd_half) answer = 1; \
- if (domain->zperiodic && fabs(dz) > domain->zprd_half) answer = 1; \
-}
-
-#ifdef _LMP_INTEL_OFFLOAD
-#pragma offload_attribute(pop)
-#endif
-
-template <class flt_t, class acc_t>
-void Neighbor::bin_atoms(void * xin, int * _noalias const atombin,
- int * _noalias const binpacked) {
- const ATOM_T * _noalias const x = (const ATOM_T * _noalias const)xin;
- int nlocal = atom->nlocal;
- const int nall = nlocal + atom->nghost;
-
- const double sboxlo0 = bboxlo[0] + mbinxlo/bininvx;
- const double sboxlo1 = bboxlo[1] + mbinylo/bininvy;
- const double sboxlo2 = bboxlo[2] + mbinzlo/bininvz;
-
- int i, ibin;
-
- for (i = 0; i < mbins; i++) binhead[i] = -1;
-
- int *mask = atom->mask;
-
- if (includegroup) {
- int bitmask = group->bitmask[includegroup];
- for (i = nall-1; i >= nlocal; i--) {
- if (mask[i] & bitmask) {
- ibin = coord2bin(atom->x[i]);
- bins[i] = binhead[ibin];
- binhead[ibin] = i;
- }
- }
- for (i = atom->nfirst-1; i >= 0; i--) {
- ibin = coord2bin(atom->x[i]);
- atombin[i] = ibin;
- bins[i] = binhead[ibin];
- binhead[ibin] = i;
- }
- } else {
- for (i = nall-1; i >= nlocal; i--) {
- ibin = coord2bin(atom->x[i]);
- bins[i] = binhead[ibin];
- binhead[ibin] = i;
- }
- for (i = nlocal-1; i >= 0; i--) {
- ibin = coord2bin(atom->x[i]);
- atombin[i]=ibin;
- bins[i] = binhead[ibin];
- binhead[ibin] = i;
- }
- }
- int newhead = 0;
- for (i = 0; i < mbins; i++) {
- int j = binhead[i];
- binhead[i] = newhead;
- for ( ; j >= 0; j = bins[j])
- binpacked[newhead++] = j;
- }
- binhead[mbins] = newhead;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with partial Newton's 3rd law
- each owned atom i checks own bin and other bins in stencil
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_no_newton_intel(NeighList *list)
-{
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- list->inum = nlocal;
-
- // Get fix for intel stuff
- FixIntel *fix = static_cast<FixIntel *>(fix_intel);
-
- const int off_end = fix->offload_end_neighbor();
- int host_start = off_end;;
- #ifdef _LMP_INTEL_OFFLOAD
- if (fix->full_host_list()) host_start = 0;
- if (exclude)
- error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
- #endif
- if (list->nstencil > INTEL_MAX_STENCIL_CHECK)
- error->all(FLERR, "Too many neighbor bins for USER-INTEL package.");
-
- int need_ic = 0;
- if (atom->molecular)
- dminimum_image_check(need_ic, cutneighmax, cutneighmax, cutneighmax);
-
- if (need_ic) {
- if (fix->precision() == FixIntel::PREC_MODE_MIXED) {
- hbnni<float,double,1>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- hbnni<float,double,1>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal,fix);
- } else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
- hbnni<double,double,1>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- hbnni<double,double,1>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix);
- } else {
- hbnni<float,float,1>(1, list, fix->get_single_buffers(),
- 0, off_end, fix);
- hbnni<float,float,1>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix);
- }
- } else {
- if (fix->precision() == FixIntel::PREC_MODE_MIXED) {
- hbnni<float,double,0>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- hbnni<float,double,0>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal,fix);
- } else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
- hbnni<double,double,0>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- hbnni<double,double,0>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix);
- } else {
- hbnni<float,float,0>(1, list, fix->get_single_buffers(),
- 0, off_end, fix);
- hbnni<float,float,0>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix);
- }
- }
-}
-
-template <class flt_t, class acc_t, int need_ic>
-void Neighbor::hbnni(const int offload, NeighList *list, void *buffers_in,
- const int astart, const int aend, void *fix_in) {
- IntelBuffers<flt_t,acc_t> *buffers = (IntelBuffers<flt_t,acc_t> *)buffers_in;
- FixIntel *fix = (FixIntel *)fix_in;
- const int nall = atom->nlocal + atom->nghost;
- int pad = 1;
-
- if (offload) {
- fix->start_watch(TIME_PACK);
- buffers->grow(nall, atom->nlocal, comm->nthreads, aend);
- buffers->grow_nbor(list, atom->nlocal, comm->nthreads, aend);
-
- ATOM_T biga;
- biga.x = INTEL_BIGP;
- biga.y = INTEL_BIGP;
- biga.z = INTEL_BIGP;
- biga.w = 1;
- buffers->get_x()[nall] = biga;
-
- const int nthreads = comm->nthreads;
- #if defined(_OPENMP)
- #pragma omp parallel default(none) shared(buffers)
- #endif
- {
- int ifrom, ito, tid;
- IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
- sizeof(ATOM_T));
- buffers->thr_pack(ifrom, ito, 0);
- }
- fix->stop_watch(TIME_PACK);
-
- fix->start_watch(TIME_HOST_NEIGHBOR);
- bin_atoms<flt_t,acc_t>(buffers->get_x(), buffers->get_atombin(),
- buffers->get_binpacked());
- if (INTEL_MIC_NBOR_PAD > 1)
- pad = INTEL_MIC_NBOR_PAD * sizeof(float) / sizeof(flt_t);
- } else {
- fix->start_watch(TIME_HOST_NEIGHBOR);
- if (INTEL_NBOR_PAD > 1)
- pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t);
- }
- const int pad_width = pad;
-
- if (aend-astart == 0) {
- fix->stop_watch(TIME_HOST_NEIGHBOR);
- return;
- }
-
- const ATOM_T * _noalias const x = buffers->get_x();
- int * _noalias const firstneigh = buffers->firstneigh(list);
-
- const int molecular = atom->molecular;
- int *ns = NULL;
- tagint *s = NULL;
- int tag_size = 0, special_size;
- if (buffers->need_tag()) tag_size = nall;
- if (molecular) {
- s = atom->special[0];
- ns = atom->nspecial[0];
- special_size = aend;
- } else {
- s = &buffers->_special_holder;
- ns = &buffers->_nspecial_holder;
- special_size = 0;
- }
- const tagint * _noalias const special = s;
- const int * _noalias const nspecial = ns;
- const int maxspecial = atom->maxspecial;
- const tagint * _noalias const tag = atom->tag;
-
- int * _noalias const ilist = list->ilist;
- int * _noalias numneigh = list->numneigh;
- int * _noalias const cnumneigh = buffers->cnumneigh(list);
- const int nstencil = list->nstencil;
- const int * _noalias const stencil = list->stencil;
- const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
- const int ntypes = atom->ntypes + 1;
- const int nlocal = atom->nlocal;
-
- #ifndef _LMP_INTEL_OFFLOAD
- int * const mask = atom->mask;
- tagint * const molecule = atom->molecule;
- #endif
-
- int tnum;
- int *overflow;
- double *timer_compute;
- if (offload) {
- timer_compute = fix->off_watch_neighbor();
- tnum = buffers->get_off_threads();
- overflow = fix->get_off_overflow_flag();
- fix->stop_watch(TIME_HOST_NEIGHBOR);
- fix->start_watch(TIME_OFFLOAD_LATENCY);
- } else {
- tnum = comm->nthreads;
- overflow = fix->get_overflow_flag();
- }
- const int nthreads = tnum;
- const int maxnbors = buffers->get_max_nbors();
- int * _noalias const atombin = buffers->get_atombin();
- const int * _noalias const binpacked = buffers->get_binpacked();
-
- const int xperiodic = domain->xperiodic;
- const int yperiodic = domain->yperiodic;
- const int zperiodic = domain->zperiodic;
- const flt_t xprd_half = domain->xprd_half;
- const flt_t yprd_half = domain->yprd_half;
- const flt_t zprd_half = domain->zprd_half;
-
- // Make sure dummy coordinates to eliminate loop remainder not within cutoff
- {
- const flt_t dx = (INTEL_BIGP - bboxhi[0]);
- const flt_t dy = (INTEL_BIGP - bboxhi[1]);
- const flt_t dz = (INTEL_BIGP - bboxhi[2]);
- if (dx * dx + dy * dy + dz * dz < static_cast<flt_t>(cutneighmaxsq))
- error->one(FLERR,
- "Intel package expects no atoms within cutoff of {1e15,1e15,1e15}.");
- }
-
- #ifdef _LMP_INTEL_OFFLOAD
- const int * _noalias const binhead = this->binhead;
- const int * _noalias const bins = this->bins;
- const int cop = fix->coprocessor_number();
- const int separate_buffers = fix->separate_buffers();
- #pragma offload target(mic:cop) if(offload) \
- in(x:length(nall+1) alloc_if(0) free_if(0)) \
- in(tag:length(tag_size) alloc_if(0) free_if(0)) \
- in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
- in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
- in(bins,binpacked:length(nall) alloc_if(0) free_if(0)) \
- in(binhead:length(mbins+1) alloc_if(0) free_if(0)) \
- in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
- in(firstneigh:length(0) alloc_if(0) free_if(0)) \
- in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
- out(numneigh:length(0) alloc_if(0) free_if(0)) \
- in(ilist:length(0) alloc_if(0) free_if(0)) \
- in(atombin:length(aend) alloc_if(0) free_if(0)) \
- in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
- in(maxnbors,nthreads,maxspecial,nstencil,pad_width,offload,nall) \
- in(separate_buffers, astart, aend, nlocal, molecular, ntypes) \
- in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \
- out(overflow:length(5) alloc_if(0) free_if(0)) \
- out(timer_compute:length(1) alloc_if(0) free_if(0)) \
- signal(tag)
- #endif
- {
- #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
- *timer_compute = MIC_Wtime();
- #endif
-
- #ifdef _LMP_INTEL_OFFLOAD
- overflow[LMP_LOCAL_MIN] = astart;
- overflow[LMP_LOCAL_MAX] = aend - 1;
- overflow[LMP_GHOST_MIN] = nall;
- overflow[LMP_GHOST_MAX] = -1;
- #endif
-
- int nstencilp = 0;
- int binstart[INTEL_MAX_STENCIL], binend[INTEL_MAX_STENCIL];
- for (int k = 0; k < nstencil; k++) {
- binstart[nstencilp] = stencil[k];
- int end = stencil[k] + 1;
- for (int kk = k + 1; kk < nstencil; kk++) {
- if (stencil[kk-1]+1 == stencil[kk]) {
- end++;
- k++;
- } else break;
- }
- binend[nstencilp] = end;
- nstencilp++;
- }
-
- #if defined(_OPENMP)
- #pragma omp parallel default(none) \
- shared(numneigh, overflow, nstencilp, binstart, binend)
- #endif
- {
- #ifdef _LMP_INTEL_OFFLOAD
- int lmin = nall, lmax = -1, gmin = nall, gmax = -1;
- #endif
-
- const int num = aend - astart;
- int tid, ifrom, ito;
- IP_PRE_omp_range_id(ifrom, ito, tid, num, nthreads);
- ifrom += astart;
- ito += astart;
-
- int which;
-
- const int list_size = (ito + tid + 1) * maxnbors;
- int ct = (ifrom + tid) * maxnbors;
- int *neighptr = firstneigh + ct;
-
- for (int i = ifrom; i < ito; i++) {
- int j, k, n, n2, itype, jtype, ibin;
- double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
-
- n = 0;
- n2 = maxnbors;
-
- xtmp = x[i].x;
- ytmp = x[i].y;
- ztmp = x[i].z;
- itype = x[i].w;
- const int ioffset = ntypes*itype;
-
- // loop over all atoms in other bins in stencil including self
- // only store pair if i < j
- // stores own/own pairs only once
- // stores own/ghost pairs on both procs
-
- ibin = atombin[i];
-
- for (k = 0; k < nstencilp; k++) {
- const int bstart = binhead[ibin + binstart[k]];
- const int bend = binhead[ibin + binend[k]];
- for (int jj = bstart; jj < bend; jj++) {
- const int j = binpacked[jj];
- if (j <= i) continue;
-
- jtype = x[j].w;
- #ifndef _LMP_INTEL_OFFLOAD
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
- #endif
-
- delx = xtmp - x[j].x;
- dely = ytmp - x[j].y;
- delz = ztmp - x[j].z;
- rsq = delx * delx + dely * dely + delz * delz;
- if (rsq <= cutneighsq[ioffset + jtype]) {
- if (j < nlocal) {
- if (need_ic) {
- int no_special;
- ominimum_image_check(no_special, delx, dely, delz);
- if (no_special)
- neighptr[n++] = -j - 1;
- else
- neighptr[n++] = j;
- } else
- neighptr[n++] = j;
- #ifdef _LMP_INTEL_OFFLOAD
- if (j < lmin) lmin = j;
- if (j > lmax) lmax = j;
- #endif
- } else {
- if (need_ic) {
- int no_special;
- ominimum_image_check(no_special, delx, dely, delz);
- if (no_special)
- neighptr[n2++] = -j - 1;
- else
- neighptr[n2++] = j;
- } else
- neighptr[n2++] = j;
- #ifdef _LMP_INTEL_OFFLOAD
- if (j < gmin) gmin = j;
- if (j > gmax) gmax = j;
- #endif
- }
- }
- }
- }
- ilist[i] = i;
-
- cnumneigh[i] = ct;
- if (n > maxnbors) *overflow = 1;
- for (k = maxnbors; k < n2; k++) neighptr[n++] = neighptr[k];
-
- const int edge = (n % pad_width);
- if (edge) {
- const int pad_end = n + (pad_width - edge);
- #if defined(LMP_SIMD_COMPILER)
- #pragma loop_count min=1, max=15, avg=8
- #endif
- for ( ; n < pad_end; n++)
- neighptr[n] = nall;
- }
- numneigh[i] = n;
- while((n % (INTEL_DATA_ALIGN / sizeof(int))) != 0) n++;
- ct += n;
- neighptr += n;
- if (ct + n + maxnbors > list_size) {
- *overflow = 1;
- ct = (ifrom + tid) * maxnbors;
- }
- }
-
- if (*overflow == 1)
- for (int i = ifrom; i < ito; i++)
- numneigh[i] = 0;
-
- #ifdef _LMP_INTEL_OFFLOAD
- if (separate_buffers) {
- #if defined(_OPENMP)
- #pragma omp critical
- #endif
- {
- if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
- if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
- if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
- if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
- }
- #pragma omp barrier
- }
-
- int ghost_offset = 0, nall_offset = nall;
- if (separate_buffers) {
- int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
- if (nghost < 0) nghost = 0;
- if (offload) {
- ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
- nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
- } else {
- ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
- nall_offset = nlocal + nghost;
- }
- }
- #endif
-
- if (molecular) {
- for (int i = ifrom; i < ito; ++i) {
- int * _noalias jlist = firstneigh + cnumneigh[i];
- const int jnum = numneigh[i];
- for (int jj = 0; jj < jnum; jj++) {
- const int j = jlist[jj];
- if (need_ic && j < 0) {
- which = 0;
- jlist[jj] = -j - 1;
- } else
- ofind_special(which, special, nspecial, i, tag[j]);
- #ifdef _LMP_INTEL_OFFLOAD
- if (j >= nlocal) {
- if (j == nall)
- jlist[jj] = nall_offset;
- else if (which)
- jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
- else jlist[jj]-=ghost_offset;
- } else
- #endif
- if (which) jlist[jj] = j ^ (which << SBBITS);
- }
- }
- }
- #ifdef _LMP_INTEL_OFFLOAD
- else if (separate_buffers) {
- for (int i = ifrom; i < ito; ++i) {
- int * _noalias jlist = firstneigh + cnumneigh[i];
- const int jnum = numneigh[i];
- int jj = 0;
- for (jj = 0; jj < jnum; jj++)
- if (jlist[jj] >= nlocal) break;
- while (jj < jnum) {
- if (jlist[jj] == nall) jlist[jj] = nall_offset;
- else jlist[jj] -= ghost_offset;
- jj++;
- }
- }
- }
- #endif
- } // end omp
- #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
- *timer_compute = MIC_Wtime() - *timer_compute;
- #endif
- } // end offload
-
- if (offload) {
- fix->stop_watch(TIME_OFFLOAD_LATENCY);
- #ifdef _LMP_INTEL_OFFLOAD
- for (int n = 0; n < aend; n++) {
- ilist[n] = n;
- numneigh[n] = 0;
- }
- #endif
- } else {
- for (int i = astart; i < aend; i++)
- list->firstneigh[i] = firstneigh + cnumneigh[i];
- fix->stop_watch(TIME_HOST_NEIGHBOR);
- #ifdef _LMP_INTEL_OFFLOAD
- if (separate_buffers) {
- fix->start_watch(TIME_PACK);
- fix->set_neighbor_host_sizes();
- buffers->pack_sep_from_single(fix->host_min_local(),
- fix->host_used_local(),
- fix->host_min_ghost(),
- fix->host_used_ghost());
- fix->stop_watch(TIME_PACK);
- }
- #endif
- }
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with full Newton's 3rd law
- each owned atom i checks its own bin and other bins in Newton stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_newton_intel(NeighList *list)
-{
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- list->inum = nlocal;
-
- // Get fix for intel stuff
- FixIntel *fix = static_cast<FixIntel *>(fix_intel);
-
- const int off_end = fix->offload_end_neighbor();
- int host_start = fix->host_start_neighbor();;
- int offload_noghost = 0;
- #ifdef _LMP_INTEL_OFFLOAD
- if (fix->full_host_list()) host_start = 0;
- offload_noghost = fix->offload_noghost();
- if (exclude)
- error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
- #endif
- if (list->nstencil / 2 > INTEL_MAX_STENCIL_CHECK)
- error->all(FLERR, "Too many neighbor bins for USER-INTEL package.");
-
- int need_ic = 0;
- if (atom->molecular)
- dminimum_image_check(need_ic, cutneighmax, cutneighmax, cutneighmax);
-
- if (need_ic) {
- if (fix->precision() == FixIntel::PREC_MODE_MIXED) {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- hbni<float,double,1,1>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- hbni<float,double,1,1>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- hbni<float,double,0,1>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- hbni<float,double,0,1>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal, fix);
- }
- } else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- hbni<double,double,1,1>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- hbni<double,double,1,1>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- hbni<double,double,0,1>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- hbni<double,double,0,1>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix);
- }
- } else {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- hbni<float,float,1,1>(1, list, fix->get_single_buffers(), 0, off_end,
- fix);
- hbni<float,float,1,1>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- hbni<float,float,0,1>(1, list, fix->get_single_buffers(), 0, off_end,
- fix);
- hbni<float,float,0,1>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix);
- }
- }
- } else {
- if (fix->precision() == FixIntel::PREC_MODE_MIXED) {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- hbni<float,double,1,0>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- hbni<float,double,1,0>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- hbni<float,double,0,0>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- hbni<float,double,0,0>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal, fix);
- }
- } else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- hbni<double,double,1,0>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- hbni<double,double,1,0>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- hbni<double,double,0,0>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- hbni<double,double,0,0>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix);
- }
- } else {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- hbni<float,float,1,0>(1, list, fix->get_single_buffers(), 0, off_end,
- fix);
- hbni<float,float,1,0>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- hbni<float,float,0,0>(1, list, fix->get_single_buffers(), 0, off_end,
- fix);
- hbni<float,float,0,0>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix);
- }
- }
- }
-}
-
-template <class flt_t, class acc_t, int offload_noghost, int need_ic>
-void Neighbor::hbni(const int offload, NeighList *list, void *buffers_in,
- const int astart, const int aend, void *fix_in,
- const int offload_end) {
- IntelBuffers<flt_t,acc_t> *buffers = (IntelBuffers<flt_t,acc_t> *)buffers_in;
- FixIntel *fix = (FixIntel *)fix_in;
- const int nall = atom->nlocal + atom->nghost;
- int pad = 1;
-
- if (offload) {
- fix->start_watch(TIME_PACK);
- buffers->grow(nall, atom->nlocal, comm->nthreads, aend);
- buffers->grow_nbor(list, atom->nlocal, comm->nthreads, aend);
-
- ATOM_T biga;
- biga.x = INTEL_BIGP;
- biga.y = INTEL_BIGP;
- biga.z = INTEL_BIGP;
- biga.w = 1;
- buffers->get_x()[nall]=biga;
-
- const int nthreads = comm->nthreads;
- #if defined(_OPENMP)
- #pragma omp parallel default(none) shared(buffers)
- #endif
- {
- int ifrom, ito, tid;
- IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
- sizeof(ATOM_T));
- buffers->thr_pack(ifrom, ito, 0);
- }
- fix->stop_watch(TIME_PACK);
-
- fix->start_watch(TIME_HOST_NEIGHBOR);
- bin_atoms<flt_t,acc_t>(buffers->get_x(), buffers->get_atombin(),
- buffers->get_binpacked());
- if (INTEL_MIC_NBOR_PAD > 1)
- pad = INTEL_MIC_NBOR_PAD * sizeof(float) / sizeof(flt_t);
- } else {
- fix->start_watch(TIME_HOST_NEIGHBOR);
- if (INTEL_NBOR_PAD > 1)
- pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t);
- }
- const int pad_width = pad;
-
- if (aend-astart == 0) {
- fix->stop_watch(TIME_HOST_NEIGHBOR);
- return;
- }
-
- const ATOM_T * _noalias const x = buffers->get_x();
- int * _noalias const firstneigh = buffers->firstneigh(list);
- int nall_t = nall;
- if (offload_noghost && offload) nall_t = atom->nlocal;
- const int e_nall = nall_t;
-
- const int molecular = atom->molecular;
- int *ns = NULL;
- tagint *s = NULL;
- int tag_size = 0, special_size;
- if (buffers->need_tag()) tag_size = e_nall;
- if (molecular) {
- s = atom->special[0];
- ns = atom->nspecial[0];
- special_size = aend;
- } else {
- s = &buffers->_special_holder;
- ns = &buffers->_nspecial_holder;
- special_size = 0;
- }
- const tagint * _noalias const special = s;
- const int * _noalias const nspecial = ns;
- const int maxspecial = atom->maxspecial;
- const tagint * _noalias const tag = atom->tag;
-
- int * _noalias const ilist = list->ilist;
- int * _noalias numneigh = list->numneigh;
- int * _noalias const cnumneigh = buffers->cnumneigh(list);
- const int nstencil = list->nstencil;
- const int * _noalias const stencil = list->stencil;
- const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
- const int ntypes = atom->ntypes + 1;
- const int nlocal = atom->nlocal;
-
- #ifndef _LMP_INTEL_OFFLOAD
- int * const mask = atom->mask;
- tagint * const molecule = atom->molecule;
- #endif
-
- int tnum;
- int *overflow;
- double *timer_compute;
- if (offload) {
- timer_compute = fix->off_watch_neighbor();
- tnum = buffers->get_off_threads();
- overflow = fix->get_off_overflow_flag();
- fix->stop_watch(TIME_HOST_NEIGHBOR);
- fix->start_watch(TIME_OFFLOAD_LATENCY);
- } else {
- tnum = comm->nthreads;
- overflow = fix->get_overflow_flag();
- }
- const int nthreads = tnum;
- const int maxnbors = buffers->get_max_nbors();
- int * _noalias const atombin = buffers->get_atombin();
- const int * _noalias const binpacked = buffers->get_binpacked();
-
- const int xperiodic = domain->xperiodic;
- const int yperiodic = domain->yperiodic;
- const int zperiodic = domain->zperiodic;
- const flt_t xprd_half = domain->xprd_half;
- const flt_t yprd_half = domain->yprd_half;
- const flt_t zprd_half = domain->zprd_half;
-
- // Make sure dummy coordinates to eliminate loop remainder not within cutoff
- {
- const flt_t dx = (INTEL_BIGP - bboxhi[0]);
- const flt_t dy = (INTEL_BIGP - bboxhi[1]);
- const flt_t dz = (INTEL_BIGP - bboxhi[2]);
- if (dx * dx + dy * dy + dz * dz < static_cast<flt_t>(cutneighmaxsq))
- error->one(FLERR,
- "Intel package expects no atoms within cutoff of {1e15,1e15,1e15}.");
- }
-
- #ifdef _LMP_INTEL_OFFLOAD
- const int * _noalias const binhead = this->binhead;
- const int * _noalias const bins = this->bins;
- const int cop = fix->coprocessor_number();
- const int separate_buffers = fix->separate_buffers();
- #pragma offload target(mic:cop) if(offload) \
- in(x:length(e_nall+1) alloc_if(0) free_if(0)) \
- in(tag:length(tag_size) alloc_if(0) free_if(0)) \
- in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
- in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
- in(bins,binpacked:length(nall) alloc_if(0) free_if(0)) \
- in(binhead:length(mbins+1) alloc_if(0) free_if(0)) \
- in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
- in(firstneigh:length(0) alloc_if(0) free_if(0)) \
- in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
- out(numneigh:length(0) alloc_if(0) free_if(0)) \
- in(ilist:length(0) alloc_if(0) free_if(0)) \
- in(atombin:length(aend) alloc_if(0) free_if(0)) \
- in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
- in(maxnbors,nthreads,maxspecial,nstencil,e_nall,offload,pad_width) \
- in(offload_end,separate_buffers,astart, aend, nlocal, molecular, ntypes) \
- in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \
- out(overflow:length(5) alloc_if(0) free_if(0)) \
- out(timer_compute:length(1) alloc_if(0) free_if(0)) \
- signal(tag)
- #endif
- {
- #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
- *timer_compute = MIC_Wtime();
- #endif
-
- #ifdef _LMP_INTEL_OFFLOAD
- overflow[LMP_LOCAL_MIN] = astart;
- overflow[LMP_LOCAL_MAX] = aend - 1;
- overflow[LMP_GHOST_MIN] = e_nall;
- overflow[LMP_GHOST_MAX] = -1;
- #endif
-
- int nstencilp = 0;
- int binstart[INTEL_MAX_STENCIL], binend[INTEL_MAX_STENCIL];
- for (int k = 0; k < nstencil; k++) {
- binstart[nstencilp] = stencil[k];
- int end = stencil[k] + 1;
- for (int kk = k + 1; kk < nstencil; kk++) {
- if (stencil[kk-1]+1 == stencil[kk]) {
- end++;
- k++;
- } else break;
- }
- binend[nstencilp] = end;
- nstencilp++;
- }
-
- #if defined(_OPENMP)
- #pragma omp parallel default(none) \
- shared(numneigh, overflow, nstencilp, binstart, binend)
- #endif
- {
- #ifdef _LMP_INTEL_OFFLOAD
- int lmin = e_nall, lmax = -1, gmin = e_nall, gmax = -1;
- #endif
-
- const int num = aend - astart;
- int tid, ifrom, ito;
-
- #ifdef OUTER_CHUNK
- const int swidth = ip_simd::SIMD_type<flt_t>::width();
- IP_PRE_omp_range_id_vec(ifrom, ito, tid, num, nthreads, swidth);
- ifrom += astart;
- ito += astart;
- int e_ito = ito;
- if (ito == num) {
- int imod = ito % swidth;
- if (imod) e_ito += swidth - imod;
- }
- const int list_size = (e_ito + tid * 2 + 2) * maxnbors;
- #else
- const int swidth = 1;
- IP_PRE_omp_range_id(ifrom, ito, tid, num, nthreads);
- ifrom += astart;
- ito += astart;
- const int list_size = (ito + tid * 2 + 2) * maxnbors;
- #endif
-
- int which;
-
- int pack_offset = maxnbors * swidth;
- int ct = (ifrom + tid * 2) * maxnbors;
- int *neighptr = firstneigh + ct;
- const int obound = pack_offset + maxnbors * 2;
-
- int max_chunk = 0;
- int lane = 0;
- for (int i = ifrom; i < ito; i++) {
- const flt_t xtmp = x[i].x;
- const flt_t ytmp = x[i].y;
- const flt_t ztmp = x[i].z;
- const int itype = x[i].w;
- const int ioffset = ntypes * itype;
-
- // loop over rest of atoms in i's bin, ghosts are at end of linked list
- // if j is owned atom, store it, since j is beyond i in linked list
- // if j is ghost, only store if j coords are "above/to the right" of i
-
- int raw_count = pack_offset;
- for (int j = bins[i]; j >= 0; j = bins[j]) {
- if (j >= nlocal) {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost && offload) continue;
- #endif
- if (x[j].z < ztmp) continue;
- if (x[j].z == ztmp) {
- if (x[j].y < ytmp) continue;
- if (x[j].y == ytmp && x[j].x < xtmp) continue;
- }
- }
- #ifdef _LMP_INTEL_OFFLOAD
- else if (offload_noghost && i < offload_end) continue;
- #endif
-
- #ifndef _LMP_INTEL_OFFLOAD
- if (exclude) {
- const int jtype = x[j].w;
- if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
- }
- #endif
-
- neighptr[raw_count++] = j;
- }
-
- // loop over all atoms in other bins in stencil, store every pair
-
- const int ibin = atombin[i];
- if (exclude) {
- for (int k = 0; k < nstencilp; k++) {
- const int bstart = binhead[ibin + binstart[k]];
- const int bend = binhead[ibin + binend[k]];
- #ifndef _LMP_INTEL_OFFLOAD
- #ifdef INTEL_VMASK
- #pragma simd
- #endif
- #endif
- for (int jj = bstart; jj < bend; jj++) {
- const int j = binpacked[jj];
-
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- if (j < nlocal) {
- if (i < offload_end) continue;
- } else if (offload) continue;
- }
- #endif
-
- #ifndef _LMP_INTEL_OFFLOAD
- const int jtype = x[j].w;
- if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
- #endif
-
- neighptr[raw_count++] = j;
- }
- }
- } else {
- for (int k = 0; k < nstencilp; k++) {
- const int bstart = binhead[ibin + binstart[k]];
- const int bend = binhead[ibin + binend[k]];
- #ifndef _LMP_INTEL_OFFLOAD
- #ifdef INTEL_VMASK
- #pragma simd
- #endif
- #endif
- for (int jj = bstart; jj < bend; jj++) {
- const int j = binpacked[jj];
-
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- if (j < nlocal) {
- if (i < offload_end) continue;
- } else if (offload) continue;
- }
- #endif
-
- neighptr[raw_count++] = j;
- }
- }
- }
-
- if (raw_count > obound) *overflow = 1;
-
- #if defined(LMP_SIMD_COMPILER)
- #ifdef _LMP_INTEL_OFFLOAD
- int vlmin = lmin, vlmax = lmax, vgmin = gmin, vgmax = gmax;
- #if __INTEL_COMPILER+0 > 1499
- #pragma vector aligned
- #pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin)
- #endif
- #else
- #pragma vector aligned
- #pragma simd
- #endif
- #endif
- for (int u = pack_offset; u < raw_count; u++) {
- int j = neighptr[u];
- const flt_t delx = xtmp - x[j].x;
- const flt_t dely = ytmp - x[j].y;
- const flt_t delz = ztmp - x[j].z;
- const int jtype = x[j].w;
- const flt_t rsq = delx * delx + dely * dely + delz * delz;
- if (rsq > cutneighsq[ioffset + jtype])
- neighptr[u] = e_nall;
- else {
- if (need_ic) {
- int no_special;
- ominimum_image_check(no_special, delx, dely, delz);
- if (no_special)
- neighptr[u] = -j - 1;
- }
- #ifdef _LMP_INTEL_OFFLOAD
- if (j < nlocal) {
- if (j < vlmin) vlmin = j;
- if (j > vlmax) vlmax = j;
- } else {
- if (j < vgmin) vgmin = j;
- if (j > vgmax) vgmax = j;
- }
- #endif
- }
- }
- #ifdef _LMP_INTEL_OFFLOAD
- lmin = MIN(lmin,vlmin);
- gmin = MIN(gmin,vgmin);
- lmax = MAX(lmax,vlmax);
- gmax = MAX(gmax,vgmax);
- #endif
-
- int n = lane, n2 = pack_offset;
- for (int u = pack_offset; u < raw_count; u++) {
- const int j = neighptr[u];
- int pj = j;
- if (pj < e_nall) {
- if (need_ic)
- if (pj < 0) pj = -pj - 1;
-
- if (pj < nlocal) {
- neighptr[n] = j;
- n += swidth;
- } else
- neighptr[n2++] = j;
- }
- }
- int ns = (n - lane) / swidth;
- for (int u = pack_offset; u < n2; u++) {
- neighptr[n] = neighptr[u];
- n += swidth;
- }
-
- ilist[i] = i;
- cnumneigh[i] = ct + lane;
- ns += n2 - pack_offset;
- #ifndef OUTER_CHUNK
- int edge = (ns % pad_width);
- if (edge) {
- const int pad_end = ns + (pad_width - edge);
- #if defined(LMP_SIMD_COMPILER)
- #pragma loop_count min=1, max=15, avg=8
- #endif
- for ( ; ns < pad_end; ns++)
- neighptr[ns] = e_nall;
- }
- #endif
- numneigh[i] = ns;
-
- #ifdef OUTER_CHUNK
- if (ns > max_chunk) max_chunk = ns;
- lane++;
- if (lane == swidth) {
- ct += max_chunk * swidth;
- const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
- int edge = (ct % alignb);
- if (edge) ct += alignb - edge;
- neighptr = firstneigh + ct;
- max_chunk = 0;
- pack_offset = maxnbors * swidth;
- lane = 0;
- if (ct + obound > list_size) {
- if (i < ito - 1) {
- *overflow = 1;
- ct = (ifrom + tid * 2) * maxnbors;
- }
- }
- }
- #else
- ct += ns;
- const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
- edge = (ct % alignb);
- if (edge) ct += alignb - edge;
- neighptr = firstneigh + ct;
- if (ct + obound > list_size) {
- if (i < ito - 1) {
- *overflow = 1;
- ct = (ifrom + tid * 2) * maxnbors;
- }
- }
- #endif
- }
-
- if (*overflow == 1)
- for (int i = ifrom; i < ito; i++)
- numneigh[i] = 0;
-
- #ifdef _LMP_INTEL_OFFLOAD
- if (separate_buffers) {
- #if defined(_OPENMP)
- #pragma omp critical
- #endif
- {
- if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
- if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
- if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
- if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
- }
- #pragma omp barrier
- }
-
- int ghost_offset = 0, nall_offset = e_nall;
- if (separate_buffers) {
- int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
- if (nghost < 0) nghost = 0;
- if (offload) {
- ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
- nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
- } else {
- ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
- nall_offset = nlocal + nghost;
- }
- }
- #endif
-
- if (molecular) {
- for (int i = ifrom; i < ito; ++i) {
- int * _noalias jlist = firstneigh + cnumneigh[i];
- const int jnum = numneigh[i];
- #ifndef OUTER_CHUNK
- #if defined(LMP_SIMD_COMPILER)
- #pragma vector aligned
- #pragma simd
- #endif
- for (int jj = 0; jj < jnum; jj++) {
- #else
- const int trip = jnum * swidth;
- for (int jj = 0; jj < trip; jj+= swidth) {
- #endif
- const int j = jlist[jj];
- if (need_ic && j < 0) {
- which = 0;
- jlist[jj] = -j - 1;
- } else
- ofind_special(which, special, nspecial, i, tag[j]);
- #ifdef _LMP_INTEL_OFFLOAD
- if (j >= nlocal) {
- if (j == e_nall)
- jlist[jj] = nall_offset;
- else if (which)
- jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
- else jlist[jj]-=ghost_offset;
- } else
- #endif
- if (which) jlist[jj] = j ^ (which << SBBITS);
- }
- }
- }
- #ifdef _LMP_INTEL_OFFLOAD
- else if (separate_buffers) {
- for (int i = ifrom; i < ito; ++i) {
- int * _noalias jlist = firstneigh + cnumneigh[i];
- const int jnum = numneigh[i];
- int jj = 0;
- for (jj = 0; jj < jnum; jj++)
- if (jlist[jj] >= nlocal) break;
- while (jj < jnum) {
- if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
- else jlist[jj] -= ghost_offset;
- jj++;
- }
- }
- }
- #endif
- } // end omp
- #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
- *timer_compute = MIC_Wtime() - *timer_compute;
- #endif
- } // end offload
-
- if (offload) {
- fix->stop_watch(TIME_OFFLOAD_LATENCY);
- #ifdef _LMP_INTEL_OFFLOAD
- for (int n = 0; n < aend; n++) {
- ilist[n] = n;
- numneigh[n] = 0;
- }
- #endif
- } else {
- for (int i = astart; i < aend; i++)
- list->firstneigh[i] = firstneigh + cnumneigh[i];
- fix->stop_watch(TIME_HOST_NEIGHBOR);
- #ifdef _LMP_INTEL_OFFLOAD
- if (separate_buffers) {
- fix->start_watch(TIME_PACK);
- fix->set_neighbor_host_sizes();
- buffers->pack_sep_from_single(fix->host_min_local(),
- fix->host_used_local(),
- fix->host_min_ghost(),
- fix->host_used_ghost());
- fix->stop_watch(TIME_PACK);
- }
- #endif
- }
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with Newton's 3rd law for triclinic
- each owned atom i checks its own bin and other bins in triclinic stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_newton_tri_intel(NeighList *list)
-{
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- list->inum = nlocal;
-
- // Get fix for intel stuff
- FixIntel *fix = static_cast<FixIntel *>(fix_intel);
-
- const int off_end = fix->offload_end_neighbor();
- int host_start = fix->host_start_neighbor();
- int offload_noghost = 0;
- #ifdef _LMP_INTEL_OFFLOAD
- if (fix->full_host_list()) host_start = 0;
- offload_noghost = fix->offload_noghost();
- if (exclude)
- error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
- #endif
- if (list->nstencil / 2 > INTEL_MAX_STENCIL_CHECK)
- error->all(FLERR, "Too many neighbor bins for USER-INTEL package.");
-
- int need_ic = 0;
- if (atom->molecular)
- dminimum_image_check(need_ic, cutneighmax, cutneighmax, cutneighmax);
-
- if (need_ic) {
- if (fix->precision() == FixIntel::PREC_MODE_MIXED) {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- hbnti<float,double,1,1>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- hbnti<float,double,1,1>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- hbnti<float,double,0,1>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- hbnti<float,double,0,1>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal, fix);
- }
- } else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- hbnti<double,double,1,1>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- hbnti<double,double,1,1>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- hbnti<double,double,0,1>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- hbnti<double,double,0,1>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix);
- }
- } else {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- hbnti<float,float,1,1>(1, list, fix->get_single_buffers(),
- 0, off_end, fix);
- hbnti<float,float,1,1>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- hbnti<float,float,0,1>(1, list, fix->get_single_buffers(),
- 0, off_end, fix);
- hbnti<float,float,0,1>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix);
- }
- }
- } else {
- if (fix->precision() == FixIntel::PREC_MODE_MIXED) {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- hbnti<float,double,1,0>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- hbnti<float,double,1,0>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- hbnti<float,double,0,0>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- hbnti<float,double,0,0>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal, fix);
- }
- } else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- hbnti<double,double,1,0>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- hbnti<double,double,1,0>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- hbnti<double,double,0,0>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- hbnti<double,double,0,0>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix);
- }
- } else {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- hbnti<float,float,1,0>(1, list, fix->get_single_buffers(),
- 0, off_end, fix);
- hbnti<float,float,1,0>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- hbnti<float,float,0,0>(1, list, fix->get_single_buffers(),
- 0, off_end, fix);
- hbnti<float,float,0,0>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix);
- }
- }
- }
-}
-
-template <class flt_t, class acc_t, int offload_noghost, int need_ic>
-void Neighbor::hbnti(const int offload, NeighList *list, void *buffers_in,
- const int astart, const int aend, void *fix_in,
- const int offload_end) {
- IntelBuffers<flt_t,acc_t> *buffers = (IntelBuffers<flt_t,acc_t> *)buffers_in;
- FixIntel *fix = (FixIntel *)fix_in;
- const int nall = atom->nlocal + atom->nghost;
- int pad = 1;
- if (list->nstencil > INTEL_MAX_STENCIL)
- error->all(FLERR, "Too many neighbor bins for USER-INTEL package.");
-
- if (offload) {
- fix->start_watch(TIME_PACK);
- buffers->grow(nall, atom->nlocal, comm->nthreads, aend);
- buffers->grow_nbor(list, atom->nlocal, comm->nthreads, aend);
-
- ATOM_T biga;
- biga.x = INTEL_BIGP;
- biga.y = INTEL_BIGP;
- biga.z = INTEL_BIGP;
- biga.w = 1;
- buffers->get_x()[nall]=biga;
-
- const int nthreads = comm->nthreads;
- #if defined(_OPENMP)
- #pragma omp parallel default(none) shared(buffers)
- #endif
- {
- int ifrom, ito, tid;
- IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
- sizeof(ATOM_T));
- buffers->thr_pack(ifrom, ito, 0);
- }
- fix->stop_watch(TIME_PACK);
-
- fix->start_watch(TIME_HOST_NEIGHBOR);
- bin_atoms<flt_t,acc_t>(buffers->get_x(), buffers->get_atombin(),
- buffers->get_binpacked());
- if (INTEL_MIC_NBOR_PAD > 1)
- pad = INTEL_MIC_NBOR_PAD * sizeof(float) / sizeof(flt_t);
- } else {
- fix->start_watch(TIME_HOST_NEIGHBOR);
- if (INTEL_NBOR_PAD > 1)
- pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t);
- }
- const int pad_width = pad;
-
- if (aend-astart == 0) {
- fix->stop_watch(TIME_HOST_NEIGHBOR);
- return;
- }
-
- const ATOM_T * _noalias const x = buffers->get_x();
- int * _noalias const firstneigh = buffers->firstneigh(list);
- int nall_t = nall;
- if (offload_noghost && offload) nall_t = atom->nlocal;
- const int e_nall = nall_t;
-
- const int molecular = atom->molecular;
- int *ns = NULL;
- tagint *s = NULL;
- int tag_size = 0, special_size;
- if (buffers->need_tag()) tag_size = e_nall;
- if (molecular) {
- s = atom->special[0];
- ns = atom->nspecial[0];
- special_size = aend;
- } else {
- s = &buffers->_special_holder;
- ns = &buffers->_nspecial_holder;
- special_size = 0;
- }
- const tagint * _noalias const special = s;
- const int * _noalias const nspecial = ns;
- const int maxspecial = atom->maxspecial;
- const tagint * _noalias const tag = atom->tag;
-
- int * _noalias const ilist = list->ilist;
- int * _noalias numneigh = list->numneigh;
- int * _noalias const cnumneigh = buffers->cnumneigh(list);
- const int nstencil = list->nstencil;
- const int * _noalias const stencil = list->stencil;
- const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
- const int ntypes = atom->ntypes + 1;
- const int nlocal = atom->nlocal;
-
- #ifndef _LMP_INTEL_OFFLOAD
- int * const mask = atom->mask;
- tagint * const molecule = atom->molecule;
- #endif
-
- int tnum;
- int *overflow;
- double *timer_compute;
- if (offload) {
- timer_compute = fix->off_watch_neighbor();
- tnum = buffers->get_off_threads();
- overflow = fix->get_off_overflow_flag();
- fix->stop_watch(TIME_HOST_NEIGHBOR);
- fix->start_watch(TIME_OFFLOAD_LATENCY);
- } else {
- tnum = comm->nthreads;
- overflow = fix->get_overflow_flag();
- }
- const int nthreads = tnum;
- const int maxnbors = buffers->get_max_nbors();
- int * _noalias const atombin = buffers->get_atombin();
- const int * _noalias const binpacked = buffers->get_binpacked();
-
- const int xperiodic = domain->xperiodic;
- const int yperiodic = domain->yperiodic;
- const int zperiodic = domain->zperiodic;
- const flt_t xprd_half = domain->xprd_half;
- const flt_t yprd_half = domain->yprd_half;
- const flt_t zprd_half = domain->zprd_half;
-
- // Make sure dummy coordinates to eliminate loop remainder not within cutoff
- {
- const flt_t dx = (INTEL_BIGP - bboxhi[0]);
- const flt_t dy = (INTEL_BIGP - bboxhi[1]);
- const flt_t dz = (INTEL_BIGP - bboxhi[2]);
- if (dx * dx + dy * dy + dz * dz < static_cast<flt_t>(cutneighmaxsq))
- error->one(FLERR,
- "Intel package expects no atoms within cutoff of {1e15,1e15,1e15}.");
- }
-
- #ifdef _LMP_INTEL_OFFLOAD
- const int * _noalias const binhead = this->binhead;
- const int * _noalias const bins = this->bins;
- const int cop = fix->coprocessor_number();
- const int separate_buffers = fix->separate_buffers();
- #pragma offload target(mic:cop) if(offload) \
- in(x:length(e_nall+1) alloc_if(0) free_if(0)) \
- in(tag:length(tag_size) alloc_if(0) free_if(0)) \
- in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
- in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
- in(bins,binpacked:length(nall) alloc_if(0) free_if(0)) \
- in(binhead:length(mbins+1) alloc_if(0) free_if(0)) \
- in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
- in(firstneigh:length(0) alloc_if(0) free_if(0)) \
- in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
- out(numneigh:length(0) alloc_if(0) free_if(0)) \
- in(ilist:length(0) alloc_if(0) free_if(0)) \
- in(atombin:length(aend) alloc_if(0) free_if(0)) \
- in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
- in(maxnbors,nthreads,maxspecial,nstencil,offload_end,pad_width,e_nall) \
- in(offload,separate_buffers, astart, aend, nlocal, molecular, ntypes) \
- in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \
- out(overflow:length(5) alloc_if(0) free_if(0)) \
- out(timer_compute:length(1) alloc_if(0) free_if(0)) \
- signal(tag)
- #endif
- {
- #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
- *timer_compute = MIC_Wtime();
- #endif
-
- #ifdef _LMP_INTEL_OFFLOAD
- overflow[LMP_LOCAL_MIN] = astart;
- overflow[LMP_LOCAL_MAX] = aend - 1;
- overflow[LMP_GHOST_MIN] = e_nall;
- overflow[LMP_GHOST_MAX] = -1;
- #endif
-
- int nstencilp = 0;
- int binstart[INTEL_MAX_STENCIL], binend[INTEL_MAX_STENCIL];
- for (int k = 0; k < nstencil; k++) {
- binstart[nstencilp] = stencil[k];
- int end = stencil[k] + 1;
- for (int kk = k + 1; kk < nstencil; kk++) {
- if (stencil[kk-1]+1 == stencil[kk]) {
- end++;
- k++;
- } else break;
- }
- binend[nstencilp] = end;
- nstencilp++;
- }
-
- #if defined(_OPENMP)
- #pragma omp parallel default(none) \
- shared(numneigh, overflow, nstencilp, binstart, binend)
- #endif
- {
- #ifdef _LMP_INTEL_OFFLOAD
- int lmin = e_nall, lmax = -1, gmin = e_nall, gmax = -1;
- #endif
-
- const int num = aend - astart;
- int tid, ifrom, ito;
- IP_PRE_omp_range_id(ifrom, ito, tid, num, nthreads);
- ifrom += astart;
- ito += astart;
-
- int which;
-
- const int list_size = (ito + tid * 2 + 2) * maxnbors;
- int ct = (ifrom + tid * 2) * maxnbors;
- int *neighptr = firstneigh + ct;
- const int obound = maxnbors * 3;
-
- for (int i = ifrom; i < ito; i++) {
- const flt_t xtmp = x[i].x;
- const flt_t ytmp = x[i].y;
- const flt_t ztmp = x[i].z;
- const int itype = x[i].w;
- const int ioffset = ntypes * itype;
-
- // loop over all atoms in bins in stencil
- // pairs for atoms j "below" i are excluded
- // below = lower z or (equal z and lower y) or (equal zy and lower x)
- // (equal zyx and j <= i)
- // latter excludes self-self interaction but allows superposed atoms
-
- const int ibin = atombin[i];
-
- int raw_count = maxnbors;
- for (int k = 0; k < nstencilp; k++) {
- const int bstart = binhead[ibin + binstart[k]];
- const int bend = binhead[ibin + binend[k]];
- for (int jj = bstart; jj < bend; jj++) {
- const int j = binpacked[jj];
-
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- if (j < nlocal) {
- if (i < offload_end) continue;
- } else if (offload) continue;
- }
- #endif
-
- if (x[j].z < ztmp) continue;
- if (x[j].z == ztmp) {
- if (x[j].y < ytmp) continue;
- if (x[j].y == ytmp) {
- if (x[j].x < xtmp) continue;
- if (x[j].x == xtmp && j <= i) continue;
- }
- }
-
- #ifndef _LMP_INTEL_OFFLOAD
- if (exclude) {
- const int jtype = x[j].w;
- if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
- }
- #endif
-
- neighptr[raw_count++] = j;
- }
- }
- if (raw_count > obound)
- *overflow = 1;
-
- #if defined(LMP_SIMD_COMPILER)
- #ifdef _LMP_INTEL_OFFLOAD
- int vlmin = lmin, vlmax = lmax, vgmin = gmin, vgmax = gmax;
- #if __INTEL_COMPILER+0 > 1499
- #pragma vector aligned
- #pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin)
- #endif
- #else
- #pragma vector aligned
- #pragma simd
- #endif
- #endif
- for (int u = maxnbors; u < raw_count; u++) {
- int j = neighptr[u];
- const flt_t delx = xtmp - x[j].x;
- const flt_t dely = ytmp - x[j].y;
- const flt_t delz = ztmp - x[j].z;
- const int jtype = x[j].w;
- const flt_t rsq = delx * delx + dely * dely + delz * delz;
- if (rsq > cutneighsq[ioffset + jtype])
- neighptr[u] = e_nall;
- else {
- if (need_ic) {
- int no_special;
- ominimum_image_check(no_special, delx, dely, delz);
- if (no_special)
- neighptr[u] = -j - 1;
- }
-
- #ifdef _LMP_INTEL_OFFLOAD
- if (j < nlocal) {
- if (j < vlmin) vlmin = j;
- if (j > vlmax) vlmax = j;
- } else {
- if (j < vgmin) vgmin = j;
- if (j > vgmax) vgmax = j;
- }
- #endif
- }
- }
-
- int n = 0, n2 = maxnbors;
- for (int u = maxnbors; u < raw_count; u++) {
- const int j = neighptr[u];
- int pj = j;
- if (pj < e_nall) {
- if (need_ic)
- if (pj < 0) pj = -pj - 1;
-
- if (pj < nlocal)
- neighptr[n++] = j;
- else
- neighptr[n2++] = j;
- }
- }
- int ns = n;
- for (int u = maxnbors; u < n2; u++)
- neighptr[n++] = neighptr[u];
-
- ilist[i] = i;
- cnumneigh[i] = ct;
- ns += n2 - maxnbors;
-
- int edge = (ns % pad_width);
- if (edge) {
- const int pad_end = ns + (pad_width - edge);
- #if defined(LMP_SIMD_COMPILER)
- #pragma loop_count min=1, max=15, avg=8
- #endif
- for ( ; ns < pad_end; ns++)
- neighptr[ns] = e_nall;
- }
- numneigh[i] = ns;
-
- ct += ns;
- const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
- edge = (ct % alignb);
- if (edge) ct += alignb - edge;
- neighptr = firstneigh + ct;
- if (ct + obound > list_size) {
- if (i < ito - 1) {
- *overflow = 1;
- ct = (ifrom + tid * 2) * maxnbors;
- }
- }
- }
-
- if (*overflow == 1)
- for (int i = ifrom; i < ito; i++)
- numneigh[i] = 0;
-
- #ifdef _LMP_INTEL_OFFLOAD
- if (separate_buffers) {
- #if defined(_OPENMP)
- #pragma omp critical
- #endif
- {
- if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
- if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
- if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
- if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
- }
- #pragma omp barrier
- }
-
- int ghost_offset = 0, nall_offset = e_nall;
- if (separate_buffers) {
- int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
- if (nghost < 0) nghost = 0;
- if (offload) {
- ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
- nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
- } else {
- ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
- nall_offset = nlocal + nghost;
- }
- }
- #endif
-
- if (molecular) {
- for (int i = ifrom; i < ito; ++i) {
- int * _noalias jlist = firstneigh + cnumneigh[i];
- const int jnum = numneigh[i];
- #if defined(LMP_SIMD_COMPILER)
- #pragma vector aligned
- #pragma simd
- #endif
- for (int jj = 0; jj < jnum; jj++) {
- const int j = jlist[jj];
- if (need_ic && j < 0) {
- which = 0;
- jlist[jj] = -j - 1;
- } else
- ofind_special(which, special, nspecial, i, tag[j]);
- #ifdef _LMP_INTEL_OFFLOAD
- if (j >= nlocal) {
- if (j == e_nall)
- jlist[jj] = nall_offset;
- else if (which)
- jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
- else jlist[jj]-=ghost_offset;
- } else
- #endif
- if (which) jlist[jj] = j ^ (which << SBBITS);
- }
- }
- }
- #ifdef _LMP_INTEL_OFFLOAD
- else if (separate_buffers) {
- for (int i = ifrom; i < ito; ++i) {
- int * _noalias jlist = firstneigh + cnumneigh[i];
- const int jnum = numneigh[i];
- int jj = 0;
- for (jj = 0; jj < jnum; jj++)
- if (jlist[jj] >= nlocal) break;
- while (jj < jnum) {
- if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
- else jlist[jj] -= ghost_offset;
- jj++;
- }
- }
- }
- #endif
- } // end omp
- #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
- *timer_compute = MIC_Wtime() - *timer_compute;
- #endif
- } // end offload
-
- if (offload) {
- fix->stop_watch(TIME_OFFLOAD_LATENCY);
- #ifdef _LMP_INTEL_OFFLOAD
- for (int n = 0; n < aend; n++) {
- ilist[n] = n;
- numneigh[n] = 0;
- }
- #endif
- } else {
- for (int i = astart; i < aend; i++)
- list->firstneigh[i] = firstneigh + cnumneigh[i];
- fix->stop_watch(TIME_HOST_NEIGHBOR);
- #ifdef _LMP_INTEL_OFFLOAD
- if (separate_buffers) {
- fix->start_watch(TIME_PACK);
- fix->set_neighbor_host_sizes();
- buffers->pack_sep_from_single(fix->host_min_local(),
- fix->host_used_local(),
- fix->host_min_ghost(),
- fix->host_used_ghost());
- fix->stop_watch(TIME_PACK);
- }
- #endif
- }
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction for all neighbors
- every neighbor pair appears in list of both atoms i and j
-------------------------------------------------------------------------- */
-
-void Neighbor::full_bin_intel(NeighList *list)
-{
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- list->inum = nlocal;
- list->gnum = 0;
-
- // Get fix for intel stuff
- FixIntel *fix = static_cast<FixIntel *>(fix_intel);
-
- const int off_end = fix->offload_end_neighbor();
- int host_start = fix->host_start_neighbor();;
- int offload_noghost = 0;
- #ifdef _LMP_INTEL_OFFLOAD
- if (fix->full_host_list()) host_start = 0;
- offload_noghost = fix->offload_noghost();
- if (exclude)
- error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
- #endif
- if (list->nstencil > INTEL_MAX_STENCIL_CHECK)
- error->all(FLERR, "Too many neighbor bins for USER-INTEL package.");
-
- int need_ic = 0;
- if (atom->molecular)
- dminimum_image_check(need_ic, cutneighmax, cutneighmax, cutneighmax);
-
- if (need_ic) {
- if (fix->precision() == FixIntel::PREC_MODE_MIXED) {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- fbi<float,double,1,1>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- fbi<float,double,1,1>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- fbi<float,double,0,1>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- fbi<float,double,0,1>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal, fix);
- }
- } else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- fbi<double,double,1,1>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- fbi<double,double,1,1>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- fbi<double,double,0,1>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- fbi<double,double,0,1>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix);
- }
- } else {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- fbi<float,float,1,1>(1, list, fix->get_single_buffers(), 0, off_end,
- fix);
- fbi<float,float,1,1>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- fbi<float,float,0,1>(1, list, fix->get_single_buffers(), 0, off_end,
- fix);
- fbi<float,float,0,1>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix);
- }
- }
- } else {
- if (fix->precision() == FixIntel::PREC_MODE_MIXED) {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- fbi<float,double,1,0>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- fbi<float,double,1,0>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- fbi<float,double,0,0>(1, list, fix->get_mixed_buffers(),
- 0, off_end, fix);
- fbi<float,double,0,0>(0, list, fix->get_mixed_buffers(),
- host_start, nlocal, fix);
- }
- } else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- fbi<double,double,1,0>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- fbi<double,double,1,0>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- fbi<double,double,0,0>(1, list, fix->get_double_buffers(),
- 0, off_end, fix);
- fbi<double,double,0,0>(0, list, fix->get_double_buffers(),
- host_start, nlocal, fix);
- }
- } else {
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- fbi<float,float,1,0>(1, list, fix->get_single_buffers(), 0, off_end,
- fix);
- fbi<float,float,1,0>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix, off_end);
- } else
- #endif
- {
- fbi<float,float,0,0>(1, list, fix->get_single_buffers(), 0, off_end,
- fix);
- fbi<float,float,0,0>(0, list, fix->get_single_buffers(),
- host_start, nlocal, fix);
- }
- }
- }
-}
-
-template <class flt_t, class acc_t, int offload_noghost, int need_ic>
-void Neighbor::fbi(const int offload, NeighList *list, void *buffers_in,
- const int astart, const int aend, void *fix_in,
- const int offload_end) {
- IntelBuffers<flt_t,acc_t> *buffers = (IntelBuffers<flt_t,acc_t> *)buffers_in;
- FixIntel *fix = (FixIntel *)fix_in;
- const int nall = atom->nlocal + atom->nghost;
- int pad = 1;
-
- const int pack_width = fix->nbor_pack_width();
-
- if (offload) {
- fix->start_watch(TIME_PACK);
- buffers->grow(nall, atom->nlocal, comm->nthreads, aend);
- buffers->grow_nbor(list, atom->nlocal, comm->nthreads, aend, pack_width);
-
- ATOM_T biga;
- biga.x = INTEL_BIGP;
- biga.y = INTEL_BIGP;
- biga.z = INTEL_BIGP;
- biga.w = 1;
- buffers->get_x()[nall]=biga;
-
- const int nthreads = comm->nthreads;
- #if defined(_OPENMP)
- #pragma omp parallel default(none) shared(buffers)
- #endif
- {
- int ifrom, ito, tid;
- IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
- sizeof(ATOM_T));
- buffers->thr_pack(ifrom, ito, 0);
- }
- fix->stop_watch(TIME_PACK);
-
- fix->start_watch(TIME_HOST_NEIGHBOR);
- bin_atoms<flt_t,acc_t>(buffers->get_x(), buffers->get_atombin(),
- buffers->get_binpacked());
- } else {
- fix->start_watch(TIME_HOST_NEIGHBOR);
- }
- const int pad_width = pad;
-
- if (aend-astart == 0) {
- fix->stop_watch(TIME_HOST_NEIGHBOR);
- return;
- }
-
- const ATOM_T * _noalias const x = buffers->get_x();
- int * _noalias const firstneigh = buffers->firstneigh(list);
- int nall_t = nall;
- if (offload_noghost && offload) nall_t = atom->nlocal;
- const int e_nall = nall_t;
-
- const int molecular = atom->molecular;
- int *ns = NULL;
- tagint *s = NULL;
- int tag_size = 0, special_size;
- if (buffers->need_tag()) tag_size = e_nall;
- if (molecular) {
- s = atom->special[0];
- ns = atom->nspecial[0];
- special_size = aend;
- } else {
- s = &buffers->_special_holder;
- ns = &buffers->_nspecial_holder;
- special_size = 0;
- }
- const tagint * _noalias const special = s;
- const int * _noalias const nspecial = ns;
- const int maxspecial = atom->maxspecial;
- const tagint * _noalias const tag = atom->tag;
-
- int * _noalias const ilist = list->ilist;
- int * _noalias numneigh = list->numneigh;
- int * _noalias const cnumneigh = buffers->cnumneigh(list);
- const int nstencil = list->nstencil;
- const int * _noalias const stencil = list->stencil;
- const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
- const int ntypes = atom->ntypes + 1;
- const int nlocal = atom->nlocal;
-
- #ifndef _LMP_INTEL_OFFLOAD
- int * const mask = atom->mask;
- tagint * const molecule = atom->molecule;
- #endif
-
- int tnum;
- int *overflow;
- double *timer_compute;
- if (offload) {
- timer_compute = fix->off_watch_neighbor();
- tnum = buffers->get_off_threads();
- overflow = fix->get_off_overflow_flag();
- fix->stop_watch(TIME_HOST_NEIGHBOR);
- fix->start_watch(TIME_OFFLOAD_LATENCY);
- } else {
- tnum = comm->nthreads;
- overflow = fix->get_overflow_flag();
- }
- const int nthreads = tnum;
- const int maxnbors = buffers->get_max_nbors();
- int * _noalias const atombin = buffers->get_atombin();
- const int * _noalias const binpacked = buffers->get_binpacked();
-
- const int xperiodic = domain->xperiodic;
- const int yperiodic = domain->yperiodic;
- const int zperiodic = domain->zperiodic;
- const flt_t xprd_half = domain->xprd_half;
- const flt_t yprd_half = domain->yprd_half;
- const flt_t zprd_half = domain->zprd_half;
-
- // Make sure dummy coordinates to eliminate loop remainder not within cutoff
- {
- const flt_t dx = (INTEL_BIGP - bboxhi[0]);
- const flt_t dy = (INTEL_BIGP - bboxhi[1]);
- const flt_t dz = (INTEL_BIGP - bboxhi[2]);
- if (dx * dx + dy * dy + dz * dz < static_cast<flt_t>(cutneighmaxsq))
- error->one(FLERR,
- "Intel package expects no atoms within cutoff of {1e15,1e15,1e15}.");
- }
-
- #ifdef _LMP_INTEL_OFFLOAD
- const int * _noalias const binhead = this->binhead;
- const int * _noalias const bins = this->bins;
- const int cop = fix->coprocessor_number();
- const int separate_buffers = fix->separate_buffers();
- #pragma offload target(mic:cop) if(offload) \
- in(x:length(e_nall+1) alloc_if(0) free_if(0)) \
- in(tag:length(tag_size) alloc_if(0) free_if(0)) \
- in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
- in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
- in(bins,binpacked:length(nall) alloc_if(0) free_if(0)) \
- in(binhead:length(mbins+1) alloc_if(0) free_if(0)) \
- in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
- in(firstneigh:length(0) alloc_if(0) free_if(0)) \
- in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
- out(numneigh:length(0) alloc_if(0) free_if(0)) \
- in(ilist:length(0) alloc_if(0) free_if(0)) \
- in(atombin:length(aend) alloc_if(0) free_if(0)) \
- in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
- in(maxnbors,nthreads,maxspecial,nstencil,e_nall,offload,pack_width) \
- in(offload_end,separate_buffers,astart, aend, nlocal, molecular, ntypes) \
- in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \
- out(overflow:length(5) alloc_if(0) free_if(0)) \
- out(timer_compute:length(1) alloc_if(0) free_if(0)) \
- signal(tag)
- #endif
- {
- #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
- *timer_compute = MIC_Wtime();
- #endif
-
- #ifdef _LMP_INTEL_OFFLOAD
- overflow[LMP_LOCAL_MIN] = astart;
- overflow[LMP_LOCAL_MAX] = aend - 1;
- overflow[LMP_GHOST_MIN] = e_nall;
- overflow[LMP_GHOST_MAX] = -1;
- #endif
-
- int nstencilp = 0;
- int binstart[INTEL_MAX_STENCIL], binend[INTEL_MAX_STENCIL];
- for (int k = 0; k < nstencil; k++) {
- binstart[nstencilp] = stencil[k];
- int end = stencil[k] + 1;
- for (int kk = k + 1; kk < nstencil; kk++) {
- if (stencil[kk-1]+1 == stencil[kk]) {
- end++;
- k++;
- } else break;
- }
- binend[nstencilp] = end;
- nstencilp++;
- }
-
- #if defined(_OPENMP)
- #pragma omp parallel default(none) \
- shared(numneigh, overflow, nstencilp, binstart, binend)
- #endif
- {
- #ifdef _LMP_INTEL_OFFLOAD
- int lmin = e_nall, lmax = -1, gmin = e_nall, gmax = -1;
- #endif
-
- const int num = aend - astart;
- int tid, ifrom, ito;
-
- IP_PRE_omp_range_id_vec(ifrom, ito, tid, num, nthreads, pack_width);
- ifrom += astart;
- ito += astart;
- int e_ito = ito;
- if (ito == num) {
- int imod = ito % pack_width;
- if (imod) e_ito += pack_width - imod;
- }
- const int list_size = (e_ito + tid * 2 + 2) * maxnbors;
- int which;
- int pack_offset = maxnbors * pack_width;
- int ct = (ifrom + tid * 2) * maxnbors;
- int *neighptr = firstneigh + ct;
- const int obound = pack_offset + maxnbors * 2;
-
- int max_chunk = 0;
- int lane = 0;
- for (int i = ifrom; i < ito; i++) {
- const flt_t xtmp = x[i].x;
- const flt_t ytmp = x[i].y;
- const flt_t ztmp = x[i].z;
- const int itype = x[i].w;
- const tagint itag = tag[i];
- const int ioffset = ntypes * itype;
-
- const int ibin = atombin[i];
- int raw_count = pack_offset;
-
- // loop over all atoms in surrounding bins in stencil including self
- // skip i = j
- if (exclude) {
- for (int k = 0; k < nstencilp; k++) {
- const int bstart = binhead[ibin + binstart[k]];
- const int bend = binhead[ibin + binend[k]];
- #ifndef _LMP_INTEL_OFFLOAD
- #ifdef INTEL_VMASK
- #pragma simd
- #endif
- #endif
- for (int jj = bstart; jj < bend; jj++) {
- int j = binpacked[jj];
-
- if (i == j) j=e_nall;
-
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- if (j < nlocal) {
- if (i < offload_end) continue;
- } else if (offload) continue;
- }
- #endif
-
- #ifndef _LMP_INTEL_OFFLOAD
- const int jtype = x[j].w;
- if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
- #endif
-
- neighptr[raw_count++] = j;
- }
- }
- } else {
- for (int k = 0; k < nstencilp; k++) {
- const int bstart = binhead[ibin + binstart[k]];
- const int bend = binhead[ibin + binend[k]];
- #ifndef _LMP_INTEL_OFFLOAD
- #ifdef INTEL_VMASK
- #pragma simd
- #endif
- #endif
- for (int jj = bstart; jj < bend; jj++) {
- int j = binpacked[jj];
-
- if (i == j) j=e_nall;
-
- #ifdef _LMP_INTEL_OFFLOAD
- if (offload_noghost) {
- if (j < nlocal) {
- if (i < offload_end) continue;
- } else if (offload) continue;
- }
- #endif
-
- neighptr[raw_count++] = j;
- }
- }
- }
-
- if (raw_count > obound) *overflow = 1;
-
- #if defined(LMP_SIMD_COMPILER)
- #ifdef _LMP_INTEL_OFFLOAD
- int vlmin = lmin, vlmax = lmax, vgmin = gmin, vgmax = gmax;
- #if __INTEL_COMPILER+0 > 1499
- #pragma vector aligned
- #pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin)
- #endif
- #else
- #pragma vector aligned
- #pragma simd
- #endif
- #endif
- for (int u = pack_offset; u < raw_count; u++) {
- int j = neighptr[u];
- const flt_t delx = xtmp - x[j].x;
- const flt_t dely = ytmp - x[j].y;
- const flt_t delz = ztmp - x[j].z;
- const int jtype = x[j].w;
- const flt_t rsq = delx * delx + dely * dely + delz * delz;
- if (rsq > cutneighsq[ioffset + jtype])
- neighptr[u] = e_nall;
- else {
- if (need_ic) {
- int no_special;
- ominimum_image_check(no_special, delx, dely, delz);
- if (no_special)
- neighptr[u] = -j - 1;
- }
- #ifdef _LMP_INTEL_OFFLOAD
- if (j < nlocal) {
- if (j < vlmin) vlmin = j;
- if (j > vlmax) vlmax = j;
- } else {
- if (j < vgmin) vgmin = j;
- if (j > vgmax) vgmax = j;
- }
- #endif
- }
- }
- #ifdef _LMP_INTEL_OFFLOAD
- lmin = MIN(lmin,vlmin);
- gmin = MIN(gmin,vgmin);
- lmax = MAX(lmax,vlmax);
- gmax = MAX(gmax,vgmax);
- #endif
-
- int n = lane, n2 = pack_offset;
- for (int u = pack_offset; u < raw_count; u++) {
- const int j = neighptr[u];
- int pj = j;
- if (pj < e_nall) {
- if (need_ic)
- if (pj < 0) pj = -pj - 1;
-
- const int jtag = tag[pj];
- int flist = 0;
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) flist = 1;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) flist = 1;
- } else {
- if (x[pj].z < ztmp) flist = 1;
- else if (x[pj].z == ztmp && x[pj].y < ytmp) flist = 1;
- else if (x[pj].z == ztmp && x[pj].y == ytmp && x[pj].x < xtmp)
- flist = 1;
- }
- if (flist) {
- neighptr[n2++] = j;
- } else {
- neighptr[n] = j;
- n += pack_width;
- }
- }
- }
- int ns = (n - lane) / pack_width;
- atombin[i] = ns;
- for (int u = pack_offset; u < n2; u++) {
- neighptr[n] = neighptr[u];
- n += pack_width;
- }
-
- ilist[i] = i;
- cnumneigh[i] = ct + lane;
- ns += n2 - pack_offset;
- numneigh[i] = ns;
-
- if (ns > max_chunk) max_chunk = ns;
- lane++;
- if (lane == pack_width) {
- ct += max_chunk * pack_width;
- const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
- const int edge = (ct % alignb);
- if (edge) ct += alignb - edge;
- neighptr = firstneigh + ct;
- max_chunk = 0;
- pack_offset = maxnbors * pack_width;
- lane = 0;
- if (ct + obound > list_size) {
- if (i < ito - 1) {
- *overflow = 1;
- ct = (ifrom + tid * 2) * maxnbors;
- }
- }
- }
- }
-
- if (*overflow == 1)
- for (int i = ifrom; i < ito; i++)
- numneigh[i] = 0;
-
- #ifdef _LMP_INTEL_OFFLOAD
- if (separate_buffers) {
- #if defined(_OPENMP)
- #pragma omp critical
- #endif
- {
- if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
- if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
- if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
- if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
- }
- #pragma omp barrier
- }
-
- int ghost_offset = 0, nall_offset = e_nall;
- if (separate_buffers) {
- int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
- if (nghost < 0) nghost = 0;
- if (offload) {
- ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
- nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
- } else {
- ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
- nall_offset = nlocal + nghost;
- }
- }
- #endif
-
- if (molecular) {
- for (int i = ifrom; i < ito; ++i) {
- int * _noalias jlist = firstneigh + cnumneigh[i];
- const int jnum = numneigh[i];
-
- const int trip = jnum * pack_width;
- for (int jj = 0; jj < trip; jj+=pack_width) {
- const int j = jlist[jj];
- if (need_ic && j < 0) {
- which = 0;
- jlist[jj] = -j - 1;
- } else
- ofind_special(which, special, nspecial, i, tag[j]);
- #ifdef _LMP_INTEL_OFFLOAD
- if (j >= nlocal) {
- if (j == e_nall)
- jlist[jj] = nall_offset;
- else if (which)
- jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
- else jlist[jj]-=ghost_offset;
- } else
- #endif
- if (which) jlist[jj] = j ^ (which << SBBITS);
- }
- }
- }
- #ifdef _LMP_INTEL_OFFLOAD
- else if (separate_buffers) {
- for (int i = ifrom; i < ito; ++i) {
- int * _noalias jlist = firstneigh + cnumneigh[i];
- const int jnum = numneigh[i];
- int jj = 0;
- for (jj = 0; jj < jnum; jj++) {
- if (jlist[jj] >= nlocal) {
- if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
- else jlist[jj] -= ghost_offset;
- }
- }
- }
- }
- #endif
- } // end omp
- #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
- *timer_compute = MIC_Wtime() - *timer_compute;
- #endif
- } // end offload
-
- if (offload) {
- fix->stop_watch(TIME_OFFLOAD_LATENCY);
- #ifdef _LMP_INTEL_OFFLOAD
- for (int n = 0; n < aend; n++) {
- ilist[n] = n;
- numneigh[n] = 0;
- }
- #endif
- } else {
- for (int i = astart; i < aend; i++)
- list->firstneigh[i] = firstneigh + cnumneigh[i];
- fix->stop_watch(TIME_HOST_NEIGHBOR);
- #ifdef _LMP_INTEL_OFFLOAD
- if (separate_buffers) {
- fix->start_watch(TIME_PACK);
- fix->set_neighbor_host_sizes();
- buffers->pack_sep_from_single(fix->host_min_local(),
- fix->host_used_local(),
- fix->host_min_ghost(),
- fix->host_used_ghost());
- fix->stop_watch(TIME_PACK);
- }
- #endif
- }
-}
-
diff --git a/src/USER-INTEL/npair_full_bin_intel.cpp b/src/USER-INTEL/npair_full_bin_intel.cpp
new file mode 100644
index 0000000000..1ec93bf113
--- /dev/null
+++ b/src/USER-INTEL/npair_full_bin_intel.cpp
@@ -0,0 +1,552 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: W. Michael Brown (Intel)
+------------------------------------------------------------------------- */
+
+#include "npair_full_bin_intel.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "comm.h"
+#include "group.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairFullBinIntel::NPairFullBinIntel(LAMMPS *lmp) : NPairIntel(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction for all neighbors
+ every neighbor pair appears in list of both atoms i and j
+------------------------------------------------------------------------- */
+
+void NPairFullBinIntel::build(NeighList *list)
+{
+ if (nstencil > INTEL_MAX_STENCIL_CHECK)
+ error->all(FLERR, "Too many neighbor bins for USER-INTEL package.");
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (exclude)
+ error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
+ #endif
+
+ if (_fix->precision() == FixIntel::PREC_MODE_MIXED)
+ fbi(list, _fix->get_mixed_buffers());
+ else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE)
+ fbi(list, _fix->get_double_buffers());
+ else
+ fbi(list, _fix->get_single_buffers());
+
+ _fix->stop_watch(TIME_HOST_NEIGHBOR);
+}
+
+template <class flt_t, class acc_t>
+void NPairFullBinIntel::
+fbi(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ list->inum = nlocal;
+ list->gnum = 0;
+
+ int host_start = _fix->host_start_neighbor();;
+ const int off_end = _fix->offload_end_neighbor();
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (off_end) grow_stencil();
+ if (_fix->full_host_list()) host_start = 0;
+ int offload_noghost = _fix->offload_noghost();
+ #endif
+
+ buffers->grow_list(list, atom->nlocal, comm->nthreads, off_end,
+ _fix->nbor_pack_width());
+
+ int need_ic = 0;
+ if (atom->molecular)
+ dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
+ neighbor->cutneighmax);
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (need_ic) {
+ if (offload_noghost) {
+ fbi<flt_t,acc_t,1,1>(1, list, buffers, 0, off_end);
+ fbi<flt_t,acc_t,1,1>(0, list, buffers, host_start, nlocal, off_end);
+ } else {
+ fbi<flt_t,acc_t,0,1>(1, list, buffers, 0, off_end);
+ fbi<flt_t,acc_t,0,1>(0, list, buffers, host_start, nlocal);
+ }
+ } else {
+ if (offload_noghost) {
+ fbi<flt_t,acc_t,1,0>(1, list, buffers, 0, off_end);
+ fbi<flt_t,acc_t,1,0>(0, list, buffers, host_start, nlocal, off_end);
+ } else {
+ fbi<flt_t,acc_t,0,0>(1, list, buffers, 0, off_end);
+ fbi<flt_t,acc_t,0,0>(0, list, buffers, host_start, nlocal);
+ }
+ }
+ #else
+ if (need_ic)
+ fbi<flt_t,acc_t,0,1>(0, list, buffers, host_start, nlocal);
+ else
+ fbi<flt_t,acc_t,0,0>(0, list, buffers, host_start, nlocal);
+ #endif
+}
+
+template <class flt_t, class acc_t, int offload_noghost, int need_ic>
+void NPairFullBinIntel::
+fbi(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
+ const int astart, const int aend, const int offload_end) {
+
+ if (aend-astart == 0) return;
+
+ const int nall = atom->nlocal + atom->nghost;
+ int pad = 1;
+ int nall_t = nall;
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload_noghost && offload) nall_t = atom->nlocal;
+ #endif
+
+ const int pack_width = _fix->nbor_pack_width();
+ const int pad_width = pad;
+
+ const ATOM_T * _noalias const x = buffers->get_x();
+ int * _noalias const firstneigh = buffers->firstneigh(list);
+ const int e_nall = nall_t;
+
+ const int molecular = atom->molecular;
+ int *ns = NULL;
+ tagint *s = NULL;
+ int tag_size = 0, special_size;
+ if (buffers->need_tag()) tag_size = e_nall;
+ if (molecular) {
+ s = atom->special[0];
+ ns = atom->nspecial[0];
+ special_size = aend;
+ } else {
+ s = &buffers->_special_holder;
+ ns = &buffers->_nspecial_holder;
+ special_size = 0;
+ }
+ const tagint * _noalias const special = s;
+ const int * _noalias const nspecial = ns;
+ const int maxspecial = atom->maxspecial;
+ const tagint * _noalias const tag = atom->tag;
+
+ int * _noalias const ilist = list->ilist;
+ int * _noalias numneigh = list->numneigh;
+ int * _noalias const cnumneigh = buffers->cnumneigh(list);
+ const int nstencil = this->nstencil;
+ const int * _noalias const stencil = this->stencil;
+ const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
+ const int ntypes = atom->ntypes + 1;
+ const int nlocal = atom->nlocal;
+
+ #ifndef _LMP_INTEL_OFFLOAD
+ int * const mask = atom->mask;
+ tagint * const molecule = atom->molecule;
+ #endif
+
+ int tnum;
+ int *overflow;
+ double *timer_compute;
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload) {
+ timer_compute = _fix->off_watch_neighbor();
+ tnum = buffers->get_off_threads();
+ overflow = _fix->get_off_overflow_flag();
+ _fix->stop_watch(TIME_HOST_NEIGHBOR);
+ _fix->start_watch(TIME_OFFLOAD_LATENCY);
+ } else
+ #endif
+ {
+ tnum = comm->nthreads;
+ overflow = _fix->get_overflow_flag();
+ }
+ const int nthreads = tnum;
+ const int maxnbors = buffers->get_max_nbors();
+ int * _noalias const atombin = buffers->get_atombin();
+ const int * _noalias const binpacked = buffers->get_binpacked();
+
+ const int xperiodic = domain->xperiodic;
+ const int yperiodic = domain->yperiodic;
+ const int zperiodic = domain->zperiodic;
+ const flt_t xprd_half = domain->xprd_half;
+ const flt_t yprd_half = domain->yprd_half;
+ const flt_t zprd_half = domain->zprd_half;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ const int * _noalias const binhead = this->binhead;
+ const int * _noalias const bins = this->bins;
+ const int cop = _fix->coprocessor_number();
+ const int separate_buffers = _fix->separate_buffers();
+ #pragma offload target(mic:cop) if(offload) \
+ in(x:length(e_nall+1) alloc_if(0) free_if(0)) \
+ in(tag:length(tag_size) alloc_if(0) free_if(0)) \
+ in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
+ in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
+ in(bins,binpacked:length(nall) alloc_if(0) free_if(0)) \
+ in(binhead:length(mbins+1) alloc_if(0) free_if(0)) \
+ in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
+ in(firstneigh:length(0) alloc_if(0) free_if(0)) \
+ in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
+ out(numneigh:length(0) alloc_if(0) free_if(0)) \
+ in(ilist:length(0) alloc_if(0) free_if(0)) \
+ in(atombin:length(aend) alloc_if(0) free_if(0)) \
+ in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
+ in(maxnbors,nthreads,maxspecial,nstencil,e_nall,offload,pack_width) \
+ in(offload_end,separate_buffers,astart, aend, nlocal, molecular, ntypes) \
+ in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \
+ out(overflow:length(5) alloc_if(0) free_if(0)) \
+ out(timer_compute:length(1) alloc_if(0) free_if(0)) \
+ signal(tag)
+ #endif
+ {
+ #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
+ *timer_compute = MIC_Wtime();
+ #endif
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ overflow[LMP_LOCAL_MIN] = astart;
+ overflow[LMP_LOCAL_MAX] = aend - 1;
+ overflow[LMP_GHOST_MIN] = e_nall;
+ overflow[LMP_GHOST_MAX] = -1;
+ #endif
+
+ int nstencilp = 0;
+ int binstart[INTEL_MAX_STENCIL], binend[INTEL_MAX_STENCIL];
+ for (int k = 0; k < nstencil; k++) {
+ binstart[nstencilp] = stencil[k];
+ int end = stencil[k] + 1;
+ for (int kk = k + 1; kk < nstencil; kk++) {
+ if (stencil[kk-1]+1 == stencil[kk]) {
+ end++;
+ k++;
+ } else break;
+ }
+ binend[nstencilp] = end;
+ nstencilp++;
+ }
+
+ #if defined(_OPENMP)
+ #pragma omp parallel default(none) \
+ shared(numneigh, overflow, nstencilp, binstart, binend)
+ #endif
+ {
+ #ifdef _LMP_INTEL_OFFLOAD
+ int lmin = e_nall, lmax = -1, gmin = e_nall, gmax = -1;
+ #endif
+
+ const int num = aend - astart;
+ int tid, ifrom, ito;
+
+ IP_PRE_omp_range_id_vec(ifrom, ito, tid, num, nthreads, pack_width);
+ ifrom += astart;
+ ito += astart;
+ int e_ito = ito;
+ if (ito == num) {
+ int imod = ito % pack_width;
+ if (imod) e_ito += pack_width - imod;
+ }
+ const int list_size = (e_ito + tid * 2 + 2) * maxnbors;
+ int which;
+ int pack_offset = maxnbors * pack_width;
+ int ct = (ifrom + tid * 2) * maxnbors;
+ int *neighptr = firstneigh + ct;
+ const int obound = pack_offset + maxnbors * 2;
+
+ int max_chunk = 0;
+ int lane = 0;
+ for (int i = ifrom; i < ito; i++) {
+ const flt_t xtmp = x[i].x;
+ const flt_t ytmp = x[i].y;
+ const flt_t ztmp = x[i].z;
+ const int itype = x[i].w;
+ const tagint itag = tag[i];
+ const int ioffset = ntypes * itype;
+
+ const int ibin = atombin[i];
+ int raw_count = pack_offset;
+
+ // loop over all atoms in surrounding bins in stencil including self
+ // skip i = j
+ if (exclude) {
+ for (int k = 0; k < nstencilp; k++) {
+ const int bstart = binhead[ibin + binstart[k]];
+ const int bend = binhead[ibin + binend[k]];
+ #ifndef _LMP_INTEL_OFFLOAD
+ #ifdef INTEL_VMASK
+ #pragma simd
+ #endif
+ #endif
+ for (int jj = bstart; jj < bend; jj++) {
+ int j = binpacked[jj];
+
+ if (i == j) j=e_nall;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload_noghost) {
+ if (j < nlocal) {
+ if (i < offload_end) continue;
+ } else if (offload) continue;
+ }
+ #endif
+
+ #ifndef _LMP_INTEL_OFFLOAD
+ const int jtype = x[j].w;
+ if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
+ #endif
+
+ neighptr[raw_count++] = j;
+ }
+ }
+ } else {
+ for (int k = 0; k < nstencilp; k++) {
+ const int bstart = binhead[ibin + binstart[k]];
+ const int bend = binhead[ibin + binend[k]];
+ #ifndef _LMP_INTEL_OFFLOAD
+ #ifdef INTEL_VMASK
+ #pragma simd
+ #endif
+ #endif
+ for (int jj = bstart; jj < bend; jj++) {
+ int j = binpacked[jj];
+
+ if (i == j) j=e_nall;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload_noghost) {
+ if (j < nlocal) {
+ if (i < offload_end) continue;
+ } else if (offload) continue;
+ }
+ #endif
+
+ neighptr[raw_count++] = j;
+ }
+ }
+ }
+
+ if (raw_count > obound) *overflow = 1;
+
+ #if defined(LMP_SIMD_COMPILER)
+ #ifdef _LMP_INTEL_OFFLOAD
+ int vlmin = lmin, vlmax = lmax, vgmin = gmin, vgmax = gmax;
+ #if __INTEL_COMPILER+0 > 1499
+ #pragma vector aligned
+ #pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin)
+ #endif
+ #else
+ #pragma vector aligned
+ #pragma simd
+ #endif
+ #endif
+ for (int u = pack_offset; u < raw_count; u++) {
+ int j = neighptr[u];
+ const flt_t delx = xtmp - x[j].x;
+ const flt_t dely = ytmp - x[j].y;
+ const flt_t delz = ztmp - x[j].z;
+ const int jtype = x[j].w;
+ const flt_t rsq = delx * delx + dely * dely + delz * delz;
+ if (rsq > cutneighsq[ioffset + jtype])
+ neighptr[u] = e_nall;
+ else {
+ if (need_ic) {
+ int no_special;
+ ominimum_image_check(no_special, delx, dely, delz);
+ if (no_special)
+ neighptr[u] = -j - 1;
+ }
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (j < nlocal) {
+ if (j < vlmin) vlmin = j;
+ if (j > vlmax) vlmax = j;
+ } else {
+ if (j < vgmin) vgmin = j;
+ if (j > vgmax) vgmax = j;
+ }
+ #endif
+ }
+ }
+ #ifdef _LMP_INTEL_OFFLOAD
+ lmin = MIN(lmin,vlmin);
+ gmin = MIN(gmin,vgmin);
+ lmax = MAX(lmax,vlmax);
+ gmax = MAX(gmax,vgmax);
+ #endif
+
+ int n = lane, n2 = pack_offset;
+ for (int u = pack_offset; u < raw_count; u++) {
+ const int j = neighptr[u];
+ int pj = j;
+ if (pj < e_nall) {
+ if (need_ic)
+ if (pj < 0) pj = -pj - 1;
+
+ const int jtag = tag[pj];
+ int flist = 0;
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) flist = 1;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) flist = 1;
+ } else {
+ if (x[pj].z < ztmp) flist = 1;
+ else if (x[pj].z == ztmp && x[pj].y < ytmp) flist = 1;
+ else if (x[pj].z == ztmp && x[pj].y == ytmp && x[pj].x < xtmp)
+ flist = 1;
+ }
+ if (flist) {
+ neighptr[n2++] = j;
+ } else {
+ neighptr[n] = j;
+ n += pack_width;
+ }
+ }
+ }
+ int ns = (n - lane) / pack_width;
+ atombin[i] = ns;
+ for (int u = pack_offset; u < n2; u++) {
+ neighptr[n] = neighptr[u];
+ n += pack_width;
+ }
+
+ ilist[i] = i;
+ cnumneigh[i] = ct + lane;
+ ns += n2 - pack_offset;
+ numneigh[i] = ns;
+
+ if (ns > max_chunk) max_chunk = ns;
+ lane++;
+ if (lane == pack_width) {
+ ct += max_chunk * pack_width;
+ const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
+ const int edge = (ct % alignb);
+ if (edge) ct += alignb - edge;
+ neighptr = firstneigh + ct;
+ max_chunk = 0;
+ pack_offset = maxnbors * pack_width;
+ lane = 0;
+ if (ct + obound > list_size) {
+ if (i < ito - 1) {
+ *overflow = 1;
+ ct = (ifrom + tid * 2) * maxnbors;
+ }
+ }
+ }
+ }
+
+ if (*overflow == 1)
+ for (int i = ifrom; i < ito; i++)
+ numneigh[i] = 0;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (separate_buffers) {
+ #if defined(_OPENMP)
+ #pragma omp critical
+ #endif
+ {
+ if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
+ if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
+ if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
+ if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
+ }
+ #pragma omp barrier
+ }
+
+ int ghost_offset = 0, nall_offset = e_nall;
+ if (separate_buffers) {
+ int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
+ if (nghost < 0) nghost = 0;
+ if (offload) {
+ ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
+ nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
+ } else {
+ ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
+ nall_offset = nlocal + nghost;
+ }
+ }
+ #endif
+
+ if (molecular) {
+ for (int i = ifrom; i < ito; ++i) {
+ int * _noalias jlist = firstneigh + cnumneigh[i];
+ const int jnum = numneigh[i];
+
+ const int trip = jnum * pack_width;
+ for (int jj = 0; jj < trip; jj+=pack_width) {
+ const int j = jlist[jj];
+ if (need_ic && j < 0) {
+ which = 0;
+ jlist[jj] = -j - 1;
+ } else
+ ofind_special(which, special, nspecial, i, tag[j]);
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (j >= nlocal) {
+ if (j == e_nall)
+ jlist[jj] = nall_offset;
+ else if (which)
+ jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
+ else jlist[jj]-=ghost_offset;
+ } else
+ #endif
+ if (which) jlist[jj] = j ^ (which << SBBITS);
+ }
+ }
+ }
+ #ifdef _LMP_INTEL_OFFLOAD
+ else if (separate_buffers) {
+ for (int i = ifrom; i < ito; ++i) {
+ int * _noalias jlist = firstneigh + cnumneigh[i];
+ const int jnum = numneigh[i];
+ int jj = 0;
+ for (jj = 0; jj < jnum; jj++) {
+ if (jlist[jj] >= nlocal) {
+ if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
+ else jlist[jj] -= ghost_offset;
+ }
+ }
+ }
+ }
+ #endif
+ } // end omp
+ #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
+ *timer_compute = MIC_Wtime() - *timer_compute;
+ #endif
+ } // end offload
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload) {
+ _fix->stop_watch(TIME_OFFLOAD_LATENCY);
+ _fix->start_watch(TIME_HOST_NEIGHBOR);
+ for (int n = 0; n < aend; n++) {
+ ilist[n] = n;
+ numneigh[n] = 0;
+ }
+ } else {
+ for (int i = astart; i < aend; i++)
+ list->firstneigh[i] = firstneigh + cnumneigh[i];
+ if (separate_buffers) {
+ _fix->start_watch(TIME_PACK);
+ _fix->set_neighbor_host_sizes();
+ buffers->pack_sep_from_single(_fix->host_min_local(),
+ _fix->host_used_local(),
+ _fix->host_min_ghost(),
+ _fix->host_used_ghost());
+ _fix->stop_watch(TIME_PACK);
+ }
+ }
+ #else
+ for (int i = astart; i < aend; i++)
+ list->firstneigh[i] = firstneigh + cnumneigh[i];
+ #endif
+}
diff --git a/src/USER-INTEL/npair_full_bin_intel.h b/src/USER-INTEL/npair_full_bin_intel.h
new file mode 100644
index 0000000000..608bd0f5dd
--- /dev/null
+++ b/src/USER-INTEL/npair_full_bin_intel.h
@@ -0,0 +1,51 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(full/bin/intel,
+ NPairFullBinIntel,
+ NP_FULL | NP_BIN | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI |
+ NP_INTEL)
+#else
+
+#ifndef LMP_NPAIR_FULL_BIN_INTEL_H
+#define LMP_NPAIR_FULL_BIN_INTEL_H
+
+#include "npair_intel.h"
+#include "fix_intel.h"
+
+namespace LAMMPS_NS {
+
+class NPairFullBinIntel : public NPairIntel {
+ public:
+ NPairFullBinIntel(class LAMMPS *);
+ ~NPairFullBinIntel() {}
+ void build(class NeighList *);
+
+ private:
+ template <class flt_t, class acc_t>
+ void fbi(NeighList *, IntelBuffers<flt_t,acc_t> *);
+ template <class flt_t, class acc_t, int, int>
+ void fbi(const int, NeighList *, IntelBuffers<flt_t,acc_t> *, const int,
+ const int, const int offload_end = 0);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-INTEL/npair_half_bin_newtoff_intel.cpp b/src/USER-INTEL/npair_half_bin_newtoff_intel.cpp
new file mode 100644
index 0000000000..1fcc3f0759
--- /dev/null
+++ b/src/USER-INTEL/npair_half_bin_newtoff_intel.cpp
@@ -0,0 +1,451 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: W. Michael Brown (Intel)
+------------------------------------------------------------------------- */
+
+#include "npair_half_bin_newtoff_intel.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "comm.h"
+#include "group.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfBinNewtoffIntel::NPairHalfBinNewtoffIntel(LAMMPS *lmp) :
+ NPairIntel(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with partial Newton's 3rd law
+ each owned atom i checks own bin and other bins in stencil
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfBinNewtoffIntel::build(NeighList *list)
+{
+ if (nstencil > INTEL_MAX_STENCIL_CHECK)
+ error->all(FLERR, "Too many neighbor bins for USER-INTEL package.");
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (exclude)
+ error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
+ #endif
+
+ if (_fix->precision() == FixIntel::PREC_MODE_MIXED)
+ hbnni(list, _fix->get_mixed_buffers());
+ else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE)
+ hbnni(list, _fix->get_double_buffers());
+ else
+ hbnni(list, _fix->get_single_buffers());
+
+ _fix->stop_watch(TIME_HOST_NEIGHBOR);
+}
+
+template <class flt_t, class acc_t>
+void NPairHalfBinNewtoffIntel::
+hbnni(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ list->inum = nlocal;
+
+ const int off_end = _fix->offload_end_neighbor();
+ int host_start = off_end;;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (off_end) grow_stencil();
+ if (_fix->full_host_list()) host_start = 0;
+ #endif
+
+ buffers->grow_list(list, atom->nlocal, comm->nthreads, off_end);
+
+ int need_ic = 0;
+ if (atom->molecular)
+ dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
+ neighbor->cutneighmax);
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (need_ic) {
+ hbnni<flt_t,acc_t,1>(1, list, buffers, 0, off_end);
+ hbnni<flt_t,acc_t,1>(0, list, buffers, host_start, nlocal);
+ } else {
+ hbnni<flt_t,acc_t,0>(1, list, buffers, 0, off_end);
+ hbnni<flt_t,acc_t,0>(0, list, buffers, host_start, nlocal);
+ }
+ #else
+ if (need_ic)
+ hbnni<flt_t,acc_t,1>(0, list, buffers, host_start, nlocal);
+ else
+ hbnni<flt_t,acc_t,0>(0, list, buffers, host_start, nlocal);
+ #endif
+}
+
+template <class flt_t, class acc_t, int need_ic>
+void NPairHalfBinNewtoffIntel::
+hbnni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
+ const int astart, const int aend) {
+
+ if (aend-astart == 0) return;
+
+ const int nall = atom->nlocal + atom->nghost;
+ int pad = 1;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload) {
+ if (INTEL_MIC_NBOR_PAD > 1)
+ pad = INTEL_MIC_NBOR_PAD * sizeof(float) / sizeof(flt_t);
+ } else
+ #endif
+ if (INTEL_NBOR_PAD > 1)
+ pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t);
+ const int pad_width = pad;
+
+ const ATOM_T * _noalias const x = buffers->get_x();
+ int * _noalias const firstneigh = buffers->firstneigh(list);
+
+ const int molecular = atom->molecular;
+ int *ns = NULL;
+ tagint *s = NULL;
+ int tag_size = 0, special_size;
+ if (buffers->need_tag()) tag_size = nall;
+ if (molecular) {
+ s = atom->special[0];
+ ns = atom->nspecial[0];
+ special_size = aend;
+ } else {
+ s = &buffers->_special_holder;
+ ns = &buffers->_nspecial_holder;
+ special_size = 0;
+ }
+ const tagint * _noalias const special = s;
+ const int * _noalias const nspecial = ns;
+ const int maxspecial = atom->maxspecial;
+ const tagint * _noalias const tag = atom->tag;
+
+ int * _noalias const ilist = list->ilist;
+ int * _noalias numneigh = list->numneigh;
+ int * _noalias const cnumneigh = buffers->cnumneigh(list);
+ const int nstencil = this->nstencil;
+ const int * _noalias const stencil = this->stencil;
+ const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
+ const int ntypes = atom->ntypes + 1;
+ const int nlocal = atom->nlocal;
+
+ #ifndef _LMP_INTEL_OFFLOAD
+ int * const mask = atom->mask;
+ tagint * const molecule = atom->molecule;
+ #endif
+
+ int tnum;
+ int *overflow;
+ double *timer_compute;
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload) {
+ timer_compute = _fix->off_watch_neighbor();
+ tnum = buffers->get_off_threads();
+ overflow = _fix->get_off_overflow_flag();
+ _fix->stop_watch(TIME_HOST_NEIGHBOR);
+ _fix->start_watch(TIME_OFFLOAD_LATENCY);
+ } else
+ #endif
+ {
+ tnum = comm->nthreads;
+ overflow = _fix->get_overflow_flag();
+ }
+ const int nthreads = tnum;
+ const int maxnbors = buffers->get_max_nbors();
+ int * _noalias const atombin = buffers->get_atombin();
+ const int * _noalias const binpacked = buffers->get_binpacked();
+
+ const int xperiodic = domain->xperiodic;
+ const int yperiodic = domain->yperiodic;
+ const int zperiodic = domain->zperiodic;
+ const flt_t xprd_half = domain->xprd_half;
+ const flt_t yprd_half = domain->yprd_half;
+ const flt_t zprd_half = domain->zprd_half;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ const int * _noalias const binhead = this->binhead;
+ const int * _noalias const bins = this->bins;
+ const int cop = _fix->coprocessor_number();
+ const int separate_buffers = _fix->separate_buffers();
+ #pragma offload target(mic:cop) if(offload) \
+ in(x:length(nall+1) alloc_if(0) free_if(0)) \
+ in(tag:length(tag_size) alloc_if(0) free_if(0)) \
+ in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
+ in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
+ in(bins,binpacked:length(nall) alloc_if(0) free_if(0)) \
+ in(binhead:length(mbins+1) alloc_if(0) free_if(0)) \
+ in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
+ in(firstneigh:length(0) alloc_if(0) free_if(0)) \
+ in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
+ out(numneigh:length(0) alloc_if(0) free_if(0)) \
+ in(ilist:length(0) alloc_if(0) free_if(0)) \
+ in(atombin:length(aend) alloc_if(0) free_if(0)) \
+ in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
+ in(maxnbors,nthreads,maxspecial,nstencil,pad_width,offload,nall) \
+ in(separate_buffers, astart, aend, nlocal, molecular, ntypes) \
+ in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \
+ out(overflow:length(5) alloc_if(0) free_if(0)) \
+ out(timer_compute:length(1) alloc_if(0) free_if(0)) \
+ signal(tag)
+ #endif
+ {
+ #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
+ *timer_compute = MIC_Wtime();
+ #endif
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ overflow[LMP_LOCAL_MIN] = astart;
+ overflow[LMP_LOCAL_MAX] = aend - 1;
+ overflow[LMP_GHOST_MIN] = nall;
+ overflow[LMP_GHOST_MAX] = -1;
+ #endif
+
+ int nstencilp = 0;
+ int binstart[INTEL_MAX_STENCIL], binend[INTEL_MAX_STENCIL];
+ for (int k = 0; k < nstencil; k++) {
+ binstart[nstencilp] = stencil[k];
+ int end = stencil[k] + 1;
+ for (int kk = k + 1; kk < nstencil; kk++) {
+ if (stencil[kk-1]+1 == stencil[kk]) {
+ end++;
+ k++;
+ } else break;
+ }
+ binend[nstencilp] = end;
+ nstencilp++;
+ }
+
+ #if defined(_OPENMP)
+ #pragma omp parallel default(none) \
+ shared(numneigh, overflow, nstencilp, binstart, binend)
+ #endif
+ {
+ #ifdef _LMP_INTEL_OFFLOAD
+ int lmin = nall, lmax = -1, gmin = nall, gmax = -1;
+ #endif
+
+ const int num = aend - astart;
+ int tid, ifrom, ito;
+ IP_PRE_omp_range_id(ifrom, ito, tid, num, nthreads);
+ ifrom += astart;
+ ito += astart;
+
+ int which;
+
+ const int list_size = (ito + tid + 1) * maxnbors;
+ int ct = (ifrom + tid) * maxnbors;
+ int *neighptr = firstneigh + ct;
+
+ for (int i = ifrom; i < ito; i++) {
+ int j, k, n, n2, itype, jtype, ibin;
+ double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
+
+ n = 0;
+ n2 = maxnbors;
+
+ xtmp = x[i].x;
+ ytmp = x[i].y;
+ ztmp = x[i].z;
+ itype = x[i].w;
+ const int ioffset = ntypes*itype;
+
+ // loop over all atoms in other bins in stencil including self
+ // only store pair if i < j
+ // stores own/own pairs only once
+ // stores own/ghost pairs on both procs
+
+ ibin = atombin[i];
+
+ for (k = 0; k < nstencilp; k++) {
+ const int bstart = binhead[ibin + binstart[k]];
+ const int bend = binhead[ibin + binend[k]];
+ for (int jj = bstart; jj < bend; jj++) {
+ const int j = binpacked[jj];
+ if (j <= i) continue;
+
+ jtype = x[j].w;
+ #ifndef _LMP_INTEL_OFFLOAD
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+ #endif
+
+ delx = xtmp - x[j].x;
+ dely = ytmp - x[j].y;
+ delz = ztmp - x[j].z;
+ rsq = delx * delx + dely * dely + delz * delz;
+ if (rsq <= cutneighsq[ioffset + jtype]) {
+ if (j < nlocal) {
+ if (need_ic) {
+ int no_special;
+ ominimum_image_check(no_special, delx, dely, delz);
+ if (no_special)
+ neighptr[n++] = -j - 1;
+ else
+ neighptr[n++] = j;
+ } else
+ neighptr[n++] = j;
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (j < lmin) lmin = j;
+ if (j > lmax) lmax = j;
+ #endif
+ } else {
+ if (need_ic) {
+ int no_special;
+ ominimum_image_check(no_special, delx, dely, delz);
+ if (no_special)
+ neighptr[n2++] = -j - 1;
+ else
+ neighptr[n2++] = j;
+ } else
+ neighptr[n2++] = j;
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (j < gmin) gmin = j;
+ if (j > gmax) gmax = j;
+ #endif
+ }
+ }
+ }
+ }
+ ilist[i] = i;
+
+ cnumneigh[i] = ct;
+ if (n > maxnbors) *overflow = 1;
+ for (k = maxnbors; k < n2; k++) neighptr[n++] = neighptr[k];
+
+ const int edge = (n % pad_width);
+ if (edge) {
+ const int pad_end = n + (pad_width - edge);
+ #if defined(LMP_SIMD_COMPILER)
+ #pragma loop_count min=1, max=15, avg=8
+ #endif
+ for ( ; n < pad_end; n++)
+ neighptr[n] = nall;
+ }
+ numneigh[i] = n;
+ while((n % (INTEL_DATA_ALIGN / sizeof(int))) != 0) n++;
+ ct += n;
+ neighptr += n;
+ if (ct + n + maxnbors > list_size) {
+ *overflow = 1;
+ ct = (ifrom + tid) * maxnbors;
+ }
+ }
+
+ if (*overflow == 1)
+ for (int i = ifrom; i < ito; i++)
+ numneigh[i] = 0;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (separate_buffers) {
+ #if defined(_OPENMP)
+ #pragma omp critical
+ #endif
+ {
+ if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
+ if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
+ if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
+ if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
+ }
+ #pragma omp barrier
+ }
+
+ int ghost_offset = 0, nall_offset = nall;
+ if (separate_buffers) {
+ int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
+ if (nghost < 0) nghost = 0;
+ if (offload) {
+ ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
+ nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
+ } else {
+ ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
+ nall_offset = nlocal + nghost;
+ }
+ }
+ #endif
+
+ if (molecular) {
+ for (int i = ifrom; i < ito; ++i) {
+ int * _noalias jlist = firstneigh + cnumneigh[i];
+ const int jnum = numneigh[i];
+ for (int jj = 0; jj < jnum; jj++) {
+ const int j = jlist[jj];
+ if (need_ic && j < 0) {
+ which = 0;
+ jlist[jj] = -j - 1;
+ } else
+ ofind_special(which, special, nspecial, i, tag[j]);
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (j >= nlocal) {
+ if (j == nall)
+ jlist[jj] = nall_offset;
+ else if (which)
+ jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
+ else jlist[jj]-=ghost_offset;
+ } else
+ #endif
+ if (which) jlist[jj] = j ^ (which << SBBITS);
+ }
+ }
+ }
+ #ifdef _LMP_INTEL_OFFLOAD
+ else if (separate_buffers) {
+ for (int i = ifrom; i < ito; ++i) {
+ int * _noalias jlist = firstneigh + cnumneigh[i];
+ const int jnum = numneigh[i];
+ int jj = 0;
+ for (jj = 0; jj < jnum; jj++)
+ if (jlist[jj] >= nlocal) break;
+ while (jj < jnum) {
+ if (jlist[jj] == nall) jlist[jj] = nall_offset;
+ else jlist[jj] -= ghost_offset;
+ jj++;
+ }
+ }
+ }
+ #endif
+ } // end omp
+ #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
+ *timer_compute = MIC_Wtime() - *timer_compute;
+ #endif
+ } // end offload
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload) {
+ _fix->stop_watch(TIME_OFFLOAD_LATENCY);
+ _fix->start_watch(TIME_HOST_NEIGHBOR);
+ for (int n = 0; n < aend; n++) {
+ ilist[n] = n;
+ numneigh[n] = 0;
+ }
+ } else {
+ for (int i = astart; i < aend; i++)
+ list->firstneigh[i] = firstneigh + cnumneigh[i];
+ if (separate_buffers) {
+ _fix->start_watch(TIME_PACK);
+ _fix->set_neighbor_host_sizes();
+ buffers->pack_sep_from_single(_fix->host_min_local(),
+ _fix->host_used_local(),
+ _fix->host_min_ghost(),
+ _fix->host_used_ghost());
+ _fix->stop_watch(TIME_PACK);
+ }
+ }
+ #else
+ for (int i = astart; i < aend; i++)
+ list->firstneigh[i] = firstneigh + cnumneigh[i];
+ #endif
+}
diff --git a/src/USER-INTEL/npair_half_bin_newtoff_intel.h b/src/USER-INTEL/npair_half_bin_newtoff_intel.h
new file mode 100644
index 0000000000..ccb4560909
--- /dev/null
+++ b/src/USER-INTEL/npair_half_bin_newtoff_intel.h
@@ -0,0 +1,52 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/bin/newtoff/intel,
+ NPairHalfBinNewtoffIntel,
+ NP_HALF | NP_BIN | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_INTEL)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_BIN_NEWTOFF_INTEL_H
+#define LMP_NPAIR_HALF_BIN_NEWTOFF_INTEL_H
+
+#include "npair_intel.h"
+#include "fix_intel.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfBinNewtoffIntel : public NPairIntel {
+ public:
+ NPairHalfBinNewtoffIntel(class LAMMPS *);
+ ~NPairHalfBinNewtoffIntel() {}
+ void build(class NeighList *);
+
+ private:
+ template <class flt_t, class acc_t>
+ void hbnni(NeighList *, IntelBuffers<flt_t,acc_t> *);
+ template <class flt_t, class acc_t, int>
+ void hbnni(const int, NeighList *, IntelBuffers<flt_t,acc_t> *, const int,
+ const int);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+
+*/
diff --git a/src/USER-INTEL/npair_half_bin_newton_intel.cpp b/src/USER-INTEL/npair_half_bin_newton_intel.cpp
new file mode 100644
index 0000000000..5584f962e9
--- /dev/null
+++ b/src/USER-INTEL/npair_half_bin_newton_intel.cpp
@@ -0,0 +1,610 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: W. Michael Brown (Intel)
+------------------------------------------------------------------------- */
+
+#include "npair_half_bin_newton_intel.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "comm.h"
+#include "group.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfBinNewtonIntel::NPairHalfBinNewtonIntel(LAMMPS *lmp) :
+ NPairIntel(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with full Newton's 3rd law
+ each owned atom i checks its own bin and other bins in Newton stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfBinNewtonIntel::build(NeighList *list)
+{
+ if (nstencil / 2 > INTEL_MAX_STENCIL_CHECK)
+ error->all(FLERR, "Too many neighbor bins for USER-INTEL package.");
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (exclude)
+ error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
+ #endif
+
+ if (_fix->precision() == FixIntel::PREC_MODE_MIXED)
+ hbni(list, _fix->get_mixed_buffers());
+ else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE)
+ hbni(list, _fix->get_double_buffers());
+ else
+ hbni(list, _fix->get_single_buffers());
+
+ _fix->stop_watch(TIME_HOST_NEIGHBOR);
+}
+
+template <class flt_t, class acc_t>
+void NPairHalfBinNewtonIntel::
+hbni(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ list->inum = nlocal;
+
+ int host_start = _fix->host_start_neighbor();
+ const int off_end = _fix->offload_end_neighbor();
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (off_end) grow_stencil();
+ if (_fix->full_host_list()) host_start = 0;
+ int offload_noghost = _fix->offload_noghost();
+ #endif
+
+ buffers->grow_list(list, atom->nlocal, comm->nthreads, off_end);
+
+ int need_ic = 0;
+ if (atom->molecular)
+ dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
+ neighbor->cutneighmax);
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (need_ic) {
+ if (offload_noghost) {
+ hbni<flt_t,acc_t,1,1>(1, list, buffers, 0, off_end);
+ hbni<flt_t,acc_t,1,1>(0, list, buffers, host_start, nlocal, off_end);
+ } else {
+ hbni<flt_t,acc_t,0,1>(1, list, buffers, 0, off_end);
+ hbni<flt_t,acc_t,0,1>(0, list, buffers, host_start, nlocal);
+ }
+ } else {
+ if (offload_noghost) {
+ hbni<flt_t,acc_t,1,0>(1, list, buffers, 0, off_end);
+ hbni<flt_t,acc_t,1,0>(0, list, buffers, host_start, nlocal, off_end);
+ } else {
+ hbni<flt_t,acc_t,0,0>(1, list, buffers, 0, off_end);
+ hbni<flt_t,acc_t,0,0>(0, list, buffers, host_start, nlocal);
+ }
+ }
+ #else
+ if (need_ic)
+ hbni<flt_t,acc_t,0,1>(0, list, buffers, host_start, nlocal);
+ else
+ hbni<flt_t,acc_t,0,0>(0, list, buffers, host_start, nlocal);
+ #endif
+}
+
+template <class flt_t, class acc_t, int offload_noghost, int need_ic>
+void NPairHalfBinNewtonIntel::
+hbni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
+ const int astart, const int aend, const int offload_end) {
+
+ if (aend-astart == 0) return;
+
+ const int nall = atom->nlocal + atom->nghost;
+ int pad = 1;
+ int nall_t = nall;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload_noghost && offload) nall_t = atom->nlocal;
+ if (offload) {
+ if (INTEL_MIC_NBOR_PAD > 1)
+ pad = INTEL_MIC_NBOR_PAD * sizeof(float) / sizeof(flt_t);
+ } else
+ #endif
+ if (INTEL_NBOR_PAD > 1)
+ pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t);
+ const int pad_width = pad;
+
+ const ATOM_T * _noalias const x = buffers->get_x();
+ int * _noalias const firstneigh = buffers->firstneigh(list);
+ const int e_nall = nall_t;
+
+ const int molecular = atom->molecular;
+ int *ns = NULL;
+ tagint *s = NULL;
+ int tag_size = 0, special_size;
+ if (buffers->need_tag()) tag_size = e_nall;
+ if (molecular) {
+ s = atom->special[0];
+ ns = atom->nspecial[0];
+ special_size = aend;
+ } else {
+ s = &buffers->_special_holder;
+ ns = &buffers->_nspecial_holder;
+ special_size = 0;
+ }
+ const tagint * _noalias const special = s;
+ const int * _noalias const nspecial = ns;
+ const int maxspecial = atom->maxspecial;
+ const tagint * _noalias const tag = atom->tag;
+
+ int * _noalias const ilist = list->ilist;
+ int * _noalias numneigh = list->numneigh;
+ int * _noalias const cnumneigh = buffers->cnumneigh(list);
+ const int nstencil = this->nstencil;
+ const int * _noalias const stencil = this->stencil;
+ const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
+ const int ntypes = atom->ntypes + 1;
+ const int nlocal = atom->nlocal;
+
+ #ifndef _LMP_INTEL_OFFLOAD
+ int * const mask = atom->mask;
+ tagint * const molecule = atom->molecule;
+ #endif
+
+ int tnum;
+ int *overflow;
+ double *timer_compute;
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload) {
+ timer_compute = _fix->off_watch_neighbor();
+ tnum = buffers->get_off_threads();
+ overflow = _fix->get_off_overflow_flag();
+ _fix->stop_watch(TIME_HOST_NEIGHBOR);
+ _fix->start_watch(TIME_OFFLOAD_LATENCY);
+ } else
+ #endif
+ {
+ tnum = comm->nthreads;
+ overflow = _fix->get_overflow_flag();
+ }
+ const int nthreads = tnum;
+ const int maxnbors = buffers->get_max_nbors();
+ int * _noalias const atombin = buffers->get_atombin();
+ const int * _noalias const binpacked = buffers->get_binpacked();
+
+ const int xperiodic = domain->xperiodic;
+ const int yperiodic = domain->yperiodic;
+ const int zperiodic = domain->zperiodic;
+ const flt_t xprd_half = domain->xprd_half;
+ const flt_t yprd_half = domain->yprd_half;
+ const flt_t zprd_half = domain->zprd_half;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ const int * _noalias const binhead = this->binhead;
+ const int * _noalias const bins = this->bins;
+ const int cop = _fix->coprocessor_number();
+ const int separate_buffers = _fix->separate_buffers();
+ #pragma offload target(mic:cop) if(offload) \
+ in(x:length(e_nall+1) alloc_if(0) free_if(0)) \
+ in(tag:length(tag_size) alloc_if(0) free_if(0)) \
+ in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
+ in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
+ in(bins,binpacked:length(nall) alloc_if(0) free_if(0)) \
+ in(binhead:length(mbins+1) alloc_if(0) free_if(0)) \
+ in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
+ in(firstneigh:length(0) alloc_if(0) free_if(0)) \
+ in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
+ out(numneigh:length(0) alloc_if(0) free_if(0)) \
+ in(ilist:length(0) alloc_if(0) free_if(0)) \
+ in(atombin:length(aend) alloc_if(0) free_if(0)) \
+ in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
+ in(maxnbors,nthreads,maxspecial,nstencil,e_nall,offload,pad_width) \
+ in(offload_end,separate_buffers,astart, aend, nlocal, molecular, ntypes) \
+ in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \
+ out(overflow:length(5) alloc_if(0) free_if(0)) \
+ out(timer_compute:length(1) alloc_if(0) free_if(0)) \
+ signal(tag)
+ #endif
+ {
+ #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
+ *timer_compute = MIC_Wtime();
+ #endif
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ overflow[LMP_LOCAL_MIN] = astart;
+ overflow[LMP_LOCAL_MAX] = aend - 1;
+ overflow[LMP_GHOST_MIN] = e_nall;
+ overflow[LMP_GHOST_MAX] = -1;
+ #endif
+
+ int nstencilp = 0;
+ int binstart[INTEL_MAX_STENCIL], binend[INTEL_MAX_STENCIL];
+ for (int k = 0; k < nstencil; k++) {
+ binstart[nstencilp] = stencil[k];
+ int end = stencil[k] + 1;
+ for (int kk = k + 1; kk < nstencil; kk++) {
+ if (stencil[kk-1]+1 == stencil[kk]) {
+ end++;
+ k++;
+ } else break;
+ }
+ binend[nstencilp] = end;
+ nstencilp++;
+ }
+
+ #if defined(_OPENMP)
+ #pragma omp parallel default(none) \
+ shared(numneigh, overflow, nstencilp, binstart, binend)
+ #endif
+ {
+ #ifdef _LMP_INTEL_OFFLOAD
+ int lmin = e_nall, lmax = -1, gmin = e_nall, gmax = -1;
+ #endif
+
+ const int num = aend - astart;
+ int tid, ifrom, ito;
+
+ #ifdef OUTER_CHUNK
+ const int swidth = ip_simd::SIMD_type<flt_t>::width();
+ IP_PRE_omp_range_id_vec(ifrom, ito, tid, num, nthreads, swidth);
+ ifrom += astart;
+ ito += astart;
+ int e_ito = ito;
+ if (ito == num) {
+ int imod = ito % swidth;
+ if (imod) e_ito += swidth - imod;
+ }
+ const int list_size = (e_ito + tid * 2 + 2) * maxnbors;
+ #else
+ const int swidth = 1;
+ IP_PRE_omp_range_id(ifrom, ito, tid, num, nthreads);
+ ifrom += astart;
+ ito += astart;
+ const int list_size = (ito + tid * 2 + 2) * maxnbors;
+ #endif
+
+ int which;
+
+ int pack_offset = maxnbors * swidth;
+ int ct = (ifrom + tid * 2) * maxnbors;
+ int *neighptr = firstneigh + ct;
+ const int obound = pack_offset + maxnbors * 2;
+
+ int max_chunk = 0;
+ int lane = 0;
+ for (int i = ifrom; i < ito; i++) {
+ const flt_t xtmp = x[i].x;
+ const flt_t ytmp = x[i].y;
+ const flt_t ztmp = x[i].z;
+ const int itype = x[i].w;
+ const int ioffset = ntypes * itype;
+
+ // loop over rest of atoms in i's bin, ghosts are at end of linked list
+ // if j is owned atom, store it, since j is beyond i in linked list
+ // if j is ghost, only store if j coords are "above/to the right" of i
+
+ int raw_count = pack_offset;
+ for (int j = bins[i]; j >= 0; j = bins[j]) {
+ if (j >= nlocal) {
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload_noghost && offload) continue;
+ #endif
+ if (x[j].z < ztmp) continue;
+ if (x[j].z == ztmp) {
+ if (x[j].y < ytmp) continue;
+ if (x[j].y == ytmp && x[j].x < xtmp) continue;
+ }
+ }
+ #ifdef _LMP_INTEL_OFFLOAD
+ else if (offload_noghost && i < offload_end) continue;
+ #endif
+
+ #ifndef _LMP_INTEL_OFFLOAD
+ if (exclude) {
+ const int jtype = x[j].w;
+ if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
+ }
+ #endif
+
+ neighptr[raw_count++] = j;
+ }
+
+ // loop over all atoms in other bins in stencil, store every pair
+
+ const int ibin = atombin[i];
+ if (exclude) {
+ for (int k = 0; k < nstencilp; k++) {
+ const int bstart = binhead[ibin + binstart[k]];
+ const int bend = binhead[ibin + binend[k]];
+ #ifndef _LMP_INTEL_OFFLOAD
+ #ifdef INTEL_VMASK
+ #pragma simd
+ #endif
+ #endif
+ for (int jj = bstart; jj < bend; jj++) {
+ const int j = binpacked[jj];
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload_noghost) {
+ if (j < nlocal) {
+ if (i < offload_end) continue;
+ } else if (offload) continue;
+ }
+ #endif
+
+ #ifndef _LMP_INTEL_OFFLOAD
+ const int jtype = x[j].w;
+ if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
+ #endif
+
+ neighptr[raw_count++] = j;
+ }
+ }
+ } else {
+ for (int k = 0; k < nstencilp; k++) {
+ const int bstart = binhead[ibin + binstart[k]];
+ const int bend = binhead[ibin + binend[k]];
+ #ifndef _LMP_INTEL_OFFLOAD
+ #ifdef INTEL_VMASK
+ #pragma simd
+ #endif
+ #endif
+ for (int jj = bstart; jj < bend; jj++) {
+ const int j = binpacked[jj];
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload_noghost) {
+ if (j < nlocal) {
+ if (i < offload_end) continue;
+ } else if (offload) continue;
+ }
+ #endif
+
+ neighptr[raw_count++] = j;
+ }
+ }
+ }
+
+ if (raw_count > obound) *overflow = 1;
+
+ #if defined(LMP_SIMD_COMPILER)
+ #ifdef _LMP_INTEL_OFFLOAD
+ int vlmin = lmin, vlmax = lmax, vgmin = gmin, vgmax = gmax;
+ #if __INTEL_COMPILER+0 > 1499
+ #pragma vector aligned
+ #pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin)
+ #endif
+ #else
+ #pragma vector aligned
+ #pragma simd
+ #endif
+ #endif
+ for (int u = pack_offset; u < raw_count; u++) {
+ int j = neighptr[u];
+ const flt_t delx = xtmp - x[j].x;
+ const flt_t dely = ytmp - x[j].y;
+ const flt_t delz = ztmp - x[j].z;
+ const int jtype = x[j].w;
+ const flt_t rsq = delx * delx + dely * dely + delz * delz;
+ if (rsq > cutneighsq[ioffset + jtype])
+ neighptr[u] = e_nall;
+ else {
+ if (need_ic) {
+ int no_special;
+ ominimum_image_check(no_special, delx, dely, delz);
+ if (no_special)
+ neighptr[u] = -j - 1;
+ }
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (j < nlocal) {
+ if (j < vlmin) vlmin = j;
+ if (j > vlmax) vlmax = j;
+ } else {
+ if (j < vgmin) vgmin = j;
+ if (j > vgmax) vgmax = j;
+ }
+ #endif
+ }
+ }
+ #ifdef _LMP_INTEL_OFFLOAD
+ lmin = MIN(lmin,vlmin);
+ gmin = MIN(gmin,vgmin);
+ lmax = MAX(lmax,vlmax);
+ gmax = MAX(gmax,vgmax);
+ #endif
+
+ int n = lane, n2 = pack_offset;
+ for (int u = pack_offset; u < raw_count; u++) {
+ const int j = neighptr[u];
+ int pj = j;
+ if (pj < e_nall) {
+ if (need_ic)
+ if (pj < 0) pj = -pj - 1;
+
+ if (pj < nlocal) {
+ neighptr[n] = j;
+ n += swidth;
+ } else
+ neighptr[n2++] = j;
+ }
+ }
+ int ns = (n - lane) / swidth;
+ for (int u = pack_offset; u < n2; u++) {
+ neighptr[n] = neighptr[u];
+ n += swidth;
+ }
+
+ ilist[i] = i;
+ cnumneigh[i] = ct + lane;
+ ns += n2 - pack_offset;
+ #ifndef OUTER_CHUNK
+ int edge = (ns % pad_width);
+ if (edge) {
+ const int pad_end = ns + (pad_width - edge);
+ #if defined(LMP_SIMD_COMPILER)
+ #pragma loop_count min=1, max=15, avg=8
+ #endif
+ for ( ; ns < pad_end; ns++)
+ neighptr[ns] = e_nall;
+ }
+ #endif
+ numneigh[i] = ns;
+
+ #ifdef OUTER_CHUNK
+ if (ns > max_chunk) max_chunk = ns;
+ lane++;
+ if (lane == swidth) {
+ ct += max_chunk * swidth;
+ const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
+ int edge = (ct % alignb);
+ if (edge) ct += alignb - edge;
+ neighptr = firstneigh + ct;
+ max_chunk = 0;
+ pack_offset = maxnbors * swidth;
+ lane = 0;
+ if (ct + obound > list_size) {
+ if (i < ito - 1) {
+ *overflow = 1;
+ ct = (ifrom + tid * 2) * maxnbors;
+ }
+ }
+ }
+ #else
+ ct += ns;
+ const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
+ edge = (ct % alignb);
+ if (edge) ct += alignb - edge;
+ neighptr = firstneigh + ct;
+ if (ct + obound > list_size) {
+ if (i < ito - 1) {
+ *overflow = 1;
+ ct = (ifrom + tid * 2) * maxnbors;
+ }
+ }
+ #endif
+ }
+
+ if (*overflow == 1)
+ for (int i = ifrom; i < ito; i++)
+ numneigh[i] = 0;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (separate_buffers) {
+ #if defined(_OPENMP)
+ #pragma omp critical
+ #endif
+ {
+ if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
+ if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
+ if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
+ if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
+ }
+ #pragma omp barrier
+ }
+
+ int ghost_offset = 0, nall_offset = e_nall;
+ if (separate_buffers) {
+ int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
+ if (nghost < 0) nghost = 0;
+ if (offload) {
+ ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
+ nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
+ } else {
+ ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
+ nall_offset = nlocal + nghost;
+ }
+ }
+ #endif
+
+ if (molecular) {
+ for (int i = ifrom; i < ito; ++i) {
+ int * _noalias jlist = firstneigh + cnumneigh[i];
+ const int jnum = numneigh[i];
+ #ifndef OUTER_CHUNK
+ #if defined(LMP_SIMD_COMPILER)
+ #pragma vector aligned
+ #pragma simd
+ #endif
+ for (int jj = 0; jj < jnum; jj++) {
+ #else
+ const int trip = jnum * swidth;
+ for (int jj = 0; jj < trip; jj+= swidth) {
+ #endif
+ const int j = jlist[jj];
+ if (need_ic && j < 0) {
+ which = 0;
+ jlist[jj] = -j - 1;
+ } else
+ ofind_special(which, special, nspecial, i, tag[j]);
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (j >= nlocal) {
+ if (j == e_nall)
+ jlist[jj] = nall_offset;
+ else if (which)
+ jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
+ else jlist[jj]-=ghost_offset;
+ } else
+ #endif
+ if (which) jlist[jj] = j ^ (which << SBBITS);
+ }
+ }
+ }
+ #ifdef _LMP_INTEL_OFFLOAD
+ else if (separate_buffers) {
+ for (int i = ifrom; i < ito; ++i) {
+ int * _noalias jlist = firstneigh + cnumneigh[i];
+ const int jnum = numneigh[i];
+ int jj = 0;
+ for (jj = 0; jj < jnum; jj++)
+ if (jlist[jj] >= nlocal) break;
+ while (jj < jnum) {
+ if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
+ else jlist[jj] -= ghost_offset;
+ jj++;
+ }
+ }
+ }
+ #endif
+ } // end omp
+ #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
+ *timer_compute = MIC_Wtime() - *timer_compute;
+ #endif
+ } // end offload
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload) {
+ _fix->stop_watch(TIME_OFFLOAD_LATENCY);
+ _fix->start_watch(TIME_HOST_NEIGHBOR);
+ for (int n = 0; n < aend; n++) {
+ ilist[n] = n;
+ numneigh[n] = 0;
+ }
+ } else {
+ for (int i = astart; i < aend; i++)
+ list->firstneigh[i] = firstneigh + cnumneigh[i];
+ if (separate_buffers) {
+ _fix->start_watch(TIME_PACK);
+ _fix->set_neighbor_host_sizes();
+ buffers->pack_sep_from_single(_fix->host_min_local(),
+ _fix->host_used_local(),
+ _fix->host_min_ghost(),
+ _fix->host_used_ghost());
+ _fix->stop_watch(TIME_PACK);
+ }
+ }
+ #else
+ for (int i = astart; i < aend; i++)
+ list->firstneigh[i] = firstneigh + cnumneigh[i];
+ #endif
+}
diff --git a/src/USER-INTEL/npair_half_bin_newton_intel.h b/src/USER-INTEL/npair_half_bin_newton_intel.h
new file mode 100644
index 0000000000..4e496986b4
--- /dev/null
+++ b/src/USER-INTEL/npair_half_bin_newton_intel.h
@@ -0,0 +1,51 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/bin/newton/intel,
+ NPairHalfBinNewtonIntel,
+ NP_HALF | NP_BIN | NP_NEWTON | NP_ORTHO | NP_INTEL)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_BIN_NEWTON_INTEL_H
+#define LMP_NPAIR_HALF_BIN_NEWTON_INTEL_H
+
+#include "npair_intel.h"
+#include "fix_intel.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfBinNewtonIntel : public NPairIntel {
+ public:
+ NPairHalfBinNewtonIntel(class LAMMPS *);
+ ~NPairHalfBinNewtonIntel() {}
+ void build(class NeighList *);
+
+ private:
+ template <class flt_t, class acc_t>
+ void hbni(NeighList *, IntelBuffers<flt_t,acc_t> *);
+ template <class flt_t, class acc_t, int, int>
+ void hbni(const int, NeighList *, IntelBuffers<flt_t,acc_t> *, const int,
+ const int, const int offload_end = 0);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp b/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp
new file mode 100644
index 0000000000..3b6d68d4de
--- /dev/null
+++ b/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp
@@ -0,0 +1,513 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: W. Michael Brown (Intel)
+------------------------------------------------------------------------- */
+
+#include "npair_half_bin_newton_tri_intel.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "comm.h"
+#include "group.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfBinNewtonTriIntel::NPairHalfBinNewtonTriIntel(LAMMPS *lmp) :
+ NPairIntel(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with Newton's 3rd law for triclinic
+ each owned atom i checks its own bin and other bins in triclinic stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfBinNewtonTriIntel::build(NeighList *list)
+{
+ if (nstencil > INTEL_MAX_STENCIL)
+ error->all(FLERR, "Too many neighbor bins for USER-INTEL package.");
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (exclude)
+ error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
+ #endif
+
+ if (_fix->precision() == FixIntel::PREC_MODE_MIXED)
+ hbnti(list, _fix->get_mixed_buffers());
+ else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE)
+ hbnti(list, _fix->get_double_buffers());
+ else
+ hbnti(list, _fix->get_single_buffers());
+
+ _fix->stop_watch(TIME_HOST_NEIGHBOR);
+}
+
+template <class flt_t, class acc_t>
+void NPairHalfBinNewtonTriIntel::
+hbnti(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ list->inum = nlocal;
+
+ int host_start = _fix->host_start_neighbor();
+ const int off_end = _fix->offload_end_neighbor();
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (off_end) grow_stencil();
+ if (_fix->full_host_list()) host_start = 0;
+ int offload_noghost = _fix->offload_noghost();
+ #endif
+
+ buffers->grow_list(list, atom->nlocal, comm->nthreads, off_end);
+
+ int need_ic = 0;
+ if (atom->molecular)
+ dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
+ neighbor->cutneighmax);
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (need_ic) {
+ if (offload_noghost) {
+ hbnti<flt_t,acc_t,1,1>(1, list, buffers, 0, off_end);
+ hbnti<flt_t,acc_t,1,1>(0, list, buffers, host_start, nlocal, off_end);
+ } else {
+ hbnti<flt_t,acc_t,0,1>(1, list, buffers, 0, off_end);
+ hbnti<flt_t,acc_t,0,1>(0, list, buffers, host_start, nlocal);
+ }
+ } else {
+ if (offload_noghost) {
+ hbnti<flt_t,acc_t,1,0>(1, list, buffers, 0, off_end);
+ hbnti<flt_t,acc_t,1,0>(0, list, buffers, host_start, nlocal, off_end);
+ } else {
+ hbnti<flt_t,acc_t,0,0>(1, list, buffers, 0, off_end);
+ hbnti<flt_t,acc_t,0,0>(0, list, buffers, host_start, nlocal);
+ }
+ }
+ #else
+ if (need_ic)
+ hbnti<flt_t,acc_t,0,1>(0, list, buffers, host_start, nlocal);
+ else
+ hbnti<flt_t,acc_t,0,0>(0, list, buffers, host_start, nlocal);
+ #endif
+}
+
+template <class flt_t, class acc_t, int offload_noghost, int need_ic>
+void NPairHalfBinNewtonTriIntel::
+hbnti(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
+ const int astart, const int aend, const int offload_end) {
+ if (aend-astart == 0) return;
+
+ const int nall = atom->nlocal + atom->nghost;
+ int pad = 1;
+ int nall_t = nall;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload_noghost && offload) nall_t = atom->nlocal;
+ if (offload) {
+ if (INTEL_MIC_NBOR_PAD > 1)
+ pad = INTEL_MIC_NBOR_PAD * sizeof(float) / sizeof(flt_t);
+ } else
+ #endif
+ if (INTEL_NBOR_PAD > 1)
+ pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t);
+ const int pad_width = pad;
+
+ const ATOM_T * _noalias const x = buffers->get_x();
+ int * _noalias const firstneigh = buffers->firstneigh(list);
+ const int e_nall = nall_t;
+
+ const int molecular = atom->molecular;
+ int *ns = NULL;
+ tagint *s = NULL;
+ int tag_size = 0, special_size;
+ if (buffers->need_tag()) tag_size = e_nall;
+ if (molecular) {
+ s = atom->special[0];
+ ns = atom->nspecial[0];
+ special_size = aend;
+ } else {
+ s = &buffers->_special_holder;
+ ns = &buffers->_nspecial_holder;
+ special_size = 0;
+ }
+ const tagint * _noalias const special = s;
+ const int * _noalias const nspecial = ns;
+ const int maxspecial = atom->maxspecial;
+ const tagint * _noalias const tag = atom->tag;
+
+ int * _noalias const ilist = list->ilist;
+ int * _noalias numneigh = list->numneigh;
+ int * _noalias const cnumneigh = buffers->cnumneigh(list);
+ const int nstencil = this->nstencil;
+ const int * _noalias const stencil = this->stencil;
+ const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
+ const int ntypes = atom->ntypes + 1;
+ const int nlocal = atom->nlocal;
+
+ #ifndef _LMP_INTEL_OFFLOAD
+ int * const mask = atom->mask;
+ tagint * const molecule = atom->molecule;
+ #endif
+
+ int tnum;
+ int *overflow;
+ double *timer_compute;
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload) {
+ timer_compute = _fix->off_watch_neighbor();
+ tnum = buffers->get_off_threads();
+ overflow = _fix->get_off_overflow_flag();
+ _fix->stop_watch(TIME_HOST_NEIGHBOR);
+ _fix->start_watch(TIME_OFFLOAD_LATENCY);
+ } else
+ #endif
+ {
+ tnum = comm->nthreads;
+ overflow = _fix->get_overflow_flag();
+ }
+ const int nthreads = tnum;
+ const int maxnbors = buffers->get_max_nbors();
+ int * _noalias const atombin = buffers->get_atombin();
+ const int * _noalias const binpacked = buffers->get_binpacked();
+
+ const int xperiodic = domain->xperiodic;
+ const int yperiodic = domain->yperiodic;
+ const int zperiodic = domain->zperiodic;
+ const flt_t xprd_half = domain->xprd_half;
+ const flt_t yprd_half = domain->yprd_half;
+ const flt_t zprd_half = domain->zprd_half;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ const int * _noalias const binhead = this->binhead;
+ const int * _noalias const bins = this->bins;
+ const int cop = _fix->coprocessor_number();
+ const int separate_buffers = _fix->separate_buffers();
+ #pragma offload target(mic:cop) if(offload) \
+ in(x:length(e_nall+1) alloc_if(0) free_if(0)) \
+ in(tag:length(tag_size) alloc_if(0) free_if(0)) \
+ in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
+ in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
+ in(bins,binpacked:length(nall) alloc_if(0) free_if(0)) \
+ in(binhead:length(mbins+1) alloc_if(0) free_if(0)) \
+ in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
+ in(firstneigh:length(0) alloc_if(0) free_if(0)) \
+ in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
+ out(numneigh:length(0) alloc_if(0) free_if(0)) \
+ in(ilist:length(0) alloc_if(0) free_if(0)) \
+ in(atombin:length(aend) alloc_if(0) free_if(0)) \
+ in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
+ in(maxnbors,nthreads,maxspecial,nstencil,offload_end,pad_width,e_nall) \
+ in(offload,separate_buffers, astart, aend, nlocal, molecular, ntypes) \
+ in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \
+ out(overflow:length(5) alloc_if(0) free_if(0)) \
+ out(timer_compute:length(1) alloc_if(0) free_if(0)) \
+ signal(tag)
+ #endif
+ {
+ #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
+ *timer_compute = MIC_Wtime();
+ #endif
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ overflow[LMP_LOCAL_MIN] = astart;
+ overflow[LMP_LOCAL_MAX] = aend - 1;
+ overflow[LMP_GHOST_MIN] = e_nall;
+ overflow[LMP_GHOST_MAX] = -1;
+ #endif
+
+ int nstencilp = 0;
+ int binstart[INTEL_MAX_STENCIL], binend[INTEL_MAX_STENCIL];
+ for (int k = 0; k < nstencil; k++) {
+ binstart[nstencilp] = stencil[k];
+ int end = stencil[k] + 1;
+ for (int kk = k + 1; kk < nstencil; kk++) {
+ if (stencil[kk-1]+1 == stencil[kk]) {
+ end++;
+ k++;
+ } else break;
+ }
+ binend[nstencilp] = end;
+ nstencilp++;
+ }
+
+ #if defined(_OPENMP)
+ #pragma omp parallel default(none) \
+ shared(numneigh, overflow, nstencilp, binstart, binend)
+ #endif
+ {
+ #ifdef _LMP_INTEL_OFFLOAD
+ int lmin = e_nall, lmax = -1, gmin = e_nall, gmax = -1;
+ #endif
+
+ const int num = aend - astart;
+ int tid, ifrom, ito;
+ IP_PRE_omp_range_id(ifrom, ito, tid, num, nthreads);
+ ifrom += astart;
+ ito += astart;
+
+ int which;
+
+ const int list_size = (ito + tid * 2 + 2) * maxnbors;
+ int ct = (ifrom + tid * 2) * maxnbors;
+ int *neighptr = firstneigh + ct;
+ const int obound = maxnbors * 3;
+
+ for (int i = ifrom; i < ito; i++) {
+ const flt_t xtmp = x[i].x;
+ const flt_t ytmp = x[i].y;
+ const flt_t ztmp = x[i].z;
+ const int itype = x[i].w;
+ const int ioffset = ntypes * itype;
+
+ // loop over all atoms in bins in stencil
+ // pairs for atoms j "below" i are excluded
+ // below = lower z or (equal z and lower y) or (equal zy and lower x)
+ // (equal zyx and j <= i)
+ // latter excludes self-self interaction but allows superposed atoms
+
+ const int ibin = atombin[i];
+
+ int raw_count = maxnbors;
+ for (int k = 0; k < nstencilp; k++) {
+ const int bstart = binhead[ibin + binstart[k]];
+ const int bend = binhead[ibin + binend[k]];
+ for (int jj = bstart; jj < bend; jj++) {
+ const int j = binpacked[jj];
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload_noghost) {
+ if (j < nlocal) {
+ if (i < offload_end) continue;
+ } else if (offload) continue;
+ }
+ #endif
+
+ if (x[j].z < ztmp) continue;
+ if (x[j].z == ztmp) {
+ if (x[j].y < ytmp) continue;
+ if (x[j].y == ytmp) {
+ if (x[j].x < xtmp) continue;
+ if (x[j].x == xtmp && j <= i) continue;
+ }
+ }
+
+ #ifndef _LMP_INTEL_OFFLOAD
+ if (exclude) {
+ const int jtype = x[j].w;
+ if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
+ }
+ #endif
+
+ neighptr[raw_count++] = j;
+ }
+ }
+ if (raw_count > obound)
+ *overflow = 1;
+
+ #if defined(LMP_SIMD_COMPILER)
+ #ifdef _LMP_INTEL_OFFLOAD
+ int vlmin = lmin, vlmax = lmax, vgmin = gmin, vgmax = gmax;
+ #if __INTEL_COMPILER+0 > 1499
+ #pragma vector aligned
+ #pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin)
+ #endif
+ #else
+ #pragma vector aligned
+ #pragma simd
+ #endif
+ #endif
+ for (int u = maxnbors; u < raw_count; u++) {
+ int j = neighptr[u];
+ const flt_t delx = xtmp - x[j].x;
+ const flt_t dely = ytmp - x[j].y;
+ const flt_t delz = ztmp - x[j].z;
+ const int jtype = x[j].w;
+ const flt_t rsq = delx * delx + dely * dely + delz * delz;
+ if (rsq > cutneighsq[ioffset + jtype])
+ neighptr[u] = e_nall;
+ else {
+ if (need_ic) {
+ int no_special;
+ ominimum_image_check(no_special, delx, dely, delz);
+ if (no_special)
+ neighptr[u] = -j - 1;
+ }
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (j < nlocal) {
+ if (j < vlmin) vlmin = j;
+ if (j > vlmax) vlmax = j;
+ } else {
+ if (j < vgmin) vgmin = j;
+ if (j > vgmax) vgmax = j;
+ }
+ #endif
+ }
+ }
+
+ int n = 0, n2 = maxnbors;
+ for (int u = maxnbors; u < raw_count; u++) {
+ const int j = neighptr[u];
+ int pj = j;
+ if (pj < e_nall) {
+ if (need_ic)
+ if (pj < 0) pj = -pj - 1;
+
+ if (pj < nlocal)
+ neighptr[n++] = j;
+ else
+ neighptr[n2++] = j;
+ }
+ }
+ int ns = n;
+ for (int u = maxnbors; u < n2; u++)
+ neighptr[n++] = neighptr[u];
+
+ ilist[i] = i;
+ cnumneigh[i] = ct;
+ ns += n2 - maxnbors;
+
+ int edge = (ns % pad_width);
+ if (edge) {
+ const int pad_end = ns + (pad_width - edge);
+ #if defined(LMP_SIMD_COMPILER)
+ #pragma loop_count min=1, max=15, avg=8
+ #endif
+ for ( ; ns < pad_end; ns++)
+ neighptr[ns] = e_nall;
+ }
+ numneigh[i] = ns;
+
+ ct += ns;
+ const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
+ edge = (ct % alignb);
+ if (edge) ct += alignb - edge;
+ neighptr = firstneigh + ct;
+ if (ct + obound > list_size) {
+ if (i < ito - 1) {
+ *overflow = 1;
+ ct = (ifrom + tid * 2) * maxnbors;
+ }
+ }
+ }
+
+ if (*overflow == 1)
+ for (int i = ifrom; i < ito; i++)
+ numneigh[i] = 0;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (separate_buffers) {
+ #if defined(_OPENMP)
+ #pragma omp critical
+ #endif
+ {
+ if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
+ if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
+ if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
+ if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
+ }
+ #pragma omp barrier
+ }
+
+ int ghost_offset = 0, nall_offset = e_nall;
+ if (separate_buffers) {
+ int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
+ if (nghost < 0) nghost = 0;
+ if (offload) {
+ ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
+ nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
+ } else {
+ ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
+ nall_offset = nlocal + nghost;
+ }
+ }
+ #endif
+
+ if (molecular) {
+ for (int i = ifrom; i < ito; ++i) {
+ int * _noalias jlist = firstneigh + cnumneigh[i];
+ const int jnum = numneigh[i];
+ #if defined(LMP_SIMD_COMPILER)
+ #pragma vector aligned
+ #pragma simd
+ #endif
+ for (int jj = 0; jj < jnum; jj++) {
+ const int j = jlist[jj];
+ if (need_ic && j < 0) {
+ which = 0;
+ jlist[jj] = -j - 1;
+ } else
+ ofind_special(which, special, nspecial, i, tag[j]);
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (j >= nlocal) {
+ if (j == e_nall)
+ jlist[jj] = nall_offset;
+ else if (which)
+ jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
+ else jlist[jj]-=ghost_offset;
+ } else
+ #endif
+ if (which) jlist[jj] = j ^ (which << SBBITS);
+ }
+ }
+ }
+ #ifdef _LMP_INTEL_OFFLOAD
+ else if (separate_buffers) {
+ for (int i = ifrom; i < ito; ++i) {
+ int * _noalias jlist = firstneigh + cnumneigh[i];
+ const int jnum = numneigh[i];
+ int jj = 0;
+ for (jj = 0; jj < jnum; jj++)
+ if (jlist[jj] >= nlocal) break;
+ while (jj < jnum) {
+ if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
+ else jlist[jj] -= ghost_offset;
+ jj++;
+ }
+ }
+ }
+ #endif
+ } // end omp
+ #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
+ *timer_compute = MIC_Wtime() - *timer_compute;
+ #endif
+ } // end offload
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (offload) {
+ _fix->stop_watch(TIME_OFFLOAD_LATENCY);
+ _fix->start_watch(TIME_HOST_NEIGHBOR);
+ for (int n = 0; n < aend; n++) {
+ ilist[n] = n;
+ numneigh[n] = 0;
+ }
+ } else {
+ for (int i = astart; i < aend; i++)
+ list->firstneigh[i] = firstneigh + cnumneigh[i];
+ if (separate_buffers) {
+ _fix->start_watch(TIME_PACK);
+ _fix->set_neighbor_host_sizes();
+ buffers->pack_sep_from_single(_fix->host_min_local(),
+ _fix->host_used_local(),
+ _fix->host_min_ghost(),
+ _fix->host_used_ghost());
+ _fix->stop_watch(TIME_PACK);
+ }
+ }
+ #else
+ for (int i = astart; i < aend; i++)
+ list->firstneigh[i] = firstneigh + cnumneigh[i];
+ #endif
+}
diff --git a/src/USER-INTEL/npair_half_bin_newton_tri_intel.h b/src/USER-INTEL/npair_half_bin_newton_tri_intel.h
new file mode 100644
index 0000000000..d1b9ee9cd1
--- /dev/null
+++ b/src/USER-INTEL/npair_half_bin_newton_tri_intel.h
@@ -0,0 +1,51 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/bin/newton/tri/intel,
+ NPairHalfBinNewtonTriIntel,
+ NP_HALF | NP_BIN | NP_NEWTON | NP_TRI | NP_INTEL)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_BIN_NEWTON_INTEL_TRI_H
+#define LMP_NPAIR_HALF_BIN_NEWTON_INTEL_TRI_H
+
+#include "npair_intel.h"
+#include "fix_intel.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfBinNewtonTriIntel : public NPairIntel {
+ public:
+ NPairHalfBinNewtonTriIntel(class LAMMPS *);
+ ~NPairHalfBinNewtonTriIntel() {}
+ void build(class NeighList *);
+
+ private:
+ template <class flt_t, class acc_t>
+ void hbnti(NeighList *, IntelBuffers<flt_t,acc_t> *);
+ template <class flt_t, class acc_t, int, int>
+ void hbnti(const int, NeighList *, IntelBuffers<flt_t,acc_t> *, const int,
+ const int, const int offload_end = 0);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp
new file mode 100644
index 0000000000..8ec40260f3
--- /dev/null
+++ b/src/USER-INTEL/npair_intel.cpp
@@ -0,0 +1,69 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: W. Michael Brown (Intel)
+------------------------------------------------------------------------- */
+
+#include "npair_intel.h"
+#include "nstencil.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairIntel::NPairIntel(LAMMPS *lmp) : NPair(lmp) {
+ int ifix = modify->find_fix("package_intel");
+ if (ifix < 0)
+ error->all(FLERR,
+ "The 'package intel' command is required for /intel styles");
+ _fix = static_cast<FixIntel *>(modify->fix[ifix]);
+ #ifdef _LMP_INTEL_OFFLOAD
+ _cop = _fix->coprocessor_number();
+ _off_map_stencil = 0;
+ #endif
+}
+
+/* ---------------------------------------------------------------------- */
+
+NPairIntel::~NPairIntel() {
+ #ifdef _LMP_INTEL_OFFLOAD
+ if (_off_map_stencil) {
+ const int * stencil = this->stencil;
+ #pragma offload_transfer target(mic:_cop) \
+ nocopy(stencil:alloc_if(0) free_if(1))
+ }
+ #endif
+}
+
+/* ----------------------------------------------------------------------
+ copy needed info from NStencil class to this build class
+------------------------------------------------------------------------- */
+
+#ifdef _LMP_INTEL_OFFLOAD
+void NPairIntel::grow_stencil()
+{
+ if (_off_map_stencil != stencil) {
+ if (_off_map_stencil) {
+ const int * stencil = _off_map_stencil;
+ #pragma offload_transfer target(mic:_cop) \
+ nocopy(stencil:alloc_if(0) free_if(1))
+ }
+ _off_map_stencil = stencil;
+ const int * stencil = _off_map_stencil;
+ const int maxstencil = ns->get_maxstencil();
+ #pragma offload_transfer target(mic:_cop) \
+ in(stencil:length(maxstencil) alloc_if(1) free_if(0))
+ }
+}
+#endif
diff --git a/src/USER-INTEL/npair_intel.h b/src/USER-INTEL/npair_intel.h
new file mode 100644
index 0000000000..06d5d79cac
--- /dev/null
+++ b/src/USER-INTEL/npair_intel.h
@@ -0,0 +1,117 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_NPAIR_INTEL_H
+#define LMP_NPAIR_INTEL_H
+
+#include "npair.h"
+#include "fix_intel.h"
+
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
+
+#ifdef LMP_USE_AVXCD
+#include "intel_simd.h"
+#endif
+
+#ifdef OUTER_CHUNK
+#include "intel_simd.h"
+#endif
+
+#ifdef _LMP_INTEL_OFFLOAD
+#pragma offload_attribute(push,target(mic))
+#endif
+
+#define ofind_special(which, special, nspecial, i, tag) \
+{ \
+ which = 0; \
+ const int n1 = nspecial[i * 3]; \
+ const int n2 = nspecial[i * 3 + 1]; \
+ const int n3 = nspecial[i * 3 + 2]; \
+ const tagint *sptr = special + i * maxspecial; \
+ for (int s = 0; s < n3; s++) { \
+ if (sptr[s] == tag) { \
+ if (s < n1) { \
+ which = 1; \
+ } else if (s < n2) { \
+ which = 2; \
+ } else { \
+ which = 3; \
+ } \
+ } \
+ } \
+}
+
+#define ominimum_image_check(answer, dx, dy, dz) \
+{ \
+ answer = 0; \
+ if (xperiodic && fabs(dx) > xprd_half) answer = 1; \
+ if (yperiodic && fabs(dy) > yprd_half) answer = 1; \
+ if (zperiodic && fabs(dz) > zprd_half) answer = 1; \
+}
+
+#define dminimum_image_check(answer, dx, dy, dz) \
+{ \
+ answer = 0; \
+ if (domain->xperiodic && fabs(dx) > domain->xprd_half) answer = 1; \
+ if (domain->yperiodic && fabs(dy) > domain->yprd_half) answer = 1; \
+ if (domain->zperiodic && fabs(dz) > domain->zprd_half) answer = 1; \
+}
+
+#ifdef _LMP_INTEL_OFFLOAD
+#pragma offload_attribute(pop)
+#endif
+
+namespace LAMMPS_NS {
+
+class NPairIntel : public NPair {
+ public:
+ NPairIntel(class LAMMPS *);
+ ~NPairIntel();
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ void grow_stencil();
+ #endif
+
+ protected:
+ FixIntel *_fix;
+
+ #ifdef _LMP_INTEL_OFFLOAD
+ int _cop;
+ int *_off_map_stencil;
+ #endif
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Exclusion lists not yet supported for Intel offload
+
+Self explanatory.
+
+E: The 'package intel' command is required for /intel styles
+
+Self explanatory.
+
+E: Too many neighbor bins for USER-INTEL package.
+
+The number of bins used in the stencil to check for neighboring atoms is too
+high for the Intel package. Either increase the bin size in the input script
+or recompile with a larger setting for INTEL_MAX_STENCIL in intel_preprocess.h.
+
+*/
+
diff --git a/src/USER-OMP/neigh_full_omp.cpp b/src/USER-OMP/neigh_full_omp.cpp
deleted file mode 100644
index e61611d41c..0000000000
--- a/src/USER-OMP/neigh_full_omp.cpp
+++ /dev/null
@@ -1,621 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "neighbor.h"
-#include "neighbor_omp.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
-#include "comm.h"
-#include "domain.h"
-#include "group.h"
-#include "my_page.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- N^2 search for all neighbors
- every neighbor pair appears in list of both atoms i and j
-------------------------------------------------------------------------- */
-
-void Neighbor::full_nsq_omp(NeighList *list)
-{
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,n,itype,jtype,which,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int nall = atom->nlocal + atom->nghost;
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- // loop over owned atoms, storing neighbors
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms, owned and ghost
- // skip i = j
-
- for (j = 0; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
- if (i == j) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
- list->gnum = 0;
-}
-
-/* ----------------------------------------------------------------------
- N^2 search for all neighbors
- include neighbors of ghost atoms, but no "special neighbors" for ghosts
- every neighbor pair appears in list of both atoms i and j
-------------------------------------------------------------------------- */
-
-void Neighbor::full_nsq_ghost_omp(NeighList *list)
-{
- const int nlocal = atom->nlocal;
- const int nall = nlocal + atom->nghost;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nall);
-
- int i,j,n,itype,jtype,which,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- // loop over owned & ghost atoms, storing neighbors
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms, owned and ghost
- // skip i = j
- // no molecular test when i = ghost atom
-
- if (i < nlocal) {
- for (j = 0; j < nall; j++) {
- if (i == j) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- } else {
- for (j = 0; j < nall; j++) {
- if (i == j) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
- list->gnum = nall - nlocal;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction for all neighbors
- every neighbor pair appears in list of both atoms i and j
-------------------------------------------------------------------------- */
-
-void Neighbor::full_bin_omp(NeighList *list)
-{
- // bin owned & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- // loop over owned atoms, storing neighbors
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in surrounding bins in stencil including self
- // skip i = j
-
- ibin = coord2bin(x[i]);
-
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (i == j) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
- list->gnum = 0;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction for all neighbors
- include neighbors of ghost atoms, but no "special neighbors" for ghosts
- every neighbor pair appears in list of both atoms i and j
-------------------------------------------------------------------------- */
-
-void Neighbor::full_bin_ghost_omp(NeighList *list)
-{
- // bin owned & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = atom->nlocal;
- const int nall = nlocal + atom->nghost;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nall);
-
- int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int xbin,ybin,zbin,xbin2,ybin2,zbin2;
- int *neighptr;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- int **stencilxyz = list->stencilxyz;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- // loop over owned & ghost atoms, storing neighbors
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in surrounding bins in stencil including self
- // when i is a ghost atom, must check if stencil bin is out of bounds
- // skip i = j
- // no molecular test when i = ghost atom
-
- if (i < nlocal) {
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (i == j) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- } else {
- ibin = coord2bin(x[i],xbin,ybin,zbin);
- for (k = 0; k < nstencil; k++) {
- xbin2 = xbin + stencilxyz[k][0];
- ybin2 = ybin + stencilxyz[k][1];
- zbin2 = zbin + stencilxyz[k][2];
- if (xbin2 < 0 || xbin2 >= mbinx ||
- ybin2 < 0 || ybin2 >= mbiny ||
- zbin2 < 0 || zbin2 >= mbinz) continue;
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (i == j) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
- list->gnum = nall - nlocal;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction for all neighbors
- multi-type stencil is itype dependent and is distance checked
- every neighbor pair appears in list of both atoms i and j
-------------------------------------------------------------------------- */
-
-void Neighbor::full_multi_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*s;
- double *cutsq,*distsq;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in other bins in stencil, including self
- // skip if i,j neighbor cutoff is less than bin distance
- // skip i = j
-
- ibin = coord2bin(x[i]);
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- cutsq = cutneighsq[itype];
- ns = nstencil_multi[itype];
- for (k = 0; k < ns; k++) {
- for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
- if (i == j) continue;
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
- list->gnum = 0;
-}
diff --git a/src/USER-OMP/neigh_gran_omp.cpp b/src/USER-OMP/neigh_gran_omp.cpp
deleted file mode 100644
index 82794ff739..0000000000
--- a/src/USER-OMP/neigh_gran_omp.cpp
+++ /dev/null
@@ -1,618 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include <string.h>
-#include "neighbor.h"
-#include "neighbor_omp.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "comm.h"
-#include "group.h"
-#include "fix_shear_history.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- granular particles
- N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
- shear history must be accounted for when a neighbor pair is added
- pair added to list if atoms i and j are both owned and i < j
- pair added if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
-{
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
-
- FixShearHistory * const fix_history = list->fix_history;
- NeighList * listgranhistory = list->listgranhistory;
-
- NEIGH_OMP_INIT;
-
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list,listgranhistory)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,m,n,nn,dnum,dnumbytes;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- double radi,radsum,cutsq;
- int *neighptr,*touchptr;
- double *shearptr;
-
- int *npartner;
- tagint **partner;
- double **shearpartner;
- int **firsttouch;
- double **firstshear;
- MyPage<int> *ipage_touch;
- MyPage<double> *dpage_shear;
-
- double **x = atom->x;
- double *radius = atom->radius;
- tagint *tag = atom->tag;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *molecule = atom->molecule;
- int nall = atom->nlocal + atom->nghost;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- if (fix_history) {
- npartner = fix_history->npartner;
- partner = fix_history->partner;
- shearpartner = fix_history->shearpartner;
- firsttouch = listgranhistory->firstneigh;
- firstshear = listgranhistory->firstdouble;
- ipage_touch = listgranhistory->ipage+tid;
- dpage_shear = listgranhistory->dpage+tid;
- dnum = listgranhistory->dnum;
- dnumbytes = dnum * sizeof(double);
- ipage_touch->reset();
- dpage_shear->reset();
- }
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
- if (fix_history) {
- nn = 0;
- touchptr = ipage_touch->vget();
- shearptr = dpage_shear->vget();
- }
-
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- radi = radius[i];
-
- // loop over remaining atoms, owned and ghost
-
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) {
- neighptr[n] = j;
-
- if (fix_history) {
- if (rsq < radsum*radsum) {
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == tag[j]) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
- nn += dnum;
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- }
-
- n++;
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (fix_history) {
- firsttouch[i] = touchptr;
- firstshear[i] = shearptr;
- ipage_touch->vgot(n);
- dpage_shear->vgot(nn);
- }
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
-}
-
-/* ----------------------------------------------------------------------
- granular particles
- N^2 / 2 search for neighbor pairs with full Newton's 3rd law
- no shear history is allowed for this option
- pair added to list if atoms i and j are both owned and i < j
- if j is ghost only me or other proc adds pair
- decision based on itag,jtag tests
-------------------------------------------------------------------------- */
-
-void Neighbor::granular_nsq_newton_omp(NeighList *list)
-{
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,n,itag,jtag;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- double radi,radsum,cutsq;
- int *neighptr;
-
- double **x = atom->x;
- double *radius = atom->radius;
- tagint *tag = atom->tag;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *molecule = atom->molecule;
- int nall = atom->nlocal + atom->nghost;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itag = tag[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- radi = radius[i];
-
- // loop over remaining atoms, owned and ghost
-
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
-
- if (j >= nlocal) {
- jtag = tag[j];
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
- }
-
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) neighptr[n++] = j;
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
-}
-
-/* ----------------------------------------------------------------------
- granular particles
- binned neighbor list construction with partial Newton's 3rd law
- shear history must be accounted for when a neighbor pair is added
- each owned atom i checks own bin and surrounding bins in non-Newton stencil
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::granular_bin_no_newton_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
-
- FixShearHistory * const fix_history = list->fix_history;
- NeighList * listgranhistory = list->listgranhistory;
-
- NEIGH_OMP_INIT;
-
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list,listgranhistory)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- double radi,radsum,cutsq;
- int *neighptr,*touchptr;
- double *shearptr;
- MyPage<int> *ipage_touch;
- MyPage<double> *dpage_shear;
-
- int *npartner;
- tagint **partner;
- double **shearpartner;
- int **firsttouch;
- double **firstshear;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- double *radius = atom->radius;
- tagint *tag = atom->tag;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *molecule = atom->molecule;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- if (fix_history) {
- npartner = fix_history->npartner;
- partner = fix_history->partner;
- shearpartner = fix_history->shearpartner;
- firsttouch = listgranhistory->firstneigh;
- firstshear = listgranhistory->firstdouble;
- ipage_touch = listgranhistory->ipage+tid;
- dpage_shear = listgranhistory->dpage+tid;
- dnum = listgranhistory->dnum;
- dnumbytes = dnum * sizeof(double);
- ipage_touch->reset();
- dpage_shear->reset();
- }
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
- if (fix_history) {
- nn = 0;
- touchptr = ipage_touch->vget();
- shearptr = dpage_shear->vget();
- }
-
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- radi = radius[i];
- ibin = coord2bin(x[i]);
-
- // loop over all atoms in surrounding bins in stencil including self
- // only store pair if i < j
- // stores own/own pairs only once
- // stores own/ghost pairs on both procs
-
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) {
- neighptr[n] = j;
-
- if (fix_history) {
- if (rsq < radsum*radsum) {
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == tag[j]) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
- nn += dnum;
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- }
-
- n++;
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (fix_history) {
- firsttouch[i] = touchptr;
- firstshear[i] = shearptr;
- ipage_touch->vgot(n);
- dpage_shear->vgot(nn);
- }
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
-}
-
-/* ----------------------------------------------------------------------
- granular particles
- binned neighbor list construction with full Newton's 3rd law
- no shear history is allowed for this option
- each owned atom i checks its own bin and other bins in Newton stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::granular_bin_newton_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,n,ibin;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- double radi,radsum,cutsq;
- int *neighptr;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- double *radius = atom->radius;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *molecule = atom->molecule;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- radi = radius[i];
-
- // loop over rest of atoms in i's bin, ghosts are at end of linked list
- // if j is owned atom, store it, since j is beyond i in linked list
- // if j is ghost, only store if j coords are "above and to the right" of i
-
- for (j = bins[i]; j >= 0; j = bins[j]) {
- if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
-
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) neighptr[n++] = j;
- }
-
- // loop over all atoms in other bins in stencil, store every pair
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) neighptr[n++] = j;
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
-}
-
-/* ----------------------------------------------------------------------
- granular particles
- binned neighbor list construction with Newton's 3rd law for triclinic
- no shear history is allowed for this option
- each owned atom i checks its own bin and other bins in triclinic stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::granular_bin_newton_tri_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,n,ibin;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- double radi,radsum,cutsq;
- int *neighptr;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- double *radius = atom->radius;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *molecule = atom->molecule;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- radi = radius[i];
-
- // loop over all atoms in bins in stencil
- // pairs for atoms j "below" i are excluded
- // below = lower z or (equal z and lower y) or (equal zy and lower x)
- // (equal zyx and j <= i)
- // latter excludes self-self interaction but allows superposed atoms
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) neighptr[n++] = j;
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
-}
diff --git a/src/USER-OMP/neigh_half_bin_omp.cpp b/src/USER-OMP/neigh_half_bin_omp.cpp
deleted file mode 100644
index 65fa07a48a..0000000000
--- a/src/USER-OMP/neigh_half_bin_omp.cpp
+++ /dev/null
@@ -1,559 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "neighbor.h"
-#include "neighbor_omp.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
-#include "comm.h"
-#include "domain.h"
-#include "my_page.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with partial Newton's 3rd law
- each owned atom i checks own bin and other bins in stencil
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_no_newton_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in other bins in stencil including self
- // only store pair if i < j
- // stores own/own pairs only once
- // stores own/ghost pairs on both procs
-
- ibin = coord2bin(x[i]);
-
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with partial Newton's 3rd law
- include neighbors of ghost atoms, but no "special neighbors" for ghosts
- owned and ghost atoms check own bin and other bins in stencil
- pair stored once if i,j are both owned and i < j
- pair stored by me if i owned and j ghost (also stored by proc owning j)
- pair stored once if i,j are both ghost and i < j
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_no_newton_ghost_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = atom->nlocal;
- const int nall = nlocal + atom->nghost;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nall);
-
- int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
- tagint tagprev;
- int xbin,ybin,zbin,xbin2,ybin2,zbin2;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- int **stencilxyz = list->stencilxyz;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in other bins in stencil including self
- // when i is a ghost atom, must check if stencil bin is out of bounds
- // only store pair if i < j
- // stores own/own pairs only once
- // stores own/ghost pairs with owned atom only, on both procs
- // stores ghost/ghost pairs only once
- // no molecular test when i = ghost atom
-
- if (i < nlocal) {
- ibin = coord2bin(x[i]);
-
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- } else {
- ibin = coord2bin(x[i],xbin,ybin,zbin);
- for (k = 0; k < nstencil; k++) {
- xbin2 = xbin + stencilxyz[k][0];
- ybin2 = ybin + stencilxyz[k][1];
- zbin2 = zbin + stencilxyz[k][2];
- if (xbin2 < 0 || xbin2 >= mbinx ||
- ybin2 < 0 || ybin2 >= mbiny ||
- zbin2 < 0 || zbin2 >= mbinz) continue;
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
- list->gnum = nall - atom->nlocal;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with full Newton's 3rd law
- each owned atom i checks its own bin and other bins in Newton stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_newton_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over rest of atoms in i's bin, ghosts are at end of linked list
- // if j is owned atom, store it, since j is beyond i in linked list
- // if j is ghost, only store if j coords are "above and to the right" of i
-
- for (j = bins[i]; j >= 0; j = bins[j]) {
- if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
-
- // loop over all atoms in other bins in stencil, store every pair
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with Newton's 3rd law for triclinic
- each owned atom i checks its own bin and other bins in triclinic stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_newton_tri_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in bins in stencil
- // pairs for atoms j "below" i are excluded
- // below = lower z or (equal z and lower y) or (equal zy and lower x)
- // (equal zyx and j <= i)
- // latter excludes self-self interaction but allows superposed atoms
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
-}
diff --git a/src/USER-OMP/neigh_half_multi_omp.cpp b/src/USER-OMP/neigh_half_multi_omp.cpp
deleted file mode 100644
index cc93bf6367..0000000000
--- a/src/USER-OMP/neigh_half_multi_omp.cpp
+++ /dev/null
@@ -1,435 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "neighbor.h"
-#include "neighbor_omp.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
-#include "comm.h"
-#include "domain.h"
-#include "my_page.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with partial Newton's 3rd law
- each owned atom i checks own bin and other bins in stencil
- multi-type stencil is itype dependent and is distance checked
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::half_multi_no_newton_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*s;
- double *cutsq,*distsq;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in other bins in stencil including self
- // only store pair if i < j
- // skip if i,j neighbor cutoff is less than bin distance
- // stores own/own pairs only once
- // stores own/ghost pairs on both procs
-
- ibin = coord2bin(x[i]);
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- cutsq = cutneighsq[itype];
- ns = nstencil_multi[itype];
- for (k = 0; k < ns; k++) {
- for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with full Newton's 3rd law
- each owned atom i checks its own bin and other bins in Newton stencil
- multi-type stencil is itype dependent and is distance checked
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_multi_newton_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*s;
- double *cutsq,*distsq;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over rest of atoms in i's bin, ghosts are at end of linked list
- // if j is owned atom, store it, since j is beyond i in linked list
- // if j is ghost, only store if j coords are "above and to the right" of i
-
- for (j = bins[i]; j >= 0; j = bins[j]) {
- if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
-
- // loop over all atoms in other bins in stencil, store every pair
- // skip if i,j neighbor cutoff is less than bin distance
-
- ibin = coord2bin(x[i]);
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- cutsq = cutneighsq[itype];
- ns = nstencil_multi[itype];
- for (k = 0; k < ns; k++) {
- for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with Newton's 3rd law for triclinic
- each owned atom i checks its own bin and other bins in triclinic stencil
- multi-type stencil is itype dependent and is distance checked
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_multi_newton_tri_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*s;
- double *cutsq,*distsq;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in bins, including self, in stencil
- // skip if i,j neighbor cutoff is less than bin distance
- // bins below self are excluded from stencil
- // pairs for atoms j "below" i are excluded
- // below = lower z or (equal z and lower y) or (equal zy and lower x)
- // (equal zyx and j <= i)
- // latter excludes self-self interaction but allows superposed atoms
-
- ibin = coord2bin(x[i]);
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- cutsq = cutneighsq[itype];
- ns = nstencil_multi[itype];
- for (k = 0; k < ns; k++) {
- for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
-}
diff --git a/src/USER-OMP/neigh_half_nsq_omp.cpp b/src/USER-OMP/neigh_half_nsq_omp.cpp
deleted file mode 100644
index ab6e8e5d8c..0000000000
--- a/src/USER-OMP/neigh_half_nsq_omp.cpp
+++ /dev/null
@@ -1,376 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "neighbor.h"
-#include "neighbor_omp.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
-#include "comm.h"
-#include "domain.h"
-#include "group.h"
-#include "my_page.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::half_nsq_no_newton_omp(NeighList *list)
-{
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
- const int nall = atom->nlocal + atom->nghost;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,n,itype,jtype,which,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- // loop over owned atoms, storing neighbors
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over remaining atoms, owned and ghost
- // only store pair if i < j
-
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
-}
-
-/* ----------------------------------------------------------------------
- N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
- include neighbors of ghost atoms, but no "special neighbors" for ghosts
- pair stored once if i,j are both owned and i < j
- pair stored by me if i owned and j ghost (also stored by proc owning j)
- pair stored once if i,j are both ghost and i < j
-------------------------------------------------------------------------- */
-
-void Neighbor::half_nsq_no_newton_ghost_omp(NeighList *list)
-{
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
- const int nall = nlocal + atom->nghost;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nall);
-
- int i,j,n,itype,jtype,which,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- // loop over owned & ghost atoms, storing neighbors
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over remaining atoms, owned and ghost
- // only store pair if i < j
- // stores own/own pairs only once
- // stores own/ghost pairs with owned atom only, on both procs
- // stores ghost/ghost pairs only once
- // no molecular test when i = ghost atom
-
- if (i < nlocal) {
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
-
- } else {
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) neighptr[n++] = j;
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = atom->nlocal;
- list->gnum = nall - atom->nlocal;
-}
-
-/* ----------------------------------------------------------------------
- N^2 / 2 search for neighbor pairs with full Newton's 3rd law
- every pair stored exactly once by some processor
- decision on ghost atoms based on itag,jtag tests
-------------------------------------------------------------------------- */
-
-void Neighbor::half_nsq_newton_omp(NeighList *list)
-{
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,n,itype,jtype,itag,jtag,which,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int nall = atom->nlocal + atom->nghost;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- for (i = ifrom; i < ito; i++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- itag = tag[i];
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over remaining atoms, owned and ghost
- // itag = jtag is possible for long cutoffs that include images of self
-
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
-
- if (j >= nlocal) {
- jtag = tag[j];
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
-}
diff --git a/src/USER-OMP/neigh_respa_omp.cpp b/src/USER-OMP/neigh_respa_omp.cpp
deleted file mode 100644
index 409090c9ea..0000000000
--- a/src/USER-OMP/neigh_respa_omp.cpp
+++ /dev/null
@@ -1,972 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "neighbor.h"
-#include "neighbor_omp.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
-#include "comm.h"
-#include "domain.h"
-#include "group.h"
-#include "my_page.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- multiple respa lists
- N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
- pair added to list if atoms i and j are both owned and i < j
- pair added if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
-{
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-
- NeighList *listinner = list->listinner;
- NeighList *listmiddle = list->listmiddle;
- const int respamiddle = list->respamiddle;
-
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list,listinner,listmiddle)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,n,itype,jtype,n_inner,n_middle,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*neighptr_inner,*neighptr_middle;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int nall = atom->nlocal + atom->nghost;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
-
- int *ilist_inner = listinner->ilist;
- int *numneigh_inner = listinner->numneigh;
- int **firstneigh_inner = listinner->firstneigh;
-
- int *ilist_middle,*numneigh_middle,**firstneigh_middle;
- if (respamiddle) {
- ilist_middle = listmiddle->ilist;
- numneigh_middle = listmiddle->numneigh;
- firstneigh_middle = listmiddle->firstneigh;
- }
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- MyPage<int> &ipage_inner = listinner->ipage[tid];
- ipage.reset();
- ipage_inner.reset();
-
- MyPage<int> *ipage_middle;
- if (respamiddle) {
- ipage_middle = listmiddle->ipage + tid;
- ipage_middle->reset();
- }
-
- int which = 0;
- int minchange = 0;
-
- for (i = ifrom; i < ito; i++) {
-
- n = n_inner = 0;
- neighptr = ipage.vget();
- neighptr_inner = ipage_inner.vget();
- if (respamiddle) {
- n_middle = 0;
- neighptr_middle = ipage_middle->vget();
- }
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over remaining atoms, owned and ghost
-
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (minchange) neighptr_inner[n_inner++] = j;
- else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (minchange) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- ilist_inner[i] = i;
- firstneigh_inner[i] = neighptr_inner;
- numneigh_inner[i] = n_inner;
- ipage.vgot(n_inner);
- if (ipage_inner.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (respamiddle) {
- ilist_middle[i] = i;
- firstneigh_middle[i] = neighptr_middle;
- numneigh_middle[i] = n_middle;
- ipage_middle->vgot(n_middle);
- if (ipage_middle->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
- listinner->inum = nlocal;
- if (respamiddle) listmiddle->inum = nlocal;
-}
-
-/* ----------------------------------------------------------------------
- multiple respa lists
- N^2 / 2 search for neighbor pairs with full Newton's 3rd law
- pair added to list if atoms i and j are both owned and i < j
- if j is ghost only me or other proc adds pair
- decision based on itag,jtag tests
-------------------------------------------------------------------------- */
-
-void Neighbor::respa_nsq_newton_omp(NeighList *list)
-{
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-
- NeighList *listinner = list->listinner;
- NeighList *listmiddle = list->listmiddle;
- const int respamiddle = list->respamiddle;
-
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list,listinner,listmiddle)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,n,itype,jtype,itag,jtag,n_inner,n_middle,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*neighptr_inner,*neighptr_middle;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int nall = atom->nlocal + atom->nghost;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
-
- int *ilist_inner = listinner->ilist;
- int *numneigh_inner = listinner->numneigh;
- int **firstneigh_inner = listinner->firstneigh;
-
- int *ilist_middle,*numneigh_middle,**firstneigh_middle;
- if (respamiddle) {
- ilist_middle = listmiddle->ilist;
- numneigh_middle = listmiddle->numneigh;
- firstneigh_middle = listmiddle->firstneigh;
- }
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- MyPage<int> &ipage_inner = listinner->ipage[tid];
- ipage.reset();
- ipage_inner.reset();
-
- MyPage<int> *ipage_middle;
- if (respamiddle) {
- ipage_middle = listmiddle->ipage + tid;
- ipage_middle->reset();
- }
-
- int which = 0;
- int minchange = 0;
-
- for (i = ifrom; i < ito; i++) {
-
- n = n_inner = 0;
- neighptr = ipage.vget();
- neighptr_inner = ipage_inner.vget();
- if (respamiddle) {
- n_middle = 0;
- neighptr_middle = ipage_middle->vget();
- }
-
- itag = tag[i];
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over remaining atoms, owned and ghost
-
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
-
- if (j >= nlocal) {
- jtag = tag[j];
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (minchange) neighptr_inner[n_inner++] = j;
- else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (minchange) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- ilist_inner[i] = i;
- firstneigh_inner[i] = neighptr_inner;
- numneigh_inner[i] = n_inner;
- ipage.vgot(n_inner);
- if (ipage_inner.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (respamiddle) {
- ilist_middle[i] = i;
- firstneigh_middle[i] = neighptr_middle;
- numneigh_middle[i] = n_middle;
- ipage_middle->vgot(n_middle);
- if (ipage_middle->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
- listinner->inum = nlocal;
- if (respamiddle) listmiddle->inum = nlocal;
-}
-
-/* ----------------------------------------------------------------------
- multiple respa lists
- binned neighbor list construction with partial Newton's 3rd law
- each owned atom i checks own bin and surrounding bins in non-Newton stencil
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::respa_bin_no_newton_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-
- NeighList *listinner = list->listinner;
- NeighList *listmiddle = list->listmiddle;
- const int respamiddle = list->respamiddle;
-
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list,listinner,listmiddle)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*neighptr_inner,*neighptr_middle;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
-
- int *ilist_inner = listinner->ilist;
- int *numneigh_inner = listinner->numneigh;
- int **firstneigh_inner = listinner->firstneigh;
-
- int *ilist_middle,*numneigh_middle,**firstneigh_middle;
- if (respamiddle) {
- ilist_middle = listmiddle->ilist;
- numneigh_middle = listmiddle->numneigh;
- firstneigh_middle = listmiddle->firstneigh;
- }
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- MyPage<int> &ipage_inner = listinner->ipage[tid];
- ipage.reset();
- ipage_inner.reset();
-
- MyPage<int> *ipage_middle;
- if (respamiddle) {
- ipage_middle = listmiddle->ipage + tid;
- ipage_middle->reset();
- }
-
- int which = 0;
- int minchange = 0;
-
- for (i = ifrom; i < ito; i++) {
-
- n = n_inner = 0;
- neighptr = ipage.vget();
- neighptr_inner = ipage_inner.vget();
- if (respamiddle) {
- n_middle = 0;
- neighptr_middle = ipage_middle->vget();
- }
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- ibin = coord2bin(x[i]);
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in surrounding bins in stencil including self
- // only store pair if i < j
- // stores own/own pairs only once
- // stores own/ghost pairs on both procs
-
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (minchange) neighptr_inner[n_inner++] = j;
- else if (which > 0)
- neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (minchange) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- ilist_inner[i] = i;
- firstneigh_inner[i] = neighptr_inner;
- numneigh_inner[i] = n_inner;
- ipage.vgot(n_inner);
- if (ipage_inner.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (respamiddle) {
- ilist_middle[i] = i;
- firstneigh_middle[i] = neighptr_middle;
- numneigh_middle[i] = n_middle;
- ipage_middle->vgot(n_middle);
- if (ipage_middle->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
- listinner->inum = nlocal;
- if (respamiddle) listmiddle->inum = nlocal;
-}
-
-/* ----------------------------------------------------------------------
- multiple respa lists
- binned neighbor list construction with full Newton's 3rd law
- each owned atom i checks its own bin and other bins in Newton stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::respa_bin_newton_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-
- NeighList *listinner = list->listinner;
- NeighList *listmiddle = list->listmiddle;
- const int respamiddle = list->respamiddle;
-
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list,listinner,listmiddle)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*neighptr_inner,*neighptr_middle;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
-
- int *ilist_inner = listinner->ilist;
- int *numneigh_inner = listinner->numneigh;
- int **firstneigh_inner = listinner->firstneigh;
-
- int *ilist_middle,*numneigh_middle,**firstneigh_middle;
- if (respamiddle) {
- ilist_middle = listmiddle->ilist;
- numneigh_middle = listmiddle->numneigh;
- firstneigh_middle = listmiddle->firstneigh;
- }
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- MyPage<int> &ipage_inner = listinner->ipage[tid];
- ipage.reset();
- ipage_inner.reset();
-
- MyPage<int> *ipage_middle;
- if (respamiddle) {
- ipage_middle = listmiddle->ipage + tid;
- ipage_middle->reset();
- }
-
- int which = 0;
- int minchange = 0;
-
- for (i = ifrom; i < ito; i++) {
-
- n = n_inner = 0;
- neighptr = ipage.vget();
- neighptr_inner = ipage_inner.vget();
- if (respamiddle) {
- n_middle = 0;
- neighptr_middle = ipage_middle->vget();
- }
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over rest of atoms in i's bin, ghosts are at end of linked list
- // if j is owned atom, store it, since j is beyond i in linked list
- // if j is ghost, only store if j coords are "above and to the right" of i
-
- for (j = bins[i]; j >= 0; j = bins[j]) {
- if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (minchange) neighptr_inner[n_inner++] = j;
- else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (minchange) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
- }
-
- // loop over all atoms in other bins in stencil, store every pair
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (minchange) neighptr_inner[n_inner++] = j;
- else if (which > 0)
- neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (minchange) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- ilist_inner[i] = i;
- firstneigh_inner[i] = neighptr_inner;
- numneigh_inner[i] = n_inner;
- ipage.vgot(n_inner);
- if (ipage_inner.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (respamiddle) {
- ilist_middle[i] = i;
- firstneigh_middle[i] = neighptr_middle;
- numneigh_middle[i] = n_middle;
- ipage_middle->vgot(n_middle);
- if (ipage_middle->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
- listinner->inum = nlocal;
- if (respamiddle) listmiddle->inum = nlocal;
-}
-
-/* ----------------------------------------------------------------------
- multiple respa lists
- binned neighbor list construction with Newton's 3rd law for triclinic
- each owned atom i checks its own bin and other bins in triclinic stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
-{
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
- const int molecular = atom->molecular;
- const int moltemplate = (molecular == 2) ? 1 : 0;
-
- NEIGH_OMP_INIT;
-
- NeighList *listinner = list->listinner;
- NeighList *listmiddle = list->listmiddle;
- const int respamiddle = list->respamiddle;
-
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list,listinner,listmiddle)
-#endif
- NEIGH_OMP_SETUP(nlocal);
-
- int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*neighptr_inner,*neighptr_middle;
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
-
- int *ilist_inner = listinner->ilist;
- int *numneigh_inner = listinner->numneigh;
- int **firstneigh_inner = listinner->firstneigh;
-
- int *ilist_middle,*numneigh_middle,**firstneigh_middle;
- if (respamiddle) {
- ilist_middle = listmiddle->ilist;
- numneigh_middle = listmiddle->numneigh;
- firstneigh_middle = listmiddle->firstneigh;
- }
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- MyPage<int> &ipage_inner = listinner->ipage[tid];
- ipage.reset();
- ipage_inner.reset();
-
- MyPage<int> *ipage_middle;
- if (respamiddle) {
- ipage_middle = listmiddle->ipage + tid;
- ipage_middle->reset();
- }
-
- int which = 0;
- int minchange = 0;
-
- for (i = ifrom; i < ito; i++) {
-
- n = n_inner = 0;
- neighptr = ipage.vget();
- neighptr_inner = ipage_inner.vget();
- if (respamiddle) {
- n_middle = 0;
- neighptr_middle = ipage_middle->vget();
- }
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in bins in stencil
- // pairs for atoms j "below" i are excluded
- // below = lower z or (equal z and lower y) or (equal zy and lower x)
- // (equal zyx and j <= i)
- // latter excludes self-self interaction but allows superposed atoms
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >=0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (minchange) neighptr_inner[n_inner++] = j;
- else if (which > 0)
- neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (minchange) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
- }
- }
-
- ilist[i] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- ilist_inner[i] = i;
- firstneigh_inner[i] = neighptr_inner;
- numneigh_inner[i] = n_inner;
- ipage.vgot(n_inner);
- if (ipage_inner.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (respamiddle) {
- ilist_middle[i] = i;
- firstneigh_middle[i] = neighptr_middle;
- numneigh_middle[i] = n_middle;
- ipage_middle->vgot(n_middle);
- if (ipage_middle->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- }
- NEIGH_OMP_CLOSE;
- list->inum = nlocal;
- listinner->inum = nlocal;
- if (respamiddle) listmiddle->inum = nlocal;
-}
diff --git a/src/USER-OMP/npair_full_bin_ghost_omp.cpp b/src/USER-OMP/npair_full_bin_ghost_omp.cpp
new file mode 100644
index 0000000000..7f7239fe63
--- /dev/null
+++ b/src/USER-OMP/npair_full_bin_ghost_omp.cpp
@@ -0,0 +1,166 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_full_bin_ghost_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace NeighConst;
+
+/* ---------------------------------------------------------------------- */
+
+NPairFullBinGhostOmp::NPairFullBinGhostOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction for all neighbors
+ include neighbors of ghost atoms, but no "special neighbors" for ghosts
+ every neighbor pair appears in list of both atoms i and j
+------------------------------------------------------------------------- */
+
+void NPairFullBinGhostOmp::build(NeighList *list)
+{
+ const int nlocal = atom->nlocal;
+ const int nall = nlocal + atom->nghost;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nall);
+
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int xbin,ybin,zbin,xbin2,ybin2,zbin2;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ // loop over owned & ghost atoms, storing neighbors
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in surrounding bins in stencil including self
+ // when i is a ghost atom, must check if stencil bin is out of bounds
+ // skip i = j
+ // no molecular test when i = ghost atom
+
+ if (i < nlocal) {
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (i == j) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ } else {
+ ibin = coord2bin(x[i],xbin,ybin,zbin);
+ for (k = 0; k < nstencil; k++) {
+ xbin2 = xbin + stencilxyz[k][0];
+ ybin2 = ybin + stencilxyz[k][1];
+ zbin2 = zbin + stencilxyz[k][2];
+ if (xbin2 < 0 || xbin2 >= mbinx ||
+ ybin2 < 0 || ybin2 >= mbiny ||
+ zbin2 < 0 || zbin2 >= mbinz) continue;
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (i == j) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+ list->gnum = nall - nlocal;
+}
diff --git a/src/USER-OMP/npair_full_bin_ghost_omp.h b/src/USER-OMP/npair_full_bin_ghost_omp.h
new file mode 100644
index 0000000000..ed1580ac3b
--- /dev/null
+++ b/src/USER-OMP/npair_full_bin_ghost_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(full/bin/ghost/omp,
+ NPairFullBinGhostOmp,
+ NP_FULL | NP_BIN | NP_GHOST | NP_OMP | NP_NEWTON | NP_NEWTOFF |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_FULL_BIN_GHOST_OMP_H
+#define LMP_NPAIR_FULL_BIN_GHOST_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairFullBinGhostOmp : public NPair {
+ public:
+ NPairFullBinGhostOmp(class LAMMPS *);
+ ~NPairFullBinGhostOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_full_bin_omp.cpp b/src/USER-OMP/npair_full_bin_omp.cpp
new file mode 100644
index 0000000000..ad9e48784e
--- /dev/null
+++ b/src/USER-OMP/npair_full_bin_omp.cpp
@@ -0,0 +1,135 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_full_bin_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace NeighConst;
+
+/* ---------------------------------------------------------------------- */
+
+NPairFullBinOmp::NPairFullBinOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction for all neighbors
+ every neighbor pair appears in list of both atoms i and j
+------------------------------------------------------------------------- */
+
+void NPairFullBinOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ // loop over owned atoms, storing neighbors
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in surrounding bins in stencil including self
+ // skip i = j
+
+ ibin = coord2bin(x[i]);
+
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (i == j) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+ list->gnum = 0;
+}
diff --git a/src/USER-OMP/npair_full_bin_omp.h b/src/USER-OMP/npair_full_bin_omp.h
new file mode 100644
index 0000000000..5aa17310e2
--- /dev/null
+++ b/src/USER-OMP/npair_full_bin_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(full/bin/omp,
+ NPairFullBinOmp,
+ NP_FULL | NP_BIN | NP_OMP | NP_NEWTON | NP_NEWTOFF |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_FULL_BIN_OMP_H
+#define LMP_NPAIR_FULL_BIN_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairFullBinOmp : public NPair {
+ public:
+ NPairFullBinOmp(class LAMMPS *);
+ ~NPairFullBinOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp
new file mode 100644
index 0000000000..eb0153d63f
--- /dev/null
+++ b/src/USER-OMP/npair_full_multi_omp.cpp
@@ -0,0 +1,143 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_full_multi_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace NeighConst;
+
+/* ---------------------------------------------------------------------- */
+
+NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction for all neighbors
+ multi-type stencil is itype dependent and is distance checked
+ every neighbor pair appears in list of both atoms i and j
+------------------------------------------------------------------------- */
+
+void NPairFullMultiOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*s;
+ double *cutsq,*distsq;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in other bins in stencil, including self
+ // skip if i,j neighbor cutoff is less than bin distance
+ // skip i = j
+
+ ibin = coord2bin(x[i]);
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ cutsq = cutneighsq[itype];
+ ns = nstencil_multi[itype];
+ for (k = 0; k < ns; k++) {
+ for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+ if (i == j) continue;
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+ list->gnum = 0;
+}
diff --git a/src/USER-OMP/npair_full_multi_omp.h b/src/USER-OMP/npair_full_multi_omp.h
new file mode 100644
index 0000000000..36a8d02e28
--- /dev/null
+++ b/src/USER-OMP/npair_full_multi_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(full/multi/omp,
+ NPairFullMultiOmp,
+ NP_FULL | NP_MULTI | NP_OMP |
+ NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_FULL_MULTI_OMP_H
+#define LMP_NPAIR_FULL_MULTI_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairFullMultiOmp : public NPair {
+ public:
+ NPairFullMultiOmp(class LAMMPS *);
+ ~NPairFullMultiOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_full_nsq_ghost_omp.cpp b/src/USER-OMP/npair_full_nsq_ghost_omp.cpp
new file mode 100644
index 0000000000..b33f76bb22
--- /dev/null
+++ b/src/USER-OMP/npair_full_nsq_ghost_omp.cpp
@@ -0,0 +1,148 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_full_nsq_ghost_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace NeighConst;
+
+/* ---------------------------------------------------------------------- */
+
+NPairFullNsqGhostOmp::NPairFullNsqGhostOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ N^2 search for all neighbors
+ include neighbors of ghost atoms, but no "special neighbors" for ghosts
+ every neighbor pair appears in list of both atoms i and j
+------------------------------------------------------------------------- */
+
+void NPairFullNsqGhostOmp::build(NeighList *list)
+{
+ const int nlocal = atom->nlocal;
+ const int nall = nlocal + atom->nghost;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nall);
+
+ int i,j,n,itype,jtype,which,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ // loop over owned & ghost atoms, storing neighbors
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms, owned and ghost
+ // skip i = j
+ // no molecular test when i = ghost atom
+
+ if (i < nlocal) {
+ for (j = 0; j < nall; j++) {
+ if (i == j) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ } else {
+ for (j = 0; j < nall; j++) {
+ if (i == j) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+ list->gnum = nall - nlocal;
+}
diff --git a/src/USER-OMP/npair_full_nsq_ghost_omp.h b/src/USER-OMP/npair_full_nsq_ghost_omp.h
new file mode 100644
index 0000000000..dbf7f81bcc
--- /dev/null
+++ b/src/USER-OMP/npair_full_nsq_ghost_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(full/nsq/ghost/omp,
+ NPairFullNsqGhostOmp,
+ NP_FULL | NP_NSQ | NP_GHOST | NP_OMP | NP_NEWTON | NP_NEWTOFF |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_FULL_NSQ_GHOST_OMP_H
+#define LMP_NPAIR_FULL_NSQ_GHOST_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairFullNsqGhostOmp : public NPair {
+ public:
+ NPairFullNsqGhostOmp(class LAMMPS *);
+ ~NPairFullNsqGhostOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_full_nsq_omp.cpp b/src/USER-OMP/npair_full_nsq_omp.cpp
new file mode 100644
index 0000000000..1d0f26d638
--- /dev/null
+++ b/src/USER-OMP/npair_full_nsq_omp.cpp
@@ -0,0 +1,134 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_full_nsq_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace NeighConst;
+
+/* ---------------------------------------------------------------------- */
+
+NPairFullNsqOmp::NPairFullNsqOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ N^2 search for all neighbors
+ every neighbor pair appears in list of both atoms i and j
+------------------------------------------------------------------------- */
+
+void NPairFullNsqOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,n,itype,jtype,which,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int nall = atom->nlocal + atom->nghost;
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ // loop over owned atoms, storing neighbors
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms, owned and ghost
+ // skip i = j
+
+ for (j = 0; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+ if (i == j) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+ list->gnum = 0;
+}
diff --git a/src/USER-OMP/npair_full_nsq_omp.h b/src/USER-OMP/npair_full_nsq_omp.h
new file mode 100644
index 0000000000..2adcb8e1bd
--- /dev/null
+++ b/src/USER-OMP/npair_full_nsq_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(full/nsq/omp,
+ NPairFullNsqOmp,
+ NP_FULL | NP_NSQ | NP_OMP | NP_NEWTON | NP_NEWTOFF |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_FULL_NSQ_OMP_H
+#define LMP_NPAIR_FULL_NSQ_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairFullNsqOmp : public NPair {
+ public:
+ NPairFullNsqOmp(class LAMMPS *);
+ ~NPairFullNsqOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp
new file mode 100644
index 0000000000..e46afebb0d
--- /dev/null
+++ b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp
@@ -0,0 +1,173 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_bin_newtoff_ghost_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfBinNewtoffGhostOmp::NPairHalfBinNewtoffGhostOmp(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with partial Newton's 3rd law
+ include neighbors of ghost atoms, but no "special neighbors" for ghosts
+ owned and ghost atoms check own bin and other bins in stencil
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if i owned and j ghost (also stored by proc owning j)
+ pair stored once if i,j are both ghost and i < j
+------------------------------------------------------------------------- */
+
+void NPairHalfBinNewtoffGhostOmp::build(NeighList *list)
+{
+ const int nlocal = atom->nlocal;
+ const int nall = nlocal + atom->nghost;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nall);
+
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
+ tagint tagprev;
+ int xbin,ybin,zbin,xbin2,ybin2,zbin2;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in other bins in stencil including self
+ // when i is a ghost atom, must check if stencil bin is out of bounds
+ // only store pair if i < j
+ // stores own/own pairs only once
+ // stores own/ghost pairs with owned atom only, on both procs
+ // stores ghost/ghost pairs only once
+ // no molecular test when i = ghost atom
+
+ if (i < nlocal) {
+ ibin = coord2bin(x[i]);
+
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (j <= i) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ } else {
+ ibin = coord2bin(x[i],xbin,ybin,zbin);
+ for (k = 0; k < nstencil; k++) {
+ xbin2 = xbin + stencilxyz[k][0];
+ ybin2 = ybin + stencilxyz[k][1];
+ zbin2 = zbin + stencilxyz[k][2];
+ if (xbin2 < 0 || xbin2 >= mbinx ||
+ ybin2 < 0 || ybin2 >= mbiny ||
+ zbin2 < 0 || zbin2 >= mbinz) continue;
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (j <= i) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+ list->gnum = nall - atom->nlocal;
+}
diff --git a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h
new file mode 100644
index 0000000000..4974c407eb
--- /dev/null
+++ b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/bin/newtoff/ghost/omp,
+ NPairHalfBinNewtoffGhostOmp,
+ NP_HALF | NP_BIN | NP_NEWTOFF | NP_GHOST | NP_OMP |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_BIN_NEWTOFF_GHOST_OMP_H
+#define LMP_NPAIR_HALF_BIN_NEWTOFF_GHOST_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfBinNewtoffGhostOmp : public NPair {
+ public:
+ NPairHalfBinNewtoffGhostOmp(class LAMMPS *);
+ ~NPairHalfBinNewtoffGhostOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_bin_newtoff_omp.cpp
new file mode 100644
index 0000000000..99698b1d30
--- /dev/null
+++ b/src/USER-OMP/npair_half_bin_newtoff_omp.cpp
@@ -0,0 +1,138 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_bin_newtoff_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfBinNewtoffOmp::NPairHalfBinNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with partial Newton's 3rd law
+ each owned atom i checks own bin and other bins in stencil
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfBinNewtoffOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in other bins in stencil including self
+ // only store pair if i < j
+ // stores own/own pairs only once
+ // stores own/ghost pairs on both procs
+
+ ibin = coord2bin(x[i]);
+
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (j <= i) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_bin_newtoff_omp.h b/src/USER-OMP/npair_half_bin_newtoff_omp.h
new file mode 100644
index 0000000000..06ef355f38
--- /dev/null
+++ b/src/USER-OMP/npair_half_bin_newtoff_omp.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/bin/newtoff/omp,
+ NPairHalfBinNewtoffOmp,
+ NP_HALF | NP_BIN | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_BIN_NEWTOFF_OMP_H
+#define LMP_NPAIR_HALF_BIN_NEWTOFF_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfBinNewtoffOmp : public NPair {
+ public:
+ NPairHalfBinNewtoffOmp(class LAMMPS *);
+ ~NPairHalfBinNewtoffOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_bin_newton_omp.cpp b/src/USER-OMP/npair_half_bin_newton_omp.cpp
new file mode 100644
index 0000000000..33d78fe55a
--- /dev/null
+++ b/src/USER-OMP/npair_half_bin_newton_omp.cpp
@@ -0,0 +1,172 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_bin_newton_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfBinNewtonOmp::NPairHalfBinNewtonOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with full Newton's 3rd law
+ each owned atom i checks its own bin and other bins in Newton stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfBinNewtonOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over rest of atoms in i's bin, ghosts are at end of linked list
+ // if j is owned atom, store it, since j is beyond i in linked list
+ // if j is ghost, only store if j coords are "above and to the right" of i
+
+ for (j = bins[i]; j >= 0; j = bins[j]) {
+ if (j >= nlocal) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ // loop over all atoms in other bins in stencil, store every pair
+
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_bin_newton_omp.h b/src/USER-OMP/npair_half_bin_newton_omp.h
new file mode 100644
index 0000000000..f2468f04ad
--- /dev/null
+++ b/src/USER-OMP/npair_half_bin_newton_omp.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/bin/newton/omp,
+ NPairHalfBinNewtonOmp,
+ NP_HALF | NP_BIN | NP_NEWTON | NP_OMP | NP_ORTHO)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_BIN_NEWTON_OMP_H
+#define LMP_NPAIR_HALF_BIN_NEWTON_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfBinNewtonOmp : public NPair {
+ public:
+ NPairHalfBinNewtonOmp(class LAMMPS *);
+ ~NPairHalfBinNewtonOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp
new file mode 100644
index 0000000000..9eb9612235
--- /dev/null
+++ b/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp
@@ -0,0 +1,144 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_bin_newton_tri_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfBinNewtonTriOmp::NPairHalfBinNewtonTriOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with Newton's 3rd law for triclinic
+ each owned atom i checks its own bin and other bins in triclinic stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfBinNewtonTriOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in bins in stencil
+ // pairs for atoms j "below" i are excluded
+ // below = lower z or (equal z and lower y) or (equal zy and lower x)
+ // (equal zyx and j <= i)
+ // latter excludes self-self interaction but allows superposed atoms
+
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_bin_newton_tri_omp.h b/src/USER-OMP/npair_half_bin_newton_tri_omp.h
new file mode 100644
index 0000000000..f04f16f653
--- /dev/null
+++ b/src/USER-OMP/npair_half_bin_newton_tri_omp.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/bin/newton/tri/omp,
+ NPairHalfBinNewtonTriOmp,
+ NP_HALF | NP_BIN | NP_NEWTON | NP_TRI | NP_OMP)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_BIN_NEWTON_TRI_OMP_H
+#define LMP_NPAIR_HALF_BIN_NEWTON_TRI_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfBinNewtonTriOmp : public NPair {
+ public:
+ NPairHalfBinNewtonTriOmp(class LAMMPS *);
+ ~NPairHalfBinNewtonTriOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp
new file mode 100644
index 0000000000..37dc805857
--- /dev/null
+++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp
@@ -0,0 +1,145 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_multi_newtoff_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with partial Newton's 3rd law
+ each owned atom i checks own bin and other bins in stencil
+ multi-type stencil is itype dependent and is distance checked
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfMultiNewtoffOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*s;
+ double *cutsq,*distsq;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in other bins in stencil including self
+ // only store pair if i < j
+ // skip if i,j neighbor cutoff is less than bin distance
+ // stores own/own pairs only once
+ // stores own/ghost pairs on both procs
+
+ ibin = coord2bin(x[i]);
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ cutsq = cutneighsq[itype];
+ ns = nstencil_multi[itype];
+ for (k = 0; k < ns; k++) {
+ for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
+ if (j <= i) continue;
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.h b/src/USER-OMP/npair_half_multi_newtoff_omp.h
new file mode 100644
index 0000000000..a7aebf6579
--- /dev/null
+++ b/src/USER-OMP/npair_half_multi_newtoff_omp.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/multi/newtoff/omp,
+ NPairHalfMultiNewtoffOmp,
+ NP_HALF | NP_MULTI | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_MULTI_NEWTOFF_OMP_H
+#define LMP_NPAIR_HALF_MULTI_NEWTOFF_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfMultiNewtoffOmp : public NPair {
+ public:
+ NPairHalfMultiNewtoffOmp(class LAMMPS *);
+ ~NPairHalfMultiNewtoffOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp
new file mode 100644
index 0000000000..9719911afa
--- /dev/null
+++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp
@@ -0,0 +1,178 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_multi_newton_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfMultiNewtonOmp::NPairHalfMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with full Newton's 3rd law
+ each owned atom i checks its own bin and other bins in Newton stencil
+ multi-type stencil is itype dependent and is distance checked
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfMultiNewtonOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*s;
+ double *cutsq,*distsq;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over rest of atoms in i's bin, ghosts are at end of linked list
+ // if j is owned atom, store it, since j is beyond i in linked list
+ // if j is ghost, only store if j coords are "above and to the right" of i
+
+ for (j = bins[i]; j >= 0; j = bins[j]) {
+ if (j >= nlocal) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ // loop over all atoms in other bins in stencil, store every pair
+ // skip if i,j neighbor cutoff is less than bin distance
+
+ ibin = coord2bin(x[i]);
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ cutsq = cutneighsq[itype];
+ ns = nstencil_multi[itype];
+ for (k = 0; k < ns; k++) {
+ for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_multi_newton_omp.h b/src/USER-OMP/npair_half_multi_newton_omp.h
new file mode 100644
index 0000000000..85df36bb09
--- /dev/null
+++ b/src/USER-OMP/npair_half_multi_newton_omp.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/multi/newton/omp,
+ NPairHalfMultiNewtonOmp,
+ NP_HALF | NP_MULTI | NP_NEWTON | NP_OMP | NP_ORTHO)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_OMP_H
+#define LMP_NPAIR_HALF_MULTI_NEWTON_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfMultiNewtonOmp : public NPair {
+ public:
+ NPairHalfMultiNewtonOmp(class LAMMPS *);
+ ~NPairHalfMultiNewtonOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp
new file mode 100644
index 0000000000..717a709386
--- /dev/null
+++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp
@@ -0,0 +1,154 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_multi_newton_tri_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with Newton's 3rd law for triclinic
+ each owned atom i checks its own bin and other bins in triclinic stencil
+ multi-type stencil is itype dependent and is distance checked
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfMultiNewtonTriOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*s;
+ double *cutsq,*distsq;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in bins, including self, in stencil
+ // skip if i,j neighbor cutoff is less than bin distance
+ // bins below self are excluded from stencil
+ // pairs for atoms j "below" i are excluded
+ // below = lower z or (equal z and lower y) or (equal zy and lower x)
+ // (equal zyx and j <= i)
+ // latter excludes self-self interaction but allows superposed atoms
+
+ ibin = coord2bin(x[i]);
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ cutsq = cutneighsq[itype];
+ ns = nstencil_multi[itype];
+ for (k = 0; k < ns; k++) {
+ for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.h b/src/USER-OMP/npair_half_multi_newton_tri_omp.h
new file mode 100644
index 0000000000..80faf8188f
--- /dev/null
+++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/multi/newton/tri/omp,
+ NPairHalfMultiNewtonTriOmp,
+ NP_HALF | NP_MULTI | NP_NEWTON | NP_TRI | NP_OMP)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_TRI_OMP_H
+#define LMP_NPAIR_HALF_MULTI_NEWTON_TRI_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfMultiNewtonTriOmp : public NPair {
+ public:
+ NPairHalfMultiNewtonTriOmp(class LAMMPS *);
+ ~NPairHalfMultiNewtonTriOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp
new file mode 100644
index 0000000000..0294658aa0
--- /dev/null
+++ b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp
@@ -0,0 +1,157 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_nsq_newtoff_ghost_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfNsqNewtoffGhostOmp::NPairHalfNsqNewtoffGhostOmp(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
+ include neighbors of ghost atoms, but no "special neighbors" for ghosts
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if i owned and j ghost (also stored by proc owning j)
+ pair stored once if i,j are both ghost and i < j
+------------------------------------------------------------------------- */
+
+void NPairHalfNsqNewtoffGhostOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
+ const int nall = nlocal + atom->nghost;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nall);
+
+ int i,j,n,itype,jtype,which,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ // loop over owned & ghost atoms, storing neighbors
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over remaining atoms, owned and ghost
+ // only store pair if i < j
+ // stores own/own pairs only once
+ // stores own/ghost pairs with owned atom only, on both procs
+ // stores ghost/ghost pairs only once
+ // no molecular test when i = ghost atom
+
+ if (i < nlocal) {
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ } else {
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) neighptr[n++] = j;
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = atom->nlocal;
+ list->gnum = nall - atom->nlocal;
+}
diff --git a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h
new file mode 100644
index 0000000000..6b565d9dd8
--- /dev/null
+++ b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/nsq/newtoff/ghost/omp,
+ NPairHalfNsqNewtoffGhostOmp,
+ NP_HALF | NP_NSQ | NP_NEWTOFF | NP_GHOST | NP_OMP |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_NSQ_NEWTOFF_GHOST_OMP_H
+#define LMP_NPAIR_HALF_NSQ_NEWTOFF_GHOST_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfNsqNewtoffGhostOmp : public NPair {
+ public:
+ NPairHalfNsqNewtoffGhostOmp(class LAMMPS *);
+ ~NPairHalfNsqNewtoffGhostOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp
new file mode 100644
index 0000000000..01da73cf1e
--- /dev/null
+++ b/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp
@@ -0,0 +1,133 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_nsq_newtoff_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfNsqNewtoffOmp::NPairHalfNsqNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfNsqNewtoffOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
+ const int nall = atom->nlocal + atom->nghost;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,n,itype,jtype,which,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ // loop over owned atoms, storing neighbors
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over remaining atoms, owned and ghost
+ // only store pair if i < j
+
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_nsq_newtoff_omp.h b/src/USER-OMP/npair_half_nsq_newtoff_omp.h
new file mode 100644
index 0000000000..23db92e10a
--- /dev/null
+++ b/src/USER-OMP/npair_half_nsq_newtoff_omp.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/nsq/newtoff/omp,
+ NPairHalfNsqNewtoffOmp,
+ NP_HALF | NP_NSQ | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_NSQ_NEWTOFF_OMP_H
+#define LMP_NPAIR_HALF_NSQ_NEWTOFF_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfNsqNewtoffOmp : public NPair {
+ public:
+ NPairHalfNsqNewtoffOmp(class LAMMPS *);
+ ~NPairHalfNsqNewtoffOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_nsq_newton_omp.cpp
new file mode 100644
index 0000000000..3815b1b85b
--- /dev/null
+++ b/src/USER-OMP/npair_half_nsq_newton_omp.cpp
@@ -0,0 +1,151 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_nsq_newton_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfNsqNewtonOmp::NPairHalfNsqNewtonOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ N^2 / 2 search for neighbor pairs with full Newton's 3rd law
+ every pair stored exactly once by some processor
+ decision on ghost atoms based on itag,jtag tests
+------------------------------------------------------------------------- */
+
+void NPairHalfNsqNewtonOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,n,itype,jtype,itag,jtag,which,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int nall = atom->nlocal + atom->nghost;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ itag = tag[i];
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over remaining atoms, owned and ghost
+ // itag = jtag is possible for long cutoffs that include images of self
+
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+
+ if (j >= nlocal) {
+ jtag = tag[j];
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_nsq_newton_omp.h b/src/USER-OMP/npair_half_nsq_newton_omp.h
new file mode 100644
index 0000000000..cd40d4217d
--- /dev/null
+++ b/src/USER-OMP/npair_half_nsq_newton_omp.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/nsq/newton/omp,
+ NPairHalfNsqNewtonOmp,
+ NP_HALF | NP_NSQ | NP_NEWTON | NP_OMP | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_NSQ_NEWTON_OMP_H
+#define LMP_NPAIR_HALF_NSQ_NEWTON_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfNsqNewtonOmp : public NPair {
+ public:
+ NPairHalfNsqNewtonOmp(class LAMMPS *);
+ ~NPairHalfNsqNewtonOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp
new file mode 100644
index 0000000000..287f11efa7
--- /dev/null
+++ b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp
@@ -0,0 +1,204 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_respa_bin_newtoff_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfRespaBinNewtoffOmp::NPairHalfRespaBinNewtoffOmp(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ multiple respa lists
+ binned neighbor list construction with partial Newton's 3rd law
+ each owned atom i checks own bin and surrounding bins in non-Newton stencil
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfRespaBinNewtoffOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+
+ NeighList *listinner = list->listinner;
+ NeighList *listmiddle = list->listmiddle;
+ const int respamiddle = list->respamiddle;
+
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list,listinner,listmiddle)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ int *ilist_inner = listinner->ilist;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ if (respamiddle) {
+ ilist_middle = listmiddle->ilist;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ }
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ MyPage<int> &ipage_inner = listinner->ipage[tid];
+ ipage.reset();
+ ipage_inner.reset();
+
+ MyPage<int> *ipage_middle;
+ if (respamiddle) {
+ ipage_middle = listmiddle->ipage + tid;
+ ipage_middle->reset();
+ }
+
+ int which = 0;
+ int minchange = 0;
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = n_inner = 0;
+ neighptr = ipage.vget();
+ neighptr_inner = ipage_inner.vget();
+ if (respamiddle) {
+ n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
+ }
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ ibin = coord2bin(x[i]);
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in surrounding bins in stencil including self
+ // only store pair if i < j
+ // stores own/own pairs only once
+ // stores own/ghost pairs on both procs
+
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (j <= i) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (minchange) neighptr_inner[n_inner++] = j;
+ else if (which > 0)
+ neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (minchange) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ ilist_inner[i] = i;
+ firstneigh_inner[i] = neighptr_inner;
+ numneigh_inner[i] = n_inner;
+ ipage.vgot(n_inner);
+ if (ipage_inner.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (respamiddle) {
+ ilist_middle[i] = i;
+ firstneigh_middle[i] = neighptr_middle;
+ numneigh_middle[i] = n_middle;
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+ listinner->inum = nlocal;
+ if (respamiddle) listmiddle->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.h b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.h
new file mode 100644
index 0000000000..257aa8fdaa
--- /dev/null
+++ b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/respa/bin/newtoff/omp,
+ NPairHalfRespaBinNewtoffOmp,
+ NP_HALF | NP_RESPA | NP_BIN | NP_NEWTOFF | NP_OMP |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_RESPA_BIN_NEWTOFF_OMP_H
+#define LMP_NPAIR_HALF_RESPA_BIN_NEWTOFF_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfRespaBinNewtoffOmp : public NPair {
+ public:
+ NPairHalfRespaBinNewtoffOmp(class LAMMPS *);
+ ~NPairHalfRespaBinNewtoffOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp
new file mode 100644
index 0000000000..30256bd20d
--- /dev/null
+++ b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp
@@ -0,0 +1,250 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_respa_bin_newton_omp.h"
+#include "neighbor.h"
+#include "npair_omp.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfRespaBinNewtonOmp::NPairHalfRespaBinNewtonOmp(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ multiple respa lists
+ binned neighbor list construction with full Newton's 3rd law
+ each owned atom i checks its own bin and other bins in Newton stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfRespaBinNewtonOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+
+ NeighList *listinner = list->listinner;
+ NeighList *listmiddle = list->listmiddle;
+ const int respamiddle = list->respamiddle;
+
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list,listinner,listmiddle)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ int *ilist_inner = listinner->ilist;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ if (respamiddle) {
+ ilist_middle = listmiddle->ilist;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ }
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ MyPage<int> &ipage_inner = listinner->ipage[tid];
+ ipage.reset();
+ ipage_inner.reset();
+
+ MyPage<int> *ipage_middle;
+ if (respamiddle) {
+ ipage_middle = listmiddle->ipage + tid;
+ ipage_middle->reset();
+ }
+
+ int which = 0;
+ int minchange = 0;
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = n_inner = 0;
+ neighptr = ipage.vget();
+ neighptr_inner = ipage_inner.vget();
+ if (respamiddle) {
+ n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
+ }
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over rest of atoms in i's bin, ghosts are at end of linked list
+ // if j is owned atom, store it, since j is beyond i in linked list
+ // if j is ghost, only store if j coords are "above and to the right" of i
+
+ for (j = bins[i]; j >= 0; j = bins[j]) {
+ if (j >= nlocal) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (minchange) neighptr_inner[n_inner++] = j;
+ else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (minchange) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
+ }
+
+ // loop over all atoms in other bins in stencil, store every pair
+
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (minchange) neighptr_inner[n_inner++] = j;
+ else if (which > 0)
+ neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (minchange) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ ilist_inner[i] = i;
+ firstneigh_inner[i] = neighptr_inner;
+ numneigh_inner[i] = n_inner;
+ ipage.vgot(n_inner);
+ if (ipage_inner.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (respamiddle) {
+ ilist_middle[i] = i;
+ firstneigh_middle[i] = neighptr_middle;
+ numneigh_middle[i] = n_middle;
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+ listinner->inum = nlocal;
+ if (respamiddle) listmiddle->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_respa_bin_newton_omp.h b/src/USER-OMP/npair_half_respa_bin_newton_omp.h
new file mode 100644
index 0000000000..c4bad0aec8
--- /dev/null
+++ b/src/USER-OMP/npair_half_respa_bin_newton_omp.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/respa/bin/newton/omp,
+ NPairHalfRespaBinNewtonOmp,
+ NP_HALF | NP_RESPA | NP_BIN | NP_NEWTON | NP_OMP | NP_ORTHO)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_RESPA_BIN_NEWTON_OMP_H
+#define LMP_NPAIR_HALF_RESPA_BIN_NEWTON_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfRespaBinNewtonOmp : public NPair {
+ public:
+ NPairHalfRespaBinNewtonOmp(class LAMMPS *);
+ ~NPairHalfRespaBinNewtonOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp
new file mode 100644
index 0000000000..27d02000c5
--- /dev/null
+++ b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp
@@ -0,0 +1,211 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_respa_bin_newton_tri_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfRespaBinNewtonTriOmp::NPairHalfRespaBinNewtonTriOmp(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ multiple respa lists
+ binned neighbor list construction with Newton's 3rd law for triclinic
+ each owned atom i checks its own bin and other bins in triclinic stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfRespaBinNewtonTriOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+
+ NeighList *listinner = list->listinner;
+ NeighList *listmiddle = list->listmiddle;
+ const int respamiddle = list->respamiddle;
+
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list,listinner,listmiddle)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ int *ilist_inner = listinner->ilist;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ if (respamiddle) {
+ ilist_middle = listmiddle->ilist;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ }
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ MyPage<int> &ipage_inner = listinner->ipage[tid];
+ ipage.reset();
+ ipage_inner.reset();
+
+ MyPage<int> *ipage_middle;
+ if (respamiddle) {
+ ipage_middle = listmiddle->ipage + tid;
+ ipage_middle->reset();
+ }
+
+ int which = 0;
+ int minchange = 0;
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = n_inner = 0;
+ neighptr = ipage.vget();
+ neighptr_inner = ipage_inner.vget();
+ if (respamiddle) {
+ n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
+ }
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in bins in stencil
+ // pairs for atoms j "below" i are excluded
+ // below = lower z or (equal z and lower y) or (equal zy and lower x)
+ // (equal zyx and j <= i)
+ // latter excludes self-self interaction but allows superposed atoms
+
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (minchange) neighptr_inner[n_inner++] = j;
+ else if (which > 0)
+ neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (minchange) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ ilist_inner[i] = i;
+ firstneigh_inner[i] = neighptr_inner;
+ numneigh_inner[i] = n_inner;
+ ipage_inner.vgot(n_inner);
+ if (ipage_inner.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (respamiddle) {
+ ilist_middle[i] = i;
+ firstneigh_middle[i] = neighptr_middle;
+ numneigh_middle[i] = n_middle;
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+ listinner->inum = nlocal;
+ if (respamiddle) listmiddle->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h
new file mode 100644
index 0000000000..ea913f5560
--- /dev/null
+++ b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/respa/bin/newton/tri/omp,
+ NPairHalfRespaBinNewtonTriOmp,
+ NP_HALF | NP_RESPA | NP_BIN | NP_NEWTON | NP_TRI | NP_OMP)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_RESPA_BIN_NEWTON_TRI_OMP_H
+#define LMP_NPAIR_HALF_RESPA_BIN_NEWTON_TRI_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfRespaBinNewtonTriOmp : public NPair {
+ public:
+ NPairHalfRespaBinNewtonTriOmp(class LAMMPS *);
+ ~NPairHalfRespaBinNewtonTriOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp
new file mode 100644
index 0000000000..80826ffa42
--- /dev/null
+++ b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp
@@ -0,0 +1,198 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_respa_nsq_newtoff_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfRespaNsqNewtoffOmp::NPairHalfRespaNsqNewtoffOmp(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ multiple respa lists
+ N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
+ pair added to list if atoms i and j are both owned and i < j
+ pair added if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfRespaNsqNewtoffOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+
+ NeighList *listinner = list->listinner;
+ NeighList *listmiddle = list->listmiddle;
+ const int respamiddle = list->respamiddle;
+
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list,listinner,listmiddle)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,n,itype,jtype,n_inner,n_middle,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int nall = atom->nlocal + atom->nghost;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ int *ilist_inner = listinner->ilist;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ if (respamiddle) {
+ ilist_middle = listmiddle->ilist;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ }
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ MyPage<int> &ipage_inner = listinner->ipage[tid];
+ ipage.reset();
+ ipage_inner.reset();
+
+ MyPage<int> *ipage_middle;
+ if (respamiddle) {
+ ipage_middle = listmiddle->ipage + tid;
+ ipage_middle->reset();
+ }
+
+ int which = 0;
+ int minchange = 0;
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = n_inner = 0;
+ neighptr = ipage.vget();
+ neighptr_inner = ipage_inner.vget();
+ if (respamiddle) {
+ n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
+ }
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over remaining atoms, owned and ghost
+
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (minchange) neighptr_inner[n_inner++] = j;
+ else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (minchange) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ ilist_inner[i] = i;
+ firstneigh_inner[i] = neighptr_inner;
+ numneigh_inner[i] = n_inner;
+ ipage.vgot(n_inner);
+ if (ipage_inner.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (respamiddle) {
+ ilist_middle[i] = i;
+ firstneigh_middle[i] = neighptr_middle;
+ numneigh_middle[i] = n_middle;
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+ listinner->inum = nlocal;
+ if (respamiddle) listmiddle->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h
new file mode 100644
index 0000000000..ebd8691635
--- /dev/null
+++ b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/respa/nsq/newtoff/omp,
+ NPairHalfRespaNsqNewtoffOmp,
+ NP_HALF | NP_RESPA | NP_NSQ | NP_NEWTOFF | NP_OMP |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_RESPA_NSQ_NEWTOFF_OMP_H
+#define LMP_NPAIR_HALF_RESPA_NSQ_NEWTOFF_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfRespaNsqNewtoffOmp : public NPair {
+ public:
+ NPairHalfRespaNsqNewtoffOmp(class LAMMPS *);
+ ~NPairHalfRespaNsqNewtoffOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp
new file mode 100644
index 0000000000..18319dc1ae
--- /dev/null
+++ b/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp
@@ -0,0 +1,217 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_respa_nsq_newton_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfRespaNsqNewtonOmp::NPairHalfRespaNsqNewtonOmp(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ multiple respa lists
+ N^2 / 2 search for neighbor pairs with full Newton's 3rd law
+ pair added to list if atoms i and j are both owned and i < j
+ if j is ghost only me or other proc adds pair
+ decision based on itag,jtag tests
+------------------------------------------------------------------------- */
+
+void NPairHalfRespaNsqNewtonOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
+ const int molecular = atom->molecular;
+ const int moltemplate = (molecular == 2) ? 1 : 0;
+
+ NPAIR_OMP_INIT;
+
+ NeighList *listinner = list->listinner;
+ NeighList *listmiddle = list->listmiddle;
+ const int respamiddle = list->respamiddle;
+
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list,listinner,listmiddle)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,n,itype,jtype,itag,jtag,n_inner,n_middle,imol,iatom;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+
+ int nall = atom->nlocal + atom->nghost;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ int *ilist_inner = listinner->ilist;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ if (respamiddle) {
+ ilist_middle = listmiddle->ilist;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ }
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ MyPage<int> &ipage_inner = listinner->ipage[tid];
+ ipage.reset();
+ ipage_inner.reset();
+
+ MyPage<int> *ipage_middle;
+ if (respamiddle) {
+ ipage_middle = listmiddle->ipage + tid;
+ ipage_middle->reset();
+ }
+
+ int which = 0;
+ int minchange = 0;
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = n_inner = 0;
+ neighptr = ipage.vget();
+ neighptr_inner = ipage_inner.vget();
+ if (respamiddle) {
+ n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
+ }
+
+ itag = tag[i];
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over remaining atoms, owned and ghost
+
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+
+ if (j >= nlocal) {
+ jtag = tag[j];
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >=0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (minchange) neighptr_inner[n_inner++] = j;
+ else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (minchange) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ ilist_inner[i] = i;
+ firstneigh_inner[i] = neighptr_inner;
+ numneigh_inner[i] = n_inner;
+ ipage.vgot(n_inner);
+ if (ipage_inner.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (respamiddle) {
+ ilist_middle[i] = i;
+ firstneigh_middle[i] = neighptr_middle;
+ numneigh_middle[i] = n_middle;
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+ listinner->inum = nlocal;
+ if (respamiddle) listmiddle->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_respa_nsq_newton_omp.h b/src/USER-OMP/npair_half_respa_nsq_newton_omp.h
new file mode 100644
index 0000000000..cf39ad8d6e
--- /dev/null
+++ b/src/USER-OMP/npair_half_respa_nsq_newton_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/respa/nsq/newton/omp,
+ NPairHalfRespaNsqNewtonOmp,
+ NP_HALF | NP_RESPA | NP_NSQ | NP_NEWTON | NP_OMP |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_RESPA_NSQ_NEWTON_OMP_H
+#define LMP_NPAIR_HALF_RESPA_NSQ_NEWTON_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfRespaNsqNewtonOmp : public NPair {
+ public:
+ NPairHalfRespaNsqNewtonOmp(class LAMMPS *);
+ ~NPairHalfRespaNsqNewtonOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
new file mode 100644
index 0000000000..89a677806a
--- /dev/null
+++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
@@ -0,0 +1,179 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "npair_half_size_bin_newtoff_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "fix_shear_history.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfSizeBinNewtoffOmp::NPairHalfSizeBinNewtoffOmp(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ size particles
+ binned neighbor list construction with partial Newton's 3rd law
+ shear history must be accounted for when a neighbor pair is added
+ each owned atom i checks own bin and surrounding bins in non-Newton stencil
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfSizeBinNewtoffOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+
+ FixShearHistory * const fix_history = list->fix_history;
+ NeighList * listgranhistory = list->listgranhistory;
+
+ NPAIR_OMP_INIT;
+
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list,listgranhistory)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ double radi,radsum,cutsq;
+ int *neighptr,*touchptr;
+ double *shearptr;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
+
+ int *npartner;
+ tagint **partner;
+ double **shearpartner;
+ int **firsttouch;
+ double **firstshear;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ double *radius = atom->radius;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *molecule = atom->molecule;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ if (fix_history) {
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ ipage_touch = listgranhistory->ipage+tid;
+ dpage_shear = listgranhistory->dpage+tid;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+ if (fix_history) {
+ nn = 0;
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
+ }
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ radi = radius[i];
+ ibin = coord2bin(x[i]);
+
+ // loop over all atoms in surrounding bins in stencil including self
+ // only store pair if i < j
+ // stores own/own pairs only once
+ // stores own/ghost pairs on both procs
+
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (j <= i) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) {
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ }
+
+ n++;
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (fix_history) {
+ firsttouch[i] = touchptr;
+ firstshear[i] = shearptr;
+ ipage_touch->vgot(n);
+ dpage_shear->vgot(nn);
+ }
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.h b/src/USER-OMP/npair_half_size_bin_newtoff_omp.h
new file mode 100644
index 0000000000..7b71aa0ea7
--- /dev/null
+++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/size/bin/newtoff/omp,
+ NPairHalfSizeBinNewtoffOmp,
+ NP_HALF | NP_SIZE | NP_BIN | NP_NEWTOFF | NP_OMP |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_SIZE_BIN_NEWTOFF_OMP_H
+#define LMP_NPAIR_HALF_SIZE_BIN_NEWTOFF_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfSizeBinNewtoffOmp : public NPair {
+ public:
+ NPairHalfSizeBinNewtoffOmp(class LAMMPS *);
+ ~NPairHalfSizeBinNewtoffOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
new file mode 100644
index 0000000000..66aa573ca8
--- /dev/null
+++ b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
@@ -0,0 +1,227 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "npair_half_size_bin_newton_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "fix_shear_history.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfSizeBinNewtonOmp::NPairHalfSizeBinNewtonOmp(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ size particles
+ binned neighbor list construction with full Newton's 3rd law
+ shear history must be accounted for when a neighbor pair is added
+ each owned atom i checks its own bin and other bins in Newton stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfSizeBinNewtonOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+
+ FixShearHistory * const fix_history = list->fix_history;
+ NeighList * listgranhistory = list->listgranhistory;
+ if (fix_history) {
+ fix_history->nlocal_neigh = nlocal;
+ fix_history->nall_neigh = nlocal + atom->nghost;
+ }
+
+ NPAIR_OMP_INIT;
+
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list,listgranhistory)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ double radi,radsum,cutsq;
+ int *neighptr,*touchptr;
+ double *shearptr;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
+
+ int *npartner;
+ tagint **partner;
+ double **shearpartner;
+ int **firsttouch;
+ double **firstshear;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ double *radius = atom->radius;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *molecule = atom->molecule;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ if (fix_history) {
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ ipage_touch = listgranhistory->ipage+tid;
+ dpage_shear = listgranhistory->dpage+tid;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+ if (fix_history) {
+ nn = 0;
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
+ }
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ radi = radius[i];
+
+ // loop over rest of atoms in i's bin, ghosts are at end of linked list
+ // if j is owned atom, store it, since j is beyond i in linked list
+ // if j is ghost, only store if j coords are "above and to the right" of i
+
+ for (j = bins[i]; j >= 0; j = bins[j]) {
+ if (j >= nlocal) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) {
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ }
+
+ n++;
+ }
+ }
+
+ // loop over all atoms in other bins in stencil, store every pair
+
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) {
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ }
+
+ n++;
+ }
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (fix_history) {
+ firsttouch[i] = touchptr;
+ firstshear[i] = shearptr;
+ ipage_touch->vgot(n);
+ dpage_shear->vgot(nn);
+ }
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.h b/src/USER-OMP/npair_half_size_bin_newton_omp.h
new file mode 100644
index 0000000000..4268ac36a1
--- /dev/null
+++ b/src/USER-OMP/npair_half_size_bin_newton_omp.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/size/bin/newton/omp,
+ NPairHalfSizeBinNewtonOmp,
+ NP_HALF | NP_SIZE | NP_BIN | NP_NEWTON | NP_OMP | NP_ORTHO)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_SIZE_BIN_NEWTON_OMP_H
+#define LMP_NPAIR_HALF_SIZE_BIN_NEWTON_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfSizeBinNewtonOmp : public NPair {
+ public:
+ NPairHalfSizeBinNewtonOmp(class LAMMPS *);
+ ~NPairHalfSizeBinNewtonOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
new file mode 100644
index 0000000000..7463a6aba6
--- /dev/null
+++ b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
@@ -0,0 +1,121 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_size_bin_newton_tri_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfSizeBinNewtonTriOmp::NPairHalfSizeBinNewtonTriOmp(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ size particles
+ binned neighbor list construction with Newton's 3rd law for triclinic
+ no shear history is allowed for this option
+ each owned atom i checks its own bin and other bins in triclinic stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfSizeBinNewtonTriOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+
+ NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,k,n,ibin;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ double radi,radsum,cutsq;
+ int *neighptr;
+
+ // loop over each atom, storing neighbors
+
+ double **x = atom->x;
+ double *radius = atom->radius;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *molecule = atom->molecule;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ radi = radius[i];
+
+ // loop over all atoms in bins in stencil
+ // pairs for atoms j "below" i are excluded
+ // below = lower z or (equal z and lower y) or (equal zy and lower x)
+ // (equal zyx and j <= i)
+ // latter excludes self-self interaction but allows superposed atoms
+
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) neighptr[n++] = j;
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.h b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.h
new file mode 100644
index 0000000000..482ea4c36e
--- /dev/null
+++ b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/size/bin/newton/tri/omp,
+ NPairHalfSizeBinNewtonTriOmp,
+ NP_HALF | NP_SIZE | NP_BIN | NP_NEWTON | NP_TRI | NP_OMP)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_SIZE_BIN_NEWTON_TRI_OMP_H
+#define LMP_NPAIR_HALF_SIZE_BIN_NEWTON_TRI_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfSizeBinNewtonTriOmp : public NPair {
+ public:
+ NPairHalfSizeBinNewtonTriOmp(class LAMMPS *);
+ ~NPairHalfSizeBinNewtonTriOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
new file mode 100644
index 0000000000..48fc846c52
--- /dev/null
+++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
@@ -0,0 +1,177 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "npair_half_size_nsq_newtoff_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "fix_shear_history.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfSizeNsqNewtoffOmp::NPairHalfSizeNsqNewtoffOmp(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ size particles
+ N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
+ shear history must be accounted for when a neighbor pair is added
+ pair added to list if atoms i and j are both owned and i < j
+ pair added if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfSizeNsqNewtoffOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
+
+ FixShearHistory * const fix_history = list->fix_history;
+ NeighList * listgranhistory = list->listgranhistory;
+ if (fix_history) {
+ fix_history->nlocal_neigh = nlocal;
+ fix_history->nall_neigh = nlocal + atom->nghost;
+ }
+
+ NPAIR_OMP_INIT;
+
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list,listgranhistory)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,m,n,nn,dnum,dnumbytes;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ double radi,radsum,cutsq;
+ int *neighptr,*touchptr;
+ double *shearptr;
+
+ int *npartner;
+ tagint **partner;
+ double **shearpartner;
+ int **firsttouch;
+ double **firstshear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
+
+ double **x = atom->x;
+ double *radius = atom->radius;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *molecule = atom->molecule;
+ int nall = atom->nlocal + atom->nghost;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ if (fix_history) {
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ ipage_touch = listgranhistory->ipage+tid;
+ dpage_shear = listgranhistory->dpage+tid;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+ if (fix_history) {
+ nn = 0;
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
+ }
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ radi = radius[i];
+
+ // loop over remaining atoms, owned and ghost
+
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) {
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ }
+
+ n++;
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (fix_history) {
+ firsttouch[i] = touchptr;
+ firstshear[i] = shearptr;
+ ipage_touch->vgot(n);
+ dpage_shear->vgot(nn);
+ }
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.h b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.h
new file mode 100644
index 0000000000..793c49335a
--- /dev/null
+++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/size/nsq/newtoff/omp,
+ NPairHalfSizeNsqNewtoffOmp,
+ NP_HALF | NP_SIZE | NP_NSQ | NP_NEWTOFF | NP_OMP |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_SIZE_NSQ_NEWTOFF_OMP_H
+#define LMP_NPAIR_HALF_SIZE_NSQ_NEWTOFF_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfSizeNsqNewtoffOmp : public NPair {
+ public:
+ NPairHalfSizeNsqNewtoffOmp(class LAMMPS *);
+ ~NPairHalfSizeNsqNewtoffOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
new file mode 100644
index 0000000000..086f08a601
--- /dev/null
+++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
@@ -0,0 +1,195 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "npair_half_size_nsq_newton_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "fix_shear_history.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfSizeNsqNewtonOmp::NPairHalfSizeNsqNewtonOmp(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ size particles
+ N^2 / 2 search for neighbor pairs with full Newton's 3rd law
+ shear history must be accounted for when a neighbor pair is added
+ pair added to list if atoms i and j are both owned and i < j
+ if j is ghost only me or other proc adds pair
+ decision based on itag,jtag tests
+------------------------------------------------------------------------- */
+
+void NPairHalfSizeNsqNewtonOmp::build(NeighList *list)
+{
+ const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
+ const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;;
+
+ FixShearHistory * const fix_history = list->fix_history;
+ NeighList * listgranhistory = list->listgranhistory;
+ if (fix_history) {
+ fix_history->nlocal_neigh = nlocal;
+ fix_history->nall_neigh = nlocal+atom->nghost;
+ }
+
+ NPAIR_OMP_INIT;
+
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list,listgranhistory)
+#endif
+ NPAIR_OMP_SETUP(nlocal);
+
+ int i,j,m,n,nn,itag,jtag,dnum,dnumbytes;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ double radi,radsum,cutsq;
+ int *neighptr,*touchptr;
+ double *shearptr;
+
+ int *npartner;
+ tagint **partner;
+ double **shearpartner;
+ int **firsttouch;
+ double **firstshear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
+
+ double **x = atom->x;
+ double *radius = atom->radius;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *molecule = atom->molecule;
+ int nall = atom->nlocal + atom->nghost;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ if (fix_history) {
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ ipage_touch = listgranhistory->ipage+tid;
+ dpage_shear = listgranhistory->dpage+tid;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
+
+ for (i = ifrom; i < ito; i++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+ if (fix_history) {
+ nn = 0;
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
+ }
+
+ itag = tag[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ radi = radius[i];
+
+ // loop over remaining atoms, owned and ghost
+
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+
+ if (j >= nlocal) {
+ jtag = tag[j];
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+ }
+
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) {
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ }
+
+ n++;
+ }
+ }
+
+ ilist[i] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (fix_history) {
+ firsttouch[i] = touchptr;
+ firstshear[i] = shearptr;
+ ipage_touch->vgot(n);
+ dpage_shear->vgot(nn);
+ }
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = nlocal;
+}
diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.h b/src/USER-OMP/npair_half_size_nsq_newton_omp.h
new file mode 100644
index 0000000000..9abdb75db0
--- /dev/null
+++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/size/nsq/newton/omp,
+ NPairHalfSizeNsqNewtonOmp,
+ NP_HALF | NP_SIZE | NP_NSQ | NP_NEWTON | NP_OMP |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_SIZE_NSQ_NEWTON_OMP_H
+#define LMP_NPAIR_HALF_SIZE_NSQ_NEWTON_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfSizeNsqNewtonOmp : public NPair {
+ public:
+ NPairHalfSizeNsqNewtonOmp(class LAMMPS *);
+ ~NPairHalfSizeNsqNewtonOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.cpp b/src/USER-OMP/npair_halffull_newtoff_omp.cpp
new file mode 100644
index 0000000000..947e4e1ad2
--- /dev/null
+++ b/src/USER-OMP/npair_halffull_newtoff_omp.cpp
@@ -0,0 +1,91 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_halffull_newtoff_omp.h"
+#include "npair_omp.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalffullNewtoffOmp::NPairHalffullNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ build half list from full list
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if j is ghost (also stored by proc owning j)
+ works if full list is a skip list
+------------------------------------------------------------------------- */
+
+void NPairHalffullNewtoffOmp::build(NeighList *list)
+{
+ const int inum_full = list->listfull->inum;
+
+ NPAIR_OMP_INIT;
+
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(list)
+#endif
+ NPAIR_OMP_SETUP(inum_full);
+
+ int i,j,ii,jj,n,jnum,joriginal;
+ int *neighptr,*jlist;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int *ilist_full = list->listfull->ilist;
+ int *numneigh_full = list->listfull->numneigh;
+ int **firstneigh_full = list->listfull->firstneigh;
+
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
+
+ // loop over atoms in full list
+
+ for (ii = ifrom; ii < ito; ii++) {
+
+ n = 0;
+ neighptr = ipage.vget();
+
+ // loop over parent full list
+
+ i = ilist_full[ii];
+ jlist = firstneigh_full[i];
+ jnum = numneigh_full[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (j > i) neighptr[n++] = joriginal;
+ }
+
+ ilist[ii] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage.vgot(n);
+ if (ipage.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+ NPAIR_OMP_CLOSE;
+ list->inum = inum_full;
+}
diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.h b/src/USER-OMP/npair_halffull_newtoff_omp.h
new file mode 100644
index 0000000000..dffef2c3d3
--- /dev/null
+++ b/src/USER-OMP/npair_halffull_newtoff_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(halffull/newtoff/omp,
+ NPairHalffullNewtoffOmp,
+ NP_HALFFULL | NP_NEWTOFF | NP_OMP |
+ NP_NSQ | NP_BIN | NP_MULTI | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALFFULL_NEWTOFF_OMP_H
+#define LMP_NPAIR_HALFFULL_NEWTOFF_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalffullNewtoffOmp : public NPair {
+ public:
+ NPairHalffullNewtoffOmp(class LAMMPS *);
+ ~NPairHalffullNewtoffOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/neigh_derive_omp.cpp b/src/USER-OMP/npair_halffull_newton_omp.cpp
similarity index 61%
rename from src/USER-OMP/neigh_derive_omp.cpp
rename to src/USER-OMP/npair_halffull_newton_omp.cpp
index 8f5fa05e81..6e158d372d 100644
--- a/src/USER-OMP/neigh_derive_omp.cpp
+++ b/src/USER-OMP/npair_halffull_newton_omp.cpp
@@ -11,77 +11,22 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "npair_halffull_newton_omp.h"
+#include "npair_omp.h"
#include "neighbor.h"
-#include "neighbor_omp.h"
#include "neigh_list.h"
#include "atom.h"
-#include "comm.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
-/* ----------------------------------------------------------------------
- build half list from full list
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
- works if full list is a skip list
-------------------------------------------------------------------------- */
-
-void Neighbor::half_from_full_no_newton_omp(NeighList *list)
-{
- const int inum_full = list->listfull->inum;
-
- NEIGH_OMP_INIT;
-
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(list)
-#endif
- NEIGH_OMP_SETUP(inum_full);
-
- int i,j,ii,jj,n,jnum,joriginal;
- int *neighptr,*jlist;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int *ilist_full = list->listfull->ilist;
- int *numneigh_full = list->listfull->numneigh;
- int **firstneigh_full = list->listfull->firstneigh;
-
- // each thread has its own page allocator
- MyPage<int> &ipage = list->ipage[tid];
- ipage.reset();
-
- // loop over atoms in full list
-
- for (ii = ifrom; ii < ito; ii++) {
-
- n = 0;
- neighptr = ipage.vget();
-
- // loop over parent full list
-
- i = ilist_full[ii];
- jlist = firstneigh_full[i];
- jnum = numneigh_full[i];
-
- for (jj = 0; jj < jnum; jj++) {
- joriginal = jlist[jj];
- j = joriginal & NEIGHMASK;
- if (j > i) neighptr[n++] = joriginal;
- }
+/* ---------------------------------------------------------------------- */
- ilist[ii] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage.vgot(n);
- if (ipage.status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
- NEIGH_OMP_CLOSE;
- list->inum = inum_full;
-}
+NPairHalffullNewtonOmp::NPairHalffullNewtonOmp(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
build half list from full list
@@ -90,15 +35,15 @@ void Neighbor::half_from_full_no_newton_omp(NeighList *list)
works if full list is a skip list
------------------------------------------------------------------------- */
-void Neighbor::half_from_full_newton_omp(NeighList *list)
+void NPairHalffullNewtonOmp::build(NeighList *list)
{
const int inum_full = list->listfull->inum;
- NEIGH_OMP_INIT;
+ NPAIR_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
- NEIGH_OMP_SETUP(inum_full);
+ NPAIR_OMP_SETUP(inum_full);
int i,j,ii,jj,n,jnum,joriginal;
int *neighptr,*jlist;
@@ -157,6 +102,6 @@ void Neighbor::half_from_full_newton_omp(NeighList *list)
if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
- NEIGH_OMP_CLOSE;
+ NPAIR_OMP_CLOSE;
list->inum = inum_full;
}
diff --git a/src/USER-OMP/npair_halffull_newton_omp.h b/src/USER-OMP/npair_halffull_newton_omp.h
new file mode 100644
index 0000000000..f7fc7c1ec7
--- /dev/null
+++ b/src/USER-OMP/npair_halffull_newton_omp.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(halffull/newton/omp,
+ NPairHalffullNewtonOmp,
+ NP_HALFFULL | NP_NEWTON | NP_OMP |
+ NP_NSQ | NP_BIN | NP_MULTI | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALFFULL_NEWTON_OMP_H
+#define LMP_NPAIR_HALFFULL_NEWTON_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalffullNewtonOmp : public NPair {
+ public:
+ NPairHalffullNewtonOmp(class LAMMPS *);
+ ~NPairHalffullNewtonOmp() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-OMP/neighbor_omp.h b/src/USER-OMP/npair_omp.h
similarity index 81%
rename from src/USER-OMP/neighbor_omp.h
rename to src/USER-OMP/npair_omp.h
index 53726109e8..7f7d4d1cc2 100644
--- a/src/USER-OMP/neighbor_omp.h
+++ b/src/USER-OMP/npair_omp.h
@@ -11,13 +11,14 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#ifndef LMP_NEIGHBOR_OMP_H
-#define LMP_NEIGHBOR_OMP_H
+#ifndef LMP_NPAIR_OMP_H
+#define LMP_NPAIR_OMP_H
#if defined(_OPENMP)
#include <omp.h>
#endif
+#include "comm.h"
#include "modify.h"
#include "timer.h"
#include "fix_omp.h"
@@ -28,13 +29,13 @@ namespace LAMMPS_NS {
// these macros hide some ugly and redundant OpenMP related stuff
#if defined(_OPENMP)
-// make sure we have at least one page for each thread
-#define NEIGH_OMP_INIT \
+// get access to number of threads and per-thread data structures via FixOMP
+#define NPAIR_OMP_INIT \
const int nthreads = comm->nthreads; \
const int ifix = modify->find_fix("package_omp")
// get thread id and then assign each thread a fixed chunk of atoms
-#define NEIGH_OMP_SETUP(num) \
+#define NPAIR_OMP_SETUP(num) \
{ \
const int tid = omp_get_thread_num(); \
const int idelta = 1 + num/nthreads; \
@@ -45,20 +46,20 @@ namespace LAMMPS_NS {
ThrData *thr = fix->get_thr(tid); \
thr->timer(Timer::START);
-#define NEIGH_OMP_CLOSE \
+#define NPAIR_OMP_CLOSE \
thr->timer(Timer::NEIGH); \
}
#else /* !defined(_OPENMP) */
-#define NEIGH_OMP_INIT
+#define NPAIR_OMP_INIT
-#define NEIGH_OMP_SETUP(num) \
+#define NPAIR_OMP_SETUP(num) \
const int tid = 0; \
const int ifrom = 0; \
const int ito = num
-#define NEIGH_OMP_CLOSE
+#define NPAIR_OMP_CLOSE
#endif
diff --git a/src/accelerator_intel.h b/src/accelerator_intel.h
deleted file mode 100644
index fab07989ff..0000000000
--- a/src/accelerator_intel.h
+++ /dev/null
@@ -1,68 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-// NOTE: this file is *supposed* to be included multiple times
-
-#ifdef LMP_USER_INTEL
-
-// true interface to USER-INTEL
-
-// this part is used inside the neighbor.h header file to
-// add functions to the Neighbor class definition
-
-#ifdef LMP_INSIDE_NEIGHBOR_H
- #ifdef LMP_INTEL_OFFLOAD
- #ifdef __INTEL_OFFLOAD
- template <class flt_t, class acc_t> friend class IntelBuffers;
- #endif
- #endif
-
- friend class FixIntel;
- void *fix_intel;
-
- template <class flt_t, class acc_t>
- void bin_atoms(void *, int *, int *);
-
- template <class flt_t, class acc_t, int, int>
- void hbni(const int, NeighList *, void *, const int, const int, void *,
- const int offload_end = 0);
- template <class flt_t, class acc_t, int>
- void hbnni(const int, NeighList *, void *, const int, const int, void *);
- template <class flt_t, class acc_t, int, int>
- void hbnti(const int, NeighList *, void *, const int, const int, void *,
- const int offload_end = 0);
- template <class flt_t, class acc_t, int, int>
- void fbi(const int, NeighList *, void *, const int, const int, void *,
- const int offload_end = 0);
-
- void half_bin_no_newton_intel(class NeighList *);
- void half_bin_newton_intel(class NeighList *);
- void half_bin_newton_tri_intel(class NeighList *);
- void full_bin_intel(class NeighList *);
-
-#endif /* !LMP_INSIDE_NEIGHBOR_H */
-
-#else /* !LMP_USER_INTEL */
-
-// needed for compiling Neighbor class when USER-Intel is not installed
-
-#ifdef LMP_INSIDE_NEIGHBOR_H
-
- void half_bin_no_newton_intel(class NeighList *) {}
- void half_bin_newton_intel(class NeighList *) {}
- void half_bin_newton_tri_intel(class NeighList *) {}
- void full_bin_intel(class NeighList *) {}
-
-#endif
-
-#endif /* !LMP_USER_INTEL */
diff --git a/src/nbin.cpp b/src/nbin.cpp
new file mode 100644
index 0000000000..ef8543fdf9
--- /dev/null
+++ b/src/nbin.cpp
@@ -0,0 +1,143 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nbin.h"
+#include "neighbor.h"
+#include "domain.h"
+#include "update.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NBin::NBin(LAMMPS *lmp) : Pointers(lmp)
+{
+ last_setup = last_bin = last_bin_memory = -1;
+ maxbin = maxatom = 0;
+ binhead = NULL;
+ bins = NULL;
+
+ // geometry settings
+
+ dimension = domain->dimension;
+ triclinic = domain->triclinic;
+}
+
+/* ---------------------------------------------------------------------- */
+
+NBin::~NBin()
+{
+ memory->destroy(binhead);
+ memory->destroy(bins);
+}
+
+/* ----------------------------------------------------------------------
+ copy needed info from Neighbor class
+------------------------------------------------------------------------- */
+
+void NBin::copy_neighbor_info()
+{
+ includegroup = neighbor->includegroup;
+ cutneighmin = neighbor->cutneighmin;
+ cutneighmax = neighbor->cutneighmax;
+ binsizeflag = neighbor->binsizeflag;
+ binsize_user = neighbor->binsize_user;
+ bboxlo = neighbor->bboxlo;
+ bboxhi = neighbor->bboxhi;
+}
+
+/* ----------------------------------------------------------------------
+ setup for bin_atoms()
+------------------------------------------------------------------------- */
+
+void NBin::bin_atoms_setup(int nall)
+{
+ // binhead = per-bin vector, mbins in length
+ // add 1 bin for USER-INTEL package
+
+ if (mbins > maxbin) {
+ maxbin = mbins;
+ memory->destroy(binhead);
+ memory->create(binhead,maxbin,"neigh:binhead");
+ last_bin_memory = update->ntimestep;
+ }
+
+ // bins = per-atom vector
+
+ if (nall > maxatom) {
+ maxatom = nall;
+ memory->destroy(bins);
+ memory->create(bins,maxatom,"neigh:bins");
+ last_bin_memory = update->ntimestep;
+ }
+
+ last_bin = update->ntimestep;
+}
+
+/* ----------------------------------------------------------------------
+ convert atom coords into local bin #
+ for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo
+ take special care to insure ghosts are in correct bins even w/ roundoff
+ hi ghost atoms = nbin,nbin+1,etc
+ owned atoms = 0 to nbin-1
+ lo ghost atoms = -1,-2,etc
+ this is necessary so that both procs on either side of PBC
+ treat a pair of atoms straddling the PBC in a consistent way
+ for triclinic, doesn't matter since stencil & neigh list built differently
+------------------------------------------------------------------------- */
+
+int NBin::coord2bin(double *x)
+{
+ int ix,iy,iz;
+
+ if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
+ error->one(FLERR,"Non-numeric positions - simulation unstable");
+
+ if (x[0] >= bboxhi[0])
+ ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx) + nbinx;
+ else if (x[0] >= bboxlo[0]) {
+ ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx);
+ ix = MIN(ix,nbinx-1);
+ } else
+ ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
+
+ if (x[1] >= bboxhi[1])
+ iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
+ else if (x[1] >= bboxlo[1]) {
+ iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy);
+ iy = MIN(iy,nbiny-1);
+ } else
+ iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
+
+ if (x[2] >= bboxhi[2])
+ iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
+ else if (x[2] >= bboxlo[2]) {
+ iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz);
+ iz = MIN(iz,nbinz-1);
+ } else
+ iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz) - 1;
+
+ return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
+}
+
+/* ---------------------------------------------------------------------- */
+
+bigint NBin::memory_usage()
+{
+ bigint bytes = 0;
+ bytes += maxbin*sizeof(int);
+ bytes += maxatom*sizeof(int);
+ return bytes;
+}
diff --git a/src/nbin.h b/src/nbin.h
new file mode 100644
index 0000000000..f000df75b0
--- /dev/null
+++ b/src/nbin.h
@@ -0,0 +1,78 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_NBIN_H
+#define LMP_NBIN_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class NBin : protected Pointers {
+ public:
+ int istyle; // 1-N index into binnames
+
+ bigint last_setup,last_bin; // timesteps for last operations performed
+ bigint last_bin_memory;
+
+ int nbinx,nbiny,nbinz; // # of global bins
+ int mbins; // # of local bins and offset on this proc
+ int mbinx,mbiny,mbinz;
+ int mbinxlo,mbinylo,mbinzlo;
+
+ double binsizex,binsizey,binsizez; // bin sizes and inverse sizes
+ double bininvx,bininvy,bininvz;
+
+ int *binhead; // index of first atom in each bin
+ int *bins; // index of next atom in same bin
+
+ NBin(class LAMMPS *);
+ ~NBin();
+ void copy_neighbor_info();
+ virtual void bin_atoms_setup(int);
+ bigint memory_usage();
+
+ virtual void setup_bins(int) = 0;
+ virtual void bin_atoms() = 0;
+
+ protected:
+
+ // data from Neighbor class
+
+ int includegroup;
+ double cutneighmin;
+ double cutneighmax;
+ int binsizeflag;
+ double binsize_user;
+ double *bboxlo,*bboxhi;
+
+ // data common to all NBin variants
+
+ int dimension;
+ int triclinic;
+
+ int maxbin; // size of binhead array
+ int maxatom; // size of bins array
+
+ // methods
+
+ int coord2bin(double *);
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp
new file mode 100644
index 0000000000..97257df717
--- /dev/null
+++ b/src/nbin_standard.cpp
@@ -0,0 +1,232 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nbin_standard.h"
+#include "neighbor.h"
+#include "atom.h"
+#include "group.h"
+#include "domain.h"
+#include "comm.h"
+#include "update.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+enum{NSQ,BIN,MULTI}; // also in Neighbor
+
+#define SMALL 1.0e-6
+#define CUT2BIN_RATIO 100
+
+/* ---------------------------------------------------------------------- */
+
+NBinStandard::NBinStandard(LAMMPS *lmp) : NBin(lmp) {}
+
+/* ----------------------------------------------------------------------
+ setup neighbor binning geometry
+ bin numbering in each dimension is global:
+ 0 = 0.0 to binsize, 1 = binsize to 2*binsize, etc
+ nbin-1,nbin,etc = bbox-binsize to bbox, bbox to bbox+binsize, etc
+ -1,-2,etc = -binsize to 0.0, -2*binsize to -binsize, etc
+ code will work for any binsize
+ since next(xyz) and stencil extend as far as necessary
+ binsize = 1/2 of cutoff is roughly optimal
+ for orthogonal boxes:
+ a dim must be filled exactly by integer # of bins
+ in periodic, procs on both sides of PBC must see same bin boundary
+ in non-periodic, coord2bin() still assumes this by use of nbin xyz
+ for triclinic boxes:
+ tilted simulation box cannot contain integer # of bins
+ stencil & neigh list built differently to account for this
+ mbinlo = lowest global bin any of my ghost atoms could fall into
+ mbinhi = highest global bin any of my ghost atoms could fall into
+ mbin = number of bins I need in a dimension
+------------------------------------------------------------------------- */
+
+void NBinStandard::setup_bins(int style)
+{
+ last_setup = update->ntimestep;
+
+ // bbox = size of bbox of entire domain
+ // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost
+ // for triclinic:
+ // bbox bounds all 8 corners of tilted box
+ // subdomain is in lamda coords
+ // include dimension-dependent extension via comm->cutghost
+ // domain->bbox() converts lamda extent to box coords and computes bbox
+
+ double bbox[3],bsubboxlo[3],bsubboxhi[3];
+ double *cutghost = comm->cutghost;
+
+ if (triclinic == 0) {
+ bsubboxlo[0] = domain->sublo[0] - cutghost[0];
+ bsubboxlo[1] = domain->sublo[1] - cutghost[1];
+ bsubboxlo[2] = domain->sublo[2] - cutghost[2];
+ bsubboxhi[0] = domain->subhi[0] + cutghost[0];
+ bsubboxhi[1] = domain->subhi[1] + cutghost[1];
+ bsubboxhi[2] = domain->subhi[2] + cutghost[2];
+ } else {
+ double lo[3],hi[3];
+ lo[0] = domain->sublo_lamda[0] - cutghost[0];
+ lo[1] = domain->sublo_lamda[1] - cutghost[1];
+ lo[2] = domain->sublo_lamda[2] - cutghost[2];
+ hi[0] = domain->subhi_lamda[0] + cutghost[0];
+ hi[1] = domain->subhi_lamda[1] + cutghost[1];
+ hi[2] = domain->subhi_lamda[2] + cutghost[2];
+ domain->bbox(lo,hi,bsubboxlo,bsubboxhi);
+ }
+
+ bbox[0] = bboxhi[0] - bboxlo[0];
+ bbox[1] = bboxhi[1] - bboxlo[1];
+ bbox[2] = bboxhi[2] - bboxlo[2];
+
+ // optimal bin size is roughly 1/2 the cutoff
+ // for BIN style, binsize = 1/2 of max neighbor cutoff
+ // for MULTI style, binsize = 1/2 of min neighbor cutoff
+ // special case of all cutoffs = 0.0, binsize = box size
+
+ double binsize_optimal;
+ if (binsizeflag) binsize_optimal = binsize_user;
+ else if (style == BIN) binsize_optimal = 0.5*cutneighmax;
+ else binsize_optimal = 0.5*cutneighmin;
+ if (binsize_optimal == 0.0) binsize_optimal = bbox[0];
+ double binsizeinv = 1.0/binsize_optimal;
+
+ // test for too many global bins in any dimension due to huge global domain
+
+ if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT ||
+ bbox[2]*binsizeinv > MAXSMALLINT)
+ error->all(FLERR,"Domain too large for neighbor bins");
+
+ // create actual bins
+ // always have one bin even if cutoff > bbox
+ // for 2d, nbinz = 1
+
+ nbinx = static_cast<int> (bbox[0]*binsizeinv);
+ nbiny = static_cast<int> (bbox[1]*binsizeinv);
+ if (dimension == 3) nbinz = static_cast<int> (bbox[2]*binsizeinv);
+ else nbinz = 1;
+
+ if (nbinx == 0) nbinx = 1;
+ if (nbiny == 0) nbiny = 1;
+ if (nbinz == 0) nbinz = 1;
+
+ // compute actual bin size for nbins to fit into box exactly
+ // error if actual bin size << cutoff, since will create a zillion bins
+ // this happens when nbin = 1 and box size << cutoff
+ // typically due to non-periodic, flat system in a particular dim
+ // in that extreme case, should use NSQ not BIN neighbor style
+
+ binsizex = bbox[0]/nbinx;
+ binsizey = bbox[1]/nbiny;
+ binsizez = bbox[2]/nbinz;
+
+ bininvx = 1.0 / binsizex;
+ bininvy = 1.0 / binsizey;
+ bininvz = 1.0 / binsizez;
+
+ if (binsize_optimal*bininvx > CUT2BIN_RATIO ||
+ binsize_optimal*bininvy > CUT2BIN_RATIO ||
+ binsize_optimal*bininvz > CUT2BIN_RATIO)
+ error->all(FLERR,"Cannot use neighbor bins - box size << cutoff");
+
+ // mbinlo/hi = lowest and highest global bins my ghost atoms could be in
+ // coord = lowest and highest values of coords for my ghost atoms
+ // static_cast(-1.5) = -1, so subract additional -1
+ // add in SMALL for round-off safety
+
+ int mbinxhi,mbinyhi,mbinzhi;
+ double coord;
+
+ coord = bsubboxlo[0] - SMALL*bbox[0];
+ mbinxlo = static_cast<int> ((coord-bboxlo[0])*bininvx);
+ if (coord < bboxlo[0]) mbinxlo = mbinxlo - 1;
+ coord = bsubboxhi[0] + SMALL*bbox[0];
+ mbinxhi = static_cast<int> ((coord-bboxlo[0])*bininvx);
+
+ coord = bsubboxlo[1] - SMALL*bbox[1];
+ mbinylo = static_cast<int> ((coord-bboxlo[1])*bininvy);
+ if (coord < bboxlo[1]) mbinylo = mbinylo - 1;
+ coord = bsubboxhi[1] + SMALL*bbox[1];
+ mbinyhi = static_cast<int> ((coord-bboxlo[1])*bininvy);
+
+ if (dimension == 3) {
+ coord = bsubboxlo[2] - SMALL*bbox[2];
+ mbinzlo = static_cast<int> ((coord-bboxlo[2])*bininvz);
+ if (coord < bboxlo[2]) mbinzlo = mbinzlo - 1;
+ coord = bsubboxhi[2] + SMALL*bbox[2];
+ mbinzhi = static_cast<int> ((coord-bboxlo[2])*bininvz);
+ }
+
+ // extend bins by 1 to insure stencil extent is included
+ // for 2d, only 1 bin in z
+
+ mbinxlo = mbinxlo - 1;
+ mbinxhi = mbinxhi + 1;
+ mbinx = mbinxhi - mbinxlo + 1;
+
+ mbinylo = mbinylo - 1;
+ mbinyhi = mbinyhi + 1;
+ mbiny = mbinyhi - mbinylo + 1;
+
+ if (dimension == 3) {
+ mbinzlo = mbinzlo - 1;
+ mbinzhi = mbinzhi + 1;
+ } else mbinzlo = mbinzhi = 0;
+ mbinz = mbinzhi - mbinzlo + 1;
+
+ bigint bbin = ((bigint) mbinx) * ((bigint) mbiny) * ((bigint) mbinz) + 1;
+ if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins");
+ mbins = bbin;
+}
+
+/* ----------------------------------------------------------------------
+ bin owned and ghost atoms
+------------------------------------------------------------------------- */
+
+void NBinStandard::bin_atoms()
+{
+ int i,ibin;
+
+ for (i = 0; i < mbins; i++) binhead[i] = -1;
+
+ // bin in reverse order so linked list will be in forward order
+ // also puts ghost atoms at end of list, which is necessary
+
+ double **x = atom->x;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+
+ if (includegroup) {
+ int bitmask = group->bitmask[includegroup];
+ for (i = nall-1; i >= nlocal; i--) {
+ if (mask[i] & bitmask) {
+ ibin = coord2bin(x[i]);
+ bins[i] = binhead[ibin];
+ binhead[ibin] = i;
+ }
+ }
+ for (i = atom->nfirst-1; i >= 0; i--) {
+ ibin = coord2bin(x[i]);
+ bins[i] = binhead[ibin];
+ binhead[ibin] = i;
+ }
+
+ } else {
+ for (i = nall-1; i >= 0; i--) {
+ ibin = coord2bin(x[i]);
+ bins[i] = binhead[ibin];
+ binhead[ibin] = i;
+ }
+ }
+}
diff --git a/src/nbin_standard.h b/src/nbin_standard.h
new file mode 100644
index 0000000000..ca96a4f133
--- /dev/null
+++ b/src/nbin_standard.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NBIN_CLASS
+
+NBinStyle(standard,
+ NBinStandard,
+ 0)
+
+#else
+
+#ifndef LMP_NBIN_STANDARD_H
+#define LMP_NBIN_STANDARD_H
+
+#include "nbin.h"
+
+namespace LAMMPS_NS {
+
+class NBinStandard : public NBin {
+ public:
+ NBinStandard(class LAMMPS *);
+ ~NBinStandard() {}
+ void setup_bins(int);
+ void bin_atoms();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/neigh_bond.cpp b/src/neigh_bond.cpp
deleted file mode 100644
index c85407c45b..0000000000
--- a/src/neigh_bond.cpp
+++ /dev/null
@@ -1,1028 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "neighbor.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
-#include "force.h"
-#include "update.h"
-#include "domain.h"
-#include "output.h"
-#include "thermo.h"
-#include "memory.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-#define BONDDELTA 10000
-
-enum{IGNORE,WARN,ERROR}; // same as thermo.cpp
-
-// bondlist, anglelist, dihedrallist, improperlist
-// no longer store atom->map() of the bond partners
-// instead store domain->closest_image() of the bond partners of atom I
-// this enables distances between list atoms to be calculated
-// w/out invoking domain->minimium_image(), e.g. in bond->compute()
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::bond_all()
-{
- int i,m,atom1;
-
- int nlocal = atom->nlocal;
- int *num_bond = atom->num_bond;
- tagint **bond_atom = atom->bond_atom;
- int **bond_type = atom->bond_type;
- tagint *tag = atom->tag;
- int newton_bond = force->newton_bond;
-
- int lostbond = output->thermo->lostbond;
- int nmissing = 0;
- nbondlist = 0;
-
- for (i = 0; i < nlocal; i++)
- for (m = 0; m < num_bond[i]; m++) {
- atom1 = atom->map(bond_atom[i][m]);
- if (atom1 == -1) {
- nmissing++;
- if (lostbond == ERROR) {
- char str[128];
- sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
- " missing on proc %d at step " BIGINT_FORMAT,
- tag[i],bond_atom[i][m],me,update->ntimestep);
- error->one(FLERR,str);
- }
- continue;
- }
- atom1 = domain->closest_image(i,atom1);
- if (newton_bond || i < atom1) {
- if (nbondlist == maxbond) {
- maxbond += BONDDELTA;
- memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
- }
- bondlist[nbondlist][0] = i;
- bondlist[nbondlist][1] = atom1;
- bondlist[nbondlist][2] = bond_type[i][m];
- nbondlist++;
- }
- }
-
- if (cluster_check) bond_check();
- if (lostbond == IGNORE) return;
-
- int all;
- MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all) {
- char str[128];
- sprintf(str,
- "Bond atoms missing at step " BIGINT_FORMAT,update->ntimestep);
- if (me == 0) error->warning(FLERR,str);
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::bond_template()
-{
- int i,m,atom1;
- int imol,iatom;
- tagint tagprev;
- int *num_bond;
- tagint **bond_atom;
- int **bond_type;
-
- Molecule **onemols = atom->avec->onemols;
-
- tagint *tag = atom->tag;
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- int nlocal = atom->nlocal;
- int newton_bond = force->newton_bond;
-
- int lostbond = output->thermo->lostbond;
- int nmissing = 0;
- nbondlist = 0;
-
- for (i = 0; i < nlocal; i++) {
- if (molindex[i] < 0) continue;
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- num_bond = onemols[imol]->num_bond;
- bond_atom = onemols[imol]->bond_atom;
- bond_type = onemols[imol]->bond_type;
-
- for (m = 0; m < num_bond[iatom]; m++) {
- if (bond_type[iatom][m] <= 0) continue;
- atom1 = atom->map(bond_atom[iatom][m]+tagprev);
- if (atom1 == -1) {
- nmissing++;
- if (lostbond == ERROR) {
- char str[128];
- sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
- " missing on proc %d at step " BIGINT_FORMAT,
- tag[i],bond_atom[iatom][m]+tagprev,me,update->ntimestep);
- error->one(FLERR,str);
- }
- continue;
- }
- atom1 = domain->closest_image(i,atom1);
- if (newton_bond || i < atom1) {
- if (nbondlist == maxbond) {
- maxbond += BONDDELTA;
- memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
- }
- bondlist[nbondlist][0] = i;
- bondlist[nbondlist][1] = atom1;
- bondlist[nbondlist][2] = bond_type[iatom][m];
- nbondlist++;
- }
- }
- }
-
- if (cluster_check) bond_check();
- if (lostbond == IGNORE) return;
-
- int all;
- MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all) {
- char str[128];
- sprintf(str,
- "Bond atoms missing at step " BIGINT_FORMAT,update->ntimestep);
- if (me == 0) error->warning(FLERR,str);
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::bond_partial()
-{
- int i,m,atom1;
-
- int nlocal = atom->nlocal;
- int *num_bond = atom->num_bond;
- tagint **bond_atom = atom->bond_atom;
- int **bond_type = atom->bond_type;
- tagint *tag = atom->tag;
- int newton_bond = force->newton_bond;
-
- int lostbond = output->thermo->lostbond;
- int nmissing = 0;
- nbondlist = 0;
-
- for (i = 0; i < nlocal; i++)
- for (m = 0; m < num_bond[i]; m++) {
- if (bond_type[i][m] <= 0) continue;
- atom1 = atom->map(bond_atom[i][m]);
- if (atom1 == -1) {
- nmissing++;
- if (lostbond == ERROR) {
- char str[128];
- sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
- " missing on proc %d at step " BIGINT_FORMAT,
- tag[i],bond_atom[i][m],me,update->ntimestep);
- error->one(FLERR,str);
- }
- continue;
- }
- atom1 = domain->closest_image(i,atom1);
- if (newton_bond || i < atom1) {
- if (nbondlist == maxbond) {
- maxbond += BONDDELTA;
- memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
- }
- bondlist[nbondlist][0] = i;
- bondlist[nbondlist][1] = atom1;
- bondlist[nbondlist][2] = bond_type[i][m];
- nbondlist++;
- }
- }
-
- if (cluster_check) bond_check();
- if (lostbond == IGNORE) return;
-
- int all;
- MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all) {
- char str[128];
- sprintf(str,
- "Bond atoms missing at step " BIGINT_FORMAT,update->ntimestep);
- if (me == 0) error->warning(FLERR,str);
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::bond_check()
-{
- int i,j;
- double dx,dy,dz,dxstart,dystart,dzstart;
-
- double **x = atom->x;
- int flag = 0;
-
- for (int m = 0; m < nbondlist; m++) {
- i = bondlist[m][0];
- j = bondlist[m][1];
- dxstart = dx = x[i][0] - x[j][0];
- dystart = dy = x[i][1] - x[j][1];
- dzstart = dz = x[i][2] - x[j][2];
- domain->minimum_image(dx,dy,dz);
- if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
- }
-
- int flag_all;
- MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
- if (flag_all) error->all(FLERR,"Bond extent > half of periodic box length");
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::angle_all()
-{
- int i,m,atom1,atom2,atom3;
-
- int nlocal = atom->nlocal;
- int *num_angle = atom->num_angle;
- tagint **angle_atom1 = atom->angle_atom1;
- tagint **angle_atom2 = atom->angle_atom2;
- tagint **angle_atom3 = atom->angle_atom3;
- int **angle_type = atom->angle_type;
- int newton_bond = force->newton_bond;
-
- int lostbond = output->thermo->lostbond;
- int nmissing = 0;
- nanglelist = 0;
-
- for (i = 0; i < nlocal; i++)
- for (m = 0; m < num_angle[i]; m++) {
- atom1 = atom->map(angle_atom1[i][m]);
- atom2 = atom->map(angle_atom2[i][m]);
- atom3 = atom->map(angle_atom3[i][m]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
- nmissing++;
- if (lostbond == ERROR) {
- char str[128];
- sprintf(str,"Angle atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
- " missing on proc %d at step " BIGINT_FORMAT,
- angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
- me,update->ntimestep);
- error->one(FLERR,str);
- }
- continue;
- }
- atom1 = domain->closest_image(i,atom1);
- atom2 = domain->closest_image(i,atom2);
- atom3 = domain->closest_image(i,atom3);
- if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
- if (nanglelist == maxangle) {
- maxangle += BONDDELTA;
- memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
- }
- anglelist[nanglelist][0] = atom1;
- anglelist[nanglelist][1] = atom2;
- anglelist[nanglelist][2] = atom3;
- anglelist[nanglelist][3] = angle_type[i][m];
- nanglelist++;
- }
- }
-
- if (cluster_check) angle_check();
- if (lostbond == IGNORE) return;
-
- int all;
- MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all) {
- char str[128];
- sprintf(str,
- "Angle atoms missing at step " BIGINT_FORMAT,update->ntimestep);
- if (me == 0) error->warning(FLERR,str);
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::angle_template()
-{
- int i,m,atom1,atom2,atom3;
- int imol,iatom;
- tagint tagprev;
- int *num_angle;
- tagint **angle_atom1,**angle_atom2,**angle_atom3;
- int **angle_type;
-
- Molecule **onemols = atom->avec->onemols;
-
- tagint *tag = atom->tag;
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- int nlocal = atom->nlocal;
- int newton_bond = force->newton_bond;
-
- int lostbond = output->thermo->lostbond;
- int nmissing = 0;
- nanglelist = 0;
-
- for (i = 0; i < nlocal; i++) {
- if (molindex[i] < 0) continue;
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- num_angle = onemols[imol]->num_angle;
- angle_atom1 = onemols[imol]->angle_atom1;
- angle_atom2 = onemols[imol]->angle_atom2;
- angle_atom3 = onemols[imol]->angle_atom3;
- angle_type = onemols[imol]->angle_type;
-
- for (m = 0; m < num_angle[iatom]; m++) {
- if (angle_type[iatom][m] <= 0) continue;
- atom1 = atom->map(angle_atom1[iatom][m]+tagprev);
- atom2 = atom->map(angle_atom2[iatom][m]+tagprev);
- atom3 = atom->map(angle_atom3[iatom][m]+tagprev);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
- nmissing++;
- if (lostbond == ERROR) {
- char str[128];
- sprintf(str,"Angle atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
- " missing on proc %d at step " BIGINT_FORMAT,
- angle_atom1[iatom][m]+tagprev,angle_atom2[iatom][m]+tagprev,
- angle_atom3[iatom][m]+tagprev,
- me,update->ntimestep);
- error->one(FLERR,str);
- }
- continue;
- }
- atom1 = domain->closest_image(i,atom1);
- atom2 = domain->closest_image(i,atom2);
- atom3 = domain->closest_image(i,atom3);
- if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
- if (nanglelist == maxangle) {
- maxangle += BONDDELTA;
- memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
- }
- anglelist[nanglelist][0] = atom1;
- anglelist[nanglelist][1] = atom2;
- anglelist[nanglelist][2] = atom3;
- anglelist[nanglelist][3] = angle_type[iatom][m];
- nanglelist++;
- }
- }
- }
-
- if (cluster_check) angle_check();
- if (lostbond == IGNORE) return;
-
- int all;
- MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all) {
- char str[128];
- sprintf(str,
- "Angle atoms missing at step " BIGINT_FORMAT,update->ntimestep);
- if (me == 0) error->warning(FLERR,str);
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::angle_partial()
-{
- int i,m,atom1,atom2,atom3;
-
- int nlocal = atom->nlocal;
- int *num_angle = atom->num_angle;
- tagint **angle_atom1 = atom->angle_atom1;
- tagint **angle_atom2 = atom->angle_atom2;
- tagint **angle_atom3 = atom->angle_atom3;
- int **angle_type = atom->angle_type;
- int newton_bond = force->newton_bond;
-
- int lostbond = output->thermo->lostbond;
- int nmissing = 0;
- nanglelist = 0;
-
- for (i = 0; i < nlocal; i++)
- for (m = 0; m < num_angle[i]; m++) {
- if (angle_type[i][m] <= 0) continue;
- atom1 = atom->map(angle_atom1[i][m]);
- atom2 = atom->map(angle_atom2[i][m]);
- atom3 = atom->map(angle_atom3[i][m]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
- nmissing++;
- if (lostbond == ERROR) {
- char str[128];
- sprintf(str,"Angle atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
- " missing on proc %d at step " BIGINT_FORMAT,
- angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
- me,update->ntimestep);
- error->one(FLERR,str);
- }
- continue;
- }
- atom1 = domain->closest_image(i,atom1);
- atom2 = domain->closest_image(i,atom2);
- atom3 = domain->closest_image(i,atom3);
- if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
- if (nanglelist == maxangle) {
- maxangle += BONDDELTA;
- memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
- }
- anglelist[nanglelist][0] = atom1;
- anglelist[nanglelist][1] = atom2;
- anglelist[nanglelist][2] = atom3;
- anglelist[nanglelist][3] = angle_type[i][m];
- nanglelist++;
- }
- }
-
- if (cluster_check) angle_check();
- if (lostbond == IGNORE) return;
-
- int all;
- MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all) {
- char str[128];
- sprintf(str,
- "Angle atoms missing at step " BIGINT_FORMAT,update->ntimestep);
- if (me == 0) error->warning(FLERR,str);
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::angle_check()
-{
- int i,j,k;
- double dx,dy,dz,dxstart,dystart,dzstart;
-
- double **x = atom->x;
- int flag = 0;
-
- // check all 3 distances
- // in case angle potential computes any of them
-
- for (int m = 0; m < nanglelist; m++) {
- i = anglelist[m][0];
- j = anglelist[m][1];
- k = anglelist[m][2];
- dxstart = dx = x[i][0] - x[j][0];
- dystart = dy = x[i][1] - x[j][1];
- dzstart = dz = x[i][2] - x[j][2];
- domain->minimum_image(dx,dy,dz);
- if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
- dxstart = dx = x[i][0] - x[k][0];
- dystart = dy = x[i][1] - x[k][1];
- dzstart = dz = x[i][2] - x[k][2];
- domain->minimum_image(dx,dy,dz);
- if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
- dxstart = dx = x[j][0] - x[k][0];
- dystart = dy = x[j][1] - x[k][1];
- dzstart = dz = x[j][2] - x[k][2];
- domain->minimum_image(dx,dy,dz);
- if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
- }
-
- int flag_all;
- MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
- if (flag_all) error->all(FLERR,"Angle extent > half of periodic box length");
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::dihedral_all()
-{
- int i,m,atom1,atom2,atom3,atom4;
-
- int nlocal = atom->nlocal;
- int *num_dihedral = atom->num_dihedral;
- tagint **dihedral_atom1 = atom->dihedral_atom1;
- tagint **dihedral_atom2 = atom->dihedral_atom2;
- tagint **dihedral_atom3 = atom->dihedral_atom3;
- tagint **dihedral_atom4 = atom->dihedral_atom4;
- int **dihedral_type = atom->dihedral_type;
- int newton_bond = force->newton_bond;
-
- int lostbond = output->thermo->lostbond;
- int nmissing = 0;
- ndihedrallist = 0;
-
- for (i = 0; i < nlocal; i++)
- for (m = 0; m < num_dihedral[i]; m++) {
- atom1 = atom->map(dihedral_atom1[i][m]);
- atom2 = atom->map(dihedral_atom2[i][m]);
- atom3 = atom->map(dihedral_atom3[i][m]);
- atom4 = atom->map(dihedral_atom4[i][m]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
- nmissing++;
- if (lostbond == ERROR) {
- char str[128];
- sprintf(str,"Dihedral atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT
- " missing on proc %d at step " BIGINT_FORMAT,
- dihedral_atom1[i][m],dihedral_atom2[i][m],
- dihedral_atom3[i][m],dihedral_atom4[i][m],
- me,update->ntimestep);
- error->one(FLERR,str);
- }
- continue;
- }
- atom1 = domain->closest_image(i,atom1);
- atom2 = domain->closest_image(i,atom2);
- atom3 = domain->closest_image(i,atom3);
- atom4 = domain->closest_image(i,atom4);
- if (newton_bond ||
- (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
- if (ndihedrallist == maxdihedral) {
- maxdihedral += BONDDELTA;
- memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
- }
- dihedrallist[ndihedrallist][0] = atom1;
- dihedrallist[ndihedrallist][1] = atom2;
- dihedrallist[ndihedrallist][2] = atom3;
- dihedrallist[ndihedrallist][3] = atom4;
- dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
- ndihedrallist++;
- }
- }
-
- if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
- if (lostbond == IGNORE) return;
-
- int all;
- MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all) {
- char str[128];
- sprintf(str,
- "Dihedral atoms missing at step " BIGINT_FORMAT,update->ntimestep);
- if (me == 0) error->warning(FLERR,str);
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::dihedral_template()
-{
- int i,m,atom1,atom2,atom3,atom4;
- int imol,iatom;
- tagint tagprev;
- int *num_dihedral;
- tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
- int **dihedral_type;
-
- Molecule **onemols = atom->avec->onemols;
-
- tagint *tag = atom->tag;
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- int nlocal = atom->nlocal;
- int newton_bond = force->newton_bond;
-
- int lostbond = output->thermo->lostbond;
- int nmissing = 0;
- ndihedrallist = 0;
-
- for (i = 0; i < nlocal; i++) {
- if (molindex[i] < 0) continue;
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- num_dihedral = onemols[imol]->num_dihedral;
- dihedral_atom1 = onemols[imol]->dihedral_atom1;
- dihedral_atom2 = onemols[imol]->dihedral_atom2;
- dihedral_atom3 = onemols[imol]->dihedral_atom3;
- dihedral_atom4 = onemols[imol]->dihedral_atom4;
- dihedral_type = onemols[imol]->dihedral_type;
-
- for (m = 0; m < num_dihedral[iatom]; m++) {
- atom1 = atom->map(dihedral_atom1[iatom][m]+tagprev);
- atom2 = atom->map(dihedral_atom2[iatom][m]+tagprev);
- atom3 = atom->map(dihedral_atom3[iatom][m]+tagprev);
- atom4 = atom->map(dihedral_atom4[iatom][m]+tagprev);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
- nmissing++;
- if (lostbond == ERROR) {
- char str[128];
- sprintf(str,"Dihedral atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT
- " missing on proc %d at step " BIGINT_FORMAT,
- dihedral_atom1[iatom][m]+tagprev,
- dihedral_atom2[iatom][m]+tagprev,
- dihedral_atom3[iatom][m]+tagprev,
- dihedral_atom4[iatom][m]+tagprev,
- me,update->ntimestep);
- error->one(FLERR,str);
- }
- continue;
- }
- atom1 = domain->closest_image(i,atom1);
- atom2 = domain->closest_image(i,atom2);
- atom3 = domain->closest_image(i,atom3);
- atom4 = domain->closest_image(i,atom4);
- if (newton_bond ||
- (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
- if (ndihedrallist == maxdihedral) {
- maxdihedral += BONDDELTA;
- memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
- }
- dihedrallist[ndihedrallist][0] = atom1;
- dihedrallist[ndihedrallist][1] = atom2;
- dihedrallist[ndihedrallist][2] = atom3;
- dihedrallist[ndihedrallist][3] = atom4;
- dihedrallist[ndihedrallist][4] = dihedral_type[iatom][m];
- ndihedrallist++;
- }
- }
- }
-
- if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
- if (lostbond == IGNORE) return;
-
- int all;
- MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all) {
- char str[128];
- sprintf(str,
- "Dihedral atoms missing at step " BIGINT_FORMAT,update->ntimestep);
- if (me == 0) error->warning(FLERR,str);
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::dihedral_partial()
-{
- int i,m,atom1,atom2,atom3,atom4;
-
- int nlocal = atom->nlocal;
- int *num_dihedral = atom->num_dihedral;
- tagint **dihedral_atom1 = atom->dihedral_atom1;
- tagint **dihedral_atom2 = atom->dihedral_atom2;
- tagint **dihedral_atom3 = atom->dihedral_atom3;
- tagint **dihedral_atom4 = atom->dihedral_atom4;
- int **dihedral_type = atom->dihedral_type;
- int newton_bond = force->newton_bond;
-
- int lostbond = output->thermo->lostbond;
- int nmissing = 0;
- ndihedrallist = 0;
-
- for (i = 0; i < nlocal; i++)
- for (m = 0; m < num_dihedral[i]; m++) {
- if (dihedral_type[i][m] <= 0) continue;
- atom1 = atom->map(dihedral_atom1[i][m]);
- atom2 = atom->map(dihedral_atom2[i][m]);
- atom3 = atom->map(dihedral_atom3[i][m]);
- atom4 = atom->map(dihedral_atom4[i][m]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
- nmissing++;
- if (lostbond == ERROR) {
- char str[128];
- sprintf(str,"Dihedral atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT
- " missing on proc %d at step " BIGINT_FORMAT,
- dihedral_atom1[i][m],dihedral_atom2[i][m],
- dihedral_atom3[i][m],dihedral_atom4[i][m],
- me,update->ntimestep);
- error->one(FLERR,str);
- }
- continue;
- }
- atom1 = domain->closest_image(i,atom1);
- atom2 = domain->closest_image(i,atom2);
- atom3 = domain->closest_image(i,atom3);
- atom4 = domain->closest_image(i,atom4);
- if (newton_bond ||
- (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
- if (ndihedrallist == maxdihedral) {
- maxdihedral += BONDDELTA;
- memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
- }
- dihedrallist[ndihedrallist][0] = atom1;
- dihedrallist[ndihedrallist][1] = atom2;
- dihedrallist[ndihedrallist][2] = atom3;
- dihedrallist[ndihedrallist][3] = atom4;
- dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
- ndihedrallist++;
- }
- }
-
- if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
- if (lostbond == IGNORE) return;
-
- int all;
- MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all) {
- char str[128];
- sprintf(str,
- "Dihedral atoms missing at step " BIGINT_FORMAT,update->ntimestep);
- if (me == 0) error->warning(FLERR,str);
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::dihedral_check(int nlist, int **list)
-{
- int i,j,k,l;
- double dx,dy,dz,dxstart,dystart,dzstart;
-
- double **x = atom->x;
- int flag = 0;
-
- // check all 6 distances
- // in case dihedral/improper potential computes any of them
-
- for (int m = 0; m < nlist; m++) {
- i = list[m][0];
- j = list[m][1];
- k = list[m][2];
- l = list[m][3];
- dxstart = dx = x[i][0] - x[j][0];
- dystart = dy = x[i][1] - x[j][1];
- dzstart = dz = x[i][2] - x[j][2];
- domain->minimum_image(dx,dy,dz);
- if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
- dxstart = dx = x[i][0] - x[k][0];
- dystart = dy = x[i][1] - x[k][1];
- dzstart = dz = x[i][2] - x[k][2];
- domain->minimum_image(dx,dy,dz);
- if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
- dxstart = dx = x[i][0] - x[l][0];
- dystart = dy = x[i][1] - x[l][1];
- dzstart = dz = x[i][2] - x[l][2];
- domain->minimum_image(dx,dy,dz);
- if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
- dxstart = dx = x[j][0] - x[k][0];
- dystart = dy = x[j][1] - x[k][1];
- dzstart = dz = x[j][2] - x[k][2];
- domain->minimum_image(dx,dy,dz);
- if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
- dxstart = dx = x[j][0] - x[l][0];
- dystart = dy = x[j][1] - x[l][1];
- dzstart = dz = x[j][2] - x[l][2];
- domain->minimum_image(dx,dy,dz);
- if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
- dxstart = dx = x[k][0] - x[l][0];
- dystart = dy = x[k][1] - x[l][1];
- dzstart = dz = x[k][2] - x[l][2];
- domain->minimum_image(dx,dy,dz);
- if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
- }
-
- int flag_all;
- MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
- if (flag_all)
- error->all(FLERR,"Dihedral/improper extent > half of periodic box length");
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::improper_all()
-{
- int i,m,atom1,atom2,atom3,atom4;
-
- int nlocal = atom->nlocal;
- int *num_improper = atom->num_improper;
- tagint **improper_atom1 = atom->improper_atom1;
- tagint **improper_atom2 = atom->improper_atom2;
- tagint **improper_atom3 = atom->improper_atom3;
- tagint **improper_atom4 = atom->improper_atom4;
- int **improper_type = atom->improper_type;
- int newton_bond = force->newton_bond;
-
- int lostbond = output->thermo->lostbond;
- int nmissing = 0;
- nimproperlist = 0;
-
- for (i = 0; i < nlocal; i++)
- for (m = 0; m < num_improper[i]; m++) {
- atom1 = atom->map(improper_atom1[i][m]);
- atom2 = atom->map(improper_atom2[i][m]);
- atom3 = atom->map(improper_atom3[i][m]);
- atom4 = atom->map(improper_atom4[i][m]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
- nmissing++;
- if (lostbond == ERROR) {
- char str[128];
- sprintf(str,"Improper atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT
- " missing on proc %d at step " BIGINT_FORMAT,
- improper_atom1[i][m],improper_atom2[i][m],
- improper_atom3[i][m],improper_atom4[i][m],
- me,update->ntimestep);
- error->one(FLERR,str);
- }
- continue;
- }
- atom1 = domain->closest_image(i,atom1);
- atom2 = domain->closest_image(i,atom2);
- atom3 = domain->closest_image(i,atom3);
- atom4 = domain-> closest_image(i,atom4);
- if (newton_bond ||
- (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
- if (nimproperlist == maximproper) {
- maximproper += BONDDELTA;
- memory->grow(improperlist,maximproper,5,"neighbor:improperlist");
- }
- improperlist[nimproperlist][0] = atom1;
- improperlist[nimproperlist][1] = atom2;
- improperlist[nimproperlist][2] = atom3;
- improperlist[nimproperlist][3] = atom4;
- improperlist[nimproperlist][4] = improper_type[i][m];
- nimproperlist++;
- }
- }
-
- if (cluster_check) dihedral_check(nimproperlist,improperlist);
- if (lostbond == IGNORE) return;
-
- int all;
- MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all) {
- char str[128];
- sprintf(str,
- "Improper atoms missing at step " BIGINT_FORMAT,update->ntimestep);
- if (me == 0) error->warning(FLERR,str);
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::improper_template()
-{
- int i,m,atom1,atom2,atom3,atom4;
- int imol,iatom;
- tagint tagprev;
- int *num_improper;
- tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
- int **improper_type;
-
- Molecule **onemols = atom->avec->onemols;
-
- tagint *tag = atom->tag;
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- int nlocal = atom->nlocal;
- int newton_bond = force->newton_bond;
-
- int lostbond = output->thermo->lostbond;
- int nmissing = 0;
- nimproperlist = 0;
-
- for (i = 0; i < nlocal; i++) {
- if (molindex[i] < 0) continue;
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- num_improper = onemols[imol]->num_improper;
- improper_atom1 = onemols[imol]->improper_atom1;
- improper_atom2 = onemols[imol]->improper_atom2;
- improper_atom3 = onemols[imol]->improper_atom3;
- improper_atom4 = onemols[imol]->improper_atom4;
- improper_type = onemols[imol]->improper_type;
-
- for (m = 0; m < num_improper[iatom]; m++) {
- atom1 = atom->map(improper_atom1[iatom][m]+tagprev);
- atom2 = atom->map(improper_atom2[iatom][m]+tagprev);
- atom3 = atom->map(improper_atom3[iatom][m]+tagprev);
- atom4 = atom->map(improper_atom4[iatom][m]+tagprev);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
- nmissing++;
- if (lostbond == ERROR) {
- char str[128];
- sprintf(str,"Improper atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT
- " missing on proc %d at step " BIGINT_FORMAT,
- improper_atom1[iatom][m]+tagprev,
- improper_atom2[iatom][m]+tagprev,
- improper_atom3[iatom][m]+tagprev,
- improper_atom4[iatom][m]+tagprev,
- me,update->ntimestep);
- error->one(FLERR,str);
- }
- continue;
- }
- atom1 = domain->closest_image(i,atom1);
- atom2 = domain->closest_image(i,atom2);
- atom3 = domain->closest_image(i,atom3);
- atom4 = domain-> closest_image(i,atom4);
- if (newton_bond ||
- (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
- if (nimproperlist == maximproper) {
- maximproper += BONDDELTA;
- memory->grow(improperlist,maximproper,5,"neighbor:improperlist");
- }
- improperlist[nimproperlist][0] = atom1;
- improperlist[nimproperlist][1] = atom2;
- improperlist[nimproperlist][2] = atom3;
- improperlist[nimproperlist][3] = atom4;
- improperlist[nimproperlist][4] = improper_type[iatom][m];
- nimproperlist++;
- }
- }
- }
-
- if (cluster_check) dihedral_check(nimproperlist,improperlist);
- if (lostbond == IGNORE) return;
-
- int all;
- MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all) {
- char str[128];
- sprintf(str,
- "Improper atoms missing at step " BIGINT_FORMAT,update->ntimestep);
- if (me == 0) error->warning(FLERR,str);
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::improper_partial()
-{
- int i,m,atom1,atom2,atom3,atom4;
-
- int nlocal = atom->nlocal;
- int *num_improper = atom->num_improper;
- tagint **improper_atom1 = atom->improper_atom1;
- tagint **improper_atom2 = atom->improper_atom2;
- tagint **improper_atom3 = atom->improper_atom3;
- tagint **improper_atom4 = atom->improper_atom4;
- int **improper_type = atom->improper_type;
- int newton_bond = force->newton_bond;
-
- int lostbond = output->thermo->lostbond;
- int nmissing = 0;
- nimproperlist = 0;
-
- for (i = 0; i < nlocal; i++)
- for (m = 0; m < num_improper[i]; m++) {
- if (improper_type[i][m] <= 0) continue;
- atom1 = atom->map(improper_atom1[i][m]);
- atom2 = atom->map(improper_atom2[i][m]);
- atom3 = atom->map(improper_atom3[i][m]);
- atom4 = atom->map(improper_atom4[i][m]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
- nmissing++;
- if (lostbond == ERROR) {
- char str[128];
- sprintf(str,"Improper atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT
- " missing on proc %d at step " BIGINT_FORMAT,
- improper_atom1[i][m],improper_atom2[i][m],
- improper_atom3[i][m],improper_atom4[i][m],
- me,update->ntimestep);
- error->one(FLERR,str);
- }
- continue;
- }
- atom1 = domain->closest_image(i,atom1);
- atom2 = domain->closest_image(i,atom2);
- atom3 = domain->closest_image(i,atom3);
- atom4 = domain->closest_image(i,atom4);
- if (newton_bond ||
- (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
- if (nimproperlist == maximproper) {
- maximproper += BONDDELTA;
- memory->grow(improperlist,maximproper,5,"neighbor:improperlist");
- }
- improperlist[nimproperlist][0] = atom1;
- improperlist[nimproperlist][1] = atom2;
- improperlist[nimproperlist][2] = atom3;
- improperlist[nimproperlist][3] = atom4;
- improperlist[nimproperlist][4] = improper_type[i][m];
- nimproperlist++;
- }
- }
-
- if (cluster_check) dihedral_check(nimproperlist,improperlist);
- if (lostbond == IGNORE) return;
-
- int all;
- MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all) {
- char str[128];
- sprintf(str,
- "Improper atoms missing at step " BIGINT_FORMAT,update->ntimestep);
- if (me == 0) error->warning(FLERR,str);
- }
-}
diff --git a/src/neigh_bond.h b/src/neigh_bond.h
deleted file mode 100644
index 894c4aebae..0000000000
--- a/src/neigh_bond.h
+++ /dev/null
@@ -1,88 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ERROR/WARNING messages:
-
-E: Bond atoms %d %d missing on proc %d at step %ld
-
-The 2nd atom needed to compute a particular bond is missing on this
-processor. Typically this is because the pairwise cutoff is set too
-short or the bond has blown apart and an atom is too far away.
-
-W: Bond atoms missing at step %ld
-
-The 2nd atom needed to compute a particular bond is missing on this
-processor. Typically this is because the pairwise cutoff is set too
-short or the bond has blown apart and an atom is too far away.
-
-E: Bond extent > half of periodic box length
-
-This error was detected by the neigh_modify check yes setting. It is
-an error because the bond atoms are so far apart it is ambiguous how
-it should be defined.
-
-E: Angle atoms %d %d %d missing on proc %d at step %ld
-
-One or more of 3 atoms needed to compute a particular angle are
-missing on this processor. Typically this is because the pairwise
-cutoff is set too short or the angle has blown apart and an atom is
-too far away.
-
-W: Angle atoms missing at step %ld
-
-One or more of 3 atoms needed to compute a particular angle are
-missing on this processor. Typically this is because the pairwise
-cutoff is set too short or the angle has blown apart and an atom is
-too far away.
-
-E: Angle extent > half of periodic box length
-
-This error was detected by the neigh_modify check yes setting. It is
-an error because the angle atoms are so far apart it is ambiguous how
-it should be defined.
-
-E: Dihedral atoms %d %d %d %d missing on proc %d at step %ld
-
-One or more of 4 atoms needed to compute a particular dihedral are
-missing on this processor. Typically this is because the pairwise
-cutoff is set too short or the dihedral has blown apart and an atom is
-too far away.
-
-W: Dihedral atoms missing at step %ld
-
-One or more of 4 atoms needed to compute a particular dihedral are
-missing on this processor. Typically this is because the pairwise
-cutoff is set too short or the dihedral has blown apart and an atom is
-too far away.
-
-E: Dihedral/improper extent > half of periodic box length
-
-This error was detected by the neigh_modify check yes setting. It is
-an error because the dihedral atoms are so far apart it is ambiguous
-how it should be defined.
-
-E: Improper atoms %d %d %d %d missing on proc %d at step %ld
-
-One or more of 4 atoms needed to compute a particular improper are
-missing on this processor. Typically this is because the pairwise
-cutoff is set too short or the improper has blown apart and an atom is
-too far away.
-
-W: Improper atoms missing at step %ld
-
-One or more of 4 atoms needed to compute a particular improper are
-missing on this processor. Typically this is because the pairwise
-cutoff is set too short or the improper has blown apart and an atom is
-too far away.
-
-*/
diff --git a/src/neigh_derive.cpp b/src/neigh_derive.cpp
deleted file mode 100644
index dcf85f844e..0000000000
--- a/src/neigh_derive.cpp
+++ /dev/null
@@ -1,845 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include <string.h>
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "domain.h"
-#include "fix_shear_history.h"
-#include "my_page.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- build half list from full list
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
- works if full list is a skip list
-------------------------------------------------------------------------- */
-
-void Neighbor::half_from_full_no_newton(NeighList *list)
-{
- int i,j,ii,jj,n,jnum,joriginal;
- int *neighptr,*jlist;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- int *ilist_full = list->listfull->ilist;
- int *numneigh_full = list->listfull->numneigh;
- int **firstneigh_full = list->listfull->firstneigh;
- int inum_full = list->listfull->inum;
-
- int inum = 0;
- ipage->reset();
-
- // loop over atoms in full list
-
- for (ii = 0; ii < inum_full; ii++) {
- n = 0;
- neighptr = ipage->vget();
-
- // loop over parent full list
-
- i = ilist_full[ii];
- jlist = firstneigh_full[i];
- jnum = numneigh_full[i];
-
- for (jj = 0; jj < jnum; jj++) {
- joriginal = jlist[jj];
- j = joriginal & NEIGHMASK;
- if (j > i) neighptr[n++] = joriginal;
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- build half list from full list
- pair stored once if i,j are both owned and i < j
- if j is ghost, only store if j coords are "above and to the right" of i
- works if full list is a skip list
-------------------------------------------------------------------------- */
-
-void Neighbor::half_from_full_newton(NeighList *list)
-{
- int i,j,ii,jj,n,jnum,joriginal;
- int *neighptr,*jlist;
- double xtmp,ytmp,ztmp;
-
- double **x = atom->x;
- int nlocal = atom->nlocal;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- int *ilist_full = list->listfull->ilist;
- int *numneigh_full = list->listfull->numneigh;
- int **firstneigh_full = list->listfull->firstneigh;
- int inum_full = list->listfull->inum;
-
- int inum = 0;
- ipage->reset();
-
- // loop over parent full list
-
- for (ii = 0; ii < inum_full; ii++) {
- n = 0;
- neighptr = ipage->vget();
-
- i = ilist_full[ii];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
-
- // loop over full neighbor list
-
- jlist = firstneigh_full[i];
- jnum = numneigh_full[i];
-
- for (jj = 0; jj < jnum; jj++) {
- joriginal = jlist[jj];
- j = joriginal & NEIGHMASK;
- if (j < nlocal) {
- if (i > j) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
- neighptr[n++] = joriginal;
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- build skip list for subset of types from parent list
- iskip and ijskip flag which atom types and type pairs to skip
- this is for half and full lists
- if ghostflag, also store neighbors of ghost atoms & set inum,gnum correctly
-------------------------------------------------------------------------- */
-
-void Neighbor::skip_from(NeighList *list)
-{
- int i,j,ii,jj,n,itype,jnum,joriginal;
- int *neighptr,*jlist;
-
- int *type = atom->type;
- int nlocal = atom->nlocal;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- int *ilist_skip = list->listskip->ilist;
- int *numneigh_skip = list->listskip->numneigh;
- int **firstneigh_skip = list->listskip->firstneigh;
- int num_skip = list->listskip->inum;
- if (list->ghostflag) num_skip += list->listskip->gnum;
-
- int *iskip = list->iskip;
- int **ijskip = list->ijskip;
-
- int inum = 0;
- ipage->reset();
-
- // loop over atoms in other list
- // skip I atom entirely if iskip is set for type[I]
- // skip I,J pair if ijskip is set for type[I],type[J]
-
- for (ii = 0; ii < num_skip; ii++) {
- i = ilist_skip[ii];
- itype = type[i];
- if (iskip[itype]) continue;
-
- n = 0;
- neighptr = ipage->vget();
-
- // loop over parent non-skip list
-
- jlist = firstneigh_skip[i];
- jnum = numneigh_skip[i];
-
- for (jj = 0; jj < jnum; jj++) {
- joriginal = jlist[jj];
- j = joriginal & NEIGHMASK;
- if (ijskip[itype][type[j]]) continue;
- neighptr[n++] = joriginal;
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
- if (list->ghostflag) {
- int num = 0;
- for (i = 0; i < inum; i++)
- if (ilist[i] < nlocal) num++;
- else break;
- list->inum = num;
- list->gnum = inum - num;
- }
-}
-
-/* ----------------------------------------------------------------------
- build skip list for subset of types from parent list
- iskip and ijskip flag which atom types and type pairs to skip
- if list requests it, preserve shear history via fix shear/history
-------------------------------------------------------------------------- */
-
-void Neighbor::skip_from_granular(NeighList *list)
-{
- int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,dnum,dnumbytes;
- tagint jtag;
- int *neighptr,*jlist,*touchptr,*touchptr_skip;
- double *shearptr,*shearptr_skip;
-
- NeighList *listgranhistory;
- int *npartner;
- tagint **partner;
- double **shearpartner;
- int **firsttouch;
- double **firstshear;
- MyPage<int> *ipage_touch;
- MyPage<double> *dpage_shear;
-
- tagint *tag = atom->tag;
- int *type = atom->type;
- int nlocal = atom->nlocal;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- int *ilist_skip = list->listskip->ilist;
- int *numneigh_skip = list->listskip->numneigh;
- int **firstneigh_skip = list->listskip->firstneigh;
- int inum_skip = list->listskip->inum;
-
- int *iskip = list->iskip;
- int **ijskip = list->ijskip;
-
- FixShearHistory *fix_history = list->fix_history;
- if (fix_history) {
- fix_history->nlocal_neigh = nlocal;
- fix_history->nall_neigh = nlocal + atom->nghost;
- npartner = fix_history->npartner;
- partner = fix_history->partner;
- shearpartner = fix_history->shearpartner;
- listgranhistory = list->listgranhistory;
- firsttouch = listgranhistory->firstneigh;
- firstshear = listgranhistory->firstdouble;
- ipage_touch = listgranhistory->ipage;
- dpage_shear = listgranhistory->dpage;
- dnum = listgranhistory->dnum;
- dnumbytes = dnum * sizeof(double);
- }
-
- int inum = 0;
- ipage->reset();
- if (fix_history) {
- ipage_touch->reset();
- dpage_shear->reset();
- }
-
- // loop over atoms in other list
- // skip I atom entirely if iskip is set for type[I]
- // skip I,J pair if ijskip is set for type[I],type[J]
-
- for (ii = 0; ii < inum_skip; ii++) {
- i = ilist_skip[ii];
- itype = type[i];
- if (iskip[itype]) continue;
-
- n = 0;
- neighptr = ipage->vget();
- if (fix_history) {
- nn = 0;
- touchptr = ipage_touch->vget();
- shearptr = dpage_shear->vget();
- }
-
- // loop over parent non-skip granular list and optionally its history info
-
- jlist = firstneigh_skip[i];
- jnum = numneigh_skip[i];
-
- for (jj = 0; jj < jnum; jj++) {
- joriginal = jlist[jj];
- j = joriginal & NEIGHMASK;
- if (ijskip[itype][type[j]]) continue;
- neighptr[n] = joriginal;
-
- // no numeric test for current touch
- // just use FSH partner list to infer it
- // would require distance calculation for spheres
- // more complex calculation for surfs
-
- if (fix_history) {
- jtag = tag[j];
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == jtag) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
- nn += dnum;
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- }
-
- n++;
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (fix_history) {
- firsttouch[i] = touchptr;
- firstshear[i] = shearptr;
- ipage_touch->vgot(n);
- dpage_shear->vgot(nn);
- }
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- build skip list for subset of types from parent list
- iskip and ijskip flag which atom types and type pairs to skip
- parent non-skip list used newton off, this skip list is newton on
- if list requests it, preserve shear history via fix shear/history
-------------------------------------------------------------------------- */
-
-void Neighbor::skip_from_granular_off2on(NeighList *list)
-{
- int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,dnum,dnumbytes;
- tagint itag,jtag;
- int *neighptr,*jlist,*touchptr,*touchptr_skip;
- double *shearptr,*shearptr_skip;
-
- NeighList *listgranhistory;
- int *npartner;
- tagint **partner;
- double **shearpartner;
- int **firsttouch;
- double **firstshear;
- MyPage<int> *ipage_touch;
- MyPage<double> *dpage_shear;
-
- tagint *tag = atom->tag;
- int *type = atom->type;
- int nlocal = atom->nlocal;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- int *ilist_skip = list->listskip->ilist;
- int *numneigh_skip = list->listskip->numneigh;
- int **firstneigh_skip = list->listskip->firstneigh;
- int inum_skip = list->listskip->inum;
-
- int *iskip = list->iskip;
- int **ijskip = list->ijskip;
-
- FixShearHistory *fix_history = list->fix_history;
- if (fix_history) {
- fix_history->nlocal_neigh = nlocal;
- fix_history->nall_neigh = nlocal + atom->nghost;
- npartner = fix_history->npartner;
- partner = fix_history->partner;
- shearpartner = fix_history->shearpartner;
- listgranhistory = list->listgranhistory;
- firsttouch = listgranhistory->firstneigh;
- firstshear = listgranhistory->firstdouble;
- ipage_touch = listgranhistory->ipage;
- dpage_shear = listgranhistory->dpage;
- dnum = listgranhistory->dnum;
- dnumbytes = dnum * sizeof(double);
- }
-
- int inum = 0;
- ipage->reset();
- if (fix_history) {
- ipage_touch->reset();
- dpage_shear->reset();
- }
-
- // loop over atoms in other list
- // skip I atom entirely if iskip is set for type[I]
- // skip I,J pair if ijskip is set for type[I],type[J]
-
- for (ii = 0; ii < inum_skip; ii++) {
- i = ilist_skip[ii];
- itype = type[i];
- if (iskip[itype]) continue;
- itag = tag[i];
-
- n = 0;
- neighptr = ipage->vget();
- if (fix_history) {
- nn = 0;
- touchptr = ipage_touch->vget();
- shearptr = dpage_shear->vget();
- }
-
- // loop over parent non-skip granular list and optionally its history info
-
- jlist = firstneigh_skip[i];
- jnum = numneigh_skip[i];
-
- for (jj = 0; jj < jnum; jj++) {
- joriginal = jlist[jj];
- j = joriginal & NEIGHMASK;
- if (ijskip[itype][type[j]]) continue;
-
- // only keep I,J when J = ghost if Itag < Jtag
-
- jtag = tag[j];
- if (j >= nlocal && jtag < itag) continue;
-
- neighptr[n] = joriginal;
-
- // no numeric test for current touch
- // just use FSH partner list to infer it
- // would require distance calculation for spheres
- // more complex calculation for surfs
-
- if (fix_history) {
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == jtag) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
- nn += dnum;
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- }
-
- n++;
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (fix_history) {
- firsttouch[i] = touchptr;
- firstshear[i] = shearptr;
- ipage_touch->vgot(n);
- dpage_shear->vgot(nn);
- }
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- build skip list for subset of types from parent list
- iskip and ijskip flag which atom types and type pairs to skip
- parent non-skip list used newton off and was not onesided,
- this skip list is newton on and onesided
- if list requests it, preserve shear history via fix shear/history
-------------------------------------------------------------------------- */
-
-void Neighbor::skip_from_granular_off2on_onesided(NeighList *list)
-{
- int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,flip,dnum,dnumbytes,tmp;
- tagint itag,jtag;
- int *surf,*neighptr,*jlist;
-
- NeighList *listgranhistory;
- int *npartner;
- tagint **partner;
- double **shearpartner;
- int **firsttouch;
- double **firstshear;
- MyPage<int> *ipage_touch;
- MyPage<double> *dpage_shear;
-
- tagint *tag = atom->tag;
- int *type = atom->type;
- int nlocal = atom->nlocal;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- int *ilist_skip = list->listskip->ilist;
- int *numneigh_skip = list->listskip->numneigh;
- int **firstneigh_skip = list->listskip->firstneigh;
- int inum_skip = list->listskip->inum;
-
- int *iskip = list->iskip;
- int **ijskip = list->ijskip;
-
- if (domain->dimension == 2) surf = atom->line;
- else surf = atom->tri;
-
- FixShearHistory *fix_history = list->fix_history;
- if (fix_history) {
- fix_history->nlocal_neigh = nlocal;
- fix_history->nall_neigh = nlocal + atom->nghost;
- npartner = fix_history->npartner;
- partner = fix_history->partner;
- shearpartner = fix_history->shearpartner;
- listgranhistory = list->listgranhistory;
- firsttouch = listgranhistory->firstneigh;
- firstshear = listgranhistory->firstdouble;
- ipage_touch = listgranhistory->ipage;
- dpage_shear = listgranhistory->dpage;
- dnum = listgranhistory->dnum;
- dnumbytes = dnum * sizeof(double);
- }
-
- int inum = 0;
- ipage->reset();
- if (fix_history) {
- ipage_touch->reset();
- dpage_shear->reset();
- }
-
- // two loops over parent list required, one to count, one to store
- // because onesided constraint means pair I,J may be stored with I or J
- // so don't know in advance how much space to alloc for each atom's neighs
-
- // first loop over atoms in other list to count neighbors
- // skip I atom entirely if iskip is set for type[I]
- // skip I,J pair if ijskip is set for type[I],type[J]
-
- for (i = 0; i < nlocal; i++) numneigh[i] = 0;
-
- for (ii = 0; ii < inum_skip; ii++) {
- i = ilist_skip[ii];
- itype = type[i];
- if (iskip[itype]) continue;
- itag = tag[i];
-
- n = 0;
-
- // loop over parent non-skip granular list
-
- jlist = firstneigh_skip[i];
- jnum = numneigh_skip[i];
-
- for (jj = 0; jj < jnum; jj++) {
- joriginal = jlist[jj];
- j = joriginal & NEIGHMASK;
- if (ijskip[itype][type[j]]) continue;
-
- // flip I,J if necessary to satisfy onesided constraint
- // do not keep if I is now ghost
-
- if (surf[i] >= 0) {
- if (j >= nlocal) continue;
- tmp = i;
- i = j;
- j = tmp;
- flip = 1;
- } else flip = 0;
-
- numneigh[i]++;
- if (flip) i = j;
- }
- }
-
- // allocate all per-atom neigh list chunks, including history
-
- for (i = 0; i < nlocal; i++) {
- if (numneigh[i] == 0) continue;
- n = numneigh[i];
- firstneigh[i] = ipage->get(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- if (fix_history) {
- firsttouch[i] = ipage_touch->get(n);
- firstshear[i] = dpage_shear->get(dnum*n);
- }
- }
-
- // second loop over atoms in other list to store neighbors
- // skip I atom entirely if iskip is set for type[I]
- // skip I,J pair if ijskip is set for type[I],type[J]
-
- for (i = 0; i < nlocal; i++) numneigh[i] = 0;
-
- for (ii = 0; ii < inum_skip; ii++) {
- i = ilist_skip[ii];
- itype = type[i];
- if (iskip[itype]) continue;
- itag = tag[i];
-
- // loop over parent non-skip granular list and optionally its history info
-
- jlist = firstneigh_skip[i];
- jnum = numneigh_skip[i];
-
- for (jj = 0; jj < jnum; jj++) {
- joriginal = jlist[jj];
- j = joriginal & NEIGHMASK;
- if (ijskip[itype][type[j]]) continue;
-
- // flip I,J if necessary to satisfy onesided constraint
- // do not keep if I is now ghost
-
- if (surf[i] >= 0) {
- if (j >= nlocal) continue;
- tmp = i;
- i = j;
- j = tmp;
- flip = 1;
- } else flip = 0;
-
- // store j in neigh list, not joriginal, like other neigh methods
- // OK, b/c there is no special list flagging for surfs
-
- firstneigh[i][numneigh[i]] = j;
-
- // no numeric test for current touch
- // just use FSH partner list to infer it
- // would require complex calculation for surfs
-
- if (fix_history) {
- jtag = tag[j];
- n = numneigh[i];
- nn = dnum*n;
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == jtag) break;
- if (m < npartner[i]) {
- firsttouch[i][n] = 1;
- memcpy(&firstshear[i][nn],&shearpartner[i][dnum*m],dnumbytes);
- } else {
- firsttouch[i][n] = 0;
- memcpy(&firstshear[i][nn],zeroes,dnumbytes);
- }
- }
-
- numneigh[i]++;
- if (flip) i = j;
- }
-
- // only add atom I to ilist if it has neighbors
- // fix shear/history allows for this in pre_exchange_onesided()
-
- if (numneigh[i]) ilist[inum++] = i;
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- build skip list for subset of types from parent list
- iskip and ijskip flag which atom types and type pairs to skip
- this is for respa lists, copy the inner/middle values from parent
-------------------------------------------------------------------------- */
-
-void Neighbor::skip_from_respa(NeighList *list)
-{
- int i,j,ii,jj,n,itype,jnum,joriginal,n_inner,n_middle;
- int *neighptr,*jlist,*neighptr_inner,*neighptr_middle;
-
- int *type = atom->type;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- int *ilist_skip = list->listskip->ilist;
- int *numneigh_skip = list->listskip->numneigh;
- int **firstneigh_skip = list->listskip->firstneigh;
- int inum_skip = list->listskip->inum;
-
- int *iskip = list->iskip;
- int **ijskip = list->ijskip;
-
- NeighList *listinner = list->listinner;
- int *ilist_inner = listinner->ilist;
- int *numneigh_inner = listinner->numneigh;
- int **firstneigh_inner = listinner->firstneigh;
- MyPage<int> *ipage_inner = listinner->ipage;
-
- int *numneigh_inner_skip = list->listskip->listinner->numneigh;
- int **firstneigh_inner_skip = list->listskip->listinner->firstneigh;
-
- NeighList *listmiddle;
- int *ilist_middle,*numneigh_middle,**firstneigh_middle;
- MyPage<int> *ipage_middle;
- int *numneigh_middle_skip,**firstneigh_middle_skip;
- int respamiddle = list->respamiddle;
- if (respamiddle) {
- listmiddle = list->listmiddle;
- ilist_middle = listmiddle->ilist;
- numneigh_middle = listmiddle->numneigh;
- firstneigh_middle = listmiddle->firstneigh;
- ipage_middle = listmiddle->ipage;
- numneigh_middle_skip = list->listskip->listmiddle->numneigh;
- firstneigh_middle_skip = list->listskip->listmiddle->firstneigh;
- }
-
- int inum = 0;
- ipage->reset();
- ipage_inner->reset();
- if (respamiddle) ipage_middle->reset();
-
- // loop over atoms in other list
- // skip I atom entirely if iskip is set for type[I]
- // skip I,J pair if ijskip is set for type[I],type[J]
-
- for (ii = 0; ii < inum_skip; ii++) {
- i = ilist_skip[ii];
- itype = type[i];
- if (iskip[itype]) continue;
-
- n = n_inner = 0;
- neighptr = ipage->vget();
- neighptr_inner = ipage_inner->vget();
- if (respamiddle) {
- n_middle = 0;
- neighptr_middle = ipage_middle->vget();
- }
-
- // loop over parent outer rRESPA list
-
- jlist = firstneigh_skip[i];
- jnum = numneigh_skip[i];
-
- for (jj = 0; jj < jnum; jj++) {
- joriginal = jlist[jj];
- j = joriginal & NEIGHMASK;
- if (ijskip[itype][type[j]]) continue;
- neighptr[n++] = joriginal;
- }
-
- // loop over parent inner rRESPA list
-
- jlist = firstneigh_inner_skip[i];
- jnum = numneigh_inner_skip[i];
-
- for (jj = 0; jj < jnum; jj++) {
- joriginal = jlist[jj];
- j = joriginal & NEIGHMASK;
- if (ijskip[itype][type[j]]) continue;
- neighptr_inner[n_inner++] = joriginal;
- }
-
- // loop over parent middle rRESPA list
-
- if (respamiddle) {
- jlist = firstneigh_middle_skip[i];
- jnum = numneigh_middle_skip[i];
-
- for (jj = 0; jj < jnum; jj++) {
- joriginal = jlist[jj];
- j = joriginal & NEIGHMASK;
- if (ijskip[itype][type[j]]) continue;
- neighptr_middle[n_middle++] = joriginal;
- }
- }
-
- ilist[inum] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- ilist_inner[inum] = i;
- firstneigh_inner[i] = neighptr_inner;
- numneigh_inner[i] = n_inner;
- ipage_inner->vgot(n);
- if (ipage_inner->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (respamiddle) {
- ilist_middle[inum] = i;
- firstneigh_middle[i] = neighptr_middle;
- numneigh_middle[i] = n_middle;
- ipage_middle->vgot(n);
- if (ipage_middle->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- inum++;
- }
-
- list->inum = inum;
- listinner->inum = inum;
- if (respamiddle) listmiddle->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- create list which is simply a copy of parent list
-------------------------------------------------------------------------- */
-
-void Neighbor::copy_from(NeighList *list)
-{
- NeighList *listcopy = list->listcopy;
-
- list->inum = listcopy->inum;
- list->gnum = listcopy->gnum;
- list->ilist = listcopy->ilist;
- list->numneigh = listcopy->numneigh;
- list->firstneigh = listcopy->firstneigh;
- list->firstdouble = listcopy->firstdouble;
- list->ipage = listcopy->ipage;
- list->dpage = listcopy->dpage;
-}
diff --git a/src/neigh_full.cpp b/src/neigh_full.cpp
deleted file mode 100644
index d9ff786d65..0000000000
--- a/src/neigh_full.cpp
+++ /dev/null
@@ -1,590 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
-#include "my_page.h"
-#include "group.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- N^2 search for all neighbors
- every neighbor pair appears in list of both atoms i and j
-------------------------------------------------------------------------- */
-
-void Neighbor::full_nsq(NeighList *list)
-{
- int i,j,n,itype,jtype,which,bitmask,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
- if (includegroup) {
- nlocal = atom->nfirst;
- bitmask = group->bitmask[includegroup];
- }
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over owned atoms, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms, owned and ghost
- // skip i = j
-
- for (j = 0; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
- if (i == j) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
- list->gnum = 0;
-}
-
-/* ----------------------------------------------------------------------
- N^2 search for all neighbors
- include neighbors of ghost atoms, but no "special neighbors" for ghosts
- every neighbor pair appears in list of both atoms i and j
-------------------------------------------------------------------------- */
-
-void Neighbor::full_nsq_ghost(NeighList *list)
-{
- int i,j,n,itype,jtype,which,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over owned & ghost atoms, storing neighbors
-
- for (i = 0; i < nall; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms, owned and ghost
- // skip i = j
- // no molecular test when i = ghost atom
-
- if (i < nlocal) {
- for (j = 0; j < nall; j++) {
- if (i == j) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- } else {
- for (j = 0; j < nall; j++) {
- if (i == j) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = atom->nlocal;
- list->gnum = inum - atom->nlocal;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction for all neighbors
- every neighbor pair appears in list of both atoms i and j
-------------------------------------------------------------------------- */
-
-void Neighbor::full_bin(NeighList *list)
-{
- int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- // bin owned & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over owned atoms, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in surrounding bins in stencil including self
- // skip i = j
-
- ibin = coord2bin(x[i]);
-
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (i == j) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
- list->gnum = 0;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction for all neighbors
- include neighbors of ghost atoms, but no "special neighbors" for ghosts
- every neighbor pair appears in list of both atoms i and j
-------------------------------------------------------------------------- */
-
-void Neighbor::full_bin_ghost(NeighList *list)
-{
- int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int xbin,ybin,zbin,xbin2,ybin2,zbin2;
- int *neighptr;
-
- // bin owned & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- int **stencilxyz = list->stencilxyz;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over owned & ghost atoms, storing neighbors
-
- for (i = 0; i < nall; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in surrounding bins in stencil including self
- // when i is a ghost atom, must check if stencil bin is out of bounds
- // skip i = j
- // no molecular test when i = ghost atom
-
- if (i < nlocal) {
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (i == j) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- } else {
- ibin = coord2bin(x[i],xbin,ybin,zbin);
- for (k = 0; k < nstencil; k++) {
- xbin2 = xbin + stencilxyz[k][0];
- ybin2 = ybin + stencilxyz[k][1];
- zbin2 = zbin + stencilxyz[k][2];
- if (xbin2 < 0 || xbin2 >= mbinx ||
- ybin2 < 0 || ybin2 >= mbiny ||
- zbin2 < 0 || zbin2 >= mbinz) continue;
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (i == j) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
- }
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = atom->nlocal;
- list->gnum = inum - atom->nlocal;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction for all neighbors
- multi-type stencil is itype dependent and is distance checked
- every neighbor pair appears in list of both atoms i and j
-------------------------------------------------------------------------- */
-
-void Neighbor::full_multi(NeighList *list)
-{
- int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*s;
- double *cutsq,*distsq;
-
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in other bins in stencil, including self
- // skip if i,j neighbor cutoff is less than bin distance
- // skip i = j
-
- ibin = coord2bin(x[i]);
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- cutsq = cutneighsq[itype];
- ns = nstencil_multi[itype];
- for (k = 0; k < ns; k++) {
- for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
- if (i == j) continue;
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
- list->gnum = 0;
-}
diff --git a/src/neigh_gran.cpp b/src/neigh_gran.cpp
deleted file mode 100644
index be724cc08c..0000000000
--- a/src/neigh_gran.cpp
+++ /dev/null
@@ -1,839 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include <string.h>
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "group.h"
-#include "fix_shear_history.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- granular particles
- N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
- shear history must be accounted for when a neighbor pair is added
- pair added to list if atoms i and j are both owned and i < j
- pair added if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::granular_nsq_no_newton(NeighList *list)
-{
- int i,j,m,n,nn,bitmask,dnum,dnumbytes;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- double radi,radsum,cutsq;
- int *neighptr,*touchptr;
- double *shearptr;
-
- NeighList *listgranhistory;
- int *npartner;
- tagint **partner;
- double **shearpartner;
- int **firsttouch;
- double **firstshear;
- MyPage<int> *ipage_touch;
- MyPage<double> *dpage_shear;
-
- double **x = atom->x;
- double *radius = atom->radius;
- tagint *tag = atom->tag;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *molecule = atom->molecule;
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
- if (includegroup) {
- nlocal = atom->nfirst;
- bitmask = group->bitmask[includegroup];
- }
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- FixShearHistory *fix_history = list->fix_history;
- if (fix_history) {
- fix_history->nlocal_neigh = nlocal;
- fix_history->nall_neigh = nall;
- npartner = fix_history->npartner;
- partner = fix_history->partner;
- shearpartner = fix_history->shearpartner;
- listgranhistory = list->listgranhistory;
- firsttouch = listgranhistory->firstneigh;
- firstshear = listgranhistory->firstdouble;
- ipage_touch = listgranhistory->ipage;
- dpage_shear = listgranhistory->dpage;
- dnum = listgranhistory->dnum;
- dnumbytes = dnum * sizeof(double);
- }
-
- int inum = 0;
- ipage->reset();
- if (fix_history) {
- ipage_touch->reset();
- dpage_shear->reset();
- }
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
- if (fix_history) {
- nn = 0;
- touchptr = ipage_touch->vget();
- shearptr = dpage_shear->vget();
- }
-
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- radi = radius[i];
-
- // loop over remaining atoms, owned and ghost
-
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) {
- neighptr[n] = j;
-
- if (fix_history) {
- if (rsq < radsum*radsum) {
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == tag[j]) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
- nn += dnum;
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- }
-
- n++;
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (fix_history) {
- firsttouch[i] = touchptr;
- firstshear[i] = shearptr;
- ipage_touch->vgot(n);
- dpage_shear->vgot(nn);
- }
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- granular particles
- N^2 / 2 search for neighbor pairs with full Newton's 3rd law
- shear history must be accounted for when a neighbor pair is added
- pair added to list if atoms i and j are both owned and i < j
- if j is ghost only me or other proc adds pair
- decision based on itag,jtag tests
-------------------------------------------------------------------------- */
-
-void Neighbor::granular_nsq_newton(NeighList *list)
-{
- int i,j,m,n,nn,itag,jtag,bitmask,dnum,dnumbytes;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- double radi,radsum,cutsq;
- int *neighptr,*touchptr;
- double *shearptr;
-
- NeighList *listgranhistory;
- int *npartner;
- tagint **partner;
- double **shearpartner;
- int **firsttouch;
- double **firstshear;
- MyPage<int> *ipage_touch;
- MyPage<double> *dpage_shear;
-
- double **x = atom->x;
- double *radius = atom->radius;
- tagint *tag = atom->tag;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *molecule = atom->molecule;
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
- if (includegroup) {
- nlocal = atom->nfirst;
- bitmask = group->bitmask[includegroup];
- }
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- FixShearHistory *fix_history = list->fix_history;
- if (fix_history) {
- fix_history->nlocal_neigh = nlocal;
- fix_history->nall_neigh = nall;
- npartner = fix_history->npartner;
- partner = fix_history->partner;
- shearpartner = fix_history->shearpartner;
- listgranhistory = list->listgranhistory;
- firsttouch = listgranhistory->firstneigh;
- firstshear = listgranhistory->firstdouble;
- ipage_touch = listgranhistory->ipage;
- dpage_shear = listgranhistory->dpage;
- dnum = listgranhistory->dnum;
- dnumbytes = dnum * sizeof(double);
- }
-
- int inum = 0;
- ipage->reset();
- if (fix_history) {
- ipage_touch->reset();
- dpage_shear->reset();
- }
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
- if (fix_history) {
- nn = 0;
- touchptr = ipage_touch->vget();
- shearptr = dpage_shear->vget();
- }
-
- itag = tag[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- radi = radius[i];
-
- // loop over remaining atoms, owned and ghost
-
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
-
- if (j >= nlocal) {
- jtag = tag[j];
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
- }
-
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) {
- neighptr[n++] = j;
-
- if (fix_history) {
- if (rsq < radsum*radsum) {
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == tag[j]) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
- nn += dnum;
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- }
-
- n++;
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (fix_history) {
- firsttouch[i] = touchptr;
- firstshear[i] = shearptr;
- ipage_touch->vgot(n);
- dpage_shear->vgot(nn);
- }
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- granular particles
- N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
- shear history must be accounted for when a neighbor pair is added
- pair added to list if atoms i and j are both owned and i < j
- pair added if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::granular_nsq_newton_onesided(NeighList *list)
-{
-}
-
-/* ----------------------------------------------------------------------
- granular particles
- binned neighbor list construction with partial Newton's 3rd law
- shear history must be accounted for when a neighbor pair is added
- each owned atom i checks own bin and surrounding bins in non-Newton stencil
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::granular_bin_no_newton(NeighList *list)
-{
- int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- double radi,radsum,cutsq;
- int *neighptr,*touchptr;
- double *shearptr;
-
- NeighList *listgranhistory;
- int *npartner;
- tagint **partner;
- double **shearpartner;
- int **firsttouch;
- double **firstshear;
- MyPage<int> *ipage_touch;
- MyPage<double> *dpage_shear;
-
- // bin local & ghost atoms
-
- bin_atoms();
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- double *radius = atom->radius;
- tagint *tag = atom->tag;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *molecule = atom->molecule;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- MyPage<int> *ipage = list->ipage;
-
- FixShearHistory *fix_history = list->fix_history;
- if (fix_history) {
- fix_history->nlocal_neigh = nlocal;
- fix_history->nall_neigh = nlocal + atom->nghost;
- npartner = fix_history->npartner;
- partner = fix_history->partner;
- shearpartner = fix_history->shearpartner;
- listgranhistory = list->listgranhistory;
- firsttouch = listgranhistory->firstneigh;
- firstshear = listgranhistory->firstdouble;
- ipage_touch = listgranhistory->ipage;
- dpage_shear = listgranhistory->dpage;
- dnum = listgranhistory->dnum;
- dnumbytes = dnum * sizeof(double);
- }
-
- int inum = 0;
- ipage->reset();
- if (fix_history) {
- ipage_touch->reset();
- dpage_shear->reset();
- }
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
- if (fix_history) {
- nn = 0;
- touchptr = ipage_touch->vget();
- shearptr = dpage_shear->vget();
- }
-
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- radi = radius[i];
- ibin = coord2bin(x[i]);
-
- // loop over all atoms in surrounding bins in stencil including self
- // only store pair if i < j
- // stores own/own pairs only once
- // stores own/ghost pairs on both procs
-
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) {
- neighptr[n] = j;
-
- if (fix_history) {
- if (rsq < radsum*radsum) {
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == tag[j]) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
- nn += dnum;
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- }
-
- n++;
- }
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (fix_history) {
- firsttouch[i] = touchptr;
- firstshear[i] = shearptr;
- ipage_touch->vgot(n);
- dpage_shear->vgot(nn);
- }
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- granular particles
- binned neighbor list construction with full Newton's 3rd law
- shear history must be accounted for when a neighbor pair is added
- each owned atom i checks its own bin and other bins in Newton stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::granular_bin_newton(NeighList *list)
-{
- int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- double radi,radsum,cutsq;
- int *neighptr,*touchptr;
- double *shearptr;
-
- NeighList *listgranhistory;
- int *npartner;
- tagint **partner;
- double **shearpartner;
- int **firsttouch;
- double **firstshear;
- MyPage<int> *ipage_touch;
- MyPage<double> *dpage_shear;
-
- // bin local & ghost atoms
-
- bin_atoms();
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- double *radius = atom->radius;
- tagint *tag = atom->tag;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *molecule = atom->molecule;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- MyPage<int> *ipage = list->ipage;
-
- FixShearHistory *fix_history = list->fix_history;
- if (fix_history) {
- fix_history->nlocal_neigh = nlocal;
- fix_history->nall_neigh = nlocal + atom->nghost;
- npartner = fix_history->npartner;
- partner = fix_history->partner;
- shearpartner = fix_history->shearpartner;
- listgranhistory = list->listgranhistory;
- firsttouch = listgranhistory->firstneigh;
- firstshear = listgranhistory->firstdouble;
- ipage_touch = listgranhistory->ipage;
- dpage_shear = listgranhistory->dpage;
- dnum = listgranhistory->dnum;
- dnumbytes = dnum * sizeof(double);
- }
-
- int inum = 0;
- ipage->reset();
- if (fix_history) {
- ipage_touch->reset();
- dpage_shear->reset();
- }
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
- if (fix_history) {
- nn = 0;
- touchptr = ipage_touch->vget();
- shearptr = dpage_shear->vget();
- }
-
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- radi = radius[i];
-
- // loop over rest of atoms in i's bin, ghosts are at end of linked list
- // if j is owned atom, store it, since j is beyond i in linked list
- // if j is ghost, only store if j coords are "above and to the right" of i
-
- for (j = bins[i]; j >= 0; j = bins[j]) {
- if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
-
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) {
- neighptr[n] = j;
-
- if (fix_history) {
- if (rsq < radsum*radsum) {
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == tag[j]) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
- nn += dnum;
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- }
-
- n++;
- }
- }
-
- // loop over all atoms in other bins in stencil, store every pair
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) {
- neighptr[n] = j;
-
- if (fix_history) {
- if (rsq < radsum*radsum) {
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == tag[j]) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
- nn += dnum;
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- }
-
- n++;
- }
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (fix_history) {
- firsttouch[i] = touchptr;
- firstshear[i] = shearptr;
- ipage_touch->vgot(n);
- dpage_shear->vgot(nn);
- }
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- granular particles
- N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
- shear history must be accounted for when a neighbor pair is added
- pair added to list if atoms i and j are both owned and i < j
- pair added if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::granular_bin_newton_onesided(NeighList *list)
-{
-}
-
-/* ----------------------------------------------------------------------
- granular particles
- binned neighbor list construction with Newton's 3rd law for triclinic
- shear history must be accounted for when a neighbor pair is added
- each owned atom i checks its own bin and other bins in triclinic stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::granular_bin_newton_tri(NeighList *list)
-{
- int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- double radi,radsum,cutsq;
- int *neighptr,*touchptr;
- double *shearptr;
-
- NeighList *listgranhistory;
- int *npartner;
- tagint **partner;
- double **shearpartner;
- int **firsttouch;
- double **firstshear;
- MyPage<int> *ipage_touch;
- MyPage<double> *dpage_shear;
-
- // bin local & ghost atoms
-
- bin_atoms();
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- double *radius = atom->radius;
- tagint *tag = atom->tag;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *molecule = atom->molecule;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- MyPage<int> *ipage = list->ipage;
-
- FixShearHistory *fix_history = list->fix_history;
- if (fix_history) {
- fix_history->nlocal_neigh = nlocal;
- fix_history->nall_neigh = nlocal + atom->nghost;
- npartner = fix_history->npartner;
- partner = fix_history->partner;
- shearpartner = fix_history->shearpartner;
- listgranhistory = list->listgranhistory;
- firsttouch = listgranhistory->firstneigh;
- firstshear = listgranhistory->firstdouble;
- ipage_touch = listgranhistory->ipage;
- dpage_shear = listgranhistory->dpage;
- dnum = listgranhistory->dnum;
- dnumbytes = dnum * sizeof(double);
- }
-
- int inum = 0;
- ipage->reset();
- if (fix_history) {
- ipage_touch->reset();
- dpage_shear->reset();
- }
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
- if (fix_history) {
- nn = 0;
- touchptr = ipage_touch->vget();
- shearptr = dpage_shear->vget();
- }
-
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- radi = radius[i];
-
- // loop over all atoms in bins in stencil
- // pairs for atoms j "below" i are excluded
- // below = lower z or (equal z and lower y) or (equal zy and lower x)
- // (equal zyx and j <= i)
- // latter excludes self-self interaction but allows superposed atoms
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) {
- neighptr[n++] = j;
-
- if (fix_history) {
- if (rsq < radsum*radsum) {
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == tag[j]) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
- nn += dnum;
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- } else {
- touchptr[n] = 0;
- memcpy(&shearptr[nn],zeroes,dnumbytes);
- nn += dnum;
- }
- }
-
- n++;
- }
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (fix_history) {
- firsttouch[i] = touchptr;
- firstshear[i] = shearptr;
- ipage_touch->vgot(n);
- dpage_shear->vgot(nn);
- }
- }
-
- list->inum = inum;
-}
diff --git a/src/neigh_half_bin.cpp b/src/neigh_half_bin.cpp
deleted file mode 100644
index 349deddae1..0000000000
--- a/src/neigh_half_bin.cpp
+++ /dev/null
@@ -1,534 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
-#include "my_page.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with partial Newton's 3rd law
- each owned atom i checks own bin and other bins in stencil
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_no_newton(NeighList *list)
-{
- int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in other bins in stencil including self
- // only store pair if i < j
- // stores own/own pairs only once
- // stores own/ghost pairs on both procs
-
- ibin = coord2bin(x[i]);
-
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with partial Newton's 3rd law
- include neighbors of ghost atoms, but no "special neighbors" for ghosts
- owned and ghost atoms check own bin and other bins in stencil
- pair stored once if i,j are both owned and i < j
- pair stored by me if i owned and j ghost (also stored by proc owning j)
- pair stored once if i,j are both ghost and i < j
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_no_newton_ghost(NeighList *list)
-{
- int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int xbin,ybin,zbin,xbin2,ybin2,zbin2;
- int *neighptr;
-
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
- if (includegroup) nlocal = atom->nfirst;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- int **stencilxyz = list->stencilxyz;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nall; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in other bins in stencil including self
- // when i is a ghost atom, must check if stencil bin is out of bounds
- // only store pair if i < j
- // stores own/own pairs only once
- // stores own/ghost pairs with owned atom only, on both procs
- // stores ghost/ghost pairs only once
- // no molecular test when i = ghost atom
-
- if (i < nlocal) {
- ibin = coord2bin(x[i]);
-
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- } else {
- ibin = coord2bin(x[i],xbin,ybin,zbin);
- for (k = 0; k < nstencil; k++) {
- xbin2 = xbin + stencilxyz[k][0];
- ybin2 = ybin + stencilxyz[k][1];
- zbin2 = zbin + stencilxyz[k][2];
- if (xbin2 < 0 || xbin2 >= mbinx ||
- ybin2 < 0 || ybin2 >= mbiny ||
- zbin2 < 0 || zbin2 >= mbinz) continue;
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
- }
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = atom->nlocal;
- list->gnum = inum - atom->nlocal;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with full Newton's 3rd law
- each owned atom i checks its own bin and other bins in Newton stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_newton(NeighList *list)
-{
- int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over rest of atoms in i's bin, ghosts are at end of linked list
- // if j is owned atom, store it, since j is beyond i in linked list
- // if j is ghost, only store if j coords are "above and to the right" of i
-
- for (j = bins[i]; j >= 0; j = bins[j]) {
- if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
-
- // loop over all atoms in other bins in stencil, store every pair
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with Newton's 3rd law for triclinic
- each owned atom i checks its own bin and other bins in triclinic stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_newton_tri(NeighList *list)
-{
- int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in bins in stencil
- // pairs for atoms j "below" i are excluded
- // below = lower z or (equal z and lower y) or (equal zy and lower x)
- // (equal zyx and j <= i)
- // latter excludes self-self interaction but allows superposed atoms
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
-}
diff --git a/src/neigh_half_multi.cpp b/src/neigh_half_multi.cpp
deleted file mode 100644
index 9d8375b68e..0000000000
--- a/src/neigh_half_multi.cpp
+++ /dev/null
@@ -1,415 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
-#include "my_page.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with partial Newton's 3rd law
- each owned atom i checks own bin and other bins in stencil
- multi-type stencil is itype dependent and is distance checked
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::half_multi_no_newton(NeighList *list)
-{
- int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*s;
- double *cutsq,*distsq;
-
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in other bins in stencil including self
- // only store pair if i < j
- // skip if i,j neighbor cutoff is less than bin distance
- // stores own/own pairs only once
- // stores own/ghost pairs on both procs
-
- ibin = coord2bin(x[i]);
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- cutsq = cutneighsq[itype];
- ns = nstencil_multi[itype];
- for (k = 0; k < ns; k++) {
- for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with full Newton's 3rd law
- each owned atom i checks its own bin and other bins in Newton stencil
- multi-type stencil is itype dependent and is distance checked
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_multi_newton(NeighList *list)
-{
- int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*s;
- double *cutsq,*distsq;
-
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over rest of atoms in i's bin, ghosts are at end of linked list
- // if j is owned atom, store it, since j is beyond i in linked list
- // if j is ghost, only store if j coords are "above and to the right" of i
-
- for (j = bins[i]; j >= 0; j = bins[j]) {
- if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
-
- // loop over all atoms in other bins in stencil, store every pair
- // skip if i,j neighbor cutoff is less than bin distance
-
- ibin = coord2bin(x[i]);
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- cutsq = cutneighsq[itype];
- ns = nstencil_multi[itype];
- for (k = 0; k < ns; k++) {
- for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with Newton's 3rd law for triclinic
- each owned atom i checks its own bin and other bins in triclinic stencil
- multi-type stencil is itype dependent and is distance checked
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_multi_newton_tri(NeighList *list)
-{
- int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*s;
- double *cutsq,*distsq;
-
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in bins, including self, in stencil
- // skip if i,j neighbor cutoff is less than bin distance
- // bins below self are excluded from stencil
- // pairs for atoms j "below" i are excluded
- // below = lower z or (equal z and lower y) or (equal zy and lower x)
- // (equal zyx and j <= i)
- // latter excludes self-self interaction but allows superposed atoms
-
- ibin = coord2bin(x[i]);
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- cutsq = cutneighsq[itype];
- ns = nstencil_multi[itype];
- for (k = 0; k < ns; k++) {
- for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
-}
diff --git a/src/neigh_half_multi.h b/src/neigh_half_multi.h
deleted file mode 100644
index 1538f7662a..0000000000
--- a/src/neigh_half_multi.h
+++ /dev/null
@@ -1,22 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ERROR/WARNING messages:
-
-E: Neighbor list overflow, boost neigh_modify one
-
-There are too many neighbors of a single atom. Use the neigh_modify
-command to increase the max number of neighbors allowed for one atom.
-You may also want to boost the page size.
-
-*/
diff --git a/src/neigh_half_nsq.cpp b/src/neigh_half_nsq.cpp
deleted file mode 100644
index 17ce63c775..0000000000
--- a/src/neigh_half_nsq.cpp
+++ /dev/null
@@ -1,360 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
-#include "group.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::half_nsq_no_newton(NeighList *list)
-{
- int i,j,n,itype,jtype,which,bitmask,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
- if (includegroup) {
- nlocal = atom->nfirst;
- bitmask = group->bitmask[includegroup];
- }
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over owned atoms, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over remaining atoms, owned and ghost
- // only store pair if i < j
-
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
- include neighbors of ghost atoms, but no "special neighbors" for ghosts
- pair stored once if i,j are both owned and i < j
- pair stored by me if i owned and j ghost (also stored by proc owning j)
- pair stored once if i,j are both ghost and i < j
-------------------------------------------------------------------------- */
-
-void Neighbor::half_nsq_no_newton_ghost(NeighList *list)
-{
- int i,j,n,itype,jtype,which,bitmask,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
- if (includegroup) {
- nlocal = atom->nfirst;
- bitmask = group->bitmask[includegroup];
- }
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over owned & ghost atoms, storing neighbors
-
- for (i = 0; i < nall; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over remaining atoms, owned and ghost
- // only store pair if i < j
- // stores own/own pairs only once
- // stores own/ghost pairs with owned atom only, on both procs
- // stores ghost/ghost pairs only once
- // no molecular test when i = ghost atom
-
- if (i < nlocal) {
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
-
- } else {
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) neighptr[n++] = j;
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = atom->nlocal;
- list->gnum = inum - atom->nlocal;
-}
-
-/* ----------------------------------------------------------------------
- N^2 / 2 search for neighbor pairs with full Newton's 3rd law
- every pair stored exactly once by some processor
- decision on ghost atoms based on itag,jtag tests
-------------------------------------------------------------------------- */
-
-void Neighbor::half_nsq_newton(NeighList *list)
-{
- int i,j,n,itype,jtype,which,bitmask,imol,iatom,moltemplate;
- tagint itag,jtag,tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
- if (includegroup) {
- nlocal = atom->nfirst;
- bitmask = group->bitmask[includegroup];
- }
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- int inum = 0;
- ipage->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = 0;
- neighptr = ipage->vget();
-
- itag = tag[i];
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over remaining atoms, owned and ghost
- // itag = jtag is possible for long cutoffs that include images of self
-
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
-
- if (j >= nlocal) {
- jtag = tag[j];
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (domain->minimum_image_check(delx,dely,delz))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
-
- ilist[inum++] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- list->inum = inum;
-}
diff --git a/src/neigh_half_nsq.h b/src/neigh_half_nsq.h
deleted file mode 100644
index 1538f7662a..0000000000
--- a/src/neigh_half_nsq.h
+++ /dev/null
@@ -1,22 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ERROR/WARNING messages:
-
-E: Neighbor list overflow, boost neigh_modify one
-
-There are too many neighbors of a single atom. Use the neigh_modify
-command to increase the max number of neighbors allowed for one atom.
-You may also want to boost the page size.
-
-*/
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index 299a8704ba..2a29c34565 100644
--- a/src/neigh_list.cpp
+++ b/src/neigh_list.cpp
@@ -25,14 +25,15 @@ using namespace LAMMPS_NS;
#define PGDELTA 1
-enum{NSQ,BIN,MULTI}; // also in neighbor.cpp
+enum{NSQ,BIN,MULTI}; // also in Neighbor
/* ---------------------------------------------------------------------- */
-NeighList::NeighList(LAMMPS *lmp) :
- Pointers(lmp)
+NeighList::NeighList(LAMMPS *lmp) : Pointers(lmp)
{
- maxatoms = 0;
+ // initializations
+
+ maxatom = 0;
inum = gnum = 0;
ilist = NULL;
@@ -40,9 +41,15 @@ NeighList::NeighList(LAMMPS *lmp) :
firstneigh = NULL;
firstdouble = NULL;
+ // defaults, but may be reset by post_constructor()
+
+ occasional = 0;
+ ghost = 0;
+ ssa = 0;
+ copy = 0;
dnum = 0;
- last_build = -1;
+ // ptrs
iskip = NULL;
ijskip = NULL;
@@ -57,74 +64,117 @@ NeighList::NeighList(LAMMPS *lmp) :
listcopy = NULL;
listskip = NULL;
+ ipage = NULL;
+ dpage = NULL;
+
// USER-DPD package
- ssaflag = 0;
ndxAIR_ssa = NULL;
maxbin_ssa = 0;
bins_ssa = NULL;
maxhead_ssa = 0;
binhead_ssa = NULL;
gbinhead_ssa = NULL;
-
- maxstencil = ghostflag = 0;
- stencil = NULL;
- stencilxyz = NULL;
-
- maxstencil_multi = 0;
- nstencil_multi = NULL;
- stencil_multi = NULL;
- distsq_multi = NULL;
-
- ipage = NULL;
- dpage = NULL;
}
/* ---------------------------------------------------------------------- */
NeighList::~NeighList()
{
- if (!listcopy) {
+ if (!copy) {
memory->destroy(ilist);
memory->destroy(numneigh);
memory->sfree(firstneigh);
memory->sfree(firstdouble);
delete [] ipage;
- if (dnum) delete [] dpage;
+ delete [] dpage;
}
delete [] iskip;
memory->destroy(ijskip);
- if (maxstencil) memory->destroy(stencil);
- if (ghostflag) memory->destroy(stencilxyz);
- if (ndxAIR_ssa) memory->sfree(ndxAIR_ssa);
- if (maxbin_ssa) memory->destroy(bins_ssa);
- if (maxhead_ssa) {
+ if (ssa) {
+ memory->sfree(ndxAIR_ssa);
+ memory->destroy(bins_ssa);
memory->destroy(binhead_ssa);
memory->destroy(gbinhead_ssa);
}
+}
- if (maxstencil_multi) {
- for (int i = 1; i <= atom->ntypes; i++) {
- memory->destroy(stencil_multi[i]);
- memory->destroy(distsq_multi[i]);
- }
- delete [] nstencil_multi;
- delete [] stencil_multi;
- delete [] distsq_multi;
+/* ----------------------------------------------------------------------
+ adjust settings to match corresponding NeighRequest
+ cannot do this in constructor b/c not all NeighLists are allocated yet
+ copy -> set listcopy for list to copy from
+ skip -> set listskip and create local copy of itype,ijtype
+ halffull -> preceeding list must be full
+ granhistory -> preceeding list must be gran, set its LGH and FH ptrs
+ respaouter -> preceeding list(s) must be inner or middle, set LM/LI ptrs
+------------------------------------------------------------------------- */
+
+void NeighList::post_constructor(NeighRequest *nq)
+{
+ occasional = nq->occasional;
+ ghost = nq->ghost;
+ ssa = nq->ssa;
+ copy = nq->copy;
+ dnum = nq->dnum;
+
+ if (nq->copy)
+ listcopy = neighbor->lists[nq->otherlist];
+
+ if (nq->skip) {
+ listskip = neighbor->lists[nq->otherlist];
+ int ntypes = atom->ntypes;
+ iskip = new int[ntypes+1];
+ memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip");
+ int i,j;
+ for (i = 1; i <= ntypes; i++) iskip[i] = nq->iskip[i];
+ for (i = 1; i <= ntypes; i++)
+ for (j = 1; j <= ntypes; j++)
+ ijskip[i][j] = nq->ijskip[i][j];
+ }
+
+ if (nq->half_from_full) {
+ NeighRequest *oq = neighbor->requests[nq->index-1];
+ if (oq->full != 1)
+ error->all(FLERR,"Neighbor half-from-full list does not follow "
+ "full list");
+ listfull = neighbor->lists[nq->index-1];
+ }
+
+ if (nq->granhistory) {
+ NeighRequest *oq = neighbor->requests[nq->index-1];
+ if (oq->gran != 1)
+ error->all(FLERR,"Neighbor granhistory list does not follow gran list");
+ neighbor->lists[nq->index-1]->listgranhistory = this;
+ neighbor->lists[nq->index-1]->fix_history = nq->fix_history;
+ }
+
+ if (nq->respaouter) {
+ NeighRequest *oq = neighbor->requests[nq->index-1];
+ if (oq->respainner) {
+ respamiddle = 0;
+ listinner = neighbor->lists[nq->index-1];
+ } else if (oq->respamiddle) {
+ respamiddle = 1;
+ listmiddle = neighbor->lists[nq->index-1];
+ oq = neighbor->requests[nq->index-2];
+ if (!oq->respainner)
+ error->all(FLERR,"Neighbor respa outer list does not follow "
+ "respa list");
+ listinner = neighbor->lists[nq->index-2];
+ } else
+ error->all(FLERR,"Neighbor respa outer list does not follow respa list");
}
}
/* ---------------------------------------------------------------------- */
-void NeighList::setup_pages(int pgsize_caller, int oneatom_caller,
- int dnum_caller)
+void NeighList::setup_pages(int pgsize_caller, int oneatom_caller)
{
pgsize = pgsize_caller;
oneatom = oneatom_caller;
- dnum = dnum_caller;
int nmypage = comm->nthreads;
ipage = new MyPage<int>[nmypage];
@@ -135,104 +185,56 @@ void NeighList::setup_pages(int pgsize_caller, int oneatom_caller,
dpage = new MyPage<double>[nmypage];
for (int i = 0; i < nmypage; i++)
dpage[i].init(dnum*oneatom,dnum*pgsize,PGDELTA);
- }
- else dpage = NULL;
+ } else dpage = NULL;
}
/* ----------------------------------------------------------------------
- grow atom arrays to allow for nmax atoms
- triggered by more atoms on a processor
- caller knows if this list stores neighs of local atoms or local+ghost
+ grow per-atom data to allow for nlocal/nall atoms
+ for parent lists:
+ also trigger grow in child list(s) which are not built themselves
+ gran calls grow() in granhistory
+ respaouter calls grow() in respainner, respamiddle
+ triggered by neighbor list build
------------------------------------------------------------------------- */
-void NeighList::grow(int nmax)
+void NeighList::grow(int nlocal, int nall)
{
- // skip if this list is already long enough to store nmax atoms
+ // trigger grow() in children before possible return
+
+ if (listgranhistory) listgranhistory->grow(nlocal,nall);
+ if (listinner) listinner->grow(nlocal,nall);
+ if (listmiddle) listmiddle->grow(nlocal,nall);
- if (nmax <= maxatoms) return;
- maxatoms = nmax;
+ // skip if data structs are already big enough
+
+ if (ghost) {
+ if (nall <= maxatom) return;
+ } else {
+ if (nlocal <= maxatom) return;
+ }
+
+ maxatom = atom->nmax;
memory->destroy(ilist);
memory->destroy(numneigh);
memory->sfree(firstneigh);
- memory->sfree(firstdouble);
-
- memory->create(ilist,maxatoms,"neighlist:ilist");
- memory->create(numneigh,maxatoms,"neighlist:numneigh");
- firstneigh = (int **) memory->smalloc(maxatoms*sizeof(int *),
+ memory->create(ilist,maxatom,"neighlist:ilist");
+ memory->create(numneigh,maxatom,"neighlist:numneigh");
+ firstneigh = (int **) memory->smalloc(maxatom*sizeof(int *),
"neighlist:firstneigh");
- if (dnum)
- firstdouble = (double **) memory->smalloc(maxatoms*sizeof(double *),
+ if (dnum) {
+ memory->sfree(firstdouble);
+ firstdouble = (double **) memory->smalloc(maxatom*sizeof(double *),
"neighlist:firstdouble");
- if (ssaflag) {
- if (ndxAIR_ssa) memory->sfree(ndxAIR_ssa);
- ndxAIR_ssa = (uint16_t (*)[8]) memory->smalloc(sizeof(uint16_t)*8*maxatoms,
- "neighlist:ndxAIR_ssa");
}
-}
-
-/* ----------------------------------------------------------------------
- insure stencils are large enough for smax bins
- style = BIN or MULTI
-------------------------------------------------------------------------- */
-
-void NeighList::stencil_allocate(int smax, int style)
-{
- int i;
-
- if (style == BIN) {
- if (smax > maxstencil) {
- maxstencil = smax;
- memory->destroy(stencil);
- memory->create(stencil,maxstencil,"neighlist:stencil");
- if (ghostflag) {
- memory->destroy(stencilxyz);
- memory->create(stencilxyz,maxstencil,3,"neighlist:stencilxyz");
- }
- }
- } else {
- int n = atom->ntypes;
- if (maxstencil_multi == 0) {
- nstencil_multi = new int[n+1];
- stencil_multi = new int*[n+1];
- distsq_multi = new double*[n+1];
- for (i = 1; i <= n; i++) {
- nstencil_multi[i] = 0;
- stencil_multi[i] = NULL;
- distsq_multi[i] = NULL;
- }
- }
- if (smax > maxstencil_multi) {
- maxstencil_multi = smax;
- for (i = 1; i <= n; i++) {
- memory->destroy(stencil_multi[i]);
- memory->destroy(distsq_multi[i]);
- memory->create(stencil_multi[i],maxstencil_multi,
- "neighlist:stencil_multi");
- memory->create(distsq_multi[i],maxstencil_multi,
- "neighlist:distsq_multi");
- }
- }
+ if (ssa) {
+ if (ndxAIR_ssa) memory->sfree(ndxAIR_ssa);
+ ndxAIR_ssa = (uint16_t (*)[8]) memory->smalloc(sizeof(uint16_t)*8*maxatom,
+ "neighlist:ndxAIR_ssa");
}
}
-/* ----------------------------------------------------------------------
- copy skip info from request rq into list's iskip,ijskip
-------------------------------------------------------------------------- */
-
-void NeighList::copy_skip_info(int *rq_iskip, int **rq_ijskip)
-{
- int ntypes = atom->ntypes;
- iskip = new int[ntypes+1];
- memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip");
- int i,j;
- for (i = 1; i <= ntypes; i++) iskip[i] = rq_iskip[i];
- for (i = 1; i <= ntypes; i++)
- for (j = 1; j <= ntypes; j++)
- ijskip[i][j] = rq_ijskip[i][j];
-}
-
/* ----------------------------------------------------------------------
print attributes of this list and associated request
------------------------------------------------------------------------- */
@@ -246,11 +248,11 @@ void NeighList::print_attributes()
printf("Neighbor list/request %d:\n",index);
printf(" %p = requestor ptr (instance %d id %d)\n",
rq->requestor,rq->requestor_instance,rq->id);
- printf(" %d = build flag\n",buildflag);
- printf(" %d = grow flag\n",growflag);
- printf(" %d = stencil flag\n",stencilflag);
- printf(" %d = ghost flag\n",ghostflag);
- printf(" %d = ssa flag\n",ssaflag);
+ printf(" %d = occasional\n",occasional);
+ printf(" %d = ghost flag\n",ghost);
+ printf(" %d = ssa flag\n",ssa);
+ printf(" %d = copy flag\n",copy);
+ printf(" %d = dnum\n",dnum);
printf("\n");
printf(" %d = pair\n",rq->pair);
printf(" %d = fix\n",rq->fix);
@@ -266,17 +268,12 @@ void NeighList::print_attributes()
printf(" %d = respaouter\n",rq->respaouter);
printf(" %d = half_from_full\n",rq->half_from_full);
printf("\n");
- printf(" %d = occasional\n",rq->occasional);
printf(" %d = newton\n",rq->newton);
printf(" %d = granonesided\n",rq->granonesided);
- printf(" %d = dnum\n",rq->dnum);
- printf(" %d = ghost\n",rq->ghost);
printf(" %d = omp\n",rq->omp);
printf(" %d = intel\n",rq->intel);
printf(" %d = kokkos host\n",rq->kokkos_host);
printf(" %d = kokkos device\n",rq->kokkos_device);
- printf(" %d = ssa\n",rq->ssa);
- printf(" %d = copy\n",rq->copy);
printf(" %d = skip\n",rq->skip);
printf(" %d = otherlist\n",rq->otherlist);
printf(" %p = listskip\n",(void *)listskip);
@@ -285,16 +282,16 @@ void NeighList::print_attributes()
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
- if growflag = 0, maxatoms & maxpage will also be 0
+ if growflag = 0, maxatom & maxpage will also be 0
if stencilflag = 0, maxstencil * maxstencil_multi will also be 0
------------------------------------------------------------------------- */
bigint NeighList::memory_usage()
{
bigint bytes = 0;
- bytes += memory->usage(ilist,maxatoms);
- bytes += memory->usage(numneigh,maxatoms);
- bytes += maxatoms * sizeof(int *);
+ bytes += memory->usage(ilist,maxatom);
+ bytes += memory->usage(numneigh,maxatom);
+ bytes += maxatom * sizeof(int *);
int nmypage = comm->nthreads;
@@ -305,24 +302,17 @@ bigint NeighList::memory_usage()
if (dnum && dpage) {
for (int i = 0; i < nmypage; i++) {
- bytes += maxatoms * sizeof(double *);
+ bytes += maxatom * sizeof(double *);
bytes += dpage[i].size();
}
}
- if (maxstencil) bytes += memory->usage(stencil,maxstencil);
- if (ghostflag) bytes += memory->usage(stencilxyz,maxstencil,3);
- if (ndxAIR_ssa) bytes += sizeof(uint16_t) * 8 * maxatoms;
+ if (ndxAIR_ssa) bytes += sizeof(uint16_t) * 8 * maxatom;
if (maxbin_ssa) bytes += memory->usage(bins_ssa,maxbin_ssa);
if (maxhead_ssa) {
bytes += memory->usage(binhead_ssa,maxhead_ssa);
bytes += memory->usage(gbinhead_ssa,maxhead_ssa);
}
- if (maxstencil_multi) {
- bytes += memory->usage(stencil_multi,atom->ntypes,maxstencil_multi);
- bytes += memory->usage(distsq_multi,atom->ntypes,maxstencil_multi);
- }
-
return bytes;
}
diff --git a/src/neigh_list.h b/src/neigh_list.h
index d76682dfc4..232892f8b4 100644
--- a/src/neigh_list.h
+++ b/src/neigh_list.h
@@ -21,14 +21,21 @@ namespace LAMMPS_NS {
class NeighList : protected Pointers {
public:
- int index; // index of which neigh list it is
- // needed when a class invokes it directly
- // also indexes the request it came from
+ int index; // index of which neigh list this is
+ // also indexes the request it came from
+ // and the npair list of NPair classes
- int buildflag; // 1 if pair_build invoked every reneigh
- int growflag; // 1 if stores atom-based arrays & pages
- int stencilflag; // 1 if stores stencil arrays
- int ghostflag; // 1 if it stores neighbors of ghosts
+ int bin_method; // 0 if no binning, else 1-N index into binnames
+ int stencil_method; // 0 if no stencil, else 1-N index into stencilnames
+ int pair_method; // 0 if no pair, else 1-N index into pairnames
+
+ // settings from NeighRequest
+
+ int occasional; // 0 if build every reneighbor, 1 if not
+ int ghost; // 1 if list stores neighbors of ghosts
+ int ssa; // 1 if list stores Shardlow data
+ int copy; // 1 if this list copied from another list
+ int dnum; // # of doubles per neighbor, 0 if none
// data structs to store neighbor pairs I,J and associated values
@@ -41,14 +48,11 @@ class NeighList : protected Pointers {
int pgsize; // size of each page
int oneatom; // max size for one atom
- int dnum; // # of doubles per neighbor, 0 if none
MyPage<int> *ipage; // pages of neighbor indices
MyPage<double> *dpage; // pages of neighbor doubles, if dnum > 0
- bigint last_build; // timestep of last build for occasional lists
-
// atom types to skip when building list
- // iskip,ijskip are just ptrs to corresponding request
+ // copied info from corresponding request into realloced vec/array
int *iskip; // iskip[i] = 1 if atoms of type I are not in list
int **ijskip; // ijskip[i][j] = 1 if pairs of type I,J are not in list
@@ -67,7 +71,6 @@ class NeighList : protected Pointers {
// USER-DPD package and Shardlow Splitting Algorithm (SSA) support
- int ssaflag; // 1 if the list has the ndxAIR_ssa array
uint16_t (*ndxAIR_ssa)[8]; // for each atom, last neighbor index of each AIR
int *bins_ssa; // index of next atom in each bin
int maxbin_ssa; // size of bins_ssa array
@@ -75,30 +78,20 @@ class NeighList : protected Pointers {
int *gbinhead_ssa; // index of 1st ghost atom in each bin
int maxhead_ssa; // size of binhead_ssa and gbinhead_ssa arrays
- // stencils of bin indices for neighbor finding
-
- int maxstencil; // max size of stencil
- int nstencil; // # of bins in stencil
- int *stencil; // list of bin offsets
- int **stencilxyz; // bin offsets in xyz dims
-
- int maxstencil_multi; // max sizes of stencils
- int *nstencil_multi; // # bins in each type-based multi stencil
- int **stencil_multi; // list of bin offsets in each stencil
- double **distsq_multi; // sq distances to bins in each stencil
+ // methods
NeighList(class LAMMPS *);
virtual ~NeighList();
- void setup_pages(int, int, int); // setup page data structures
- void grow(int); // grow maxlocal
+ void post_constructor(class NeighRequest *);
+ void setup_pages(int, int); // setup page data structures
+ void grow(int,int); // grow all data structs
void stencil_allocate(int, int); // allocate stencil arrays
- void copy_skip_info(int *, int **); // copy skip info from a neigh request
void print_attributes(); // debug routine
- int get_maxlocal() {return maxatoms;}
+ int get_maxlocal() {return maxatom;}
bigint memory_usage();
protected:
- int maxatoms; // size of allocated atom arrays
+ int maxatom; // size of allocated per-atom arrays
};
}
diff --git a/src/neigh_request.cpp b/src/neigh_request.cpp
index cc8c0d7c99..4a3eb14933 100644
--- a/src/neigh_request.cpp
+++ b/src/neigh_request.cpp
@@ -24,7 +24,6 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
// default ID = 0
id = 0;
- unprocessed = 1;
// class user of list: default is pair request
// only one is set to 1
@@ -37,16 +36,19 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
half = 1;
full = 0;
- full_cluster = 0;
- gran = 0;
+ gran = granhistory = 0;
respainner = respamiddle = respaouter = 0;
half_from_full = 0;
+ full_cluster = 0;
+
+ // only set when command = 1;
+
+ command_style = NULL;
// combination of settings, mutiple can be set to 1
// default is every reneighboring
// default is use newton_pair setting in force
- // default is encode special bond flags
- // default is no granular history (when gran = 1)
+ // default is no size history (when gran = 1)
// default is no one-sided sphere/surface interactions (when gran = 1)
// default is no auxiliary floating point values
// default is no neighbors of ghosts
@@ -56,8 +58,6 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
occasional = 0;
newton = 0;
- //special = 1;
- granhistory = 0;
granonesided = 0;
dnum = 0;
ghost = 0;
@@ -73,6 +73,7 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
skip = 0;
iskip = NULL;
ijskip = NULL;
+ off2on = 0;
otherlist = -1;
}
@@ -113,8 +114,6 @@ int NeighRequest::identical(NeighRequest *other)
// and appearing to be old, when it is really new
// only needed for classes with persistent neigh lists: Fix, Compute, Pair
- if (other->unprocessed) same = 0;
-
if (requestor != other->requestor) same = 0;
if (requestor_instance != other->requestor_instance) same = 0;
if (id != other->id) same = 0;
@@ -134,7 +133,6 @@ int NeighRequest::identical(NeighRequest *other)
if (newton != other->newton) same = 0;
if (occasional != other->occasional) same = 0;
- //if (special != other->special) same = 0;
if (granhistory != other->granhistory) same = 0;
if (granonesided != other->granonesided) same = 0;
if (dnum != other->dnum) same = 0;
diff --git a/src/neigh_request.h b/src/neigh_request.h
index 16d4dfddaf..0b561710e7 100644
--- a/src/neigh_request.h
+++ b/src/neigh_request.h
@@ -20,12 +20,11 @@ namespace LAMMPS_NS {
class NeighRequest : protected Pointers {
public:
+ int index; // index of which neigh request this is
void *requestor; // class that made request
int requestor_instance; // instance of that class (only Fix, Compute, Pair)
int id; // ID of request as stored by requestor
// used to track multiple requests from one class
- int unprocessed; // 1 when first requested
- // 0 after processed by Neighbor class
// which class style requests the list, one flag is 1, others are 0
@@ -35,16 +34,20 @@ class NeighRequest : protected Pointers {
int command;
// kind of list requested, one flag is 1, others are 0
+ // NOTE: should make only the first 3 settings be unique,
+ // allow others as add-on flags
+ // this will require changed flags in pair requestors
+ // this will lead to simpler logic in Neighbor::choose_build()
int half; // 1 if half neigh list (set by default)
int full; // 1 if full neigh list
- int full_cluster; // only used by Kokkos pair styles
+ int half_from_full; // 1 if half list computed from previous full list
int gran; // 1 if granular list
int granhistory; // 1 if history info for granular contact pairs
int respainner; // 1 if a rRESPA inner list
int respamiddle; // 1 if a rRESPA middle list
int respaouter; // 1 if a rRESPA outer list
- int half_from_full; // 1 if half list computed from previous full list
+ int full_cluster; // only used by Kokkos pair styles
// command_style only set if command = 1
// allows print_pair_info() to access command name
@@ -52,7 +55,7 @@ class NeighRequest : protected Pointers {
const char *command_style;
// -----------------
- // optional settings
+ // optional settings, set by caller, all are 0 by default
// -----------------
// 0 if needed every reneighboring during run
@@ -66,11 +69,6 @@ class NeighRequest : protected Pointers {
int newton;
- // 0 if user of list wants no encoding of special bond flags and all neighs
- // 1 if user of list wants special bond flags encoded, set by default
-
- //int special;
-
// 1 if one-sided granular list for sphere/surf interactions (gran = 1)
int granonesided;
@@ -96,9 +94,13 @@ class NeighRequest : protected Pointers {
// 1 if using Shardlow Splitting Algorithm (SSA) neighbor list build
int ssa;
+
+ // -----------------
+ // end of optional settings
+ // -----------------
- // set by neighbor and pair_hybrid after all requests are made
- // these settings do not change kind value
+ // set by pair_hybrid and neighbor after all requests are made
+ // these settings do not change kind value or optional settings
int copy; // 1 if this list copied from another list
diff --git a/src/neigh_respa.cpp b/src/neigh_respa.cpp
deleted file mode 100644
index 777534746b..0000000000
--- a/src/neigh_respa.cpp
+++ /dev/null
@@ -1,928 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
-#include "group.h"
-#include "my_page.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- multiple respa lists
- N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
- pair added to list if atoms i and j are both owned and i < j
- pair added if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::respa_nsq_no_newton(NeighList *list)
-{
- int i,j,n,itype,jtype,n_inner,n_middle,bitmask,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*neighptr_inner,*neighptr_middle;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
- if (includegroup) {
- nlocal = atom->nfirst;
- bitmask = group->bitmask[includegroup];
- }
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- NeighList *listinner = list->listinner;
- int *ilist_inner = listinner->ilist;
- int *numneigh_inner = listinner->numneigh;
- int **firstneigh_inner = listinner->firstneigh;
- MyPage<int> *ipage_inner = listinner->ipage;
-
- NeighList *listmiddle;
- int *ilist_middle,*numneigh_middle,**firstneigh_middle;
- MyPage<int> *ipage_middle;
- int respamiddle = list->respamiddle;
- if (respamiddle) {
- listmiddle = list->listmiddle;
- ilist_middle = listmiddle->ilist;
- numneigh_middle = listmiddle->numneigh;
- firstneigh_middle = listmiddle->firstneigh;
- ipage_middle = listmiddle->ipage;
- }
-
- int inum = 0;
- int which = 0;
- int minchange = 0;
- ipage->reset();
- ipage_inner->reset();
- if (respamiddle) ipage_middle->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = n_inner = 0;
- neighptr = ipage->vget();
- neighptr_inner = ipage_inner->vget();
- if (respamiddle) {
- n_middle = 0;
- neighptr_middle = ipage_middle->vget();
- }
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over remaining atoms, owned and ghost
-
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (minchange) neighptr_inner[n_inner++] = j;
- else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (minchange) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
- }
-
- ilist[inum] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- ilist_inner[inum] = i;
- firstneigh_inner[i] = neighptr_inner;
- numneigh_inner[i] = n_inner;
- ipage_inner->vgot(n_inner);
- if (ipage_inner->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (respamiddle) {
- ilist_middle[inum] = i;
- firstneigh_middle[i] = neighptr_middle;
- numneigh_middle[i] = n_middle;
- ipage_middle->vgot(n_middle);
- if (ipage_middle->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- inum++;
- }
-
- list->inum = inum;
- listinner->inum = inum;
- if (respamiddle) listmiddle->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- multiple respa lists
- N^2 / 2 search for neighbor pairs with full Newton's 3rd law
- pair added to list if atoms i and j are both owned and i < j
- if j is ghost only me or other proc adds pair
- decision based on itag,jtag tests
-------------------------------------------------------------------------- */
-
-void Neighbor::respa_nsq_newton(NeighList *list)
-{
- int i,j,n,itype,jtype,itag,jtag,n_inner,n_middle,bitmask;
- int imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*neighptr_inner,*neighptr_middle;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
- if (includegroup) {
- nlocal = atom->nfirst;
- bitmask = group->bitmask[includegroup];
- }
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- MyPage<int> *ipage = list->ipage;
-
- NeighList *listinner = list->listinner;
- int *ilist_inner = listinner->ilist;
- int *numneigh_inner = listinner->numneigh;
- int **firstneigh_inner = listinner->firstneigh;
- MyPage<int> *ipage_inner = listinner->ipage;
-
- NeighList *listmiddle;
- int *ilist_middle,*numneigh_middle,**firstneigh_middle;
- MyPage<int> *ipage_middle;
- int respamiddle = list->respamiddle;
- if (respamiddle) {
- listmiddle = list->listmiddle;
- ilist_middle = listmiddle->ilist;
- numneigh_middle = listmiddle->numneigh;
- firstneigh_middle = listmiddle->firstneigh;
- ipage_middle = listmiddle->ipage;
- }
-
- int inum = 0;
- int which = 0;
- int minchange = 0;
- ipage->reset();
- ipage_inner->reset();
- if (respamiddle) ipage_middle->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = n_inner = 0;
- neighptr = ipage->vget();
- neighptr_inner = ipage_inner->vget();
- if (respamiddle) {
- n_middle = 0;
- neighptr_middle = ipage_middle->vget();
- }
-
- itag = tag[i];
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over remaining atoms, owned and ghost
-
- for (j = i+1; j < nall; j++) {
- if (includegroup && !(mask[j] & bitmask)) continue;
-
- if (j >= nlocal) {
- jtag = tag[j];
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (minchange) neighptr_inner[n_inner++] = j;
- else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (minchange) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
- }
-
- ilist[inum] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- ilist_inner[inum] = i;
- firstneigh_inner[i] = neighptr_inner;
- numneigh_inner[i] = n_inner;
- ipage_inner->vgot(n_inner);
- if (ipage_inner->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (respamiddle) {
- ilist_middle[inum] = i;
- firstneigh_middle[i] = neighptr_middle;
- numneigh_middle[i] = n_middle;
- ipage_middle->vgot(n_middle);
- if (ipage_middle->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- inum++;
- }
-
- list->inum = inum;
- listinner->inum = inum;
- if (respamiddle) listmiddle->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- multiple respa lists
- binned neighbor list construction with partial Newton's 3rd law
- each owned atom i checks own bin and surrounding bins in non-Newton stencil
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::respa_bin_no_newton(NeighList *list)
-{
- int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*neighptr_inner,*neighptr_middle;
-
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- MyPage<int> *ipage = list->ipage;
-
- NeighList *listinner = list->listinner;
- int *ilist_inner = listinner->ilist;
- int *numneigh_inner = listinner->numneigh;
- int **firstneigh_inner = listinner->firstneigh;
- MyPage<int> *ipage_inner = listinner->ipage;
-
- NeighList *listmiddle;
- int *ilist_middle,*numneigh_middle,**firstneigh_middle;
- MyPage<int> *ipage_middle;
- int respamiddle = list->respamiddle;
- if (respamiddle) {
- listmiddle = list->listmiddle;
- ilist_middle = listmiddle->ilist;
- numneigh_middle = listmiddle->numneigh;
- firstneigh_middle = listmiddle->firstneigh;
- ipage_middle = listmiddle->ipage;
- }
-
- int inum = 0;
- int which = 0;
- int minchange = 0;
- ipage->reset();
- ipage_inner->reset();
- if (respamiddle) ipage_middle->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = n_inner = 0;
- neighptr = ipage->vget();
- neighptr_inner = ipage_inner->vget();
- if (respamiddle) {
- n_middle = 0;
- neighptr_middle = ipage_middle->vget();
- }
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- ibin = coord2bin(x[i]);
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in surrounding bins in stencil including self
- // only store pair if i < j
- // stores own/own pairs only once
- // stores own/ghost pairs on both procs
-
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (minchange) neighptr_inner[n_inner++] = j;
- else if (which > 0)
- neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (minchange) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
- }
- }
-
- ilist[inum] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- ilist_inner[inum] = i;
- firstneigh_inner[i] = neighptr_inner;
- numneigh_inner[i] = n_inner;
- ipage_inner->vgot(n_inner);
- if (ipage_inner->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (respamiddle) {
- ilist_middle[inum] = i;
- firstneigh_middle[i] = neighptr_middle;
- numneigh_middle[i] = n_middle;
- ipage_middle->vgot(n_middle);
- if (ipage_middle->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- inum++;
- }
-
- list->inum = inum;
- listinner->inum = inum;
- if (respamiddle) listmiddle->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- multiple respa lists
- binned neighbor list construction with full Newton's 3rd law
- each owned atom i checks its own bin and other bins in Newton stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::respa_bin_newton(NeighList *list)
-{
- int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*neighptr_inner,*neighptr_middle;
-
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- MyPage<int> *ipage = list->ipage;
-
- NeighList *listinner = list->listinner;
- int *ilist_inner = listinner->ilist;
- int *numneigh_inner = listinner->numneigh;
- int **firstneigh_inner = listinner->firstneigh;
- MyPage<int> *ipage_inner = listinner->ipage;
-
- NeighList *listmiddle;
- int *ilist_middle,*numneigh_middle,**firstneigh_middle;
- MyPage<int> *ipage_middle;
- int respamiddle = list->respamiddle;
- if (respamiddle) {
- listmiddle = list->listmiddle;
- ilist_middle = listmiddle->ilist;
- numneigh_middle = listmiddle->numneigh;
- firstneigh_middle = listmiddle->firstneigh;
- ipage_middle = listmiddle->ipage;
- }
-
- int inum = 0;
- int which = 0;
- int minchange = 0;
- ipage->reset();
- ipage_inner->reset();
- if (respamiddle) ipage_middle->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = n_inner = 0;
- neighptr = ipage->vget();
- neighptr_inner = ipage_inner->vget();
- if (respamiddle) {
- n_middle = 0;
- neighptr_middle = ipage_middle->vget();
- }
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over rest of atoms in i's bin, ghosts are at end of linked list
- // if j is owned atom, store it, since j is beyond i in linked list
- // if j is ghost, only store if j coords are "above and to the right" of i
-
- for (j = bins[i]; j >= 0; j = bins[j]) {
- if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (minchange) neighptr_inner[n_inner++] = j;
- else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (minchange) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
- }
-
- // loop over all atoms in other bins in stencil, store every pair
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (minchange) neighptr_inner[n_inner++] = j;
- else if (which > 0)
- neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (minchange) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
- }
- }
-
- ilist[inum] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- ilist_inner[inum] = i;
- firstneigh_inner[i] = neighptr_inner;
- numneigh_inner[i] = n_inner;
- ipage_inner->vgot(n_inner);
- if (ipage_inner->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (respamiddle) {
- ilist_middle[inum] = i;
- firstneigh_middle[i] = neighptr_middle;
- numneigh_middle[i] = n_middle;
- ipage_middle->vgot(n_middle);
- if (ipage_middle->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- inum++;
- }
-
- list->inum = inum;
- listinner->inum = inum;
- if (respamiddle) listmiddle->inum = inum;
-}
-
-/* ----------------------------------------------------------------------
- multiple respa lists
- binned neighbor list construction with Newton's 3rd law for triclinic
- each owned atom i checks its own bin and other bins in triclinic stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::respa_bin_newton_tri(NeighList *list)
-{
- int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom,moltemplate;
- tagint tagprev;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*neighptr_inner,*neighptr_middle;
-
- // bin local & ghost atoms
-
- if (binatomflag) bin_atoms();
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- tagint *molecule = atom->molecule;
- tagint **special = atom->special;
- int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
-
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
- int molecular = atom->molecular;
- if (molecular == 2) moltemplate = 1;
- else moltemplate = 0;
-
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
- int nstencil = list->nstencil;
- int *stencil = list->stencil;
- MyPage<int> *ipage = list->ipage;
-
- NeighList *listinner = list->listinner;
- int *ilist_inner = listinner->ilist;
- int *numneigh_inner = listinner->numneigh;
- int **firstneigh_inner = listinner->firstneigh;
- MyPage<int> *ipage_inner = listinner->ipage;
-
- NeighList *listmiddle;
- int *ilist_middle,*numneigh_middle,**firstneigh_middle;
- MyPage<int> *ipage_middle;
- int respamiddle = list->respamiddle;
- if (respamiddle) {
- listmiddle = list->listmiddle;
- ilist_middle = listmiddle->ilist;
- numneigh_middle = listmiddle->numneigh;
- firstneigh_middle = listmiddle->firstneigh;
- ipage_middle = listmiddle->ipage;
- }
-
- int inum = 0;
- int which = 0;
- int minchange = 0;
- ipage->reset();
- ipage_inner->reset();
- if (respamiddle) ipage_middle->reset();
-
- // loop over each atom, storing neighbors
-
- for (i = 0; i < nlocal; i++) {
- n = n_inner = 0;
- neighptr = ipage->vget();
- neighptr_inner = ipage_inner->vget();
- if (respamiddle) {
- n_middle = 0;
- neighptr_middle = ipage_middle->vget();
- }
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- if (moltemplate) {
- imol = molindex[i];
- iatom = molatom[i];
- tagprev = tag[i] - iatom - 1;
- }
-
- // loop over all atoms in bins in stencil
- // pairs for atoms j "below" i are excluded
- // below = lower z or (equal z and lower y) or (equal zy and lower x)
- // (equal zyx and j <= i)
- // latter excludes self-self interaction but allows superposed atoms
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- if (!moltemplate)
- which = find_special(special[i],nspecial[i],tag[j]);
- else if (imol >= 0)
- which = find_special(onemols[imol]->special[iatom],
- onemols[imol]->nspecial[iatom],
- tag[j]-tagprev);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
- neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (minchange) neighptr_inner[n_inner++] = j;
- else if (which > 0)
- neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (minchange) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
- }
- }
-
- ilist[inum] = i;
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- ipage->vgot(n);
- if (ipage->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- ilist_inner[inum] = i;
- firstneigh_inner[i] = neighptr_inner;
- numneigh_inner[i] = n_inner;
- ipage_inner->vgot(n_inner);
- if (ipage_inner->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-
- if (respamiddle) {
- ilist_middle[inum] = i;
- firstneigh_middle[i] = neighptr_middle;
- numneigh_middle[i] = n_middle;
- ipage_middle->vgot(n_middle);
- if (ipage_middle->status())
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
- }
-
- inum++;
- }
-
- list->inum = inum;
- listinner->inum = inum;
- if (respamiddle) listmiddle->inum = inum;
-}
diff --git a/src/neigh_respa.h b/src/neigh_respa.h
deleted file mode 100644
index 1538f7662a..0000000000
--- a/src/neigh_respa.h
+++ /dev/null
@@ -1,22 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ERROR/WARNING messages:
-
-E: Neighbor list overflow, boost neigh_modify one
-
-There are too many neighbors of a single atom. Use the neigh_modify
-command to increase the max number of neighbors allowed for one atom.
-You may also want to boost the page size.
-
-*/
diff --git a/src/neigh_shardlow.h b/src/neigh_shardlow.h
deleted file mode 100644
index 1538f7662a..0000000000
--- a/src/neigh_shardlow.h
+++ /dev/null
@@ -1,22 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ERROR/WARNING messages:
-
-E: Neighbor list overflow, boost neigh_modify one
-
-There are too many neighbors of a single atom. Use the neigh_modify
-command to increase the max number of neighbors allowed for one atom.
-You may also want to boost the page size.
-
-*/
diff --git a/src/neigh_stencil.cpp b/src/neigh_stencil.cpp
deleted file mode 100644
index 65fd860d2b..0000000000
--- a/src/neigh_stencil.cpp
+++ /dev/null
@@ -1,536 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "atom.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- routines to create a stencil = list of bin offsets
- stencil = bins whose closest corner to central bin is within cutoff
- sx,sy,sz = bin bounds = furthest the stencil could possibly extend
- 3d creates xyz stencil, 2d creates xy stencil
- for half list with newton off:
- stencil is all surrounding bins including self
- regardless of triclinic
- for half list with newton on:
- stencil is bins to the "upper right" of central bin
- stencil does not include self
- for half list with triclinic:
- stencil is all bins in z-plane of self and above, but not below
- in 2d is all bins in y-plane of self and above, but not below
- stencil includes self
- for full list:
- stencil is all surrounding bins including self
- regardless of newton on/off or triclinic
- for multi:
- create one stencil for each atom type
- stencil is same bin bounds as newton on/off, triclinic, half/full
- cutoff is not cutneighmaxsq, but max cutoff for that atom type
-------------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_bin_2d_no_newton(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j;
- int *stencil = list->stencil;
- int nstencil = 0;
-
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil[nstencil++] = j*mbinx + i;
-
- list->nstencil = nstencil;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_ghost_bin_2d_no_newton(NeighList *list,
- int sx, int sy, int sz)
-{
- int *stencil = list->stencil;
- int **stencilxyz = list->stencilxyz;
- int nstencil = 0;
-
- for (int j = -sy; j <= sy; j++)
- for (int i = -sx; i <= sx; i++)
- if (bin_distance(i,j,0) < cutneighmaxsq) {
- stencilxyz[nstencil][0] = i;
- stencilxyz[nstencil][1] = j;
- stencilxyz[nstencil][2] = 0;
- stencil[nstencil++] = j*mbinx + i;
- }
-
- list->nstencil = nstencil;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_bin_3d_no_newton(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,k;
- int *stencil = list->stencil;
- int nstencil = 0;
-
- for (k = -sz; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,k) < cutneighmaxsq)
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
-
- list->nstencil = nstencil;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_ghost_bin_3d_no_newton(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,k;
- int *stencil = list->stencil;
- int **stencilxyz = list->stencilxyz;
- int nstencil = 0;
-
- for (k = -sz; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,k) < cutneighmaxsq) {
- stencilxyz[nstencil][0] = i;
- stencilxyz[nstencil][1] = j;
- stencilxyz[nstencil][2] = k;
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
- }
-
- list->nstencil = nstencil;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_bin_2d_newton(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j;
- int *stencil = list->stencil;
- int nstencil = 0;
-
- for (j = 0; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (j > 0 || (j == 0 && i > 0))
- if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil[nstencil++] = j*mbinx + i;
-
- list->nstencil = nstencil;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_bin_3d_newton(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,k;
- int *stencil = list->stencil;
- int nstencil = 0;
-
- for (k = 0; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (k > 0 || j > 0 || (j == 0 && i > 0))
- if (bin_distance(i,j,k) < cutneighmaxsq)
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
-
- list->nstencil = nstencil;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_bin_2d_newton_tri(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j;
- int *stencil = list->stencil;
- int nstencil = 0;
-
- for (j = 0; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil[nstencil++] = j*mbinx + i;
-
- list->nstencil = nstencil;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_bin_3d_newton_tri(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,k;
- int *stencil = list->stencil;
- int nstencil = 0;
-
- for (k = 0; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,k) < cutneighmaxsq)
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
-
- list->nstencil = nstencil;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_multi_2d_no_newton(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,n;
- double rsq,typesq;
- int *s;
- double *distsq;
-
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
-
- int ntypes = atom->ntypes;
- for (int itype = 1; itype <= ntypes; itype++) {
- typesq = cuttypesq[itype];
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- n = 0;
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,0);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = j*mbinx + i;
- }
- }
- nstencil_multi[itype] = n;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_multi_3d_no_newton(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,k,n;
- double rsq,typesq;
- int *s;
- double *distsq;
-
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
-
- int ntypes = atom->ntypes;
- for (int itype = 1; itype <= ntypes; itype++) {
- typesq = cuttypesq[itype];
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- n = 0;
- for (k = -sz; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,k);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = k*mbiny*mbinx + j*mbinx + i;
- }
- }
- nstencil_multi[itype] = n;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_multi_2d_newton(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,n;
- double rsq,typesq;
- int *s;
- double *distsq;
-
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
-
- int ntypes = atom->ntypes;
- for (int itype = 1; itype <= ntypes; itype++) {
- typesq = cuttypesq[itype];
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- n = 0;
- for (j = 0; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (j > 0 || (j == 0 && i > 0)) {
- rsq = bin_distance(i,j,0);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = j*mbinx + i;
- }
- }
- nstencil_multi[itype] = n;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_multi_3d_newton(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,k,n;
- double rsq,typesq;
- int *s;
- double *distsq;
-
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
-
- int ntypes = atom->ntypes;
- for (int itype = 1; itype <= ntypes; itype++) {
- typesq = cuttypesq[itype];
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- n = 0;
- for (k = 0; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (k > 0 || j > 0 || (j == 0 && i > 0)) {
- rsq = bin_distance(i,j,k);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = k*mbiny*mbinx + j*mbinx + i;
- }
- }
- nstencil_multi[itype] = n;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_multi_2d_newton_tri(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,n;
- double rsq,typesq;
- int *s;
- double *distsq;
-
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
-
- int ntypes = atom->ntypes;
- for (int itype = 1; itype <= ntypes; itype++) {
- typesq = cuttypesq[itype];
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- n = 0;
- for (j = 0; j <= sy; j++)
- for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,0);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = j*mbinx + i;
- }
- }
- nstencil_multi[itype] = n;
- }
-}
-
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_multi_3d_newton_tri(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,k,n;
- double rsq,typesq;
- int *s;
- double *distsq;
-
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
-
- int ntypes = atom->ntypes;
- for (int itype = 1; itype <= ntypes; itype++) {
- typesq = cuttypesq[itype];
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- n = 0;
- for (k = 0; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,k);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = k*mbiny*mbinx + j*mbinx + i;
- }
- }
- nstencil_multi[itype] = n;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_full_bin_2d(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j;
- int *stencil = list->stencil;
- int nstencil = 0;
-
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil[nstencil++] = j*mbinx + i;
-
- list->nstencil = nstencil;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_full_ghost_bin_2d(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j;
- int *stencil = list->stencil;
- int **stencilxyz = list->stencilxyz;
- int nstencil = 0;
-
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,0) < cutneighmaxsq) {
- stencilxyz[nstencil][0] = i;
- stencilxyz[nstencil][1] = j;
- stencilxyz[nstencil][2] = 0;
- stencil[nstencil++] = j*mbinx + i;
- }
-
- list->nstencil = nstencil;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_full_bin_3d(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,k;
- int *stencil = list->stencil;
- int nstencil = 0;
-
- for (k = -sz; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,k) < cutneighmaxsq)
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
-
- list->nstencil = nstencil;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_full_ghost_bin_3d(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,k;
- int *stencil = list->stencil;
- int **stencilxyz = list->stencilxyz;
- int nstencil = 0;
-
- for (k = -sz; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,k) < cutneighmaxsq) {
- stencilxyz[nstencil][0] = i;
- stencilxyz[nstencil][1] = j;
- stencilxyz[nstencil][2] = k;
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
- }
-
- list->nstencil = nstencil;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_full_multi_2d(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,n;
- double rsq,typesq;
- int *s;
- double *distsq;
-
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
-
- int ntypes = atom->ntypes;
- for (int itype = 1; itype <= ntypes; itype++) {
- typesq = cuttypesq[itype];
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- n = 0;
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,0);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = j*mbinx + i;
- }
- }
- nstencil_multi[itype] = n;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_full_multi_3d(NeighList *list,
- int sx, int sy, int sz)
-{
- int i,j,k,n;
- double rsq,typesq;
- int *s;
- double *distsq;
-
- int *nstencil_multi = list->nstencil_multi;
- int **stencil_multi = list->stencil_multi;
- double **distsq_multi = list->distsq_multi;
-
- int ntypes = atom->ntypes;
- for (int itype = 1; itype <= ntypes; itype++) {
- typesq = cuttypesq[itype];
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- n = 0;
- for (k = -sz; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,k);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = k*mbiny*mbinx + j*mbinx + i;
- }
- }
- nstencil_multi[itype] = n;
- }
-}
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index de6835da87..e58fc7126e 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -22,6 +22,10 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
+#include "style_nbin.h"
+#include "style_nstencil.h"
+#include "style_npair.h"
+#include "style_ntopo.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
@@ -39,17 +43,18 @@
#include "memory.h"
#include "error.h"
+#include <map>
+
using namespace LAMMPS_NS;
+using namespace NeighConst;
#define RQDELTA 1
#define EXDELTA 1
-#define LB_FACTOR 1.5
-#define SMALL 1.0e-6
#define BIG 1.0e20
-#define CUT2BIN_RATIO 100
-enum{NSQ,BIN,MULTI}; // also in neigh_list.cpp
+enum{NSQ,BIN,MULTI}; // also in NBin, NeighList, NStencil
+enum{NONE,ALL,PARTIAL,TEMPLATE};
static const char cite_neigh_multi[] =
"neighbor multi command:\n\n"
@@ -73,6 +78,8 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
+ firsttime = 1;
+
style = BIN;
every = 1;
delay = 10;
@@ -82,7 +89,6 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
binsizeflag = 0;
build_once = 0;
cluster_check = 0;
- binatomflag = 1;
ago = -1;
cutneighmax = 0.0;
@@ -92,44 +98,24 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
cuttypesq = NULL;
fixchecklist = NULL;
- // coords at last neighboring
-
- maxhold = 0;
- xhold = NULL;
- lastcall = -1;
-
- // binning
+ // pairwise neighbor lists and associated data structs
- maxhead = 0;
- binhead = NULL;
- maxbin = 0;
- bins = NULL;
-
- // pair exclusion list info
-
- includegroup = 0;
-
- nex_type = maxex_type = 0;
- ex1_type = ex2_type = NULL;
- ex_type = NULL;
+ nlist = 0;
+ lists = NULL;
- nex_group = maxex_group = 0;
- ex1_group = ex2_group = ex1_bit = ex2_bit = NULL;
+ nbin = 0;
+ neigh_bin = NULL;
- nex_mol = maxex_mol = 0;
- ex_mol_group = ex_mol_bit = NULL;
+ nstencil = 0;
+ neigh_stencil = NULL;
- // pair lists
+ neigh_pair = NULL;
- maxatom = 0;
- nblist = nglist = nslist = 0;
+ nstencil_perpetual = 0;
+ slist = NULL;
- nlist = 0;
- lists = NULL;
- pair_build = NULL;
- stencil_create = NULL;
- blist = glist = slist = NULL;
- anyghostlist = 0;
+ npair_perpetual = 0;
+ plist = NULL;
nrequest = maxrequest = 0;
requests = NULL;
@@ -141,23 +127,47 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
old_triclinic = 0;
old_pgsize = pgsize;
old_oneatom = oneatom;
- old_every = every;
- old_delay = delay;
- old_check = dist_check;
- old_cutoff = cutneighmax;
zeroes = NULL;
- // bond lists
+ binclass = NULL;
+ binnames = NULL;
+ binmasks = NULL;
+ stencilclass = NULL;
+ stencilnames = NULL;
+ stencilmasks = NULL;
+
+ // topology lists
+
+ bondwhich = anglewhich = dihedralwhich = improperwhich = NONE;
+
+ neigh_bond = NULL;
+ neigh_angle = NULL;
+ neigh_dihedral = NULL;
+ neigh_improper = NULL;
+
+ // coords at last neighboring
+
+ maxhold = 0;
+ xhold = NULL;
+ lastcall = -1;
+ last_setup_bins = -1;
+
+ // pair exclusion list info
+
+ includegroup = 0;
+
+ nex_type = maxex_type = 0;
+ ex1_type = ex2_type = NULL;
+ ex_type = NULL;
+
+ nex_group = maxex_group = 0;
+ ex1_group = ex2_group = ex1_bit = ex2_bit = NULL;
+
+ nex_mol = maxex_mol = 0;
+ ex_mol_group = ex_mol_bit = NULL;
- maxbond = 0;
- bondlist = NULL;
- maxangle = 0;
- anglelist = NULL;
- maxdihedral = 0;
- dihedrallist = NULL;
- maximproper = 0;
- improperlist = NULL;
+ // Kokkos setting
copymode = 0;
}
@@ -174,10 +184,41 @@ Neighbor::~Neighbor()
delete [] cuttypesq;
delete [] fixchecklist;
- memory->destroy(xhold);
+ for (int i = 0; i < nlist; i++) delete lists[i];
+ for (int i = 0; i < nbin; i++) delete neigh_bin[i];
+ for (int i = 0; i < nstencil; i++) delete neigh_stencil[i];
+ for (int i = 0; i < nlist; i++) delete neigh_pair[i];
+ delete [] lists;
+ delete [] neigh_bin;
+ delete [] neigh_stencil;
+ delete [] neigh_pair;
+
+ delete [] slist;
+ delete [] plist;
+
+ for (int i = 0; i < nrequest; i++) delete requests[i];
+ memory->sfree(requests);
+ for (int i = 0; i < old_nrequest; i++) delete old_requests[i];
+ memory->sfree(old_requests);
+
+ delete [] zeroes;
- memory->destroy(binhead);
- memory->destroy(bins);
+ delete [] binclass;
+ delete [] binnames;
+ delete [] binmasks;
+ delete [] stencilclass;
+ delete [] stencilnames;
+ delete [] stencilmasks;
+ delete [] pairclass;
+ delete [] pairnames;
+ delete [] pairmasks;
+
+ delete neigh_bond;
+ delete neigh_angle;
+ delete neigh_dihedral;
+ delete neigh_improper;
+
+ memory->destroy(xhold);
memory->destroy(ex1_type);
memory->destroy(ex2_type);
@@ -190,33 +231,13 @@ Neighbor::~Neighbor()
memory->destroy(ex_mol_group);
delete [] ex_mol_bit;
-
- for (int i = 0; i < nlist; i++) delete lists[i];
- delete [] lists;
- delete [] pair_build;
- delete [] stencil_create;
- delete [] blist;
- delete [] glist;
- delete [] slist;
-
- for (int i = 0; i < nrequest; i++) delete requests[i];
- memory->sfree(requests);
- for (int i = 0; i < old_nrequest; i++) delete old_requests[i];
- memory->sfree(old_requests);
-
- delete [] zeroes;
-
- memory->destroy(bondlist);
- memory->destroy(anglelist);
- memory->destroy(dihedrallist);
- memory->destroy(improperlist);
}
/* ---------------------------------------------------------------------- */
void Neighbor::init()
{
- int i,j,m,n;
+ int i,j,n;
ncalls = ndanger = 0;
dimension = domain->dimension;
@@ -234,7 +255,7 @@ void Neighbor::init()
// ------------------------------------------------------------------
// settings
- // bbox lo/hi = bounding box of entire domain, stored by Domain
+ // bbox lo/hi ptrs = bounding box of entire domain, stored by Domain
if (triclinic == 0) {
bboxlo = domain->boxlo;
@@ -293,7 +314,23 @@ void Neighbor::init()
}
cutneighmaxsq = cutneighmax * cutneighmax;
- // check other classes that can induce reneighboring in decide()
+ // rRESPA cutoffs
+
+ int respa = 0;
+ if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
+ if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
+ if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
+ }
+
+ if (respa) {
+ double *cut_respa = ((Respa *) update->integrate)->cutoff;
+ cut_inner_sq = (cut_respa[1] + skin) * (cut_respa[1] + skin);
+ cut_middle_sq = (cut_respa[3] + skin) * (cut_respa[3] + skin);
+ cut_middle_inside_sq = (cut_respa[0] - skin) * (cut_respa[0] - skin);
+ if (cut_respa[0]-skin < 0) cut_middle_inside_sq = 0.0;
+ }
+
+ // fixchecklist = other classes that can induce reneighboring in decide()
restart_check = 0;
if (output->restart_flag) restart_check = 1;
@@ -347,26 +384,10 @@ void Neighbor::init()
if (special_flag[2] == 2) maxwt = 3;
if (special_flag[3] == 2) maxwt = 4;
- // rRESPA cutoffs
-
- int respa = 0;
- if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
- if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
- if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
- }
-
- if (respa) {
- double *cut_respa = ((Respa *) update->integrate)->cutoff;
- cut_inner_sq = (cut_respa[1] + skin) * (cut_respa[1] + skin);
- cut_middle_sq = (cut_respa[3] + skin) * (cut_respa[3] + skin);
- cut_middle_inside_sq = (cut_respa[0] - skin) * (cut_respa[0] - skin);
- if (cut_respa[0]-skin < 0) cut_middle_inside_sq = 0.0;
- }
-
// ------------------------------------------------------------------
- // xhold, bins, exclusion lists
+ // xhold array
- // free xhold and bins if not needed for this run
+ // free if not needed for this run
if (dist_check == 0) {
memory->destroy(xhold);
@@ -374,15 +395,7 @@ void Neighbor::init()
xhold = NULL;
}
- if (style == NSQ) {
- memory->destroy(bins);
- memory->destroy(binhead);
- maxbin = maxhead = 0;
- binhead = NULL;
- bins = NULL;
- }
-
- // 1st time allocation of xhold and bins
+ // first time allocation
if (dist_check) {
if (maxhold == 0) {
@@ -391,14 +404,10 @@ void Neighbor::init()
}
}
- if (style != NSQ) {
- if (maxbin == 0) {
- maxbin = atom->nmax;
- memory->create(bins,maxbin,"bins");
- }
- }
+ // ------------------------------------------------------------------
+ // exclusion lists
- // exclusion lists for type, group, molecule settings from neigh_modify
+ // depend on type, group, molecule settings from neigh_modify
// warn if exclusions used with KSpace solver
n = atom->ntypes;
@@ -460,18 +469,132 @@ void Neighbor::init()
"may give inconsistent Coulombic energies");
// ------------------------------------------------------------------
- // pairwise lists
+ // create pairwise lists
+ // one-time call to init_styles() to scan style files and setup
+ // init_pair() creates auxiliary classes: NBin, NStencil, NPair
+
+ if (firsttime) init_styles();
+ firsttime = 0;
+
+ init_pair();
+
+ // invoke copy_neighbor_info() in Bin,Stencil,Pair classes
+ // copied once per run in case any cutoff, exclusion, special info changed
+
+ for (i = 0; i < nbin; i++) neigh_bin[i]->copy_neighbor_info();
+ for (i = 0; i < nstencil; i++) neigh_stencil[i]->copy_neighbor_info();
+ for (i = 0; i < nlist; i++)
+ if (neigh_pair[i]) neigh_pair[i]->copy_neighbor_info();
+
+ if (!same && comm->me == 0) print_pairwise_info();
+ requests_new2old();
+
+ // ------------------------------------------------------------------
+ // create topology lists
+ // instantiated topo styles can change from run to run
+
+ init_topology();
+}
+
+/* ----------------------------------------------------------------------
+ create and initialize lists of Nbin, Nstencil, NPair classes
+ lists have info on all classes in 3 style*.h files
+ cannot do this in constructor, b/c too early to instantiate classes
+------------------------------------------------------------------------- */
+
+void Neighbor::init_styles()
+{
+ // extract info from NBin classes listed in style_nbin.h
+
+ nbclass = 0;
+
+#define NBIN_CLASS
+#define NBinStyle(key,Class,bitmasks) nbclass++;
+#include "style_nbin.h"
+#undef NBinStyle
+#undef NBIN_CLASS
+
+ binclass = new BinCreator[nbclass];
+ binnames = new char*[nbclass];
+ binmasks = new int[nbclass];
+ nbclass = 0;
+
+#define NBIN_CLASS
+#define NBinStyle(key,Class,bitmasks) \
+ binnames[nbclass] = (char *) #key; \
+ binclass[nbclass] = &bin_creator<Class>; \
+ binmasks[nbclass++] = bitmasks;
+#include "style_nbin.h"
+#undef NBinStyle
+#undef NBIN_CLASS
+
+ // extract info from NStencil classes listed in style_nstencil.h
+
+ nsclass = 0;
+
+#define NSTENCIL_CLASS
+#define NStencilStyle(key,Class,bitmasks) nsclass++;
+#include "style_nstencil.h"
+#undef NStencilStyle
+#undef NSTENCIL_CLASS
+
+ stencilclass = new StencilCreator[nsclass];
+ stencilnames = new char*[nsclass];
+ stencilmasks = new int[nsclass];
+ nsclass = 0;
+
+#define NSTENCIL_CLASS
+#define NStencilStyle(key,Class,bitmasks) \
+ stencilnames[nsclass] = (char *) #key; \
+ stencilclass[nsclass] = &stencil_creator<Class>; \
+ stencilmasks[nsclass++] = bitmasks;
+#include "style_nstencil.h"
+#undef NStencilStyle
+#undef NSTENCIL_CLASS
+
+ // extract info from NPair classes listed in style_npair.h
+
+ npclass = 0;
+
+#define NPAIR_CLASS
+#define NPairStyle(key,Class,bitmasks) npclass++;
+#include "style_npair.h"
+#undef NPairStyle
+#undef NPAIR_CLASS
+
+ pairclass = new PairCreator[npclass];
+ pairnames = new char*[npclass];
+ pairmasks = new int[npclass];
+ npclass = 0;
+
+#define NPAIR_CLASS
+#define NPairStyle(key,Class,bitmasks) \
+ pairnames[npclass] = (char *) #key; \
+ pairclass[npclass] = &pair_creator<Class>; \
+ pairmasks[npclass++] = bitmasks;
+#include "style_npair.h"
+#undef NPairStyle
+#undef NPAIR_CLASS
+}
+
+/* ----------------------------------------------------------------------
+ create and initialize NPair classes
+------------------------------------------------------------------------- */
+
+void Neighbor::init_pair()
+{
+ int i,j,k,m;
// test if pairwise lists need to be re-created
// no need to re-create if:
// neigh style, triclinic, pgsize, oneatom have not changed
// current requests = old requests
// first archive request params for current requests
- // before Neighbor possibly changes them below
+ // before possibly changing them below
for (i = 0; i < nrequest; i++) requests[i]->archive();
- int same = 1;
+ same = 1;
if (style != old_style) same = 0;
if (triclinic != old_triclinic) same = 0;
if (pgsize != old_pgsize) same = 0;
@@ -485,438 +608,346 @@ void Neighbor::init()
if (comm->me == 0) printf("SAME flag %d\n",same);
#endif
- // if old and new are not the same, create new pairwise lists
-
- if (!same) {
-
- // delete old lists and create new ones
-
- for (i = 0; i < nlist; i++) delete lists[i];
- delete [] lists;
- delete [] pair_build;
- delete [] stencil_create;
-
- if (lmp->kokkos) nlist = init_lists_kokkos();
- else nlist = nrequest;
-
- lists = new NeighList*[nrequest];
- pair_build = new PairPtr[nrequest];
- stencil_create = new StencilPtr[nrequest];
+ if (same) return;
+
+ // delete old lists and create new ones
- // initialize to NULL since some may be Kokkos lists
+ for (i = 0; i < nlist; i++) delete lists[i];
+ for (i = 0; i < nbin; i++) delete neigh_bin[i];
+ for (i = 0; i < nstencil; i++) delete neigh_stencil[i];
+ for (i = 0; i < nlist; i++) delete neigh_pair[i];
+ delete [] lists;
+ delete [] neigh_bin;
+ delete [] neigh_stencil;
+ delete [] neigh_pair;
- for (i = 0; i < nrequest; i++) {
+ if (lmp->kokkos) nlist = init_lists_kokkos();
+ else nlist = nrequest;
+
+ lists = new NeighList*[nrequest];
+ neigh_bin = new NBin*[nrequest];
+ neigh_stencil = new NStencil*[nrequest];
+ neigh_pair = new NPair*[nrequest];
+
+ // create individual lists, one per request
+ // pass list ptr back to requestor (except for Command class)
+ // wait to allocate initial pages until copy lists are detected
+
+ for (i = 0; i < nrequest; i++) {
+ if (requests[i]->kokkos_host || requests[i]->kokkos_device) {
lists[i] = NULL;
- pair_build[i] = NULL;
- stencil_create[i] = NULL;
+ continue;
}
-
- // create individual lists, one per request
- // pass list ptr back to requestor (except for Command class)
- // wait to allocate initial pages until copy lists are detected
-
- for (i = 0; i < nrequest; i++) {
- if (requests[i]->kokkos_host || requests[i]->kokkos_device) continue;
- lists[i] = new NeighList(lmp);
- lists[i]->index = i;
-
- if (requests[i]->pair) {
- Pair *pair = (Pair *) requests[i]->requestor;
- pair->init_list(requests[i]->id,lists[i]);
- } else if (requests[i]->fix) {
- Fix *fix = (Fix *) requests[i]->requestor;
- fix->init_list(requests[i]->id,lists[i]);
- } else if (requests[i]->compute) {
- Compute *compute = (Compute *) requests[i]->requestor;
- compute->init_list(requests[i]->id,lists[i]);
- }
+ lists[i] = new NeighList(lmp);
+ lists[i]->index = i;
+
+ if (requests[i]->pair) {
+ Pair *pair = (Pair *) requests[i]->requestor;
+ pair->init_list(requests[i]->id,lists[i]);
+ } else if (requests[i]->fix) {
+ Fix *fix = (Fix *) requests[i]->requestor;
+ fix->init_list(requests[i]->id,lists[i]);
+ } else if (requests[i]->compute) {
+ Compute *compute = (Compute *) requests[i]->requestor;
+ compute->init_list(requests[i]->id,lists[i]);
}
+ }
- // detect lists that are connected to other lists
- // if-then-else sequence and processed flag is important
- // since don't want to re-process skip or copy lists further down
-
- int processed;
-
- for (i = 0; i < nrequest; i++) {
- if (!lists[i]) continue;
- processed = 0;
-
- // copy: point this list at request->otherlist, could be a skip list
-
- if (requests[i]->copy) {
- lists[i]->listcopy = lists[requests[i]->otherlist];
- processed = 1;
-
- // skip: point this list at request->otherlist,
- // copy skip info from request
- // skip list still needs to have granhistory or respa info added below
-
- } else if (requests[i]->skip) {
- lists[i]->listskip = lists[requests[i]->otherlist];
- lists[i]->copy_skip_info(requests[i]->iskip,requests[i]->ijskip);
- processed = 1;
-
- // half_from_full: point this list at full list that comes right before
- // will only be case if pair style requested one after other
-
- } else if (requests[i]->half_from_full) {
- lists[i]->listfull = lists[i-1];
- processed = 1;
- }
-
- // granhistory: set preceeding list's listgranhistory to this list
- // also set FH ptr in preceeding list to FSH class created by pair
-
- if (requests[i]->granhistory) {
- lists[i-1]->listgranhistory = lists[i];
- lists[i-1]->fix_history = requests[i]->fix_history;
- processed = 1;
+ // morph requests via A,B,C rules
+ // this is to avoid duplicate or inefficient builds
+ // update both request and list when morph
- // respaouter: point this list at preceeding 1/2 inner/middle lists
+ // (A) rule:
+ // invoke post_constructor() for all lists
+ // processes copy,skip,half_from_full,granhistory,respaouter lists
+ // error checks and resets internal ptrs to other lists that now exist
- } else if (requests[i]->respaouter) {
- if (requests[i-1]->respainner) {
- lists[i]->respamiddle = 0;
- lists[i]->listinner = lists[i-1];
- } else {
- lists[i]->respamiddle = 1;
- lists[i]->listmiddle = lists[i-1];
- lists[i]->listinner = lists[i-2];
- }
- processed = 1;
+ for (i = 0; i < nrequest; i++) {
+ if (!lists[i]) continue;
+ lists[i]->post_constructor(requests[i]);
+ }
+
+ // (B) rule:
+ // if request = pair, half, newton != 2
+ // and full perpetual non-skip/copy list exists,
+ // then morph to half_from_full of matching parent list
+ // NOTE: should be OK if parent is skip list?
+ // see build method comments
+ // parent can be pair or fix, so long as perpetual fix
+ // NOTE: could remove newton != 2 restriction if added
+ // half_from_full_newtoff_ghost NPair class
+ // this would require full list having ghost info
+ // would be useful when reax/c used in hybrid mode, e.g. with airebo
+
+ for (i = 0; i < nrequest; i++) {
+ if (lists[i] == NULL) continue; // Kokkos
+ if (requests[i]->pair && requests[i]->half && requests[i]->newton != 2) {
+ for (j = 0; j < nrequest; j++) {
+ if (lists[j] == NULL) continue; // Kokkos
+ if (requests[j]->full && requests[j]->occasional == 0 &&
+ !requests[j]->skip && !requests[j]->copy) break;
}
-
- if (processed) continue;
-
- // pair and half and newton != 2:
- // if there is a full non-occasional non-skip list
- // change this list to half_from_full and point at the full list
- // parent could be copy list or pair or fix
- // could remove newton != 2 check if added half_from_full_no_newton_ghost
- // option in neigh_derive.cpp and below in choose_build()
- // this would require full list had ghost info
- // would be useful when reax/c used in hybrid mode, e.g. with airebo
-
- if (requests[i]->pair && requests[i]->half && requests[i]->newton != 2) {
- for (j = 0; j < nrequest; j++) {
- if (!lists[j]) continue;
- if (requests[j]->full && requests[j]->occasional == 0 &&
- requests[j]->skip == 0) break;
- }
- if (j < nrequest) {
- requests[i]->half = 0;
- requests[i]->half_from_full = 1;
- lists[i]->listfull = lists[j];
- }
-
- // fix/compute requests:
- // whether request is occasional or not doesn't matter
- // if request = half and non-skip pair half/respaouter exists,
- // if request = full and non-skip pair full exists,
- // if request = half and non-skip pair full exists,
- // if no matches, do nothing
- // fix/compute list will be built independently as needed
- // ok if parent is itself a copy list
-
- } else if (requests[i]->fix || requests[i]->compute) {
- for (j = 0; j < nrequest; j++) {
- if (!lists[j]) continue;
- if (requests[i]->half && requests[j]->pair &&
- requests[j]->skip == 0 && requests[j]->half) break;
- if (requests[i]->full && requests[j]->pair &&
- requests[j]->skip == 0 && requests[j]->full) break;
- if (requests[i]->gran && requests[j]->pair &&
- requests[j]->skip == 0 && requests[j]->gran) break;
- if (requests[i]->half && requests[j]->pair &&
- requests[j]->skip == 0 && requests[j]->respaouter) break;
- }
- if (j < nrequest) {
- requests[i]->copy = 1;
- requests[i]->otherlist = j;
- lists[i]->listcopy = lists[j];
- } else {
- for (j = 0; j < nrequest; j++) {
- if (!lists[j]) continue;
- if (requests[i]->half && requests[j]->pair &&
- requests[j]->skip == 0 && requests[j]->full) break;
- }
- if (j < nrequest) {
- requests[i]->half = 0;
- requests[i]->half_from_full = 1;
- lists[i]->listfull = lists[j];
- }
- }
+ if (j < nrequest) {
+ requests[i]->half = 0;
+ requests[i]->half_from_full = 1;
+ lists[i]->listfull = lists[j];
}
}
-
- // allocate initial pages for each list, except if listcopy set
- // allocate dnum vector of zeroes if set
-
- int dnummax = 0;
- for (i = 0; i < nrequest; i++) {
- if (!lists[i]) continue;
- if (!lists[i]->listcopy) {
- lists[i]->setup_pages(pgsize,oneatom,requests[i]->dnum);
- dnummax = MAX(dnummax,requests[i]->dnum);
- }
+ }
+
+ // (C) rule:
+ // for fix/compute requests, occasional or not does not matter
+ // 1st check:
+ // if request = half and non-skip/copy pair half/respaouter request exists,
+ // or if request = full and non-skip/copy pair full request exists,
+ // or if request = gran and non-skip/copy pair gran request exists,
+ // then morph to copy of the matching parent list
+ // 2nd check: only if no match to 1st check
+ // if request = half and non-skip/copy pair full request exists,
+ // then morph to half_from_full of the matching parent list
+ // for 1st or 2nd check, parent can be copy list or pair or fix
+
+ for (i = 0; i < nrequest; i++) {
+ if (lists[i] == NULL) continue; // Kokkos
+ if (!requests[i]->fix && !requests[i]->compute) continue;
+ for (j = 0; j < nrequest; j++) {
+ if (lists[j] == NULL) continue; // Kokkos
+ if (requests[i]->half && requests[j]->pair &&
+ !requests[j]->skip && requests[j]->half && !requests[j]->copy)
+ break;
+ if (requests[i]->half && requests[j]->pair &&
+ !requests[j]->skip && requests[j]->respaouter && !requests[j]->copy)
+ break;
+ if (requests[i]->full && requests[j]->pair &&
+ !requests[j]->skip && requests[j]->full && !requests[j]->copy)
+ break;
+ if (requests[i]->gran && requests[j]->pair &&
+ !requests[j]->skip && requests[j]->gran && !requests[j]->copy)
+ break;
}
-
- if (dnummax) {
- delete [] zeroes;
- zeroes = new double[dnummax];
- for (i = 0; i < dnummax; i++) zeroes[i] = 0.0;
+ if (j < nrequest) {
+ requests[i]->copy = 1;
+ requests[i]->otherlist = j;
+ lists[i]->copy = 1;
+ lists[i]->listcopy = lists[j];
+ continue;
}
-
- // set ptrs to pair_build and stencil_create functions for each list
- // ptrs set to NULL if not set explicitly
-
- for (i = 0; i < nrequest; i++) {
- choose_build(i,requests[i]);
- if (style != NSQ) choose_stencil(i,requests[i]);
- else stencil_create[i] = NULL;
+ for (j = 0; j < nrequest; j++) {
+ if (lists[j] == NULL) continue; // Kokkos
+ if (requests[i]->half && requests[j]->pair &&
+ !requests[j]->skip && requests[j]->full && !requests[j]->copy)
+ break;
}
-
- // set each list's build/grow/stencil/ghost flags based on neigh request
- // buildflag = 1 if its pair_build() invoked every reneighbor
- // growflag = 1 if it stores atom-based arrays and pages
- // stencilflag = 1 if it stores stencil arrays
- // ghostflag = 1 if it stores neighbors of ghosts
- // anyghostlist = 1 if any non-occasional list stores neighbors of ghosts
-
- anyghostlist = 0;
- int anybuild = 0;
-
- for (i = 0; i < nrequest; i++) {
- if (lists[i]) {
- lists[i]->buildflag = 1;
- if (pair_build[i] == NULL) lists[i]->buildflag = 0;
- if (requests[i]->occasional) lists[i]->buildflag = 0;
- if (lists[i]->buildflag) anybuild = 1;
-
- lists[i]->growflag = 1;
- if (requests[i]->copy) lists[i]->growflag = 0;
-
- lists[i]->stencilflag = 1;
- if (style == NSQ) lists[i]->stencilflag = 0;
- if (stencil_create[i] == NULL) lists[i]->stencilflag = 0;
-
- lists[i]->ghostflag = 0;
- if (requests[i]->ghost) lists[i]->ghostflag = 1;
- if (requests[i]->ghost && !requests[i]->occasional) anyghostlist = 1;
-
- lists[i]->ssaflag = 0;
- if (requests[i]->ssa) lists[i]->ssaflag = 1;
- } else init_list_flags1_kokkos(i);
+ if (j < nrequest) {
+ requests[i]->half = 0;
+ requests[i]->half_from_full = 1;
+ lists[i]->listfull = lists[j];
}
+ }
+
+ // assign Bin,Stencil,Pair style to each list
+
+ int flag;
+ for (i = 0; i < nrequest; i++) {
+ flag = choose_bin(requests[i]);
+ lists[i]->bin_method = flag;
+ if (flag < 0)
+ error->all(FLERR,"Requested neighbor bin option does not exist");
+
+ flag = choose_stencil(requests[i]);
+ lists[i]->stencil_method = flag;
+ if (flag < 0)
+ error->all(FLERR,"Requested neighbor stencil method does not exist");
+
+ flag = choose_pair(requests[i]);
+ lists[i]->pair_method = flag;
+ if (flag < 0)
+ error->all(FLERR,"Requested neighbor pair method does not exist");
+ }
- // no request has the buildflag set, so set it for the first request only
- // this insure binning is done for any occasional neighbor lists
+ // instantiate unique Bin,Stencil classes in neigh_bin & neigh_stencil vecs
+ // instantiate one Pair class per list in neigh_pair vec
+
+ nbin = 0;
+ for (i = 0; i < nrequest; i++) {
+ flag = lists[i]->bin_method;
+ if (flag == 0) continue;
+ for (j = 0; j < nbin; j++)
+ if (neigh_bin[j]->istyle == flag) break;
+ if (j < nbin) continue;
+ BinCreator bin_creator = binclass[flag-1];
+ neigh_bin[nbin] = bin_creator(lmp);
+ neigh_bin[nbin]->istyle = flag;
+ nbin++;
+ }
- if (!anybuild) {
- for (i = 0; i < nrequest; i++) {
- if (lists[i]) {
- lists[i]->buildflag = 1;
- break;
- }
+ nstencil = 0;
+ for (i = 0; i < nrequest; i++) {
+ flag = lists[i]->stencil_method;
+ if (flag == 0) continue;
+ for (j = 0; j < nstencil; j++)
+ if (neigh_stencil[j]->istyle == flag) break;
+ if (j < nstencil) continue;
+ StencilCreator stencil_creator = stencilclass[flag-1];
+ neigh_stencil[nstencil] = stencil_creator(lmp);
+ neigh_stencil[nstencil]->istyle = flag;
+ int bin_method = lists[i]->bin_method;
+ for (k = 0; k < nbin; k++) {
+ if (neigh_bin[k]->istyle == bin_method) {
+ neigh_stencil[nstencil]->nb = neigh_bin[k];
+ break;
}
}
+ if (k == nbin)
+ error->all(FLERR,"Could not assign bin method to neighbor stencil");
+ nstencil++;
+ }
-#ifdef NEIGH_LIST_DEBUG
- for (i = 0; i < nrequest; i++)
- if (comm->me == 0) printf("Build/stencil methods: %d: %p %p\n",
- i,pair_build[i],stencil_create[i]);
- for (i = 0; i < nrequest; i++) lists[i]->print_attributes();
-#endif
-
- // allocate atom arrays for neighbor lists that store them
-
- maxatom = atom->nmax;
- for (i = 0; i < nrequest; i++) {
- if (lists[i]) {
- if (lists[i]->growflag) lists[i]->grow(maxatom);
- } else init_list_grow_kokkos(i);
+ for (i = 0; i < nrequest; i++) {
+ flag = lists[i]->pair_method;
+ if (flag == 0) {
+ neigh_pair[i] = NULL;
+ continue;
}
+ PairCreator pair_creator = pairclass[flag-1];
+ neigh_pair[i] = pair_creator(lmp);
+ neigh_pair[i]->istyle = flag;
- // setup 3 vectors of pairwise neighbor lists
- // blist = lists whose pair_build() is invoked every reneighbor
- // glist = lists who store atom arrays which are used every reneighbor
- // slist = lists who store stencil arrays which are used every reneighbor
- // blist and glist vectors are used by neighbor::build()
- // slist vector is used by neighbor::setup_bins()
-
- nblist = nglist = nslist = 0;
- delete [] blist;
- delete [] glist;
- delete [] slist;
- blist = new int[nrequest];
- glist = new int[nrequest];
- slist = new int[nrequest];
-
- for (i = 0; i < nrequest; i++) {
- if (lists[i]) {
- if (lists[i]->buildflag) blist[nblist++] = i;
- if (lists[i]->growflag && requests[i]->occasional == 0)
- glist[nglist++] = i;
- if (lists[i]->stencilflag && requests[i]->occasional == 0)
- slist[nslist++] = i;
- } else init_list_flags2_kokkos(i);
+ int bin_method = lists[i]->bin_method;
+ if (bin_method == 0) neigh_pair[i]->nb = NULL;
+ else {
+ for (k = 0; k < nbin; k++) {
+ if (neigh_bin[k]->istyle == bin_method) {
+ neigh_pair[i]->nb = neigh_bin[k];
+ break;
+ }
+ }
+ if (k == nbin)
+ error->all(FLERR,"Could not assign bin method to neighbor pair");
}
-
- // no request had buildflag set, so we set it for the first request
- // we also need to set other occasional neighbor list properties
-
- if (!anybuild)
- for (i = 0; i < nrequest; i++)
- if (lists[i] && lists[i]->buildflag) {
- if (lists[i]->growflag) glist[nglist++] = i;
- if (lists[i]->stencilflag) slist[nslist++] = i;
+ int stencil_method = lists[i]->stencil_method;
+ if (stencil_method == 0) neigh_pair[i]->ns = NULL;
+ else {
+ for (k = 0; k < nstencil; k++) {
+ if (neigh_stencil[k]->istyle == stencil_method) {
+ neigh_pair[i]->ns = neigh_stencil[k];
+ break;
}
-
-#ifdef NEIGH_LIST_DEBUG
- print_lists_of_lists();
-#endif
-
- // reorder build vector if necessary
- // relevant for lists that copy/skip/half-full from parent
- // the derived list must appear in blist after the parent list
- // no occasional lists are in build vector
- // swap two lists within blist when dependency is mis-ordered
- // done when entire pass thru blist results in no swaps
-
- int done = 0;
- while (!done) {
- done = 1;
- for (i = 0; i < nblist; i++) {
- if (!lists[blist[i]]) continue;
- NeighList *ptr = NULL;
- if (lists[blist[i]]->listfull) ptr = lists[blist[i]]->listfull;
- if (lists[blist[i]]->listcopy) ptr = lists[blist[i]]->listcopy;
- if (lists[blist[i]]->listskip) ptr = lists[blist[i]]->listskip;
- if (ptr == NULL) continue;
- for (m = 0; m < nrequest; m++)
- if (ptr == lists[m]) break;
- for (j = 0; j < nblist; j++)
- if (m == blist[j]) break;
- if (j < i) continue;
- int tmp = blist[i];
- blist[i] = blist[j];
- blist[j] = tmp;
- done = 0;
- break;
}
+ if (k == nstencil)
+ error->all(FLERR,"Could not assign stencil method to neighbor pair");
}
+ }
-#ifdef NEIGH_LIST_DEBUG
- print_lists_of_lists();
-#endif
+ // allocate initial pages for each list, except if copy flag set
+ // allocate dnum vector of zeroes if set
+
+ int dnummax = 0;
+ for (i = 0; i < nlist; i++) {
+ if (lists[i] == NULL) continue; // Kokkos
+ if (lists[i]->copy) continue;
+ lists[i]->setup_pages(pgsize,oneatom);
+ dnummax = MAX(dnummax,lists[i]->dnum);
+ }
+
+ if (dnummax) {
+ delete [] zeroes;
+ zeroes = new double[dnummax];
+ for (i = 0; i < dnummax; i++) zeroes[i] = 0.0;
}
- // output neighbor list info, only first time or when info changes
-
- if (!same || every != old_every || delay != old_delay ||
- old_check != dist_check || old_cutoff != cutneighmax) {
- if (me == 0) {
- const double cutghost = MAX(cutneighmax,comm->cutghostuser);
-
- double binsize, bbox[3];
- bbox[0] = bboxhi[0]-bboxlo[0];
- bbox[1] = bboxhi[1]-bboxlo[1];
- bbox[2] = bboxhi[2]-bboxlo[2];
- if (binsizeflag) binsize = binsize_user;
- else if (style == BIN) binsize = 0.5*cutneighmax;
- else binsize = 0.5*cutneighmin;
- if (binsize == 0.0) binsize = bbox[0];
-
- if (logfile) {
- fprintf(logfile,"Neighbor list info ...\n");
- fprintf(logfile," %d neighbor list requests\n",nrequest);
- fprintf(logfile," update every %d steps, delay %d steps, check %s\n",
- every,delay,dist_check ? "yes" : "no");
- fprintf(logfile," max neighbors/atom: %d, page size: %d\n",
- oneatom, pgsize);
- fprintf(logfile," master list distance cutoff = %g\n",cutneighmax);
- fprintf(logfile," ghost atom cutoff = %g\n",cutghost);
- if (style != NSQ)
- fprintf(logfile," binsize = %g -> bins = %g %g %g\n",binsize,
- ceil(bbox[0]/binsize), ceil(bbox[1]/binsize),
- ceil(bbox[2]/binsize));
- }
- if (screen) {
- fprintf(screen,"Neighbor list info ...\n");
- fprintf(screen," %d neighbor list requests\n",nrequest);
- fprintf(screen," update every %d steps, delay %d steps, check %s\n",
- every,delay,dist_check ? "yes" : "no");
- fprintf(screen," max neighbors/atom: %d, page size: %d\n",
- oneatom, pgsize);
- fprintf(screen," master list distance cutoff = %g\n",cutneighmax);
- fprintf(screen," ghost atom cutoff = %g\n",cutghost);
- if (style != NSQ)
- fprintf(screen," binsize = %g, bins = %g %g %g\n",binsize,
- ceil(bbox[0]/binsize), ceil(bbox[1]/binsize),
- ceil(bbox[2]/binsize));
- }
+ // first-time allocation of per-atom data for lists that are built and store
+ // lists that are not built: granhistory, respa inner/middle (no neigh_pair)
+ // lists that do not store: copy
+ // use atom->nmax for both grow() args
+ // i.e. grow first time to expanded size to avoid future reallocs
+ // also Kokkos list initialization
+
+ int maxatom = atom->nmax;
+ for (i = 0; i < nlist; i++) {
+ if (lists[i]) {
+ if (neigh_pair[i] && !lists[i]->copy) lists[i]->grow(maxatom,maxatom);
+ } else {
+ init_list_flags1_kokkos(i);
+ init_list_grow_kokkos(i);
}
}
- // mark all current requests as processed
- // delete old requests
- // copy current requests and style to old for next run
-
- for (i = 0; i < nrequest; i++) requests[i]->unprocessed = 0;
- for (i = 0; i < old_nrequest; i++) delete old_requests[i];
- memory->sfree(old_requests);
-
- old_nrequest = nrequest;
- old_requests = requests;
- nrequest = maxrequest = 0;
- requests = NULL;
- old_style = style;
- old_triclinic = triclinic;
- old_pgsize = pgsize;
- old_oneatom = oneatom;
- old_every = every;
- old_delay = delay;
- old_check = dist_check;
- old_cutoff = cutneighmax;
-
- // ------------------------------------------------------------------
- // topology lists
-
- // 1st time allocation of topology lists
-
- if (lmp->kokkos) {
- init_topology_kokkos();
- return;
+ // plist = indices of perpetual NPair classes
+ // perpetual = non-occasional, re-built at every reneighboring
+ // slist = indices of perpetual NStencil classes
+ // perpetual = used by any perpetual NPair class
+
+ delete [] slist;
+ delete [] plist;
+ nstencil_perpetual = npair_perpetual = 0;
+ slist = new int[nstencil];
+ plist = new int[nlist];
+
+ for (i = 0; i < nlist; i++) {
+ if (lists[i]) {
+ if (lists[i]->occasional == 0 && lists[i]->pair_method)
+ plist[npair_perpetual++] = i;
+ } else init_list_flags2_kokkos(i);
}
-
- if (atom->molecular && atom->nbonds && maxbond == 0) {
- if (nprocs == 1) maxbond = atom->nbonds;
- else maxbond = static_cast<int> (LB_FACTOR * atom->nbonds / nprocs);
- memory->create(bondlist,maxbond,3,"neigh:bondlist");
+
+ for (i = 0; i < nstencil; i++) {
+ flag = 0;
+ for (j = 0; j < npair_perpetual; j++)
+ if (lists[plist[j]]->stencil_method == neigh_stencil[i]->istyle) flag = 1;
+ if (flag) slist[nstencil_perpetual++] = i;
}
- if (atom->molecular && atom->nangles && maxangle == 0) {
- if (nprocs == 1) maxangle = atom->nangles;
- else maxangle = static_cast<int> (LB_FACTOR * atom->nangles / nprocs);
- memory->create(anglelist,maxangle,4,"neigh:anglelist");
+ // reorder plist vector if necessary
+ // relevant for lists that copy/skip/half-full from parent
+ // the child index must appear in plist after the parent index
+ // swap two indices within plist when dependency is mis-ordered
+ // done when entire pass thru plist results in no swaps
+
+ NeighList *ptr;
+
+ int done = 0;
+ while (!done) {
+ done = 1;
+ for (i = 0; i < npair_perpetual; i++) {
+ if (!lists[plist[i]]) continue; // Kokkos check
+ ptr = NULL;
+ if (lists[plist[i]]->listcopy) ptr = lists[plist[i]]->listcopy;
+ if (lists[plist[i]]->listskip) ptr = lists[plist[i]]->listskip;
+ if (lists[plist[i]]->listfull) ptr = lists[plist[i]]->listfull;
+ if (ptr == NULL) continue;
+ for (m = 0; m < nrequest; m++)
+ if (ptr == lists[m]) break;
+ for (j = 0; j < npair_perpetual; j++)
+ if (m == plist[j]) break;
+ if (j < i) continue;
+ int tmp = plist[i]; // swap I,J indices
+ plist[i] = plist[j];
+ plist[j] = tmp;
+ done = 0;
+ break;
+ }
}
- if (atom->molecular && atom->ndihedrals && maxdihedral == 0) {
- if (nprocs == 1) maxdihedral = atom->ndihedrals;
- else maxdihedral = static_cast<int>
- (LB_FACTOR * atom->ndihedrals / nprocs);
- memory->create(dihedrallist,maxdihedral,5,"neigh:dihedrallist");
- }
+ // debug output
- if (atom->molecular && atom->nimpropers && maximproper == 0) {
- if (nprocs == 1) maximproper = atom->nimpropers;
- else maximproper = static_cast<int>
- (LB_FACTOR * atom->nimpropers / nprocs);
- memory->create(improperlist,maximproper,5,"neigh:improperlist");
- }
+#ifdef NEIGH_LIST_DEBUG
+ for (i = 0; i < nrequest; i++) lists[i]->print_attributes();
+#endif
+}
+
+/* ----------------------------------------------------------------------
+ create and initialize NTopo classes
+------------------------------------------------------------------------- */
+
+void Neighbor::init_topology()
+{
+ int i,m;
- // set flags that determine which topology neighboring routines to use
+ if (!atom->molecular) return;
+
+ // set flags that determine which topology neighbor classes to use
+ // these settings could change from run to run, depending on fixes defined
// bonds,etc can only be broken for atom->molecular = 1, not 2
// SHAKE sets bonds and angles negative
// gcmc sets all bonds, angles, etc negative
@@ -971,502 +1002,560 @@ void Neighbor::init()
// sync on/off settings across all procs
- int on_or_off = bond_off;
- MPI_Allreduce(&on_or_off,&bond_off,1,MPI_INT,MPI_MAX,world);
- on_or_off = angle_off;
- MPI_Allreduce(&on_or_off,&angle_off,1,MPI_INT,MPI_MAX,world);
- on_or_off = dihedral_off;
- MPI_Allreduce(&on_or_off,&dihedral_off,1,MPI_INT,MPI_MAX,world);
- on_or_off = improper_off;
- MPI_Allreduce(&on_or_off,&improper_off,1,MPI_INT,MPI_MAX,world);
-
- // set ptrs to topology build functions
+ int onoff = bond_off;
+ MPI_Allreduce(&onoff,&bond_off,1,MPI_INT,MPI_MAX,world);
+ onoff = angle_off;
+ MPI_Allreduce(&onoff,&angle_off,1,MPI_INT,MPI_MAX,world);
+ onoff = dihedral_off;
+ MPI_Allreduce(&onoff,&dihedral_off,1,MPI_INT,MPI_MAX,world);
+ onoff = improper_off;
+ MPI_Allreduce(&onoff,&improper_off,1,MPI_INT,MPI_MAX,world);
+
+ // instantiate NTopo classes
+
+ if (atom->avec->bonds_allow) {
+ int old_bondwhich = bondwhich;
+ if (atom->molecular == 2) bondwhich = TEMPLATE;
+ else if (bond_off) bondwhich = PARTIAL;
+ else bondwhich = ALL;
+ if (!neigh_bond || bondwhich != old_bondwhich) {
+ delete neigh_bond;
+ if (bondwhich == ALL)
+ neigh_bond = new NTopoBondAll(lmp);
+ else if (bondwhich == PARTIAL)
+ neigh_bond = new NTopoBondPartial(lmp);
+ else if (bondwhich == TEMPLATE)
+ neigh_bond = new NTopoBondTemplate(lmp);
+ }
+ }
- if (atom->molecular == 2) bond_build = &Neighbor::bond_template;
- else if (bond_off) bond_build = &Neighbor::bond_partial;
- else bond_build = &Neighbor::bond_all;
+ if (atom->avec->angles_allow) {
+ int old_anglewhich = anglewhich;
+ if (atom->molecular == 2) anglewhich = TEMPLATE;
+ else if (angle_off) anglewhich = PARTIAL;
+ else anglewhich = ALL;
+ if (!neigh_angle || anglewhich != old_anglewhich) {
+ delete neigh_angle;
+ if (anglewhich == ALL)
+ neigh_angle = new NTopoAngleAll(lmp);
+ else if (anglewhich == PARTIAL)
+ neigh_angle = new NTopoAnglePartial(lmp);
+ else if (anglewhich == TEMPLATE)
+ neigh_angle = new NTopoAngleTemplate(lmp);
+ }
+ }
- if (atom->molecular == 2) angle_build = &Neighbor::angle_template;
- else if (angle_off) angle_build = &Neighbor::angle_partial;
- else angle_build = &Neighbor::angle_all;
+ if (atom->avec->dihedrals_allow) {
+ int old_dihedralwhich = dihedralwhich;
+ if (atom->molecular == 2) dihedralwhich = TEMPLATE;
+ else if (dihedral_off) dihedralwhich = PARTIAL;
+ else dihedralwhich = ALL;
+ if (!neigh_dihedral || dihedralwhich != old_dihedralwhich) {
+ delete neigh_dihedral;
+ if (dihedralwhich == ALL)
+ neigh_dihedral = new NTopoDihedralAll(lmp);
+ else if (dihedralwhich == PARTIAL)
+ neigh_dihedral = new NTopoDihedralPartial(lmp);
+ else if (dihedralwhich == TEMPLATE)
+ neigh_dihedral = new NTopoDihedralTemplate(lmp);
+ }
+ }
- if (atom->molecular == 2) dihedral_build = &Neighbor::dihedral_template;
- else if (dihedral_off) dihedral_build = &Neighbor::dihedral_partial;
- else dihedral_build = &Neighbor::dihedral_all;
+ if (atom->avec->impropers_allow) {
+ int old_improperwhich = improperwhich;
+ if (atom->molecular == 2) improperwhich = TEMPLATE;
+ else if (improper_off) improperwhich = PARTIAL;
+ else improperwhich = ALL;
+ if (!neigh_improper || improperwhich != old_improperwhich) {
+ delete neigh_improper;
+ if (improperwhich == ALL)
+ neigh_improper = new NTopoImproperAll(lmp);
+ else if (improperwhich == PARTIAL)
+ neigh_improper = new NTopoImproperPartial(lmp);
+ else if (improperwhich == TEMPLATE)
+ neigh_improper = new NTopoImproperTemplate(lmp);
+ }
+ }
+}
- if (atom->molecular == 2) improper_build = &Neighbor::improper_template;
- else if (improper_off) improper_build = &Neighbor::improper_partial;
- else improper_build = &Neighbor::improper_all;
+/* ----------------------------------------------------------------------
+ output summary of pairwise neighbor list info
+ only called by proc 0
+------------------------------------------------------------------------- */
- // set topology neighbor list counts to 0
- // in case all are turned off but potential is still defined
+void Neighbor::print_pairwise_info()
+{
+ int i,j,m;
+ char str[128];
+ const char *kind;
+ FILE *out;
+
+ const double cutghost = MAX(cutneighmax,comm->cutghostuser);
+
+ double binsize, bbox[3];
+ bbox[0] = bboxhi[0]-bboxlo[0];
+ bbox[1] = bboxhi[1]-bboxlo[1];
+ bbox[2] = bboxhi[2]-bboxlo[2];
+ if (binsizeflag) binsize = binsize_user;
+ else if (style == BIN) binsize = 0.5*cutneighmax;
+ else binsize = 0.5*cutneighmin;
+ if (binsize == 0.0) binsize = bbox[0];
+
+ int nperpetual = 0;
+ int noccasional = 0;
+ int nextra = 0;
+ for (i = 0; i < nlist; i++) {
+ if (lists[i]->pair_method == 0) nextra++;
+ else if (lists[i]->occasional) noccasional++;
+ else nperpetual++;
+ }
- nbondlist = nanglelist = ndihedrallist = nimproperlist = 0;
+ for (m = 0; m < 2; m++) {
+ if (m == 0) out = screen;
+ else out = logfile;
+
+ if (out) {
+ fprintf(out,"Neighbor list info ...\n");
+ fprintf(out," update every %d steps, delay %d steps, check %s\n",
+ every,delay,dist_check ? "yes" : "no");
+ fprintf(out," max neighbors/atom: %d, page size: %d\n",
+ oneatom, pgsize);
+ fprintf(out," master list distance cutoff = %g\n",cutneighmax);
+ fprintf(out," ghost atom cutoff = %g\n",cutghost);
+ if (style != NSQ)
+ fprintf(out," binsize = %g, bins = %g %g %g\n",binsize,
+ ceil(bbox[0]/binsize), ceil(bbox[1]/binsize),
+ ceil(bbox[2]/binsize));
+
+ fprintf(out," %d neighbor lists, "
+ "perpetual/occasional/extra = %d %d %d\n",
+ nlist,nperpetual,noccasional,nextra);
+
+ for (i = 0; i < nlist; i++) {
+ if (requests[i]->pair) {
+ char *pname = force->pair_match_ptr((Pair *) requests[i]->requestor);
+ sprintf(str," (%d) pair %s",i+1,pname);
+ } else if (requests[i]->fix) {
+ sprintf(str," (%d) fix %s",i+1,
+ ((Fix *) requests[i]->requestor)->style);
+ } else if (requests[i]->compute) {
+ sprintf(str," (%d) compute %s",i+1,
+ ((Compute *) requests[i]->requestor)->style);
+ } else {
+ sprintf(str," (%d) command %s",i+1,requests[i]->command_style);
+ }
+ fprintf(out,"%s\n",str);
+
+ if (requests[i]->half) kind = "half";
+ else if (requests[i]->full) kind = "full";
+ else if (requests[i]->gran) kind = "size";
+ else if (requests[i]->granhistory) kind = "size/history";
+ else if (requests[i]->respainner) kind = "respa/inner";
+ else if (requests[i]->respamiddle) kind = "respa/middle";
+ else if (requests[i]->respaouter) kind = "respa/outer";
+ else if (requests[i]->half_from_full) kind = "half/from/full";
+ else if (requests[i]->full_cluster) kind = "full/cluster"; // Kokkos
+ fprintf(out," kind: %s",kind);
+
+ if (requests[i]->occasional) fprintf(out,", occasional");
+ else fprintf(out,", perpetual");
+ if (requests[i]->ghost) fprintf(out,", ghost");
+ if (requests[i]->ssa) fprintf(out,", ssa");
+ if (requests[i]->omp) fprintf(out,", omp");
+ if (requests[i]->intel) fprintf(out,", intel");
+ if (requests[i]->copy)
+ fprintf(out,", copy from (%d)",requests[i]->otherlist+1);
+ if (requests[i]->skip)
+ fprintf(out,", skip from (%d)",requests[i]->otherlist+1);
+ if (requests[i]->off2on) fprintf(out,", off2on");
+ fprintf(out,"\n");
+
+ if (lists[i]->pair_method == 0) fprintf(out," pair build: none\n");
+ else fprintf(out," pair build: %s\n",
+ pairnames[lists[i]->pair_method-1]);
+
+ if (lists[i]->stencil_method == 0) fprintf(out," stencil: none\n");
+ else fprintf(out," stencil: %s\n",
+ stencilnames[lists[i]->stencil_method-1]);
+
+ if (lists[i]->bin_method == 0) fprintf(out," bin: none\n");
+ else fprintf(out," bin: %s\n",binnames[lists[i]->bin_method-1]);
+ }
+
+ /*
+ fprintf(out," %d stencil methods\n",nstencil);
+ for (i = 0; i < nstencil; i++)
+ fprintf(out," (%d) %s\n",
+ i+1,stencilnames[neigh_stencil[i]->istyle-1]);
+
+ fprintf(out," %d bin methods\n",nbin);
+ for (i = 0; i < nbin; i++)
+ fprintf(out," (%d) %s\n",i+1,binnames[neigh_bin[i]->istyle-1]);
+ */
+ }
+ }
}
+
+/* ----------------------------------------------------------------------
+ delete old NeighRequests
+ copy current requests and params to old for next run
+------------------------------------------------------------------------- */
-/* ---------------------------------------------------------------------- */
+void Neighbor::requests_new2old()
+{
+ for (int i = 0; i < old_nrequest; i++) delete old_requests[i];
+ memory->sfree(old_requests);
-int Neighbor::request(void *requestor, int instance)
+ old_nrequest = nrequest;
+ old_requests = requests;
+ nrequest = maxrequest = 0;
+ requests = NULL;
+ old_style = style;
+ old_triclinic = triclinic;
+ old_pgsize = pgsize;
+ old_oneatom = oneatom;
+}
+
+/* ----------------------------------------------------------------------
+ assign NBin class to a NeighList
+ use neigh request settings to build mask
+ match mask to list of masks of known Nbin classes
+ return index+1 of match in list of masks
+ return 0 for no binning
+ return -1 if no match
+------------------------------------------------------------------------- */
+
+int Neighbor::choose_bin(NeighRequest *rq)
{
- if (nrequest == maxrequest) {
- maxrequest += RQDELTA;
- requests = (NeighRequest **)
- memory->srealloc(requests,maxrequest*sizeof(NeighRequest *),
- "neighbor:requests");
+ // no binning needed
+
+ if (style == NSQ) return 0;
+ if (rq->skip || rq->copy || rq->half_from_full) return 0;
+ if (rq->granhistory) return 0;
+ if (rq->respainner || rq->respamiddle) return 0;
+
+ // flags for settings the request + system requires of NBin class
+ // ssaflag = no/yes ssa request
+ // intelflag = no/yes intel request
+
+ int ssaflag,intelflag;
+
+ ssaflag = intelflag = 0;
+
+ if (rq->ssa) ssaflag = NB_SSA;
+ if (rq->intel) intelflag = NB_INTEL;
+
+ // use flags to match exactly one of NBin class masks, bit by bit
+
+ int mask;
+
+ for (int i = 0; i < nbclass; i++) {
+ mask = binmasks[i];
+
+ if (ssaflag != (mask & NB_SSA)) continue;
+ if (intelflag != (mask & NB_INTEL)) continue;
+
+ return i+1;
}
- requests[nrequest] = new NeighRequest(lmp);
- requests[nrequest]->requestor = requestor;
- requests[nrequest]->requestor_instance = instance;
- nrequest++;
- return nrequest-1;
+ // error return if matched none
+
+ return -1;
}
/* ----------------------------------------------------------------------
- determine which pair_build function each neigh list needs
- based on settings of neigh request
- copy -> copy_from function
- skip -> granular function if gran, several options
- respa function if respaouter,
- skip_from function for everything else
- ssa -> special case for USER-DPD pair styles
- half_from_full, half, full, gran, respaouter ->
- choose by newton and rq->newton and triclinic settings
- style NSQ options = newton off, newton on
- style BIN options = newton off, newton on and not tri, newton on and tri
- stlye MULTI options = same options as BIN
- if none of these, ptr = NULL since pair_build is not invoked for this list
- use "else if" logic b/c skip,copy can be set in addition to half,full,etc
+ assign NStencil class to a NeighList
+ use neigh request settings to build mask
+ match mask to list of masks of known NStencil classes
+ return index+1 of match in list of masks
+ return 0 for no binning
+ return -1 if no match
------------------------------------------------------------------------- */
-void Neighbor::choose_build(int index, NeighRequest *rq)
+int Neighbor::choose_stencil(NeighRequest *rq)
{
- PairPtr pb = NULL;
-
- if (rq->omp == 0 && rq->intel == 0) {
-
- if (rq->copy) pb = &Neighbor::copy_from;
-
- else if (rq->skip) {
- if (rq->gran) {
- NeighRequest *otherrq = requests[rq->otherlist];
- if (otherrq->newton == 0) {
- pb = &Neighbor::skip_from_granular;
- } else if (otherrq->newton == 1) {
- error->all(FLERR,"Neighbor build method not supported");
- } else if (otherrq->newton == 2) {
- if (rq->granonesided == 0)
- pb = &Neighbor::skip_from_granular_off2on;
- else if (rq->granonesided == 1)
- pb = &Neighbor::skip_from_granular_off2on_onesided;
- }
- }
- else if (rq->respaouter) pb = &Neighbor::skip_from_respa;
- else pb = &Neighbor::skip_from;
-
- } else if (rq->ssa) {
- if (rq->half_from_full) pb = &Neighbor::half_from_full_newton_ssa;
- else pb = &Neighbor::half_bin_newton_ssa;
-
- } else if (rq->half_from_full) {
- if (rq->newton == 0) {
- if (newton_pair == 0) pb = &Neighbor::half_from_full_no_newton;
- else if (newton_pair == 1) pb = &Neighbor::half_from_full_newton;
- } else if (rq->newton == 1) {
- pb = &Neighbor::half_from_full_newton;
- } else if (rq->newton == 2) {
- pb = &Neighbor::half_from_full_no_newton;
- }
+ // no stencil creation needed
- } else if (rq->half) {
- if (style == NSQ) {
- if (rq->newton == 0) {
- if (newton_pair == 0) {
- if (rq->ghost == 0) pb = &Neighbor::half_nsq_no_newton;
- else if (includegroup)
- error->all(FLERR,"Neighbor include group not allowed "
- "with ghost neighbors");
- else pb = &Neighbor::half_nsq_no_newton_ghost;
- } else if (newton_pair == 1) pb = &Neighbor::half_nsq_newton;
- } else if (rq->newton == 1) {
- pb = &Neighbor::half_nsq_newton;
- } else if (rq->newton == 2) {
- if (rq->ghost == 0) pb = &Neighbor::half_nsq_no_newton;
- else if (includegroup)
- error->all(FLERR,"Neighbor include group not allowed "
- "with ghost neighbors");
- else pb = &Neighbor::half_nsq_no_newton_ghost;
- }
- } else if (style == BIN) {
- if (rq->newton == 0) {
- if (newton_pair == 0) {
- if (rq->ghost == 0) pb = &Neighbor::half_bin_no_newton;
- else if (includegroup)
- error->all(FLERR,"Neighbor include group not allowed "
- "with ghost neighbors");
- else pb = &Neighbor::half_bin_no_newton_ghost;
- } else if (triclinic == 0) {
- pb = &Neighbor::half_bin_newton;
- } else if (triclinic == 1)
- pb = &Neighbor::half_bin_newton_tri;
- } else if (rq->newton == 1) {
- if (triclinic == 0) pb = &Neighbor::half_bin_newton;
- else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri;
- } else if (rq->newton == 2) {
- if (rq->ghost == 0) pb = &Neighbor::half_bin_no_newton;
- else if (includegroup)
- error->all(FLERR,"Neighbor include group not allowed "
- "with ghost neighbors");
- else pb = &Neighbor::half_bin_no_newton_ghost;
- }
- } else if (style == MULTI) {
- if (rq->ghost == 1)
- error->all(FLERR,
- "Neighbor multi not yet enabled for ghost neighbors");
- if (rq->newton == 0) {
- if (newton_pair == 0) pb = &Neighbor::half_multi_no_newton;
- else if (triclinic == 0) pb = &Neighbor::half_multi_newton;
- else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri;
- } else if (rq->newton == 1) {
- if (triclinic == 0) pb = &Neighbor::half_multi_newton;
- else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri;
- } else if (rq->newton == 2) pb = &Neighbor::half_multi_no_newton;
- }
+ if (style == NSQ) return 0;
+ if (rq->skip || rq->copy || rq->half_from_full) return 0;
+ if (rq->granhistory) return 0;
+ if (rq->respainner || rq->respamiddle) return 0;
- } else if (rq->full) {
- if (style == NSQ) {
- if (rq->ghost == 0) pb = &Neighbor::full_nsq;
- else if (includegroup)
- error->all(FLERR,
- "Neighbor include group not allowed with ghost neighbors");
- else pb = &Neighbor::full_nsq_ghost;
- } else if (style == BIN) {
- if (rq->ghost == 0) pb = &Neighbor::full_bin;
- else if (includegroup)
- error->all(FLERR,
- "Neighbor include group not allowed with ghost neighbors");
- else pb = &Neighbor::full_bin_ghost;
- } else if (style == MULTI) {
- if (rq->ghost == 1)
- error->all(FLERR,
- "Neighbor multi not yet enabled for ghost neighbors");
- pb = &Neighbor::full_multi;
- }
+ // flags for settings the request + system requires of NStencil class
+ // halfflag = half request (gran and respa are also half lists)
+ // fullflag = full request
+ // ghostflag = no/yes ghost request
+ // ssaflag = no/yes ssa request
+ // dimension = 2d/3d
+ // newtflag = newton off/on request
+ // triclinic = orthgonal/triclinic box
- } else if (rq->gran) {
- if (rq->newton == 0) {
- if (style == NSQ) {
- if (newton_pair == 0) pb = &Neighbor::granular_nsq_no_newton;
- else if (newton_pair == 1) {
- if (rq->granonesided == 0) pb = &Neighbor::granular_nsq_newton;
- else pb = &Neighbor::granular_nsq_newton_onesided;
- }
- } else if (style == BIN) {
- if (newton_pair == 0) pb = &Neighbor::granular_bin_no_newton;
- else if (newton_pair == 1) {
- if (triclinic == 0) {
- if (rq->granonesided == 0) pb = &Neighbor::granular_bin_newton;
- else pb = &Neighbor::granular_bin_newton_onesided;
- } else if (triclinic == 1) {
- if (rq->granonesided == 0)
- pb = &Neighbor::granular_bin_newton_tri;
- else error->all(FLERR,"Neighbor build method not supported");
- }
- }
- } else if (style == MULTI)
- error->all(FLERR,"Neighbor multi not yet enabled for granular");
- } else if (rq->newton == 1) {
- error->all(FLERR,"Neighbor build method not yet supported");
- } else if (rq->newton == 2) {
- if (style == NSQ) pb = &Neighbor::granular_nsq_no_newton;
- else if (style == BIN) {
- if (triclinic == 0) pb = &Neighbor::granular_bin_no_newton;
- else if (triclinic == 1)
- error->all(FLERR,"Neighbor build method not yet supported");
- } else if (style == MULTI)
- error->all(FLERR,"Neighbor multi not yet enabled for granular");
- }
-
- } else if (rq->respaouter) {
- if (style == NSQ) {
- if (newton_pair == 0) pb = &Neighbor::respa_nsq_no_newton;
- else if (newton_pair == 1) pb = &Neighbor::respa_nsq_newton;
- } else if (style == BIN) {
- if (newton_pair == 0) pb = &Neighbor::respa_bin_no_newton;
- else if (triclinic == 0) pb = &Neighbor::respa_bin_newton;
- else if (triclinic == 1) pb = &Neighbor::respa_bin_newton_tri;
- } else if (style == MULTI)
- error->all(FLERR,"Neighbor multi not yet enabled for rRESPA");
- }
+ int halfflag,fullflag,ghostflag,ssaflag;
- // OMP versions of build methods
+ halfflag = fullflag = ghostflag = ssaflag = 0;
- } else {
+ if (rq->half) halfflag = 1;
+ if (rq->full) fullflag = 1;
+ if (rq->gran) halfflag = 1;
+ if (rq->respaouter) halfflag = 1;
- if (rq->copy) pb = &Neighbor::copy_from;
-
- else if (rq->skip) {
- if (rq->gran && lists[index]->listgranhistory)
- pb = &Neighbor::skip_from_granular;
- else if (rq->respaouter) pb = &Neighbor::skip_from_respa;
- else pb = &Neighbor::skip_from;
-
- } else if (rq->half_from_full) {
- if (newton_pair == 0) pb = &Neighbor::half_from_full_no_newton_omp;
- else if (newton_pair == 1) pb = &Neighbor::half_from_full_newton_omp;
-
- } else if (rq->half) {
- if (style == NSQ) {
- if (rq->newton == 0) {
- if (newton_pair == 0) {
- if (rq->ghost == 0) pb = &Neighbor::half_nsq_no_newton_omp;
- else if (includegroup)
- error->all(FLERR,"Neighbor include group not allowed "
- "with ghost neighbors");
- else pb = &Neighbor::half_nsq_no_newton_ghost_omp;
- } else if (newton_pair == 1) pb = &Neighbor::half_nsq_newton_omp;
- } else if (rq->newton == 1) {
- pb = &Neighbor::half_nsq_newton_omp;
- } else if (rq->newton == 2) {
- if (rq->ghost == 0) pb = &Neighbor::half_nsq_no_newton_omp;
- else if (includegroup)
- error->all(FLERR,"Neighbor include group not allowed "
- "with ghost neighbors");
- else pb = &Neighbor::half_nsq_no_newton_ghost_omp;
- }
- } else if (style == BIN) {
- if (rq->newton == 0) {
- if (newton_pair == 0) {
- if (rq->ghost == 0) {
- if (rq->intel) pb = &Neighbor::half_bin_no_newton_intel;
- else pb = &Neighbor::half_bin_no_newton_omp;
- } else if (includegroup)
- error->all(FLERR,"Neighbor include group not allowed "
- "with ghost neighbors");
- else pb = &Neighbor::half_bin_no_newton_ghost_omp;
- } else if (triclinic == 0) {
- if (rq->intel) pb = &Neighbor::half_bin_newton_intel;
- else pb = &Neighbor::half_bin_newton_omp;
- } else if (triclinic == 1) {
- if (rq->intel) pb = &Neighbor::half_bin_newton_tri_intel;
- else pb = &Neighbor::half_bin_newton_tri_omp;
- }
- } else if (rq->newton == 1) {
- if (triclinic == 0) {
- if (rq->intel) pb = &Neighbor::half_bin_newton_intel;
- else pb = &Neighbor::half_bin_newton_omp;
- } else if (triclinic == 1) {
- if (rq->intel) pb = &Neighbor::half_bin_newton_tri_intel;
- else pb = &Neighbor::half_bin_newton_tri_omp;
- }
- } else if (rq->newton == 2) {
- if (rq->ghost == 0) {
- if (rq->intel) pb = &Neighbor::half_bin_no_newton_intel;
- else pb = &Neighbor::half_bin_no_newton_omp;
- } else if (includegroup)
- error->all(FLERR,"Neighbor include group not allowed "
- "with ghost neighbors");
- else pb = &Neighbor::half_bin_no_newton_ghost_omp;
- }
- } else if (style == MULTI) {
- if (rq->ghost == 1)
- error->all(FLERR,
- "Neighbor multi not yet enabled for ghost neighbors");
- if (rq->newton == 0) {
- if (newton_pair == 0) pb = &Neighbor::half_multi_no_newton_omp;
- else if (triclinic == 0) pb = &Neighbor::half_multi_newton_omp;
- else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri_omp;
- } else if (rq->newton == 1) {
- if (triclinic == 0) pb = &Neighbor::half_multi_newton_omp;
- else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri_omp;
- } else if (rq->newton == 2) pb = &Neighbor::half_multi_no_newton_omp;
- }
+ if (rq->ghost) ghostflag = NS_GHOST;
+ if (rq->ssa) ssaflag = NS_SSA;
- } else if (rq->full) {
- if (style == NSQ) {
- if (rq->ghost == 0) pb = &Neighbor::full_nsq_omp;
- else if (includegroup)
- error->all(FLERR,
- "Neighbor include group not allowed with ghost neighbors");
- else pb = &Neighbor::full_nsq_ghost_omp;
- } else if (style == BIN) {
- if (rq->ghost == 0) {
- if (rq->intel) pb = &Neighbor::full_bin_intel;
- else pb = &Neighbor::full_bin_omp;
- } else if (includegroup)
- error->all(FLERR,
- "Neighbor include group not allowed with ghost neighbors");
- else pb = &Neighbor::full_bin_ghost_omp;
- } else if (style == MULTI) {
- if (rq->ghost == 1)
- error->all(FLERR,
- "Neighbor multi not yet enabled for ghost neighbors");
- pb = &Neighbor::full_multi_omp;
- }
+ int newtflag;
+ if (rq->newton == 0 && newton_pair) newtflag = 1;
+ else if (rq->newton == 0 && !newton_pair) newtflag = 0;
+ else if (rq->newton == 1) newtflag = 1;
+ else if (rq->newton == 2) newtflag = 0;
+
+ // use flags to match exactly one of NStencil class masks, bit by bit
+ // exactly one of halfflag,fullflag is set and thus must match
+
+ int mask;
+
+ for (int i = 0; i < nsclass; i++) {
+ mask = stencilmasks[i];
- } else if (rq->gran) {
- if (style == NSQ) {
- if (newton_pair == 0) pb = &Neighbor::granular_nsq_no_newton_omp;
- else if (newton_pair == 1) pb = &Neighbor::granular_nsq_newton_omp;
- } else if (style == BIN) {
- if (newton_pair == 0) pb = &Neighbor::granular_bin_no_newton_omp;
- else if (triclinic == 0) pb = &Neighbor::granular_bin_newton_omp;
- else if (triclinic == 1) pb = &Neighbor::granular_bin_newton_tri_omp;
- } else if (style == MULTI)
- error->all(FLERR,"Neighbor multi not yet enabled for granular");
-
- } else if (rq->respaouter) {
- if (style == NSQ) {
- if (newton_pair == 0) pb = &Neighbor::respa_nsq_no_newton_omp;
- else if (newton_pair == 1) pb = &Neighbor::respa_nsq_newton_omp;
- } else if (style == BIN) {
- if (newton_pair == 0) pb = &Neighbor::respa_bin_no_newton_omp;
- else if (triclinic == 0) pb = &Neighbor::respa_bin_newton_omp;
- else if (triclinic == 1) pb = &Neighbor::respa_bin_newton_tri_omp;
- } else if (style == MULTI)
- error->all(FLERR,"Neighbor multi not yet enabled for rRESPA");
+ if (halfflag) {
+ if (!(mask & NS_HALF)) continue;
+ } else if (fullflag) {
+ if (!(mask & NS_FULL)) continue;
}
+
+ if (ghostflag != (mask & NS_GHOST)) continue;
+ if (ssaflag != (mask & NS_SSA)) continue;
+
+ if (style == BIN && !(mask & NS_BIN)) continue;
+ if (style == MULTI && !(mask & NS_MULTI)) continue;
+
+ if (dimension == 2 && !(mask & NS_2D)) continue;
+ if (dimension == 3 && !(mask & NS_3D)) continue;
+
+ if (newtflag && !(mask & NS_NEWTON)) continue;
+ if (!newtflag && !(mask & NS_NEWTOFF)) continue;
+
+ if (!triclinic && !(mask & NS_ORTHO)) continue;
+ if (triclinic && !(mask & NS_TRI)) continue;
+
+ return i+1;
}
- pair_build[index] = pb;
+ // error return if matched none
+
+ return -1;
}
/* ----------------------------------------------------------------------
- determine which stencil_create function each neigh list needs
- based on settings of neigh request, only called if style != NSQ
- skip or copy or half_from_full -> no stencil
- ssa = special case for USER-DPD pair styles
- half, gran, respaouter, full -> choose by newton and tri and dimension
- if none of these, ptr = NULL since this list needs no stencils
- use "else if" b/c skip,copy can be set in addition to half,full,etc
+ assign NPair class to a NeighList
+ use neigh request settings to build mask
+ match mask to list of masks of known NPair classes
+ return index+1 of match in list of masks
+ return 0 for no binning
+ return -1 if no match
------------------------------------------------------------------------- */
-void Neighbor::choose_stencil(int index, NeighRequest *rq)
+int Neighbor::choose_pair(NeighRequest *rq)
{
- StencilPtr sc = NULL;
-
- if (rq->skip || rq->copy || rq->half_from_full) sc = NULL;
-
- else if (rq->ssa) {
- if (dimension == 2) sc = &Neighbor::stencil_half_bin_2d_ssa;
- else if (dimension == 3) sc = &Neighbor::stencil_half_bin_3d_ssa;
-
- } else if (rq->half || rq->gran || rq->respaouter) {
- if (style == BIN) {
- if (rq->newton == 0) {
- if (newton_pair == 0) {
- if (dimension == 2) {
- if (rq->ghost) sc = &Neighbor::stencil_half_ghost_bin_2d_no_newton;
- else sc = &Neighbor::stencil_half_bin_2d_no_newton;
- } else if (dimension == 3) {
- if (rq->ghost) sc = &Neighbor::stencil_half_ghost_bin_3d_no_newton;
- else sc = &Neighbor::stencil_half_bin_3d_no_newton;
- }
- } else if (triclinic == 0) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_bin_2d_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_bin_3d_newton;
- } else if (triclinic == 1) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_bin_2d_newton_tri;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_bin_3d_newton_tri;
- }
- } else if (rq->newton == 1) {
- if (triclinic == 0) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_bin_2d_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_bin_3d_newton;
- } else if (triclinic == 1) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_bin_2d_newton_tri;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_bin_3d_newton_tri;
- }
- } else if (rq->newton == 2) {
- if (dimension == 2)
- if (rq->ghost) sc = &Neighbor::stencil_half_ghost_bin_2d_no_newton;
- else sc = &Neighbor::stencil_half_bin_2d_no_newton;
- else if (dimension == 3) {
- if (rq->ghost) sc = &Neighbor::stencil_half_ghost_bin_3d_no_newton;
- else sc = &Neighbor::stencil_half_bin_3d_no_newton;
- }
- }
+ // no NPair build performed
+
+ if (rq->granhistory) return 0;
+ if (rq->respainner || rq->respamiddle) return 0;
+
+ // error check for includegroup with ghost neighbor request
+
+ if (includegroup && rq->ghost)
+ error->all(FLERR,"Neighbor include group not allowed "
+ "with ghost neighbors");
+
+ // flags for settings the request + system requires of NPair class
+ // copyflag = no/yes copy request
+ // skipflag = no/yes skip request
+ // halfflag = half request (gran and respa are also half lists)
+ // fullflag = full request
+ // halffullflag = half_from_full request
+ // sizeflag = no/yes gran request for finite-size particles
+ // ghostflag = no/yes ghost request
+ // respaflag = no/yes respa request
+ // off2onflag = no/yes off2on request
+ // onesideflag = no/yes granonesided request
+ // ssaflag = no/yes request
+ // ompflag = no/yes omp request
+ // intelflag = no/yes intel request
+ // newtflag = newton off/on request
+ // style = NSQ/BIN/MULTI neighbor style
+ // triclinic = orthgonal/triclinic box
+
+ int copyflag,skipflag,halfflag,fullflag,halffullflag,sizeflag,respaflag,
+ ghostflag,off2onflag,onesideflag,ssaflag,ompflag,intelflag;
+
+ copyflag = skipflag = halfflag = fullflag = halffullflag = sizeflag =
+ ghostflag = respaflag = off2onflag = onesideflag = ssaflag =
+ ompflag = intelflag = 0;
+
+ if (rq->copy) copyflag = NP_COPY;
+ if (rq->skip) skipflag = NP_SKIP;
+
+ // NOTE: exactly one of these request flags is set (see neigh_request.h)
+ // this requires gran/respaouter also set halfflag
+ // can simplify this logic, if follow NOTE in neigh_request.h
+ // all why do size/off2on and size/off2on/oneside set NP_HALF
+ // either should set both half & full, or half should be in file name
+ // to be consistent with how other NP classes use "half"
+
+ if (rq->half) halfflag = 1;
+ if (rq->full) fullflag = 1;
+ if (rq->half_from_full) halffullflag = 1;
+ if (rq->gran) {
+ sizeflag = NP_SIZE;
+ halfflag = 1;
+ }
+ if (rq->respaouter) {
+ respaflag = NP_RESPA;
+ halfflag = 1;
+ }
- } else if (style == MULTI) {
- if (rq->newton == 0) {
- if (newton_pair == 0) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_multi_2d_no_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_multi_3d_no_newton;
- } else if (triclinic == 0) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_multi_2d_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_multi_3d_newton;
- } else if (triclinic == 1) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_multi_2d_newton_tri;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_multi_3d_newton_tri;
- }
- } else if (rq->newton == 1) {
- if (triclinic == 0) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_multi_2d_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_multi_3d_newton;
- } else if (triclinic == 1) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_multi_2d_newton_tri;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_multi_3d_newton_tri;
- }
- } else if (rq->newton == 2) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_multi_2d_no_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_multi_3d_no_newton;
- }
+ if (rq->ghost) ghostflag = NP_GHOST;
+ if (rq->off2on) off2onflag = NP_OFF2ON;
+ if (rq->granonesided) onesideflag = NP_ONESIDE;
+ if (rq->ssa) ssaflag = NP_SSA;
+ if (rq->omp) ompflag = NP_OMP;
+ if (rq->intel) intelflag = NP_INTEL;
+
+ int newtflag;
+ if (rq->newton == 0 && newton_pair) newtflag = 1;
+ else if (rq->newton == 0 && !newton_pair) newtflag = 0;
+ else if (rq->newton == 1) newtflag = 1;
+ else if (rq->newton == 2) newtflag = 0;
+
+ // use flags to match exactly one of NPair class masks, bit by bit
+ // copyflag match returns with no further checks
+ // exactly one of halfflag,fullflag,halffullflag is set and thus must match
+
+ int mask;
+
+ //printf("FLAGS: %d %d %d %d %d %d %d %d %d %d %d %d %d %d\n",
+ // copyflag,skipflag,halfflag,fullflag,halffullflag,
+ // sizeflag,respaflag,ghostflag,off2onflag,onesideflag,ssaflag,
+ // ompflag,intelflag,newtflag);
+
+ for (int i = 0; i < npclass; i++) {
+ mask = pairmasks[i];
+
+ if (copyflag && (mask & NP_COPY)) return i+1;
+ if (skipflag != (mask & NP_SKIP)) continue;
+
+ if (halfflag) {
+ if (!(mask & NP_HALF)) continue;
+ } else if (fullflag) {
+ if (!(mask & NP_FULL)) continue;
+ } else if (halffullflag) {
+ if (!(mask & NP_HALFFULL)) continue;
}
- } else if (rq->full) {
- if (style == BIN) {
- if (dimension == 2) {
- if (rq->ghost) sc = &Neighbor::stencil_full_ghost_bin_2d;
- else sc = &Neighbor::stencil_full_bin_2d;
- }
- else if (dimension == 3) {
- if (rq->ghost) sc = &Neighbor::stencil_full_ghost_bin_3d;
- else sc = &Neighbor::stencil_full_bin_3d;
- }
- } else if (style == MULTI) {
- if (dimension == 2) sc = &Neighbor::stencil_full_multi_2d;
- else if (dimension == 3) sc = &Neighbor::stencil_full_multi_3d;
- }
+ if (sizeflag != (mask & NP_SIZE)) continue;
+ if (respaflag != (mask & NP_RESPA)) continue;
+ if (ghostflag != (mask & NP_GHOST)) continue;
+ if (off2onflag != (mask & NP_OFF2ON)) continue;
+ if (onesideflag != (mask & NP_ONESIDE)) continue;
+ if (ssaflag != (mask & NP_SSA)) continue;
+ if (ompflag != (mask & NP_OMP)) continue;
+ if (intelflag != (mask & NP_INTEL)) continue;
+
+ if (style == NSQ && !(mask & NP_NSQ)) continue;
+ if (style == BIN && !(mask & NP_BIN)) continue;
+ if (style == MULTI && !(mask & NP_MULTI)) continue;
+
+ if (newtflag && !(mask & NP_NEWTON)) continue;
+ if (!newtflag && !(mask & NP_NEWTOFF)) continue;
+
+ if (!triclinic && !(mask & NP_ORTHO)) continue;
+ if (triclinic && !(mask & NP_TRI)) continue;
+
+ return i+1;
}
- stencil_create[index] = sc;
+ //printf("NO MATCH\n");
+
+ // error return if matched none
+
+ return -1;
}
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+ called by other classes to request a pairwise neighbor list
+------------------------------------------------------------------------- */
-void Neighbor::print_lists_of_lists()
+int Neighbor::request(void *requestor, int instance)
{
- if (comm->me == 0) {
- printf("Build lists = %d: ",nblist);
- for (int i = 0; i < nblist; i++) printf("%d ",blist[i]);
- printf("\n");
- printf("Grow lists = %d: ",nglist);
- for (int i = 0; i < nglist; i++) printf("%d ",glist[i]);
- printf("\n");
- printf("Stencil lists = %d: ",nslist);
- for (int i = 0; i < nslist; i++) printf("%d ",slist[i]);
- printf("\n");
+ if (nrequest == maxrequest) {
+ maxrequest += RQDELTA;
+ requests = (NeighRequest **)
+ memory->srealloc(requests,maxrequest*sizeof(NeighRequest *),
+ "neighbor:requests");
}
+
+ requests[nrequest] = new NeighRequest(lmp);
+ requests[nrequest]->index = nrequest;
+ requests[nrequest]->requestor = requestor;
+ requests[nrequest]->requestor_instance = instance;
+ nrequest++;
+ return nrequest-1;
+}
+
+/* ----------------------------------------------------------------------
+ one instance per entry in style_neigh_bin.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+NBin *Neighbor::bin_creator(LAMMPS *lmp)
+{
+ return new T(lmp);
+}
+
+/* ----------------------------------------------------------------------
+ one instance per entry in style_neigh_stencil.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+NStencil *Neighbor::stencil_creator(LAMMPS *lmp)
+{
+ return new T(lmp);
+}
+
+/* ----------------------------------------------------------------------
+ one instance per entry in style_neigh_pair.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+NPair *Neighbor::pair_creator(LAMMPS *lmp)
+{
+ return new T(lmp);
+}
+
+/* ----------------------------------------------------------------------
+ setup neighbor binning and neighbor stencils
+ called before run and every reneighbor if box size/shape changes
+ only operates on perpetual lists
+ build_one() operates on occasional lists
+------------------------------------------------------------------------- */
+
+void Neighbor::setup_bins()
+{
+ // invoke setup_bins() for all NBin
+ // actual binning is performed in build()
+
+ for (int i = 0; i < nbin; i++)
+ neigh_bin[i]->setup_bins(style);
+
+ // invoke create_setup() and create() for all perpetual NStencil
+ // same ops performed for occasional lists in build_one()
+
+ for (int i = 0; i < nstencil_perpetual; i++) {
+ neigh_stencil[slist[i]]->create_setup();
+ neigh_stencil[slist[i]]->create();
+ }
+
+ last_setup_bins = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
@@ -1554,22 +1643,29 @@ int Neighbor::check_distance()
/* ----------------------------------------------------------------------
build perpetual neighbor lists
called at setup and every few timesteps during run or minimization
- topology lists also built if topoflag = 1, USER-CUDA calls with topoflag = 0
+ topology lists also built if topoflag = 1 (Kokkos calls with topoflag=0)
------------------------------------------------------------------------- */
void Neighbor::build(int topoflag)
{
- int i;
+ int i,m;
ago = 0;
ncalls++;
lastcall = update->ntimestep;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+
+ // check that using special bond flags will not overflow neigh lists
+
+ if (nall > NEIGHMASK)
+ error->one(FLERR,"Too many local+ghost atoms for neighbor list");
+
// store current atom positions and box size if needed
if (dist_check) {
double **x = atom->x;
- int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
if (atom->nmax > maxhold) {
maxhold = atom->nmax;
@@ -1601,53 +1697,61 @@ void Neighbor::build(int topoflag)
}
}
- // if any lists store neighbors of ghosts:
- // invoke grow() if nlocal+nghost exceeds previous list size
- // else only invoke grow() if nlocal exceeds previous list size
- // only for lists with growflag set and which are perpetual (glist)
-
- if (anyghostlist && atom->nmax > maxatom) {
- maxatom = atom->nmax;
- for (i = 0; i < nglist; i++) lists[glist[i]]->grow(maxatom);
- } else if (atom->nmax > maxatom) {
- maxatom = atom->nmax;
- for (i = 0; i < nglist; i++) lists[glist[i]]->grow(maxatom);
- }
-
- // extend atom bin list if necessary
+ // bin atoms for all NBin instances
+ // not just NBin associated with perpetual lists
+ // b/c cannot wait to bin occasional lists in build_one() call
+ // if bin then, atoms may have moved outside of proc domain & bin extent,
+ // leading to errors or even a crash
- if (style != NSQ && atom->nmax > maxbin) {
- maxbin = atom->nmax;
- memory->destroy(bins);
- memory->create(bins,maxbin,"bins");
+ if (style != NSQ) {
+ for (int i = 0; i < nbin; i++) {
+ neigh_bin[i]->bin_atoms_setup(nall);
+ neigh_bin[i]->bin_atoms();
+ }
}
- // check that using special bond flags will not overflow neigh lists
+ // build pairwise lists for all perpetual NPair/NeighList
+ // grow() with nlocal/nall args so that only realloc if have to
- if (atom->nlocal+atom->nghost > NEIGHMASK)
- error->one(FLERR,"Too many local+ghost atoms for neighbor list");
-
- // invoke building of pair and molecular topology neighbor lists
- // only for pairwise lists with buildflag set
- // blist is for standard neigh lists, otherwise is a Kokkos list
+ for (i = 0; i < npair_perpetual; i++) {
+ m = plist[i];
+ lists[m]->grow(nlocal,nall);
+ neigh_pair[m]->build_setup();
+ neigh_pair[m]->build(lists[m]);
+ }
- for (i = 0; i < nblist; i++)
- (this->*pair_build[blist[i]])(lists[blist[i]]);
+ // build topology lists for bonds/angles/etc
if (atom->molecular && topoflag) build_topology();
}
/* ----------------------------------------------------------------------
- build all topology neighbor lists every few timesteps
- normally built with pair lists, but USER-CUDA separates them
+ build topology neighbor lists: bond, angle, dihedral, improper
+ copy their list info back to Neighbor for access by bond/angle/etc classes
------------------------------------------------------------------------- */
void Neighbor::build_topology()
{
- if (force->bond) (this->*bond_build)();
- if (force->angle) (this->*angle_build)();
- if (force->dihedral) (this->*dihedral_build)();
- if (force->improper) (this->*improper_build)();
+ if (force->bond) {
+ neigh_bond->build();
+ nbondlist = neigh_bond->nbondlist;
+ bondlist = neigh_bond->bondlist;
+ }
+ if (force->angle) {
+ neigh_angle->build();
+ nanglelist = neigh_angle->nanglelist;
+ anglelist = neigh_angle->anglelist;
+ }
+ if (force->dihedral) {
+ neigh_dihedral->build();
+ ndihedrallist = neigh_dihedral->ndihedrallist;
+ dihedrallist = neigh_dihedral->dihedrallist;
+ }
+ if (force->improper) {
+ neigh_improper->build();
+ nimproperlist = neigh_improper->nimproperlist;
+ improperlist = neigh_improper->improperlist;
+ }
}
/* ----------------------------------------------------------------------
@@ -1663,254 +1767,45 @@ void Neighbor::build_one(class NeighList *mylist, int preflag)
error->all(FLERR,"Trying to build an occasional neighbor list "
"before initialization completed");
+ // build_one() should never be invoked on a perpetual list
+
+ if (!mylist->occasional)
+ error->all(FLERR,"Neighbor build one invoked on perpetual list");
+
// no need to build if already built since last re-neighbor
// preflag is set by fix bond/create and fix bond/swap
// b/c they invoke build_one() on same step neigh list is re-built,
// but before re-build, so need to use ">" instead of ">="
+ NPair *np = neigh_pair[mylist->index];
+
if (preflag) {
- if (mylist->last_build > lastcall) return;
+ if (np->last_build > lastcall) return;
} else {
- if (mylist->last_build >= lastcall) return;
+ if (np->last_build >= lastcall) return;
}
- mylist->last_build = update->ntimestep;
+ // if this is copy list and parent is occasional list,
+ // or this is half_from_full and parent is occasional list,
+ // insure parent is current
- // update stencils and grow atom arrays as needed
- // only for relevant settings of stencilflag and growflag
- // grow atom array for this list to current size of perpetual lists
-
- if (mylist->stencilflag) {
- mylist->stencil_allocate(smax,style);
- (this->*stencil_create[mylist->index])(mylist,sx,sy,sz);
- }
+ if (mylist->listcopy && mylist->listcopy->occasional)
+ build_one(mylist->listcopy,preflag);
+ if (mylist->listfull && mylist->listfull->occasional)
+ build_one(mylist->listfull,preflag);
- if (mylist->growflag) mylist->grow(maxatom);
+ // create stencil if hasn't been created since last setup_bins() call
- // build list I, turning off atom binning
- // binning results from last re-neighbor should be used instead
- // if re-bin now, atoms may have moved outside of proc domain & bin extent,
- // leading to errors or even a crash
-
- binatomflag = 0;
- (this->*pair_build[mylist->index])(mylist);
- binatomflag = 1;
-}
-
-/* ----------------------------------------------------------------------
- setup neighbor binning parameters
- bin numbering in each dimension is global:
- 0 = 0.0 to binsize, 1 = binsize to 2*binsize, etc
- nbin-1,nbin,etc = bbox-binsize to bbox, bbox to bbox+binsize, etc
- -1,-2,etc = -binsize to 0.0, -2*binsize to -binsize, etc
- code will work for any binsize
- since next(xyz) and stencil extend as far as necessary
- binsize = 1/2 of cutoff is roughly optimal
- for orthogonal boxes:
- a dim must be filled exactly by integer # of bins
- in periodic, procs on both sides of PBC must see same bin boundary
- in non-periodic, coord2bin() still assumes this by use of nbin xyz
- for triclinic boxes:
- tilted simulation box cannot contain integer # of bins
- stencil & neigh list built differently to account for this
- mbinlo = lowest global bin any of my ghost atoms could fall into
- mbinhi = highest global bin any of my ghost atoms could fall into
- mbin = number of bins I need in a dimension
-------------------------------------------------------------------------- */
-
-void Neighbor::setup_bins()
-{
- // bbox = size of bbox of entire domain
- // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost
- // for triclinic:
- // bbox bounds all 8 corners of tilted box
- // subdomain is in lamda coords
- // include dimension-dependent extension via comm->cutghost
- // domain->bbox() converts lamda extent to box coords and computes bbox
-
- double bbox[3],bsubboxlo[3],bsubboxhi[3];
- double *cutghost = comm->cutghost;
-
- if (triclinic == 0) {
- bsubboxlo[0] = domain->sublo[0] - cutghost[0];
- bsubboxlo[1] = domain->sublo[1] - cutghost[1];
- bsubboxlo[2] = domain->sublo[2] - cutghost[2];
- bsubboxhi[0] = domain->subhi[0] + cutghost[0];
- bsubboxhi[1] = domain->subhi[1] + cutghost[1];
- bsubboxhi[2] = domain->subhi[2] + cutghost[2];
- } else {
- double lo[3],hi[3];
- lo[0] = domain->sublo_lamda[0] - cutghost[0];
- lo[1] = domain->sublo_lamda[1] - cutghost[1];
- lo[2] = domain->sublo_lamda[2] - cutghost[2];
- hi[0] = domain->subhi_lamda[0] + cutghost[0];
- hi[1] = domain->subhi_lamda[1] + cutghost[1];
- hi[2] = domain->subhi_lamda[2] + cutghost[2];
- domain->bbox(lo,hi,bsubboxlo,bsubboxhi);
- }
-
- bbox[0] = bboxhi[0] - bboxlo[0];
- bbox[1] = bboxhi[1] - bboxlo[1];
- bbox[2] = bboxhi[2] - bboxlo[2];
-
- // optimal bin size is roughly 1/2 the cutoff
- // for BIN style, binsize = 1/2 of max neighbor cutoff
- // for MULTI style, binsize = 1/2 of min neighbor cutoff
- // special case of all cutoffs = 0.0, binsize = box size
-
- double binsize_optimal;
- if (binsizeflag) binsize_optimal = binsize_user;
- else if (style == BIN) binsize_optimal = 0.5*cutneighmax;
- else binsize_optimal = 0.5*cutneighmin;
- if (binsize_optimal == 0.0) binsize_optimal = bbox[0];
- double binsizeinv = 1.0/binsize_optimal;
-
- // test for too many global bins in any dimension due to huge global domain
-
- if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT ||
- bbox[2]*binsizeinv > MAXSMALLINT)
- error->all(FLERR,"Domain too large for neighbor bins");
-
- // create actual bins
- // always have one bin even if cutoff > bbox
- // for 2d, nbinz = 1
-
- nbinx = static_cast<int> (bbox[0]*binsizeinv);
- nbiny = static_cast<int> (bbox[1]*binsizeinv);
- if (dimension == 3) nbinz = static_cast<int> (bbox[2]*binsizeinv);
- else nbinz = 1;
-
- if (nbinx == 0) nbinx = 1;
- if (nbiny == 0) nbiny = 1;
- if (nbinz == 0) nbinz = 1;
-
- // compute actual bin size for nbins to fit into box exactly
- // error if actual bin size << cutoff, since will create a zillion bins
- // this happens when nbin = 1 and box size << cutoff
- // typically due to non-periodic, flat system in a particular dim
- // in that extreme case, should use NSQ not BIN neighbor style
-
- binsizex = bbox[0]/nbinx;
- binsizey = bbox[1]/nbiny;
- binsizez = bbox[2]/nbinz;
-
- bininvx = 1.0 / binsizex;
- bininvy = 1.0 / binsizey;
- bininvz = 1.0 / binsizez;
-
- if (binsize_optimal*bininvx > CUT2BIN_RATIO ||
- binsize_optimal*bininvy > CUT2BIN_RATIO ||
- binsize_optimal*bininvz > CUT2BIN_RATIO)
- error->all(FLERR,"Cannot use neighbor bins - box size << cutoff");
-
- // mbinlo/hi = lowest and highest global bins my ghost atoms could be in
- // coord = lowest and highest values of coords for my ghost atoms
- // static_cast(-1.5) = -1, so subract additional -1
- // add in SMALL for round-off safety
-
- int mbinxhi,mbinyhi,mbinzhi;
- double coord;
-
- coord = bsubboxlo[0] - SMALL*bbox[0];
- mbinxlo = static_cast<int> ((coord-bboxlo[0])*bininvx);
- if (coord < bboxlo[0]) mbinxlo = mbinxlo - 1;
- coord = bsubboxhi[0] + SMALL*bbox[0];
- mbinxhi = static_cast<int> ((coord-bboxlo[0])*bininvx);
-
- coord = bsubboxlo[1] - SMALL*bbox[1];
- mbinylo = static_cast<int> ((coord-bboxlo[1])*bininvy);
- if (coord < bboxlo[1]) mbinylo = mbinylo - 1;
- coord = bsubboxhi[1] + SMALL*bbox[1];
- mbinyhi = static_cast<int> ((coord-bboxlo[1])*bininvy);
-
- if (dimension == 3) {
- coord = bsubboxlo[2] - SMALL*bbox[2];
- mbinzlo = static_cast<int> ((coord-bboxlo[2])*bininvz);
- if (coord < bboxlo[2]) mbinzlo = mbinzlo - 1;
- coord = bsubboxhi[2] + SMALL*bbox[2];
- mbinzhi = static_cast<int> ((coord-bboxlo[2])*bininvz);
- }
-
- // extend bins by 1 to insure stencil extent is included
- // if 2d, only 1 bin in z
-
- mbinxlo = mbinxlo - 1;
- mbinxhi = mbinxhi + 1;
- mbinx = mbinxhi - mbinxlo + 1;
-
- mbinylo = mbinylo - 1;
- mbinyhi = mbinyhi + 1;
- mbiny = mbinyhi - mbinylo + 1;
-
- if (dimension == 3) {
- mbinzlo = mbinzlo - 1;
- mbinzhi = mbinzhi + 1;
- } else mbinzlo = mbinzhi = 0;
- mbinz = mbinzhi - mbinzlo + 1;
-
- // memory for bin ptrs
-
- bigint bbin = ((bigint) mbinx) * ((bigint) mbiny) * ((bigint) mbinz);
- if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins");
- mbins = bbin;
- if (mbins > maxhead) {
- maxhead = mbins;
- memory->destroy(binhead);
-
- // USER-INTEL package requires one additional element
- #if defined(LMP_USER_INTEL)
- memory->create(binhead,maxhead + 1,"neigh:binhead");
- #else
- memory->create(binhead,maxhead,"neigh:binhead");
- #endif
+ NStencil *ns = np->ns;
+ if (ns && ns->last_create < last_setup_bins) {
+ ns->create_setup();
+ ns->create();
}
- // create stencil of bins to search over in neighbor list construction
- // sx,sy,sz = max range of stencil in each dim
- // smax = max possible size of entire 3d stencil
- // stencil is empty if cutneighmax = 0.0
-
- sx = static_cast<int> (cutneighmax*bininvx);
- if (sx*binsizex < cutneighmax) sx++;
- sy = static_cast<int> (cutneighmax*bininvy);
- if (sy*binsizey < cutneighmax) sy++;
- sz = static_cast<int> (cutneighmax*bininvz);
- if (sz*binsizez < cutneighmax) sz++;
- if (dimension == 2) sz = 0;
- smax = (2*sx+1) * (2*sy+1) * (2*sz+1);
-
- // create stencils for pairwise neighbor lists
- // only done for lists with stencilflag and buildflag set
-
- for (int i = 0; i < nslist; i++) {
- if (lists[slist[i]]) {
- lists[slist[i]]->stencil_allocate(smax,style);
- (this->*stencil_create[slist[i]])(lists[slist[i]],sx,sy,sz);
- } else setup_bins_kokkos(i);
- }
-}
-
-/* ----------------------------------------------------------------------
- compute closest distance between central bin (0,0,0) and bin (i,j,k)
-------------------------------------------------------------------------- */
-
-double Neighbor::bin_distance(int i, int j, int k)
-{
- double delx,dely,delz;
-
- if (i > 0) delx = (i-1)*binsizex;
- else if (i == 0) delx = 0.0;
- else delx = (i+1)*binsizex;
-
- if (j > 0) dely = (j-1)*binsizey;
- else if (j == 0) dely = 0.0;
- else dely = (j+1)*binsizey;
+ // build the list
- if (k > 0) delz = (k-1)*binsizez;
- else if (k == 0) delz = 0.0;
- else delz = (k+1)*binsizez;
-
- return (delx*delx + dely*dely + delz*delz);
+ np->build_setup();
+ np->build(mylist);
}
/* ----------------------------------------------------------------------
@@ -1933,14 +1828,31 @@ void Neighbor::set(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- reset timestamps in all NeighList classes
+ reset timestamps in all NeignBin, NStencil, NPair classes
so that neighbor lists will rebuild properly with timestep change
------------------------------------------------------------------------- */
void Neighbor::reset_timestep(bigint ntimestep)
{
- for (int i = 0; i < nlist; i++)
- lists[i]->last_build = -1;
+ for (int i = 0; i < nbin; i++) {
+ neigh_bin[i]->last_setup = -1;
+ neigh_bin[i]->last_bin = -1;
+ neigh_bin[i]->last_bin_memory = -1;
+ }
+
+ for (int i = 0; i < nstencil; i++) {
+ neigh_stencil[i]->last_create = -1;
+ neigh_stencil[i]->last_stencil_memory = -1;
+ neigh_stencil[i]->last_copy_bin = -1;
+ }
+
+ for (int i = 0; i < nlist; i++) {
+ if (!neigh_pair[i]) continue;
+ neigh_pair[i]->last_build = -1;
+ neigh_pair[i]->last_copy_bin_setup = -1;
+ neigh_pair[i]->last_copy_bin = -1;
+ neigh_pair[i]->last_copy_stencil = -1;
+ }
}
/* ----------------------------------------------------------------------
@@ -2061,161 +1973,6 @@ void Neighbor::modify_params(int narg, char **arg)
}
}
-/* ----------------------------------------------------------------------
- bin owned and ghost atoms
-------------------------------------------------------------------------- */
-
-void Neighbor::bin_atoms()
-{
- int i,ibin;
-
- for (i = 0; i < mbins; i++) binhead[i] = -1;
-
- // bin in reverse order so linked list will be in forward order
- // also puts ghost atoms at end of list, which is necessary
-
- double **x = atom->x;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
-
- if (includegroup) {
- int bitmask = group->bitmask[includegroup];
- for (i = nall-1; i >= nlocal; i--) {
- if (mask[i] & bitmask) {
- ibin = coord2bin(x[i]);
- bins[i] = binhead[ibin];
- binhead[ibin] = i;
- }
- }
- for (i = atom->nfirst-1; i >= 0; i--) {
- ibin = coord2bin(x[i]);
- bins[i] = binhead[ibin];
- binhead[ibin] = i;
- }
-
- } else {
- for (i = nall-1; i >= 0; i--) {
- ibin = coord2bin(x[i]);
- bins[i] = binhead[ibin];
- binhead[ibin] = i;
- }
- }
-}
-
-/* ----------------------------------------------------------------------
- convert atom coords into local bin #
- for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo
- take special care to insure ghosts are in correct bins even w/ roundoff
- hi ghost atoms = nbin,nbin+1,etc
- owned atoms = 0 to nbin-1
- lo ghost atoms = -1,-2,etc
- this is necessary so that both procs on either side of PBC
- treat a pair of atoms straddling the PBC in a consistent way
- for triclinic, doesn't matter since stencil & neigh list built differently
-------------------------------------------------------------------------- */
-
-int Neighbor::coord2bin(double *x)
-{
- int ix,iy,iz;
-
- if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
- error->one(FLERR,"Non-numeric positions - simulation unstable");
-
- if (x[0] >= bboxhi[0])
- ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx) + nbinx;
- else if (x[0] >= bboxlo[0]) {
- ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx);
- ix = MIN(ix,nbinx-1);
- } else
- ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
-
- if (x[1] >= bboxhi[1])
- iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
- else if (x[1] >= bboxlo[1]) {
- iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy);
- iy = MIN(iy,nbiny-1);
- } else
- iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
-
- if (x[2] >= bboxhi[2])
- iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
- else if (x[2] >= bboxlo[2]) {
- iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz);
- iz = MIN(iz,nbinz-1);
- } else
- iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz) - 1;
-
- return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
-}
-
-/* ----------------------------------------------------------------------
- same as coord2bin, but also return ix,iy,iz offsets in each dim
-------------------------------------------------------------------------- */
-
-int Neighbor::coord2bin(double *x, int &ix, int &iy, int &iz)
-{
- if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
- error->one(FLERR,"Non-numeric positions - simulation unstable");
-
- if (x[0] >= bboxhi[0])
- ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx) + nbinx;
- else if (x[0] >= bboxlo[0]) {
- ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx);
- ix = MIN(ix,nbinx-1);
- } else
- ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
-
- if (x[1] >= bboxhi[1])
- iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
- else if (x[1] >= bboxlo[1]) {
- iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy);
- iy = MIN(iy,nbiny-1);
- } else
- iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
-
- if (x[2] >= bboxhi[2])
- iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
- else if (x[2] >= bboxlo[2]) {
- iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz);
- iz = MIN(iz,nbinz-1);
- } else
- iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz) - 1;
-
- ix -= mbinxlo;
- iy -= mbinylo;
- iz -= mbinzlo;
- return iz*mbiny*mbinx + iy*mbinx + ix;
-}
-
-/* ----------------------------------------------------------------------
- test if atom pair i,j is excluded from neighbor list
- due to type, group, molecule settings from neigh_modify command
- return 1 if should be excluded, 0 if included
-------------------------------------------------------------------------- */
-
-int Neighbor::exclusion(int i, int j, int itype, int jtype,
- int *mask, tagint *molecule) const {
- int m;
-
- if (nex_type && ex_type[itype][jtype]) return 1;
-
- if (nex_group) {
- for (m = 0; m < nex_group; m++) {
- if (mask[i] & ex1_bit[m] && mask[j] & ex2_bit[m]) return 1;
- if (mask[i] & ex2_bit[m] && mask[j] & ex1_bit[m]) return 1;
- }
- }
-
- if (nex_mol) {
- for (m = 0; m < nex_mol; m++)
- if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
- molecule[i] == molecule[j]) return 1;
- }
-
- return 0;
-}
-
/* ----------------------------------------------------------------------
remove the first group-group exclusion matching group1, group2
------------------------------------------------------------------------- */
@@ -2240,6 +1997,16 @@ void Neighbor::exclusion_group_group_delete(int group1, int group2)
nex_group--;
}
+
+/* ----------------------------------------------------------------------
+ return the value of exclude - used to check compatibility with GPU
+------------------------------------------------------------------------- */
+
+int Neighbor::exclude_setting()
+{
+ return exclude;
+}
+
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
@@ -2249,27 +2016,17 @@ bigint Neighbor::memory_usage()
bigint bytes = 0;
bytes += memory->usage(xhold,maxhold,3);
- if (style != NSQ) {
- bytes += memory->usage(bins,maxbin);
- bytes += memory->usage(binhead,maxhead);
- }
-
- for (int i = 0; i < nrequest; i++)
+ for (int i = 0; i < nlist; i++)
if (lists[i]) bytes += lists[i]->memory_usage();
+ for (int i = 0; i < nstencil; i++)
+ bytes += neigh_stencil[i]->memory_usage();
+ for (int i = 0; i < nbin; i++)
+ bytes += neigh_bin[i]->memory_usage();
- bytes += memory->usage(bondlist,maxbond,3);
- bytes += memory->usage(anglelist,maxangle,4);
- bytes += memory->usage(dihedrallist,maxdihedral,5);
- bytes += memory->usage(improperlist,maximproper,5);
+ if (neigh_bond) bytes += neigh_bond->memory_usage();
+ if (neigh_angle) bytes += neigh_angle->memory_usage();
+ if (neigh_dihedral) bytes += neigh_dihedral->memory_usage();
+ if (neigh_improper) bytes += neigh_improper->memory_usage();
return bytes;
}
-
-/* ----------------------------------------------------------------------
- return the value of exclude - used to check compatibility with GPU
-------------------------------------------------------------------------- */
-
-int Neighbor::exclude_setting()
-{
- return exclude;
-}
diff --git a/src/neighbor.h b/src/neighbor.h
index 23fd663e2b..9655cca545 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -15,12 +15,11 @@
#define LMP_NEIGHBOR_H
#include "pointers.h"
+#include <map>
namespace LAMMPS_NS {
class Neighbor : protected Pointers {
- friend class Cuda;
-
public:
int style; // 0,1,2 = nsq, bin, multi
int every; // build every this many steps
@@ -31,12 +30,18 @@ class Neighbor : protected Pointers {
int oneatom; // max # of neighbors for one atom
int includegroup; // only build pairwise lists for this group
int build_once; // 1 if only build lists once per run
- int cudable; // GPU <-> CPU communication flag for CUDA
double skin; // skin distance
double cutneighmin; // min neighbor cutoff for all type pairs
double cutneighmax; // max neighbor cutoff for all type pairs
+ double cutneighmaxsq; // cutneighmax squared
+ double **cutneighsq; // neighbor cutneigh sq for each type pair
+ double **cutneighghostsq; // cutneigh sq for each ghost type pair
double *cuttype; // for each type, max neigh cut w/ others
+ double *cuttypesq; // cuttype squared
+ double cut_inner_sq; // outer cutoff for inner neighbor list
+ double cut_middle_sq; // outer cutoff for middle neighbor list
+ double cut_middle_inside_sq; // inner cutoff for middle neighbor list
int binsizeflag; // user-chosen bin size
double binsize_user; // set externally by some accelerator pkgs
@@ -45,20 +50,47 @@ class Neighbor : protected Pointers {
bigint ndanger; // # of dangerous builds
bigint lastcall; // timestep of last neighbor::build() call
- int nrequest; // requests for pairwise neighbor lists
- class NeighRequest **requests; // from Pair, Fix, Compute, Command classes
- int maxrequest;
+ // geometry and static info, used by other Neigh classes
- int old_style,old_nrequest; // previous run info to avoid
- int old_triclinic,old_pgsize; // re-creation of pairwise neighbor lists
- int old_oneatom,old_every;
- int old_delay,old_check;
- double old_cutoff;
+ double *bboxlo,*bboxhi; // ptrs to full domain bounding box
+ // different for orthog vs triclinic
+ double *zeroes; // vector of zeroes for shear history init
- class NeighRequest **old_requests;
+ // exclusion info, used by NeighPair
+
+ int exclude; // 0 if no type/group exclusions, 1 if yes
+
+ int nex_type; // # of entries in type exclusion list
+ int *ex1_type,*ex2_type; // pairs of types to exclude
+ int **ex_type; // 2d array of excluded type pairs
+
+ int nex_group; // # of entries in group exclusion list
+ int *ex1_group,*ex2_group; // pairs of group #'s to exclude
+ int *ex1_bit,*ex2_bit; // pairs of group bits to exclude
+
+ int nex_mol; // # of entries in molecule exclusion list
+ int *ex_mol_group; // molecule group #'s to exclude
+ int *ex_mol_bit; // molecule group bits to exclude
+
+ // special info, used by NeighPair
+
+ int special_flag[4]; // flags for 1-2, 1-3, 1-4 neighbors
+
+ // cluster setting, used by NeighTopo
+
+ int cluster_check; // 1 if check bond/angle/etc satisfies minimg
+
+ // pairwise neighbor lists and corresponding requests
+
+ int nlist; // # of pairwise neighbor lists
+ int nrequest; // # of requests, same as nlist
+ int old_nrequest; // RQ count for run that just finished
- int nlist; // pairwise neighbor lists
class NeighList **lists;
+ class NeighRequest **requests; // from Pair,Fix,Compute,Command classes
+ class NeighRequest **old_requests; // accessed by Finish
+
+ // data from topology neighbor lists
int nbondlist; // list of bonds to compute
int **bondlist;
@@ -69,128 +101,123 @@ class Neighbor : protected Pointers {
int nimproperlist; // list of impropers to compute
int **improperlist;
- int cluster_check; // 1 if check bond/angle/etc satisfies minimg
-
- // methods
+ // public methods
Neighbor(class LAMMPS *);
virtual ~Neighbor();
virtual void init();
- int request(void *, int instance=0); // another class requests a neigh list
- void print_lists_of_lists(); // debug print out
+ int request(void *, int instance=0);
int decide(); // decide whether to build or not
virtual int check_distance(); // check max distance moved since last build
void setup_bins(); // setup bins based on box and cutoff
- virtual void build(int topoflag=1); // create all neighbor lists (pair,bond)
- virtual void build_topology(); // create all topology neighbor lists
- void build_one(class NeighList *list,
- int preflag=0); // create a single one-time neigh list
+ virtual void build(int topoflag=1); // build all perpetual neighbor lists
+ virtual void build_topology(); // pairwise topology neighbor lists
+ void build_one(class NeighList *list, int preflag=0);
+ // create a one-time pairwise neigh list
void set(int, char **); // set neighbor style and skin distance
void reset_timestep(bigint); // reset of timestep counter
- void modify_params(int, char**); // modify parameters that control builds
- bigint memory_usage();
- int exclude_setting();
+ void modify_params(int, char**); // modify params that control builds
+
void exclusion_group_group_delete(int, int); // rm a group-group exclusion
+ int exclude_setting(); // return exclude value to accelerator pkg
+
+ bigint memory_usage();
protected:
int me,nprocs;
+ int firsttime; // flag for calling init_styles() only once
- int maxatom; // size of atom-based NeighList arrays
- int maxbond,maxangle,maxdihedral,maximproper; // size of bond lists
- int maxwt; // max weighting factor applied + 1
+ int dimension; // 2/3 for 2d/3d
+ int triclinic; // 0 if domain is orthog, 1 if triclinic
+ int newton_pair; // 0 if newton off for pairwise, 1 if on
int must_check; // 1 if must check other classes to reneigh
int restart_check; // 1 if restart enabled, 0 if no
int fix_check; // # of fixes that induce reneigh
int *fixchecklist; // which fixes to check
- double **cutneighsq; // neighbor cutneigh sq for each type pair
- double **cutneighghostsq; // neighbor cutnsq for each ghost type pair
- double cutneighmaxsq; // cutneighmax squared
- double *cuttypesq; // cuttype squared
+ bigint last_setup_bins; // step of last neighbor::setup_bins() call
double triggersq; // trigger = build when atom moves this dist
double **xhold; // atom coords at last neighbor build
int maxhold; // size of xhold array
+
int boxcheck; // 1 if need to store box size
double boxlo_hold[3],boxhi_hold[3]; // box size at last neighbor build
double corners_hold[8][3]; // box corners at last neighbor build
+ double (*corners)[3]; // ptr to 8 corners of triclinic box
- int binatomflag; // bin atoms or not when build neigh list
- // turned off by build_one()
-
- int nbinx,nbiny,nbinz; // # of global bins
- int *bins; // ptr to next atom in each bin
- int maxbin; // size of bins array
-
- int *binhead; // ptr to 1st atom in each bin
- int maxhead; // size of binhead array
-
- int mbins; // # of local bins and offset
- int mbinx,mbiny,mbinz;
- int mbinxlo,mbinylo,mbinzlo;
+ double inner[2],middle[2]; // rRESPA cutoffs for extra lists
- double binsizex,binsizey,binsizez; // actual bin sizes and inverse sizes
- double bininvx,bininvy,bininvz;
+ int same; // 1 if NeighRequests are same as last run
+ int old_style,old_triclinic; // previous run info
+ int old_pgsize,old_oneatom; // used to avoid re-creating neigh lists
- int sx,sy,sz,smax; // bin stencil extents
+ int nstencil_perpetual; // # of perpetual NeighStencil classes
+ int npair_perpetual; // # of perpetual NeighPair classes
+ int *slist; // indices of them in neigh_stencil
+ int *plist; // indices of them in neigh_pair
- int dimension; // 2/3 for 2d/3d
- int triclinic; // 0 if domain is orthog, 1 if triclinic
- int newton_pair; // 0 if newton off, 1 if on for pairwise
-
- double *bboxlo,*bboxhi; // ptrs to full domain bounding box
- double (*corners)[3]; // ptr to 8 corners of triclinic box
+ int maxex_type; // max # in exclusion type list
+ int maxex_group; // max # in exclusion group list
+ int maxex_mol; // max # in exclusion molecule list
- double inner[2],middle[2]; // rRESPA cutoffs for extra lists
- double cut_inner_sq; // outer cutoff for inner neighbor list
- double cut_middle_sq; // outer cutoff for middle neighbor list
- double cut_middle_inside_sq; // inner cutoff for middle neighbor list
+ int maxatom; // size of atom-based NeighList arrays
+ int maxrequest; // size of NeighRequest list
+ int maxwt; // max weighting factor applied + 1
- int special_flag[4]; // flags for 1-2, 1-3, 1-4 neighbors
+ // info for other Neigh classes: NBin,NStencil,NPair,NTopo
- int anyghostlist; // 1 if any non-occasional list
- // stores neighbors of ghosts
+ int nbin,nstencil;
+ int nbclass,nsclass,npclass;
+ int bondwhich,anglewhich,dihedralwhich,improperwhich;
- int exclude; // 0 if no type/group exclusions, 1 if yes
+ typedef class NBin *(*BinCreator)(class LAMMPS *);
+ BinCreator *binclass;
+ char **binnames;
+ int *binmasks;
+ class NBin **neigh_bin;
- int nex_type; // # of entries in type exclusion list
- int maxex_type; // max # in type list
- int *ex1_type,*ex2_type; // pairs of types to exclude
- int **ex_type; // 2d array of excluded type pairs
+ typedef class NStencil *(*StencilCreator)(class LAMMPS *);
+ StencilCreator *stencilclass;
+ char **stencilnames;
+ int *stencilmasks;
+ class NStencil **neigh_stencil;
- int nex_group; // # of entries in group exclusion list
- int maxex_group; // max # in group list
- int *ex1_group,*ex2_group; // pairs of group #'s to exclude
- int *ex1_bit,*ex2_bit; // pairs of group bits to exclude
+ typedef class NPair *(*PairCreator)(class LAMMPS *);
+ PairCreator *pairclass;
+ char **pairnames;
+ int *pairmasks;
+ class NPair **neigh_pair;
- int nex_mol; // # of entries in molecule exclusion list
- int maxex_mol; // max # in molecule list
- int *ex_mol_group; // molecule group #'s to exclude
- int *ex_mol_bit; // molecule group bits to exclude
+ class NTopo *neigh_bond;
+ class NTopo *neigh_angle;
+ class NTopo *neigh_dihedral;
+ class NTopo *neigh_improper;
- int nblist,nglist,nslist; // # of pairwise neigh lists of various kinds
- int *blist; // lists to build every reneighboring
- int *glist; // lists to grow atom arrays every reneigh
- int *slist; // lists to grow stencil arrays every reneigh
+ // internal methods
+ // including creator methods for Nbin,Nstencil,Npair instances
- double *zeroes; // vector of zeroes for shear history init
+ void init_styles();
+ void init_pair();
+ void init_topology();
- // methods
+ void print_pairwise_info();
+ void requests_new2old();
- void bin_atoms(); // bin all atoms
- double bin_distance(int, int, int); // distance between binx
- int coord2bin(double *); // mapping atom coord to a bin
- int coord2bin(double *, int &, int &, int&); // ditto
+ int choose_bin(class NeighRequest *);
+ int choose_stencil(class NeighRequest *);
+ int choose_pair(class NeighRequest *);
- int exclusion(int, int, int,
- int, int *, tagint *) const; // test for pair exclusion
+ template <typename T> static NBin *bin_creator(class LAMMPS *);
+ template <typename T> static NStencil *stencil_creator(class LAMMPS *);
+ template <typename T> static NPair *pair_creator(class LAMMPS *);
- virtual void choose_build(int, class NeighRequest *);
- void choose_stencil(int, class NeighRequest *);
+ // dummy functions provided by NeighborKokkos, called in init()
+ // otherwise NeighborKokkos would have to overwrite init()
- // dummy functions provided by NeighborKokkos
+ int copymode;
virtual void init_cutneighsq_kokkos(int) {}
virtual int init_lists_kokkos() {return 0;}
@@ -200,164 +227,47 @@ class Neighbor : protected Pointers {
virtual void init_ex_bit_kokkos() {}
virtual void init_ex_mol_bit_kokkos() {}
virtual void init_list_grow_kokkos(int) {}
- virtual void build_kokkos(int) {}
- virtual void setup_bins_kokkos(int) {}
- virtual void init_topology_kokkos() {}
- virtual void build_topology_kokkos() {}
-
- int copymode;
-
- // pairwise build functions
-
- typedef void (Neighbor::*PairPtr)(class NeighList *);
- PairPtr *pair_build;
-
- void half_nsq_no_newton(class NeighList *);
- void half_nsq_no_newton_ghost(class NeighList *);
- void half_nsq_newton(class NeighList *);
-
- void half_bin_no_newton(class NeighList *);
- void half_bin_no_newton_ghost(class NeighList *);
- void half_bin_newton(class NeighList *);
- void half_bin_newton_tri(class NeighList *);
-
- void half_multi_no_newton(class NeighList *);
- void half_multi_newton(class NeighList *);
- void half_multi_newton_tri(class NeighList *);
-
- void full_nsq(class NeighList *);
- void full_nsq_ghost(class NeighList *);
- void full_bin(class NeighList *);
- void full_bin_ghost(class NeighList *);
- void full_multi(class NeighList *);
-
- void granular_nsq_no_newton(class NeighList *);
- void granular_nsq_newton(class NeighList *);
- void granular_nsq_newton_onesided(class NeighList *);
- void granular_bin_no_newton(class NeighList *);
- void granular_bin_newton(class NeighList *);
- void granular_bin_newton_onesided(class NeighList *);
- void granular_bin_newton_tri(class NeighList *);
-
- void respa_nsq_no_newton(class NeighList *);
- void respa_nsq_newton(class NeighList *);
- void respa_bin_no_newton(class NeighList *);
- void respa_bin_newton(class NeighList *);
- void respa_bin_newton_tri(class NeighList *);
-
- void half_from_full_no_newton(class NeighList *);
- void half_from_full_newton(class NeighList *);
- void skip_from(class NeighList *);
- void skip_from_granular(class NeighList *);
- void skip_from_granular_off2on(class NeighList *);
- void skip_from_granular_off2on_onesided(class NeighList *);
- void skip_from_respa(class NeighList *);
- void copy_from(class NeighList *);
-
- // include prototypes for multi-threaded neighbor lists
- // builds or their corresponding dummy versions
-
-#define LMP_INSIDE_NEIGHBOR_H
-#include "accelerator_omp.h"
-#include "accelerator_intel.h"
-#undef LMP_INSIDE_NEIGHBOR_H
-
- // pairwise stencil creation functions
-
- typedef void (Neighbor::*StencilPtr)(class NeighList *, int, int, int);
- StencilPtr *stencil_create;
-
- void stencil_half_bin_2d_no_newton(class NeighList *, int, int, int);
- void stencil_half_ghost_bin_2d_no_newton(class NeighList *, int, int, int);
- void stencil_half_bin_3d_no_newton(class NeighList *, int, int, int);
- void stencil_half_ghost_bin_3d_no_newton(class NeighList *, int, int, int);
- void stencil_half_bin_2d_newton(class NeighList *, int, int, int);
- void stencil_half_bin_3d_newton(class NeighList *, int, int, int);
- void stencil_half_bin_2d_newton_tri(class NeighList *, int, int, int);
- void stencil_half_bin_3d_newton_tri(class NeighList *, int, int, int);
-
- void stencil_half_multi_2d_no_newton(class NeighList *, int, int, int);
- void stencil_half_multi_3d_no_newton(class NeighList *, int, int, int);
- void stencil_half_multi_2d_newton(class NeighList *, int, int, int);
- void stencil_half_multi_3d_newton(class NeighList *, int, int, int);
- void stencil_half_multi_2d_newton_tri(class NeighList *, int, int, int);
- void stencil_half_multi_3d_newton_tri(class NeighList *, int, int, int);
-
- void stencil_full_bin_2d(class NeighList *, int, int, int);
- void stencil_full_ghost_bin_2d(class NeighList *, int, int, int);
- void stencil_full_bin_3d(class NeighList *, int, int, int);
- void stencil_full_ghost_bin_3d(class NeighList *, int, int, int);
- void stencil_full_multi_2d(class NeighList *, int, int, int);
- void stencil_full_multi_3d(class NeighList *, int, int, int);
-
- // topology build functions
-
- typedef void (Neighbor::*BondPtr)(); // ptrs to topology build functions
-
- BondPtr bond_build; // ptr to bond list functions
- void bond_all(); // bond list with all bonds
- void bond_template(); // bond list with templated bonds
- void bond_partial(); // exclude certain bonds
- void bond_check();
-
- BondPtr angle_build; // ptr to angle list functions
- void angle_all(); // angle list with all angles
- void angle_template(); // angle list with templated bonds
- void angle_partial(); // exclude certain angles
- void angle_check();
-
- BondPtr dihedral_build; // ptr to dihedral list functions
- void dihedral_all(); // dihedral list with all dihedrals
- void dihedral_template(); // dihedral list with templated bonds
- void dihedral_partial(); // exclude certain dihedrals
- void dihedral_check(int, int **);
-
- BondPtr improper_build; // ptr to improper list functions
- void improper_all(); // improper list with all impropers
- void improper_template(); // improper list with templated bonds
- void improper_partial(); // exclude certain impropers
-
- // SSA neighboring for USER-DPD
-
- void half_bin_newton_ssa(NeighList *);
- void half_from_full_newton_ssa(class NeighList *);
- void stencil_half_bin_2d_ssa(class NeighList *, int, int, int);
- void stencil_half_bin_3d_ssa(class NeighList *, int, int, int);
-
- // find_special: determine if atom j is in special list of atom i
- // if it is not, return 0
- // if it is and special flag is 0 (both coeffs are 0.0), return -1
- // if it is and special flag is 1 (both coeffs are 1.0), return 0
- // if it is and special flag is 2 (otherwise), return 1,2,3
- // for which level of neighbor it is (and which coeff it maps to)
-
- inline int find_special(const tagint *list, const int *nspecial,
- const tagint tag) const {
- const int n1 = nspecial[0];
- const int n2 = nspecial[1];
- const int n3 = nspecial[2];
-
- for (int i = 0; i < n3; i++) {
- if (list[i] == tag) {
- if (i < n1) {
- if (special_flag[1] == 0) return -1;
- else if (special_flag[1] == 1) return 0;
- else return 1;
- } else if (i < n2) {
- if (special_flag[2] == 0) return -1;
- else if (special_flag[2] == 1) return 0;
- else return 2;
- } else {
- if (special_flag[3] == 0) return -1;
- else if (special_flag[3] == 1) return 0;
- else return 3;
- }
- }
- }
- return 0;
- };
};
+namespace NeighConst {
+ static const int NB_SSA = 1<<0;
+ static const int NB_INTEL = 1<<1;
+
+ static const int NS_HALF = 1<<0;
+ static const int NS_FULL = 1<<1;
+ static const int NS_GHOST = 1<<2;
+ static const int NS_SSA = 1<<3;
+ static const int NS_BIN = 1<<4;
+ static const int NS_MULTI = 1<<5;
+ static const int NS_2D = 1<<6;
+ static const int NS_3D = 1<<7;
+ static const int NS_NEWTON = 1<<8;
+ static const int NS_NEWTOFF = 1<<9;
+ static const int NS_ORTHO = 1<<10;
+ static const int NS_TRI = 1<<11;
+
+ static const int NP_COPY = 1<<0;
+ static const int NP_SKIP = 1<<1;
+ static const int NP_HALF = 1<<2;
+ static const int NP_FULL = 1<<3;
+ static const int NP_HALFFULL = 1<<4;
+ static const int NP_SIZE = 1<<5;
+ static const int NP_RESPA = 1<<6;
+ static const int NP_GHOST = 1<<7;
+ static const int NP_OFF2ON = 1<<8;
+ static const int NP_ONESIDE = 1<<9;
+ static const int NP_SSA = 1<<10;
+ static const int NP_OMP = 1<<11;
+ static const int NP_INTEL = 1<<12;
+ static const int NP_NSQ = 1<<13;
+ static const int NP_BIN = 1<<14;
+ static const int NP_MULTI = 1<<15;
+ static const int NP_NEWTON = 1<<16;
+ static const int NP_NEWTOFF = 1<<17;
+ static const int NP_ORTHO = 1<<18;
+ static const int NP_TRI = 1<<19;
+}
+
}
#endif
diff --git a/src/npair.cpp b/src/npair.cpp
new file mode 100644
index 0000000000..20522cde48
--- /dev/null
+++ b/src/npair.cpp
@@ -0,0 +1,258 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include "npair.h"
+#include "neighbor.h"
+#include "nbin.h"
+#include "nstencil.h"
+#include "atom.h"
+#include "update.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPair::NPair(LAMMPS *lmp) : Pointers(lmp)
+{
+ last_build = -1;
+ last_copy_bin_setup = last_copy_bin = last_copy_stencil = -1;
+
+ molecular = atom->molecular;
+}
+
+/* ----------------------------------------------------------------------
+ copy needed info from Neighbor class to this build class
+------------------------------------------------------------------------- */
+
+void NPair::copy_neighbor_info()
+{
+ // general params
+
+ includegroup = neighbor->includegroup;
+ exclude = neighbor->exclude;
+ skin = neighbor->skin;
+ cutneighsq = neighbor->cutneighsq;
+ cutneighghostsq = neighbor->cutneighghostsq;
+ cut_inner_sq = neighbor->cut_inner_sq;
+ cut_middle_sq = neighbor->cut_middle_sq;
+ cut_middle_inside_sq = neighbor->cut_middle_inside_sq;
+ zeroes = neighbor->zeroes;
+ bboxlo = neighbor->bboxlo;
+ bboxhi = neighbor->bboxhi;
+
+ // exclusion info
+
+ nex_type = neighbor->nex_type;
+ ex1_type = neighbor->ex1_type;
+ ex2_type = neighbor->ex2_type;
+ ex_type = neighbor->ex_type;
+
+ nex_group = neighbor->nex_group;
+ ex1_group = neighbor->ex1_group;
+ ex2_group = neighbor->ex2_group;
+ ex1_bit = neighbor->ex1_bit;
+ ex2_bit = neighbor->ex2_bit;
+
+ nex_mol = neighbor->nex_mol;
+ ex_mol_group = neighbor->ex_mol_group;
+ ex_mol_bit = neighbor->ex_mol_bit;
+
+ // special info
+
+ special_flag = neighbor->special_flag;
+}
+
+/* ----------------------------------------------------------------------
+ copy bin geometry info from NBin class to this build class
+------------------------------------------------------------------------- */
+
+void NPair::copy_bin_setup_info()
+{
+ nbinx = nb->nbinx;
+ nbiny = nb->nbiny;
+ nbinz = nb->nbinz;
+ mbins = nb->mbins;
+ mbinx = nb->mbinx;
+ mbiny = nb->mbiny;
+ mbinz = nb->mbinz;
+ mbinxlo = nb->mbinxlo;
+ mbinylo = nb->mbinylo;
+ mbinzlo = nb->mbinzlo;
+
+ bininvx = nb->bininvx;
+ bininvy = nb->bininvy;
+ bininvz = nb->bininvz;
+}
+
+/* ----------------------------------------------------------------------
+ copy per-atom and per-bin vectors from NBin class to this build class
+------------------------------------------------------------------------- */
+
+void NPair::copy_bin_info()
+{
+ bins = nb->bins;
+ binhead = nb->binhead;
+}
+
+/* ----------------------------------------------------------------------
+ copy needed info from NStencil class to this build class
+------------------------------------------------------------------------- */
+
+void NPair::copy_stencil_info()
+{
+ nstencil = ns->nstencil;
+ nstencil_ssa = ns->nstencil_ssa;
+ stencil = ns->stencil;
+ stencilxyz = ns->stencilxyz;
+ nstencil_multi = ns->nstencil_multi;
+ stencil_multi = ns->stencil_multi;
+ distsq_multi = ns->distsq_multi;
+}
+
+/* ----------------------------------------------------------------------
+ copy needed info from NStencil class to this build class
+------------------------------------------------------------------------- */
+
+void NPair::build_setup()
+{
+ if (nb && last_copy_bin_setup < nb->last_setup) {
+ copy_bin_setup_info();
+ last_copy_bin_setup = update->ntimestep;
+ }
+ if (nb && last_copy_bin < nb->last_bin_memory) {
+ copy_bin_info();
+ last_copy_bin = update->ntimestep;
+ }
+ if (ns && last_copy_stencil < ns->last_create) {
+ copy_stencil_info();
+ last_copy_stencil = update->ntimestep;
+ }
+
+ last_build = update->ntimestep;
+}
+
+/* ----------------------------------------------------------------------
+ test if atom pair i,j is excluded from neighbor list
+ due to type, group, molecule settings from neigh_modify command
+ return 1 if should be excluded, 0 if included
+------------------------------------------------------------------------- */
+
+int NPair::exclusion(int i, int j, int itype, int jtype,
+ int *mask, tagint *molecule) const {
+ int m;
+
+ if (nex_type && ex_type[itype][jtype]) return 1;
+
+ if (nex_group) {
+ for (m = 0; m < nex_group; m++) {
+ if (mask[i] & ex1_bit[m] && mask[j] & ex2_bit[m]) return 1;
+ if (mask[i] & ex2_bit[m] && mask[j] & ex1_bit[m]) return 1;
+ }
+ }
+
+ if (nex_mol) {
+ for (m = 0; m < nex_mol; m++)
+ if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
+ molecule[i] == molecule[j]) return 1;
+ }
+
+ return 0;
+}
+
+/* ----------------------------------------------------------------------
+ convert atom coords into local bin #
+ for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo
+ take special care to insure ghosts are in correct bins even w/ roundoff
+ hi ghost atoms = nbin,nbin+1,etc
+ owned atoms = 0 to nbin-1
+ lo ghost atoms = -1,-2,etc
+ this is necessary so that both procs on either side of PBC
+ treat a pair of atoms straddling the PBC in a consistent way
+ for triclinic, doesn't matter since stencil & neigh list built differently
+------------------------------------------------------------------------- */
+
+int NPair::coord2bin(double *x)
+{
+ int ix,iy,iz;
+
+ if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
+ error->one(FLERR,"Non-numeric positions - simulation unstable");
+
+ if (x[0] >= bboxhi[0])
+ ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx) + nbinx;
+ else if (x[0] >= bboxlo[0]) {
+ ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx);
+ ix = MIN(ix,nbinx-1);
+ } else
+ ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
+
+ if (x[1] >= bboxhi[1])
+ iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
+ else if (x[1] >= bboxlo[1]) {
+ iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy);
+ iy = MIN(iy,nbiny-1);
+ } else
+ iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
+
+ if (x[2] >= bboxhi[2])
+ iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
+ else if (x[2] >= bboxlo[2]) {
+ iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz);
+ iz = MIN(iz,nbinz-1);
+ } else
+ iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz) - 1;
+
+ return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
+}
+
+/* ----------------------------------------------------------------------
+ same as coord2bin, but also return ix,iy,iz offsets in each dim
+------------------------------------------------------------------------- */
+
+int NPair::coord2bin(double *x, int &ix, int &iy, int &iz)
+{
+ if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
+ error->one(FLERR,"Non-numeric positions - simulation unstable");
+
+ if (x[0] >= bboxhi[0])
+ ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx) + nbinx;
+ else if (x[0] >= bboxlo[0]) {
+ ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx);
+ ix = MIN(ix,nbinx-1);
+ } else
+ ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
+
+ if (x[1] >= bboxhi[1])
+ iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
+ else if (x[1] >= bboxlo[1]) {
+ iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy);
+ iy = MIN(iy,nbiny-1);
+ } else
+ iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
+
+ if (x[2] >= bboxhi[2])
+ iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
+ else if (x[2] >= bboxlo[2]) {
+ iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz);
+ iz = MIN(iz,nbinz-1);
+ } else
+ iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz) - 1;
+
+ ix -= mbinxlo;
+ iy -= mbinylo;
+ iz -= mbinzlo;
+ return iz*mbiny*mbinx + iy*mbinx + ix;
+}
+
diff --git a/src/npair.h b/src/npair.h
new file mode 100644
index 0000000000..aba7256d73
--- /dev/null
+++ b/src/npair.h
@@ -0,0 +1,146 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_NPAIR_H
+#define LMP_NPAIR_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class NPair : protected Pointers {
+ public:
+ int istyle; // 1-N index into pairnames
+ class NBin *nb; // ptr to NBin instance I depend on
+ class NStencil *ns; // ptr to NStencil instance I depend on
+
+ bigint last_build; // last timestep build performed
+ bigint last_copy_bin_setup; // last timestep I invoked copy_bin_setup_info()
+ bigint last_copy_bin; // last step I invoked copy_bin_info()
+ bigint last_copy_stencil; // last step I invoked copy_bin_stencil_info()
+
+ NPair(class LAMMPS *);
+ virtual ~NPair() {}
+ void copy_neighbor_info();
+ void build_setup();
+ virtual void build(class NeighList *) = 0;
+
+ protected:
+
+ // data from Neighbor class
+
+ int includegroup;
+ int exclude;
+ double skin;
+ double **cutneighsq;
+ double **cutneighghostsq;
+ double cut_inner_sq;
+ double cut_middle_sq;
+ double cut_middle_inside_sq;
+ double *zeroes;
+ double *bboxlo,*bboxhi;
+
+ // exclusion data from Neighbor class
+
+ int nex_type; // # of entries in type exclusion list
+ int *ex1_type,*ex2_type; // pairs of types to exclude
+ int **ex_type; // 2d array of excluded type pairs
+
+ int nex_group; // # of entries in group exclusion list
+ int *ex1_group,*ex2_group; // pairs of group #'s to exclude
+ int *ex1_bit,*ex2_bit; // pairs of group bits to exclude
+
+ int nex_mol; // # of entries in molecule exclusion list
+ int *ex_mol_group; // molecule group #'s to exclude
+ int *ex_mol_bit; // molecule group bits to exclude
+
+ // special data from Neighbor class
+
+ int *special_flag;
+
+ // data from NBin class
+
+ int nbinx,nbiny,nbinz;
+ int mbins;
+ int mbinx,mbiny,mbinz;
+ int mbinxlo,mbinylo,mbinzlo;
+ double bininvx,bininvy,bininvz;
+ int *bins;
+ int *binhead;
+
+ // data from NStencil class
+
+ int nstencil;
+ int nstencil_ssa;
+ int *stencil;
+ int **stencilxyz;
+ int *nstencil_multi;
+ int **stencil_multi;
+ double **distsq_multi;
+
+ // data common to all NPair variants
+
+ int molecular;
+
+ // methods for all NPair variants
+
+ void copy_bin_setup_info();
+ void copy_bin_info();
+ void copy_stencil_info();
+
+ int exclusion(int, int, int,
+ int, int *, tagint *) const; // test for pair exclusion
+ int coord2bin(double *); // mapping atom coord to a bin
+ int coord2bin(double *, int &, int &, int&); // ditto
+
+ // find_special: determine if atom j is in special list of atom i
+ // if it is not, return 0
+ // if it is and special flag is 0 (both coeffs are 0.0), return -1
+ // if it is and special flag is 1 (both coeffs are 1.0), return 0
+ // if it is and special flag is 2 (otherwise), return 1,2,3
+ // for which level of neighbor it is (and which coeff it maps to)
+
+ inline int find_special(const tagint *list, const int *nspecial,
+ const tagint tag) const {
+ const int n1 = nspecial[0];
+ const int n2 = nspecial[1];
+ const int n3 = nspecial[2];
+
+ for (int i = 0; i < n3; i++) {
+ if (list[i] == tag) {
+ if (i < n1) {
+ if (special_flag[1] == 0) return -1;
+ else if (special_flag[1] == 1) return 0;
+ else return 1;
+ } else if (i < n2) {
+ if (special_flag[2] == 0) return -1;
+ else if (special_flag[2] == 1) return 0;
+ else return 2;
+ } else {
+ if (special_flag[3] == 0) return -1;
+ else if (special_flag[3] == 1) return 0;
+ else return 3;
+ }
+ }
+ }
+ return 0;
+ };
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_copy.cpp b/src/npair_copy.cpp
new file mode 100644
index 0000000000..1799d48fed
--- /dev/null
+++ b/src/npair_copy.cpp
@@ -0,0 +1,46 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_copy.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairCopy::NPairCopy(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create list which is simply a copy of parent list
+------------------------------------------------------------------------- */
+
+void NPairCopy::build(NeighList *list)
+{
+ NeighList *listcopy = list->listcopy;
+
+ list->inum = listcopy->inum;
+ list->gnum = listcopy->gnum;
+ list->ilist = listcopy->ilist;
+ list->numneigh = listcopy->numneigh;
+ list->firstneigh = listcopy->firstneigh;
+ list->firstdouble = listcopy->firstdouble;
+ list->ipage = listcopy->ipage;
+ list->dpage = listcopy->dpage;
+}
diff --git a/src/neigh_gran.h b/src/npair_copy.h
similarity index 67%
rename from src/neigh_gran.h
rename to src/npair_copy.h
index 1538f7662a..62467c2d20 100644
--- a/src/neigh_gran.h
+++ b/src/npair_copy.h
@@ -11,12 +11,33 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-/* ERROR/WARNING messages:
+#ifdef NPAIR_CLASS
+
+NPairStyle(copy,
+ NPairCopy,
+ NP_COPY)
+
+#else
+
+#ifndef LMP_NPAIR_COPY_H
+#define LMP_NPAIR_COPY_H
+
+#include "npair.h"
-E: Neighbor list overflow, boost neigh_modify one
+namespace LAMMPS_NS {
-There are too many neighbors of a single atom. Use the neigh_modify
-command to increase the max number of neighbors allowed for one atom.
-You may also want to boost the page size.
+class NPairCopy : public NPair {
+ public:
+ NPairCopy(class LAMMPS *);
+ ~NPairCopy() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
*/
diff --git a/src/npair_full_bin.cpp b/src/npair_full_bin.cpp
new file mode 100644
index 0000000000..a29acb67ab
--- /dev/null
+++ b/src/npair_full_bin.cpp
@@ -0,0 +1,125 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_full_bin.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairFullBin::NPairFullBin(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction for all neighbors
+ every neighbor pair appears in list of both atoms i and j
+------------------------------------------------------------------------- */
+
+void NPairFullBin::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in surrounding bins in stencil including self
+ // skip i = j
+
+ ibin = coord2bin(x[i]);
+
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (i == j) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+ list->gnum = 0;
+}
diff --git a/src/npair_full_bin.h b/src/npair_full_bin.h
new file mode 100644
index 0000000000..c6acde578c
--- /dev/null
+++ b/src/npair_full_bin.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(full/bin,
+ NPairFullBin,
+ NP_FULL | NP_BIN | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_FULL_BIN_H
+#define LMP_NPAIR_FULL_BIN_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairFullBin : public NPair {
+ public:
+ NPairFullBin(class LAMMPS *);
+ ~NPairFullBin() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_full_bin_ghost.cpp b/src/npair_full_bin_ghost.cpp
new file mode 100644
index 0000000000..1e258cf518
--- /dev/null
+++ b/src/npair_full_bin_ghost.cpp
@@ -0,0 +1,156 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_full_bin_ghost.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairFullBinGhost::NPairFullBinGhost(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction for all neighbors
+ include neighbors of ghost atoms, but no "special neighbors" for ghosts
+ every neighbor pair appears in list of both atoms i and j
+------------------------------------------------------------------------- */
+
+void NPairFullBinGhost::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int xbin,ybin,zbin,xbin2,ybin2,zbin2;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ // loop over owned & ghost atoms, storing neighbors
+
+ for (i = 0; i < nall; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in surrounding bins in stencil including self
+ // when i is a ghost atom, must check if stencil bin is out of bounds
+ // skip i = j
+ // no molecular test when i = ghost atom
+
+ if (i < nlocal) {
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (i == j) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ } else {
+ ibin = coord2bin(x[i],xbin,ybin,zbin);
+ for (k = 0; k < nstencil; k++) {
+ xbin2 = xbin + stencilxyz[k][0];
+ ybin2 = ybin + stencilxyz[k][1];
+ zbin2 = zbin + stencilxyz[k][2];
+ if (xbin2 < 0 || xbin2 >= mbinx ||
+ ybin2 < 0 || ybin2 >= mbiny ||
+ zbin2 < 0 || zbin2 >= mbinz) continue;
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (i == j) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = atom->nlocal;
+ list->gnum = inum - atom->nlocal;
+}
diff --git a/src/npair_full_bin_ghost.h b/src/npair_full_bin_ghost.h
new file mode 100644
index 0000000000..a09aab8512
--- /dev/null
+++ b/src/npair_full_bin_ghost.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(full/bin/ghost,
+ NPairFullBinGhost,
+ NP_FULL | NP_BIN | NP_GHOST | NP_NEWTON | NP_NEWTOFF |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_FULL_BIN_GHOST_H
+#define LMP_NPAIR_FULL_BIN_GHOST_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairFullBinGhost : public NPair {
+ public:
+ NPairFullBinGhost(class LAMMPS *);
+ ~NPairFullBinGhost() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp
new file mode 100644
index 0000000000..628a706e7a
--- /dev/null
+++ b/src/npair_full_multi.cpp
@@ -0,0 +1,132 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_full_multi.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction for all neighbors
+ multi-type stencil is itype dependent and is distance checked
+ every neighbor pair appears in list of both atoms i and j
+------------------------------------------------------------------------- */
+
+void NPairFullMulti::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*s;
+ double *cutsq,*distsq;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in other bins in stencil, including self
+ // skip if i,j neighbor cutoff is less than bin distance
+ // skip i = j
+
+ ibin = coord2bin(x[i]);
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ cutsq = cutneighsq[itype];
+ ns = nstencil_multi[itype];
+ for (k = 0; k < ns; k++) {
+ for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+ if (i == j) continue;
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+ list->gnum = 0;
+}
diff --git a/src/npair_full_multi.h b/src/npair_full_multi.h
new file mode 100644
index 0000000000..c778978c01
--- /dev/null
+++ b/src/npair_full_multi.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(full/multi,
+ NPairFullMulti,
+ NP_FULL | NP_MULTI | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_FULL_MULTI_H
+#define LMP_NPAIR_FULL_MULTI_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairFullMulti : public NPair {
+ public:
+ NPairFullMulti(class LAMMPS *);
+ ~NPairFullMulti() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_full_nsq.cpp b/src/npair_full_nsq.cpp
new file mode 100644
index 0000000000..1b404ffc94
--- /dev/null
+++ b/src/npair_full_nsq.cpp
@@ -0,0 +1,125 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_full_nsq.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairFullNsq::NPairFullNsq(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ N^2 search for all neighbors
+ every neighbor pair appears in list of both atoms i and j
+------------------------------------------------------------------------- */
+
+void NPairFullNsq::build(NeighList *list)
+{
+ int i,j,n,itype,jtype,which,bitmask,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+ if (includegroup) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[includegroup];
+ }
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms, owned and ghost
+ // skip i = j
+
+ for (j = 0; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+ if (i == j) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+ list->gnum = 0;
+}
diff --git a/src/npair_full_nsq.h b/src/npair_full_nsq.h
new file mode 100644
index 0000000000..a1eaf8463a
--- /dev/null
+++ b/src/npair_full_nsq.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(full/nsq,
+ NPairFullNsq,
+ NP_FULL | NP_NSQ | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_FULL_NSQ_H
+#define LMP_NPAIR_FULL_NSQ_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairFullNsq : public NPair {
+ public:
+ NPairFullNsq(class LAMMPS *);
+ ~NPairFullNsq() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_full_nsq_ghost.cpp b/src/npair_full_nsq_ghost.cpp
new file mode 100644
index 0000000000..1727b2905e
--- /dev/null
+++ b/src/npair_full_nsq_ghost.cpp
@@ -0,0 +1,138 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_full_nsq_ghost.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairFullNsqGhost::NPairFullNsqGhost(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ N^2 search for all neighbors
+ include neighbors of ghost atoms, but no "special neighbors" for ghosts
+ every neighbor pair appears in list of both atoms i and j
+------------------------------------------------------------------------- */
+
+void NPairFullNsqGhost::build(NeighList *list)
+{
+ int i,j,n,itype,jtype,which,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ // loop over owned & ghost atoms, storing neighbors
+
+ for (i = 0; i < nall; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms, owned and ghost
+ // skip i = j
+ // no molecular test when i = ghost atom
+
+ if (i < nlocal) {
+ for (j = 0; j < nall; j++) {
+ if (i == j) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ } else {
+ for (j = 0; j < nall; j++) {
+ if (i == j) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = atom->nlocal;
+ list->gnum = inum - atom->nlocal;
+}
diff --git a/src/npair_full_nsq_ghost.h b/src/npair_full_nsq_ghost.h
new file mode 100644
index 0000000000..3e259ed098
--- /dev/null
+++ b/src/npair_full_nsq_ghost.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(full/nsq/ghost,
+ NPairFullNsqGhost,
+ NP_FULL | NP_NSQ | NP_GHOST | NP_NEWTON | NP_NEWTOFF |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_FULL_NSQ_GHOST_H
+#define LMP_NPAIR_FULL_NSQ_GHOST_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairFullNsqGhost : public NPair {
+ public:
+ NPairFullNsqGhost(class LAMMPS *);
+ ~NPairFullNsqGhost() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_bin_newtoff.cpp b/src/npair_half_bin_newtoff.cpp
new file mode 100644
index 0000000000..dd072508a9
--- /dev/null
+++ b/src/npair_half_bin_newtoff.cpp
@@ -0,0 +1,129 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_bin_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfBinNewtoff::NPairHalfBinNewtoff(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with partial Newton's 3rd law
+ each owned atom i checks own bin and other bins in stencil
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfBinNewtoff::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in other bins in stencil including self
+ // only store pair if i < j
+ // stores own/own pairs only once
+ // stores own/ghost pairs on both procs
+
+ ibin = coord2bin(x[i]);
+
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (j <= i) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_half_bin_newtoff.h b/src/npair_half_bin_newtoff.h
new file mode 100644
index 0000000000..f6025ac095
--- /dev/null
+++ b/src/npair_half_bin_newtoff.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/bin/newtoff,
+ NPairHalfBinNewtoff,
+ NP_HALF | NP_BIN | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_BIN_NEWTOFF_H
+#define LMP_NPAIR_HALF_BIN_NEWTOFF_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfBinNewtoff : public NPair {
+ public:
+ NPairHalfBinNewtoff(class LAMMPS *);
+ ~NPairHalfBinNewtoff() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_bin_newtoff_ghost.cpp b/src/npair_half_bin_newtoff_ghost.cpp
new file mode 100644
index 0000000000..f486df105a
--- /dev/null
+++ b/src/npair_half_bin_newtoff_ghost.cpp
@@ -0,0 +1,162 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_bin_newtoff_ghost.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfBinNewtoffGhost::NPairHalfBinNewtoffGhost(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with partial Newton's 3rd law
+ include neighbors of ghost atoms, but no "special neighbors" for ghosts
+ owned and ghost atoms check own bin and other bins in stencil
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if i owned and j ghost (also stored by proc owning j)
+ pair stored once if i,j are both ghost and i < j
+------------------------------------------------------------------------- */
+
+void NPairHalfBinNewtoffGhost::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int xbin,ybin,zbin,xbin2,ybin2,zbin2;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ for (i = 0; i < nall; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in other bins in stencil including self
+ // when i is a ghost atom, must check if stencil bin is out of bounds
+ // only store pair if i < j
+ // stores own/own pairs only once
+ // stores own/ghost pairs with owned atom only, on both procs
+ // stores ghost/ghost pairs only once
+ // no molecular test when i = ghost atom
+
+ if (i < nlocal) {
+ ibin = coord2bin(x[i]);
+
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (j <= i) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ } else {
+ ibin = coord2bin(x[i],xbin,ybin,zbin);
+ for (k = 0; k < nstencil; k++) {
+ xbin2 = xbin + stencilxyz[k][0];
+ ybin2 = ybin + stencilxyz[k][1];
+ zbin2 = zbin + stencilxyz[k][2];
+ if (xbin2 < 0 || xbin2 >= mbinx ||
+ ybin2 < 0 || ybin2 >= mbiny ||
+ zbin2 < 0 || zbin2 >= mbinz) continue;
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (j <= i) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = atom->nlocal;
+ list->gnum = inum - atom->nlocal;
+}
diff --git a/src/npair_half_bin_newtoff_ghost.h b/src/npair_half_bin_newtoff_ghost.h
new file mode 100644
index 0000000000..ffdf097f7e
--- /dev/null
+++ b/src/npair_half_bin_newtoff_ghost.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/bin/newtoff/ghost,
+ NPairHalfBinNewtoffGhost,
+ NP_HALF | NP_BIN | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_BIN_NEWTOFF_GHOST_H
+#define LMP_NPAIR_HALF_BIN_NEWTOFF_GHOST_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfBinNewtoffGhost : public NPair {
+ public:
+ NPairHalfBinNewtoffGhost(class LAMMPS *);
+ ~NPairHalfBinNewtoffGhost() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_bin_newton.cpp b/src/npair_half_bin_newton.cpp
new file mode 100644
index 0000000000..f1fc203403
--- /dev/null
+++ b/src/npair_half_bin_newton.cpp
@@ -0,0 +1,161 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_bin_newton.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfBinNewton::NPairHalfBinNewton(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with full Newton's 3rd law
+ each owned atom i checks its own bin and other bins in Newton stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfBinNewton::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over rest of atoms in i's bin, ghosts are at end of linked list
+ // if j is owned atom, store it, since j is beyond i in linked list
+ // if j is ghost, only store if j coords are "above and to the right" of i
+
+ for (j = bins[i]; j >= 0; j = bins[j]) {
+ if (j >= nlocal) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ // loop over all atoms in other bins in stencil, store every pair
+
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_half_bin_newton.h b/src/npair_half_bin_newton.h
new file mode 100644
index 0000000000..c20e3dbef5
--- /dev/null
+++ b/src/npair_half_bin_newton.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/bin/newton,
+ NPairHalfBinNewton,
+ NP_HALF | NP_BIN | NP_NEWTON | NP_ORTHO)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_BIN_NEWTON_H
+#define LMP_NPAIR_HALF_BIN_NEWTON_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfBinNewton : public NPair {
+ public:
+ NPairHalfBinNewton(class LAMMPS *);
+ ~NPairHalfBinNewton() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_bin_newton_ssa.cpp b/src/npair_half_bin_newton_ssa.cpp
new file mode 100644
index 0000000000..b529121a0a
--- /dev/null
+++ b/src/npair_half_bin_newton_ssa.cpp
@@ -0,0 +1,311 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors:
+ James Larentzos and Timothy I. Mattox (Engility Corporation)
+------------------------------------------------------------------------- */
+
+#include "npair_half_bin_newton_ssa.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "group.h"
+#include "memory.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+// allocate space for static class variable
+// prototype for non-class function
+
+static int *ssaAIRptr;
+static int cmp_ssaAIR(const void *, const void *);
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfBinNewtonSSA::NPairHalfBinNewtonSSA(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with full Newton's 3rd law
+ for use by Shardlow Spliting Algorithm
+ each owned atom i checks its own bin and other bins in Newton stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfBinNewtonSSA::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+ if (includegroup) nlocal = atom->nfirst;
+ int *ssaAIR = atom->ssaAIR;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ int molecular = atom->molecular;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+
+ // bin owned and ghost atoms for use by Shardlow Splitting Algorithm
+ // exclude ghost atoms that are not in the Active Interaction Regions (AIR)
+
+ // NOTE to Tim: this binatomflag no longer exists
+ // the logic up higher assures that binning has been done
+ // before this build() method is called
+ // maybe this code below needs to be in a new NBinShardlow class?
+ // this class also inherits NPair::nb from its parent
+ // which points to the NBin class that did the binning
+ // there are last_step variables stored there which indicate
+ // the last time binning was done
+ // the basic question is what data is created/stored by SSA binning
+ // and in what class should it live?
+ // if it is created by the binning operation, then I think
+ // it should be in a new NBinShardlow class
+
+ if (true /* binatomflag */) { // only false in Neighbor::build_one
+
+ if (mbins > list->maxhead_ssa) {
+ list->maxhead_ssa = mbins;
+ memory->destroy(list->gbinhead_ssa);
+ memory->destroy(list->binhead_ssa);
+ memory->create(list->binhead_ssa,list->maxhead_ssa,"binhead_ssa");
+ memory->create(list->gbinhead_ssa,list->maxhead_ssa,"gbinhead_ssa");
+ }
+ for (i = 0; i < mbins; i++) {
+ list->gbinhead_ssa[i] = -1;
+ list->binhead_ssa[i] = -1;
+ }
+
+ if (nall > list->maxbin_ssa) {
+ list->maxbin_ssa = nall;
+ memory->destroy(list->bins_ssa);
+ memory->create(list->bins_ssa,list->maxbin_ssa,"bins_ssa");
+ }
+
+ // bin in reverse order so linked list will be in forward order
+
+ if (includegroup) {
+ int bitmask = group->bitmask[includegroup];
+ int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above
+ for (i = nall-1; i >= nowned; i--) {
+ if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
+ if (mask[i] & bitmask) {
+ ibin = coord2bin(x[i]);
+ list->bins_ssa[i] = list->gbinhead_ssa[ibin];
+ list->gbinhead_ssa[ibin] = i;
+ }
+ }
+ } else {
+ for (i = nall-1; i >= nlocal; i--) {
+ if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
+ ibin = coord2bin(x[i]);
+ list->bins_ssa[i] = list->gbinhead_ssa[ibin];
+ list->gbinhead_ssa[ibin] = i;
+ }
+ }
+ for (i = nlocal-1; i >= 0; i--) {
+ ibin = coord2bin(x[i]);
+ list->bins_ssa[i] = list->binhead_ssa[ibin];
+ list->binhead_ssa[ibin] = i;
+ }
+ } // else reuse previous binning. See Neighbor::build_one comment
+
+ ipage->reset();
+
+ // loop over owned atoms, storing half of the neighbors
+
+ for (i = 0; i < nlocal; i++) {
+ int AIRct[8] = { 0 };
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over rest of local atoms in i's bin
+ // just store them, since j is beyond i in linked list
+
+ for (j = list->bins_ssa[i]; j >= 0; j = list->bins_ssa[j]) {
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ ibin = coord2bin(x[i]);
+
+ // loop over all local atoms in other bins in "half" stencil
+
+ for (k = 0; k < nstencil; k++) {
+ for (j = list->binhead_ssa[ibin+stencil[k]]; j >= 0;
+ j = list->bins_ssa[j]) {
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+ AIRct[0] = n;
+
+ // loop over AIR ghost atoms in all bins in "full" stencil
+ // Note: the non-AIR ghost atoms have already been filtered out
+ // That is a significant time savings because of the "full" stencil
+ // Note2: only non-pure locals can have ghosts as neighbors
+
+ if (ssaAIR[i] == 1) for (k = 0; k < nstencil_ssa; k++) {
+ for (j = list->gbinhead_ssa[ibin+stencil[k]]; j >= 0;
+ j = list->bins_ssa[j]) {
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) {
+ neighptr[n++] = j;
+ ++(AIRct[ssaAIR[j] - 1]);
+ } else if (domain->minimum_image_check(delx,dely,delz)) {
+ neighptr[n++] = j;
+ ++(AIRct[ssaAIR[j] - 1]);
+ } else if (which > 0) {
+ neighptr[n++] = j ^ (which << SBBITS);
+ ++(AIRct[ssaAIR[j] - 1]);
+ }
+ } else {
+ neighptr[n++] = j;
+ ++(AIRct[ssaAIR[j] - 1]);
+ }
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ // sort the ghosts in the neighbor list by their ssaAIR number
+
+ ssaAIRptr = atom->ssaAIR;
+ qsort(&(neighptr[AIRct[0]]), n - AIRct[0], sizeof(int), cmp_ssaAIR);
+
+ // do a prefix sum on the counts to turn them into indexes
+
+ list->ndxAIR_ssa[i][0] = AIRct[0];
+ for (int ndx = 1; ndx < 8; ++ndx) {
+ list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
+ }
+ }
+
+ list->inum = inum;
+}
+
+/* ----------------------------------------------------------------------
+ comparison function invoked by qsort()
+ accesses static class member ssaAIRptr, set before call to qsort()
+------------------------------------------------------------------------- */
+
+static int cmp_ssaAIR(const void *iptr, const void *jptr)
+{
+ int i = *((int *) iptr);
+ int j = *((int *) jptr);
+ if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
+ if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
+ return 0;
+}
+
diff --git a/src/npair_half_bin_newton_ssa.h b/src/npair_half_bin_newton_ssa.h
new file mode 100644
index 0000000000..a2e72d772b
--- /dev/null
+++ b/src/npair_half_bin_newton_ssa.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/bin/newton/ssa,
+ NPairHalfBinNewtonSSA,
+ NP_BIN | NP_NEWTON | NP_ORTHO | NP_SSA)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_BIN_NEWTON_SSA_H
+#define LMP_NPAIR_HALF_BIN_NEWTON_SSA_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfBinNewtonSSA : public NPair {
+ public:
+ NPairHalfBinNewtonSSA(class LAMMPS *);
+ ~NPairHalfBinNewtonSSA() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_bin_newton_tri.cpp b/src/npair_half_bin_newton_tri.cpp
new file mode 100644
index 0000000000..3ef8c3260e
--- /dev/null
+++ b/src/npair_half_bin_newton_tri.cpp
@@ -0,0 +1,134 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_bin_newton_tri.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfBinNewtonTri::NPairHalfBinNewtonTri(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with Newton's 3rd law for triclinic
+ each owned atom i checks its own bin and other bins in triclinic stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfBinNewtonTri::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in bins in stencil
+ // pairs for atoms j "below" i are excluded
+ // below = lower z or (equal z and lower y) or (equal zy and lower x)
+ // (equal zyx and j <= i)
+ // latter excludes self-self interaction but allows superposed atoms
+
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_half_bin_newton_tri.h b/src/npair_half_bin_newton_tri.h
new file mode 100644
index 0000000000..e6b09f58f4
--- /dev/null
+++ b/src/npair_half_bin_newton_tri.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/bin/newton/tri,
+ NPairHalfBinNewtonTri,
+ NP_HALF | NP_BIN | NP_NEWTON | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_BIN_NEWTON_TRI_H
+#define LMP_NPAIR_HALF_BIN_NEWTON_TRI_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfBinNewtonTri : public NPair {
+ public:
+ NPairHalfBinNewtonTri(class LAMMPS *);
+ ~NPairHalfBinNewtonTri() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp
new file mode 100644
index 0000000000..11e45d91ff
--- /dev/null
+++ b/src/npair_half_multi_newtoff.cpp
@@ -0,0 +1,135 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_multi_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with partial Newton's 3rd law
+ each owned atom i checks own bin and other bins in stencil
+ multi-type stencil is itype dependent and is distance checked
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfMultiNewtoff::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*s;
+ double *cutsq,*distsq;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in other bins in stencil including self
+ // only store pair if i < j
+ // skip if i,j neighbor cutoff is less than bin distance
+ // stores own/own pairs only once
+ // stores own/ghost pairs on both procs
+
+ ibin = coord2bin(x[i]);
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ cutsq = cutneighsq[itype];
+ ns = nstencil_multi[itype];
+ for (k = 0; k < ns; k++) {
+ for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
+ if (j <= i) continue;
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_half_multi_newtoff.h b/src/npair_half_multi_newtoff.h
new file mode 100644
index 0000000000..4c57c9bfe7
--- /dev/null
+++ b/src/npair_half_multi_newtoff.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/multi/newtoff,
+ NPairHalfMultiNewtoff,
+ NP_HALF | NP_MULTI | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_MULTI_NEWTOFF_H
+#define LMP_NPAIR_HALF_MULTI_NEWTOFF_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfMultiNewtoff : public NPair {
+ public:
+ NPairHalfMultiNewtoff(class LAMMPS *);
+ ~NPairHalfMultiNewtoff() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp
new file mode 100644
index 0000000000..cd3a37821f
--- /dev/null
+++ b/src/npair_half_multi_newton.cpp
@@ -0,0 +1,168 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_multi_newton.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with full Newton's 3rd law
+ each owned atom i checks its own bin and other bins in Newton stencil
+ multi-type stencil is itype dependent and is distance checked
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfMultiNewton::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*s;
+ double *cutsq,*distsq;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over rest of atoms in i's bin, ghosts are at end of linked list
+ // if j is owned atom, store it, since j is beyond i in linked list
+ // if j is ghost, only store if j coords are "above and to the right" of i
+
+ for (j = bins[i]; j >= 0; j = bins[j]) {
+ if (j >= nlocal) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ // loop over all atoms in other bins in stencil, store every pair
+ // skip if i,j neighbor cutoff is less than bin distance
+
+ ibin = coord2bin(x[i]);
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ cutsq = cutneighsq[itype];
+ ns = nstencil_multi[itype];
+ for (k = 0; k < ns; k++) {
+ for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_half_multi_newton.h b/src/npair_half_multi_newton.h
new file mode 100644
index 0000000000..64021a9f58
--- /dev/null
+++ b/src/npair_half_multi_newton.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/multi/newton,
+ NPairHalfMultiNewton,
+ NP_HALF | NP_MULTI | NP_NEWTON | NP_ORTHO)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_H
+#define LMP_NPAIR_HALF_MULTI_NEWTON_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfMultiNewton : public NPair {
+ public:
+ NPairHalfMultiNewton(class LAMMPS *);
+ ~NPairHalfMultiNewton() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp
new file mode 100644
index 0000000000..f9aaeb0414
--- /dev/null
+++ b/src/npair_half_multi_newton_tri.cpp
@@ -0,0 +1,143 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_multi_newton_tri.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ binned neighbor list construction with Newton's 3rd law for triclinic
+ each owned atom i checks its own bin and other bins in triclinic stencil
+ multi-type stencil is itype dependent and is distance checked
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfMultiNewtonTri::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*s;
+ double *cutsq,*distsq;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in bins, including self, in stencil
+ // skip if i,j neighbor cutoff is less than bin distance
+ // bins below self are excluded from stencil
+ // pairs for atoms j "below" i are excluded
+ // below = lower z or (equal z and lower y) or (equal zy and lower x)
+ // (equal zyx and j <= i)
+ // latter excludes self-self interaction but allows superposed atoms
+
+ ibin = coord2bin(x[i]);
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ cutsq = cutneighsq[itype];
+ ns = nstencil_multi[itype];
+ for (k = 0; k < ns; k++) {
+ for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_half_multi_newton_tri.h b/src/npair_half_multi_newton_tri.h
new file mode 100644
index 0000000000..51b720e0c4
--- /dev/null
+++ b/src/npair_half_multi_newton_tri.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/multi/newton/tri,
+ NPairHalfMultiNewtonTri,
+ NP_HALF | NP_MULTI | NP_NEWTON | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_TRI_H
+#define LMP_NPAIR_HALF_MULTI_NEWTON_TRI_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfMultiNewtonTri : public NPair {
+ public:
+ NPairHalfMultiNewtonTri(class LAMMPS *);
+ ~NPairHalfMultiNewtonTri() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_nsq_newtoff.cpp b/src/npair_half_nsq_newtoff.cpp
new file mode 100644
index 0000000000..06e8344332
--- /dev/null
+++ b/src/npair_half_nsq_newtoff.cpp
@@ -0,0 +1,125 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_nsq_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfNsqNewtoff::NPairHalfNsqNewtoff(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfNsqNewtoff::build(NeighList *list)
+{
+ int i,j,n,itype,jtype,which,bitmask,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+ if (includegroup) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[includegroup];
+ }
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over remaining atoms, owned and ghost
+ // only store pair if i < j
+
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_half_nsq_newtoff.h b/src/npair_half_nsq_newtoff.h
new file mode 100644
index 0000000000..90a1990f7f
--- /dev/null
+++ b/src/npair_half_nsq_newtoff.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/nsq/newtoff,
+ NPairHalfNsqNewtoff,
+ NP_HALF | NP_NSQ | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_NSQ_NEWTOFF_H
+#define LMP_NPAIR_HALF_NSQ_NEWTOFF_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfNsqNewtoff : public NPair {
+ public:
+ NPairHalfNsqNewtoff(class LAMMPS *);
+ ~NPairHalfNsqNewtoff() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_nsq_newtoff_ghost.cpp b/src/npair_half_nsq_newtoff_ghost.cpp
new file mode 100644
index 0000000000..1865061a8b
--- /dev/null
+++ b/src/npair_half_nsq_newtoff_ghost.cpp
@@ -0,0 +1,150 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_nsq_newtoff_ghost.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfNsqNewtoffGhost::NPairHalfNsqNewtoffGhost(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
+ include neighbors of ghost atoms, but no "special neighbors" for ghosts
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if i owned and j ghost (also stored by proc owning j)
+ pair stored once if i,j are both ghost and i < j
+------------------------------------------------------------------------- */
+
+void NPairHalfNsqNewtoffGhost::build(NeighList *list)
+{
+ int i,j,n,itype,jtype,which,bitmask,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+ if (includegroup) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[includegroup];
+ }
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ // loop over owned & ghost atoms, storing neighbors
+
+ for (i = 0; i < nall; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over remaining atoms, owned and ghost
+ // only store pair if i < j
+ // stores own/own pairs only once
+ // stores own/ghost pairs with owned atom only, on both procs
+ // stores ghost/ghost pairs only once
+ // no molecular test when i = ghost atom
+
+ if (i < nlocal) {
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ } else {
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) neighptr[n++] = j;
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = atom->nlocal;
+ list->gnum = inum - atom->nlocal;
+}
diff --git a/src/npair_half_nsq_newtoff_ghost.h b/src/npair_half_nsq_newtoff_ghost.h
new file mode 100644
index 0000000000..e772b4b5c4
--- /dev/null
+++ b/src/npair_half_nsq_newtoff_ghost.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/nsq/newtoff/ghost,
+ NPairHalfNsqNewtoffGhost,
+ NP_HALF | NP_NSQ | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_NSQ_NEWTOFF_GHOST_H
+#define LMP_NPAIR_HALF_NSQ_NEWTOFF_GHOST_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfNsqNewtoffGhost : public NPair {
+ public:
+ NPairHalfNsqNewtoffGhost(class LAMMPS *);
+ ~NPairHalfNsqNewtoffGhost() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_nsq_newton.cpp b/src/npair_half_nsq_newton.cpp
new file mode 100644
index 0000000000..11c71d5609
--- /dev/null
+++ b/src/npair_half_nsq_newton.cpp
@@ -0,0 +1,142 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_nsq_newton.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfNsqNewton::NPairHalfNsqNewton(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ N^2 / 2 search for neighbor pairs with full Newton's 3rd law
+ every pair stored exactly once by some processor
+ decision on ghost atoms based on itag,jtag tests
+------------------------------------------------------------------------- */
+
+void NPairHalfNsqNewton::build(NeighList *list)
+{
+ int i,j,n,itype,jtype,which,bitmask,imol,iatom,moltemplate;
+ tagint itag,jtag,tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+ if (includegroup) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[includegroup];
+ }
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int inum = 0;
+ ipage->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ itag = tag[i];
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over remaining atoms, owned and ghost
+ // itag = jtag is possible for long cutoffs that include images of self
+
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+
+ if (j >= nlocal) {
+ jtag = tag[j];
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if (domain->minimum_image_check(delx,dely,delz))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_half_nsq_newton.h b/src/npair_half_nsq_newton.h
new file mode 100644
index 0000000000..7373c44f1a
--- /dev/null
+++ b/src/npair_half_nsq_newton.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/nsq/newton,
+ NPairHalfNsqNewton,
+ NP_HALF | NP_NSQ | NP_NEWTON | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_NSQ_NEWTON_H
+#define LMP_NPAIR_HALF_NSQ_NEWTON_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfNsqNewton : public NPair {
+ public:
+ NPairHalfNsqNewton(class LAMMPS *);
+ ~NPairHalfNsqNewton() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_respa_bin_newtoff.cpp b/src/npair_half_respa_bin_newtoff.cpp
new file mode 100644
index 0000000000..39f68a289d
--- /dev/null
+++ b/src/npair_half_respa_bin_newtoff.cpp
@@ -0,0 +1,190 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_respa_bin_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfRespaBinNewtoff::NPairHalfRespaBinNewtoff(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ multiple respa lists
+ binned neighbor list construction with partial Newton's 3rd law
+ each owned atom i checks own bin and surrounding bins in non-Newton stencil
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfRespaBinNewtoff::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ NeighList *listinner = list->listinner;
+ int *ilist_inner = listinner->ilist;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+ MyPage<int> *ipage_inner = listinner->ipage;
+
+ NeighList *listmiddle;
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ MyPage<int> *ipage_middle;
+ int respamiddle = list->respamiddle;
+ if (respamiddle) {
+ listmiddle = list->listmiddle;
+ ilist_middle = listmiddle->ilist;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ ipage_middle = listmiddle->ipage;
+ }
+
+ int inum = 0;
+ int which = 0;
+ int minchange = 0;
+ ipage->reset();
+ ipage_inner->reset();
+ if (respamiddle) ipage_middle->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = n_inner = 0;
+ neighptr = ipage->vget();
+ neighptr_inner = ipage_inner->vget();
+ if (respamiddle) {
+ n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
+ }
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ ibin = coord2bin(x[i]);
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in surrounding bins in stencil including self
+ // only store pair if i < j
+ // stores own/own pairs only once
+ // stores own/ghost pairs on both procs
+
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (j <= i) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (minchange) neighptr_inner[n_inner++] = j;
+ else if (which > 0)
+ neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (minchange) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
+ }
+ }
+
+ ilist[inum] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ ilist_inner[inum] = i;
+ firstneigh_inner[i] = neighptr_inner;
+ numneigh_inner[i] = n_inner;
+ ipage_inner->vgot(n_inner);
+ if (ipage_inner->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (respamiddle) {
+ ilist_middle[inum] = i;
+ firstneigh_middle[i] = neighptr_middle;
+ numneigh_middle[i] = n_middle;
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ inum++;
+ }
+
+ list->inum = inum;
+ listinner->inum = inum;
+ if (respamiddle) listmiddle->inum = inum;
+}
diff --git a/src/npair_half_respa_bin_newtoff.h b/src/npair_half_respa_bin_newtoff.h
new file mode 100644
index 0000000000..290783d8fe
--- /dev/null
+++ b/src/npair_half_respa_bin_newtoff.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/respa/bin/newtoff,
+ NPairHalfRespaBinNewtoff,
+ NP_HALF | NP_RESPA | NP_BIN | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_RESPA_BIN_NEWTOFF_H
+#define LMP_NPAIR_HALF_RESPA_BIN_NEWTOFF_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfRespaBinNewtoff : public NPair {
+ public:
+ NPairHalfRespaBinNewtoff(class LAMMPS *);
+ ~NPairHalfRespaBinNewtoff() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_respa_bin_newton.cpp b/src/npair_half_respa_bin_newton.cpp
new file mode 100644
index 0000000000..537a72d0c1
--- /dev/null
+++ b/src/npair_half_respa_bin_newton.cpp
@@ -0,0 +1,236 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_respa_bin_newton.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfRespaBinNewton::NPairHalfRespaBinNewton(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ multiple respa lists
+ binned neighbor list construction with full Newton's 3rd law
+ each owned atom i checks its own bin and other bins in Newton stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfRespaBinNewton::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ NeighList *listinner = list->listinner;
+ int *ilist_inner = listinner->ilist;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+ MyPage<int> *ipage_inner = listinner->ipage;
+
+ NeighList *listmiddle;
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ MyPage<int> *ipage_middle;
+ int respamiddle = list->respamiddle;
+ if (respamiddle) {
+ listmiddle = list->listmiddle;
+ ilist_middle = listmiddle->ilist;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ ipage_middle = listmiddle->ipage;
+ }
+
+ int inum = 0;
+ int which = 0;
+ int minchange = 0;
+ ipage->reset();
+ ipage_inner->reset();
+ if (respamiddle) ipage_middle->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = n_inner = 0;
+ neighptr = ipage->vget();
+ neighptr_inner = ipage_inner->vget();
+ if (respamiddle) {
+ n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
+ }
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over rest of atoms in i's bin, ghosts are at end of linked list
+ // if j is owned atom, store it, since j is beyond i in linked list
+ // if j is ghost, only store if j coords are "above and to the right" of i
+
+ for (j = bins[i]; j >= 0; j = bins[j]) {
+ if (j >= nlocal) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (minchange) neighptr_inner[n_inner++] = j;
+ else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (minchange) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
+ }
+
+ // loop over all atoms in other bins in stencil, store every pair
+
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (minchange) neighptr_inner[n_inner++] = j;
+ else if (which > 0)
+ neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (minchange) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
+ }
+ }
+
+ ilist[inum] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ ilist_inner[inum] = i;
+ firstneigh_inner[i] = neighptr_inner;
+ numneigh_inner[i] = n_inner;
+ ipage_inner->vgot(n_inner);
+ if (ipage_inner->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (respamiddle) {
+ ilist_middle[inum] = i;
+ firstneigh_middle[i] = neighptr_middle;
+ numneigh_middle[i] = n_middle;
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ inum++;
+ }
+
+ list->inum = inum;
+ listinner->inum = inum;
+ if (respamiddle) listmiddle->inum = inum;
+}
diff --git a/src/npair_half_respa_bin_newton.h b/src/npair_half_respa_bin_newton.h
new file mode 100644
index 0000000000..d1566ee943
--- /dev/null
+++ b/src/npair_half_respa_bin_newton.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/respa/bin/newton,
+ NPairHalfRespaBinNewton,
+ NP_HALF | NP_RESPA | NP_BIN | NP_NEWTON | NP_ORTHO)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_RESPA_BIN_NEWTON_H
+#define LMP_NPAIR_HALF_RESPA_BIN_NEWTON_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfRespaBinNewton : public NPair {
+ public:
+ NPairHalfRespaBinNewton(class LAMMPS *);
+ ~NPairHalfRespaBinNewton() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_respa_bin_newton_tri.cpp b/src/npair_half_respa_bin_newton_tri.cpp
new file mode 100644
index 0000000000..9c5fd39fbe
--- /dev/null
+++ b/src/npair_half_respa_bin_newton_tri.cpp
@@ -0,0 +1,198 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_respa_bin_newton_tri.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfRespaBinNewtonTri::NPairHalfRespaBinNewtonTri(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ multiple respa lists
+ binned neighbor list construction with Newton's 3rd law for triclinic
+ each owned atom i checks its own bin and other bins in triclinic stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfRespaBinNewtonTri::build(NeighList *list)
+{
+ int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ NeighList *listinner = list->listinner;
+ int *ilist_inner = listinner->ilist;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+ MyPage<int> *ipage_inner = listinner->ipage;
+
+ NeighList *listmiddle;
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ MyPage<int> *ipage_middle;
+ int respamiddle = list->respamiddle;
+ if (respamiddle) {
+ listmiddle = list->listmiddle;
+ ilist_middle = listmiddle->ilist;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ ipage_middle = listmiddle->ipage;
+ }
+
+ int inum = 0;
+ int which = 0;
+ int minchange = 0;
+ ipage->reset();
+ ipage_inner->reset();
+ if (respamiddle) ipage_middle->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = n_inner = 0;
+ neighptr = ipage->vget();
+ neighptr_inner = ipage_inner->vget();
+ if (respamiddle) {
+ n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
+ }
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over all atoms in bins in stencil
+ // pairs for atoms j "below" i are excluded
+ // below = lower z or (equal z and lower y) or (equal zy and lower x)
+ // (equal zyx and j <= i)
+ // latter excludes self-self interaction but allows superposed atoms
+
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (minchange) neighptr_inner[n_inner++] = j;
+ else if (which > 0)
+ neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (minchange) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
+ }
+ }
+
+ ilist[inum] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ ilist_inner[inum] = i;
+ firstneigh_inner[i] = neighptr_inner;
+ numneigh_inner[i] = n_inner;
+ ipage_inner->vgot(n_inner);
+ if (ipage_inner->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (respamiddle) {
+ ilist_middle[inum] = i;
+ firstneigh_middle[i] = neighptr_middle;
+ numneigh_middle[i] = n_middle;
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ inum++;
+ }
+
+ list->inum = inum;
+ listinner->inum = inum;
+ if (respamiddle) listmiddle->inum = inum;
+}
diff --git a/src/npair_half_respa_bin_newton_tri.h b/src/npair_half_respa_bin_newton_tri.h
new file mode 100644
index 0000000000..779a3cd1db
--- /dev/null
+++ b/src/npair_half_respa_bin_newton_tri.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/respa/bin/newton/tri,
+ NPairHalfRespaBinNewtonTri,
+ NP_HALF | NP_RESPA | NP_BIN | NP_NEWTON | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_RESPA_BIN_NEWTON_TRI_H
+#define LMP_NPAIR_HALF_RESPA_BIN_NEWTON_TRI_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfRespaBinNewtonTri : public NPair {
+ public:
+ NPairHalfRespaBinNewtonTri(class LAMMPS *);
+ ~NPairHalfRespaBinNewtonTri() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_respa_nsq_newtoff.cpp b/src/npair_half_respa_nsq_newtoff.cpp
new file mode 100644
index 0000000000..1bb2034384
--- /dev/null
+++ b/src/npair_half_respa_nsq_newtoff.cpp
@@ -0,0 +1,185 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_respa_nsq_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfRespaNsqNewtoff::NPairHalfRespaNsqNewtoff(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ multiple respa lists
+ N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
+ pair added to list if atoms i and j are both owned and i < j
+ pair added if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfRespaNsqNewtoff::build(NeighList *list)
+{
+ int i,j,n,itype,jtype,n_inner,n_middle,bitmask,imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+ if (includegroup) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[includegroup];
+ }
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ NeighList *listinner = list->listinner;
+ int *ilist_inner = listinner->ilist;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+ MyPage<int> *ipage_inner = listinner->ipage;
+
+ NeighList *listmiddle;
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ MyPage<int> *ipage_middle;
+ int respamiddle = list->respamiddle;
+ if (respamiddle) {
+ listmiddle = list->listmiddle;
+ ilist_middle = listmiddle->ilist;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ ipage_middle = listmiddle->ipage;
+ }
+
+ int inum = 0;
+ int which = 0;
+ int minchange = 0;
+ ipage->reset();
+ ipage_inner->reset();
+ if (respamiddle) ipage_middle->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = n_inner = 0;
+ neighptr = ipage->vget();
+ neighptr_inner = ipage_inner->vget();
+ if (respamiddle) {
+ n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
+ }
+
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over remaining atoms, owned and ghost
+
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (minchange) neighptr_inner[n_inner++] = j;
+ else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (minchange) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
+ }
+
+ ilist[inum] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ ilist_inner[inum] = i;
+ firstneigh_inner[i] = neighptr_inner;
+ numneigh_inner[i] = n_inner;
+ ipage_inner->vgot(n_inner);
+ if (ipage_inner->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (respamiddle) {
+ ilist_middle[inum] = i;
+ firstneigh_middle[i] = neighptr_middle;
+ numneigh_middle[i] = n_middle;
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ inum++;
+ }
+
+ list->inum = inum;
+ listinner->inum = inum;
+ if (respamiddle) listmiddle->inum = inum;
+}
diff --git a/src/npair_half_respa_nsq_newtoff.h b/src/npair_half_respa_nsq_newtoff.h
new file mode 100644
index 0000000000..71f936c4ae
--- /dev/null
+++ b/src/npair_half_respa_nsq_newtoff.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/respa/nsq/newtoff,
+ NPairHalfRespaNsqNewtoff,
+ NP_HALF | NP_RESPA | NP_NSQ | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_RESPA_NSQ_NEWTOFF_H
+#define LMP_NPAIR_HALF_RESPA_NSQ_NEWTOFF_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfRespaNsqNewtoff : public NPair {
+ public:
+ NPairHalfRespaNsqNewtoff(class LAMMPS *);
+ ~NPairHalfRespaNsqNewtoff() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_respa_nsq_newton.cpp b/src/npair_half_respa_nsq_newton.cpp
new file mode 100644
index 0000000000..9aacc702cc
--- /dev/null
+++ b/src/npair_half_respa_nsq_newton.cpp
@@ -0,0 +1,205 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_half_respa_nsq_newton.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfRespaNsqNewton::NPairHalfRespaNsqNewton(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ multiple respa lists
+ N^2 / 2 search for neighbor pairs with full Newton's 3rd law
+ pair added to list if atoms i and j are both owned and i < j
+ if j is ghost only me or other proc adds pair
+ decision based on itag,jtag tests
+------------------------------------------------------------------------- */
+
+void NPairHalfRespaNsqNewton::build(NeighList *list)
+{
+ int i,j,n,itype,jtype,itag,jtag,n_inner,n_middle,bitmask;
+ int imol,iatom,moltemplate;
+ tagint tagprev;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ tagint *molecule = atom->molecule;
+ tagint **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+ if (includegroup) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[includegroup];
+ }
+
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ Molecule **onemols = atom->avec->onemols;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ NeighList *listinner = list->listinner;
+ int *ilist_inner = listinner->ilist;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+ MyPage<int> *ipage_inner = listinner->ipage;
+
+ NeighList *listmiddle;
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ MyPage<int> *ipage_middle;
+ int respamiddle = list->respamiddle;
+ if (respamiddle) {
+ listmiddle = list->listmiddle;
+ ilist_middle = listmiddle->ilist;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ ipage_middle = listmiddle->ipage;
+ }
+
+ int inum = 0;
+ int which = 0;
+ int minchange = 0;
+ ipage->reset();
+ ipage_inner->reset();
+ if (respamiddle) ipage_middle->reset();
+
+ for (i = 0; i < nlocal; i++) {
+ n = n_inner = 0;
+ neighptr = ipage->vget();
+ neighptr_inner = ipage_inner->vget();
+ if (respamiddle) {
+ n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
+ }
+
+ itag = tag[i];
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ if (moltemplate) {
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ }
+
+ // loop over remaining atoms, owned and ghost
+
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+
+ if (j >= nlocal) {
+ jtag = tag[j];
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(special[i],nspecial[i],tag[j]);
+ else if (imol >= 0)
+ which = find_special(onemols[imol]->special[iatom],
+ onemols[imol]->nspecial[iatom],
+ tag[j]-tagprev);
+ else which = 0;
+ if (which == 0) neighptr[n++] = j;
+ else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
+ neighptr[n++] = j;
+ else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (minchange) neighptr_inner[n_inner++] = j;
+ else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (minchange) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
+ }
+
+ ilist[inum] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ ilist_inner[inum] = i;
+ firstneigh_inner[i] = neighptr_inner;
+ numneigh_inner[i] = n_inner;
+ ipage_inner->vgot(n_inner);
+ if (ipage_inner->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (respamiddle) {
+ ilist_middle[inum] = i;
+ firstneigh_middle[i] = neighptr_middle;
+ numneigh_middle[i] = n_middle;
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ inum++;
+ }
+
+ list->inum = inum;
+ listinner->inum = inum;
+ if (respamiddle) listmiddle->inum = inum;
+}
diff --git a/src/npair_half_respa_nsq_newton.h b/src/npair_half_respa_nsq_newton.h
new file mode 100644
index 0000000000..ad6828b46a
--- /dev/null
+++ b/src/npair_half_respa_nsq_newton.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/respa/nsq/newton,
+ NPairHalfRespaNsqNewton,
+ NP_HALF | NP_RESPA | NP_NSQ | NP_NEWTON | NP_ORTHO)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_RESPA_NSQ_NEWTON_H
+#define LMP_NPAIR_HALF_RESPA_NSQ_NEWTON_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfRespaNsqNewton : public NPair {
+ public:
+ NPairHalfRespaNsqNewton(class LAMMPS *);
+ ~NPairHalfRespaNsqNewton() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp
new file mode 100644
index 0000000000..b87bede312
--- /dev/null
+++ b/src/npair_half_size_bin_newtoff.cpp
@@ -0,0 +1,171 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "npair_half_size_bin_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "fix_shear_history.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfSizeBinNewtoff::NPairHalfSizeBinNewtoff(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ size particles
+ binned neighbor list construction with partial Newton's 3rd law
+ shear history must be accounted for when a neighbor pair is added
+ each owned atom i checks own bin and surrounding bins in non-Newton stencil
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfSizeBinNewtoff::build(NeighList *list)
+{
+ int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ double radi,radsum,cutsq;
+ int *neighptr,*touchptr;
+ double *shearptr;
+
+ int *npartner;
+ tagint **partner;
+ double **shearpartner;
+ int **firsttouch;
+ double **firstshear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
+ NeighList *listgranhistory;
+
+ double **x = atom->x;
+ double *radius = atom->radius;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *molecule = atom->molecule;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ FixShearHistory *fix_history = list->fix_history;
+ if (fix_history) {
+ fix_history->nlocal_neigh = nlocal;
+ fix_history->nall_neigh = nlocal + atom->nghost;
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ listgranhistory = list->listgranhistory;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ ipage_touch = listgranhistory->ipage;
+ dpage_shear = listgranhistory->dpage;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
+ }
+
+ int inum = 0;
+ ipage->reset();
+ if (fix_history) {
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+ if (fix_history) {
+ nn = 0;
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
+ }
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ radi = radius[i];
+ ibin = coord2bin(x[i]);
+
+ // loop over all atoms in surrounding bins in stencil including self
+ // only store pair if i < j
+ // stores own/own pairs only once
+ // stores own/ghost pairs on both procs
+
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (j <= i) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) {
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ }
+
+ n++;
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (fix_history) {
+ firsttouch[i] = touchptr;
+ firstshear[i] = shearptr;
+ ipage_touch->vgot(n);
+ dpage_shear->vgot(nn);
+ }
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_half_size_bin_newtoff.h b/src/npair_half_size_bin_newtoff.h
new file mode 100644
index 0000000000..ec3b1af7e9
--- /dev/null
+++ b/src/npair_half_size_bin_newtoff.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/size/bin/newtoff,
+ NPairHalfSizeBinNewtoff,
+ NP_HALF | NP_SIZE | NP_BIN | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_SIZE_BIN_NEWTOFF_H
+#define LMP_NPAIR_HALF_SIZE_BIN_NEWTOFF_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfSizeBinNewtoff : public NPair {
+ public:
+ NPairHalfSizeBinNewtoff(class LAMMPS *);
+ ~NPairHalfSizeBinNewtoff() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp
new file mode 100644
index 0000000000..8a32f4e6d6
--- /dev/null
+++ b/src/npair_half_size_bin_newton.cpp
@@ -0,0 +1,215 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "npair_half_size_bin_newton.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "fix_shear_history.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfSizeBinNewton::NPairHalfSizeBinNewton(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ size particles
+ binned neighbor list construction with full Newton's 3rd law
+ shear history must be accounted for when a neighbor pair is added
+ each owned atom i checks its own bin and other bins in Newton stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfSizeBinNewton::build(NeighList *list)
+{
+ int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ double radi,radsum,cutsq;
+ int *neighptr,*touchptr;
+ double *shearptr;
+
+ int *npartner;
+ tagint **partner;
+ double **shearpartner;
+ int **firsttouch;
+ double **firstshear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
+ NeighList *listgranhistory;
+
+ double **x = atom->x;
+ double *radius = atom->radius;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *molecule = atom->molecule;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ FixShearHistory *fix_history = list->fix_history;
+ if (fix_history) {
+ fix_history->nlocal_neigh = nlocal;
+ fix_history->nall_neigh = nlocal + atom->nghost;
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ listgranhistory = list->listgranhistory;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ ipage_touch = listgranhistory->ipage;
+ dpage_shear = listgranhistory->dpage;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
+ }
+
+ int inum = 0;
+ ipage->reset();
+ if (fix_history) {
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+ if (fix_history) {
+ nn = 0;
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
+ }
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ radi = radius[i];
+
+ // loop over rest of atoms in i's bin, ghosts are at end of linked list
+ // if j is owned atom, store it, since j is beyond i in linked list
+ // if j is ghost, only store if j coords are "above and to the right" of i
+
+ for (j = bins[i]; j >= 0; j = bins[j]) {
+ if (j >= nlocal) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) {
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ }
+
+ n++;
+ }
+ }
+
+ // loop over all atoms in other bins in stencil, store every pair
+
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) {
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ }
+
+ n++;
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (fix_history) {
+ firsttouch[i] = touchptr;
+ firstshear[i] = shearptr;
+ ipage_touch->vgot(n);
+ dpage_shear->vgot(nn);
+ }
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_half_size_bin_newton.h b/src/npair_half_size_bin_newton.h
new file mode 100644
index 0000000000..71ec9c5a37
--- /dev/null
+++ b/src/npair_half_size_bin_newton.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/size/bin/newton,
+ NPairHalfSizeBinNewton,
+ NP_HALF | NP_SIZE | NP_BIN | NP_NEWTON | NP_ORTHO)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_SIZE_BIN_NEWTON_H
+#define LMP_NPAIR_HALF_SIZE_BIN_NEWTON_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfSizeBinNewton : public NPair {
+ public:
+ NPairHalfSizeBinNewton(class LAMMPS *);
+ ~NPairHalfSizeBinNewton() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_size_bin_newton_tri.cpp b/src/npair_half_size_bin_newton_tri.cpp
new file mode 100644
index 0000000000..620a07159e
--- /dev/null
+++ b/src/npair_half_size_bin_newton_tri.cpp
@@ -0,0 +1,180 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "npair_half_size_bin_newton_tri.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "fix_shear_history.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfSizeBinNewtonTri::NPairHalfSizeBinNewtonTri(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ size particles
+ binned neighbor list construction with Newton's 3rd law for triclinic
+ shear history must be accounted for when a neighbor pair is added
+ each owned atom i checks its own bin and other bins in triclinic stencil
+ every pair stored exactly once by some processor
+------------------------------------------------------------------------- */
+
+void NPairHalfSizeBinNewtonTri::build(NeighList *list)
+{
+ int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ double radi,radsum,cutsq;
+ int *neighptr,*touchptr;
+ double *shearptr;
+
+ int *npartner;
+ tagint **partner;
+ double **shearpartner;
+ int **firsttouch;
+ double **firstshear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
+ NeighList *listgranhistory;
+
+ double **x = atom->x;
+ double *radius = atom->radius;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *molecule = atom->molecule;
+ int nlocal = atom->nlocal;
+ if (includegroup) nlocal = atom->nfirst;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ FixShearHistory *fix_history = list->fix_history;
+ if (fix_history) {
+ fix_history->nlocal_neigh = nlocal;
+ fix_history->nall_neigh = nlocal + atom->nghost;
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ listgranhistory = list->listgranhistory;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ ipage_touch = listgranhistory->ipage;
+ dpage_shear = listgranhistory->dpage;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
+ }
+
+ int inum = 0;
+ ipage->reset();
+ if (fix_history) {
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+ if (fix_history) {
+ nn = 0;
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
+ }
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ radi = radius[i];
+
+ // loop over all atoms in bins in stencil
+ // pairs for atoms j "below" i are excluded
+ // below = lower z or (equal z and lower y) or (equal zy and lower x)
+ // (equal zyx and j <= i)
+ // latter excludes self-self interaction but allows superposed atoms
+
+ ibin = coord2bin(x[i]);
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) {
+ neighptr[n++] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ }
+
+ n++;
+ }
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (fix_history) {
+ firsttouch[i] = touchptr;
+ firstshear[i] = shearptr;
+ ipage_touch->vgot(n);
+ dpage_shear->vgot(nn);
+ }
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_half_size_bin_newton_tri.h b/src/npair_half_size_bin_newton_tri.h
new file mode 100644
index 0000000000..bf956aa7fe
--- /dev/null
+++ b/src/npair_half_size_bin_newton_tri.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/size/bin/newton/tri,
+ NPairHalfSizeBinNewtonTri,
+ NP_HALF | NP_SIZE | NP_BIN | NP_NEWTON | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_SIZE_BIN_NEWTON_TRI_H
+#define LMP_NPAIR_HALF_SIZE_BIN_NEWTON_TRI_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfSizeBinNewtonTri : public NPair {
+ public:
+ NPairHalfSizeBinNewtonTri(class LAMMPS *);
+ ~NPairHalfSizeBinNewtonTri() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_size_nsq_newtoff.cpp b/src/npair_half_size_nsq_newtoff.cpp
new file mode 100644
index 0000000000..1c2d079893
--- /dev/null
+++ b/src/npair_half_size_nsq_newtoff.cpp
@@ -0,0 +1,169 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "npair_half_size_nsq_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "fix_shear_history.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfSizeNsqNewtoff::NPairHalfSizeNsqNewtoff(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ size particles
+ N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
+ shear history must be accounted for when a neighbor pair is added
+ pair added to list if atoms i and j are both owned and i < j
+ pair added if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfSizeNsqNewtoff::build(NeighList *list)
+{
+ int i,j,m,n,nn,bitmask,dnum,dnumbytes;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ double radi,radsum,cutsq;
+ int *neighptr,*touchptr;
+ double *shearptr;
+
+ int *npartner;
+ tagint **partner;
+ double **shearpartner;
+ int **firsttouch;
+ double **firstshear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
+ NeighList *listgranhistory;
+
+ double **x = atom->x;
+ double *radius = atom->radius;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *molecule = atom->molecule;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+ if (includegroup) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[includegroup];
+ }
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ FixShearHistory *fix_history = list->fix_history;
+ if (fix_history) {
+ fix_history->nlocal_neigh = nlocal;
+ fix_history->nall_neigh = nall;
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ listgranhistory = list->listgranhistory;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ ipage_touch = listgranhistory->ipage;
+ dpage_shear = listgranhistory->dpage;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
+ }
+
+ int inum = 0;
+ ipage->reset();
+ if (fix_history) {
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+ if (fix_history) {
+ nn = 0;
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
+ }
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ radi = radius[i];
+
+ // loop over remaining atoms, owned and ghost
+
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) {
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ }
+
+ n++;
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (fix_history) {
+ firsttouch[i] = touchptr;
+ firstshear[i] = shearptr;
+ ipage_touch->vgot(n);
+ dpage_shear->vgot(nn);
+ }
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_half_size_nsq_newtoff.h b/src/npair_half_size_nsq_newtoff.h
new file mode 100644
index 0000000000..0446208cbb
--- /dev/null
+++ b/src/npair_half_size_nsq_newtoff.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/size/nsq/newtoff,
+ NPairHalfSizeNsqNewtoff,
+ NP_HALF | NP_SIZE | NP_NSQ | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_SIZE_NSQ_NEWTOFF_H
+#define LMP_NPAIR_HALF_SIZE_NSQ_NEWTOFF_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfSizeNsqNewtoff : public NPair {
+ public:
+ NPairHalfSizeNsqNewtoff(class LAMMPS *);
+ ~NPairHalfSizeNsqNewtoff() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_half_size_nsq_newton.cpp b/src/npair_half_size_nsq_newton.cpp
new file mode 100644
index 0000000000..914a4e7e7d
--- /dev/null
+++ b/src/npair_half_size_nsq_newton.cpp
@@ -0,0 +1,187 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "npair_half_size_nsq_newton.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "fix_shear_history.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfSizeNsqNewton::NPairHalfSizeNsqNewton(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ size particles
+ N^2 / 2 search for neighbor pairs with full Newton's 3rd law
+ shear history must be accounted for when a neighbor pair is added
+ pair added to list if atoms i and j are both owned and i < j
+ if j is ghost only me or other proc adds pair
+ decision based on itag,jtag tests
+------------------------------------------------------------------------- */
+
+void NPairHalfSizeNsqNewton::build(NeighList *list)
+{
+ int i,j,m,n,nn,itag,jtag,bitmask,dnum,dnumbytes;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ double radi,radsum,cutsq;
+ int *neighptr,*touchptr;
+ double *shearptr;
+
+ int *npartner;
+ tagint **partner;
+ double **shearpartner;
+ int **firsttouch;
+ double **firstshear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
+ NeighList *listgranhistory;
+
+ double **x = atom->x;
+ double *radius = atom->radius;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ tagint *molecule = atom->molecule;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+ if (includegroup) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[includegroup];
+ }
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ FixShearHistory *fix_history = list->fix_history;
+ if (fix_history) {
+ fix_history->nlocal_neigh = nlocal;
+ fix_history->nall_neigh = nall;
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ listgranhistory = list->listgranhistory;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ ipage_touch = listgranhistory->ipage;
+ dpage_shear = listgranhistory->dpage;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
+ }
+
+ int inum = 0;
+ ipage->reset();
+ if (fix_history) {
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
+
+ for (i = 0; i < nlocal; i++) {
+ n = 0;
+ neighptr = ipage->vget();
+ if (fix_history) {
+ nn = 0;
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
+ }
+
+ itag = tag[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ radi = radius[i];
+
+ // loop over remaining atoms, owned and ghost
+
+ for (j = i+1; j < nall; j++) {
+ if (includegroup && !(mask[j] & bitmask)) continue;
+
+ if (j >= nlocal) {
+ jtag = tag[j];
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+ }
+
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) {
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ }
+
+ n++;
+ }
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (fix_history) {
+ firsttouch[i] = touchptr;
+ firstshear[i] = shearptr;
+ ipage_touch->vgot(n);
+ dpage_shear->vgot(nn);
+ }
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_half_size_nsq_newton.h b/src/npair_half_size_nsq_newton.h
new file mode 100644
index 0000000000..3550d6c7f5
--- /dev/null
+++ b/src/npair_half_size_nsq_newton.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(half/size/nsq/newton,
+ NPairHalfSizeNsqNewton,
+ NP_HALF | NP_SIZE | NP_NSQ | NP_NEWTON | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALF_SIZE_NSQ_NEWTON_H
+#define LMP_NPAIR_HALF_SIZE_NSQ_NEWTON_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalfSizeNsqNewton : public NPair {
+ public:
+ NPairHalfSizeNsqNewton(class LAMMPS *);
+ ~NPairHalfSizeNsqNewton() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_halffull_newtoff.cpp b/src/npair_halffull_newtoff.cpp
new file mode 100644
index 0000000000..bd7cc4dd59
--- /dev/null
+++ b/src/npair_halffull_newtoff.cpp
@@ -0,0 +1,82 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_halffull_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalffullNewtoff::NPairHalffullNewtoff(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ build half list from full list
+ pair stored once if i,j are both owned and i < j
+ pair stored by me if j is ghost (also stored by proc owning j)
+ works if full list is a skip list
+------------------------------------------------------------------------- */
+
+void NPairHalffullNewtoff::build(NeighList *list)
+{
+ int i,j,ii,jj,n,jnum,joriginal;
+ int *neighptr,*jlist;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int *ilist_full = list->listfull->ilist;
+ int *numneigh_full = list->listfull->numneigh;
+ int **firstneigh_full = list->listfull->firstneigh;
+ int inum_full = list->listfull->inum;
+
+ int inum = 0;
+ ipage->reset();
+
+ // loop over atoms in full list
+
+ for (ii = 0; ii < inum_full; ii++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ // loop over parent full list
+
+ i = ilist_full[ii];
+ jlist = firstneigh_full[i];
+ jnum = numneigh_full[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (j > i) neighptr[n++] = joriginal;
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_halffull_newtoff.h b/src/npair_halffull_newtoff.h
new file mode 100644
index 0000000000..20ceeabaad
--- /dev/null
+++ b/src/npair_halffull_newtoff.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(halffull/newtoff,
+ NPairHalffullNewtoff,
+ NP_HALFFULL | NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTOFF |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALFFULL_NEWTOFF_H
+#define LMP_NPAIR_HALFFULL_NEWTOFF_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalffullNewtoff : public NPair {
+ public:
+ NPairHalffullNewtoff(class LAMMPS *);
+ ~NPairHalffullNewtoff() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_halffull_newton.cpp b/src/npair_halffull_newton.cpp
new file mode 100644
index 0000000000..371bbd33a8
--- /dev/null
+++ b/src/npair_halffull_newton.cpp
@@ -0,0 +1,99 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_halffull_newton.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalffullNewton::NPairHalffullNewton(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ build half list from full list
+ pair stored once if i,j are both owned and i < j
+ if j is ghost, only store if j coords are "above and to the right" of i
+ works if full list is a skip list
+------------------------------------------------------------------------- */
+
+void NPairHalffullNewton::build(NeighList *list)
+{
+ int i,j,ii,jj,n,jnum,joriginal;
+ int *neighptr,*jlist;
+ double xtmp,ytmp,ztmp;
+
+ double **x = atom->x;
+ int nlocal = atom->nlocal;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int *ilist_full = list->listfull->ilist;
+ int *numneigh_full = list->listfull->numneigh;
+ int **firstneigh_full = list->listfull->firstneigh;
+ int inum_full = list->listfull->inum;
+
+ int inum = 0;
+ ipage->reset();
+
+ // loop over parent full list
+
+ for (ii = 0; ii < inum_full; ii++) {
+ n = 0;
+ neighptr = ipage->vget();
+
+ i = ilist_full[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+
+ // loop over full neighbor list
+
+ jlist = firstneigh_full[i];
+ jnum = numneigh_full[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (j < nlocal) {
+ if (i > j) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+ neighptr[n++] = joriginal;
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_halffull_newton.h b/src/npair_halffull_newton.h
new file mode 100644
index 0000000000..0f0aee58dc
--- /dev/null
+++ b/src/npair_halffull_newton.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(halffull/newton,
+ NPairHalffullNewton,
+ NP_HALFFULL | NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_HALFFULL_NEWTON_H
+#define LMP_NPAIR_HALFFULL_NEWTON_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalffullNewton : public NPair {
+ public:
+ NPairHalffullNewton(class LAMMPS *);
+ ~NPairHalffullNewton() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_halffull_newton_ssa.cpp b/src/npair_halffull_newton_ssa.cpp
new file mode 100644
index 0000000000..f09a2c3ae1
--- /dev/null
+++ b/src/npair_halffull_newton_ssa.cpp
@@ -0,0 +1,132 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors:
+ James Larentzos and Timothy I. Mattox (Engility Corporation)
+------------------------------------------------------------------------- */
+
+#include "npair_halffull_newton_ssa.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+// allocate space for static class variable
+// prototype for non-class function
+
+static int *ssaAIRptr;
+static int cmp_ssaAIR(const void *, const void *);
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalffullNewtonSSA::NPairHalffullNewtonSSA(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ build half list from full list for use by Shardlow Spliting Algorithm
+ pair stored once if i,j are both owned and i < j
+ if j is ghost, only store if j coords are "above and to the right" of i
+ works if full list is a skip list
+------------------------------------------------------------------------- */
+
+void NPairHalffullNewtonSSA::build(NeighList *list)
+{
+ int i,j,ii,jj,n,jnum,joriginal;
+ int *neighptr,*jlist;
+
+ int nlocal = atom->nlocal;
+ int *ssaAIR = atom->ssaAIR;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int *ilist_full = list->listfull->ilist;
+ int *numneigh_full = list->listfull->numneigh;
+ int **firstneigh_full = list->listfull->firstneigh;
+ int inum_full = list->listfull->inum;
+
+ int inum = 0;
+ ipage->reset();
+
+ // loop over parent full list
+
+ for (ii = 0; ii < inum_full; ii++) {
+ int AIRct[8] = { 0 };
+ n = 0;
+ neighptr = ipage->vget();
+
+ i = ilist_full[ii];
+
+ // loop over full neighbor list
+
+ jlist = firstneigh_full[i];
+ jnum = numneigh_full[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (j < nlocal) {
+ if (i > j) continue;
+ ++(AIRct[0]);
+ } else {
+ if (ssaAIR[j] < 2) continue; // skip ghost atoms not in AIR
+ ++(AIRct[ssaAIR[j] - 1]);
+ }
+ neighptr[n++] = joriginal;
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ // sort the locals+ghosts in the neighbor list by their ssaAIR number
+
+ ssaAIRptr = atom->ssaAIR;
+ qsort(&(neighptr[0]), n, sizeof(int), cmp_ssaAIR);
+
+ // do a prefix sum on the counts to turn them into indexes
+
+ list->ndxAIR_ssa[i][0] = AIRct[0];
+ for (int ndx = 1; ndx < 8; ++ndx) {
+ list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
+ }
+ }
+
+ list->inum = inum;
+}
+
+/* ----------------------------------------------------------------------
+ comparison function invoked by qsort()
+ accesses static class member ssaAIRptr, set before call to qsort()
+------------------------------------------------------------------------- */
+
+static int cmp_ssaAIR(const void *iptr, const void *jptr)
+{
+ int i = *((int *) iptr);
+ int j = *((int *) jptr);
+ if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
+ if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
+ return 0;
+}
+
diff --git a/src/npair_halffull_newton_ssa.h b/src/npair_halffull_newton_ssa.h
new file mode 100644
index 0000000000..4935349f77
--- /dev/null
+++ b/src/npair_halffull_newton_ssa.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(halffull/newton/ssa,
+ NPairHalffullNewtonSSA,
+ NP_HALFFULL | NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON |
+ NP_ORTHO | NP_TRI | NP_SSA)
+
+#else
+
+#ifndef LMP_NPAIR_HALFFULL_NEWTON_SSA_H
+#define LMP_NPAIR_HALFFULL_NEWTON_SSA_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalffullNewtonSSA : public NPair {
+ public:
+ NPairHalffullNewtonSSA(class LAMMPS *);
+ ~NPairHalffullNewtonSSA() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_skip.cpp b/src/npair_skip.cpp
new file mode 100644
index 0000000000..3048460859
--- /dev/null
+++ b/src/npair_skip.cpp
@@ -0,0 +1,103 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_skip.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairSkip::NPairSkip(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ build skip list for subset of types from parent list
+ iskip and ijskip flag which atom types and type pairs to skip
+ this is for half and full lists
+ if ghost, also store neighbors of ghost atoms & set inum,gnum correctly
+------------------------------------------------------------------------- */
+
+void NPairSkip::build(NeighList *list)
+{
+ int i,j,ii,jj,n,itype,jnum,joriginal;
+ int *neighptr,*jlist;
+
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int *ilist_skip = list->listskip->ilist;
+ int *numneigh_skip = list->listskip->numneigh;
+ int **firstneigh_skip = list->listskip->firstneigh;
+ int num_skip = list->listskip->inum;
+ if (list->ghost) num_skip += list->listskip->gnum;
+
+ int *iskip = list->iskip;
+ int **ijskip = list->ijskip;
+
+ int inum = 0;
+ ipage->reset();
+
+ // loop over atoms in other list
+ // skip I atom entirely if iskip is set for type[I]
+ // skip I,J pair if ijskip is set for type[I],type[J]
+
+ for (ii = 0; ii < num_skip; ii++) {
+ i = ilist_skip[ii];
+ itype = type[i];
+ if (iskip[itype]) continue;
+
+ n = 0;
+ neighptr = ipage->vget();
+
+ // loop over parent non-skip list
+
+ jlist = firstneigh_skip[i];
+ jnum = numneigh_skip[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (ijskip[itype][type[j]]) continue;
+ neighptr[n++] = joriginal;
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ list->inum = inum;
+ if (list->ghost) {
+ int num = 0;
+ for (i = 0; i < inum; i++)
+ if (ilist[i] < nlocal) num++;
+ else break;
+ list->inum = num;
+ list->gnum = inum - num;
+ }
+}
diff --git a/src/npair_skip.h b/src/npair_skip.h
new file mode 100644
index 0000000000..872fd9cb58
--- /dev/null
+++ b/src/npair_skip.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(skip,
+ NPairSkip,
+ NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI |
+ NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_SKIP_H
+#define LMP_NPAIR_SKIP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairSkip : public NPair {
+ public:
+ NPairSkip(class LAMMPS *);
+ ~NPairSkip() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_skip_respa.cpp b/src/npair_skip_respa.cpp
new file mode 100644
index 0000000000..31420b32d1
--- /dev/null
+++ b/src/npair_skip_respa.cpp
@@ -0,0 +1,169 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_skip_respa.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairSkipRespa::NPairSkipRespa(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ build skip list for subset of types from parent list
+ iskip and ijskip flag which atom types and type pairs to skip
+ this is for respa lists, copy the inner/middle values from parent
+------------------------------------------------------------------------- */
+
+void NPairSkipRespa::build(NeighList *list)
+{
+ int i,j,ii,jj,n,itype,jnum,joriginal,n_inner,n_middle;
+ int *neighptr,*jlist,*neighptr_inner,*neighptr_middle;
+
+ int *type = atom->type;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int *ilist_skip = list->listskip->ilist;
+ int *numneigh_skip = list->listskip->numneigh;
+ int **firstneigh_skip = list->listskip->firstneigh;
+ int inum_skip = list->listskip->inum;
+
+ int *iskip = list->iskip;
+ int **ijskip = list->ijskip;
+
+ NeighList *listinner = list->listinner;
+ int *ilist_inner = listinner->ilist;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+ MyPage<int> *ipage_inner = listinner->ipage;
+
+ int *numneigh_inner_skip = list->listskip->listinner->numneigh;
+ int **firstneigh_inner_skip = list->listskip->listinner->firstneigh;
+
+ NeighList *listmiddle;
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ MyPage<int> *ipage_middle;
+ int *numneigh_middle_skip,**firstneigh_middle_skip;
+ int respamiddle = list->respamiddle;
+ if (respamiddle) {
+ listmiddle = list->listmiddle;
+ ilist_middle = listmiddle->ilist;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ ipage_middle = listmiddle->ipage;
+ numneigh_middle_skip = list->listskip->listmiddle->numneigh;
+ firstneigh_middle_skip = list->listskip->listmiddle->firstneigh;
+ }
+
+ int inum = 0;
+ ipage->reset();
+ ipage_inner->reset();
+ if (respamiddle) ipage_middle->reset();
+
+ // loop over atoms in other list
+ // skip I atom entirely if iskip is set for type[I]
+ // skip I,J pair if ijskip is set for type[I],type[J]
+
+ for (ii = 0; ii < inum_skip; ii++) {
+ i = ilist_skip[ii];
+ itype = type[i];
+ if (iskip[itype]) continue;
+
+ n = n_inner = 0;
+ neighptr = ipage->vget();
+ neighptr_inner = ipage_inner->vget();
+ if (respamiddle) {
+ n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
+ }
+
+ // loop over parent outer rRESPA list
+
+ jlist = firstneigh_skip[i];
+ jnum = numneigh_skip[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (ijskip[itype][type[j]]) continue;
+ neighptr[n++] = joriginal;
+ }
+
+ // loop over parent inner rRESPA list
+
+ jlist = firstneigh_inner_skip[i];
+ jnum = numneigh_inner_skip[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (ijskip[itype][type[j]]) continue;
+ neighptr_inner[n_inner++] = joriginal;
+ }
+
+ // loop over parent middle rRESPA list
+
+ if (respamiddle) {
+ jlist = firstneigh_middle_skip[i];
+ jnum = numneigh_middle_skip[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (ijskip[itype][type[j]]) continue;
+ neighptr_middle[n_middle++] = joriginal;
+ }
+ }
+
+ ilist[inum] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ ilist_inner[inum] = i;
+ firstneigh_inner[i] = neighptr_inner;
+ numneigh_inner[i] = n_inner;
+ ipage_inner->vgot(n);
+ if (ipage_inner->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (respamiddle) {
+ ilist_middle[inum] = i;
+ firstneigh_middle[i] = neighptr_middle;
+ numneigh_middle[i] = n_middle;
+ ipage_middle->vgot(n);
+ if (ipage_middle->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+
+ inum++;
+ }
+
+ list->inum = inum;
+ listinner->inum = inum;
+ if (respamiddle) listmiddle->inum = inum;
+}
diff --git a/src/npair_skip_respa.h b/src/npair_skip_respa.h
new file mode 100644
index 0000000000..62077f85df
--- /dev/null
+++ b/src/npair_skip_respa.h
@@ -0,0 +1,45 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(skip/half/respa,
+ NPairSkipRespa,
+ NP_SKIP | NP_RESPA | NP_HALF | NP_FULL |
+ NP_NSQ | NP_BIN | NP_MULTI |
+ NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_SKIP_RESPA_H
+#define LMP_NPAIR_SKIP_RESPA_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairSkipRespa : public NPair {
+ public:
+ NPairSkipRespa(class LAMMPS *);
+ ~NPairSkipRespa() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_skip_size.cpp b/src/npair_skip_size.cpp
new file mode 100644
index 0000000000..c69b16d1df
--- /dev/null
+++ b/src/npair_skip_size.cpp
@@ -0,0 +1,161 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "npair_skip_size.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "fix_shear_history.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairSkipSize::NPairSkipSize(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ build skip list for subset of types from parent list
+ iskip and ijskip flag which atom types and type pairs to skip
+ if list requests it, preserve shear history via fix shear/history
+------------------------------------------------------------------------- */
+
+void NPairSkipSize::build(NeighList *list)
+{
+ int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,dnum,dnumbytes;
+ tagint jtag;
+ int *neighptr,*jlist,*touchptr;
+ double *shearptr;
+
+ int *npartner;
+ tagint **partner;
+ double **shearpartner;
+ int **firsttouch;
+ double **firstshear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
+ NeighList *listgranhistory;
+
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int *ilist_skip = list->listskip->ilist;
+ int *numneigh_skip = list->listskip->numneigh;
+ int **firstneigh_skip = list->listskip->firstneigh;
+ int inum_skip = list->listskip->inum;
+
+ int *iskip = list->iskip;
+ int **ijskip = list->ijskip;
+
+ FixShearHistory *fix_history = list->fix_history;
+ if (fix_history) {
+ fix_history->nlocal_neigh = nlocal;
+ fix_history->nall_neigh = nlocal + atom->nghost;
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ listgranhistory = list->listgranhistory;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ ipage_touch = listgranhistory->ipage;
+ dpage_shear = listgranhistory->dpage;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
+ }
+
+ int inum = 0;
+ ipage->reset();
+ if (fix_history) {
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
+
+ // loop over atoms in other list
+ // skip I atom entirely if iskip is set for type[I]
+ // skip I,J pair if ijskip is set for type[I],type[J]
+
+ for (ii = 0; ii < inum_skip; ii++) {
+ i = ilist_skip[ii];
+ itype = type[i];
+ if (iskip[itype]) continue;
+
+ n = 0;
+ neighptr = ipage->vget();
+ if (fix_history) {
+ nn = 0;
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
+ }
+
+ // loop over parent non-skip size list and optionally its history info
+
+ jlist = firstneigh_skip[i];
+ jnum = numneigh_skip[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (ijskip[itype][type[j]]) continue;
+ neighptr[n] = joriginal;
+
+ // no numeric test for current touch
+ // just use FSH partner list to infer it
+ // would require distance calculation for spheres
+ // more complex calculation for surfs
+
+ if (fix_history) {
+ jtag = tag[j];
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == jtag) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ }
+
+ n++;
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (fix_history) {
+ firsttouch[i] = touchptr;
+ firstshear[i] = shearptr;
+ ipage_touch->vgot(n);
+ dpage_shear->vgot(nn);
+ }
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_skip_size.h b/src/npair_skip_size.h
new file mode 100644
index 0000000000..9573396641
--- /dev/null
+++ b/src/npair_skip_size.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(skip/half/size,
+ NPairSkipSize,
+ NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI |
+ NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_SKIP_SIZE_H
+#define LMP_NPAIR_SKIP_SIZE_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairSkipSize : public NPair {
+ public:
+ NPairSkipSize(class LAMMPS *);
+ ~NPairSkipSize() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_skip_size_off2on.cpp b/src/npair_skip_size_off2on.cpp
new file mode 100644
index 0000000000..bd509327f1
--- /dev/null
+++ b/src/npair_skip_size_off2on.cpp
@@ -0,0 +1,168 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "npair_skip_size_off2on.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "fix_shear_history.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairSkipSizeOff2on::NPairSkipSizeOff2on(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ build skip list for subset of types from parent list
+ iskip and ijskip flag which atom types and type pairs to skip
+ parent non-skip list used newton off, this skip list is newton on
+ if list requests it, preserve shear history via fix shear/history
+------------------------------------------------------------------------- */
+
+void NPairSkipSizeOff2on::build(NeighList *list)
+{
+ int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,dnum,dnumbytes;
+ tagint itag,jtag;
+ int *neighptr,*jlist,*touchptr;
+ double *shearptr;
+
+ int *npartner;
+ tagint **partner;
+ double **shearpartner;
+ int **firsttouch;
+ double **firstshear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
+ NeighList *listgranhistory;
+
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int *ilist_skip = list->listskip->ilist;
+ int *numneigh_skip = list->listskip->numneigh;
+ int **firstneigh_skip = list->listskip->firstneigh;
+ int inum_skip = list->listskip->inum;
+
+ int *iskip = list->iskip;
+ int **ijskip = list->ijskip;
+
+ FixShearHistory *fix_history = list->fix_history;
+ if (fix_history) {
+ fix_history->nlocal_neigh = nlocal;
+ fix_history->nall_neigh = nlocal + atom->nghost;
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ listgranhistory = list->listgranhistory;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ ipage_touch = listgranhistory->ipage;
+ dpage_shear = listgranhistory->dpage;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
+ }
+
+ int inum = 0;
+ ipage->reset();
+ if (fix_history) {
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
+
+ // loop over atoms in other list
+ // skip I atom entirely if iskip is set for type[I]
+ // skip I,J pair if ijskip is set for type[I],type[J]
+
+ for (ii = 0; ii < inum_skip; ii++) {
+ i = ilist_skip[ii];
+ itype = type[i];
+ if (iskip[itype]) continue;
+ itag = tag[i];
+
+ n = 0;
+ neighptr = ipage->vget();
+ if (fix_history) {
+ nn = 0;
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
+ }
+
+ // loop over parent non-skip size list and optionally its history info
+
+ jlist = firstneigh_skip[i];
+ jnum = numneigh_skip[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (ijskip[itype][type[j]]) continue;
+
+ // only keep I,J when J = ghost if Itag < Jtag
+
+ jtag = tag[j];
+ if (j >= nlocal && jtag < itag) continue;
+
+ neighptr[n] = joriginal;
+
+ // no numeric test for current touch
+ // just use FSH partner list to infer it
+ // would require distance calculation for spheres
+ // more complex calculation for surfs
+
+ if (fix_history) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == jtag) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
+ } else {
+ touchptr[n] = 0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
+ }
+ }
+
+ n++;
+ }
+
+ ilist[inum++] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ if (fix_history) {
+ firsttouch[i] = touchptr;
+ firstshear[i] = shearptr;
+ ipage_touch->vgot(n);
+ dpage_shear->vgot(nn);
+ }
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_skip_size_off2on.h b/src/npair_skip_size_off2on.h
new file mode 100644
index 0000000000..4b4e9a9c29
--- /dev/null
+++ b/src/npair_skip_size_off2on.h
@@ -0,0 +1,45 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(skip/size/off2on,
+ NPairSkipSizeOff2on,
+ NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF |
+ NP_NSQ | NP_BIN | NP_MULTI |
+ NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_SKIP_SIZE_OFF2ON_H
+#define LMP_NPAIR_SKIP_SIZE_OFF2ON_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairSkipSizeOff2on : public NPair {
+ public:
+ NPairSkipSizeOff2on(class LAMMPS *);
+ ~NPairSkipSizeOff2on() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp
new file mode 100644
index 0000000000..12123741d0
--- /dev/null
+++ b/src/npair_skip_size_off2on_oneside.cpp
@@ -0,0 +1,223 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "npair_skip_size_off2on_oneside.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "fix_shear_history.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairSkipSizeOff2onOneside::NPairSkipSizeOff2onOneside(LAMMPS *lmp) :
+ NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+ build skip list for subset of types from parent list
+ iskip and ijskip flag which atom types and type pairs to skip
+ parent non-skip list used newton off and was not onesided,
+ this skip list is newton on and onesided
+ if list requests it, preserve shear history via fix shear/history
+------------------------------------------------------------------------- */
+
+void NPairSkipSizeOff2onOneside::build(NeighList *list)
+{
+ int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,flip,dnum,dnumbytes,tmp;
+ tagint jtag;
+ int *surf,*jlist;
+
+ int *npartner;
+ tagint **partner;
+ double **shearpartner;
+ int **firsttouch;
+ double **firstshear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
+ NeighList *listgranhistory;
+
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ MyPage<int> *ipage = list->ipage;
+
+ int *ilist_skip = list->listskip->ilist;
+ int *numneigh_skip = list->listskip->numneigh;
+ int **firstneigh_skip = list->listskip->firstneigh;
+ int inum_skip = list->listskip->inum;
+
+ int *iskip = list->iskip;
+ int **ijskip = list->ijskip;
+
+ if (domain->dimension == 2) surf = atom->line;
+ else surf = atom->tri;
+
+ FixShearHistory *fix_history = list->fix_history;
+ if (fix_history) {
+ fix_history->nlocal_neigh = nlocal;
+ fix_history->nall_neigh = nlocal + atom->nghost;
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ listgranhistory = list->listgranhistory;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ ipage_touch = listgranhistory->ipage;
+ dpage_shear = listgranhistory->dpage;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
+ }
+
+ int inum = 0;
+ ipage->reset();
+ if (fix_history) {
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
+
+ // two loops over parent list required, one to count, one to store
+ // because onesided constraint means pair I,J may be stored with I or J
+ // so don't know in advance how much space to alloc for each atom's neighs
+
+ // first loop over atoms in other list to count neighbors
+ // skip I atom entirely if iskip is set for type[I]
+ // skip I,J pair if ijskip is set for type[I],type[J]
+
+ for (i = 0; i < nlocal; i++) numneigh[i] = 0;
+
+ for (ii = 0; ii < inum_skip; ii++) {
+ i = ilist_skip[ii];
+ itype = type[i];
+ if (iskip[itype]) continue;
+
+ n = 0;
+
+ // loop over parent non-skip size list
+
+ jlist = firstneigh_skip[i];
+ jnum = numneigh_skip[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (ijskip[itype][type[j]]) continue;
+
+ // flip I,J if necessary to satisfy onesided constraint
+ // do not keep if I is now ghost
+
+ if (surf[i] >= 0) {
+ if (j >= nlocal) continue;
+ tmp = i;
+ i = j;
+ j = tmp;
+ flip = 1;
+ } else flip = 0;
+
+ numneigh[i]++;
+ if (flip) i = j;
+ }
+ }
+
+ // allocate all per-atom neigh list chunks, including history
+
+ for (i = 0; i < nlocal; i++) {
+ if (numneigh[i] == 0) continue;
+ n = numneigh[i];
+ firstneigh[i] = ipage->get(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ if (fix_history) {
+ firsttouch[i] = ipage_touch->get(n);
+ firstshear[i] = dpage_shear->get(dnum*n);
+ }
+ }
+
+ // second loop over atoms in other list to store neighbors
+ // skip I atom entirely if iskip is set for type[I]
+ // skip I,J pair if ijskip is set for type[I],type[J]
+
+ for (i = 0; i < nlocal; i++) numneigh[i] = 0;
+
+ for (ii = 0; ii < inum_skip; ii++) {
+ i = ilist_skip[ii];
+ itype = type[i];
+ if (iskip[itype]) continue;
+
+ // loop over parent non-skip size list and optionally its history info
+
+ jlist = firstneigh_skip[i];
+ jnum = numneigh_skip[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (ijskip[itype][type[j]]) continue;
+
+ // flip I,J if necessary to satisfy onesided constraint
+ // do not keep if I is now ghost
+
+ if (surf[i] >= 0) {
+ if (j >= nlocal) continue;
+ tmp = i;
+ i = j;
+ j = tmp;
+ flip = 1;
+ } else flip = 0;
+
+ // store j in neigh list, not joriginal, like other neigh methods
+ // OK, b/c there is no special list flagging for surfs
+
+ firstneigh[i][numneigh[i]] = j;
+
+ // no numeric test for current touch
+ // just use FSH partner list to infer it
+ // would require complex calculation for surfs
+
+ if (fix_history) {
+ jtag = tag[j];
+ n = numneigh[i];
+ nn = dnum*n;
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == jtag) break;
+ if (m < npartner[i]) {
+ firsttouch[i][n] = 1;
+ memcpy(&firstshear[i][nn],&shearpartner[i][dnum*m],dnumbytes);
+ } else {
+ firsttouch[i][n] = 0;
+ memcpy(&firstshear[i][nn],zeroes,dnumbytes);
+ }
+ }
+
+ numneigh[i]++;
+ if (flip) i = j;
+ }
+
+ // only add atom I to ilist if it has neighbors
+ // fix shear/history allows for this in pre_exchange_onesided()
+
+ if (numneigh[i]) ilist[inum++] = i;
+ }
+
+ list->inum = inum;
+}
diff --git a/src/npair_skip_size_off2on_oneside.h b/src/npair_skip_size_off2on_oneside.h
new file mode 100644
index 0000000000..9f3c06e7bc
--- /dev/null
+++ b/src/npair_skip_size_off2on_oneside.h
@@ -0,0 +1,45 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(skip/size/off2on/oneside,
+ NPairSkipSizeOff2onOneside,
+ NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF |
+ NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON | NP_NEWTOFF |
+ NP_ORTHO | NP_TRI)
+
+#else
+
+#ifndef LMP_NPAIR_SKIP_SIZE_OFF2ON_ONESIDE_H
+#define LMP_NPAIR_SKIP_SIZE_OFF2ON_ONESIDE_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairSkipSizeOff2onOneside : public NPair {
+ public:
+ NPairSkipSizeOff2onOneside(class LAMMPS *);
+ ~NPairSkipSizeOff2onOneside() {}
+ void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil.cpp b/src/nstencil.cpp
new file mode 100644
index 0000000000..5f403d7511
--- /dev/null
+++ b/src/nstencil.cpp
@@ -0,0 +1,230 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil.h"
+#include "neighbor.h"
+#include "nbin.h"
+#include "atom.h"
+#include "update.h"
+#include "domain.h"
+#include "memory.h"
+
+using namespace LAMMPS_NS;
+
+enum{NSQ,BIN,MULTI}; // also in Neighbor
+
+/* ----------------------------------------------------------------------
+ NStencil classes
+ each has method to create a stencil = list of bin offsets
+ invoked each time simulation box size/shape changes
+ since induces change in bins
+ stencil = bins whose closest corner to central bin is within cutoff
+ sx,sy,sz = bin bounds = furthest the stencil could possibly extend
+ calculated below in create_setup()
+ 3d creates xyz stencil, 2d creates xy stencil
+ for half list with newton off:
+ stencil is all surrounding bins including self
+ regardless of triclinic
+ for half list with newton on:
+ stencil is bins to the "upper right" of central bin
+ stencil does not include self
+ no versions that allow ghost on (no callers need it?)
+ for half list with newton on and triclinic:
+ stencil is all bins in z-plane of self and above, but not below
+ in 2d is all bins in y-plane of self and above, but not below
+ stencil includes self
+ no versions that allow ghost on (no callers need it?)
+ for full list:
+ stencil is all surrounding bins including self
+ regardless of newton on/off or triclinic
+ for multi:
+ create one stencil for each atom type
+ stencil follows same rules for half/full, newton on/off, triclinic
+ cutoff is not cutneighmaxsq, but max cutoff for that atom type
+ no versions that allow ghost on (any need for it?)
+------------------------------------------------------------------------- */
+
+NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp)
+{
+ last_create = last_stencil_memory = -1;
+ last_copy_bin = -1;
+
+ xyzflag = 0;
+
+ maxstencil = maxstencil_multi = 0;
+ stencil = NULL;
+ stencilxyz = NULL;
+ nstencil_multi = NULL;
+ stencil_multi = NULL;
+ distsq_multi = NULL;
+
+ dimension = domain->dimension;
+}
+
+/* ---------------------------------------------------------------------- */
+
+NStencil::~NStencil()
+{
+ memory->destroy(stencil);
+ memory->destroy(stencilxyz);
+ memory->destroy(nstencil_multi);
+
+ if (!stencil_multi) return;
+
+ int n = atom->ntypes;
+ for (int i = 1; i <= n; i++) {
+ memory->destroy(stencil_multi[i]);
+ memory->destroy(distsq_multi[i]);
+ }
+ delete [] stencil_multi;
+ delete [] distsq_multi;
+}
+
+/* ----------------------------------------------------------------------
+ copy needed info from Neighbor class to this stencil class
+------------------------------------------------------------------------- */
+
+void NStencil::copy_neighbor_info()
+{
+ neighstyle = neighbor->style;
+ cutneighmax = neighbor->cutneighmax;
+ cutneighmaxsq = neighbor->cutneighmaxsq;
+ cuttypesq = neighbor->cuttypesq;
+}
+
+/* ----------------------------------------------------------------------
+ copy needed info from NBin class to this stencil class
+------------------------------------------------------------------------- */
+
+void NStencil::copy_bin_info()
+{
+ mbinx = nb->mbinx;
+ mbiny = nb->mbiny;
+ mbinz = nb->mbinz;
+ binsizex = nb->binsizex;
+ binsizey = nb->binsizey;
+ binsizez = nb->binsizez;
+ bininvx = nb->bininvx;
+ bininvy = nb->bininvy;
+ bininvz = nb->bininvz;
+}
+
+/* ----------------------------------------------------------------------
+ insure NBin data is current
+ insure stencils are allocated large enough
+------------------------------------------------------------------------- */
+
+void NStencil::create_setup()
+{
+ if (nb && last_copy_bin < nb->last_setup) {
+ copy_bin_info();
+ last_copy_bin = update->ntimestep;
+ }
+
+ // sx,sy,sz = max range of stencil in each dim
+ // smax = max possible size of entire 3d stencil
+ // stencil will be empty if cutneighmax = 0.0
+
+ sx = static_cast<int> (cutneighmax*bininvx);
+ if (sx*binsizex < cutneighmax) sx++;
+ sy = static_cast<int> (cutneighmax*bininvy);
+ if (sy*binsizey < cutneighmax) sy++;
+ sz = static_cast<int> (cutneighmax*bininvz);
+ if (sz*binsizez < cutneighmax) sz++;
+ if (dimension == 2) sz = 0;
+
+ int smax = (2*sx+1) * (2*sy+1) * (2*sz+1);
+
+ // reallocate stencil structs if necessary
+ // for BIN and MULTI styles
+
+ if (neighstyle == BIN) {
+ if (smax > maxstencil) {
+ maxstencil = smax;
+ memory->destroy(stencil);
+ memory->create(stencil,maxstencil,"neighstencil:stencil");
+ if (xyzflag) {
+ memory->destroy(stencilxyz);
+ memory->create(stencilxyz,maxstencil,3,"neighstencil:stencilxyz");
+ }
+ last_stencil_memory = update->ntimestep;
+ }
+
+ } else {
+ int i;
+ int n = atom->ntypes;
+ if (maxstencil_multi == 0) {
+ nstencil_multi = new int[n+1];
+ stencil_multi = new int*[n+1];
+ distsq_multi = new double*[n+1];
+ for (i = 1; i <= n; i++) {
+ nstencil_multi[i] = 0;
+ stencil_multi[i] = NULL;
+ distsq_multi[i] = NULL;
+ }
+ last_stencil_memory = update->ntimestep;
+ }
+ if (smax > maxstencil_multi) {
+ maxstencil_multi = smax;
+ for (i = 1; i <= n; i++) {
+ memory->destroy(stencil_multi[i]);
+ memory->destroy(distsq_multi[i]);
+ memory->create(stencil_multi[i],maxstencil_multi,
+ "neighstencil:stencil_multi");
+ memory->create(distsq_multi[i],maxstencil_multi,
+ "neighstencil:distsq_multi");
+ last_stencil_memory = update->ntimestep;
+ }
+ }
+ }
+
+ last_create = update->ntimestep;
+}
+
+/* ----------------------------------------------------------------------
+ compute closest distance between central bin (0,0,0) and bin (i,j,k)
+------------------------------------------------------------------------- */
+
+double NStencil::bin_distance(int i, int j, int k)
+{
+ double delx,dely,delz;
+
+ if (i > 0) delx = (i-1)*binsizex;
+ else if (i == 0) delx = 0.0;
+ else delx = (i+1)*binsizex;
+
+ if (j > 0) dely = (j-1)*binsizey;
+ else if (j == 0) dely = 0.0;
+ else dely = (j+1)*binsizey;
+
+ if (k > 0) delz = (k-1)*binsizez;
+ else if (k == 0) delz = 0.0;
+ else delz = (k+1)*binsizez;
+
+ return (delx*delx + dely*dely + delz*delz);
+}
+
+/* ---------------------------------------------------------------------- */
+
+bigint NStencil::memory_usage()
+{
+ bigint bytes = 0;
+ if (neighstyle == BIN) {
+ bytes += memory->usage(stencil,maxstencil);
+ bytes += memory->usage(stencilxyz,maxstencil,3);
+ } else if (neighstyle == MULTI) {
+ bytes += atom->ntypes*maxstencil_multi * sizeof(int);
+ bytes += atom->ntypes*maxstencil_multi * sizeof(double);
+ }
+ return bytes;
+}
diff --git a/src/nstencil.h b/src/nstencil.h
new file mode 100644
index 0000000000..c0ecfe2754
--- /dev/null
+++ b/src/nstencil.h
@@ -0,0 +1,84 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_NSTENCIL_H
+#define LMP_NSTENCIL_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class NStencil : protected Pointers {
+ public:
+ int istyle; // 1-N index into binnames
+ class NBin *nb; // ptr to NBin instance I depend on
+
+ bigint last_create; // timesteps for last operations performed
+ bigint last_stencil_memory;
+ bigint last_copy_bin;
+
+ int nstencil; // # of bins in stencil
+ int nstencil_ssa; // # of total bins in SSA stencil
+ int *stencil; // list of bin offsets
+ int **stencilxyz; // bin offsets in xyz dims
+ int *nstencil_multi; // # bins in each type-based multi stencil
+ int **stencil_multi; // list of bin offsets in each stencil
+ double **distsq_multi; // sq distances to bins in each stencil
+
+ NStencil(class LAMMPS *);
+ virtual ~NStencil();
+ void copy_neighbor_info();
+ void create_setup();
+ bigint memory_usage();
+
+ virtual void create() = 0;
+
+ inline int get_maxstencil() {return maxstencil;}
+
+ protected:
+
+ // data from Neighbor class
+
+ int neighstyle;
+ double cutneighmax;
+ double cutneighmaxsq;
+ double *cuttypesq;
+
+ // data from NBin class
+
+ int mbinx,mbiny,mbinz;
+ double binsizex,binsizey,binsizez;
+ double bininvx,bininvy,bininvz;
+
+ // data common to all NStencil variants
+
+ int xyzflag; // 1 if stencilxyz is allocated
+ int maxstencil; // max size of stencil
+ int maxstencil_multi; // max sizes of stencils
+ int sx,sy,sz; // extent of stencil in each dim
+
+ int dimension;
+
+ // methods for all NStencil variants
+
+ void copy_bin_info(); // copy info from NBin class
+ double bin_distance(int, int, int); // distance between bin corners
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_full_bin_2d.cpp b/src/nstencil_full_bin_2d.cpp
new file mode 100644
index 0000000000..1f2b666dfb
--- /dev/null
+++ b/src/nstencil_full_bin_2d.cpp
@@ -0,0 +1,38 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_full_bin_2d.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilFullBin2d::NStencilFullBin2d(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilFullBin2d::create()
+{
+ int i,j;
+
+ nstencil = 0;
+
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,0) < cutneighmaxsq)
+ stencil[nstencil++] = j*mbinx + i;
+}
diff --git a/src/nstencil_full_bin_2d.h b/src/nstencil_full_bin_2d.h
new file mode 100644
index 0000000000..18f848f275
--- /dev/null
+++ b/src/nstencil_full_bin_2d.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(full/bin/2d,
+ NStencilFullBin2d,
+ NS_FULL | NS_BIN | NS_2D |
+ NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_FULL_BIN_2D_H
+#define LMP_NSTENCIL_FULL_BIN_2D_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilFullBin2d : public NStencil {
+ public:
+ NStencilFullBin2d(class LAMMPS *);
+ ~NStencilFullBin2d() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_full_bin_3d.cpp b/src/nstencil_full_bin_3d.cpp
new file mode 100644
index 0000000000..b6a2198132
--- /dev/null
+++ b/src/nstencil_full_bin_3d.cpp
@@ -0,0 +1,39 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_full_bin_3d.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilFullBin3d::NStencilFullBin3d(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilFullBin3d::create()
+{
+ int i,j,k;
+
+ nstencil = 0;
+
+ for (k = -sz; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+}
diff --git a/src/nstencil_full_bin_3d.h b/src/nstencil_full_bin_3d.h
new file mode 100644
index 0000000000..d9acc9c535
--- /dev/null
+++ b/src/nstencil_full_bin_3d.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(full/bin/3d,
+ NStencilFullBin3d,
+ NS_FULL | NS_BIN | NS_3D |
+ NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_FULL_BIN_3D_H
+#define LMP_NSTENCIL_FULL_BIN_3D_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilFullBin3d : public NStencil {
+ public:
+ NStencilFullBin3d(class LAMMPS *);
+ ~NStencilFullBin3d() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_full_ghost_bin_2d.cpp b/src/nstencil_full_ghost_bin_2d.cpp
new file mode 100644
index 0000000000..bbbf1a4466
--- /dev/null
+++ b/src/nstencil_full_ghost_bin_2d.cpp
@@ -0,0 +1,45 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_full_ghost_bin_2d.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilFullGhostBin2d::NStencilFullGhostBin2d(LAMMPS *lmp) : NStencil(lmp)
+{
+ xyzflag = 1;
+}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilFullGhostBin2d::create()
+{
+ int i,j;
+
+ nstencil = 0;
+
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,0) < cutneighmaxsq) {
+ stencilxyz[nstencil][0] = i;
+ stencilxyz[nstencil][1] = j;
+ stencilxyz[nstencil][2] = 0;
+ stencil[nstencil++] = j*mbinx + i;
+ }
+}
diff --git a/src/nstencil_full_ghost_bin_2d.h b/src/nstencil_full_ghost_bin_2d.h
new file mode 100644
index 0000000000..af47913e7f
--- /dev/null
+++ b/src/nstencil_full_ghost_bin_2d.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(full/ghost/bin/2d,
+ NStencilFullGhostBin2d,
+ NS_FULL | NS_GHOST | NS_BIN | NS_2D |
+ NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_FULL_GHOST_BIN_2D_H
+#define LMP_NSTENCIL_FULL_GHOST_BIN_2D_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilFullGhostBin2d : public NStencil {
+ public:
+ NStencilFullGhostBin2d(class LAMMPS *);
+ ~NStencilFullGhostBin2d() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_full_ghost_bin_3d.cpp b/src/nstencil_full_ghost_bin_3d.cpp
new file mode 100644
index 0000000000..e9abca2174
--- /dev/null
+++ b/src/nstencil_full_ghost_bin_3d.cpp
@@ -0,0 +1,46 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_full_ghost_bin_3d.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilFullGhostBin3d::NStencilFullGhostBin3d(LAMMPS *lmp) : NStencil(lmp)
+{
+ xyzflag = 1;
+}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilFullGhostBin3d::create()
+{
+ int i,j,k;
+
+ nstencil = 0;
+
+ for (k = -sz; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,k) < cutneighmaxsq) {
+ stencilxyz[nstencil][0] = i;
+ stencilxyz[nstencil][1] = j;
+ stencilxyz[nstencil][2] = k;
+ stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+}
diff --git a/src/nstencil_full_ghost_bin_3d.h b/src/nstencil_full_ghost_bin_3d.h
new file mode 100644
index 0000000000..beca6573de
--- /dev/null
+++ b/src/nstencil_full_ghost_bin_3d.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(full/ghost/bin/3d,
+ NStencilFullGhostBin3d,
+ NS_FULL | NS_GHOST | NS_BIN | NS_3D |
+ NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_FULL_GHOST_BIN_3D_H
+#define LMP_NSTENCIL_FULL_GHOST_BIN_3D_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilFullGhostBin3d : public NStencil {
+ public:
+ NStencilFullGhostBin3d(class LAMMPS *);
+ ~NStencilFullGhostBin3d() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp
new file mode 100644
index 0000000000..ed2ffe11dc
--- /dev/null
+++ b/src/nstencil_full_multi_2d.cpp
@@ -0,0 +1,52 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_full_multi_2d.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilFullMulti2d::NStencilFullMulti2d(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilFullMulti2d::create()
+{
+ int i,j,n;
+ double rsq,typesq;
+ int *s;
+ double *distsq;
+
+ int ntypes = atom->ntypes;
+ for (int itype = 1; itype <= ntypes; itype++) {
+ typesq = cuttypesq[itype];
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ n = 0;
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++) {
+ rsq = bin_distance(i,j,0);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = j*mbinx + i;
+ }
+ }
+ nstencil_multi[itype] = n;
+ }
+}
diff --git a/src/nstencil_full_multi_2d.h b/src/nstencil_full_multi_2d.h
new file mode 100644
index 0000000000..8154144eda
--- /dev/null
+++ b/src/nstencil_full_multi_2d.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(full/multi/2d,
+ NStencilFullMulti2d,
+ NS_FULL | NS_MULTI | NS_2D |
+ NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_FULL_MULTI_2D_H
+#define LMP_NSTENCIL_FULL_MULTI_2D_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilFullMulti2d : public NStencil {
+ public:
+ NStencilFullMulti2d(class LAMMPS *);
+ ~NStencilFullMulti2d() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp
new file mode 100644
index 0000000000..c171bfadc5
--- /dev/null
+++ b/src/nstencil_full_multi_3d.cpp
@@ -0,0 +1,53 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_full_multi_3d.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilFullMulti3d::NStencilFullMulti3d(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilFullMulti3d::create()
+{
+ int i,j,k,n;
+ double rsq,typesq;
+ int *s;
+ double *distsq;
+
+ int ntypes = atom->ntypes;
+ for (int itype = 1; itype <= ntypes; itype++) {
+ typesq = cuttypesq[itype];
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ n = 0;
+ for (k = -sz; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++) {
+ rsq = bin_distance(i,j,k);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+ }
+ nstencil_multi[itype] = n;
+ }
+}
diff --git a/src/nstencil_full_multi_3d.h b/src/nstencil_full_multi_3d.h
new file mode 100644
index 0000000000..9e3696f5d2
--- /dev/null
+++ b/src/nstencil_full_multi_3d.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(full/multi/3d,
+ NStencilFullMulti3d,
+ NS_FULL | NS_MULTI | NS_3D |
+ NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_FULL_MULTI_3D_H
+#define LMP_NSTENCIL_FULL_MULTI_3D_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilFullMulti3d : public NStencil {
+ public:
+ NStencilFullMulti3d(class LAMMPS *);
+ ~NStencilFullMulti3d() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_bin_2d_newtoff.cpp b/src/nstencil_half_bin_2d_newtoff.cpp
new file mode 100644
index 0000000000..be5bc81dbf
--- /dev/null
+++ b/src/nstencil_half_bin_2d_newtoff.cpp
@@ -0,0 +1,39 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_bin_2d_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfBin2dNewtoff::NStencilHalfBin2dNewtoff(LAMMPS *lmp) :
+ NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfBin2dNewtoff::create()
+{
+ int i,j;
+
+ nstencil = 0;
+
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,0) < cutneighmaxsq)
+ stencil[nstencil++] = j*mbinx + i;
+}
diff --git a/src/nstencil_half_bin_2d_newtoff.h b/src/nstencil_half_bin_2d_newtoff.h
new file mode 100644
index 0000000000..7a350df1bc
--- /dev/null
+++ b/src/nstencil_half_bin_2d_newtoff.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/bin/2d/newtoff,
+ NStencilHalfBin2dNewtoff,
+ NS_HALF | NS_BIN | NS_2D | NS_NEWTOFF | NS_ORTHO | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTOFF_H
+#define LMP_NSTENCIL_HALF_BIN_2D_NEWTOFF_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfBin2dNewtoff : public NStencil {
+ public:
+ NStencilHalfBin2dNewtoff(class LAMMPS *);
+ ~NStencilHalfBin2dNewtoff() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_bin_2d_newton.cpp b/src/nstencil_half_bin_2d_newton.cpp
new file mode 100644
index 0000000000..9479bbf0c8
--- /dev/null
+++ b/src/nstencil_half_bin_2d_newton.cpp
@@ -0,0 +1,39 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_bin_2d_newton.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfBin2dNewton::NStencilHalfBin2dNewton(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfBin2dNewton::create()
+{
+ int i,j;
+
+ nstencil = 0;
+
+ for (j = 0; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (j > 0 || (j == 0 && i > 0))
+ if (bin_distance(i,j,0) < cutneighmaxsq)
+ stencil[nstencil++] = j*mbinx + i;
+}
diff --git a/src/nstencil_half_bin_2d_newton.h b/src/nstencil_half_bin_2d_newton.h
new file mode 100644
index 0000000000..64bbfc5fe4
--- /dev/null
+++ b/src/nstencil_half_bin_2d_newton.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/bin/2d/newton,
+ NStencilHalfBin2dNewton,
+ NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_ORTHO)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_H
+#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfBin2dNewton : public NStencil {
+ public:
+ NStencilHalfBin2dNewton(class LAMMPS *);
+ ~NStencilHalfBin2dNewton() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_bin_2d_newton_ssa.cpp b/src/nstencil_half_bin_2d_newton_ssa.cpp
new file mode 100644
index 0000000000..8c53abfe80
--- /dev/null
+++ b/src/nstencil_half_bin_2d_newton_ssa.cpp
@@ -0,0 +1,64 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors:
+ James Larentzos and Timothy I. Mattox (Engility Corporation)
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_bin_2d_newton_ssa.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) :
+ NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+ stencil = bins whose closest corner to central bin is within cutoff
+ sx,sy,sz = bin bounds = furthest the stencil could possibly extend
+ 3d creates xyz stencil, 2d creates xy stencil
+ for half list with newton on:
+ stencil is bins to the "upper right" of central bin
+ stencil does not include self
+ additionally, includes the bins beyond nstencil that are needed
+ to locate all the Active Interaction Region (AIR) ghosts for SSA
+------------------------------------------------------------------------- */
+
+void NStencilHalfBin2dNewtonSSA::create()
+{
+ int i,j,pos = 0;
+
+ for (j = 0; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (j > 0 || (j == 0 && i > 0))
+ if (bin_distance(i,j,0) < cutneighmaxsq)
+ stencil[pos++] = j*mbinx + i;
+
+ nstencil = pos; // record where normal half stencil ends
+
+ // include additional bins for AIR ghosts only
+
+ for (j = -sy; j <= 0; j++)
+ for (i = -sx; i <= sx; i++) {
+ if (j == 0 && i > 0) continue;
+ if (bin_distance(i,j,0) < cutneighmaxsq)
+ stencil[pos++] = j*mbinx + i;
+ }
+
+ nstencil_ssa = pos; // record where full stencil ends
+}
diff --git a/src/nstencil_half_bin_2d_newton_ssa.h b/src/nstencil_half_bin_2d_newton_ssa.h
new file mode 100644
index 0000000000..319a8ce670
--- /dev/null
+++ b/src/nstencil_half_bin_2d_newton_ssa.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/bin/2d/newton/ssa,
+ NStencilHalfBin2dNewtonSSA,
+ NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_SSA | NS_ORTHO)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H
+#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfBin2dNewtonSSA : public NStencil {
+ public:
+ NStencilHalfBin2dNewtonSSA(class LAMMPS *);
+ ~NStencilHalfBin2dNewtonSSA() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_bin_2d_newton_tri.cpp b/src/nstencil_half_bin_2d_newton_tri.cpp
new file mode 100644
index 0000000000..3a645a7434
--- /dev/null
+++ b/src/nstencil_half_bin_2d_newton_tri.cpp
@@ -0,0 +1,39 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_bin_2d_newton_tri.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfBin2dNewtonTri::NStencilHalfBin2dNewtonTri(LAMMPS *lmp) :
+ NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfBin2dNewtonTri::create()
+{
+ int i,j;
+
+ nstencil = 0;
+
+ for (j = 0; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,0) < cutneighmaxsq)
+ stencil[nstencil++] = j*mbinx + i;
+}
diff --git a/src/nstencil_half_bin_2d_newton_tri.h b/src/nstencil_half_bin_2d_newton_tri.h
new file mode 100644
index 0000000000..b9926608d7
--- /dev/null
+++ b/src/nstencil_half_bin_2d_newton_tri.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/bin/2d/newton/tri,
+ NStencilHalfBin2dNewtonTri,
+ NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_TRI_H
+#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_TRI_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfBin2dNewtonTri : public NStencil {
+ public:
+ NStencilHalfBin2dNewtonTri(class LAMMPS *);
+ ~NStencilHalfBin2dNewtonTri() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_bin_3d_newtoff.cpp b/src/nstencil_half_bin_3d_newtoff.cpp
new file mode 100644
index 0000000000..44678b05df
--- /dev/null
+++ b/src/nstencil_half_bin_3d_newtoff.cpp
@@ -0,0 +1,40 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_bin_3d_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfBin3dNewtoff::NStencilHalfBin3dNewtoff(LAMMPS *lmp) :
+ NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfBin3dNewtoff::create()
+{
+ int i,j,k;
+
+ nstencil = 0;
+
+ for (k = -sz; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+}
diff --git a/src/nstencil_half_bin_3d_newtoff.h b/src/nstencil_half_bin_3d_newtoff.h
new file mode 100644
index 0000000000..d1eac666cc
--- /dev/null
+++ b/src/nstencil_half_bin_3d_newtoff.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/bin/3d/newtoff,
+ NStencilHalfBin3dNewtoff,
+ NS_HALF | NS_BIN | NS_3D | NS_NEWTOFF | NS_ORTHO | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTOFF_H
+#define LMP_NSTENCIL_HALF_BIN_3D_NEWTOFF_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfBin3dNewtoff : public NStencil {
+ public:
+ NStencilHalfBin3dNewtoff(class LAMMPS *);
+ ~NStencilHalfBin3dNewtoff() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_bin_3d_newton.cpp b/src/nstencil_half_bin_3d_newton.cpp
new file mode 100644
index 0000000000..24c234c004
--- /dev/null
+++ b/src/nstencil_half_bin_3d_newton.cpp
@@ -0,0 +1,40 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_bin_3d_newton.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfBin3dNewton::NStencilHalfBin3dNewton(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfBin3dNewton::create()
+{
+ int i,j,k;
+
+ nstencil = 0;
+
+ for (k = 0; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (k > 0 || j > 0 || (j == 0 && i > 0))
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+}
diff --git a/src/nstencil_half_bin_3d_newton.h b/src/nstencil_half_bin_3d_newton.h
new file mode 100644
index 0000000000..96f19adae1
--- /dev/null
+++ b/src/nstencil_half_bin_3d_newton.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/bin/3d/newton,
+ NStencilHalfBin3dNewton,
+ NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_ORTHO)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_H
+#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfBin3dNewton : public NStencil {
+ public:
+ NStencilHalfBin3dNewton(class LAMMPS *);
+ ~NStencilHalfBin3dNewton() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_bin_3d_newton_ssa.cpp b/src/nstencil_half_bin_3d_newton_ssa.cpp
new file mode 100644
index 0000000000..1ac15fe61e
--- /dev/null
+++ b/src/nstencil_half_bin_3d_newton_ssa.cpp
@@ -0,0 +1,74 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors:
+ James Larentzos and Timothy I. Mattox (Engility Corporation)
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_bin_3d_newton_ssa.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) :
+ NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+ stencil = bins whose closest corner to central bin is within cutoff
+ sx,sy,sz = bin bounds = furthest the stencil could possibly extend
+ 3d creates xyz stencil, 2d creates xy stencil
+ for half list with newton on:
+ stencil is bins to the "upper right" of central bin
+ stencil does not include self
+ additionally, includes the bins beyond nstencil that are needed
+ to locate all the Active Interaction Region (AIR) ghosts for SSA
+------------------------------------------------------------------------- */
+
+void NStencilHalfBin3dNewtonSSA::create()
+{
+ int i,j,k,pos = 0;
+
+ for (k = 0; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (k > 0 || j > 0 || (j == 0 && i > 0))
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;
+
+ nstencil = pos; // record where normal half stencil ends
+
+ // include additional bins for AIR ghosts only
+
+ for (k = -sz; k < 0; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;
+
+ // For k==0, make sure to skip already included bins
+
+ k = 0;
+ for (j = -sy; j <= 0; j++)
+ for (i = -sx; i <= sx; i++) {
+ if (j == 0 && i > 0) continue;
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+
+ nstencil_ssa = pos; // record where full stencil ends
+}
diff --git a/src/nstencil_half_bin_3d_newton_ssa.h b/src/nstencil_half_bin_3d_newton_ssa.h
new file mode 100644
index 0000000000..8cb130a712
--- /dev/null
+++ b/src/nstencil_half_bin_3d_newton_ssa.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/bin/3d/newton/ssa,
+ NStencilHalfBin3dNewtonSSA,
+ NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_SSA | NS_ORTHO)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H
+#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfBin3dNewtonSSA : public NStencil {
+ public:
+ NStencilHalfBin3dNewtonSSA(class LAMMPS *);
+ ~NStencilHalfBin3dNewtonSSA() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_bin_3d_newton_tri.cpp b/src/nstencil_half_bin_3d_newton_tri.cpp
new file mode 100644
index 0000000000..9e8c41f97a
--- /dev/null
+++ b/src/nstencil_half_bin_3d_newton_tri.cpp
@@ -0,0 +1,40 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_bin_3d_newton_tri.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfBin3dNewtonTri::NStencilHalfBin3dNewtonTri(LAMMPS *lmp) :
+ NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfBin3dNewtonTri::create()
+{
+ int i,j,k;
+
+ nstencil = 0;
+
+ for (k = 0; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+}
diff --git a/src/nstencil_half_bin_3d_newton_tri.h b/src/nstencil_half_bin_3d_newton_tri.h
new file mode 100644
index 0000000000..8c265acb46
--- /dev/null
+++ b/src/nstencil_half_bin_3d_newton_tri.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/bin/3d/newton/tri,
+ NStencilHalfBin3dNewtonTri,
+ NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_TRI_H
+#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_TRI_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfBin3dNewtonTri : public NStencil {
+ public:
+ NStencilHalfBin3dNewtonTri(class LAMMPS *);
+ ~NStencilHalfBin3dNewtonTri() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_ghost_bin_2d_newtoff.cpp b/src/nstencil_half_ghost_bin_2d_newtoff.cpp
new file mode 100644
index 0000000000..4bb0ecafe2
--- /dev/null
+++ b/src/nstencil_half_ghost_bin_2d_newtoff.cpp
@@ -0,0 +1,46 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_ghost_bin_2d_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfGhostBin2dNewtoff::
+NStencilHalfGhostBin2dNewtoff(LAMMPS *lmp) : NStencil(lmp)
+{
+ xyzflag = 1;
+}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfGhostBin2dNewtoff::create()
+{
+ int i,j;
+
+ nstencil = 0;
+
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,0) < cutneighmaxsq) {
+ stencilxyz[nstencil][0] = i;
+ stencilxyz[nstencil][1] = j;
+ stencilxyz[nstencil][2] = 0;
+ stencil[nstencil++] = j*mbinx + i;
+ }
+}
diff --git a/src/nstencil_half_ghost_bin_2d_newtoff.h b/src/nstencil_half_ghost_bin_2d_newtoff.h
new file mode 100644
index 0000000000..3b70f0042a
--- /dev/null
+++ b/src/nstencil_half_ghost_bin_2d_newtoff.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/ghost/bin/2d/newtoff,
+ NStencilHalfGhostBin2dNewtoff,
+ NS_HALF | NS_GHOST | NS_BIN | NS_2D |
+ NS_NEWTOFF | NS_ORTHO | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_GHOST_BIN_2D_NEWTOFF_H
+#define LMP_NSTENCIL_HALF_GHOST_BIN_2D_NEWTOFF_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfGhostBin2dNewtoff : public NStencil {
+ public:
+ NStencilHalfGhostBin2dNewtoff(class LAMMPS *);
+ ~NStencilHalfGhostBin2dNewtoff() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_ghost_bin_3d_newtoff.cpp b/src/nstencil_half_ghost_bin_3d_newtoff.cpp
new file mode 100644
index 0000000000..1026b11542
--- /dev/null
+++ b/src/nstencil_half_ghost_bin_3d_newtoff.cpp
@@ -0,0 +1,47 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_ghost_bin_3d_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfGhostBin3dNewtoff::
+NStencilHalfGhostBin3dNewtoff(LAMMPS *lmp) : NStencil(lmp)
+{
+ xyzflag = 1;
+}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfGhostBin3dNewtoff::create()
+{
+ int i,j,k;
+
+ nstencil = 0;
+
+ for (k = -sz; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,k) < cutneighmaxsq) {
+ stencilxyz[nstencil][0] = i;
+ stencilxyz[nstencil][1] = j;
+ stencilxyz[nstencil][2] = k;
+ stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+}
diff --git a/src/nstencil_half_ghost_bin_3d_newtoff.h b/src/nstencil_half_ghost_bin_3d_newtoff.h
new file mode 100644
index 0000000000..ee58c29342
--- /dev/null
+++ b/src/nstencil_half_ghost_bin_3d_newtoff.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/ghost/bin/3d/newtoff,
+ NStencilHalfGhostBin3dNewtoff,
+ NS_HALF | NS_GHOST | NS_BIN | NS_3D |
+ NS_NEWTOFF | NS_ORTHO | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_GHOST_BIN_3D_NEWTOFF_H
+#define LMP_NSTENCIL_HALF_GHOST_BIN_3D_NEWTOFF_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfGhostBin3dNewtoff : public NStencil {
+ public:
+ NStencilHalfGhostBin3dNewtoff(class LAMMPS *);
+ ~NStencilHalfGhostBin3dNewtoff() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_multi_2d_newtoff.cpp b/src/nstencil_half_multi_2d_newtoff.cpp
new file mode 100644
index 0000000000..567abe2878
--- /dev/null
+++ b/src/nstencil_half_multi_2d_newtoff.cpp
@@ -0,0 +1,53 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_multi_2d_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfMulti2dNewtoff::
+NStencilHalfMulti2dNewtoff(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfMulti2dNewtoff::create()
+{
+ int i,j,n;
+ double rsq,typesq;
+ int *s;
+ double *distsq;
+
+ int ntypes = atom->ntypes;
+ for (int itype = 1; itype <= ntypes; itype++) {
+ typesq = cuttypesq[itype];
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ n = 0;
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++) {
+ rsq = bin_distance(i,j,0);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = j*mbinx + i;
+ }
+ }
+ nstencil_multi[itype] = n;
+ }
+}
diff --git a/src/nstencil_half_multi_2d_newtoff.h b/src/nstencil_half_multi_2d_newtoff.h
new file mode 100644
index 0000000000..5603f37beb
--- /dev/null
+++ b/src/nstencil_half_multi_2d_newtoff.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/multi/2d/newtoff,
+ NStencilHalfMulti2dNewtoff,
+ NS_HALF | NS_MULTI | NS_2D | NS_NEWTOFF | NS_ORTHO | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_MULTI_2D_NEWTOFF_H
+#define LMP_NSTENCIL_HALF_MULTI_2D_NEWTOFF_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfMulti2dNewtoff : public NStencil {
+ public:
+ NStencilHalfMulti2dNewtoff(class LAMMPS *);
+ ~NStencilHalfMulti2dNewtoff() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_multi_2d_newton.cpp b/src/nstencil_half_multi_2d_newton.cpp
new file mode 100644
index 0000000000..5dc2c37148
--- /dev/null
+++ b/src/nstencil_half_multi_2d_newton.cpp
@@ -0,0 +1,54 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_multi_2d_newton.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfMulti2dNewton::
+NStencilHalfMulti2dNewton(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfMulti2dNewton::create()
+{
+ int i,j,n;
+ double rsq,typesq;
+ int *s;
+ double *distsq;
+
+ int ntypes = atom->ntypes;
+ for (int itype = 1; itype <= ntypes; itype++) {
+ typesq = cuttypesq[itype];
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ n = 0;
+ for (j = 0; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (j > 0 || (j == 0 && i > 0)) {
+ rsq = bin_distance(i,j,0);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = j*mbinx + i;
+ }
+ }
+ nstencil_multi[itype] = n;
+ }
+}
diff --git a/src/nstencil_half_multi_2d_newton.h b/src/nstencil_half_multi_2d_newton.h
new file mode 100644
index 0000000000..9ecac4c696
--- /dev/null
+++ b/src/nstencil_half_multi_2d_newton.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/multi/2d/newton,
+ NStencilHalfMulti2dNewton,
+ NS_HALF | NS_MULTI | NS_2D | NS_NEWTON | NS_ORTHO)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_H
+#define LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfMulti2dNewton : public NStencil {
+ public:
+ NStencilHalfMulti2dNewton(class LAMMPS *);
+ ~NStencilHalfMulti2dNewton() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_multi_2d_newton_tri.cpp b/src/nstencil_half_multi_2d_newton_tri.cpp
new file mode 100644
index 0000000000..59a5a1d19e
--- /dev/null
+++ b/src/nstencil_half_multi_2d_newton_tri.cpp
@@ -0,0 +1,53 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_multi_2d_newton_tri.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfMulti2dNewtonTri::
+NStencilHalfMulti2dNewtonTri(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfMulti2dNewtonTri::create()
+{
+ int i,j,n;
+ double rsq,typesq;
+ int *s;
+ double *distsq;
+
+ int ntypes = atom->ntypes;
+ for (int itype = 1; itype <= ntypes; itype++) {
+ typesq = cuttypesq[itype];
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ n = 0;
+ for (j = 0; j <= sy; j++)
+ for (i = -sx; i <= sx; i++) {
+ rsq = bin_distance(i,j,0);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = j*mbinx + i;
+ }
+ }
+ nstencil_multi[itype] = n;
+ }
+}
diff --git a/src/nstencil_half_multi_2d_newton_tri.h b/src/nstencil_half_multi_2d_newton_tri.h
new file mode 100644
index 0000000000..62d7dfdebf
--- /dev/null
+++ b/src/nstencil_half_multi_2d_newton_tri.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/multi/2d/newton/tri,
+ NStencilHalfMulti2dNewtonTri,
+ NS_HALF | NS_MULTI | NS_2D | NS_NEWTON | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_TRI_H
+#define LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_TRI_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfMulti2dNewtonTri : public NStencil {
+ public:
+ NStencilHalfMulti2dNewtonTri(class LAMMPS *);
+ ~NStencilHalfMulti2dNewtonTri() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_multi_3d_newtoff.cpp b/src/nstencil_half_multi_3d_newtoff.cpp
new file mode 100644
index 0000000000..72b882dddc
--- /dev/null
+++ b/src/nstencil_half_multi_3d_newtoff.cpp
@@ -0,0 +1,54 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_multi_3d_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfMulti3dNewtoff::
+NStencilHalfMulti3dNewtoff(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfMulti3dNewtoff::create()
+{
+ int i,j,k,n;
+ double rsq,typesq;
+ int *s;
+ double *distsq;
+
+ int ntypes = atom->ntypes;
+ for (int itype = 1; itype <= ntypes; itype++) {
+ typesq = cuttypesq[itype];
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ n = 0;
+ for (k = -sz; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++) {
+ rsq = bin_distance(i,j,k);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+ }
+ nstencil_multi[itype] = n;
+ }
+}
diff --git a/src/nstencil_half_multi_3d_newtoff.h b/src/nstencil_half_multi_3d_newtoff.h
new file mode 100644
index 0000000000..99428deb6a
--- /dev/null
+++ b/src/nstencil_half_multi_3d_newtoff.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/multi/3d/newtoff,
+ NStencilHalfMulti3dNewtoff,
+ NS_HALF | NS_MULTI | NS_3D | NS_NEWTOFF | NS_ORTHO | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_MULTI_3D_NEWTOFF_H
+#define LMP_NSTENCIL_HALF_MULTI_3D_NEWTOFF_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfMulti3dNewtoff : public NStencil {
+ public:
+ NStencilHalfMulti3dNewtoff(class LAMMPS *);
+ ~NStencilHalfMulti3dNewtoff() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_multi_3d_newton.cpp b/src/nstencil_half_multi_3d_newton.cpp
new file mode 100644
index 0000000000..9a5d5cab65
--- /dev/null
+++ b/src/nstencil_half_multi_3d_newton.cpp
@@ -0,0 +1,55 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_multi_3d_newton.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfMulti3dNewton::
+NStencilHalfMulti3dNewton(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfMulti3dNewton::create()
+{
+ int i,j,k,n;
+ double rsq,typesq;
+ int *s;
+ double *distsq;
+
+ int ntypes = atom->ntypes;
+ for (int itype = 1; itype <= ntypes; itype++) {
+ typesq = cuttypesq[itype];
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ n = 0;
+ for (k = 0; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (k > 0 || j > 0 || (j == 0 && i > 0)) {
+ rsq = bin_distance(i,j,k);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+ }
+ nstencil_multi[itype] = n;
+ }
+}
diff --git a/src/nstencil_half_multi_3d_newton.h b/src/nstencil_half_multi_3d_newton.h
new file mode 100644
index 0000000000..bbdc7752c6
--- /dev/null
+++ b/src/nstencil_half_multi_3d_newton.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/multi/3d/newton,
+ NStencilHalfMulti3dNewton,
+ NS_HALF | NS_MULTI | NS_3D | NS_NEWTON | NS_ORTHO)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_H
+#define LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfMulti3dNewton : public NStencil {
+ public:
+ NStencilHalfMulti3dNewton(class LAMMPS *);
+ ~NStencilHalfMulti3dNewton() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/nstencil_half_multi_3d_newton_tri.cpp b/src/nstencil_half_multi_3d_newton_tri.cpp
new file mode 100644
index 0000000000..953beb3211
--- /dev/null
+++ b/src/nstencil_half_multi_3d_newton_tri.cpp
@@ -0,0 +1,54 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nstencil_half_multi_3d_newton_tri.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NStencilHalfMulti3dNewtonTri::
+NStencilHalfMulti3dNewtonTri(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+ create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+void NStencilHalfMulti3dNewtonTri::create()
+{
+ int i,j,k,n;
+ double rsq,typesq;
+ int *s;
+ double *distsq;
+
+ int ntypes = atom->ntypes;
+ for (int itype = 1; itype <= ntypes; itype++) {
+ typesq = cuttypesq[itype];
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ n = 0;
+ for (k = 0; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++) {
+ rsq = bin_distance(i,j,k);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+ }
+ nstencil_multi[itype] = n;
+ }
+}
diff --git a/src/nstencil_half_multi_3d_newton_tri.h b/src/nstencil_half_multi_3d_newton_tri.h
new file mode 100644
index 0000000000..f6866489a4
--- /dev/null
+++ b/src/nstencil_half_multi_3d_newton_tri.h
@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+
+NStencilStyle(half/multi/3d/newton/tri,
+ NStencilHalfMulti3dNewtonTri,
+ NS_HALF | NS_MULTI | NS_3D | NS_NEWTON | NS_TRI)
+
+#else
+
+#ifndef LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_TRI_H
+#define LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_TRI_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+class NStencilHalfMulti3dNewtonTri : public NStencil {
+ public:
+ NStencilHalfMulti3dNewtonTri(class LAMMPS *);
+ ~NStencilHalfMulti3dNewtonTri() {}
+ void create();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/ntopo.cpp b/src/ntopo.cpp
new file mode 100644
index 0000000000..124fa6687c
--- /dev/null
+++ b/src/ntopo.cpp
@@ -0,0 +1,218 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include "ntopo.h"
+#include "atom.h"
+#include "neighbor.h"
+#include "comm.h"
+#include "domain.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define LB_FACTOR 1.5
+
+/* ---------------------------------------------------------------------- */
+
+NTopo::NTopo(LAMMPS *lmp) : Pointers(lmp)
+{
+ me = comm->me;
+ nprocs = comm->nprocs;
+
+ nbondlist = nanglelist = ndihedrallist = nimproperlist = 0;
+ maxbond = maxangle = maxdihedral = maximproper = 0;
+ bondlist = anglelist = dihedrallist = improperlist = NULL;
+
+ cluster_check = neighbor->cluster_check;
+}
+
+/* ---------------------------------------------------------------------- */
+
+NTopo::~NTopo()
+{
+ memory->destroy(bondlist);
+ memory->destroy(anglelist);
+ memory->destroy(dihedrallist);
+ memory->destroy(improperlist);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopo::allocate_bond()
+{
+ if (nprocs == 1) maxbond = atom->nbonds;
+ else maxbond = static_cast<int> (LB_FACTOR * atom->nbonds / nprocs);
+ memory->create(bondlist,maxbond,3,"neigh_topo:bondlist");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopo::allocate_angle()
+{
+ if (nprocs == 1) maxangle = atom->nangles;
+ else maxangle = static_cast<int> (LB_FACTOR * atom->nangles / nprocs);
+ memory->create(anglelist,maxangle,4,"neigh_topo:anglelist");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopo::allocate_dihedral()
+{
+ if (nprocs == 1) maxdihedral = atom->ndihedrals;
+ else maxdihedral = static_cast<int> (LB_FACTOR * atom->ndihedrals / nprocs);
+ memory->create(dihedrallist,maxdihedral,5,"neigh_topo:dihedrallist");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopo::allocate_improper()
+{
+ if (nprocs == 1) maximproper = atom->nimpropers;
+ else maximproper = static_cast<int> (LB_FACTOR * atom->nimpropers / nprocs);
+ memory->create(improperlist,maximproper,5,"neigh_topo:improperlist");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopo::bond_check()
+{
+ int i,j;
+ double dx,dy,dz,dxstart,dystart,dzstart;
+
+ double **x = atom->x;
+ int flag = 0;
+
+ for (int m = 0; m < nbondlist; m++) {
+ i = bondlist[m][0];
+ j = bondlist[m][1];
+ dxstart = dx = x[i][0] - x[j][0];
+ dystart = dy = x[i][1] - x[j][1];
+ dzstart = dz = x[i][2] - x[j][2];
+ domain->minimum_image(dx,dy,dz);
+ if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+ }
+
+ int flag_all;
+ MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
+ if (flag_all) error->all(FLERR,"Bond extent > half of periodic box length");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopo::angle_check()
+{
+ int i,j,k;
+ double dx,dy,dz,dxstart,dystart,dzstart;
+
+ double **x = atom->x;
+ int flag = 0;
+
+ // check all 3 distances
+ // in case angle potential computes any of them
+
+ for (int m = 0; m < nanglelist; m++) {
+ i = anglelist[m][0];
+ j = anglelist[m][1];
+ k = anglelist[m][2];
+ dxstart = dx = x[i][0] - x[j][0];
+ dystart = dy = x[i][1] - x[j][1];
+ dzstart = dz = x[i][2] - x[j][2];
+ domain->minimum_image(dx,dy,dz);
+ if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+ dxstart = dx = x[i][0] - x[k][0];
+ dystart = dy = x[i][1] - x[k][1];
+ dzstart = dz = x[i][2] - x[k][2];
+ domain->minimum_image(dx,dy,dz);
+ if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+ dxstart = dx = x[j][0] - x[k][0];
+ dystart = dy = x[j][1] - x[k][1];
+ dzstart = dz = x[j][2] - x[k][2];
+ domain->minimum_image(dx,dy,dz);
+ if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+ }
+
+ int flag_all;
+ MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
+ if (flag_all) error->all(FLERR,"Angle extent > half of periodic box length");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopo::dihedral_check(int nlist, int **list)
+{
+ int i,j,k,l;
+ double dx,dy,dz,dxstart,dystart,dzstart;
+
+ double **x = atom->x;
+ int flag = 0;
+
+ // check all 6 distances
+ // in case dihedral/improper potential computes any of them
+
+ for (int m = 0; m < nlist; m++) {
+ i = list[m][0];
+ j = list[m][1];
+ k = list[m][2];
+ l = list[m][3];
+ dxstart = dx = x[i][0] - x[j][0];
+ dystart = dy = x[i][1] - x[j][1];
+ dzstart = dz = x[i][2] - x[j][2];
+ domain->minimum_image(dx,dy,dz);
+ if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+ dxstart = dx = x[i][0] - x[k][0];
+ dystart = dy = x[i][1] - x[k][1];
+ dzstart = dz = x[i][2] - x[k][2];
+ domain->minimum_image(dx,dy,dz);
+ if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+ dxstart = dx = x[i][0] - x[l][0];
+ dystart = dy = x[i][1] - x[l][1];
+ dzstart = dz = x[i][2] - x[l][2];
+ domain->minimum_image(dx,dy,dz);
+ if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+ dxstart = dx = x[j][0] - x[k][0];
+ dystart = dy = x[j][1] - x[k][1];
+ dzstart = dz = x[j][2] - x[k][2];
+ domain->minimum_image(dx,dy,dz);
+ if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+ dxstart = dx = x[j][0] - x[l][0];
+ dystart = dy = x[j][1] - x[l][1];
+ dzstart = dz = x[j][2] - x[l][2];
+ domain->minimum_image(dx,dy,dz);
+ if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+ dxstart = dx = x[k][0] - x[l][0];
+ dystart = dy = x[k][1] - x[l][1];
+ dzstart = dz = x[k][2] - x[l][2];
+ domain->minimum_image(dx,dy,dz);
+ if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+ }
+
+ int flag_all;
+ MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
+ if (flag_all)
+ error->all(FLERR,"Dihedral/improper extent > half of periodic box length");
+}
+
+/* ---------------------------------------------------------------------- */
+
+bigint NTopo::memory_usage()
+{
+ bigint bytes = 0;
+ bytes += 3*maxbond * sizeof(int);
+ bytes += 4*maxangle * sizeof(int);
+ bytes += 5*maxdihedral * sizeof(int);
+ bytes += 5*maximproper * sizeof(int);
+ return bytes;
+}
+
diff --git a/src/ntopo.h b/src/ntopo.h
new file mode 100644
index 0000000000..672a82e367
--- /dev/null
+++ b/src/ntopo.h
@@ -0,0 +1,56 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_NTOPO_H
+#define LMP_NTOPO_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class NTopo : protected Pointers {
+ public:
+ int nbondlist,nanglelist,ndihedrallist,nimproperlist;
+ int **bondlist,**anglelist,**dihedrallist,**improperlist;
+
+ NTopo(class LAMMPS *);
+ virtual ~NTopo();
+
+ virtual void build() = 0;
+
+ bigint memory_usage();
+
+ protected:
+ enum{IGNORE,WARN,ERROR}; // same as thermo.cpp
+
+ int me,nprocs;
+ int maxbond,maxangle,maxdihedral,maximproper;
+ int cluster_check; // copy from Neighbor
+
+ void allocate_bond();
+ void allocate_angle();
+ void allocate_dihedral();
+ void allocate_improper();
+
+ void bond_check();
+ void angle_check();
+ void dihedral_check(int, int **);
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/ntopo_angle_all.cpp b/src/ntopo_angle_all.cpp
new file mode 100644
index 0000000000..3a079ab467
--- /dev/null
+++ b/src/ntopo_angle_all.cpp
@@ -0,0 +1,99 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include "ntopo_angle_all.h"
+#include "atom.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoAngleAll::NTopoAngleAll(LAMMPS *lmp) : NTopo(lmp)
+{
+ allocate_angle();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoAngleAll::build()
+{
+ int i,m,atom1,atom2,atom3;
+
+ int nlocal = atom->nlocal;
+ int *num_angle = atom->num_angle;
+ tagint **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom2 = atom->angle_atom2;
+ tagint **angle_atom3 = atom->angle_atom3;
+ int **angle_type = atom->angle_type;
+ int newton_bond = force->newton_bond;
+
+ int lostbond = output->thermo->lostbond;
+ int nmissing = 0;
+ nanglelist = 0;
+
+ for (i = 0; i < nlocal; i++)
+ for (m = 0; m < num_angle[i]; m++) {
+ atom1 = atom->map(angle_atom1[i][m]);
+ atom2 = atom->map(angle_atom2[i][m]);
+ atom3 = atom->map(angle_atom3[i][m]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
+ nmissing++;
+ if (lostbond == ERROR) {
+ char str[128];
+ sprintf(str,"Angle atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ continue;
+ }
+ atom1 = domain->closest_image(i,atom1);
+ atom2 = domain->closest_image(i,atom2);
+ atom3 = domain->closest_image(i,atom3);
+ if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
+ if (nanglelist == maxangle) {
+ maxangle += DELTA;
+ memory->grow(anglelist,maxangle,4,"neigh_topo:anglelist");
+ }
+ anglelist[nanglelist][0] = atom1;
+ anglelist[nanglelist][1] = atom2;
+ anglelist[nanglelist][2] = atom3;
+ anglelist[nanglelist][3] = angle_type[i][m];
+ nanglelist++;
+ }
+ }
+
+ if (cluster_check) angle_check();
+ if (lostbond == IGNORE) return;
+
+ int all;
+ MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+ if (all) {
+ char str[128];
+ sprintf(str,
+ "Angle atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+ if (me == 0) error->warning(FLERR,str);
+ }
+}
diff --git a/src/neigh_full.h b/src/ntopo_angle_all.h
similarity index 68%
rename from src/neigh_full.h
rename to src/ntopo_angle_all.h
index 1538f7662a..fad611a1eb 100644
--- a/src/neigh_full.h
+++ b/src/ntopo_angle_all.h
@@ -11,12 +11,31 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-/* ERROR/WARNING messages:
+#ifdef NTOPO_CLASS
+
+NTopoStyle(NTOPO_ANGLE_ALL,NTopoAngleAll)
+
+#else
+
+#ifndef LMP_TOPO_ANGLE_ALL_H
+#define LMP_TOPO_ANGLE_ALL_H
+
+#include "ntopo.h"
-E: Neighbor list overflow, boost neigh_modify one
+namespace LAMMPS_NS {
-There are too many neighbors of a single atom. Use the neigh_modify
-command to increase the max number of neighbors allowed for one atom.
-You may also want to boost the page size.
+class NTopoAngleAll : public NTopo {
+ public:
+ NTopoAngleAll(class LAMMPS *);
+ ~NTopoAngleAll() {}
+ void build();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
*/
diff --git a/src/ntopo_angle_partial.cpp b/src/ntopo_angle_partial.cpp
new file mode 100644
index 0000000000..f1d668a3ba
--- /dev/null
+++ b/src/ntopo_angle_partial.cpp
@@ -0,0 +1,100 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include "ntopo_angle_partial.h"
+#include "atom.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoAnglePartial::NTopoAnglePartial(LAMMPS *lmp) : NTopo(lmp)
+{
+ allocate_angle();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoAnglePartial::build()
+{
+ int i,m,atom1,atom2,atom3;
+
+ int nlocal = atom->nlocal;
+ int *num_angle = atom->num_angle;
+ tagint **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom2 = atom->angle_atom2;
+ tagint **angle_atom3 = atom->angle_atom3;
+ int **angle_type = atom->angle_type;
+ int newton_bond = force->newton_bond;
+
+ int lostbond = output->thermo->lostbond;
+ int nmissing = 0;
+ nanglelist = 0;
+
+ for (i = 0; i < nlocal; i++)
+ for (m = 0; m < num_angle[i]; m++) {
+ if (angle_type[i][m] <= 0) continue;
+ atom1 = atom->map(angle_atom1[i][m]);
+ atom2 = atom->map(angle_atom2[i][m]);
+ atom3 = atom->map(angle_atom3[i][m]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
+ nmissing++;
+ if (lostbond == ERROR) {
+ char str[128];
+ sprintf(str,"Angle atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ continue;
+ }
+ atom1 = domain->closest_image(i,atom1);
+ atom2 = domain->closest_image(i,atom2);
+ atom3 = domain->closest_image(i,atom3);
+ if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
+ if (nanglelist == maxangle) {
+ maxangle += DELTA;
+ memory->grow(anglelist,maxangle,4,"neigh_topo:anglelist");
+ }
+ anglelist[nanglelist][0] = atom1;
+ anglelist[nanglelist][1] = atom2;
+ anglelist[nanglelist][2] = atom3;
+ anglelist[nanglelist][3] = angle_type[i][m];
+ nanglelist++;
+ }
+ }
+
+ if (cluster_check) angle_check();
+ if (lostbond == IGNORE) return;
+
+ int all;
+ MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+ if (all) {
+ char str[128];
+ sprintf(str,
+ "Angle atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+ if (me == 0) error->warning(FLERR,str);
+ }
+}
diff --git a/src/ntopo_angle_partial.h b/src/ntopo_angle_partial.h
new file mode 100644
index 0000000000..57ebcec558
--- /dev/null
+++ b/src/ntopo_angle_partial.h
@@ -0,0 +1,41 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NTOPO_CLASS
+
+NTopoStyle(NTOPO_ANGLE_PARTIAL,NTopoAnglePartial)
+
+#else
+
+#ifndef LMP_TOPO_ANGLE_PARTIAL_H
+#define LMP_TOPO_ANGLE_PARTIAL_H
+
+#include "ntopo.h"
+
+namespace LAMMPS_NS {
+
+class NTopoAnglePartial : public NTopo {
+ public:
+ NTopoAnglePartial(class LAMMPS *);
+ ~NTopoAnglePartial() {}
+ void build();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/ntopo_angle_template.cpp b/src/ntopo_angle_template.cpp
new file mode 100644
index 0000000000..05d5de28a4
--- /dev/null
+++ b/src/ntopo_angle_template.cpp
@@ -0,0 +1,119 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include "ntopo_angle_template.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "molecule.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoAngleTemplate::NTopoAngleTemplate(LAMMPS *lmp) : NTopo(lmp)
+{
+ allocate_angle();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoAngleTemplate::build()
+{
+ int i,m,atom1,atom2,atom3;
+ int imol,iatom;
+ tagint tagprev;
+ int *num_angle;
+ tagint **angle_atom1,**angle_atom2,**angle_atom3;
+ int **angle_type;
+
+ Molecule **onemols = atom->avec->onemols;
+
+ tagint *tag = atom->tag;
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ int nlocal = atom->nlocal;
+ int newton_bond = force->newton_bond;
+
+ int lostbond = output->thermo->lostbond;
+ int nmissing = 0;
+ nanglelist = 0;
+
+ for (i = 0; i < nlocal; i++) {
+ if (molindex[i] < 0) continue;
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ num_angle = onemols[imol]->num_angle;
+ angle_atom1 = onemols[imol]->angle_atom1;
+ angle_atom2 = onemols[imol]->angle_atom2;
+ angle_atom3 = onemols[imol]->angle_atom3;
+ angle_type = onemols[imol]->angle_type;
+
+ for (m = 0; m < num_angle[iatom]; m++) {
+ if (angle_type[iatom][m] <= 0) continue;
+ atom1 = atom->map(angle_atom1[iatom][m]+tagprev);
+ atom2 = atom->map(angle_atom2[iatom][m]+tagprev);
+ atom3 = atom->map(angle_atom3[iatom][m]+tagprev);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
+ nmissing++;
+ if (lostbond == ERROR) {
+ char str[128];
+ sprintf(str,"Angle atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ angle_atom1[iatom][m]+tagprev,angle_atom2[iatom][m]+tagprev,
+ angle_atom3[iatom][m]+tagprev,
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ continue;
+ }
+ atom1 = domain->closest_image(i,atom1);
+ atom2 = domain->closest_image(i,atom2);
+ atom3 = domain->closest_image(i,atom3);
+ if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
+ if (nanglelist == maxangle) {
+ maxangle += DELTA;
+ memory->grow(anglelist,maxangle,4,"neigh_topo:anglelist");
+ }
+ anglelist[nanglelist][0] = atom1;
+ anglelist[nanglelist][1] = atom2;
+ anglelist[nanglelist][2] = atom3;
+ anglelist[nanglelist][3] = angle_type[iatom][m];
+ nanglelist++;
+ }
+ }
+ }
+
+ if (cluster_check) angle_check();
+ if (lostbond == IGNORE) return;
+
+ int all;
+ MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+ if (all) {
+ char str[128];
+ sprintf(str,
+ "Angle atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+ if (me == 0) error->warning(FLERR,str);
+ }
+}
diff --git a/src/ntopo_angle_template.h b/src/ntopo_angle_template.h
new file mode 100644
index 0000000000..fc94a07b02
--- /dev/null
+++ b/src/ntopo_angle_template.h
@@ -0,0 +1,41 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NTOPO_CLASS
+
+NTopoStyle(NTOPO_ANGLE_TEMPLATE,NTopoAngleTemplate)
+
+#else
+
+#ifndef LMP_TOPO_ANGLE_TEMPLATE_H
+#define LMP_TOPO_ANGLE_TEMPLATE_H
+
+#include "ntopo.h"
+
+namespace LAMMPS_NS {
+
+class NTopoAngleTemplate : public NTopo {
+ public:
+ NTopoAngleTemplate(class LAMMPS *);
+ ~NTopoAngleTemplate() {}
+ void build();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/ntopo_bond_all.cpp b/src/ntopo_bond_all.cpp
new file mode 100644
index 0000000000..03cb2ad86b
--- /dev/null
+++ b/src/ntopo_bond_all.cpp
@@ -0,0 +1,91 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include "ntopo_bond_all.h"
+#include "atom.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoBondAll::NTopoBondAll(LAMMPS *lmp) : NTopo(lmp)
+{
+ allocate_bond();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoBondAll::build()
+{
+ int i,m,atom1;
+
+ int nlocal = atom->nlocal;
+ int *num_bond = atom->num_bond;
+ tagint **bond_atom = atom->bond_atom;
+ int **bond_type = atom->bond_type;
+ tagint *tag = atom->tag;
+ int newton_bond = force->newton_bond;
+
+ int lostbond = output->thermo->lostbond;
+ int nmissing = 0;
+ nbondlist = 0;
+
+ for (i = 0; i < nlocal; i++)
+ for (m = 0; m < num_bond[i]; m++) {
+ atom1 = atom->map(bond_atom[i][m]);
+ if (atom1 == -1) {
+ nmissing++;
+ if (lostbond == ERROR) {
+ char str[128];
+ sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ tag[i],bond_atom[i][m],me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ continue;
+ }
+ atom1 = domain->closest_image(i,atom1);
+ if (newton_bond || i < atom1) {
+ if (nbondlist == maxbond) {
+ maxbond += DELTA;
+ memory->grow(bondlist,maxbond,3,"neigh_topo:bondlist");
+ }
+ bondlist[nbondlist][0] = i;
+ bondlist[nbondlist][1] = atom1;
+ bondlist[nbondlist][2] = bond_type[i][m];
+ nbondlist++;
+ }
+ }
+
+ if (cluster_check) bond_check();
+ if (lostbond == IGNORE) return;
+
+ int all;
+ MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+ if (all) {
+ char str[128];
+ sprintf(str,
+ "Bond atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+ if (me == 0) error->warning(FLERR,str);
+ }
+}
diff --git a/src/neigh_derive.h b/src/ntopo_bond_all.h
similarity index 68%
rename from src/neigh_derive.h
rename to src/ntopo_bond_all.h
index 1538f7662a..8c89d66431 100644
--- a/src/neigh_derive.h
+++ b/src/ntopo_bond_all.h
@@ -11,12 +11,31 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-/* ERROR/WARNING messages:
+#ifdef NTOPO_CLASS
+
+NTopoStyle(NTOPO_BOND_ALL,NTopoBondAll)
+
+#else
+
+#ifndef LMP_TOPO_BOND_ALL_H
+#define LMP_TOPO_BOND_ALL_H
+
+#include "ntopo.h"
-E: Neighbor list overflow, boost neigh_modify one
+namespace LAMMPS_NS {
-There are too many neighbors of a single atom. Use the neigh_modify
-command to increase the max number of neighbors allowed for one atom.
-You may also want to boost the page size.
+class NTopoBondAll : public NTopo {
+ public:
+ NTopoBondAll(class LAMMPS *);
+ ~NTopoBondAll() {}
+ void build();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
*/
diff --git a/src/ntopo_bond_partial.cpp b/src/ntopo_bond_partial.cpp
new file mode 100644
index 0000000000..cda4bdcf09
--- /dev/null
+++ b/src/ntopo_bond_partial.cpp
@@ -0,0 +1,92 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include "ntopo_bond_partial.h"
+#include "atom.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoBondPartial::NTopoBondPartial(LAMMPS *lmp) : NTopo(lmp)
+{
+ allocate_bond();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoBondPartial::build()
+{
+ int i,m,atom1;
+
+ int nlocal = atom->nlocal;
+ int *num_bond = atom->num_bond;
+ tagint **bond_atom = atom->bond_atom;
+ int **bond_type = atom->bond_type;
+ tagint *tag = atom->tag;
+ int newton_bond = force->newton_bond;
+
+ int lostbond = output->thermo->lostbond;
+ int nmissing = 0;
+ nbondlist = 0;
+
+ for (i = 0; i < nlocal; i++)
+ for (m = 0; m < num_bond[i]; m++) {
+ if (bond_type[i][m] <= 0) continue;
+ atom1 = atom->map(bond_atom[i][m]);
+ if (atom1 == -1) {
+ nmissing++;
+ if (lostbond == ERROR) {
+ char str[128];
+ sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ tag[i],bond_atom[i][m],me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ continue;
+ }
+ atom1 = domain->closest_image(i,atom1);
+ if (newton_bond || i < atom1) {
+ if (nbondlist == maxbond) {
+ maxbond += DELTA;
+ memory->grow(bondlist,maxbond,3,"neigh_topo:bondlist");
+ }
+ bondlist[nbondlist][0] = i;
+ bondlist[nbondlist][1] = atom1;
+ bondlist[nbondlist][2] = bond_type[i][m];
+ nbondlist++;
+ }
+ }
+
+ if (cluster_check) bond_check();
+ if (lostbond == IGNORE) return;
+
+ int all;
+ MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+ if (all) {
+ char str[128];
+ sprintf(str,
+ "Bond atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+ if (me == 0) error->warning(FLERR,str);
+ }
+}
diff --git a/src/neigh_half_bin.h b/src/ntopo_bond_partial.h
similarity index 66%
rename from src/neigh_half_bin.h
rename to src/ntopo_bond_partial.h
index 1538f7662a..b0a2c274b2 100644
--- a/src/neigh_half_bin.h
+++ b/src/ntopo_bond_partial.h
@@ -11,12 +11,31 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-/* ERROR/WARNING messages:
+#ifdef NTOPO_CLASS
+
+NTopoStyle(NTOPO_BOND_PARTIAL,NTopoBondPartial)
+
+#else
+
+#ifndef LMP_TOPO_BOND_PARTIAL_H
+#define LMP_TOPO_BOND_PARTIAL_H
+
+#include "ntopo.h"
-E: Neighbor list overflow, boost neigh_modify one
+namespace LAMMPS_NS {
-There are too many neighbors of a single atom. Use the neigh_modify
-command to increase the max number of neighbors allowed for one atom.
-You may also want to boost the page size.
+class NTopoBondPartial : public NTopo {
+ public:
+ NTopoBondPartial(class LAMMPS *);
+ ~NTopoBondPartial() {}
+ void build();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
*/
diff --git a/src/ntopo_bond_template.cpp b/src/ntopo_bond_template.cpp
new file mode 100644
index 0000000000..de16d78585
--- /dev/null
+++ b/src/ntopo_bond_template.cpp
@@ -0,0 +1,109 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include "ntopo_bond_template.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "molecule.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoBondTemplate::NTopoBondTemplate(LAMMPS *lmp) : NTopo(lmp)
+{
+ allocate_bond();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoBondTemplate::build()
+{
+ int i,m,atom1;
+ int imol,iatom;
+ tagint tagprev;
+ int *num_bond;
+ tagint **bond_atom;
+ int **bond_type;
+
+ Molecule **onemols = atom->avec->onemols;
+
+ tagint *tag = atom->tag;
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ int nlocal = atom->nlocal;
+ int newton_bond = force->newton_bond;
+
+ int lostbond = output->thermo->lostbond;
+ int nmissing = 0;
+ nbondlist = 0;
+
+ for (i = 0; i < nlocal; i++) {
+ if (molindex[i] < 0) continue;
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ num_bond = onemols[imol]->num_bond;
+ bond_atom = onemols[imol]->bond_atom;
+ bond_type = onemols[imol]->bond_type;
+
+ for (m = 0; m < num_bond[iatom]; m++) {
+ if (bond_type[iatom][m] <= 0) continue;
+ atom1 = atom->map(bond_atom[iatom][m]+tagprev);
+ if (atom1 == -1) {
+ nmissing++;
+ if (lostbond == ERROR) {
+ char str[128];
+ sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ tag[i],bond_atom[iatom][m]+tagprev,me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ continue;
+ }
+ atom1 = domain->closest_image(i,atom1);
+ if (newton_bond || i < atom1) {
+ if (nbondlist == maxbond) {
+ maxbond += DELTA;
+ memory->grow(bondlist,maxbond,3,"neigh_topo:bondlist");
+ }
+ bondlist[nbondlist][0] = i;
+ bondlist[nbondlist][1] = atom1;
+ bondlist[nbondlist][2] = bond_type[iatom][m];
+ nbondlist++;
+ }
+ }
+ }
+
+ if (cluster_check) bond_check();
+ if (lostbond == IGNORE) return;
+
+ int all;
+ MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+ if (all) {
+ char str[128];
+ sprintf(str,
+ "Bond atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+ if (me == 0) error->warning(FLERR,str);
+ }
+}
diff --git a/src/ntopo_bond_template.h b/src/ntopo_bond_template.h
new file mode 100644
index 0000000000..6d0aeb001f
--- /dev/null
+++ b/src/ntopo_bond_template.h
@@ -0,0 +1,41 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NTOPO_CLASS
+
+NTopoStyle(NTOPO_BOND_TEMPLATE,NTopoBondTemplate)
+
+#else
+
+#ifndef LMP_TOPO_BOND_TEMPLATE_H
+#define LMP_TOPO_BOND_TEMPLATE_H
+
+#include "ntopo.h"
+
+namespace LAMMPS_NS {
+
+class NTopoBondTemplate : public NTopo {
+ public:
+ NTopoBondTemplate(class LAMMPS *);
+ ~NTopoBondTemplate() {}
+ void build();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/ntopo_dihedral_all.cpp b/src/ntopo_dihedral_all.cpp
new file mode 100644
index 0000000000..7a5b350fa0
--- /dev/null
+++ b/src/ntopo_dihedral_all.cpp
@@ -0,0 +1,106 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include "ntopo_dihedral_all.h"
+#include "atom.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoDihedralAll::NTopoDihedralAll(LAMMPS *lmp) : NTopo(lmp)
+{
+ allocate_dihedral();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoDihedralAll::build()
+{
+ int i,m,atom1,atom2,atom3,atom4;
+
+ int nlocal = atom->nlocal;
+ int *num_dihedral = atom->num_dihedral;
+ tagint **dihedral_atom1 = atom->dihedral_atom1;
+ tagint **dihedral_atom2 = atom->dihedral_atom2;
+ tagint **dihedral_atom3 = atom->dihedral_atom3;
+ tagint **dihedral_atom4 = atom->dihedral_atom4;
+ int **dihedral_type = atom->dihedral_type;
+ int newton_bond = force->newton_bond;
+
+ int lostbond = output->thermo->lostbond;
+ int nmissing = 0;
+ ndihedrallist = 0;
+
+ for (i = 0; i < nlocal; i++)
+ for (m = 0; m < num_dihedral[i]; m++) {
+ atom1 = atom->map(dihedral_atom1[i][m]);
+ atom2 = atom->map(dihedral_atom2[i][m]);
+ atom3 = atom->map(dihedral_atom3[i][m]);
+ atom4 = atom->map(dihedral_atom4[i][m]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
+ nmissing++;
+ if (lostbond == ERROR) {
+ char str[128];
+ sprintf(str,"Dihedral atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ dihedral_atom1[i][m],dihedral_atom2[i][m],
+ dihedral_atom3[i][m],dihedral_atom4[i][m],
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ continue;
+ }
+ atom1 = domain->closest_image(i,atom1);
+ atom2 = domain->closest_image(i,atom2);
+ atom3 = domain->closest_image(i,atom3);
+ atom4 = domain->closest_image(i,atom4);
+ if (newton_bond ||
+ (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
+ if (ndihedrallist == maxdihedral) {
+ maxdihedral += DELTA;
+ memory->grow(dihedrallist,maxdihedral,5,"neigh_topo:dihedrallist");
+ }
+ dihedrallist[ndihedrallist][0] = atom1;
+ dihedrallist[ndihedrallist][1] = atom2;
+ dihedrallist[ndihedrallist][2] = atom3;
+ dihedrallist[ndihedrallist][3] = atom4;
+ dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
+ ndihedrallist++;
+ }
+ }
+
+ if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
+ if (lostbond == IGNORE) return;
+
+ int all;
+ MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+ if (all) {
+ char str[128];
+ sprintf(str,
+ "Dihedral atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+ if (me == 0) error->warning(FLERR,str);
+ }
+}
diff --git a/src/ntopo_dihedral_all.h b/src/ntopo_dihedral_all.h
new file mode 100644
index 0000000000..45a5711687
--- /dev/null
+++ b/src/ntopo_dihedral_all.h
@@ -0,0 +1,41 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NTOPO_CLASS
+
+NTopoStyle(NTOPO_DIHEDRAL_ALL,NTopoDihedralAll)
+
+#else
+
+#ifndef LMP_TOPO_DIHEDRAL_ALL_H
+#define LMP_TOPO_DIHEDRAL_ALL_H
+
+#include "ntopo.h"
+
+namespace LAMMPS_NS {
+
+class NTopoDihedralAll : public NTopo {
+ public:
+ NTopoDihedralAll(class LAMMPS *);
+ ~NTopoDihedralAll() {}
+ void build();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp
new file mode 100644
index 0000000000..abfc30ba31
--- /dev/null
+++ b/src/ntopo_dihedral_partial.cpp
@@ -0,0 +1,108 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include "ntopo_dihedral_partial.h"
+#include "atom.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoDihedralPartial::NTopoDihedralPartial(LAMMPS *lmp) :
+ NTopo(lmp)
+{
+ allocate_dihedral();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoDihedralPartial::build()
+{
+ int i,m,atom1,atom2,atom3,atom4;
+
+ int nlocal = atom->nlocal;
+ int *num_dihedral = atom->num_dihedral;
+ tagint **dihedral_atom1 = atom->dihedral_atom1;
+ tagint **dihedral_atom2 = atom->dihedral_atom2;
+ tagint **dihedral_atom3 = atom->dihedral_atom3;
+ tagint **dihedral_atom4 = atom->dihedral_atom4;
+ int **dihedral_type = atom->dihedral_type;
+ int newton_bond = force->newton_bond;
+
+ int lostbond = output->thermo->lostbond;
+ int nmissing = 0;
+ ndihedrallist = 0;
+
+ for (i = 0; i < nlocal; i++)
+ for (m = 0; m < num_dihedral[i]; m++) {
+ if (dihedral_type[i][m] <= 0) continue;
+ atom1 = atom->map(dihedral_atom1[i][m]);
+ atom2 = atom->map(dihedral_atom2[i][m]);
+ atom3 = atom->map(dihedral_atom3[i][m]);
+ atom4 = atom->map(dihedral_atom4[i][m]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
+ nmissing++;
+ if (lostbond == ERROR) {
+ char str[128];
+ sprintf(str,"Dihedral atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ dihedral_atom1[i][m],dihedral_atom2[i][m],
+ dihedral_atom3[i][m],dihedral_atom4[i][m],
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ continue;
+ }
+ atom1 = domain->closest_image(i,atom1);
+ atom2 = domain->closest_image(i,atom2);
+ atom3 = domain->closest_image(i,atom3);
+ atom4 = domain->closest_image(i,atom4);
+ if (newton_bond ||
+ (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
+ if (ndihedrallist == maxdihedral) {
+ maxdihedral += DELTA;
+ memory->grow(dihedrallist,maxdihedral,5,"neigh_topo:dihedrallist");
+ }
+ dihedrallist[ndihedrallist][0] = atom1;
+ dihedrallist[ndihedrallist][1] = atom2;
+ dihedrallist[ndihedrallist][2] = atom3;
+ dihedrallist[ndihedrallist][3] = atom4;
+ dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
+ ndihedrallist++;
+ }
+ }
+
+ if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
+ if (lostbond == IGNORE) return;
+
+ int all;
+ MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+ if (all) {
+ char str[128];
+ sprintf(str,
+ "Dihedral atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+ if (me == 0) error->warning(FLERR,str);
+ }
+}
diff --git a/src/ntopo_dihedral_partial.h b/src/ntopo_dihedral_partial.h
new file mode 100644
index 0000000000..a71022a601
--- /dev/null
+++ b/src/ntopo_dihedral_partial.h
@@ -0,0 +1,41 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NTOPO_CLASS
+
+NTopoStyle(NTOPO_DIHEDRAL_PARTIAL,NTopoDihedralPartial)
+
+#else
+
+#ifndef LMP_TOPO_DIHEDRAL_PARTIAL_H
+#define LMP_TOPO_DIHEDRAL_PARTIAL_H
+
+#include "ntopo.h"
+
+namespace LAMMPS_NS {
+
+class NTopoDihedralPartial : public NTopo {
+ public:
+ NTopoDihedralPartial(class LAMMPS *);
+ ~NTopoDihedralPartial() {}
+ void build();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp
new file mode 100644
index 0000000000..8ef60de237
--- /dev/null
+++ b/src/ntopo_dihedral_template.cpp
@@ -0,0 +1,127 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include "ntopo_dihedral_template.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "molecule.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoDihedralTemplate::NTopoDihedralTemplate(LAMMPS *lmp) :
+ NTopo(lmp)
+{
+ allocate_dihedral();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoDihedralTemplate::build()
+{
+ int i,m,atom1,atom2,atom3,atom4;
+ int imol,iatom;
+ tagint tagprev;
+ int *num_dihedral;
+ tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
+ int **dihedral_type;
+
+ Molecule **onemols = atom->avec->onemols;
+
+ tagint *tag = atom->tag;
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ int nlocal = atom->nlocal;
+ int newton_bond = force->newton_bond;
+
+ int lostbond = output->thermo->lostbond;
+ int nmissing = 0;
+ ndihedrallist = 0;
+
+ for (i = 0; i < nlocal; i++) {
+ if (molindex[i] < 0) continue;
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ num_dihedral = onemols[imol]->num_dihedral;
+ dihedral_atom1 = onemols[imol]->dihedral_atom1;
+ dihedral_atom2 = onemols[imol]->dihedral_atom2;
+ dihedral_atom3 = onemols[imol]->dihedral_atom3;
+ dihedral_atom4 = onemols[imol]->dihedral_atom4;
+ dihedral_type = onemols[imol]->dihedral_type;
+
+ for (m = 0; m < num_dihedral[iatom]; m++) {
+ atom1 = atom->map(dihedral_atom1[iatom][m]+tagprev);
+ atom2 = atom->map(dihedral_atom2[iatom][m]+tagprev);
+ atom3 = atom->map(dihedral_atom3[iatom][m]+tagprev);
+ atom4 = atom->map(dihedral_atom4[iatom][m]+tagprev);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
+ nmissing++;
+ if (lostbond == ERROR) {
+ char str[128];
+ sprintf(str,"Dihedral atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ dihedral_atom1[iatom][m]+tagprev,
+ dihedral_atom2[iatom][m]+tagprev,
+ dihedral_atom3[iatom][m]+tagprev,
+ dihedral_atom4[iatom][m]+tagprev,
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ continue;
+ }
+ atom1 = domain->closest_image(i,atom1);
+ atom2 = domain->closest_image(i,atom2);
+ atom3 = domain->closest_image(i,atom3);
+ atom4 = domain->closest_image(i,atom4);
+ if (newton_bond ||
+ (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
+ if (ndihedrallist == maxdihedral) {
+ maxdihedral += DELTA;
+ memory->grow(dihedrallist,maxdihedral,5,"neigh_topo:dihedrallist");
+ }
+ dihedrallist[ndihedrallist][0] = atom1;
+ dihedrallist[ndihedrallist][1] = atom2;
+ dihedrallist[ndihedrallist][2] = atom3;
+ dihedrallist[ndihedrallist][3] = atom4;
+ dihedrallist[ndihedrallist][4] = dihedral_type[iatom][m];
+ ndihedrallist++;
+ }
+ }
+ }
+
+ if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
+ if (lostbond == IGNORE) return;
+
+ int all;
+ MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+ if (all) {
+ char str[128];
+ sprintf(str,
+ "Dihedral atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+ if (me == 0) error->warning(FLERR,str);
+ }
+}
diff --git a/src/ntopo_dihedral_template.h b/src/ntopo_dihedral_template.h
new file mode 100644
index 0000000000..c289fb6b7d
--- /dev/null
+++ b/src/ntopo_dihedral_template.h
@@ -0,0 +1,41 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NTOPO_CLASS
+
+NTopoStyle(NTOPO_DIHEDRAL_TEMPLATE,NTopoDihedralTemplate)
+
+#else
+
+#ifndef LMP_TOPO_DIHEDRAL_TEMPLATE_H
+#define LMP_TOPO_DIHEDRAL_TEMPLATE_H
+
+#include "ntopo.h"
+
+namespace LAMMPS_NS {
+
+class NTopoDihedralTemplate : public NTopo {
+ public:
+ NTopoDihedralTemplate(class LAMMPS *);
+ ~NTopoDihedralTemplate() {}
+ void build();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/ntopo_improper_all.cpp b/src/ntopo_improper_all.cpp
new file mode 100644
index 0000000000..ada3927e79
--- /dev/null
+++ b/src/ntopo_improper_all.cpp
@@ -0,0 +1,106 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include "ntopo_improper_all.h"
+#include "atom.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoImproperAll::NTopoImproperAll(LAMMPS *lmp) : NTopo(lmp)
+{
+ allocate_improper();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoImproperAll::build()
+{
+ int i,m,atom1,atom2,atom3,atom4;
+
+ int nlocal = atom->nlocal;
+ int *num_improper = atom->num_improper;
+ tagint **improper_atom1 = atom->improper_atom1;
+ tagint **improper_atom2 = atom->improper_atom2;
+ tagint **improper_atom3 = atom->improper_atom3;
+ tagint **improper_atom4 = atom->improper_atom4;
+ int **improper_type = atom->improper_type;
+ int newton_bond = force->newton_bond;
+
+ int lostbond = output->thermo->lostbond;
+ int nmissing = 0;
+ nimproperlist = 0;
+
+ for (i = 0; i < nlocal; i++)
+ for (m = 0; m < num_improper[i]; m++) {
+ atom1 = atom->map(improper_atom1[i][m]);
+ atom2 = atom->map(improper_atom2[i][m]);
+ atom3 = atom->map(improper_atom3[i][m]);
+ atom4 = atom->map(improper_atom4[i][m]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
+ nmissing++;
+ if (lostbond == ERROR) {
+ char str[128];
+ sprintf(str,"Improper atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ improper_atom1[i][m],improper_atom2[i][m],
+ improper_atom3[i][m],improper_atom4[i][m],
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ continue;
+ }
+ atom1 = domain->closest_image(i,atom1);
+ atom2 = domain->closest_image(i,atom2);
+ atom3 = domain->closest_image(i,atom3);
+ atom4 = domain-> closest_image(i,atom4);
+ if (newton_bond ||
+ (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
+ if (nimproperlist == maximproper) {
+ maximproper += DELTA;
+ memory->grow(improperlist,maximproper,5,"neigh_topo:improperlist");
+ }
+ improperlist[nimproperlist][0] = atom1;
+ improperlist[nimproperlist][1] = atom2;
+ improperlist[nimproperlist][2] = atom3;
+ improperlist[nimproperlist][3] = atom4;
+ improperlist[nimproperlist][4] = improper_type[i][m];
+ nimproperlist++;
+ }
+ }
+
+ if (cluster_check) dihedral_check(nimproperlist,improperlist);
+ if (lostbond == IGNORE) return;
+
+ int all;
+ MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+ if (all) {
+ char str[128];
+ sprintf(str,
+ "Improper atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+ if (me == 0) error->warning(FLERR,str);
+ }
+}
diff --git a/src/ntopo_improper_all.h b/src/ntopo_improper_all.h
new file mode 100644
index 0000000000..b7d9a9f049
--- /dev/null
+++ b/src/ntopo_improper_all.h
@@ -0,0 +1,41 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NTOPO_CLASS
+
+NTopoStyle(NTOPO_IMPROPER_ALL,NTopoImproperAll)
+
+#else
+
+#ifndef LMP_TOPO_IMPROPER_ALL_H
+#define LMP_TOPO_IMPROPER_ALL_H
+
+#include "ntopo.h"
+
+namespace LAMMPS_NS {
+
+class NTopoImproperAll : public NTopo {
+ public:
+ NTopoImproperAll(class LAMMPS *);
+ ~NTopoImproperAll() {}
+ void build();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp
new file mode 100644
index 0000000000..f8f06cf41b
--- /dev/null
+++ b/src/ntopo_improper_partial.cpp
@@ -0,0 +1,108 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include "ntopo_improper_partial.h"
+#include "atom.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoImproperPartial::NTopoImproperPartial(LAMMPS *lmp) :
+ NTopo(lmp)
+{
+ allocate_improper();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoImproperPartial::build()
+{
+ int i,m,atom1,atom2,atom3,atom4;
+
+ int nlocal = atom->nlocal;
+ int *num_improper = atom->num_improper;
+ tagint **improper_atom1 = atom->improper_atom1;
+ tagint **improper_atom2 = atom->improper_atom2;
+ tagint **improper_atom3 = atom->improper_atom3;
+ tagint **improper_atom4 = atom->improper_atom4;
+ int **improper_type = atom->improper_type;
+ int newton_bond = force->newton_bond;
+
+ int lostbond = output->thermo->lostbond;
+ int nmissing = 0;
+ nimproperlist = 0;
+
+ for (i = 0; i < nlocal; i++)
+ for (m = 0; m < num_improper[i]; m++) {
+ if (improper_type[i][m] <= 0) continue;
+ atom1 = atom->map(improper_atom1[i][m]);
+ atom2 = atom->map(improper_atom2[i][m]);
+ atom3 = atom->map(improper_atom3[i][m]);
+ atom4 = atom->map(improper_atom4[i][m]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
+ nmissing++;
+ if (lostbond == ERROR) {
+ char str[128];
+ sprintf(str,"Improper atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ improper_atom1[i][m],improper_atom2[i][m],
+ improper_atom3[i][m],improper_atom4[i][m],
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ continue;
+ }
+ atom1 = domain->closest_image(i,atom1);
+ atom2 = domain->closest_image(i,atom2);
+ atom3 = domain->closest_image(i,atom3);
+ atom4 = domain->closest_image(i,atom4);
+ if (newton_bond ||
+ (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
+ if (nimproperlist == maximproper) {
+ maximproper += DELTA;
+ memory->grow(improperlist,maximproper,5,"neigh_topo:improperlist");
+ }
+ improperlist[nimproperlist][0] = atom1;
+ improperlist[nimproperlist][1] = atom2;
+ improperlist[nimproperlist][2] = atom3;
+ improperlist[nimproperlist][3] = atom4;
+ improperlist[nimproperlist][4] = improper_type[i][m];
+ nimproperlist++;
+ }
+ }
+
+ if (cluster_check) dihedral_check(nimproperlist,improperlist);
+ if (lostbond == IGNORE) return;
+
+ int all;
+ MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+ if (all) {
+ char str[128];
+ sprintf(str,
+ "Improper atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+ if (me == 0) error->warning(FLERR,str);
+ }
+}
diff --git a/src/ntopo_improper_partial.h b/src/ntopo_improper_partial.h
new file mode 100644
index 0000000000..45a9673e67
--- /dev/null
+++ b/src/ntopo_improper_partial.h
@@ -0,0 +1,41 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NTOPO_CLASS
+
+NTopoStyle(NTOPO_IMPROPER_PARTIAL,NTopoImproperPartial)
+
+#else
+
+#ifndef LMP_TOPO_IMPROPER_PARTIAL_H
+#define LMP_TOPO_IMPROPER_PARTIAL_H
+
+#include "ntopo.h"
+
+namespace LAMMPS_NS {
+
+class NTopoImproperPartial : public NTopo {
+ public:
+ NTopoImproperPartial(class LAMMPS *);
+ ~NTopoImproperPartial() {}
+ void build();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp
new file mode 100644
index 0000000000..4662e3693f
--- /dev/null
+++ b/src/ntopo_improper_template.cpp
@@ -0,0 +1,127 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Templatel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include "ntopo_improper_template.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "molecule.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoImproperTemplate::NTopoImproperTemplate(LAMMPS *lmp) :
+ NTopo(lmp)
+{
+ allocate_improper();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoImproperTemplate::build()
+{
+ int i,m,atom1,atom2,atom3,atom4;
+ int imol,iatom;
+ tagint tagprev;
+ int *num_improper;
+ tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
+ int **improper_type;
+
+ Molecule **onemols = atom->avec->onemols;
+
+ tagint *tag = atom->tag;
+ int *molindex = atom->molindex;
+ int *molatom = atom->molatom;
+ int nlocal = atom->nlocal;
+ int newton_bond = force->newton_bond;
+
+ int lostbond = output->thermo->lostbond;
+ int nmissing = 0;
+ nimproperlist = 0;
+
+ for (i = 0; i < nlocal; i++) {
+ if (molindex[i] < 0) continue;
+ imol = molindex[i];
+ iatom = molatom[i];
+ tagprev = tag[i] - iatom - 1;
+ num_improper = onemols[imol]->num_improper;
+ improper_atom1 = onemols[imol]->improper_atom1;
+ improper_atom2 = onemols[imol]->improper_atom2;
+ improper_atom3 = onemols[imol]->improper_atom3;
+ improper_atom4 = onemols[imol]->improper_atom4;
+ improper_type = onemols[imol]->improper_type;
+
+ for (m = 0; m < num_improper[iatom]; m++) {
+ atom1 = atom->map(improper_atom1[iatom][m]+tagprev);
+ atom2 = atom->map(improper_atom2[iatom][m]+tagprev);
+ atom3 = atom->map(improper_atom3[iatom][m]+tagprev);
+ atom4 = atom->map(improper_atom4[iatom][m]+tagprev);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
+ nmissing++;
+ if (lostbond == ERROR) {
+ char str[128];
+ sprintf(str,"Improper atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ improper_atom1[iatom][m]+tagprev,
+ improper_atom2[iatom][m]+tagprev,
+ improper_atom3[iatom][m]+tagprev,
+ improper_atom4[iatom][m]+tagprev,
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ continue;
+ }
+ atom1 = domain->closest_image(i,atom1);
+ atom2 = domain->closest_image(i,atom2);
+ atom3 = domain->closest_image(i,atom3);
+ atom4 = domain-> closest_image(i,atom4);
+ if (newton_bond ||
+ (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
+ if (nimproperlist == maximproper) {
+ maximproper += DELTA;
+ memory->grow(improperlist,maximproper,5,"neigh_topo:improperlist");
+ }
+ improperlist[nimproperlist][0] = atom1;
+ improperlist[nimproperlist][1] = atom2;
+ improperlist[nimproperlist][2] = atom3;
+ improperlist[nimproperlist][3] = atom4;
+ improperlist[nimproperlist][4] = improper_type[iatom][m];
+ nimproperlist++;
+ }
+ }
+ }
+
+ if (cluster_check) dihedral_check(nimproperlist,improperlist);
+ if (lostbond == IGNORE) return;
+
+ int all;
+ MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+ if (all) {
+ char str[128];
+ sprintf(str,
+ "Improper atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+ if (me == 0) error->warning(FLERR,str);
+ }
+}
diff --git a/src/ntopo_improper_template.h b/src/ntopo_improper_template.h
new file mode 100644
index 0000000000..fc760d021e
--- /dev/null
+++ b/src/ntopo_improper_template.h
@@ -0,0 +1,41 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NTOPO_CLASS
+
+NTopoStyle(NTOPO_IMPROPER_TEMPLATE,NTopoImproperTemplate)
+
+#else
+
+#ifndef LMP_TOPO_IMPROPER_TEMPLATE_H
+#define LMP_TOPO_IMPROPER_TEMPLATE_H
+
+#include "ntopo.h"
+
+namespace LAMMPS_NS {
+
+class NTopoImproperTemplate : public NTopo {
+ public:
+ NTopoImproperTemplate(class LAMMPS *);
+ ~NTopoImproperTemplate() {}
+ void build();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
--
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