From b1b014aed3e15e2d8ca02b68a0cf567edcff67e8 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Fri, 2 Oct 2020 15:09:47 -0600 Subject: [PATCH 01/73] Fixing merge conflicts --- src/comm.cpp | 6 + src/comm.h | 1 + src/comm_brick.cpp | 6 + src/nbin.cpp | 9 + src/nbin.h | 14 + src/nbin_bytype.cpp | 466 ++++++++++++++++++++++++ src/nbin_bytype.h | 56 +++ src/nbin_standard.h | 2 +- src/neighbor.cpp | 17 +- src/neighbor.h | 6 +- src/npair_full_bytype.cpp | 144 ++++++++ src/npair_full_bytype.h | 43 +++ src/npair_half_bytype_newton.cpp | 219 +++++++++++ src/npair_half_bytype_newton.h | 43 +++ src/npair_half_size_bytype_newtoff.cpp | 130 +++++++ src/npair_half_size_bytype_newtoff.h | 43 +++ src/npair_half_size_bytype_newton.cpp | 189 ++++++++++ src/npair_half_size_bytype_newton.h | 43 +++ src/nstencil.h | 4 + src/nstencil_full_bytype_3d.cpp | 192 ++++++++++ src/nstencil_full_bytype_3d.h | 53 +++ src/nstencil_half_bytype_2d_newton.cpp | 192 ++++++++++ src/nstencil_half_bytype_2d_newton.h | 52 +++ src/nstencil_half_bytype_3d_newtoff.cpp | 190 ++++++++++ src/nstencil_half_bytype_3d_newtoff.h | 51 +++ src/nstencil_half_bytype_3d_newton.cpp | 194 ++++++++++ src/nstencil_half_bytype_3d_newton.h | 52 +++ 27 files changed, 2413 insertions(+), 4 deletions(-) create mode 100644 src/nbin_bytype.cpp create mode 100644 src/nbin_bytype.h create mode 100644 src/npair_full_bytype.cpp create mode 100644 src/npair_full_bytype.h create mode 100755 src/npair_half_bytype_newton.cpp create mode 100755 src/npair_half_bytype_newton.h create mode 100644 src/npair_half_size_bytype_newtoff.cpp create mode 100644 src/npair_half_size_bytype_newtoff.h create mode 100755 src/npair_half_size_bytype_newton.cpp create mode 100755 src/npair_half_size_bytype_newton.h create mode 100644 src/nstencil_full_bytype_3d.cpp create mode 100644 src/nstencil_full_bytype_3d.h create mode 100644 src/nstencil_half_bytype_2d_newton.cpp create mode 100644 src/nstencil_half_bytype_2d_newton.h create mode 100644 src/nstencil_half_bytype_3d_newtoff.cpp create mode 100644 src/nstencil_half_bytype_3d_newtoff.h create mode 100644 src/nstencil_half_bytype_3d_newton.cpp create mode 100644 src/nstencil_half_bytype_3d_newton.h diff --git a/src/comm.cpp b/src/comm.cpp index 32a4152294..1efe966459 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -76,6 +76,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) grid2proc = nullptr; xsplit = ysplit = zsplit = nullptr; rcbnew = 0; + multi_bytype = 0; // use of OpenMP threads // query OpenMP for number of threads/process set by user at run-time @@ -326,6 +327,11 @@ void Comm::modify_params(int narg, char **arg) for (i=nlo; i<=nhi; ++i) cutusermulti[i] = cut; iarg += 3; + } else if (strcmp(arg[iarg],"cutoff/bytype") == 0) { + if (mode == Comm::SINGLE) + error->all(FLERR,"Use cutoff/bytype in mode multi only"); + multi_bytype = 1; + iarg += 1; } else if (strcmp(arg[iarg],"vel") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command"); if (strcmp(arg[iarg+1],"yes") == 0) ghost_velocity = 1; diff --git a/src/comm.h b/src/comm.h index c8d7add79c..e5fc1bdee4 100644 --- a/src/comm.h +++ b/src/comm.h @@ -161,6 +161,7 @@ class Comm : protected Pointers { int (*)(int, char *, int &, int *&, char *&, void *), int, char *&, int, void *, int); void rendezvous_stats(int, int, int, int, int, int, bigint); + int multi_bytype; // 1 if multi cutoff is intra-type cutoff public: enum{MULTIPLE}; diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 374c394b0b..57703b578c 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -181,6 +181,12 @@ void CommBrick::setup() cutghostmulti[i][0] = MAX(cut,cuttype[i]); cutghostmulti[i][1] = MAX(cut,cuttype[i]); cutghostmulti[i][2] = MAX(cut,cuttype[i]); + if (multi_bytype == 1) { + // Set the BYTYPE cutoff + cutghostmulti[i][0] = sqrt(neighbor->cutneighsq[i][i]); + cutghostmulti[i][1] = sqrt(neighbor->cutneighsq[i][i]); + cutghostmulti[i][2] = sqrt(neighbor->cutneighsq[i][i]); + } } } diff --git a/src/nbin.cpp b/src/nbin.cpp index 1fe011e9f2..64ae7e7b83 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -150,6 +150,15 @@ int NBin::coord2bin(double *x) return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo); } +/* ---------------------------------------------------------------------- + to be overridden by NBinType + ------------------------------------------------------------------------- */ + +int NBin::coord2bin(double * x, int itype) +{ + error->all(FLERR,"coord2bin(x, itype) not available.\n"); + return -1; +} /* ---------------------------------------------------------------------- */ diff --git a/src/nbin.h b/src/nbin.h index 4bfe579514..96cc7eac64 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -37,6 +37,18 @@ class NBin : protected Pointers { double cutoff_custom; // cutoff set by requestor + // Analogues for NBinType + int * nbinx_type, * nbiny_type, * nbinz_type; + int * mbins_type; + int * mbinx_type, * mbiny_type, * mbinz_type; + int * mbinxlo_type, * mbinylo_type, * mbinzlo_type; + double * binsizex_type, * binsizey_type, * binsizez_type; + double * bininvx_type, * bininvy_type, * bininvz_type; + + int ** binhead_type; + int ** bins_type; + int ** atom2bin_type; + NBin(class LAMMPS *); ~NBin(); void post_constructor(class NeighRequest *); @@ -50,6 +62,8 @@ class NBin : protected Pointers { // Kokkos package int kokkos; // 1 if class stores Kokkos data + // For NBinType + virtual int coord2bin(double *, int); protected: diff --git a/src/nbin_bytype.cpp b/src/nbin_bytype.cpp new file mode 100644 index 0000000000..f719ed116f --- /dev/null +++ b/src/nbin_bytype.cpp @@ -0,0 +1,466 @@ +/* ---------------------------------------------------------------------- + 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_bytype.h" +#include "neighbor.h" +#include "atom.h" +#include "group.h" +#include "domain.h" +#include "comm.h" +#include "update.h" +#include "error.h" + +#include +#include "memory.h" + +using namespace LAMMPS_NS; + +#define SMALL 1.0e-6 // Duplicated from NBinStandard +#define CUT2BIN_RATIO 100 // Duplicated from NBinStandard + +/* ---------------------------------------------------------------------- */ + +NBinBytype::NBinBytype(LAMMPS *lmp) : NBin(lmp) { + + nbinx_type = NULL; nbiny_type = NULL; nbinz_type = NULL; + mbins_type = NULL; + mbinx_type = NULL; mbiny_type = NULL, mbinz_type = NULL; + mbinxlo_type = NULL; + mbinylo_type = NULL; + mbinzlo_type = NULL; + binsizex_type = NULL; binsizey_type = NULL; binsizez_type = NULL; + bininvx_type = NULL; bininvy_type = NULL; bininvz_type = NULL; + binhead_type = NULL; + bins_type = NULL; + atom2bin_type = NULL; + maxtypes = 0; + maxbins_type = NULL; +} + +NBinBytype::~NBinBytype() { + + memory->destroy(nbinx_type); + memory->destroy(nbiny_type); + memory->destroy(nbinz_type); + memory->destroy(mbins_type); + memory->destroy(mbinx_type); + memory->destroy(mbiny_type); + memory->destroy(mbinz_type); + memory->destroy(mbinxlo_type); + memory->destroy(mbinylo_type); + memory->destroy(mbinzlo_type); + + memory->destroy(binsizex_type); + memory->destroy(binsizey_type); + memory->destroy(binsizez_type); + memory->destroy(bininvx_type); + memory->destroy(bininvy_type); + memory->destroy(bininvz_type); + + for (int n = 1; n <= maxtypes; n++) { + memory->destroy(binhead_type[n]); + memory->destroy(bins_type[n]); + memory->destroy(atom2bin_type[n]); + } + delete [] binhead_type; + delete [] bins_type; + delete [] atom2bin_type; + + memory->destroy(maxbins_type); +} + +/* ---------------------------------------------------------------------- + arrange storage for types + allows ntypes to change, but not currently expected after initialisation + ------------------------------------------------------------------------- */ + +void NBinBytype::setup_types() { + + int n; + + if (atom->ntypes > maxtypes) { + + // Clear any/all memory for existing types + + for (n = 1; n <= maxtypes; n++) { + memory->destroy(atom2bin_type[n]); + memory->destroy(binhead_type[n]); + memory->destroy(bins_type[n]); + } + delete [] atom2bin_type; + delete [] binhead_type; + delete [] bins_type; + + // Realloacte at updated maxtypes + + maxtypes = atom->ntypes; + + atom2bin_type = new int*[maxtypes+1](); + binhead_type = new int*[maxtypes+1](); + bins_type = new int*[maxtypes+1](); + + memory->destroy(nbinx_type); + memory->destroy(nbiny_type); + memory->destroy(nbinz_type); + memory->create(nbinx_type, maxtypes+1, "nBinType:nbinx_type"); + memory->create(nbiny_type, maxtypes+1, "nBinType:nbiny_type"); + memory->create(nbinz_type, maxtypes+1, "nBinType:nbinz_type"); + + memory->destroy(mbins_type); + memory->destroy(mbinx_type); + memory->destroy(mbiny_type); + memory->destroy(mbinz_type); + memory->create(mbins_type, maxtypes+1, "nBinType:mbins_type"); + memory->create(mbinx_type, maxtypes+1, "nBinType:mbinx_type"); + memory->create(mbiny_type, maxtypes+1, "nBinType:mbiny_type"); + memory->create(mbinz_type, maxtypes+1, "nBinType:mbinz_type"); + + memory->destroy(mbinxlo_type); + memory->destroy(mbinylo_type); + memory->destroy(mbinzlo_type); + memory->create(mbinxlo_type, maxtypes+1, "nBinType:mbinxlo_type"); + memory->create(mbinylo_type, maxtypes+1, "nBinType:mbinylo_type"); + memory->create(mbinzlo_type, maxtypes+1, "nBinType:mbinzlo_type"); + + memory->destroy(binsizex_type); + memory->destroy(binsizey_type); + memory->destroy(binsizez_type); + memory->create(binsizex_type, maxtypes+1, "nBinType:binsizex_type"); + memory->create(binsizey_type, maxtypes+1, "nBinType:binsizey_type"); + memory->create(binsizez_type, maxtypes+1, "nBinType:binsizez_type"); + + memory->destroy(bininvx_type); + memory->destroy(bininvy_type); + memory->destroy(bininvz_type); + memory->create(bininvx_type, maxtypes+1, "nBinType:bininvx_type"); + memory->create(bininvy_type, maxtypes+1, "nBinType:bininvy_type"); + memory->create(bininvz_type, maxtypes+1, "nBinType:bininvz_type"); + + memory->destroy(maxbins_type); + memory->create(maxbins_type, maxtypes+1, "nBinType:maxbins_type"); + // make sure reallocation occurs in bin_atoms_setup() + for (n = 1; n <= maxtypes; n++) { + maxbins_type[n] = 0; + } + maxatom = 0; + } + +} + +/* --------------------------------------------------------------------- + identify index of type with smallest cutoff + --------------------------------------------------------------------- */ + +int NBinBytype::itype_min() { + + int itypemin = 1; + double ** cutneighsq; + + cutneighsq = neighbor->cutneighsq; + + for (int n = 1; n <= atom->ntypes; n++) { + if (cutneighsq[n][n] < cutneighsq[itypemin][itypemin]) { + itypemin = n; + } + } + + return itypemin; +} + +/* ---------------------------------------------------------------------- + setup neighbor binning geometry + ---------------------------------------------------------------------- */ + +void NBinBytype::setup_bins(int style) +{ + int n; + int itypemin; + + setup_types(); + itypemin = itype_min(); + + // 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]; + + // For each type... + + for (n = 1; n <= atom->ntypes; n++) { + // binsize_user only relates to smallest type + // optimal bin size is roughly 1/2 the type-type cutoff + // special case of all cutoffs = 0.0, binsize = box size + + double binsize_optimal; + if (n == itypemin && binsizeflag) binsize_optimal = binsize_user; + else binsize_optimal = 0.5*sqrt(neighbor->cutneighsq[n][n]); + 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_type[n] = 1 + + nbinx_type[n] = static_cast (bbox[0]*binsizeinv); + nbiny_type[n] = static_cast (bbox[1]*binsizeinv); + if (dimension == 3) nbinz_type[n] = static_cast (bbox[2]*binsizeinv); + else nbinz_type[n] = 1; + + if (nbinx_type[n] == 0) nbinx_type[n] = 1; + if (nbiny_type[n] == 0) nbiny_type[n] = 1; + if (nbinz_type[n] == 0) nbinz_type[n] = 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_type[n] = bbox[0]/nbinx_type[n]; + binsizey_type[n] = bbox[1]/nbiny_type[n]; + binsizez_type[n] = bbox[2]/nbinz_type[n]; + + bininvx_type[n] = 1.0 / binsizex_type[n]; + bininvy_type[n] = 1.0 / binsizey_type[n]; + bininvz_type[n] = 1.0 / binsizez_type[n]; + + if (binsize_optimal*bininvx_type[n] > CUT2BIN_RATIO || + binsize_optimal*bininvy_type[n] > CUT2BIN_RATIO || + binsize_optimal*bininvz_type[n] > 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_type[n] = static_cast ((coord-bboxlo[0])*bininvx_type[n]); + if (coord < bboxlo[0]) mbinxlo_type[n] = mbinxlo_type[n] - 1; + coord = bsubboxhi[0] + SMALL*bbox[0]; + mbinxhi = static_cast ((coord-bboxlo[0])*bininvx_type[n]); + + coord = bsubboxlo[1] - SMALL*bbox[1]; + mbinylo_type[n] = static_cast ((coord-bboxlo[1])*bininvy_type[n]); + if (coord < bboxlo[1]) mbinylo_type[n] = mbinylo_type[n] - 1; + coord = bsubboxhi[1] + SMALL*bbox[1]; + mbinyhi = static_cast ((coord-bboxlo[1])*bininvy_type[n]); + + if (dimension == 3) { + coord = bsubboxlo[2] - SMALL*bbox[2]; + mbinzlo_type[n] = static_cast ((coord-bboxlo[2])*bininvz_type[n]); + if (coord < bboxlo[2]) mbinzlo_type[n] = mbinzlo_type[n] - 1; + coord = bsubboxhi[2] + SMALL*bbox[2]; + mbinzhi = static_cast ((coord-bboxlo[2])*bininvz_type[n]); + } + + // extend bins by 1 to insure stencil extent is included + // for 2d, only 1 bin in z + + mbinxlo_type[n] = mbinxlo_type[n] - 1; + mbinxhi = mbinxhi + 1; + mbinx_type[n] = mbinxhi - mbinxlo_type[n] + 1; + + mbinylo_type[n] = mbinylo_type[n] - 1; + mbinyhi = mbinyhi + 1; + mbiny_type[n] = mbinyhi - mbinylo_type[n] + 1; + + if (dimension == 3) { + mbinzlo_type[n] = mbinzlo_type[n] - 1; + mbinzhi = mbinzhi + 1; + } else mbinzlo_type[n] = mbinzhi = 0; + mbinz_type[n] = mbinzhi - mbinzlo_type[n] + 1; + + bigint bbin = ((bigint) mbinx_type[n]) + * ((bigint) mbiny_type[n]) * ((bigint) mbinz_type[n]) + 1; + if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins"); + mbins_type[n] = bbin; + } + +} + +/* ---------------------------------------------------------------------- + bin owned and ghost atoms by type +------------------------------------------------------------------------- */ + +void NBinBytype::bin_atoms() +{ + int i,ibin,n; + + last_bin = update->ntimestep; + for (n = 1; n <= maxtypes; n++) { + for (i = 0; i < mbins_type[n]; i++) binhead_type[n][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 *type = atom->type; + 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) { + n = type[i]; + ibin = coord2bin(x[i], n); + atom2bin_type[n][i] = ibin; + bins_type[n][i] = binhead_type[n][ibin]; + binhead_type[n][ibin] = i; + } + } + for (i = atom->nfirst-1; i >= 0; i--) { + n = type[i]; + ibin = coord2bin(x[i], n); + atom2bin_type[n][i] = ibin; + bins_type[n][i] = binhead_type[n][ibin]; + binhead_type[n][ibin] = i; + } + } else { + for (i = nall-1; i >= 0; i--) { + n = type[i]; + ibin = coord2bin(x[i], n); + atom2bin_type[n][i] = ibin; + bins_type[n][i] = binhead_type[n][ibin]; + binhead_type[n][ibin] = i; + } + } +} + + +/* ---------------------------------------------------------------------- + allocate/reallocate vectors +------------------------------------------------------------------------- */ + +void NBinBytype::bin_atoms_setup(int nall) { + + // all atom2bin, bins must be of length nall + if (nall > maxatom) { + for (int n = 1; n <= maxtypes; n++) { + memory->destroy(bins_type[n]); + memory->destroy(atom2bin_type[n]); + memory->create(bins_type[n], nall, "NBinBytype:bin_type"); + memory->create(atom2bin_type[n], nall, "NBinBytype:atom2bin_type"); + } + maxatom = nall; + } + + for (int n = 1; n <= maxtypes; n++) { + if (mbins_type[n] > maxbins_type[n]) { + maxbins_type[n] = mbins_type[n]; + memory->destroy(binhead_type[n]); + memory->create(binhead_type[n], mbins_type[n], "NBinBytype:mbins_type"); + } + } + +} + + +/* ---------------------------------------------------------------------- + convert atom coords into local bin # for bin type it +------------------------------------------------------------------------- */ + +int NBinBytype::coord2bin(double *x, int it) +{ + int ix,iy,iz; + int ibin; + + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx_type[it]) + nbinx_type[it]; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx_type[it]); + ix = MIN(ix,nbinx_type[it]-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx_type[it]) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy_type[it]) + nbiny_type[it]; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy_type[it]); + iy = MIN(iy,nbiny_type[it]-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy_type[it]) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz_type[it]) + nbinz_type[it]; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz_type[it]); + iz = MIN(iz,nbinz_type[it]-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz_type[it]) - 1; + + + ibin = (iz-mbinzlo_type[it])*mbiny_type[it]*mbinx_type[it] + + (iy-mbinylo_type[it])*mbinx_type[it] + + (ix-mbinxlo_type[it]); + return ibin; +} + + +/* ---------------------------------------------------------------------- + tot up for types + ---------------------------------------------------------------------- */ + +bigint NBinBytype::memory_usage() +{ + bigint bytes = 0; + + for (int m = 1; m < maxtypes; m++) { + bytes += 2*maxatom*sizeof(int); + bytes += maxbins_type[m]*sizeof(int); + } + return bytes; +} diff --git a/src/nbin_bytype.h b/src/nbin_bytype.h new file mode 100644 index 0000000000..89e6ca3650 --- /dev/null +++ b/src/nbin_bytype.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. +------------------------------------------------------------------------- */ + +#ifdef NBIN_CLASS + +NBinStyle(bytype, + NBinBytype, + NB_BYTYPE) + +#else + +#ifndef LMP_NBIN_BYTYPE_H +#define LMP_NBIN_BYTYPE_H + +#include "nbin.h" + +namespace LAMMPS_NS { + +class NBinBytype : public NBin { + public: + + NBinBytype(class LAMMPS *); + ~NBinBytype(); + void bin_atoms_setup(int); + void setup_bins(int); + void bin_atoms(); + + int coord2bin(double *x, int itype); + bigint memory_usage(); + + private: + int maxtypes; + int * maxbins_type; + + void setup_types(); + int itype_min(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nbin_standard.h b/src/nbin_standard.h index 14b587c24c..06defdb101 100644 --- a/src/nbin_standard.h +++ b/src/nbin_standard.h @@ -15,7 +15,7 @@ NBinStyle(standard, NBinStandard, - 0) + NB_STANDARD) #else diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 58737b815d..6e861b5a2b 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1620,6 +1620,14 @@ int Neighbor::choose_bin(NeighRequest *rq) if (!rq->kokkos_device != !(mask & NB_KOKKOS_DEVICE)) continue; if (!rq->kokkos_host != !(mask & NB_KOKKOS_HOST)) continue; + // neighbor style is BIN or MULTI or BYTYPE and must match + + if (style == Neighbor::BIN || style == Neighbor::MULTI) { + if (!(mask & NB_STANDARD)) continue; + } else if (style == Neighbor::BYTYPE) { + if (!(mask & NB_BYTYPE)) continue; + } + return i+1; } @@ -1690,12 +1698,14 @@ int Neighbor::choose_stencil(NeighRequest *rq) if (!rq->ghost != !(mask & NS_GHOST)) continue; if (!rq->ssa != !(mask & NS_SSA)) continue; - // neighbor style is BIN or MULTI and must match + // neighbor style is one of BIN, MULTI or BYTYPE and must match if (style == Neighbor::BIN) { if (!(mask & NS_BIN)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NS_MULTI)) continue; + } else if (style == Neighbor::BYTYPE) { + if (!(mask & NS_BYTYPE)) continue; } // dimension is 2 or 3 and must match @@ -1825,7 +1835,7 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!rq->halffull != !(mask & NP_HALF_FULL)) continue; if (!rq->off2on != !(mask & NP_OFF2ON)) continue; - // neighbor style is one of NSQ,BIN,MULTI and must match + // neighbor style is one of NSQ,BIN,MULTI or BYTYPE and must match if (style == Neighbor::NSQ) { if (!(mask & NP_NSQ)) continue; @@ -1833,6 +1843,8 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!(mask & NP_BIN)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NP_MULTI)) continue; + } else if (style == Neighbor::BYTYPE) { + if (!(mask & NP_BYTYPE)) continue; } // domain triclinic flag is on or off and must match @@ -2199,6 +2211,7 @@ void Neighbor::set(int narg, char **arg) if (strcmp(arg[1],"nsq") == 0) style = Neighbor::NSQ; else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN; else if (strcmp(arg[1],"multi") == 0) style = Neighbor::MULTI; + else if (strcmp(arg[1],"bytype") == 0) style = Neighbor::BYTYPE; else error->all(FLERR,"Illegal neighbor command"); if (style == Neighbor::MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi); diff --git a/src/neighbor.h b/src/neighbor.h index 9ee2af9c75..e5b76dd41b 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -20,7 +20,7 @@ namespace LAMMPS_NS { class Neighbor : protected Pointers { public: - enum{NSQ,BIN,MULTI}; + enum{NSQ,BIN,MULTI,BYTYPE}; int style; // 0,1,2 = nsq, bin, multi int every; // build every this many steps int delay; // delay build for this many steps @@ -239,6 +239,8 @@ namespace NeighConst { static const int NB_KOKKOS_DEVICE = 1<<1; static const int NB_KOKKOS_HOST = 1<<2; static const int NB_SSA = 1<<3; + static const int NB_BYTYPE = 1<<4; + static const int NB_STANDARD = 1<<5; static const int NS_BIN = 1<<0; static const int NS_MULTI = 1<<1; @@ -252,6 +254,7 @@ namespace NeighConst { static const int NS_TRI = 1<<9; static const int NS_GHOST = 1<<10; static const int NS_SSA = 1<<11; + static const int NS_BYTYPE = 1<<12; static const int NP_NSQ = 1<<0; static const int NP_BIN = 1<<1; @@ -278,6 +281,7 @@ namespace NeighConst { static const int NP_SKIP = 1<<22; static const int NP_HALF_FULL = 1<<23; static const int NP_OFF2ON = 1<<24; + static const int NP_BYTYPE = 1<<25; } } diff --git a/src/npair_full_bytype.cpp b/src/npair_full_bytype.cpp new file mode 100644 index 0000000000..d244c263ed --- /dev/null +++ b/src/npair_full_bytype.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_full_bytype.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" + +#include "nbin.h" +#include "nstencil.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairFullBytype::NPairFullBytype(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 + KS ADJUST +------------------------------------------------------------------------- */ + +void NPairFullBytype::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 **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 *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 + + int kbin; + ibin = nb->atom2bin_type[itype][i]; + for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + kbin = ibin; + } + else { + // Locate i in ktype bin + kbin = nb->coord2bin(x[i], ktype); + } + + s = this->ns->stencil_type[itype][ktype]; + ns = this->ns->nstencil_type[itype][ktype]; + for (k = 0; k < ns; k++) { + int js = this->nb->binhead_type[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = this->nb->bins_type[ktype][j]) { + jtype = type[j]; + 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_bytype.h b/src/npair_full_bytype.h new file mode 100644 index 0000000000..9ce221ff22 --- /dev/null +++ b/src/npair_full_bytype.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/bytype, + NPairFullBytype, + NP_FULL | NP_BYTYPE | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_FULL_BYTYPE_H +#define LMP_NPAIR_FULL_BYTYPE_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairFullBytype : public NPair { + public: + NPairFullBytype(class LAMMPS *); + ~NPairFullBytype() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/npair_half_bytype_newton.cpp b/src/npair_half_bytype_newton.cpp new file mode 100755 index 0000000000..66899564be --- /dev/null +++ b/src/npair_half_bytype_newton.cpp @@ -0,0 +1,219 @@ +/* ---------------------------------------------------------------------- + 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 +#include "npair_half_bytype_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" + +#include "nbin.h" +#include "nstencil.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfBytypeNewton::NPairHalfBytypeNewton(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + KS REWRTIE + 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 NPairHalfBytypeNewton::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 **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 *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; + } + + int js; + int kbin; + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = nb->atom2bin_type[itype][i]; + + for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // own bin ... + js = nb->bins_type[itype][i]; + for (j = js; j >= 0; j = nb->bins_type[itype][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 + + s = this->ns->stencil_type[itype][itype]; + ns = this->ns->nstencil_type[itype][itype]; + for (k = 0; k < ns; k++) { + js = nb->binhead_type[itype][ibin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[itype][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; + } + } + } + + } + else { + // smaller -> larger: locate i in the ktype bin structure + + kbin = nb->coord2bin(x[i], ktype); + s = this->ns->stencil_type[itype][ktype]; + ns = this->ns->nstencil_type[itype][ktype]; + + for (k = 0; k < ns; k++) { + js = nb->binhead_type[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[ktype][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; + } + } + } + } + } + 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_bytype_newton.h b/src/npair_half_bytype_newton.h new file mode 100755 index 0000000000..8be7292219 --- /dev/null +++ b/src/npair_half_bytype_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/bytype/newton, + NPairHalfBytypeNewton, + NP_HALF | NP_BYTYPE | NP_NEWTON | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_BYTYPE_NEWTON_H +#define LMP_NPAIR_HALF_BYTYPE_NEWTON_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfBytypeNewton : public NPair { + public: + NPairHalfBytypeNewton(class LAMMPS *); + ~NPairHalfBytypeNewton() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/npair_half_size_bytype_newtoff.cpp b/src/npair_half_size_bytype_newtoff.cpp new file mode 100644 index 0000000000..f065c60736 --- /dev/null +++ b/src/npair_half_size_bytype_newtoff.cpp @@ -0,0 +1,130 @@ +/* ---------------------------------------------------------------------- + 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 +es 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 +#include "npair_half_size_bytype_newtoff.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +#include "nbin.h" +#include "nstencil.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeBytypeNewtoff::NPairHalfSizeBytypeNewtoff(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + REWRITE + 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 NPairHalfSizeBytypeNewtoff::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + 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]; + radi = radius[i]; + + // 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 + + int kbin; + + ibin = nb->atom2bin_type[itype][i]; + for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + kbin = ibin; + } + else { + // Locate i in ktype bin + kbin = nb->coord2bin(x[i], ktype); + } + s = this->ns->stencil_type[itype][ktype]; + ns = this->ns->nstencil_type[itype][ktype]; + for (k = 0; k < ns; k++) { + int js = nb->binhead_type[ktype][kbin + s[k]]; + for (j = js; j >=0; j = nb->bins_type[ktype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + 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_size_bytype_newtoff.h b/src/npair_half_size_bytype_newtoff.h new file mode 100644 index 0000000000..e131a12f4b --- /dev/null +++ b/src/npair_half_size_bytype_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/bytype/newtoff, + NPairHalfSizeBytypeNewtoff, + NP_HALF | NP_SIZE | NP_BYTYPE | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTOFF_H +#define LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTOFF_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeBytypeNewtoff : public NPair { + public: + NPairHalfSizeBytypeNewtoff(class LAMMPS *); + ~NPairHalfSizeBytypeNewtoff() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/npair_half_size_bytype_newton.cpp b/src/npair_half_size_bytype_newton.cpp new file mode 100755 index 0000000000..3981635439 --- /dev/null +++ b/src/npair_half_size_bytype_newton.cpp @@ -0,0 +1,189 @@ +/* ---------------------------------------------------------------------- + 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 +#include "npair_half_size_bytype_newton.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +#include "nbin.h" +#include "nstencil.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeBytypeNewton::NPairHalfSizeBytypeNewton(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + KS REWRTIE + 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 NPairHalfSizeBytypeNewton::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + 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]; + radi = radius[i]; + + int js; + int kbin; + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = nb->atom2bin_type[itype][i]; + + for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // own bin ... + js = nb->bins_type[itype][i]; + for (j = js; j >= 0; j = nb->bins_type[itype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + 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 + + s = this->ns->stencil_type[itype][itype]; + ns = this->ns->nstencil_type[itype][itype]; + for (k = 0; k < ns; k++) { + js = nb->binhead_type[itype][ibin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[itype][j]) { + jtype = type[j]; + // KS. CHECK ME 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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + } + else { + // KS + // smaller -> larger: locate i in the ktype bin structure + kbin = nb->coord2bin(x[i], ktype); + + s = this->ns->stencil_type[itype][ktype]; + ns = this->ns->nstencil_type[itype][ktype]; + for (k = 0; k < ns; k++) { + js = nb->binhead_type[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[ktype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + 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_size_bytype_newton.h b/src/npair_half_size_bytype_newton.h new file mode 100755 index 0000000000..a6bb7a00a8 --- /dev/null +++ b/src/npair_half_size_bytype_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/bytype/newton, + NPairHalfSizeBytypeNewton, + NP_HALF | NP_SIZE | NP_BYTYPE | NP_NEWTON | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_H +#define LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeBytypeNewton : public NPair { + public: + NPairHalfSizeBytypeNewton(class LAMMPS *); + ~NPairHalfSizeBytypeNewton() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil.h b/src/nstencil.h index 75e678b483..bdd656b937 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -34,6 +34,10 @@ class NStencil : protected Pointers { double cutoff_custom; // cutoff set by requestor + // BYTYPE stencils + int ** nstencil_type; // No. of bins for stencil[itype][jtype] + int *** stencil_type; // Stencil for [itype][jtype] + NStencil(class LAMMPS *); virtual ~NStencil(); void post_constructor(class NeighRequest *); diff --git a/src/nstencil_full_bytype_3d.cpp b/src/nstencil_full_bytype_3d.cpp new file mode 100644 index 0000000000..3936ec2483 --- /dev/null +++ b/src/nstencil_full_bytype_3d.cpp @@ -0,0 +1,192 @@ +/* ---------------------------------------------------------------------- + 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_bytype_3d.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilFullBytype3d::NStencilFullBytype3d(LAMMPS *lmp) : + NStencil(lmp) +{ + maxstencil_type = NULL; +} + +NStencilFullBytype3d::~NStencilFullBytype3d() { + + if (maxstencil_type) { + memory->destroy(nstencil_type); + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = 0; j <= atom->ntypes; j++) { + if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); + } + delete [] stencil_type[i]; + } + delete [] stencil_type; + memory->destroy(maxstencil_type); + } +} + +void NStencilFullBytype3d::copy_bin_info_bytype(int itype) { + + mbinx = nb->mbinx_type[itype]; + mbiny = nb->mbiny_type[itype]; + mbinz = nb->mbinz_type[itype]; + binsizex = nb->binsizex_type[itype]; + binsizey = nb->binsizey_type[itype]; + binsizez = nb->binsizez_type[itype]; + bininvx = nb->bininvx_type[itype]; + bininvy = nb->bininvy_type[itype]; + bininvz = nb->bininvz_type[itype]; +} + +int NStencilFullBytype3d::copy_neigh_info_bytype(int itype) { + + cutneighmaxsq = neighbor->cutneighsq[itype][itype]; + cutneighmax = sqrt(cutneighmaxsq); + cuttypesq = neighbor->cuttypesq; + + // 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 (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + return ((2*sx+1) * (2*sy+1) * (2*sz+1)); +} + +void NStencilFullBytype3d::create_setup() +{ + + int itype, jtype; + int maxtypes; + int smax; + + //printf("NStencilFullBytype3d::create_steup()\n"); + maxtypes = atom->ntypes; + + if (maxstencil_type == NULL) { + memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "BAD A"); + memory->create(nstencil_type, maxtypes+1, maxtypes+1, "BAD B"); + stencil_type = new int**[maxtypes+1](); + for (itype = 1; itype <= maxtypes; ++itype) { + stencil_type[itype] = new int*[maxtypes+1](); + for (jtype = 1; jtype <= maxtypes; ++jtype) { + maxstencil_type[itype][jtype] = 0; + } + } + } + + // like -> like => use standard newtoff stencil at bin + + for (itype = 1; itype <= maxtypes; ++itype) { + copy_bin_info_bytype(itype); + smax = copy_neigh_info_bytype(itype); + if (smax > maxstencil_type[itype][itype]) { + maxstencil_type[itype][itype] = smax; + memory->destroy(stencil_type[itype][itype]); + memory->create(stencil_type[itype][itype], smax, + "NStencilFullBytype::create_steup() stencil"); + } + create_newtoff(itype, itype, cutneighmaxsq); + } + + // smaller -> larger => use existing newtoff stencil in larger bin + // larger -> smaller => use multi-like stencil for small-large in smaller bin + // If types are same cutoff, use existing like-like stencil. + + for (itype = 1; itype <= maxtypes; ++itype) { + for (jtype = 1; jtype <= maxtypes; ++jtype) { + if (itype == jtype) continue; + if (cuttypesq[itype] <= cuttypesq[jtype]) { + // Potential destroy/create problem? + nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; + stencil_type[itype][jtype] = stencil_type[jtype][jtype]; + } + else { + copy_bin_info_bytype(jtype); + // smax = copy_neigh_info_bytype(jtype); + + cutneighmaxsq = cuttypesq[jtype]; + cutneighmax = sqrt(cutneighmaxsq); + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + smax = (2*sx+1) * (2*sy+1) * (2*sz+1); + if (smax > maxstencil_type[itype][jtype]) { + maxstencil_type[itype][jtype] = smax; + memory->destroy(stencil_type[itype][jtype]); + memory->create(stencil_type[itype][jtype], smax, "Bad C"); + } + create_newtoff(itype, jtype, cuttypesq[jtype]); + } + } + } + + //for (itype = 1; itype <= maxtypes; itype++) { + // for (jtype = 1; jtype <= maxtypes; jtype++) { + // printf("i j n %d %d %d\n", itype, jtype, nstencil_type[itype][jtype]); + // printf("i j n %d %d %d\n", itype, jtype, maxstencil_type[itype][jtype]); + // } + // } + +} + +void NStencilFullBytype3d::create_newtoff(int itype, int jtype, double cutsq) { + + int i, j, k, ns; + + ns = 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) < cutsq) + stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; + + nstencil_type[itype][jtype] = ns; +} + +/* ---------------------------------------------------------------------- + create stencil based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilFullBytype3d::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_bytype_3d.h b/src/nstencil_full_bytype_3d.h new file mode 100644 index 0000000000..6e61365d17 --- /dev/null +++ b/src/nstencil_full_bytype_3d.h @@ -0,0 +1,53 @@ +/* -*- 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/bytype/3d, + NStencilFullBytype3d, + NS_FULL | NS_BYTYPE | NS_3D | + NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_FULL_BYTYPE_3D_H +#define LMP_NSTENCIL_FULL_BYTYPE_3D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilFullBytype3d : public NStencil { + public: + NStencilFullBytype3d(class LAMMPS *); + ~NStencilFullBytype3d(); + void create(); + void create_setup(); + +private: + int ** maxstencil_type; + + void copy_bin_info_bytype(int); + int copy_neigh_info_bytype(int); + void create_newtoff(int, int, double); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_bytype_2d_newton.cpp b/src/nstencil_half_bytype_2d_newton.cpp new file mode 100644 index 0000000000..18ed0972ff --- /dev/null +++ b/src/nstencil_half_bytype_2d_newton.cpp @@ -0,0 +1,192 @@ +/* ---------------------------------------------------------------------- + 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_bytype_2d_newton.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfBytype2dNewton::NStencilHalfBytype2dNewton(LAMMPS *lmp) : + NStencil(lmp) +{ + maxstencil_type = NULL; +} + +NStencilHalfBytype2dNewton::~NStencilHalfBytype2dNewton() { + + memory->destroy(nstencil_type); + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = 0; j <= atom->ntypes; j++) { + if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); + } + delete [] stencil_type[i]; + } + delete [] stencil_type; + memory->destroy(maxstencil_type); +} + +// KS To superclass +void NStencilHalfBytype2dNewton::copy_bin_info_bytype(int itype) { + + mbinx = nb->mbinx_type[itype]; + mbiny = nb->mbiny_type[itype]; + mbinz = nb->mbinz_type[itype]; + binsizex = nb->binsizex_type[itype]; + binsizey = nb->binsizey_type[itype]; + binsizez = nb->binsizez_type[itype]; + bininvx = nb->bininvx_type[itype]; + bininvy = nb->bininvy_type[itype]; + bininvz = nb->bininvz_type[itype]; +} + +// KS To superclass? +int NStencilHalfBytype2dNewton::copy_neigh_info_bytype(int itype) { + + cutneighmaxsq = neighbor->cutneighsq[itype][itype]; + cutneighmax = sqrt(cutneighmaxsq); + cuttypesq = neighbor->cuttypesq; + + // sx,sy,sz = max range of stencil in each dim + // smax = max possible size of entire 2d stencil + // stencil will be empty if cutneighmax = 0.0 + + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + return ((2*sx+1) * (2*sy+1) * (2*sz+1)); +} + +void NStencilHalfBytype2dNewton::create_setup() +{ + + int itype, jtype; + int maxtypes; + int smax; + + // maxstencil_type to superclass? + maxtypes = atom->ntypes; + + if (maxstencil_type == NULL) { + memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "maxstencil_type"); + memory->create(nstencil_type, maxtypes+1, maxtypes+1, "nstencil_type"); + stencil_type = new int**[maxtypes+1](); + for (itype = 1; itype <= maxtypes; ++itype) { + stencil_type[itype] = new int*[maxtypes+1](); + for (jtype = 1; jtype <= maxtypes; ++jtype) { + maxstencil_type[itype][jtype] = 0; + nstencil_type[itype][jtype] = 0; + } + } + } + + // like -> like => use standard Newton stencil at bin + + for (itype = 1; itype <= maxtypes; ++itype) { + copy_bin_info_bytype(itype); + smax = copy_neigh_info_bytype(itype); + if (smax > maxstencil_type[itype][itype]) { + maxstencil_type[itype][itype] = smax; + memory->destroy(stencil_type[itype][itype]); + memory->create(stencil_type[itype][itype], smax, + "NStencilHalfBytypeNewton::create_steup() stencil"); + } + create_newton(itype, itype, cutneighmaxsq); + } + + // Cross types: "Newton on" reached by using Newton off stencil and + // looking one way through hierarchy + // smaller -> larger => use Newton off stencil in larger bin + // larger -> smaller => no nstecil required + // If cut offs are same, use existing type-type stencil + + for (itype = 1; itype <= maxtypes; ++itype) { + for (jtype = 1; jtype <= maxtypes; ++jtype) { + if (itype == jtype) continue; + if (cuttypesq[itype] == cuttypesq[jtype]) { + nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; + stencil_type[itype][jtype] = stencil_type[jtype][jtype]; + } + else if (cuttypesq[itype] < cuttypesq[jtype]) { + copy_bin_info_bytype(jtype); + + cutneighmaxsq = cuttypesq[jtype]; + cutneighmax = sqrt(cutneighmaxsq); + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + smax = (2*sx+1) * (2*sy+1) * (2*sz+1); + if (smax > maxstencil_type[itype][jtype]) { + maxstencil_type[itype][jtype] = smax; + memory->destroy(stencil_type[itype][jtype]); + memory->create(stencil_type[itype][jtype], smax, "stencil_type[]"); + } + create_newtoff(itype, jtype, cuttypesq[jtype]); + } + } + } + +} + +void NStencilHalfBytype2dNewton::create_newton(int itype, int jtype, double cutsq) { + + int i, j, ns; + + ns = 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) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + } + nstencil_type[itype][jtype] = ns; +} + +void NStencilHalfBytype2dNewton::create_newtoff(int itype, int jtype, double cutsq) { + + int i, j, ns; + + ns = 0; + + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,0) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + + nstencil_type[itype][jtype] = ns; +} + +/* ---------------------------------------------------------------------- + create stencil based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfBytype2dNewton::create() +{ + // KS. Move "creation" here. +} diff --git a/src/nstencil_half_bytype_2d_newton.h b/src/nstencil_half_bytype_2d_newton.h new file mode 100644 index 0000000000..4d33c26a71 --- /dev/null +++ b/src/nstencil_half_bytype_2d_newton.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 NSTENCIL_CLASS + +NStencilStyle(half/bytype/2d/newton, + NStencilHalfBytype2dNewton, + NS_HALF | NS_BYTYPE | NS_2D | NS_NEWTON | NS_ORTHO) + +#else + +#ifndef LMP_NSTENCIL_HALF_BYTYPE_2D_NEWTON_H +#define LMP_NSTENCIL_HALF_BYTYPE_2D_NEWTON_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfBytype2dNewton : public NStencil { + public: + NStencilHalfBytype2dNewton(class LAMMPS *); + ~NStencilHalfBytype2dNewton(); + void create_setup(); + void create(); + + private: + int ** maxstencil_type; + + void copy_bin_info_bytype(int); + int copy_neigh_info_bytype(int); + void create_newton(int, int, double); + void create_newtoff(int, int, double); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_bytype_3d_newtoff.cpp b/src/nstencil_half_bytype_3d_newtoff.cpp new file mode 100644 index 0000000000..f111715e5d --- /dev/null +++ b/src/nstencil_half_bytype_3d_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 "nstencil_half_bytype_3d_newtoff.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfBytype3dNewtoff::NStencilHalfBytype3dNewtoff(LAMMPS *lmp) : + NStencil(lmp) +{ + maxstencil_type = NULL; +} + +NStencilHalfBytype3dNewtoff::~NStencilHalfBytype3dNewtoff() { + + memory->destroy(nstencil_type); + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = 0; j <= atom->ntypes; j++) { + if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); + } + delete [] stencil_type[i]; + } + delete [] stencil_type; + memory->destroy(maxstencil_type); +} + +void NStencilHalfBytype3dNewtoff::copy_bin_info_bytype(int itype) { + + mbinx = nb->mbinx_type[itype]; + mbiny = nb->mbiny_type[itype]; + mbinz = nb->mbinz_type[itype]; + binsizex = nb->binsizex_type[itype]; + binsizey = nb->binsizey_type[itype]; + binsizez = nb->binsizez_type[itype]; + bininvx = nb->bininvx_type[itype]; + bininvy = nb->bininvy_type[itype]; + bininvz = nb->bininvz_type[itype]; +} + +int NStencilHalfBytype3dNewtoff::copy_neigh_info_bytype(int itype) { + + cutneighmaxsq = neighbor->cutneighsq[itype][itype]; + cutneighmax = sqrt(cutneighmaxsq); + cuttypesq = neighbor->cuttypesq; + + // 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 (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + return ((2*sx+1) * (2*sy+1) * (2*sz+1)); +} + +void NStencilHalfBytype3dNewtoff::create_setup() +{ + + int itype, jtype; + int maxtypes; + int smax; + + //printf("NStencilHalfBytype3dNewtoff::create_steup()\n"); + maxtypes = atom->ntypes; + + if (maxstencil_type == NULL) { + memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "BAD A"); + memory->create(nstencil_type, maxtypes+1, maxtypes+1, "BAD B"); + stencil_type = new int**[maxtypes+1](); + for (itype = 1; itype <= maxtypes; ++itype) { + stencil_type[itype] = new int*[maxtypes+1](); + for (jtype = 1; jtype <= maxtypes; ++jtype) { + maxstencil_type[itype][jtype] = 0; + } + } + } + + // like -> like => use standard newtoff stencil at bin + + for (itype = 1; itype <= maxtypes; ++itype) { + copy_bin_info_bytype(itype); + smax = copy_neigh_info_bytype(itype); + if (smax > maxstencil_type[itype][itype]) { + maxstencil_type[itype][itype] = smax; + memory->destroy(stencil_type[itype][itype]); + memory->create(stencil_type[itype][itype], smax, + "NStencilHalfBytypeNewtoff::create_steup() stencil"); + } + create_newtoff(itype, itype, cutneighmaxsq); + } + + // smaller -> larger => use existing newtoff stencil in larger bin + // larger -> smaller => use multi-like stencil for small-large in smaller bin + // If types are same cutoff, use existing like-like stencil. + + for (itype = 1; itype <= maxtypes; ++itype) { + for (jtype = 1; jtype <= maxtypes; ++jtype) { + if (itype == jtype) continue; + if (cuttypesq[itype] <= cuttypesq[jtype]) { + // Potential destroy/create problem? + nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; + stencil_type[itype][jtype] = stencil_type[jtype][jtype]; + } + else { + copy_bin_info_bytype(jtype); + // smax = copy_neigh_info_bytype(jtype); + + cutneighmaxsq = cuttypesq[jtype]; + cutneighmax = sqrt(cutneighmaxsq); + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + smax = (2*sx+1) * (2*sy+1) * (2*sz+1); + if (smax > maxstencil_type[itype][jtype]) { + maxstencil_type[itype][jtype] = smax; + memory->destroy(stencil_type[itype][jtype]); + memory->create(stencil_type[itype][jtype], smax, "Bad C"); + } + create_newtoff(itype, jtype, cuttypesq[jtype]); + } + } + } + + //for (itype = 1; itype <= maxtypes; itype++) { + // for (jtype = 1; jtype <= maxtypes; jtype++) { + // printf("i j n %d %d %d\n", itype, jtype, nstencil_type[itype][jtype]); + // printf("i j n %d %d %d\n", itype, jtype, maxstencil_type[itype][jtype]); + // } + // } + +} + +void NStencilHalfBytype3dNewtoff::create_newtoff(int itype, int jtype, double cutsq) { + + int i, j, k, ns; + + ns = 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) < cutsq) + stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; + + nstencil_type[itype][jtype] = ns; +} + +/* ---------------------------------------------------------------------- + create stencil based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfBytype3dNewtoff::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_bytype_3d_newtoff.h b/src/nstencil_half_bytype_3d_newtoff.h new file mode 100644 index 0000000000..bf83a31e9a --- /dev/null +++ b/src/nstencil_half_bytype_3d_newtoff.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 NSTENCIL_CLASS + +NStencilStyle(half/bytype/3d/newtoff, + NStencilHalfBytype3dNewtoff, + NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTOFF | NS_ORTHO | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTOFF_H +#define LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTOFF_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfBytype3dNewtoff : public NStencil { + public: + NStencilHalfBytype3dNewtoff(class LAMMPS *); + ~NStencilHalfBytype3dNewtoff(); + void create_setup(); + void create(); + + private: + int ** maxstencil_type; + + void copy_bin_info_bytype(int); + int copy_neigh_info_bytype(int); + void create_newtoff(int, int, double); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_bytype_3d_newton.cpp b/src/nstencil_half_bytype_3d_newton.cpp new file mode 100644 index 0000000000..94c1ecd94d --- /dev/null +++ b/src/nstencil_half_bytype_3d_newton.cpp @@ -0,0 +1,194 @@ +/* ---------------------------------------------------------------------- + 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_bytype_3d_newton.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfBytype3dNewton::NStencilHalfBytype3dNewton(LAMMPS *lmp) : + NStencil(lmp) +{ + maxstencil_type = NULL; +} + +NStencilHalfBytype3dNewton::~NStencilHalfBytype3dNewton() { + + memory->destroy(nstencil_type); + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = 0; j <= atom->ntypes; j++) { + if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); + } + delete [] stencil_type[i]; + } + delete [] stencil_type; + memory->destroy(maxstencil_type); +} + +// KS To superclass +void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { + + mbinx = nb->mbinx_type[itype]; + mbiny = nb->mbiny_type[itype]; + mbinz = nb->mbinz_type[itype]; + binsizex = nb->binsizex_type[itype]; + binsizey = nb->binsizey_type[itype]; + binsizez = nb->binsizez_type[itype]; + bininvx = nb->bininvx_type[itype]; + bininvy = nb->bininvy_type[itype]; + bininvz = nb->bininvz_type[itype]; +} + +// KS To superclass? +int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { + + cutneighmaxsq = neighbor->cutneighsq[itype][itype]; + cutneighmax = sqrt(cutneighmaxsq); + cuttypesq = neighbor->cuttypesq; + + // 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 (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + return ((2*sx+1) * (2*sy+1) * (2*sz+1)); +} + +void NStencilHalfBytype3dNewton::create_setup() +{ + + int itype, jtype; + int maxtypes; + int smax; + + // maxstencil_type to superclass? + maxtypes = atom->ntypes; + + if (maxstencil_type == NULL) { + memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "maxstencil_type"); + memory->create(nstencil_type, maxtypes+1, maxtypes+1, "nstencil_type"); + stencil_type = new int**[maxtypes+1](); + for (itype = 1; itype <= maxtypes; ++itype) { + stencil_type[itype] = new int*[maxtypes+1](); + for (jtype = 1; jtype <= maxtypes; ++jtype) { + maxstencil_type[itype][jtype] = 0; + nstencil_type[itype][jtype] = 0; + } + } + } + + // like -> like => use standard Newton stencil at bin + + for (itype = 1; itype <= maxtypes; ++itype) { + copy_bin_info_bytype(itype); + smax = copy_neigh_info_bytype(itype); + if (smax > maxstencil_type[itype][itype]) { + maxstencil_type[itype][itype] = smax; + memory->destroy(stencil_type[itype][itype]); + memory->create(stencil_type[itype][itype], smax, + "NStencilHalfBytypeNewton::create_steup() stencil"); + } + create_newton(itype, itype, cutneighmaxsq); + } + + // Cross types: "Newton on" reached by using Newton off stencil and + // looking one way through hierarchy + // smaller -> larger => use Newton off stencil in larger bin + // larger -> smaller => no nstecil required + // If cut offs are same, use existing type-type stencil + + for (itype = 1; itype <= maxtypes; ++itype) { + for (jtype = 1; jtype <= maxtypes; ++jtype) { + if (itype == jtype) continue; + if (cuttypesq[itype] == cuttypesq[jtype]) { + nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; + stencil_type[itype][jtype] = stencil_type[jtype][jtype]; + } + else if (cuttypesq[itype] < cuttypesq[jtype]) { + copy_bin_info_bytype(jtype); + + cutneighmaxsq = cuttypesq[jtype]; + cutneighmax = sqrt(cutneighmaxsq); + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + smax = (2*sx+1) * (2*sy+1) * (2*sz+1); + if (smax > maxstencil_type[itype][jtype]) { + maxstencil_type[itype][jtype] = smax; + memory->destroy(stencil_type[itype][jtype]); + memory->create(stencil_type[itype][jtype], smax, "stencil_type[]"); + } + create_newtoff(itype, jtype, cuttypesq[jtype]); + } + } + } + +} + +void NStencilHalfBytype3dNewton::create_newton(int itype, int jtype, double cutsq) { + + int i, j, k, ns; + + ns = 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) < cutsq) + stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; + } + nstencil_type[itype][jtype] = ns; +} + +void NStencilHalfBytype3dNewton::create_newtoff(int itype, int jtype, double cutsq) { + + int i, j, k, ns; + + ns = 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) < cutsq) + stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; + + nstencil_type[itype][jtype] = ns; +} + +/* ---------------------------------------------------------------------- + create stencil based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfBytype3dNewton::create() +{ + // KS. Move "creation" here. +} diff --git a/src/nstencil_half_bytype_3d_newton.h b/src/nstencil_half_bytype_3d_newton.h new file mode 100644 index 0000000000..1245e2cd08 --- /dev/null +++ b/src/nstencil_half_bytype_3d_newton.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 NSTENCIL_CLASS + +NStencilStyle(half/bytype/3d/newton, + NStencilHalfBytype3dNewton, + NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTON | NS_ORTHO | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H +#define LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfBytype3dNewton : public NStencil { + public: + NStencilHalfBytype3dNewton(class LAMMPS *); + ~NStencilHalfBytype3dNewton(); + void create_setup(); + void create(); + + private: + int ** maxstencil_type; + + void copy_bin_info_bytype(int); + int copy_neigh_info_bytype(int); + void create_newton(int, int, double); + void create_newtoff(int, int, double); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ From e125d464d1977df0cc76a28043cc324e74827fb0 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 5 Oct 2020 16:09:50 -0600 Subject: [PATCH 02/73] Replacing molecular enumeration --- src/npair_full_bytype.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/npair_full_bytype.cpp b/src/npair_full_bytype.cpp index d244c263ed..6f13d77672 100644 --- a/src/npair_full_bytype.cpp +++ b/src/npair_full_bytype.cpp @@ -57,7 +57,7 @@ void NPairFullBytype::build(NeighList *list) int *molindex = atom->molindex; int *molatom = atom->molatom; Molecule **onemols = atom->avec->onemols; - if (molecular == 2) moltemplate = 1; + if (molecular == Atom::TEMPLATE) moltemplate = 1; else moltemplate = 0; int *ilist = list->ilist; @@ -113,7 +113,7 @@ void NPairFullBytype::build(NeighList *list) rsq = delx*delx + dely*dely + delz*delz; if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { + if (molecular != Atom::ATOMIC) { if (!moltemplate) which = find_special(special[i],nspecial[i],tag[j]); else if (imol >= 0) From 58e27a9c51047efe50770f86bdf21c4bfdd61ea7 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Fri, 9 Oct 2020 13:50:20 -0600 Subject: [PATCH 03/73] More edits and documentation --- doc/src/comm_modify.rst | 9 ++++++++- doc/src/neighbor.rst | 16 +++++++++++++++- src/comm.h | 4 ++++ src/comm_tiled.cpp | 6 ++++++ src/nbin_bytype.cpp | 16 +++++++--------- src/nbin_bytype.h | 16 ++++++++++++++++ src/npair_full_bytype.cpp | 6 ++---- src/npair_full_bytype.h | 4 ++++ src/npair_half_size_bytype_newtoff.cpp | 2 -- src/npair_half_size_bytype_newtoff.h | 4 ++++ src/npair_half_size_bytype_newton.cpp | 2 -- src/npair_half_size_bytype_newton.h | 6 +++++- src/nstencil_full_bytype_3d.cpp | 12 ++++++++++-- src/nstencil_half_bytype_2d_newton.cpp | 11 ++++++++++- src/nstencil_half_bytype_3d_newtoff.cpp | 12 ++++++++++-- src/nstencil_half_bytype_3d_newton.cpp | 13 ++++++++++++- 16 files changed, 113 insertions(+), 26 deletions(-) diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 9a2ae60f1e..2940b14283 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -11,7 +11,7 @@ Syntax comm_modify keyword value ... * zero or more keyword/value pairs may be appended -* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel* +* keyword = *mode* or *cutoff* or *cutoff/multi* or *cutoff/bytype* or *group* or *vel* .. parsed-literal:: @@ -20,6 +20,7 @@ Syntax *cutoff/multi* type value type = atom type or type range (supports asterisk notation) value = Rcut (distance units) = communicate atoms for selected types from this far away + *cutoff/byptype* arg = none = communicate atoms for each type by a distance equal to the largest interaction distance for that type *group* value = group-ID = only communicate atoms in the group *vel* value = *yes* or *no* = do or do not communicate velocity info with ghost atoms @@ -92,6 +93,12 @@ cutoffs are determined per atom type, a type specifier is needed and cutoff for one or multiple types can be extended. Also ranges of types using the usual asterisk notation can be given. +The *cutoff/bytype* option applies to *multi* and automtically sets communication +cutoffs for each particle type based on the largest interaction distance +between two particles of the same type. This method is only compatible +with Newton on and the *bytype* neighbor style. See the :doc:`neighbor bytype ` +command for more information. + These are simulation scenarios in which it may be useful or even necessary to set a ghost cutoff > neighbor cutoff: diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index 1bb591587c..8db9131545 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -11,7 +11,7 @@ Syntax neighbor skin style * skin = extra distance beyond force cutoff (distance units) -* style = *bin* or *nsq* or *multi* +* style = *bin* or *nsq* or *multi* or *bytype* Examples """""""" @@ -60,6 +60,14 @@ This imposes some extra setup overhead, but the searches themselves may be much faster for the short-cutoff cases. See the :doc:`comm_modify mode multi ` command for a communication option that may also be beneficial for simulations of this kind. +The *bytype* style is an extension of the *multi* style that was +presented by Shire, Hanley, and Stratford :ref:`(Shire) `. +For style *bytype*, different bin lists are created for each different +type and separate bin sizes are generated. Whether *bytype* or *multi* +is faster may depend on the specifics of your system. See the +:doc:`comm_modify mode bytype ` command for a compatible +communication option. + The :doc:`neigh_modify ` command has additional options that control how often neighbor lists are built and which pairs are stored in the list. @@ -86,3 +94,9 @@ Default | 0.001 bin for units = si, skin = 0.001 meters = 1.0 mm | 0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm | + +---------- + +.. _bytype-Shire: + +**(Shire)** Shire, Hanley and Stratford, Comp Part Mech, (2020). diff --git a/src/comm.h b/src/comm.h index e5fc1bdee4..3105e09a61 100644 --- a/src/comm.h +++ b/src/comm.h @@ -199,6 +199,10 @@ E: Use cutoff keyword to set cutoff in single mode Mode is single so cutoff/multi keyword cannot be used. +E: Use cutoff/bytype in mode multi only + +Mode is single so cutoff/bytype keyword cannot be used. + E: Cannot set cutoff/multi before simulation box is defined Self-explanatory. diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index dbdc887097..4759639bff 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -183,6 +183,12 @@ void CommTiled::setup() cutghostmulti[i][0] = MAX(cut,cuttype[i]); cutghostmulti[i][1] = MAX(cut,cuttype[i]); cutghostmulti[i][2] = MAX(cut,cuttype[i]); + if (multi_bytype == 1) { + // Set the BYTYPE cutoff + cutghostmulti[i][0] = sqrt(neighbor->cutneighsq[i][i]); + cutghostmulti[i][1] = sqrt(neighbor->cutneighsq[i][i]); + cutghostmulti[i][2] = sqrt(neighbor->cutneighsq[i][i]); + } } } diff --git a/src/nbin_bytype.cpp b/src/nbin_bytype.cpp index f719ed116f..70732a4b97 100644 --- a/src/nbin_bytype.cpp +++ b/src/nbin_bytype.cpp @@ -19,14 +19,12 @@ #include "comm.h" #include "update.h" #include "error.h" - -#include #include "memory.h" using namespace LAMMPS_NS; -#define SMALL 1.0e-6 // Duplicated from NBinStandard -#define CUT2BIN_RATIO 100 // Duplicated from NBinStandard +#define SMALL 1.0e-6 +#define CUT2BIN_RATIO 100 /* ---------------------------------------------------------------------- */ @@ -238,7 +236,7 @@ void NBinBytype::setup_bins(int style) // 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) + bbox[2]*binsizeinv > MAXSMALLINT) error->all(FLERR,"Domain too large for neighbor bins"); // create actual bins @@ -269,8 +267,8 @@ void NBinBytype::setup_bins(int style) bininvz_type[n] = 1.0 / binsizez_type[n]; if (binsize_optimal*bininvx_type[n] > CUT2BIN_RATIO || - binsize_optimal*bininvy_type[n] > CUT2BIN_RATIO || - binsize_optimal*bininvz_type[n] > CUT2BIN_RATIO) + binsize_optimal*bininvy_type[n] > CUT2BIN_RATIO || + binsize_optimal*bininvz_type[n] > 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 @@ -352,8 +350,8 @@ void NBinBytype::bin_atoms() int bitmask = group->bitmask[includegroup]; for (i = nall-1; i >= nlocal; i--) { if (mask[i] & bitmask) { - n = type[i]; - ibin = coord2bin(x[i], n); + n = type[i]; + ibin = coord2bin(x[i], n); atom2bin_type[n][i] = ibin; bins_type[n][i] = binhead_type[n][ibin]; binhead_type[n][ibin] = i; diff --git a/src/nbin_bytype.h b/src/nbin_bytype.h index 89e6ca3650..ad2b95ef4b 100644 --- a/src/nbin_bytype.h +++ b/src/nbin_bytype.h @@ -53,4 +53,20 @@ class NBinBytype : public NBin { /* ERROR/WARNING messages: +E: Domain too large for neighbor bins + +UNDOCUMENTED + +E: Cannot use neighbor bins - box size << cutoff + +UNDOCUMENTED + +E: Too many neighbor bins + +UNDOCUMENTED + +E Non-numeric positions - simulation unstable + +UNDOCUMENTED + */ diff --git a/src/npair_full_bytype.cpp b/src/npair_full_bytype.cpp index 6f13d77672..3b9a89bb56 100644 --- a/src/npair_full_bytype.cpp +++ b/src/npair_full_bytype.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_bytype.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -20,7 +19,6 @@ #include "domain.h" #include "my_page.h" #include "error.h" - #include "nbin.h" #include "nstencil.h" @@ -102,9 +100,9 @@ void NPairFullBytype::build(NeighList *list) for (k = 0; k < ns; k++) { int js = this->nb->binhead_type[ktype][kbin + s[k]]; for (j = js; j >= 0; j = this->nb->bins_type[ktype][j]) { - jtype = type[j]; if (i == j) continue; - + + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/npair_full_bytype.h b/src/npair_full_bytype.h index 9ce221ff22..fdcd6b5fb1 100644 --- a/src/npair_full_bytype.h +++ b/src/npair_full_bytype.h @@ -40,4 +40,8 @@ class NPairFullBytype : public NPair { /* ERROR/WARNING messages: +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + */ diff --git a/src/npair_half_size_bytype_newtoff.cpp b/src/npair_half_size_bytype_newtoff.cpp index f065c60736..220ae747a7 100644 --- a/src/npair_half_size_bytype_newtoff.cpp +++ b/src/npair_half_size_bytype_newtoff.cpp @@ -13,13 +13,11 @@ es certain rights in this software. This software is distributed under #include #include "npair_half_size_bytype_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "my_page.h" #include "error.h" - #include "nbin.h" #include "nstencil.h" diff --git a/src/npair_half_size_bytype_newtoff.h b/src/npair_half_size_bytype_newtoff.h index e131a12f4b..183bd39fb3 100644 --- a/src/npair_half_size_bytype_newtoff.h +++ b/src/npair_half_size_bytype_newtoff.h @@ -40,4 +40,8 @@ class NPairHalfSizeBytypeNewtoff : public NPair { /* ERROR/WARNING messages: +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + */ diff --git a/src/npair_half_size_bytype_newton.cpp b/src/npair_half_size_bytype_newton.cpp index 3981635439..339c4859a6 100755 --- a/src/npair_half_size_bytype_newton.cpp +++ b/src/npair_half_size_bytype_newton.cpp @@ -13,13 +13,11 @@ #include #include "npair_half_size_bytype_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "my_page.h" #include "error.h" - #include "nbin.h" #include "nstencil.h" diff --git a/src/npair_half_size_bytype_newton.h b/src/npair_half_size_bytype_newton.h index a6bb7a00a8..3cd1ee05d1 100755 --- a/src/npair_half_size_bytype_newton.h +++ b/src/npair_half_size_bytype_newton.h @@ -40,4 +40,8 @@ class NPairHalfSizeBytypeNewton : public NPair { /* ERROR/WARNING messages: -*/ +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + +*/ \ No newline at end of file diff --git a/src/nstencil_full_bytype_3d.cpp b/src/nstencil_full_bytype_3d.cpp index 3936ec2483..cecccdfb14 100644 --- a/src/nstencil_full_bytype_3d.cpp +++ b/src/nstencil_full_bytype_3d.cpp @@ -17,7 +17,6 @@ #include "nbin.h" #include "memory.h" #include "atom.h" - #include using namespace LAMMPS_NS; @@ -30,6 +29,8 @@ NStencilFullBytype3d::NStencilFullBytype3d(LAMMPS *lmp) : maxstencil_type = NULL; } +/* ---------------------------------------------------------------------- */ + NStencilFullBytype3d::~NStencilFullBytype3d() { if (maxstencil_type) { @@ -45,6 +46,8 @@ NStencilFullBytype3d::~NStencilFullBytype3d() { } } +/* ---------------------------------------------------------------------- */ + void NStencilFullBytype3d::copy_bin_info_bytype(int itype) { mbinx = nb->mbinx_type[itype]; @@ -58,6 +61,8 @@ void NStencilFullBytype3d::copy_bin_info_bytype(int itype) { bininvz = nb->bininvz_type[itype]; } +/* ---------------------------------------------------------------------- */ + int NStencilFullBytype3d::copy_neigh_info_bytype(int itype) { cutneighmaxsq = neighbor->cutneighsq[itype][itype]; @@ -78,6 +83,8 @@ int NStencilFullBytype3d::copy_neigh_info_bytype(int itype) { return ((2*sx+1) * (2*sy+1) * (2*sz+1)); } +/* ---------------------------------------------------------------------- */ + void NStencilFullBytype3d::create_setup() { @@ -85,7 +92,6 @@ void NStencilFullBytype3d::create_setup() int maxtypes; int smax; - //printf("NStencilFullBytype3d::create_steup()\n"); maxtypes = atom->ntypes; if (maxstencil_type == NULL) { @@ -159,6 +165,8 @@ void NStencilFullBytype3d::create_setup() } +/* ---------------------------------------------------------------------- */ + void NStencilFullBytype3d::create_newtoff(int itype, int jtype, double cutsq) { int i, j, k, ns; diff --git a/src/nstencil_half_bytype_2d_newton.cpp b/src/nstencil_half_bytype_2d_newton.cpp index 18ed0972ff..66158202bf 100644 --- a/src/nstencil_half_bytype_2d_newton.cpp +++ b/src/nstencil_half_bytype_2d_newton.cpp @@ -17,7 +17,6 @@ #include "nbin.h" #include "memory.h" #include "atom.h" - #include using namespace LAMMPS_NS; @@ -43,6 +42,8 @@ NStencilHalfBytype2dNewton::~NStencilHalfBytype2dNewton() { memory->destroy(maxstencil_type); } +/* ---------------------------------------------------------------------- */ + // KS To superclass void NStencilHalfBytype2dNewton::copy_bin_info_bytype(int itype) { @@ -57,6 +58,8 @@ void NStencilHalfBytype2dNewton::copy_bin_info_bytype(int itype) { bininvz = nb->bininvz_type[itype]; } +/* ---------------------------------------------------------------------- */ + // KS To superclass? int NStencilHalfBytype2dNewton::copy_neigh_info_bytype(int itype) { @@ -78,6 +81,8 @@ int NStencilHalfBytype2dNewton::copy_neigh_info_bytype(int itype) { return ((2*sx+1) * (2*sy+1) * (2*sz+1)); } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype2dNewton::create_setup() { @@ -153,6 +158,8 @@ void NStencilHalfBytype2dNewton::create_setup() } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype2dNewton::create_newton(int itype, int jtype, double cutsq) { int i, j, ns; @@ -168,6 +175,8 @@ void NStencilHalfBytype2dNewton::create_newton(int itype, int jtype, double cuts nstencil_type[itype][jtype] = ns; } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype2dNewton::create_newtoff(int itype, int jtype, double cutsq) { int i, j, ns; diff --git a/src/nstencil_half_bytype_3d_newtoff.cpp b/src/nstencil_half_bytype_3d_newtoff.cpp index f111715e5d..fedc8060ce 100644 --- a/src/nstencil_half_bytype_3d_newtoff.cpp +++ b/src/nstencil_half_bytype_3d_newtoff.cpp @@ -17,7 +17,6 @@ #include "nbin.h" #include "memory.h" #include "atom.h" - #include using namespace LAMMPS_NS; @@ -30,6 +29,8 @@ NStencilHalfBytype3dNewtoff::NStencilHalfBytype3dNewtoff(LAMMPS *lmp) : maxstencil_type = NULL; } +/* ---------------------------------------------------------------------- */ + NStencilHalfBytype3dNewtoff::~NStencilHalfBytype3dNewtoff() { memory->destroy(nstencil_type); @@ -43,6 +44,8 @@ NStencilHalfBytype3dNewtoff::~NStencilHalfBytype3dNewtoff() { memory->destroy(maxstencil_type); } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype3dNewtoff::copy_bin_info_bytype(int itype) { mbinx = nb->mbinx_type[itype]; @@ -56,6 +59,8 @@ void NStencilHalfBytype3dNewtoff::copy_bin_info_bytype(int itype) { bininvz = nb->bininvz_type[itype]; } +/* ---------------------------------------------------------------------- */ + int NStencilHalfBytype3dNewtoff::copy_neigh_info_bytype(int itype) { cutneighmaxsq = neighbor->cutneighsq[itype][itype]; @@ -76,6 +81,8 @@ int NStencilHalfBytype3dNewtoff::copy_neigh_info_bytype(int itype) { return ((2*sx+1) * (2*sy+1) * (2*sz+1)); } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype3dNewtoff::create_setup() { @@ -83,7 +90,6 @@ void NStencilHalfBytype3dNewtoff::create_setup() int maxtypes; int smax; - //printf("NStencilHalfBytype3dNewtoff::create_steup()\n"); maxtypes = atom->ntypes; if (maxstencil_type == NULL) { @@ -157,6 +163,8 @@ void NStencilHalfBytype3dNewtoff::create_setup() } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype3dNewtoff::create_newtoff(int itype, int jtype, double cutsq) { int i, j, k, ns; diff --git a/src/nstencil_half_bytype_3d_newton.cpp b/src/nstencil_half_bytype_3d_newton.cpp index 94c1ecd94d..7fc53fe762 100644 --- a/src/nstencil_half_bytype_3d_newton.cpp +++ b/src/nstencil_half_bytype_3d_newton.cpp @@ -17,7 +17,6 @@ #include "nbin.h" #include "memory.h" #include "atom.h" - #include using namespace LAMMPS_NS; @@ -30,6 +29,8 @@ NStencilHalfBytype3dNewton::NStencilHalfBytype3dNewton(LAMMPS *lmp) : maxstencil_type = NULL; } +/* ---------------------------------------------------------------------- */ + NStencilHalfBytype3dNewton::~NStencilHalfBytype3dNewton() { memory->destroy(nstencil_type); @@ -43,6 +44,8 @@ NStencilHalfBytype3dNewton::~NStencilHalfBytype3dNewton() { memory->destroy(maxstencil_type); } +/* ---------------------------------------------------------------------- */ + // KS To superclass void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { @@ -57,6 +60,8 @@ void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { bininvz = nb->bininvz_type[itype]; } +/* ---------------------------------------------------------------------- */ + // KS To superclass? int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { @@ -78,6 +83,8 @@ int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { return ((2*sx+1) * (2*sy+1) * (2*sz+1)); } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype3dNewton::create_setup() { @@ -153,6 +160,8 @@ void NStencilHalfBytype3dNewton::create_setup() } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype3dNewton::create_newton(int itype, int jtype, double cutsq) { int i, j, k, ns; @@ -169,6 +178,8 @@ void NStencilHalfBytype3dNewton::create_newton(int itype, int jtype, double cuts nstencil_type[itype][jtype] = ns; } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype3dNewton::create_newtoff(int itype, int jtype, double cutsq) { int i, j, k, ns; From 557ef57526e7a61bb466f3904a46a8a0c1983113 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Thu, 29 Oct 2020 15:13:28 -0600 Subject: [PATCH 04/73] Adding initial support for triclinic boundaries --- src/npair_half_bytype_newton_tri.cpp | 190 +++++++++++++++++++ src/npair_half_bytype_newton_tri.h | 43 +++++ src/npair_half_size_bytype_newton_tri.cpp | 166 +++++++++++++++++ src/npair_half_size_bytype_newton_tri.h | 47 +++++ src/nstencil_half_bytype_3d_newton.h | 2 +- src/nstencil_half_bytype_3d_newton_tri.cpp | 203 +++++++++++++++++++++ src/nstencil_half_bytype_3d_newton_tri.h | 52 ++++++ 7 files changed, 702 insertions(+), 1 deletion(-) create mode 100755 src/npair_half_bytype_newton_tri.cpp create mode 100755 src/npair_half_bytype_newton_tri.h create mode 100755 src/npair_half_size_bytype_newton_tri.cpp create mode 100755 src/npair_half_size_bytype_newton_tri.h create mode 100755 src/nstencil_half_bytype_3d_newton_tri.cpp create mode 100755 src/nstencil_half_bytype_3d_newton_tri.h diff --git a/src/npair_half_bytype_newton_tri.cpp b/src/npair_half_bytype_newton_tri.cpp new file mode 100755 index 0000000000..6b28e76789 --- /dev/null +++ b/src/npair_half_bytype_newton_tri.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 +#include "npair_half_bytype_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" + +#include "nbin.h" +#include "nstencil.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfBytypeNewtonTri::NPairHalfBytypeNewtonTri(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + KS REWRTIE + 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 NPairHalfBytypeNewtonTri::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 **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 *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; + } + + int js; + int kbin; + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = nb->atom2bin_type[itype][i]; + + for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = this->ns->stencil_type[itype][itype]; + ns = this->ns->nstencil_type[itype][itype]; + for (k = 0; k < ns; k++) { + js = nb->binhead_type[itype][ibin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[itype][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; + } + } + } + + } + else { + // smaller -> larger: locate i in the ktype bin structure + + kbin = nb->coord2bin(x[i], ktype); + s = this->ns->stencil_type[itype][ktype]; + ns = this->ns->nstencil_type[itype][ktype]; + + for (k = 0; k < ns; k++) { + js = nb->binhead_type[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[ktype][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; + } + } + } + } + } + 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_bytype_newton_tri.h b/src/npair_half_bytype_newton_tri.h new file mode 100755 index 0000000000..0582801028 --- /dev/null +++ b/src/npair_half_bytype_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/bytype/newton/tri, + NPairHalfBytypeNewtonTri, + NP_HALF | NP_BYTYPE | NP_NEWTON | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_BYTYPE_NEWTON_TRI_H +#define LMP_NPAIR_HALF_BYTYPE_NEWTON_TRI_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfBytypeNewtonTri : public NPair { + public: + NPairHalfBytypeNewtonTri(class LAMMPS *); + ~NPairHalfBytypeNewtonTri() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/npair_half_size_bytype_newton_tri.cpp b/src/npair_half_size_bytype_newton_tri.cpp new file mode 100755 index 0000000000..62d499b10f --- /dev/null +++ b/src/npair_half_size_bytype_newton_tri.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 +#include "npair_half_size_bytype_newton_tri.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" +#include "nbin.h" +#include "nstencil.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeBytypeNewtonTri::NPairHalfSizeBytypeNewtonTri(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + KS REWRTIE + 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 NPairHalfSizeBytypeNewtonTri::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + 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]; + radi = radius[i]; + + int js; + int kbin; + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = nb->atom2bin_type[itype][i]; + + for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = this->ns->stencil_type[itype][itype]; + ns = this->ns->nstencil_type[itype][itype]; + for (k = 0; k < ns; k++) { + js = nb->binhead_type[itype][ibin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[itype][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]; + // KS. CHECK ME 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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + } + else { + // KS + // smaller -> larger: locate i in the ktype bin structure + kbin = nb->coord2bin(x[i], ktype); + + s = this->ns->stencil_type[itype][ktype]; + ns = this->ns->nstencil_type[itype][ktype]; + for (k = 0; k < ns; k++) { + js = nb->binhead_type[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[ktype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + 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_size_bytype_newton_tri.h b/src/npair_half_size_bytype_newton_tri.h new file mode 100755 index 0000000000..0f770e780d --- /dev/null +++ b/src/npair_half_size_bytype_newton_tri.h @@ -0,0 +1,47 @@ +/* -*- 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/bytype/newton/tri, + NPairHalfSizeBytypeNewtonTri, + NP_HALF | NP_SIZE | NP_BYTYPE | NP_NEWTON | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_TRI_H +#define LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_TRI_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeBytypeNewtonTri : public NPair { + public: + NPairHalfSizeBytypeNewtonTri(class LAMMPS *); + ~NPairHalfSizeBytypeNewtonTri() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + +*/ \ No newline at end of file diff --git a/src/nstencil_half_bytype_3d_newton.h b/src/nstencil_half_bytype_3d_newton.h index 1245e2cd08..cbb88fcb1d 100644 --- a/src/nstencil_half_bytype_3d_newton.h +++ b/src/nstencil_half_bytype_3d_newton.h @@ -15,7 +15,7 @@ NStencilStyle(half/bytype/3d/newton, NStencilHalfBytype3dNewton, - NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTON | NS_ORTHO | NS_TRI) + NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTON | NS_ORTHO) #else diff --git a/src/nstencil_half_bytype_3d_newton_tri.cpp b/src/nstencil_half_bytype_3d_newton_tri.cpp new file mode 100755 index 0000000000..f1ab713725 --- /dev/null +++ b/src/nstencil_half_bytype_3d_newton_tri.cpp @@ -0,0 +1,203 @@ +/* ---------------------------------------------------------------------- + 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_bytype_3d_newton.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfBytype3dNewton::NStencilHalfBytype3dNewton(LAMMPS *lmp) : + NStencil(lmp) +{ + maxstencil_type = NULL; +} + +/* ---------------------------------------------------------------------- */ + +NStencilHalfBytype3dNewton::~NStencilHalfBytype3dNewton() { + + memory->destroy(nstencil_type); + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = 0; j <= atom->ntypes; j++) { + if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); + } + delete [] stencil_type[i]; + } + delete [] stencil_type; + memory->destroy(maxstencil_type); +} + +/* ---------------------------------------------------------------------- */ + +// KS To superclass +void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { + + mbinx = nb->mbinx_type[itype]; + mbiny = nb->mbiny_type[itype]; + mbinz = nb->mbinz_type[itype]; + binsizex = nb->binsizex_type[itype]; + binsizey = nb->binsizey_type[itype]; + binsizez = nb->binsizez_type[itype]; + bininvx = nb->bininvx_type[itype]; + bininvy = nb->bininvy_type[itype]; + bininvz = nb->bininvz_type[itype]; +} + +/* ---------------------------------------------------------------------- */ + +// KS To superclass? +int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { + + cutneighmaxsq = neighbor->cutneighsq[itype][itype]; + cutneighmax = sqrt(cutneighmaxsq); + cuttypesq = neighbor->cuttypesq; + + // 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 (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + return ((2*sx+1) * (2*sy+1) * (2*sz+1)); +} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfBytype3dNewton::create_setup() +{ + + int itype, jtype; + int maxtypes; + int smax; + + // maxstencil_type to superclass? + maxtypes = atom->ntypes; + + if (maxstencil_type == NULL) { + memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "maxstencil_type"); + memory->create(nstencil_type, maxtypes+1, maxtypes+1, "nstencil_type"); + stencil_type = new int**[maxtypes+1](); + for (itype = 1; itype <= maxtypes; ++itype) { + stencil_type[itype] = new int*[maxtypes+1](); + for (jtype = 1; jtype <= maxtypes; ++jtype) { + maxstencil_type[itype][jtype] = 0; + nstencil_type[itype][jtype] = 0; + } + } + } + + // like -> like => use standard Newton stencil at bin + + for (itype = 1; itype <= maxtypes; ++itype) { + copy_bin_info_bytype(itype); + smax = copy_neigh_info_bytype(itype); + if (smax > maxstencil_type[itype][itype]) { + maxstencil_type[itype][itype] = smax; + memory->destroy(stencil_type[itype][itype]); + memory->create(stencil_type[itype][itype], smax, + "NStencilHalfBytypeNewton::create_steup() stencil"); + } + create_newton(itype, itype, cutneighmaxsq); + } + + // Cross types: "Newton on" reached by using Newton off stencil and + // looking one way through hierarchy + // smaller -> larger => use Newton off stencil in larger bin + // larger -> smaller => no nstecil required + // If cut offs are same, use existing type-type stencil + + for (itype = 1; itype <= maxtypes; ++itype) { + for (jtype = 1; jtype <= maxtypes; ++jtype) { + if (itype == jtype) continue; + if (cuttypesq[itype] == cuttypesq[jtype]) { + nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; + stencil_type[itype][jtype] = stencil_type[jtype][jtype]; + } + else if (cuttypesq[itype] < cuttypesq[jtype]) { + copy_bin_info_bytype(jtype); + + cutneighmaxsq = cuttypesq[jtype]; + cutneighmax = sqrt(cutneighmaxsq); + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + smax = (2*sx+1) * (2*sy+1) * (2*sz+1); + if (smax > maxstencil_type[itype][jtype]) { + maxstencil_type[itype][jtype] = smax; + memory->destroy(stencil_type[itype][jtype]); + memory->create(stencil_type[itype][jtype], smax, "stencil_type[]"); + } + create_newtoff(itype, jtype, cuttypesq[jtype]); + } + } + } + +} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfBytype3dNewton::create_newton(int itype, int jtype, double cutsq) { + + int i, j, k, ns; + + ns = 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) < cutsq) + stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; + nstencil_type[itype][jtype] = ns; +} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfBytype3dNewton::create_newtoff(int itype, int jtype, double cutsq) { + + int i, j, k, ns; + + ns = 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) < cutsq) + stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; + + nstencil_type[itype][jtype] = ns; +} + +/* ---------------------------------------------------------------------- + create stencil based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfBytype3dNewton::create() +{ + // KS. Move "creation" here. +} diff --git a/src/nstencil_half_bytype_3d_newton_tri.h b/src/nstencil_half_bytype_3d_newton_tri.h new file mode 100755 index 0000000000..e419161bb5 --- /dev/null +++ b/src/nstencil_half_bytype_3d_newton_tri.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 NSTENCIL_CLASS + +NStencilStyle(half/bytype/3d/newton, + NStencilHalfBytype3dNewton, + NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTON | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H +#define LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfBytype3dNewton : public NStencil { + public: + NStencilHalfBytype3dNewton(class LAMMPS *); + ~NStencilHalfBytype3dNewton(); + void create_setup(); + void create(); + + private: + int ** maxstencil_type; + + void copy_bin_info_bytype(int); + int copy_neigh_info_bytype(int); + void create_newton(int, int, double); + void create_newtoff(int, int, double); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ From 12288630f576273a2848f6a2bd0e272b142b2e29 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 9 Nov 2020 16:32:11 -0700 Subject: [PATCH 05/73] Fixing comm and renaming bytype --- src/comm.cpp | 12 ++-- src/comm.h | 6 +- src/comm_brick.cpp | 58 +++++++++++++------ src/comm_tiled.cpp | 33 ++++++----- ...{nbin_bytype.cpp => nbin_multi_tiered.cpp} | 0 src/{nbin_bytype.h => nbin_multi_tiered.h} | 0 src/neighbor.cpp | 20 +++---- src/neighbor.h | 32 +++++----- ...bytype.cpp => npair_full_multi_tiered.cpp} | 0 ...ull_bytype.h => npair_full_multi_tiered.h} | 0 ...cpp => npair_half_multi_tiered_newton.cpp} | 0 ...ton.h => npair_half_multi_tiered_newton.h} | 0 ...=> npair_half_multi_tiered_newton_tri.cpp} | 0 ...h => npair_half_multi_tiered_newton_tri.h} | 0 ... npair_half_size_multi_tiered_newtoff.cpp} | 0 ...=> npair_half_size_multi_tiered_newtoff.h} | 0 ...> npair_half_size_multi_tiered_newton.cpp} | 0 ... => npair_half_size_multi_tiered_newton.h} | 0 ...air_half_size_multi_tiered_newton_tri.cpp} | 0 ...npair_half_size_multi_tiered_newton_tri.h} | 0 ....cpp => nstencil_full_multi_tiered_3d.cpp} | 0 ...e_3d.h => nstencil_full_multi_tiered_3d.h} | 0 ... nstencil_half_multi_tiered_2d_newton.cpp} | 0 ...=> nstencil_half_multi_tiered_2d_newton.h} | 0 ...nstencil_half_multi_tiered_3d_newtoff.cpp} | 0 ...> nstencil_half_multi_tiered_3d_newtoff.h} | 0 ... nstencil_half_multi_tiered_3d_newton.cpp} | 0 ...=> nstencil_half_multi_tiered_3d_newton.h} | 0 ...encil_half_multi_tiered_3d_newton_tri.cpp} | 0 ...stencil_half_multi_tiered_3d_newton_tri.h} | 0 30 files changed, 98 insertions(+), 63 deletions(-) rename src/{nbin_bytype.cpp => nbin_multi_tiered.cpp} (100%) rename src/{nbin_bytype.h => nbin_multi_tiered.h} (100%) rename src/{npair_full_bytype.cpp => npair_full_multi_tiered.cpp} (100%) rename src/{npair_full_bytype.h => npair_full_multi_tiered.h} (100%) rename src/{npair_half_bytype_newton.cpp => npair_half_multi_tiered_newton.cpp} (100%) rename src/{npair_half_bytype_newton.h => npair_half_multi_tiered_newton.h} (100%) rename src/{npair_half_bytype_newton_tri.cpp => npair_half_multi_tiered_newton_tri.cpp} (100%) rename src/{npair_half_bytype_newton_tri.h => npair_half_multi_tiered_newton_tri.h} (100%) rename src/{npair_half_size_bytype_newtoff.cpp => npair_half_size_multi_tiered_newtoff.cpp} (100%) rename src/{npair_half_size_bytype_newtoff.h => npair_half_size_multi_tiered_newtoff.h} (100%) rename src/{npair_half_size_bytype_newton.cpp => npair_half_size_multi_tiered_newton.cpp} (100%) rename src/{npair_half_size_bytype_newton.h => npair_half_size_multi_tiered_newton.h} (100%) rename src/{npair_half_size_bytype_newton_tri.cpp => npair_half_size_multi_tiered_newton_tri.cpp} (100%) rename src/{npair_half_size_bytype_newton_tri.h => npair_half_size_multi_tiered_newton_tri.h} (100%) rename src/{nstencil_full_bytype_3d.cpp => nstencil_full_multi_tiered_3d.cpp} (100%) rename src/{nstencil_full_bytype_3d.h => nstencil_full_multi_tiered_3d.h} (100%) rename src/{nstencil_half_bytype_2d_newton.cpp => nstencil_half_multi_tiered_2d_newton.cpp} (100%) rename src/{nstencil_half_bytype_2d_newton.h => nstencil_half_multi_tiered_2d_newton.h} (100%) rename src/{nstencil_half_bytype_3d_newtoff.cpp => nstencil_half_multi_tiered_3d_newtoff.cpp} (100%) rename src/{nstencil_half_bytype_3d_newtoff.h => nstencil_half_multi_tiered_3d_newtoff.h} (100%) rename src/{nstencil_half_bytype_3d_newton.cpp => nstencil_half_multi_tiered_3d_newton.cpp} (100%) rename src/{nstencil_half_bytype_3d_newton.h => nstencil_half_multi_tiered_3d_newton.h} (100%) rename src/{nstencil_half_bytype_3d_newton_tri.cpp => nstencil_half_multi_tiered_3d_newton_tri.cpp} (100%) rename src/{nstencil_half_bytype_3d_newton_tri.h => nstencil_half_multi_tiered_3d_newton_tri.h} (100%) diff --git a/src/comm.cpp b/src/comm.cpp index 1efe966459..b6f905d9a2 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -76,7 +76,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) grid2proc = nullptr; xsplit = ysplit = zsplit = nullptr; rcbnew = 0; - multi_bytype = 0; + multi_tiered = 0; // use of OpenMP threads // query OpenMP for number of threads/process set by user at run-time @@ -241,6 +241,10 @@ void Comm::init() maxexchange_fix_dynamic = 0; for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; + + // Can't used multi/tiered communication with Newton off + if (force->newton == 0 && multi_tiered) + error->all(FLERR,"Cannot use multi/tiered communication with Newton off"); } /* ---------------------------------------------------------------------- @@ -327,10 +331,10 @@ void Comm::modify_params(int narg, char **arg) for (i=nlo; i<=nhi; ++i) cutusermulti[i] = cut; iarg += 3; - } else if (strcmp(arg[iarg],"cutoff/bytype") == 0) { + } else if (strcmp(arg[iarg],"cutoff/tiered") == 0) { if (mode == Comm::SINGLE) - error->all(FLERR,"Use cutoff/bytype in mode multi only"); - multi_bytype = 1; + error->all(FLERR,"Use cutoff/tiered in mode multi only"); + multi_tiered = 1; iarg += 1; } else if (strcmp(arg[iarg],"vel") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command"); diff --git a/src/comm.h b/src/comm.h index 3105e09a61..037eaab348 100644 --- a/src/comm.h +++ b/src/comm.h @@ -161,7 +161,7 @@ class Comm : protected Pointers { int (*)(int, char *, int &, int *&, char *&, void *), int, char *&, int, void *, int); void rendezvous_stats(int, int, int, int, int, int, bigint); - int multi_bytype; // 1 if multi cutoff is intra-type cutoff + int multi_tiered; // 1 if multi cutoff is intra-type cutoff public: enum{MULTIPLE}; @@ -247,6 +247,10 @@ E: Processor count in z must be 1 for 2d simulation Self-explanatory. +E: Cannot use multi/tiered communication with Newton off + +Self-explanatory. + E: Cannot put data on ring from nullptr pointer W: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 57703b578c..c9fd00e9f5 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -174,18 +174,25 @@ void CommBrick::setup() cutghost[0] = cutghost[1] = cutghost[2] = cut; if (mode == Comm::MULTI) { - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,cuttype[i]); - cutghostmulti[i][1] = MAX(cut,cuttype[i]); - cutghostmulti[i][2] = MAX(cut,cuttype[i]); - if (multi_bytype == 1) { - // Set the BYTYPE cutoff - cutghostmulti[i][0] = sqrt(neighbor->cutneighsq[i][i]); - cutghostmulti[i][1] = sqrt(neighbor->cutneighsq[i][i]); - cutghostmulti[i][2] = sqrt(neighbor->cutneighsq[i][i]); + if (multi_tiered) { + // If using tiered binlists, use the itype-itype interaction distance for communication + double **cutneighsq = neighbor->cutneighsq; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) cut = cutusermulti[i]; + cutghostmulti[i][0] = MAX(cut,sqrt(cutneighsq[i][i])); + cutghostmulti[i][1] = MAX(cut,sqrt(cutneighsq[i][i])); + cutghostmulti[i][2] = MAX(cut,sqrt(cutneighsq[i][i])); + } + } else { + // If using a single binlist, use the max itype-jtype interaction distance for communication + double *cuttype = neighbor->cuttype; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) cut = cutusermulti[i]; + cutghostmulti[i][0] = MAX(cut,cuttype[i]); + cutghostmulti[i][1] = MAX(cut,cuttype[i]); + cutghostmulti[i][2] = MAX(cut,cuttype[i]); } } } @@ -204,13 +211,26 @@ void CommBrick::setup() cutghost[2] = cut * length2; if (mode == Comm::MULTI) { - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = length0 * MAX(cut,cuttype[i]); - cutghostmulti[i][1] = length1 * MAX(cut,cuttype[i]); - cutghostmulti[i][2] = length2 * MAX(cut,cuttype[i]); + if (multi_tiered) { + // If using tiered binlists, use the itype-itype interaction distance for communication + double **cutneighsq = neighbor->cutneighsq; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) cut = cutusermulti[i]; + cutghostmulti[i][0] = length0 * MAX(cut,sqrt(cutneighsq[i][i])); + cutghostmulti[i][1] = length1 * MAX(cut,sqrt(cutneighsq[i][i])); + cutghostmulti[i][2] = length2 * MAX(cut,sqrt(cutneighsq[i][i])); + } + } else { + // If using a single binlist, use the max itype-jtype interaction distance for communication + double *cuttype = neighbor->cuttype; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) cut = cutusermulti[i]; + cutghostmulti[i][0] = length0 * MAX(cut,cuttype[i]); + cutghostmulti[i][1] = length1 * MAX(cut,cuttype[i]); + cutghostmulti[i][2] = length2 * MAX(cut,cuttype[i]); + } } } } diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 4759639bff..b82d54b3ab 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -175,20 +175,27 @@ void CommTiled::setup() // check that cutoff < any periodic box length if (mode == Comm::MULTI) { - double *cuttype = neighbor->cuttype; double cut; - for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,cuttype[i]); - cutghostmulti[i][1] = MAX(cut,cuttype[i]); - cutghostmulti[i][2] = MAX(cut,cuttype[i]); - if (multi_bytype == 1) { - // Set the BYTYPE cutoff - cutghostmulti[i][0] = sqrt(neighbor->cutneighsq[i][i]); - cutghostmulti[i][1] = sqrt(neighbor->cutneighsq[i][i]); - cutghostmulti[i][2] = sqrt(neighbor->cutneighsq[i][i]); - } + if (multi_tiered) { + // If using tiered binlists, use the itype-itype interaction distance for communication + double **cutneighsq = neighbor->cutneighsq; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) cut = cutusermulti[i]; + cutghostmulti[i][0] = MAX(cut,sqrt(cutneighsq[i][i])); + cutghostmulti[i][1] = MAX(cut,sqrt(cutneighsq[i][i])); + cutghostmulti[i][2] = MAX(cut,sqrt(cutneighsq[i][i])); + } + } else { + // If using a single binlist, use the max itype-jtype interaction distance for communication + double *cuttype = neighbor->cuttype; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) cut = cutusermulti[i]; + cutghostmulti[i][0] = MAX(cut,cuttype[i]); + cutghostmulti[i][1] = MAX(cut,cuttype[i]); + cutghostmulti[i][2] = MAX(cut,cuttype[i]); + } } } diff --git a/src/nbin_bytype.cpp b/src/nbin_multi_tiered.cpp similarity index 100% rename from src/nbin_bytype.cpp rename to src/nbin_multi_tiered.cpp diff --git a/src/nbin_bytype.h b/src/nbin_multi_tiered.h similarity index 100% rename from src/nbin_bytype.h rename to src/nbin_multi_tiered.h diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 6e861b5a2b..740b16b66e 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1620,12 +1620,12 @@ int Neighbor::choose_bin(NeighRequest *rq) if (!rq->kokkos_device != !(mask & NB_KOKKOS_DEVICE)) continue; if (!rq->kokkos_host != !(mask & NB_KOKKOS_HOST)) continue; - // neighbor style is BIN or MULTI or BYTYPE and must match + // neighbor style is BIN or MULTI or MULTI/TIERED and must match if (style == Neighbor::BIN || style == Neighbor::MULTI) { if (!(mask & NB_STANDARD)) continue; - } else if (style == Neighbor::BYTYPE) { - if (!(mask & NB_BYTYPE)) continue; + } else if (style == Neighbor::MULTI_TIERED) { + if (!(mask & NB_MULTI_TIERED)) continue; } return i+1; @@ -1698,14 +1698,14 @@ int Neighbor::choose_stencil(NeighRequest *rq) if (!rq->ghost != !(mask & NS_GHOST)) continue; if (!rq->ssa != !(mask & NS_SSA)) continue; - // neighbor style is one of BIN, MULTI or BYTYPE and must match + // neighbor style is one of BIN, MULTI, or MULT/TIERED and must match if (style == Neighbor::BIN) { if (!(mask & NS_BIN)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NS_MULTI)) continue; - } else if (style == Neighbor::BYTYPE) { - if (!(mask & NS_BYTYPE)) continue; + } else if (style == Neighbor::MULT_TIERED) { + if (!(mask & NS_MULT_TIERED)) continue; } // dimension is 2 or 3 and must match @@ -1835,7 +1835,7 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!rq->halffull != !(mask & NP_HALF_FULL)) continue; if (!rq->off2on != !(mask & NP_OFF2ON)) continue; - // neighbor style is one of NSQ,BIN,MULTI or BYTYPE and must match + // neighbor style is one of NSQ, BIN, MULTI, or MULTI/TIERED and must match if (style == Neighbor::NSQ) { if (!(mask & NP_NSQ)) continue; @@ -1843,8 +1843,8 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!(mask & NP_BIN)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NP_MULTI)) continue; - } else if (style == Neighbor::BYTYPE) { - if (!(mask & NP_BYTYPE)) continue; + } else if (style == Neighbor::MULT_TIERED) { + if (!(mask & NP_MULT_TIERED)) continue; } // domain triclinic flag is on or off and must match @@ -2211,7 +2211,7 @@ void Neighbor::set(int narg, char **arg) if (strcmp(arg[1],"nsq") == 0) style = Neighbor::NSQ; else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN; else if (strcmp(arg[1],"multi") == 0) style = Neighbor::MULTI; - else if (strcmp(arg[1],"bytype") == 0) style = Neighbor::BYTYPE; + else if (strcmp(arg[1],"multi/tiered") == 0) style = Neighbor::MULT_TIERED; else error->all(FLERR,"Illegal neighbor command"); if (style == Neighbor::MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi); diff --git a/src/neighbor.h b/src/neighbor.h index e5b76dd41b..fd8cc49067 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -20,7 +20,7 @@ namespace LAMMPS_NS { class Neighbor : protected Pointers { public: - enum{NSQ,BIN,MULTI,BYTYPE}; + enum{NSQ,BIN,MULTI,MULTI_TIERED}; int style; // 0,1,2 = nsq, bin, multi int every; // build every this many steps int delay; // delay build for this many steps @@ -239,22 +239,22 @@ namespace NeighConst { static const int NB_KOKKOS_DEVICE = 1<<1; static const int NB_KOKKOS_HOST = 1<<2; static const int NB_SSA = 1<<3; - static const int NB_BYTYPE = 1<<4; + static const int NB_MULTI_TIERED = 1<<4; static const int NB_STANDARD = 1<<5; - static const int NS_BIN = 1<<0; - static const int NS_MULTI = 1<<1; - static const int NS_HALF = 1<<2; - static const int NS_FULL = 1<<3; - static const int NS_2D = 1<<4; - static const int NS_3D = 1<<5; - static const int NS_NEWTON = 1<<6; - static const int NS_NEWTOFF = 1<<7; - static const int NS_ORTHO = 1<<8; - static const int NS_TRI = 1<<9; - static const int NS_GHOST = 1<<10; - static const int NS_SSA = 1<<11; - static const int NS_BYTYPE = 1<<12; + static const int NS_BIN = 1<<0; + static const int NS_MULTI = 1<<1; + static const int NS_HALF = 1<<2; + static const int NS_FULL = 1<<3; + static const int NS_2D = 1<<4; + static const int NS_3D = 1<<5; + static const int NS_NEWTON = 1<<6; + static const int NS_NEWTOFF = 1<<7; + static const int NS_ORTHO = 1<<8; + static const int NS_TRI = 1<<9; + static const int NS_GHOST = 1<<10; + static const int NS_SSA = 1<<11; + static const int NS_MULTI_TIERED = 1<<12; static const int NP_NSQ = 1<<0; static const int NP_BIN = 1<<1; @@ -281,7 +281,7 @@ namespace NeighConst { static const int NP_SKIP = 1<<22; static const int NP_HALF_FULL = 1<<23; static const int NP_OFF2ON = 1<<24; - static const int NP_BYTYPE = 1<<25; + static const int NP_MULTI_TIERED = 1<<25; } } diff --git a/src/npair_full_bytype.cpp b/src/npair_full_multi_tiered.cpp similarity index 100% rename from src/npair_full_bytype.cpp rename to src/npair_full_multi_tiered.cpp diff --git a/src/npair_full_bytype.h b/src/npair_full_multi_tiered.h similarity index 100% rename from src/npair_full_bytype.h rename to src/npair_full_multi_tiered.h diff --git a/src/npair_half_bytype_newton.cpp b/src/npair_half_multi_tiered_newton.cpp similarity index 100% rename from src/npair_half_bytype_newton.cpp rename to src/npair_half_multi_tiered_newton.cpp diff --git a/src/npair_half_bytype_newton.h b/src/npair_half_multi_tiered_newton.h similarity index 100% rename from src/npair_half_bytype_newton.h rename to src/npair_half_multi_tiered_newton.h diff --git a/src/npair_half_bytype_newton_tri.cpp b/src/npair_half_multi_tiered_newton_tri.cpp similarity index 100% rename from src/npair_half_bytype_newton_tri.cpp rename to src/npair_half_multi_tiered_newton_tri.cpp diff --git a/src/npair_half_bytype_newton_tri.h b/src/npair_half_multi_tiered_newton_tri.h similarity index 100% rename from src/npair_half_bytype_newton_tri.h rename to src/npair_half_multi_tiered_newton_tri.h diff --git a/src/npair_half_size_bytype_newtoff.cpp b/src/npair_half_size_multi_tiered_newtoff.cpp similarity index 100% rename from src/npair_half_size_bytype_newtoff.cpp rename to src/npair_half_size_multi_tiered_newtoff.cpp diff --git a/src/npair_half_size_bytype_newtoff.h b/src/npair_half_size_multi_tiered_newtoff.h similarity index 100% rename from src/npair_half_size_bytype_newtoff.h rename to src/npair_half_size_multi_tiered_newtoff.h diff --git a/src/npair_half_size_bytype_newton.cpp b/src/npair_half_size_multi_tiered_newton.cpp similarity index 100% rename from src/npair_half_size_bytype_newton.cpp rename to src/npair_half_size_multi_tiered_newton.cpp diff --git a/src/npair_half_size_bytype_newton.h b/src/npair_half_size_multi_tiered_newton.h similarity index 100% rename from src/npair_half_size_bytype_newton.h rename to src/npair_half_size_multi_tiered_newton.h diff --git a/src/npair_half_size_bytype_newton_tri.cpp b/src/npair_half_size_multi_tiered_newton_tri.cpp similarity index 100% rename from src/npair_half_size_bytype_newton_tri.cpp rename to src/npair_half_size_multi_tiered_newton_tri.cpp diff --git a/src/npair_half_size_bytype_newton_tri.h b/src/npair_half_size_multi_tiered_newton_tri.h similarity index 100% rename from src/npair_half_size_bytype_newton_tri.h rename to src/npair_half_size_multi_tiered_newton_tri.h diff --git a/src/nstencil_full_bytype_3d.cpp b/src/nstencil_full_multi_tiered_3d.cpp similarity index 100% rename from src/nstencil_full_bytype_3d.cpp rename to src/nstencil_full_multi_tiered_3d.cpp diff --git a/src/nstencil_full_bytype_3d.h b/src/nstencil_full_multi_tiered_3d.h similarity index 100% rename from src/nstencil_full_bytype_3d.h rename to src/nstencil_full_multi_tiered_3d.h diff --git a/src/nstencil_half_bytype_2d_newton.cpp b/src/nstencil_half_multi_tiered_2d_newton.cpp similarity index 100% rename from src/nstencil_half_bytype_2d_newton.cpp rename to src/nstencil_half_multi_tiered_2d_newton.cpp diff --git a/src/nstencil_half_bytype_2d_newton.h b/src/nstencil_half_multi_tiered_2d_newton.h similarity index 100% rename from src/nstencil_half_bytype_2d_newton.h rename to src/nstencil_half_multi_tiered_2d_newton.h diff --git a/src/nstencil_half_bytype_3d_newtoff.cpp b/src/nstencil_half_multi_tiered_3d_newtoff.cpp similarity index 100% rename from src/nstencil_half_bytype_3d_newtoff.cpp rename to src/nstencil_half_multi_tiered_3d_newtoff.cpp diff --git a/src/nstencil_half_bytype_3d_newtoff.h b/src/nstencil_half_multi_tiered_3d_newtoff.h similarity index 100% rename from src/nstencil_half_bytype_3d_newtoff.h rename to src/nstencil_half_multi_tiered_3d_newtoff.h diff --git a/src/nstencil_half_bytype_3d_newton.cpp b/src/nstencil_half_multi_tiered_3d_newton.cpp similarity index 100% rename from src/nstencil_half_bytype_3d_newton.cpp rename to src/nstencil_half_multi_tiered_3d_newton.cpp diff --git a/src/nstencil_half_bytype_3d_newton.h b/src/nstencil_half_multi_tiered_3d_newton.h similarity index 100% rename from src/nstencil_half_bytype_3d_newton.h rename to src/nstencil_half_multi_tiered_3d_newton.h diff --git a/src/nstencil_half_bytype_3d_newton_tri.cpp b/src/nstencil_half_multi_tiered_3d_newton_tri.cpp similarity index 100% rename from src/nstencil_half_bytype_3d_newton_tri.cpp rename to src/nstencil_half_multi_tiered_3d_newton_tri.cpp diff --git a/src/nstencil_half_bytype_3d_newton_tri.h b/src/nstencil_half_multi_tiered_3d_newton_tri.h similarity index 100% rename from src/nstencil_half_bytype_3d_newton_tri.h rename to src/nstencil_half_multi_tiered_3d_newton_tri.h From 943a187be722c94cd669a6c80da6b6c85084bb4f Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 10 Nov 2020 16:39:56 -0700 Subject: [PATCH 06/73] Renamed to multi2, initial stencil edits --- src/comm.cpp | 14 +- src/comm.h | 2 +- src/comm_brick.cpp | 4 +- src/comm_tiled.cpp | 4 +- src/nbin.cpp | 138 ++---- src/nbin.h | 47 +- src/nbin_multi2.cpp | 414 ++++++++++++++++ src/{nbin_multi_tiered.h => nbin_multi2.h} | 26 +- src/nbin_multi_tiered.cpp | 464 ------------------ src/nbin_standard.cpp | 85 ++++ src/nbin_standard.h | 6 + src/neighbor.cpp | 20 +- src/neighbor.h | 8 +- ...ewton.cpp => npair_half_multi2_newton.cpp} | 0 ...ed_newton.h => npair_half_multi2_newton.h} | 0 ...i.cpp => npair_half_multi2_newton_tri.cpp} | 0 ...n_tri.h => npair_half_multi2_newton_tri.h} | 0 ...cpp => npair_half_size_multi2_newtoff.cpp} | 0 ...off.h => npair_half_size_multi2_newtoff.h} | 0 ....cpp => npair_half_size_multi2_newton.cpp} | 0 ...wton.h => npair_half_size_multi2_newton.h} | 0 ... => npair_half_size_multi2_newton_tri.cpp} | 0 ....h => npair_half_size_multi2_newton_tri.h} | 0 src/nstencil.cpp | 250 +++++++--- src/nstencil.h | 30 +- ...red_3d.cpp => nstencil_full_multi2_3d.cpp} | 24 +- ..._tiered_3d.h => nstencil_full_multi2_3d.h} | 11 +- ...cpp => nstencil_half_multi2_2d_newton.cpp} | 0 ...ton.h => nstencil_half_multi2_2d_newton.h} | 0 ...pp => nstencil_half_multi2_3d_newtoff.cpp} | 0 ...ff.h => nstencil_half_multi2_3d_newtoff.h} | 0 ...cpp => nstencil_half_multi2_3d_newton.cpp} | 0 ...ton.h => nstencil_half_multi2_3d_newton.h} | 0 ...=> nstencil_half_multi2_3d_newton_tri.cpp} | 0 ...h => nstencil_half_multi2_3d_newton_tri.h} | 0 35 files changed, 845 insertions(+), 702 deletions(-) create mode 100644 src/nbin_multi2.cpp rename src/{nbin_multi_tiered.h => nbin_multi2.h} (75%) delete mode 100644 src/nbin_multi_tiered.cpp rename src/{npair_half_multi_tiered_newton.cpp => npair_half_multi2_newton.cpp} (100%) rename src/{npair_half_multi_tiered_newton.h => npair_half_multi2_newton.h} (100%) rename src/{npair_half_multi_tiered_newton_tri.cpp => npair_half_multi2_newton_tri.cpp} (100%) rename src/{npair_half_multi_tiered_newton_tri.h => npair_half_multi2_newton_tri.h} (100%) rename src/{npair_half_size_multi_tiered_newtoff.cpp => npair_half_size_multi2_newtoff.cpp} (100%) rename src/{npair_half_size_multi_tiered_newtoff.h => npair_half_size_multi2_newtoff.h} (100%) rename src/{npair_half_size_multi_tiered_newton.cpp => npair_half_size_multi2_newton.cpp} (100%) rename src/{npair_half_size_multi_tiered_newton.h => npair_half_size_multi2_newton.h} (100%) rename src/{npair_half_size_multi_tiered_newton_tri.cpp => npair_half_size_multi2_newton_tri.cpp} (100%) rename src/{npair_half_size_multi_tiered_newton_tri.h => npair_half_size_multi2_newton_tri.h} (100%) rename src/{nstencil_full_multi_tiered_3d.cpp => nstencil_full_multi2_3d.cpp} (90%) rename src/{nstencil_full_multi_tiered_3d.h => nstencil_full_multi2_3d.h} (83%) rename src/{nstencil_half_multi_tiered_2d_newton.cpp => nstencil_half_multi2_2d_newton.cpp} (100%) rename src/{nstencil_half_multi_tiered_2d_newton.h => nstencil_half_multi2_2d_newton.h} (100%) rename src/{nstencil_half_multi_tiered_3d_newtoff.cpp => nstencil_half_multi2_3d_newtoff.cpp} (100%) rename src/{nstencil_half_multi_tiered_3d_newtoff.h => nstencil_half_multi2_3d_newtoff.h} (100%) rename src/{nstencil_half_multi_tiered_3d_newton.cpp => nstencil_half_multi2_3d_newton.cpp} (100%) rename src/{nstencil_half_multi_tiered_3d_newton.h => nstencil_half_multi2_3d_newton.h} (100%) rename src/{nstencil_half_multi_tiered_3d_newton_tri.cpp => nstencil_half_multi2_3d_newton_tri.cpp} (100%) rename src/{nstencil_half_multi_tiered_3d_newton_tri.h => nstencil_half_multi2_3d_newton_tri.h} (100%) diff --git a/src/comm.cpp b/src/comm.cpp index b6f905d9a2..ad0c836432 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -76,7 +76,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) grid2proc = nullptr; xsplit = ysplit = zsplit = nullptr; rcbnew = 0; - multi_tiered = 0; + multi2 = 0; // use of OpenMP threads // query OpenMP for number of threads/process set by user at run-time @@ -242,9 +242,9 @@ void Comm::init() for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; - // Can't used multi/tiered communication with Newton off - if (force->newton == 0 && multi_tiered) - error->all(FLERR,"Cannot use multi/tiered communication with Newton off"); + // Can't used multi2 communication with Newton off + if (force->newton == 0 && multi2) + error->all(FLERR,"Cannot use multi2 communication with Newton off"); } /* ---------------------------------------------------------------------- @@ -331,10 +331,10 @@ void Comm::modify_params(int narg, char **arg) for (i=nlo; i<=nhi; ++i) cutusermulti[i] = cut; iarg += 3; - } else if (strcmp(arg[iarg],"cutoff/tiered") == 0) { + } else if (strcmp(arg[iarg],"cutoff/multi2") == 0) { if (mode == Comm::SINGLE) - error->all(FLERR,"Use cutoff/tiered in mode multi only"); - multi_tiered = 1; + error->all(FLERR,"Use cutoff/multi2 in mode multi only"); + multi2 = 1; iarg += 1; } else if (strcmp(arg[iarg],"vel") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command"); diff --git a/src/comm.h b/src/comm.h index 037eaab348..d8d842ace5 100644 --- a/src/comm.h +++ b/src/comm.h @@ -161,7 +161,7 @@ class Comm : protected Pointers { int (*)(int, char *, int &, int *&, char *&, void *), int, char *&, int, void *, int); void rendezvous_stats(int, int, int, int, int, int, bigint); - int multi_tiered; // 1 if multi cutoff is intra-type cutoff + int multi2; // 1 if multi cutoff is intra-type cutoff public: enum{MULTIPLE}; diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index c9fd00e9f5..981e86c2a4 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -174,8 +174,8 @@ void CommBrick::setup() cutghost[0] = cutghost[1] = cutghost[2] = cut; if (mode == Comm::MULTI) { - if (multi_tiered) { - // If using tiered binlists, use the itype-itype interaction distance for communication + if (multi2) { + // If using multi2 binlists, use the itype-itype interaction distance for communication double **cutneighsq = neighbor->cutneighsq; for (i = 1; i <= ntypes; i++) { cut = 0.0; diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index b82d54b3ab..16ae86b4a3 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -176,8 +176,8 @@ void CommTiled::setup() if (mode == Comm::MULTI) { double cut; - if (multi_tiered) { - // If using tiered binlists, use the itype-itype interaction distance for communication + if (multi2) { + // If using multi2 binlists, use the itype-itype interaction distance for communication double **cutneighsq = neighbor->cutneighsq; for (i = 1; i <= ntypes; i++) { cut = 0.0; diff --git a/src/nbin.cpp b/src/nbin.cpp index 64ae7e7b83..4ab3270287 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -31,6 +31,21 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) bins = nullptr; atom2bin = nullptr; + nbinx_tiered = nullptr; nbiny_tiered = nullptr; nbinz_tiered = nullptr; + mbins_tiered = nullptr; + mbinx_tiered = nullptr; mbiny_tiered = nullptr, mbinz_tiered = nullptr; + mbinxlo_tiered = nullptr; + mbinylo_tiered = nullptr; + mbinzlo_tiered = nullptr; + binsizex_tiered = nullptr; binsizey_tiered = nullptr; binsizez_tiered = nullptr; + bininvx_tiered = nullptr; bininvy_tiered = nullptr; bininvz_tiered = nullptr; + binhead_tiered = nullptr; + bins_tiered = nullptr; + atom2bin_tiered = nullptr; + maxbins_tiered = nullptr; + + maxtypes = 0; + neighbor->last_setup_bins = -1; // geometry settings @@ -48,6 +63,37 @@ NBin::~NBin() memory->destroy(binhead); memory->destroy(bins); memory->destroy(atom2bin); + + if (!bins_tiered) return; + + memory->destroy(nbinx_tiered); + memory->destroy(nbiny_tiered); + memory->destroy(nbinz_tiered); + memory->destroy(mbins_tiered); + memory->destroy(mbinx_tiered); + memory->destroy(mbiny_tiered); + memory->destroy(mbinz_tiered); + memory->destroy(mbinxlo_tiered); + memory->destroy(mbinylo_tiered); + memory->destroy(mbinzlo_tiered); + + memory->destroy(binsizex_tiered); + memory->destroy(binsizey_tiered); + memory->destroy(binsizez_tiered); + memory->destroy(bininvx_tiered); + memory->destroy(bininvy_tiered); + memory->destroy(bininvz_tiered); + + for (int n = 1; n <= maxtypes; n++) { + memory->destroy(binhead_tiered[n]); + memory->destroy(bins_tiered[n]); + memory->destroy(atom2bin_tiered[n]); + } + delete [] binhead_tiered; + delete [] bins_tiered; + delete [] atom2bin_tiered; + + memory->destroy(maxbins_tiered); } /* ---------------------------------------------------------------------- */ @@ -77,95 +123,3 @@ void NBin::copy_neighbor_info() if (cutoff_custom > 0.0) cutneighmax = cutoff_custom; } - -/* ---------------------------------------------------------------------- - 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"); - } - - // bins and atom2bin = per-atom vectors - // for both local and ghost atoms - - if (nall > maxatom) { - maxatom = nall; - memory->destroy(bins); - memory->create(bins,maxatom,"neigh:bins"); - memory->destroy(atom2bin); - memory->create(atom2bin,maxatom,"neigh:atom2bin"); - } -} - -/* ---------------------------------------------------------------------- - 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 (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable"); - - if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx) + nbinx; - else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx); - ix = MIN(ix,nbinx-1); - } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx) - 1; - - if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy) + nbiny; - else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy); - iy = MIN(iy,nbiny-1); - } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy) - 1; - - if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz) + nbinz; - else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz); - iz = MIN(iz,nbinz-1); - } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz) - 1; - - return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo); -} -/* ---------------------------------------------------------------------- - to be overridden by NBinType - ------------------------------------------------------------------------- */ - -int NBin::coord2bin(double * x, int itype) -{ - error->all(FLERR,"coord2bin(x, itype) not available.\n"); - return -1; -} - -/* ---------------------------------------------------------------------- */ - -double NBin::memory_usage() -{ - double bytes = 0; - bytes += maxbin*sizeof(int); - bytes += 2*maxatom*sizeof(int); - return bytes; -} diff --git a/src/nbin.h b/src/nbin.h index 96cc7eac64..33b93ef79c 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -22,6 +22,9 @@ class NBin : protected Pointers { public: int istyle; // 1-N index into binnames bigint last_bin; // last timestep atoms were binned + double cutoff_custom; // cutoff set by requestor + + // Variables for NBinStandard int nbinx,nbiny,nbinz; // # of global bins int mbins; // # of local bins and offset on this proc @@ -35,35 +38,32 @@ class NBin : protected Pointers { int *bins; // index of next atom in same bin int *atom2bin; // bin assignment for each atom (local+ghost) - double cutoff_custom; // cutoff set by requestor - - // Analogues for NBinType - int * nbinx_type, * nbiny_type, * nbinz_type; - int * mbins_type; - int * mbinx_type, * mbiny_type, * mbinz_type; - int * mbinxlo_type, * mbinylo_type, * mbinzlo_type; - double * binsizex_type, * binsizey_type, * binsizez_type; - double * bininvx_type, * bininvy_type, * bininvz_type; - - int ** binhead_type; - int ** bins_type; - int ** atom2bin_type; + // Analogues for NBinMultimulti2 + + int *nbinx_multi2, *nbiny_multi2, *nbinz_multi2; + int *mbins_multi2; + int *mbinx_multi2, *mbiny_multi2, *mbinz_multi2; + int *mbinxlo_multi2, *mbinylo_multi2, *mbinzlo_multi2; + double *binsizex_multi2, *binsizey_multi2, *binsizez_multi2; + double *bininvx_multi2, *bininvy_multi2, *bininvz_multi2; + int **binhead_multi2; + int **bins_multi2; + int **atom2bin_multi2; + NBin(class LAMMPS *); ~NBin(); void post_constructor(class NeighRequest *); virtual void copy_neighbor_info(); - virtual void bin_atoms_setup(int); - double memory_usage(); + virtual void bin_atoms_setup(int) = 0; virtual void setup_bins(int) = 0; virtual void bin_atoms() = 0; + virtual double memory_usage() {return 0.0;} // Kokkos package int kokkos; // 1 if class stores Kokkos data - // For NBinType - virtual int coord2bin(double *, int); protected: @@ -81,12 +81,23 @@ class NBin : protected Pointers { int dimension; int triclinic; - int maxbin; // size of binhead array + // data for standard NBin + int maxatom; // size of bins array + // data for standard NBin + + int maxbin; // size of binhead array + + // data for multi/multi2 NBin + + int maxtypes; // size of multi2 arrays + int * maxbins_multi2; // size of 2nd dimension of binhead_multi2 array + // methods int coord2bin(double *); + int coord2bin(double *, int); }; } diff --git a/src/nbin_multi2.cpp b/src/nbin_multi2.cpp new file mode 100644 index 0000000000..7a87ba940c --- /dev/null +++ b/src/nbin_multi2.cpp @@ -0,0 +1,414 @@ +/* ---------------------------------------------------------------------- + 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_multi2.h" +#include "neighbor.h" +#include "atom.h" +#include "group.h" +#include "domain.h" +#include "comm.h" +#include "update.h" +#include "error.h" +#include "memory.h" + +using namespace LAMMPS_NS; + +#define SMALL 1.0e-6 +#define CUT2BIN_RATIO 100 + +/* ---------------------------------------------------------------------- */ + +NBinMulti2::NBinMulti2(LAMMPS *lmp) : NBin(lmp) {} + +/* ---------------------------------------------------------------------- + setup for bin_atoms() +------------------------------------------------------------------------- */ + +void NBinMulti2::bin_atoms_setup(int nall) +{ + // binhead_multi2[n] = per-bin vector mbins in length mbins_multi2[n] + + for (int n = 1; n <= maxtypes; n++) { + if (mbins_multi2[n] > maxbins_multi2[n]) { + maxbins_multi2[n] = mbins_multi2[n]; + memory->destroy(binhead_multi2[n]); + memory->create(binhead_multi2[n], mbins_multi2[n], "neigh:mbins_multi2"); + } + } + + // bins_multi2[n] and atom2bin_multi2[n] = per-atom vectors + // for both local and ghost atoms + + if (nall > maxatom) { + maxatom = nall; + for (int n = 1; n <= maxtypes; n++) { + memory->destroy(bins_multi2[n]); + memory->destroy(atom2bin_multi2[n]); + memory->create(bins_multi2[n], maxatom, "neigh:bin_multi2"); + memory->create(atom2bin_multi2[n], maxatom, "neigh:atom2bin_multi2"); + } + } +} + +/* --------------------------------------------------------------------- + Identify index of type with smallest cutoff +------------------------------------------------------------------------ */ + +int NBinMulti2::itype_min() { + + int itypemin = 1; + double ** cutneighsq; + + cutneighsq = neighbor->cutneighsq; + + for (int n = 1; n <= atom->ntypes; n++) { + if (cutneighsq[n][n] < cutneighsq[itypemin][itypemin]) { + itypemin = n; + } + } + + return itypemin; +} + +/* ---------------------------------------------------------------------- + setup neighbor binning geometry + ---------------------------------------------------------------------- */ + +void NBinMulti2::setup_bins(int style) +{ + int n; + int itypemin; + + // Initialize arrays + + if (atom->ntypes > maxtypes) { + + // Clear any/all memory for existing types + + for (n = 1; n <= maxtypes; n++) { + memory->destroy(atom2bin_multi2[n]); + memory->destroy(binhead_multi2[n]); + memory->destroy(bins_multi2[n]); + } + delete [] atom2bin_multi2; + delete [] binhead_multi2; + delete [] bins_multi2; + + // Realloacte at updated maxtypes + + maxtypes = atom->ntypes; + + atom2bin_multi2 = new int*[maxtypes+1](); + binhead_multi2 = new int*[maxtypes+1](); + bins_multi2 = new int*[maxtypes+1](); + + memory->destroy(nbinx_multi2); + memory->destroy(nbiny_multi2); + memory->destroy(nbinz_multi2); + memory->create(nbinx_multi2, maxtypes+1, "neigh:nbinx_multi2"); + memory->create(nbiny_multi2, maxtypes+1, "neigh:nbiny_multi2"); + memory->create(nbinz_multi2, maxtypes+1, "neigh:nbinz_multi2"); + + memory->destroy(mbins_multi2); + memory->destroy(mbinx_multi2); + memory->destroy(mbiny_multi2); + memory->destroy(mbinz_multi2); + memory->create(mbins_multi2, maxtypes+1, "neigh:mbins_multi2"); + memory->create(mbinx_multi2, maxtypes+1, "neigh:mbinx_multi2"); + memory->create(mbiny_multi2, maxtypes+1, "neigh:mbiny_multi2"); + memory->create(mbinz_multi2, maxtypes+1, "neigh:mbinz_multi2"); + + memory->destroy(mbinxlo_multi2); + memory->destroy(mbinylo_multi2); + memory->destroy(mbinzlo_multi2); + memory->create(mbinxlo_multi2, maxtypes+1, "neigh:mbinxlo_multi2"); + memory->create(mbinylo_multi2, maxtypes+1, "neigh:mbinylo_multi2"); + memory->create(mbinzlo_multi2, maxtypes+1, "neigh:mbinzlo_multi2"); + + memory->destroy(binsizex_multi2); + memory->destroy(binsizey_multi2); + memory->destroy(binsizez_multi2); + memory->create(binsizex_multi2, maxtypes+1, "neigh:binsizex_multi2"); + memory->create(binsizey_multi2, maxtypes+1, "neigh:binsizey_multi2"); + memory->create(binsizez_multi2, maxtypes+1, "neigh:binsizez_multi2"); + + memory->destroy(bininvx_multi2); + memory->destroy(bininvy_multi2); + memory->destroy(bininvz_multi2); + memory->create(bininvx_multi2, maxtypes+1, "neigh:bininvx_multi2"); + memory->create(bininvy_multi2, maxtypes+1, "neigh:bininvy_multi2"); + memory->create(bininvz_multi2, maxtypes+1, "neigh:bininvz_multi2"); + + memory->destroy(maxbins_multi2); + memory->create(maxbins_multi2, maxtypes+1, "neigh:maxbins_multi2"); + // make sure reallocation occurs in bin_atoms_setup() + for (n = 1; n <= maxtypes; n++) { + maxbins_multi2[n] = 0; + } + maxatom = 0; + } + + itypemin = itype_min(); + + // 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]; + + // For each type... + + for (n = 1; n <= atom->ntypes; n++) { + // binsize_user only relates to smallest type + // optimal bin size is roughly 1/2 the type-type cutoff + // special case of all cutoffs = 0.0, binsize = box size + + double binsize_optimal; + if (n == itypemin && binsizeflag) binsize_optimal = binsize_user; + else binsize_optimal = 0.5*sqrt(neighbor->cutneighsq[n][n]); + 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_multi2[n] = 1 + + nbinx_multi2[n] = static_cast (bbox[0]*binsizeinv); + nbiny_multi2[n] = static_cast (bbox[1]*binsizeinv); + if (dimension == 3) nbinz_multi2[n] = static_cast (bbox[2]*binsizeinv); + else nbinz_multi2[n] = 1; + + if (nbinx_multi2[n] == 0) nbinx_multi2[n] = 1; + if (nbiny_multi2[n] == 0) nbiny_multi2[n] = 1; + if (nbinz_multi2[n] == 0) nbinz_multi2[n] = 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_multi2[n] = bbox[0]/nbinx_multi2[n]; + binsizey_multi2[n] = bbox[1]/nbiny_multi2[n]; + binsizez_multi2[n] = bbox[2]/nbinz_multi2[n]; + + bininvx_multi2[n] = 1.0 / binsizex_multi2[n]; + bininvy_multi2[n] = 1.0 / binsizey_multi2[n]; + bininvz_multi2[n] = 1.0 / binsizez_multi2[n]; + + if (binsize_optimal*bininvx_multi2[n] > CUT2BIN_RATIO || + binsize_optimal*bininvy_multi2[n] > CUT2BIN_RATIO || + binsize_optimal*bininvz_multi2[n] > 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_multi2[n] = static_cast ((coord-bboxlo[0])*bininvx_multi2[n]); + if (coord < bboxlo[0]) mbinxlo_multi2[n] = mbinxlo_multi2[n] - 1; + coord = bsubboxhi[0] + SMALL*bbox[0]; + mbinxhi = static_cast ((coord-bboxlo[0])*bininvx_multi2[n]); + + coord = bsubboxlo[1] - SMALL*bbox[1]; + mbinylo_multi2[n] = static_cast ((coord-bboxlo[1])*bininvy_multi2[n]); + if (coord < bboxlo[1]) mbinylo_multi2[n] = mbinylo_multi2[n] - 1; + coord = bsubboxhi[1] + SMALL*bbox[1]; + mbinyhi = static_cast ((coord-bboxlo[1])*bininvy_multi2[n]); + + if (dimension == 3) { + coord = bsubboxlo[2] - SMALL*bbox[2]; + mbinzlo_multi2[n] = static_cast ((coord-bboxlo[2])*bininvz_multi2[n]); + if (coord < bboxlo[2]) mbinzlo_multi2[n] = mbinzlo_multi2[n] - 1; + coord = bsubboxhi[2] + SMALL*bbox[2]; + mbinzhi = static_cast ((coord-bboxlo[2])*bininvz_multi2[n]); + } + + // extend bins by 1 to insure stencil extent is included + // for 2d, only 1 bin in z + + mbinxlo_multi2[n] = mbinxlo_multi2[n] - 1; + mbinxhi = mbinxhi + 1; + mbinx_multi2[n] = mbinxhi - mbinxlo_multi2[n] + 1; + + mbinylo_multi2[n] = mbinylo_multi2[n] - 1; + mbinyhi = mbinyhi + 1; + mbiny_multi2[n] = mbinyhi - mbinylo_multi2[n] + 1; + + if (dimension == 3) { + mbinzlo_multi2[n] = mbinzlo_multi2[n] - 1; + mbinzhi = mbinzhi + 1; + } else mbinzlo_multi2[n] = mbinzhi = 0; + mbinz_multi2[n] = mbinzhi - mbinzlo_multi2[n] + 1; + + bigint bbin = ((bigint) mbinx_multi2[n]) + * ((bigint) mbiny_multi2[n]) * ((bigint) mbinz_multi2[n]) + 1; + if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins"); + mbins_multi2[n] = bbin; + } + +} + +/* ---------------------------------------------------------------------- + bin owned and ghost atoms by type +------------------------------------------------------------------------- */ + +void NBinMulti2::bin_atoms() +{ + int i,ibin,n; + + last_bin = update->ntimestep; + for (n = 1; n <= maxtypes; n++) { + for (i = 0; i < mbins_multi2[n]; i++) binhead_multi2[n][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 *type = atom->type; + 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) { + n = type[i]; + ibin = coord2bin(x[i], n); + atom2bin_multi2[n][i] = ibin; + bins_multi2[n][i] = binhead_multi2[n][ibin]; + binhead_multi2[n][ibin] = i; + } + } + for (i = atom->nfirst-1; i >= 0; i--) { + n = type[i]; + ibin = coord2bin(x[i], n); + atom2bin_multi2[n][i] = ibin; + bins_multi2[n][i] = binhead_multi2[n][ibin]; + binhead_multi2[n][ibin] = i; + } + } else { + for (i = nall-1; i >= 0; i--) { + n = type[i]; + ibin = coord2bin(x[i], n); + atom2bin_multi2[n][i] = ibin; + bins_multi2[n][i] = binhead_multi2[n][ibin]; + binhead_multi2[n][ibin] = i; + } + } +} + +/* ---------------------------------------------------------------------- + convert atom coords into local bin # for a particular type + 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 NBinMulti2::coord2bin(double *x, int it) +{ + int ix,iy,iz; + int ibin; + + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi2[it]) + nbinx_multi2[it]; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]); + ix = MIN(ix,nbinx_multi2[it]-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi2[it]) + nbiny_multi2[it]; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]); + iy = MIN(iy,nbiny_multi2[it]-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi2[it]) + nbinz_multi2[it]; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]); + iz = MIN(iz,nbinz_multi2[it]-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]) - 1; + + + ibin = (iz-mbinzlo_multi2[it])*mbiny_multi2[it]*mbinx_multi2[it] + + (iy-mbinylo_multi2[it])*mbinx_multi2[it] + + (ix-mbinxlo_multi2[it]); + return ibin; +} + + +/* ---------------------------------------------------------------------- */ + +double NBinMulti2::memory_usage() +{ + double bytes = 0; + + for (int m = 1; m < maxtypes; m++) { + bytes += maxbins_multi2[m]*sizeof(int); + bytes += 2*maxatom*sizeof(int); + } + return bytes; +} diff --git a/src/nbin_multi_tiered.h b/src/nbin_multi2.h similarity index 75% rename from src/nbin_multi_tiered.h rename to src/nbin_multi2.h index ad2b95ef4b..8cca7b1023 100644 --- a/src/nbin_multi_tiered.h +++ b/src/nbin_multi2.h @@ -13,36 +13,32 @@ #ifdef NBIN_CLASS -NBinStyle(bytype, - NBinBytype, - NB_BYTYPE) +NBinStyle(multi2, + NBinMulti2, + NB_MULTI2) #else -#ifndef LMP_NBIN_BYTYPE_H -#define LMP_NBIN_BYTYPE_H +#ifndef LMP_NBIN_MULTI2_H +#define LMP_NBIN_MULTI2_H #include "nbin.h" namespace LAMMPS_NS { -class NBinBytype : public NBin { +class NBinMulti2 : public NBin { public: - NBinBytype(class LAMMPS *); - ~NBinBytype(); + NBinMulti2(class LAMMPS *); + ~NBinMulti2() {} void bin_atoms_setup(int); void setup_bins(int); - void bin_atoms(); - - int coord2bin(double *x, int itype); - bigint memory_usage(); + void bin_atoms(); + double memory_usage(); private: - int maxtypes; - int * maxbins_type; - void setup_types(); + int coord2bin(double *, int); int itype_min(); }; diff --git a/src/nbin_multi_tiered.cpp b/src/nbin_multi_tiered.cpp deleted file mode 100644 index 70732a4b97..0000000000 --- a/src/nbin_multi_tiered.cpp +++ /dev/null @@ -1,464 +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 "nbin_bytype.h" -#include "neighbor.h" -#include "atom.h" -#include "group.h" -#include "domain.h" -#include "comm.h" -#include "update.h" -#include "error.h" -#include "memory.h" - -using namespace LAMMPS_NS; - -#define SMALL 1.0e-6 -#define CUT2BIN_RATIO 100 - -/* ---------------------------------------------------------------------- */ - -NBinBytype::NBinBytype(LAMMPS *lmp) : NBin(lmp) { - - nbinx_type = NULL; nbiny_type = NULL; nbinz_type = NULL; - mbins_type = NULL; - mbinx_type = NULL; mbiny_type = NULL, mbinz_type = NULL; - mbinxlo_type = NULL; - mbinylo_type = NULL; - mbinzlo_type = NULL; - binsizex_type = NULL; binsizey_type = NULL; binsizez_type = NULL; - bininvx_type = NULL; bininvy_type = NULL; bininvz_type = NULL; - binhead_type = NULL; - bins_type = NULL; - atom2bin_type = NULL; - maxtypes = 0; - maxbins_type = NULL; -} - -NBinBytype::~NBinBytype() { - - memory->destroy(nbinx_type); - memory->destroy(nbiny_type); - memory->destroy(nbinz_type); - memory->destroy(mbins_type); - memory->destroy(mbinx_type); - memory->destroy(mbiny_type); - memory->destroy(mbinz_type); - memory->destroy(mbinxlo_type); - memory->destroy(mbinylo_type); - memory->destroy(mbinzlo_type); - - memory->destroy(binsizex_type); - memory->destroy(binsizey_type); - memory->destroy(binsizez_type); - memory->destroy(bininvx_type); - memory->destroy(bininvy_type); - memory->destroy(bininvz_type); - - for (int n = 1; n <= maxtypes; n++) { - memory->destroy(binhead_type[n]); - memory->destroy(bins_type[n]); - memory->destroy(atom2bin_type[n]); - } - delete [] binhead_type; - delete [] bins_type; - delete [] atom2bin_type; - - memory->destroy(maxbins_type); -} - -/* ---------------------------------------------------------------------- - arrange storage for types - allows ntypes to change, but not currently expected after initialisation - ------------------------------------------------------------------------- */ - -void NBinBytype::setup_types() { - - int n; - - if (atom->ntypes > maxtypes) { - - // Clear any/all memory for existing types - - for (n = 1; n <= maxtypes; n++) { - memory->destroy(atom2bin_type[n]); - memory->destroy(binhead_type[n]); - memory->destroy(bins_type[n]); - } - delete [] atom2bin_type; - delete [] binhead_type; - delete [] bins_type; - - // Realloacte at updated maxtypes - - maxtypes = atom->ntypes; - - atom2bin_type = new int*[maxtypes+1](); - binhead_type = new int*[maxtypes+1](); - bins_type = new int*[maxtypes+1](); - - memory->destroy(nbinx_type); - memory->destroy(nbiny_type); - memory->destroy(nbinz_type); - memory->create(nbinx_type, maxtypes+1, "nBinType:nbinx_type"); - memory->create(nbiny_type, maxtypes+1, "nBinType:nbiny_type"); - memory->create(nbinz_type, maxtypes+1, "nBinType:nbinz_type"); - - memory->destroy(mbins_type); - memory->destroy(mbinx_type); - memory->destroy(mbiny_type); - memory->destroy(mbinz_type); - memory->create(mbins_type, maxtypes+1, "nBinType:mbins_type"); - memory->create(mbinx_type, maxtypes+1, "nBinType:mbinx_type"); - memory->create(mbiny_type, maxtypes+1, "nBinType:mbiny_type"); - memory->create(mbinz_type, maxtypes+1, "nBinType:mbinz_type"); - - memory->destroy(mbinxlo_type); - memory->destroy(mbinylo_type); - memory->destroy(mbinzlo_type); - memory->create(mbinxlo_type, maxtypes+1, "nBinType:mbinxlo_type"); - memory->create(mbinylo_type, maxtypes+1, "nBinType:mbinylo_type"); - memory->create(mbinzlo_type, maxtypes+1, "nBinType:mbinzlo_type"); - - memory->destroy(binsizex_type); - memory->destroy(binsizey_type); - memory->destroy(binsizez_type); - memory->create(binsizex_type, maxtypes+1, "nBinType:binsizex_type"); - memory->create(binsizey_type, maxtypes+1, "nBinType:binsizey_type"); - memory->create(binsizez_type, maxtypes+1, "nBinType:binsizez_type"); - - memory->destroy(bininvx_type); - memory->destroy(bininvy_type); - memory->destroy(bininvz_type); - memory->create(bininvx_type, maxtypes+1, "nBinType:bininvx_type"); - memory->create(bininvy_type, maxtypes+1, "nBinType:bininvy_type"); - memory->create(bininvz_type, maxtypes+1, "nBinType:bininvz_type"); - - memory->destroy(maxbins_type); - memory->create(maxbins_type, maxtypes+1, "nBinType:maxbins_type"); - // make sure reallocation occurs in bin_atoms_setup() - for (n = 1; n <= maxtypes; n++) { - maxbins_type[n] = 0; - } - maxatom = 0; - } - -} - -/* --------------------------------------------------------------------- - identify index of type with smallest cutoff - --------------------------------------------------------------------- */ - -int NBinBytype::itype_min() { - - int itypemin = 1; - double ** cutneighsq; - - cutneighsq = neighbor->cutneighsq; - - for (int n = 1; n <= atom->ntypes; n++) { - if (cutneighsq[n][n] < cutneighsq[itypemin][itypemin]) { - itypemin = n; - } - } - - return itypemin; -} - -/* ---------------------------------------------------------------------- - setup neighbor binning geometry - ---------------------------------------------------------------------- */ - -void NBinBytype::setup_bins(int style) -{ - int n; - int itypemin; - - setup_types(); - itypemin = itype_min(); - - // 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]; - - // For each type... - - for (n = 1; n <= atom->ntypes; n++) { - // binsize_user only relates to smallest type - // optimal bin size is roughly 1/2 the type-type cutoff - // special case of all cutoffs = 0.0, binsize = box size - - double binsize_optimal; - if (n == itypemin && binsizeflag) binsize_optimal = binsize_user; - else binsize_optimal = 0.5*sqrt(neighbor->cutneighsq[n][n]); - 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_type[n] = 1 - - nbinx_type[n] = static_cast (bbox[0]*binsizeinv); - nbiny_type[n] = static_cast (bbox[1]*binsizeinv); - if (dimension == 3) nbinz_type[n] = static_cast (bbox[2]*binsizeinv); - else nbinz_type[n] = 1; - - if (nbinx_type[n] == 0) nbinx_type[n] = 1; - if (nbiny_type[n] == 0) nbiny_type[n] = 1; - if (nbinz_type[n] == 0) nbinz_type[n] = 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_type[n] = bbox[0]/nbinx_type[n]; - binsizey_type[n] = bbox[1]/nbiny_type[n]; - binsizez_type[n] = bbox[2]/nbinz_type[n]; - - bininvx_type[n] = 1.0 / binsizex_type[n]; - bininvy_type[n] = 1.0 / binsizey_type[n]; - bininvz_type[n] = 1.0 / binsizez_type[n]; - - if (binsize_optimal*bininvx_type[n] > CUT2BIN_RATIO || - binsize_optimal*bininvy_type[n] > CUT2BIN_RATIO || - binsize_optimal*bininvz_type[n] > 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_type[n] = static_cast ((coord-bboxlo[0])*bininvx_type[n]); - if (coord < bboxlo[0]) mbinxlo_type[n] = mbinxlo_type[n] - 1; - coord = bsubboxhi[0] + SMALL*bbox[0]; - mbinxhi = static_cast ((coord-bboxlo[0])*bininvx_type[n]); - - coord = bsubboxlo[1] - SMALL*bbox[1]; - mbinylo_type[n] = static_cast ((coord-bboxlo[1])*bininvy_type[n]); - if (coord < bboxlo[1]) mbinylo_type[n] = mbinylo_type[n] - 1; - coord = bsubboxhi[1] + SMALL*bbox[1]; - mbinyhi = static_cast ((coord-bboxlo[1])*bininvy_type[n]); - - if (dimension == 3) { - coord = bsubboxlo[2] - SMALL*bbox[2]; - mbinzlo_type[n] = static_cast ((coord-bboxlo[2])*bininvz_type[n]); - if (coord < bboxlo[2]) mbinzlo_type[n] = mbinzlo_type[n] - 1; - coord = bsubboxhi[2] + SMALL*bbox[2]; - mbinzhi = static_cast ((coord-bboxlo[2])*bininvz_type[n]); - } - - // extend bins by 1 to insure stencil extent is included - // for 2d, only 1 bin in z - - mbinxlo_type[n] = mbinxlo_type[n] - 1; - mbinxhi = mbinxhi + 1; - mbinx_type[n] = mbinxhi - mbinxlo_type[n] + 1; - - mbinylo_type[n] = mbinylo_type[n] - 1; - mbinyhi = mbinyhi + 1; - mbiny_type[n] = mbinyhi - mbinylo_type[n] + 1; - - if (dimension == 3) { - mbinzlo_type[n] = mbinzlo_type[n] - 1; - mbinzhi = mbinzhi + 1; - } else mbinzlo_type[n] = mbinzhi = 0; - mbinz_type[n] = mbinzhi - mbinzlo_type[n] + 1; - - bigint bbin = ((bigint) mbinx_type[n]) - * ((bigint) mbiny_type[n]) * ((bigint) mbinz_type[n]) + 1; - if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins"); - mbins_type[n] = bbin; - } - -} - -/* ---------------------------------------------------------------------- - bin owned and ghost atoms by type -------------------------------------------------------------------------- */ - -void NBinBytype::bin_atoms() -{ - int i,ibin,n; - - last_bin = update->ntimestep; - for (n = 1; n <= maxtypes; n++) { - for (i = 0; i < mbins_type[n]; i++) binhead_type[n][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 *type = atom->type; - 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) { - n = type[i]; - ibin = coord2bin(x[i], n); - atom2bin_type[n][i] = ibin; - bins_type[n][i] = binhead_type[n][ibin]; - binhead_type[n][ibin] = i; - } - } - for (i = atom->nfirst-1; i >= 0; i--) { - n = type[i]; - ibin = coord2bin(x[i], n); - atom2bin_type[n][i] = ibin; - bins_type[n][i] = binhead_type[n][ibin]; - binhead_type[n][ibin] = i; - } - } else { - for (i = nall-1; i >= 0; i--) { - n = type[i]; - ibin = coord2bin(x[i], n); - atom2bin_type[n][i] = ibin; - bins_type[n][i] = binhead_type[n][ibin]; - binhead_type[n][ibin] = i; - } - } -} - - -/* ---------------------------------------------------------------------- - allocate/reallocate vectors -------------------------------------------------------------------------- */ - -void NBinBytype::bin_atoms_setup(int nall) { - - // all atom2bin, bins must be of length nall - if (nall > maxatom) { - for (int n = 1; n <= maxtypes; n++) { - memory->destroy(bins_type[n]); - memory->destroy(atom2bin_type[n]); - memory->create(bins_type[n], nall, "NBinBytype:bin_type"); - memory->create(atom2bin_type[n], nall, "NBinBytype:atom2bin_type"); - } - maxatom = nall; - } - - for (int n = 1; n <= maxtypes; n++) { - if (mbins_type[n] > maxbins_type[n]) { - maxbins_type[n] = mbins_type[n]; - memory->destroy(binhead_type[n]); - memory->create(binhead_type[n], mbins_type[n], "NBinBytype:mbins_type"); - } - } - -} - - -/* ---------------------------------------------------------------------- - convert atom coords into local bin # for bin type it -------------------------------------------------------------------------- */ - -int NBinBytype::coord2bin(double *x, int it) -{ - int ix,iy,iz; - int ibin; - - if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable"); - - if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_type[it]) + nbinx_type[it]; - else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_type[it]); - ix = MIN(ix,nbinx_type[it]-1); - } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_type[it]) - 1; - - if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_type[it]) + nbiny_type[it]; - else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_type[it]); - iy = MIN(iy,nbiny_type[it]-1); - } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_type[it]) - 1; - - if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_type[it]) + nbinz_type[it]; - else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_type[it]); - iz = MIN(iz,nbinz_type[it]-1); - } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_type[it]) - 1; - - - ibin = (iz-mbinzlo_type[it])*mbiny_type[it]*mbinx_type[it] - + (iy-mbinylo_type[it])*mbinx_type[it] - + (ix-mbinxlo_type[it]); - return ibin; -} - - -/* ---------------------------------------------------------------------- - tot up for types - ---------------------------------------------------------------------- */ - -bigint NBinBytype::memory_usage() -{ - bigint bytes = 0; - - for (int m = 1; m < maxtypes; m++) { - bytes += 2*maxatom*sizeof(int); - bytes += maxbins_type[m]*sizeof(int); - } - return bytes; -} diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp index 9a28121384..e63c8dcd56 100644 --- a/src/nbin_standard.cpp +++ b/src/nbin_standard.cpp @@ -29,6 +29,33 @@ using namespace LAMMPS_NS; NBinStandard::NBinStandard(LAMMPS *lmp) : NBin(lmp) {} +/* ---------------------------------------------------------------------- + setup for bin_atoms() +------------------------------------------------------------------------- */ + +void NBinStandard::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"); + } + + // bins and atom2bin = per-atom vectors + // for both local and ghost atoms + + if (nall > maxatom) { + maxatom = nall; + memory->destroy(bins); + memory->create(bins,maxatom,"neigh:bins"); + memory->destroy(atom2bin); + memory->create(atom2bin,maxatom,"neigh:atom2bin"); + } +} + /* ---------------------------------------------------------------------- setup neighbor binning geometry bin numbering in each dimension is global: @@ -230,3 +257,61 @@ void NBinStandard::bin_atoms() } } } + + +/* ---------------------------------------------------------------------- + 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 NBinStandard::coord2bin(double *x) +{ + int ix,iy,iz; + + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx) + nbinx; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx); + ix = MIN(ix,nbinx-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy) + nbiny; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy); + iy = MIN(iy,nbiny-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz) + nbinz; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz); + iz = MIN(iz,nbinz-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz) - 1; + + return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo); +} + + +/* ---------------------------------------------------------------------- */ + +double NBinStandard::memory_usage() +{ + double bytes = 0; + bytes += maxbin*sizeof(int); + bytes += 2*maxatom*sizeof(int); + return bytes; +} diff --git a/src/nbin_standard.h b/src/nbin_standard.h index 06defdb101..d8ecb435b7 100644 --- a/src/nbin_standard.h +++ b/src/nbin_standard.h @@ -30,8 +30,14 @@ class NBinStandard : public NBin { public: NBinStandard(class LAMMPS *); ~NBinStandard() {} + void bin_atoms_setup(int); void setup_bins(int); void bin_atoms(); + double memory_usage(); + + private: + + int coord2bin(double *); }; } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 740b16b66e..d4a2727662 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1620,12 +1620,12 @@ int Neighbor::choose_bin(NeighRequest *rq) if (!rq->kokkos_device != !(mask & NB_KOKKOS_DEVICE)) continue; if (!rq->kokkos_host != !(mask & NB_KOKKOS_HOST)) continue; - // neighbor style is BIN or MULTI or MULTI/TIERED and must match + // neighbor style is BIN or MULTI or MULTI2 and must match if (style == Neighbor::BIN || style == Neighbor::MULTI) { if (!(mask & NB_STANDARD)) continue; - } else if (style == Neighbor::MULTI_TIERED) { - if (!(mask & NB_MULTI_TIERED)) continue; + } else if (style == Neighbor::MULTI2) { + if (!(mask & NB_MULTI2)) continue; } return i+1; @@ -1698,14 +1698,14 @@ int Neighbor::choose_stencil(NeighRequest *rq) if (!rq->ghost != !(mask & NS_GHOST)) continue; if (!rq->ssa != !(mask & NS_SSA)) continue; - // neighbor style is one of BIN, MULTI, or MULT/TIERED and must match + // neighbor style is one of BIN, MULTI, or MULTI2 and must match if (style == Neighbor::BIN) { if (!(mask & NS_BIN)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NS_MULTI)) continue; - } else if (style == Neighbor::MULT_TIERED) { - if (!(mask & NS_MULT_TIERED)) continue; + } else if (style == Neighbor::MULTI2) { + if (!(mask & NS_MULTI2)) continue; } // dimension is 2 or 3 and must match @@ -1835,7 +1835,7 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!rq->halffull != !(mask & NP_HALF_FULL)) continue; if (!rq->off2on != !(mask & NP_OFF2ON)) continue; - // neighbor style is one of NSQ, BIN, MULTI, or MULTI/TIERED and must match + // neighbor style is one of NSQ, BIN, MULTI, or MULTI2 and must match if (style == Neighbor::NSQ) { if (!(mask & NP_NSQ)) continue; @@ -1843,8 +1843,8 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!(mask & NP_BIN)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NP_MULTI)) continue; - } else if (style == Neighbor::MULT_TIERED) { - if (!(mask & NP_MULT_TIERED)) continue; + } else if (style == Neighbor::MULTI2) { + if (!(mask & NP_MULTI2)) continue; } // domain triclinic flag is on or off and must match @@ -2211,7 +2211,7 @@ void Neighbor::set(int narg, char **arg) if (strcmp(arg[1],"nsq") == 0) style = Neighbor::NSQ; else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN; else if (strcmp(arg[1],"multi") == 0) style = Neighbor::MULTI; - else if (strcmp(arg[1],"multi/tiered") == 0) style = Neighbor::MULT_TIERED; + else if (strcmp(arg[1],"multi2") == 0) style = Neighbor::MULTI2; else error->all(FLERR,"Illegal neighbor command"); if (style == Neighbor::MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi); diff --git a/src/neighbor.h b/src/neighbor.h index fd8cc49067..0012cb29fa 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -20,7 +20,7 @@ namespace LAMMPS_NS { class Neighbor : protected Pointers { public: - enum{NSQ,BIN,MULTI,MULTI_TIERED}; + enum{NSQ,BIN,MULTI,MULTI2}; int style; // 0,1,2 = nsq, bin, multi int every; // build every this many steps int delay; // delay build for this many steps @@ -239,7 +239,7 @@ namespace NeighConst { static const int NB_KOKKOS_DEVICE = 1<<1; static const int NB_KOKKOS_HOST = 1<<2; static const int NB_SSA = 1<<3; - static const int NB_MULTI_TIERED = 1<<4; + static const int NB_MULTI2 = 1<<4; static const int NB_STANDARD = 1<<5; static const int NS_BIN = 1<<0; @@ -254,7 +254,7 @@ namespace NeighConst { static const int NS_TRI = 1<<9; static const int NS_GHOST = 1<<10; static const int NS_SSA = 1<<11; - static const int NS_MULTI_TIERED = 1<<12; + static const int NS_MULTI2 = 1<<12; static const int NP_NSQ = 1<<0; static const int NP_BIN = 1<<1; @@ -281,7 +281,7 @@ namespace NeighConst { static const int NP_SKIP = 1<<22; static const int NP_HALF_FULL = 1<<23; static const int NP_OFF2ON = 1<<24; - static const int NP_MULTI_TIERED = 1<<25; + static const int NP_MULTI2 = 1<<25; } } diff --git a/src/npair_half_multi_tiered_newton.cpp b/src/npair_half_multi2_newton.cpp similarity index 100% rename from src/npair_half_multi_tiered_newton.cpp rename to src/npair_half_multi2_newton.cpp diff --git a/src/npair_half_multi_tiered_newton.h b/src/npair_half_multi2_newton.h similarity index 100% rename from src/npair_half_multi_tiered_newton.h rename to src/npair_half_multi2_newton.h diff --git a/src/npair_half_multi_tiered_newton_tri.cpp b/src/npair_half_multi2_newton_tri.cpp similarity index 100% rename from src/npair_half_multi_tiered_newton_tri.cpp rename to src/npair_half_multi2_newton_tri.cpp diff --git a/src/npair_half_multi_tiered_newton_tri.h b/src/npair_half_multi2_newton_tri.h similarity index 100% rename from src/npair_half_multi_tiered_newton_tri.h rename to src/npair_half_multi2_newton_tri.h diff --git a/src/npair_half_size_multi_tiered_newtoff.cpp b/src/npair_half_size_multi2_newtoff.cpp similarity index 100% rename from src/npair_half_size_multi_tiered_newtoff.cpp rename to src/npair_half_size_multi2_newtoff.cpp diff --git a/src/npair_half_size_multi_tiered_newtoff.h b/src/npair_half_size_multi2_newtoff.h similarity index 100% rename from src/npair_half_size_multi_tiered_newtoff.h rename to src/npair_half_size_multi2_newtoff.h diff --git a/src/npair_half_size_multi_tiered_newton.cpp b/src/npair_half_size_multi2_newton.cpp similarity index 100% rename from src/npair_half_size_multi_tiered_newton.cpp rename to src/npair_half_size_multi2_newton.cpp diff --git a/src/npair_half_size_multi_tiered_newton.h b/src/npair_half_size_multi2_newton.h similarity index 100% rename from src/npair_half_size_multi_tiered_newton.h rename to src/npair_half_size_multi2_newton.h diff --git a/src/npair_half_size_multi_tiered_newton_tri.cpp b/src/npair_half_size_multi2_newton_tri.cpp similarity index 100% rename from src/npair_half_size_multi_tiered_newton_tri.cpp rename to src/npair_half_size_multi2_newton_tri.cpp diff --git a/src/npair_half_size_multi_tiered_newton_tri.h b/src/npair_half_size_multi2_newton_tri.h similarity index 100% rename from src/npair_half_size_multi_tiered_newton_tri.h rename to src/npair_half_size_multi2_newton_tri.h diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 861fcd537e..3518b7db55 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -51,6 +51,15 @@ using namespace LAMMPS_NS; 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?) + for multi/tiered: + create one stencil for each itype-jtype pairing + stencils do not generally follow the same rules for half/full or newton on/off + whole stencils including all surrounding bins are always used except + for same-type stencils with newton on which uses a split stencil + for orthogonal boxes, a split stencil includes bins to the "upper right" of central bin + for triclinic, a split stencil includes bins in the z (3D) or y (2D) plane of self and above + 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) @@ -64,6 +73,11 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) nstencil_multi = nullptr; stencil_multi = nullptr; distsq_multi = nullptr; + + stencil_split = nullptr; + stencil_skip = nullptr; + stencil_bin_type = nullptr; + stencil_cut = nullptr; dimension = domain->dimension; } @@ -75,16 +89,44 @@ NStencil::~NStencil() memory->destroy(stencil); memory->destroy(stencilxyz); - if (!stencil_multi) return; + if (stencil_multi) { - int n = atom->ntypes; - for (int i = 1; i <= n; i++) { - memory->destroy(stencil_multi[i]); - memory->destroy(distsq_multi[i]); + int n = atom->ntypes; + for (int i = 1; i <= n; i++) { + memory->destroy(stencil_multi[i]); + memory->destroy(distsq_multi[i]); + } + delete [] nstencil_multi; + delete [] stencil_multi; + delete [] distsq_multi; + } + + if (stencil_multi_tiered) { + + int n = atom->ntypes; + memory->destroy(nstencil_multi_tiered); + for (int i = 1; i <= n; i++) { + for (int j = 0; j <= n; j++) { + if (! stencil_skip[i][j]) + memory->destroy(stencil_multi_tiered[i][j]); + } + delete [] stencil_multi_tiered[i]; + } + delete [] stencil_multi_tiered; + memory->destroy(maxstencil_multi_tiered); + memory->destroy(stencil_split); + memory->destroy(stencil_skip); + memory->destroy(stencil_bin_type); + memory->destroy(stencil_cut); + + memory->destroy(sx_multi_tiered); + memory->destroy(sy_multi_tiered); + memory->destroy(sz_multi_tiered); + + memory->destroy(binsizex_multi_tiered); + memory->destroy(binsizey_multi_tiered); + memory->destroy(binsizez_multi_tiered); } - delete [] nstencil_multi; - delete [] stencil_multi; - delete [] distsq_multi; } /* ---------------------------------------------------------------------- */ @@ -105,6 +147,7 @@ void NStencil::copy_neighbor_info() cutneighmax = neighbor->cutneighmax; cutneighmaxsq = neighbor->cutneighmaxsq; cuttypesq = neighbor->cuttypesq; + cutneighsq = neighbor->cutneighsq; // overwrite Neighbor cutoff with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -132,6 +175,23 @@ void NStencil::copy_bin_info() bininvz = nb->bininvz; } +/* ---------------------------------------------------------------------- + copy needed info for a given type from NBin class to this stencil class +------------------------------------------------------------------------- */ + +void NStencil::copy_bin_info_multi_tiered(int type) +{ + mbinx = nb->mbinx_tiered[type]; + mbiny = nb->mbiny_tiered[type]; + mbinz = nb->mbinz_tiered[type]; + binsizex = nb->binsizex_tiered[type]; + binsizey = nb->binsizey_tiered[type]; + binsizez = nb->binsizez_tiered[type]; + bininvx = nb->bininvx_tiered[type]; + bininvy = nb->bininvy_tiered[type]; + bininvz = nb->bininvz_tiered[type]; +} + /* ---------------------------------------------------------------------- insure NBin data is current insure stencils are allocated large enough @@ -139,59 +199,131 @@ void NStencil::copy_bin_info() void NStencil::create_setup() { - if (nb) copy_bin_info(); - last_stencil = 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 (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (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 == Neighbor::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"); + + if (neighstyle != Neighbor::MULTI_TIERED){ + if (nb) copy_bin_info(); + last_stencil = 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 (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (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 == Neighbor::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"); + } + } + + } 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] = nullptr; + distsq_multi[i] = nullptr; + } + } + 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"); + } } } - } else { - int i; + int i, j, bin_type, smax; + double stencil_range; 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] = nullptr; - distsq_multi[i] = nullptr; - } - } - 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"); + + // Allocate arrays to store stencil information + memory->create(stencil_split, n, n, + "neighstencil:stencil_split");" + memory->create(stencil_skip, n, n, + "neighstencil:stencil_skip");" + memory->create(stencil_bin_type, n, n, + "neighstencil:stencil_bin_type");" + memory->create(stencil_cut, n, n, + "neighstencil:stencil_cut");" + + memory->create(sx_multi_tiered, n, n, + "neighstencil:sx_multi_tiered");" + memory->create(sy_multi_tiered, n, n, + "neighstencil:sy_multi_tiered");" + memory->create(sz_multi_tiered, n, n, + "neighstencil:sz_multi_tiered");" + + memory->create(binsizex_multi_tiered, n, n, + "neighstencil:binsizex_multi_tiered");" + memory->create(binsizey_multi_tiered, n, n, + "neighstencil:binsizey_multi_tiered");" + memory->create(binsizez_multi_tiered, n, n, + "neighstencil:binsizez_multi_tiered");" + + // Determine which stencils need to be built + set_stencil_properties(); + + for (i = 1; i <= n; ++i) { + for (j = 1; j <= n; ++j) { + + // Skip creation of unused stencils + if (stencil_skip[i][j]) continue; + + // Copy bin info for this particular pair of types + bin_type = stencil_bin_type[i][j]; + copy_bin_info_bytype(bin_type); + + binsizex_multi_tiered[i][j] = binsizex; + binsizey_multi_tiered[i][j] = binsizey; + binsizez_multi_tiered[i][j] = binsizez; + + stencil_range = stencil_cut[i][j]; + + sx = static_cast (stencil_range*bininvx); + if (sx*binsizex < stencil_range) sx++; + sy = static_cast (stencil_range*bininvy); + if (sy*binsizey < stencil_range) sy++; + sz = static_cast (stencil_range*bininvz); + if (sz*binsizez < stencil_range) sz++; + + sx_multi_tiered[i][j] = sx; + sy_multi_tiered[i][j] = sy; + sz_multi_tiered[i][j] = sz; + + smax = ((2*sx+1) * (2*sy+1) * (2*sz+1)); + + if (smax > maxstencil_multi_tiered[i][j]) { + maxstencil_multi_tiered[i][j] = smax; + memory->destroy(stencil_multi_tiered[i][j]); + memory->create(stencil_multi_tiered[i][j], smax, + "neighstencil::stencil_multi_tiered"); + } } } } @@ -231,6 +363,10 @@ double NStencil::memory_usage() } else if (neighstyle == Neighbor::MULTI) { bytes += atom->ntypes*maxstencil_multi * sizeof(int); bytes += atom->ntypes*maxstencil_multi * sizeof(double); + } else if (neighstyle == Neighbor::MULTI_TIERED) { + bytes += atom->ntypes*maxstencil_multi * sizeof(int); + 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 index bdd656b937..58c39ee13c 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -29,14 +29,22 @@ class NStencil : protected Pointers { 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 + int ** nstencil_multi_tiered; // # bins bins in each itype-jtype tiered multi stencil + int *** stencil_multi_tiered; // list of bin offsets in each tiered multi stencil + int ** maxstencil_type; // max double **distsq_multi; // sq distances to bins in each stencil int sx,sy,sz; // extent of stencil in each dim + int **sx_multi_tiered; // analogs for multi tiered + int **sy_multi_tiered; + int **sz_multi_tiered; - double cutoff_custom; // cutoff set by requestor - - // BYTYPE stencils - int ** nstencil_type; // No. of bins for stencil[itype][jtype] - int *** stencil_type; // Stencil for [itype][jtype] + double cutoff_custom; // cutoff set by requestor + + // Arrays to store options for multi/tiered itype-jtype stencils + bool **stencil_half; // flag creation of a half stencil for itype-jtype + bool **stencil_skip; // skip creation of itype-jtype stencils (for newton on) + int **stencil_bin_type; // what type to use for bin information + double **stencil_cut; // cutoff used for stencil size NStencil(class LAMMPS *); virtual ~NStencil(); @@ -57,12 +65,19 @@ class NStencil : protected Pointers { double cutneighmax; double cutneighmaxsq; double *cuttypesq; + double *cutneighsq; // data from NBin class int mbinx,mbiny,mbinz; double binsizex,binsizey,binsizez; double bininvx,bininvy,bininvz; + + // analogs for multi-tiered + + double **binsizex_multi_tiered; + double **binsizey_multi_tiered; + double **binsizez_multi_tiered; // data common to all NStencil variants @@ -76,6 +91,11 @@ class NStencil : protected Pointers { void copy_bin_info(); // copy info from NBin class double bin_distance(int, int, int); // distance between bin corners + + // methods for multi/tiered NStencil + + void copy_bin_info_multi_tiered(int); // copy mult/tiered info from NBin class + void set_stencil_properties(); // determine which stencils to build and how }; } diff --git a/src/nstencil_full_multi_tiered_3d.cpp b/src/nstencil_full_multi2_3d.cpp similarity index 90% rename from src/nstencil_full_multi_tiered_3d.cpp rename to src/nstencil_full_multi2_3d.cpp index cecccdfb14..099e2adeb8 100644 --- a/src/nstencil_full_multi_tiered_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -46,23 +46,9 @@ NStencilFullBytype3d::~NStencilFullBytype3d() { } } -/* ---------------------------------------------------------------------- */ - -void NStencilFullBytype3d::copy_bin_info_bytype(int itype) { - - mbinx = nb->mbinx_type[itype]; - mbiny = nb->mbiny_type[itype]; - mbinz = nb->mbinz_type[itype]; - binsizex = nb->binsizex_type[itype]; - binsizey = nb->binsizey_type[itype]; - binsizez = nb->binsizez_type[itype]; - bininvx = nb->bininvx_type[itype]; - bininvy = nb->bininvy_type[itype]; - bininvz = nb->bininvz_type[itype]; -} /* ---------------------------------------------------------------------- */ - +INCORPORTE INTO CREATE THEN DELETE, NOTE NAME OF CUTNEIGHMAX ETC int NStencilFullBytype3d::copy_neigh_info_bytype(int itype) { cutneighmaxsq = neighbor->cutneighsq[itype][itype]; @@ -104,13 +90,13 @@ void NStencilFullBytype3d::create_setup() maxstencil_type[itype][jtype] = 0; } } - } + } MOVE TO PARENT CLASS // like -> like => use standard newtoff stencil at bin for (itype = 1; itype <= maxtypes; ++itype) { copy_bin_info_bytype(itype); - smax = copy_neigh_info_bytype(itype); + smax = copy_neigh_info_bytype(itype); uses cutneighsq[itype][itype] to create s's if (smax > maxstencil_type[itype][itype]) { maxstencil_type[itype][itype] = smax; memory->destroy(stencil_type[itype][itype]); @@ -127,7 +113,7 @@ void NStencilFullBytype3d::create_setup() for (itype = 1; itype <= maxtypes; ++itype) { for (jtype = 1; jtype <= maxtypes; ++jtype) { if (itype == jtype) continue; - if (cuttypesq[itype] <= cuttypesq[jtype]) { + if (cuttypesq[itype] <= cuttypesq[jtype]) { This does work to say which prticle is smller // Potential destroy/create problem? nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; stencil_type[itype][jtype] = stencil_type[jtype][jtype]; @@ -136,7 +122,7 @@ void NStencilFullBytype3d::create_setup() copy_bin_info_bytype(jtype); // smax = copy_neigh_info_bytype(jtype); - cutneighmaxsq = cuttypesq[jtype]; + cutneighmaxsq = cuttypesq[jtype]; Does it need to be this big? Can't I use cutneighsq[i][j]? cutneighmax = sqrt(cutneighmaxsq); sx = static_cast (cutneighmax*bininvx); if (sx*binsizex < cutneighmax) sx++; diff --git a/src/nstencil_full_multi_tiered_3d.h b/src/nstencil_full_multi2_3d.h similarity index 83% rename from src/nstencil_full_multi_tiered_3d.h rename to src/nstencil_full_multi2_3d.h index 6e61365d17..b9b835fd24 100644 --- a/src/nstencil_full_multi_tiered_3d.h +++ b/src/nstencil_full_multi2_3d.h @@ -13,15 +13,15 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(full/bytype/3d, - NStencilFullBytype3d, - NS_FULL | NS_BYTYPE | NS_3D | +NStencilStyle(full/multi/tiered/3d, + NStencilFullMultiTiered3d, + NS_FULL | NS_Multi_Tiered | NS_3D | NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) #else -#ifndef LMP_NSTENCIL_FULL_BYTYPE_3D_H -#define LMP_NSTENCIL_FULL_BYTYPE_3D_H +#ifndef LMP_NSTENCIL_FULL_MULTI_TIERED_3D_H +#define LMP_NSTENCIL_FULL_MULTI_TIERED_3D_H #include "nstencil.h" @@ -37,7 +37,6 @@ class NStencilFullBytype3d : public NStencil { private: int ** maxstencil_type; - void copy_bin_info_bytype(int); int copy_neigh_info_bytype(int); void create_newtoff(int, int, double); diff --git a/src/nstencil_half_multi_tiered_2d_newton.cpp b/src/nstencil_half_multi2_2d_newton.cpp similarity index 100% rename from src/nstencil_half_multi_tiered_2d_newton.cpp rename to src/nstencil_half_multi2_2d_newton.cpp diff --git a/src/nstencil_half_multi_tiered_2d_newton.h b/src/nstencil_half_multi2_2d_newton.h similarity index 100% rename from src/nstencil_half_multi_tiered_2d_newton.h rename to src/nstencil_half_multi2_2d_newton.h diff --git a/src/nstencil_half_multi_tiered_3d_newtoff.cpp b/src/nstencil_half_multi2_3d_newtoff.cpp similarity index 100% rename from src/nstencil_half_multi_tiered_3d_newtoff.cpp rename to src/nstencil_half_multi2_3d_newtoff.cpp diff --git a/src/nstencil_half_multi_tiered_3d_newtoff.h b/src/nstencil_half_multi2_3d_newtoff.h similarity index 100% rename from src/nstencil_half_multi_tiered_3d_newtoff.h rename to src/nstencil_half_multi2_3d_newtoff.h diff --git a/src/nstencil_half_multi_tiered_3d_newton.cpp b/src/nstencil_half_multi2_3d_newton.cpp similarity index 100% rename from src/nstencil_half_multi_tiered_3d_newton.cpp rename to src/nstencil_half_multi2_3d_newton.cpp diff --git a/src/nstencil_half_multi_tiered_3d_newton.h b/src/nstencil_half_multi2_3d_newton.h similarity index 100% rename from src/nstencil_half_multi_tiered_3d_newton.h rename to src/nstencil_half_multi2_3d_newton.h diff --git a/src/nstencil_half_multi_tiered_3d_newton_tri.cpp b/src/nstencil_half_multi2_3d_newton_tri.cpp similarity index 100% rename from src/nstencil_half_multi_tiered_3d_newton_tri.cpp rename to src/nstencil_half_multi2_3d_newton_tri.cpp diff --git a/src/nstencil_half_multi_tiered_3d_newton_tri.h b/src/nstencil_half_multi2_3d_newton_tri.h similarity index 100% rename from src/nstencil_half_multi_tiered_3d_newton_tri.h rename to src/nstencil_half_multi2_3d_newton_tri.h From af57879416adc0578f88a1470115075c7a460da0 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 10 Nov 2020 17:15:28 -0700 Subject: [PATCH 07/73] Labelling stencils half/full, removing unnecessary newton on/off designation --- src/neighbor.cpp | 29 ++- src/neighbor.h | 12 +- src/nstencil_full_bin_2d.h | 3 +- src/nstencil_full_bin_3d.h | 3 +- src/nstencil_full_ghost_bin_2d.h | 3 +- src/nstencil_full_ghost_bin_3d.h | 3 +- src/nstencil_full_multi2_3d.h | 4 +- src/nstencil_full_multi_2d.h | 3 +- src/nstencil_full_multi_3d.h | 3 +- ...2d_newton.cpp => nstencil_half_bin_2d.cpp} | 6 +- ...bin_3d_newton.h => nstencil_half_bin_2d.h} | 16 +- src/nstencil_half_bin_2d_newtoff.cpp | 37 ---- src/nstencil_half_bin_2d_newtoff.h | 43 ---- src/nstencil_half_bin_2d_newton_tri.h | 43 ---- ...n_tri.cpp => nstencil_half_bin_2d_tri.cpp} | 6 +- ...2d_newton.h => nstencil_half_bin_2d_tri.h} | 16 +- ...3d_newton.cpp => nstencil_half_bin_3d.cpp} | 6 +- ...lti_2d_newton.h => nstencil_half_bin_3d.h} | 16 +- src/nstencil_half_bin_3d_newtoff.cpp | 38 ---- src/nstencil_half_bin_3d_newtoff.h | 43 ---- src/nstencil_half_bin_3d_newton_tri.h | 43 ---- ...n_tri.cpp => nstencil_half_bin_3d_tri.cpp} | 6 +- ...3d_newton.h => nstencil_half_bin_3d_tri.h} | 16 +- src/nstencil_half_ghost_bin_2d_newtoff.cpp | 44 ---- src/nstencil_half_ghost_bin_2d_newtoff.h | 44 ---- src/nstencil_half_ghost_bin_3d_newtoff.cpp | 45 ---- src/nstencil_half_ghost_bin_3d_newtoff.h | 44 ---- src/nstencil_half_multi2_2d_newton.cpp | 201 ------------------ src/nstencil_half_multi2_2d_newton.h | 52 ----- ...newton.cpp => nstencil_half_multi2_3d.cpp} | 0 ...newton_tri.h => nstencil_half_multi2_3d.h} | 9 +- ...> nstencil_half_multi2_3d_delete_noff.cpp} | 0 ... => nstencil_half_multi2_3d_delete_noff.h} | 0 ...ri.cpp => nstencil_half_multi2_3d_tri.cpp} | 0 ...newton.h => nstencil_half_multi2_3d_tri.h} | 9 +- ..._newton.cpp => nstencil_half_multi_2d.cpp} | 8 +- src/nstencil_half_multi_2d.h | 42 ++++ src/nstencil_half_multi_2d_newtoff.cpp | 51 ----- src/nstencil_half_multi_2d_newtoff.h | 43 ---- src/nstencil_half_multi_2d_newton_tri.h | 43 ---- ...tri.cpp => nstencil_half_multi_2d_tri.cpp} | 8 +- src/nstencil_half_multi_2d_tri.h | 42 ++++ ..._newton.cpp => nstencil_half_multi_3d.cpp} | 8 +- src/nstencil_half_multi_3d.h | 42 ++++ src/nstencil_half_multi_3d_newtoff.cpp | 52 ----- src/nstencil_half_multi_3d_newtoff.h | 43 ---- src/nstencil_half_multi_3d_newton_tri.h | 43 ---- ...tri.cpp => nstencil_half_multi_3d_tri.cpp} | 8 +- src/nstencil_half_multi_3d_tri.h | 42 ++++ 49 files changed, 261 insertions(+), 1060 deletions(-) rename src/{nstencil_half_bin_2d_newton.cpp => nstencil_half_bin_2d.cpp} (87%) rename src/{nstencil_half_bin_3d_newton.h => nstencil_half_bin_2d.h} (69%) delete mode 100644 src/nstencil_half_bin_2d_newtoff.cpp delete mode 100644 src/nstencil_half_bin_2d_newtoff.h delete mode 100644 src/nstencil_half_bin_2d_newton_tri.h rename src/{nstencil_half_bin_2d_newton_tri.cpp => nstencil_half_bin_2d_tri.cpp} (87%) rename src/{nstencil_half_bin_2d_newton.h => nstencil_half_bin_2d_tri.h} (69%) rename src/{nstencil_half_bin_3d_newton.cpp => nstencil_half_bin_3d.cpp} (88%) rename src/{nstencil_half_multi_2d_newton.h => nstencil_half_bin_3d.h} (68%) delete mode 100644 src/nstencil_half_bin_3d_newtoff.cpp delete mode 100644 src/nstencil_half_bin_3d_newtoff.h delete mode 100644 src/nstencil_half_bin_3d_newton_tri.h rename src/{nstencil_half_bin_3d_newton_tri.cpp => nstencil_half_bin_3d_tri.cpp} (88%) rename src/{nstencil_half_multi_3d_newton.h => nstencil_half_bin_3d_tri.h} (68%) delete mode 100644 src/nstencil_half_ghost_bin_2d_newtoff.cpp delete mode 100644 src/nstencil_half_ghost_bin_2d_newtoff.h delete mode 100644 src/nstencil_half_ghost_bin_3d_newtoff.cpp delete mode 100644 src/nstencil_half_ghost_bin_3d_newtoff.h delete mode 100644 src/nstencil_half_multi2_2d_newton.cpp delete mode 100644 src/nstencil_half_multi2_2d_newton.h rename src/{nstencil_half_multi2_3d_newton.cpp => nstencil_half_multi2_3d.cpp} (100%) rename src/{nstencil_half_multi2_3d_newton_tri.h => nstencil_half_multi2_3d.h} (82%) mode change 100755 => 100644 rename src/{nstencil_half_multi2_3d_newtoff.cpp => nstencil_half_multi2_3d_delete_noff.cpp} (100%) rename src/{nstencil_half_multi2_3d_newtoff.h => nstencil_half_multi2_3d_delete_noff.h} (100%) rename src/{nstencil_half_multi2_3d_newton_tri.cpp => nstencil_half_multi2_3d_tri.cpp} (100%) rename src/{nstencil_half_multi2_3d_newton.h => nstencil_half_multi2_3d_tri.h} (82%) mode change 100644 => 100755 rename src/{nstencil_half_multi_2d_newton.cpp => nstencil_half_multi_2d.cpp} (89%) create mode 100644 src/nstencil_half_multi_2d.h delete mode 100644 src/nstencil_half_multi_2d_newtoff.cpp delete mode 100644 src/nstencil_half_multi_2d_newtoff.h delete mode 100644 src/nstencil_half_multi_2d_newton_tri.h rename src/{nstencil_half_multi_2d_newton_tri.cpp => nstencil_half_multi_2d_tri.cpp} (88%) create mode 100644 src/nstencil_half_multi_2d_tri.h rename src/{nstencil_half_multi_3d_newton.cpp => nstencil_half_multi_3d.cpp} (90%) create mode 100644 src/nstencil_half_multi_3d.h delete mode 100644 src/nstencil_half_multi_3d_newtoff.cpp delete mode 100644 src/nstencil_half_multi_3d_newtoff.h delete mode 100644 src/nstencil_half_multi_3d_newton_tri.h rename src/{nstencil_half_multi_3d_newton_tri.cpp => nstencil_half_multi_3d_tri.cpp} (89%) create mode 100644 src/nstencil_half_multi_3d_tri.h diff --git a/src/neighbor.cpp b/src/neighbor.cpp index d4a2727662..2b4911958f 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1660,9 +1660,15 @@ int Neighbor::choose_stencil(NeighRequest *rq) else if (rq->newton == 1) newtflag = 1; else if (rq->newton == 2) newtflag = 0; - //printf("STENCIL RQ FLAGS: hff %d %d n %d g %d s %d newtflag %d\n", + // request a full stencil if building full neighbor list or newton is off + + int fullflag = 0; + if (rq->full) fullflag = 1; + if (!newtflag) fullflag = 1; + + //printf("STENCIL RQ FLAGS: hff %d %d n %d g %d s %d newtflag %d fullflag %d\n", // rq->half,rq->full,rq->newton,rq->ghost,rq->ssa, - // newtflag); + // newtflag, fullflag); // use request and system settings to match exactly one NStencil class mask // checks are bitwise using NeighConst bit masks @@ -1672,24 +1678,15 @@ int Neighbor::choose_stencil(NeighRequest *rq) for (int i = 0; i < nsclass; i++) { mask = stencilmasks[i]; - //printf("III %d: half %d full %d newton %d newtoff %d ghost %d ssa %d\n", - // i,mask & NS_HALF,mask & NS_FULL,mask & NS_NEWTON, - // mask & NS_NEWTOFF,mask & NS_GHOST,mask & NS_SSA); + //printf("III %d: half %d full %d ghost %d ssa %d\n", + // i,mask & NS_HALF,mask & NS_FULL,mask & NS_GHOST,mask & NS_SSA); // exactly one of half or full is set and must match - if (rq->half) { - if (!(mask & NS_HALF)) continue; - } else if (rq->full) { + if (fullflag) { if (!(mask & NS_FULL)) continue; - } - - // newtflag is on or off and must match - - if (newtflag) { - if (!(mask & NS_NEWTON)) continue; - } else if (!newtflag) { - if (!(mask & NS_NEWTOFF)) continue; + } else { + if (!(mask & NS_HALF)) continue; } // require match of these request flags and mask bits diff --git a/src/neighbor.h b/src/neighbor.h index 0012cb29fa..b1cc95f5e7 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -248,13 +248,11 @@ namespace NeighConst { static const int NS_FULL = 1<<3; static const int NS_2D = 1<<4; static const int NS_3D = 1<<5; - static const int NS_NEWTON = 1<<6; - static const int NS_NEWTOFF = 1<<7; - static const int NS_ORTHO = 1<<8; - static const int NS_TRI = 1<<9; - static const int NS_GHOST = 1<<10; - static const int NS_SSA = 1<<11; - static const int NS_MULTI2 = 1<<12; + static const int NS_ORTHO = 1<<6; + static const int NS_TRI = 1<<7; + static const int NS_GHOST = 1<<8; + static const int NS_SSA = 1<<9; + static const int NS_MULTI2 = 1<<10; static const int NP_NSQ = 1<<0; static const int NP_BIN = 1<<1; diff --git a/src/nstencil_full_bin_2d.h b/src/nstencil_full_bin_2d.h index d85063596f..0d97cc2634 100644 --- a/src/nstencil_full_bin_2d.h +++ b/src/nstencil_full_bin_2d.h @@ -15,8 +15,7 @@ NStencilStyle(full/bin/2d, NStencilFullBin2d, - NS_FULL | NS_BIN | NS_2D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_BIN | NS_2D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_bin_3d.h b/src/nstencil_full_bin_3d.h index facddd8ead..47f84aebcc 100644 --- a/src/nstencil_full_bin_3d.h +++ b/src/nstencil_full_bin_3d.h @@ -15,8 +15,7 @@ NStencilStyle(full/bin/3d, NStencilFullBin3d, - NS_FULL | NS_BIN | NS_3D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_BIN | NS_3D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_ghost_bin_2d.h b/src/nstencil_full_ghost_bin_2d.h index 531c7d2eb1..db870f9c04 100644 --- a/src/nstencil_full_ghost_bin_2d.h +++ b/src/nstencil_full_ghost_bin_2d.h @@ -15,8 +15,7 @@ NStencilStyle(full/ghost/bin/2d, NStencilFullGhostBin2d, - NS_FULL | NS_GHOST | NS_BIN | NS_2D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_GHOST | NS_BIN | NS_2D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_ghost_bin_3d.h b/src/nstencil_full_ghost_bin_3d.h index ed4ca6c4d6..d99be6d869 100644 --- a/src/nstencil_full_ghost_bin_3d.h +++ b/src/nstencil_full_ghost_bin_3d.h @@ -15,8 +15,7 @@ NStencilStyle(full/ghost/bin/3d, NStencilFullGhostBin3d, - NS_FULL | NS_GHOST | NS_BIN | NS_3D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_GHOST | NS_BIN | NS_3D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_multi2_3d.h b/src/nstencil_full_multi2_3d.h index b9b835fd24..48bdfd2611 100644 --- a/src/nstencil_full_multi2_3d.h +++ b/src/nstencil_full_multi2_3d.h @@ -14,9 +14,7 @@ #ifdef NSTENCIL_CLASS NStencilStyle(full/multi/tiered/3d, - NStencilFullMultiTiered3d, - NS_FULL | NS_Multi_Tiered | NS_3D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NStencilFullMultiTiered3d, NS_FULL | NS_Multi_Tiered | NS_3D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_multi_2d.h b/src/nstencil_full_multi_2d.h index f78eecc55f..2c28bb56bf 100644 --- a/src/nstencil_full_multi_2d.h +++ b/src/nstencil_full_multi_2d.h @@ -15,8 +15,7 @@ NStencilStyle(full/multi/2d, NStencilFullMulti2d, - NS_FULL | NS_MULTI | NS_2D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_MULTI | NS_2D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_multi_3d.h b/src/nstencil_full_multi_3d.h index 9e3696f5d2..b2edfd8b0d 100644 --- a/src/nstencil_full_multi_3d.h +++ b/src/nstencil_full_multi_3d.h @@ -15,8 +15,7 @@ NStencilStyle(full/multi/3d, NStencilFullMulti3d, - NS_FULL | NS_MULTI | NS_3D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_MULTI | NS_3D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_half_bin_2d_newton.cpp b/src/nstencil_half_bin_2d.cpp similarity index 87% rename from src/nstencil_half_bin_2d_newton.cpp rename to src/nstencil_half_bin_2d.cpp index 8fdc8f1aa9..fc7b552118 100644 --- a/src/nstencil_half_bin_2d_newton.cpp +++ b/src/nstencil_half_bin_2d.cpp @@ -11,19 +11,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_2d_newton.h" +#include "nstencil_half_bin_2d.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin2dNewton::NStencilHalfBin2dNewton(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfBin2d::NStencilHalfBin2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBin2dNewton::create() +void NStencilHalfBin2d::create() { int i,j; diff --git a/src/nstencil_half_bin_3d_newton.h b/src/nstencil_half_bin_2d.h similarity index 69% rename from src/nstencil_half_bin_3d_newton.h rename to src/nstencil_half_bin_2d.h index 96f19adae1..29a8868221 100644 --- a/src/nstencil_half_bin_3d_newton.h +++ b/src/nstencil_half_bin_2d.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bin/3d/newton, - NStencilHalfBin3dNewton, - NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_ORTHO) +NStencilStyle(half/bin/2d, + NStencilHalfBin2d, + NS_HALF | NS_BIN | NS_2D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_H -#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_BIN_2D_H +#define LMP_NSTENCIL_HALF_BIN_2D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfBin3dNewton : public NStencil { +class NStencilHalfBin2d : public NStencil { public: - NStencilHalfBin3dNewton(class LAMMPS *); - ~NStencilHalfBin3dNewton() {} + NStencilHalfBin2d(class LAMMPS *); + ~NStencilHalfBin2d() {} void create(); }; diff --git a/src/nstencil_half_bin_2d_newtoff.cpp b/src/nstencil_half_bin_2d_newtoff.cpp deleted file mode 100644 index f3a6c5d08b..0000000000 --- a/src/nstencil_half_bin_2d_newtoff.cpp +++ /dev/null @@ -1,37 +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 "nstencil_half_bin_2d_newtoff.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 deleted file mode 100644 index 7a350df1bc..0000000000 --- a/src/nstencil_half_bin_2d_newtoff.h +++ /dev/null @@ -1,43 +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. -------------------------------------------------------------------------- */ - -#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_tri.h b/src/nstencil_half_bin_2d_newton_tri.h deleted file mode 100644 index b9926608d7..0000000000 --- a/src/nstencil_half_bin_2d_newton_tri.h +++ /dev/null @@ -1,43 +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. -------------------------------------------------------------------------- */ - -#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_2d_newton_tri.cpp b/src/nstencil_half_bin_2d_tri.cpp similarity index 87% rename from src/nstencil_half_bin_2d_newton_tri.cpp rename to src/nstencil_half_bin_2d_tri.cpp index 30d064fb29..0ad5456d62 100644 --- a/src/nstencil_half_bin_2d_newton_tri.cpp +++ b/src/nstencil_half_bin_2d_tri.cpp @@ -11,20 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_2d_newton_tri.h" +#include "nstencil_half_bin_2d_tri.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin2dNewtonTri::NStencilHalfBin2dNewtonTri(LAMMPS *lmp) : +NStencilHalfBin2dTri::NStencilHalfBin2dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBin2dNewtonTri::create() +void NStencilHalfBin2dTri::create() { int i,j; diff --git a/src/nstencil_half_bin_2d_newton.h b/src/nstencil_half_bin_2d_tri.h similarity index 69% rename from src/nstencil_half_bin_2d_newton.h rename to src/nstencil_half_bin_2d_tri.h index 64bbfc5fe4..4dba9151ba 100644 --- a/src/nstencil_half_bin_2d_newton.h +++ b/src/nstencil_half_bin_2d_tri.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bin/2d/newton, - NStencilHalfBin2dNewton, - NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_ORTHO) +NStencilStyle(half/bin/2d/tri, + NStencilHalfBin2dTri, + NS_HALF | NS_BIN | NS_2D | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_H -#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_BIN_2D_TRI_H +#define LMP_NSTENCIL_HALF_BIN_2D_TRI_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfBin2dNewton : public NStencil { +class NStencilHalfBin2dTri : public NStencil { public: - NStencilHalfBin2dNewton(class LAMMPS *); - ~NStencilHalfBin2dNewton() {} + NStencilHalfBin2dTri(class LAMMPS *); + ~NStencilHalfBin2dTri() {} void create(); }; diff --git a/src/nstencil_half_bin_3d_newton.cpp b/src/nstencil_half_bin_3d.cpp similarity index 88% rename from src/nstencil_half_bin_3d_newton.cpp rename to src/nstencil_half_bin_3d.cpp index 998ed28afe..43dcd2b648 100644 --- a/src/nstencil_half_bin_3d_newton.cpp +++ b/src/nstencil_half_bin_3d.cpp @@ -11,19 +11,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_3d_newton.h" +#include "nstencil_half_bin_3d.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin3dNewton::NStencilHalfBin3dNewton(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfBin3d::NStencilHalfBin3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBin3dNewton::create() +void NStencilHalfBin3d::create() { int i,j,k; diff --git a/src/nstencil_half_multi_2d_newton.h b/src/nstencil_half_bin_3d.h similarity index 68% rename from src/nstencil_half_multi_2d_newton.h rename to src/nstencil_half_bin_3d.h index 9ecac4c696..729dcf9c91 100644 --- a/src/nstencil_half_multi_2d_newton.h +++ b/src/nstencil_half_bin_3d.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi/2d/newton, - NStencilHalfMulti2dNewton, - NS_HALF | NS_MULTI | NS_2D | NS_NEWTON | NS_ORTHO) +NStencilStyle(half/bin/3d, + NStencilHalfBin3d, + NS_HALF | NS_BIN | NS_3D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_H -#define LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_BIN_3D_H +#define LMP_NSTENCIL_HALF_BIN_3D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti2dNewton : public NStencil { +class NStencilHalfBin3d : public NStencil { public: - NStencilHalfMulti2dNewton(class LAMMPS *); - ~NStencilHalfMulti2dNewton() {} + NStencilHalfBin3d(class LAMMPS *); + ~NStencilHalfBin3d() {} void create(); }; diff --git a/src/nstencil_half_bin_3d_newtoff.cpp b/src/nstencil_half_bin_3d_newtoff.cpp deleted file mode 100644 index e44a93d47d..0000000000 --- a/src/nstencil_half_bin_3d_newtoff.cpp +++ /dev/null @@ -1,38 +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 "nstencil_half_bin_3d_newtoff.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 deleted file mode 100644 index d1eac666cc..0000000000 --- a/src/nstencil_half_bin_3d_newtoff.h +++ /dev/null @@ -1,43 +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. -------------------------------------------------------------------------- */ - -#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_tri.h b/src/nstencil_half_bin_3d_newton_tri.h deleted file mode 100644 index 8c265acb46..0000000000 --- a/src/nstencil_half_bin_3d_newton_tri.h +++ /dev/null @@ -1,43 +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. -------------------------------------------------------------------------- */ - -#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_bin_3d_newton_tri.cpp b/src/nstencil_half_bin_3d_tri.cpp similarity index 88% rename from src/nstencil_half_bin_3d_newton_tri.cpp rename to src/nstencil_half_bin_3d_tri.cpp index 2aae44ceaf..ca016d956a 100644 --- a/src/nstencil_half_bin_3d_newton_tri.cpp +++ b/src/nstencil_half_bin_3d_tri.cpp @@ -11,20 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_3d_newton_tri.h" +#include "nstencil_half_bin_3d_tri.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin3dNewtonTri::NStencilHalfBin3dNewtonTri(LAMMPS *lmp) : +NStencilHalfBin3dTri::NStencilHalfBin3dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBin3dNewtonTri::create() +void NStencilHalfBin3dTri::create() { int i,j,k; diff --git a/src/nstencil_half_multi_3d_newton.h b/src/nstencil_half_bin_3d_tri.h similarity index 68% rename from src/nstencil_half_multi_3d_newton.h rename to src/nstencil_half_bin_3d_tri.h index bbdc7752c6..33183cd318 100644 --- a/src/nstencil_half_multi_3d_newton.h +++ b/src/nstencil_half_bin_3d_tri.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi/3d/newton, - NStencilHalfMulti3dNewton, - NS_HALF | NS_MULTI | NS_3D | NS_NEWTON | NS_ORTHO) +NStencilStyle(half/bin/3d/tri, + NStencilHalfBin3dTri, + NS_HALF | NS_BIN | NS_3D | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_H -#define LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_BIN_3D_TRI_H +#define LMP_NSTENCIL_HALF_BIN_3D_TRI_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti3dNewton : public NStencil { +class NStencilHalfBin3dTri : public NStencil { public: - NStencilHalfMulti3dNewton(class LAMMPS *); - ~NStencilHalfMulti3dNewton() {} + NStencilHalfBin3dTri(class LAMMPS *); + ~NStencilHalfBin3dTri() {} void create(); }; diff --git a/src/nstencil_half_ghost_bin_2d_newtoff.cpp b/src/nstencil_half_ghost_bin_2d_newtoff.cpp deleted file mode 100644 index 6f9a7585fe..0000000000 --- a/src/nstencil_half_ghost_bin_2d_newtoff.cpp +++ /dev/null @@ -1,44 +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 "nstencil_half_ghost_bin_2d_newtoff.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 deleted file mode 100644 index 3286810c1c..0000000000 --- a/src/nstencil_half_ghost_bin_2d_newtoff.h +++ /dev/null @@ -1,44 +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. -------------------------------------------------------------------------- */ - -#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 deleted file mode 100644 index 6492fe4a4e..0000000000 --- a/src/nstencil_half_ghost_bin_3d_newtoff.cpp +++ /dev/null @@ -1,45 +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 "nstencil_half_ghost_bin_3d_newtoff.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 deleted file mode 100644 index ee58c29342..0000000000 --- a/src/nstencil_half_ghost_bin_3d_newtoff.h +++ /dev/null @@ -1,44 +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. -------------------------------------------------------------------------- */ - -#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_multi2_2d_newton.cpp b/src/nstencil_half_multi2_2d_newton.cpp deleted file mode 100644 index 66158202bf..0000000000 --- a/src/nstencil_half_multi2_2d_newton.cpp +++ /dev/null @@ -1,201 +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 "nstencil_half_bytype_2d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "nbin.h" -#include "memory.h" -#include "atom.h" -#include - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBytype2dNewton::NStencilHalfBytype2dNewton(LAMMPS *lmp) : - NStencil(lmp) -{ - maxstencil_type = NULL; -} - -NStencilHalfBytype2dNewton::~NStencilHalfBytype2dNewton() { - - memory->destroy(nstencil_type); - for (int i = 1; i <= atom->ntypes; i++) { - for (int j = 0; j <= atom->ntypes; j++) { - if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); - } - delete [] stencil_type[i]; - } - delete [] stencil_type; - memory->destroy(maxstencil_type); -} - -/* ---------------------------------------------------------------------- */ - -// KS To superclass -void NStencilHalfBytype2dNewton::copy_bin_info_bytype(int itype) { - - mbinx = nb->mbinx_type[itype]; - mbiny = nb->mbiny_type[itype]; - mbinz = nb->mbinz_type[itype]; - binsizex = nb->binsizex_type[itype]; - binsizey = nb->binsizey_type[itype]; - binsizez = nb->binsizez_type[itype]; - bininvx = nb->bininvx_type[itype]; - bininvy = nb->bininvy_type[itype]; - bininvz = nb->bininvz_type[itype]; -} - -/* ---------------------------------------------------------------------- */ - -// KS To superclass? -int NStencilHalfBytype2dNewton::copy_neigh_info_bytype(int itype) { - - cutneighmaxsq = neighbor->cutneighsq[itype][itype]; - cutneighmax = sqrt(cutneighmaxsq); - cuttypesq = neighbor->cuttypesq; - - // sx,sy,sz = max range of stencil in each dim - // smax = max possible size of entire 2d stencil - // stencil will be empty if cutneighmax = 0.0 - - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - return ((2*sx+1) * (2*sy+1) * (2*sz+1)); -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype2dNewton::create_setup() -{ - - int itype, jtype; - int maxtypes; - int smax; - - // maxstencil_type to superclass? - maxtypes = atom->ntypes; - - if (maxstencil_type == NULL) { - memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "maxstencil_type"); - memory->create(nstencil_type, maxtypes+1, maxtypes+1, "nstencil_type"); - stencil_type = new int**[maxtypes+1](); - for (itype = 1; itype <= maxtypes; ++itype) { - stencil_type[itype] = new int*[maxtypes+1](); - for (jtype = 1; jtype <= maxtypes; ++jtype) { - maxstencil_type[itype][jtype] = 0; - nstencil_type[itype][jtype] = 0; - } - } - } - - // like -> like => use standard Newton stencil at bin - - for (itype = 1; itype <= maxtypes; ++itype) { - copy_bin_info_bytype(itype); - smax = copy_neigh_info_bytype(itype); - if (smax > maxstencil_type[itype][itype]) { - maxstencil_type[itype][itype] = smax; - memory->destroy(stencil_type[itype][itype]); - memory->create(stencil_type[itype][itype], smax, - "NStencilHalfBytypeNewton::create_steup() stencil"); - } - create_newton(itype, itype, cutneighmaxsq); - } - - // Cross types: "Newton on" reached by using Newton off stencil and - // looking one way through hierarchy - // smaller -> larger => use Newton off stencil in larger bin - // larger -> smaller => no nstecil required - // If cut offs are same, use existing type-type stencil - - for (itype = 1; itype <= maxtypes; ++itype) { - for (jtype = 1; jtype <= maxtypes; ++jtype) { - if (itype == jtype) continue; - if (cuttypesq[itype] == cuttypesq[jtype]) { - nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; - stencil_type[itype][jtype] = stencil_type[jtype][jtype]; - } - else if (cuttypesq[itype] < cuttypesq[jtype]) { - copy_bin_info_bytype(jtype); - - cutneighmaxsq = cuttypesq[jtype]; - cutneighmax = sqrt(cutneighmaxsq); - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - smax = (2*sx+1) * (2*sy+1) * (2*sz+1); - if (smax > maxstencil_type[itype][jtype]) { - maxstencil_type[itype][jtype] = smax; - memory->destroy(stencil_type[itype][jtype]); - memory->create(stencil_type[itype][jtype], smax, "stencil_type[]"); - } - create_newtoff(itype, jtype, cuttypesq[jtype]); - } - } - } - -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype2dNewton::create_newton(int itype, int jtype, double cutsq) { - - int i, j, ns; - - ns = 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) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; - } - nstencil_type[itype][jtype] = ns; -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype2dNewton::create_newtoff(int itype, int jtype, double cutsq) { - - int i, j, ns; - - ns = 0; - - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; - - nstencil_type[itype][jtype] = ns; -} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfBytype2dNewton::create() -{ - // KS. Move "creation" here. -} diff --git a/src/nstencil_half_multi2_2d_newton.h b/src/nstencil_half_multi2_2d_newton.h deleted file mode 100644 index 4d33c26a71..0000000000 --- a/src/nstencil_half_multi2_2d_newton.h +++ /dev/null @@ -1,52 +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. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/bytype/2d/newton, - NStencilHalfBytype2dNewton, - NS_HALF | NS_BYTYPE | NS_2D | NS_NEWTON | NS_ORTHO) - -#else - -#ifndef LMP_NSTENCIL_HALF_BYTYPE_2D_NEWTON_H -#define LMP_NSTENCIL_HALF_BYTYPE_2D_NEWTON_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfBytype2dNewton : public NStencil { - public: - NStencilHalfBytype2dNewton(class LAMMPS *); - ~NStencilHalfBytype2dNewton(); - void create_setup(); - void create(); - - private: - int ** maxstencil_type; - - void copy_bin_info_bytype(int); - int copy_neigh_info_bytype(int); - void create_newton(int, int, double); - void create_newtoff(int, int, double); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi2_3d_newton.cpp b/src/nstencil_half_multi2_3d.cpp similarity index 100% rename from src/nstencil_half_multi2_3d_newton.cpp rename to src/nstencil_half_multi2_3d.cpp diff --git a/src/nstencil_half_multi2_3d_newton_tri.h b/src/nstencil_half_multi2_3d.h old mode 100755 new mode 100644 similarity index 82% rename from src/nstencil_half_multi2_3d_newton_tri.h rename to src/nstencil_half_multi2_3d.h index e419161bb5..e39db1c1e1 --- a/src/nstencil_half_multi2_3d_newton_tri.h +++ b/src/nstencil_half_multi2_3d.h @@ -13,14 +13,13 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bytype/3d/newton, - NStencilHalfBytype3dNewton, - NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTON | NS_TRI) +NStencilStyle(half/bytype/3d, + NStencilHalfBytype3dNewton, NS_HALF | NS_BYTYPE | NS_3D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H -#define LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_H +#define LMP_NSTENCIL_HALF_BYTYPE_3D_H #include "nstencil.h" diff --git a/src/nstencil_half_multi2_3d_newtoff.cpp b/src/nstencil_half_multi2_3d_delete_noff.cpp similarity index 100% rename from src/nstencil_half_multi2_3d_newtoff.cpp rename to src/nstencil_half_multi2_3d_delete_noff.cpp diff --git a/src/nstencil_half_multi2_3d_newtoff.h b/src/nstencil_half_multi2_3d_delete_noff.h similarity index 100% rename from src/nstencil_half_multi2_3d_newtoff.h rename to src/nstencil_half_multi2_3d_delete_noff.h diff --git a/src/nstencil_half_multi2_3d_newton_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp similarity index 100% rename from src/nstencil_half_multi2_3d_newton_tri.cpp rename to src/nstencil_half_multi2_3d_tri.cpp diff --git a/src/nstencil_half_multi2_3d_newton.h b/src/nstencil_half_multi2_3d_tri.h old mode 100644 new mode 100755 similarity index 82% rename from src/nstencil_half_multi2_3d_newton.h rename to src/nstencil_half_multi2_3d_tri.h index cbb88fcb1d..5424d73f11 --- a/src/nstencil_half_multi2_3d_newton.h +++ b/src/nstencil_half_multi2_3d_tri.h @@ -13,14 +13,13 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bytype/3d/newton, - NStencilHalfBytype3dNewton, - NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTON | NS_ORTHO) +NStencilStyle(half/bytype/3d, + NStencilHalfBytype3d, NS_HALF | NS_BYTYPE | NS_3D | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H -#define LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_H +#define LMP_NSTENCIL_HALF_BYTYPE_3D_H #include "nstencil.h" diff --git a/src/nstencil_half_multi_2d_newton.cpp b/src/nstencil_half_multi_2d.cpp similarity index 89% rename from src/nstencil_half_multi_2d_newton.cpp rename to src/nstencil_half_multi_2d.cpp index f6f6c488a5..db009030cf 100644 --- a/src/nstencil_half_multi_2d_newton.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_2d_newton.h" +#include "nstencil_half_multi_2d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti2dNewton:: -NStencilHalfMulti2dNewton(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMulti2d:: +NStencilHalfMulti2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti2dNewton::create() +void NStencilHalfMulti2d::create() { int i,j,n; double rsq,typesq; diff --git a/src/nstencil_half_multi_2d.h b/src/nstencil_half_multi_2d.h new file mode 100644 index 0000000000..128d37a2e9 --- /dev/null +++ b/src/nstencil_half_multi_2d.h @@ -0,0 +1,42 @@ +/* -*- 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, + NStencilHalfMulti2d, NS_HALF | NS_MULTI | NS_2D | NS_ORTHO) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_2D_H +#define LMP_NSTENCIL_HALF_MULTI_2D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti2d : public NStencil { + public: + NStencilHalfMulti2d(class LAMMPS *); + ~NStencilHalfMulti2d() {} + 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 deleted file mode 100644 index 63cd3fd524..0000000000 --- a/src/nstencil_half_multi_2d_newtoff.cpp +++ /dev/null @@ -1,51 +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 "nstencil_half_multi_2d_newtoff.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 deleted file mode 100644 index 5603f37beb..0000000000 --- a/src/nstencil_half_multi_2d_newtoff.h +++ /dev/null @@ -1,43 +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. -------------------------------------------------------------------------- */ - -#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_tri.h b/src/nstencil_half_multi_2d_newton_tri.h deleted file mode 100644 index 62d7dfdebf..0000000000 --- a/src/nstencil_half_multi_2d_newton_tri.h +++ /dev/null @@ -1,43 +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. -------------------------------------------------------------------------- */ - -#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_2d_newton_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp similarity index 88% rename from src/nstencil_half_multi_2d_newton_tri.cpp rename to src/nstencil_half_multi_2d_tri.cpp index b44ab36ea0..fef551f3e0 100644 --- a/src/nstencil_half_multi_2d_newton_tri.cpp +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_2d_newton_tri.h" +#include "nstencil_half_multi_2d_tri.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti2dNewtonTri:: -NStencilHalfMulti2dNewtonTri(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMulti2dTri:: +NStencilHalfMulti2dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti2dNewtonTri::create() +void NStencilHalfMulti2dTri::create() { int i,j,n; double rsq,typesq; diff --git a/src/nstencil_half_multi_2d_tri.h b/src/nstencil_half_multi_2d_tri.h new file mode 100644 index 0000000000..776c42e96b --- /dev/null +++ b/src/nstencil_half_multi_2d_tri.h @@ -0,0 +1,42 @@ +/* -*- 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/tri, + NStencilHalfMulti2dTri, NS_HALF | NS_MULTI | NS_2D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_2D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_2D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti2dTri : public NStencil { + public: + NStencilHalfMulti2dTri(class LAMMPS *); + ~NStencilHalfMulti2dTri() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi_3d_newton.cpp b/src/nstencil_half_multi_3d.cpp similarity index 90% rename from src/nstencil_half_multi_3d_newton.cpp rename to src/nstencil_half_multi_3d.cpp index 5b0c7f9f63..ca1c7f2f02 100644 --- a/src/nstencil_half_multi_3d_newton.cpp +++ b/src/nstencil_half_multi_3d.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_3d_newton.h" +#include "nstencil_half_multi_3d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti3dNewton:: -NStencilHalfMulti3dNewton(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMulti3d:: +NStencilHalfMulti3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti3dNewton::create() +void NStencilHalfMulti3d::create() { int i,j,k,n; double rsq,typesq; diff --git a/src/nstencil_half_multi_3d.h b/src/nstencil_half_multi_3d.h new file mode 100644 index 0000000000..51cf9d5c29 --- /dev/null +++ b/src/nstencil_half_multi_3d.h @@ -0,0 +1,42 @@ +/* -*- 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, + NStencilHalfMulti3d, NS_HALF | NS_MULTI | NS_3D | NS_ORTHO) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_3D_H +#define LMP_NSTENCIL_HALF_MULTI_3D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti3d : public NStencil { + public: + NStencilHalfMulti3d(class LAMMPS *); + ~NStencilHalfMulti3d() {} + 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 deleted file mode 100644 index 5a83c4e002..0000000000 --- a/src/nstencil_half_multi_3d_newtoff.cpp +++ /dev/null @@ -1,52 +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 "nstencil_half_multi_3d_newtoff.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 deleted file mode 100644 index 99428deb6a..0000000000 --- a/src/nstencil_half_multi_3d_newtoff.h +++ /dev/null @@ -1,43 +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. -------------------------------------------------------------------------- */ - -#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_tri.h b/src/nstencil_half_multi_3d_newton_tri.h deleted file mode 100644 index f6866489a4..0000000000 --- a/src/nstencil_half_multi_3d_newton_tri.h +++ /dev/null @@ -1,43 +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. -------------------------------------------------------------------------- */ - -#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/nstencil_half_multi_3d_newton_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp similarity index 89% rename from src/nstencil_half_multi_3d_newton_tri.cpp rename to src/nstencil_half_multi_3d_tri.cpp index b25a0d0bdb..2970977a1e 100644 --- a/src/nstencil_half_multi_3d_newton_tri.cpp +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_3d_newton_tri.h" +#include "nstencil_half_multi_3d_tri.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti3dNewtonTri:: -NStencilHalfMulti3dNewtonTri(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMulti3dTri:: +NStencilHalfMulti3dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti3dNewtonTri::create() +void NStencilHalfMulti3dTri::create() { int i,j,k,n; double rsq,typesq; diff --git a/src/nstencil_half_multi_3d_tri.h b/src/nstencil_half_multi_3d_tri.h new file mode 100644 index 0000000000..f33f65cfea --- /dev/null +++ b/src/nstencil_half_multi_3d_tri.h @@ -0,0 +1,42 @@ +/* -*- 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/tri, + NStencilHalfMulti3dTri, NS_HALF | NS_MULTI | NS_3D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_3D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_3D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti3dTri : public NStencil { + public: + NStencilHalfMulti3dTri(class LAMMPS *); + ~NStencilHalfMulti3dTri() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ From dd1cce1da5dfd7da50b55e792e64883871c9cd1e Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 10 Nov 2020 20:03:00 -0700 Subject: [PATCH 08/73] Finish stencil classes --- src/nstencil.cpp | 173 +++++++------ src/nstencil.h | 23 +- src/nstencil_full_multi2_2d.cpp | 97 +++++++ ...elete_noff.h => nstencil_full_multi2_2d.h} | 23 +- src/nstencil_full_multi2_3d.cpp | 203 +++++---------- src/nstencil_full_multi2_3d.h | 22 +- src/nstencil_half_multi2_2d.cpp | 111 ++++++++ src/nstencil_half_multi2_2d.h | 46 ++++ src/nstencil_half_multi2_2d_tri.cpp | 108 ++++++++ src/nstencil_half_multi2_2d_tri.h | 45 ++++ src/nstencil_half_multi2_3d.cpp | 240 ++++++------------ src/nstencil_half_multi2_3d.h | 23 +- src/nstencil_half_multi2_3d_delete_noff.cpp | 198 --------------- src/nstencil_half_multi2_3d_tri.cpp | 150 ++++++----- src/nstencil_half_multi2_3d_tri.h | 24 +- 15 files changed, 779 insertions(+), 707 deletions(-) create mode 100644 src/nstencil_full_multi2_2d.cpp rename src/{nstencil_half_multi2_3d_delete_noff.h => nstencil_full_multi2_2d.h} (58%) create mode 100644 src/nstencil_half_multi2_2d.cpp create mode 100644 src/nstencil_half_multi2_2d.h create mode 100755 src/nstencil_half_multi2_2d_tri.cpp create mode 100755 src/nstencil_half_multi2_2d_tri.h delete mode 100644 src/nstencil_half_multi2_3d_delete_noff.cpp diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 3518b7db55..525369d573 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -31,33 +31,33 @@ using namespace LAMMPS_NS; 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: + for full list or half list with newton off + use a full stencil stencil is all surrounding bins including self regardless of triclinic - for half list with newton on: + for half list with newton on + use a half stencil 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: + use a half stencil 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?) - for multi/tiered: + for multi2: create one stencil for each itype-jtype pairing stencils do not generally follow the same rules for half/full or newton on/off - whole stencils including all surrounding bins are always used except - for same-type stencils with newton on which uses a split stencil - for orthogonal boxes, a split stencil includes bins to the "upper right" of central bin - for triclinic, a split stencil includes bins in the z (3D) or y (2D) plane of self and above + full stencils including all surrounding bins are always used except + for same-type stencils with newton on which uses a half stencil + for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin + for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above cutoff is not cutneighmaxsq, but max cutoff for that atom type no versions that allow ghost on (any need for it?) ------------------------------------------------------------------------- */ @@ -74,7 +74,7 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) stencil_multi = nullptr; distsq_multi = nullptr; - stencil_split = nullptr; + stencil_half = nullptr; stencil_skip = nullptr; stencil_bin_type = nullptr; stencil_cut = nullptr; @@ -101,31 +101,31 @@ NStencil::~NStencil() delete [] distsq_multi; } - if (stencil_multi_tiered) { + if (stencil_multi2) { int n = atom->ntypes; - memory->destroy(nstencil_multi_tiered); + memory->destroy(nstencil_multi2); for (int i = 1; i <= n; i++) { for (int j = 0; j <= n; j++) { if (! stencil_skip[i][j]) - memory->destroy(stencil_multi_tiered[i][j]); + memory->destroy(stencil_multi2[i][j]); } - delete [] stencil_multi_tiered[i]; + delete [] stencil_multi2[i]; } - delete [] stencil_multi_tiered; - memory->destroy(maxstencil_multi_tiered); - memory->destroy(stencil_split); + delete [] stencil_multi2; + memory->destroy(maxstencil_multi2); + memory->destroy(stencil_half); memory->destroy(stencil_skip); memory->destroy(stencil_bin_type); memory->destroy(stencil_cut); - memory->destroy(sx_multi_tiered); - memory->destroy(sy_multi_tiered); - memory->destroy(sz_multi_tiered); + memory->destroy(sx_multi2); + memory->destroy(sy_multi2); + memory->destroy(sz_multi2); - memory->destroy(binsizex_multi_tiered); - memory->destroy(binsizey_multi_tiered); - memory->destroy(binsizez_multi_tiered); + memory->destroy(binsizex_multi2); + memory->destroy(binsizey_multi2); + memory->destroy(binsizez_multi2); } } @@ -179,17 +179,17 @@ void NStencil::copy_bin_info() copy needed info for a given type from NBin class to this stencil class ------------------------------------------------------------------------- */ -void NStencil::copy_bin_info_multi_tiered(int type) +void NStencil::copy_bin_info_multi2(int type) { - mbinx = nb->mbinx_tiered[type]; - mbiny = nb->mbiny_tiered[type]; - mbinz = nb->mbinz_tiered[type]; - binsizex = nb->binsizex_tiered[type]; - binsizey = nb->binsizey_tiered[type]; - binsizez = nb->binsizez_tiered[type]; - bininvx = nb->bininvx_tiered[type]; - bininvy = nb->bininvy_tiered[type]; - bininvz = nb->bininvz_tiered[type]; + mbinx = nb->mbinx2[type]; + mbiny = nb->mbiny2[type]; + mbinz = nb->mbinz2[type]; + binsizex = nb->binsizex2[type]; + binsizey = nb->binsizey2[type]; + binsizez = nb->binsizez2[type]; + bininvx = nb->bininvx2[type]; + bininvy = nb->bininvy2[type]; + bininvz = nb->bininvz2[type]; } /* ---------------------------------------------------------------------- @@ -200,7 +200,7 @@ void NStencil::copy_bin_info_multi_tiered(int type) void NStencil::create_setup() { - if (neighstyle != Neighbor::MULTI_TIERED){ + if (neighstyle != Neighbor::MULTI2){ if (nb) copy_bin_info(); last_stencil = update->ntimestep; @@ -263,34 +263,53 @@ void NStencil::create_setup() int n = atom->ntypes; // Allocate arrays to store stencil information - memory->create(stencil_split, n, n, - "neighstencil:stencil_split");" - memory->create(stencil_skip, n, n, - "neighstencil:stencil_skip");" - memory->create(stencil_bin_type, n, n, - "neighstencil:stencil_bin_type");" - memory->create(stencil_cut, n, n, - "neighstencil:stencil_cut");" + memory->create(stencil_half, n+1, n+1, + "neighstencil:stencil_half"); + memory->create(stencil_skip, n+1, n+1, + "neighstencil:stencil_skip"); + memory->create(stencil_bin_type, n+1, n+1, + "neighstencil:stencil_bin_type"); + memory->create(stencil_cut, n+1, n+1, + "neighstencil:stencil_cut"); - memory->create(sx_multi_tiered, n, n, - "neighstencil:sx_multi_tiered");" - memory->create(sy_multi_tiered, n, n, - "neighstencil:sy_multi_tiered");" - memory->create(sz_multi_tiered, n, n, - "neighstencil:sz_multi_tiered");" + memory->create(sx_multi2, n+1, n+1, "neighstencil:sx_multi2"); + memory->create(sy_multi2, n+1, n+1, "neighstencil:sy_multi2"); + memory->create(sz_multi2, n+1, n+1, "neighstencil:sz_multi2"); - memory->create(binsizex_multi_tiered, n, n, - "neighstencil:binsizex_multi_tiered");" - memory->create(binsizey_multi_tiered, n, n, - "neighstencil:binsizey_multi_tiered");" - memory->create(binsizez_multi_tiered, n, n, - "neighstencil:binsizez_multi_tiered");" - + memory->create(binsizex_multi2, n+1, n+1, + "neighstencil:binsizex_multi2"); + memory->create(binsizey_multi2, n+1, n+1, + "neighstencil:binsizey_multi2"); + memory->create(binsizez_multi2, n+1, n+1, + "neighstencil:binsizez_multi2"); + + // Skip all stencils by default, initialize smax + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + stencil_skip[i][j] = 1; + maxstencil_multi2[i][j] = 0; + } + } + // Determine which stencils need to be built set_stencil_properties(); - for (i = 1; i <= n; ++i) { - for (j = 1; j <= n; ++j) { + // Allocate arrays to store stencils + + if (!maxstencil_multi2) { + memory->create(maxstencil_multi2, n+1, n+1, "neighstencil::stencil_multi2"); + memory->create(nstencil_multi2, n+1, n+1, "neighstencil::nstencil_multi2"); + stencil_multi2 = new int**[n+1](); + for (i = 1; i <= n; ++i) { + stencil_multi2[i] = new int*[n+1](); + for (j = 1; j <= n; ++j) { + maxstencil_multi2[i][j] = 0; + } + } + } + + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { // Skip creation of unused stencils if (stencil_skip[i][j]) continue; @@ -299,9 +318,9 @@ void NStencil::create_setup() bin_type = stencil_bin_type[i][j]; copy_bin_info_bytype(bin_type); - binsizex_multi_tiered[i][j] = binsizex; - binsizey_multi_tiered[i][j] = binsizey; - binsizez_multi_tiered[i][j] = binsizez; + binsizex_multi2[i][j] = binsizex; + binsizey_multi2[i][j] = binsizey; + binsizez_multi2[i][j] = binsizez; stencil_range = stencil_cut[i][j]; @@ -312,17 +331,17 @@ void NStencil::create_setup() sz = static_cast (stencil_range*bininvz); if (sz*binsizez < stencil_range) sz++; - sx_multi_tiered[i][j] = sx; - sy_multi_tiered[i][j] = sy; - sz_multi_tiered[i][j] = sz; + sx_multi2[i][j] = sx; + sy_multi2[i][j] = sy; + sz_multi2[i][j] = sz; smax = ((2*sx+1) * (2*sy+1) * (2*sz+1)); - if (smax > maxstencil_multi_tiered[i][j]) { - maxstencil_multi_tiered[i][j] = smax; - memory->destroy(stencil_multi_tiered[i][j]); - memory->create(stencil_multi_tiered[i][j], smax, - "neighstencil::stencil_multi_tiered"); + if (smax > maxstencil_multi2[i][j]) { + maxstencil_multi2[i][j] = smax; + memory->destroy(stencil_multi2[i][j]); + memory->create(stencil_multi2[i][j], smax, + "neighstencil::stencil_multi2"); } } } @@ -363,10 +382,18 @@ double NStencil::memory_usage() } else if (neighstyle == Neighbor::MULTI) { bytes += atom->ntypes*maxstencil_multi * sizeof(int); bytes += atom->ntypes*maxstencil_multi * sizeof(double); - } else if (neighstyle == Neighbor::MULTI_TIERED) { - bytes += atom->ntypes*maxstencil_multi * sizeof(int); - bytes += atom->ntypes*maxstencil_multi * sizeof(int); - bytes += atom->ntypes*maxstencil_multi * sizeof(double); + } else if (neighstyle == Neighbor::MULTI2) { + int n = atom->ntypes; + for (i = 1; i <= n; ++i) { + for (j = 1; j <= n; ++j) { + bytes += maxstencil_multi2[i][j] * sizeof(int); + bytes += maxstencil_multi2[i][j] * sizeof(int); + bytes += maxstencil_multi2[i][j] * sizeof(double); + } + } + bytes += 2 * n * n * sizeof(bool); + bytes += 6 * n * n * sizeof(int); + bytes += 4 * n * n * sizeof(double); } return bytes; } diff --git a/src/nstencil.h b/src/nstencil.h index 58c39ee13c..7c6a04a56a 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -29,14 +29,17 @@ class NStencil : protected Pointers { 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 - int ** nstencil_multi_tiered; // # bins bins in each itype-jtype tiered multi stencil - int *** stencil_multi_tiered; // list of bin offsets in each tiered multi stencil - int ** maxstencil_type; // max double **distsq_multi; // sq distances to bins in each stencil + int ** nstencil_multi2; // # bins bins in each itype-jtype multi2 stencil + int *** stencil_multi2; // list of bin offsets in each multi2 stencil + int ** maxstencil_multi2; // max stencil size for each multi2 stencil + + ^do i need a multi 2 analog to distsq_multi? + int sx,sy,sz; // extent of stencil in each dim - int **sx_multi_tiered; // analogs for multi tiered - int **sy_multi_tiered; - int **sz_multi_tiered; + int **sx_multi2; // analogs for multi tiered + int **sy_multi2; + int **sz_multi2; double cutoff_custom; // cutoff set by requestor @@ -75,9 +78,9 @@ class NStencil : protected Pointers { // analogs for multi-tiered - double **binsizex_multi_tiered; - double **binsizey_multi_tiered; - double **binsizez_multi_tiered; + double **binsizex_multi2; + double **binsizey_multi2; + double **binsizez_multi2; // data common to all NStencil variants @@ -94,7 +97,7 @@ class NStencil : protected Pointers { // methods for multi/tiered NStencil - void copy_bin_info_multi_tiered(int); // copy mult/tiered info from NBin class + void copy_bin_info_multi2(int); // copy mult/tiered info from NBin class void set_stencil_properties(); // determine which stencils to build and how }; diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp new file mode 100644 index 0000000000..f62cddb0b5 --- /dev/null +++ b/src/nstencil_full_multi2_2d.cpp @@ -0,0 +1,97 @@ +/* ---------------------------------------------------------------------- + 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_multi2_2d.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilFullMulti22d::NStencilFullMulti22d(LAMMPS *lmp) : NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilFullMulti22d::set_stencil_properties() +{ + int n = atom->ntypes; + int i, j; + + // like -> like => use half stencil + for (i = 1; i <= n; i++) { + stencil_half[i][i] = 0; + stencil_skip[i][i] = 0; + stencil_bin_type[i][i] = i; + stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + } + + // smaller -> larger => use existing newtoff stencil in larger bin + // larger -> smaller => use multi-like stencil for small-large in smaller bin + // If types are same cutoff, use existing like-like stencil. + + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + if(i == j) continue; + + stencil_half[i][j] = 0; + stencil_skip[i][j] = 0; + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + + if(cuttypesq[i] <= cuttypesq[j]){ + stencil_bin_type[i][j] = i; + } else { + stencil_bin_type[i][j] = j; + } + } + } +} + +/* ---------------------------------------------------------------------- + create stencils based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilFullMulti22d::create() +{ + int itype, jtype, i, j, k, ns; + int n = atom->ntypes; + double cutsq; + + + for (itype = 1; itype <= n; itype++) { + for (jtype = 1; jtype <= n; jtype++) { + if (stencil_skip[itype][jtype]) continue; + + ns = 0; + + sx = sx_multi2[itype][jtype]; + sy = sy_multi2[itype][jtype]; + + mbinx = mbinx_multi2[itype][jtype]; + mbiny = mbiny_multi2[itype][jtype]; + + cutsq = stencil_cut[itype][jtype]; + + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,0) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + + nstencil_multi2[itype][jtype] = ns; + } + } +} diff --git a/src/nstencil_half_multi2_3d_delete_noff.h b/src/nstencil_full_multi2_2d.h similarity index 58% rename from src/nstencil_half_multi2_3d_delete_noff.h rename to src/nstencil_full_multi2_2d.h index bf83a31e9a..1dfc5ae4d6 100644 --- a/src/nstencil_half_multi2_3d_delete_noff.h +++ b/src/nstencil_full_multi2_2d.h @@ -13,32 +13,27 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bytype/3d/newtoff, - NStencilHalfBytype3dNewtoff, - NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTOFF | NS_ORTHO | NS_TRI) +NStencilStyle(full/multi2/2d, + NStencilFullMulti22d, NS_FULL | NS_Multi2 | NS_2D | NS_ORTHO | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTOFF_H +#ifndef LMP_NSTENCIL_FULL_MULTI2_2D_H +#define LMP_NSTENCIL_FULL_MULTI2_2D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfBytype3dNewtoff : public NStencil { +class NStencilFullMulti22d : public NStencil { public: - NStencilHalfBytype3dNewtoff(class LAMMPS *); - ~NStencilHalfBytype3dNewtoff(); - void create_setup(); + NStencilFullMulti22d(class LAMMPS *); + ~NStencilFullMulti22d(); void create(); - private: - int ** maxstencil_type; + protected: + void set_stencil_properties(); - void copy_bin_info_bytype(int); - int copy_neigh_info_bytype(int); - void create_newtoff(int, int, double); }; } diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 099e2adeb8..77ae62738c 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_full_bytype_3d.h" +#include "nstencil_full_multi2_3d.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,164 +23,79 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilFullBytype3d::NStencilFullBytype3d(LAMMPS *lmp) : - NStencil(lmp) +NStencilFullMulti23d::NStencilFullMulti23d(LAMMPS *lmp) : NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilFullMulti23d::set_stencil_properties() { - maxstencil_type = NULL; -} - -/* ---------------------------------------------------------------------- */ - -NStencilFullBytype3d::~NStencilFullBytype3d() { - - if (maxstencil_type) { - memory->destroy(nstencil_type); - for (int i = 1; i <= atom->ntypes; i++) { - for (int j = 0; j <= atom->ntypes; j++) { - if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); - } - delete [] stencil_type[i]; - } - delete [] stencil_type; - memory->destroy(maxstencil_type); - } -} - - -/* ---------------------------------------------------------------------- */ -INCORPORTE INTO CREATE THEN DELETE, NOTE NAME OF CUTNEIGHMAX ETC -int NStencilFullBytype3d::copy_neigh_info_bytype(int itype) { - - cutneighmaxsq = neighbor->cutneighsq[itype][itype]; - cutneighmax = sqrt(cutneighmaxsq); - cuttypesq = neighbor->cuttypesq; - - // 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 (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - return ((2*sx+1) * (2*sy+1) * (2*sz+1)); -} - -/* ---------------------------------------------------------------------- */ - -void NStencilFullBytype3d::create_setup() -{ - - int itype, jtype; - int maxtypes; - int smax; - - maxtypes = atom->ntypes; - - if (maxstencil_type == NULL) { - memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "BAD A"); - memory->create(nstencil_type, maxtypes+1, maxtypes+1, "BAD B"); - stencil_type = new int**[maxtypes+1](); - for (itype = 1; itype <= maxtypes; ++itype) { - stencil_type[itype] = new int*[maxtypes+1](); - for (jtype = 1; jtype <= maxtypes; ++jtype) { - maxstencil_type[itype][jtype] = 0; - } - } - } MOVE TO PARENT CLASS - - // like -> like => use standard newtoff stencil at bin - - for (itype = 1; itype <= maxtypes; ++itype) { - copy_bin_info_bytype(itype); - smax = copy_neigh_info_bytype(itype); uses cutneighsq[itype][itype] to create s's - if (smax > maxstencil_type[itype][itype]) { - maxstencil_type[itype][itype] = smax; - memory->destroy(stencil_type[itype][itype]); - memory->create(stencil_type[itype][itype], smax, - "NStencilFullBytype::create_steup() stencil"); - } - create_newtoff(itype, itype, cutneighmaxsq); + int n = atom->ntypes; + int i, j; + + // like -> like => use half stencil + for (i = 1; i <= n; i++) { + stencil_half[i][i] = 0; + stencil_skip[i][i] = 0; + stencil_bin_type[i][i] = i; + stencil_cut[i][i] = sqrt(cutneighsq[i][i]); } // smaller -> larger => use existing newtoff stencil in larger bin // larger -> smaller => use multi-like stencil for small-large in smaller bin // If types are same cutoff, use existing like-like stencil. - for (itype = 1; itype <= maxtypes; ++itype) { - for (jtype = 1; jtype <= maxtypes; ++jtype) { - if (itype == jtype) continue; - if (cuttypesq[itype] <= cuttypesq[jtype]) { This does work to say which prticle is smller - // Potential destroy/create problem? - nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; - stencil_type[itype][jtype] = stencil_type[jtype][jtype]; - } - else { - copy_bin_info_bytype(jtype); - // smax = copy_neigh_info_bytype(jtype); + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + if(i == j) continue; - cutneighmaxsq = cuttypesq[jtype]; Does it need to be this big? Can't I use cutneighsq[i][j]? - cutneighmax = sqrt(cutneighmaxsq); - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - smax = (2*sx+1) * (2*sy+1) * (2*sz+1); - if (smax > maxstencil_type[itype][jtype]) { - maxstencil_type[itype][jtype] = smax; - memory->destroy(stencil_type[itype][jtype]); - memory->create(stencil_type[itype][jtype], smax, "Bad C"); - } - create_newtoff(itype, jtype, cuttypesq[jtype]); + stencil_half[i][j] = 0; + stencil_skip[i][j] = 0; + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + + if(cuttypesq[i] <= cuttypesq[j]){ + stencil_bin_type[i][j] = i; + } else { + stencil_bin_type[i][j] = j; } } } - - //for (itype = 1; itype <= maxtypes; itype++) { - // for (jtype = 1; jtype <= maxtypes; jtype++) { - // printf("i j n %d %d %d\n", itype, jtype, nstencil_type[itype][jtype]); - // printf("i j n %d %d %d\n", itype, jtype, maxstencil_type[itype][jtype]); - // } - // } - -} - -/* ---------------------------------------------------------------------- */ - -void NStencilFullBytype3d::create_newtoff(int itype, int jtype, double cutsq) { - - int i, j, k, ns; - - ns = 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) < cutsq) - stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - - nstencil_type[itype][jtype] = ns; } /* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff + create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilFullBytype3d::create() +void NStencilFullMulti23d::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; + int itype, jtype, i, j, k, ns; + int n = atom->ntypes; + double cutsq; + + + for (itype = 1; itype <= n; itype++) { + for (jtype = 1; jtype <= n; jtype++) { + if (stencil_skip[itype][jtype]) continue; + + ns = 0; + + sx = sx_multi2[itype][jtype]; + sy = sy_multi2[itype][jtype]; + sz = sz_multi2[itype][jtype]; + + mbinx = mbinx_multi2[itype][jtype]; + mbiny = mbiny_multi2[itype][jtype]; + mbinz = mbinz_multi2[itype][jtype]; + + cutsq = stencil_cut[itype][jtype]; + + for (k = -sz; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = + k*mbiny*mbinx + j*mbinx + i; + + nstencil_multi2[itype][jtype] = ns; + } + } } diff --git a/src/nstencil_full_multi2_3d.h b/src/nstencil_full_multi2_3d.h index 48bdfd2611..f7baefc8e9 100644 --- a/src/nstencil_full_multi2_3d.h +++ b/src/nstencil_full_multi2_3d.h @@ -13,30 +13,26 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(full/multi/tiered/3d, - NStencilFullMultiTiered3d, NS_FULL | NS_Multi_Tiered | NS_3D | NS_ORTHO | NS_TRI) +NStencilStyle(full/multi2/3d, + NStencilFullMulti23d, NS_FULL | NS_Multi2 | NS_3D | NS_ORTHO | NS_TRI) #else -#ifndef LMP_NSTENCIL_FULL_MULTI_TIERED_3D_H -#define LMP_NSTENCIL_FULL_MULTI_TIERED_3D_H +#ifndef LMP_NSTENCIL_FULL_MULTI2_3D_H +#define LMP_NSTENCIL_FULL_MULTI2_3D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilFullBytype3d : public NStencil { +class NStencilFullMulti23d : public NStencil { public: - NStencilFullBytype3d(class LAMMPS *); - ~NStencilFullBytype3d(); + NStencilFullMulti23d(class LAMMPS *); + ~NStencilFullMulti23d(); void create(); - void create_setup(); -private: - int ** maxstencil_type; - - int copy_neigh_info_bytype(int); - void create_newtoff(int, int, double); + protected: + void set_stencil_properties(); }; diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp new file mode 100644 index 0000000000..86da6ea91e --- /dev/null +++ b/src/nstencil_half_multi2_2d.cpp @@ -0,0 +1,111 @@ +/* ---------------------------------------------------------------------- + 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_multi2_2d.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfMulti22d::NStencilHalfMulti23d(LAMMPS *lmp) : + NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfMulti23d::set_stencil_properties() +{ + int n = atom->ntypes; + int i, j; + + // like -> like => use half stencil + for (i = 1; i <= n; i++) { + stencil_half[i][i] = 1; + stencil_skip[i][i] = 0; + stencil_bin_type[i][i] = i; + stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + } + + // Cross types: use full stencil, looking one way through hierarchy + // smaller -> larger => use full stencil in larger bin + // larger -> smaller => no nstecil required + // If cut offs are same, use existing type-type stencil + + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + if(i == j) continue; + if(cuttypesq[i] > cuttypesq[j]) continue; + + stencil_skip[i][j] = 0; + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + + if(cuttypesq[i] == cuttypesq[j]){ + stencil_half[i][j] = 1; + stencil_bin_type[i][j] = i; + } else { + stencil_half[i][j] = 0; + stencil_bin_type[i][j] = j; + } + } + } +} + +/* ---------------------------------------------------------------------- + create stencils based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfMulti23d::create() +{ + int itype, jtype, i, j, ns; + int n = atom->ntypes; + double cutsq; + + + for (itype = 1; itype <= n; itype++) { + for (jtype = 1; jtype <= n; jtype++) { + if (stencil_skip[itype][jtype]) continue; + + ns = 0; + + sx = sx_multi2[itype][jtype]; + sy = sy_multi2[itype][jtype]; + + mbinx = mbinx_multi2[itype][jtype]; + mbiny = mbiny_multi2[itype][jtype]; + + cutsq = stencil_cut[itype][jtype]; + + if (stencil_half[itype][jtype]) { + 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) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + } + } else { + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,0) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + } + + nstencil_multi2[itype][jtype] = ns; + } + } +} + diff --git a/src/nstencil_half_multi2_2d.h b/src/nstencil_half_multi2_2d.h new file mode 100644 index 0000000000..ba3a471833 --- /dev/null +++ b/src/nstencil_half_multi2_2d.h @@ -0,0 +1,46 @@ +/* -*- 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/multi2/2d, + NStencilHalfMulti22d, NS_HALF | NS_MULTI2 | NS_2D | NS_ORTHO) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI2_2D_H +#define LMP_NSTENCIL_HALF_MULTI2_2D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti22d : public NStencil { + public: + NStencilHalfMulti22d(class LAMMPS *); + ~NStencilHalfMulti22d(); + void create(); + + protected: + void set_stencil_properties(); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp new file mode 100755 index 0000000000..46f55300ce --- /dev/null +++ b/src/nstencil_half_multi2_2d_tri.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 "nstencil_half_multi2_2d_tri.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfMulti22dTri::NStencilHalfMulti22d(LAMMPS *lmp) : + NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfMulti22d::set_stencil_properties() +{ + int n = atom->ntypes; + int i, j; + + // like -> like => use half stencil + for (i = 1; i <= n; i++) { + stencil_half[i][i] = 1; + stencil_skip[i][i] = 0; + stencil_bin_type[i][i] = i; + stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + } + + // Cross types: use full stencil, looking one way through hierarchy + // smaller -> larger => use full stencil in larger bin + // larger -> smaller => no nstecil required + // If cut offs are same, use existing type-type stencil + + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + if(i == j) continue; + if(cuttypesq[i] > cuttypesq[j]) continue; + + stencil_skip[i][j] = 0; + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + + if(cuttypesq[i] == cuttypesq[j]){ + stencil_half[i][j] = 1; + stencil_bin_type[i][j] = i; + } else { + stencil_half[i][j] = 0; + stencil_bin_type[i][j] = j; + } + } + } +} + +/* ---------------------------------------------------------------------- + create stencils based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfMulti22d::create() +{ + int itype, jtype, i, j, ns; + int n = atom->ntypes; + double cutsq; + + + for (itype = 1; itype <= n; itype++) { + for (jtype = 1; jtype <= n; jtype++) { + if (stencil_skip[itype][jtype]) continue; + + ns = 0; + + sx = sx_multi2[itype][jtype]; + sy = sy_multi2[itype][jtype]; + + mbinx = mbinx_multi2[itype][jtype]; + mbiny = mbiny_multi2[itype][jtype]; + + cutsq = stencil_cut[itype][jtype]; + + if (stencil_half[itype][jtype]) { + for (j = 0; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,0) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + } else { + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,0) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + } + + nstencil_multi2[itype][jtype] = ns; + } + } +} diff --git a/src/nstencil_half_multi2_2d_tri.h b/src/nstencil_half_multi2_2d_tri.h new file mode 100755 index 0000000000..1d25e56776 --- /dev/null +++ b/src/nstencil_half_multi2_2d_tri.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 NSTENCIL_CLASS + +NStencilStyle(half/multi2/2d/tri, + NStencilHalfMulti22dTri, NS_HALF | NS_MULTI2 | NS_2D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI2_2D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI2_2D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti22dTri : public NStencil { + public: + NStencilHalfMulti22dTri(class LAMMPS *); + ~NStencilHalfMulti22dTri(); + void create(); + + protected: + void set_stencil_properties(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 7fc53fe762..02a65bd3a1 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bytype_3d_newton.h" +#include "nstencil_half_multi2_3d.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,183 +23,95 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBytype3dNewton::NStencilHalfBytype3dNewton(LAMMPS *lmp) : - NStencil(lmp) +NStencilHalfMulti23d::NStencilHalfMulti23d(LAMMPS *lmp) : + NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfMulti23d::set_stencil_properties() { - maxstencil_type = NULL; -} - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBytype3dNewton::~NStencilHalfBytype3dNewton() { - - memory->destroy(nstencil_type); - for (int i = 1; i <= atom->ntypes; i++) { - for (int j = 0; j <= atom->ntypes; j++) { - if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); - } - delete [] stencil_type[i]; - } - delete [] stencil_type; - memory->destroy(maxstencil_type); -} - -/* ---------------------------------------------------------------------- */ - -// KS To superclass -void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { - - mbinx = nb->mbinx_type[itype]; - mbiny = nb->mbiny_type[itype]; - mbinz = nb->mbinz_type[itype]; - binsizex = nb->binsizex_type[itype]; - binsizey = nb->binsizey_type[itype]; - binsizez = nb->binsizez_type[itype]; - bininvx = nb->bininvx_type[itype]; - bininvy = nb->bininvy_type[itype]; - bininvz = nb->bininvz_type[itype]; -} - -/* ---------------------------------------------------------------------- */ - -// KS To superclass? -int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { - - cutneighmaxsq = neighbor->cutneighsq[itype][itype]; - cutneighmax = sqrt(cutneighmaxsq); - cuttypesq = neighbor->cuttypesq; - - // 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 (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - return ((2*sx+1) * (2*sy+1) * (2*sz+1)); -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewton::create_setup() -{ - - int itype, jtype; - int maxtypes; - int smax; - - // maxstencil_type to superclass? - maxtypes = atom->ntypes; - - if (maxstencil_type == NULL) { - memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "maxstencil_type"); - memory->create(nstencil_type, maxtypes+1, maxtypes+1, "nstencil_type"); - stencil_type = new int**[maxtypes+1](); - for (itype = 1; itype <= maxtypes; ++itype) { - stencil_type[itype] = new int*[maxtypes+1](); - for (jtype = 1; jtype <= maxtypes; ++jtype) { - maxstencil_type[itype][jtype] = 0; - nstencil_type[itype][jtype] = 0; - } - } + int n = atom->ntypes; + int i, j; + + // like -> like => use half stencil + for (i = 1; i <= n; i++) { + stencil_half[i][i] = 1; + stencil_skip[i][i] = 0; + stencil_bin_type[i][i] = i; + stencil_cut[i][i] = sqrt(cutneighsq[i][i]); } - // like -> like => use standard Newton stencil at bin - - for (itype = 1; itype <= maxtypes; ++itype) { - copy_bin_info_bytype(itype); - smax = copy_neigh_info_bytype(itype); - if (smax > maxstencil_type[itype][itype]) { - maxstencil_type[itype][itype] = smax; - memory->destroy(stencil_type[itype][itype]); - memory->create(stencil_type[itype][itype], smax, - "NStencilHalfBytypeNewton::create_steup() stencil"); - } - create_newton(itype, itype, cutneighmaxsq); - } - - // Cross types: "Newton on" reached by using Newton off stencil and - // looking one way through hierarchy - // smaller -> larger => use Newton off stencil in larger bin + // Cross types: use full stencil, looking one way through hierarchy + // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstecil required // If cut offs are same, use existing type-type stencil - for (itype = 1; itype <= maxtypes; ++itype) { - for (jtype = 1; jtype <= maxtypes; ++jtype) { - if (itype == jtype) continue; - if (cuttypesq[itype] == cuttypesq[jtype]) { - nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; - stencil_type[itype][jtype] = stencil_type[jtype][jtype]; - } - else if (cuttypesq[itype] < cuttypesq[jtype]) { - copy_bin_info_bytype(jtype); + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + if(i == j) continue; + if(cuttypesq[i] > cuttypesq[j]) continue; - cutneighmaxsq = cuttypesq[jtype]; - cutneighmax = sqrt(cutneighmaxsq); - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - smax = (2*sx+1) * (2*sy+1) * (2*sz+1); - if (smax > maxstencil_type[itype][jtype]) { - maxstencil_type[itype][jtype] = smax; - memory->destroy(stencil_type[itype][jtype]); - memory->create(stencil_type[itype][jtype], smax, "stencil_type[]"); - } - create_newtoff(itype, jtype, cuttypesq[jtype]); + stencil_skip[i][j] = 0; + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + + if(cuttypesq[i] == cuttypesq[j]){ + stencil_half[i][j] = 1; + stencil_bin_type[i][j] = i; + } else { + stencil_half[i][j] = 0; + stencil_bin_type[i][j] = j; } } } - -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewton::create_newton(int itype, int jtype, double cutsq) { - - int i, j, k, ns; - - ns = 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) < cutsq) - stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - } - nstencil_type[itype][jtype] = ns; -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewton::create_newtoff(int itype, int jtype, double cutsq) { - - int i, j, k, ns; - - ns = 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) < cutsq) - stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - - nstencil_type[itype][jtype] = ns; } /* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff + create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBytype3dNewton::create() +void NStencilHalfMulti23d::create() { - // KS. Move "creation" here. + int itype, jtype, i, j, k, ns; + int n = atom->ntypes; + double cutsq; + + + for (itype = 1; itype <= n; itype++) { + for (jtype = 1; jtype <= n; jtype++) { + if (stencil_skip[itype][jtype]) continue; + + ns = 0; + + sx = sx_multi2[itype][jtype]; + sy = sy_multi2[itype][jtype]; + sz = sz_multi2[itype][jtype]; + + mbinx = mbinx_multi2[itype][jtype]; + mbiny = mbiny_multi2[itype][jtype]; + mbinz = mbinz_multi2[itype][jtype]; + + cutsq = stencil_cut[itype][jtype]; + + if (stencil_half[itype][jtype]) { + 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) < cutsq) + stencil_type[itype][jtype][ns++] = + k*mbiny*mbinx + j*mbinx + i; + } + } else { + for (k = -sz; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = + k*mbiny*mbinx + j*mbinx + i; + } + + nstencil_multi2[itype][jtype] = ns; + } + } } + diff --git a/src/nstencil_half_multi2_3d.h b/src/nstencil_half_multi2_3d.h index e39db1c1e1..9cae8269cb 100644 --- a/src/nstencil_half_multi2_3d.h +++ b/src/nstencil_half_multi2_3d.h @@ -13,32 +13,27 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bytype/3d, - NStencilHalfBytype3dNewton, NS_HALF | NS_BYTYPE | NS_3D | NS_ORTHO) +NStencilStyle(half/multi2/3d, + NStencilHalfMulti23d, NS_HALF | NS_MULTI2 | NS_3D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_H -#define LMP_NSTENCIL_HALF_BYTYPE_3D_H +#ifndef LMP_NSTENCIL_HALF_MULTI2_3D_H +#define LMP_NSTENCIL_HALF_MULTI2_3D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfBytype3dNewton : public NStencil { +class NStencilHalfMulti23d : public NStencil { public: - NStencilHalfBytype3dNewton(class LAMMPS *); - ~NStencilHalfBytype3dNewton(); - void create_setup(); + NStencilHalfMulti23d(class LAMMPS *); + ~NStencilHalfMulti23d(); void create(); - private: - int ** maxstencil_type; + protected: + void set_stencil_properties(); - void copy_bin_info_bytype(int); - int copy_neigh_info_bytype(int); - void create_newton(int, int, double); - void create_newtoff(int, int, double); }; } diff --git a/src/nstencil_half_multi2_3d_delete_noff.cpp b/src/nstencil_half_multi2_3d_delete_noff.cpp deleted file mode 100644 index fedc8060ce..0000000000 --- a/src/nstencil_half_multi2_3d_delete_noff.cpp +++ /dev/null @@ -1,198 +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 "nstencil_half_bytype_3d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "nbin.h" -#include "memory.h" -#include "atom.h" -#include - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBytype3dNewtoff::NStencilHalfBytype3dNewtoff(LAMMPS *lmp) : - NStencil(lmp) -{ - maxstencil_type = NULL; -} - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBytype3dNewtoff::~NStencilHalfBytype3dNewtoff() { - - memory->destroy(nstencil_type); - for (int i = 1; i <= atom->ntypes; i++) { - for (int j = 0; j <= atom->ntypes; j++) { - if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); - } - delete [] stencil_type[i]; - } - delete [] stencil_type; - memory->destroy(maxstencil_type); -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewtoff::copy_bin_info_bytype(int itype) { - - mbinx = nb->mbinx_type[itype]; - mbiny = nb->mbiny_type[itype]; - mbinz = nb->mbinz_type[itype]; - binsizex = nb->binsizex_type[itype]; - binsizey = nb->binsizey_type[itype]; - binsizez = nb->binsizez_type[itype]; - bininvx = nb->bininvx_type[itype]; - bininvy = nb->bininvy_type[itype]; - bininvz = nb->bininvz_type[itype]; -} - -/* ---------------------------------------------------------------------- */ - -int NStencilHalfBytype3dNewtoff::copy_neigh_info_bytype(int itype) { - - cutneighmaxsq = neighbor->cutneighsq[itype][itype]; - cutneighmax = sqrt(cutneighmaxsq); - cuttypesq = neighbor->cuttypesq; - - // 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 (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - return ((2*sx+1) * (2*sy+1) * (2*sz+1)); -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewtoff::create_setup() -{ - - int itype, jtype; - int maxtypes; - int smax; - - maxtypes = atom->ntypes; - - if (maxstencil_type == NULL) { - memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "BAD A"); - memory->create(nstencil_type, maxtypes+1, maxtypes+1, "BAD B"); - stencil_type = new int**[maxtypes+1](); - for (itype = 1; itype <= maxtypes; ++itype) { - stencil_type[itype] = new int*[maxtypes+1](); - for (jtype = 1; jtype <= maxtypes; ++jtype) { - maxstencil_type[itype][jtype] = 0; - } - } - } - - // like -> like => use standard newtoff stencil at bin - - for (itype = 1; itype <= maxtypes; ++itype) { - copy_bin_info_bytype(itype); - smax = copy_neigh_info_bytype(itype); - if (smax > maxstencil_type[itype][itype]) { - maxstencil_type[itype][itype] = smax; - memory->destroy(stencil_type[itype][itype]); - memory->create(stencil_type[itype][itype], smax, - "NStencilHalfBytypeNewtoff::create_steup() stencil"); - } - create_newtoff(itype, itype, cutneighmaxsq); - } - - // smaller -> larger => use existing newtoff stencil in larger bin - // larger -> smaller => use multi-like stencil for small-large in smaller bin - // If types are same cutoff, use existing like-like stencil. - - for (itype = 1; itype <= maxtypes; ++itype) { - for (jtype = 1; jtype <= maxtypes; ++jtype) { - if (itype == jtype) continue; - if (cuttypesq[itype] <= cuttypesq[jtype]) { - // Potential destroy/create problem? - nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; - stencil_type[itype][jtype] = stencil_type[jtype][jtype]; - } - else { - copy_bin_info_bytype(jtype); - // smax = copy_neigh_info_bytype(jtype); - - cutneighmaxsq = cuttypesq[jtype]; - cutneighmax = sqrt(cutneighmaxsq); - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - smax = (2*sx+1) * (2*sy+1) * (2*sz+1); - if (smax > maxstencil_type[itype][jtype]) { - maxstencil_type[itype][jtype] = smax; - memory->destroy(stencil_type[itype][jtype]); - memory->create(stencil_type[itype][jtype], smax, "Bad C"); - } - create_newtoff(itype, jtype, cuttypesq[jtype]); - } - } - } - - //for (itype = 1; itype <= maxtypes; itype++) { - // for (jtype = 1; jtype <= maxtypes; jtype++) { - // printf("i j n %d %d %d\n", itype, jtype, nstencil_type[itype][jtype]); - // printf("i j n %d %d %d\n", itype, jtype, maxstencil_type[itype][jtype]); - // } - // } - -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewtoff::create_newtoff(int itype, int jtype, double cutsq) { - - int i, j, k, ns; - - ns = 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) < cutsq) - stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - - nstencil_type[itype][jtype] = ns; -} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewtoff::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_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index f1ab713725..bcaf22abbd 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bytype_3d_newton.h" +#include "nstencil_half_multi2_3d_tri.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,31 +23,100 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBytype3dNewton::NStencilHalfBytype3dNewton(LAMMPS *lmp) : - NStencil(lmp) -{ - maxstencil_type = NULL; -} +NStencilHalfMulti23dTri::NStencilHalfMulti23d(LAMMPS *lmp) : + NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -NStencilHalfBytype3dNewton::~NStencilHalfBytype3dNewton() { - - memory->destroy(nstencil_type); - for (int i = 1; i <= atom->ntypes; i++) { - for (int j = 0; j <= atom->ntypes; j++) { - if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); - } - delete [] stencil_type[i]; +void NStencilHalfMulti23d::set_stencil_properties() +{ + int n = atom->ntypes; + int i, j; + + // like -> like => use half stencil + for (i = 1; i <= n; i++) { + stencil_half[i][i] = 1; + stencil_skip[i][i] = 0; + stencil_bin_type[i][i] = i; + stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + } + + // Cross types: use full stencil, looking one way through hierarchy + // smaller -> larger => use full stencil in larger bin + // larger -> smaller => no nstecil required + // If cut offs are same, use existing type-type stencil + + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + if(i == j) continue; + if(cuttypesq[i] > cuttypesq[j]) continue; + + stencil_skip[i][j] = 0; + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + + if(cuttypesq[i] == cuttypesq[j]){ + stencil_half[i][j] = 1; + stencil_bin_type[i][j] = i; + } else { + stencil_half[i][j] = 0; + stencil_bin_type[i][j] = j; + } + } + } +} + +/* ---------------------------------------------------------------------- + create stencils based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfMulti23d::create() +{ + int itype, jtype, i, j, k, ns; + int n = atom->ntypes; + double cutsq; + + + for (itype = 1; itype <= n; itype++) { + for (jtype = 1; jtype <= n; jtype++) { + if (stencil_skip[itype][jtype]) continue; + + ns = 0; + + sx = sx_multi2[itype][jtype]; + sy = sy_multi2[itype][jtype]; + sz = sz_multi2[itype][jtype]; + + mbinx = mbinx_multi2[itype][jtype]; + mbiny = mbiny_multi2[itype][jtype]; + mbinz = mbinz_multi2[itype][jtype]; + + cutsq = stencil_cut[itype][jtype]; + + if (stencil_half[itype][jtype]) { + for (k = 0; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = + k*mbiny*mbinx + j*mbinx + i; + } else { + for (k = -sz; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = + k*mbiny*mbinx + j*mbinx + i; + } + + nstencil_multi2[itype][jtype] = ns; + } } - delete [] stencil_type; - memory->destroy(maxstencil_type); } /* ---------------------------------------------------------------------- */ // KS To superclass -void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { +void NStencilHalfMulti23d::copy_bin_info_bytype(int itype) { mbinx = nb->mbinx_type[itype]; mbiny = nb->mbiny_type[itype]; @@ -63,7 +132,7 @@ void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { /* ---------------------------------------------------------------------- */ // KS To superclass? -int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { +int NStencilHalfMulti23d::copy_neigh_info_bytype(int itype) { cutneighmaxsq = neighbor->cutneighsq[itype][itype]; cutneighmax = sqrt(cutneighmaxsq); @@ -85,7 +154,7 @@ int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { /* ---------------------------------------------------------------------- */ -void NStencilHalfBytype3dNewton::create_setup() +void NStencilHalfMulti23d::create_setup() { int itype, jtype; @@ -157,47 +226,4 @@ void NStencilHalfBytype3dNewton::create_setup() } } } - -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewton::create_newton(int itype, int jtype, double cutsq) { - - int i, j, k, ns; - - ns = 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) < cutsq) - stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - nstencil_type[itype][jtype] = ns; -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewton::create_newtoff(int itype, int jtype, double cutsq) { - - int i, j, k, ns; - - ns = 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) < cutsq) - stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - - nstencil_type[itype][jtype] = ns; -} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewton::create() -{ - // KS. Move "creation" here. } diff --git a/src/nstencil_half_multi2_3d_tri.h b/src/nstencil_half_multi2_3d_tri.h index 5424d73f11..f4b37ebebe 100755 --- a/src/nstencil_half_multi2_3d_tri.h +++ b/src/nstencil_half_multi2_3d_tri.h @@ -13,32 +13,26 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bytype/3d, - NStencilHalfBytype3d, NS_HALF | NS_BYTYPE | NS_3D | NS_TRI) +NStencilStyle(half/multi2/3d/tri, + NStencilHalfMulti23dTri, NS_HALF | NS_MULTI2 | NS_3D | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_H -#define LMP_NSTENCIL_HALF_BYTYPE_3D_H +#ifndef LMP_NSTENCIL_HALF_MULTI2_3D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI2_3D_TRI_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfBytype3dNewton : public NStencil { +class NStencilHalfMulti23dTri : public NStencil { public: - NStencilHalfBytype3dNewton(class LAMMPS *); - ~NStencilHalfBytype3dNewton(); - void create_setup(); + NStencilHalfMulti23dTri(class LAMMPS *); + ~NStencilHalfMulti23dTri(); void create(); - private: - int ** maxstencil_type; - - void copy_bin_info_bytype(int); - int copy_neigh_info_bytype(int); - void create_newton(int, int, double); - void create_newtoff(int, int, double); + protected: + void set_stencil_properties(); }; } From bdc21c87b211f6f08be703471c3d4bee5934bc89 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 10 Nov 2020 20:15:54 -0700 Subject: [PATCH 09/73] Clarifying multi2 stencil label --- src/nstencil.cpp | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 525369d573..b7cfe4dc72 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -53,9 +53,10 @@ using namespace LAMMPS_NS; no versions that allow ghost on (any need for it?) for multi2: create one stencil for each itype-jtype pairing - stencils do not generally follow the same rules for half/full or newton on/off - full stencils including all surrounding bins are always used except - for same-type stencils with newton on which uses a half stencil + the full/half stencil label refers to the same-type stencil + a half list with newton on has a half same-type stencil + a full list or half list with newton of has a full same-type stencil + cross type stencils are always full to allow small-to-large lookups for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above cutoff is not cutneighmaxsq, but max cutoff for that atom type From 061229093cb7c28058fdbdcff2fd13c9226d78de Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 10 Nov 2020 22:44:55 -0700 Subject: [PATCH 10/73] Adding npair classes --- src/npair.cpp | 65 +++++ src/npair.h | 14 ++ ...multi_tiered.cpp => npair_full_multi2.cpp} | 83 ++++--- ...ull_multi_tiered.h => npair_full_multi2.h} | 16 +- src/npair_half_multi2_newtoff.cpp | 143 +++++++++++ src/npair_half_multi2_newtoff.h | 47 ++++ src/npair_half_multi2_newton.cpp | 225 +++++++++--------- src/npair_half_multi2_newton.h | 16 +- src/npair_half_multi2_newton_tri.cpp | 172 +++++++------ src/npair_half_multi2_newton_tri.h | 16 +- src/npair_half_size_multi2_newtoff.cpp | 68 +++--- src/npair_half_size_multi2_newtoff.h | 16 +- src/npair_half_size_multi2_newton.cpp | 183 +++++++------- src/npair_half_size_multi2_newton.h | 16 +- src/npair_half_size_multi2_newton_tri.cpp | 145 ++++++----- src/npair_half_size_multi2_newton_tri.h | 16 +- src/nstencil.h | 4 +- 17 files changed, 738 insertions(+), 507 deletions(-) rename src/{npair_full_multi_tiered.cpp => npair_full_multi2.cpp} (63%) rename src/{npair_full_multi_tiered.h => npair_full_multi2.h} (75%) create mode 100755 src/npair_half_multi2_newtoff.cpp create mode 100755 src/npair_half_multi2_newtoff.h diff --git a/src/npair.cpp b/src/npair.cpp index 698ff28067..920728a692 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -134,6 +134,25 @@ void NPair::copy_bin_info() atom2bin = nb->atom2bin; bins = nb->bins; binhead = nb->binhead; + + nbinx_multi2 = nb->nbinx_multi2; + nbiny_multi2 = nb->nbiny_multi2; + nbinz_multi2 = nb->nbinz_multi2; + mbins_multi2 = nb->mbins_multi2; + mbinx_multi2 = nb->mbinx_multi2; + mbiny_multi2 = nb->mbiny_multi2; + mbinz_multi2 = nb->mbinz_multi2; + mbinxlo_multi2 = nb->mbinxlo_multi2; + mbinylo_multi2 = nb->mbinylo_multi2; + mbinzlo_multi2 = nb->mbinzlo_multi2; + + bininvx_multi2 = nb->bininvx_multi2; + bininvy_multi2 = nb->bininvy_multi2; + bininvz_multi2 = nb->bininvz_multi2; + + atom2bin_multi2 = nb->atom2bin_multi2; + bins_multi2 = nb->bins_multi2; + binhead_multi2 = nb->binhead_multi2; } /* ---------------------------------------------------------------------- @@ -148,6 +167,9 @@ void NPair::copy_stencil_info() nstencil_multi = ns->nstencil_multi; stencil_multi = ns->stencil_multi; distsq_multi = ns->distsq_multi; + + nstencil_multi2 = ns->nstencil_multi2; + stencil_multi2 = ns->stencil_multi2; } /* ---------------------------------------------------------------------- @@ -241,3 +263,46 @@ int NPair::coord2bin(double *x, int &ix, int &iy, int &iz) return iz*mbiny*mbinx + iy*mbinx + ix; } + +/* ---------------------------------------------------------------------- + same as coord2bin in NbinMulti2 +------------------------------------------------------------------------- */ + +int NPair::coord2bin(double *x, int it) +{ + int ix,iy,iz; + int ibin; + + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi2[it]) + nbinx_multi2[it]; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]); + ix = MIN(ix,nbinx_multi2[it]-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi2[it]) + nbiny_multi2[it]; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]); + iy = MIN(iy,nbiny_multi2[it]-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi2[it]) + nbinz_multi2[it]; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]); + iz = MIN(iz,nbinz_multi2[it]-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]) - 1; + + + ibin = (iz-mbinzlo_multi2[it])*mbiny_multi2[it]*mbinx_multi2[it] + + (iy-mbinylo_multi2[it])*mbinx_multi2[it] + + (ix-mbinxlo_multi2[it]); + return ibin; +} \ No newline at end of file diff --git a/src/npair.h b/src/npair.h index ec75042302..87b2584521 100644 --- a/src/npair.h +++ b/src/npair.h @@ -79,6 +79,14 @@ class NPair : protected Pointers { int *atom2bin,*bins; int *binhead; + int *nbinx_multi2, *nbiny_multi2, *nbinz_multi2; + int *mbins_multi2; + int *mbinx_multi2, *mbiny_multi2, *mbinz_multi2; + int *mbinxlo_multi2, *mbinylo_multi2, *mbinzlo_multi2; + double *bininvx_multi2, *bininvy_multi2, *bininvz_multi2; + int **binhead_multi2,**bins_multi2; + int **atom2bin_multi2; + // data from NStencil class int nstencil; @@ -88,6 +96,9 @@ class NPair : protected Pointers { int **stencil_multi; double **distsq_multi; + int ** nstencil_multi2; + int *** stencil_multi2; + // data common to all NPair variants int molecular; @@ -102,6 +113,9 @@ class NPair : protected Pointers { int coord2bin(double *); // mapping atom coord to a bin int coord2bin(double *, int &, int &, int&); // ditto + int coord2bin(double *, int); // mapping atom coord to type bin + + // 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 diff --git a/src/npair_full_multi_tiered.cpp b/src/npair_full_multi2.cpp similarity index 63% rename from src/npair_full_multi_tiered.cpp rename to src/npair_full_multi2.cpp index 3b9a89bb56..4fbdc6148b 100644 --- a/src/npair_full_multi_tiered.cpp +++ b/src/npair_full_multi2.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_full_bytype.h" +#include "npair_full_multi2.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -19,28 +19,27 @@ #include "domain.h" #include "my_page.h" #include "error.h" -#include "nbin.h" -#include "nstencil.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairFullBytype::NPairFullBytype(LAMMPS *lmp) : NPair(lmp) {} +NPairFullMulti2::NPairFullMulti2(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- + REWRITE 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 - KS ADJUST ------------------------------------------------------------------------- */ -void NPairFullBytype::build(NeighList *list) +void NPairFullMulti2::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; + int js; double **x = atom->x; int *type = atom->type; @@ -84,48 +83,46 @@ void NPairFullBytype::build(NeighList *list) // skip if i,j neighbor cutoff is less than bin distance // skip i = j - int kbin; - ibin = nb->atom2bin_type[itype][i]; - for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + ibin = atom2bin_multi2[itype][i]; + for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { - kbin = ibin; - } - else { - // Locate i in ktype bin - kbin = nb->coord2bin(x[i], ktype); + kbin = ibin; + } else { + // Locate i in ktype bin + kbin = coord2bin(x[i], ktype); } - s = this->ns->stencil_type[itype][ktype]; - ns = this->ns->nstencil_type[itype][ktype]; + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; for (k = 0; k < ns; k++) { - int js = this->nb->binhead_type[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = this->nb->bins_type[ktype][j]) { - if (i == j) continue; + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if (i == j) continue; - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) 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 != Atom::ATOMIC) { - 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; - } - } + 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 != Atom::ATOMIC) { + 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; + } + } } } diff --git a/src/npair_full_multi_tiered.h b/src/npair_full_multi2.h similarity index 75% rename from src/npair_full_multi_tiered.h rename to src/npair_full_multi2.h index fdcd6b5fb1..f552e5bf47 100644 --- a/src/npair_full_multi_tiered.h +++ b/src/npair_full_multi2.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(full/bytype, - NPairFullBytype, - NP_FULL | NP_BYTYPE | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(full/multi2, + NPairFullMulti2, + NP_FULL | NP_MULTI2 | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_FULL_BYTYPE_H -#define LMP_NPAIR_FULL_BYTYPE_H +#ifndef LMP_NPAIR_FULL_MULTI2_H +#define LMP_NPAIR_FULL_MULTI2_H #include "npair.h" namespace LAMMPS_NS { -class NPairFullBytype : public NPair { +class NPairFullMulti2 : public NPair { public: - NPairFullBytype(class LAMMPS *); - ~NPairFullBytype() {} + NPairFullMulti2(class LAMMPS *); + ~NPairFullMulti2() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi2_newtoff.cpp b/src/npair_half_multi2_newtoff.cpp new file mode 100755 index 0000000000..83a8054247 --- /dev/null +++ b/src/npair_half_multi2_newtoff.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_multi2_newtoff.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; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMulti2Newtoff::NPairHalfMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + REWRITE + 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 NPairHalfMulti2Newtoff::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + int js; + + 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 == Atom::TEMPLATE) moltemplate = 1; + else moltemplate = 0; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *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 = nb->atom2bin_type[itype][i]; + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + kbin = ibin; + } else { + // Locate i in ktype bin + kbin = coord2bin(x[i], ktype); + } + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >=0; j = nb->bins_multi2[ktype][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 != Atom::ATOMIC) { + 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_multi2_newtoff.h b/src/npair_half_multi2_newtoff.h new file mode 100755 index 0000000000..30a6d3164d --- /dev/null +++ b/src/npair_half_multi2_newtoff.h @@ -0,0 +1,47 @@ +/* -*- 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/multi2/newtoff, + NPairHalfMulti2Newtoff, + NP_HALF | NP_MULTI2 | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI2_NEWTOFF_H +#define LMP_NPAIR_HALF_MULTI2_NEWTOFF_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMulti2Newtoff : public NPair { + public: + NPairHalfMulti2Newtoff(class LAMMPS *); + ~NPairHalfMulti2Newtoff() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + +*/ diff --git a/src/npair_half_multi2_newton.cpp b/src/npair_half_multi2_newton.cpp index 66899564be..58397f645e 100755 --- a/src/npair_half_multi2_newton.cpp +++ b/src/npair_half_multi2_newton.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include "npair_half_bytype_newton.h" -#include "neighbor.h" +#include "npair_half_multi2_newton.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,14 +20,11 @@ #include "my_page.h" #include "error.h" -#include "nbin.h" -#include "nstencil.h" - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfBytypeNewton::NPairHalfBytypeNewton(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMulti2Newton::NPairHalfMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- KS REWRTIE @@ -39,12 +34,13 @@ NPairHalfBytypeNewton::NPairHalfBytypeNewton(LAMMPS *lmp) : NPair(lmp) {} every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfBytypeNewton::build(NeighList *list) +void NPairHalfMulti2Newton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; + int js; double **x = atom->x; int *type = atom->type; @@ -84,129 +80,124 @@ void NPairHalfBytypeNewton::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - int js; - int kbin; - // own type: loop over atoms ahead in bin, including ghosts at end of list // if j is owned atom, store by virtue of being ahead of i in list // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = nb->atom2bin_type[itype][i]; - - for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + ibin = atom2bin_multi2[itype][i]; + for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { - // own bin ... - js = nb->bins_type[itype][i]; - for (j = js; j >= 0; j = nb->bins_type[itype][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; + // own bin ... + js = bins_multi2[itype][i]; + for (j = js; j >= 0; j = bins_multi2[itype][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; + } } - } - 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 - - s = this->ns->stencil_type[itype][itype]; - ns = this->ns->nstencil_type[itype][itype]; - for (k = 0; k < ns; k++) { - js = nb->binhead_type[itype][ibin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[itype][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; + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][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; + } + } } - } - } - - } - else { + } else { // smaller -> larger: locate i in the ktype bin structure - kbin = nb->coord2bin(x[i], ktype); - s = this->ns->stencil_type[itype][ktype]; - ns = this->ns->nstencil_type[itype][ktype]; - - for (k = 0; k < ns; k++) { - js = nb->binhead_type[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[ktype][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; + kbin = coord2bin(x[i], ktype); + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][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; + } + } } - } - } } } + ilist[inum++] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/npair_half_multi2_newton.h b/src/npair_half_multi2_newton.h index 8be7292219..8037d2e172 100755 --- a/src/npair_half_multi2_newton.h +++ b/src/npair_half_multi2_newton.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/bytype/newton, - NPairHalfBytypeNewton, - NP_HALF | NP_BYTYPE | NP_NEWTON | NP_ORTHO) +NPairStyle(half/multi2/newton, + NPairHalfMulti2Newton, + NP_HALF | NP_MULTI2 | NP_NEWTON | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_BYTYPE_NEWTON_H -#define LMP_NPAIR_HALF_BYTYPE_NEWTON_H +#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_H +#define LMP_NPAIR_HALF_MULTI2_NEWTON_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfBytypeNewton : public NPair { +class NPairHalfMulti2Newton : public NPair { public: - NPairHalfBytypeNewton(class LAMMPS *); - ~NPairHalfBytypeNewton() {} + NPairHalfMulti2Newton(class LAMMPS *); + ~NPairHalfMulti2Newton() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi2_newton_tri.cpp b/src/npair_half_multi2_newton_tri.cpp index 6b28e76789..c741a860f1 100755 --- a/src/npair_half_multi2_newton_tri.cpp +++ b/src/npair_half_multi2_newton_tri.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include "npair_half_bytype_newton_tri.h" -#include "neighbor.h" +#include "npair_half_multi2_newton_tri.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,14 +20,11 @@ #include "my_page.h" #include "error.h" -#include "nbin.h" -#include "nstencil.h" - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfBytypeNewtonTri::NPairHalfBytypeNewtonTri(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMulti2NewtonTri::NPairHalfMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- KS REWRTIE @@ -39,12 +34,13 @@ NPairHalfBytypeNewtonTri::NPairHalfBytypeNewtonTri(LAMMPS *lmp) : NPair(lmp) {} every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfBytypeNewtonTri::build(NeighList *list) +void NPairHalfMulti2NewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; + int js; double **x = atom->x; int *type = atom->type; @@ -83,101 +79,97 @@ void NPairHalfBytypeNewtonTri::build(NeighList *list) iatom = molatom[i]; tagprev = tag[i] - iatom - 1; } - - int js; - int kbin; - + // own type: loop over atoms ahead in bin, including ghosts at end of list // if j is owned atom, store by virtue of being ahead of i in list // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = nb->atom2bin_type[itype][i]; + ibin = atom2bin_multi2[itype][i]; - for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = this->ns->stencil_type[itype][itype]; - ns = this->ns->nstencil_type[itype][itype]; - for (k = 0; k < ns; k++) { - js = nb->binhead_type[itype][ibin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[itype][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; + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][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; + } + } } - } - } - - } - else { + } else { // smaller -> larger: locate i in the ktype bin structure - kbin = nb->coord2bin(x[i], ktype); - s = this->ns->stencil_type[itype][ktype]; - ns = this->ns->nstencil_type[itype][ktype]; - - for (k = 0; k < ns; k++) { - js = nb->binhead_type[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[ktype][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; + kbin = coord2bin(x[i], ktype); + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][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; + } + } } - } - } } } + ilist[inum++] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/npair_half_multi2_newton_tri.h b/src/npair_half_multi2_newton_tri.h index 0582801028..0787860c52 100755 --- a/src/npair_half_multi2_newton_tri.h +++ b/src/npair_half_multi2_newton_tri.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/bytype/newton/tri, - NPairHalfBytypeNewtonTri, - NP_HALF | NP_BYTYPE | NP_NEWTON | NP_TRI) +NPairStyle(half/multi2/newton/tri, + NPairHalfMulti2NewtonTri, + NP_HALF | NP_MULTI2 | NP_NEWTON | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_BYTYPE_NEWTON_TRI_H -#define LMP_NPAIR_HALF_BYTYPE_NEWTON_TRI_H +#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_H +#define LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfBytypeNewtonTri : public NPair { +class NPairHalfMulti2NewtonTri : public NPair { public: - NPairHalfBytypeNewtonTri(class LAMMPS *); - ~NPairHalfBytypeNewtonTri() {} + NPairHalfMulti2NewtonTri(class LAMMPS *); + ~NPairHalfMulti2NewtonTri() {} void build(class NeighList *); }; diff --git a/src/npair_half_size_multi2_newtoff.cpp b/src/npair_half_size_multi2_newtoff.cpp index 220ae747a7..0ea9e493ce 100644 --- a/src/npair_half_size_multi2_newtoff.cpp +++ b/src/npair_half_size_multi2_newtoff.cpp @@ -12,20 +12,18 @@ es certain rights in this software. This software is distributed under ------------------------------------------------------------------------- */ #include -#include "npair_half_size_bytype_newtoff.h" +#include "npair_half_size_multi2_newtoff.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "my_page.h" #include "error.h" -#include "nbin.h" -#include "nstencil.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeBytypeNewtoff::NPairHalfSizeBytypeNewtoff(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMulti2Newtoff::NPairHalfSizeMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- REWRITE @@ -36,12 +34,13 @@ NPairHalfSizeBytypeNewtoff::NPairHalfSizeBytypeNewtoff(LAMMPS *lmp) : NPair(lmp) pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfSizeBytypeNewtoff::build(NeighList *list) +void NPairHalfSizeMulti2Newtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; + int js; double **x = atom->x; double *radius = atom->radius; @@ -78,41 +77,40 @@ void NPairHalfSizeBytypeNewtoff::build(NeighList *list) // stores own/own pairs only once // stores own/ghost pairs on both procs - int kbin; - ibin = nb->atom2bin_type[itype][i]; - for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { - kbin = ibin; + kbin = ibin; + } else { + // Locate i in ktype bin + kbin = coord2bin(x[i], ktype); } - else { - // Locate i in ktype bin - kbin = nb->coord2bin(x[i], ktype); - } - s = this->ns->stencil_type[itype][ktype]; - ns = this->ns->nstencil_type[itype][ktype]; + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; for (k = 0; k < ns; k++) { - int js = nb->binhead_type[ktype][kbin + s[k]]; - for (j = js; j >=0; j = nb->bins_type[ktype][j]) { - if (j <= i) continue; - jtype = type[j]; + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >=0; j = nb->bins_multi2[ktype][j]) { + if (j <= i) continue; + + jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) 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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); - 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]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } } } diff --git a/src/npair_half_size_multi2_newtoff.h b/src/npair_half_size_multi2_newtoff.h index 183bd39fb3..15540666c3 100644 --- a/src/npair_half_size_multi2_newtoff.h +++ b/src/npair_half_size_multi2_newtoff.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/size/bytype/newtoff, - NPairHalfSizeBytypeNewtoff, - NP_HALF | NP_SIZE | NP_BYTYPE | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(half/size/multi2/newtoff, + NPairHalfSizeMulti2Newtoff, + NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTOFF_H -#define LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTOFF_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_H +#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfSizeBytypeNewtoff : public NPair { +class NPairHalfSizeMulti2Newtoff : public NPair { public: - NPairHalfSizeBytypeNewtoff(class LAMMPS *); - ~NPairHalfSizeBytypeNewtoff() {} + NPairHalfSizeMulti2Newtoff(class LAMMPS *); + ~NPairHalfSizeMulti2Newtoff() {} void build(class NeighList *); }; diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi2_newton.cpp index 339c4859a6..3b89c259ec 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi2_newton.cpp @@ -11,21 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include "npair_half_size_bytype_newton.h" +#include "npair_half_size_multi2_newton.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "my_page.h" #include "error.h" -#include "nbin.h" -#include "nstencil.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeBytypeNewton::NPairHalfSizeBytypeNewton(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMulti2Newton::NPairHalfSizeMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- KS REWRTIE @@ -35,9 +32,9 @@ NPairHalfSizeBytypeNewton::NPairHalfSizeBytypeNewton(LAMMPS *lmp) : NPair(lmp) { every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeBytypeNewton::build(NeighList *list) +void NPairHalfSizeMulti2Newton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -71,110 +68,104 @@ void NPairHalfSizeBytypeNewton::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - int js; - int kbin; - // own type: loop over atoms ahead in bin, including ghosts at end of list // if j is owned atom, store by virtue of being ahead of i in list // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = nb->atom2bin_type[itype][i]; + ibin = nb->atom2bin_multi2[itype][i]; - for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { - // own bin ... - js = nb->bins_type[itype][i]; - for (j = js; j >= 0; j = nb->bins_type[itype][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; + // own bin ... + js = bins_multi2[itype][i]; + for (j = js; j >= 0; j = bins_multi2[itype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - 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 - - s = this->ns->stencil_type[itype][itype]; - ns = this->ns->nstencil_type[itype][itype]; - for (k = 0; k < ns; k++) { - js = nb->binhead_type[itype][ibin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[itype][j]) { - jtype = type[j]; - // KS. CHECK ME 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - 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 + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } } - } - } - - } - else { - // KS + } else { // smaller -> larger: locate i in the ktype bin structure - kbin = nb->coord2bin(x[i], ktype); - - s = this->ns->stencil_type[itype][ktype]; - ns = this->ns->nstencil_type[itype][ktype]; - for (k = 0; k < ns; k++) { - js = nb->binhead_type[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[ktype][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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + kbin = coord2bin(x[i], ktype); + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } } - } - } } } + ilist[inum++] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/npair_half_size_multi2_newton.h b/src/npair_half_size_multi2_newton.h index 3cd1ee05d1..8c7bc1cc9e 100755 --- a/src/npair_half_size_multi2_newton.h +++ b/src/npair_half_size_multi2_newton.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/size/bytype/newton, - NPairHalfSizeBytypeNewton, - NP_HALF | NP_SIZE | NP_BYTYPE | NP_NEWTON | NP_ORTHO) +NPairStyle(half/size/multi2/newton, + NPairHalfSizeMulti2Newton, + NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_H -#define LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_H +#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfSizeBytypeNewton : public NPair { +class NPairHalfSizeMulti2Newton : public NPair { public: - NPairHalfSizeBytypeNewton(class LAMMPS *); - ~NPairHalfSizeBytypeNewton() {} + NPairHalfSizeMulti2Newton(class LAMMPS *); + ~NPairHalfSizeMulti2Newton() {} void build(class NeighList *); }; diff --git a/src/npair_half_size_multi2_newton_tri.cpp b/src/npair_half_size_multi2_newton_tri.cpp index 62d499b10f..1c0c1d514f 100755 --- a/src/npair_half_size_multi2_newton_tri.cpp +++ b/src/npair_half_size_multi2_newton_tri.cpp @@ -11,21 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include "npair_half_size_bytype_newton_tri.h" +#include "npair_half_size_multi2_newton_tri.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "my_page.h" #include "error.h" -#include "nbin.h" -#include "nstencil.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeBytypeNewtonTri::NPairHalfSizeBytypeNewtonTri(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMulti2NewtonTri::NPairHalfSizeMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- KS REWRTIE @@ -35,9 +32,9 @@ NPairHalfSizeBytypeNewtonTri::NPairHalfSizeBytypeNewtonTri(LAMMPS *lmp) : NPair( every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeBytypeNewtonTri::build(NeighList *list) +void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -71,89 +68,83 @@ void NPairHalfSizeBytypeNewtonTri::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - int js; - int kbin; - // own type: loop over atoms ahead in bin, including ghosts at end of list // if j is owned atom, store by virtue of being ahead of i in list // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = nb->atom2bin_type[itype][i]; + ibin = atom2bin_multi2[itype][i]; - for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = this->ns->stencil_type[itype][itype]; - ns = this->ns->nstencil_type[itype][itype]; - for (k = 0; k < ns; k++) { - js = nb->binhead_type[itype][ibin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[itype][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]; - // KS. CHECK ME 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - 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 + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } } - } - } - - } - else { - // KS + } else { // smaller -> larger: locate i in the ktype bin structure - kbin = nb->coord2bin(x[i], ktype); - - s = this->ns->stencil_type[itype][ktype]; - ns = this->ns->nstencil_type[itype][ktype]; - for (k = 0; k < ns; k++) { - js = nb->binhead_type[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[ktype][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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + kbin = coord2bin(x[i], ktype); + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } } - } - } } } + ilist[inum++] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/npair_half_size_multi2_newton_tri.h b/src/npair_half_size_multi2_newton_tri.h index 0f770e780d..6ce4f6d2fb 100755 --- a/src/npair_half_size_multi2_newton_tri.h +++ b/src/npair_half_size_multi2_newton_tri.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/size/bytype/newton/tri, - NPairHalfSizeBytypeNewtonTri, - NP_HALF | NP_SIZE | NP_BYTYPE | NP_NEWTON | NP_TRI) +NPairStyle(half/size/multi2/newton/tri, + NPairHalfSizeMulti2NewtonTri, + NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_TRI_H -#define LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_TRI_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_H +#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfSizeBytypeNewtonTri : public NPair { +class NPairHalfSizeMulti2NewtonTri : public NPair { public: - NPairHalfSizeBytypeNewtonTri(class LAMMPS *); - ~NPairHalfSizeBytypeNewtonTri() {} + NPairHalfSizeMulti2NewtonTri(class LAMMPS *); + ~NPairHalfSizeMulti2NewtonTri() {} void build(class NeighList *); }; diff --git a/src/nstencil.h b/src/nstencil.h index 7c6a04a56a..faf4ca0872 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -34,7 +34,9 @@ class NStencil : protected Pointers { int *** stencil_multi2; // list of bin offsets in each multi2 stencil int ** maxstencil_multi2; // max stencil size for each multi2 stencil - ^do i need a multi 2 analog to distsq_multi? + // Note distsq_multi is used in multi to quickly skip bins beyond interaction cutoff + // Not quite sure why bins are beyond this distance? Have to think + // Probably not needed for multi2 since bins are more efficiently chosen int sx,sy,sz; // extent of stencil in each dim int **sx_multi2; // analogs for multi tiered From 9a3ece75f25c9b6d8aa0ab1b6f2af6e8cf9c8875 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 10 Nov 2020 23:30:58 -0700 Subject: [PATCH 11/73] Batch 1 of typo/bug fixes --- src/comm_brick.cpp | 4 +- src/nbin.cpp | 72 +++++++------- src/npair_half_size_multi2_newtoff.cpp | 4 +- src/nstencil.cpp | 8 ++ src/nstencil.h | 5 +- src/nstencil_full_multi2_2d.h | 2 +- src/nstencil_full_multi2_3d.cpp | 2 +- src/nstencil_full_multi2_3d.h | 2 +- src/nstencil_half_multi2_2d.cpp | 10 +- src/nstencil_half_multi2_2d_tri.cpp | 10 +- src/nstencil_half_multi2_3d_tri.cpp | 125 +------------------------ 11 files changed, 70 insertions(+), 174 deletions(-) diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 981e86c2a4..e283e08e20 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -211,8 +211,8 @@ void CommBrick::setup() cutghost[2] = cut * length2; if (mode == Comm::MULTI) { - if (multi_tiered) { - // If using tiered binlists, use the itype-itype interaction distance for communication + if (multi2) { + // If using multi2 binlists, use the itype-itype interaction distance for communication double **cutneighsq = neighbor->cutneighsq; for (i = 1; i <= ntypes; i++) { cut = 0.0; diff --git a/src/nbin.cpp b/src/nbin.cpp index 4ab3270287..cf6ef3ddd4 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -31,18 +31,18 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) bins = nullptr; atom2bin = nullptr; - nbinx_tiered = nullptr; nbiny_tiered = nullptr; nbinz_tiered = nullptr; - mbins_tiered = nullptr; - mbinx_tiered = nullptr; mbiny_tiered = nullptr, mbinz_tiered = nullptr; - mbinxlo_tiered = nullptr; - mbinylo_tiered = nullptr; - mbinzlo_tiered = nullptr; - binsizex_tiered = nullptr; binsizey_tiered = nullptr; binsizez_tiered = nullptr; - bininvx_tiered = nullptr; bininvy_tiered = nullptr; bininvz_tiered = nullptr; - binhead_tiered = nullptr; - bins_tiered = nullptr; - atom2bin_tiered = nullptr; - maxbins_tiered = nullptr; + nbinx_multi2 = nullptr; nbiny_multi2 = nullptr; nbinz_multi2 = nullptr; + mbins_multi2 = nullptr; + mbinx_multi2 = nullptr; mbiny_multi2 = nullptr, mbinz_multi2 = nullptr; + mbinxlo_multi2 = nullptr; + mbinylo_multi2 = nullptr; + mbinzlo_multi2 = nullptr; + binsizex_multi2 = nullptr; binsizey_multi2 = nullptr; binsizez_multi2 = nullptr; + bininvx_multi2 = nullptr; bininvy_multi2 = nullptr; bininvz_multi2 = nullptr; + binhead_multi2 = nullptr; + bins_multi2 = nullptr; + atom2bin_multi2 = nullptr; + maxbins_multi2 = nullptr; maxtypes = 0; @@ -64,36 +64,36 @@ NBin::~NBin() memory->destroy(bins); memory->destroy(atom2bin); - if (!bins_tiered) return; + if (!bins_multi2) return; - memory->destroy(nbinx_tiered); - memory->destroy(nbiny_tiered); - memory->destroy(nbinz_tiered); - memory->destroy(mbins_tiered); - memory->destroy(mbinx_tiered); - memory->destroy(mbiny_tiered); - memory->destroy(mbinz_tiered); - memory->destroy(mbinxlo_tiered); - memory->destroy(mbinylo_tiered); - memory->destroy(mbinzlo_tiered); + memory->destroy(nbinx_multi2); + memory->destroy(nbiny_multi2); + memory->destroy(nbinz_multi2); + memory->destroy(mbins_multi2); + memory->destroy(mbinx_multi2); + memory->destroy(mbiny_multi2); + memory->destroy(mbinz_multi2); + memory->destroy(mbinxlo_multi2); + memory->destroy(mbinylo_multi2); + memory->destroy(mbinzlo_multi2); - memory->destroy(binsizex_tiered); - memory->destroy(binsizey_tiered); - memory->destroy(binsizez_tiered); - memory->destroy(bininvx_tiered); - memory->destroy(bininvy_tiered); - memory->destroy(bininvz_tiered); + memory->destroy(binsizex_multi2); + memory->destroy(binsizey_multi2); + memory->destroy(binsizez_multi2); + memory->destroy(bininvx_multi2); + memory->destroy(bininvy_multi2); + memory->destroy(bininvz_multi2); for (int n = 1; n <= maxtypes; n++) { - memory->destroy(binhead_tiered[n]); - memory->destroy(bins_tiered[n]); - memory->destroy(atom2bin_tiered[n]); + memory->destroy(binhead_multi2[n]); + memory->destroy(bins_multi2[n]); + memory->destroy(atom2bin_multi2[n]); } - delete [] binhead_tiered; - delete [] bins_tiered; - delete [] atom2bin_tiered; + delete [] binhead_multi2; + delete [] bins_multi2; + delete [] atom2bin_multi2; - memory->destroy(maxbins_tiered); + memory->destroy(maxbins_multi2); } /* ---------------------------------------------------------------------- */ diff --git a/src/npair_half_size_multi2_newtoff.cpp b/src/npair_half_size_multi2_newtoff.cpp index 0ea9e493ce..0e0137a77e 100644 --- a/src/npair_half_size_multi2_newtoff.cpp +++ b/src/npair_half_size_multi2_newtoff.cpp @@ -77,7 +77,7 @@ void NPairHalfSizeMulti2Newtoff::build(NeighList *list) // stores own/own pairs only once // stores own/ghost pairs on both procs - ibin = nb->atom2bin_type[itype][i]; + ibin = atom2bin_multi2[itype][i]; for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { kbin = ibin; @@ -90,7 +90,7 @@ void NPairHalfSizeMulti2Newtoff::build(NeighList *list) ns = nstencil_multi2[itype][ktype]; for (k = 0; k < ns; k++) { js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >=0; j = nb->bins_multi2[ktype][j]) { + for (j = js; j >=0; j = bins_multi2[ktype][j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/nstencil.cpp b/src/nstencil.cpp index b7cfe4dc72..bcde1024b3 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -284,6 +284,10 @@ void NStencil::create_setup() memory->create(binsizez_multi2, n+1, n+1, "neighstencil:binsizez_multi2"); + memory->create(mbinx_multi2, n+1, n+1,"neighstencil:mbinx_multi2"); + memory->create(mbiney_multi2, n+1, n+1, "neighstencil:mbiny_multi2"); + memory->create(mbinz_multi2, n+1, n+1, "neighstencil:mbinz_multi2"); + // Skip all stencils by default, initialize smax for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { @@ -323,6 +327,10 @@ void NStencil::create_setup() binsizey_multi2[i][j] = binsizey; binsizez_multi2[i][j] = binsizez; + mbinx_multi2[i][j] = mbinx; + mbiny_multi2[i][j] = mbiny; + mbinz_multi2[i][j] = mbinz; + stencil_range = stencil_cut[i][j]; sx = static_cast (stencil_range*bininvx); diff --git a/src/nstencil.h b/src/nstencil.h index faf4ca0872..158ced07d2 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -70,7 +70,7 @@ class NStencil : protected Pointers { double cutneighmax; double cutneighmaxsq; double *cuttypesq; - double *cutneighsq; + double **cutneighsq; // data from NBin class @@ -80,6 +80,9 @@ class NStencil : protected Pointers { // analogs for multi-tiered + int **mbinx_multi2; + int **mbiny_multi2; + int **mbinz_multi2; double **binsizex_multi2; double **binsizey_multi2; double **binsizez_multi2; diff --git a/src/nstencil_full_multi2_2d.h b/src/nstencil_full_multi2_2d.h index 1dfc5ae4d6..b9f46056c5 100644 --- a/src/nstencil_full_multi2_2d.h +++ b/src/nstencil_full_multi2_2d.h @@ -14,7 +14,7 @@ #ifdef NSTENCIL_CLASS NStencilStyle(full/multi2/2d, - NStencilFullMulti22d, NS_FULL | NS_Multi2 | NS_2D | NS_ORTHO | NS_TRI) + NStencilFullMulti22d, NS_FULL | NS_MULTI2 | NS_2D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 77ae62738c..808c2d334d 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -92,7 +92,7 @@ void NStencilFullMulti23d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = + stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; nstencil_multi2[itype][jtype] = ns; diff --git a/src/nstencil_full_multi2_3d.h b/src/nstencil_full_multi2_3d.h index f7baefc8e9..102471f2c7 100644 --- a/src/nstencil_full_multi2_3d.h +++ b/src/nstencil_full_multi2_3d.h @@ -14,7 +14,7 @@ #ifdef NSTENCIL_CLASS NStencilStyle(full/multi2/3d, - NStencilFullMulti23d, NS_FULL | NS_Multi2 | NS_3D | NS_ORTHO | NS_TRI) + NStencilFullMulti23d, NS_FULL | NS_MULTI2 | NS_3D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 86da6ea91e..3daf872fa9 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti22d::NStencilHalfMulti23d(LAMMPS *lmp) : +NStencilHalfMulti22d::NStencilHalfMulti22d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti23d::set_stencil_properties() +void NStencilHalfMulti22d::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -69,7 +69,7 @@ void NStencilHalfMulti23d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti23d::create() +void NStencilHalfMulti22d::create() { int itype, jtype, i, j, ns; int n = atom->ntypes; @@ -95,13 +95,13 @@ void NStencilHalfMulti23d::create() for (i = -sx; i <= sx; i++) if (j > 0 || (j == 0 && i > 0)) { if (bin_distance(i,j,0) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; + stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,0) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; + stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } nstencil_multi2[itype][jtype] = ns; diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index 46f55300ce..9e8ae81036 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti22dTri::NStencilHalfMulti22d(LAMMPS *lmp) : +NStencilHalfMulti22dTri::NStencilHalfMulti22dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti22d::set_stencil_properties() +void NStencilHalfMulti22dTri::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -69,7 +69,7 @@ void NStencilHalfMulti22d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti22d::create() +void NStencilHalfMulti22dTri::create() { int itype, jtype, i, j, ns; int n = atom->ntypes; @@ -94,12 +94,12 @@ void NStencilHalfMulti22d::create() for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,0) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; + stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,0) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; + stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } nstencil_multi2[itype][jtype] = ns; diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index bcaf22abbd..652b1ed60f 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti23dTri::NStencilHalfMulti23d(LAMMPS *lmp) : +NStencilHalfMulti23dTri::NStencilHalfMulti23dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti23d::set_stencil_properties() +void NStencilHalfMulti23dTri::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -69,7 +69,7 @@ void NStencilHalfMulti23d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti23d::create() +void NStencilHalfMulti23dTri::create() { int itype, jtype, i, j, k, ns; int n = atom->ntypes; @@ -97,14 +97,14 @@ void NStencilHalfMulti23d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = + stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = + stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } @@ -112,118 +112,3 @@ void NStencilHalfMulti23d::create() } } } - -/* ---------------------------------------------------------------------- */ - -// KS To superclass -void NStencilHalfMulti23d::copy_bin_info_bytype(int itype) { - - mbinx = nb->mbinx_type[itype]; - mbiny = nb->mbiny_type[itype]; - mbinz = nb->mbinz_type[itype]; - binsizex = nb->binsizex_type[itype]; - binsizey = nb->binsizey_type[itype]; - binsizez = nb->binsizez_type[itype]; - bininvx = nb->bininvx_type[itype]; - bininvy = nb->bininvy_type[itype]; - bininvz = nb->bininvz_type[itype]; -} - -/* ---------------------------------------------------------------------- */ - -// KS To superclass? -int NStencilHalfMulti23d::copy_neigh_info_bytype(int itype) { - - cutneighmaxsq = neighbor->cutneighsq[itype][itype]; - cutneighmax = sqrt(cutneighmaxsq); - cuttypesq = neighbor->cuttypesq; - - // 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 (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - return ((2*sx+1) * (2*sy+1) * (2*sz+1)); -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfMulti23d::create_setup() -{ - - int itype, jtype; - int maxtypes; - int smax; - - // maxstencil_type to superclass? - maxtypes = atom->ntypes; - - if (maxstencil_type == NULL) { - memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "maxstencil_type"); - memory->create(nstencil_type, maxtypes+1, maxtypes+1, "nstencil_type"); - stencil_type = new int**[maxtypes+1](); - for (itype = 1; itype <= maxtypes; ++itype) { - stencil_type[itype] = new int*[maxtypes+1](); - for (jtype = 1; jtype <= maxtypes; ++jtype) { - maxstencil_type[itype][jtype] = 0; - nstencil_type[itype][jtype] = 0; - } - } - } - - // like -> like => use standard Newton stencil at bin - - for (itype = 1; itype <= maxtypes; ++itype) { - copy_bin_info_bytype(itype); - smax = copy_neigh_info_bytype(itype); - if (smax > maxstencil_type[itype][itype]) { - maxstencil_type[itype][itype] = smax; - memory->destroy(stencil_type[itype][itype]); - memory->create(stencil_type[itype][itype], smax, - "NStencilHalfBytypeNewton::create_steup() stencil"); - } - create_newton(itype, itype, cutneighmaxsq); - } - - // Cross types: "Newton on" reached by using Newton off stencil and - // looking one way through hierarchy - // smaller -> larger => use Newton off stencil in larger bin - // larger -> smaller => no nstecil required - // If cut offs are same, use existing type-type stencil - - for (itype = 1; itype <= maxtypes; ++itype) { - for (jtype = 1; jtype <= maxtypes; ++jtype) { - if (itype == jtype) continue; - if (cuttypesq[itype] == cuttypesq[jtype]) { - nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; - stencil_type[itype][jtype] = stencil_type[jtype][jtype]; - } - else if (cuttypesq[itype] < cuttypesq[jtype]) { - copy_bin_info_bytype(jtype); - - cutneighmaxsq = cuttypesq[jtype]; - cutneighmax = sqrt(cutneighmaxsq); - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - smax = (2*sx+1) * (2*sy+1) * (2*sz+1); - if (smax > maxstencil_type[itype][jtype]) { - maxstencil_type[itype][jtype] = smax; - memory->destroy(stencil_type[itype][jtype]); - memory->create(stencil_type[itype][jtype], smax, "stencil_type[]"); - } - create_newtoff(itype, jtype, cuttypesq[jtype]); - } - } - } -} From f94c82910d542ea194ec9e959da9f81966e41f03 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Wed, 11 Nov 2020 10:11:49 -0700 Subject: [PATCH 12/73] Fixing remaining bugs to compile --- src/nbin_standard.cpp | 1 + src/npair_half_multi2_newtoff.cpp | 4 ++-- src/npair_half_size_multi2_newton.cpp | 2 +- src/nstencil.cpp | 28 +++++++++++++-------------- src/nstencil.h | 4 ++-- src/nstencil_full_multi2_2d.cpp | 2 +- src/nstencil_full_multi2_2d.h | 2 +- src/nstencil_full_multi2_3d.h | 2 +- src/nstencil_half_multi2_2d.h | 2 +- src/nstencil_half_multi2_2d_tri.h | 2 +- src/nstencil_half_multi2_3d.cpp | 4 ++-- src/nstencil_half_multi2_3d.h | 2 +- src/nstencil_half_multi2_3d_tri.h | 2 +- 13 files changed, 29 insertions(+), 28 deletions(-) diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp index e63c8dcd56..07dfd3a6cb 100644 --- a/src/nbin_standard.cpp +++ b/src/nbin_standard.cpp @@ -19,6 +19,7 @@ #include "comm.h" #include "update.h" #include "error.h" +#include "memory.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_multi2_newtoff.cpp b/src/npair_half_multi2_newtoff.cpp index 83a8054247..b44f2bcc62 100755 --- a/src/npair_half_multi2_newtoff.cpp +++ b/src/npair_half_multi2_newtoff.cpp @@ -87,7 +87,7 @@ void NPairHalfMulti2Newtoff::build(NeighList *list) // stores own/own pairs only once // stores own/ghost pairs on both procs - ibin = nb->atom2bin_type[itype][i]; + ibin = atom2bin_multi2[itype][i]; for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { kbin = ibin; @@ -100,7 +100,7 @@ void NPairHalfMulti2Newtoff::build(NeighList *list) ns = nstencil_multi2[itype][ktype]; for (k = 0; k < ns; k++) { js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >=0; j = nb->bins_multi2[ktype][j]) { + for (j = js; j >=0; j = bins_multi2[ktype][j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi2_newton.cpp index 3b89c259ec..a1832f6a49 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi2_newton.cpp @@ -72,7 +72,7 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) // if j is owned atom, store by virtue of being ahead of i in list // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = nb->atom2bin_multi2[itype][i]; + ibin = atom2bin_multi2[itype][i]; for (ktype = 1; ktype <= atom->ntypes; ktype++) { diff --git a/src/nstencil.cpp b/src/nstencil.cpp index bcde1024b3..033d79e279 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -182,15 +182,15 @@ void NStencil::copy_bin_info() void NStencil::copy_bin_info_multi2(int type) { - mbinx = nb->mbinx2[type]; - mbiny = nb->mbiny2[type]; - mbinz = nb->mbinz2[type]; - binsizex = nb->binsizex2[type]; - binsizey = nb->binsizey2[type]; - binsizez = nb->binsizez2[type]; - bininvx = nb->bininvx2[type]; - bininvy = nb->bininvy2[type]; - bininvz = nb->bininvz2[type]; + mbinx = nb->mbinx_multi2[type]; + mbiny = nb->mbiny_multi2[type]; + mbinz = nb->mbinz_multi2[type]; + binsizex = nb->binsizex_multi2[type]; + binsizey = nb->binsizey_multi2[type]; + binsizez = nb->binsizez_multi2[type]; + bininvx = nb->bininvx_multi2[type]; + bininvy = nb->bininvy_multi2[type]; + bininvz = nb->bininvz_multi2[type]; } /* ---------------------------------------------------------------------- @@ -284,8 +284,8 @@ void NStencil::create_setup() memory->create(binsizez_multi2, n+1, n+1, "neighstencil:binsizez_multi2"); - memory->create(mbinx_multi2, n+1, n+1,"neighstencil:mbinx_multi2"); - memory->create(mbiney_multi2, n+1, n+1, "neighstencil:mbiny_multi2"); + memory->create(mbinx_multi2, n+1, n+1, "neighstencil:mbinx_multi2"); + memory->create(mbiny_multi2, n+1, n+1, "neighstencil:mbiny_multi2"); memory->create(mbinz_multi2, n+1, n+1, "neighstencil:mbinz_multi2"); // Skip all stencils by default, initialize smax @@ -321,7 +321,7 @@ void NStencil::create_setup() // Copy bin info for this particular pair of types bin_type = stencil_bin_type[i][j]; - copy_bin_info_bytype(bin_type); + copy_bin_info_multi2(bin_type); binsizex_multi2[i][j] = binsizex; binsizey_multi2[i][j] = binsizey; @@ -393,8 +393,8 @@ double NStencil::memory_usage() bytes += atom->ntypes*maxstencil_multi * sizeof(double); } else if (neighstyle == Neighbor::MULTI2) { int n = atom->ntypes; - for (i = 1; i <= n; ++i) { - for (j = 1; j <= n; ++j) { + for (int i = 1; i <= n; i++) { + for (int j = 1; j <= n; j++) { bytes += maxstencil_multi2[i][j] * sizeof(int); bytes += maxstencil_multi2[i][j] * sizeof(int); bytes += maxstencil_multi2[i][j] * sizeof(double); diff --git a/src/nstencil.h b/src/nstencil.h index 158ced07d2..5f010cb377 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -102,8 +102,8 @@ class NStencil : protected Pointers { // methods for multi/tiered NStencil - void copy_bin_info_multi2(int); // copy mult/tiered info from NBin class - void set_stencil_properties(); // determine which stencils to build and how + void copy_bin_info_multi2(int); // copy mult/tiered info from NBin class + virtual void set_stencil_properties(){} // determine which stencils to build and how }; } diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index f62cddb0b5..ba503fd5f5 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -89,7 +89,7 @@ void NStencilFullMulti22d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,0) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; + stencil_multi2[itype][jtype][ns++] = j*mbinx + i; nstencil_multi2[itype][jtype] = ns; } diff --git a/src/nstencil_full_multi2_2d.h b/src/nstencil_full_multi2_2d.h index b9f46056c5..46e12db039 100644 --- a/src/nstencil_full_multi2_2d.h +++ b/src/nstencil_full_multi2_2d.h @@ -28,7 +28,7 @@ namespace LAMMPS_NS { class NStencilFullMulti22d : public NStencil { public: NStencilFullMulti22d(class LAMMPS *); - ~NStencilFullMulti22d(); + ~NStencilFullMulti22d() {} void create(); protected: diff --git a/src/nstencil_full_multi2_3d.h b/src/nstencil_full_multi2_3d.h index 102471f2c7..fb6a19ec6f 100644 --- a/src/nstencil_full_multi2_3d.h +++ b/src/nstencil_full_multi2_3d.h @@ -28,7 +28,7 @@ namespace LAMMPS_NS { class NStencilFullMulti23d : public NStencil { public: NStencilFullMulti23d(class LAMMPS *); - ~NStencilFullMulti23d(); + ~NStencilFullMulti23d(){} void create(); protected: diff --git a/src/nstencil_half_multi2_2d.h b/src/nstencil_half_multi2_2d.h index ba3a471833..8e79fd0541 100644 --- a/src/nstencil_half_multi2_2d.h +++ b/src/nstencil_half_multi2_2d.h @@ -28,7 +28,7 @@ namespace LAMMPS_NS { class NStencilHalfMulti22d : public NStencil { public: NStencilHalfMulti22d(class LAMMPS *); - ~NStencilHalfMulti22d(); + ~NStencilHalfMulti22d() {} void create(); protected: diff --git a/src/nstencil_half_multi2_2d_tri.h b/src/nstencil_half_multi2_2d_tri.h index 1d25e56776..4072c6d31b 100755 --- a/src/nstencil_half_multi2_2d_tri.h +++ b/src/nstencil_half_multi2_2d_tri.h @@ -28,7 +28,7 @@ namespace LAMMPS_NS { class NStencilHalfMulti22dTri : public NStencil { public: NStencilHalfMulti22dTri(class LAMMPS *); - ~NStencilHalfMulti22dTri(); + ~NStencilHalfMulti22dTri() {} void create(); protected: diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 02a65bd3a1..a129d6b53b 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -98,7 +98,7 @@ void NStencilHalfMulti23d::create() for (i = -sx; i <= sx; i++) if (k > 0 || j > 0 || (j == 0 && i > 0)) { if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = + stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } } else { @@ -106,7 +106,7 @@ void NStencilHalfMulti23d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = + stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } diff --git a/src/nstencil_half_multi2_3d.h b/src/nstencil_half_multi2_3d.h index 9cae8269cb..6a0d8f90a2 100644 --- a/src/nstencil_half_multi2_3d.h +++ b/src/nstencil_half_multi2_3d.h @@ -28,7 +28,7 @@ namespace LAMMPS_NS { class NStencilHalfMulti23d : public NStencil { public: NStencilHalfMulti23d(class LAMMPS *); - ~NStencilHalfMulti23d(); + ~NStencilHalfMulti23d() {} void create(); protected: diff --git a/src/nstencil_half_multi2_3d_tri.h b/src/nstencil_half_multi2_3d_tri.h index f4b37ebebe..de449ce1d8 100755 --- a/src/nstencil_half_multi2_3d_tri.h +++ b/src/nstencil_half_multi2_3d_tri.h @@ -28,7 +28,7 @@ namespace LAMMPS_NS { class NStencilHalfMulti23dTri : public NStencil { public: NStencilHalfMulti23dTri(class LAMMPS *); - ~NStencilHalfMulti23dTri(); + ~NStencilHalfMulti23dTri() {} void create(); protected: From ac527f4615b8a845c3fea69f66b782fbf2e2df0d Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Wed, 11 Nov 2020 15:39:53 -0700 Subject: [PATCH 13/73] Fixing bugs in nstencil --- src/nstencil.cpp | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 033d79e279..c537767d64 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -74,7 +74,11 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) nstencil_multi = nullptr; stencil_multi = nullptr; distsq_multi = nullptr; - + + nstencil_multi2 = nullptr; + stencil_multi2 = nullptr; + maxstencil_multi2 = nullptr; + stencil_half = nullptr; stencil_skip = nullptr; stencil_bin_type = nullptr; @@ -292,7 +296,6 @@ void NStencil::create_setup() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { stencil_skip[i][j] = 1; - maxstencil_multi2[i][j] = 0; } } From b6dfc28e38c122c0a284a3d0d791e50f2621ad4d Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Wed, 11 Nov 2020 22:50:59 -0700 Subject: [PATCH 14/73] Resetting bin sizes in stencils --- src/nstencil_full_multi2_2d.cpp | 5 +++++ src/nstencil_full_multi2_3d.cpp | 5 +++++ src/nstencil_half_multi2_2d.cpp | 5 +++++ src/nstencil_half_multi2_2d_tri.cpp | 5 +++++ src/nstencil_half_multi2_3d.cpp | 5 +++++ src/nstencil_half_multi2_3d_tri.cpp | 5 +++++ 6 files changed, 30 insertions(+) diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index ba503fd5f5..8ff504b48d 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -84,6 +84,11 @@ void NStencilFullMulti22d::create() mbinx = mbinx_multi2[itype][jtype]; mbiny = mbiny_multi2[itype][jtype]; + // Redefine for use in bin_distance() + binsizex = binsizex_multi2[itype][jtype]; + binsizey = binsizey_multi2[itype][jtype]; + binsizez = binsizez_multi2[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; for (j = -sy; j <= sy; j++) diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 808c2d334d..1257650c5e 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -86,6 +86,11 @@ void NStencilFullMulti23d::create() mbiny = mbiny_multi2[itype][jtype]; mbinz = mbinz_multi2[itype][jtype]; + // Redefine for use in bin_distance() + binsizex = binsizex_multi2[itype][jtype]; + binsizey = binsizey_multi2[itype][jtype]; + binsizez = binsizez_multi2[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; for (k = -sz; k <= sz; k++) diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 3daf872fa9..89d2903f1c 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -88,6 +88,11 @@ void NStencilHalfMulti22d::create() mbinx = mbinx_multi2[itype][jtype]; mbiny = mbiny_multi2[itype][jtype]; + // Redefine for use in bin_distance() + binsizex = binsizex_multi2[itype][jtype]; + binsizey = binsizey_multi2[itype][jtype]; + binsizez = binsizez_multi2[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; if (stencil_half[itype][jtype]) { diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index 9e8ae81036..4b4019cef2 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -88,6 +88,11 @@ void NStencilHalfMulti22dTri::create() mbinx = mbinx_multi2[itype][jtype]; mbiny = mbiny_multi2[itype][jtype]; + // Redefine for use in bin_distance() + binsizex = binsizex_multi2[itype][jtype]; + binsizey = binsizey_multi2[itype][jtype]; + binsizez = binsizez_multi2[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; if (stencil_half[itype][jtype]) { diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index a129d6b53b..1777e748de 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -90,6 +90,11 @@ void NStencilHalfMulti23d::create() mbiny = mbiny_multi2[itype][jtype]; mbinz = mbinz_multi2[itype][jtype]; + // Redefine for use in bin_distance() + binsizex = binsizex_multi2[itype][jtype]; + binsizey = binsizey_multi2[itype][jtype]; + binsizez = binsizez_multi2[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; if (stencil_half[itype][jtype]) { diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index 652b1ed60f..4a9ba63b20 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -90,6 +90,11 @@ void NStencilHalfMulti23dTri::create() mbiny = mbiny_multi2[itype][jtype]; mbinz = mbinz_multi2[itype][jtype]; + // Redefine for use in bin_distance() + binsizex = binsizex_multi2[itype][jtype]; + binsizey = binsizey_multi2[itype][jtype]; + binsizez = binsizez_multi2[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; if (stencil_half[itype][jtype]) { From 6909839ff0fde523596878d2e7138d6e5e399c1c Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Thu, 12 Nov 2020 15:03:44 -0700 Subject: [PATCH 15/73] Fix full multi stencil --- src/nstencil_full_multi2_2d.cpp | 5 +++-- src/nstencil_full_multi2_3d.cpp | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index 8ff504b48d..c59edbe90d 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -50,11 +50,12 @@ void NStencilFullMulti22d::set_stencil_properties() stencil_half[i][j] = 0; stencil_skip[i][j] = 0; - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); if(cuttypesq[i] <= cuttypesq[j]){ - stencil_bin_type[i][j] = i; + stencil_cut[i][j] = sqrt(cutneighsq[j][j]); + stencil_bin_type[i][j] = j; } else { + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); stencil_bin_type[i][j] = j; } } diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 1257650c5e..6021382022 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -50,11 +50,12 @@ void NStencilFullMulti23d::set_stencil_properties() stencil_half[i][j] = 0; stencil_skip[i][j] = 0; - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); if(cuttypesq[i] <= cuttypesq[j]){ - stencil_bin_type[i][j] = i; + stencil_cut[i][j] = sqrt(cutneighsq[j][j]); + stencil_bin_type[i][j] = j; } else { + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); stencil_bin_type[i][j] = j; } } From af11a54a272831e3383b1184871057ab88708928 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Thu, 12 Nov 2020 18:37:53 -0700 Subject: [PATCH 16/73] Copying more variables to classes and moving/clarifying definitions --- src/nbin.cpp | 93 ++++++++++++++++++++++ src/nbin.h | 2 +- src/nbin_multi2.cpp | 58 +------------- src/nbin_multi2.h | 1 - src/nbin_standard.cpp | 48 ----------- src/nbin_standard.h | 4 - src/nstencil.cpp | 119 ++++++++++++++++++---------- src/nstencil.h | 47 +++++++---- src/nstencil_full_multi2_2d.cpp | 17 ++-- src/nstencil_full_multi2_3d.cpp | 21 +++-- src/nstencil_half_multi2_2d.cpp | 13 +-- src/nstencil_half_multi2_2d_tri.cpp | 19 ++--- src/nstencil_half_multi2_3d.cpp | 23 +++--- src/nstencil_half_multi2_3d_tri.cpp | 23 +++--- 14 files changed, 252 insertions(+), 236 deletions(-) diff --git a/src/nbin.cpp b/src/nbin.cpp index cf6ef3ddd4..39c7ce6447 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -123,3 +123,96 @@ void NBin::copy_neighbor_info() if (cutoff_custom > 0.0) cutneighmax = cutoff_custom; } + + + +/* ---------------------------------------------------------------------- + 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 (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx) + nbinx; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx); + ix = MIN(ix,nbinx-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy) + nbiny; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy); + iy = MIN(iy,nbiny-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz) + nbinz; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz); + iz = MIN(iz,nbinz-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz) - 1; + + return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo); +} + + +/* ---------------------------------------------------------------------- + convert atom coords into local bin # for a particular type +------------------------------------------------------------------------- */ + +int NBin::coord2bin_multi2(double *x, int it) +{ + int ix,iy,iz; + int ibin; + + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi2[it]) + nbinx_multi2[it]; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]); + ix = MIN(ix,nbinx_multi2[it]-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi2[it]) + nbiny_multi2[it]; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]); + iy = MIN(iy,nbiny_multi2[it]-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi2[it]) + nbinz_multi2[it]; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]); + iz = MIN(iz,nbinz_multi2[it]-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]) - 1; + + + ibin = (iz-mbinzlo_multi2[it])*mbiny_multi2[it]*mbinx_multi2[it] + + (iy-mbinylo_multi2[it])*mbinx_multi2[it] + + (ix-mbinxlo_multi2[it]); + return ibin; +} + diff --git a/src/nbin.h b/src/nbin.h index 33b93ef79c..441e4815dd 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -97,7 +97,7 @@ class NBin : protected Pointers { // methods int coord2bin(double *); - int coord2bin(double *, int); + int coord2bin_multi2(double *, int); }; } diff --git a/src/nbin_multi2.cpp b/src/nbin_multi2.cpp index 7a87ba940c..f57558a36c 100644 --- a/src/nbin_multi2.cpp +++ b/src/nbin_multi2.cpp @@ -324,7 +324,7 @@ void NBinMulti2::bin_atoms() for (i = nall-1; i >= nlocal; i--) { if (mask[i] & bitmask) { n = type[i]; - ibin = coord2bin(x[i], n); + ibin = coord2bin_multi2(x[i], n); atom2bin_multi2[n][i] = ibin; bins_multi2[n][i] = binhead_multi2[n][ibin]; binhead_multi2[n][ibin] = i; @@ -332,7 +332,7 @@ void NBinMulti2::bin_atoms() } for (i = atom->nfirst-1; i >= 0; i--) { n = type[i]; - ibin = coord2bin(x[i], n); + ibin = coord2bin_multi2(x[i], n); atom2bin_multi2[n][i] = ibin; bins_multi2[n][i] = binhead_multi2[n][ibin]; binhead_multi2[n][ibin] = i; @@ -340,7 +340,7 @@ void NBinMulti2::bin_atoms() } else { for (i = nall-1; i >= 0; i--) { n = type[i]; - ibin = coord2bin(x[i], n); + ibin = coord2bin_multi2(x[i], n); atom2bin_multi2[n][i] = ibin; bins_multi2[n][i] = binhead_multi2[n][ibin]; binhead_multi2[n][ibin] = i; @@ -348,58 +348,6 @@ void NBinMulti2::bin_atoms() } } -/* ---------------------------------------------------------------------- - convert atom coords into local bin # for a particular type - 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 NBinMulti2::coord2bin(double *x, int it) -{ - int ix,iy,iz; - int ibin; - - if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable"); - - if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi2[it]) + nbinx_multi2[it]; - else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]); - ix = MIN(ix,nbinx_multi2[it]-1); - } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]) - 1; - - if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi2[it]) + nbiny_multi2[it]; - else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]); - iy = MIN(iy,nbiny_multi2[it]-1); - } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]) - 1; - - if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi2[it]) + nbinz_multi2[it]; - else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]); - iz = MIN(iz,nbinz_multi2[it]-1); - } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]) - 1; - - - ibin = (iz-mbinzlo_multi2[it])*mbiny_multi2[it]*mbinx_multi2[it] - + (iy-mbinylo_multi2[it])*mbinx_multi2[it] - + (ix-mbinxlo_multi2[it]); - return ibin; -} - - /* ---------------------------------------------------------------------- */ double NBinMulti2::memory_usage() diff --git a/src/nbin_multi2.h b/src/nbin_multi2.h index 8cca7b1023..3094027f64 100644 --- a/src/nbin_multi2.h +++ b/src/nbin_multi2.h @@ -38,7 +38,6 @@ class NBinMulti2 : public NBin { private: - int coord2bin(double *, int); int itype_min(); }; diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp index 07dfd3a6cb..4298a9670c 100644 --- a/src/nbin_standard.cpp +++ b/src/nbin_standard.cpp @@ -259,54 +259,6 @@ void NBinStandard::bin_atoms() } } - -/* ---------------------------------------------------------------------- - 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 NBinStandard::coord2bin(double *x) -{ - int ix,iy,iz; - - if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable"); - - if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx) + nbinx; - else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx); - ix = MIN(ix,nbinx-1); - } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx) - 1; - - if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy) + nbiny; - else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy); - iy = MIN(iy,nbiny-1); - } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy) - 1; - - if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz) + nbinz; - else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz); - iz = MIN(iz,nbinz-1); - } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz) - 1; - - return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo); -} - - /* ---------------------------------------------------------------------- */ double NBinStandard::memory_usage() diff --git a/src/nbin_standard.h b/src/nbin_standard.h index d8ecb435b7..89b749c948 100644 --- a/src/nbin_standard.h +++ b/src/nbin_standard.h @@ -34,10 +34,6 @@ class NBinStandard : public NBin { void setup_bins(int); void bin_atoms(); double memory_usage(); - - private: - - int coord2bin(double *); }; } diff --git a/src/nstencil.cpp b/src/nstencil.cpp index c537767d64..2ace1125e8 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -124,13 +124,17 @@ NStencil::~NStencil() memory->destroy(stencil_bin_type); memory->destroy(stencil_cut); - memory->destroy(sx_multi2); - memory->destroy(sy_multi2); - memory->destroy(sz_multi2); + memory->destroy(stencil_sx_multi2); + memory->destroy(stencil_sy_multi2); + memory->destroy(stencil_sz_multi2); + + memory->destroy(stencil_mbinx_multi2); + memory->destroy(stencil_mbiny_multi2); + memory->destroy(stencil_mbinz_multi2); - memory->destroy(binsizex_multi2); - memory->destroy(binsizey_multi2); - memory->destroy(binsizez_multi2); + memory->destroy(stencil_binsizex_multi2); + memory->destroy(stencil_binsizey_multi2); + memory->destroy(stencil_binsizez_multi2); } } @@ -181,20 +185,20 @@ void NStencil::copy_bin_info() } /* ---------------------------------------------------------------------- - copy needed info for a given type from NBin class to this stencil class + copy needed info for multi2 from NBin class to this stencil class ------------------------------------------------------------------------- */ -void NStencil::copy_bin_info_multi2(int type) +void NStencil::copy_bin_info_multi2() { - mbinx = nb->mbinx_multi2[type]; - mbiny = nb->mbiny_multi2[type]; - mbinz = nb->mbinz_multi2[type]; - binsizex = nb->binsizex_multi2[type]; - binsizey = nb->binsizey_multi2[type]; - binsizez = nb->binsizez_multi2[type]; - bininvx = nb->bininvx_multi2[type]; - bininvy = nb->bininvy_multi2[type]; - bininvz = nb->bininvz_multi2[type]; + mbinx_multi2 = nb->mbinx_multi2; + mbiny_multi2 = nb->mbiny_multi2; + mbinz_multi2 = nb->mbinz_multi2; + binsizex_multi2 = nb->binsizex_multi2; + binsizey_multi2 = nb->binsizey_multi2; + binsizez_multi2 = nb->binsizez_multi2; + bininvx_multi2 = nb->bininvx_multi2; + bininvy_multi2 = nb->bininvy_multi2; + bininvz_multi2 = nb->bininvz_multi2; } /* ---------------------------------------------------------------------- @@ -266,6 +270,8 @@ void NStencil::create_setup() int i, j, bin_type, smax; double stencil_range; int n = atom->ntypes; + + if(nb) copy_bin_info_multi2(); // Allocate arrays to store stencil information memory->create(stencil_half, n+1, n+1, @@ -277,20 +283,26 @@ void NStencil::create_setup() memory->create(stencil_cut, n+1, n+1, "neighstencil:stencil_cut"); - memory->create(sx_multi2, n+1, n+1, "neighstencil:sx_multi2"); - memory->create(sy_multi2, n+1, n+1, "neighstencil:sy_multi2"); - memory->create(sz_multi2, n+1, n+1, "neighstencil:sz_multi2"); + memory->create(stencil_sx_multi2, n+1, n+1, + "neighstencil:stencil_sx_multi2"); + memory->create(stencil_sy_multi2, n+1, n+1, + "neighstencil:stencil_sy_multi2"); + memory->create(stencil_sz_multi2, n+1, n+1, + "neighstencil:stencil_sz_multi2"); - memory->create(binsizex_multi2, n+1, n+1, - "neighstencil:binsizex_multi2"); - memory->create(binsizey_multi2, n+1, n+1, - "neighstencil:binsizey_multi2"); - memory->create(binsizez_multi2, n+1, n+1, - "neighstencil:binsizez_multi2"); + memory->create(stencil_binsizex_multi2, n+1, n+1, + "neighstencil:stencil_binsizex_multi2"); + memory->create(stencil_binsizey_multi2, n+1, n+1, + "neighstencil:stencil_binsizey_multi2"); + memory->create(stencil_binsizez_multi2, n+1, n+1, + "neighstencil:stencil_binsizez_multi2"); - memory->create(mbinx_multi2, n+1, n+1, "neighstencil:mbinx_multi2"); - memory->create(mbiny_multi2, n+1, n+1, "neighstencil:mbiny_multi2"); - memory->create(mbinz_multi2, n+1, n+1, "neighstencil:mbinz_multi2"); + memory->create(stencil_mbinx_multi2, n+1, n+1, + "neighstencil:stencil_mbinx_multi2"); + memory->create(stencil_mbiny_multi2, n+1, n+1, + "neighstencil:stencil_mbiny_multi2"); + memory->create(stencil_mbinz_multi2, n+1, n+1, + "neighstencil:stencil_mbinz_multi2"); // Skip all stencils by default, initialize smax for (i = 1; i <= n; i++) { @@ -324,28 +336,27 @@ void NStencil::create_setup() // Copy bin info for this particular pair of types bin_type = stencil_bin_type[i][j]; - copy_bin_info_multi2(bin_type); - binsizex_multi2[i][j] = binsizex; - binsizey_multi2[i][j] = binsizey; - binsizez_multi2[i][j] = binsizez; + stencil_binsizex_multi2[i][j] = binsizex_multi2[bin_type]; + stencil_binsizey_multi2[i][j] = binsizey_multi2[bin_type]; + stencil_binsizez_multi2[i][j] = binsizez_multi2[bin_type]; - mbinx_multi2[i][j] = mbinx; - mbiny_multi2[i][j] = mbiny; - mbinz_multi2[i][j] = mbinz; + stencil_mbinx_multi2[i][j] = mbinx_multi2[bin_type]; + stencil_mbiny_multi2[i][j] = mbiny_multi2[bin_type]; + stencil_mbinz_multi2[i][j] = mbinz_multi2[bin_type]; stencil_range = stencil_cut[i][j]; - sx = static_cast (stencil_range*bininvx); + sx = static_cast (stencil_range*bininvx_multi2[bin_type]); if (sx*binsizex < stencil_range) sx++; - sy = static_cast (stencil_range*bininvy); + sy = static_cast (stencil_range*bininvy_multi2[bin_type]); if (sy*binsizey < stencil_range) sy++; - sz = static_cast (stencil_range*bininvz); + sz = static_cast (stencil_range*bininvz_multi2[bin_type]); if (sz*binsizez < stencil_range) sz++; - sx_multi2[i][j] = sx; - sy_multi2[i][j] = sy; - sz_multi2[i][j] = sz; + stencil_sx_multi2[i][j] = sx; + stencil_sy_multi2[i][j] = sy; + stencil_sz_multi2[i][j] = sz; smax = ((2*sx+1) * (2*sy+1) * (2*sz+1)); @@ -383,6 +394,30 @@ double NStencil::bin_distance(int i, int j, int k) return (delx*delx + dely*dely + delz*delz); } + +/* ---------------------------------------------------------------------- + compute closest distance for a given atom type +------------------------------------------------------------------------- */ + +double NStencil::bin_distance_multi2(int i, int j, int k, int type) +{ + double delx,dely,delz; + + if (i > 0) delx = (i-1)*binsizex_multi2[type]; + else if (i == 0) delx = 0.0; + else delx = (i+1)*binsizex_multi2[type]; + + if (j > 0) dely = (j-1)*binsizey_multi2[type]; + else if (j == 0) dely = 0.0; + else dely = (j+1)*binsizey_multi2[type]; + + if (k > 0) delz = (k-1)*binsizez_multi2[type]; + else if (k == 0) delz = 0.0; + else delz = (k+1)*binsizez_multi2[type]; + + return (delx*delx + dely*dely + delz*delz); +} + /* ---------------------------------------------------------------------- */ double NStencil::memory_usage() diff --git a/src/nstencil.h b/src/nstencil.h index 5f010cb377..68c7702f79 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -39,13 +39,13 @@ class NStencil : protected Pointers { // Probably not needed for multi2 since bins are more efficiently chosen int sx,sy,sz; // extent of stencil in each dim - int **sx_multi2; // analogs for multi tiered - int **sy_multi2; - int **sz_multi2; + int **stencil_sx_multi2; // analogs for each multi2 stencil + int **stencil_sy_multi2; + int **stencil_sz_multi2; double cutoff_custom; // cutoff set by requestor - // Arrays to store options for multi/tiered itype-jtype stencils + // Arrays to store options for multi2 itype-jtype stencils bool **stencil_half; // flag creation of a half stencil for itype-jtype bool **stencil_skip; // skip creation of itype-jtype stencils (for newton on) int **stencil_bin_type; // what type to use for bin information @@ -78,15 +78,27 @@ class NStencil : protected Pointers { double binsizex,binsizey,binsizez; double bininvx,bininvy,bininvz; - // analogs for multi-tiered + // data from NBin class for multi2 + + int *mbinx_multi2; + int *mbiny_multi2; + int *mbinz_multi2; + double *binsizex_multi2; + double *binsizey_multi2; + double *binsizez_multi2; + double *bininvx_multi2; + double *bininvy_multi2; + double *bininvz_multi2; + + // Stored bin information for each stencil + + int **stencil_mbinx_multi2; + int **stencil_mbiny_multi2; + int **stencil_mbinz_multi2; + double **stencil_binsizex_multi2; + double **stencil_binsizey_multi2; + double **stencil_binsizez_multi2; - int **mbinx_multi2; - int **mbiny_multi2; - int **mbinz_multi2; - double **binsizex_multi2; - double **binsizey_multi2; - double **binsizez_multi2; - // data common to all NStencil variants int xyzflag; // 1 if stencilxyz is allocated @@ -95,15 +107,16 @@ class NStencil : protected Pointers { int dimension; - // methods for all NStencil variants + // methods for standard NStencil variants void copy_bin_info(); // copy info from NBin class double bin_distance(int, int, int); // distance between bin corners - // methods for multi/tiered NStencil - - void copy_bin_info_multi2(int); // copy mult/tiered info from NBin class - virtual void set_stencil_properties(){} // determine which stencils to build and how + // methods for multi2 NStencil + + double bin_distance_multi2(int, int, int, int); // distance between bin corners for different types + void copy_bin_info_multi2(); // copy mult2 info from NBin class + virtual void set_stencil_properties(){} // determine which stencils to build and how }; } diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index c59edbe90d..627a1e2f9e 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -68,7 +68,7 @@ void NStencilFullMulti22d::set_stencil_properties() void NStencilFullMulti22d::create() { - int itype, jtype, i, j, k, ns; + int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; double cutsq; @@ -79,22 +79,19 @@ void NStencilFullMulti22d::create() ns = 0; - sx = sx_multi2[itype][jtype]; - sy = sy_multi2[itype][jtype]; + sx = stencil_sx_multi2[itype][jtype]; + sy = stencil_sy_multi2[itype][jtype]; - mbinx = mbinx_multi2[itype][jtype]; - mbiny = mbiny_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi2[itype][jtype]; + mbiny = stencil_mbiny_multi2[itype][jtype]; - // Redefine for use in bin_distance() - binsizex = binsizex_multi2[itype][jtype]; - binsizey = binsizey_multi2[itype][jtype]; - binsizez = binsizez_multi2[itype][jtype]; + bin_type = stencil_bin_type[i][j]; cutsq = stencil_cut[itype][jtype]; for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutsq) + if (bin_distance_multi2(i,j,0,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = j*mbinx + i; nstencil_multi2[itype][jtype] = ns; diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 6021382022..19bf30ec07 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -68,7 +68,7 @@ void NStencilFullMulti23d::set_stencil_properties() void NStencilFullMulti23d::create() { - int itype, jtype, i, j, k, ns; + int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; double cutsq; @@ -79,25 +79,22 @@ void NStencilFullMulti23d::create() ns = 0; - sx = sx_multi2[itype][jtype]; - sy = sy_multi2[itype][jtype]; - sz = sz_multi2[itype][jtype]; + sx = stencil_sx_multi2[itype][jtype]; + sy = stencil_sy_multi2[itype][jtype]; + sz = stencil_sz_multi2[itype][jtype]; - mbinx = mbinx_multi2[itype][jtype]; - mbiny = mbiny_multi2[itype][jtype]; - mbinz = mbinz_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi2[itype][jtype]; + mbiny = stencil_mbiny_multi2[itype][jtype]; + mbinz = stencil_mbinz_multi2[itype][jtype]; - // Redefine for use in bin_distance() - binsizex = binsizex_multi2[itype][jtype]; - binsizey = binsizey_multi2[itype][jtype]; - binsizez = binsizez_multi2[itype][jtype]; + bin_type = stencil_bin_type[i][j]; cutsq = stencil_cut[itype][jtype]; for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutsq) + if (bin_distance_multi2(i,j,k,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 89d2903f1c..2a3c8da45c 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -82,16 +82,11 @@ void NStencilHalfMulti22d::create() ns = 0; - sx = sx_multi2[itype][jtype]; - sy = sy_multi2[itype][jtype]; + sx = stencil_sx_multi2[itype][jtype]; + sy = stencil_sy_multi2[itype][jtype]; - mbinx = mbinx_multi2[itype][jtype]; - mbiny = mbiny_multi2[itype][jtype]; - - // Redefine for use in bin_distance() - binsizex = binsizex_multi2[itype][jtype]; - binsizey = binsizey_multi2[itype][jtype]; - binsizez = binsizez_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi2[itype][jtype]; + mbiny = stencil_mbiny_multi2[itype][jtype]; cutsq = stencil_cut[itype][jtype]; diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index 4b4019cef2..08568139ad 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -71,7 +71,7 @@ void NStencilHalfMulti22dTri::set_stencil_properties() void NStencilHalfMulti22dTri::create() { - int itype, jtype, i, j, ns; + int itype, jtype, bin_type, i, j, ns; int n = atom->ntypes; double cutsq; @@ -82,28 +82,25 @@ void NStencilHalfMulti22dTri::create() ns = 0; - sx = sx_multi2[itype][jtype]; - sy = sy_multi2[itype][jtype]; + sx = stencil_sx_multi2[itype][jtype]; + sy = stencil_sy_multi2[itype][jtype]; - mbinx = mbinx_multi2[itype][jtype]; - mbiny = mbiny_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi2[itype][jtype]; + mbiny = stencil_mbiny_multi2[itype][jtype]; - // Redefine for use in bin_distance() - binsizex = binsizex_multi2[itype][jtype]; - binsizey = binsizey_multi2[itype][jtype]; - binsizez = binsizez_multi2[itype][jtype]; + bin_type = stencil_bin_type[i][j]; cutsq = stencil_cut[itype][jtype]; if (stencil_half[itype][jtype]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutsq) + if (bin_distance_multi2(i,j,0,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutsq) + if (bin_distance_multi2(i,j,0,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 1777e748de..21bd29269a 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -71,7 +71,7 @@ void NStencilHalfMulti23d::set_stencil_properties() void NStencilHalfMulti23d::create() { - int itype, jtype, i, j, k, ns; + int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; double cutsq; @@ -82,18 +82,15 @@ void NStencilHalfMulti23d::create() ns = 0; - sx = sx_multi2[itype][jtype]; - sy = sy_multi2[itype][jtype]; - sz = sz_multi2[itype][jtype]; + sx = stencil_sx_multi2[itype][jtype]; + sy = stencil_sy_multi2[itype][jtype]; + sz = stencil_sz_multi2[itype][jtype]; - mbinx = mbinx_multi2[itype][jtype]; - mbiny = mbiny_multi2[itype][jtype]; - mbinz = mbinz_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi2[itype][jtype]; + mbiny = stencil_mbiny_multi2[itype][jtype]; + mbinz = stencil_mbinz_multi2[itype][jtype]; - // Redefine for use in bin_distance() - binsizex = binsizex_multi2[itype][jtype]; - binsizey = binsizey_multi2[itype][jtype]; - binsizez = binsizez_multi2[itype][jtype]; + bin_type = stencil_bin_type[i][j]; cutsq = stencil_cut[itype][jtype]; @@ -102,7 +99,7 @@ void NStencilHalfMulti23d::create() 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) < cutsq) + if (bin_distance_multi2(i,j,k,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } @@ -110,7 +107,7 @@ void NStencilHalfMulti23d::create() for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutsq) + if (bin_distance_multi2(i,j,k,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index 4a9ba63b20..1b71a096e3 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -71,7 +71,7 @@ void NStencilHalfMulti23dTri::set_stencil_properties() void NStencilHalfMulti23dTri::create() { - int itype, jtype, i, j, k, ns; + int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; double cutsq; @@ -82,18 +82,15 @@ void NStencilHalfMulti23dTri::create() ns = 0; - sx = sx_multi2[itype][jtype]; - sy = sy_multi2[itype][jtype]; - sz = sz_multi2[itype][jtype]; + sx = stencil_sx_multi2[itype][jtype]; + sy = stencil_sy_multi2[itype][jtype]; + sz = stencil_sz_multi2[itype][jtype]; - mbinx = mbinx_multi2[itype][jtype]; - mbiny = mbiny_multi2[itype][jtype]; - mbinz = mbinz_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi2[itype][jtype]; + mbiny = stencil_mbiny_multi2[itype][jtype]; + mbinz = stencil_mbinz_multi2[itype][jtype]; - // Redefine for use in bin_distance() - binsizex = binsizex_multi2[itype][jtype]; - binsizey = binsizey_multi2[itype][jtype]; - binsizez = binsizez_multi2[itype][jtype]; + bin_type = stencil_bin_type[i][j]; cutsq = stencil_cut[itype][jtype]; @@ -101,14 +98,14 @@ void NStencilHalfMulti23dTri::create() for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutsq) + if (bin_distance_multi2(i,j,k,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutsq) + if (bin_distance_multi2(i,j,k,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } From 00a74558ff441d39b537de9892542c2d83ae5a47 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 22 Nov 2020 20:01:14 -0700 Subject: [PATCH 17/73] Fixing typos --- src/comm_brick.cpp | 46 +++++++++++++++++++++-------- src/comm_tiled.cpp | 27 +++++++++++------ src/nstencil.cpp | 1 + src/nstencil_full_multi2_2d.cpp | 2 +- src/nstencil_full_multi2_3d.cpp | 2 +- src/nstencil_half_multi2_2d.cpp | 8 +++-- src/nstencil_half_multi2_2d_tri.cpp | 2 +- src/nstencil_half_multi2_3d.cpp | 2 +- src/nstencil_half_multi2_3d_tri.cpp | 2 +- 9 files changed, 63 insertions(+), 29 deletions(-) diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index e283e08e20..ad8669d6c1 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -158,7 +158,7 @@ void CommBrick::setup() // for multi: // cutghostmulti = same as cutghost, only for each atom type - int i; + int i,j; int ntypes = atom->ntypes; double *prd,*sublo,*subhi; @@ -175,14 +175,23 @@ void CommBrick::setup() if (mode == Comm::MULTI) { if (multi2) { - // If using multi2 binlists, use the itype-itype interaction distance for communication + // If using multi2 binlists, communicate itype particles a distance + // equal to the max of itype-jtype interaction given smaller jtype particles double **cutneighsq = neighbor->cutneighsq; - for (i = 1; i <= ntypes; i++) { + double *cuttypesq = neighbor->cuttypesq; + for (i = 1; i <= ntypes; i++) { cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,sqrt(cutneighsq[i][i])); - cutghostmulti[i][1] = MAX(cut,sqrt(cutneighsq[i][i])); - cutghostmulti[i][2] = MAX(cut,sqrt(cutneighsq[i][i])); + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } + for (j = 1; j <= ntypes; j++){ + if(cuttypesq[j] > cuttypesq[i]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); + } } } else { // If using a single binlist, use the max itype-jtype interaction distance for communication @@ -212,14 +221,27 @@ void CommBrick::setup() if (mode == Comm::MULTI) { if (multi2) { - // If using multi2 binlists, use the itype-itype interaction distance for communication + // If using multi2 binlists, communicate itype particles a distance + // equal to the max of itype-jtype interaction given smaller jtype particles double **cutneighsq = neighbor->cutneighsq; + double *cuttypesq = neighbor->cuttypesq; for (i = 1; i <= ntypes; i++) { cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = length0 * MAX(cut,sqrt(cutneighsq[i][i])); - cutghostmulti[i][1] = length1 * MAX(cut,sqrt(cutneighsq[i][i])); - cutghostmulti[i][2] = length2 * MAX(cut,sqrt(cutneighsq[i][i])); + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } + for (j = 1; j <= ntypes; j++){ + if(cuttypesq[j] > cuttypesq[i]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); + } + + cutghostmulti[i][0] *= length0; + cutghostmulti[i][1] *= length1; + cutghostmulti[i][2] *= length2; } } else { // If using a single binlist, use the max itype-jtype interaction distance for communication diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 16ae86b4a3..4835251b77 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -177,15 +177,24 @@ void CommTiled::setup() if (mode == Comm::MULTI) { double cut; if (multi2) { - // If using multi2 binlists, use the itype-itype interaction distance for communication - double **cutneighsq = neighbor->cutneighsq; - for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,sqrt(cutneighsq[i][i])); - cutghostmulti[i][1] = MAX(cut,sqrt(cutneighsq[i][i])); - cutghostmulti[i][2] = MAX(cut,sqrt(cutneighsq[i][i])); - } + // If using multi2 binlists, communicate itype particles a distance + // equal to the max of itype-jtype interaction given smaller jtype particles + double **cutneighsq = neighbor->cutneighsq; + double *cuttypesq = neighbor->cuttypesq; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } + for (j = 1; j <= ntypes; j++){ + if(cuttypesq[j] > cuttypesq[i]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); + } + } } else { // If using a single binlist, use the max itype-jtype interaction distance for communication double *cuttype = neighbor->cuttype; diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 2ace1125e8..57aff6a71b 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -324,6 +324,7 @@ void NStencil::create_setup() stencil_multi2[i] = new int*[n+1](); for (j = 1; j <= n; ++j) { maxstencil_multi2[i][j] = 0; + nstencil_multi2[i][j] = 0; } } } diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index 627a1e2f9e..2a31f95dad 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -85,7 +85,7 @@ void NStencilFullMulti22d::create() mbinx = stencil_mbinx_multi2[itype][jtype]; mbiny = stencil_mbiny_multi2[itype][jtype]; - bin_type = stencil_bin_type[i][j]; + bin_type = stencil_bin_type[itype][jtype]; cutsq = stencil_cut[itype][jtype]; diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 19bf30ec07..e028e631a8 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -87,7 +87,7 @@ void NStencilFullMulti23d::create() mbiny = stencil_mbiny_multi2[itype][jtype]; mbinz = stencil_mbinz_multi2[itype][jtype]; - bin_type = stencil_bin_type[i][j]; + bin_type = stencil_bin_type[itype][jtype]; cutsq = stencil_cut[itype][jtype]; diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 2a3c8da45c..70aa24f9f2 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -71,7 +71,7 @@ void NStencilHalfMulti22d::set_stencil_properties() void NStencilHalfMulti22d::create() { - int itype, jtype, i, j, ns; + int itype, jtype, bin_type, i, j, ns; int n = atom->ntypes; double cutsq; @@ -88,19 +88,21 @@ void NStencilHalfMulti22d::create() mbinx = stencil_mbinx_multi2[itype][jtype]; mbiny = stencil_mbiny_multi2[itype][jtype]; + bin_type = stencil_bin_type[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; if (stencil_half[itype][jtype]) { 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) < cutsq) + if (bin_distance_multi2(i,j,0,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutsq) + if (bin_distance_multi2(i,j,0,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index 08568139ad..739803c0db 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -88,7 +88,7 @@ void NStencilHalfMulti22dTri::create() mbinx = stencil_mbinx_multi2[itype][jtype]; mbiny = stencil_mbiny_multi2[itype][jtype]; - bin_type = stencil_bin_type[i][j]; + bin_type = stencil_bin_type[itype][jtype]; cutsq = stencil_cut[itype][jtype]; diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 21bd29269a..1433273f27 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -90,7 +90,7 @@ void NStencilHalfMulti23d::create() mbiny = stencil_mbiny_multi2[itype][jtype]; mbinz = stencil_mbinz_multi2[itype][jtype]; - bin_type = stencil_bin_type[i][j]; + bin_type = stencil_bin_type[itype][jtype]; cutsq = stencil_cut[itype][jtype]; diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index 1b71a096e3..b62993caa2 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -90,7 +90,7 @@ void NStencilHalfMulti23dTri::create() mbiny = stencil_mbiny_multi2[itype][jtype]; mbinz = stencil_mbinz_multi2[itype][jtype]; - bin_type = stencil_bin_type[i][j]; + bin_type = stencil_bin_type[itype][jtype]; cutsq = stencil_cut[itype][jtype]; From de5df539c9f244f62949efdbf51aa8ec75c68bdf Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 22 Nov 2020 20:40:47 -0700 Subject: [PATCH 18/73] Changing particle size metric to neighcutsq --- src/nstencil_full_multi2_2d.cpp | 2 +- src/nstencil_full_multi2_3d.cpp | 2 +- src/nstencil_half_multi2_2d.cpp | 4 ++-- src/nstencil_half_multi2_2d_tri.cpp | 4 ++-- src/nstencil_half_multi2_3d.cpp | 4 ++-- src/nstencil_half_multi2_3d_tri.cpp | 4 ++-- 6 files changed, 10 insertions(+), 10 deletions(-) diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index 2a31f95dad..0170fc5cab 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -51,7 +51,7 @@ void NStencilFullMulti22d::set_stencil_properties() stencil_half[i][j] = 0; stencil_skip[i][j] = 0; - if(cuttypesq[i] <= cuttypesq[j]){ + if(cutneighsq[i][i] <= cutneighsq[j][j]){ stencil_cut[i][j] = sqrt(cutneighsq[j][j]); stencil_bin_type[i][j] = j; } else { diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index e028e631a8..72da5b379f 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -51,7 +51,7 @@ void NStencilFullMulti23d::set_stencil_properties() stencil_half[i][j] = 0; stencil_skip[i][j] = 0; - if(cuttypesq[i] <= cuttypesq[j]){ + if(cutneighsq[i][i] <= cutneighsq[j][j]){ stencil_cut[i][j] = sqrt(cutneighsq[j][j]); stencil_bin_type[i][j] = j; } else { diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 70aa24f9f2..2a84fc0e34 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -49,12 +49,12 @@ void NStencilHalfMulti22d::set_stencil_properties() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { if(i == j) continue; - if(cuttypesq[i] > cuttypesq[j]) continue; + if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; stencil_cut[i][j] = sqrt(cutneighsq[i][j]); - if(cuttypesq[i] == cuttypesq[j]){ + if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; stencil_bin_type[i][j] = i; } else { diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index 739803c0db..f91e0f6524 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -49,12 +49,12 @@ void NStencilHalfMulti22dTri::set_stencil_properties() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { if(i == j) continue; - if(cuttypesq[i] > cuttypesq[j]) continue; + if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; stencil_cut[i][j] = sqrt(cutneighsq[i][j]); - if(cuttypesq[i] == cuttypesq[j]){ + if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; stencil_bin_type[i][j] = i; } else { diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 1433273f27..fb6b5d8cd9 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -49,12 +49,12 @@ void NStencilHalfMulti23d::set_stencil_properties() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { if(i == j) continue; - if(cuttypesq[i] > cuttypesq[j]) continue; + if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; stencil_cut[i][j] = sqrt(cutneighsq[i][j]); - if(cuttypesq[i] == cuttypesq[j]){ + if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; stencil_bin_type[i][j] = i; } else { diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index b62993caa2..013688081e 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -49,12 +49,12 @@ void NStencilHalfMulti23dTri::set_stencil_properties() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { if(i == j) continue; - if(cuttypesq[i] > cuttypesq[j]) continue; + if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; stencil_cut[i][j] = sqrt(cutneighsq[i][j]); - if(cuttypesq[i] == cuttypesq[j]){ + if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; stencil_bin_type[i][j] = i; } else { From d7047245f412fb969ef0bd120a9d83a0d37eb1d0 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 22 Nov 2020 21:22:29 -0700 Subject: [PATCH 19/73] Add cross type self bin check for newton --- src/npair_half_multi2_newton.cpp | 39 +++++++++++++++++++++++ src/npair_half_multi2_newton_tri.cpp | 13 ++++++++ src/npair_half_size_multi2_newton.cpp | 33 +++++++++++++++++++ src/npair_half_size_multi2_newton_tri.cpp | 13 ++++++++ 4 files changed, 98 insertions(+) diff --git a/src/npair_half_multi2_newton.cpp b/src/npair_half_multi2_newton.cpp index 58397f645e..413da06284 100755 --- a/src/npair_half_multi2_newton.cpp +++ b/src/npair_half_multi2_newton.cpp @@ -163,6 +163,45 @@ void NPairHalfMulti2Newton::build(NeighList *list) // smaller -> larger: locate i in the ktype bin structure kbin = coord2bin(x[i], ktype); + + // if same size, use half list so check own bin + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + js = binhead_multi2[ktype][kbin]; + for (j = js; j >= 0; j = bins_multi2[ktype][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; + } + } + } + s = stencil_multi2[itype][ktype]; ns = nstencil_multi2[itype][ktype]; diff --git a/src/npair_half_multi2_newton_tri.cpp b/src/npair_half_multi2_newton_tri.cpp index c741a860f1..7970ee94a0 100755 --- a/src/npair_half_multi2_newton_tri.cpp +++ b/src/npair_half_multi2_newton_tri.cpp @@ -143,6 +143,19 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) for (j = js; j >= 0; j = bins_multi2[ktype][j]) { jtype = type[j]; + + // if same size, use half stencil + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + 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]; diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi2_newton.cpp index a1832f6a49..3b34b1a514 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi2_newton.cpp @@ -138,6 +138,39 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) // smaller -> larger: locate i in the ktype bin structure kbin = coord2bin(x[i], ktype); + // if same size, use half list so check own bin + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + js = binhead_multi2[ktype][kbin]; + for (j = js; j >= 0; j = bins_multi2[ktype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + // Check other stencils + s = stencil_multi2[itype][ktype]; ns = nstencil_multi2[itype][ktype]; for (k = 0; k < ns; k++) { diff --git a/src/npair_half_size_multi2_newton_tri.cpp b/src/npair_half_size_multi2_newton_tri.cpp index 1c0c1d514f..3a2065c36e 100755 --- a/src/npair_half_size_multi2_newton_tri.cpp +++ b/src/npair_half_size_multi2_newton_tri.cpp @@ -115,6 +115,7 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) } } else { // smaller -> larger: locate i in the ktype bin structure + kbin = coord2bin(x[i], ktype); s = stencil_multi2[itype][ktype]; @@ -124,6 +125,18 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) for (j = js; j >= 0; j = bins_multi2[ktype][j]) { jtype = type[j]; + + // if same size, use half stencil + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + 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; From 9b9e5022d67dd341c3126e965c6f161a9905049f Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Thu, 26 Nov 2020 14:57:48 -0700 Subject: [PATCH 20/73] initializing comm distances, temporarily sorting nlit dumps --- src/comm_brick.cpp | 18 ++++++++++++---- src/comm_tiled.cpp | 9 ++++++-- src/compute_property_local.cpp | 38 +++++++++++++++++++++++++--------- 3 files changed, 49 insertions(+), 16 deletions(-) diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index ad8669d6c1..9daca70233 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -180,14 +180,19 @@ void CommBrick::setup() double **cutneighsq = neighbor->cutneighsq; double *cuttypesq = neighbor->cuttypesq; for (i = 1; i <= ntypes; i++) { - cut = 0.0; + if (cutusermulti) { cutghostmulti[i][0] = cutusermulti[i]; cutghostmulti[i][1] = cutusermulti[i]; cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; } + for (j = 1; j <= ntypes; j++){ - if(cuttypesq[j] > cuttypesq[i]) continue; + if(cutneighsq[j][j] > cutneighsq[i][i]) continue; cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); @@ -226,14 +231,19 @@ void CommBrick::setup() double **cutneighsq = neighbor->cutneighsq; double *cuttypesq = neighbor->cuttypesq; for (i = 1; i <= ntypes; i++) { - cut = 0.0; + if (cutusermulti) { cutghostmulti[i][0] = cutusermulti[i]; cutghostmulti[i][1] = cutusermulti[i]; cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; } + for (j = 1; j <= ntypes; j++){ - if(cuttypesq[j] > cuttypesq[i]) continue; + if(cutneighsq[j][j] > cutneighsq[i][i]) continue; cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 4835251b77..6657977eee 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -182,14 +182,19 @@ void CommTiled::setup() double **cutneighsq = neighbor->cutneighsq; double *cuttypesq = neighbor->cuttypesq; for (i = 1; i <= ntypes; i++) { - cut = 0.0; + if (cutusermulti) { cutghostmulti[i][0] = cutusermulti[i]; cutghostmulti[i][1] = cutusermulti[i]; cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; } + for (j = 1; j <= ntypes; j++){ - if(cuttypesq[j] > cuttypesq[i]) continue; + if(cutneighsq[j][j] > cutneighsq[i][i]) continue; cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index 36940164aa..fd0391831c 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -665,12 +665,16 @@ double ComputePropertyLocal::memory_usage() void ComputePropertyLocal::pack_patom1(int n) { - int i; + int i,j; tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { i = indices[m][0]; - buf[n] = tag[i]; + j = indices[m][1]; + if(tag[i] < tag[j]) + buf[n] = tag[i]; + else + buf[n] = tag[j]; n += nvalues; } } @@ -679,12 +683,16 @@ void ComputePropertyLocal::pack_patom1(int n) void ComputePropertyLocal::pack_patom2(int n) { - int i; + int i,j; tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { - i = indices[m][1]; - buf[n] = tag[i]; + i = indices[m][0]; + j = indices[m][1]; + if(tag[i] > tag[j]) + buf[n] = tag[i]; + else + buf[n] = tag[j]; n += nvalues; } } @@ -693,12 +701,17 @@ void ComputePropertyLocal::pack_patom2(int n) void ComputePropertyLocal::pack_ptype1(int n) { - int i; + int i,j; int *type = atom->type; + tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { i = indices[m][0]; - buf[n] = type[i]; + j = indices[m][1]; + if(tag[i] < tag[j]) + buf[n] = type[i]; + else + buf[n] = type[j]; n += nvalues; } } @@ -707,12 +720,17 @@ void ComputePropertyLocal::pack_ptype1(int n) void ComputePropertyLocal::pack_ptype2(int n) { - int i; + int i,j; int *type = atom->type; + tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { - i = indices[m][1]; - buf[n] = type[i]; + i = indices[m][0]; + j = indices[m][1]; + if(tag[i] > tag[j]) + buf[n] = type[i]; + else + buf[n] = type[j]; n += nvalues; } } From 73a6bb36216f8049ce0ba92162f85a8acae71b52 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Thu, 26 Nov 2020 15:58:05 -0700 Subject: [PATCH 21/73] Fixing mistake with stencil cutoffs not being squ squared --- src/nstencil.cpp | 10 +++++----- src/nstencil.h | 2 +- src/nstencil_full_multi2_2d.cpp | 8 ++++---- src/nstencil_full_multi2_3d.cpp | 8 ++++---- src/nstencil_half_multi2_2d.cpp | 6 +++--- src/nstencil_half_multi2_2d_tri.cpp | 6 +++--- src/nstencil_half_multi2_3d.cpp | 6 +++--- src/nstencil_half_multi2_3d_tri.cpp | 6 +++--- 8 files changed, 26 insertions(+), 26 deletions(-) diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 57aff6a71b..e362662dde 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -82,7 +82,7 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) stencil_half = nullptr; stencil_skip = nullptr; stencil_bin_type = nullptr; - stencil_cut = nullptr; + stencil_cutsq = nullptr; dimension = domain->dimension; } @@ -122,7 +122,7 @@ NStencil::~NStencil() memory->destroy(stencil_half); memory->destroy(stencil_skip); memory->destroy(stencil_bin_type); - memory->destroy(stencil_cut); + memory->destroy(stencil_cutsq); memory->destroy(stencil_sx_multi2); memory->destroy(stencil_sy_multi2); @@ -280,8 +280,8 @@ void NStencil::create_setup() "neighstencil:stencil_skip"); memory->create(stencil_bin_type, n+1, n+1, "neighstencil:stencil_bin_type"); - memory->create(stencil_cut, n+1, n+1, - "neighstencil:stencil_cut"); + memory->create(stencil_cutsq, n+1, n+1, + "neighstencil:stencil_cutsq"); memory->create(stencil_sx_multi2, n+1, n+1, "neighstencil:stencil_sx_multi2"); @@ -346,7 +346,7 @@ void NStencil::create_setup() stencil_mbiny_multi2[i][j] = mbiny_multi2[bin_type]; stencil_mbinz_multi2[i][j] = mbinz_multi2[bin_type]; - stencil_range = stencil_cut[i][j]; + stencil_range = sqrt(stencil_cutsq[i][j]); sx = static_cast (stencil_range*bininvx_multi2[bin_type]); if (sx*binsizex < stencil_range) sx++; diff --git a/src/nstencil.h b/src/nstencil.h index 68c7702f79..3c10221603 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -49,7 +49,7 @@ class NStencil : protected Pointers { bool **stencil_half; // flag creation of a half stencil for itype-jtype bool **stencil_skip; // skip creation of itype-jtype stencils (for newton on) int **stencil_bin_type; // what type to use for bin information - double **stencil_cut; // cutoff used for stencil size + double **stencil_cutsq; // cutoff used for stencil size NStencil(class LAMMPS *); virtual ~NStencil(); diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index 0170fc5cab..a10798677d 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -37,7 +37,7 @@ void NStencilFullMulti22d::set_stencil_properties() stencil_half[i][i] = 0; stencil_skip[i][i] = 0; stencil_bin_type[i][i] = i; - stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + stencil_cutsq[i][i] = cutneighsq[i][i]; } // smaller -> larger => use existing newtoff stencil in larger bin @@ -52,10 +52,10 @@ void NStencilFullMulti22d::set_stencil_properties() stencil_skip[i][j] = 0; if(cutneighsq[i][i] <= cutneighsq[j][j]){ - stencil_cut[i][j] = sqrt(cutneighsq[j][j]); + stencil_cutsq[i][j] = cutneighsq[j][j]; stencil_bin_type[i][j] = j; } else { - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + stencil_cutsq[i][j] = cutneighsq[i][j]; stencil_bin_type[i][j] = j; } } @@ -87,7 +87,7 @@ void NStencilFullMulti22d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cut[itype][jtype]; + cutsq = stencil_cutsq[itype][jtype]; for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 72da5b379f..7e224be7ab 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -37,7 +37,7 @@ void NStencilFullMulti23d::set_stencil_properties() stencil_half[i][i] = 0; stencil_skip[i][i] = 0; stencil_bin_type[i][i] = i; - stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + stencil_cutsq[i][i] = cutneighsq[i][i]; } // smaller -> larger => use existing newtoff stencil in larger bin @@ -52,10 +52,10 @@ void NStencilFullMulti23d::set_stencil_properties() stencil_skip[i][j] = 0; if(cutneighsq[i][i] <= cutneighsq[j][j]){ - stencil_cut[i][j] = sqrt(cutneighsq[j][j]); + stencil_cutsq[i][j] = cutneighsq[j][j]; stencil_bin_type[i][j] = j; } else { - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + stencil_cutsq[i][j] = cutneighsq[i][j]; stencil_bin_type[i][j] = j; } } @@ -89,7 +89,7 @@ void NStencilFullMulti23d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cut[itype][jtype]; + cutsq = stencil_cutsq[itype][jtype]; for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 2a84fc0e34..7ea058e70b 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -38,7 +38,7 @@ void NStencilHalfMulti22d::set_stencil_properties() stencil_half[i][i] = 1; stencil_skip[i][i] = 0; stencil_bin_type[i][i] = i; - stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + stencil_cutsq[i][i] = cutneighsq[i][i]; } // Cross types: use full stencil, looking one way through hierarchy @@ -52,7 +52,7 @@ void NStencilHalfMulti22d::set_stencil_properties() if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -90,7 +90,7 @@ void NStencilHalfMulti22d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cut[itype][jtype]; + cutsq = stencil_cutsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (j = 0; j <= sy; j++) diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index f91e0f6524..fb974877af 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -38,7 +38,7 @@ void NStencilHalfMulti22dTri::set_stencil_properties() stencil_half[i][i] = 1; stencil_skip[i][i] = 0; stencil_bin_type[i][i] = i; - stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + stencil_cutsq[i][i] = cutneighsq[i][i]; } // Cross types: use full stencil, looking one way through hierarchy @@ -52,7 +52,7 @@ void NStencilHalfMulti22dTri::set_stencil_properties() if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -90,7 +90,7 @@ void NStencilHalfMulti22dTri::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cut[itype][jtype]; + cutsq = stencil_cutsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (j = 0; j <= sy; j++) diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index fb6b5d8cd9..92cdc4e5e6 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -38,7 +38,7 @@ void NStencilHalfMulti23d::set_stencil_properties() stencil_half[i][i] = 1; stencil_skip[i][i] = 0; stencil_bin_type[i][i] = i; - stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + stencil_cutsq[i][i] = cutneighsq[i][i]; } // Cross types: use full stencil, looking one way through hierarchy @@ -52,7 +52,7 @@ void NStencilHalfMulti23d::set_stencil_properties() if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -92,7 +92,7 @@ void NStencilHalfMulti23d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cut[itype][jtype]; + cutsq = stencil_cutsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (k = 0; k <= sz; k++) diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index 013688081e..d114635113 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -38,7 +38,7 @@ void NStencilHalfMulti23dTri::set_stencil_properties() stencil_half[i][i] = 1; stencil_skip[i][i] = 0; stencil_bin_type[i][i] = i; - stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + stencil_cutsq[i][i] = cutneighsq[i][i]; } // Cross types: use full stencil, looking one way through hierarchy @@ -52,7 +52,7 @@ void NStencilHalfMulti23dTri::set_stencil_properties() if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -92,7 +92,7 @@ void NStencilHalfMulti23dTri::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cut[itype][jtype]; + cutsq = stencil_cutsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (k = 0; k <= sz; k++) From f8d35139c359803938e85eceb1a8f16ab6dfc7eb Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Fri, 27 Nov 2020 17:16:52 -0700 Subject: [PATCH 22/73] Adding files for OMP --- src/USER-OMP/npair_full_multi2_omp.cpp | 149 ++++++++++ src/USER-OMP/npair_full_multi2_omp.h | 44 +++ .../npair_half_multi2_newtoff_omp.cpp | 154 +++++++++++ src/USER-OMP/npair_half_multi2_newtoff_omp.h | 43 +++ src/USER-OMP/npair_half_multi2_newton_omp.cpp | 259 ++++++++++++++++++ src/USER-OMP/npair_half_multi2_newton_omp.h | 43 +++ .../npair_half_multi2_newton_tri_omp.cpp | 206 ++++++++++++++ .../npair_half_multi2_newton_tri_omp.h | 43 +++ .../npair_half_size_multi2_newtoff_omp.cpp | 135 +++++++++ .../npair_half_size_multi2_newtoff_omp.h | 43 +++ .../npair_half_size_multi2_newton_omp.cpp | 221 +++++++++++++++ .../npair_half_size_multi2_newton_omp.h | 43 +++ .../npair_half_size_multi2_newton_tri_omp.cpp | 181 ++++++++++++ .../npair_half_size_multi2_newton_tri_omp.h | 43 +++ 14 files changed, 1607 insertions(+) create mode 100755 src/USER-OMP/npair_full_multi2_omp.cpp create mode 100755 src/USER-OMP/npair_full_multi2_omp.h create mode 100755 src/USER-OMP/npair_half_multi2_newtoff_omp.cpp create mode 100755 src/USER-OMP/npair_half_multi2_newtoff_omp.h create mode 100755 src/USER-OMP/npair_half_multi2_newton_omp.cpp create mode 100755 src/USER-OMP/npair_half_multi2_newton_omp.h create mode 100755 src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp create mode 100755 src/USER-OMP/npair_half_multi2_newton_tri_omp.h create mode 100755 src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp create mode 100755 src/USER-OMP/npair_half_size_multi2_newtoff_omp.h create mode 100755 src/USER-OMP/npair_half_size_multi2_newton_omp.cpp create mode 100755 src/USER-OMP/npair_half_size_multi2_newton_omp.h create mode 100755 src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp create mode 100755 src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h diff --git a/src/USER-OMP/npair_full_multi2_omp.cpp b/src/USER-OMP/npair_full_multi2_omp.cpp new file mode 100755 index 0000000000..8e025806c9 --- /dev/null +++ b/src/USER-OMP/npair_full_multi2_omp.cpp @@ -0,0 +1,149 @@ +/* ---------------------------------------------------------------------- + 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 "omp_compat.h" +#include "npair_full_multi2_omp.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; + +/* ---------------------------------------------------------------------- */ + +NPairFullMulti2Omp::NPairFullMulti2Omp(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 NPairFullMulti2Omp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int molecular = atom->molecular; + const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + int js; + + // 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 &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 = atom2bin_multi2[itype][i]; + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + kbin = ibin; + } else { + // Locate i in ktype bin + kbin = coord2bin(x[i], ktype); + } + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][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 != Atom::ATOMIC) { + 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_multi2_omp.h b/src/USER-OMP/npair_full_multi2_omp.h new file mode 100755 index 0000000000..d2bc478532 --- /dev/null +++ b/src/USER-OMP/npair_full_multi2_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/multi2/omp, + NPairFullMulti2Omp, + NP_FULL | NP_MULTI2 | NP_OMP | + NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_FULL_MULTI2_OMP_H +#define LMP_NPAIR_FULL_MULTI2_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairFullMulti2Omp : public NPair { + public: + NPairFullMulti2Omp(class LAMMPS *); + ~NPairFullMulti2Omp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp new file mode 100755 index 0000000000..44689e1efc --- /dev/null +++ b/src/USER-OMP/npair_half_multi2_newtoff_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 "omp_compat.h" +#include "npair_half_multi2_newtoff_omp.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; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMulti2NewtoffOmp::NPairHalfMulti2NewtoffOmp(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 NPairHalfMulti2NewtoffOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int molecular = atom->molecular; + const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + int js; + + // 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 &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 = atom2bin_multi2[itype][i]; + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + kbin = ibin; + } else { + // Locate i in ktype bin + kbin = coord2bin(x[i], ktype); + } + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >=0; j = bins_multi2[ktype][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 != Atom::ATOMIC) { + 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_multi2_newtoff_omp.h b/src/USER-OMP/npair_half_multi2_newtoff_omp.h new file mode 100755 index 0000000000..a9e9a842cb --- /dev/null +++ b/src/USER-OMP/npair_half_multi2_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/multi2/newtoff/omp, + NPairHalfMulti2NewtoffOmp, + NP_HALF | NP_MULTI2 | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI2_NEWTOFF_OMP_H +#define LMP_NPAIR_HALF_MULTI2_NEWTOFF_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMulti2NewtoffOmp : public NPair { + public: + NPairHalfMulti2NewtoffOmp(class LAMMPS *); + ~NPairHalfMulti2NewtoffOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_multi2_newton_omp.cpp new file mode 100755 index 0000000000..cc86410fa9 --- /dev/null +++ b/src/USER-OMP/npair_half_multi2_newton_omp.cpp @@ -0,0 +1,259 @@ +/* ---------------------------------------------------------------------- + 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 "omp_compat.h" +#include "npair_half_multi2_newton_omp.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; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMulti2NewtonOmp::NPairHalfMulti2NewtonOmp(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 NPairHalfMulti2NewtonOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int molecular = atom->molecular; + const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + int js; + + // 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 &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; + } + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = atom2bin_multi2[itype][i]; + + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + + // own bin ... + js = bins_multi2[itype][i]; + for (j = js; j >= 0; j = bins_multi2[itype][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 + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][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; + } + } + } + } else { + // smaller -> larger: locate i in the ktype bin structure + + kbin = coord2bin(x[i], ktype); + + // if same size, use half list so check own bin + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + js = binhead_multi2[ktype][kbin]; + for (j = js; j >= 0; j = bins_multi2[ktype][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; + } + } + } + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][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; + } + } + } + } + } + + 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_multi2_newton_omp.h b/src/USER-OMP/npair_half_multi2_newton_omp.h new file mode 100755 index 0000000000..2ea2bd1ad0 --- /dev/null +++ b/src/USER-OMP/npair_half_multi2_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/multi2/newton/omp, + NPairHalfMulti2NewtonOmp, + NP_HALF | NP_MULTI2 | NP_NEWTON | NP_OMP | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_OMP_H +#define LMP_NPAIR_HALF_MULTI2_NEWTON_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMulti2NewtonOmp : public NPair { + public: + NPairHalfMulti2NewtonOmp(class LAMMPS *); + ~NPairHalfMulti2NewtonOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp new file mode 100755 index 0000000000..707c247607 --- /dev/null +++ b/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp @@ -0,0 +1,206 @@ +/* ---------------------------------------------------------------------- + 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 "omp_compat.h" +#include "npair_half_multi2_newton_tri_omp.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; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMulti2NewtonTriOmp::NPairHalfMulti2NewtonTriOmp(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 NPairHalfMulti2NewtonTriOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int molecular = atom->molecular; + const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + int js; + + // 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 &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; + } + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = atom2bin_multi2[itype][i]; + + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][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; + } + } + } + } else { + // smaller -> larger: locate i in the ktype bin structure + + kbin = coord2bin(x[i], ktype); + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + + jtype = type[j]; + + // if same size, use half stencil + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + 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_multi2_newton_tri_omp.h b/src/USER-OMP/npair_half_multi2_newton_tri_omp.h new file mode 100755 index 0000000000..dd9eea6847 --- /dev/null +++ b/src/USER-OMP/npair_half_multi2_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/multi2/newton/tri/omp, + NPairHalfMulti2NewtonTriOmp, + NP_HALF | NP_MULTI2 | NP_NEWTON | NP_TRI | NP_OMP) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_OMP_H +#define LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMulti2NewtonTriOmp : public NPair { + public: + NPairHalfMulti2NewtonTriOmp(class LAMMPS *); + ~NPairHalfMulti2NewtonTriOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp new file mode 100755 index 0000000000..d4578985ed --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi2_newtoff_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 "omp_compat.h" +#include "npair_half_size_multi2_newtoff_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMulti2NewtoffOmp::NPairHalfSizeMulti2NewtoffOmp(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 NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int history = list->history; + const int mask_history = 3 << SBBITS; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + int js; + + // 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 &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]; + radi = radius[i]; + + // 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 = atom2bin_multi2[itype][i]; + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + kbin = ibin; + } else { + // Locate i in ktype bin + kbin = coord2bin(x[i], ktype); + } + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >=0; j = bins_multi2[ktype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + 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_size_multi2_newtoff_omp.h b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.h new file mode 100755 index 0000000000..fd592d839c --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi2_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/size/multi2/newtoff/omp, + NPairHalfSizeMulti2NewtoffOmp, + NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMulti2NewtoffOmp : public NPair { + public: + NPairHalfSizeMulti2NewtoffOmp(class LAMMPS *); + ~NPairHalfSizeMulti2NewtoffOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp new file mode 100755 index 0000000000..5d8080f913 --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp @@ -0,0 +1,221 @@ +/* ---------------------------------------------------------------------- + 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 "omp_compat.h" +#include "npair_half_size_multi2_newton_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMulti2NewtonOmp::NPairHalfSizeMulti2NewtonOmp(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 NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int history = list->history; + const int mask_history = 3 << SBBITS; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + int js; + + // 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 &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]; + radi = radius[i]; + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = atom2bin_multi2[itype][i]; + + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // own bin ... + js = bins_multi2[itype][i]; + for (j = js; j >= 0; j = bins_multi2[itype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + 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 + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } else { + // smaller -> larger: locate i in the ktype bin structure + kbin = coord2bin(x[i], ktype); + + // if same size, use half list so check own bin + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + js = binhead_multi2[ktype][kbin]; + for (j = js; j >= 0; j = bins_multi2[ktype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + // Check other stencils + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + 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_size_multi2_newton_omp.h b/src/USER-OMP/npair_half_size_multi2_newton_omp.h new file mode 100755 index 0000000000..38b4dde272 --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi2_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/multi2/newton/omp, + NPairHalfSizeMulti2NewtonOmp, + NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_OMP | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMulti2NewtonOmp : public NPair { + public: + NPairHalfSizeMulti2NewtonOmp(class LAMMPS *); + ~NPairHalfSizeMulti2NewtonOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp new file mode 100755 index 0000000000..12365ff27c --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp @@ -0,0 +1,181 @@ +/* ---------------------------------------------------------------------- + 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 "omp_compat.h" +#include "npair_half_size_multi2_newton_tri_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMulti2NewtonTriOmp::NPairHalfSizeMulti2NewtonTriOmp(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 NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int history = list->history; + const int mask_history = 3 << SBBITS; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + int js; + + // 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 &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]; + radi = radius[i]; + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = atom2bin_multi2[itype][i]; + + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } else { + // smaller -> larger: locate i in the ktype bin structure + + kbin = coord2bin(x[i], ktype); + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + + jtype = type[j]; + + // if same size, use half stencil + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + 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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + 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_size_multi2_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h new file mode 100755 index 0000000000..494a419c8f --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi2_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/multi2/newton/tri/omp, + NPairHalfSizeMulti2NewtonTriOmp, + NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_TRI | NP_OMP) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMulti2NewtonTriOmp : public NPair { + public: + NPairHalfSizeMulti2NewtonTriOmp(class LAMMPS *); + ~NPairHalfSizeMulti2NewtonTriOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ From cea20da5be0d8088468cf301d66cd0f91fb9965e Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 29 Nov 2020 16:07:20 -0700 Subject: [PATCH 23/73] Simplifying stencils --- src/nstencil.cpp | 6 +----- src/nstencil.h | 1 - src/nstencil_full_multi2_2d.cpp | 25 +++---------------------- src/nstencil_full_multi2_3d.cpp | 26 ++++---------------------- src/nstencil_half_multi2_2d.cpp | 16 +++------------- src/nstencil_half_multi2_2d_tri.cpp | 16 +++------------- src/nstencil_half_multi2_3d.cpp | 16 +++------------- src/nstencil_half_multi2_3d_tri.cpp | 16 +++------------- 8 files changed, 20 insertions(+), 102 deletions(-) diff --git a/src/nstencil.cpp b/src/nstencil.cpp index e362662dde..1658654e5a 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -82,7 +82,6 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) stencil_half = nullptr; stencil_skip = nullptr; stencil_bin_type = nullptr; - stencil_cutsq = nullptr; dimension = domain->dimension; } @@ -122,7 +121,6 @@ NStencil::~NStencil() memory->destroy(stencil_half); memory->destroy(stencil_skip); memory->destroy(stencil_bin_type); - memory->destroy(stencil_cutsq); memory->destroy(stencil_sx_multi2); memory->destroy(stencil_sy_multi2); @@ -280,8 +278,6 @@ void NStencil::create_setup() "neighstencil:stencil_skip"); memory->create(stencil_bin_type, n+1, n+1, "neighstencil:stencil_bin_type"); - memory->create(stencil_cutsq, n+1, n+1, - "neighstencil:stencil_cutsq"); memory->create(stencil_sx_multi2, n+1, n+1, "neighstencil:stencil_sx_multi2"); @@ -346,7 +342,7 @@ void NStencil::create_setup() stencil_mbiny_multi2[i][j] = mbiny_multi2[bin_type]; stencil_mbinz_multi2[i][j] = mbinz_multi2[bin_type]; - stencil_range = sqrt(stencil_cutsq[i][j]); + stencil_range = sqrt(cutneighsq[i][j]); sx = static_cast (stencil_range*bininvx_multi2[bin_type]); if (sx*binsizex < stencil_range) sx++; diff --git a/src/nstencil.h b/src/nstencil.h index 3c10221603..60e584b2a0 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -49,7 +49,6 @@ class NStencil : protected Pointers { bool **stencil_half; // flag creation of a half stencil for itype-jtype bool **stencil_skip; // skip creation of itype-jtype stencils (for newton on) int **stencil_bin_type; // what type to use for bin information - double **stencil_cutsq; // cutoff used for stencil size NStencil(class LAMMPS *); virtual ~NStencil(); diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index a10798677d..658dba1c28 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -32,32 +32,13 @@ void NStencilFullMulti22d::set_stencil_properties() int n = atom->ntypes; int i, j; - // like -> like => use half stencil - for (i = 1; i <= n; i++) { - stencil_half[i][i] = 0; - stencil_skip[i][i] = 0; - stencil_bin_type[i][i] = i; - stencil_cutsq[i][i] = cutneighsq[i][i]; - } - - // smaller -> larger => use existing newtoff stencil in larger bin - // larger -> smaller => use multi-like stencil for small-large in smaller bin - // If types are same cutoff, use existing like-like stencil. + // Always look up neighbor using full stencil and neighbor's bin for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - if(i == j) continue; - stencil_half[i][j] = 0; stencil_skip[i][j] = 0; - - if(cutneighsq[i][i] <= cutneighsq[j][j]){ - stencil_cutsq[i][j] = cutneighsq[j][j]; - stencil_bin_type[i][j] = j; - } else { - stencil_cutsq[i][j] = cutneighsq[i][j]; - stencil_bin_type[i][j] = j; - } + stencil_bin_type[i][j] = j; } } } @@ -87,7 +68,7 @@ void NStencilFullMulti22d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cutsq[itype][jtype]; + cutsq = cutneighsq[itype][jtype]; for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 7e224be7ab..7bbe5208f2 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -32,32 +32,14 @@ void NStencilFullMulti23d::set_stencil_properties() int n = atom->ntypes; int i, j; - // like -> like => use half stencil - for (i = 1; i <= n; i++) { - stencil_half[i][i] = 0; - stencil_skip[i][i] = 0; - stencil_bin_type[i][i] = i; - stencil_cutsq[i][i] = cutneighsq[i][i]; - } - - // smaller -> larger => use existing newtoff stencil in larger bin - // larger -> smaller => use multi-like stencil for small-large in smaller bin - // If types are same cutoff, use existing like-like stencil. + // Always look up neighbor using full stencil and neighbor's bin + // Stencil cutoff set by i-j cutoff for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - if(i == j) continue; - stencil_half[i][j] = 0; stencil_skip[i][j] = 0; - - if(cutneighsq[i][i] <= cutneighsq[j][j]){ - stencil_cutsq[i][j] = cutneighsq[j][j]; - stencil_bin_type[i][j] = j; - } else { - stencil_cutsq[i][j] = cutneighsq[i][j]; - stencil_bin_type[i][j] = j; - } + stencil_bin_type[i][j] = j; } } } @@ -89,7 +71,7 @@ void NStencilFullMulti23d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cutsq[itype][jtype]; + cutsq = cutneighsq[itype][jtype]; for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 7ea058e70b..c2f2127548 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -32,27 +32,17 @@ void NStencilHalfMulti22d::set_stencil_properties() { int n = atom->ntypes; int i, j; - - // like -> like => use half stencil - for (i = 1; i <= n; i++) { - stencil_half[i][i] = 1; - stencil_skip[i][i] = 0; - stencil_bin_type[i][i] = i; - stencil_cutsq[i][i] = cutneighsq[i][i]; - } // Cross types: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin - // larger -> smaller => no nstecil required - // If cut offs are same, use existing type-type stencil + // larger -> smaller => no nstencil required + // If cut offs are same, use half stencil for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - if(i == j) continue; if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -90,7 +80,7 @@ void NStencilHalfMulti22d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cutsq[itype][jtype]; + cutsq = cutneighsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (j = 0; j <= sy; j++) diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index fb974877af..7143378305 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -32,27 +32,17 @@ void NStencilHalfMulti22dTri::set_stencil_properties() { int n = atom->ntypes; int i, j; - - // like -> like => use half stencil - for (i = 1; i <= n; i++) { - stencil_half[i][i] = 1; - stencil_skip[i][i] = 0; - stencil_bin_type[i][i] = i; - stencil_cutsq[i][i] = cutneighsq[i][i]; - } // Cross types: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin - // larger -> smaller => no nstecil required - // If cut offs are same, use existing type-type stencil + // larger -> smaller => no nstencil required + // If cut offs are same, use half stencil for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - if(i == j) continue; if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -90,7 +80,7 @@ void NStencilHalfMulti22dTri::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cutsq[itype][jtype]; + cutsq = cutneighsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (j = 0; j <= sy; j++) diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 92cdc4e5e6..57702cdb50 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -32,27 +32,17 @@ void NStencilHalfMulti23d::set_stencil_properties() { int n = atom->ntypes; int i, j; - - // like -> like => use half stencil - for (i = 1; i <= n; i++) { - stencil_half[i][i] = 1; - stencil_skip[i][i] = 0; - stencil_bin_type[i][i] = i; - stencil_cutsq[i][i] = cutneighsq[i][i]; - } // Cross types: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin - // larger -> smaller => no nstecil required - // If cut offs are same, use existing type-type stencil + // larger -> smaller => no nstencil required + // If cut offs are same, use half stencil for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - if(i == j) continue; if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -92,7 +82,7 @@ void NStencilHalfMulti23d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cutsq[itype][jtype]; + cutsq = cutneighsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (k = 0; k <= sz; k++) diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index d114635113..33915d4741 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -33,26 +33,16 @@ void NStencilHalfMulti23dTri::set_stencil_properties() int n = atom->ntypes; int i, j; - // like -> like => use half stencil - for (i = 1; i <= n; i++) { - stencil_half[i][i] = 1; - stencil_skip[i][i] = 0; - stencil_bin_type[i][i] = i; - stencil_cutsq[i][i] = cutneighsq[i][i]; - } - // Cross types: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin - // larger -> smaller => no nstecil required - // If cut offs are same, use existing type-type stencil + // larger -> smaller => no nstencil required + // If cut offs are same, use half stencil for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - if(i == j) continue; if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -92,7 +82,7 @@ void NStencilHalfMulti23dTri::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cutsq[itype][jtype]; + cutsq = cutneighsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (k = 0; k <= sz; k++) From 2c79fbebe8ab700c226715c571d06e5fd47ff4a9 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 29 Nov 2020 17:48:43 -0700 Subject: [PATCH 24/73] Adding todo note for comm, testing for full nlist --- src/comm.cpp | 2 + src/pair_full_print.cpp | 341 ++++++++++++++++++++++++++++++++++++++++ src/pair_full_print.h | 72 +++++++++ 3 files changed, 415 insertions(+) create mode 100644 src/pair_full_print.cpp create mode 100644 src/pair_full_print.h diff --git a/src/comm.cpp b/src/comm.cpp index ad0c836432..7930b08f87 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -243,6 +243,8 @@ void Comm::init() if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; // Can't used multi2 communication with Newton off + // TODO: need to somehow restrict this option with full neighbor lists + // CANNOT use multi2 communication with full nlist if (force->newton == 0 && multi2) error->all(FLERR,"Cannot use multi2 communication with Newton off"); } diff --git a/src/pair_full_print.cpp b/src/pair_full_print.cpp new file mode 100644 index 0000000000..bf42a81288 --- /dev/null +++ b/src/pair_full_print.cpp @@ -0,0 +1,341 @@ +/* ---------------------------------------------------------------------- + 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 "pair_full_print.h" + +#include +#include +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairFullPrint::PairFullPrint(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairFullPrint::~PairFullPrint() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(prefactor); + memory->destroy(cut); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairFullPrint::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double r,rsq,arg,factor_lj; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + tagint *tag = atom->tag; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + printf("NLIST %d %d %d %d\n", tag[i], tag[j], type[i], type[j]); + r = sqrt(rsq); + arg = MY_PI*r/cut[itype][jtype]; + if (r > 0.0) fpair = factor_lj * prefactor[itype][jtype] * + sin(arg) * MY_PI/cut[itype][jtype]/r; + else fpair = 0.0; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + + if (eflag) + evdwl = factor_lj * prefactor[itype][jtype] * (1.0+cos(arg)); + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairFullPrint::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(prefactor,n+1,n+1,"pair:prefactor"); + memory->create(cut,n+1,n+1,"pair:cut"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairFullPrint::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + + cut_global = utils::numeric(FLERR,arg[0],false,lmp); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairFullPrint::coeff(int narg, char **arg) +{ + if (narg < 3 || narg > 4) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + double prefactor_one = utils::numeric(FLERR,arg[2],false,lmp); + + double cut_one = cut_global; + if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],false,lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + prefactor[i][j] = prefactor_one; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style + ------------------------------------------------------------------------- */ + +void PairFullPrint::init_style() { + // need a full neighbor list + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; +} + + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairFullPrint::init_one(int i, int j) +{ + // always mix prefactors geometrically + + if (setflag[i][j] == 0) { + prefactor[i][j] = sqrt(prefactor[i][i]*prefactor[j][j]); + cut[i][j] = mix_distance(cut[i][i],cut[j][j]); + } + + prefactor[j][i] = prefactor[i][j]; + cut[j][i] = cut[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairFullPrint::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&prefactor[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairFullPrint::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + utils::sfread(FLERR,&prefactor[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + } + MPI_Bcast(&prefactor[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairFullPrint::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairFullPrint::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); + } + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairFullPrint::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g\n",i,prefactor[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairFullPrint::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g\n",i,j,prefactor[i][j],cut[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairFullPrint::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, + double &fforce) +{ + double r,arg,philj; + + r = sqrt(rsq); + arg = MY_PI*r/cut[itype][jtype]; + fforce = factor_lj * prefactor[itype][jtype] * + sin(arg) * MY_PI/cut[itype][jtype]/r; + + philj = prefactor[itype][jtype] * (1.0+cos(arg)); + return factor_lj*philj; +} + +/* ---------------------------------------------------------------------- */ + +void *PairFullPrint::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"a") == 0) return (void *) prefactor; + return nullptr; +} diff --git a/src/pair_full_print.h b/src/pair_full_print.h new file mode 100644 index 0000000000..31b51f4e97 --- /dev/null +++ b/src/pair_full_print.h @@ -0,0 +1,72 @@ +/* -*- 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 PAIR_CLASS + +PairStyle(full/print,PairFullPrint) + +#else + +#ifndef LMP_PAIR_FULL_PRINT_H +#define LMP_PAIR_FULL_PRINT_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairFullPrint : public Pair { + friend class Pair; + + public: + PairFullPrint(class LAMMPS *); + virtual ~PairFullPrint(); + void init_style(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + double single(int, int, int, int, double, double, double, double &); + void *extract(const char *, int &); + + protected: + double cut_global; + double **prefactor; + double **cut; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +*/ From 8a0dac90ca1c850a4017410fd0e50d26f713a393 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 29 Nov 2020 19:57:14 -0700 Subject: [PATCH 25/73] Removing redundant k variables in npair --- src/USER-OMP/npair_full_multi2_omp.cpp | 21 ++++++------- .../npair_half_multi2_newtoff_omp.cpp | 24 +++++++------- src/USER-OMP/npair_half_multi2_newton_omp.cpp | 28 +++++++---------- .../npair_half_multi2_newton_tri_omp.cpp | 26 +++++++--------- .../npair_half_size_multi2_newtoff_omp.cpp | 24 +++++++------- .../npair_half_size_multi2_newton_omp.cpp | 31 ++++++++----------- .../npair_half_size_multi2_newton_tri_omp.cpp | 25 +++++++-------- src/comm.cpp | 3 ++ src/npair_full_multi2.cpp | 21 ++++++------- src/npair_half_multi2_newton.cpp | 28 +++++++---------- src/npair_half_multi2_newton_tri.cpp | 26 +++++++--------- src/npair_half_size_multi2_newtoff.cpp | 24 +++++++------- src/npair_half_size_multi2_newton.cpp | 31 ++++++++----------- src/npair_half_size_multi2_newton_tri.cpp | 25 +++++++-------- 14 files changed, 152 insertions(+), 185 deletions(-) diff --git a/src/USER-OMP/npair_full_multi2_omp.cpp b/src/USER-OMP/npair_full_multi2_omp.cpp index 8e025806c9..33ac289375 100755 --- a/src/USER-OMP/npair_full_multi2_omp.cpp +++ b/src/USER-OMP/npair_full_multi2_omp.cpp @@ -46,7 +46,7 @@ void NPairFullMulti2Omp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -94,22 +94,21 @@ void NPairFullMulti2Omp::build(NeighList *list) // skip i = j ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { - kbin = ibin; + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { + jbin = ibin; } else { - // Locate i in ktype bin - kbin = coord2bin(x[i], ktype); + // Locate i in jtype bin + jbin = coord2bin(x[i], jtype); } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (i == j) continue; - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp index 44689e1efc..f440865bc7 100755 --- a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp @@ -48,7 +48,7 @@ void NPairHalfMulti2NewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -98,23 +98,21 @@ void NPairHalfMulti2NewtoffOmp::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { - kbin = ibin; + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { + jbin = ibin; } else { - // Locate i in ktype bin - kbin = coord2bin(x[i], ktype); + // Locate i in jtype bin + jbin = coord2bin(x[i], jtype); } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi2[jtype][j]) { if (j <= i) continue; - - jtype = type[j]; - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_multi2_newton_omp.cpp index cc86410fa9..4035a44a8e 100755 --- a/src/USER-OMP/npair_half_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi2_newton_omp.cpp @@ -47,7 +47,7 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -96,8 +96,8 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { // own bin ... js = bins_multi2[itype][i]; @@ -110,7 +110,6 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -144,7 +143,6 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) js = binhead_multi2[itype][ibin + s[k]]; for (j = js; j >= 0; j = bins_multi2[itype][j]) { - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -170,14 +168,14 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure + // smaller -> larger: locate i in the jtype bin structure - kbin = coord2bin(x[i], ktype); + jbin = coord2bin(x[i], jtype); // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ - js = binhead_multi2[ktype][kbin]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -186,7 +184,6 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -212,14 +209,13 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) } } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp index 707c247607..25f49a5b09 100755 --- a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp @@ -48,7 +48,7 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -97,9 +97,9 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == ktype) { + if (itype == jtype) { // loop over all atoms in other bins in stencil, store every pair // skip if i,j neighbor cutoff is less than bin distance @@ -117,7 +117,7 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) 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]; @@ -143,20 +143,18 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure + // smaller -> larger: locate i in the jtype bin structure - kbin = coord2bin(x[i], ktype); - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + jbin = coord2bin(x[i], jtype); + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { - - jtype = type[j]; - + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp index d4578985ed..8e95b2c5b8 100755 --- a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp @@ -46,7 +46,7 @@ void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + int i,j,k,n,itype,jtype,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -86,23 +86,21 @@ void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { - kbin = ibin; + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { + jbin = ibin; } else { - // Locate i in ktype bin - kbin = coord2bin(x[i], ktype); + // Locate i in jtype bin + jbin = coord2bin(x[i], jtype); } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi2[jtype][j]) { if (j <= i) continue; - - jtype = type[j]; - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp index 5d8080f913..ae490fe837 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp @@ -45,7 +45,7 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + int i,j,k,n,itype,jtype,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -84,9 +84,9 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == ktype) { + if (itype == jtype) { // own bin ... js = bins_multi2[itype][i]; @@ -99,7 +99,6 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -125,7 +124,6 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi2[itype][ibin + s[k]]; for (j = js; j >= 0; j = bins_multi2[itype][j]) { - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; @@ -145,13 +143,13 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure - kbin = coord2bin(x[i], ktype); + // smaller -> larger: locate i in the jtype bin structure + jbin = coord2bin(x[i], jtype); // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ - js = binhead_multi2[ktype][kbin]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -160,7 +158,6 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -181,14 +178,12 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) // Check other stencils - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { - - jtype = type[j]; - + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp index 12365ff27c..c1dea8ca79 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp @@ -46,7 +46,7 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + int i,j,k,n,itype,jtype,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -85,9 +85,9 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == ktype) { + if (itype == jtype) { // loop over all atoms in other bins in stencil, store every pair // skip if i,j neighbor cutoff is less than bin distance @@ -105,7 +105,6 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) if (x[j][0] == xtmp && j <= i) continue; } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; @@ -125,20 +124,18 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure + // smaller -> larger: locate i in the jtype bin structure - kbin = coord2bin(x[i], ktype); + jbin = coord2bin(x[i], jtype); - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { - - jtype = type[j]; - + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/comm.cpp b/src/comm.cpp index 7930b08f87..2e1192e150 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -245,6 +245,9 @@ void Comm::init() // Can't used multi2 communication with Newton off // TODO: need to somehow restrict this option with full neighbor lists // CANNOT use multi2 communication with full nlist + // Could remove NP_NEWTON from npair_full_*multi2*, but could be cryptic + // Also could be cases where you want newton off (hybrid) but don't use multi2 comm + // Could add check on neighbor build, if full and comm->multi2 error... if (force->newton == 0 && multi2) error->all(FLERR,"Cannot use multi2 communication with Newton off"); } diff --git a/src/npair_full_multi2.cpp b/src/npair_full_multi2.cpp index 4fbdc6148b..8af77aea22 100644 --- a/src/npair_full_multi2.cpp +++ b/src/npair_full_multi2.cpp @@ -35,7 +35,7 @@ NPairFullMulti2::NPairFullMulti2(LAMMPS *lmp) : NPair(lmp) {} void NPairFullMulti2::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -84,22 +84,21 @@ void NPairFullMulti2::build(NeighList *list) // skip i = j ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { - kbin = ibin; + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { + jbin = ibin; } else { - // Locate i in ktype bin - kbin = coord2bin(x[i], ktype); + // Locate i in jtype bin + jbin = coord2bin(x[i], jtype); } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (i == j) continue; - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/npair_half_multi2_newton.cpp b/src/npair_half_multi2_newton.cpp index 413da06284..ee3114ec8b 100755 --- a/src/npair_half_multi2_newton.cpp +++ b/src/npair_half_multi2_newton.cpp @@ -36,7 +36,7 @@ NPairHalfMulti2Newton::NPairHalfMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} void NPairHalfMulti2Newton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -86,8 +86,8 @@ void NPairHalfMulti2Newton::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { // own bin ... js = bins_multi2[itype][i]; @@ -100,7 +100,6 @@ void NPairHalfMulti2Newton::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -134,7 +133,6 @@ void NPairHalfMulti2Newton::build(NeighList *list) js = binhead_multi2[itype][ibin + s[k]]; for (j = js; j >= 0; j = bins_multi2[itype][j]) { - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -160,14 +158,14 @@ void NPairHalfMulti2Newton::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure + // smaller -> larger: locate i in the jtype bin structure - kbin = coord2bin(x[i], ktype); + jbin = coord2bin(x[i], jtype); // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ - js = binhead_multi2[ktype][kbin]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -176,7 +174,6 @@ void NPairHalfMulti2Newton::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -202,14 +199,13 @@ void NPairHalfMulti2Newton::build(NeighList *list) } } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/npair_half_multi2_newton_tri.cpp b/src/npair_half_multi2_newton_tri.cpp index 7970ee94a0..6c0fc35985 100755 --- a/src/npair_half_multi2_newton_tri.cpp +++ b/src/npair_half_multi2_newton_tri.cpp @@ -36,7 +36,7 @@ NPairHalfMulti2NewtonTri::NPairHalfMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} void NPairHalfMulti2NewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -86,9 +86,9 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == ktype) { + if (itype == jtype) { // loop over all atoms in other bins in stencil, store every pair // skip if i,j neighbor cutoff is less than bin distance @@ -106,7 +106,7 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) 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]; @@ -132,20 +132,18 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure + // smaller -> larger: locate i in the jtype bin structure - kbin = coord2bin(x[i], ktype); - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + jbin = coord2bin(x[i], jtype); + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { - - jtype = type[j]; - + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/npair_half_size_multi2_newtoff.cpp b/src/npair_half_size_multi2_newtoff.cpp index 0e0137a77e..efbd8f2fe4 100644 --- a/src/npair_half_size_multi2_newtoff.cpp +++ b/src/npair_half_size_multi2_newtoff.cpp @@ -36,7 +36,7 @@ NPairHalfSizeMulti2Newtoff::NPairHalfSizeMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) void NPairHalfSizeMulti2Newtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + int i,j,k,n,itype,jtype,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -78,23 +78,21 @@ void NPairHalfSizeMulti2Newtoff::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { - kbin = ibin; + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { + jbin = ibin; } else { - // Locate i in ktype bin - kbin = coord2bin(x[i], ktype); + // Locate i in jtype bin + jbin = coord2bin(x[i], jtype); } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi2[jtype][j]) { if (j <= i) continue; - - jtype = type[j]; - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi2_newton.cpp index 3b34b1a514..8a143124fd 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi2_newton.cpp @@ -34,7 +34,7 @@ NPairHalfSizeMulti2Newton::NPairHalfSizeMulti2Newton(LAMMPS *lmp) : NPair(lmp) { void NPairHalfSizeMulti2Newton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns,js; + int i,j,k,n,itype,jtype,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -74,9 +74,9 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == ktype) { + if (itype == jtype) { // own bin ... js = bins_multi2[itype][i]; @@ -89,7 +89,6 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -115,7 +114,6 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi2[itype][ibin + s[k]]; for (j = js; j >= 0; j = bins_multi2[itype][j]) { - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; @@ -135,13 +133,13 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure - kbin = coord2bin(x[i], ktype); + // smaller -> larger: locate i in the jtype bin structure + jbin = coord2bin(x[i], jtype); // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ - js = binhead_multi2[ktype][kbin]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -150,7 +148,6 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -171,14 +168,12 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) // Check other stencils - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { - - jtype = type[j]; - + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/npair_half_size_multi2_newton_tri.cpp b/src/npair_half_size_multi2_newton_tri.cpp index 3a2065c36e..e5b3b414ec 100755 --- a/src/npair_half_size_multi2_newton_tri.cpp +++ b/src/npair_half_size_multi2_newton_tri.cpp @@ -34,7 +34,7 @@ NPairHalfSizeMulti2NewtonTri::NPairHalfSizeMulti2NewtonTri(LAMMPS *lmp) : NPair( void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns,js; + int i,j,k,n,itype,jtype,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -74,9 +74,9 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == ktype) { + if (itype == jtype) { // loop over all atoms in other bins in stencil, store every pair // skip if i,j neighbor cutoff is less than bin distance @@ -94,7 +94,6 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) if (x[j][0] == xtmp && j <= i) continue; } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; @@ -114,20 +113,18 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure + // smaller -> larger: locate i in the jtype bin structure - kbin = coord2bin(x[i], ktype); + jbin = coord2bin(x[i], jtype); - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { - - jtype = type[j]; - + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; From 6c9bb854c017b92b1a1f0f28da4deeda3aa6735a Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 30 Nov 2020 10:51:15 -0700 Subject: [PATCH 26/73] Revamping multi2 npair classes, fixed bug if two types had same cut, better comments --- src/USER-OMP/npair_full_multi2_omp.cpp | 23 ++- .../npair_half_multi2_newtoff_omp.cpp | 28 +-- src/USER-OMP/npair_half_multi2_newton_omp.cpp | 192 ++++++++--------- .../npair_half_multi2_newton_tri_omp.cpp | 136 +++++------- .../npair_half_size_multi2_newtoff_omp.cpp | 29 +-- .../npair_half_size_multi2_newton_omp.cpp | 160 +++++++-------- .../npair_half_size_multi2_newton_tri_omp.cpp | 113 ++++------ src/npair_full_multi2.cpp | 24 +-- src/npair_half_multi2_newtoff.cpp | 44 ++-- src/npair_half_multi2_newton.cpp | 193 ++++++++---------- src/npair_half_multi2_newton_tri.cpp | 137 +++++-------- src/npair_half_size_multi2_newtoff.cpp | 29 +-- src/npair_half_size_multi2_newton.cpp | 161 +++++++-------- src/npair_half_size_multi2_newton_tri.cpp | 116 ++++------- 14 files changed, 600 insertions(+), 785 deletions(-) diff --git a/src/USER-OMP/npair_full_multi2_omp.cpp b/src/USER-OMP/npair_full_multi2_omp.cpp index 33ac289375..39f711fe4f 100755 --- a/src/USER-OMP/npair_full_multi2_omp.cpp +++ b/src/USER-OMP/npair_full_multi2_omp.cpp @@ -30,7 +30,7 @@ NPairFullMulti2Omp::NPairFullMulti2Omp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi-type stencil is itype dependent and is distance checked + multi2-type stencil is itype-jtype dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ @@ -89,21 +89,22 @@ void NPairFullMulti2Omp::build(NeighList *list) 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 = atom2bin_multi2[itype][i]; + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { - jbin = ibin; - } else { - // Locate i in jtype bin - jbin = coord2bin(x[i], jtype); - } + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + + // loop over all atoms in surrounding bins in stencil including self + // skip i = j + // use full stencil for all type combinations s = stencil_multi2[itype][jtype]; ns = nstencil_multi2[itype][jtype]; + for (k = 0; k < ns; k++) { js = binhead_multi2[jtype][jbin + s[k]]; for (j = js; j >= 0; j = bins_multi2[jtype][j]) { diff --git a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp index f440865bc7..bfd0d34a6c 100755 --- a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp @@ -30,8 +30,8 @@ NPairHalfMulti2NewtoffOmp::NPairHalfMulti2NewtoffOmp(LAMMPS *lmp) : NPair(lmp) { /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law + multi2-type stencil is itype-jtype dependent 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) ------------------------------------------------------------------------- */ @@ -91,23 +91,24 @@ void NPairHalfMulti2NewtoffOmp::build(NeighList *list) 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 = atom2bin_multi2[itype][i]; + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { - jbin = ibin; - } else { - // Locate i in jtype bin - jbin = coord2bin(x[i], jtype); - } + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + // 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 + // use full stencil for all type combinations + s = stencil_multi2[itype][jtype]; ns = nstencil_multi2[itype][jtype]; + for (k = 0; k < ns; k++) { js = binhead_multi2[jtype][jbin + s[k]]; for (j = js; j >=0; j = bins_multi2[jtype][j]) { @@ -139,7 +140,6 @@ void NPairHalfMulti2NewtoffOmp::build(NeighList *list) } } - ilist[i] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/USER-OMP/npair_half_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_multi2_newton_omp.cpp index 4035a44a8e..cbdbd69f50 100755 --- a/src/USER-OMP/npair_half_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi2_newton_omp.cpp @@ -30,8 +30,8 @@ NPairHalfMulti2NewtonOmp::NPairHalfMulti2NewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law + multi2-type stencil is itype-jtype dependent 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 ------------------------------------------------------------------------- */ @@ -90,91 +90,27 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = atom2bin_multi2[itype][i]; - + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); - // own bin ... - js = bins_multi2[itype][i]; - for (j = js; j >= 0; j = bins_multi2[itype][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(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + + // if same size: use half stencil + if(itype == jtype){ + + // if same type, implement with: + // 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 + + js = bins_multi2[itype][i]; - 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 - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][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 { - // smaller -> larger: locate i in the jtype bin structure - - jbin = coord2bin(x[i], jtype); - - // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - js = binhead_multi2[jtype][jbin]; for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -183,7 +119,7 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) if (x[j][1] == ytmp && x[j][0] < xtmp) continue; } } - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -207,40 +143,88 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) } else neighptr[n++] = j; } } - } - - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + } else { + + // if different types, implement with: + // loop over all atoms in jtype bin + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - + if(j < i) continue; + + 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,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); + 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; } + } + } + } + + // for all types, loop over all atoms in other bins in stencil, store every pair + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][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 != Atom::ATOMIC) { + 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; diff --git a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp index 25f49a5b09..5d0d724b58 100755 --- a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp @@ -31,8 +31,8 @@ NPairHalfMulti2NewtonTriOmp::NPairHalfMulti2NewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic + multi2-type stencil is itype-jtype dependent 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 ------------------------------------------------------------------------- */ @@ -90,25 +90,34 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) iatom = molatom[i]; tagprev = tag[i] - iatom - 1; } - - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] ibin = atom2bin_multi2[itype][i]; - + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + + // loop over all atoms in bins in stencil + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + // if half: 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 - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + + // if same size (e.g. same type), use half stencil + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -116,80 +125,33 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) 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; - } + } + } + + 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 != Atom::ATOMIC) { + 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 { - // smaller -> larger: locate i in the jtype bin structure - - jbin = coord2bin(x[i], jtype); - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; - - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - - // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - 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; diff --git a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp index 8e95b2c5b8..3b1f979a8e 100755 --- a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp @@ -27,9 +27,10 @@ using namespace LAMMPS_NS; NPairHalfSizeMulti2NewtoffOmp::NPairHalfSizeMulti2NewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- + size particles binned neighbor list construction with partial Newton's 3rd law + multi2-type stencil is itype-jtype dependent 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) ------------------------------------------------------------------------- */ @@ -79,23 +80,24 @@ void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - // 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 = atom2bin_multi2[itype][i]; + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { - jbin = ibin; - } else { - // Locate i in jtype bin - jbin = coord2bin(x[i], jtype); - } + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + // 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 + // use full stencil for all type combinations + s = stencil_multi2[itype][jtype]; ns = nstencil_multi2[itype][jtype]; + for (k = 0; k < ns; k++) { js = binhead_multi2[jtype][jbin + s[k]]; for (j = js; j >=0; j = bins_multi2[jtype][j]) { @@ -120,7 +122,6 @@ void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) } } - ilist[i] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp index ae490fe837..b7367abd57 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp @@ -27,9 +27,10 @@ using namespace LAMMPS_NS; NPairHalfSizeMulti2NewtonOmp::NPairHalfSizeMulti2NewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- + size particles binned neighbor list construction with full Newton's 3rd law + multi2-type stencil is itype-jtype dependent 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 ------------------------------------------------------------------------- */ @@ -78,77 +79,27 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = atom2bin_multi2[itype][i]; - + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); - if (itype == jtype) { - - // own bin ... - js = bins_multi2[itype][i]; - for (j = js; j >= 0; j = bins_multi2[itype][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(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + + // if same size: use half stencil + if(itype == jtype){ + + // if same type, implement with: + // 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 + + js = bins_multi2[itype][i]; - 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - 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 - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } - } - } else { - // smaller -> larger: locate i in the jtype bin structure - jbin = coord2bin(x[i], jtype); - - // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - js = binhead_multi2[jtype][jbin]; for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -157,41 +108,82 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) if (x[j][1] == ytmp && x[j][0] < xtmp) 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; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); - + if (rsq <= cutdistsq) { if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; } - } - } - - // Check other stencils + } + } else { + + // if different types, implement with: + // loop over all atoms in jtype bin + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - + if(j < i) continue; + + 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,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; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } + + // for all types, loop over all atoms in other bins in stencil, store every pair + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); if (rsq <= cutdistsq) { if (history && rsq < radsum*radsum) diff --git a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp index c1dea8ca79..66f9cbce0a 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp @@ -28,9 +28,10 @@ NPairHalfSizeMulti2NewtonTriOmp::NPairHalfSizeMulti2NewtonTriOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- + size particles binned neighbor list construction with Newton's 3rd law for triclinic + multi2-type stencil is itype-jtype dependent 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 ------------------------------------------------------------------------- */ @@ -79,24 +80,34 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = atom2bin_multi2[itype][i]; + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { + + // loop over all atoms in bins in stencil + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + // if half: 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 + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + + // if same size (e.g. same type), use half stencil + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -104,66 +115,26 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) if (x[j][0] < xtmp) continue; if (x[j][0] == xtmp && j <= i) continue; } - } + } + } + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } + 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]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; } } - } else { - // smaller -> larger: locate i in the jtype bin structure - - jbin = coord2bin(x[i], jtype); - - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - - // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } - } - } + } } ilist[i] = i; diff --git a/src/npair_full_multi2.cpp b/src/npair_full_multi2.cpp index 8af77aea22..732c5e581e 100644 --- a/src/npair_full_multi2.cpp +++ b/src/npair_full_multi2.cpp @@ -27,9 +27,8 @@ using namespace LAMMPS_NS; NPairFullMulti2::NPairFullMulti2(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - REWRITE binned neighbor list construction for all neighbors - multi-type stencil is itype dependent and is distance checked + multi2-type stencil is itype-jtype dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ @@ -79,21 +78,22 @@ void NPairFullMulti2::build(NeighList *list) 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 = atom2bin_multi2[itype][i]; + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { - jbin = ibin; - } else { - // Locate i in jtype bin - jbin = coord2bin(x[i], jtype); - } + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + + // loop over all atoms in surrounding bins in stencil including self + // skip i = j + // use full stencil for all type combinations s = stencil_multi2[itype][jtype]; ns = nstencil_multi2[itype][jtype]; + for (k = 0; k < ns; k++) { js = binhead_multi2[jtype][jbin + s[k]]; for (j = js; j >= 0; j = bins_multi2[jtype][j]) { diff --git a/src/npair_half_multi2_newtoff.cpp b/src/npair_half_multi2_newtoff.cpp index b44f2bcc62..ecd97fe689 100755 --- a/src/npair_half_multi2_newtoff.cpp +++ b/src/npair_half_multi2_newtoff.cpp @@ -27,17 +27,16 @@ using namespace LAMMPS_NS; NPairHalfMulti2Newtoff::NPairHalfMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - REWRITE binned neighbor list construction with partial Newton's 3rd law + multi2-type stencil is itype-jtype dependent 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 NPairHalfMulti2Newtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -81,30 +80,29 @@ void NPairHalfMulti2Newtoff::build(NeighList *list) 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 = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { - kbin = ibin; - } else { - // Locate i in ktype bin - kbin = coord2bin(x[i], ktype); - } + + // loop through stencils for all types + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + + // 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 + // use full stencil for all type combinations + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi2[jtype][j]) { if (j <= i) continue; - - jtype = type[j]; - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/npair_half_multi2_newton.cpp b/src/npair_half_multi2_newton.cpp index ee3114ec8b..6a7f52168a 100755 --- a/src/npair_half_multi2_newton.cpp +++ b/src/npair_half_multi2_newton.cpp @@ -27,10 +27,9 @@ using namespace LAMMPS_NS; NPairHalfMulti2Newton::NPairHalfMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - KS REWRTIE binned neighbor list construction with full Newton's 3rd law + multi2-type stencil is itype-jtype dependent 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 ------------------------------------------------------------------------- */ @@ -80,91 +79,27 @@ void NPairHalfMulti2Newton::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = atom2bin_multi2[itype][i]; - + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); - // own bin ... - js = bins_multi2[itype][i]; - for (j = js; j >= 0; j = bins_multi2[itype][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(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + + // if same size: use half stencil + if(itype == jtype){ + + // if same type, implement with: + // 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 + + js = bins_multi2[itype][i]; - 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 - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][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 { - // smaller -> larger: locate i in the jtype bin structure - - jbin = coord2bin(x[i], jtype); - - // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - js = binhead_multi2[jtype][jbin]; for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -173,7 +108,7 @@ void NPairHalfMulti2Newton::build(NeighList *list) if (x[j][1] == ytmp && x[j][0] < xtmp) continue; } } - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -197,40 +132,88 @@ void NPairHalfMulti2Newton::build(NeighList *list) } else neighptr[n++] = j; } } - } - - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + } else { + + // if different types, implement with: + // loop over all atoms in jtype bin + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - + if(j < i) continue; + + 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,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); + 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; } + } + } + } + + // for all types, loop over all atoms in other bins in stencil, store every pair + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][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 != Atom::ATOMIC) { + 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; diff --git a/src/npair_half_multi2_newton_tri.cpp b/src/npair_half_multi2_newton_tri.cpp index 6c0fc35985..9d0db60d50 100755 --- a/src/npair_half_multi2_newton_tri.cpp +++ b/src/npair_half_multi2_newton_tri.cpp @@ -27,10 +27,9 @@ using namespace LAMMPS_NS; NPairHalfMulti2NewtonTri::NPairHalfMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - KS REWRTIE binned neighbor list construction with Newton's 3rd law for triclinic + multi2-type stencil is itype-jtype dependent 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 ------------------------------------------------------------------------- */ @@ -79,25 +78,34 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) iatom = molatom[i]; tagprev = tag[i] - iatom - 1; } - - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] ibin = atom2bin_multi2[itype][i]; - + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + + // loop over all atoms in bins in stencil + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + // if half: 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 - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + + // if same size (e.g. same type), use half stencil + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -105,80 +113,33 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) 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; - } + } + } + + 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 != Atom::ATOMIC) { + 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 { - // smaller -> larger: locate i in the jtype bin structure - - jbin = coord2bin(x[i], jtype); - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; - - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - - // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - 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; diff --git a/src/npair_half_size_multi2_newtoff.cpp b/src/npair_half_size_multi2_newtoff.cpp index efbd8f2fe4..b559f83414 100644 --- a/src/npair_half_size_multi2_newtoff.cpp +++ b/src/npair_half_size_multi2_newtoff.cpp @@ -26,10 +26,10 @@ using namespace LAMMPS_NS; NPairHalfSizeMulti2Newtoff::NPairHalfSizeMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - REWRITE + size particles binned neighbor list construction with partial Newton's 3rd law + multi2-type stencil is itype-jtype dependent 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) ------------------------------------------------------------------------- */ @@ -71,23 +71,24 @@ void NPairHalfSizeMulti2Newtoff::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - // 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 = atom2bin_multi2[itype][i]; + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { - jbin = ibin; - } else { - // Locate i in jtype bin - jbin = coord2bin(x[i], jtype); - } + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + // 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 + // use full stencil for all type combinations + s = stencil_multi2[itype][jtype]; ns = nstencil_multi2[itype][jtype]; + for (k = 0; k < ns; k++) { js = binhead_multi2[jtype][jbin + s[k]]; for (j = js; j >=0; j = bins_multi2[jtype][j]) { diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi2_newton.cpp index 8a143124fd..bd5c6f6146 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi2_newton.cpp @@ -25,10 +25,10 @@ using namespace LAMMPS_NS; NPairHalfSizeMulti2Newton::NPairHalfSizeMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - KS REWRTIE + size particles binned neighbor list construction with full Newton's 3rd law + multi2-type stencil is itype-jtype dependent 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 ------------------------------------------------------------------------- */ @@ -68,77 +68,27 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = atom2bin_multi2[itype][i]; - + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); - if (itype == jtype) { - - // own bin ... - js = bins_multi2[itype][i]; - for (j = js; j >= 0; j = bins_multi2[itype][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(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + + // if same size: use half stencil + if(itype == jtype){ + + // if same type, implement with: + // 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 + + js = bins_multi2[itype][i]; - 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - 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 - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } - } - } else { - // smaller -> larger: locate i in the jtype bin structure - jbin = coord2bin(x[i], jtype); - - // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - js = binhead_multi2[jtype][jbin]; for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -147,41 +97,82 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) if (x[j][1] == ytmp && x[j][0] < xtmp) 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; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); - + if (rsq <= cutdistsq) { if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; } - } - } - - // Check other stencils + } + } else { + + // if different types, implement with: + // loop over all atoms in jtype bin + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - + if(j < i) continue; + + 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,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; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } + + // for all types, loop over all atoms in other bins in stencil, store every pair + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); if (rsq <= cutdistsq) { if (history && rsq < radsum*radsum) diff --git a/src/npair_half_size_multi2_newton_tri.cpp b/src/npair_half_size_multi2_newton_tri.cpp index e5b3b414ec..8cde0cbb36 100755 --- a/src/npair_half_size_multi2_newton_tri.cpp +++ b/src/npair_half_size_multi2_newton_tri.cpp @@ -25,10 +25,10 @@ using namespace LAMMPS_NS; NPairHalfSizeMulti2NewtonTri::NPairHalfSizeMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - KS REWRTIE + size particles binned neighbor list construction with Newton's 3rd law for triclinic + multi2-type stencil is itype-jtype dependent 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 ------------------------------------------------------------------------- */ @@ -68,24 +68,34 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = atom2bin_multi2[itype][i]; + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { + + // loop over all atoms in bins in stencil + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + // if half: 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 + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + + // if same size (e.g. same type), use half stencil + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -93,68 +103,28 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) if (x[j][0] < xtmp) continue; if (x[j][0] == xtmp && j <= i) continue; } - } + } + } + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } + 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]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; } } - } else { - // smaller -> larger: locate i in the jtype bin structure - - jbin = coord2bin(x[i], jtype); - - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - - // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } - } - } + } } - + ilist[inum++] = i; firstneigh[i] = neighptr; numneigh[i] = n; From e716abd34aafcdab1e29054475646aabf00fd932 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 30 Nov 2020 11:00:53 -0700 Subject: [PATCH 27/73] Fixing bad bracket --- .../npair_half_size_multi2_newton_omp.cpp | 19 +++++++++---------- src/npair_half_size_multi2_newton.cpp | 17 ++++++++--------- 2 files changed, 17 insertions(+), 19 deletions(-) diff --git a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp index b7367abd57..3a3a2fbe74 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp @@ -179,21 +179,20 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; - else + else neighptr[n++] = j; - } } } - } + } } ilist[i] = i; diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi2_newton.cpp index bd5c6f6146..bc6116b21c 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi2_newton.cpp @@ -168,18 +168,17 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; - else + else neighptr[n++] = j; - } } } } From 6308248a44a8dbc4cb07e2c73e94cbc835756726 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 30 Nov 2020 20:55:04 -0700 Subject: [PATCH 28/73] Replacing binsizex with multi2 version --- src/comm.cpp | 1 + src/nstencil.cpp | 6 +++--- src/nstencil_half_multi2_2d.cpp | 2 +- src/nstencil_half_multi2_3d.cpp | 2 +- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index 2e1192e150..fdafdbaf17 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -248,6 +248,7 @@ void Comm::init() // Could remove NP_NEWTON from npair_full_*multi2*, but could be cryptic // Also could be cases where you want newton off (hybrid) but don't use multi2 comm // Could add check on neighbor build, if full and comm->multi2 error... + // or just add check on comm setup - is that run before every run? Only if box change... if (force->newton == 0 && multi2) error->all(FLERR,"Cannot use multi2 communication with Newton off"); } diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 1658654e5a..709b48a257 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -345,11 +345,11 @@ void NStencil::create_setup() stencil_range = sqrt(cutneighsq[i][j]); sx = static_cast (stencil_range*bininvx_multi2[bin_type]); - if (sx*binsizex < stencil_range) sx++; + if (sx*binsizex_multi2[bin_type] < stencil_range) sx++; sy = static_cast (stencil_range*bininvy_multi2[bin_type]); - if (sy*binsizey < stencil_range) sy++; + if (sy*binsizey_multi2[bin_type] < stencil_range) sy++; sz = static_cast (stencil_range*bininvz_multi2[bin_type]); - if (sz*binsizez < stencil_range) sz++; + if (sz*binsizez_multi2[bin_type] < stencil_range) sz++; stencil_sx_multi2[i][j] = sx; stencil_sy_multi2[i][j] = sy; diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index c2f2127548..f240d87b54 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -88,7 +88,7 @@ void NStencilHalfMulti22d::create() if (j > 0 || (j == 0 && i > 0)) { if (bin_distance_multi2(i,j,0,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = j*mbinx + i; - } + } } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 57702cdb50..83ecb24cba 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -92,7 +92,7 @@ void NStencilHalfMulti23d::create() if (bin_distance_multi2(i,j,k,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - } + } } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) From 4fa48edb815406dec5c162b389c9625a56d5ae8a Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Thu, 10 Dec 2020 11:36:15 -0700 Subject: [PATCH 29/73] Adding size/multi npair files --- src/npair_half_size_multi_newtoff.cpp | 117 +++++++++++++++++++ src/npair_half_size_multi_newtoff.h | 46 ++++++++ src/npair_half_size_multi_newton.cpp | 143 +++++++++++++++++++++++ src/npair_half_size_multi_newton.h | 46 ++++++++ src/npair_half_size_multi_newton_tri.cpp | 125 ++++++++++++++++++++ src/npair_half_size_multi_newton_tri.h | 46 ++++++++ 6 files changed, 523 insertions(+) create mode 100644 src/npair_half_size_multi_newtoff.cpp create mode 100644 src/npair_half_size_multi_newtoff.h create mode 100644 src/npair_half_size_multi_newton.cpp create mode 100644 src/npair_half_size_multi_newton.h create mode 100644 src/npair_half_size_multi_newton_tri.cpp create mode 100644 src/npair_half_size_multi_newton_tri.h diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp new file mode 100644 index 0000000000..9dd9c9f38b --- /dev/null +++ b/src/npair_half_size_multi_newtoff.cpp @@ -0,0 +1,117 @@ +/* ---------------------------------------------------------------------- + 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_multi_newtoff.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + size particles + 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 NPairHalfSizeMultiNewtoff::build(NeighList *list) +{ + int i,j,k,m,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + 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]; + radi = radius[i]; + + // 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 = atom2bin[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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + 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_size_multi_newtoff.h b/src/npair_half_size_multi_newtoff.h new file mode 100644 index 0000000000..6f88240db6 --- /dev/null +++ b/src/npair_half_size_multi_newtoff.h @@ -0,0 +1,46 @@ +/* -*- 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/multi/newtoff, + NPairHalfSizeMultiNewtoff, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiNewtoff : public NPair { + public: + NPairHalfSizeMultiNewtoff(class LAMMPS *); + ~NPairHalfSizeMultiNewtoff() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp new file mode 100644 index 0000000000..631ba72340 --- /dev/null +++ b/src/npair_half_size_multi_newton.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_size_multi_newton.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + size particles + 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 NPairHalfSizeMultiNewton::build(NeighList *list) +{ + int i,j,k,m,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + 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]; + 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; + } + } + + 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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + 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 = atom2bin[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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + 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_size_multi_newton.h b/src/npair_half_size_multi_newton.h new file mode 100644 index 0000000000..2be10aa3d2 --- /dev/null +++ b/src/npair_half_size_multi_newton.h @@ -0,0 +1,46 @@ +/* -*- 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/multi/newton, + NPairHalfSizeMultiNewton, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiNewton : public NPair { + public: + NPairHalfSizeMultiNewton(class LAMMPS *); + ~NPairHalfSizeMultiNewton() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp new file mode 100644 index 0000000000..49745a87b0 --- /dev/null +++ b/src/npair_half_size_multi_newton_tri.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_size_multi_newton_tri.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(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 NPairHalfSizeMultiNewtonTri::build(NeighList *list) +{ + int i,j,k,m,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + 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]; + radi = radius[i]; + + + // 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 = atom2bin[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; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + 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_size_multi_newton_tri.h b/src/npair_half_size_multi_newton_tri.h new file mode 100644 index 0000000000..5a24d3437b --- /dev/null +++ b/src/npair_half_size_multi_newton_tri.h @@ -0,0 +1,46 @@ +/* -*- 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/multi/newton/tri, + NPairHalfSizeMultiNewtonTri, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiNewtonTri : public NPair { + public: + NPairHalfSizeMultiNewtonTri(class LAMMPS *); + ~NPairHalfSizeMultiNewtonTri() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ From a9c6d6f117a72829823b2a3f99ceca8992086a71 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 14:11:46 -0700 Subject: [PATCH 30/73] Removing temporary utilities --- src/compute_property_local.cpp | 48 ++--- src/pair_full_print.cpp | 341 --------------------------------- src/pair_full_print.h | 72 ------- 3 files changed, 15 insertions(+), 446 deletions(-) delete mode 100644 src/pair_full_print.cpp delete mode 100644 src/pair_full_print.h diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index fd0391831c..651e1190b1 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -35,7 +35,7 @@ enum{TYPE,RADIUS}; ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - vlocal(nullptr), alocal(nullptr), indices(nullptr), pack_choice(nullptr) + vlocal(NULL), alocal(NULL), indices(NULL), pack_choice(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute property/local command"); @@ -233,7 +233,7 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) : // error check - if (atom->molecular == Atom::TEMPLATE && (kindflag == BOND || kindflag == ANGLE || + if (atom->molecular == 2 && (kindflag == BOND || kindflag == ANGLE || kindflag == DIHEDRAL || kindflag == IMPROPER)) error->all(FLERR,"Compute property/local does not (yet) work " "with atom_style template"); @@ -254,8 +254,8 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute property/local requires atom attribute radius"); nmax = 0; - vlocal = nullptr; - alocal = nullptr; + vlocal = NULL; + alocal = NULL; } /* ---------------------------------------------------------------------- */ @@ -273,7 +273,7 @@ ComputePropertyLocal::~ComputePropertyLocal() void ComputePropertyLocal::init() { if (kindflag == NEIGH || kindflag == PAIR) { - if (force->pair == nullptr) + if (force->pair == NULL) error->all(FLERR,"No pair style is defined for compute property/local"); if (force->pair->single_enable == 0) error->all(FLERR,"Pair style does not support compute property/local"); @@ -665,16 +665,12 @@ double ComputePropertyLocal::memory_usage() void ComputePropertyLocal::pack_patom1(int n) { - int i,j; + int i; tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { i = indices[m][0]; - j = indices[m][1]; - if(tag[i] < tag[j]) - buf[n] = tag[i]; - else - buf[n] = tag[j]; + buf[n] = tag[i]; n += nvalues; } } @@ -683,16 +679,12 @@ void ComputePropertyLocal::pack_patom1(int n) void ComputePropertyLocal::pack_patom2(int n) { - int i,j; + int i; tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { - i = indices[m][0]; - j = indices[m][1]; - if(tag[i] > tag[j]) - buf[n] = tag[i]; - else - buf[n] = tag[j]; + i = indices[m][1]; + buf[n] = tag[i]; n += nvalues; } } @@ -701,17 +693,12 @@ void ComputePropertyLocal::pack_patom2(int n) void ComputePropertyLocal::pack_ptype1(int n) { - int i,j; + int i; int *type = atom->type; - tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { i = indices[m][0]; - j = indices[m][1]; - if(tag[i] < tag[j]) - buf[n] = type[i]; - else - buf[n] = type[j]; + buf[n] = type[i]; n += nvalues; } } @@ -720,17 +707,12 @@ void ComputePropertyLocal::pack_ptype1(int n) void ComputePropertyLocal::pack_ptype2(int n) { - int i,j; + int i; int *type = atom->type; - tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { - i = indices[m][0]; - j = indices[m][1]; - if(tag[i] > tag[j]) - buf[n] = type[i]; - else - buf[n] = type[j]; + i = indices[m][1]; + buf[n] = type[i]; n += nvalues; } } diff --git a/src/pair_full_print.cpp b/src/pair_full_print.cpp deleted file mode 100644 index bf42a81288..0000000000 --- a/src/pair_full_print.cpp +++ /dev/null @@ -1,341 +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 "pair_full_print.h" - -#include -#include -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "neighbor.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" - - -using namespace LAMMPS_NS; -using namespace MathConst; - -/* ---------------------------------------------------------------------- */ - -PairFullPrint::PairFullPrint(LAMMPS *lmp) : Pair(lmp) -{ - writedata = 1; -} - -/* ---------------------------------------------------------------------- */ - -PairFullPrint::~PairFullPrint() -{ - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - memory->destroy(prefactor); - memory->destroy(cut); - } -} - -/* ---------------------------------------------------------------------- */ - -void PairFullPrint::compute(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; - double r,rsq,arg,factor_lj; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = 0.0; - ev_init(eflag,vflag); - - double **x = atom->x; - double **f = atom->f; - tagint *tag = atom->tag; - int *type = atom->type; - int nlocal = atom->nlocal; - double *special_lj = force->special_lj; - int newton_pair = force->newton_pair; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // loop over neighbors of my atoms - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - factor_lj = special_lj[sbmask(j)]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - jtype = type[j]; - - if (rsq < cutsq[itype][jtype]) { - printf("NLIST %d %d %d %d\n", tag[i], tag[j], type[i], type[j]); - r = sqrt(rsq); - arg = MY_PI*r/cut[itype][jtype]; - if (r > 0.0) fpair = factor_lj * prefactor[itype][jtype] * - sin(arg) * MY_PI/cut[itype][jtype]/r; - else fpair = 0.0; - - f[i][0] += delx*fpair; - f[i][1] += dely*fpair; - f[i][2] += delz*fpair; - - if (eflag) - evdwl = factor_lj * prefactor[itype][jtype] * (1.0+cos(arg)); - - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,0.0,fpair,delx,dely,delz); - } - } - } - - if (vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairFullPrint::allocate() -{ - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - - memory->create(prefactor,n+1,n+1,"pair:prefactor"); - memory->create(cut,n+1,n+1,"pair:cut"); -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairFullPrint::settings(int narg, char **arg) -{ - if (narg != 1) error->all(FLERR,"Illegal pair_style command"); - - cut_global = utils::numeric(FLERR,arg[0],false,lmp); - - // reset cutoffs that have been explicitly set - - if (allocated) { - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) - if (setflag[i][j]) cut[i][j] = cut_global; - } -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairFullPrint::coeff(int narg, char **arg) -{ - if (narg < 3 || narg > 4) - error->all(FLERR,"Incorrect args for pair coefficients"); - if (!allocated) allocate(); - - int ilo,ihi,jlo,jhi; - utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); - utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); - - double prefactor_one = utils::numeric(FLERR,arg[2],false,lmp); - - double cut_one = cut_global; - if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],false,lmp); - - int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - prefactor[i][j] = prefactor_one; - cut[i][j] = cut_one; - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - -/* ---------------------------------------------------------------------- - init specific to this pair style - ------------------------------------------------------------------------- */ - -void PairFullPrint::init_style() { - // need a full neighbor list - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; -} - - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairFullPrint::init_one(int i, int j) -{ - // always mix prefactors geometrically - - if (setflag[i][j] == 0) { - prefactor[i][j] = sqrt(prefactor[i][i]*prefactor[j][j]); - cut[i][j] = mix_distance(cut[i][i],cut[j][j]); - } - - prefactor[j][i] = prefactor[i][j]; - cut[j][i] = cut[i][j]; - - return cut[i][j]; -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairFullPrint::write_restart(FILE *fp) -{ - write_restart_settings(fp); - - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) { - fwrite(&setflag[i][j],sizeof(int),1,fp); - if (setflag[i][j]) { - fwrite(&prefactor[i][j],sizeof(double),1,fp); - fwrite(&cut[i][j],sizeof(double),1,fp); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairFullPrint::read_restart(FILE *fp) -{ - read_restart_settings(fp); - - allocate(); - - int i,j; - int me = comm->me; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) { - if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); - if (setflag[i][j]) { - if (me == 0) { - utils::sfread(FLERR,&prefactor[i][j],sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); - } - MPI_Bcast(&prefactor[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairFullPrint::write_restart_settings(FILE *fp) -{ - fwrite(&cut_global,sizeof(double),1,fp); - fwrite(&mix_flag,sizeof(int),1,fp); -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairFullPrint::read_restart_settings(FILE *fp) -{ - if (comm->me == 0) { - utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); - } - MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); - MPI_Bcast(&mix_flag,1,MPI_INT,0,world); -} - -/* ---------------------------------------------------------------------- - proc 0 writes to data file -------------------------------------------------------------------------- */ - -void PairFullPrint::write_data(FILE *fp) -{ - for (int i = 1; i <= atom->ntypes; i++) - fprintf(fp,"%d %g\n",i,prefactor[i][i]); -} - -/* ---------------------------------------------------------------------- - proc 0 writes all pairs to data file -------------------------------------------------------------------------- */ - -void PairFullPrint::write_data_all(FILE *fp) -{ - for (int i = 1; i <= atom->ntypes; i++) - for (int j = i; j <= atom->ntypes; j++) - fprintf(fp,"%d %d %g %g\n",i,j,prefactor[i][j],cut[i][j]); -} - -/* ---------------------------------------------------------------------- */ - -double PairFullPrint::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, - double /*factor_coul*/, double factor_lj, - double &fforce) -{ - double r,arg,philj; - - r = sqrt(rsq); - arg = MY_PI*r/cut[itype][jtype]; - fforce = factor_lj * prefactor[itype][jtype] * - sin(arg) * MY_PI/cut[itype][jtype]/r; - - philj = prefactor[itype][jtype] * (1.0+cos(arg)); - return factor_lj*philj; -} - -/* ---------------------------------------------------------------------- */ - -void *PairFullPrint::extract(const char *str, int &dim) -{ - dim = 2; - if (strcmp(str,"a") == 0) return (void *) prefactor; - return nullptr; -} diff --git a/src/pair_full_print.h b/src/pair_full_print.h deleted file mode 100644 index 31b51f4e97..0000000000 --- a/src/pair_full_print.h +++ /dev/null @@ -1,72 +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. -------------------------------------------------------------------------- */ - -#ifdef PAIR_CLASS - -PairStyle(full/print,PairFullPrint) - -#else - -#ifndef LMP_PAIR_FULL_PRINT_H -#define LMP_PAIR_FULL_PRINT_H - -#include "pair.h" - -namespace LAMMPS_NS { - -class PairFullPrint : public Pair { - friend class Pair; - - public: - PairFullPrint(class LAMMPS *); - virtual ~PairFullPrint(); - void init_style(); - virtual void compute(int, int); - void settings(int, char **); - void coeff(int, char **); - double init_one(int, int); - void write_restart(FILE *); - void read_restart(FILE *); - void write_restart_settings(FILE *); - void read_restart_settings(FILE *); - void write_data(FILE *); - void write_data_all(FILE *); - double single(int, int, int, int, double, double, double, double &); - void *extract(const char *, int &); - - protected: - double cut_global; - double **prefactor; - double **cut; - - void allocate(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Incorrect args for pair coefficients - -Self-explanatory. Check the input script or data file. - -*/ From 0549da668d1556dddcd49c5f031732ff82dda0ca Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 16:06:47 -0700 Subject: [PATCH 31/73] Renaming multi->multi/old, updating lmpcite --- ...i_omp.cpp => npair_full_multi_old_omp.cpp} | 6 +-- ...multi_omp.h => npair_full_multi_old_omp.h} | 16 +++---- ...p => npair_half_multi_old_newtoff_omp.cpp} | 6 +-- ...p.h => npair_half_multi_old_newtoff_omp.h} | 16 +++---- ...pp => npair_half_multi_old_newton_omp.cpp} | 6 +-- ...mp.h => npair_half_multi_old_newton_omp.h} | 16 +++---- ...> npair_half_multi_old_newton_tri_omp.cpp} | 6 +-- ... => npair_half_multi_old_newton_tri_omp.h} | 16 +++---- .../npair_half_size_multi_newton_omp.h | 43 ----------------- .../npair_half_size_multi_newton_tri_omp.h | 43 ----------------- ...npair_half_size_multi_old_newtoff_omp.cpp} | 6 +-- ...> npair_half_size_multi_old_newtoff_omp.h} | 16 +++---- ... npair_half_size_multi_old_newton_omp.cpp} | 6 +-- .../npair_half_size_multi_old_newton_omp.h | 43 +++++++++++++++++ ...ir_half_size_multi_old_newton_tri_omp.cpp} | 6 +-- ...npair_half_size_multi_old_newton_tri_omp.h | 43 +++++++++++++++++ src/USER-OMP/npair_halffull_newtoff_omp.h | 4 +- src/USER-OMP/npair_halffull_newton_omp.h | 4 +- src/USER-OMP/npair_skip_omp.h | 12 ++--- src/comm.h | 2 +- src/nbin_standard.cpp | 2 +- src/neighbor.cpp | 41 +++++++++++++---- src/neighbor.h | 10 ++-- ...ull_multi.cpp => npair_full_multi_old.cpp} | 6 +-- ...ir_full_multi.h => npair_full_multi_old.h} | 16 +++---- ...f.cpp => npair_half_multi_old_newtoff.cpp} | 6 +-- ...ewton.h => npair_half_multi_old_newtoff.h} | 16 +++---- ...on.cpp => npair_half_multi_old_newton.cpp} | 6 +-- ...ewtoff.h => npair_half_multi_old_newton.h} | 16 +++---- ...pp => npair_half_multi_old_newton_tri.cpp} | 6 +-- ...ri.h => npair_half_multi_old_newton_tri.h} | 16 +++---- src/npair_half_size_multi_newtoff.h | 46 ------------------- src/npair_half_size_multi_newton.h | 46 ------------------- src/npair_half_size_multi_newton_tri.h | 46 ------------------- ... => npair_half_size_multi_old_newtoff.cpp} | 6 +-- src/npair_half_size_multi_old_newtoff.h | 46 +++++++++++++++++++ ...p => npair_half_size_multi_old_newton.cpp} | 6 +-- src/npair_half_size_multi_old_newton.h | 46 +++++++++++++++++++ ... npair_half_size_multi_old_newton_tri.cpp} | 8 ++-- src/npair_half_size_multi_old_newton_tri.h | 46 +++++++++++++++++++ src/npair_halffull_newtoff.h | 8 ++-- src/npair_halffull_newton.h | 4 +- src/npair_skip.h | 4 +- src/npair_skip_respa.h | 2 +- src/npair_skip_size.h | 2 +- src/npair_skip_size_off2on.h | 2 +- src/npair_skip_size_off2on_oneside.h | 2 +- 47 files changed, 399 insertions(+), 378 deletions(-) rename src/USER-OMP/{npair_full_multi_omp.cpp => npair_full_multi_old_omp.cpp} (96%) rename src/USER-OMP/{npair_full_multi_omp.h => npair_full_multi_old_omp.h} (73%) rename src/USER-OMP/{npair_half_multi_newtoff_omp.cpp => npair_half_multi_old_newtoff_omp.cpp} (95%) rename src/USER-OMP/{npair_half_multi_newton_tri_omp.h => npair_half_multi_old_newtoff_omp.h} (67%) rename src/USER-OMP/{npair_half_multi_newton_omp.cpp => npair_half_multi_old_newton_omp.cpp} (96%) rename src/USER-OMP/{npair_half_multi_newton_omp.h => npair_half_multi_old_newton_omp.h} (68%) rename src/USER-OMP/{npair_half_multi_newton_tri_omp.cpp => npair_half_multi_old_newton_tri_omp.cpp} (96%) rename src/USER-OMP/{npair_half_multi_newtoff_omp.h => npair_half_multi_old_newton_tri_omp.h} (67%) delete mode 100644 src/USER-OMP/npair_half_size_multi_newton_omp.h delete mode 100644 src/USER-OMP/npair_half_size_multi_newton_tri_omp.h rename src/USER-OMP/{npair_half_size_multi_newtoff_omp.cpp => npair_half_size_multi_old_newtoff_omp.cpp} (95%) rename src/USER-OMP/{npair_half_size_multi_newtoff_omp.h => npair_half_size_multi_old_newtoff_omp.h} (67%) rename src/USER-OMP/{npair_half_size_multi_newton_omp.cpp => npair_half_size_multi_old_newton_omp.cpp} (95%) create mode 100644 src/USER-OMP/npair_half_size_multi_old_newton_omp.h rename src/USER-OMP/{npair_half_size_multi_newton_tri_omp.cpp => npair_half_size_multi_old_newton_tri_omp.cpp} (95%) create mode 100644 src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h rename src/{npair_full_multi.cpp => npair_full_multi_old.cpp} (96%) rename src/{npair_full_multi.h => npair_full_multi_old.h} (73%) rename src/{npair_half_multi_newtoff.cpp => npair_half_multi_old_newtoff.cpp} (95%) rename src/{npair_half_multi_newton.h => npair_half_multi_old_newtoff.h} (71%) rename src/{npair_half_multi_newton.cpp => npair_half_multi_old_newton.cpp} (96%) rename src/{npair_half_multi_newtoff.h => npair_half_multi_old_newton.h} (72%) rename src/{npair_half_multi_newton_tri.cpp => npair_half_multi_old_newton_tri.cpp} (96%) rename src/{npair_half_multi_newton_tri.h => npair_half_multi_old_newton_tri.h} (70%) delete mode 100644 src/npair_half_size_multi_newtoff.h delete mode 100644 src/npair_half_size_multi_newton.h delete mode 100644 src/npair_half_size_multi_newton_tri.h rename src/{npair_half_size_multi_newtoff.cpp => npair_half_size_multi_old_newtoff.cpp} (94%) create mode 100644 src/npair_half_size_multi_old_newtoff.h rename src/{npair_half_size_multi_newton.cpp => npair_half_size_multi_old_newton.cpp} (95%) create mode 100644 src/npair_half_size_multi_old_newton.h rename src/{npair_half_size_multi_newton_tri.cpp => npair_half_size_multi_old_newton_tri.cpp} (92%) create mode 100644 src/npair_half_size_multi_old_newton_tri.h diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_old_omp.cpp similarity index 96% rename from src/USER-OMP/npair_full_multi_omp.cpp rename to src/USER-OMP/npair_full_multi_old_omp.cpp index ce17b4a5a9..ef4c4ef5e4 100644 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_old_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_full_multi_omp.h" +#include "npair_full_multi_old_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,7 +26,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairFullMultiOldOmp::NPairFullMultiOldOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors @@ -34,7 +34,7 @@ NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {} every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ -void NPairFullMultiOmp::build(NeighList *list) +void NPairFullMultiOldOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; diff --git a/src/USER-OMP/npair_full_multi_omp.h b/src/USER-OMP/npair_full_multi_old_omp.h similarity index 73% rename from src/USER-OMP/npair_full_multi_omp.h rename to src/USER-OMP/npair_full_multi_old_omp.h index 882e649183..2c1711f257 100644 --- a/src/USER-OMP/npair_full_multi_omp.h +++ b/src/USER-OMP/npair_full_multi_old_omp.h @@ -13,24 +13,24 @@ #ifdef NPAIR_CLASS -NPairStyle(full/multi/omp, - NPairFullMultiOmp, - NP_FULL | NP_MULTI | NP_OMP | +NPairStyle(full/multi/old/omp, + NPairFullMultiOldOmp, + NP_FULL | NP_MULTI_OLD | 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 +#ifndef LMP_NPAIR_FULL_MULTI_OLD_OMP_H +#define LMP_NPAIR_FULL_MULTI_OLD_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairFullMultiOmp : public NPair { +class NPairFullMultiOldOmp : public NPair { public: - NPairFullMultiOmp(class LAMMPS *); - ~NPairFullMultiOmp() {} + NPairFullMultiOldOmp(class LAMMPS *); + ~NPairFullMultiOldOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp similarity index 95% rename from src/USER-OMP/npair_half_multi_newtoff_omp.cpp rename to src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp index 2bc90838d6..2839ebfa14 100644 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_multi_newtoff_omp.h" +#include "npair_half_multi_old_newtoff_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,7 +26,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiOldNewtoffOmp::NPairHalfMultiOldNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law @@ -36,7 +36,7 @@ NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfMultiNewtoffOmp::build(NeighList *list) +void NPairHalfMultiOldNewtoffOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.h b/src/USER-OMP/npair_half_multi_old_newtoff_omp.h similarity index 67% rename from src/USER-OMP/npair_half_multi_newton_tri_omp.h rename to src/USER-OMP/npair_half_multi_old_newtoff_omp.h index 80faf8188f..0487be35ef 100644 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.h +++ b/src/USER-OMP/npair_half_multi_old_newtoff_omp.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi/newton/tri/omp, - NPairHalfMultiNewtonTriOmp, - NP_HALF | NP_MULTI | NP_NEWTON | NP_TRI | NP_OMP) +NPairStyle(half/multi/old/newtoff/omp, + NPairHalfMultiOldNewtoffOmp, + NP_HALF | NP_MULTI_OLD | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_TRI_OMP_H -#define LMP_NPAIR_HALF_MULTI_NEWTON_TRI_OMP_H +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_OMP_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMultiNewtonTriOmp : public NPair { +class NPairHalfMultiOldNewtoffOmp : public NPair { public: - NPairHalfMultiNewtonTriOmp(class LAMMPS *); - ~NPairHalfMultiNewtonTriOmp() {} + NPairHalfMultiOldNewtoffOmp(class LAMMPS *); + ~NPairHalfMultiOldNewtoffOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_old_newton_omp.cpp similarity index 96% rename from src/USER-OMP/npair_half_multi_newton_omp.cpp rename to src/USER-OMP/npair_half_multi_old_newton_omp.cpp index dbaad2adec..bc77cc518b 100644 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_old_newton_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_multi_newton_omp.h" +#include "npair_half_multi_old_newton_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,7 +26,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMultiNewtonOmp::NPairHalfMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiOldNewtonOmp::NPairHalfMultiOldNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law @@ -35,7 +35,7 @@ NPairHalfMultiNewtonOmp::NPairHalfMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMultiNewtonOmp::build(NeighList *list) +void NPairHalfMultiOldNewtonOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; diff --git a/src/USER-OMP/npair_half_multi_newton_omp.h b/src/USER-OMP/npair_half_multi_old_newton_omp.h similarity index 68% rename from src/USER-OMP/npair_half_multi_newton_omp.h rename to src/USER-OMP/npair_half_multi_old_newton_omp.h index 85df36bb09..145ef9d0be 100644 --- a/src/USER-OMP/npair_half_multi_newton_omp.h +++ b/src/USER-OMP/npair_half_multi_old_newton_omp.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi/newton/omp, - NPairHalfMultiNewtonOmp, - NP_HALF | NP_MULTI | NP_NEWTON | NP_OMP | NP_ORTHO) +NPairStyle(half/multi/old/newton/omp, + NPairHalfMultiOldNewtonOmp, + NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_OMP | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_OMP_H -#define LMP_NPAIR_HALF_MULTI_NEWTON_OMP_H +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_OMP_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMultiNewtonOmp : public NPair { +class NPairHalfMultiOldNewtonOmp : public NPair { public: - NPairHalfMultiNewtonOmp(class LAMMPS *); - ~NPairHalfMultiNewtonOmp() {} + NPairHalfMultiOldNewtonOmp(class LAMMPS *); + ~NPairHalfMultiOldNewtonOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp similarity index 96% rename from src/USER-OMP/npair_half_multi_newton_tri_omp.cpp rename to src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp index dd219a616e..3d5a577396 100644 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_multi_newton_tri_omp.h" +#include "npair_half_multi_old_newton_tri_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,7 +26,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) : +NPairHalfMultiOldNewtonTriOmp::NPairHalfMultiOldNewtonTriOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- @@ -36,7 +36,7 @@ NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) : every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMultiNewtonTriOmp::build(NeighList *list) +void NPairHalfMultiOldNewtonTriOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.h b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.h similarity index 67% rename from src/USER-OMP/npair_half_multi_newtoff_omp.h rename to src/USER-OMP/npair_half_multi_old_newton_tri_omp.h index a7aebf6579..29bb456570 100644 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.h +++ b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi/newtoff/omp, - NPairHalfMultiNewtoffOmp, - NP_HALF | NP_MULTI | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) +NPairStyle(half/multi/old/newton/tri/omp, + NPairHalfMultiOldNewtonTriOmp, + NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_TRI | NP_OMP) #else -#ifndef LMP_NPAIR_HALF_MULTI_NEWTOFF_OMP_H -#define LMP_NPAIR_HALF_MULTI_NEWTOFF_OMP_H +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_OMP_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMultiNewtoffOmp : public NPair { +class NPairHalfMultiOldNewtonTriOmp : public NPair { public: - NPairHalfMultiNewtoffOmp(class LAMMPS *); - ~NPairHalfMultiNewtoffOmp() {} + NPairHalfMultiOldNewtonTriOmp(class LAMMPS *); + ~NPairHalfMultiOldNewtonTriOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.h b/src/USER-OMP/npair_half_size_multi_newton_omp.h deleted file mode 100644 index 03d712145f..0000000000 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.h +++ /dev/null @@ -1,43 +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. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi/newton/omp, - NPairHalfSizeMultiNewtonOmp, - NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_OMP | NP_ORTHO) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_OMP_H -#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_OMP_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMultiNewtonOmp : public NPair { - public: - NPairHalfSizeMultiNewtonOmp(class LAMMPS *); - ~NPairHalfSizeMultiNewtonOmp() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h deleted file mode 100644 index 6e936c8da4..0000000000 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h +++ /dev/null @@ -1,43 +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. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi/newton/tri/omp, - NPairHalfSizeMultiNewtonTriOmp, - NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_TRI | NP_OMP) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_OMP_H -#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_OMP_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMultiNewtonTriOmp : public NPair { - public: - NPairHalfSizeMultiNewtonTriOmp(class LAMMPS *); - ~NPairHalfSizeMultiNewtonTriOmp() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp similarity index 95% rename from src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp rename to src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp index 33722eb9d3..e3001185c1 100644 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_size_multi_newtoff_omp.h" +#include "npair_half_size_multi_old_newtoff_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : +NPairHalfSizeMultiNewtoffOldOmp::NPairHalfSizeMultiNewtoffOldOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- @@ -36,7 +36,7 @@ NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) +void NPairHalfSizeMultiNewtoffOldOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.h b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.h similarity index 67% rename from src/USER-OMP/npair_half_size_multi_newtoff_omp.h rename to src/USER-OMP/npair_half_size_multi_old_newtoff_omp.h index dd883d7f3c..b7a7d9f4ac 100644 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.h +++ b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.h @@ -13,24 +13,24 @@ #ifdef NPAIR_CLASS -NPairStyle(half/size/multi/newtoff/omp, - NPairHalfSizeMultiNewtoffOmp, - NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_OMP | +NPairStyle(half/size/multi/old/newtoff/omp, + NPairHalfSizeMultiOldNewtoffOmp, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_OMP_H -#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_OMP_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfSizeMultiNewtoffOmp : public NPair { +class NPairHalfSizeMultiOldNewtoffOmp : public NPair { public: - NPairHalfSizeMultiNewtoffOmp(class LAMMPS *); - ~NPairHalfSizeMultiNewtoffOmp() {} + NPairHalfSizeMultiOldNewtoffOmp(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtoffOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp similarity index 95% rename from src/USER-OMP/npair_half_size_multi_newton_omp.cpp rename to src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp index 0be87457e3..ee166a57cf 100644 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_size_multi_newton_omp.h" +#include "npair_half_size_multi_old_newton_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) : +NPairHalfSizeMultiNewtonOldOmp::NPairHalfSizeMultiNewtonOldOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- @@ -35,7 +35,7 @@ NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) : every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) +void NPairHalfSizeMultiNewtonOldOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_omp.h b/src/USER-OMP/npair_half_size_multi_old_newton_omp.h new file mode 100644 index 0000000000..7573b8c89e --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi_old_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/multi/old/newton/omp, + NPairHalfSizeMultiOldNewtonOmp, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_OMP | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewtonOmp : public NPair { + public: + NPairHalfSizeMultiOldNewtonOmp(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtonOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp similarity index 95% rename from src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp rename to src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp index ef26a5f2bd..81e896db6c 100644 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_size_multi_newton_tri_omp.h" +#include "npair_half_size_multi_old_newton_tri_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) : +NPairHalfSizeMultiOldNewtonTriOmp::NPairHalfSizeMultiOldNewtonTriOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- @@ -35,7 +35,7 @@ NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) : every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) +void NPairHalfSizeMultiOldNewtonTriOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h new file mode 100644 index 0000000000..4cd1c58e6f --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi_old_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/multi/old/newton/tri/omp, + NPairHalfSizeMultiOldNewtonTriOmp, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_TRI | NP_OMP) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewtonTriOmp : public NPair { + public: + NPairHalfSizeMultiOldNewtonTriOmp(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtonTriOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.h b/src/USER-OMP/npair_halffull_newtoff_omp.h index 961544a952..010921d13e 100644 --- a/src/USER-OMP/npair_halffull_newtoff_omp.h +++ b/src/USER-OMP/npair_halffull_newtoff_omp.h @@ -15,12 +15,12 @@ NPairStyle(halffull/newtoff/omp, NPairHalffullNewtoffOmp, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI |NP_OMP) NPairStyle(halffull/newtoff/skip/omp, NPairHalffullNewtoffOmp, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI | NP_SKIP | NP_OMP) #else diff --git a/src/USER-OMP/npair_halffull_newton_omp.h b/src/USER-OMP/npair_halffull_newton_omp.h index ef8be32a74..88dbc3653b 100644 --- a/src/USER-OMP/npair_halffull_newton_omp.h +++ b/src/USER-OMP/npair_halffull_newton_omp.h @@ -15,12 +15,12 @@ NPairStyle(halffull/newton/omp, NPairHalffullNewtonOmp, - NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_ORTHO | NP_TRI| NP_OMP) NPairStyle(halffull/newton/skip/omp, NPairHalffullNewtonOmp, - NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_ORTHO | NP_TRI | NP_SKIP | NP_OMP) #else diff --git a/src/USER-OMP/npair_skip_omp.h b/src/USER-OMP/npair_skip_omp.h index a6ee1930d4..c080296e36 100644 --- a/src/USER-OMP/npair_skip_omp.h +++ b/src/USER-OMP/npair_skip_omp.h @@ -19,36 +19,36 @@ NPairStyle(skip/omp, NPairSkip, NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/half/respa/omp, NPairSkipRespa, NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/half/size/omp, NPairSkipSize, - NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | + NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/size/off2on/omp, NPairSkipSizeOff2on, NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/size/off2on/oneside/omp, NPairSkipSizeOff2onOneside, NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON | NP_NEWTOFF | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/ghost/omp, NPairSkip, NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP | NP_GHOST) #endif diff --git a/src/comm.h b/src/comm.h index d8d842ace5..5cd47bd5cd 100644 --- a/src/comm.h +++ b/src/comm.h @@ -152,6 +152,7 @@ class Comm : protected Pointers { int ncores; // # of cores per node int coregrid[3]; // 3d grid of cores within a node int user_coregrid[3]; // user request for cores in each dim + int multi2; // 1 if multi cutoff is intra-type cutoff void init_exchange(); int rendezvous_irregular(int, char *, int, int, int *, @@ -161,7 +162,6 @@ class Comm : protected Pointers { int (*)(int, char *, int &, int *&, char *&, void *), int, char *&, int, void *, int); void rendezvous_stats(int, int, int, int, int, int, bigint); - int multi2; // 1 if multi cutoff is intra-type cutoff public: enum{MULTIPLE}; diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp index 8295a621fb..ebf7114d94 100644 --- a/src/nbin_standard.cpp +++ b/src/nbin_standard.cpp @@ -115,7 +115,7 @@ void NBinStandard::setup_bins(int style) // 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 + // for MULTI_OLD style, binsize = 1/2 of min neighbor cutoff // special case of all cutoffs = 0.0, binsize = box size double binsize_optimal; diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 401bd7298b..0854dee227 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -58,6 +58,19 @@ using namespace NeighConst; enum{NONE,ALL,PARTIAL,TEMPLATE}; +static const char cite_neigh_multi_old[] = + "neighbor multi/old command:\n\n" + "@Article{Intveld08,\n" + " author = {P.{\\,}J.~in{\\,}'t~Veld and S.{\\,}J.~Plimpton" + " and G.{\\,}S.~Grest},\n" + " title = {Accurate and Efficient Methods for Modeling Colloidal\n" + " Mixtures in an Explicit Solvent using Molecular Dynamics},\n" + " journal = {Comp.~Phys.~Comm.},\n" + " year = 2008,\n" + " volume = 179,\n" + " pages = {320--329}\n" + "}\n\n"; + static const char cite_neigh_multi[] = "neighbor multi command:\n\n" "@Article{Intveld08,\n" @@ -69,6 +82,13 @@ static const char cite_neigh_multi[] = " year = 2008,\n" " volume = 179,\n" " pages = {320--329}\n" + "}\n\n" + "@article{Shire2020,\n" + " author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},\n" + " title = {DEM simulations of polydisperse media: efficient contact\n" + " detection applied to investigate the quasi-static limit},\n" + " journal = {Computational Particle Mechanics},\n" + " year = {2020}\n" "}\n\n"; //#define NEIGH_LIST_DEBUG 1 @@ -1622,10 +1642,10 @@ int Neighbor::choose_bin(NeighRequest *rq) // neighbor style is BIN or MULTI or MULTI2 and must match - if (style == Neighbor::BIN || style == Neighbor::MULTI) { + if (style == Neighbor::BIN || style == Neighbor::MULTI_OLD) { if (!(mask & NB_STANDARD)) continue; - } else if (style == Neighbor::MULTI2) { - if (!(mask & NB_MULTI2)) continue; + } else if (style == Neighbor::MULTI) { + if (!(mask & NB_MULTI)) continue; } return i+1; @@ -1695,14 +1715,14 @@ int Neighbor::choose_stencil(NeighRequest *rq) if (!rq->ghost != !(mask & NS_GHOST)) continue; if (!rq->ssa != !(mask & NS_SSA)) continue; - // neighbor style is one of BIN, MULTI, or MULTI2 and must match + // neighbor style is one of BIN, MULTI_OLD, or MULTI and must match if (style == Neighbor::BIN) { if (!(mask & NS_BIN)) continue; + } else if (style == Neighbor::MULTI_OLD) { + if (!(mask & NS_MULTI_OLD)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NS_MULTI)) continue; - } else if (style == Neighbor::MULTI2) { - if (!(mask & NS_MULTI2)) continue; } // dimension is 2 or 3 and must match @@ -1832,16 +1852,16 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!rq->halffull != !(mask & NP_HALF_FULL)) continue; if (!rq->off2on != !(mask & NP_OFF2ON)) continue; - // neighbor style is one of NSQ, BIN, MULTI, or MULTI2 and must match + // neighbor style is one of NSQ, BIN, MULTI_OLD, or MULTI and must match if (style == Neighbor::NSQ) { if (!(mask & NP_NSQ)) continue; } else if (style == Neighbor::BIN) { if (!(mask & NP_BIN)) continue; + } else if (style == Neighbor::MULTI_OLD) { + if (!(mask & NP_MULTI_OLD)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NP_MULTI)) continue; - } else if (style == Neighbor::MULTI2) { - if (!(mask & NP_MULTI2)) continue; } // domain triclinic flag is on or off and must match @@ -2211,9 +2231,10 @@ void Neighbor::set(int narg, char **arg) if (strcmp(arg[1],"nsq") == 0) style = Neighbor::NSQ; else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN; else if (strcmp(arg[1],"multi") == 0) style = Neighbor::MULTI; - else if (strcmp(arg[1],"multi2") == 0) style = Neighbor::MULTI2; + else if (strcmp(arg[1],"multi/old") == 0) style = Neighbor::MULTI_OLD; else error->all(FLERR,"Illegal neighbor command"); + if (style == Neighbor::MULTI_OLD && lmp->citeme) lmp->citeme->add(cite_neigh_multi_old); if (style == Neighbor::MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi); } diff --git a/src/neighbor.h b/src/neighbor.h index b1cc95f5e7..2943f7e082 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -20,8 +20,8 @@ namespace LAMMPS_NS { class Neighbor : protected Pointers { public: - enum{NSQ,BIN,MULTI,MULTI2}; - int style; // 0,1,2 = nsq, bin, multi + enum{NSQ,BIN,MULTI_OLD,MULTI}; + int style; // 0,1,2 = nsq, bin, multi/old, multi int every; // build every this many steps int delay; // delay build for this many steps int dist_check; // 0 = always build, 1 = only if 1/2 dist @@ -239,7 +239,7 @@ namespace NeighConst { static const int NB_KOKKOS_DEVICE = 1<<1; static const int NB_KOKKOS_HOST = 1<<2; static const int NB_SSA = 1<<3; - static const int NB_MULTI2 = 1<<4; + static const int NB_MULTI = 1<<4; static const int NB_STANDARD = 1<<5; static const int NS_BIN = 1<<0; @@ -252,7 +252,7 @@ namespace NeighConst { static const int NS_TRI = 1<<7; static const int NS_GHOST = 1<<8; static const int NS_SSA = 1<<9; - static const int NS_MULTI2 = 1<<10; + static const int NS_MULTI_OLD = 1<<10; static const int NP_NSQ = 1<<0; static const int NP_BIN = 1<<1; @@ -279,7 +279,7 @@ namespace NeighConst { static const int NP_SKIP = 1<<22; static const int NP_HALF_FULL = 1<<23; static const int NP_OFF2ON = 1<<24; - static const int NP_MULTI2 = 1<<25; + static const int NP_MULTI_OLD = 1<<25; } } diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi_old.cpp similarity index 96% rename from src/npair_full_multi.cpp rename to src/npair_full_multi_old.cpp index 79a9c7cec3..9a800a80b5 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi_old.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_full_multi.h" +#include "npair_full_multi_old.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {} +NPairFullMultiOld::NPairFullMultiOld(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors @@ -32,7 +32,7 @@ NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {} every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ -void NPairFullMulti::build(NeighList *list) +void NPairFullMultiOld::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; tagint tagprev; diff --git a/src/npair_full_multi.h b/src/npair_full_multi_old.h similarity index 73% rename from src/npair_full_multi.h rename to src/npair_full_multi_old.h index 481a673060..f53b6451e2 100644 --- a/src/npair_full_multi.h +++ b/src/npair_full_multi_old.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(full/multi, - NPairFullMulti, - NP_FULL | NP_MULTI | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(full/multi/old, + NPairFullMultiOld, + NP_FULL | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_FULL_MULTI_H -#define LMP_NPAIR_FULL_MULTI_H +#ifndef LMP_NPAIR_FULL_MULTI_OLD_H +#define LMP_NPAIR_FULL_MULTI_OLD_H #include "npair.h" namespace LAMMPS_NS { -class NPairFullMulti : public NPair { +class NPairFullMultiOld : public NPair { public: - NPairFullMulti(class LAMMPS *); - ~NPairFullMulti() {} + NPairFullMultiOld(class LAMMPS *); + ~NPairFullMultiOld() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_old_newtoff.cpp similarity index 95% rename from src/npair_half_multi_newtoff.cpp rename to src/npair_half_multi_old_newtoff.cpp index 3979e494a9..351fd65c32 100644 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_old_newtoff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_multi_newtoff.h" +#include "npair_half_multi_old_newtoff.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiOldNewtoff::NPairHalfMultiOldNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law @@ -34,7 +34,7 @@ NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfMultiNewtoff::build(NeighList *list) +void NPairHalfMultiOldNewtoff::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; tagint tagprev; diff --git a/src/npair_half_multi_newton.h b/src/npair_half_multi_old_newtoff.h similarity index 71% rename from src/npair_half_multi_newton.h rename to src/npair_half_multi_old_newtoff.h index 427b771780..7a3e7b3671 100644 --- a/src/npair_half_multi_newton.h +++ b/src/npair_half_multi_old_newtoff.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi/newton, - NPairHalfMultiNewton, - NP_HALF | NP_MULTI | NP_NEWTON | NP_ORTHO) +NPairStyle(half/multi/old/newtoff, + NPairHalfMultiOldNewtoff, + NP_HALF | NP_MULTI_OLD | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_H -#define LMP_NPAIR_HALF_MULTI_NEWTON_H +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMultiNewton : public NPair { +class NPairHalfMultiOldNewtoff : public NPair { public: - NPairHalfMultiNewton(class LAMMPS *); - ~NPairHalfMultiNewton() {} + NPairHalfMultiOldNewtoff(class LAMMPS *); + ~NPairHalfMultiOldNewtoff() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_old_newton.cpp similarity index 96% rename from src/npair_half_multi_newton.cpp rename to src/npair_half_multi_old_newton.cpp index 7ea58d29ad..5af420017d 100644 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_old_newton.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_multi_newton.h" +#include "npair_half_multi_old_newton.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiOldNewton::NPairHalfMultiOldNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law @@ -33,7 +33,7 @@ NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {} every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMultiNewton::build(NeighList *list) +void NPairHalfMultiOldNewton::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; tagint tagprev; diff --git a/src/npair_half_multi_newtoff.h b/src/npair_half_multi_old_newton.h similarity index 72% rename from src/npair_half_multi_newtoff.h rename to src/npair_half_multi_old_newton.h index 593e2c1d9d..337e54abed 100644 --- a/src/npair_half_multi_newtoff.h +++ b/src/npair_half_multi_old_newton.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi/newtoff, - NPairHalfMultiNewtoff, - NP_HALF | NP_MULTI | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(half/multi/old/newton, + NPairHalfMultiOldNewton, + NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_MULTI_NEWTOFF_H -#define LMP_NPAIR_HALF_MULTI_NEWTOFF_H +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMultiNewtoff : public NPair { +class NPairHalfMultiOldNewton : public NPair { public: - NPairHalfMultiNewtoff(class LAMMPS *); - ~NPairHalfMultiNewtoff() {} + NPairHalfMultiOldNewton(class LAMMPS *); + ~NPairHalfMultiOldNewton() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_old_newton_tri.cpp similarity index 96% rename from src/npair_half_multi_newton_tri.cpp rename to src/npair_half_multi_old_newton_tri.cpp index a1095c3fe2..f22e0fbf4f 100644 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_old_newton_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_multi_newton_tri.h" +#include "npair_half_multi_old_newton_tri.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiOldNewtonTri::NPairHalfMultiOldNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic @@ -33,7 +33,7 @@ NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMultiNewtonTri::build(NeighList *list) +void NPairHalfMultiOldNewtonTri::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; tagint tagprev; diff --git a/src/npair_half_multi_newton_tri.h b/src/npair_half_multi_old_newton_tri.h similarity index 70% rename from src/npair_half_multi_newton_tri.h rename to src/npair_half_multi_old_newton_tri.h index 6fe7577259..3c9202992a 100644 --- a/src/npair_half_multi_newton_tri.h +++ b/src/npair_half_multi_old_newton_tri.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi/newton/tri, - NPairHalfMultiNewtonTri, - NP_HALF | NP_MULTI | NP_NEWTON | NP_TRI) +NPairStyle(half/multi/old/newton/tri, + NPairHalfMultiOldNewtonTri, + NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_TRI_H -#define LMP_NPAIR_HALF_MULTI_NEWTON_TRI_H +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMultiNewtonTri : public NPair { +class NPairHalfMultiOldNewtonTri : public NPair { public: - NPairHalfMultiNewtonTri(class LAMMPS *); - ~NPairHalfMultiNewtonTri() {} + NPairHalfMultiOldNewtonTri(class LAMMPS *); + ~NPairHalfMultiOldNewtonTri() {} void build(class NeighList *); }; diff --git a/src/npair_half_size_multi_newtoff.h b/src/npair_half_size_multi_newtoff.h deleted file mode 100644 index f255f9a17d..0000000000 --- a/src/npair_half_size_multi_newtoff.h +++ /dev/null @@ -1,46 +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. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi/newtoff, - NPairHalfSizeMultiNewtoff, - NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_ORTHO | NP_TRI) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H -#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMultiNewtoff : public NPair { - public: - NPairHalfSizeMultiNewtoff(class LAMMPS *); - ~NPairHalfSizeMultiNewtoff() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Neighbor list overflow, boost neigh_modify one - -UNDOCUMENTED -*/ diff --git a/src/npair_half_size_multi_newton.h b/src/npair_half_size_multi_newton.h deleted file mode 100644 index 3e3d6f4180..0000000000 --- a/src/npair_half_size_multi_newton.h +++ /dev/null @@ -1,46 +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. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi/newton, - NPairHalfSizeMultiNewton, - NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_ORTHO) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H -#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMultiNewton : public NPair { - public: - NPairHalfSizeMultiNewton(class LAMMPS *); - ~NPairHalfSizeMultiNewton() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Neighbor list overflow, boost neigh_modify one - -UNDOCUMENTED -*/ diff --git a/src/npair_half_size_multi_newton_tri.h b/src/npair_half_size_multi_newton_tri.h deleted file mode 100644 index 6afe8201a7..0000000000 --- a/src/npair_half_size_multi_newton_tri.h +++ /dev/null @@ -1,46 +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. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi/newton/tri, - NPairHalfSizeMultiNewtonTri, - NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_TRI) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H -#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMultiNewtonTri : public NPair { - public: - NPairHalfSizeMultiNewtonTri(class LAMMPS *); - ~NPairHalfSizeMultiNewtonTri() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Neighbor list overflow, boost neigh_modify one - -UNDOCUMENTED -*/ diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_old_newtoff.cpp similarity index 94% rename from src/npair_half_size_multi_newtoff.cpp rename to src/npair_half_size_multi_old_newtoff.cpp index 813a642b96..394ad58981 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_old_newtoff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_size_multi_newtoff.h" +#include "npair_half_size_multi_old_newtoff.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,7 +22,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiOldNewtoff::NPairHalfSizeMultiOldNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles @@ -33,7 +33,7 @@ NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) { pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtoff::build(NeighList *list) +void NPairHalfSizeMultiOldNewtoff::build(NeighList *list) { int i,j,k,m,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; diff --git a/src/npair_half_size_multi_old_newtoff.h b/src/npair_half_size_multi_old_newtoff.h new file mode 100644 index 0000000000..ca429d8914 --- /dev/null +++ b/src/npair_half_size_multi_old_newtoff.h @@ -0,0 +1,46 @@ +/* -*- 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/multi/old/newtoff, + NPairHalfSizeMultiOldNewtoff, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewtoff : public NPair { + public: + NPairHalfSizeMultiOldNewtoff(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtoff() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_old_newton.cpp similarity index 95% rename from src/npair_half_size_multi_newton.cpp rename to src/npair_half_size_multi_old_newton.cpp index 0d12924629..65b197a86b 100644 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_old_newton.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_size_multi_newton.h" +#include "npair_half_size_multi_old_newton.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,7 +22,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiOldNewton::NPairHalfSizeMultiOldNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles @@ -32,7 +32,7 @@ NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {} every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewton::build(NeighList *list) +void NPairHalfSizeMultiOldNewton::build(NeighList *list) { int i,j,k,m,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; diff --git a/src/npair_half_size_multi_old_newton.h b/src/npair_half_size_multi_old_newton.h new file mode 100644 index 0000000000..e954ee07b1 --- /dev/null +++ b/src/npair_half_size_multi_old_newton.h @@ -0,0 +1,46 @@ +g/* -*- 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/multi/old/newton, + NPairHalfSizeMultiOldNewton, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewton : public NPair { + public: + NPairHalfSizeMultiOldNewton(class LAMMPS *); + ~NPairHalfSizeMultiOldNewton() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_old_newton_tri.cpp similarity index 92% rename from src/npair_half_size_multi_newton_tri.cpp rename to src/npair_half_size_multi_old_newton_tri.cpp index adc4c080ec..93d3beeb0a 100644 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_old_newton_tri.cpp @@ -1,4 +1,4 @@ -/* ---------------------------------------------------------------------- +re/* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_size_multi_newton_tri.h" +#include "npair_half_size_multi_old_newton_tri.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,7 +22,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiOldNewtonTri::NPairHalfSizeMultiOldNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic @@ -31,7 +31,7 @@ NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lm every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtonTri::build(NeighList *list) +void NPairHalfSizeMultiOldNewtonTri::build(NeighList *list) { int i,j,k,m,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; diff --git a/src/npair_half_size_multi_old_newton_tri.h b/src/npair_half_size_multi_old_newton_tri.h new file mode 100644 index 0000000000..126735e9c8 --- /dev/null +++ b/src/npair_half_size_multi_old_newton_tri.h @@ -0,0 +1,46 @@ +/* -*- 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/multi/old/newton/tri, + NPairHalfSizeMultiOldNewtonTri, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewtonTri : public NPair { + public: + NPairHalfSizeMultiOldNewtonTri(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtonTri() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ diff --git a/src/npair_halffull_newtoff.h b/src/npair_halffull_newtoff.h index 2f711629be..307156ef13 100644 --- a/src/npair_halffull_newtoff.h +++ b/src/npair_halffull_newtoff.h @@ -15,22 +15,22 @@ NPairStyle(halffull/newtoff, NPairHalffullNewtoff, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI) NPairStyle(halffull/newtoff/skip, NPairHalffullNewtoff, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI | NP_SKIP) NPairStyle(halffull/newtoff/ghost, NPairHalffullNewtoff, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI | NP_GHOST) NPairStyle(halffull/newtoff/skip/ghost, NPairHalffullNewtoff, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI | NP_SKIP | NP_GHOST) #else diff --git a/src/npair_halffull_newton.h b/src/npair_halffull_newton.h index dc82225216..f5f36b9e8c 100644 --- a/src/npair_halffull_newton.h +++ b/src/npair_halffull_newton.h @@ -15,12 +15,12 @@ NPairStyle(halffull/newton, NPairHalffullNewton, - NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_ORTHO | NP_TRI) NPairStyle(halffull/newton/skip, NPairHalffullNewton, - NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_ORTHO | NP_TRI | NP_SKIP) #else diff --git a/src/npair_skip.h b/src/npair_skip.h index 5fde8e7039..aae8abf6e4 100644 --- a/src/npair_skip.h +++ b/src/npair_skip.h @@ -16,13 +16,13 @@ NPairStyle(skip, NPairSkip, NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) NPairStyle(skip/ghost, NPairSkip, NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_GHOST) #else diff --git a/src/npair_skip_respa.h b/src/npair_skip_respa.h index a309d47124..31bcf0b510 100644 --- a/src/npair_skip_respa.h +++ b/src/npair_skip_respa.h @@ -16,7 +16,7 @@ NPairStyle(skip/half/respa, NPairSkipRespa, NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else diff --git a/src/npair_skip_size.h b/src/npair_skip_size.h index ae3f77d6ed..76f810bdc1 100644 --- a/src/npair_skip_size.h +++ b/src/npair_skip_size.h @@ -15,7 +15,7 @@ NPairStyle(skip/half/size, NPairSkipSize, - NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | + NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else diff --git a/src/npair_skip_size_off2on.h b/src/npair_skip_size_off2on.h index 59fc0878ef..7236e9e993 100644 --- a/src/npair_skip_size_off2on.h +++ b/src/npair_skip_size_off2on.h @@ -16,7 +16,7 @@ NPairStyle(skip/size/off2on, NPairSkipSizeOff2on, NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else diff --git a/src/npair_skip_size_off2on_oneside.h b/src/npair_skip_size_off2on_oneside.h index f7ae2338b7..e8b5977a34 100644 --- a/src/npair_skip_size_off2on_oneside.h +++ b/src/npair_skip_size_off2on_oneside.h @@ -16,7 +16,7 @@ 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_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else From 42278e87665404fa5df52214ffbee9b3934ffb99 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 17:09:11 -0700 Subject: [PATCH 32/73] Renaming multi2->multi npair classes, renaming npair multi variables --- src/USER-OMP/npair_full_multi_old_omp.cpp | 6 +- ...ulti2_omp.cpp => npair_full_multi_omp.cpp} | 18 ++--- ...ll_multi2_omp.h => npair_full_multi_omp.h} | 16 ++--- ...p.cpp => npair_half_multi_newtoff_omp.cpp} | 18 ++--- src/USER-OMP/npair_half_multi_newtoff_omp.h | 43 ++++++++++++ ...mp.cpp => npair_half_multi_newton_omp.cpp} | 26 +++---- ...on_omp.h => npair_half_multi_newton_omp.h} | 16 ++--- ...pp => npair_half_multi_newton_tri_omp.cpp} | 18 ++--- .../npair_half_multi_newton_tri_omp.h | 43 ++++++++++++ .../npair_half_multi_old_newtoff_omp.cpp | 6 +- .../npair_half_multi_old_newton_omp.cpp | 6 +- .../npair_half_multi_old_newton_tri_omp.cpp | 6 +- .../npair_half_size_multi2_newtoff_omp.h | 43 ------------ .../npair_half_size_multi2_newton_omp.h | 43 ------------ .../npair_half_size_multi2_newton_tri_omp.h | 43 ------------ ... => npair_half_size_multi_newtoff_omp.cpp} | 18 ++--- ....h => npair_half_size_multi_newtoff_omp.h} | 16 ++--- ...p => npair_half_size_multi_newton_omp.cpp} | 26 +++---- ...p.h => npair_half_size_multi_newton_omp.h} | 16 ++--- ... npair_half_size_multi_newton_tri_omp.cpp} | 18 ++--- .../npair_half_size_multi_newton_tri_omp.h | 43 ++++++++++++ .../npair_half_size_multi_old_newtoff_omp.cpp | 6 +- .../npair_half_size_multi_old_newton_omp.cpp | 6 +- ...air_half_size_multi_old_newton_tri_omp.cpp | 6 +- src/npair.cpp | 70 +++++++++---------- src/npair.h | 24 +++---- ...r_full_multi2.cpp => npair_full_multi.cpp} | 18 ++--- ...npair_full_multi2.h => npair_full_multi.h} | 16 ++--- src/npair_full_multi_old.cpp | 6 +- ...wtoff.cpp => npair_half_multi_newtoff.cpp} | 18 ++--- ...2_newtoff.h => npair_half_multi_newtoff.h} | 16 ++--- ...newton.cpp => npair_half_multi_newton.cpp} | 26 +++---- ...ti2_newton.h => npair_half_multi_newton.h} | 16 ++--- ...ri.cpp => npair_half_multi_newton_tri.cpp} | 18 ++--- ...on_tri.h => npair_half_multi_newton_tri.h} | 16 ++--- src/npair_half_multi_old_newtoff.cpp | 6 +- src/npair_half_multi_old_newton.cpp | 6 +- src/npair_half_multi_old_newton_tri.cpp | 6 +- src/npair_half_size_multi2_newton_tri.h | 47 ------------- ....cpp => npair_half_size_multi_newtoff.cpp} | 18 ++--- ...toff.h => npair_half_size_multi_newtoff.h} | 16 ++--- ...n.cpp => npair_half_size_multi_newton.cpp} | 26 +++---- ...ewton.h => npair_half_size_multi_newton.h} | 16 ++--- ...p => npair_half_size_multi_newton_tri.cpp} | 18 ++--- src/npair_half_size_multi_newton_tri.h | 47 +++++++++++++ src/npair_half_size_multi_old_newtoff.cpp | 6 +- src/npair_half_size_multi_old_newton.cpp | 6 +- src/npair_half_size_multi_old_newton_tri.cpp | 6 +- 48 files changed, 487 insertions(+), 487 deletions(-) rename src/USER-OMP/{npair_full_multi2_omp.cpp => npair_full_multi_omp.cpp} (90%) rename src/USER-OMP/{npair_full_multi2_omp.h => npair_full_multi_omp.h} (75%) rename src/USER-OMP/{npair_half_multi2_newtoff_omp.cpp => npair_half_multi_newtoff_omp.cpp} (90%) create mode 100755 src/USER-OMP/npair_half_multi_newtoff_omp.h rename src/USER-OMP/{npair_half_multi2_newton_omp.cpp => npair_half_multi_newton_omp.cpp} (91%) rename src/USER-OMP/{npair_half_multi2_newton_omp.h => npair_half_multi_newton_omp.h} (69%) rename src/USER-OMP/{npair_half_multi2_newton_tri_omp.cpp => npair_half_multi_newton_tri_omp.cpp} (91%) create mode 100755 src/USER-OMP/npair_half_multi_newton_tri_omp.h delete mode 100755 src/USER-OMP/npair_half_size_multi2_newtoff_omp.h delete mode 100755 src/USER-OMP/npair_half_size_multi2_newton_omp.h delete mode 100755 src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h rename src/USER-OMP/{npair_half_size_multi2_newtoff_omp.cpp => npair_half_size_multi_newtoff_omp.cpp} (88%) rename src/USER-OMP/{npair_half_multi2_newtoff_omp.h => npair_half_size_multi_newtoff_omp.h} (66%) rename src/USER-OMP/{npair_half_size_multi2_newton_omp.cpp => npair_half_size_multi_newton_omp.cpp} (89%) rename src/USER-OMP/{npair_half_multi2_newton_tri_omp.h => npair_half_size_multi_newton_omp.h} (67%) rename src/USER-OMP/{npair_half_size_multi2_newton_tri_omp.cpp => npair_half_size_multi_newton_tri_omp.cpp} (90%) create mode 100755 src/USER-OMP/npair_half_size_multi_newton_tri_omp.h rename src/{npair_full_multi2.cpp => npair_full_multi.cpp} (90%) rename src/{npair_full_multi2.h => npair_full_multi.h} (74%) rename src/{npair_half_multi2_newtoff.cpp => npair_half_multi_newtoff.cpp} (90%) rename src/{npair_half_multi2_newtoff.h => npair_half_multi_newtoff.h} (72%) rename src/{npair_half_multi2_newton.cpp => npair_half_multi_newton.cpp} (91%) rename src/{npair_half_multi2_newton.h => npair_half_multi_newton.h} (71%) rename src/{npair_half_multi2_newton_tri.cpp => npair_half_multi_newton_tri.cpp} (91%) rename src/{npair_half_multi2_newton_tri.h => npair_half_multi_newton_tri.h} (70%) delete mode 100755 src/npair_half_size_multi2_newton_tri.h rename src/{npair_half_size_multi2_newtoff.cpp => npair_half_size_multi_newtoff.cpp} (87%) rename src/{npair_half_size_multi2_newtoff.h => npair_half_size_multi_newtoff.h} (69%) rename src/{npair_half_size_multi2_newton.cpp => npair_half_size_multi_newton.cpp} (89%) rename src/{npair_half_size_multi2_newton.h => npair_half_size_multi_newton.h} (70%) rename src/{npair_half_size_multi2_newton_tri.cpp => npair_half_size_multi_newton_tri.cpp} (89%) create mode 100755 src/npair_half_size_multi_newton_tri.h diff --git a/src/USER-OMP/npair_full_multi_old_omp.cpp b/src/USER-OMP/npair_full_multi_old_omp.cpp index ef4c4ef5e4..46890f6438 100644 --- a/src/USER-OMP/npair_full_multi_old_omp.cpp +++ b/src/USER-OMP/npair_full_multi_old_omp.cpp @@ -94,10 +94,10 @@ void NPairFullMultiOldOmp::build(NeighList *list) // skip i = j ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/USER-OMP/npair_full_multi2_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp similarity index 90% rename from src/USER-OMP/npair_full_multi2_omp.cpp rename to src/USER-OMP/npair_full_multi_omp.cpp index 39f711fe4f..cf897f9dea 100755 --- a/src/USER-OMP/npair_full_multi2_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_full_multi2_omp.h" +#include "npair_full_multi_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,15 +26,15 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairFullMulti2Omp::NPairFullMulti2Omp(LAMMPS *lmp) : NPair(lmp) {} +NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ -void NPairFullMulti2Omp::build(NeighList *list) +void NPairFullMultiOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -89,7 +89,7 @@ void NPairFullMulti2Omp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -102,12 +102,12 @@ void NPairFullMulti2Omp::build(NeighList *list) // skip i = j // use full stencil for all type combinations - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (i == j) continue; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/USER-OMP/npair_full_multi2_omp.h b/src/USER-OMP/npair_full_multi_omp.h similarity index 75% rename from src/USER-OMP/npair_full_multi2_omp.h rename to src/USER-OMP/npair_full_multi_omp.h index d2bc478532..882e649183 100755 --- a/src/USER-OMP/npair_full_multi2_omp.h +++ b/src/USER-OMP/npair_full_multi_omp.h @@ -13,24 +13,24 @@ #ifdef NPAIR_CLASS -NPairStyle(full/multi2/omp, - NPairFullMulti2Omp, - NP_FULL | NP_MULTI2 | NP_OMP | +NPairStyle(full/multi/omp, + NPairFullMultiOmp, + NP_FULL | NP_MULTI | NP_OMP | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_FULL_MULTI2_OMP_H -#define LMP_NPAIR_FULL_MULTI2_OMP_H +#ifndef LMP_NPAIR_FULL_MULTI_OMP_H +#define LMP_NPAIR_FULL_MULTI_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairFullMulti2Omp : public NPair { +class NPairFullMultiOmp : public NPair { public: - NPairFullMulti2Omp(class LAMMPS *); - ~NPairFullMulti2Omp() {} + NPairFullMultiOmp(class LAMMPS *); + ~NPairFullMultiOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp similarity index 90% rename from src/USER-OMP/npair_half_multi2_newtoff_omp.cpp rename to src/USER-OMP/npair_half_multi_newtoff_omp.cpp index bfd0d34a6c..bf7644f01f 100755 --- a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_multi2_newtoff_omp.h" +#include "npair_half_multi_newtoff_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,17 +26,17 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMulti2NewtoffOmp::NPairHalfMulti2NewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent 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 NPairHalfMulti2NewtoffOmp::build(NeighList *list) +void NPairHalfMultiNewtoffOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -91,7 +91,7 @@ void NPairHalfMulti2NewtoffOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -106,12 +106,12 @@ void NPairHalfMulti2NewtoffOmp::build(NeighList *list) // stores own/ghost pairs on both procs // use full stencil for all type combinations - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jtype][j]) { if (j <= i) continue; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; 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 100755 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_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp similarity index 91% rename from src/USER-OMP/npair_half_multi2_newton_omp.cpp rename to src/USER-OMP/npair_half_multi_newton_omp.cpp index cbdbd69f50..c68a3a150f 100755 --- a/src/USER-OMP/npair_half_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_multi2_newton_omp.h" +#include "npair_half_multi_newton_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,16 +26,16 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMulti2NewtonOmp::NPairHalfMulti2NewtonOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiNewtonOmp::NPairHalfMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMulti2NewtonOmp::build(NeighList *list) +void NPairHalfMultiNewtonOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -90,7 +90,7 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -109,9 +109,9 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *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 - js = bins_multi2[itype][i]; + js = bins_multi[itype][i]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -150,9 +150,9 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi2[jtype][jbin]; + js = binhead_multi[jtype][jbin]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if(j < i) continue; if (j >= nlocal) { @@ -194,12 +194,12 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/USER-OMP/npair_half_multi2_newton_omp.h b/src/USER-OMP/npair_half_multi_newton_omp.h similarity index 69% rename from src/USER-OMP/npair_half_multi2_newton_omp.h rename to src/USER-OMP/npair_half_multi_newton_omp.h index 2ea2bd1ad0..85df36bb09 100755 --- a/src/USER-OMP/npair_half_multi2_newton_omp.h +++ b/src/USER-OMP/npair_half_multi_newton_omp.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi2/newton/omp, - NPairHalfMulti2NewtonOmp, - NP_HALF | NP_MULTI2 | NP_NEWTON | NP_OMP | NP_ORTHO) +NPairStyle(half/multi/newton/omp, + NPairHalfMultiNewtonOmp, + NP_HALF | NP_MULTI | NP_NEWTON | NP_OMP | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_OMP_H -#define LMP_NPAIR_HALF_MULTI2_NEWTON_OMP_H +#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_OMP_H +#define LMP_NPAIR_HALF_MULTI_NEWTON_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMulti2NewtonOmp : public NPair { +class NPairHalfMultiNewtonOmp : public NPair { public: - NPairHalfMulti2NewtonOmp(class LAMMPS *); - ~NPairHalfMulti2NewtonOmp() {} + NPairHalfMultiNewtonOmp(class LAMMPS *); + ~NPairHalfMultiNewtonOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp similarity index 91% rename from src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp rename to src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index 5d0d724b58..3f3ac37b6d 100755 --- a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_multi2_newton_tri_omp.h" +#include "npair_half_multi_newton_tri_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,17 +26,17 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMulti2NewtonTriOmp::NPairHalfMulti2NewtonTriOmp(LAMMPS *lmp) : +NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) +void NPairHalfMultiNewtonTriOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -91,7 +91,7 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -109,12 +109,12 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { // if same size (e.g. same type), use half stencil if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ 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 100755 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_multi_old_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp index 2839ebfa14..961bac8fb7 100644 --- a/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp @@ -98,10 +98,10 @@ void NPairHalfMultiOldNewtoffOmp::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { if (j <= i) continue; diff --git a/src/USER-OMP/npair_half_multi_old_newton_omp.cpp b/src/USER-OMP/npair_half_multi_old_newton_omp.cpp index bc77cc518b..affae74dbd 100644 --- a/src/USER-OMP/npair_half_multi_old_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_old_newton_omp.cpp @@ -132,10 +132,10 @@ void NPairHalfMultiOldNewtonOmp::build(NeighList *list) // skip if i,j neighbor cutoff is less than bin distance ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp index 3d5a577396..c023b08cb7 100644 --- a/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp @@ -100,10 +100,10 @@ void NPairHalfMultiOldNewtonTriOmp::build(NeighList *list) // latter excludes self-self interaction but allows superposed atoms ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.h b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.h deleted file mode 100755 index fd592d839c..0000000000 --- a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.h +++ /dev/null @@ -1,43 +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. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi2/newtoff/omp, - NPairHalfSizeMulti2NewtoffOmp, - NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_OMP_H -#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_OMP_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMulti2NewtoffOmp : public NPair { - public: - NPairHalfSizeMulti2NewtoffOmp(class LAMMPS *); - ~NPairHalfSizeMulti2NewtoffOmp() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/USER-OMP/npair_half_size_multi2_newton_omp.h b/src/USER-OMP/npair_half_size_multi2_newton_omp.h deleted file mode 100755 index 38b4dde272..0000000000 --- a/src/USER-OMP/npair_half_size_multi2_newton_omp.h +++ /dev/null @@ -1,43 +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. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi2/newton/omp, - NPairHalfSizeMulti2NewtonOmp, - NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_OMP | NP_ORTHO) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_OMP_H -#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_OMP_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMulti2NewtonOmp : public NPair { - public: - NPairHalfSizeMulti2NewtonOmp(class LAMMPS *); - ~NPairHalfSizeMulti2NewtonOmp() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h deleted file mode 100755 index 494a419c8f..0000000000 --- a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h +++ /dev/null @@ -1,43 +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. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi2/newton/tri/omp, - NPairHalfSizeMulti2NewtonTriOmp, - NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_TRI | NP_OMP) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_OMP_H -#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_OMP_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMulti2NewtonTriOmp : public NPair { - public: - NPairHalfSizeMulti2NewtonTriOmp(class LAMMPS *); - ~NPairHalfSizeMulti2NewtonTriOmp() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp similarity index 88% rename from src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp rename to src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp index 3b1f979a8e..8201ba8cb6 100755 --- a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_size_multi2_newtoff_omp.h" +#include "npair_half_size_multi_newtoff_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -24,18 +24,18 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMulti2NewtoffOmp::NPairHalfSizeMulti2NewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent 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 NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) +void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; @@ -80,7 +80,7 @@ void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -95,12 +95,12 @@ void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) // stores own/ghost pairs on both procs // use full stencil for all type combinations - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jtype][j]) { if (j <= i) continue; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/USER-OMP/npair_half_multi2_newtoff_omp.h b/src/USER-OMP/npair_half_size_multi_newtoff_omp.h similarity index 66% rename from src/USER-OMP/npair_half_multi2_newtoff_omp.h rename to src/USER-OMP/npair_half_size_multi_newtoff_omp.h index a9e9a842cb..b25a372186 100755 --- a/src/USER-OMP/npair_half_multi2_newtoff_omp.h +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi2/newtoff/omp, - NPairHalfMulti2NewtoffOmp, - NP_HALF | NP_MULTI2 | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) +NPairStyle(half/size/multi/newtoff/omp, + NPairHalfSizeMultiNewtoffOmp, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_MULTI2_NEWTOFF_OMP_H -#define LMP_NPAIR_HALF_MULTI2_NEWTOFF_OMP_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMulti2NewtoffOmp : public NPair { +class NPairHalfSizeMultiNewtoffOmp : public NPair { public: - NPairHalfMulti2NewtoffOmp(class LAMMPS *); - ~NPairHalfMulti2NewtoffOmp() {} + NPairHalfSizeMultiNewtoffOmp(class LAMMPS *); + ~NPairHalfSizeMultiNewtoffOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp similarity index 89% rename from src/USER-OMP/npair_half_size_multi2_newton_omp.cpp rename to src/USER-OMP/npair_half_size_multi_newton_omp.cpp index 3a3a2fbe74..197b41c12e 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_size_multi2_newton_omp.h" +#include "npair_half_size_multi_newton_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -24,17 +24,17 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMulti2NewtonOmp::NPairHalfSizeMulti2NewtonOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) +void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; @@ -79,7 +79,7 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -98,9 +98,9 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *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 - js = bins_multi2[itype][i]; + js = bins_multi[itype][i]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -132,9 +132,9 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi2[jtype][jbin]; + js = binhead_multi[jtype][jbin]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if(j < i) continue; if (j >= nlocal) { @@ -169,12 +169,12 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/USER-OMP/npair_half_multi2_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi_newton_omp.h similarity index 67% rename from src/USER-OMP/npair_half_multi2_newton_tri_omp.h rename to src/USER-OMP/npair_half_size_multi_newton_omp.h index dd9eea6847..03d712145f 100755 --- a/src/USER-OMP/npair_half_multi2_newton_tri_omp.h +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi2/newton/tri/omp, - NPairHalfMulti2NewtonTriOmp, - NP_HALF | NP_MULTI2 | NP_NEWTON | NP_TRI | NP_OMP) +NPairStyle(half/size/multi/newton/omp, + NPairHalfSizeMultiNewtonOmp, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_OMP | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_OMP_H -#define LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_OMP_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMulti2NewtonTriOmp : public NPair { +class NPairHalfSizeMultiNewtonOmp : public NPair { public: - NPairHalfMulti2NewtonTriOmp(class LAMMPS *); - ~NPairHalfMulti2NewtonTriOmp() {} + NPairHalfSizeMultiNewtonOmp(class LAMMPS *); + ~NPairHalfSizeMultiNewtonOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp similarity index 90% rename from src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp rename to src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp index 66f9cbce0a..cd123202b1 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_size_multi2_newton_tri_omp.h" +#include "npair_half_size_multi_newton_tri_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -24,18 +24,18 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMulti2NewtonTriOmp::NPairHalfSizeMulti2NewtonTriOmp(LAMMPS *lmp) : +NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) +void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; @@ -80,7 +80,7 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -99,12 +99,12 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { // if same size (e.g. same type), use half stencil if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h new file mode 100755 index 0000000000..6e936c8da4 --- /dev/null +++ b/src/USER-OMP/npair_half_size_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/size/multi/newton/tri/omp, + NPairHalfSizeMultiNewtonTriOmp, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_TRI | NP_OMP) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiNewtonTriOmp : public NPair { + public: + NPairHalfSizeMultiNewtonTriOmp(class LAMMPS *); + ~NPairHalfSizeMultiNewtonTriOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp index e3001185c1..3ed703586d 100644 --- a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp @@ -86,10 +86,10 @@ void NPairHalfSizeMultiNewtoffOldOmp::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { if (j <= i) continue; diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp index ee166a57cf..37203c53db 100644 --- a/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp @@ -112,10 +112,10 @@ void NPairHalfSizeMultiNewtonOldOmp::build(NeighList *list) // skip if i,j neighbor cutoff is less than bin distance ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp index 81e896db6c..8352e28643 100644 --- a/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp @@ -87,10 +87,10 @@ void NPairHalfSizeMultiOldNewtonTriOmp::build(NeighList *list) // latter excludes self-self interaction but allows superposed atoms ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair.cpp b/src/npair.cpp index 4d86badf76..07e476e1dd 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -135,24 +135,24 @@ void NPair::copy_bin_info() bins = nb->bins; binhead = nb->binhead; - nbinx_multi2 = nb->nbinx_multi2; - nbiny_multi2 = nb->nbiny_multi2; - nbinz_multi2 = nb->nbinz_multi2; - mbins_multi2 = nb->mbins_multi2; - mbinx_multi2 = nb->mbinx_multi2; - mbiny_multi2 = nb->mbiny_multi2; - mbinz_multi2 = nb->mbinz_multi2; - mbinxlo_multi2 = nb->mbinxlo_multi2; - mbinylo_multi2 = nb->mbinylo_multi2; - mbinzlo_multi2 = nb->mbinzlo_multi2; + nbinx_multi = nb->nbinx_multi; + nbiny_multi = nb->nbiny_multi; + nbinz_multi = nb->nbinz_multi; + mbins_multi = nb->mbins_multi; + mbinx_multi = nb->mbinx_multi; + mbiny_multi = nb->mbiny_multi; + mbinz_multi = nb->mbinz_multi; + mbinxlo_multi = nb->mbinxlo_multi; + mbinylo_multi = nb->mbinylo_multi; + mbinzlo_multi = nb->mbinzlo_multi; - bininvx_multi2 = nb->bininvx_multi2; - bininvy_multi2 = nb->bininvy_multi2; - bininvz_multi2 = nb->bininvz_multi2; + bininvx_multi = nb->bininvx_multi; + bininvy_multi = nb->bininvy_multi; + bininvz_multi = nb->bininvz_multi; - atom2bin_multi2 = nb->atom2bin_multi2; - bins_multi2 = nb->bins_multi2; - binhead_multi2 = nb->binhead_multi2; + atom2bin_multi = nb->atom2bin_multi; + bins_multi = nb->bins_multi; + binhead_multi = nb->binhead_multi; } /* ---------------------------------------------------------------------- @@ -164,12 +164,12 @@ void NPair::copy_stencil_info() nstencil = ns->nstencil; stencil = ns->stencil; stencilxyz = ns->stencilxyz; + nstencil_multi_old = ns->nstencil_multi_old; + stencil_multi_old = ns->stencil_multi_old; + distsq_multi_old = ns->distsq_multi_old; + nstencil_multi = ns->nstencil_multi; stencil_multi = ns->stencil_multi; - distsq_multi = ns->distsq_multi; - - nstencil_multi2 = ns->nstencil_multi2; - stencil_multi2 = ns->stencil_multi2; } /* ---------------------------------------------------------------------- @@ -277,32 +277,32 @@ int NPair::coord2bin(double *x, int it) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi2[it]) + nbinx_multi2[it]; + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[it]) + nbinx_multi[it]; else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]); - ix = MIN(ix,nbinx_multi2[it]-1); + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]); + ix = MIN(ix,nbinx_multi[it]-1); } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]) - 1; + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]) - 1; if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi2[it]) + nbiny_multi2[it]; + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[it]) + nbiny_multi[it]; else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]); - iy = MIN(iy,nbiny_multi2[it]-1); + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]); + iy = MIN(iy,nbiny_multi[it]-1); } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]) - 1; + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]) - 1; if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi2[it]) + nbinz_multi2[it]; + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[it]) + nbinz_multi[it]; else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]); - iz = MIN(iz,nbinz_multi2[it]-1); + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]); + iz = MIN(iz,nbinz_multi[it]-1); } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]) - 1; + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]) - 1; - ibin = (iz-mbinzlo_multi2[it])*mbiny_multi2[it]*mbinx_multi2[it] - + (iy-mbinylo_multi2[it])*mbinx_multi2[it] - + (ix-mbinxlo_multi2[it]); + ibin = (iz-mbinzlo_multi[it])*mbiny_multi[it]*mbinx_multi[it] + + (iy-mbinylo_multi[it])*mbinx_multi[it] + + (ix-mbinxlo_multi[it]); return ibin; } \ No newline at end of file diff --git a/src/npair.h b/src/npair.h index 87b2584521..c56c6bdb20 100644 --- a/src/npair.h +++ b/src/npair.h @@ -79,25 +79,25 @@ class NPair : protected Pointers { int *atom2bin,*bins; int *binhead; - int *nbinx_multi2, *nbiny_multi2, *nbinz_multi2; - int *mbins_multi2; - int *mbinx_multi2, *mbiny_multi2, *mbinz_multi2; - int *mbinxlo_multi2, *mbinylo_multi2, *mbinzlo_multi2; - double *bininvx_multi2, *bininvy_multi2, *bininvz_multi2; - int **binhead_multi2,**bins_multi2; - int **atom2bin_multi2; + int *nbinx_multi, *nbiny_multi, *nbinz_multi; + int *mbins_multi; + int *mbinx_multi, *mbiny_multi, *mbinz_multi; + int *mbinxlo_multi, *mbinylo_multi, *mbinzlo_multi; + double *bininvx_multi, *bininvy_multi, *bininvz_multi; + int **binhead_multi,**bins_multi; + int **atom2bin_multi; // data from NStencil class int nstencil; int *stencil; int **stencilxyz; - int *nstencil_multi; - int **stencil_multi; - double **distsq_multi; + int *nstencil_multi_old; + int **stencil_multi_old; + double **distsq_multi_old; - int ** nstencil_multi2; - int *** stencil_multi2; + int ** nstencil_multi; + int *** stencil_multi; // data common to all NPair variants diff --git a/src/npair_full_multi2.cpp b/src/npair_full_multi.cpp similarity index 90% rename from src/npair_full_multi2.cpp rename to src/npair_full_multi.cpp index 732c5e581e..4463964d5f 100644 --- a/src/npair_full_multi2.cpp +++ b/src/npair_full_multi.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_full_multi2.h" +#include "npair_full_multi.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,15 +24,15 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairFullMulti2::NPairFullMulti2(LAMMPS *lmp) : NPair(lmp) {} +NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ -void NPairFullMulti2::build(NeighList *list) +void NPairFullMulti::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; @@ -78,7 +78,7 @@ void NPairFullMulti2::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -91,12 +91,12 @@ void NPairFullMulti2::build(NeighList *list) // skip i = j // use full stencil for all type combinations - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (i == j) continue; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_full_multi2.h b/src/npair_full_multi.h similarity index 74% rename from src/npair_full_multi2.h rename to src/npair_full_multi.h index f552e5bf47..481a673060 100644 --- a/src/npair_full_multi2.h +++ b/src/npair_full_multi.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(full/multi2, - NPairFullMulti2, - NP_FULL | NP_MULTI2 | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(full/multi, + NPairFullMulti, + NP_FULL | NP_MULTI | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_FULL_MULTI2_H -#define LMP_NPAIR_FULL_MULTI2_H +#ifndef LMP_NPAIR_FULL_MULTI_H +#define LMP_NPAIR_FULL_MULTI_H #include "npair.h" namespace LAMMPS_NS { -class NPairFullMulti2 : public NPair { +class NPairFullMulti : public NPair { public: - NPairFullMulti2(class LAMMPS *); - ~NPairFullMulti2() {} + NPairFullMulti(class LAMMPS *); + ~NPairFullMulti() {} void build(class NeighList *); }; diff --git a/src/npair_full_multi_old.cpp b/src/npair_full_multi_old.cpp index 9a800a80b5..328b3325ab 100644 --- a/src/npair_full_multi_old.cpp +++ b/src/npair_full_multi_old.cpp @@ -83,10 +83,10 @@ void NPairFullMultiOld::build(NeighList *list) // skip i = j ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair_half_multi2_newtoff.cpp b/src/npair_half_multi_newtoff.cpp similarity index 90% rename from src/npair_half_multi2_newtoff.cpp rename to src/npair_half_multi_newtoff.cpp index ecd97fe689..c0dcaf0c98 100755 --- a/src/npair_half_multi2_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_multi2_newtoff.h" +#include "npair_half_multi_newtoff.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,17 +24,17 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMulti2Newtoff::NPairHalfMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent 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 NPairHalfMulti2Newtoff::build(NeighList *list) +void NPairHalfMultiNewtoff::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; @@ -80,7 +80,7 @@ void NPairHalfMulti2Newtoff::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -95,12 +95,12 @@ void NPairHalfMulti2Newtoff::build(NeighList *list) // stores own/ghost pairs on both procs // use full stencil for all type combinations - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jtype][j]) { if (j <= i) continue; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_half_multi2_newtoff.h b/src/npair_half_multi_newtoff.h similarity index 72% rename from src/npair_half_multi2_newtoff.h rename to src/npair_half_multi_newtoff.h index 30a6d3164d..593e2c1d9d 100755 --- a/src/npair_half_multi2_newtoff.h +++ b/src/npair_half_multi_newtoff.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi2/newtoff, - NPairHalfMulti2Newtoff, - NP_HALF | NP_MULTI2 | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(half/multi/newtoff, + NPairHalfMultiNewtoff, + NP_HALF | NP_MULTI | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_MULTI2_NEWTOFF_H -#define LMP_NPAIR_HALF_MULTI2_NEWTOFF_H +#ifndef LMP_NPAIR_HALF_MULTI_NEWTOFF_H +#define LMP_NPAIR_HALF_MULTI_NEWTOFF_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMulti2Newtoff : public NPair { +class NPairHalfMultiNewtoff : public NPair { public: - NPairHalfMulti2Newtoff(class LAMMPS *); - ~NPairHalfMulti2Newtoff() {} + NPairHalfMultiNewtoff(class LAMMPS *); + ~NPairHalfMultiNewtoff() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi2_newton.cpp b/src/npair_half_multi_newton.cpp similarity index 91% rename from src/npair_half_multi2_newton.cpp rename to src/npair_half_multi_newton.cpp index 6a7f52168a..e097052fe5 100755 --- a/src/npair_half_multi2_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_multi2_newton.h" +#include "npair_half_multi_newton.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,16 +24,16 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMulti2Newton::NPairHalfMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMulti2Newton::build(NeighList *list) +void NPairHalfMultiNewton::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; @@ -79,7 +79,7 @@ void NPairHalfMulti2Newton::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -98,9 +98,9 @@ void NPairHalfMulti2Newton::build(NeighList *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 - js = bins_multi2[itype][i]; + js = bins_multi[itype][i]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -139,9 +139,9 @@ void NPairHalfMulti2Newton::build(NeighList *list) // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi2[jtype][jbin]; + js = binhead_multi[jtype][jbin]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if(j < i) continue; if (j >= nlocal) { @@ -183,12 +183,12 @@ void NPairHalfMulti2Newton::build(NeighList *list) // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_half_multi2_newton.h b/src/npair_half_multi_newton.h similarity index 71% rename from src/npair_half_multi2_newton.h rename to src/npair_half_multi_newton.h index 8037d2e172..64021a9f58 100755 --- a/src/npair_half_multi2_newton.h +++ b/src/npair_half_multi_newton.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi2/newton, - NPairHalfMulti2Newton, - NP_HALF | NP_MULTI2 | NP_NEWTON | NP_ORTHO) +NPairStyle(half/multi/newton, + NPairHalfMultiNewton, + NP_HALF | NP_MULTI | NP_NEWTON | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_H -#define LMP_NPAIR_HALF_MULTI2_NEWTON_H +#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_H +#define LMP_NPAIR_HALF_MULTI_NEWTON_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMulti2Newton : public NPair { +class NPairHalfMultiNewton : public NPair { public: - NPairHalfMulti2Newton(class LAMMPS *); - ~NPairHalfMulti2Newton() {} + NPairHalfMultiNewton(class LAMMPS *); + ~NPairHalfMultiNewton() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi2_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp similarity index 91% rename from src/npair_half_multi2_newton_tri.cpp rename to src/npair_half_multi_newton_tri.cpp index 9d0db60d50..fabaf5f202 100755 --- a/src/npair_half_multi2_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_multi2_newton_tri.h" +#include "npair_half_multi_newton_tri.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,16 +24,16 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMulti2NewtonTri::NPairHalfMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMulti2NewtonTri::build(NeighList *list) +void NPairHalfMultiNewtonTri::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; @@ -79,7 +79,7 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -97,12 +97,12 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { // if same size (e.g. same type), use half stencil if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ diff --git a/src/npair_half_multi2_newton_tri.h b/src/npair_half_multi_newton_tri.h similarity index 70% rename from src/npair_half_multi2_newton_tri.h rename to src/npair_half_multi_newton_tri.h index 0787860c52..51b720e0c4 100755 --- a/src/npair_half_multi2_newton_tri.h +++ b/src/npair_half_multi_newton_tri.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi2/newton/tri, - NPairHalfMulti2NewtonTri, - NP_HALF | NP_MULTI2 | NP_NEWTON | NP_TRI) +NPairStyle(half/multi/newton/tri, + NPairHalfMultiNewtonTri, + NP_HALF | NP_MULTI | NP_NEWTON | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_H -#define LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_H +#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_TRI_H +#define LMP_NPAIR_HALF_MULTI_NEWTON_TRI_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMulti2NewtonTri : public NPair { +class NPairHalfMultiNewtonTri : public NPair { public: - NPairHalfMulti2NewtonTri(class LAMMPS *); - ~NPairHalfMulti2NewtonTri() {} + NPairHalfMultiNewtonTri(class LAMMPS *); + ~NPairHalfMultiNewtonTri() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi_old_newtoff.cpp b/src/npair_half_multi_old_newtoff.cpp index 351fd65c32..fa9544aa68 100644 --- a/src/npair_half_multi_old_newtoff.cpp +++ b/src/npair_half_multi_old_newtoff.cpp @@ -87,10 +87,10 @@ void NPairHalfMultiOldNewtoff::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { if (j <= i) continue; diff --git a/src/npair_half_multi_old_newton.cpp b/src/npair_half_multi_old_newton.cpp index 5af420017d..db3a7c015c 100644 --- a/src/npair_half_multi_old_newton.cpp +++ b/src/npair_half_multi_old_newton.cpp @@ -121,10 +121,10 @@ void NPairHalfMultiOldNewton::build(NeighList *list) // skip if i,j neighbor cutoff is less than bin distance ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair_half_multi_old_newton_tri.cpp b/src/npair_half_multi_old_newton_tri.cpp index f22e0fbf4f..1b142aa9ab 100644 --- a/src/npair_half_multi_old_newton_tri.cpp +++ b/src/npair_half_multi_old_newton_tri.cpp @@ -88,10 +88,10 @@ void NPairHalfMultiOldNewtonTri::build(NeighList *list) // latter excludes self-self interaction but allows superposed atoms ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair_half_size_multi2_newton_tri.h b/src/npair_half_size_multi2_newton_tri.h deleted file mode 100755 index 6ce4f6d2fb..0000000000 --- a/src/npair_half_size_multi2_newton_tri.h +++ /dev/null @@ -1,47 +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. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi2/newton/tri, - NPairHalfSizeMulti2NewtonTri, - NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_TRI) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_H -#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMulti2NewtonTri : public NPair { - public: - NPairHalfSizeMulti2NewtonTri(class LAMMPS *); - ~NPairHalfSizeMulti2NewtonTri() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Neighbor list overflow, boost neigh_modify one - -UNDOCUMENTED - -*/ \ No newline at end of file diff --git a/src/npair_half_size_multi2_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp similarity index 87% rename from src/npair_half_size_multi2_newtoff.cpp rename to src/npair_half_size_multi_newtoff.cpp index b559f83414..65b6b68fb2 100644 --- a/src/npair_half_size_multi2_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -12,7 +12,7 @@ es certain rights in this software. This software is distributed under ------------------------------------------------------------------------- */ #include -#include "npair_half_size_multi2_newtoff.h" +#include "npair_half_size_multi_newtoff.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -23,18 +23,18 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMulti2Newtoff::NPairHalfSizeMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent 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 NPairHalfSizeMulti2Newtoff::build(NeighList *list) +void NPairHalfSizeMultiNewtoff::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; @@ -71,7 +71,7 @@ void NPairHalfSizeMulti2Newtoff::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -86,12 +86,12 @@ void NPairHalfSizeMulti2Newtoff::build(NeighList *list) // stores own/ghost pairs on both procs // use full stencil for all type combinations - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jtype][j]) { if (j <= i) continue; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_half_size_multi2_newtoff.h b/src/npair_half_size_multi_newtoff.h similarity index 69% rename from src/npair_half_size_multi2_newtoff.h rename to src/npair_half_size_multi_newtoff.h index 15540666c3..47c922cb7e 100644 --- a/src/npair_half_size_multi2_newtoff.h +++ b/src/npair_half_size_multi_newtoff.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/size/multi2/newtoff, - NPairHalfSizeMulti2Newtoff, - NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(half/size/multi/newtoff, + NPairHalfSizeMultiNewtoff, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_H -#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfSizeMulti2Newtoff : public NPair { +class NPairHalfSizeMultiNewtoff : public NPair { public: - NPairHalfSizeMulti2Newtoff(class LAMMPS *); - ~NPairHalfSizeMulti2Newtoff() {} + NPairHalfSizeMultiNewtoff(class LAMMPS *); + ~NPairHalfSizeMultiNewtoff() {} void build(class NeighList *); }; diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi_newton.cpp similarity index 89% rename from src/npair_half_size_multi2_newton.cpp rename to src/npair_half_size_multi_newton.cpp index bc6116b21c..8fa3b9bc1b 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_size_multi2_newton.h" +#include "npair_half_size_multi_newton.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,17 +22,17 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMulti2Newton::NPairHalfSizeMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMulti2Newton::build(NeighList *list) +void NPairHalfSizeMultiNewton::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; @@ -68,7 +68,7 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -87,9 +87,9 @@ void NPairHalfSizeMulti2Newton::build(NeighList *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 - js = bins_multi2[itype][i]; + js = bins_multi[itype][i]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -121,9 +121,9 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi2[jtype][jbin]; + js = binhead_multi[jtype][jbin]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if(j < i) continue; if (j >= nlocal) { @@ -158,12 +158,12 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_half_size_multi2_newton.h b/src/npair_half_size_multi_newton.h similarity index 70% rename from src/npair_half_size_multi2_newton.h rename to src/npair_half_size_multi_newton.h index 8c7bc1cc9e..d31496873d 100755 --- a/src/npair_half_size_multi2_newton.h +++ b/src/npair_half_size_multi_newton.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/size/multi2/newton, - NPairHalfSizeMulti2Newton, - NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_ORTHO) +NPairStyle(half/size/multi/newton, + NPairHalfSizeMultiNewton, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_H -#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfSizeMulti2Newton : public NPair { +class NPairHalfSizeMultiNewton : public NPair { public: - NPairHalfSizeMulti2Newton(class LAMMPS *); - ~NPairHalfSizeMulti2Newton() {} + NPairHalfSizeMultiNewton(class LAMMPS *); + ~NPairHalfSizeMultiNewton() {} void build(class NeighList *); }; diff --git a/src/npair_half_size_multi2_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp similarity index 89% rename from src/npair_half_size_multi2_newton_tri.cpp rename to src/npair_half_size_multi_newton_tri.cpp index 8cde0cbb36..780fa95f0b 100755 --- a/src/npair_half_size_multi2_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_size_multi2_newton_tri.h" +#include "npair_half_size_multi_newton_tri.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,17 +22,17 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMulti2NewtonTri::NPairHalfSizeMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) +void NPairHalfSizeMultiNewtonTri::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; @@ -68,7 +68,7 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -87,12 +87,12 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { // if same size (e.g. same type), use half stencil if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ diff --git a/src/npair_half_size_multi_newton_tri.h b/src/npair_half_size_multi_newton_tri.h new file mode 100755 index 0000000000..9bc1238e77 --- /dev/null +++ b/src/npair_half_size_multi_newton_tri.h @@ -0,0 +1,47 @@ +/* -*- 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/multi/newton/tri, + NPairHalfSizeMultiNewtonTri, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiNewtonTri : public NPair { + public: + NPairHalfSizeMultiNewtonTri(class LAMMPS *); + ~NPairHalfSizeMultiNewtonTri() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + +*/ \ No newline at end of file diff --git a/src/npair_half_size_multi_old_newtoff.cpp b/src/npair_half_size_multi_old_newtoff.cpp index 394ad58981..35095b4856 100644 --- a/src/npair_half_size_multi_old_newtoff.cpp +++ b/src/npair_half_size_multi_old_newtoff.cpp @@ -77,10 +77,10 @@ void NPairHalfSizeMultiOldNewtoff::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { if (j <= i) continue; diff --git a/src/npair_half_size_multi_old_newton.cpp b/src/npair_half_size_multi_old_newton.cpp index 65b197a86b..0112c0593f 100644 --- a/src/npair_half_size_multi_old_newton.cpp +++ b/src/npair_half_size_multi_old_newton.cpp @@ -104,10 +104,10 @@ void NPairHalfSizeMultiOldNewton::build(NeighList *list) // skip if i,j neighbor cutoff is less than bin distance ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair_half_size_multi_old_newton_tri.cpp b/src/npair_half_size_multi_old_newton_tri.cpp index 93d3beeb0a..2b63e116d7 100644 --- a/src/npair_half_size_multi_old_newton_tri.cpp +++ b/src/npair_half_size_multi_old_newton_tri.cpp @@ -78,10 +78,10 @@ void NPairHalfSizeMultiOldNewtonTri::build(NeighList *list) // latter excludes self-self interaction but allows superposed atoms ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; From 42e5130893a4842a86e4b09db30bb4980318eb10 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 17:18:54 -0700 Subject: [PATCH 33/73] Renaming multi->multi2 in nbin files --- src/nbin.cpp | 104 +++++------ src/nbin.h | 28 +-- src/{nbin_multi2.cpp => nbin_multi.cpp} | 222 ++++++++++++------------ src/{nbin_multi2.h => nbin_multi.h} | 16 +- 4 files changed, 185 insertions(+), 185 deletions(-) rename src/{nbin_multi2.cpp => nbin_multi.cpp} (55%) rename src/{nbin_multi2.h => nbin_multi.h} (85%) diff --git a/src/nbin.cpp b/src/nbin.cpp index 26aebd3a3a..084d3bfc4a 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -31,18 +31,18 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) bins = nullptr; atom2bin = nullptr; - nbinx_multi2 = nullptr; nbiny_multi2 = nullptr; nbinz_multi2 = nullptr; - mbins_multi2 = nullptr; - mbinx_multi2 = nullptr; mbiny_multi2 = nullptr, mbinz_multi2 = nullptr; - mbinxlo_multi2 = nullptr; - mbinylo_multi2 = nullptr; - mbinzlo_multi2 = nullptr; - binsizex_multi2 = nullptr; binsizey_multi2 = nullptr; binsizez_multi2 = nullptr; - bininvx_multi2 = nullptr; bininvy_multi2 = nullptr; bininvz_multi2 = nullptr; - binhead_multi2 = nullptr; - bins_multi2 = nullptr; - atom2bin_multi2 = nullptr; - maxbins_multi2 = nullptr; + nbinx_multi = nullptr; nbiny_multi = nullptr; nbinz_multi = nullptr; + mbins_multi = nullptr; + mbinx_multi = nullptr; mbiny_multi = nullptr, mbinz_multi = nullptr; + mbinxlo_multi = nullptr; + mbinylo_multi = nullptr; + mbinzlo_multi = nullptr; + binsizex_multi = nullptr; binsizey_multi = nullptr; binsizez_multi = nullptr; + bininvx_multi = nullptr; bininvy_multi = nullptr; bininvz_multi = nullptr; + binhead_multi = nullptr; + bins_multi = nullptr; + atom2bin_multi = nullptr; + maxbins_multi = nullptr; maxtypes = 0; @@ -64,36 +64,36 @@ NBin::~NBin() memory->destroy(bins); memory->destroy(atom2bin); - if (!bins_multi2) return; + if (!bins_multi) return; - memory->destroy(nbinx_multi2); - memory->destroy(nbiny_multi2); - memory->destroy(nbinz_multi2); - memory->destroy(mbins_multi2); - memory->destroy(mbinx_multi2); - memory->destroy(mbiny_multi2); - memory->destroy(mbinz_multi2); - memory->destroy(mbinxlo_multi2); - memory->destroy(mbinylo_multi2); - memory->destroy(mbinzlo_multi2); + memory->destroy(nbinx_multi); + memory->destroy(nbiny_multi); + memory->destroy(nbinz_multi); + memory->destroy(mbins_multi); + memory->destroy(mbinx_multi); + memory->destroy(mbiny_multi); + memory->destroy(mbinz_multi); + memory->destroy(mbinxlo_multi); + memory->destroy(mbinylo_multi); + memory->destroy(mbinzlo_multi); - memory->destroy(binsizex_multi2); - memory->destroy(binsizey_multi2); - memory->destroy(binsizez_multi2); - memory->destroy(bininvx_multi2); - memory->destroy(bininvy_multi2); - memory->destroy(bininvz_multi2); + memory->destroy(binsizex_multi); + memory->destroy(binsizey_multi); + memory->destroy(binsizez_multi); + memory->destroy(bininvx_multi); + memory->destroy(bininvy_multi); + memory->destroy(bininvz_multi); for (int n = 1; n <= maxtypes; n++) { - memory->destroy(binhead_multi2[n]); - memory->destroy(bins_multi2[n]); - memory->destroy(atom2bin_multi2[n]); + memory->destroy(binhead_multi[n]); + memory->destroy(bins_multi[n]); + memory->destroy(atom2bin_multi[n]); } - delete [] binhead_multi2; - delete [] bins_multi2; - delete [] atom2bin_multi2; + delete [] binhead_multi; + delete [] bins_multi; + delete [] atom2bin_multi; - memory->destroy(maxbins_multi2); + memory->destroy(maxbins_multi); } /* ---------------------------------------------------------------------- */ @@ -177,7 +177,7 @@ int NBin::coord2bin(double *x) convert atom coords into local bin # for a particular type ------------------------------------------------------------------------- */ -int NBin::coord2bin_multi2(double *x, int it) +int NBin::coord2bin_multi(double *x, int it) { int ix,iy,iz; int ibin; @@ -186,33 +186,33 @@ int NBin::coord2bin_multi2(double *x, int it) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi2[it]) + nbinx_multi2[it]; + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[it]) + nbinx_multi[it]; else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]); - ix = MIN(ix,nbinx_multi2[it]-1); + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]); + ix = MIN(ix,nbinx_multi[it]-1); } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]) - 1; + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]) - 1; if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi2[it]) + nbiny_multi2[it]; + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[it]) + nbiny_multi[it]; else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]); - iy = MIN(iy,nbiny_multi2[it]-1); + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]); + iy = MIN(iy,nbiny_multi[it]-1); } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]) - 1; + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]) - 1; if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi2[it]) + nbinz_multi2[it]; + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[it]) + nbinz_multi[it]; else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]); - iz = MIN(iz,nbinz_multi2[it]-1); + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]); + iz = MIN(iz,nbinz_multi[it]-1); } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]) - 1; + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]) - 1; - ibin = (iz-mbinzlo_multi2[it])*mbiny_multi2[it]*mbinx_multi2[it] - + (iy-mbinylo_multi2[it])*mbinx_multi2[it] - + (ix-mbinxlo_multi2[it]); + ibin = (iz-mbinzlo_multi[it])*mbiny_multi[it]*mbinx_multi[it] + + (iy-mbinylo_multi[it])*mbinx_multi[it] + + (ix-mbinxlo_multi[it]); return ibin; } diff --git a/src/nbin.h b/src/nbin.h index 441e4815dd..8f95ad987e 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -38,18 +38,18 @@ class NBin : protected Pointers { int *bins; // index of next atom in same bin int *atom2bin; // bin assignment for each atom (local+ghost) - // Analogues for NBinMultimulti2 + // Analogues for NBinMultimulti - int *nbinx_multi2, *nbiny_multi2, *nbinz_multi2; - int *mbins_multi2; - int *mbinx_multi2, *mbiny_multi2, *mbinz_multi2; - int *mbinxlo_multi2, *mbinylo_multi2, *mbinzlo_multi2; - double *binsizex_multi2, *binsizey_multi2, *binsizez_multi2; - double *bininvx_multi2, *bininvy_multi2, *bininvz_multi2; + int *nbinx_multi, *nbiny_multi, *nbinz_multi; + int *mbins_multi; + int *mbinx_multi, *mbiny_multi, *mbinz_multi; + int *mbinxlo_multi, *mbinylo_multi, *mbinzlo_multi; + double *binsizex_multi, *binsizey_multi, *binsizez_multi; + double *bininvx_multi, *bininvy_multi, *bininvz_multi; - int **binhead_multi2; - int **bins_multi2; - int **atom2bin_multi2; + int **binhead_multi; + int **bins_multi; + int **atom2bin_multi; NBin(class LAMMPS *); ~NBin(); @@ -89,15 +89,15 @@ class NBin : protected Pointers { int maxbin; // size of binhead array - // data for multi/multi2 NBin + // data for multi/multi NBin - int maxtypes; // size of multi2 arrays - int * maxbins_multi2; // size of 2nd dimension of binhead_multi2 array + int maxtypes; // size of multi arrays + int * maxbins_multi; // size of 2nd dimension of binhead_multi array // methods int coord2bin(double *); - int coord2bin_multi2(double *, int); + int coord2bin_multi(double *, int); }; } diff --git a/src/nbin_multi2.cpp b/src/nbin_multi.cpp similarity index 55% rename from src/nbin_multi2.cpp rename to src/nbin_multi.cpp index f57558a36c..302fe30d88 100644 --- a/src/nbin_multi2.cpp +++ b/src/nbin_multi.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nbin_multi2.h" +#include "nbin_multi.h" #include "neighbor.h" #include "atom.h" #include "group.h" @@ -28,34 +28,34 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NBinMulti2::NBinMulti2(LAMMPS *lmp) : NBin(lmp) {} +NBinMulti::NBinMulti(LAMMPS *lmp) : NBin(lmp) {} /* ---------------------------------------------------------------------- setup for bin_atoms() ------------------------------------------------------------------------- */ -void NBinMulti2::bin_atoms_setup(int nall) +void NBinMulti::bin_atoms_setup(int nall) { - // binhead_multi2[n] = per-bin vector mbins in length mbins_multi2[n] + // binhead_multi[n] = per-bin vector mbins in length mbins_multi[n] for (int n = 1; n <= maxtypes; n++) { - if (mbins_multi2[n] > maxbins_multi2[n]) { - maxbins_multi2[n] = mbins_multi2[n]; - memory->destroy(binhead_multi2[n]); - memory->create(binhead_multi2[n], mbins_multi2[n], "neigh:mbins_multi2"); + if (mbins_multi[n] > maxbins_multi[n]) { + maxbins_multi[n] = mbins_multi[n]; + memory->destroy(binhead_multi[n]); + memory->create(binhead_multi[n], mbins_multi[n], "neigh:mbins_multi"); } } - // bins_multi2[n] and atom2bin_multi2[n] = per-atom vectors + // bins_multi[n] and atom2bin_multi[n] = per-atom vectors // for both local and ghost atoms if (nall > maxatom) { maxatom = nall; for (int n = 1; n <= maxtypes; n++) { - memory->destroy(bins_multi2[n]); - memory->destroy(atom2bin_multi2[n]); - memory->create(bins_multi2[n], maxatom, "neigh:bin_multi2"); - memory->create(atom2bin_multi2[n], maxatom, "neigh:atom2bin_multi2"); + memory->destroy(bins_multi[n]); + memory->destroy(atom2bin_multi[n]); + memory->create(bins_multi[n], maxatom, "neigh:bin_multi"); + memory->create(atom2bin_multi[n], maxatom, "neigh:atom2bin_multi"); } } } @@ -64,7 +64,7 @@ void NBinMulti2::bin_atoms_setup(int nall) Identify index of type with smallest cutoff ------------------------------------------------------------------------ */ -int NBinMulti2::itype_min() { +int NBinMulti::itype_min() { int itypemin = 1; double ** cutneighsq; @@ -84,7 +84,7 @@ int NBinMulti2::itype_min() { setup neighbor binning geometry ---------------------------------------------------------------------- */ -void NBinMulti2::setup_bins(int style) +void NBinMulti::setup_bins(int style) { int n; int itypemin; @@ -96,64 +96,64 @@ void NBinMulti2::setup_bins(int style) // Clear any/all memory for existing types for (n = 1; n <= maxtypes; n++) { - memory->destroy(atom2bin_multi2[n]); - memory->destroy(binhead_multi2[n]); - memory->destroy(bins_multi2[n]); + memory->destroy(atom2bin_multi[n]); + memory->destroy(binhead_multi[n]); + memory->destroy(bins_multi[n]); } - delete [] atom2bin_multi2; - delete [] binhead_multi2; - delete [] bins_multi2; + delete [] atom2bin_multi; + delete [] binhead_multi; + delete [] bins_multi; // Realloacte at updated maxtypes maxtypes = atom->ntypes; - atom2bin_multi2 = new int*[maxtypes+1](); - binhead_multi2 = new int*[maxtypes+1](); - bins_multi2 = new int*[maxtypes+1](); + atom2bin_multi = new int*[maxtypes+1](); + binhead_multi = new int*[maxtypes+1](); + bins_multi = new int*[maxtypes+1](); - memory->destroy(nbinx_multi2); - memory->destroy(nbiny_multi2); - memory->destroy(nbinz_multi2); - memory->create(nbinx_multi2, maxtypes+1, "neigh:nbinx_multi2"); - memory->create(nbiny_multi2, maxtypes+1, "neigh:nbiny_multi2"); - memory->create(nbinz_multi2, maxtypes+1, "neigh:nbinz_multi2"); + memory->destroy(nbinx_multi); + memory->destroy(nbiny_multi); + memory->destroy(nbinz_multi); + memory->create(nbinx_multi, maxtypes+1, "neigh:nbinx_multi"); + memory->create(nbiny_multi, maxtypes+1, "neigh:nbiny_multi"); + memory->create(nbinz_multi, maxtypes+1, "neigh:nbinz_multi"); - memory->destroy(mbins_multi2); - memory->destroy(mbinx_multi2); - memory->destroy(mbiny_multi2); - memory->destroy(mbinz_multi2); - memory->create(mbins_multi2, maxtypes+1, "neigh:mbins_multi2"); - memory->create(mbinx_multi2, maxtypes+1, "neigh:mbinx_multi2"); - memory->create(mbiny_multi2, maxtypes+1, "neigh:mbiny_multi2"); - memory->create(mbinz_multi2, maxtypes+1, "neigh:mbinz_multi2"); + memory->destroy(mbins_multi); + memory->destroy(mbinx_multi); + memory->destroy(mbiny_multi); + memory->destroy(mbinz_multi); + memory->create(mbins_multi, maxtypes+1, "neigh:mbins_multi"); + memory->create(mbinx_multi, maxtypes+1, "neigh:mbinx_multi"); + memory->create(mbiny_multi, maxtypes+1, "neigh:mbiny_multi"); + memory->create(mbinz_multi, maxtypes+1, "neigh:mbinz_multi"); - memory->destroy(mbinxlo_multi2); - memory->destroy(mbinylo_multi2); - memory->destroy(mbinzlo_multi2); - memory->create(mbinxlo_multi2, maxtypes+1, "neigh:mbinxlo_multi2"); - memory->create(mbinylo_multi2, maxtypes+1, "neigh:mbinylo_multi2"); - memory->create(mbinzlo_multi2, maxtypes+1, "neigh:mbinzlo_multi2"); + memory->destroy(mbinxlo_multi); + memory->destroy(mbinylo_multi); + memory->destroy(mbinzlo_multi); + memory->create(mbinxlo_multi, maxtypes+1, "neigh:mbinxlo_multi"); + memory->create(mbinylo_multi, maxtypes+1, "neigh:mbinylo_multi"); + memory->create(mbinzlo_multi, maxtypes+1, "neigh:mbinzlo_multi"); - memory->destroy(binsizex_multi2); - memory->destroy(binsizey_multi2); - memory->destroy(binsizez_multi2); - memory->create(binsizex_multi2, maxtypes+1, "neigh:binsizex_multi2"); - memory->create(binsizey_multi2, maxtypes+1, "neigh:binsizey_multi2"); - memory->create(binsizez_multi2, maxtypes+1, "neigh:binsizez_multi2"); + memory->destroy(binsizex_multi); + memory->destroy(binsizey_multi); + memory->destroy(binsizez_multi); + memory->create(binsizex_multi, maxtypes+1, "neigh:binsizex_multi"); + memory->create(binsizey_multi, maxtypes+1, "neigh:binsizey_multi"); + memory->create(binsizez_multi, maxtypes+1, "neigh:binsizez_multi"); - memory->destroy(bininvx_multi2); - memory->destroy(bininvy_multi2); - memory->destroy(bininvz_multi2); - memory->create(bininvx_multi2, maxtypes+1, "neigh:bininvx_multi2"); - memory->create(bininvy_multi2, maxtypes+1, "neigh:bininvy_multi2"); - memory->create(bininvz_multi2, maxtypes+1, "neigh:bininvz_multi2"); + memory->destroy(bininvx_multi); + memory->destroy(bininvy_multi); + memory->destroy(bininvz_multi); + memory->create(bininvx_multi, maxtypes+1, "neigh:bininvx_multi"); + memory->create(bininvy_multi, maxtypes+1, "neigh:bininvy_multi"); + memory->create(bininvz_multi, maxtypes+1, "neigh:bininvz_multi"); - memory->destroy(maxbins_multi2); - memory->create(maxbins_multi2, maxtypes+1, "neigh:maxbins_multi2"); + memory->destroy(maxbins_multi); + memory->create(maxbins_multi, maxtypes+1, "neigh:maxbins_multi"); // make sure reallocation occurs in bin_atoms_setup() for (n = 1; n <= maxtypes; n++) { - maxbins_multi2[n] = 0; + maxbins_multi[n] = 0; } maxatom = 0; } @@ -214,16 +214,16 @@ void NBinMulti2::setup_bins(int style) // create actual bins // always have one bin even if cutoff > bbox - // for 2d, nbinz_multi2[n] = 1 + // for 2d, nbinz_multi[n] = 1 - nbinx_multi2[n] = static_cast (bbox[0]*binsizeinv); - nbiny_multi2[n] = static_cast (bbox[1]*binsizeinv); - if (dimension == 3) nbinz_multi2[n] = static_cast (bbox[2]*binsizeinv); - else nbinz_multi2[n] = 1; + nbinx_multi[n] = static_cast (bbox[0]*binsizeinv); + nbiny_multi[n] = static_cast (bbox[1]*binsizeinv); + if (dimension == 3) nbinz_multi[n] = static_cast (bbox[2]*binsizeinv); + else nbinz_multi[n] = 1; - if (nbinx_multi2[n] == 0) nbinx_multi2[n] = 1; - if (nbiny_multi2[n] == 0) nbiny_multi2[n] = 1; - if (nbinz_multi2[n] == 0) nbinz_multi2[n] = 1; + if (nbinx_multi[n] == 0) nbinx_multi[n] = 1; + if (nbiny_multi[n] == 0) nbiny_multi[n] = 1; + if (nbinz_multi[n] == 0) nbinz_multi[n] = 1; // compute actual bin size for nbins to fit into box exactly // error if actual bin size << cutoff, since will create a zillion bins @@ -231,17 +231,17 @@ void NBinMulti2::setup_bins(int style) // typically due to non-periodic, flat system in a particular dim // in that extreme case, should use NSQ not BIN neighbor style - binsizex_multi2[n] = bbox[0]/nbinx_multi2[n]; - binsizey_multi2[n] = bbox[1]/nbiny_multi2[n]; - binsizez_multi2[n] = bbox[2]/nbinz_multi2[n]; + binsizex_multi[n] = bbox[0]/nbinx_multi[n]; + binsizey_multi[n] = bbox[1]/nbiny_multi[n]; + binsizez_multi[n] = bbox[2]/nbinz_multi[n]; - bininvx_multi2[n] = 1.0 / binsizex_multi2[n]; - bininvy_multi2[n] = 1.0 / binsizey_multi2[n]; - bininvz_multi2[n] = 1.0 / binsizez_multi2[n]; + bininvx_multi[n] = 1.0 / binsizex_multi[n]; + bininvy_multi[n] = 1.0 / binsizey_multi[n]; + bininvz_multi[n] = 1.0 / binsizez_multi[n]; - if (binsize_optimal*bininvx_multi2[n] > CUT2BIN_RATIO || - binsize_optimal*bininvy_multi2[n] > CUT2BIN_RATIO || - binsize_optimal*bininvz_multi2[n] > CUT2BIN_RATIO) + if (binsize_optimal*bininvx_multi[n] > CUT2BIN_RATIO || + binsize_optimal*bininvy_multi[n] > CUT2BIN_RATIO || + binsize_optimal*bininvz_multi[n] > 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 @@ -253,46 +253,46 @@ void NBinMulti2::setup_bins(int style) double coord; coord = bsubboxlo[0] - SMALL*bbox[0]; - mbinxlo_multi2[n] = static_cast ((coord-bboxlo[0])*bininvx_multi2[n]); - if (coord < bboxlo[0]) mbinxlo_multi2[n] = mbinxlo_multi2[n] - 1; + mbinxlo_multi[n] = static_cast ((coord-bboxlo[0])*bininvx_multi[n]); + if (coord < bboxlo[0]) mbinxlo_multi[n] = mbinxlo_multi[n] - 1; coord = bsubboxhi[0] + SMALL*bbox[0]; - mbinxhi = static_cast ((coord-bboxlo[0])*bininvx_multi2[n]); + mbinxhi = static_cast ((coord-bboxlo[0])*bininvx_multi[n]); coord = bsubboxlo[1] - SMALL*bbox[1]; - mbinylo_multi2[n] = static_cast ((coord-bboxlo[1])*bininvy_multi2[n]); - if (coord < bboxlo[1]) mbinylo_multi2[n] = mbinylo_multi2[n] - 1; + mbinylo_multi[n] = static_cast ((coord-bboxlo[1])*bininvy_multi[n]); + if (coord < bboxlo[1]) mbinylo_multi[n] = mbinylo_multi[n] - 1; coord = bsubboxhi[1] + SMALL*bbox[1]; - mbinyhi = static_cast ((coord-bboxlo[1])*bininvy_multi2[n]); + mbinyhi = static_cast ((coord-bboxlo[1])*bininvy_multi[n]); if (dimension == 3) { coord = bsubboxlo[2] - SMALL*bbox[2]; - mbinzlo_multi2[n] = static_cast ((coord-bboxlo[2])*bininvz_multi2[n]); - if (coord < bboxlo[2]) mbinzlo_multi2[n] = mbinzlo_multi2[n] - 1; + mbinzlo_multi[n] = static_cast ((coord-bboxlo[2])*bininvz_multi[n]); + if (coord < bboxlo[2]) mbinzlo_multi[n] = mbinzlo_multi[n] - 1; coord = bsubboxhi[2] + SMALL*bbox[2]; - mbinzhi = static_cast ((coord-bboxlo[2])*bininvz_multi2[n]); + mbinzhi = static_cast ((coord-bboxlo[2])*bininvz_multi[n]); } // extend bins by 1 to insure stencil extent is included // for 2d, only 1 bin in z - mbinxlo_multi2[n] = mbinxlo_multi2[n] - 1; + mbinxlo_multi[n] = mbinxlo_multi[n] - 1; mbinxhi = mbinxhi + 1; - mbinx_multi2[n] = mbinxhi - mbinxlo_multi2[n] + 1; + mbinx_multi[n] = mbinxhi - mbinxlo_multi[n] + 1; - mbinylo_multi2[n] = mbinylo_multi2[n] - 1; + mbinylo_multi[n] = mbinylo_multi[n] - 1; mbinyhi = mbinyhi + 1; - mbiny_multi2[n] = mbinyhi - mbinylo_multi2[n] + 1; + mbiny_multi[n] = mbinyhi - mbinylo_multi[n] + 1; if (dimension == 3) { - mbinzlo_multi2[n] = mbinzlo_multi2[n] - 1; + mbinzlo_multi[n] = mbinzlo_multi[n] - 1; mbinzhi = mbinzhi + 1; - } else mbinzlo_multi2[n] = mbinzhi = 0; - mbinz_multi2[n] = mbinzhi - mbinzlo_multi2[n] + 1; + } else mbinzlo_multi[n] = mbinzhi = 0; + mbinz_multi[n] = mbinzhi - mbinzlo_multi[n] + 1; - bigint bbin = ((bigint) mbinx_multi2[n]) - * ((bigint) mbiny_multi2[n]) * ((bigint) mbinz_multi2[n]) + 1; + bigint bbin = ((bigint) mbinx_multi[n]) + * ((bigint) mbiny_multi[n]) * ((bigint) mbinz_multi[n]) + 1; if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins"); - mbins_multi2[n] = bbin; + mbins_multi[n] = bbin; } } @@ -301,13 +301,13 @@ void NBinMulti2::setup_bins(int style) bin owned and ghost atoms by type ------------------------------------------------------------------------- */ -void NBinMulti2::bin_atoms() +void NBinMulti::bin_atoms() { int i,ibin,n; last_bin = update->ntimestep; for (n = 1; n <= maxtypes; n++) { - for (i = 0; i < mbins_multi2[n]; i++) binhead_multi2[n][i] = -1; + for (i = 0; i < mbins_multi[n]; i++) binhead_multi[n][i] = -1; } // bin in reverse order so linked list will be in forward order @@ -324,38 +324,38 @@ void NBinMulti2::bin_atoms() for (i = nall-1; i >= nlocal; i--) { if (mask[i] & bitmask) { n = type[i]; - ibin = coord2bin_multi2(x[i], n); - atom2bin_multi2[n][i] = ibin; - bins_multi2[n][i] = binhead_multi2[n][ibin]; - binhead_multi2[n][ibin] = i; + ibin = coord2bin_multi(x[i], n); + atom2bin_multi[n][i] = ibin; + bins_multi[n][i] = binhead_multi[n][ibin]; + binhead_multi[n][ibin] = i; } } for (i = atom->nfirst-1; i >= 0; i--) { n = type[i]; - ibin = coord2bin_multi2(x[i], n); - atom2bin_multi2[n][i] = ibin; - bins_multi2[n][i] = binhead_multi2[n][ibin]; - binhead_multi2[n][ibin] = i; + ibin = coord2bin_multi(x[i], n); + atom2bin_multi[n][i] = ibin; + bins_multi[n][i] = binhead_multi[n][ibin]; + binhead_multi[n][ibin] = i; } } else { for (i = nall-1; i >= 0; i--) { n = type[i]; - ibin = coord2bin_multi2(x[i], n); - atom2bin_multi2[n][i] = ibin; - bins_multi2[n][i] = binhead_multi2[n][ibin]; - binhead_multi2[n][ibin] = i; + ibin = coord2bin_multi(x[i], n); + atom2bin_multi[n][i] = ibin; + bins_multi[n][i] = binhead_multi[n][ibin]; + binhead_multi[n][ibin] = i; } } } /* ---------------------------------------------------------------------- */ -double NBinMulti2::memory_usage() +double NBinMulti::memory_usage() { double bytes = 0; for (int m = 1; m < maxtypes; m++) { - bytes += maxbins_multi2[m]*sizeof(int); + bytes += maxbins_multi[m]*sizeof(int); bytes += 2*maxatom*sizeof(int); } return bytes; diff --git a/src/nbin_multi2.h b/src/nbin_multi.h similarity index 85% rename from src/nbin_multi2.h rename to src/nbin_multi.h index 3094027f64..856f3fa722 100644 --- a/src/nbin_multi2.h +++ b/src/nbin_multi.h @@ -13,24 +13,24 @@ #ifdef NBIN_CLASS -NBinStyle(multi2, - NBinMulti2, - NB_MULTI2) +NBinStyle(multi, + NBinMulti, + NB_MULTI) #else -#ifndef LMP_NBIN_MULTI2_H -#define LMP_NBIN_MULTI2_H +#ifndef LMP_NBIN_MULTI_H +#define LMP_NBIN_MULTI_H #include "nbin.h" namespace LAMMPS_NS { -class NBinMulti2 : public NBin { +class NBinMulti : public NBin { public: - NBinMulti2(class LAMMPS *); - ~NBinMulti2() {} + NBinMulti(class LAMMPS *); + ~NBinMulti() {} void bin_atoms_setup(int); void setup_bins(int); void bin_atoms(); From 4a85afcde21dc63a8b35c5a1b789042bbb43dd07 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 17:22:42 -0700 Subject: [PATCH 34/73] Removing redundant stencils --- src/nstencil_half_bin_2d_newtoff.cpp | 37 --------------- src/nstencil_half_bin_3d_newtoff.cpp | 38 ---------------- src/nstencil_half_ghost_bin_2d_newtoff.cpp | 44 ------------------ src/nstencil_half_ghost_bin_3d_newtoff.cpp | 45 ------------------- src/nstencil_half_multi_2d_newtoff.cpp | 51 --------------------- src/nstencil_half_multi_3d_newtoff.cpp | 52 ---------------------- 6 files changed, 267 deletions(-) delete mode 100644 src/nstencil_half_bin_2d_newtoff.cpp delete mode 100644 src/nstencil_half_bin_3d_newtoff.cpp delete mode 100644 src/nstencil_half_ghost_bin_2d_newtoff.cpp delete mode 100644 src/nstencil_half_ghost_bin_3d_newtoff.cpp delete mode 100644 src/nstencil_half_multi_2d_newtoff.cpp delete mode 100644 src/nstencil_half_multi_3d_newtoff.cpp diff --git a/src/nstencil_half_bin_2d_newtoff.cpp b/src/nstencil_half_bin_2d_newtoff.cpp deleted file mode 100644 index 09c74d8b69..0000000000 --- a/src/nstencil_half_bin_2d_newtoff.cpp +++ /dev/null @@ -1,37 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://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" - -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_3d_newtoff.cpp b/src/nstencil_half_bin_3d_newtoff.cpp deleted file mode 100644 index 36b2a11c66..0000000000 --- a/src/nstencil_half_bin_3d_newtoff.cpp +++ /dev/null @@ -1,38 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://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" - -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_ghost_bin_2d_newtoff.cpp b/src/nstencil_half_ghost_bin_2d_newtoff.cpp deleted file mode 100644 index 0aa5202da8..0000000000 --- a/src/nstencil_half_ghost_bin_2d_newtoff.cpp +++ /dev/null @@ -1,44 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://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" - -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_3d_newtoff.cpp b/src/nstencil_half_ghost_bin_3d_newtoff.cpp deleted file mode 100644 index 95016108e4..0000000000 --- a/src/nstencil_half_ghost_bin_3d_newtoff.cpp +++ /dev/null @@ -1,45 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://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" - -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_multi_2d_newtoff.cpp b/src/nstencil_half_multi_2d_newtoff.cpp deleted file mode 100644 index 9b6ea08862..0000000000 --- a/src/nstencil_half_multi_2d_newtoff.cpp +++ /dev/null @@ -1,51 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://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 "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_3d_newtoff.cpp b/src/nstencil_half_multi_3d_newtoff.cpp deleted file mode 100644 index 533ba21c3a..0000000000 --- a/src/nstencil_half_multi_3d_newtoff.cpp +++ /dev/null @@ -1,52 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://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 "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; - } -} From 1c52ff15c37df375d8b91b1f1b7c81aefed481da Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 17:39:20 -0700 Subject: [PATCH 35/73] Renaming multi nstencils to multi/old --- src/nstencil.cpp | 232 +++++++++--------- src/nstencil.h | 60 +++-- ..._2d.cpp => nstencil_full_multi_old_2d.cpp} | 12 +- src/nstencil_full_multi_old_2d.h | 43 ++++ ..._3d.cpp => nstencil_full_multi_old_3d.cpp} | 12 +- src/nstencil_full_multi_old_3d.h | 43 ++++ src/nstencil_half_multi_3d.h | 42 ---- src/nstencil_half_multi_3d_tri.h | 42 ---- ..._2d.cpp => nstencil_half_multi_old_2d.cpp} | 14 +- ..._2d_tri.h => nstencil_half_multi_old_2d.h} | 14 +- ...cpp => nstencil_half_multi_old_2d_tri.cpp} | 14 +- ..._2d.h => nstencil_half_multi_old_2d_tri.h} | 14 +- ..._3d.cpp => nstencil_half_multi_old_3d.cpp} | 14 +- ...ulti_2d.h => nstencil_half_multi_old_3d.h} | 15 +- ...cpp => nstencil_half_multi_old_3d_tri.cpp} | 14 +- ..._3d.h => nstencil_half_multi_old_3d_tri.h} | 15 +- 16 files changed, 298 insertions(+), 302 deletions(-) rename src/{nstencil_full_multi_2d.cpp => nstencil_full_multi_old_2d.cpp} (83%) create mode 100644 src/nstencil_full_multi_old_2d.h rename src/{nstencil_full_multi_3d.cpp => nstencil_full_multi_old_3d.cpp} (84%) create mode 100644 src/nstencil_full_multi_old_3d.h delete mode 100644 src/nstencil_half_multi_3d.h delete mode 100644 src/nstencil_half_multi_3d_tri.h rename src/{nstencil_half_multi_2d.cpp => nstencil_half_multi_old_2d.cpp} (84%) rename src/{nstencil_half_multi_2d_tri.h => nstencil_half_multi_old_2d.h} (71%) rename src/{nstencil_half_multi_2d_tri.cpp => nstencil_half_multi_old_2d_tri.cpp} (82%) rename src/{nstencil_half_multi_2d.h => nstencil_half_multi_old_2d_tri.h} (69%) rename src/{nstencil_half_multi_3d.cpp => nstencil_half_multi_old_3d.cpp} (84%) rename src/{nstencil_full_multi_2d.h => nstencil_half_multi_old_3d.h} (71%) rename src/{nstencil_half_multi_3d_tri.cpp => nstencil_half_multi_old_3d_tri.cpp} (83%) rename src/{nstencil_full_multi_3d.h => nstencil_half_multi_old_3d_tri.h} (69%) diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 6fece15dcd..42ddbaff30 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -46,12 +46,12 @@ using namespace LAMMPS_NS; 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 multi: + for multi/old: 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?) - for multi2: + for multi: create one stencil for each itype-jtype pairing the full/half stencil label refers to the same-type stencil a half list with newton on has a half same-type stencil @@ -68,16 +68,16 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) last_stencil = -1; xyzflag = 0; - maxstencil = maxstencil_multi = 0; + maxstencil = maxstencil_multi_old = 0; stencil = nullptr; stencilxyz = nullptr; - nstencil_multi = nullptr; - stencil_multi = nullptr; - distsq_multi = nullptr; + nstencil_multi_old = nullptr; + stencil_multi_old = nullptr; + distsq_multi_old = nullptr; - nstencil_multi2 = nullptr; - stencil_multi2 = nullptr; - maxstencil_multi2 = nullptr; + nstencil_multi = nullptr; + stencil_multi = nullptr; + maxstencil_multi = nullptr; stencil_half = nullptr; stencil_skip = nullptr; @@ -93,46 +93,46 @@ NStencil::~NStencil() memory->destroy(stencil); memory->destroy(stencilxyz); - if (stencil_multi) { + if (stencil_multi_old) { int n = atom->ntypes; for (int i = 1; i <= n; i++) { - memory->destroy(stencil_multi[i]); - memory->destroy(distsq_multi[i]); + memory->destroy(stencil_multi_old[i]); + memory->destroy(distsq_multi_old[i]); } - delete [] nstencil_multi; - delete [] stencil_multi; - delete [] distsq_multi; + delete [] nstencil_multi_old; + delete [] stencil_multi_old; + delete [] distsq_multi_old; } - if (stencil_multi2) { + if (stencil_multi) { int n = atom->ntypes; - memory->destroy(nstencil_multi2); + memory->destroy(nstencil_multi); for (int i = 1; i <= n; i++) { for (int j = 0; j <= n; j++) { if (! stencil_skip[i][j]) - memory->destroy(stencil_multi2[i][j]); + memory->destroy(stencil_multi[i][j]); } - delete [] stencil_multi2[i]; + delete [] stencil_multi[i]; } - delete [] stencil_multi2; - memory->destroy(maxstencil_multi2); + delete [] stencil_multi; + memory->destroy(maxstencil_multi); memory->destroy(stencil_half); memory->destroy(stencil_skip); memory->destroy(stencil_bin_type); - memory->destroy(stencil_sx_multi2); - memory->destroy(stencil_sy_multi2); - memory->destroy(stencil_sz_multi2); + memory->destroy(stencil_sx_multi); + memory->destroy(stencil_sy_multi); + memory->destroy(stencil_sz_multi); - memory->destroy(stencil_mbinx_multi2); - memory->destroy(stencil_mbiny_multi2); - memory->destroy(stencil_mbinz_multi2); + memory->destroy(stencil_mbinx_multi); + memory->destroy(stencil_mbiny_multi); + memory->destroy(stencil_mbinz_multi); - memory->destroy(stencil_binsizex_multi2); - memory->destroy(stencil_binsizey_multi2); - memory->destroy(stencil_binsizez_multi2); + memory->destroy(stencil_binsizex_multi); + memory->destroy(stencil_binsizey_multi); + memory->destroy(stencil_binsizez_multi); } } @@ -183,20 +183,20 @@ void NStencil::copy_bin_info() } /* ---------------------------------------------------------------------- - copy needed info for multi2 from NBin class to this stencil class + copy needed info for multi from NBin class to this stencil class ------------------------------------------------------------------------- */ -void NStencil::copy_bin_info_multi2() +void NStencil::copy_bin_info_multi() { - mbinx_multi2 = nb->mbinx_multi2; - mbiny_multi2 = nb->mbiny_multi2; - mbinz_multi2 = nb->mbinz_multi2; - binsizex_multi2 = nb->binsizex_multi2; - binsizey_multi2 = nb->binsizey_multi2; - binsizez_multi2 = nb->binsizez_multi2; - bininvx_multi2 = nb->bininvx_multi2; - bininvy_multi2 = nb->bininvy_multi2; - bininvz_multi2 = nb->bininvz_multi2; + mbinx_multi = nb->mbinx_multi; + mbiny_multi = nb->mbiny_multi; + mbinz_multi = nb->mbinz_multi; + binsizex_multi = nb->binsizex_multi; + binsizey_multi = nb->binsizey_multi; + binsizez_multi = nb->binsizez_multi; + bininvx_multi = nb->bininvx_multi; + bininvy_multi = nb->bininvy_multi; + bininvz_multi = nb->bininvz_multi; } /* ---------------------------------------------------------------------- @@ -207,7 +207,7 @@ void NStencil::copy_bin_info_multi2() void NStencil::create_setup() { - if (neighstyle != Neighbor::MULTI2){ + if (neighstyle != Neighbor::MULTI){ if (nb) copy_bin_info(); last_stencil = update->ntimestep; @@ -242,25 +242,25 @@ void NStencil::create_setup() } 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]; + if (maxstencil_multi_old == 0) { + nstencil_multi_old = new int[n+1]; + stencil_multi_old = new int*[n+1]; + distsq_multi_old = new double*[n+1]; for (i = 1; i <= n; i++) { - nstencil_multi[i] = 0; - stencil_multi[i] = nullptr; - distsq_multi[i] = nullptr; + nstencil_multi_old[i] = 0; + stencil_multi_old[i] = nullptr; + distsq_multi_old[i] = nullptr; } } - if (smax > maxstencil_multi) { - maxstencil_multi = smax; + if (smax > maxstencil_multi_old) { + maxstencil_multi_old = 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"); + memory->destroy(stencil_multi_old[i]); + memory->destroy(distsq_multi_old[i]); + memory->create(stencil_multi_old[i],maxstencil_multi_old, + "neighstencil:stencil_multi_old"); + memory->create(distsq_multi_old[i],maxstencil_multi_old, + "neighstencil:distsq_multi_old"); } } } @@ -269,7 +269,7 @@ void NStencil::create_setup() double stencil_range; int n = atom->ntypes; - if(nb) copy_bin_info_multi2(); + if(nb) copy_bin_info_multi(); // Allocate arrays to store stencil information memory->create(stencil_half, n+1, n+1, @@ -279,26 +279,26 @@ void NStencil::create_setup() memory->create(stencil_bin_type, n+1, n+1, "neighstencil:stencil_bin_type"); - memory->create(stencil_sx_multi2, n+1, n+1, - "neighstencil:stencil_sx_multi2"); - memory->create(stencil_sy_multi2, n+1, n+1, - "neighstencil:stencil_sy_multi2"); - memory->create(stencil_sz_multi2, n+1, n+1, - "neighstencil:stencil_sz_multi2"); + memory->create(stencil_sx_multi, n+1, n+1, + "neighstencil:stencil_sx_multi"); + memory->create(stencil_sy_multi, n+1, n+1, + "neighstencil:stencil_sy_multi"); + memory->create(stencil_sz_multi, n+1, n+1, + "neighstencil:stencil_sz_multi"); - memory->create(stencil_binsizex_multi2, n+1, n+1, - "neighstencil:stencil_binsizex_multi2"); - memory->create(stencil_binsizey_multi2, n+1, n+1, - "neighstencil:stencil_binsizey_multi2"); - memory->create(stencil_binsizez_multi2, n+1, n+1, - "neighstencil:stencil_binsizez_multi2"); + memory->create(stencil_binsizex_multi, n+1, n+1, + "neighstencil:stencil_binsizex_multi"); + memory->create(stencil_binsizey_multi, n+1, n+1, + "neighstencil:stencil_binsizey_multi"); + memory->create(stencil_binsizez_multi, n+1, n+1, + "neighstencil:stencil_binsizez_multi"); - memory->create(stencil_mbinx_multi2, n+1, n+1, - "neighstencil:stencil_mbinx_multi2"); - memory->create(stencil_mbiny_multi2, n+1, n+1, - "neighstencil:stencil_mbiny_multi2"); - memory->create(stencil_mbinz_multi2, n+1, n+1, - "neighstencil:stencil_mbinz_multi2"); + memory->create(stencil_mbinx_multi, n+1, n+1, + "neighstencil:stencil_mbinx_multi"); + memory->create(stencil_mbiny_multi, n+1, n+1, + "neighstencil:stencil_mbiny_multi"); + memory->create(stencil_mbinz_multi, n+1, n+1, + "neighstencil:stencil_mbinz_multi"); // Skip all stencils by default, initialize smax for (i = 1; i <= n; i++) { @@ -312,15 +312,15 @@ void NStencil::create_setup() // Allocate arrays to store stencils - if (!maxstencil_multi2) { - memory->create(maxstencil_multi2, n+1, n+1, "neighstencil::stencil_multi2"); - memory->create(nstencil_multi2, n+1, n+1, "neighstencil::nstencil_multi2"); - stencil_multi2 = new int**[n+1](); + if (!maxstencil_multi) { + memory->create(maxstencil_multi, n+1, n+1, "neighstencil::stencil_multi"); + memory->create(nstencil_multi, n+1, n+1, "neighstencil::nstencil_multi"); + stencil_multi = new int**[n+1](); for (i = 1; i <= n; ++i) { - stencil_multi2[i] = new int*[n+1](); + stencil_multi[i] = new int*[n+1](); for (j = 1; j <= n; ++j) { - maxstencil_multi2[i][j] = 0; - nstencil_multi2[i][j] = 0; + maxstencil_multi[i][j] = 0; + nstencil_multi[i][j] = 0; } } } @@ -334,34 +334,34 @@ void NStencil::create_setup() // Copy bin info for this particular pair of types bin_type = stencil_bin_type[i][j]; - stencil_binsizex_multi2[i][j] = binsizex_multi2[bin_type]; - stencil_binsizey_multi2[i][j] = binsizey_multi2[bin_type]; - stencil_binsizez_multi2[i][j] = binsizez_multi2[bin_type]; + stencil_binsizex_multi[i][j] = binsizex_multi[bin_type]; + stencil_binsizey_multi[i][j] = binsizey_multi[bin_type]; + stencil_binsizez_multi[i][j] = binsizez_multi[bin_type]; - stencil_mbinx_multi2[i][j] = mbinx_multi2[bin_type]; - stencil_mbiny_multi2[i][j] = mbiny_multi2[bin_type]; - stencil_mbinz_multi2[i][j] = mbinz_multi2[bin_type]; + stencil_mbinx_multi[i][j] = mbinx_multi[bin_type]; + stencil_mbiny_multi[i][j] = mbiny_multi[bin_type]; + stencil_mbinz_multi[i][j] = mbinz_multi[bin_type]; stencil_range = sqrt(cutneighsq[i][j]); - sx = static_cast (stencil_range*bininvx_multi2[bin_type]); - if (sx*binsizex_multi2[bin_type] < stencil_range) sx++; - sy = static_cast (stencil_range*bininvy_multi2[bin_type]); - if (sy*binsizey_multi2[bin_type] < stencil_range) sy++; - sz = static_cast (stencil_range*bininvz_multi2[bin_type]); - if (sz*binsizez_multi2[bin_type] < stencil_range) sz++; + sx = static_cast (stencil_range*bininvx_multi[bin_type]); + if (sx*binsizex_multi[bin_type] < stencil_range) sx++; + sy = static_cast (stencil_range*bininvy_multi[bin_type]); + if (sy*binsizey_multi[bin_type] < stencil_range) sy++; + sz = static_cast (stencil_range*bininvz_multi[bin_type]); + if (sz*binsizez_multi[bin_type] < stencil_range) sz++; - stencil_sx_multi2[i][j] = sx; - stencil_sy_multi2[i][j] = sy; - stencil_sz_multi2[i][j] = sz; + stencil_sx_multi[i][j] = sx; + stencil_sy_multi[i][j] = sy; + stencil_sz_multi[i][j] = sz; smax = ((2*sx+1) * (2*sy+1) * (2*sz+1)); - if (smax > maxstencil_multi2[i][j]) { - maxstencil_multi2[i][j] = smax; - memory->destroy(stencil_multi2[i][j]); - memory->create(stencil_multi2[i][j], smax, - "neighstencil::stencil_multi2"); + if (smax > maxstencil_multi[i][j]) { + maxstencil_multi[i][j] = smax; + memory->destroy(stencil_multi[i][j]); + memory->create(stencil_multi[i][j], smax, + "neighstencil::stencil_multi"); } } } @@ -396,21 +396,21 @@ double NStencil::bin_distance(int i, int j, int k) compute closest distance for a given atom type ------------------------------------------------------------------------- */ -double NStencil::bin_distance_multi2(int i, int j, int k, int type) +double NStencil::bin_distance_multi(int i, int j, int k, int type) { double delx,dely,delz; - if (i > 0) delx = (i-1)*binsizex_multi2[type]; + if (i > 0) delx = (i-1)*binsizex_multi[type]; else if (i == 0) delx = 0.0; - else delx = (i+1)*binsizex_multi2[type]; + else delx = (i+1)*binsizex_multi[type]; - if (j > 0) dely = (j-1)*binsizey_multi2[type]; + if (j > 0) dely = (j-1)*binsizey_multi[type]; else if (j == 0) dely = 0.0; - else dely = (j+1)*binsizey_multi2[type]; + else dely = (j+1)*binsizey_multi[type]; - if (k > 0) delz = (k-1)*binsizez_multi2[type]; + if (k > 0) delz = (k-1)*binsizez_multi[type]; else if (k == 0) delz = 0.0; - else delz = (k+1)*binsizez_multi2[type]; + else delz = (k+1)*binsizez_multi[type]; return (delx*delx + dely*dely + delz*delz); } @@ -423,16 +423,16 @@ double NStencil::memory_usage() if (neighstyle == Neighbor::BIN) { bytes += memory->usage(stencil,maxstencil); bytes += memory->usage(stencilxyz,maxstencil,3); + } else if (neighstyle == Neighbor::MULTI_OLD) { + bytes += atom->ntypes*maxstencil_multi_old * sizeof(int); + bytes += atom->ntypes*maxstencil_multi_old * sizeof(double); } else if (neighstyle == Neighbor::MULTI) { - bytes += atom->ntypes*maxstencil_multi * sizeof(int); - bytes += atom->ntypes*maxstencil_multi * sizeof(double); - } else if (neighstyle == Neighbor::MULTI2) { int n = atom->ntypes; for (int i = 1; i <= n; i++) { for (int j = 1; j <= n; j++) { - bytes += maxstencil_multi2[i][j] * sizeof(int); - bytes += maxstencil_multi2[i][j] * sizeof(int); - bytes += maxstencil_multi2[i][j] * sizeof(double); + bytes += maxstencil_multi[i][j] * sizeof(int); + bytes += maxstencil_multi[i][j] * sizeof(int); + bytes += maxstencil_multi[i][j] * sizeof(double); } } bytes += 2 * n * n * sizeof(bool); diff --git a/src/nstencil.h b/src/nstencil.h index 60e584b2a0..28c7fb0ec2 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -27,21 +27,17 @@ class NStencil : protected Pointers { int nstencil; // # of bins in 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 - int ** nstencil_multi2; // # bins bins in each itype-jtype multi2 stencil - int *** stencil_multi2; // list of bin offsets in each multi2 stencil - int ** maxstencil_multi2; // max stencil size for each multi2 stencil - - // Note distsq_multi is used in multi to quickly skip bins beyond interaction cutoff - // Not quite sure why bins are beyond this distance? Have to think - // Probably not needed for multi2 since bins are more efficiently chosen + int *nstencil_multi_old; // # bins in each type-based old multi stencil + int **stencil_multi_old; // list of bin offsets in each stencil + double **distsq_multi_old; // sq distances to bins in each stencil + int ** nstencil_multi; // # bins bins in each itype-jtype multi stencil + int *** stencil_multi; // list of bin offsets in each multi stencil + int ** maxstencil_multi; // max stencil size for each multi stencil int sx,sy,sz; // extent of stencil in each dim - int **stencil_sx_multi2; // analogs for each multi2 stencil - int **stencil_sy_multi2; - int **stencil_sz_multi2; + int **stencil_sx_multi; // analogs for each multi stencil + int **stencil_sy_multi; + int **stencil_sz_multi; double cutoff_custom; // cutoff set by requestor @@ -77,32 +73,32 @@ class NStencil : protected Pointers { double binsizex,binsizey,binsizez; double bininvx,bininvy,bininvz; - // data from NBin class for multi2 + // data from NBin class for multi - int *mbinx_multi2; - int *mbiny_multi2; - int *mbinz_multi2; - double *binsizex_multi2; - double *binsizey_multi2; - double *binsizez_multi2; - double *bininvx_multi2; - double *bininvy_multi2; - double *bininvz_multi2; + int *mbinx_multi; + int *mbiny_multi; + int *mbinz_multi; + double *binsizex_multi; + double *binsizey_multi; + double *binsizez_multi; + double *bininvx_multi; + double *bininvy_multi; + double *bininvz_multi; // Stored bin information for each stencil - int **stencil_mbinx_multi2; - int **stencil_mbiny_multi2; - int **stencil_mbinz_multi2; - double **stencil_binsizex_multi2; - double **stencil_binsizey_multi2; - double **stencil_binsizez_multi2; + int **stencil_mbinx_multi; + int **stencil_mbiny_multi; + int **stencil_mbinz_multi; + double **stencil_binsizex_multi; + double **stencil_binsizey_multi; + double **stencil_binsizez_multi; // 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 maxstencil_multi_old; // max sizes of stencils int dimension; @@ -113,8 +109,8 @@ class NStencil : protected Pointers { // methods for multi2 NStencil - double bin_distance_multi2(int, int, int, int); // distance between bin corners for different types - void copy_bin_info_multi2(); // copy mult2 info from NBin class + double bin_distance_multi(int, int, int, int); // distance between bin corners for different types + void copy_bin_info_multi(); // copy multi info from NBin class virtual void set_stencil_properties(){} // determine which stencils to build and how }; diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_old_2d.cpp similarity index 83% rename from src/nstencil_full_multi_2d.cpp rename to src/nstencil_full_multi_old_2d.cpp index b71ca5e55d..ec2dba322e 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_old_2d.cpp @@ -11,20 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_full_multi_2d.h" +#include "nstencil_full_multi_old_2d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilFullMulti2d::NStencilFullMulti2d(LAMMPS *lmp) : NStencil(lmp) {} +NStencilFullMultiOld2d::NStencilFullMultiOld2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilFullMulti2d::create() +void NStencilFullMultiOld2d::create() { int i,j,n; double rsq,typesq; @@ -34,8 +34,8 @@ void NStencilFullMulti2d::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) { @@ -45,6 +45,6 @@ void NStencilFullMulti2d::create() s[n++] = j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_full_multi_old_2d.h b/src/nstencil_full_multi_old_2d.h new file mode 100644 index 0000000000..d75df8bce7 --- /dev/null +++ b/src/nstencil_full_multi_old_2d.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(full/multi/old/2d, + NStencilFullMultiOld2d, + NS_FULL | NS_MULTI_OLD | NS_2D | NS_ORTHO | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_FULL_MULTI_OLD_2D_H +#define LMP_NSTENCIL_FULL_MULTI_OLD_2D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilFullMultiOld2d : public NStencil { + public: + NStencilFullMultiOld2d(class LAMMPS *); + ~NStencilFullMultiOld2d() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_old_3d.cpp similarity index 84% rename from src/nstencil_full_multi_3d.cpp rename to src/nstencil_full_multi_old_3d.cpp index 2c63476ae6..2bfd962261 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_old_3d.cpp @@ -11,20 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_full_multi_3d.h" +#include "nstencil_full_multi_old_3d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilFullMulti3d::NStencilFullMulti3d(LAMMPS *lmp) : NStencil(lmp) {} +NStencilFullMultiOld3d::NStencilFullMultiOld3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilFullMulti3d::create() +void NStencilFullMultiOld3d::create() { int i,j,k,n; double rsq,typesq; @@ -34,8 +34,8 @@ void NStencilFullMulti3d::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) @@ -46,6 +46,6 @@ void NStencilFullMulti3d::create() s[n++] = k*mbiny*mbinx + j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_full_multi_old_3d.h b/src/nstencil_full_multi_old_3d.h new file mode 100644 index 0000000000..bcc6f551a0 --- /dev/null +++ b/src/nstencil_full_multi_old_3d.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(full/multi/old/3d, + NStencilFullMultiOld3d, + NS_FULL | NS_MULTI_OLD | NS_3D | NS_ORTHO | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_FULL_MULTI_OLD_3D_H +#define LMP_NSTENCIL_FULL_MULTI_OLD_3D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilFullMultiOld3d : public NStencil { + public: + NStencilFullMultiOld3d(class LAMMPS *); + ~NStencilFullMultiOld3d() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi_3d.h b/src/nstencil_half_multi_3d.h deleted file mode 100644 index 51cf9d5c29..0000000000 --- a/src/nstencil_half_multi_3d.h +++ /dev/null @@ -1,42 +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. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi/3d, - NStencilHalfMulti3d, NS_HALF | NS_MULTI | NS_3D | NS_ORTHO) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI_3D_H -#define LMP_NSTENCIL_HALF_MULTI_3D_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti3d : public NStencil { - public: - NStencilHalfMulti3d(class LAMMPS *); - ~NStencilHalfMulti3d() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi_3d_tri.h b/src/nstencil_half_multi_3d_tri.h deleted file mode 100644 index f33f65cfea..0000000000 --- a/src/nstencil_half_multi_3d_tri.h +++ /dev/null @@ -1,42 +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. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi/3d/tri, - NStencilHalfMulti3dTri, NS_HALF | NS_MULTI | NS_3D | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI_3D_TRI_H -#define LMP_NSTENCIL_HALF_MULTI_3D_TRI_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti3dTri : public NStencil { - public: - NStencilHalfMulti3dTri(class LAMMPS *); - ~NStencilHalfMulti3dTri() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_old_2d.cpp similarity index 84% rename from src/nstencil_half_multi_2d.cpp rename to src/nstencil_half_multi_old_2d.cpp index 6642c2decd..18efc14703 100644 --- a/src/nstencil_half_multi_2d.cpp +++ b/src/nstencil_half_multi_old_2d.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_2d.h" +#include "nstencil_half_multi_old_2d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti2d:: -NStencilHalfMulti2d(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMultiOld2d:: +NStencilHalfMultiOld2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti2d::create() +void NStencilHalfMultiOld2d::create() { int i,j,n; double rsq,typesq; @@ -35,8 +35,8 @@ void NStencilHalfMulti2d::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) @@ -47,6 +47,6 @@ void NStencilHalfMulti2d::create() s[n++] = j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_half_multi_2d_tri.h b/src/nstencil_half_multi_old_2d.h similarity index 71% rename from src/nstencil_half_multi_2d_tri.h rename to src/nstencil_half_multi_old_2d.h index 776c42e96b..ef9e127978 100644 --- a/src/nstencil_half_multi_2d_tri.h +++ b/src/nstencil_half_multi_old_2d.h @@ -13,22 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi/2d/tri, - NStencilHalfMulti2dTri, NS_HALF | NS_MULTI | NS_2D | NS_TRI) +NStencilStyle(half/multi/old/2d, + NStencilHalfMultiOld2d, NS_HALF | NS_MULTI_OLD | NS_2D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_MULTI_2D_TRI_H -#define LMP_NSTENCIL_HALF_MULTI_2D_TRI_H +#ifndef LMP_NSTENCIL_HALF_MULTI_OLD_2D_H +#define LMP_NSTENCIL_HALF_MULTI_OLD_2D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti2dTri : public NStencil { +class NStencilHalfMultiOld2d : public NStencil { public: - NStencilHalfMulti2dTri(class LAMMPS *); - ~NStencilHalfMulti2dTri() {} + NStencilHalfMultiOld2d(class LAMMPS *); + ~NStencilHalfMultiOld2d() {} void create(); }; diff --git a/src/nstencil_half_multi_2d_tri.cpp b/src/nstencil_half_multi_old_2d_tri.cpp similarity index 82% rename from src/nstencil_half_multi_2d_tri.cpp rename to src/nstencil_half_multi_old_2d_tri.cpp index f9ed49404c..24056c2ada 100644 --- a/src/nstencil_half_multi_2d_tri.cpp +++ b/src/nstencil_half_multi_old_2d_tri.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_2d_tri.h" +#include "nstencil_half_multi_old_2d_tri.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti2dTri:: -NStencilHalfMulti2dTri(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMultiOld2dTri:: +NStencilHalfMultiOld2dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti2dTri::create() +void NStencilHalfMultiOld2dTri::create() { int i,j,n; double rsq,typesq; @@ -35,8 +35,8 @@ void NStencilHalfMulti2dTri::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) { @@ -46,6 +46,6 @@ void NStencilHalfMulti2dTri::create() s[n++] = j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_half_multi_2d.h b/src/nstencil_half_multi_old_2d_tri.h similarity index 69% rename from src/nstencil_half_multi_2d.h rename to src/nstencil_half_multi_old_2d_tri.h index 128d37a2e9..0c79ae8c96 100644 --- a/src/nstencil_half_multi_2d.h +++ b/src/nstencil_half_multi_old_2d_tri.h @@ -13,22 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi/2d, - NStencilHalfMulti2d, NS_HALF | NS_MULTI | NS_2D | NS_ORTHO) +NStencilStyle(half/multi/old/2d/tri, + NStencilHalfMultiOld2dTri, NS_HALF | NS_MULTI_OLD | NS_2D | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_MULTI_2D_H -#define LMP_NSTENCIL_HALF_MULTI_2D_H +#ifndef LMP_NSTENCIL_HALF_MULTI_OLD_2D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_OLD_2D_TRI_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti2d : public NStencil { +class NStencilHalfMultiOld2dTri : public NStencil { public: - NStencilHalfMulti2d(class LAMMPS *); - ~NStencilHalfMulti2d() {} + NStencilHalfMultiOld2dTri(class LAMMPS *); + ~NStencilHalfMultiOld2dTri() {} void create(); }; diff --git a/src/nstencil_half_multi_3d.cpp b/src/nstencil_half_multi_old_3d.cpp similarity index 84% rename from src/nstencil_half_multi_3d.cpp rename to src/nstencil_half_multi_old_3d.cpp index 119398f960..ebdd09674d 100644 --- a/src/nstencil_half_multi_3d.cpp +++ b/src/nstencil_half_multi_old_3d.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_3d.h" +#include "nstencil_half_multi_old_3d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti3d:: -NStencilHalfMulti3d(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMultiOld3d:: +NStencilHalfMultiOld3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti3d::create() +void NStencilHalfMultiOld3d::create() { int i,j,k,n; double rsq,typesq; @@ -35,8 +35,8 @@ void NStencilHalfMulti3d::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) @@ -48,6 +48,6 @@ void NStencilHalfMulti3d::create() s[n++] = k*mbiny*mbinx + j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_full_multi_2d.h b/src/nstencil_half_multi_old_3d.h similarity index 71% rename from src/nstencil_full_multi_2d.h rename to src/nstencil_half_multi_old_3d.h index 2c28bb56bf..b37134b4cc 100644 --- a/src/nstencil_full_multi_2d.h +++ b/src/nstencil_half_multi_old_3d.h @@ -13,23 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(full/multi/2d, - NStencilFullMulti2d, - NS_FULL | NS_MULTI | NS_2D | NS_ORTHO | NS_TRI) +NStencilStyle(half/multi_old/3d, + NStencilHalfMultiOld3d, NS_HALF | NS_MULTI_OLD | NS_3D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_FULL_MULTI_2D_H -#define LMP_NSTENCIL_FULL_MULTI_2D_H +#ifndef LMP_NSTENCIL_HALF_MULTI_OLD_3D_H +#define LMP_NSTENCIL_HALF_MULTI_OLD_3D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilFullMulti2d : public NStencil { +class NStencilHalfMultiOld3d : public NStencil { public: - NStencilFullMulti2d(class LAMMPS *); - ~NStencilFullMulti2d() {} + NStencilHalfMultiOld3d(class LAMMPS *); + ~NStencilHalfMultiOld3d() {} void create(); }; diff --git a/src/nstencil_half_multi_3d_tri.cpp b/src/nstencil_half_multi_old_3d_tri.cpp similarity index 83% rename from src/nstencil_half_multi_3d_tri.cpp rename to src/nstencil_half_multi_old_3d_tri.cpp index ca31a5a073..27dd320c6b 100644 --- a/src/nstencil_half_multi_3d_tri.cpp +++ b/src/nstencil_half_multi_old_3d_tri.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_3d_tri.h" +#include "nstencil_half_multi_old_3d_tri.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti3dTri:: -NStencilHalfMulti3dTri(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMultiOld3dTri:: +NStencilHalfMultiOld3dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti3dTri::create() +void NStencilHalfMultiOld3dTri::create() { int i,j,k,n; double rsq,typesq; @@ -35,8 +35,8 @@ void NStencilHalfMulti3dTri::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) @@ -47,6 +47,6 @@ void NStencilHalfMulti3dTri::create() s[n++] = k*mbiny*mbinx + j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_full_multi_3d.h b/src/nstencil_half_multi_old_3d_tri.h similarity index 69% rename from src/nstencil_full_multi_3d.h rename to src/nstencil_half_multi_old_3d_tri.h index b2edfd8b0d..cbc98a8ba8 100644 --- a/src/nstencil_full_multi_3d.h +++ b/src/nstencil_half_multi_old_3d_tri.h @@ -13,23 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(full/multi/3d, - NStencilFullMulti3d, - NS_FULL | NS_MULTI | NS_3D | NS_ORTHO | NS_TRI) +NStencilStyle(half/multi/old/3d/tri, + NStencilHalfMultiOld3dTri, NS_HALF | NS_MULTI_OLD | NS_3D | NS_TRI) #else -#ifndef LMP_NSTENCIL_FULL_MULTI_3D_H -#define LMP_NSTENCIL_FULL_MULTI_3D_H +#ifndef LMP_NSTENCIL_HALF_MULTI_OLD_3D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_OLD_3D_TRI_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilFullMulti3d : public NStencil { +class NStencilHalfMultiOld3dTri : public NStencil { public: - NStencilFullMulti3d(class LAMMPS *); - ~NStencilFullMulti3d() {} + NStencilHalfMultiOld3dTri(class LAMMPS *); + ~NStencilHalfMultiOld3dTri() {} void create(); }; From 5d097845e78e801dd819670c8fd9af4a06eb529a Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 17:45:46 -0700 Subject: [PATCH 36/73] Renaming multi2->multi in nstencil --- src/nstencil.h | 4 +- ...lti2_2d.cpp => nstencil_full_multi_2d.cpp} | 22 ++++----- ...l_multi2_3d.h => nstencil_full_multi_2d.h} | 14 +++--- ...lti2_3d.cpp => nstencil_full_multi_3d.cpp} | 26 +++++------ ...f_multi2_2d.h => nstencil_full_multi_3d.h} | 14 +++--- src/nstencil_half_multi2_2d_tri.h | 45 ------------------- src/nstencil_half_multi2_3d_tri.h | 45 ------------------- ...lti2_2d.cpp => nstencil_half_multi_2d.cpp} | 26 +++++------ ...f_multi2_3d.h => nstencil_half_multi_2d.h} | 14 +++--- ...tri.cpp => nstencil_half_multi_2d_tri.cpp} | 26 +++++------ src/nstencil_half_multi_2d_tri.h | 45 +++++++++++++++++++ ...lti2_3d.cpp => nstencil_half_multi_3d.cpp} | 30 ++++++------- ...l_multi2_2d.h => nstencil_half_multi_3d.h} | 14 +++--- ...tri.cpp => nstencil_half_multi_3d_tri.cpp} | 30 ++++++------- src/nstencil_half_multi_3d_tri.h | 45 +++++++++++++++++++ 15 files changed, 200 insertions(+), 200 deletions(-) rename src/{nstencil_full_multi2_2d.cpp => nstencil_full_multi_2d.cpp} (77%) rename src/{nstencil_full_multi2_3d.h => nstencil_full_multi_2d.h} (73%) rename src/{nstencil_full_multi2_3d.cpp => nstencil_full_multi_3d.cpp} (75%) rename src/{nstencil_half_multi2_2d.h => nstencil_full_multi_3d.h} (73%) delete mode 100755 src/nstencil_half_multi2_2d_tri.h delete mode 100755 src/nstencil_half_multi2_3d_tri.h rename src/{nstencil_half_multi2_2d.cpp => nstencil_half_multi_2d.cpp} (78%) rename src/{nstencil_half_multi2_3d.h => nstencil_half_multi_2d.h} (73%) rename src/{nstencil_half_multi2_2d_tri.cpp => nstencil_half_multi_2d_tri.cpp} (78%) create mode 100755 src/nstencil_half_multi_2d_tri.h rename src/{nstencil_half_multi2_3d.cpp => nstencil_half_multi_3d.cpp} (78%) rename src/{nstencil_full_multi2_2d.h => nstencil_half_multi_3d.h} (73%) rename src/{nstencil_half_multi2_3d_tri.cpp => nstencil_half_multi_3d_tri.cpp} (77%) create mode 100755 src/nstencil_half_multi_3d_tri.h diff --git a/src/nstencil.h b/src/nstencil.h index 28c7fb0ec2..5bff8cbfac 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -41,7 +41,7 @@ class NStencil : protected Pointers { double cutoff_custom; // cutoff set by requestor - // Arrays to store options for multi2 itype-jtype stencils + // Arrays to store options for multi itype-jtype stencils bool **stencil_half; // flag creation of a half stencil for itype-jtype bool **stencil_skip; // skip creation of itype-jtype stencils (for newton on) int **stencil_bin_type; // what type to use for bin information @@ -107,7 +107,7 @@ class NStencil : protected Pointers { void copy_bin_info(); // copy info from NBin class double bin_distance(int, int, int); // distance between bin corners - // methods for multi2 NStencil + // methods for multi NStencil double bin_distance_multi(int, int, int, int); // distance between bin corners for different types void copy_bin_info_multi(); // copy multi info from NBin class diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi_2d.cpp similarity index 77% rename from src/nstencil_full_multi2_2d.cpp rename to src/nstencil_full_multi_2d.cpp index 658dba1c28..9712db7ac8 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_full_multi2_2d.h" +#include "nstencil_full_multi_2d.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,11 +23,11 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilFullMulti22d::NStencilFullMulti22d(LAMMPS *lmp) : NStencil(lmp) {} +NStencilFullMulti2d::NStencilFullMulti2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilFullMulti22d::set_stencil_properties() +void NStencilFullMulti2d::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -47,7 +47,7 @@ void NStencilFullMulti22d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilFullMulti22d::create() +void NStencilFullMulti2d::create() { int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; @@ -60,11 +60,11 @@ void NStencilFullMulti22d::create() ns = 0; - sx = stencil_sx_multi2[itype][jtype]; - sy = stencil_sy_multi2[itype][jtype]; + sx = stencil_sx_multi[itype][jtype]; + sy = stencil_sy_multi[itype][jtype]; - mbinx = stencil_mbinx_multi2[itype][jtype]; - mbiny = stencil_mbiny_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi[itype][jtype]; + mbiny = stencil_mbiny_multi[itype][jtype]; bin_type = stencil_bin_type[itype][jtype]; @@ -72,10 +72,10 @@ void NStencilFullMulti22d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,0,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = j*mbinx + i; - nstencil_multi2[itype][jtype] = ns; + nstencil_multi[itype][jtype] = ns; } } } diff --git a/src/nstencil_full_multi2_3d.h b/src/nstencil_full_multi_2d.h similarity index 73% rename from src/nstencil_full_multi2_3d.h rename to src/nstencil_full_multi_2d.h index fb6a19ec6f..9990716b3a 100644 --- a/src/nstencil_full_multi2_3d.h +++ b/src/nstencil_full_multi_2d.h @@ -13,22 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(full/multi2/3d, - NStencilFullMulti23d, NS_FULL | NS_MULTI2 | NS_3D | NS_ORTHO | NS_TRI) +NStencilStyle(full/multi/2d, + NStencilFullMulti2d, NS_FULL | NS_MULTI | NS_2D | NS_ORTHO | NS_TRI) #else -#ifndef LMP_NSTENCIL_FULL_MULTI2_3D_H -#define LMP_NSTENCIL_FULL_MULTI2_3D_H +#ifndef LMP_NSTENCIL_FULL_MULTI_2D_H +#define LMP_NSTENCIL_FULL_MULTI_2D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilFullMulti23d : public NStencil { +class NStencilFullMulti2d : public NStencil { public: - NStencilFullMulti23d(class LAMMPS *); - ~NStencilFullMulti23d(){} + NStencilFullMulti2d(class LAMMPS *); + ~NStencilFullMulti2d() {} void create(); protected: diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi_3d.cpp similarity index 75% rename from src/nstencil_full_multi2_3d.cpp rename to src/nstencil_full_multi_3d.cpp index 7bbe5208f2..b3f8db53b7 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_full_multi2_3d.h" +#include "nstencil_full_multi_3d.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,11 +23,11 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilFullMulti23d::NStencilFullMulti23d(LAMMPS *lmp) : NStencil(lmp) {} +NStencilFullMulti3d::NStencilFullMulti3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilFullMulti23d::set_stencil_properties() +void NStencilFullMulti3d::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -48,7 +48,7 @@ void NStencilFullMulti23d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilFullMulti23d::create() +void NStencilFullMulti3d::create() { int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; @@ -61,13 +61,13 @@ void NStencilFullMulti23d::create() ns = 0; - sx = stencil_sx_multi2[itype][jtype]; - sy = stencil_sy_multi2[itype][jtype]; - sz = stencil_sz_multi2[itype][jtype]; + sx = stencil_sx_multi[itype][jtype]; + sy = stencil_sy_multi[itype][jtype]; + sz = stencil_sz_multi[itype][jtype]; - mbinx = stencil_mbinx_multi2[itype][jtype]; - mbiny = stencil_mbiny_multi2[itype][jtype]; - mbinz = stencil_mbinz_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi[itype][jtype]; + mbiny = stencil_mbiny_multi[itype][jtype]; + mbinz = stencil_mbinz_multi[itype][jtype]; bin_type = stencil_bin_type[itype][jtype]; @@ -76,11 +76,11 @@ void NStencilFullMulti23d::create() for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,k,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - nstencil_multi2[itype][jtype] = ns; + nstencil_multi[itype][jtype] = ns; } } } diff --git a/src/nstencil_half_multi2_2d.h b/src/nstencil_full_multi_3d.h similarity index 73% rename from src/nstencil_half_multi2_2d.h rename to src/nstencil_full_multi_3d.h index 8e79fd0541..ed3401b2bd 100644 --- a/src/nstencil_half_multi2_2d.h +++ b/src/nstencil_full_multi_3d.h @@ -13,22 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi2/2d, - NStencilHalfMulti22d, NS_HALF | NS_MULTI2 | NS_2D | NS_ORTHO) +NStencilStyle(full/multi/3d, + NStencilFullMulti3d, NS_FULL | NS_MULTI | NS_3D | NS_ORTHO | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_MULTI2_2D_H -#define LMP_NSTENCIL_HALF_MULTI2_2D_H +#ifndef LMP_NSTENCIL_FULL_MULTI_3D_H +#define LMP_NSTENCIL_FULL_MULTI_3D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti22d : public NStencil { +class NStencilFullMulti3d : public NStencil { public: - NStencilHalfMulti22d(class LAMMPS *); - ~NStencilHalfMulti22d() {} + NStencilFullMulti3d(class LAMMPS *); + ~NStencilFullMulti3d(){} void create(); protected: diff --git a/src/nstencil_half_multi2_2d_tri.h b/src/nstencil_half_multi2_2d_tri.h deleted file mode 100755 index 4072c6d31b..0000000000 --- a/src/nstencil_half_multi2_2d_tri.h +++ /dev/null @@ -1,45 +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. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi2/2d/tri, - NStencilHalfMulti22dTri, NS_HALF | NS_MULTI2 | NS_2D | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI2_2D_TRI_H -#define LMP_NSTENCIL_HALF_MULTI2_2D_TRI_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti22dTri : public NStencil { - public: - NStencilHalfMulti22dTri(class LAMMPS *); - ~NStencilHalfMulti22dTri() {} - void create(); - - protected: - void set_stencil_properties(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi2_3d_tri.h b/src/nstencil_half_multi2_3d_tri.h deleted file mode 100755 index de449ce1d8..0000000000 --- a/src/nstencil_half_multi2_3d_tri.h +++ /dev/null @@ -1,45 +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. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi2/3d/tri, - NStencilHalfMulti23dTri, NS_HALF | NS_MULTI2 | NS_3D | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI2_3D_TRI_H -#define LMP_NSTENCIL_HALF_MULTI2_3D_TRI_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti23dTri : public NStencil { - public: - NStencilHalfMulti23dTri(class LAMMPS *); - ~NStencilHalfMulti23dTri() {} - void create(); - - protected: - void set_stencil_properties(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi_2d.cpp similarity index 78% rename from src/nstencil_half_multi2_2d.cpp rename to src/nstencil_half_multi_2d.cpp index f240d87b54..0b320394b7 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi2_2d.h" +#include "nstencil_half_multi_2d.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti22d::NStencilHalfMulti22d(LAMMPS *lmp) : +NStencilHalfMulti2d::NStencilHalfMulti2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti22d::set_stencil_properties() +void NStencilHalfMulti2d::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -59,7 +59,7 @@ void NStencilHalfMulti22d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti22d::create() +void NStencilHalfMulti2d::create() { int itype, jtype, bin_type, i, j, ns; int n = atom->ntypes; @@ -72,11 +72,11 @@ void NStencilHalfMulti22d::create() ns = 0; - sx = stencil_sx_multi2[itype][jtype]; - sy = stencil_sy_multi2[itype][jtype]; + sx = stencil_sx_multi[itype][jtype]; + sy = stencil_sy_multi[itype][jtype]; - mbinx = stencil_mbinx_multi2[itype][jtype]; - mbiny = stencil_mbiny_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi[itype][jtype]; + mbiny = stencil_mbiny_multi[itype][jtype]; bin_type = stencil_bin_type[itype][jtype]; @@ -86,17 +86,17 @@ void NStencilHalfMulti22d::create() for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) if (j > 0 || (j == 0 && i > 0)) { - if (bin_distance_multi2(i,j,0,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = j*mbinx + i; } } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,0,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = j*mbinx + i; } - nstencil_multi2[itype][jtype] = ns; + nstencil_multi[itype][jtype] = ns; } } } diff --git a/src/nstencil_half_multi2_3d.h b/src/nstencil_half_multi_2d.h similarity index 73% rename from src/nstencil_half_multi2_3d.h rename to src/nstencil_half_multi_2d.h index 6a0d8f90a2..2c18bb7b07 100644 --- a/src/nstencil_half_multi2_3d.h +++ b/src/nstencil_half_multi_2d.h @@ -13,22 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi2/3d, - NStencilHalfMulti23d, NS_HALF | NS_MULTI2 | NS_3D | NS_ORTHO) +NStencilStyle(half/multi/2d, + NStencilHalfMulti2d, NS_HALF | NS_MULTI | NS_2D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_MULTI2_3D_H -#define LMP_NSTENCIL_HALF_MULTI2_3D_H +#ifndef LMP_NSTENCIL_HALF_MULTI_2D_H +#define LMP_NSTENCIL_HALF_MULTI_2D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti23d : public NStencil { +class NStencilHalfMulti2d : public NStencil { public: - NStencilHalfMulti23d(class LAMMPS *); - ~NStencilHalfMulti23d() {} + NStencilHalfMulti2d(class LAMMPS *); + ~NStencilHalfMulti2d() {} void create(); protected: diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp similarity index 78% rename from src/nstencil_half_multi2_2d_tri.cpp rename to src/nstencil_half_multi_2d_tri.cpp index 7143378305..95b0b483c5 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi2_2d_tri.h" +#include "nstencil_half_multi_2d_tri.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti22dTri::NStencilHalfMulti22dTri(LAMMPS *lmp) : +NStencilHalfMulti2dTri::NStencilHalfMulti2dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti22dTri::set_stencil_properties() +void NStencilHalfMulti2dTri::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -59,7 +59,7 @@ void NStencilHalfMulti22dTri::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti22dTri::create() +void NStencilHalfMulti2dTri::create() { int itype, jtype, bin_type, i, j, ns; int n = atom->ntypes; @@ -72,11 +72,11 @@ void NStencilHalfMulti22dTri::create() ns = 0; - sx = stencil_sx_multi2[itype][jtype]; - sy = stencil_sy_multi2[itype][jtype]; + sx = stencil_sx_multi[itype][jtype]; + sy = stencil_sy_multi[itype][jtype]; - mbinx = stencil_mbinx_multi2[itype][jtype]; - mbiny = stencil_mbiny_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi[itype][jtype]; + mbiny = stencil_mbiny_multi[itype][jtype]; bin_type = stencil_bin_type[itype][jtype]; @@ -85,16 +85,16 @@ void NStencilHalfMulti22dTri::create() if (stencil_half[itype][jtype]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,0,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = j*mbinx + i; } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,0,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = j*mbinx + i; } - nstencil_multi2[itype][jtype] = ns; + nstencil_multi[itype][jtype] = ns; } } } diff --git a/src/nstencil_half_multi_2d_tri.h b/src/nstencil_half_multi_2d_tri.h new file mode 100755 index 0000000000..3cd49caa9d --- /dev/null +++ b/src/nstencil_half_multi_2d_tri.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 NSTENCIL_CLASS + +NStencilStyle(half/multi/2d/tri, + NStencilHalfMulti2dTri, NS_HALF | NS_MULTI | NS_2D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_2D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_2D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti2dTri : public NStencil { + public: + NStencilHalfMulti2dTri(class LAMMPS *); + ~NStencilHalfMulti2dTri() {} + void create(); + + protected: + void set_stencil_properties(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi_3d.cpp similarity index 78% rename from src/nstencil_half_multi2_3d.cpp rename to src/nstencil_half_multi_3d.cpp index 83ecb24cba..1f94fb16cd 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi_3d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi2_3d.h" +#include "nstencil_half_multi_3d.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti23d::NStencilHalfMulti23d(LAMMPS *lmp) : +NStencilHalfMulti3d::NStencilHalfMulti3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti23d::set_stencil_properties() +void NStencilHalfMulti3d::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -59,7 +59,7 @@ void NStencilHalfMulti23d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti23d::create() +void NStencilHalfMulti3d::create() { int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; @@ -72,13 +72,13 @@ void NStencilHalfMulti23d::create() ns = 0; - sx = stencil_sx_multi2[itype][jtype]; - sy = stencil_sy_multi2[itype][jtype]; - sz = stencil_sz_multi2[itype][jtype]; + sx = stencil_sx_multi[itype][jtype]; + sy = stencil_sy_multi[itype][jtype]; + sz = stencil_sz_multi[itype][jtype]; - mbinx = stencil_mbinx_multi2[itype][jtype]; - mbiny = stencil_mbiny_multi2[itype][jtype]; - mbinz = stencil_mbinz_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi[itype][jtype]; + mbiny = stencil_mbiny_multi[itype][jtype]; + mbinz = stencil_mbinz_multi[itype][jtype]; bin_type = stencil_bin_type[itype][jtype]; @@ -89,20 +89,20 @@ void NStencilHalfMulti23d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (k > 0 || j > 0 || (j == 0 && i > 0)) { - if (bin_distance_multi2(i,j,k,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,k,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } - nstencil_multi2[itype][jtype] = ns; + nstencil_multi[itype][jtype] = ns; } } } diff --git a/src/nstencil_full_multi2_2d.h b/src/nstencil_half_multi_3d.h similarity index 73% rename from src/nstencil_full_multi2_2d.h rename to src/nstencil_half_multi_3d.h index 46e12db039..a020192243 100644 --- a/src/nstencil_full_multi2_2d.h +++ b/src/nstencil_half_multi_3d.h @@ -13,22 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(full/multi2/2d, - NStencilFullMulti22d, NS_FULL | NS_MULTI2 | NS_2D | NS_ORTHO | NS_TRI) +NStencilStyle(half/multi/3d, + NStencilHalfMulti3d, NS_HALF | NS_MULTI | NS_3D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_FULL_MULTI2_2D_H -#define LMP_NSTENCIL_FULL_MULTI2_2D_H +#ifndef LMP_NSTENCIL_HALF_MULTI_3D_H +#define LMP_NSTENCIL_HALF_MULTI_3D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilFullMulti22d : public NStencil { +class NStencilHalfMulti3d : public NStencil { public: - NStencilFullMulti22d(class LAMMPS *); - ~NStencilFullMulti22d() {} + NStencilHalfMulti3d(class LAMMPS *); + ~NStencilHalfMulti3d() {} void create(); protected: diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp similarity index 77% rename from src/nstencil_half_multi2_3d_tri.cpp rename to src/nstencil_half_multi_3d_tri.cpp index 33915d4741..30e59e92e8 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi2_3d_tri.h" +#include "nstencil_half_multi_3d_tri.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti23dTri::NStencilHalfMulti23dTri(LAMMPS *lmp) : +NStencilHalfMulti3dTri::NStencilHalfMulti3dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti23dTri::set_stencil_properties() +void NStencilHalfMulti3dTri::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -59,7 +59,7 @@ void NStencilHalfMulti23dTri::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti23dTri::create() +void NStencilHalfMulti3dTri::create() { int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; @@ -72,13 +72,13 @@ void NStencilHalfMulti23dTri::create() ns = 0; - sx = stencil_sx_multi2[itype][jtype]; - sy = stencil_sy_multi2[itype][jtype]; - sz = stencil_sz_multi2[itype][jtype]; + sx = stencil_sx_multi[itype][jtype]; + sy = stencil_sy_multi[itype][jtype]; + sz = stencil_sz_multi[itype][jtype]; - mbinx = stencil_mbinx_multi2[itype][jtype]; - mbiny = stencil_mbiny_multi2[itype][jtype]; - mbinz = stencil_mbinz_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi[itype][jtype]; + mbiny = stencil_mbiny_multi[itype][jtype]; + mbinz = stencil_mbinz_multi[itype][jtype]; bin_type = stencil_bin_type[itype][jtype]; @@ -88,19 +88,19 @@ void NStencilHalfMulti23dTri::create() for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,k,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,k,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } - nstencil_multi2[itype][jtype] = ns; + nstencil_multi[itype][jtype] = ns; } } } diff --git a/src/nstencil_half_multi_3d_tri.h b/src/nstencil_half_multi_3d_tri.h new file mode 100755 index 0000000000..eb76e6fb2c --- /dev/null +++ b/src/nstencil_half_multi_3d_tri.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 NSTENCIL_CLASS + +NStencilStyle(half/multi/3d/tri, + NStencilHalfMulti3dTri, NS_HALF | NS_MULTI | NS_3D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_3D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_3D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti3dTri : public NStencil { + public: + NStencilHalfMulti3dTri(class LAMMPS *); + ~NStencilHalfMulti3dTri() {} + void create(); + + protected: + void set_stencil_properties(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ From 0a36baf86d87b5aa1ce403e9c417afd6427d9634 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 17:51:09 -0700 Subject: [PATCH 37/73] Updating naming in other classes --- src/comm.cpp | 22 +++++++++++----------- src/comm.h | 2 +- src/comm_brick.cpp | 8 ++++---- src/comm_tiled.cpp | 4 ++-- src/neighbor.cpp | 2 +- 5 files changed, 19 insertions(+), 19 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index f814c804c9..afd4d891ee 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -76,7 +76,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) grid2proc = nullptr; xsplit = ysplit = zsplit = nullptr; rcbnew = 0; - multi2 = 0; + multi_reduce = 0; // use of OpenMP threads // query OpenMP for number of threads/process set by user at run-time @@ -242,15 +242,15 @@ void Comm::init() for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; - // Can't used multi2 communication with Newton off + // Can't used multi_reduce communication with Newton off // TODO: need to somehow restrict this option with full neighbor lists - // CANNOT use multi2 communication with full nlist - // Could remove NP_NEWTON from npair_full_*multi2*, but could be cryptic - // Also could be cases where you want newton off (hybrid) but don't use multi2 comm - // Could add check on neighbor build, if full and comm->multi2 error... + // CANNOT use multi_reduce communication with full nlist + // Could remove NP_NEWTON from npair_full_*multi_reduce*, but could be cryptic + // Also could be cases where you want newton off (hybrid) but don't use multi_reduce comm + // Could add check on neighbor build, if full and comm->multi_reduce error... // or just add check on comm setup - is that run before every run? Only if box change... - if (force->newton == 0 && multi2) - error->all(FLERR,"Cannot use multi2 communication with Newton off"); + if (force->newton == 0 && multi_reduce) + error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); } /* ---------------------------------------------------------------------- @@ -337,10 +337,10 @@ void Comm::modify_params(int narg, char **arg) for (i=nlo; i<=nhi; ++i) cutusermulti[i] = cut; iarg += 3; - } else if (strcmp(arg[iarg],"cutoff/multi2") == 0) { + } else if (strcmp(arg[iarg],"multi/reduce") == 0) { if (mode == Comm::SINGLE) - error->all(FLERR,"Use cutoff/multi2 in mode multi only"); - multi2 = 1; + error->all(FLERR,"Use multi/reduce in mode multi only"); + multi_reduce = 1; iarg += 1; } else if (strcmp(arg[iarg],"vel") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command"); diff --git a/src/comm.h b/src/comm.h index 5cd47bd5cd..4ae4faf7fd 100644 --- a/src/comm.h +++ b/src/comm.h @@ -152,7 +152,7 @@ class Comm : protected Pointers { int ncores; // # of cores per node int coregrid[3]; // 3d grid of cores within a node int user_coregrid[3]; // user request for cores in each dim - int multi2; // 1 if multi cutoff is intra-type cutoff + int multi_reduce; // 1 if multi cutoff is intra-type cutoff void init_exchange(); int rendezvous_irregular(int, char *, int, int, int *, diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index b22c254e3a..7f84d619e4 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -174,8 +174,8 @@ void CommBrick::setup() cutghost[0] = cutghost[1] = cutghost[2] = cut; if (mode == Comm::MULTI) { - if (multi2) { - // If using multi2 binlists, communicate itype particles a distance + if (multi_reduce) { + // If using multi/reduce binlists, communicate itype particles a distance // equal to the max of itype-jtype interaction given smaller jtype particles double **cutneighsq = neighbor->cutneighsq; double *cuttypesq = neighbor->cuttypesq; @@ -225,8 +225,8 @@ void CommBrick::setup() cutghost[2] = cut * length2; if (mode == Comm::MULTI) { - if (multi2) { - // If using multi2 binlists, communicate itype particles a distance + if (multi_reduce) { + // If using multi/reduce binlists, communicate itype particles a distance // equal to the max of itype-jtype interaction given smaller jtype particles double **cutneighsq = neighbor->cutneighsq; double *cuttypesq = neighbor->cuttypesq; diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 4ff4774cd7..ce76fa7442 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -176,8 +176,8 @@ void CommTiled::setup() if (mode == Comm::MULTI) { double cut; - if (multi2) { - // If using multi2 binlists, communicate itype particles a distance + if (multi_reduce) { + // If using multi/reduce binlists, communicate itype particles a distance // equal to the max of itype-jtype interaction given smaller jtype particles double **cutneighsq = neighbor->cutneighsq; double *cuttypesq = neighbor->cuttypesq; diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 0854dee227..fe34e738b0 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1640,7 +1640,7 @@ int Neighbor::choose_bin(NeighRequest *rq) if (!rq->kokkos_device != !(mask & NB_KOKKOS_DEVICE)) continue; if (!rq->kokkos_host != !(mask & NB_KOKKOS_HOST)) continue; - // neighbor style is BIN or MULTI or MULTI2 and must match + // neighbor style is BIN or MULTI or MULTI_OLD and must match if (style == Neighbor::BIN || style == Neighbor::MULTI_OLD) { if (!(mask & NB_STANDARD)) continue; From fee6df1ab69ec546566d941e5cee2a263f2edf2d Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 18:07:10 -0700 Subject: [PATCH 38/73] Fixing typos --- src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp | 4 ++-- src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp | 4 ++-- src/npair_half_size_multi_old_newton.h | 2 +- src/npair_half_size_multi_old_newton_tri.cpp | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp index 3ed703586d..204f811ca2 100644 --- a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtoffOldOmp::NPairHalfSizeMultiNewtoffOldOmp(LAMMPS *lmp) : +NPairHalfSizeMultiOldNewtoffOmp::NPairHalfSizeMultiOldNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- @@ -36,7 +36,7 @@ NPairHalfSizeMultiNewtoffOldOmp::NPairHalfSizeMultiNewtoffOldOmp(LAMMPS *lmp) : pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtoffOldOmp::build(NeighList *list) +void NPairHalfSizeMultiOldNewtoffOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp index 37203c53db..6248004ce6 100644 --- a/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtonOldOmp::NPairHalfSizeMultiNewtonOldOmp(LAMMPS *lmp) : +NPairHalfSizeMultiOldNewtonOmp::NPairHalfSizeMultiOldNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- @@ -35,7 +35,7 @@ NPairHalfSizeMultiNewtonOldOmp::NPairHalfSizeMultiNewtonOldOmp(LAMMPS *lmp) : every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtonOldOmp::build(NeighList *list) +void NPairHalfSizeMultiOldNewtonOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; diff --git a/src/npair_half_size_multi_old_newton.h b/src/npair_half_size_multi_old_newton.h index e954ee07b1..edd87a72ed 100644 --- a/src/npair_half_size_multi_old_newton.h +++ b/src/npair_half_size_multi_old_newton.h @@ -1,4 +1,4 @@ -g/* -*- c++ -*- ---------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov diff --git a/src/npair_half_size_multi_old_newton_tri.cpp b/src/npair_half_size_multi_old_newton_tri.cpp index 2b63e116d7..f29c323944 100644 --- a/src/npair_half_size_multi_old_newton_tri.cpp +++ b/src/npair_half_size_multi_old_newton_tri.cpp @@ -1,4 +1,4 @@ -re/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov From bce37abe8f18a62e42e3d3ba501d03bc14c158cd Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 20 Dec 2020 15:15:19 -0700 Subject: [PATCH 39/73] Clarifying variable names --- src/nstencil.cpp | 34 +++++++++++++++--------------- src/nstencil.h | 6 +++--- src/nstencil_full_multi_2d.cpp | 10 ++++----- src/nstencil_full_multi_3d.cpp | 10 ++++----- src/nstencil_half_multi_2d.cpp | 16 +++++++------- src/nstencil_half_multi_2d_tri.cpp | 16 +++++++------- src/nstencil_half_multi_3d.cpp | 16 +++++++------- src/nstencil_half_multi_3d_tri.cpp | 16 +++++++------- 8 files changed, 62 insertions(+), 62 deletions(-) diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 42ddbaff30..f6281a1964 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -79,9 +79,9 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) stencil_multi = nullptr; maxstencil_multi = nullptr; - stencil_half = nullptr; - stencil_skip = nullptr; - stencil_bin_type = nullptr; + flag_half_multi = nullptr; + flag_skip_multi = nullptr; + bin_type_multi = nullptr; dimension = domain->dimension; } @@ -111,16 +111,16 @@ NStencil::~NStencil() memory->destroy(nstencil_multi); for (int i = 1; i <= n; i++) { for (int j = 0; j <= n; j++) { - if (! stencil_skip[i][j]) + if (! flag_skip_multi[i][j]) memory->destroy(stencil_multi[i][j]); } delete [] stencil_multi[i]; } delete [] stencil_multi; memory->destroy(maxstencil_multi); - memory->destroy(stencil_half); - memory->destroy(stencil_skip); - memory->destroy(stencil_bin_type); + memory->destroy(flag_half_multi); + memory->destroy(flag_skip_multi); + memory->destroy(bin_type_multi); memory->destroy(stencil_sx_multi); memory->destroy(stencil_sy_multi); @@ -272,12 +272,12 @@ void NStencil::create_setup() if(nb) copy_bin_info_multi(); // Allocate arrays to store stencil information - memory->create(stencil_half, n+1, n+1, - "neighstencil:stencil_half"); - memory->create(stencil_skip, n+1, n+1, - "neighstencil:stencil_skip"); - memory->create(stencil_bin_type, n+1, n+1, - "neighstencil:stencil_bin_type"); + memory->create(flag_half_multi, n+1, n+1, + "neighstencil:flag_half_multi"); + memory->create(flag_skip_multi, n+1, n+1, + "neighstencil:flag_skip_multi"); + memory->create(bin_type_multi, n+1, n+1, + "neighstencil:bin_type_multi"); memory->create(stencil_sx_multi, n+1, n+1, "neighstencil:stencil_sx_multi"); @@ -303,7 +303,7 @@ void NStencil::create_setup() // Skip all stencils by default, initialize smax for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - stencil_skip[i][j] = 1; + flag_skip_multi[i][j] = 1; } } @@ -329,10 +329,10 @@ void NStencil::create_setup() for (j = 1; j <= n; j++) { // Skip creation of unused stencils - if (stencil_skip[i][j]) continue; + if (flag_skip_multi[i][j]) continue; - // Copy bin info for this particular pair of types - bin_type = stencil_bin_type[i][j]; + // Copy bin info for this pair of atom types + bin_type = bin_type_multi[i][j]; stencil_binsizex_multi[i][j] = binsizex_multi[bin_type]; stencil_binsizey_multi[i][j] = binsizey_multi[bin_type]; diff --git a/src/nstencil.h b/src/nstencil.h index 5bff8cbfac..9ca8bab55d 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -42,9 +42,9 @@ class NStencil : protected Pointers { double cutoff_custom; // cutoff set by requestor // Arrays to store options for multi itype-jtype stencils - bool **stencil_half; // flag creation of a half stencil for itype-jtype - bool **stencil_skip; // skip creation of itype-jtype stencils (for newton on) - int **stencil_bin_type; // what type to use for bin information + bool **flag_half_multi; // flag creation of a half stencil for itype-jtype + bool **flag_skip_multi; // skip creation of itype-jtype stencils (for newton on) + int **bin_type_multi; // what type to use for bin information NStencil(class LAMMPS *); virtual ~NStencil(); diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index 9712db7ac8..61557f2d00 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -36,9 +36,9 @@ void NStencilFullMulti2d::set_stencil_properties() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - stencil_half[i][j] = 0; - stencil_skip[i][j] = 0; - stencil_bin_type[i][j] = j; + flag_half_multi[i][j] = 0; + flag_skip_multi[i][j] = 0; + bin_type_multi[i][j] = j; } } } @@ -56,7 +56,7 @@ void NStencilFullMulti2d::create() for (itype = 1; itype <= n; itype++) { for (jtype = 1; jtype <= n; jtype++) { - if (stencil_skip[itype][jtype]) continue; + if (flag_skip_multi[itype][jtype]) continue; ns = 0; @@ -66,7 +66,7 @@ void NStencilFullMulti2d::create() mbinx = stencil_mbinx_multi[itype][jtype]; mbiny = stencil_mbiny_multi[itype][jtype]; - bin_type = stencil_bin_type[itype][jtype]; + bin_type = bin_type_multi[itype][jtype]; cutsq = cutneighsq[itype][jtype]; diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp index b3f8db53b7..f4935b70e0 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -37,9 +37,9 @@ void NStencilFullMulti3d::set_stencil_properties() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - stencil_half[i][j] = 0; - stencil_skip[i][j] = 0; - stencil_bin_type[i][j] = j; + flag_half_multi[i][j] = 0; + flag_skip_multi[i][j] = 0; + bin_type_multi[i][j] = j; } } } @@ -57,7 +57,7 @@ void NStencilFullMulti3d::create() for (itype = 1; itype <= n; itype++) { for (jtype = 1; jtype <= n; jtype++) { - if (stencil_skip[itype][jtype]) continue; + if (flag_skip_multi[itype][jtype]) continue; ns = 0; @@ -69,7 +69,7 @@ void NStencilFullMulti3d::create() mbiny = stencil_mbiny_multi[itype][jtype]; mbinz = stencil_mbinz_multi[itype][jtype]; - bin_type = stencil_bin_type[itype][jtype]; + bin_type = bin_type_multi[itype][jtype]; cutsq = cutneighsq[itype][jtype]; diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_2d.cpp index 0b320394b7..b407746602 100644 --- a/src/nstencil_half_multi_2d.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -42,14 +42,14 @@ void NStencilHalfMulti2d::set_stencil_properties() for (j = 1; j <= n; j++) { if(cutneighsq[i][i] > cutneighsq[j][j]) continue; - stencil_skip[i][j] = 0; + flag_skip_multi[i][j] = 0; if(cutneighsq[i][i] == cutneighsq[j][j]){ - stencil_half[i][j] = 1; - stencil_bin_type[i][j] = i; + flag_half_multi[i][j] = 1; + bin_type_multi[i][j] = i; } else { - stencil_half[i][j] = 0; - stencil_bin_type[i][j] = j; + flag_half_multi[i][j] = 0; + bin_type_multi[i][j] = j; } } } @@ -68,7 +68,7 @@ void NStencilHalfMulti2d::create() for (itype = 1; itype <= n; itype++) { for (jtype = 1; jtype <= n; jtype++) { - if (stencil_skip[itype][jtype]) continue; + if (flag_skip_multi[itype][jtype]) continue; ns = 0; @@ -78,11 +78,11 @@ void NStencilHalfMulti2d::create() mbinx = stencil_mbinx_multi[itype][jtype]; mbiny = stencil_mbiny_multi[itype][jtype]; - bin_type = stencil_bin_type[itype][jtype]; + bin_type = bin_type_multi[itype][jtype]; cutsq = cutneighsq[itype][jtype]; - if (stencil_half[itype][jtype]) { + if (flag_half_multi[itype][jtype]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) if (j > 0 || (j == 0 && i > 0)) { diff --git a/src/nstencil_half_multi_2d_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp index 95b0b483c5..cd9f85da60 100755 --- a/src/nstencil_half_multi_2d_tri.cpp +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -42,14 +42,14 @@ void NStencilHalfMulti2dTri::set_stencil_properties() for (j = 1; j <= n; j++) { if(cutneighsq[i][i] > cutneighsq[j][j]) continue; - stencil_skip[i][j] = 0; + flag_skip_multi[i][j] = 0; if(cutneighsq[i][i] == cutneighsq[j][j]){ - stencil_half[i][j] = 1; - stencil_bin_type[i][j] = i; + flag_half_multi[i][j] = 1; + bin_type_multi[i][j] = i; } else { - stencil_half[i][j] = 0; - stencil_bin_type[i][j] = j; + flag_half_multi[i][j] = 0; + bin_type_multi[i][j] = j; } } } @@ -68,7 +68,7 @@ void NStencilHalfMulti2dTri::create() for (itype = 1; itype <= n; itype++) { for (jtype = 1; jtype <= n; jtype++) { - if (stencil_skip[itype][jtype]) continue; + if (flag_skip_multi[itype][jtype]) continue; ns = 0; @@ -78,11 +78,11 @@ void NStencilHalfMulti2dTri::create() mbinx = stencil_mbinx_multi[itype][jtype]; mbiny = stencil_mbiny_multi[itype][jtype]; - bin_type = stencil_bin_type[itype][jtype]; + bin_type = bin_type_multi[itype][jtype]; cutsq = cutneighsq[itype][jtype]; - if (stencil_half[itype][jtype]) { + if (flag_half_multi[itype][jtype]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance_multi(i,j,0,bin_type) < cutsq) diff --git a/src/nstencil_half_multi_3d.cpp b/src/nstencil_half_multi_3d.cpp index 1f94fb16cd..d66cfe98b9 100644 --- a/src/nstencil_half_multi_3d.cpp +++ b/src/nstencil_half_multi_3d.cpp @@ -42,14 +42,14 @@ void NStencilHalfMulti3d::set_stencil_properties() for (j = 1; j <= n; j++) { if(cutneighsq[i][i] > cutneighsq[j][j]) continue; - stencil_skip[i][j] = 0; + flag_skip_multi[i][j] = 0; if(cutneighsq[i][i] == cutneighsq[j][j]){ - stencil_half[i][j] = 1; - stencil_bin_type[i][j] = i; + flag_half_multi[i][j] = 1; + bin_type_multi[i][j] = i; } else { - stencil_half[i][j] = 0; - stencil_bin_type[i][j] = j; + flag_half_multi[i][j] = 0; + bin_type_multi[i][j] = j; } } } @@ -68,7 +68,7 @@ void NStencilHalfMulti3d::create() for (itype = 1; itype <= n; itype++) { for (jtype = 1; jtype <= n; jtype++) { - if (stencil_skip[itype][jtype]) continue; + if (flag_skip_multi[itype][jtype]) continue; ns = 0; @@ -80,11 +80,11 @@ void NStencilHalfMulti3d::create() mbiny = stencil_mbiny_multi[itype][jtype]; mbinz = stencil_mbinz_multi[itype][jtype]; - bin_type = stencil_bin_type[itype][jtype]; + bin_type = bin_type_multi[itype][jtype]; cutsq = cutneighsq[itype][jtype]; - if (stencil_half[itype][jtype]) { + if (flag_half_multi[itype][jtype]) { for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) diff --git a/src/nstencil_half_multi_3d_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp index 30e59e92e8..e4a5747ca6 100755 --- a/src/nstencil_half_multi_3d_tri.cpp +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -42,14 +42,14 @@ void NStencilHalfMulti3dTri::set_stencil_properties() for (j = 1; j <= n; j++) { if(cutneighsq[i][i] > cutneighsq[j][j]) continue; - stencil_skip[i][j] = 0; + flag_skip_multi[i][j] = 0; if(cutneighsq[i][i] == cutneighsq[j][j]){ - stencil_half[i][j] = 1; - stencil_bin_type[i][j] = i; + flag_half_multi[i][j] = 1; + bin_type_multi[i][j] = i; } else { - stencil_half[i][j] = 0; - stencil_bin_type[i][j] = j; + flag_half_multi[i][j] = 0; + bin_type_multi[i][j] = j; } } } @@ -68,7 +68,7 @@ void NStencilHalfMulti3dTri::create() for (itype = 1; itype <= n; itype++) { for (jtype = 1; jtype <= n; jtype++) { - if (stencil_skip[itype][jtype]) continue; + if (flag_skip_multi[itype][jtype]) continue; ns = 0; @@ -80,11 +80,11 @@ void NStencilHalfMulti3dTri::create() mbiny = stencil_mbiny_multi[itype][jtype]; mbinz = stencil_mbinz_multi[itype][jtype]; - bin_type = stencil_bin_type[itype][jtype]; + bin_type = bin_type_multi[itype][jtype]; cutsq = cutneighsq[itype][jtype]; - if (stencil_half[itype][jtype]) { + if (flag_half_multi[itype][jtype]) { for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) From 5ae32146eb7069cbe16c14903ca4a9bc66f31fd2 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 20 Dec 2020 17:18:32 -0700 Subject: [PATCH 40/73] Adding full neighbor list check for new reduced comm --- src/comm.cpp | 16 +++++++--------- src/neighbor.cpp | 13 +++++++++++++ src/neighbor.h | 1 + 3 files changed, 21 insertions(+), 9 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index afd4d891ee..84e3b9ad65 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -242,15 +242,13 @@ void Comm::init() for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; - // Can't used multi_reduce communication with Newton off - // TODO: need to somehow restrict this option with full neighbor lists - // CANNOT use multi_reduce communication with full nlist - // Could remove NP_NEWTON from npair_full_*multi_reduce*, but could be cryptic - // Also could be cases where you want newton off (hybrid) but don't use multi_reduce comm - // Could add check on neighbor build, if full and comm->multi_reduce error... - // or just add check on comm setup - is that run before every run? Only if box change... - if (force->newton == 0 && multi_reduce) - error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); + // Can't used multi/reduce communication with Newton off or full neighbor lits + if(multi_reduce){ + if (force->newton == 0) + error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); + if (neighbor->any_full()) + error->all(FLERR,"Cannot use multi/reduce communication with a full neighbor list"); + } } /* ---------------------------------------------------------------------- diff --git a/src/neighbor.cpp b/src/neighbor.cpp index fe34e738b0..d130219931 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -2420,6 +2420,19 @@ int Neighbor::exclude_setting() return exclude; } +/* ---------------------------------------------------------------------- + check if any of the old requested neighbor lists are full +------------------------------------------------------------------------- */ + +int Neighbor::any_full() +{ + int any_full = 0; + for(int i = 0; i < old_nrequest; i++) { + if(old_requests[i]->full) any_full = 1; + } + return any_full; +} + /* ---------------------------------------------------------------------- return # of bytes of allocated memory ------------------------------------------------------------------------- */ diff --git a/src/neighbor.h b/src/neighbor.h index 2943f7e082..d1a5cf9112 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -122,6 +122,7 @@ class Neighbor : protected Pointers { void exclusion_group_group_delete(int, int); // rm a group-group exclusion int exclude_setting(); // return exclude value to accelerator pkg class NeighRequest *find_request(void *); // find a neighbor request + int any_full(); // Check if any old requests had full neighbor lists double memory_usage(); From b421c3d67652aa6fd0657542e5914a633c73bf47 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 22 Dec 2020 10:20:06 -0700 Subject: [PATCH 41/73] Adding arguments, initialization, and communication for custom groupings --- src/comm_brick.cpp | 44 ++++++++++++----------- src/comm_tiled.cpp | 46 +++++++++++++----------- src/neighbor.cpp | 87 +++++++++++++++++++++++++++++++++++++++++++++- src/neighbor.h | 9 ++++- 4 files changed, 143 insertions(+), 43 deletions(-) diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 7f84d619e4..528456ab7c 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -175,10 +175,11 @@ void CommBrick::setup() if (mode == Comm::MULTI) { if (multi_reduce) { - // If using multi/reduce binlists, communicate itype particles a distance - // equal to the max of itype-jtype interaction given smaller jtype particles - double **cutneighsq = neighbor->cutneighsq; - double *cuttypesq = neighbor->cuttypesq; + // If using multi/reduce, communicate itype particles a distance equal + // to the max of itype-jtype group interaction given smaller jtype group + int igroup, jgroup; + double **cutmultisq = neighbor->cutmultisq; + int *map_type_multi = neighbor->map_type_multi; for (i = 1; i <= ntypes; i++) { if (cutusermulti) { @@ -191,11 +192,14 @@ void CommBrick::setup() cutghostmulti[i][2] = 0.0; } + igroup = map_type_multi[i]; for (j = 1; j <= ntypes; j++){ - if(cutneighsq[j][j] > cutneighsq[i][i]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); + jgroup = map_type_multi[j]; + + if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); } } } else { @@ -226,10 +230,11 @@ void CommBrick::setup() if (mode == Comm::MULTI) { if (multi_reduce) { - // If using multi/reduce binlists, communicate itype particles a distance - // equal to the max of itype-jtype interaction given smaller jtype particles - double **cutneighsq = neighbor->cutneighsq; - double *cuttypesq = neighbor->cuttypesq; + // If using multi/reduce, communicate itype particles a distance equal + // to the max of itype-jtype group interaction given smaller jtype group + int igroup, jgroup; + double **cutmultisq = neighbor->cutmultisq; + int *map_type_multi = neighbor->map_type_multi; for (i = 1; i <= ntypes; i++) { if (cutusermulti) { @@ -242,16 +247,15 @@ void CommBrick::setup() cutghostmulti[i][2] = 0.0; } + igroup = map_type_multi[i]; for (j = 1; j <= ntypes; j++){ - if(cutneighsq[j][j] > cutneighsq[i][i]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); + jgroup = map_type_multi[j]; + + if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); } - - cutghostmulti[i][0] *= length0; - cutghostmulti[i][1] *= length1; - cutghostmulti[i][2] *= length2; } } else { // If using a single binlist, use the max itype-jtype interaction distance for communication diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index ce76fa7442..64d1207a64 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -177,29 +177,33 @@ void CommTiled::setup() if (mode == Comm::MULTI) { double cut; if (multi_reduce) { - // If using multi/reduce binlists, communicate itype particles a distance - // equal to the max of itype-jtype interaction given smaller jtype particles - double **cutneighsq = neighbor->cutneighsq; - double *cuttypesq = neighbor->cuttypesq; - for (i = 1; i <= ntypes; i++) { + // If using multi/reduce, communicate itype particles a distance equal + // to the max of itype-jtype group interaction given smaller jtype group + int igroup, jgroup; + double **cutmultisq = neighbor->cutmultisq; + int *map_type_multi = neighbor->map_type_multi; + for (i = 1; i <= ntypes; i++) { - if (cutusermulti) { - cutghostmulti[i][0] = cutusermulti[i]; - cutghostmulti[i][1] = cutusermulti[i]; - cutghostmulti[i][2] = cutusermulti[i]; - } else { - cutghostmulti[i][0] = 0.0; - cutghostmulti[i][1] = 0.0; - cutghostmulti[i][2] = 0.0; - } - - for (j = 1; j <= ntypes; j++){ - if(cutneighsq[j][j] > cutneighsq[i][i]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); - } + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; } + + igroup = map_type_multi[i]; + for (j = 1; j <= ntypes; j++){ + jgroup = map_type_multi[j]; + + if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); + } + } } else { // If using a single binlist, use the max itype-jtype interaction distance for communication double *cuttype = neighbor->cuttype; diff --git a/src/neighbor.cpp b/src/neighbor.cpp index d130219931..b08de6cb02 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -188,6 +188,12 @@ pairclass(nullptr), pairnames(nullptr), pairmasks(nullptr) nex_mol = maxex_mol = 0; ex_mol_group = ex_mol_bit = ex_mol_intra = nullptr; + // Multi data + + map_type_multi = nullptr; + cutmultisq = nullptr; + multi_groups = 0; + // Kokkos setting copymode = 0; @@ -253,6 +259,9 @@ Neighbor::~Neighbor() memory->destroy(ex_mol_group); delete [] ex_mol_bit; memory->destroy(ex_mol_intra); + + memory->destroy(map_type_multi); + memory->destroy(cutmultisq); } /* ---------------------------------------------------------------------- */ @@ -336,6 +345,35 @@ void Neighbor::init() } cutneighmaxsq = cutneighmax * cutneighmax; + // multi cutoffs + if(style == Neighbor::MULTI){ + int igroup, jgroup; + // If not defined, create default mapping + if(not map_type_multi) { + memory->create(map_type_multi,n+1,"neigh:map_type_multi"); + n_multi_groups = n; + for(i = 1; i <= n; i++) + map_type_multi[i] = i-1; + } + + // Define maximum interaction distance for each pair of groups + memory->grow(cutmultisq, n_multi_groups, n_multi_groups, "neigh:cutmultisq"); + for(i = 0; i < n_multi_groups; i++) + for(j = 0; j < n_multi_groups; j++) + cutmultisq[i][j] = 0.0; + + for(i = 1; i <= n; i++){ + igroup = map_type_multi[i]; + for(j = 1; j <= n; j++){ + jgroup = map_type_multi[j]; + if(cutneighsq[i][j] > cutmultisq[igroup][jgroup]) { + cutmultisq[igroup][jgroup] = cutneighsq[i][j]; + cutmultisq[jgroup][igroup] = cutneighsq[i][j]; + } + } + } + } + // rRESPA cutoffs int respa = 0; @@ -1934,6 +1972,7 @@ NPair *Neighbor::pair_creator(LAMMPS *lmp) /* ---------------------------------------------------------------------- setup neighbor binning and neighbor stencils called before run and every reneighbor if box size/shape changes + initialize default settings for multi before run only operates on perpetual lists build_one() operates on occasional lists ------------------------------------------------------------------------- */ @@ -2379,9 +2418,55 @@ void Neighbor::modify_params(int narg, char **arg) } else if (strcmp(arg[iarg+1],"none") == 0) { nex_type = nex_group = nex_mol = 0; iarg += 2; - + } else error->all(FLERR,"Illegal neigh_modify command"); + } else if (strcmp(arg[iarg],"multi/custom") == 0) { + if(style != Neighbor::MULTI) + error->all(FLERR,"Cannot use multi/custom command without multi setting"); + + if(iarg+2 > narg) + error->all(FLERR,"Invalid multi/custom command"); + int nextra = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if(iarg+1+nextra > narg) + error->all(FLERR,"Invalid multi/custom command"); + int ntypes = atom->ntypes; + int n, nlo, nhi, i, j, igroup, jgroup; + + if(not map_type_multi) + memory->create(map_type_multi,ntypes+1,"neigh:map_type_multi"); + + // Erase previous mapping + for(i = 1; i <= ntypes; i++) + map_type_multi[i] = -1; + + // For each custom range, define mapping for types in interval + n_multi_groups = 0; + char *id; + for(i = 0; i < nextra; i++){ + n = strlen(arg[iarg+2+i]) + 1; + id = new char[n]; + strcpy(id,arg[iarg+2+i]); + utils::bounds(FLERR,id,1,ntypes,nlo,nhi,error); + delete [] id; + + for (j = nlo; j <= nhi; j++) { + if(map_type_multi[j] != -1) + error->all(FLERR,"Type specified more than once in multi/custom commnd"); + map_type_multi[j] = n_multi_groups; + } + n_multi_groups += 1; + } + + // Create seprate group for each undefined atom type + for(i = 1; i <= ntypes; i++){ + if(map_type_multi[i] == -1){ + map_type_multi[i] = n_multi_groups; + n_multi_groups += 1; + } + } + + iarg += 2 + nextra; } else error->all(FLERR,"Illegal neigh_modify command"); } } diff --git a/src/neighbor.h b/src/neighbor.h index d1a5cf9112..ad3de851cf 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -21,7 +21,7 @@ namespace LAMMPS_NS { class Neighbor : protected Pointers { public: enum{NSQ,BIN,MULTI_OLD,MULTI}; - int style; // 0,1,2 = nsq, bin, multi/old, multi + int style; // 0,1,2,3 = nsq, bin, multi/old, multi int every; // build every this many steps int delay; // delay build for this many steps int dist_check; // 0 = always build, 1 = only if 1/2 dist @@ -102,6 +102,13 @@ class Neighbor : protected Pointers { int nimproperlist; // list of impropers to compute int **improperlist; + // optional type grouping for multi + + int multi_groups; // 1 if custom groupings are defined for multi + int n_multi_groups; // # of custom groupings + int *map_type_multi; // ntype array mapping types to custom groupings + double **cutmultisq; // cutoffs for each combination of custom groupings + // public methods Neighbor(class LAMMPS *); From 2458eaf4f9bb4e58a5a277f02475b7b1f04ca7c6 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 26 Dec 2020 11:03:29 -0700 Subject: [PATCH 42/73] Adding custom grouping option --- src/USER-OMP/npair_full_multi_omp.cpp | 28 ++-- src/USER-OMP/npair_half_multi_newtoff_omp.cpp | 28 ++-- src/USER-OMP/npair_half_multi_newton_omp.cpp | 54 ++++---- .../npair_half_multi_newton_tri_omp.cpp | 30 +++-- .../npair_half_size_multi_newtoff_omp.cpp | 28 ++-- .../npair_half_size_multi_newton_omp.cpp | 48 ++++--- .../npair_half_size_multi_newton_tri_omp.cpp | 30 +++-- src/comm_brick.cpp | 6 +- src/nbin.cpp | 45 ++++--- src/nbin.h | 12 +- src/nbin_multi.cpp | 98 +++++++------- src/nbin_multi.h | 2 +- src/neighbor.cpp | 2 +- src/npair.cpp | 40 +++--- src/npair.h | 5 +- src/npair_full_multi.cpp | 33 ++--- src/npair_half_multi_newtoff.cpp | 31 ++--- src/npair_half_multi_newton.cpp | 57 ++++---- src/npair_half_multi_newton_tri.cpp | 35 ++--- src/npair_half_size_multi_newtoff.cpp | 31 ++--- src/npair_half_size_multi_newton.cpp | 59 ++++---- src/npair_half_size_multi_newton_tri.cpp | 31 ++--- src/nstencil.cpp | 126 +++++++++--------- src/nstencil.h | 7 +- src/nstencil_full_multi_2d.cpp | 36 ++--- src/nstencil_full_multi_3d.cpp | 40 +++--- src/nstencil_half_multi_2d.cpp | 50 +++---- src/nstencil_half_multi_2d_tri.cpp | 50 +++---- src/nstencil_half_multi_3d.cpp | 54 ++++---- src/nstencil_half_multi_3d_tri.cpp | 54 ++++---- 30 files changed, 599 insertions(+), 551 deletions(-) diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index cf897f9dea..11b8bae196 100755 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -30,7 +30,7 @@ NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ @@ -46,7 +46,7 @@ void NPairFullMultiOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -80,6 +80,7 @@ void NPairFullMultiOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -89,27 +90,28 @@ void NPairFullMultiOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in surrounding bins in stencil including self // skip i = j - // use full stencil for all type combinations + // use full stencil for all group combinations - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if (i == j) continue; + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp index bf7644f01f..e3e03ee8ed 100755 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -30,7 +30,7 @@ NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent 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) @@ -48,7 +48,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -82,6 +82,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -91,29 +92,30 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // 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 - // use full stencil for all type combinations + // use full stencil for all group combinations - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jgroup][j]) { if (j <= i) continue; + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index c68a3a150f..28db1b3c0d 100755 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -30,7 +30,7 @@ NPairHalfMultiNewtonOmp::NPairHalfMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -47,7 +47,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -81,6 +81,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -90,28 +91,28 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ // if same size: use half stencil - if(itype == jtype){ + if(igroup == jgroup){ - // if same type, implement with: + // if same group, implement with: // 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 - js = bins_multi[itype][i]; + js = bins_multi[igroup][i]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -120,6 +121,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) } } + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -145,14 +147,14 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) } } else { - // if different types, implement with: - // loop over all atoms in jtype bin + // if different groups, implement with: + // loop over all atoms in jgroup bin // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi[jtype][jbin]; + js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if(j < i) continue; if (j >= nlocal) { @@ -163,8 +165,9 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) } } + 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]; @@ -189,20 +192,21 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) } } - // for all types, loop over all atoms in other bins in stencil, store every pair + // for all groups, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][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]; diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index 3f3ac37b6d..0289967d30 100755 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -31,7 +31,7 @@ NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -48,7 +48,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,ibin,jbin,igroup,jgroup,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -82,6 +82,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -91,14 +92,14 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in bins in stencil // stencil is empty if i larger than j @@ -109,15 +110,15 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { - // if same size (e.g. same type), use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + // if same size (same group), use half stencil + if(cutmultisq[igroup][igroup] == cutmutlisq[jgroup][jgroup]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -128,6 +129,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) } } + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp index 8201ba8cb6..35cfaad5e6 100755 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp @@ -29,7 +29,7 @@ NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : NPair( /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent 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) @@ -47,7 +47,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,ns; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -75,34 +75,36 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // 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 - // use full stencil for all type combinations + // use full stencil for all group combinations - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jgroup][j]) { if (j <= i) continue; + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index 197b41c12e..974b8c5809 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -29,7 +29,7 @@ NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) : NPair(lm /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -46,7 +46,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,ns; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -74,33 +74,34 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_group; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ // if same size: use half stencil - if(itype == jtype){ + if(igroup == jgroup){ - // if same type, implement with: + // if same group, implement with: // 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 - js = bins_multi[itype][i]; + js = bins_multi[igroup][i]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -109,6 +110,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) } } + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -127,14 +129,14 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) } } else { - // if different types, implement with: - // loop over all atoms in jtype bin + // if different groups, implement with: + // loop over all atoms in jgroup bin // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi[jtype][jbin]; + js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if(j < i) continue; if (j >= nlocal) { @@ -145,6 +147,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) } } + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -164,18 +167,19 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) } } - // for all types, loop over all atoms in other bins in stencil, store every pair + // for all groups, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp index cd123202b1..d1c5a97498 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp @@ -30,7 +30,7 @@ NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -47,7 +47,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,ns; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -75,19 +75,20 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in bins in stencil @@ -99,15 +100,15 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { - // if same size (e.g. same type), use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + // if same size (same group), use half stencil + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -118,6 +119,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) } } + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 528456ab7c..74865476f5 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -252,9 +252,9 @@ void CommBrick::setup() jgroup = map_type_multi[j]; if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][0] = length0 * MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][1] = length1 * MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][2] = length2 * MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); } } } else { diff --git a/src/nbin.cpp b/src/nbin.cpp index 084d3bfc4a..cb10014b36 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -43,8 +43,11 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) bins_multi = nullptr; atom2bin_multi = nullptr; maxbins_multi = nullptr; + + map_type_multi = nullptr; + cutmultisq = nullptr; - maxtypes = 0; + maxgroups = 0; neighbor->last_setup_bins = -1; @@ -84,7 +87,7 @@ NBin::~NBin() memory->destroy(bininvy_multi); memory->destroy(bininvz_multi); - for (int n = 1; n <= maxtypes; n++) { + for (int n = 0; n < maxgroups; n++) { memory->destroy(binhead_multi[n]); memory->destroy(bins_multi[n]); memory->destroy(atom2bin_multi[n]); @@ -117,6 +120,10 @@ void NBin::copy_neighbor_info() binsize_user = neighbor->binsize_user; bboxlo = neighbor->bboxlo; bboxhi = neighbor->bboxhi; + + n_multi_groups = neighbor->n_multi_groups; + map_type_multi = neighbor->map_type_multi; + cutmultisq = neighbor->cutmultisq; // overwrite Neighbor cutoff with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -174,10 +181,10 @@ int NBin::coord2bin(double *x) /* ---------------------------------------------------------------------- - convert atom coords into local bin # for a particular type + convert atom coords into local bin # for a particular grouping ------------------------------------------------------------------------- */ -int NBin::coord2bin_multi(double *x, int it) +int NBin::coord2bin_multi(double *x, int ig) { int ix,iy,iz; int ibin; @@ -186,33 +193,33 @@ int NBin::coord2bin_multi(double *x, int it) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[it]) + nbinx_multi[it]; + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ig]) + nbinx_multi[ig]; else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]); - ix = MIN(ix,nbinx_multi[it]-1); + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]); + ix = MIN(ix,nbinx_multi[ig]-1); } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]) - 1; + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]) - 1; if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[it]) + nbiny_multi[it]; + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ig]) + nbiny_multi[ig]; else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]); - iy = MIN(iy,nbiny_multi[it]-1); + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]); + iy = MIN(iy,nbiny_multi[ig]-1); } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]) - 1; + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]) - 1; if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[it]) + nbinz_multi[it]; + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ig]) + nbinz_multi[ig]; else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]); - iz = MIN(iz,nbinz_multi[it]-1); + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]); + iz = MIN(iz,nbinz_multi[ig]-1); } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]) - 1; + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]) - 1; - ibin = (iz-mbinzlo_multi[it])*mbiny_multi[it]*mbinx_multi[it] - + (iy-mbinylo_multi[it])*mbinx_multi[it] - + (ix-mbinxlo_multi[it]); + ibin = (iz-mbinzlo_multi[ig])*mbiny_multi[ig]*mbinx_multi[ig] + + (iy-mbinylo_multi[ig])*mbinx_multi[ig] + + (ix-mbinxlo_multi[ig]); return ibin; } diff --git a/src/nbin.h b/src/nbin.h index 8f95ad987e..19035d619e 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -75,6 +75,9 @@ class NBin : protected Pointers { int binsizeflag; double binsize_user; double *bboxlo,*bboxhi; + int n_multi_groups; + int *map_type_multi; + double **cutmultisq; // data common to all NBin variants @@ -84,15 +87,12 @@ class NBin : protected Pointers { // data for standard NBin int maxatom; // size of bins array - - // data for standard NBin - int maxbin; // size of binhead array - // data for multi/multi NBin + // data for multi NBin - int maxtypes; // size of multi arrays - int * maxbins_multi; // size of 2nd dimension of binhead_multi array + int maxgroups; // size of multi arrays + int * maxbins_multi; // size of 2nd dimension of binhead_multi array // methods diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index 302fe30d88..b39489c3fe 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -38,7 +38,7 @@ void NBinMulti::bin_atoms_setup(int nall) { // binhead_multi[n] = per-bin vector mbins in length mbins_multi[n] - for (int n = 1; n <= maxtypes; n++) { + for (int n = 0; n < maxgroups; n++) { if (mbins_multi[n] > maxbins_multi[n]) { maxbins_multi[n] = mbins_multi[n]; memory->destroy(binhead_multi[n]); @@ -48,10 +48,12 @@ void NBinMulti::bin_atoms_setup(int nall) // bins_multi[n] and atom2bin_multi[n] = per-atom vectors // for both local and ghost atoms + + // TODO: maxatom should be maxatom per group if (nall > maxatom) { maxatom = nall; - for (int n = 1; n <= maxtypes; n++) { + for (int n = 0; n < maxgroups; n++) { memory->destroy(bins_multi[n]); memory->destroy(atom2bin_multi[n]); memory->create(bins_multi[n], maxatom, "neigh:bin_multi"); @@ -61,23 +63,16 @@ void NBinMulti::bin_atoms_setup(int nall) } /* --------------------------------------------------------------------- - Identify index of type with smallest cutoff + Identify index of group with smallest cutoff ------------------------------------------------------------------------ */ -int NBinMulti::itype_min() { +int NBinMulti::igroup_min() +{ + int imin = 0; + for (int n = 0; n < maxgroups; n++) + if (cutmultisq[n][n] < cutmultisq[imin][imin]) imin = n; - int itypemin = 1; - double ** cutneighsq; - - cutneighsq = neighbor->cutneighsq; - - for (int n = 1; n <= atom->ntypes; n++) { - if (cutneighsq[n][n] < cutneighsq[itypemin][itypemin]) { - itypemin = n; - } - } - - return itypemin; + return imin; } /* ---------------------------------------------------------------------- @@ -87,15 +82,15 @@ int NBinMulti::itype_min() { void NBinMulti::setup_bins(int style) { int n; - int itypemin; + int igroupmin; // Initialize arrays - if (atom->ntypes > maxtypes) { + if (n_multi_groups > maxgroups) { // Clear any/all memory for existing types - for (n = 1; n <= maxtypes; n++) { + for (n = 0; n < maxgroups; n++) { memory->destroy(atom2bin_multi[n]); memory->destroy(binhead_multi[n]); memory->destroy(bins_multi[n]); @@ -106,59 +101,60 @@ void NBinMulti::setup_bins(int style) // Realloacte at updated maxtypes - maxtypes = atom->ntypes; + maxgroups = n_multi_groups; - atom2bin_multi = new int*[maxtypes+1](); - binhead_multi = new int*[maxtypes+1](); - bins_multi = new int*[maxtypes+1](); + atom2bin_multi = new int*[maxgroups](); + binhead_multi = new int*[maxgroups](); + bins_multi = new int*[maxgroups](); memory->destroy(nbinx_multi); memory->destroy(nbiny_multi); memory->destroy(nbinz_multi); - memory->create(nbinx_multi, maxtypes+1, "neigh:nbinx_multi"); - memory->create(nbiny_multi, maxtypes+1, "neigh:nbiny_multi"); - memory->create(nbinz_multi, maxtypes+1, "neigh:nbinz_multi"); + memory->create(nbinx_multi, maxgroups, "neigh:nbinx_multi"); + memory->create(nbiny_multi, maxgroups, "neigh:nbiny_multi"); + memory->create(nbinz_multi, maxgroups, "neigh:nbinz_multi"); memory->destroy(mbins_multi); memory->destroy(mbinx_multi); memory->destroy(mbiny_multi); memory->destroy(mbinz_multi); - memory->create(mbins_multi, maxtypes+1, "neigh:mbins_multi"); - memory->create(mbinx_multi, maxtypes+1, "neigh:mbinx_multi"); - memory->create(mbiny_multi, maxtypes+1, "neigh:mbiny_multi"); - memory->create(mbinz_multi, maxtypes+1, "neigh:mbinz_multi"); + memory->create(mbins_multi, maxgroups, "neigh:mbins_multi"); + memory->create(mbinx_multi, maxgroups, "neigh:mbinx_multi"); + memory->create(mbiny_multi, maxgroups, "neigh:mbiny_multi"); + memory->create(mbinz_multi, maxgroups, "neigh:mbinz_multi"); memory->destroy(mbinxlo_multi); memory->destroy(mbinylo_multi); memory->destroy(mbinzlo_multi); - memory->create(mbinxlo_multi, maxtypes+1, "neigh:mbinxlo_multi"); - memory->create(mbinylo_multi, maxtypes+1, "neigh:mbinylo_multi"); - memory->create(mbinzlo_multi, maxtypes+1, "neigh:mbinzlo_multi"); + memory->create(mbinxlo_multi, maxgroups, "neigh:mbinxlo_multi"); + memory->create(mbinylo_multi, maxgroups, "neigh:mbinylo_multi"); + memory->create(mbinzlo_multi, maxgroups, "neigh:mbinzlo_multi"); memory->destroy(binsizex_multi); memory->destroy(binsizey_multi); memory->destroy(binsizez_multi); - memory->create(binsizex_multi, maxtypes+1, "neigh:binsizex_multi"); - memory->create(binsizey_multi, maxtypes+1, "neigh:binsizey_multi"); - memory->create(binsizez_multi, maxtypes+1, "neigh:binsizez_multi"); + memory->create(binsizex_multi, maxgroups, "neigh:binsizex_multi"); + memory->create(binsizey_multi, maxgroups, "neigh:binsizey_multi"); + memory->create(binsizez_multi, maxgroups, "neigh:binsizez_multi"); memory->destroy(bininvx_multi); memory->destroy(bininvy_multi); memory->destroy(bininvz_multi); - memory->create(bininvx_multi, maxtypes+1, "neigh:bininvx_multi"); - memory->create(bininvy_multi, maxtypes+1, "neigh:bininvy_multi"); - memory->create(bininvz_multi, maxtypes+1, "neigh:bininvz_multi"); + memory->create(bininvx_multi, maxgroups, "neigh:bininvx_multi"); + memory->create(bininvy_multi, maxgroups, "neigh:bininvy_multi"); + memory->create(bininvz_multi, maxgroups, "neigh:bininvz_multi"); memory->destroy(maxbins_multi); - memory->create(maxbins_multi, maxtypes+1, "neigh:maxbins_multi"); + memory->create(maxbins_multi, maxgroups, "neigh:maxbins_multi"); + // make sure reallocation occurs in bin_atoms_setup() - for (n = 1; n <= maxtypes; n++) { + for (n = 0; n < maxgroups; n++) { maxbins_multi[n] = 0; } maxatom = 0; } - itypemin = itype_min(); + igroupmin = igroup_min(); // bbox = size of bbox of entire domain // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost @@ -193,16 +189,16 @@ void NBinMulti::setup_bins(int style) bbox[1] = bboxhi[1] - bboxlo[1]; bbox[2] = bboxhi[2] - bboxlo[2]; - // For each type... + // For each grouping... - for (n = 1; n <= atom->ntypes; n++) { + for (n = 0; n < maxgroups; n++) { // binsize_user only relates to smallest type // optimal bin size is roughly 1/2 the type-type cutoff // special case of all cutoffs = 0.0, binsize = box size double binsize_optimal; - if (n == itypemin && binsizeflag) binsize_optimal = binsize_user; - else binsize_optimal = 0.5*sqrt(neighbor->cutneighsq[n][n]); + if (n == igroupmin && binsizeflag) binsize_optimal = binsize_user; + else binsize_optimal = 0.5*sqrt(cutmultisq[n][n]); if (binsize_optimal == 0.0) binsize_optimal = bbox[0]; double binsizeinv = 1.0/binsize_optimal; @@ -306,7 +302,7 @@ void NBinMulti::bin_atoms() int i,ibin,n; last_bin = update->ntimestep; - for (n = 1; n <= maxtypes; n++) { + for (n = 0; n < maxgroups; n++) { for (i = 0; i < mbins_multi[n]; i++) binhead_multi[n][i] = -1; } @@ -323,7 +319,7 @@ void NBinMulti::bin_atoms() int bitmask = group->bitmask[includegroup]; for (i = nall-1; i >= nlocal; i--) { if (mask[i] & bitmask) { - n = type[i]; + n = map_type_multi[type[i]]; ibin = coord2bin_multi(x[i], n); atom2bin_multi[n][i] = ibin; bins_multi[n][i] = binhead_multi[n][ibin]; @@ -331,7 +327,7 @@ void NBinMulti::bin_atoms() } } for (i = atom->nfirst-1; i >= 0; i--) { - n = type[i]; + n = map_type_multi[type[i]]; ibin = coord2bin_multi(x[i], n); atom2bin_multi[n][i] = ibin; bins_multi[n][i] = binhead_multi[n][ibin]; @@ -339,7 +335,7 @@ void NBinMulti::bin_atoms() } } else { for (i = nall-1; i >= 0; i--) { - n = type[i]; + n = map_type_multi[type[i]]; ibin = coord2bin_multi(x[i], n); atom2bin_multi[n][i] = ibin; bins_multi[n][i] = binhead_multi[n][ibin]; @@ -354,7 +350,7 @@ double NBinMulti::memory_usage() { double bytes = 0; - for (int m = 1; m < maxtypes; m++) { + for (int m = 0; m < maxgroups; m++) { bytes += maxbins_multi[m]*sizeof(int); bytes += 2*maxatom*sizeof(int); } diff --git a/src/nbin_multi.h b/src/nbin_multi.h index 856f3fa722..84ec0348bc 100644 --- a/src/nbin_multi.h +++ b/src/nbin_multi.h @@ -38,7 +38,7 @@ class NBinMulti : public NBin { private: - int itype_min(); + int igroup_min(); }; } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index b08de6cb02..94add1f324 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -350,8 +350,8 @@ void Neighbor::init() int igroup, jgroup; // If not defined, create default mapping if(not map_type_multi) { - memory->create(map_type_multi,n+1,"neigh:map_type_multi"); n_multi_groups = n; + memory->create(map_type_multi,n+1,"neigh:map_type_multi"); for(i = 1; i <= n; i++) map_type_multi[i] = i-1; } diff --git a/src/npair.cpp b/src/npair.cpp index 07e476e1dd..b2ecc953ea 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -95,6 +95,12 @@ void NPair::copy_neighbor_info() special_flag = neighbor->special_flag; + // multi info + + n_multi_groups = neighbor->n_multi_groups; + map_type_multi = neighbor->map_type_multi; + cutmultisq = neighbor->cutmultisq; + // overwrite per-type Neighbor cutoffs with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -265,10 +271,10 @@ int NPair::coord2bin(double *x, int &ix, int &iy, int &iz) /* ---------------------------------------------------------------------- - same as coord2bin in NbinMulti2 + multi version of coord2bin for a given grouping ------------------------------------------------------------------------- */ -int NPair::coord2bin(double *x, int it) +int NPair::coord2bin(double *x, int ig) { int ix,iy,iz; int ibin; @@ -277,32 +283,32 @@ int NPair::coord2bin(double *x, int it) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[it]) + nbinx_multi[it]; + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ig]) + nbinx_multi[ig]; else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]); - ix = MIN(ix,nbinx_multi[it]-1); + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]); + ix = MIN(ix,nbinx_multi[ig]-1); } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]) - 1; + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]) - 1; if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[it]) + nbiny_multi[it]; + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ig]) + nbiny_multi[ig]; else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]); - iy = MIN(iy,nbiny_multi[it]-1); + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]); + iy = MIN(iy,nbiny_multi[ig]-1); } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]) - 1; + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]) - 1; if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[it]) + nbinz_multi[it]; + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ig]) + nbinz_multi[ig]; else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]); - iz = MIN(iz,nbinz_multi[it]-1); + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]); + iz = MIN(iz,nbinz_multi[ig]-1); } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]) - 1; + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]) - 1; - ibin = (iz-mbinzlo_multi[it])*mbiny_multi[it]*mbinx_multi[it] - + (iy-mbinylo_multi[it])*mbinx_multi[it] - + (ix-mbinxlo_multi[it]); + ibin = (iz-mbinzlo_multi[ig])*mbiny_multi[ig]*mbinx_multi[ig] + + (iy-mbinylo_multi[ig])*mbinx_multi[ig] + + (ix-mbinxlo_multi[ig]); return ibin; } \ No newline at end of file diff --git a/src/npair.h b/src/npair.h index c56c6bdb20..4d99e3a8e6 100644 --- a/src/npair.h +++ b/src/npair.h @@ -48,7 +48,10 @@ class NPair : protected Pointers { double cut_middle_sq; double cut_middle_inside_sq; double *bboxlo,*bboxhi; - + int n_multi_groups; + int *map_type_multi; + double **cutmultisq; + // exclusion data from Neighbor class int nex_type; // # of entries in type exclusion list diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp index 4463964d5f..f29f04107a 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi.cpp @@ -28,13 +28,13 @@ NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent 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,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -67,8 +67,8 @@ void NPairFullMulti::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -78,29 +78,30 @@ void NPairFullMulti::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in surrounding bins in stencil including self // skip i = j - // use full stencil for all type combinations + // use full stencil for all group combinations - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if (i == j) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) 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]; diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index c0dcaf0c98..85832b11b1 100755 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -28,7 +28,7 @@ NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent 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) @@ -36,7 +36,7 @@ NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} void NPairHalfMultiNewtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -69,8 +69,8 @@ void NPairHalfMultiNewtoff::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -80,30 +80,31 @@ void NPairHalfMultiNewtoff::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // 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 - // use full stencil for all type combinations + // use full stencil for all group combinations - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jgroup][j]) { if (j <= i) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index e097052fe5..d18b009460 100755 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -28,14 +28,14 @@ NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfMultiNewton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -68,8 +68,8 @@ void NPairHalfMultiNewton::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -79,28 +79,28 @@ void NPairHalfMultiNewton::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ // if same size: use half stencil - if(itype == jtype){ + if(igroup == jgroup){ - // if same type, implement with: + // if same group, implement with: // 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 - js = bins_multi[itype][i]; + js = bins_multi[igroup][i]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -109,7 +109,8 @@ void NPairHalfMultiNewton::build(NeighList *list) } } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; @@ -134,14 +135,14 @@ void NPairHalfMultiNewton::build(NeighList *list) } } else { - // if different types, implement with: - // loop over all atoms in jtype bin + // if different groups, implement with: + // loop over all atoms in jgroup bin // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi[jtype][jbin]; + js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if(j < i) continue; if (j >= nlocal) { @@ -152,7 +153,8 @@ void NPairHalfMultiNewton::build(NeighList *list) } } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; @@ -178,20 +180,21 @@ void NPairHalfMultiNewton::build(NeighList *list) } } - // for all types, loop over all atoms in other bins in stencil, store every pair + // for all groups, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][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]; diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index fabaf5f202..ebf871ad99 100755 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -28,14 +28,14 @@ NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfMultiNewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -68,8 +68,8 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -79,14 +79,14 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in bins in stencil // stencil is empty if i larger than j @@ -97,15 +97,15 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { - // if same size (e.g. same type), use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + // if same size (same group), use half stencil + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -116,8 +116,9 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) } } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) 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]; diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index 65b6b68fb2..ec4fbad9aa 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -28,7 +28,7 @@ NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) { /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent 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) @@ -36,7 +36,7 @@ NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) { void NPairHalfSizeMultiNewtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,jbin,ns; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -64,37 +64,38 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // 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 - // use full stencil for all type combinations + // use full stencil for all group combinations - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jgroup][j]) { if (j <= i) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index 8fa3b9bc1b..c3a13f4b81 100755 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -27,14 +27,14 @@ NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfSizeMultiNewton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,jbin,ns,js; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -61,35 +61,35 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ // if same size: use half stencil - if(itype == jtype){ + if(igroup == jgroup){ - // if same type, implement with: + // if same group, implement with: // 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 - js = bins_multi[itype][i]; + js = bins_multi[igroup][i]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -98,7 +98,8 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) } } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; @@ -116,14 +117,14 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) } } else { - // if different types, implement with: - // loop over all atoms in jtype bin + // if different groups, implement with: + // loop over all atoms in jgroup bin // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi[jtype][jbin]; + js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if(j < i) continue; if (j >= nlocal) { @@ -134,8 +135,9 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) } } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) 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]; @@ -153,20 +155,21 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) } } - // for all types, loop over all atoms in other bins in stencil, store every pair + // for all groups, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) 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]; diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 780fa95f0b..7c792c6a19 100755 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -27,14 +27,14 @@ NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lm /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,jbin,ns,js; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -61,21 +61,21 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in bins in stencil @@ -87,15 +87,15 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { - // if same size (e.g. same type), use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + // if same size (same group), use half stencil + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -106,6 +106,7 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) } } + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/nstencil.cpp b/src/nstencil.cpp index f6281a1964..acd7272245 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -52,14 +52,14 @@ using namespace LAMMPS_NS; cutoff is not cutneighmaxsq, but max cutoff for that atom type no versions that allow ghost on (any need for it?) for multi: - create one stencil for each itype-jtype pairing - the full/half stencil label refers to the same-type stencil - a half list with newton on has a half same-type stencil - a full list or half list with newton of has a full same-type stencil - cross type stencils are always full to allow small-to-large lookups + create one stencil for each igroup-jgroup pairing + the full/half stencil label refers to the same-group stencil + a half list with newton on has a half same-group stencil + a full list or half list with newton of has a full same-group stencil + cross group stencils are always full to allow small-to-large lookups for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above - cutoff is not cutneighmaxsq, but max cutoff for that atom type + cutoff is not cutneighmaxsq, but max cutoff for that atom group no versions that allow ghost on (any need for it?) ------------------------------------------------------------------------- */ @@ -81,7 +81,7 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) flag_half_multi = nullptr; flag_skip_multi = nullptr; - bin_type_multi = nullptr; + bin_group_multi = nullptr; dimension = domain->dimension; } @@ -107,10 +107,10 @@ NStencil::~NStencil() if (stencil_multi) { - int n = atom->ntypes; + int n = n_multi_groups; memory->destroy(nstencil_multi); - for (int i = 1; i <= n; i++) { - for (int j = 0; j <= n; j++) { + for (int i = 0; i < n; i++) { + for (int j = 0; j < n; j++) { if (! flag_skip_multi[i][j]) memory->destroy(stencil_multi[i][j]); } @@ -120,7 +120,7 @@ NStencil::~NStencil() memory->destroy(maxstencil_multi); memory->destroy(flag_half_multi); memory->destroy(flag_skip_multi); - memory->destroy(bin_type_multi); + memory->destroy(bin_group_multi); memory->destroy(stencil_sx_multi); memory->destroy(stencil_sy_multi); @@ -155,6 +155,10 @@ void NStencil::copy_neighbor_info() cutneighmaxsq = neighbor->cutneighmaxsq; cuttypesq = neighbor->cuttypesq; cutneighsq = neighbor->cutneighsq; + + n_multi_groups = neighbor->n_multi_groups; + map_type_multi = neighbor->map_type_multi; + cutmultisq = neighbor->cutmultisq; // overwrite Neighbor cutoff with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -265,44 +269,44 @@ void NStencil::create_setup() } } } else { - int i, j, bin_type, smax; + int i, j, bin_group, smax; double stencil_range; - int n = atom->ntypes; + int n = n_multi_groups; if(nb) copy_bin_info_multi(); // Allocate arrays to store stencil information - memory->create(flag_half_multi, n+1, n+1, + memory->create(flag_half_multi, n, n, "neighstencil:flag_half_multi"); - memory->create(flag_skip_multi, n+1, n+1, + memory->create(flag_skip_multi, n, n, "neighstencil:flag_skip_multi"); - memory->create(bin_type_multi, n+1, n+1, - "neighstencil:bin_type_multi"); + memory->create(bin_group_multi, n, n, + "neighstencil:bin_group_multi"); - memory->create(stencil_sx_multi, n+1, n+1, + memory->create(stencil_sx_multi, n, n, "neighstencil:stencil_sx_multi"); - memory->create(stencil_sy_multi, n+1, n+1, + memory->create(stencil_sy_multi, n, n, "neighstencil:stencil_sy_multi"); - memory->create(stencil_sz_multi, n+1, n+1, + memory->create(stencil_sz_multi, n, n, "neighstencil:stencil_sz_multi"); - memory->create(stencil_binsizex_multi, n+1, n+1, + memory->create(stencil_binsizex_multi, n, n, "neighstencil:stencil_binsizex_multi"); - memory->create(stencil_binsizey_multi, n+1, n+1, + memory->create(stencil_binsizey_multi, n, n, "neighstencil:stencil_binsizey_multi"); - memory->create(stencil_binsizez_multi, n+1, n+1, + memory->create(stencil_binsizez_multi, n, n, "neighstencil:stencil_binsizez_multi"); - memory->create(stencil_mbinx_multi, n+1, n+1, + memory->create(stencil_mbinx_multi, n, n, "neighstencil:stencil_mbinx_multi"); - memory->create(stencil_mbiny_multi, n+1, n+1, + memory->create(stencil_mbiny_multi, n, n, "neighstencil:stencil_mbiny_multi"); - memory->create(stencil_mbinz_multi, n+1, n+1, + memory->create(stencil_mbinz_multi, n, n, "neighstencil:stencil_mbinz_multi"); // Skip all stencils by default, initialize smax - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { flag_skip_multi[i][j] = 1; } } @@ -313,43 +317,43 @@ void NStencil::create_setup() // Allocate arrays to store stencils if (!maxstencil_multi) { - memory->create(maxstencil_multi, n+1, n+1, "neighstencil::stencil_multi"); - memory->create(nstencil_multi, n+1, n+1, "neighstencil::nstencil_multi"); - stencil_multi = new int**[n+1](); - for (i = 1; i <= n; ++i) { - stencil_multi[i] = new int*[n+1](); - for (j = 1; j <= n; ++j) { + memory->create(maxstencil_multi, n, n, "neighstencil::stencil_multi"); + memory->create(nstencil_multi, n, n, "neighstencil::nstencil_multi"); + stencil_multi = new int**[n](); + for (i = 0; i < n; ++i) { + stencil_multi[i] = new int*[n](); + for (j = 0; j < n; ++j) { maxstencil_multi[i][j] = 0; nstencil_multi[i][j] = 0; } } } - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { // Skip creation of unused stencils if (flag_skip_multi[i][j]) continue; // Copy bin info for this pair of atom types - bin_type = bin_type_multi[i][j]; + bin_group = bin_group_multi[i][j]; - stencil_binsizex_multi[i][j] = binsizex_multi[bin_type]; - stencil_binsizey_multi[i][j] = binsizey_multi[bin_type]; - stencil_binsizez_multi[i][j] = binsizez_multi[bin_type]; + stencil_binsizex_multi[i][j] = binsizex_multi[bin_group]; + stencil_binsizey_multi[i][j] = binsizey_multi[bin_group]; + stencil_binsizez_multi[i][j] = binsizez_multi[bin_group]; - stencil_mbinx_multi[i][j] = mbinx_multi[bin_type]; - stencil_mbiny_multi[i][j] = mbiny_multi[bin_type]; - stencil_mbinz_multi[i][j] = mbinz_multi[bin_type]; + stencil_mbinx_multi[i][j] = mbinx_multi[bin_group]; + stencil_mbiny_multi[i][j] = mbiny_multi[bin_group]; + stencil_mbinz_multi[i][j] = mbinz_multi[bin_group]; - stencil_range = sqrt(cutneighsq[i][j]); + stencil_range = sqrt(cutmultisq[i][j]); - sx = static_cast (stencil_range*bininvx_multi[bin_type]); - if (sx*binsizex_multi[bin_type] < stencil_range) sx++; - sy = static_cast (stencil_range*bininvy_multi[bin_type]); - if (sy*binsizey_multi[bin_type] < stencil_range) sy++; - sz = static_cast (stencil_range*bininvz_multi[bin_type]); - if (sz*binsizez_multi[bin_type] < stencil_range) sz++; + sx = static_cast (stencil_range*bininvx_multi[bin_group]); + if (sx*binsizex_multi[bin_group] < stencil_range) sx++; + sy = static_cast (stencil_range*bininvy_multi[bin_group]); + if (sy*binsizey_multi[bin_group] < stencil_range) sy++; + sz = static_cast (stencil_range*bininvz_multi[bin_group]); + if (sz*binsizez_multi[bin_group] < stencil_range) sz++; stencil_sx_multi[i][j] = sx; stencil_sy_multi[i][j] = sy; @@ -393,24 +397,24 @@ double NStencil::bin_distance(int i, int j, int k) /* ---------------------------------------------------------------------- - compute closest distance for a given atom type + compute closest distance for a given atom grouping ------------------------------------------------------------------------- */ -double NStencil::bin_distance_multi(int i, int j, int k, int type) +double NStencil::bin_distance_multi(int i, int j, int k, int group) { double delx,dely,delz; - if (i > 0) delx = (i-1)*binsizex_multi[type]; + if (i > 0) delx = (i-1)*binsizex_multi[group]; else if (i == 0) delx = 0.0; - else delx = (i+1)*binsizex_multi[type]; + else delx = (i+1)*binsizex_multi[group]; - if (j > 0) dely = (j-1)*binsizey_multi[type]; + if (j > 0) dely = (j-1)*binsizey_multi[group]; else if (j == 0) dely = 0.0; - else dely = (j+1)*binsizey_multi[type]; + else dely = (j+1)*binsizey_multi[group]; - if (k > 0) delz = (k-1)*binsizez_multi[type]; + if (k > 0) delz = (k-1)*binsizez_multi[group]; else if (k == 0) delz = 0.0; - else delz = (k+1)*binsizez_multi[type]; + else delz = (k+1)*binsizez_multi[group]; return (delx*delx + dely*dely + delz*delz); } @@ -427,9 +431,9 @@ double NStencil::memory_usage() bytes += atom->ntypes*maxstencil_multi_old * sizeof(int); bytes += atom->ntypes*maxstencil_multi_old * sizeof(double); } else if (neighstyle == Neighbor::MULTI) { - int n = atom->ntypes; - for (int i = 1; i <= n; i++) { - for (int j = 1; j <= n; j++) { + int n = n_multi_groups; + for (int i = 0; i < n; i++) { + for (int j = 0; j < n; j++) { bytes += maxstencil_multi[i][j] * sizeof(int); bytes += maxstencil_multi[i][j] * sizeof(int); bytes += maxstencil_multi[i][j] * sizeof(double); diff --git a/src/nstencil.h b/src/nstencil.h index 9ca8bab55d..b06f340d6f 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -44,7 +44,7 @@ class NStencil : protected Pointers { // Arrays to store options for multi itype-jtype stencils bool **flag_half_multi; // flag creation of a half stencil for itype-jtype bool **flag_skip_multi; // skip creation of itype-jtype stencils (for newton on) - int **bin_type_multi; // what type to use for bin information + int **bin_group_multi; // what group to use for bin information NStencil(class LAMMPS *); virtual ~NStencil(); @@ -66,7 +66,10 @@ class NStencil : protected Pointers { double cutneighmaxsq; double *cuttypesq; double **cutneighsq; - + double **cutmultisq; + int n_multi_groups; + int *map_type_multi; + // data from NBin class int mbinx,mbiny,mbinz; diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index 61557f2d00..4c96f41a56 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -29,16 +29,16 @@ NStencilFullMulti2d::NStencilFullMulti2d(LAMMPS *lmp) : NStencil(lmp) {} void NStencilFullMulti2d::set_stencil_properties() { - int n = atom->ntypes; + int n = n_multi_groups; int i, j; // Always look up neighbor using full stencil and neighbor's bin - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { flag_half_multi[i][j] = 0; flag_skip_multi[i][j] = 0; - bin_type_multi[i][j] = j; + bin_group_multi[i][j] = j; } } } @@ -49,33 +49,33 @@ void NStencilFullMulti2d::set_stencil_properties() void NStencilFullMulti2d::create() { - int itype, jtype, bin_type, i, j, k, ns; - int n = atom->ntypes; + int igroup, jgroup, bin_group, i, j, k, ns; + int n = n_multi_groups; double cutsq; - for (itype = 1; itype <= n; itype++) { - for (jtype = 1; jtype <= n; jtype++) { - if (flag_skip_multi[itype][jtype]) continue; + for (igroup = 0; igroup < n; igroup++) { + for (jgroup = 0; jgroup < n; jgroup++) { + if (flag_skip_multi[igroup][jgroup]) continue; ns = 0; - sx = stencil_sx_multi[itype][jtype]; - sy = stencil_sy_multi[itype][jtype]; + sx = stencil_sx_multi[igroup][jgroup]; + sy = stencil_sy_multi[igroup][jgroup]; - mbinx = stencil_mbinx_multi[itype][jtype]; - mbiny = stencil_mbiny_multi[itype][jtype]; + mbinx = stencil_mbinx_multi[igroup][jgroup]; + mbiny = stencil_mbiny_multi[igroup][jgroup]; - bin_type = bin_type_multi[itype][jtype]; + bin_group = bin_group_multi[igroup][jgroup]; - cutsq = cutneighsq[itype][jtype]; + cutsq = cutmultisq[igroup][jgroup]; for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; - nstencil_multi[itype][jtype] = ns; + nstencil_multi[igroup][jgroup] = ns; } } } diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp index f4935b70e0..bc76433723 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -29,17 +29,17 @@ NStencilFullMulti3d::NStencilFullMulti3d(LAMMPS *lmp) : NStencil(lmp) {} void NStencilFullMulti3d::set_stencil_properties() { - int n = atom->ntypes; + int n = n_multi_groups; int i, j; // Always look up neighbor using full stencil and neighbor's bin // Stencil cutoff set by i-j cutoff - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { flag_half_multi[i][j] = 0; flag_skip_multi[i][j] = 0; - bin_type_multi[i][j] = j; + bin_group_multi[i][j] = j; } } } @@ -50,37 +50,37 @@ void NStencilFullMulti3d::set_stencil_properties() void NStencilFullMulti3d::create() { - int itype, jtype, bin_type, i, j, k, ns; - int n = atom->ntypes; + int igroup, jgroup, bin_group, i, j, k, ns; + int n = n_multi_groups; double cutsq; - for (itype = 1; itype <= n; itype++) { - for (jtype = 1; jtype <= n; jtype++) { - if (flag_skip_multi[itype][jtype]) continue; + for (igroup = 0; igroup < n; igroup++) { + for (jgroup = 0; jgroup < n; jgroup++) { + if (flag_skip_multi[igroup][jgroup]) continue; ns = 0; - sx = stencil_sx_multi[itype][jtype]; - sy = stencil_sy_multi[itype][jtype]; - sz = stencil_sz_multi[itype][jtype]; + sx = stencil_sx_multi[igroup][jgroup]; + sy = stencil_sy_multi[igroup][jgroup]; + sz = stencil_sz_multi[igroup][jgroup]; - mbinx = stencil_mbinx_multi[itype][jtype]; - mbiny = stencil_mbiny_multi[itype][jtype]; - mbinz = stencil_mbinz_multi[itype][jtype]; + mbinx = stencil_mbinx_multi[igroup][jgroup]; + mbiny = stencil_mbiny_multi[igroup][jgroup]; + mbinz = stencil_mbinz_multi[igroup][jgroup]; - bin_type = bin_type_multi[itype][jtype]; + bin_group = bin_group_multi[igroup][jgroup]; - cutsq = cutneighsq[itype][jtype]; + cutsq = cutmultisq[igroup][jgroup]; for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = k*mbiny*mbinx + j*mbinx + i; - nstencil_multi[itype][jtype] = ns; + nstencil_multi[igroup][jgroup] = ns; } } } diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_2d.cpp index b407746602..8be8a1c151 100644 --- a/src/nstencil_half_multi_2d.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti2d::NStencilHalfMulti2d(LAMMPS *lmp) : void NStencilHalfMulti2d::set_stencil_properties() { - int n = atom->ntypes; + int n = n_multi_groups; int i, j; - // Cross types: use full stencil, looking one way through hierarchy + // Cross groups: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { - if(cutneighsq[i][i] > cutneighsq[j][j]) continue; + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + if(cutmultisq[i][i] > cutmultisq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutneighsq[i][i] == cutneighsq[j][j]){ + if(cutmultisq[i][i] == cutmultisq[j][j]){ flag_half_multi[i][j] = 1; - bin_type_multi[i][j] = i; + bin_group_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_type_multi[i][j] = j; + bin_group_multi[i][j] = j; } } } @@ -61,42 +61,42 @@ void NStencilHalfMulti2d::set_stencil_properties() void NStencilHalfMulti2d::create() { - int itype, jtype, bin_type, i, j, ns; - int n = atom->ntypes; + int igroup, jgroup, bin_group, i, j, ns; + int n = n_multi_groups; double cutsq; - for (itype = 1; itype <= n; itype++) { - for (jtype = 1; jtype <= n; jtype++) { - if (flag_skip_multi[itype][jtype]) continue; + for (igroup = 0; igroup < n; igroup++) { + for (jgroup = 0; jgroup < n; jgroup++) { + if (flag_skip_multi[igroup][jgroup]) continue; ns = 0; - sx = stencil_sx_multi[itype][jtype]; - sy = stencil_sy_multi[itype][jtype]; + sx = stencil_sx_multi[igroup][jgroup]; + sy = stencil_sy_multi[igroup][jgroup]; - mbinx = stencil_mbinx_multi[itype][jtype]; - mbiny = stencil_mbiny_multi[itype][jtype]; + mbinx = stencil_mbinx_multi[igroup][jgroup]; + mbiny = stencil_mbiny_multi[igroup][jgroup]; - bin_type = bin_type_multi[itype][jtype]; + bin_group = bin_group_multi[igroup][jgroup]; - cutsq = cutneighsq[itype][jtype]; + cutsq = cutmultisq[igroup][jgroup]; - if (flag_half_multi[itype][jtype]) { + if (flag_half_multi[igroup][jgroup]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) if (j > 0 || (j == 0 && i > 0)) { - if (bin_distance_multi(i,j,0,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; } } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; } - nstencil_multi[itype][jtype] = ns; + nstencil_multi[igroup][jgroup] = ns; } } } diff --git a/src/nstencil_half_multi_2d_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp index cd9f85da60..4a4e74c4a0 100755 --- a/src/nstencil_half_multi_2d_tri.cpp +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti2dTri::NStencilHalfMulti2dTri(LAMMPS *lmp) : void NStencilHalfMulti2dTri::set_stencil_properties() { - int n = atom->ntypes; + int n = n_multi_groups; int i, j; - // Cross types: use full stencil, looking one way through hierarchy + // Cross groups: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { - if(cutneighsq[i][i] > cutneighsq[j][j]) continue; + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + if(cutmultisq[i][i] > cutmultisq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutneighsq[i][i] == cutneighsq[j][j]){ + if(cutmultisq[i][i] == cutmultisq[j][j]){ flag_half_multi[i][j] = 1; - bin_type_multi[i][j] = i; + bin_group_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_type_multi[i][j] = j; + bin_group_multi[i][j] = j; } } } @@ -61,40 +61,40 @@ void NStencilHalfMulti2dTri::set_stencil_properties() void NStencilHalfMulti2dTri::create() { - int itype, jtype, bin_type, i, j, ns; - int n = atom->ntypes; + int igroup, jgroup, bin_group, i, j, ns; + int n = n_multi_groups; double cutsq; - for (itype = 1; itype <= n; itype++) { - for (jtype = 1; jtype <= n; jtype++) { - if (flag_skip_multi[itype][jtype]) continue; + for (igroup = 0; igroup < n; igroup++) { + for (jgroup = 0; jgroup < n; jgroup++) { + if (flag_skip_multi[igroup][jgroup]) continue; ns = 0; - sx = stencil_sx_multi[itype][jtype]; - sy = stencil_sy_multi[itype][jtype]; + sx = stencil_sx_multi[igroup][jgroup]; + sy = stencil_sy_multi[igroup][jgroup]; - mbinx = stencil_mbinx_multi[itype][jtype]; - mbiny = stencil_mbiny_multi[itype][jtype]; + mbinx = stencil_mbinx_multi[igroup][jgroup]; + mbiny = stencil_mbiny_multi[igroup][jgroup]; - bin_type = bin_type_multi[itype][jtype]; + bin_group = bin_group_multi[igroup][jgroup]; - cutsq = cutneighsq[itype][jtype]; + cutsq = cutmultisq[igroup][jgroup]; - if (flag_half_multi[itype][jtype]) { + if (flag_half_multi[igroup][jgroup]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; } - nstencil_multi[itype][jtype] = ns; + nstencil_multi[igroup][jgroup] = ns; } } } diff --git a/src/nstencil_half_multi_3d.cpp b/src/nstencil_half_multi_3d.cpp index d66cfe98b9..ad4970603c 100644 --- a/src/nstencil_half_multi_3d.cpp +++ b/src/nstencil_half_multi_3d.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti3d::NStencilHalfMulti3d(LAMMPS *lmp) : void NStencilHalfMulti3d::set_stencil_properties() { - int n = atom->ntypes; + int n = n_multi_groups; int i, j; - // Cross types: use full stencil, looking one way through hierarchy + // Cross groups: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { - if(cutneighsq[i][i] > cutneighsq[j][j]) continue; + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + if(cutmultisq[i][i] > cutmultisq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutneighsq[i][i] == cutneighsq[j][j]){ + if(cutmultisq[i][i] == cutmultisq[j][j]){ flag_half_multi[i][j] = 1; - bin_type_multi[i][j] = i; + bin_group_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_type_multi[i][j] = j; + bin_group_multi[i][j] = j; } } } @@ -61,48 +61,48 @@ void NStencilHalfMulti3d::set_stencil_properties() void NStencilHalfMulti3d::create() { - int itype, jtype, bin_type, i, j, k, ns; - int n = atom->ntypes; + int igroup, jgroup, bin_group, i, j, k, ns; + int n = n_multi_groups; double cutsq; - for (itype = 1; itype <= n; itype++) { - for (jtype = 1; jtype <= n; jtype++) { - if (flag_skip_multi[itype][jtype]) continue; + for (igroup = 0; igroup < n; igroup++) { + for (jgroup = 0; jgroup < n; jgroup++) { + if (flag_skip_multi[igroup][jgroup]) continue; ns = 0; - sx = stencil_sx_multi[itype][jtype]; - sy = stencil_sy_multi[itype][jtype]; - sz = stencil_sz_multi[itype][jtype]; + sx = stencil_sx_multi[igroup][jgroup]; + sy = stencil_sy_multi[igroup][jgroup]; + sz = stencil_sz_multi[igroup][jgroup]; - mbinx = stencil_mbinx_multi[itype][jtype]; - mbiny = stencil_mbiny_multi[itype][jtype]; - mbinz = stencil_mbinz_multi[itype][jtype]; + mbinx = stencil_mbinx_multi[igroup][jgroup]; + mbiny = stencil_mbiny_multi[igroup][jgroup]; + mbinz = stencil_mbinz_multi[igroup][jgroup]; - bin_type = bin_type_multi[itype][jtype]; + bin_group = bin_group_multi[igroup][jgroup]; - cutsq = cutneighsq[itype][jtype]; + cutsq = cutmultisq[igroup][jgroup]; - if (flag_half_multi[itype][jtype]) { + if (flag_half_multi[igroup][jgroup]) { 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_multi(i,j,k,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = k*mbiny*mbinx + j*mbinx + i; } } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = k*mbiny*mbinx + j*mbinx + i; } - nstencil_multi[itype][jtype] = ns; + nstencil_multi[igroup][jgroup] = ns; } } } diff --git a/src/nstencil_half_multi_3d_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp index e4a5747ca6..779f0865a5 100755 --- a/src/nstencil_half_multi_3d_tri.cpp +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti3dTri::NStencilHalfMulti3dTri(LAMMPS *lmp) : void NStencilHalfMulti3dTri::set_stencil_properties() { - int n = atom->ntypes; + int n = n_multi_groups; int i, j; - // Cross types: use full stencil, looking one way through hierarchy + // Cross groups: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { - if(cutneighsq[i][i] > cutneighsq[j][j]) continue; + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + if(cutmultisq[i][i] > cutmultisq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutneighsq[i][i] == cutneighsq[j][j]){ + if(cutmultisq[i][i] == cutmultisq[j][j]){ flag_half_multi[i][j] = 1; - bin_type_multi[i][j] = i; + bin_group_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_type_multi[i][j] = j; + bin_group_multi[i][j] = j; } } } @@ -61,46 +61,46 @@ void NStencilHalfMulti3dTri::set_stencil_properties() void NStencilHalfMulti3dTri::create() { - int itype, jtype, bin_type, i, j, k, ns; - int n = atom->ntypes; + int igroup, jgroup, bin_group, i, j, k, ns; + int n = n_multi_groups; double cutsq; - for (itype = 1; itype <= n; itype++) { - for (jtype = 1; jtype <= n; jtype++) { - if (flag_skip_multi[itype][jtype]) continue; + for (igroup = 0; igroup < n; igroup++) { + for (jgroup = 0; jgroup < n; jgroup++) { + if (flag_skip_multi[igroup][jgroup]) continue; ns = 0; - sx = stencil_sx_multi[itype][jtype]; - sy = stencil_sy_multi[itype][jtype]; - sz = stencil_sz_multi[itype][jtype]; + sx = stencil_sx_multi[igroup][jgroup]; + sy = stencil_sy_multi[igroup][jgroup]; + sz = stencil_sz_multi[igroup][jgroup]; - mbinx = stencil_mbinx_multi[itype][jtype]; - mbiny = stencil_mbiny_multi[itype][jtype]; - mbinz = stencil_mbinz_multi[itype][jtype]; + mbinx = stencil_mbinx_multi[igroup][jgroup]; + mbiny = stencil_mbiny_multi[igroup][jgroup]; + mbinz = stencil_mbinz_multi[igroup][jgroup]; - bin_type = bin_type_multi[itype][jtype]; + bin_group = bin_group_multi[igroup][jgroup]; - cutsq = cutneighsq[itype][jtype]; + cutsq = cutmultisq[igroup][jgroup]; - if (flag_half_multi[itype][jtype]) { + if (flag_half_multi[igroup][jgroup]) { for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = k*mbiny*mbinx + j*mbinx + i; } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = k*mbiny*mbinx + j*mbinx + i; } - nstencil_multi[itype][jtype] = ns; + nstencil_multi[igroup][jgroup] = ns; } } } From a88fab75587bfbe6e86fd65a20fe5f081c89538c Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 26 Dec 2020 11:07:48 -0700 Subject: [PATCH 43/73] Missed typos in user-omp --- src/USER-OMP/npair_half_multi_newton_tri_omp.cpp | 2 +- src/USER-OMP/npair_half_size_multi_newton_omp.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index 0289967d30..2e4cf0ec19 100755 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -118,7 +118,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) for (j = js; j >= 0; j = bins_multi[jgroup][j]) { // if same size (same group), use half stencil - if(cutmultisq[igroup][igroup] == cutmutlisq[jgroup][jgroup]){ + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index 974b8c5809..87b4fa1601 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -83,7 +83,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) ibin = atom2bin_multi[igroup][i]; // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_group; jgroup++) { + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { // if same group use own bin if(igroup == jgroup) jbin = ibin; From 50be21902ef87bd6a789144f509ac919812861f0 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 26 Dec 2020 16:00:33 -0700 Subject: [PATCH 44/73] Reducing memory consumption for multi --- src/USER-OMP/npair_full_multi_omp.cpp | 4 +- src/USER-OMP/npair_half_multi_newtoff_omp.cpp | 4 +- src/USER-OMP/npair_half_multi_newton_omp.cpp | 10 ++--- .../npair_half_multi_newton_tri_omp.cpp | 4 +- .../npair_half_size_multi_newtoff_omp.cpp | 4 +- .../npair_half_size_multi_newton_omp.cpp | 10 ++--- .../npair_half_size_multi_newton_tri_omp.cpp | 4 +- src/nbin.cpp | 8 +--- src/nbin.h | 2 - src/nbin_multi.cpp | 37 +++++++------------ src/npair.cpp | 2 - src/npair.h | 3 +- src/npair_full_multi.cpp | 4 +- src/npair_half_multi_newtoff.cpp | 4 +- src/npair_half_multi_newton.cpp | 10 ++--- src/npair_half_multi_newton_tri.cpp | 4 +- src/npair_half_size_multi_newtoff.cpp | 4 +- src/npair_half_size_multi_newton.cpp | 10 ++--- src/npair_half_size_multi_newton_tri.cpp | 4 +- 19 files changed, 56 insertions(+), 76 deletions(-) diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index 11b8bae196..4b38e660d4 100755 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -90,7 +90,7 @@ void NPairFullMultiOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -108,7 +108,7 @@ void NPairFullMultiOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if (i == j) continue; jtype = type[j]; diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp index e3e03ee8ed..93d150f445 100755 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -92,7 +92,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -112,7 +112,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jgroup][j]) { + for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index 28db1b3c0d..a7a3e6d6f7 100755 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -91,7 +91,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -110,9 +110,9 @@ void NPairHalfMultiNewtonOmp::build(NeighList *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 - js = bins_multi[igroup][i]; + js = bins[i]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -154,7 +154,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if(j < i) continue; if (j >= nlocal) { @@ -202,7 +202,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index 2e4cf0ec19..b5882580a8 100755 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -92,7 +92,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -115,7 +115,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { // if same size (same group), use half stencil if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp index 35cfaad5e6..0d588b2f24 100755 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp @@ -81,7 +81,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -101,7 +101,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jgroup][j]) { + for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index 87b4fa1601..0137873600 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -80,7 +80,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -99,9 +99,9 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *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 - js = bins_multi[igroup][i]; + js = bins[i]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -136,7 +136,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if(j < i) continue; if (j >= nlocal) { @@ -177,7 +177,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp index d1c5a97498..396e870846 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp @@ -81,7 +81,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -105,7 +105,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { // if same size (same group), use half stencil if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ diff --git a/src/nbin.cpp b/src/nbin.cpp index cb10014b36..c28c22882c 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -40,8 +40,6 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) binsizex_multi = nullptr; binsizey_multi = nullptr; binsizez_multi = nullptr; bininvx_multi = nullptr; bininvy_multi = nullptr; bininvz_multi = nullptr; binhead_multi = nullptr; - bins_multi = nullptr; - atom2bin_multi = nullptr; maxbins_multi = nullptr; map_type_multi = nullptr; @@ -67,7 +65,7 @@ NBin::~NBin() memory->destroy(bins); memory->destroy(atom2bin); - if (!bins_multi) return; + if (!binhead_multi) return; memory->destroy(nbinx_multi); memory->destroy(nbiny_multi); @@ -89,12 +87,8 @@ NBin::~NBin() for (int n = 0; n < maxgroups; n++) { memory->destroy(binhead_multi[n]); - memory->destroy(bins_multi[n]); - memory->destroy(atom2bin_multi[n]); } delete [] binhead_multi; - delete [] bins_multi; - delete [] atom2bin_multi; memory->destroy(maxbins_multi); } diff --git a/src/nbin.h b/src/nbin.h index 19035d619e..e31e5bab99 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -48,8 +48,6 @@ class NBin : protected Pointers { double *bininvx_multi, *bininvy_multi, *bininvz_multi; int **binhead_multi; - int **bins_multi; - int **atom2bin_multi; NBin(class LAMMPS *); ~NBin(); diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index b39489c3fe..b8832bdfea 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -46,19 +46,16 @@ void NBinMulti::bin_atoms_setup(int nall) } } - // bins_multi[n] and atom2bin_multi[n] = per-atom vectors + // bins and atom2bin = per-atom vectors // for both local and ghost atoms - - // TODO: maxatom should be maxatom per group + // for multi, bins and atom2bin correspond to different binlists if (nall > maxatom) { maxatom = nall; - for (int n = 0; n < maxgroups; n++) { - memory->destroy(bins_multi[n]); - memory->destroy(atom2bin_multi[n]); - memory->create(bins_multi[n], maxatom, "neigh:bin_multi"); - memory->create(atom2bin_multi[n], maxatom, "neigh:atom2bin_multi"); - } + memory->destroy(bins); + memory->create(bins,maxatom,"neigh:bins"); + memory->destroy(atom2bin); + memory->create(atom2bin,maxatom,"neigh:atom2bin"); } } @@ -90,22 +87,16 @@ void NBinMulti::setup_bins(int style) // Clear any/all memory for existing types - for (n = 0; n < maxgroups; n++) { - memory->destroy(atom2bin_multi[n]); + for (n = 0; n < maxgroups; n++) memory->destroy(binhead_multi[n]); - memory->destroy(bins_multi[n]); - } - delete [] atom2bin_multi; + delete [] binhead_multi; - delete [] bins_multi; // Realloacte at updated maxtypes maxgroups = n_multi_groups; - atom2bin_multi = new int*[maxgroups](); binhead_multi = new int*[maxgroups](); - bins_multi = new int*[maxgroups](); memory->destroy(nbinx_multi); memory->destroy(nbiny_multi); @@ -321,24 +312,24 @@ void NBinMulti::bin_atoms() if (mask[i] & bitmask) { n = map_type_multi[type[i]]; ibin = coord2bin_multi(x[i], n); - atom2bin_multi[n][i] = ibin; - bins_multi[n][i] = binhead_multi[n][ibin]; + atom2bin[i] = ibin; + bins[i] = binhead_multi[n][ibin]; binhead_multi[n][ibin] = i; } } for (i = atom->nfirst-1; i >= 0; i--) { n = map_type_multi[type[i]]; ibin = coord2bin_multi(x[i], n); - atom2bin_multi[n][i] = ibin; - bins_multi[n][i] = binhead_multi[n][ibin]; + atom2bin[i] = ibin; + bins[i] = binhead_multi[n][ibin]; binhead_multi[n][ibin] = i; } } else { for (i = nall-1; i >= 0; i--) { n = map_type_multi[type[i]]; ibin = coord2bin_multi(x[i], n); - atom2bin_multi[n][i] = ibin; - bins_multi[n][i] = binhead_multi[n][ibin]; + atom2bin[i] = ibin; + bins[i] = binhead_multi[n][ibin]; binhead_multi[n][ibin] = i; } } diff --git a/src/npair.cpp b/src/npair.cpp index b2ecc953ea..facd9086d1 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -156,8 +156,6 @@ void NPair::copy_bin_info() bininvy_multi = nb->bininvy_multi; bininvz_multi = nb->bininvz_multi; - atom2bin_multi = nb->atom2bin_multi; - bins_multi = nb->bins_multi; binhead_multi = nb->binhead_multi; } diff --git a/src/npair.h b/src/npair.h index 4d99e3a8e6..d1fcf2e6b2 100644 --- a/src/npair.h +++ b/src/npair.h @@ -87,8 +87,7 @@ class NPair : protected Pointers { int *mbinx_multi, *mbiny_multi, *mbinz_multi; int *mbinxlo_multi, *mbinylo_multi, *mbinzlo_multi; double *bininvx_multi, *bininvy_multi, *bininvz_multi; - int **binhead_multi,**bins_multi; - int **atom2bin_multi; + int **binhead_multi; // data from NStencil class diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp index f29f04107a..c78f7b2d1d 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi.cpp @@ -78,7 +78,7 @@ void NPairFullMulti::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -96,7 +96,7 @@ void NPairFullMulti::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if (i == j) continue; jtype = type[j]; diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index 85832b11b1..11bab91e6a 100755 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -80,7 +80,7 @@ void NPairHalfMultiNewtoff::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -100,7 +100,7 @@ void NPairHalfMultiNewtoff::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jgroup][j]) { + for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index d18b009460..777aab5826 100755 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -79,7 +79,7 @@ void NPairHalfMultiNewton::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -98,9 +98,9 @@ void NPairHalfMultiNewton::build(NeighList *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 - js = bins_multi[igroup][i]; + js = bins[i]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -142,7 +142,7 @@ void NPairHalfMultiNewton::build(NeighList *list) js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if(j < i) continue; if (j >= nlocal) { @@ -190,7 +190,7 @@ void NPairHalfMultiNewton::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index ebf871ad99..6969c9cfab 100755 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -79,7 +79,7 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -102,7 +102,7 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { // if same size (same group), use half stencil if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index ec4fbad9aa..e361bbce76 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -71,7 +71,7 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -91,7 +91,7 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jgroup][j]) { + for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index c3a13f4b81..500e06bc35 100755 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -68,7 +68,7 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -87,9 +87,9 @@ void NPairHalfSizeMultiNewton::build(NeighList *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 - js = bins_multi[igroup][i]; + js = bins[i]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -124,7 +124,7 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if(j < i) continue; if (j >= nlocal) { @@ -165,7 +165,7 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 7c792c6a19..0000f7b4d3 100755 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -68,7 +68,7 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -92,7 +92,7 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { // if same size (same group), use half stencil if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ From d5f34f62967070da33a64f9dd800bf93267be9dd Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Fri, 8 Jan 2021 15:27:23 -0700 Subject: [PATCH 45/73] Examples and documentation --- doc/src/comm_modify.rst | 16 +- doc/src/neigh_modify.rst | 20 +- doc/src/neighbor.rst | 32 +-- examples/multi/in.colloid | 67 +++++++ examples/multi/in.granular | 58 ++++++ examples/multi/log.30Nov20.colloid.intel.1 | 183 ++++++++++++++++++ examples/multi/log.30Nov20.colloid.intel.4 | 183 ++++++++++++++++++ .../multi/log.30Nov20.colloid.old.intel.1 | 183 ++++++++++++++++++ .../multi/log.30Nov20.colloid.old.intel.4 | 183 ++++++++++++++++++ examples/multi/log.30Nov20.granular.intel.1 | 175 +++++++++++++++++ examples/multi/log.30Nov20.granular.intel.4 | 175 +++++++++++++++++ .../multi/log.30Nov20.granular.old.intel.1 | 175 +++++++++++++++++ .../multi/log.30Nov20.granular.old.intel.4 | 175 +++++++++++++++++ src/comm.cpp | 2 + 14 files changed, 1604 insertions(+), 23 deletions(-) create mode 100644 examples/multi/in.colloid create mode 100644 examples/multi/in.granular create mode 100644 examples/multi/log.30Nov20.colloid.intel.1 create mode 100644 examples/multi/log.30Nov20.colloid.intel.4 create mode 100644 examples/multi/log.30Nov20.colloid.old.intel.1 create mode 100644 examples/multi/log.30Nov20.colloid.old.intel.4 create mode 100644 examples/multi/log.30Nov20.granular.intel.1 create mode 100644 examples/multi/log.30Nov20.granular.intel.4 create mode 100644 examples/multi/log.30Nov20.granular.old.intel.1 create mode 100644 examples/multi/log.30Nov20.granular.old.intel.4 diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 895d3cf4fd..5f084561a1 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -66,9 +66,10 @@ For many systems this is an efficient algorithm, but for systems with widely varying cutoffs for different type pairs, the *multi* mode can be faster. In this case, each atom type is assigned its own distance cutoff for communication purposes, and fewer atoms will be -communicated. See the :doc:`neighbor multi ` command for a +communicated. See the :doc:`neighbor multi ` command for a neighbor list construction option that may also be beneficial for -simulations of this kind. +simulations of this kind. The *multi* mode is compatable with both the +*multi* and *multi/old* neighbor styles. The *cutoff* keyword allows you to extend the ghost cutoff distance for communication mode *single*\ , which is the distance from the borders @@ -95,11 +96,12 @@ using the usual asterisk notation can be given. For granular pair styles, the default cutoff is set to the sum of the current maximum atomic radii for each type. -The *cutoff/bytype* option applies to *multi* and automtically sets communication -cutoffs for each particle type based on the largest interaction distance -between two particles of the same type. This method is only compatible -with Newton on and the *bytype* neighbor style. See the :doc:`neighbor bytype ` -command for more information. +The *multi/reduce* option applies to *multi* and automatically sets communication +cutoffs for different sized particles based on the largest interaction distance +between two particles in the same multi grouping. This reduces the number of +ghost that need to be communicated This method is only compatible with the +*multi* neighbor style and requires only half neighbor lists and Newton on. +See the :doc:`neighbor multi ` command for more information. These are simulation scenarios in which it may be useful or even necessary to set a ghost cutoff > neighbor cutoff: diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 2618953dd7..33f24af96e 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -14,7 +14,7 @@ Syntax .. parsed-literal:: - keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* + keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *multi/custom* *delay* value = N N = delay building until this many steps since last build *every* value = M @@ -47,6 +47,9 @@ Syntax N = max number of neighbors of one atom *binsize* value = size size = bin size for neighbor list construction (distance units) + *multi/custom* values = N types + N = number of custom groups + types = N separate types or groups of types (see below) Examples """""""" @@ -58,6 +61,7 @@ Examples neigh_modify exclude group frozen frozen check no neigh_modify exclude group residue1 chain3 neigh_modify exclude molecule/intra rigid + neigh_modify multi/custom 2 1*2 3*4 Description """"""""""" @@ -197,6 +201,20 @@ small, the optimal number of atoms is checked, but bin overhead goes up. If you set the binsize to 0.0, LAMMPS will use the default binsize of 1/2 the cutoff. +The *multi/custom* option allows you to define custom groups of atom +types for the *multi* neighbor mode. By grouping atom types with +similar cutoffs, one may be able to improve performance by reducing +overhead. You must first specify the number of custom groups N to be +defined followed by N ranges of types. The range can be specified as a +single numeric value, or a wildcard asterisk can be used to specify a range +of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For +example, if N = the number of atom types, then an asterisk with no numeric +values means all types from 1 to N. A leading asterisk means all types +from 1 to n (inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n (inclusive). +Note that any atom types not included in a custom group will be automatically +placed within a new, separate group. + Restrictions """""""""""" diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index f638160d21..52d59dae75 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -11,7 +11,7 @@ Syntax neighbor skin style * skin = extra distance beyond force cutoff (distance units) -* style = *bin* or *nsq* or *multi* or *bytype* +* style = *bin* or *nsq* or *multi* or *multi/old* Examples """""""" @@ -55,22 +55,24 @@ For the *bin* style, the bin size is set to 1/2 of the largest cutoff distance between any pair of atom types and a single set of bins is defined to search over for all atom types. This can be inefficient if one pair of types has a very long cutoff, but -other type pairs have a much shorter cutoff. For style *multi* the -bin size is set to 1/2 of the shortest cutoff distance and multiple -sets of bins are defined to search over for different atom types. +other type pairs have a much shorter cutoff. The *multi* style uses +different sized bins for groups of different sized particles. Different +sets of bins are then used to construct the neighbor lists as as further +described by Shire, Hanley, and Stratford :ref:`(Shire) `. This imposes some extra setup overhead, but the searches themselves -may be much faster for the short-cutoff cases. -See the :doc:`comm_modify mode multi ` command for a -communication option that may also be beneficial for simulations of -this kind. +may be much faster. By default, separate groups of particles are defined +for each atom type. For systems with two or more types with similar +cutoffs, one can reduce the extra overhead by defining custom groupings +using the :doc:`neigh_modify ` command. See the +:doc:`comm_modify mode bytype ` command for compatible +communication options that may be beneficial for simulations of this kind. -The *bytype* style is an extension of the *multi* style that was -presented by Shire, Hanley, and Stratford :ref:`(Shire) `. -For style *bytype*, different bin lists are created for each different -type and separate bin sizes are generated. Whether *bytype* or *multi* -is faster may depend on the specifics of your system. See the -:doc:`comm_modify mode bytype ` command for a compatible -communication option. +An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest +cutoff distance and multiple sets of bins are defined to search over for +different atom types. This algorithm used to be the default *multi* +algorithm in LAMMPS but was found to be significantly slower than the new +approach. Although, there may be instances where the *multi/old* style +could outperform the new style. The :doc:`neigh_modify ` command has additional options that control how often neighbor lists are built and which pairs are diff --git a/examples/multi/in.colloid b/examples/multi/in.colloid new file mode 100644 index 0000000000..b332560777 --- /dev/null +++ b/examples/multi/in.colloid @@ -0,0 +1,67 @@ +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +create_atoms 1 box + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +set group all type/fraction 3 0.333 43684 +set group all type/fraction 4 0.250 87811 + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +delete_atoms region sphere2 +create_atoms 5 single 60.0 60.0 0.0 units box +create_atoms 5 single 130.0 130.0 0.0 units box + +set type 1 mass 400 +set type 2 mass 1 + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 multi/custom 2 1*4 5 +comm_modify mode multi multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 & + mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +#dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 diff --git a/examples/multi/in.granular b/examples/multi/in.granular new file mode 100644 index 0000000000..00dd4ad2bb --- /dev/null +++ b/examples/multi/in.granular @@ -0,0 +1,58 @@ +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +create_atoms 1 box +change_box all triclinic + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +delete_atoms region sphere2 +create_atoms 2 single 20.0 20.0 0.0 units box +create_atoms 2 single 60.0 60.0 0.0 units box + +set type 2 mass 400 +set type 1 mass 1 +set type 2 diameter 20 +set type 1 diameter 1 + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 +comm_modify mode multi vel yes multi/reduce + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +#dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 diff --git a/examples/multi/log.30Nov20.colloid.intel.1 b/examples/multi/log.30Nov20.colloid.intel.1 new file mode 100644 index 0000000000..2bc82eaab0 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.intel.1 @@ -0,0 +1,183 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #/old +neigh_modify delay 0 multi/custom 2 1*4 5 +comm_modify mode multi multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d + bin: multi +Per MPI rank memory allocation (min/avg/max) = 5.538 | 5.538 | 5.538 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69 + 3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12 + 4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299 + 5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92 + 6000 2.0797015 -0.086800285 1.992214 0.082095164 78182.702 + 7000 2.0867886 -0.10960963 1.9764893 0.10103655 63990.386 + 8000 2.0803886 -0.12736298 1.9523381 0.12561727 52648.372 + 9000 2.0605661 -0.14572043 1.9141648 0.15154081 44589.764 + 10000 2.0636909 -0.18556771 1.8774412 0.1604707 38996.941 + 11000 2.0498344 -0.20303461 1.8461224 0.18295046 34927.993 + 12000 2.0466611 -0.2217963 1.8241884 0.23031182 31760.363 + 13000 2.0441824 -0.24716826 1.7963386 0.22167931 29178.226 + 14000 2.047513 -0.26988172 1.7769547 0.24070752 26991.372 + 15000 2.0154283 -0.26144354 1.7533187 0.27587713 25247.715 + 16000 2.0160849 -0.28106984 1.7343488 0.32297139 23703.607 + 17000 2.0184729 -0.31071368 1.7070922 0.29815613 22300.6 + 18000 2.0237288 -0.33944941 1.6836106 0.3262795 21098.856 + 19000 2.0329827 -0.35438937 1.6779215 0.33691952 19989.867 + 20000 2.021113 -0.37316841 1.6472766 0.39687648 18978.666 + 21000 2.0352439 -0.40857976 1.6259915 0.38632613 18146.277 + 22000 2.0158566 -0.41271329 1.6024771 0.41480502 17409.593 + 23000 2.0170409 -0.42611776 1.5902566 0.40446612 16748.968 + 24000 2.0108878 -0.43899286 1.5712304 0.42075035 16086.941 + 25000 2.0218394 -0.47012156 1.5510497 0.46655183 15460.154 + 26000 2.0100713 -0.47985916 1.5295479 0.45575323 15013.774 + 27000 2.0251738 -0.5016665 1.5228381 0.50151992 14591.521 + 28000 2.0062966 -0.50284394 1.5027897 0.5462034 14135.093 + 29000 2.0146666 -0.53126035 1.4827405 0.60379062 13725.945 + 30000 2.0036455 -0.53246643 1.4705169 0.56784088 13417.305 + 31000 2.0127662 -0.54487777 1.4672233 0.6427741 13139.392 + 32000 2.0221816 -0.5625554 1.4589579 0.60695012 12779.609 + 33000 2.024983 -0.59515221 1.4291616 0.60005385 12584.572 + 34000 2.0184045 -0.59033569 1.4274018 0.62519753 12355.49 + 35000 2.0155635 -0.61190466 1.4029927 0.71044196 12106.819 + 36000 2.0252503 -0.61581601 1.408765 0.68805882 11728.608 + 37000 2.0112487 -0.64540754 1.3651765 0.66981639 11475.772 + 38000 2.0147475 -0.64161981 1.3724619 0.71130901 11285.511 + 39000 2.0213092 -0.67174661 1.3488946 0.6969697 11044.647 + 40000 2.0178739 -0.67924699 1.3379601 0.77309897 10824.198 + 41000 1.9952353 -0.67490899 1.3196669 0.76592358 10646.649 + 42000 2.002415 -0.70533555 1.2964178 0.81084741 10519.804 + 43000 2.0211625 -0.71370366 1.3067909 0.77355048 10434.893 + 44000 2.0252106 -0.72635544 1.2981859 0.83770143 10132.262 + 45000 2.0126446 -0.75197714 1.2600024 0.88927993 9946.7842 + 46000 2.0431159 -0.78445975 1.257981 0.84492327 9869.8151 + 47000 2.0199724 -0.76967899 1.2496259 0.90977181 9653.4334 + 48000 2.0109636 -0.78968551 1.2206135 0.89458323 9496.7246 + 49000 2.0131059 -0.79687252 1.2155681 0.91239613 9418.3093 + 50000 2.0073361 -0.79981468 1.206858 0.98524334 9289.4715 +Loop time of 20.4651 on 1 procs for 50000 steps with 3026 atoms + +Performance: 1055453.279 tau/day, 2443.179 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.099 | 11.099 | 11.099 | 0.0 | 54.23 +Neigh | 2.7536 | 2.7536 | 2.7536 | 0.0 | 13.46 +Comm | 0.53353 | 0.53353 | 0.53353 | 0.0 | 2.61 +Output | 0.11209 | 0.11209 | 0.11209 | 0.0 | 0.55 +Modify | 5.1627 | 5.1627 | 5.1627 | 0.0 | 25.23 +Other | | 0.8046 | | | 3.93 + +Nlocal: 3026.00 ave 3026 max 3026 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 584.000 ave 584 max 584 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 25892.0 ave 25892 max 25892 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 25892 +Ave neighs/atom = 8.5565102 +Neighbor list builds = 4330 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:20 diff --git a/examples/multi/log.30Nov20.colloid.intel.4 b/examples/multi/log.30Nov20.colloid.intel.4 new file mode 100644 index 0000000000..48a5846a09 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.intel.4 @@ -0,0 +1,183 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #/old +neigh_modify delay 0 multi/custom 2 1*4 5 +comm_modify mode multi multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d + bin: multi +Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.382 | 5.384 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688 + 3000 1.8956738 -0.090814176 1.8042332 0.075557943 77825.289 + 4000 1.9570462 -0.072505537 1.8838939 0.072824365 90931.708 + 5000 2.0376745 -0.083247829 1.9537533 0.068496975 90055.295 + 6000 2.0744887 -0.085395371 1.9884077 0.0821927 78070.648 + 7000 2.1002183 -0.11654617 1.9829781 0.10523249 63934.448 + 8000 2.0818325 -0.13271654 1.948428 0.11909162 52636.484 + 9000 2.0693987 -0.16404154 1.9046733 0.14702552 44539.609 + 10000 2.0667772 -0.19779488 1.8682993 0.17245383 38822.542 + 11000 2.0640582 -0.22114917 1.842227 0.18083079 34788.927 + 12000 2.0308462 -0.20353105 1.8266441 0.20640739 31706.009 + 13000 2.0395895 -0.24217765 1.7967378 0.21832952 29152.654 + 14000 2.030848 -0.2586169 1.77156 0.26577748 27068.89 + 15000 2.0222966 -0.27554585 1.7460825 0.2777169 25272.786 + 16000 2.0398867 -0.31547563 1.723737 0.27763622 23666.792 + 17000 2.03026 -0.32453791 1.7050512 0.28099246 22272.809 + 18000 2.0345512 -0.35026242 1.6836164 0.36600779 21023.172 + 19000 2.0242864 -0.35813231 1.6654851 0.33415432 19941.244 + 20000 2.0132465 -0.36563904 1.6469422 0.403365 18979.884 + 21000 2.0280384 -0.4075867 1.6197815 0.37205362 18152.487 + 22000 2.0206494 -0.40600336 1.6139782 0.42704594 17370.812 + 23000 2.0395761 -0.45083258 1.5880695 0.40276343 16700.427 + 24000 2.017203 -0.44930293 1.5672335 0.43867313 16161.79 + 25000 2.0191846 -0.4672218 1.5512955 0.47031215 15622.756 + 26000 2.0131624 -0.46436088 1.5481363 0.51717944 15141.645 + 27000 2.0322461 -0.50659994 1.5249745 0.49218933 14627.657 + 28000 2.0169304 -0.50555565 1.5107082 0.55547935 14186.079 + 29000 2.024656 -0.52258414 1.5014028 0.59125812 13759.99 + 30000 2.0153725 -0.53585947 1.478847 0.57235811 13384.355 + 31000 2.0163261 -0.56383766 1.4518221 0.58232057 13098.196 + 32000 2.0109673 -0.56784395 1.4424588 0.58282178 12831.934 + 33000 2.0099169 -0.57625621 1.4329964 0.65139601 12479.442 + 34000 2.0238152 -0.60189607 1.4212503 0.62659152 12210.628 + 35000 2.0359989 -0.62654733 1.4087787 0.67574446 11972.725 + 36000 2.0222689 -0.62880837 1.3927923 0.66602146 11690.049 + 37000 1.9982569 -0.62746376 1.3701328 0.71326589 11433.825 + 38000 1.9969836 -0.63975181 1.3565719 0.72799891 11285.497 + 39000 2.0071087 -0.65781805 1.3486274 0.79121297 11107.469 + 40000 2.0243046 -0.6881221 1.3355135 0.77519099 10943.846 + 41000 2.0351657 -0.70309175 1.3314014 0.68815156 10742.515 + 42000 2.0224788 -0.70975664 1.3120538 0.80484619 10505.657 + 43000 2.0123135 -0.70818545 1.3034631 0.84204556 10353.024 + 44000 1.999883 -0.70981202 1.2894101 0.94070546 10212.224 + 45000 2.0127291 -0.73338075 1.2786832 0.82095205 10109.959 + 46000 2.0109037 -0.75130029 1.2589389 0.88538358 9953.4822 + 47000 1.9879175 -0.73152019 1.2557404 0.92089629 9832.892 + 48000 2.0108204 -0.76655178 1.2436041 0.95379465 9633.6453 + 49000 1.9868193 -0.76613798 1.2200247 0.88790224 9504.2918 + 50000 2.0141467 -0.80029827 1.2131829 1.0064263 9346.3268 +Loop time of 7.28248 on 4 procs for 50000 steps with 3026 atoms + +Performance: 2966022.789 tau/day, 6865.793 timesteps/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.1624 | 2.5918 | 2.9227 | 17.4 | 35.59 +Neigh | 0.62508 | 0.7436 | 0.83321 | 9.2 | 10.21 +Comm | 1.1035 | 1.5265 | 2.0746 | 29.3 | 20.96 +Output | 0.050094 | 0.050233 | 0.05062 | 0.1 | 0.69 +Modify | 1.8164 | 1.8966 | 1.9583 | 4.2 | 26.04 +Other | | 0.4737 | | | 6.50 + +Nlocal: 756.500 ave 839 max 673 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Nghost: 292.500 ave 307 max 282 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 6435.25 ave 7367 max 5493 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 25741 +Ave neighs/atom = 8.5066094 +Neighbor list builds = 4335 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:07 diff --git a/examples/multi/log.30Nov20.colloid.old.intel.1 b/examples/multi/log.30Nov20.colloid.old.intel.1 new file mode 100644 index 0000000000..291e8f89df --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.old.intel.1 @@ -0,0 +1,183 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old +neigh_modify delay 0 #multi/custom 2 1*4 5 +comm_modify mode multi #multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/old/newton + stencil: half/multi/old/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.611 | 5.611 | 5.611 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69 + 3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12 + 4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299 + 5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92 + 6000 2.0797015 -0.086800284 1.992214 0.082095164 78182.702 + 7000 2.086794 -0.10961479 1.9764895 0.10103993 63990.387 + 8000 2.082863 -0.12779588 1.9543788 0.12672452 52629.802 + 9000 2.0718275 -0.15189022 1.9192526 0.14728063 44541.722 + 10000 2.0603856 -0.18054161 1.8791631 0.16715133 38940.135 + 11000 2.046791 -0.20458359 1.841531 0.19532742 34907.116 + 12000 2.0406846 -0.2252868 1.8147234 0.2036178 31740.208 + 13000 2.0369763 -0.23721632 1.7990869 0.25542564 29079.901 + 14000 2.0376121 -0.26282517 1.7741135 0.24722118 26947.344 + 15000 2.0312772 -0.2851101 1.7454959 0.2801199 25180.963 + 16000 2.0080448 -0.28992973 1.7174515 0.30099318 23723.043 + 17000 2.0234993 -0.30440169 1.7184289 0.3193226 22342.977 + 18000 2.0216103 -0.32036933 1.7005729 0.3460322 21068.99 + 19000 2.0493952 -0.37711533 1.6716026 0.33804972 20013.325 + 20000 2.0307894 -0.38462795 1.6454903 0.37041981 19092.745 + 21000 2.0328577 -0.39442652 1.6377594 0.36327057 18260.298 + 22000 2.0325613 -0.40481002 1.6270796 0.42756691 17447.199 + 23000 2.0199358 -0.42175719 1.5975111 0.40948041 16768.71 + 24000 2.0149952 -0.43618764 1.5781417 0.45406069 16187.334 + 25000 2.0153221 -0.45884172 1.5558143 0.52717203 15605.577 + 26000 2.0099026 -0.47080566 1.5384327 0.49181459 15088.041 + 27000 2.0128537 -0.49799999 1.5141885 0.53907465 14590.392 + 28000 2.0287266 -0.53112525 1.4969309 0.59750714 14208.419 + 29000 2.0143609 -0.53175704 1.4819381 0.56118773 13840.642 + 30000 2.0235262 -0.53923416 1.4836234 0.52579997 13500.15 + 31000 2.0390444 -0.57976823 1.4586023 0.5760349 13082.091 + 32000 2.018046 -0.57797686 1.4394022 0.59127933 12761.726 + 33000 2.0059068 -0.57185148 1.4333925 0.58992758 12473.866 + 34000 1.9828456 -0.57147221 1.4107181 0.77593228 12208.869 + 35000 1.9900097 -0.58349168 1.4058604 0.681968 11937.285 + 36000 2.0271405 -0.64374859 1.382722 0.63152587 11675.264 + 37000 2.0032809 -0.63520712 1.3674117 0.71639384 11440.274 + 38000 2.0000566 -0.63941617 1.3599795 0.74099652 11235.252 + 39000 1.9872705 -0.64765522 1.3389586 0.7575743 11080.857 + 40000 2.0224403 -0.6795645 1.3422075 0.82918546 10861.905 + 41000 2.0137595 -0.69863075 1.3144633 0.80397759 10712.981 + 42000 1.9950915 -0.68892531 1.3055069 0.77631365 10632.931 + 43000 2.0080851 -0.70534369 1.3020778 0.82408436 10408.82 + 44000 2.0239806 -0.73189482 1.2914169 0.83228695 10227.18 + 45000 2.0019542 -0.72613202 1.2751606 0.9145618 10044.013 + 46000 2.0173095 -0.75370218 1.2629407 0.99791312 9837.9611 + 47000 1.9921201 -0.75875076 1.232711 1.0047839 9711.2083 + 48000 2.0283587 -0.79063641 1.237052 0.83617499 9610.9933 + 49000 2.0051919 -0.79078067 1.2137485 0.95651813 9411.7165 + 50000 2.0140985 -0.81796958 1.1954634 0.93791038 9296.069 +Loop time of 29.8066 on 1 procs for 50000 steps with 3026 atoms + +Performance: 724671.093 tau/day, 1677.479 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.698 | 11.698 | 11.698 | 0.0 | 39.25 +Neigh | 10.292 | 10.292 | 10.292 | 0.0 | 34.53 +Comm | 1.405 | 1.405 | 1.405 | 0.0 | 4.71 +Output | 0.11474 | 0.11474 | 0.11474 | 0.0 | 0.38 +Modify | 5.3019 | 5.3019 | 5.3019 | 0.0 | 17.79 +Other | | 0.9947 | | | 3.34 + +Nlocal: 3026.00 ave 3026 max 3026 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2292.00 ave 2292 max 2292 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 25767.0 ave 25767 max 25767 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 25767 +Ave neighs/atom = 8.5152016 +Neighbor list builds = 4332 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:29 diff --git a/examples/multi/log.30Nov20.colloid.old.intel.4 b/examples/multi/log.30Nov20.colloid.old.intel.4 new file mode 100644 index 0000000000..0eae8cc8e7 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.old.intel.4 @@ -0,0 +1,183 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old +neigh_modify delay 0 #multi/custom 2 1*4 5 +comm_modify mode multi #multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/old/newton + stencil: half/multi/old/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.438 | 5.441 | 5.444 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688 + 3000 1.8956738 -0.090814168 1.8042332 0.075557943 77825.289 + 4000 1.9567884 -0.072243657 1.8838981 0.072836007 90931.521 + 5000 2.0386455 -0.084279096 1.9536927 0.06867562 90054.581 + 6000 2.0816461 -0.093158646 1.9877995 0.082802397 78084.994 + 7000 2.0854943 -0.10553618 1.979269 0.10230351 63886.068 + 8000 2.0923948 -0.14072173 1.9509816 0.11775174 52590.899 + 9000 2.0687841 -0.15957251 1.9085279 0.14963059 44575.69 + 10000 2.0607467 -0.18970216 1.8703636 0.17210861 39016.271 + 11000 2.0538523 -0.20866031 1.8445133 0.18554787 34992.223 + 12000 2.0408745 -0.22276635 1.8174337 0.21228473 31794.869 + 13000 2.0366678 -0.24217764 1.7938171 0.22999314 29186.441 + 14000 2.0470314 -0.26923854 1.7771164 0.2576977 26941.432 + 15000 2.0262458 -0.27296827 1.7526079 0.25960813 25184.491 + 16000 2.0410096 -0.30940081 1.7309343 0.27842776 23619.633 + 17000 2.027379 -0.32411477 1.7025943 0.32102949 22231.582 + 18000 2.0338405 -0.34468182 1.6884866 0.3306203 21028.933 + 19000 2.032206 -0.36558904 1.6659454 0.33926726 19958.945 + 20000 2.0347643 -0.3915229 1.642569 0.33718716 19054.271 + 21000 2.0242901 -0.38913219 1.634489 0.38062225 18190.934 + 22000 2.0207557 -0.41078199 1.6093059 0.40143768 17422.03 + 23000 2.0069068 -0.42062708 1.5856165 0.40146954 16717.999 + 24000 2.0300595 -0.4536262 1.5757624 0.49229743 16097.323 + 25000 2.0347548 -0.47655047 1.5575319 0.46787969 15564.848 + 26000 2.0180789 -0.46537586 1.5520362 0.48541997 15072.597 + 27000 2.0150506 -0.4886202 1.5257645 0.53829749 14621.24 + 28000 2.0175464 -0.50951413 1.5073655 0.50140171 14253.441 + 29000 2.0186127 -0.53911975 1.4788258 0.52955802 13930.266 + 30000 2.0006844 -0.52621334 1.4738099 0.60130639 13650.051 + 31000 2.0179614 -0.54573939 1.4715551 0.58747508 13285.903 + 32000 2.0333208 -0.57431851 1.4583303 0.62631039 12894.077 + 33000 2.0017273 -0.57778326 1.4232825 0.61159622 12595.987 + 34000 2.0063025 -0.58192939 1.4237101 0.66174764 12316.964 + 35000 2.0174782 -0.60591394 1.4108976 0.63571024 12063.433 + 36000 2.025112 -0.64319133 1.3812514 0.62829458 11930.246 + 37000 2.0431268 -0.64342323 1.3990283 0.68038546 11651.664 + 38000 2.0064271 -0.63716263 1.3686014 0.72167175 11345.421 + 39000 2.0284014 -0.67236471 1.3553663 0.68693225 11062.293 + 40000 2.0181711 -0.6962559 1.3212483 0.76033095 10864.176 + 41000 1.9908152 -0.66607906 1.3240783 0.90250403 10812.599 + 42000 2.0007084 -0.68853623 1.311511 0.88096905 10627.922 + 43000 1.998883 -0.69053805 1.3076844 0.81765345 10469.928 + 44000 2.0197069 -0.72507021 1.2939693 0.87004916 10194.954 + 45000 2.0112835 -0.72638581 1.284233 0.99236207 9968.2662 + 46000 2.0195002 -0.75152677 1.2673061 0.92706763 9751.1162 + 47000 1.983694 -0.75006702 1.2329714 0.8945741 9652.1453 + 48000 1.9977505 -0.77207122 1.225019 0.92107083 9647.1543 + 49000 2.0000901 -0.76254934 1.2368798 1.0320945 9536.2823 + 50000 2.0150929 -0.80463979 1.2097872 0.99556424 9324.0277 +Loop time of 11.239 on 4 procs for 50000 steps with 3026 atoms + +Performance: 1921872.705 tau/day, 4448.779 timesteps/s +98.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.3936 | 2.7411 | 3.1078 | 16.7 | 24.39 +Neigh | 2.2948 | 2.6755 | 3.1013 | 18.5 | 23.81 +Comm | 2.522 | 3.3135 | 4.0361 | 31.7 | 29.48 +Output | 0.040863 | 0.041031 | 0.041456 | 0.1 | 0.37 +Modify | 1.844 | 1.9014 | 1.9701 | 3.4 | 16.92 +Other | | 0.5666 | | | 5.04 + +Nlocal: 756.500 ave 838 max 693 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1282.50 ave 1333 max 1216 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Neighs: 6426.25 ave 7350 max 5786 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 25705 +Ave neighs/atom = 8.4947125 +Neighbor list builds = 4326 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:11 diff --git a/examples/multi/log.30Nov20.granular.intel.1 b/examples/multi/log.30Nov20.granular.intel.1 new file mode 100644 index 0000000000..2e313231ca --- /dev/null +++ b/examples/multi/log.30Nov20.granular.intel.1 @@ -0,0 +1,175 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #/old +neigh_modify delay 0 +comm_modify mode multi vel yes + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 11.78 | 11.78 | 11.78 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.016370159 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156551 0 0.014152248 0.021324815 5815.4665 + 12000 0.013725406 0 0.013721235 0.021159958 5483.6304 + 13000 0.013215746 0 0.013211729 0.021685712 5165.4758 + 14000 0.012398153 0 0.012394384 0.024155434 4862.8657 + 15000 0.011842796 0 0.011839196 0.028503991 4577.9008 + 16000 0.011433182 0 0.011429706 0.033564839 4309.8792 + 17000 0.011166574 0 0.01116318 0.040592677 4058.9964 + 18000 0.01100067 0 0.010997326 0.04899206 3825.155 + 19000 0.010224474 0 0.010221366 0.063670337 3607.6577 + 20000 0.0091360559 0 0.0091332789 0.088230111 3408.5658 + 21000 0.007733647 0 0.0077312964 0.11769368 3227.7002 + 22000 0.0060202358 0 0.0060184059 0.15272491 3064.3986 + 23000 0.004670574 0 0.0046691543 0.19450724 2918.0014 + 24000 0.0040248313 0 0.004023608 0.24161742 2788.4113 + 25000 0.0032075275 0 0.0032065526 0.2897693 2674.5604 + 26000 0.0021358024 0 0.0021351532 0.33635617 2574.9564 + 27000 0.0016902752 0 0.0016897614 0.37624266 2487.2379 + 28000 0.0014038218 0 0.0014033951 0.41492104 2409.2461 + 29000 0.00090262506 0 0.0009023507 0.45392905 2340.0308 + 30000 0.00049466342 0 0.00049451306 0.49295072 2279.2316 + 31000 0.00056998139 0 0.00056980815 0.53299515 2226.5683 + 32000 0.00057326945 0 0.0005730952 0.56856537 2181.7092 + 33000 0.00044845112 0 0.00044831481 0.59623471 2142.7573 + 34000 0.00059840183 0 0.00059821994 0.61758983 2107.1253 + 35000 0.00075310993 0 0.00075288103 0.63756827 2072.7217 + 36000 0.00053774066 0 0.00053757721 0.66026064 2039.1655 + 37000 0.00030440106 0 0.00030430853 0.69059102 2007.7903 + 38000 0.00034436264 0 0.00034425797 0.72166344 1980.7137 + 39000 0.00039693498 0 0.00039681433 0.74680327 1957.9531 + 40000 0.00035425567 0 0.000354148 0.76604186 1937.3834 + 41000 0.0003094733 0 0.00030937924 0.78323163 1916.7027 + 42000 0.00027259246 0 0.0002725096 0.80315535 1895.0714 + 43000 0.00020659817 0 0.00020653538 0.8274603 1873.5407 + 44000 0.00016023333 0 0.00016018463 0.85418969 1853.8674 + 45000 0.00016111931 0 0.00016107034 0.87913944 1837.1141 + 46000 0.00016130888 0 0.00016125985 0.89921705 1822.7354 + 47000 0.00015755049 0 0.0001575026 0.91653538 1809.0285 + 48000 0.00017794781 0 0.00017789372 0.93582908 1794.7041 + 49000 0.00018878437 0 0.00018872699 0.95775203 1780.032 + 50000 0.0001778042 0 0.00017775016 0.97893714 1765.9439 +Loop time of 77.4487 on 1 procs for 50000 steps with 3290 atoms + +Performance: 278894.354 tau/day, 645.589 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 60.017 | 60.017 | 60.017 | 0.0 | 77.49 +Neigh | 0.47 | 0.47 | 0.47 | 0.0 | 0.61 +Comm | 6.6765 | 6.6765 | 6.6765 | 0.0 | 8.62 +Output | 0.24799 | 0.24799 | 0.24799 | 0.0 | 0.32 +Modify | 8.8677 | 8.8677 | 8.8677 | 0.0 | 11.45 +Other | | 1.17 | | | 1.51 + +Nlocal: 3290.00 ave 3290 max 3290 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 6295.00 ave 6295 max 6295 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 53729.0 ave 53729 max 53729 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 53729 +Ave neighs/atom = 16.331003 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:17 diff --git a/examples/multi/log.30Nov20.granular.intel.4 b/examples/multi/log.30Nov20.granular.intel.4 new file mode 100644 index 0000000000..d53684c596 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.intel.4 @@ -0,0 +1,175 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 +comm_modify mode multi vel yes multi/reduce + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 11.33 | 11.33 | 11.33 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.01637016 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156553 0 0.01415225 0.021324818 5815.4665 + 12000 0.013725412 0 0.01372124 0.021159958 5483.6304 + 13000 0.013215733 0 0.013211716 0.021685624 5165.4758 + 14000 0.012398179 0 0.012394411 0.024155572 4862.8657 + 15000 0.01184269 0 0.01183909 0.028504106 4577.901 + 16000 0.01143291 0 0.011429435 0.033564204 4309.88 + 17000 0.011166204 0 0.01116281 0.040588854 4058.9972 + 18000 0.011000875 0 0.010997532 0.048998904 3825.1569 + 19000 0.010225905 0 0.010222797 0.063669586 3607.6622 + 20000 0.0091390249 0 0.0091362471 0.088165396 3408.567 + 21000 0.0077382016 0 0.0077358496 0.11770473 3227.6936 + 22000 0.0060173113 0 0.0060154823 0.15261992 3064.3873 + 23000 0.0046667554 0 0.004665337 0.19453813 2917.9782 + 24000 0.0040425764 0 0.0040413476 0.24145834 2788.3897 + 25000 0.0031933187 0 0.0031923481 0.28989732 2674.5164 + 26000 0.0021139018 0 0.0021132592 0.33598721 2574.9313 + 27000 0.0017005052 0 0.0016999884 0.37665029 2487.1628 + 28000 0.001443434 0 0.0014429952 0.41572112 2409.3271 + 29000 0.00089885805 0 0.00089858484 0.45343123 2340.2314 + 30000 0.00048558336 0 0.00048543577 0.49175966 2279.2156 + 31000 0.00058132898 0 0.00058115228 0.53236819 2226.2347 + 32000 0.00057751441 0 0.00057733887 0.56915062 2181.2736 + 33000 0.00044720497 0 0.00044706904 0.59696122 2142.5709 + 34000 0.00060927898 0 0.00060909379 0.61734988 2107.128 + 35000 0.00077422577 0 0.00077399045 0.63696024 2072.6004 + 36000 0.00055753008 0 0.00055736062 0.65981839 2038.8237 + 37000 0.0003140158 0 0.00031392035 0.69018918 2007.323 + 38000 0.00034970199 0 0.0003495957 0.72155094 1980.1702 + 39000 0.00041435514 0 0.00041422919 0.7468053 1957.3837 + 40000 0.00037229543 0 0.00037218227 0.76581519 1936.8032 + 41000 0.00031027679 0 0.00031018248 0.78321128 1916.1103 + 42000 0.00026621832 0 0.00026613741 0.80267694 1894.4646 + 43000 0.00020544063 0 0.00020537818 0.82714181 1872.768 + 44000 0.00015635243 0 0.00015630491 0.85496512 1853.0303 + 45000 0.00014985611 0 0.00014981056 0.87924561 1836.4779 + 46000 0.00015645346 0 0.00015640591 0.89896131 1822.2004 + 47000 0.00016007816 0 0.00016002951 0.91662026 1808.4601 + 48000 0.00017439363 0 0.00017434063 0.93565314 1794.1244 + 49000 0.00018647711 0 0.00018642043 0.95733125 1779.401 + 50000 0.00018463414 0 0.00018457802 0.96449755 1765.1506 +Loop time of 22.3987 on 4 procs for 50000 steps with 3290 atoms + +Performance: 964340.770 tau/day, 2232.270 timesteps/s +99.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.5158 | 12.318 | 15.836 | 92.1 | 54.99 +Neigh | 0.092527 | 0.11392 | 0.13595 | 5.6 | 0.51 +Comm | 2.7127 | 6.2337 | 10.096 | 131.0 | 27.83 +Output | 0.088027 | 0.088284 | 0.088812 | 0.1 | 0.39 +Modify | 2.8544 | 3.0435 | 3.2034 | 9.2 | 13.59 +Other | | 0.6017 | | | 2.69 + +Nlocal: 822.500 ave 859 max 785 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 395.750 ave 424 max 368 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 13439.5 ave 14346 max 12017 min +Histogram: 1 0 0 0 0 1 0 0 0 2 + +Total # of neighbors = 53758 +Ave neighs/atom = 16.339818 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:22 diff --git a/examples/multi/log.30Nov20.granular.old.intel.1 b/examples/multi/log.30Nov20.granular.old.intel.1 new file mode 100644 index 0000000000..ad827423c5 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.old.intel.1 @@ -0,0 +1,175 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old +neigh_modify delay 0 +comm_modify mode multi vel yes + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/old/newton/tri + stencil: half/multi/old/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.75 | 11.75 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.016370159 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156551 0 0.014152248 0.021324815 5815.4665 + 12000 0.013725406 0 0.013721235 0.021159958 5483.6304 + 13000 0.013215746 0 0.013211729 0.021685712 5165.4758 + 14000 0.012398153 0 0.012394384 0.024155434 4862.8657 + 15000 0.011842796 0 0.011839196 0.028503991 4577.9008 + 16000 0.011433182 0 0.011429706 0.033564839 4309.8792 + 17000 0.011166574 0 0.01116318 0.040592677 4058.9964 + 18000 0.01100067 0 0.010997326 0.04899206 3825.155 + 19000 0.010224474 0 0.010221366 0.063670337 3607.6577 + 20000 0.0091360558 0 0.0091332789 0.088230111 3408.5658 + 21000 0.0077336471 0 0.0077312964 0.11769368 3227.7002 + 22000 0.0060202357 0 0.0060184059 0.15272492 3064.3986 + 23000 0.0046705738 0 0.0046691542 0.19450723 2918.0014 + 24000 0.0040248311 0 0.0040236078 0.24161743 2788.4113 + 25000 0.0032075267 0 0.0032065518 0.28976925 2674.5604 + 26000 0.0021358008 0 0.0021351516 0.33635615 2574.9564 + 27000 0.0016902771 0 0.0016897633 0.37624261 2487.2379 + 28000 0.0014038216 0 0.0014033949 0.41492061 2409.2461 + 29000 0.00090262588 0 0.00090235152 0.45392924 2340.0308 + 30000 0.00049466445 0 0.0004945141 0.49295063 2279.2316 + 31000 0.00056998139 0 0.00056980814 0.53299532 2226.5683 + 32000 0.00057327032 0 0.00057309607 0.56856551 2181.7093 + 33000 0.00044845449 0 0.00044831818 0.59623461 2142.7574 + 34000 0.00059840346 0 0.00059822157 0.61758978 2107.1254 + 35000 0.00075311121 0 0.0007528823 0.63756791 2072.7217 + 36000 0.00053773653 0 0.00053757309 0.66026022 2039.1654 + 37000 0.00030439696 0 0.00030430444 0.69059127 2007.7901 + 38000 0.00034435616 0 0.00034425149 0.72166346 1980.7136 + 39000 0.00039692535 0 0.0003968047 0.7468036 1957.9531 + 40000 0.0003542502 0 0.00035414252 0.76604173 1937.3834 + 41000 0.0003094667 0 0.00030937263 0.78323183 1916.7027 + 42000 0.00027258976 0 0.0002725069 0.80315572 1895.0714 + 43000 0.00020659987 0 0.00020653707 0.82746098 1873.5408 + 44000 0.00016023865 0 0.00016018994 0.85418945 1853.8677 + 45000 0.00016112731 0 0.00016107833 0.87913874 1837.1144 + 46000 0.00016131366 0 0.00016126463 0.89921653 1822.7355 + 47000 0.00015754747 0 0.00015749958 0.91653641 1809.0285 + 48000 0.00017794764 0 0.00017789356 0.93582953 1794.7043 + 49000 0.00018879338 0 0.000188736 0.95775166 1780.0323 + 50000 0.00017781117 0 0.00017775712 0.97893641 1765.9442 +Loop time of 80.8597 on 1 procs for 50000 steps with 3290 atoms + +Performance: 267129.375 tau/day, 618.355 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 61.524 | 61.524 | 61.524 | 0.0 | 76.09 +Neigh | 2.2021 | 2.2021 | 2.2021 | 0.0 | 2.72 +Comm | 6.748 | 6.748 | 6.748 | 0.0 | 8.35 +Output | 0.25904 | 0.25904 | 0.25904 | 0.0 | 0.32 +Modify | 8.9408 | 8.9408 | 8.9408 | 0.0 | 11.06 +Other | | 1.186 | | | 1.47 + +Nlocal: 3290.00 ave 3290 max 3290 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 6295.00 ave 6295 max 6295 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 53729.0 ave 53729 max 53729 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 53729 +Ave neighs/atom = 16.331003 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:20 diff --git a/examples/multi/log.30Nov20.granular.old.intel.4 b/examples/multi/log.30Nov20.granular.old.intel.4 new file mode 100644 index 0000000000..e41741b536 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.old.intel.4 @@ -0,0 +1,175 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old +neigh_modify delay 0 +comm_modify mode multi vel yes #multi/reduce + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/old/newton/tri + stencil: half/multi/old/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.48 | 11.48 | 11.49 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.01637016 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156553 0 0.01415225 0.021324818 5815.4665 + 12000 0.013725412 0 0.01372124 0.021159958 5483.6304 + 13000 0.013215733 0 0.013211716 0.021685624 5165.4758 + 14000 0.012398179 0 0.012394411 0.024155572 4862.8657 + 15000 0.01184269 0 0.01183909 0.028504106 4577.901 + 16000 0.01143291 0 0.011429435 0.033564204 4309.88 + 17000 0.011166204 0 0.01116281 0.040588854 4058.9972 + 18000 0.011000875 0 0.010997532 0.048998904 3825.1569 + 19000 0.010225905 0 0.010222797 0.063669588 3607.6622 + 20000 0.0091390255 0 0.0091362477 0.088165402 3408.567 + 21000 0.0077382041 0 0.0077358521 0.11770474 3227.6936 + 22000 0.00601731 0 0.0060154811 0.15261994 3064.3873 + 23000 0.0046667591 0 0.0046653407 0.19453819 2917.9782 + 24000 0.0040425749 0 0.0040413461 0.24145833 2788.3897 + 25000 0.0031933217 0 0.0031923511 0.28989713 2674.5164 + 26000 0.0021138997 0 0.0021132571 0.33598673 2574.9312 + 27000 0.001700508 0 0.0016999912 0.37665013 2487.1626 + 28000 0.0014434246 0 0.0014429859 0.41572163 2409.327 + 29000 0.00089885063 0 0.00089857742 0.453431 2340.2313 + 30000 0.00048556478 0 0.00048541719 0.49176025 2279.2155 + 31000 0.00058130972 0 0.00058113303 0.53236818 2226.2349 + 32000 0.00057749847 0 0.00057732294 0.5691506 2181.2738 + 33000 0.00044719326 0 0.00044705733 0.59696179 2142.571 + 34000 0.00060924828 0 0.0006090631 0.61735036 2107.1282 + 35000 0.00077419805 0 0.00077396273 0.63696098 2072.6008 + 36000 0.00055752003 0 0.00055735057 0.65981842 2038.8242 + 37000 0.00031402452 0 0.00031392907 0.69018949 2007.3235 + 38000 0.00034969879 0 0.0003495925 0.72155053 1980.1706 + 39000 0.00041434197 0 0.00041421603 0.74680715 1957.3838 + 40000 0.00037229243 0 0.00037217927 0.76581686 1936.8034 + 41000 0.00031028842 0 0.00031019411 0.78321059 1916.1108 + 42000 0.00026623668 0 0.00026615575 0.80267329 1894.4649 + 43000 0.00020543723 0 0.00020537479 0.82714001 1872.7672 + 44000 0.0001563321 0 0.00015628458 0.85496396 1853.0284 + 45000 0.00014981713 0 0.00014977159 0.87924842 1836.4755 + 46000 0.00015641585 0 0.00015636831 0.89896936 1822.1989 + 47000 0.00016004701 0 0.00015999837 0.91661933 1808.4606 + 48000 0.00017437702 0 0.00017432402 0.93565475 1794.1258 + 49000 0.00018645903 0 0.00018640235 0.95733183 1779.4032 + 50000 0.00018469122 0 0.00018463508 0.96446925 1765.1534 +Loop time of 30.9351 on 4 procs for 50000 steps with 3290 atoms + +Performance: 698235.574 tau/day, 1616.286 timesteps/s +89.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.3702 | 12.796 | 16.045 | 84.3 | 41.36 +Neigh | 0.43499 | 0.55158 | 0.64861 | 12.8 | 1.78 +Comm | 10.183 | 13.476 | 16.961 | 83.7 | 43.56 +Output | 0.088474 | 0.088715 | 0.089272 | 0.1 | 0.29 +Modify | 3.0446 | 3.1809 | 3.3227 | 7.4 | 10.28 +Other | | 0.8418 | | | 2.72 + +Nlocal: 822.500 ave 859 max 785 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 3049.75 ave 3089 max 2999 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 13440.5 ave 14459 max 11964 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 53762 +Ave neighs/atom = 16.341033 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:30 diff --git a/src/comm.cpp b/src/comm.cpp index 84e3b9ad65..542ddfdf10 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -248,6 +248,8 @@ void Comm::init() error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); if (neighbor->any_full()) error->all(FLERR,"Cannot use multi/reduce communication with a full neighbor list"); + if (neighbor->style != Neighbor::MULTI) + error->all(FLERR,"Cannot use multi/reduce communication without multi-style neighbor lists"); } } From a25c77e512762a6eee146e20baa477143b83ef6f Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 12 Jan 2021 23:04:14 -0700 Subject: [PATCH 46/73] Misc comments, typos, and cleanups --- doc/src/comm_modify.rst | 8 +- doc/src/neigh_modify.rst | 12 +- examples/multi/in.granular | 2 +- src/USER-OMP/npair_half_multi_newton_omp.cpp | 125 ++++++----------- .../npair_half_size_multi_newton_omp.cpp | 100 +++++-------- src/comm.cpp | 1 - src/comm_brick.cpp | 132 +++++++----------- src/comm_tiled.cpp | 16 +-- src/nbin_multi.cpp | 69 ++++----- src/nbin_multi.h | 4 - src/neighbor.cpp | 21 +-- src/npair.cpp | 10 +- src/npair.h | 2 +- src/npair_half_multi_newton.cpp | 123 ++++++---------- src/npair_half_size_multi_newton.cpp | 100 +++++-------- src/npair_half_size_multi_newton_tri.cpp | 1 - src/nstencil.cpp | 29 ++-- src/nstencil.h | 6 +- 18 files changed, 285 insertions(+), 476 deletions(-) diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 5f084561a1..a3f7dba4eb 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -11,7 +11,7 @@ Syntax comm_modify keyword value ... * zero or more keyword/value pairs may be appended -* keyword = *mode* or *cutoff* or *cutoff/multi* or *cutoff/bytype* or *group* or *vel* +* keyword = *mode* or *cutoff* or *cutoff/multi* or *multi/reduce* or *group* or *vel* .. parsed-literal:: @@ -20,7 +20,7 @@ Syntax *cutoff/multi* type value type = atom type or type range (supports asterisk notation) value = Rcut (distance units) = communicate atoms for selected types from this far away - *cutoff/byptype* arg = none = communicate atoms for each type by a distance equal to the largest interaction distance for that type + *multi/reduce* arg = none = reduce number of communicated ghost atoms for multi style *group* value = group-ID = only communicate atoms in the group *vel* value = *yes* or *no* = do or do not communicate velocity info with ghost atoms @@ -96,10 +96,10 @@ using the usual asterisk notation can be given. For granular pair styles, the default cutoff is set to the sum of the current maximum atomic radii for each type. -The *multi/reduce* option applies to *multi* and automatically sets communication +The *multi/reduce* option applies to *multi* and sets communication cutoffs for different sized particles based on the largest interaction distance between two particles in the same multi grouping. This reduces the number of -ghost that need to be communicated This method is only compatible with the +ghost atoms that need to be communicated. This method is only compatible with the *multi* neighbor style and requires only half neighbor lists and Newton on. See the :doc:`neighbor multi ` command for more information. diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 33f24af96e..c6f573ef08 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -47,9 +47,9 @@ Syntax N = max number of neighbors of one atom *binsize* value = size size = bin size for neighbor list construction (distance units) - *multi/custom* values = N types + *multi/custom* values = N arg1 ... argN N = number of custom groups - types = N separate types or groups of types (see below) + arg = N separate types or ranges of types (see below) Examples """""""" @@ -208,12 +208,12 @@ overhead. You must first specify the number of custom groups N to be defined followed by N ranges of types. The range can be specified as a single numeric value, or a wildcard asterisk can be used to specify a range of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For -example, if N = the number of atom types, then an asterisk with no numeric -values means all types from 1 to N. A leading asterisk means all types -from 1 to n (inclusive). A trailing asterisk means all types from n to N +example, if M = the number of atom types, then an asterisk with no numeric +values means all types from 1 to M. A leading asterisk means all types +from 1 to n (inclusive). A trailing asterisk means all types from n to M (inclusive). A middle asterisk means all types from m to n (inclusive). Note that any atom types not included in a custom group will be automatically -placed within a new, separate group. +placed within a separate group. Restrictions """""""""""" diff --git a/examples/multi/in.granular b/examples/multi/in.granular index 00dd4ad2bb..8f1743f90d 100644 --- a/examples/multi/in.granular +++ b/examples/multi/in.granular @@ -1,4 +1,4 @@ -# Big colloid particles and small LJ particles +# Bidisperse set of grains units lj atom_style sphere diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index a7a3e6d6f7..11a84a3040 100755 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -100,96 +100,55 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) if(igroup == jgroup) jbin = ibin; else jbin = coord2bin(x[i], jgroup); + // if same size: uses half stencil so check central bin if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ - // if same size: use half stencil - if(igroup == jgroup){ - - // if same group, implement with: - // 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 - - js = bins[i]; + if(igroup == jgroup) js = bins[i]; + else js = binhead_multi[jgroup][jbin]; - for (j = js; 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; - } - } - } else { - - // if different groups, implement with: - // loop over all atoms in jgroup bin - // if j is owned atom, store it if j > i - // if j is ghost, only store if j coords are "above and to the right" of i + // if same group, + // 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 - js = binhead_multi[jgroup][jbin]; + // if different groups, + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - for (j = js; j >= 0; j = bins[j]) { - if(j < i) continue; + for (j = js; j >= 0; j = bins[j]) { + if(igroup != jgroup and j < i) continue; - 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 (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; - } - } - } + } + + 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; + } + } } // for all groups, loop over all atoms in other bins in stencil, store every pair diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index 0137873600..cec3edd02b 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -89,80 +89,46 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) if(igroup == jgroup) jbin = ibin; else jbin = coord2bin(x[i], jgroup); + // if same size: uses half stencil so check central bin if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ - - // if same size: use half stencil - if(igroup == jgroup){ - - // if same group, implement with: - // 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 - - js = bins[i]; - - for (j = js; 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + if(igroup == jgroup) js = bins[i]; + else js = binhead_multi[jgroup][jbin]; + + // if same group, + // 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 + + // if different groups, + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + for (j = js; j >= 0; j = bins[j]) { + if(igroup != jgroup and j < i) continue; + + 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; } } - } else { - - // if different groups, implement with: - // loop over all atoms in jgroup bin - // if j is owned atom, store it if j > i - // if j is ghost, only store if j coords are "above and to the right" of i + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - js = binhead_multi[jgroup][jbin]; + 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]; + cutdistsq = (radsum+skin) * (radsum+skin); - for (j = js; j >= 0; j = bins[j]) { - if(j < i) continue; - - 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; } } } diff --git a/src/comm.cpp b/src/comm.cpp index 542ddfdf10..867eab6256 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -242,7 +242,6 @@ void Comm::init() for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; - // Can't used multi/reduce communication with Newton off or full neighbor lits if(multi_reduce){ if (force->newton == 0) error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 74865476f5..939669fb75 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -167,54 +167,55 @@ void CommBrick::setup() error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " "will be generated. Atoms may get lost."); + + if (mode == Comm::MULTI) { + if (multi_reduce) { + // If using multi/reduce, communicate itype particles a distance equal + // to the max of itype-jtype group interaction + // only consider smaller jtype groups + int igroup, jgroup; + double **cutmultisq = neighbor->cutmultisq; + int *map_type_multi = neighbor->map_type_multi; + for (i = 1; i <= ntypes; i++) { + + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; + } + + igroup = map_type_multi[i]; + for (j = 1; j <= ntypes; j++){ + jgroup = map_type_multi[j]; + + if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); + } + } + } else { + // otherwise, communicate a distance equal to the maximum interaction distance for each type + double *cuttype = neighbor->cuttype; + for (i = 1; i <= ntypes; i++) { + double tmp = 0.0; + if (cutusermulti) tmp = cutusermulti[i]; + cutghostmulti[i][0] = MAX(tmp,cuttype[i]); + cutghostmulti[i][1] = MAX(tmp,cuttype[i]); + cutghostmulti[i][2] = MAX(tmp,cuttype[i]); + } + } + } + if (triclinic == 0) { prd = domain->prd; sublo = domain->sublo; subhi = domain->subhi; cutghost[0] = cutghost[1] = cutghost[2] = cut; - - if (mode == Comm::MULTI) { - if (multi_reduce) { - // If using multi/reduce, communicate itype particles a distance equal - // to the max of itype-jtype group interaction given smaller jtype group - int igroup, jgroup; - double **cutmultisq = neighbor->cutmultisq; - int *map_type_multi = neighbor->map_type_multi; - for (i = 1; i <= ntypes; i++) { - - if (cutusermulti) { - cutghostmulti[i][0] = cutusermulti[i]; - cutghostmulti[i][1] = cutusermulti[i]; - cutghostmulti[i][2] = cutusermulti[i]; - } else { - cutghostmulti[i][0] = 0.0; - cutghostmulti[i][1] = 0.0; - cutghostmulti[i][2] = 0.0; - } - - igroup = map_type_multi[i]; - for (j = 1; j <= ntypes; j++){ - jgroup = map_type_multi[j]; - - if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); - } - } - } else { - // If using a single binlist, use the max itype-jtype interaction distance for communication - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,cuttype[i]); - cutghostmulti[i][1] = MAX(cut,cuttype[i]); - cutghostmulti[i][2] = MAX(cut,cuttype[i]); - } - } - } - } else { prd = domain->prd_lamda; sublo = domain->sublo_lamda; @@ -227,46 +228,11 @@ void CommBrick::setup() cutghost[1] = cut * length1; length2 = h_inv[2]; cutghost[2] = cut * length2; - - if (mode == Comm::MULTI) { - if (multi_reduce) { - // If using multi/reduce, communicate itype particles a distance equal - // to the max of itype-jtype group interaction given smaller jtype group - int igroup, jgroup; - double **cutmultisq = neighbor->cutmultisq; - int *map_type_multi = neighbor->map_type_multi; - for (i = 1; i <= ntypes; i++) { - - if (cutusermulti) { - cutghostmulti[i][0] = cutusermulti[i]; - cutghostmulti[i][1] = cutusermulti[i]; - cutghostmulti[i][2] = cutusermulti[i]; - } else { - cutghostmulti[i][0] = 0.0; - cutghostmulti[i][1] = 0.0; - cutghostmulti[i][2] = 0.0; - } - - igroup = map_type_multi[i]; - for (j = 1; j <= ntypes; j++){ - jgroup = map_type_multi[j]; - - if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; - cutghostmulti[i][0] = length0 * MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][1] = length1 * MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][2] = length2 * MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); - } - } - } else { - // If using a single binlist, use the max itype-jtype interaction distance for communication - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = length0 * MAX(cut,cuttype[i]); - cutghostmulti[i][1] = length1 * MAX(cut,cuttype[i]); - cutghostmulti[i][2] = length2 * MAX(cut,cuttype[i]); - } + if (mode == Comm::MULTI){ + for (i = 1; i <= ntypes; i++) { + cutghostmulti[i][0] *= length0; + cutghostmulti[i][1] *= length1; + cutghostmulti[i][2] *= length2; } } } diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 64d1207a64..06edbf7416 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -175,10 +175,10 @@ void CommTiled::setup() // check that cutoff < any periodic box length if (mode == Comm::MULTI) { - double cut; if (multi_reduce) { // If using multi/reduce, communicate itype particles a distance equal - // to the max of itype-jtype group interaction given smaller jtype group + // to the max of itype-jtype group interaction + // only consider smaller jtype groups int igroup, jgroup; double **cutmultisq = neighbor->cutmultisq; int *map_type_multi = neighbor->map_type_multi; @@ -205,14 +205,14 @@ void CommTiled::setup() } } } else { - // If using a single binlist, use the max itype-jtype interaction distance for communication + // otherwise, communicate a distance equal to the maximum interaction distance for each type double *cuttype = neighbor->cuttype; for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,cuttype[i]); - cutghostmulti[i][1] = MAX(cut,cuttype[i]); - cutghostmulti[i][2] = MAX(cut,cuttype[i]); + double tmp = 0.0; + if (cutusermulti) tmp = cutusermulti[i]; + cutghostmulti[i][0] = MAX(tmp,cuttype[i]); + cutghostmulti[i][1] = MAX(tmp,cuttype[i]); + cutghostmulti[i][2] = MAX(tmp,cuttype[i]); } } } diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index b8832bdfea..04756ff803 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -59,41 +59,41 @@ void NBinMulti::bin_atoms_setup(int nall) } } -/* --------------------------------------------------------------------- - Identify index of group with smallest cutoff ------------------------------------------------------------------------- */ - -int NBinMulti::igroup_min() -{ - int imin = 0; - for (int n = 0; n < maxgroups; n++) - if (cutmultisq[n][n] < cutmultisq[imin][imin]) imin = n; - - return imin; -} - /* ---------------------------------------------------------------------- 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_multi = lowest global bin any of my ghost atoms could fall into for each grouping + mbinhi_multi = highest global bin any of my ghost atoms could fall into for each grouping + mbin_multi = number of bins I need in a dimension for each grouping +------------------------------------------------------------------------- */ void NBinMulti::setup_bins(int style) { int n; - int igroupmin; // Initialize arrays - if (n_multi_groups > maxgroups) { - // Clear any/all memory for existing types - + // Clear any/all memory for existing groupings for (n = 0; n < maxgroups; n++) memory->destroy(binhead_multi[n]); delete [] binhead_multi; - // Realloacte at updated maxtypes - + // Realloacte at updated maxgroups maxgroups = n_multi_groups; binhead_multi = new int*[maxgroups](); @@ -138,14 +138,18 @@ void NBinMulti::setup_bins(int style) memory->destroy(maxbins_multi); memory->create(maxbins_multi, maxgroups, "neigh:maxbins_multi"); - // make sure reallocation occurs in bin_atoms_setup() + // ensure reallocation occurs in bin_atoms_setup() for (n = 0; n < maxgroups; n++) { maxbins_multi[n] = 0; } maxatom = 0; } - igroupmin = igroup_min(); + // Identify smallest group + int igroupmin = 0; + for (n = 0; n < maxgroups; n++) + if (cutmultisq[n][n] < cutmultisq[igroupmin][igroupmin]) + igroupmin = n; // bbox = size of bbox of entire domain // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost @@ -182,16 +186,18 @@ void NBinMulti::setup_bins(int style) // For each grouping... + double binsize_optimal, binsizeinv, coord; + int mbinxhi,mbinyhi,mbinzhi; + for (n = 0; n < maxgroups; n++) { - // binsize_user only relates to smallest type - // optimal bin size is roughly 1/2 the type-type cutoff + // binsize_user only relates to smallest group + // optimal bin size is roughly 1/2 the group-group cutoff // special case of all cutoffs = 0.0, binsize = box size - double binsize_optimal; if (n == igroupmin && binsizeflag) binsize_optimal = binsize_user; else binsize_optimal = 0.5*sqrt(cutmultisq[n][n]); if (binsize_optimal == 0.0) binsize_optimal = bbox[0]; - double binsizeinv = 1.0/binsize_optimal; + binsizeinv = 1.0/binsize_optimal; // test for too many global bins in any dimension due to huge global domain @@ -216,7 +222,7 @@ void NBinMulti::setup_bins(int style) // 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 + // in that extreme case, cannot use multi, should use NSQ not BIN neighbor style binsizex_multi[n] = bbox[0]/nbinx_multi[n]; binsizey_multi[n] = bbox[1]/nbiny_multi[n]; @@ -236,9 +242,6 @@ void NBinMulti::setup_bins(int style) // 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_multi[n] = static_cast ((coord-bboxlo[0])*bininvx_multi[n]); if (coord < bboxlo[0]) mbinxlo_multi[n] = mbinxlo_multi[n] - 1; @@ -340,10 +343,8 @@ void NBinMulti::bin_atoms() double NBinMulti::memory_usage() { double bytes = 0; - - for (int m = 0; m < maxgroups; m++) { + for (int m = 0; m < maxgroups; m++) bytes += maxbins_multi[m]*sizeof(int); - bytes += 2*maxatom*sizeof(int); - } + bytes += 2*maxatom*sizeof(int); return bytes; } diff --git a/src/nbin_multi.h b/src/nbin_multi.h index 84ec0348bc..490af10dbb 100644 --- a/src/nbin_multi.h +++ b/src/nbin_multi.h @@ -35,10 +35,6 @@ class NBinMulti : public NBin { void setup_bins(int); void bin_atoms(); double memory_usage(); - - private: - - int igroup_min(); }; } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 94add1f324..5c8d8ec594 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -83,6 +83,11 @@ static const char cite_neigh_multi[] = " volume = 179,\n" " pages = {320--329}\n" "}\n\n" + "@article{Stratford2018,\n" + " author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin},\n" + " title = {Implementation of multi-level contact detection in LAMMPS},\n" + " year = {2018}\n" + "}\n\n" "@article{Shire2020,\n" " author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},\n" " title = {DEM simulations of polydisperse media: efficient contact\n" @@ -348,7 +353,8 @@ void Neighbor::init() // multi cutoffs if(style == Neighbor::MULTI){ int igroup, jgroup; - // If not defined, create default mapping + + // If not defined from custom grouping, create default map if(not map_type_multi) { n_multi_groups = n; memory->create(map_type_multi,n+1,"neigh:map_type_multi"); @@ -1678,12 +1684,11 @@ int Neighbor::choose_bin(NeighRequest *rq) if (!rq->kokkos_device != !(mask & NB_KOKKOS_DEVICE)) continue; if (!rq->kokkos_host != !(mask & NB_KOKKOS_HOST)) continue; - // neighbor style is BIN or MULTI or MULTI_OLD and must match - - if (style == Neighbor::BIN || style == Neighbor::MULTI_OLD) { - if (!(mask & NB_STANDARD)) continue; - } else if (style == Neighbor::MULTI) { + // multi neighbor style require multi bin style + if (style == Neighbor::MULTI) { if (!(mask & NB_MULTI)) continue; + } else { + if (!(mask & NB_STANDARD)) continue; } return i+1; @@ -1719,7 +1724,6 @@ int Neighbor::choose_stencil(NeighRequest *rq) else if (rq->newton == 2) newtflag = 0; // request a full stencil if building full neighbor list or newton is off - int fullflag = 0; if (rq->full) fullflag = 1; if (!newtflag) fullflag = 1; @@ -1972,7 +1976,6 @@ NPair *Neighbor::pair_creator(LAMMPS *lmp) /* ---------------------------------------------------------------------- setup neighbor binning and neighbor stencils called before run and every reneighbor if box size/shape changes - initialize default settings for multi before run only operates on perpetual lists build_one() operates on occasional lists ------------------------------------------------------------------------- */ @@ -2458,7 +2461,7 @@ void Neighbor::modify_params(int narg, char **arg) n_multi_groups += 1; } - // Create seprate group for each undefined atom type + // Create separate group for each undefined atom type for(i = 1; i <= ntypes; i++){ if(map_type_multi[i] == -1){ map_type_multi[i] = n_multi_groups; diff --git a/src/npair.cpp b/src/npair.cpp index facd9086d1..95a61fbefa 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -304,9 +304,9 @@ int NPair::coord2bin(double *x, int ig) } else iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]) - 1; - - ibin = (iz-mbinzlo_multi[ig])*mbiny_multi[ig]*mbinx_multi[ig] - + (iy-mbinylo_multi[ig])*mbinx_multi[ig] - + (ix-mbinxlo_multi[ig]); + ix -= mbinxlo_multi[ig]; + iy -= mbinylo_multi[ig]; + iz -= mbinzlo_multi[ig]; + ibin = iz*mbiny_multi[ig]*mbinx_multi[ig] + iy*mbinx_multi[ig] + ix; return ibin; -} \ No newline at end of file +} diff --git a/src/npair.h b/src/npair.h index d1fcf2e6b2..c857ec0924 100644 --- a/src/npair.h +++ b/src/npair.h @@ -115,7 +115,7 @@ class NPair : protected Pointers { int coord2bin(double *); // mapping atom coord to a bin int coord2bin(double *, int &, int &, int&); // ditto - int coord2bin(double *, int); // mapping atom coord to type bin + int coord2bin(double *, int); // mapping atom coord to group bin // find_special: determine if atom j is in special list of atom i diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index 777aab5826..aa8f606242 100755 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -88,96 +88,55 @@ void NPairHalfMultiNewton::build(NeighList *list) if(igroup == jgroup) jbin = ibin; else jbin = coord2bin(x[i], jgroup); + // if same size: uses half stencil so check central bin if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ - // if same size: use half stencil - if(igroup == jgroup){ - - // if same group, implement with: - // 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 - - js = bins[i]; + if(igroup == jgroup) js = bins[i]; + else js = binhead_multi[jgroup][jbin]; - for (j = js; 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; - } - } - } else { - - // if different groups, implement with: - // loop over all atoms in jgroup bin - // if j is owned atom, store it if j > i - // if j is ghost, only store if j coords are "above and to the right" of i + // if same group, + // 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 - js = binhead_multi[jgroup][jbin]; + // if different groups, + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - for (j = js; j >= 0; j = bins[j]) { - if(j < i) continue; + for (j = js; j >= 0; j = bins[j]) { + if(igroup != jgroup and j < i) continue; - 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 (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; - } - } - } + 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; + } + } } // for all groups, loop over all atoms in other bins in stencil, store every pair diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index 500e06bc35..84571a3b02 100755 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -77,80 +77,46 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) if(igroup == jgroup) jbin = ibin; else jbin = coord2bin(x[i], jgroup); + // if same size: uses half stencil so check central bin if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ - - // if same size: use half stencil - if(igroup == jgroup){ - - // if same group, implement with: - // 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 - - js = bins[i]; - - for (j = js; 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + if(igroup == jgroup) js = bins[i]; + else js = binhead_multi[jgroup][jbin]; + + // if same group, + // 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 + + // if different groups, + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + for (j = js; j >= 0; j = bins[j]) { + if(igroup != jgroup and j < i) continue; + + 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; } } - } else { - - // if different groups, implement with: - // loop over all atoms in jgroup bin - // if j is owned atom, store it if j > i - // if j is ghost, only store if j coords are "above and to the right" of i + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - js = binhead_multi[jgroup][jbin]; + 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]; + cutdistsq = (radsum+skin) * (radsum+skin); - for (j = js; j >= 0; j = bins[j]) { - if(j < i) continue; - - 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; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; } } } diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 0000f7b4d3..2000927c63 100755 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -77,7 +77,6 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) if(igroup == jgroup) jbin = ibin; else jbin = coord2bin(x[i], jgroup); - // loop over all atoms in bins in stencil // stencil is empty if i larger than j // stencil is half if i same size as j diff --git a/src/nstencil.cpp b/src/nstencil.cpp index acd7272245..3d86b57b9e 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -55,7 +55,7 @@ using namespace LAMMPS_NS; create one stencil for each igroup-jgroup pairing the full/half stencil label refers to the same-group stencil a half list with newton on has a half same-group stencil - a full list or half list with newton of has a full same-group stencil + a full list or half list with newton off has a full same-group stencil cross group stencils are always full to allow small-to-large lookups for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above @@ -76,7 +76,7 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) distsq_multi_old = nullptr; nstencil_multi = nullptr; - stencil_multi = nullptr; + stencil_multi = nullptr; maxstencil_multi = nullptr; flag_half_multi = nullptr; @@ -230,7 +230,7 @@ void NStencil::create_setup() int smax = (2*sx+1) * (2*sy+1) * (2*sz+1); // reallocate stencil structs if necessary - // for BIN and MULTI styles + // for BIN and MULTI_OLD styles if (neighstyle == Neighbor::BIN) { if (smax > maxstencil) { @@ -315,9 +315,8 @@ void NStencil::create_setup() set_stencil_properties(); // Allocate arrays to store stencils - if (!maxstencil_multi) { - memory->create(maxstencil_multi, n, n, "neighstencil::stencil_multi"); + memory->create(maxstencil_multi, n, n, "neighstencil::maxstencil_multi"); memory->create(nstencil_multi, n, n, "neighstencil::nstencil_multi"); stencil_multi = new int**[n](); for (i = 0; i < n; ++i) { @@ -325,6 +324,7 @@ void NStencil::create_setup() for (j = 0; j < n; ++j) { maxstencil_multi[i][j] = 0; nstencil_multi[i][j] = 0; + stencil_multi[i][j] = nullptr; } } } @@ -400,21 +400,21 @@ double NStencil::bin_distance(int i, int j, int k) compute closest distance for a given atom grouping ------------------------------------------------------------------------- */ -double NStencil::bin_distance_multi(int i, int j, int k, int group) +double NStencil::bin_distance_multi(int i, int j, int k, int ig) { double delx,dely,delz; - if (i > 0) delx = (i-1)*binsizex_multi[group]; + if (i > 0) delx = (i-1)*binsizex_multi[ig]; else if (i == 0) delx = 0.0; - else delx = (i+1)*binsizex_multi[group]; + else delx = (i+1)*binsizex_multi[ig]; - if (j > 0) dely = (j-1)*binsizey_multi[group]; + if (j > 0) dely = (j-1)*binsizey_multi[ig]; else if (j == 0) dely = 0.0; - else dely = (j+1)*binsizey_multi[group]; + else dely = (j+1)*binsizey_multi[ig]; - if (k > 0) delz = (k-1)*binsizez_multi[group]; + if (k > 0) delz = (k-1)*binsizez_multi[ig]; else if (k == 0) delz = 0.0; - else delz = (k+1)*binsizez_multi[group]; + else delz = (k+1)*binsizez_multi[ig]; return (delx*delx + dely*dely + delz*delz); } @@ -435,13 +435,8 @@ double NStencil::memory_usage() for (int i = 0; i < n; i++) { for (int j = 0; j < n; j++) { bytes += maxstencil_multi[i][j] * sizeof(int); - bytes += maxstencil_multi[i][j] * sizeof(int); - bytes += maxstencil_multi[i][j] * sizeof(double); } } - bytes += 2 * n * n * sizeof(bool); - bytes += 6 * n * n * sizeof(int); - bytes += 4 * n * n * sizeof(double); } return bytes; } diff --git a/src/nstencil.h b/src/nstencil.h index b06f340d6f..b38276b45f 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -30,7 +30,7 @@ class NStencil : protected Pointers { int *nstencil_multi_old; // # bins in each type-based old multi stencil int **stencil_multi_old; // list of bin offsets in each stencil double **distsq_multi_old; // sq distances to bins in each stencil - int ** nstencil_multi; // # bins bins in each itype-jtype multi stencil + int ** nstencil_multi; // # bins bins in each igroup-jgroup multi stencil int *** stencil_multi; // list of bin offsets in each multi stencil int ** maxstencil_multi; // max stencil size for each multi stencil @@ -42,8 +42,8 @@ class NStencil : protected Pointers { double cutoff_custom; // cutoff set by requestor // Arrays to store options for multi itype-jtype stencils - bool **flag_half_multi; // flag creation of a half stencil for itype-jtype - bool **flag_skip_multi; // skip creation of itype-jtype stencils (for newton on) + bool **flag_half_multi; // flag creation of a half stencil for igroup-jgroup + bool **flag_skip_multi; // skip creation of igroup-jgroup stencils (for newton on) int **bin_group_multi; // what group to use for bin information NStencil(class LAMMPS *); From d79a2c3a02b295dd1d8c1cb636546d8de6c16015 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 2 Feb 2021 09:39:13 -0700 Subject: [PATCH 47/73] Adding collection array, new user arguments, and multi communication --- src/GRANULAR/pair_gran_hooke_history.cpp | 21 + src/GRANULAR/pair_gran_hooke_history.h | 2 + src/GRANULAR/pair_granular.cpp | 48 ++ src/GRANULAR/pair_granular.h | 2 + ...n_ssa.cpp => nstencil_half_bin_2d_ssa.cpp} | 6 +- ...ewton_ssa.h => nstencil_half_bin_2d_ssa.h} | 16 +- ...n_ssa.cpp => nstencil_half_bin_3d_ssa.cpp} | 6 +- ...ewton_ssa.h => nstencil_half_bin_3d_ssa.h} | 16 +- src/USER-OMP/npair_full_multi_omp.cpp | 26 +- src/USER-OMP/npair_half_multi_newtoff_omp.cpp | 26 +- src/USER-OMP/npair_half_multi_newton_omp.cpp | 38 +- .../npair_half_multi_newton_tri_omp.cpp | 28 +- .../npair_half_size_multi_newtoff_omp.cpp | 26 +- .../npair_half_size_multi_newton_omp.cpp | 38 +- .../npair_half_size_multi_newton_tri_omp.cpp | 28 +- src/comm.cpp | 70 +- src/comm.h | 11 +- src/comm_brick.cpp | 219 +++-- src/comm_brick.h | 10 +- src/comm_tiled.cpp | 294 +++++-- src/comm_tiled.h | 10 +- src/init | 789 ++++++++++++++++++ src/nbin.cpp | 46 +- src/nbin.h | 7 +- src/nbin_multi.cpp | 90 +- src/neighbor.cpp | 255 ++++-- src/neighbor.h | 16 +- src/npair.cpp | 44 +- src/npair.h | 5 +- src/npair_full_multi.cpp | 26 +- src/npair_half_multi_newtoff.cpp | 26 +- src/npair_half_multi_newton.cpp | 38 +- src/npair_half_multi_newton_tri.cpp | 30 +- src/npair_half_size_multi_newtoff.cpp | 26 +- src/npair_half_size_multi_newton.cpp | 38 +- src/npair_half_size_multi_newton_tri.cpp | 28 +- src/npair_half_size_multi_old_newtoff.cpp | 2 +- src/npair_half_size_multi_old_newton.cpp | 2 +- src/npair_half_size_multi_old_newton_tri.cpp | 2 +- src/nstencil.cpp | 80 +- src/nstencil.h | 12 +- src/nstencil_full_multi_2d.cpp | 32 +- src/nstencil_full_multi_3d.cpp | 36 +- src/nstencil_half_multi_2d.cpp | 46 +- src/nstencil_half_multi_2d_tri.cpp | 46 +- src/nstencil_half_multi_3d.cpp | 50 +- src/nstencil_half_multi_3d_tri.cpp | 50 +- src/pair.cpp | 1 + src/pair.h | 3 + src/pair_hybrid.cpp | 37 + src/pair_hybrid.h | 2 + 51 files changed, 2109 insertions(+), 697 deletions(-) rename src/USER-DPD/{nstencil_half_bin_2d_newton_ssa.cpp => nstencil_half_bin_2d_ssa.cpp} (95%) rename src/USER-DPD/{nstencil_half_bin_2d_newton_ssa.h => nstencil_half_bin_2d_ssa.h} (66%) rename src/USER-DPD/{nstencil_half_bin_3d_newton_ssa.cpp => nstencil_half_bin_3d_ssa.cpp} (97%) rename src/USER-DPD/{nstencil_half_bin_3d_newton_ssa.h => nstencil_half_bin_3d_ssa.h} (66%) create mode 100644 src/init diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 7b7586d355..46b41126aa 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -43,6 +43,7 @@ PairGranHookeHistory::PairGranHookeHistory(LAMMPS *lmp) : Pair(lmp) single_enable = 1; no_virial_fdotr_compute = 1; centroidstressflag = CENTROID_NOTAVAIL; + finitecutflag = 1; history = 1; size_history = 3; @@ -796,3 +797,23 @@ double PairGranHookeHistory::memory_usage() double bytes = nmax * sizeof(double); return bytes; } + +/* ---------------------------------------------------------------------- + self-interaction range of particle +------------------------------------------------------------------------- */ + +double PairGranHookeHistory::atom2cut(int i) +{ + double cut = atom->radius[i]*2; + return cut; +} + +/* ---------------------------------------------------------------------- + maximum interaction range for two finite particles +------------------------------------------------------------------------- */ + +double PairGranHookeHistory::radii2cut(double r1, double r2) +{ + double cut = r1+r2; + return cut; +} \ No newline at end of file diff --git a/src/GRANULAR/pair_gran_hooke_history.h b/src/GRANULAR/pair_gran_hooke_history.h index c27ce8a9af..9575c49d0c 100644 --- a/src/GRANULAR/pair_gran_hooke_history.h +++ b/src/GRANULAR/pair_gran_hooke_history.h @@ -42,6 +42,8 @@ class PairGranHookeHistory : public Pair { int pack_forward_comm(int, int *, double *, int, int *); void unpack_forward_comm(int, int, double *); double memory_usage(); + double atom2cut(int); + double radii2cut(double,double); protected: double kn,kt,gamman,gammat,xmu; diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 215926e23e..0f1fbd49f3 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -67,6 +67,7 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp) single_enable = 1; no_virial_fdotr_compute = 1; centroidstressflag = CENTROID_NOTAVAIL; + finitecutflag = 1; single_extra = 12; svector = new double[single_extra]; @@ -1819,3 +1820,50 @@ void PairGranular::transfer_history(double* source, double* target) for (int i = 0; i < size_history; i++) target[i] = history_transfer_factors[i]*source[i]; } + +/* ---------------------------------------------------------------------- + self-interaction range of particle +------------------------------------------------------------------------- */ + +double PairGranular::atom2cut(int i) +{ + double cut; + + cut = atom->radius[i]*2; + if(beyond_contact) { + int itype = atom->type[i] + if(normal_model[itype][itype] == JKR) { + cut += pulloffdistance(cut, cut, itype, itype); + } + } + + return cut; +} + +/* ---------------------------------------------------------------------- + maximum interaction range for two finite particles +------------------------------------------------------------------------- */ + +double PairGranular::radii2cut(double r1, double r2) +{ + double cut = 0.0; + + if(beyond_contact) { + int n = atom->ntypes; + double temp; + + // Check all combinations of i and j to find theoretical maximum pull off distance + for(int i = 0; i < n; i++){ + for(int j = 0; j < n; j++){ + if(normal_model[i][j] == JKR) { + temp = pulloffdistance(r1, r2, i, j); + if(temp > cut) cut = temp; + } + } + } + } + + cut += r1 + r2; + + return cut; +} diff --git a/src/GRANULAR/pair_granular.h b/src/GRANULAR/pair_granular.h index 7ef4f2af98..7fe47b3275 100644 --- a/src/GRANULAR/pair_granular.h +++ b/src/GRANULAR/pair_granular.h @@ -40,6 +40,8 @@ class PairGranular : public Pair { int pack_forward_comm(int, int *, double *, int, int *); void unpack_forward_comm(int, int, double *); double memory_usage(); + double atom2cut(int); + double radii2cut(double,double); protected: double dt; diff --git a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_2d_ssa.cpp similarity index 95% rename from src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp rename to src/USER-DPD/nstencil_half_bin_2d_ssa.cpp index 803a80f3e3..aca7b9df09 100644 --- a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp +++ b/src/USER-DPD/nstencil_half_bin_2d_ssa.cpp @@ -16,13 +16,13 @@ James Larentzos and Timothy I. Mattox (Engility Corporation) ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_2d_newton_ssa.h" +#include "nstencil_half_bin_2d_ssa.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) : +NStencilHalfBin2dSSA::NStencilHalfBin2dSSA(LAMMPS *lmp) : NStencilSSA(lmp) {} /* ---------------------------------------------------------------------- @@ -37,7 +37,7 @@ NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) : to locate all the Active Interaction Region (AIR) ghosts for SSA ------------------------------------------------------------------------- */ -void NStencilHalfBin2dNewtonSSA::create() +void NStencilHalfBin2dSSA::create() { int i,j,pos = 0; nstencil_ssa[0] = 0; // redundant info, but saves a conditional diff --git a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h b/src/USER-DPD/nstencil_half_bin_2d_ssa.h similarity index 66% rename from src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h rename to src/USER-DPD/nstencil_half_bin_2d_ssa.h index 1d5cc3f6b2..a50c852670 100644 --- a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h +++ b/src/USER-DPD/nstencil_half_bin_2d_ssa.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bin/2d/newton/ssa, - NStencilHalfBin2dNewtonSSA, - NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_SSA | NS_ORTHO | NS_GHOST) +NStencilStyle(half/bin/2d/ssa, + NStencilHalfBin2dSSA, + NS_HALF | NS_BIN | NS_2D | NS_SSA | NS_ORTHO | NS_GHOST) #else -#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H -#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H +#ifndef LMP_NSTENCIL_HALF_BIN_2D_SSA_H +#define LMP_NSTENCIL_HALF_BIN_2D_SSA_H #include "nstencil_ssa.h" namespace LAMMPS_NS { -class NStencilHalfBin2dNewtonSSA : public NStencilSSA { +class NStencilHalfBin2dSSA : public NStencilSSA { public: - NStencilHalfBin2dNewtonSSA(class LAMMPS *); - ~NStencilHalfBin2dNewtonSSA() {} + NStencilHalfBin2dSSA(class LAMMPS *); + ~NStencilHalfBin2dSSA() {} void create(); }; diff --git a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_3d_ssa.cpp similarity index 97% rename from src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp rename to src/USER-DPD/nstencil_half_bin_3d_ssa.cpp index c20dabe28f..8e33f5414f 100644 --- a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp +++ b/src/USER-DPD/nstencil_half_bin_3d_ssa.cpp @@ -16,13 +16,13 @@ James Larentzos and Timothy I. Mattox (Engility Corporation) ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_3d_newton_ssa.h" +#include "nstencil_half_bin_3d_ssa.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) : +NStencilHalfBin3dSSA::NStencilHalfBin3dSSA(LAMMPS *lmp) : NStencilSSA(lmp) {} /* ---------------------------------------------------------------------- @@ -37,7 +37,7 @@ NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) : to locate all the Active Interaction Region (AIR) ghosts for SSA ------------------------------------------------------------------------- */ -void NStencilHalfBin3dNewtonSSA::create() +void NStencilHalfBin3dSSA::create() { int i,j,k,pos = 0; nstencil_ssa[0] = 0; // redundant info, but saves a conditional diff --git a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h b/src/USER-DPD/nstencil_half_bin_3d_ssa.h similarity index 66% rename from src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h rename to src/USER-DPD/nstencil_half_bin_3d_ssa.h index 450a696e46..94f8fb4142 100644 --- a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h +++ b/src/USER-DPD/nstencil_half_bin_3d_ssa.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bin/3d/newton/ssa, - NStencilHalfBin3dNewtonSSA, - NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_SSA | NS_ORTHO | NS_GHOST) +NStencilStyle(half/bin/3d/ssa, + NStencilHalfBin3dSSA, + NS_HALF | NS_BIN | NS_3D | NS_SSA | NS_ORTHO | NS_GHOST) #else -#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H -#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H +#ifndef LMP_NSTENCIL_HALF_BIN_3D_SSA_H +#define LMP_NSTENCIL_HALF_BIN_3D_SSA_H #include "nstencil_ssa.h" namespace LAMMPS_NS { -class NStencilHalfBin3dNewtonSSA : public NStencilSSA { +class NStencilHalfBin3dSSA : public NStencilSSA { public: - NStencilHalfBin3dNewtonSSA(class LAMMPS *); - ~NStencilHalfBin3dNewtonSSA() {} + NStencilHalfBin3dSSA(class LAMMPS *); + ~NStencilHalfBin3dSSA() {} void create(); }; diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index 4b38e660d4..4fc6fb4a68 100755 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_full_multi_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -30,7 +31,7 @@ NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ @@ -46,7 +47,7 @@ void NPairFullMultiOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -54,6 +55,7 @@ void NPairFullMultiOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -80,7 +82,7 @@ void NPairFullMultiOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -92,22 +94,22 @@ void NPairFullMultiOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in surrounding bins in stencil including self // skip i = j - // use full stencil for all group combinations + // use full stencil for all collection combinations - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { if (i == j) continue; diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp index 93d150f445..ed0e770b2f 100755 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #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" @@ -30,7 +31,7 @@ NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent 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) @@ -48,7 +49,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -56,6 +57,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -82,7 +84,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -94,24 +96,24 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // 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 - // use full stencil for all group combinations + // use full stencil for all collection combinations - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index 11a84a3040..13d286ab5b 100755 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #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" @@ -30,7 +31,7 @@ NPairHalfMultiNewtonOmp::NPairHalfMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -47,7 +48,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -55,6 +56,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -81,7 +83,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -93,29 +95,29 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(igroup == jgroup) js = bins[i]; - else js = binhead_multi[jgroup][jbin]; + if(icollection == jcollection) js = bins[i]; + else js = binhead_multi[jcollection][jbin]; - // if same group, + // if same collection, // 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 - // if different groups, + // if different collections, // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(igroup != jgroup and j < i) continue; + if(icollection != jcollection and j < i) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -151,16 +153,16 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) } } - // for all groups, loop over all atoms in other bins in stencil, store every pair + // for all collections, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index b5882580a8..cb758673d4 100755 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #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" @@ -31,7 +32,7 @@ NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -48,7 +49,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,igroup,jgroup,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,ibin,jbin,icollection,jcollection,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -56,6 +57,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -82,7 +84,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -94,12 +96,12 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil // stencil is empty if i larger than j @@ -110,15 +112,15 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { - // if same size (same group), use half stencil - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + // if same size (same collection), use half stencil + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp index 0d588b2f24..0efb4f067a 100755 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_half_size_multi_newtoff_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -29,7 +30,7 @@ NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : NPair( /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent 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) @@ -47,7 +48,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -55,6 +56,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -75,7 +77,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -83,24 +85,24 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // 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 - // use full stencil for all group combinations + // use full stencil for all collection combinations - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index cec3edd02b..68885fb453 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_half_size_multi_newton_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -29,7 +30,7 @@ NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) : NPair(lm /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -46,7 +47,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -54,6 +55,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -74,7 +76,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -82,29 +84,29 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(igroup == jgroup) js = bins[i]; - else js = binhead_multi[jgroup][jbin]; + if(icollection == jcollection) js = bins[i]; + else js = binhead_multi[jcollection][jbin]; - // if same group, + // if same collection, // 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 - // if different groups, + // if different collections, // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(igroup != jgroup and j < i) continue; + if(icollection != jcollection and j < i) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -133,16 +135,16 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) } } - // for all groups, loop over all atoms in other bins in stencil, store every pair + // for all collections, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp index 396e870846..76f61b8792 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_half_size_multi_newton_tri_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -30,7 +31,7 @@ NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -47,7 +48,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -55,6 +56,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -75,7 +77,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -83,12 +85,12 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil @@ -100,15 +102,15 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { - // if same size (same group), use half stencil - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + // if same size (same collection), use half stencil + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/comm.cpp b/src/comm.cpp index 867eab6256..3f2d4ecde6 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -58,6 +58,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) bordergroup = 0; cutghostuser = 0.0; cutusermulti = nullptr; + cutusermultiold = nullptr; ghost_velocity = 0; user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0; @@ -118,6 +119,7 @@ Comm::~Comm() memory->destroy(ysplit); memory->destroy(zsplit); memory->destroy(cutusermulti); + memory->destroy(cutusermultiold); delete [] customfile; delete [] outfile; } @@ -146,8 +148,13 @@ void Comm::copy_arrays(Comm *oldcomm) } if (oldcomm->cutusermulti) { - memory->create(cutusermulti,atom->ntypes+1,"comm:cutusermulti"); - memcpy(cutusermulti,oldcomm->cutusermulti,atom->ntypes+1); + memory->create(cutusermulti,ncollections,"comm:cutusermulti"); + memcpy(cutusermulti,oldcomm->cutusermulti,ncollections); + } + + if (oldcomm->cutusermultiold) { + memory->create(cutusermultiold,atom->ntypes+1,"comm:cutusermultiold"); + memcpy(cutusermultiold,oldcomm->cutusermultiold,atom->ntypes+1); } if (customfile) { @@ -242,13 +249,16 @@ void Comm::init() for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; + if(mode == Comm::MULTI and neighbor->style != Neighbor::MULTI) + error->all(FLERR,"Cannot use comm mode multi without multi-style neighbor lists"); + if(multi_reduce){ if (force->newton == 0) error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); if (neighbor->any_full()) error->all(FLERR,"Cannot use multi/reduce communication with a full neighbor list"); - if (neighbor->style != Neighbor::MULTI) - error->all(FLERR,"Cannot use multi/reduce communication without multi-style neighbor lists"); + if(mode != Comm::MULTI) + error->all(FLERR,"Cannot use multi/reduce communication without mode multi"); } } @@ -285,13 +295,20 @@ void Comm::modify_params(int narg, char **arg) if (strcmp(arg[iarg+1],"single") == 0) { // need to reset cutghostuser when switching comm mode if (mode == Comm::MULTI) cutghostuser = 0.0; + if (mode == Comm::MULTIOLD) cutghostuser = 0.0; memory->destroy(cutusermulti); cutusermulti = nullptr; mode = Comm::SINGLE; } else if (strcmp(arg[iarg+1],"multi") == 0) { // need to reset cutghostuser when switching comm mode if (mode == Comm::SINGLE) cutghostuser = 0.0; + if (mode == Comm::MULTIOLD) cutghostuser = 0.0; mode = Comm::MULTI; + } else if (strcmp(arg[iarg+1],"multi/old") == 0) { + // need to reset cutghostuser when switching comm mode + if (mode == Comm::SINGLE) cutghostuser = 0.0; + if (mode == Comm::MULTI) cutghostuser = 0.0; + mode = Comm::MULTIOLD; } else error->all(FLERR,"Illegal comm_modify command"); iarg += 2; } else if (strcmp(arg[iarg],"group") == 0) { @@ -308,6 +325,9 @@ void Comm::modify_params(int narg, char **arg) if (mode == Comm::MULTI) error->all(FLERR, "Use cutoff/multi keyword to set cutoff in multi mode"); + if (mode == Comm::MULTIOLD) + error->all(FLERR, + "Use cutoff/multi/old keyword to set cutoff in multi mode"); cutghostuser = utils::numeric(FLERR,arg[iarg+1],false,lmp); if (cutghostuser < 0.0) error->all(FLERR,"Invalid cutoff in comm_modify command"); @@ -317,18 +337,20 @@ void Comm::modify_params(int narg, char **arg) double cut; if (mode == Comm::SINGLE) error->all(FLERR,"Use cutoff keyword to set cutoff in single mode"); - if (domain->box_exist == 0) + if (mode == Comm::MULTIOLD) + error->all(FLERR,"Use cutoff/multi/old keyword to set cutoff in multi/old mode"); + if (domain->box_exist == 0) error->all(FLERR, "Cannot set cutoff/multi before simulation box is defined"); - const int ntypes = atom->ntypes; + ncollections = neighbor->ncollections; if (iarg+3 > narg) error->all(FLERR,"Illegal comm_modify command"); if (cutusermulti == nullptr) { - memory->create(cutusermulti,ntypes+1,"comm:cutusermulti"); - for (i=0; i < ntypes+1; ++i) + memory->create(cutusermulti,ncollections,"comm:cutusermulti"); + for (i=0; i < ncollections; ++i) cutusermulti[i] = -1.0; } - utils::bounds(FLERR,arg[iarg+1],1,ntypes,nlo,nhi,error); + utils::bounds(FLERR,arg[iarg+1],1,ncollections,nlo,nhi,error); cut = utils::numeric(FLERR,arg[iarg+2],false,lmp); cutghostuser = MAX(cutghostuser,cut); if (cut < 0.0) @@ -336,9 +358,35 @@ void Comm::modify_params(int narg, char **arg) for (i=nlo; i<=nhi; ++i) cutusermulti[i] = cut; iarg += 3; - } else if (strcmp(arg[iarg],"multi/reduce") == 0) { + } else if (strcmp(arg[iarg],"cutoff/multi/old") == 0) { + int i,nlo,nhi; + double cut; if (mode == Comm::SINGLE) - error->all(FLERR,"Use multi/reduce in mode multi only"); + error->all(FLERR,"Use cutoff keyword to set cutoff in single mode"); + if (mode == Comm::MULTI) + error->all(FLERR,"Use cutoff/multi keyword to set cutoff in multi mode"); + if (domain->box_exist == 0) + error->all(FLERR, + "Cannot set cutoff/multi before simulation box is defined"); + const int ntypes = atom->ntypes; + if (iarg+3 > narg) + error->all(FLERR,"Illegal comm_modify command"); + if (cutusermultiold == nullptr) { + memory->create(cutusermultiold,ntypes+1,"comm:cutusermultiold"); + for (i=0; i < ntypes+1; ++i) + cutusermultiold[i] = -1.0; + } + utils::bounds(FLERR,arg[iarg+1],1,ntypes,nlo,nhi,error); + cut = utils::numeric(FLERR,arg[iarg+2],false,lmp); + cutghostuser = MAX(cutghostuser,cut); + if (cut < 0.0) + error->all(FLERR,"Invalid cutoff in comm_modify command"); + for (i=nlo; i<=nhi; ++i) + cutusermultiold[i] = cut; + iarg += 3; + } else if (strcmp(arg[iarg],"reduce/multi") == 0) { + if (mode == Comm::SINGLE) + error->all(FLERR,"Use reduce/multi in mode multi only"); multi_reduce = 1; iarg += 1; } else if (strcmp(arg[iarg],"vel") == 0) { diff --git a/src/comm.h b/src/comm.h index 4ae4faf7fd..877941523c 100644 --- a/src/comm.h +++ b/src/comm.h @@ -25,14 +25,15 @@ class Comm : protected Pointers { // LAYOUT_NONUNIFORM = logical bricks, but diff sizes via LB // LAYOUT_TILED = general tiling, due to RCB LB enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; - int mode; // 0 = single cutoff, 1 = multi-type cutoff - enum{SINGLE,MULTI}; + int mode; // 0 = single cutoff, 1 = multi-collection cutoff, 2 = multiold-type cutoff + enum{SINGLE,MULTI,MULTIOLD}; int me,nprocs; // proc info int ghost_velocity; // 1 if ghost atoms have velocity, 0 if not double cutghost[3]; // cutoffs used for acquiring ghost atoms double cutghostuser; // user-specified ghost cutoff (mode == 0) - double *cutusermulti; // per type user ghost cutoff (mode == 1) + double *cutusermulti; // per collection user ghost cutoff (mode == 1) + double *cutusermultiold; // per type user ghost cutoff (mode == 2) int recv_from_partition; // recv proc layout from this partition int send_to_partition; // send my proc layout to this partition // -1 if no recv or send @@ -152,7 +153,9 @@ class Comm : protected Pointers { int ncores; // # of cores per node int coregrid[3]; // 3d grid of cores within a node int user_coregrid[3]; // user request for cores in each dim - int multi_reduce; // 1 if multi cutoff is intra-type cutoff + int multi_reduce; // 1 if multi cutoff is intra-collection cutoff + int ncollections; // number of collection cutoffs defined for multi + int ncollections_prior; // value of ncollections at last setup void init_exchange(); int rendezvous_irregular(int, char *, int, int, int *, diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 939669fb75..ca0fea8757 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -46,6 +46,7 @@ CommBrick::CommBrick(LAMMPS *lmp) : size_reverse_send(nullptr), size_reverse_recv(nullptr), slablo(nullptr), slabhi(nullptr), multilo(nullptr), multihi(nullptr), cutghostmulti(nullptr), pbc_flag(nullptr), pbc(nullptr), firstrecv(nullptr), + multioldlo(nullptr), multioldhi(nullptr), cutghostmultiold(nullptr), sendlist(nullptr), localsendlist(nullptr), maxsendlist(nullptr), buf_send(nullptr), buf_recv(nullptr) { @@ -65,6 +66,11 @@ CommBrick::~CommBrick() memory->destroy(cutghostmulti); } + if (mode == Comm::MULTIOLD) { + free_multiold(); + memory->destroy(cutghostmultiold); + } + if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]); if (localsendlist) memory->destroy(localsendlist); memory->sfree(sendlist); @@ -101,6 +107,9 @@ void CommBrick::init_buffers() multilo = multihi = nullptr; cutghostmulti = nullptr; + multioldlo = multioldhi = nullptr; + cutghostmultiold = nullptr; + buf_send = buf_recv = nullptr; maxsend = maxrecv = BUFMIN; grow_send(maxsend,2); @@ -128,23 +137,37 @@ void CommBrick::init() init_exchange(); if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2); - // memory for multi-style communication + // memory for multi style communication + // allocate in setup if (mode == Comm::MULTI && multilo == nullptr) { allocate_multi(maxswap); - memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti"); - } - if (mode == Comm::SINGLE && multilo) { + memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); + ncollections_prior = ncollections; + } + if ((mode == Comm::SINGLE or mode == Comm::MULTIOLD) && multilo) { free_multi(); memory->destroy(cutghostmulti); } + + // memory for multi/old-style communication + + if (mode == Comm::MULTIOLD && multioldlo == nullptr) { + allocate_multiold(maxswap); + memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold"); + } + if ((mode == Comm::SINGLE or mode == Comm::MULTI) && multioldlo) { + free_multiold(); + memory->destroy(cutghostmultiold); + } } /* ---------------------------------------------------------------------- setup spatial-decomposition communication patterns function of neighbor cutoff(s) & cutghostuser & current box size single mode sets slab boundaries (slablo,slabhi) based on max cutoff - multi mode sets type-dependent slab boundaries (multilo,multihi) + multi mode sets collection-dependent slab boundaries (multilo,multihi) + multi/old mode sets type-dependent slab boundaries (multioldlo,multioldhi) ------------------------------------------------------------------------- */ void CommBrick::setup() @@ -156,8 +179,10 @@ void CommBrick::setup() // neigh->cutghost = distance between tilted planes in box coords // cutghost is in lamda coords = distance between those planes // for multi: - // cutghostmulti = same as cutghost, only for each atom type - + // cutghostmulti = same as cutghost, only for each atom collection + // for multi/old: + // cutghostmultiold = same as cutghost, only for each atom type + int i,j; int ntypes = atom->ntypes; double *prd,*sublo,*subhi; @@ -167,49 +192,58 @@ void CommBrick::setup() error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " "will be generated. Atoms may get lost."); - if (mode == Comm::MULTI) { - if (multi_reduce) { - // If using multi/reduce, communicate itype particles a distance equal - // to the max of itype-jtype group interaction - // only consider smaller jtype groups - int igroup, jgroup; - double **cutmultisq = neighbor->cutmultisq; - int *map_type_multi = neighbor->map_type_multi; - for (i = 1; i <= ntypes; i++) { - - if (cutusermulti) { - cutghostmulti[i][0] = cutusermulti[i]; - cutghostmulti[i][1] = cutusermulti[i]; - cutghostmulti[i][2] = cutusermulti[i]; - } else { - cutghostmulti[i][0] = 0.0; - cutghostmulti[i][1] = 0.0; - cutghostmulti[i][2] = 0.0; - } - - igroup = map_type_multi[i]; - for (j = 1; j <= ntypes; j++){ - jgroup = map_type_multi[j]; - - if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); - } + // build initial collection array + neighbor->build_collection(0); + + if(cutusermulti and ncollections != neighbor->ncollections) + error->all(FLERR, "Cannot change number of collections after defining comm_modify multi/cutoff"); + else ncollections = neighbor->ncollections; + + // reallocate memory for multi-style communication at setup if ncollections change + if(ncollections_prior != ncollections){ + if(multilo) free_multi(); + if(cutghostmulti) memory->destroy(cutghostmulti); + + allocate_multi(maxswap); + memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); + ncollections_prior = ncollections; + } + + double **cutcollectionsq = neighbor->cutcollectionsq; + // If using multi/reduce, communicate particles a distance equal + // to the max cutoff with equally sized or smaller collections + // If not, communicate the maximum cutoff of the entire collection + for (i = 0; i < ncollections; i++) { + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; } - } else { - // otherwise, communicate a distance equal to the maximum interaction distance for each type - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - double tmp = 0.0; - if (cutusermulti) tmp = cutusermulti[i]; - cutghostmulti[i][0] = MAX(tmp,cuttype[i]); - cutghostmulti[i][1] = MAX(tmp,cuttype[i]); - cutghostmulti[i][2] = MAX(tmp,cuttype[i]); + + for (j = 0; j < ncollections; j++){ + if(multi_reduce and cutcollectionsq[j][j] > cutcollectionsq[i][i]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j])); } } } + + if (mode == Comm::MULTIOLD) { + double *cuttype = neighbor->cuttype; + for (i = 1; i <= ntypes; i++) { + double tmp = 0.0; + if (cutusermultiold) tmp = cutusermultiold[i]; + cutghostmultiold[i][0] = MAX(tmp,cuttype[i]); + cutghostmultiold[i][1] = MAX(tmp,cuttype[i]); + cutghostmultiold[i][2] = MAX(tmp,cuttype[i]); + } + } if (triclinic == 0) { prd = domain->prd; @@ -228,13 +262,21 @@ void CommBrick::setup() cutghost[1] = cut * length1; length2 = h_inv[2]; cutghost[2] = cut * length2; - if (mode == Comm::MULTI){ - for (i = 1; i <= ntypes; i++) { + if (mode == Comm::MULTI) { + for (i = 0; i < ncollections; i++) { cutghostmulti[i][0] *= length0; cutghostmulti[i][1] *= length1; cutghostmulti[i][2] *= length2; } } + + if (mode == Comm::MULTIOLD) { + for (i = 1; i <= ntypes; i++) { + cutghostmultiold[i][0] *= length0; + cutghostmultiold[i][1] *= length1; + cutghostmultiold[i][2] *= length2; + } + } } // recvneed[idim][0/1] = # of procs away I recv atoms from, within cutghost @@ -378,12 +420,18 @@ void CommBrick::setup() if (ineed < 2) slablo[iswap] = -BIG; else slablo[iswap] = 0.5 * (sublo[dim] + subhi[dim]); slabhi[iswap] = sublo[dim] + cutghost[dim]; - } else { - for (i = 1; i <= ntypes; i++) { + } else if (mode == Comm::MULTI) { + for (i = 0; i < ncollections; i++) { if (ineed < 2) multilo[iswap][i] = -BIG; else multilo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); multihi[iswap][i] = sublo[dim] + cutghostmulti[i][dim]; } + } else { + for (i = 1; i <= ntypes; i++) { + if (ineed < 2) multioldlo[iswap][i] = -BIG; + else multioldlo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); + multioldhi[iswap][i] = sublo[dim] + cutghostmultiold[i][dim]; + } } if (myloc[dim] == 0) { pbc_flag[iswap] = 1; @@ -401,12 +449,18 @@ void CommBrick::setup() slablo[iswap] = subhi[dim] - cutghost[dim]; if (ineed < 2) slabhi[iswap] = BIG; else slabhi[iswap] = 0.5 * (sublo[dim] + subhi[dim]); - } else { - for (i = 1; i <= ntypes; i++) { + } else if (mode == Comm::MULTI) { + for (i = 0; i < ncollections; i++) { multilo[iswap][i] = subhi[dim] - cutghostmulti[i][dim]; if (ineed < 2) multihi[iswap][i] = BIG; else multihi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); } + } else { + for (i = 1; i <= ntypes; i++) { + multioldlo[iswap][i] = subhi[dim] - cutghostmultiold[i][dim]; + if (ineed < 2) multioldhi[iswap][i] = BIG; + else multioldhi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); + } } if (myloc[dim] == procgrid[dim]-1) { pbc_flag[iswap] = 1; @@ -727,15 +781,19 @@ void CommBrick::exchange() void CommBrick::borders() { - int i,n,itype,iswap,dim,ineed,twoneed; - int nsend,nrecv,sendflag,nfirst,nlast,ngroup; + int i,n,itype,icollection,iswap,dim,ineed,twoneed; + int nsend,nrecv,sendflag,nfirst,nlast,ngroup,nprior; double lo,hi; int *type; + int *collection; double **x; double *buf,*mlo,*mhi; MPI_Request request; AtomVec *avec = atom->avec; + // After exchanging/sorting, need to reconstruct collection array for border communication + if(mode == Comm::MULTI) neighbor->build_collection(0); + // do swaps over all 3 dimensions iswap = 0; @@ -756,10 +814,14 @@ void CommBrick::borders() if (mode == Comm::SINGLE) { lo = slablo[iswap]; hi = slabhi[iswap]; - } else { - type = atom->type; + } else if (mode == Comm::MULTI) { + collection = neighbor->collection; mlo = multilo[iswap]; mhi = multihi[iswap]; + } else { + type = atom->type; + mlo = multioldlo[iswap]; + mhi = multioldhi[iswap]; } if (ineed % 2 == 0) { nfirst = nlast; @@ -788,6 +850,14 @@ void CommBrick::borders() if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); sendlist[iswap][nsend++] = i; } + } else if (mode == Comm::MULTI) { + for (i = nfirst; i < nlast; i++) { + icollection = collection[i]; + if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) { + if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); + sendlist[iswap][nsend++] = i; + } + } } else { for (i = nfirst; i < nlast; i++) { itype = type[i]; @@ -878,7 +948,10 @@ void CommBrick::borders() size_reverse_send[iswap] = nrecv*size_reverse; size_reverse_recv[iswap] = nsend*size_reverse; firstrecv[iswap] = atom->nlocal + atom->nghost; + nprior = atom->nlocal + atom->nghost; atom->nghost += nrecv; + if(neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); + iswap++; } } @@ -1431,6 +1504,12 @@ void CommBrick::grow_swap(int n) allocate_multi(n); } + if (mode == Comm::MULTIOLD) { + free_multiold(); + allocate_multiold(n); + } + + sendlist = (int **) memory->srealloc(sendlist,n*sizeof(int *),"comm:sendlist"); memory->grow(maxsendlist,n,"comm:maxsendlist"); @@ -1462,15 +1541,26 @@ void CommBrick::allocate_swap(int n) } /* ---------------------------------------------------------------------- - allocation of multi-type swap info + allocation of multi-collection swap info ------------------------------------------------------------------------- */ void CommBrick::allocate_multi(int n) { - multilo = memory->create(multilo,n,atom->ntypes+1,"comm:multilo"); - multihi = memory->create(multihi,n,atom->ntypes+1,"comm:multihi"); + multilo = memory->create(multilo,n,ncollections,"comm:multilo"); + multihi = memory->create(multihi,n,ncollections,"comm:multihi"); } +/* ---------------------------------------------------------------------- + allocation of multi/old-type swap info +------------------------------------------------------------------------- */ + +void CommBrick::allocate_multiold(int n) +{ + multioldlo = memory->create(multioldlo,n,atom->ntypes+1,"comm:multioldlo"); + multioldhi = memory->create(multioldhi,n,atom->ntypes+1,"comm:multioldhi"); +} + + /* ---------------------------------------------------------------------- free memory for swaps ------------------------------------------------------------------------- */ @@ -1492,7 +1582,7 @@ void CommBrick::free_swap() } /* ---------------------------------------------------------------------- - free memory for multi-type swaps + free memory for multi-collection swaps ------------------------------------------------------------------------- */ void CommBrick::free_multi() @@ -1502,6 +1592,17 @@ void CommBrick::free_multi() multilo = multihi = nullptr; } +/* ---------------------------------------------------------------------- + free memory for multi/old-type swaps +------------------------------------------------------------------------- */ + +void CommBrick::free_multiold() +{ + memory->destroy(multioldlo); + memory->destroy(multioldhi); + multioldlo = multioldhi = nullptr; +} + /* ---------------------------------------------------------------------- extract data potentially useful to other classes ------------------------------------------------------------------------- */ diff --git a/src/comm_brick.h b/src/comm_brick.h index 6165f54de5..a1794fdb7b 100644 --- a/src/comm_brick.h +++ b/src/comm_brick.h @@ -61,8 +61,10 @@ class CommBrick : public Comm { int *size_reverse_send; // # to send in each reverse comm int *size_reverse_recv; // # to recv in each reverse comm double *slablo,*slabhi; // bounds of slab to send at each swap - double **multilo,**multihi; // bounds of slabs for multi-type swap - double **cutghostmulti; // cutghost on a per-type basis + double **multilo,**multihi; // bounds of slabs for multi-collection swap + double **multioldlo,**multioldhi; // bounds of slabs for multi-type swap + double **cutghostmulti; // cutghost on a per-collection basis + double **cutghostmultiold; // cutghost on a per-type basis int *pbc_flag; // general flag for sending atoms thru PBC int **pbc; // dimension flags for PBC adjustments @@ -84,11 +86,13 @@ class CommBrick : public Comm { virtual void grow_send(int, int); // reallocate send buffer virtual void grow_recv(int); // free/allocate recv buffer virtual void grow_list(int, int); // reallocate one sendlist - virtual void grow_swap(int); // grow swap and multi arrays + virtual void grow_swap(int); // grow swap, multi, and multi/old arrays virtual void allocate_swap(int); // allocate swap arrays virtual void allocate_multi(int); // allocate multi arrays + virtual void allocate_multiold(int); // allocate multi/old arrays virtual void free_swap(); // free swap arrays virtual void free_multi(); // free multi arrays + virtual void free_multiold(); // free multi/old arrays }; } diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 2e916e7e1e..accdbf7b04 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -53,6 +53,7 @@ CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp) overlap = nullptr; rcbinfo = nullptr; cutghostmulti = nullptr; + cutghostmultiold = nullptr; init_buffers(); } @@ -81,6 +82,7 @@ CommTiled::~CommTiled() deallocate_swap(maxswap); memory->sfree(rcbinfo); memory->destroy(cutghostmulti); + memory->destroy(cutghostmultiold); } /* ---------------------------------------------------------------------- @@ -98,7 +100,9 @@ void CommTiled::init_buffers() overlap = nullptr; rcbinfo = nullptr; cutghostmulti = nullptr; + cutghostmultiold = nullptr; sendbox_multi = nullptr; + sendbox_multiold = nullptr; maxswap = 6; allocate_swap(maxswap); @@ -115,9 +119,10 @@ void CommTiled::init() nswap = 2*domain->dimension; - memory->destroy(cutghostmulti); - if (mode == Comm::MULTI) - memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti"); + memory->destroy(cutghostmultiold); + if (mode == Comm::MULTIOLD) + memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold"); + int bufextra_old = bufextra; init_exchange(); @@ -173,49 +178,62 @@ void CommTiled::setup() // set cutoff for comm forward and comm reverse // check that cutoff < any periodic box length - + if (mode == Comm::MULTI) { - if (multi_reduce) { - // If using multi/reduce, communicate itype particles a distance equal - // to the max of itype-jtype group interaction - // only consider smaller jtype groups - int igroup, jgroup; - double **cutmultisq = neighbor->cutmultisq; - int *map_type_multi = neighbor->map_type_multi; - for (i = 1; i <= ntypes; i++) { - - if (cutusermulti) { - cutghostmulti[i][0] = cutusermulti[i]; - cutghostmulti[i][1] = cutusermulti[i]; - cutghostmulti[i][2] = cutusermulti[i]; - } else { - cutghostmulti[i][0] = 0.0; - cutghostmulti[i][1] = 0.0; - cutghostmulti[i][2] = 0.0; - } + // build collection from scratch as it is needed for atom exchange + neighbor->build_collection(0); + + if(cutusermulti and ncollections != neighbor->ncollections) + error->all(FLERR, "Cannot change number of collections after defining comm_modify multi/cutoff"); + + ncollections = neighbor->ncollections; + + // allocate memory for multi-style communication at setup as ncollections can change + if(ncollections_prior != ncollections){ + memory->destroy(cutghostmulti); + if (mode == Comm::MULTI) + memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - igroup = map_type_multi[i]; - for (j = 1; j <= ntypes; j++){ - jgroup = map_type_multi[j]; - - if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); - } + for(i = 0; i < maxswap; i ++) + grow_swap_send_multi(i,DELTA_PROCS); + + ncollections_prior = ncollections; + } + + double **cutcollectionsq = neighbor->cutcollectionsq; + // If using multi/reduce, communicate particles a distance equal + // to the max cutoff with equally sized or smaller collections + // If not, communicate the maximum cutoff of the entire collection + for (i = 0; i < ncollections; i++) { + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; } - } else { - // otherwise, communicate a distance equal to the maximum interaction distance for each type - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - double tmp = 0.0; - if (cutusermulti) tmp = cutusermulti[i]; - cutghostmulti[i][0] = MAX(tmp,cuttype[i]); - cutghostmulti[i][1] = MAX(tmp,cuttype[i]); - cutghostmulti[i][2] = MAX(tmp,cuttype[i]); + + for (j = 0; j < ncollections; j++){ + if(multi_reduce and cutcollectionsq[j][j] > cutcollectionsq[i][i]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j])); } } } + + if (mode == Comm::MULTIOLD) { + double *cuttype = neighbor->cuttype; + for (i = 1; i <= ntypes; i++) { + double tmp = 0.0; + if (cutusermultiold) tmp = cutusermultiold[i]; + cutghostmultiold[i][0] = MAX(tmp,cuttype[i]); + cutghostmultiold[i][1] = MAX(tmp,cuttype[i]); + cutghostmultiold[i][2] = MAX(tmp,cuttype[i]); + } + } double cut = get_comm_cutoff(); if ((cut == 0.0) && (me == 0)) @@ -233,12 +251,20 @@ void CommTiled::setup() length2 = h_inv[2]; cutghost[2] = cut * length2; if (mode == Comm::MULTI) { - for (i = 1; i <= ntypes; i++) { + for (i = 0; i < ncollections; i++) { cutghostmulti[i][0] *= length0; cutghostmulti[i][1] *= length1; cutghostmulti[i][2] *= length2; } } + + if (mode == Comm::MULTIOLD) { + for (i = 1; i <= ntypes; i++) { + cutghostmultiold[i][0] *= length0; + cutghostmultiold[i][1] *= length1; + cutghostmultiold[i][2] *= length2; + } + } } if ((periodicity[0] && cutghost[0] > prd[0]) || @@ -376,7 +402,7 @@ void CommTiled::setup() // extend sbox in those lower dims to include ghost atoms // single mode and multi mode - double oboxlo[3],oboxhi[3],sbox[6],sbox_multi[6]; + double oboxlo[3],oboxhi[3],sbox[6],sbox_multi[6],sbox_multiold[6]; if (mode == Comm::SINGLE) { for (i = 0; i < noverlap; i++) { @@ -465,7 +491,7 @@ void CommTiled::setup() sbox[5] = MIN(oboxhi[2],hi2[2]); } - for (int itype = 1; itype <= atom->ntypes; itype++) { + for (int icollection = 0; icollection < ncollections; icollection++) { sbox_multi[0] = sbox[0]; sbox_multi[1] = sbox[1]; sbox_multi[2] = sbox[2]; @@ -476,36 +502,112 @@ void CommTiled::setup() sbox_multi[idim] = sublo[idim]; if (i < noverlap1) sbox_multi[3+idim] = - MIN(sbox_multi[3+idim]+cutghostmulti[itype][idim],subhi[idim]); + MIN(sbox_multi[3+idim]+cutghostmulti[icollection][idim],subhi[idim]); else sbox_multi[3+idim] = - MIN(sbox_multi[3+idim]-prd[idim]+cutghostmulti[itype][idim], + MIN(sbox_multi[3+idim]-prd[idim]+cutghostmulti[icollection][idim], subhi[idim]); } else { if (i < noverlap1) sbox_multi[idim] = - MAX(sbox_multi[idim]-cutghostmulti[itype][idim],sublo[idim]); + MAX(sbox_multi[idim]-cutghostmulti[icollection][idim],sublo[idim]); else sbox_multi[idim] = - MAX(sbox_multi[idim]+prd[idim]-cutghostmulti[itype][idim], + MAX(sbox_multi[idim]+prd[idim]-cutghostmulti[icollection][idim], sublo[idim]); sbox_multi[3+idim] = subhi[idim]; } if (idim >= 1) { if (sbox_multi[0] == oboxlo[0]) - sbox_multi[0] -= cutghostmulti[itype][idim]; + sbox_multi[0] -= cutghostmulti[icollection][idim]; if (sbox_multi[3] == oboxhi[0]) - sbox_multi[3] += cutghostmulti[itype][idim]; + sbox_multi[3] += cutghostmulti[icollection][idim]; } if (idim == 2) { if (sbox_multi[1] == oboxlo[1]) - sbox_multi[1] -= cutghostmulti[itype][idim]; + sbox_multi[1] -= cutghostmulti[icollection][idim]; if (sbox_multi[4] == oboxhi[1]) - sbox_multi[4] += cutghostmulti[itype][idim]; + sbox_multi[4] += cutghostmulti[icollection][idim]; } - memcpy(sendbox_multi[iswap][i][itype],sbox_multi,6*sizeof(double)); + memcpy(sendbox_multi[iswap][i][icollection],sbox_multi,6*sizeof(double)); + } + } + } + + if (mode == Comm::MULTIOLD) { + for (i = 0; i < noverlap; i++) { + pbc_flag[iswap][i] = 0; + pbc[iswap][i][0] = pbc[iswap][i][1] = pbc[iswap][i][2] = + pbc[iswap][i][3] = pbc[iswap][i][4] = pbc[iswap][i][5] = 0; + + (this->*box_other)(idim,idir,overlap[i],oboxlo,oboxhi); + + if (i < noverlap1) { + sbox[0] = MAX(oboxlo[0],lo1[0]); + sbox[1] = MAX(oboxlo[1],lo1[1]); + sbox[2] = MAX(oboxlo[2],lo1[2]); + sbox[3] = MIN(oboxhi[0],hi1[0]); + sbox[4] = MIN(oboxhi[1],hi1[1]); + sbox[5] = MIN(oboxhi[2],hi1[2]); + } else { + pbc_flag[iswap][i] = 1; + if (idir == 0) pbc[iswap][i][idim] = 1; + else pbc[iswap][i][idim] = -1; + if (triclinic) { + if (idim == 1) pbc[iswap][i][5] = pbc[iswap][i][idim]; + if (idim == 2) pbc[iswap][i][4] = pbc[iswap][i][3] = pbc[iswap][i][idim]; + } + sbox[0] = MAX(oboxlo[0],lo2[0]); + sbox[1] = MAX(oboxlo[1],lo2[1]); + sbox[2] = MAX(oboxlo[2],lo2[2]); + sbox[3] = MIN(oboxhi[0],hi2[0]); + sbox[4] = MIN(oboxhi[1],hi2[1]); + sbox[5] = MIN(oboxhi[2],hi2[2]); + } + + for (int itype = 1; itype <= atom->ntypes; itype++) { + sbox_multiold[0] = sbox[0]; + sbox_multiold[1] = sbox[1]; + sbox_multiold[2] = sbox[2]; + sbox_multiold[3] = sbox[3]; + sbox_multiold[4] = sbox[4]; + sbox_multiold[5] = sbox[5]; + if (idir == 0) { + sbox_multiold[idim] = sublo[idim]; + if (i < noverlap1) + sbox_multiold[3+idim] = + MIN(sbox_multiold[3+idim]+cutghostmultiold[itype][idim],subhi[idim]); + else + sbox_multiold[3+idim] = + MIN(sbox_multiold[3+idim]-prd[idim]+cutghostmultiold[itype][idim], + subhi[idim]); + } else { + if (i < noverlap1) + sbox_multiold[idim] = + MAX(sbox_multiold[idim]-cutghostmultiold[itype][idim],sublo[idim]); + else + sbox_multiold[idim] = + MAX(sbox_multiold[idim]+prd[idim]-cutghostmultiold[itype][idim], + sublo[idim]); + sbox_multiold[3+idim] = subhi[idim]; + } + + if (idim >= 1) { + if (sbox_multiold[0] == oboxlo[0]) + sbox_multiold[0] -= cutghostmultiold[itype][idim]; + if (sbox_multiold[3] == oboxhi[0]) + sbox_multiold[3] += cutghostmultiold[itype][idim]; + } + if (idim == 2) { + if (sbox_multiold[1] == oboxlo[1]) + sbox_multiold[1] -= cutghostmultiold[itype][idim]; + if (sbox_multiold[4] == oboxhi[1]) + sbox_multiold[4] += cutghostmultiold[itype][idim]; + } + + memcpy(sendbox_multiold[iswap][i][itype],sbox_multiold,6*sizeof(double)); } } } @@ -937,11 +1039,14 @@ void CommTiled::exchange() void CommTiled::borders() { - int i,m,n,nlast,nsend,nrecv,ngroup,ncount,ncountall; + int i,m,n,nlast,nsend,nrecv,ngroup,nprior,ncount,ncountall; double xlo,xhi,ylo,yhi,zlo,zhi; double *bbox; double **x; AtomVec *avec = atom->avec; + + // After exchanging, need to reconstruct collection array for border communication + if(mode == Comm::MULTI) neighbor->build_collection(0); // send/recv max one = max # of atoms in single send/recv for any swap // send/recv max all = max # of atoms in all sends/recvs within any swap @@ -1008,6 +1113,56 @@ void CommTiled::borders() smaxone = MAX(smaxone,ncount); ncountall += ncount; + } else if (mode == Comm::MULTI) { + + int* collection=neighbor->collection; + int icollection; + ncount = 0; + + if (!bordergroup) { + for (i = 0; i < nlast; i++) { + icollection=collection[i]; + bbox = sendbox_multi[iswap][m][icollection]; + xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; + xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; + if (x[i][0] >= xlo && x[i][0] < xhi && + x[i][1] >= ylo && x[i][1] < yhi && + x[i][2] >= zlo && x[i][2] < zhi) { + if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount); + sendlist[iswap][m][ncount++] = i; + } + } + } else { + ngroup = atom->nfirst; + for (i = 0; i < ngroup; i++) { + icollection=collection[i]; + bbox = sendbox_multi[iswap][m][icollection]; + xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; + xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; + if (x[i][0] >= xlo && x[i][0] < xhi && + x[i][1] >= ylo && x[i][1] < yhi && + x[i][2] >= zlo && x[i][2] < zhi) { + if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount); + sendlist[iswap][m][ncount++] = i; + } + } + for (i = atom->nlocal; i < nlast; i++) { + icollection=collection[i]; + bbox = sendbox_multi[iswap][m][icollection]; + xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; + xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; + if (x[i][0] >= xlo && x[i][0] < xhi && + x[i][1] >= ylo && x[i][1] < yhi && + x[i][2] >= zlo && x[i][2] < zhi) { + if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount); + sendlist[iswap][m][ncount++] = i; + } + } + } + + sendnum[iswap][m] = ncount; + smaxone = MAX(smaxone,ncount); + ncountall += ncount; } else { int* type=atom->type; @@ -1017,7 +1172,7 @@ void CommTiled::borders() if (!bordergroup) { for (i = 0; i < nlast; i++) { itype=type[i]; - bbox = sendbox_multi[iswap][m][itype]; + bbox = sendbox_multiold[iswap][m][itype]; xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; if (x[i][0] >= xlo && x[i][0] < xhi && @@ -1031,7 +1186,7 @@ void CommTiled::borders() ngroup = atom->nfirst; for (i = 0; i < ngroup; i++) { itype=type[i]; - bbox = sendbox_multi[iswap][m][itype]; + bbox = sendbox_multiold[iswap][m][itype]; xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; if (x[i][0] >= xlo && x[i][0] < xhi && @@ -1043,7 +1198,7 @@ void CommTiled::borders() } for (i = atom->nlocal; i < nlast; i++) { itype=type[i]; - bbox = sendbox_multi[iswap][m][itype]; + bbox = sendbox_multiold[iswap][m][itype]; xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; if (x[i][0] >= xlo && x[i][0] < xhi && @@ -1179,8 +1334,11 @@ void CommTiled::borders() // increment ghost atoms n = nrecvproc[iswap]; - if (n) + if (n) { + nprior = atom->nghost + atom->nlocal; atom->nghost += forward_recv_offset[iswap][n-1] + recvnum[iswap][n-1]; + if(neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); + } } // For molecular systems we lose some bits for local atom indices due @@ -2120,6 +2278,7 @@ void CommTiled::allocate_swap(int n) pbc = new int**[n]; sendbox = new double**[n]; sendbox_multi = new double***[n]; + sendbox_multiold = new double***[n]; maxsendlist = new int*[n]; sendlist = new int**[n]; @@ -2134,6 +2293,7 @@ void CommTiled::allocate_swap(int n) pbc[i] = nullptr; sendbox[i] = nullptr; sendbox_multi[i] = nullptr; + sendbox_multiold[i] = nullptr; maxsendlist[i] = nullptr; sendlist[i] = nullptr; } @@ -2182,8 +2342,9 @@ void CommTiled::grow_swap_send(int i, int n, int nold) memory->create(pbc[i],n,6,"comm:pbc_flag"); memory->destroy(sendbox[i]); memory->create(sendbox[i],n,6,"comm:sendbox"); - memory->destroy(sendbox_multi[i]); - memory->create(sendbox_multi[i],n,atom->ntypes+1,6,"comm:sendbox_multi"); + grow_swap_send_multi(i,n); + memory->destroy(sendbox_multiold[i]); + memory->create(sendbox_multiold[i],n,atom->ntypes+1,6,"comm:sendbox_multiold"); delete [] maxsendlist[i]; maxsendlist[i] = new int[n]; @@ -2215,6 +2376,19 @@ void CommTiled::grow_swap_recv(int i, int n) size_reverse_send[i] = new int[n]; } + +/* ---------------------------------------------------------------------- + grow info for swap I for multi as ncollections can change +------------------------------------------------------------------------- */ + +void CommTiled::grow_swap_send_multi(int i, int n) +{ + memory->destroy(sendbox_multi[i]); + + if(ncollections > 0) + memory->create(sendbox_multi[i],n,ncollections,6,"comm:sendbox_multi"); +} + /* ---------------------------------------------------------------------- deallocate swap info ------------------------------------------------------------------------- */ @@ -2243,6 +2417,7 @@ void CommTiled::deallocate_swap(int n) memory->destroy(pbc[i]); memory->destroy(sendbox[i]); memory->destroy(sendbox_multi[i]); + memory->destroy(sendbox_multiold[i]); delete [] maxsendlist[i]; @@ -2265,6 +2440,7 @@ void CommTiled::deallocate_swap(int n) delete [] pbc; delete [] sendbox; delete [] sendbox_multi; + delete [] sendbox_multiold; delete [] maxsendlist; delete [] sendlist; diff --git a/src/comm_tiled.h b/src/comm_tiled.h index fa2c76e6e9..fdb175117e 100644 --- a/src/comm_tiled.h +++ b/src/comm_tiled.h @@ -77,9 +77,12 @@ class CommTiled : public Comm { double ***sendbox; // bounding box of atoms to send per swap/proc - double **cutghostmulti; // cutghost on a per-type basis + double **cutghostmulti; // cutghost on a per-collection basis + double **cutghostmultiold; // cutghost on a per-type basis double ****sendbox_multi; // bounding box of atoms to send // per swap/proc for multi comm + double ****sendbox_multiold; // bounding box of atoms to send + // per swap/proc for multi/old comm // exchange comm info, proc lists do not include self @@ -148,6 +151,7 @@ class CommTiled : public Comm { void grow_list(int, int, int); // reallocate sendlist for one swap/proc void allocate_swap(int); // allocate swap arrays void grow_swap_send(int, int, int); // grow swap arrays for send and recv + void grow_swap_send_multi(int, int); // grow multi swap arrays for send and recv void grow_swap_recv(int, int); void deallocate_swap(int); // deallocate swap arrays @@ -163,10 +167,6 @@ E: Cannot yet use comm_style tiled with triclinic box Self-explanatory. -E: Cannot yet use comm_style tiled with multi-mode comm - -Self-explanatory. - E: Communication cutoff for comm_style tiled cannot exceed periodic box length Self-explanatory. diff --git a/src/init b/src/init new file mode 100644 index 0000000000..617c9effa3 --- /dev/null +++ b/src/init @@ -0,0 +1,789 @@ +angle_charmm.cpp: if (comm->me == 0) { +angle_cosine.cpp: if (comm->me == 0) utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,nullptr,error); +angle_cosine_periodic.cpp: if (comm->me == 0) { +angle_cosine_squared.cpp: if (comm->me == 0) { +angle.cpp: memory->create(eatom,comm->nthreads*maxeatom,"angle:eatom"); +angle.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"angle:vatom"); +angle.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"angle:cvatom"); +angle.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); +angle.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); +angle.cpp: bytes += comm->nthreads*maxcvatom*9 * sizeof(double); +angle_deprecated.cpp: if (lmp->comm->me == 0) +angle_harmonic.cpp: if (comm->me == 0) { +angle_hybrid.cpp: const int nthreads = comm->nthreads; +angle_hybrid.cpp: if (comm->nthreads > 1) { +angle_hybrid.cpp: int me = comm->me; +angle_table.cpp: if (comm->me == 0) { +angle_zero.cpp: if (comm->me == 0) { +atom.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +atom.cpp: if (comm->myloc[0] == 0) sublo[0] -= epsilon[0]; +atom.cpp: if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += epsilon[0]; +atom.cpp: if (comm->myloc[1] == 0) sublo[1] -= epsilon[1]; +atom.cpp: if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += epsilon[1]; +atom.cpp: if (comm->myloc[2] == 0) sublo[2] -= epsilon[2]; +atom.cpp: if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += epsilon[2]; +atom.cpp: if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0]; +atom.cpp: if (comm->mysplit[0][1] == 1.0) subhi[0] += epsilon[0]; +atom.cpp: if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1]; +atom.cpp: if (comm->mysplit[1][1] == 1.0) subhi[1] += epsilon[1]; +atom.cpp: if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2]; +atom.cpp: if (comm->mysplit[2][1] == 1.0) subhi[2] += epsilon[2]; +atom.cpp: if (comm->me == 0) { +atom.cpp: called by comm->exchange() if atom_modify first group is set +atom.cpp: always called between comm->exchange() and comm->borders() +atom.cpp: if (comm->me == 0) +atom_map.cpp: int nper = static_cast (natoms/comm->nprocs); +atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); +atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); +atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); +atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); +atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); +atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); +atom_vec.cpp: f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f"); +atom_vec.cpp: const int nthreads = threads[i] ? comm->nthreads : 1; +atom_vec.cpp: bytes += memory->usage(f,nmax*comm->nthreads,3); +atom_vec.cpp: const int nthreads = threads[i] ? comm->nthreads : 1; +atom_vec_hybrid.cpp: if (mass_pertype && mass_peratom && comm->me == 0) +atom_vec_hybrid.cpp: if ((ptr && strstr(ptr+1,dup)) && (comm->me == 0)) +atom_vec_line.cpp: //if (comm->me == 1 && update->ntimestep == 873) +atom_vec_line.cpp: printf("BAD vecline ptrs: %s: %d %d: %d\n",str,comm->me, +atom_vec_line.cpp: str,comm->me,update->ntimestep,count,nlocal_bonus); +balance.cpp: int *procgrid = comm->procgrid; +balance.cpp: if (style == BISECTION && comm->style == 0) +balance.cpp: // init entire system since comm->setup is done +balance.cpp: comm->setup(); +balance.cpp: comm->exchange(); +balance.cpp: if (comm->layout == Comm::LAYOUT_TILED && style != BISECTION) { +balance.cpp: if (comm->layout == Comm::LAYOUT_UNIFORM) { +balance.cpp: comm->layout = Comm::LAYOUT_NONUNIFORM; +balance.cpp: } else if (comm->layout == Comm::LAYOUT_NONUNIFORM) { +balance.cpp: comm->layout = Comm::LAYOUT_UNIFORM; +balance.cpp: } else if (comm->layout == Comm::LAYOUT_TILED) { +balance.cpp: comm->layout = Comm::LAYOUT_UNIFORM; +balance.cpp: else comm->layout = Comm::LAYOUT_NONUNIFORM; +balance.cpp: comm->xsplit[i] = i * 1.0/procgrid[0]; +balance.cpp: comm->xsplit[procgrid[0]] = 1.0; +balance.cpp: for (int i = 0; i <= procgrid[0]; i++) comm->xsplit[i] = user_xsplit[i]; +balance.cpp: comm->ysplit[i] = i * 1.0/procgrid[1]; +balance.cpp: comm->ysplit[procgrid[1]] = 1.0; +balance.cpp: for (int i = 0; i <= procgrid[1]; i++) comm->ysplit[i] = user_ysplit[i]; +balance.cpp: comm->zsplit[i] = i * 1.0/procgrid[2]; +balance.cpp: comm->zsplit[procgrid[2]] = 1.0; +balance.cpp: for (int i = 0; i <= procgrid[2]; i++) comm->zsplit[i] = user_zsplit[i]; +balance.cpp: comm->layout = Comm::LAYOUT_NONUNIFORM; +balance.cpp: comm->layout = Comm::LAYOUT_TILED; +balance.cpp: for (int i = 0; i <= comm->procgrid[0]; i++) +balance.cpp: mesg += fmt::format(" {:.8}",comm->xsplit[i]); +balance.cpp: for (int i = 0; i <= comm->procgrid[1]; i++) +balance.cpp: mesg += fmt::format(" {:.8}",comm->ysplit[i]); +balance.cpp: for (int i = 0; i <= comm->procgrid[2]; i++) +balance.cpp: mesg += fmt::format(" {:.8}",comm->zsplit[i]); +balance.cpp: if (outflag && comm->me == 0) { +balance.cpp: comm->rcbnew = 1; +balance.cpp: if (idim >= 0) comm->rcbcutfrac = (rcb->cut - boxlo[idim]) / prd[idim]; +balance.cpp: else comm->rcbcutfrac = 0.0; +balance.cpp: comm->rcbcutdim = idim; +balance.cpp: double (*mysplit)[2] = comm->mysplit; +balance.cpp: int max = MAX(comm->procgrid[0],comm->procgrid[1]); +balance.cpp: max = MAX(max,comm->procgrid[2]); +balance.cpp: if (comm->layout == Comm::LAYOUT_TILED) { +balance.cpp: int *procgrid = comm->procgrid; +balance.cpp: double *xsplit = comm->xsplit; +balance.cpp: double *ysplit = comm->ysplit; +balance.cpp: double *zsplit = comm->zsplit; +balance.cpp: int *procgrid = comm->procgrid; +balance.cpp: split = comm->xsplit; +balance.cpp: split = comm->ysplit; +balance.cpp: split = comm->zsplit; +balance.cpp: double *xsplit = comm->xsplit; +balance.cpp: double *ysplit = comm->ysplit; +balance.cpp: double *zsplit = comm->zsplit; +balance.cpp: int nx = comm->procgrid[0]; +balance.cpp: int ny = comm->procgrid[1]; +balance.cpp: int nz = comm->procgrid[2]; +bond.cpp: memory->create(eatom,comm->nthreads*maxeatom,"bond:eatom"); +bond.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"bond:vatom"); +bond.cpp: if (comm->me == 0) { +bond.cpp: if (comm->me == 0) { +bond.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); +bond.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); +bond_deprecated.cpp: if (lmp->comm->me == 0) +bond_fene.cpp: if (comm->me == 0) +bond_fene.cpp: if (comm->me == 0) { +bond_fene_expand.cpp: if (comm->me == 0) +bond_fene_expand.cpp: if (comm->me == 0) { +bond_gromos.cpp: if (comm->me == 0) { +bond_harmonic.cpp: if (comm->me == 0) { +bond_hybrid.cpp: const int nthreads = comm->nthreads; +bond_hybrid.cpp: int me = comm->me; +bond_morse.cpp: if (comm->me == 0) { +bond_nonlinear.cpp: if (comm->me == 0) { +bond_quartic.cpp: if (comm->me == 0) { +bond_table.cpp: if (comm->me == 0) { +bond_zero.cpp: if (comm->me == 0) { +change_box.cpp: if (comm->me == 0) utils::logmesg(lmp,"Changing box ...\n"); +change_box.cpp: if (natoms != atom->natoms && comm->me == 0) +comm_brick.cpp: if (oldcomm->layout == Comm::LAYOUT_TILED) +comm_brick.cpp: layout = oldcomm->layout; +comm.cpp: if (oldcomm->grid2proc) { +comm.cpp: memcpy(&grid2proc[0][0][0],&oldcomm->grid2proc[0][0][0], +comm.cpp: memcpy(xsplit,oldcomm->xsplit,(procgrid[0]+1)*sizeof(double)); +comm.cpp: memcpy(ysplit,oldcomm->ysplit,(procgrid[1]+1)*sizeof(double)); +comm.cpp: memcpy(zsplit,oldcomm->zsplit,(procgrid[2]+1)*sizeof(double)); +comm.cpp: if (oldcomm->cutusermulti) { +comm.cpp: memcpy(cutusermulti,oldcomm->cutusermulti,ncollections); +comm.cpp: if (oldcomm->cutusermultiold) { +comm.cpp: memcpy(cutusermultiold,oldcomm->cutusermultiold,atom->ntypes+1); +comm.cpp: int n = strlen(oldcomm->customfile) + 1; +comm.cpp: strcpy(customfile,oldcomm->customfile); +comm.cpp: int n = strlen(oldcomm->outfile) + 1; +comm.cpp: strcpy(outfile,oldcomm->outfile); +comm_tiled.cpp: layout = oldcomm->layout; +compute_adf.cpp: if (mycutneigh > comm->cutghostuser) +compute_aggregate_atom.cpp: if (count > 1 && comm->me == 0) +compute_aggregate_atom.cpp: comm->forward_comm_compute(this); +compute_aggregate_atom.cpp: comm->forward_comm_compute(this); +compute_aggregate_atom.cpp: comm->reverse_comm_compute(this); +compute_bond_local.cpp: if (velflag && !comm->ghost_velocity) ghostvelflag = 1; +compute_bond_local.cpp: if (ghostvelflag && !initflag) comm->forward_comm_compute(this); +compute_centro_atom.cpp: if (count > 1 && comm->me == 0) +compute_centroid_stress_atom.cpp: comm->reverse_comm_compute(this); +compute_chunk_atom.cpp: int nprocs = comm->nprocs; +compute_chunk_atom.cpp: comm->ring(n,sizeof(int),list,1,idring,nullptr,(void *)this,0); +compute_chunk_atom.cpp: callback from comm->ring() +compute_chunk_atom.cpp: if (flagall && comm->me == 0) +compute_cluster_atom.cpp: if (count > 1 && comm->me == 0) +compute_cluster_atom.cpp: comm->forward_comm_compute(this); +compute_cluster_atom.cpp: comm->forward_comm_compute(this); +compute_cluster_atom.cpp: comm->forward_comm_compute(this); +compute_cna_atom.cpp: comm->me == 0) +compute_cna_atom.cpp: if (count > 1 && comm->me == 0) +compute_cna_atom.cpp: if (nerrorall && comm->me == 0) +compute_cna_atom.cpp: if (nerrorall && comm->me == 0) +compute_contact_atom.cpp: if (count > 1 && comm->me == 0) +compute_contact_atom.cpp: if (force->newton_pair) comm->reverse_comm_compute(this); +compute_coord_atom.cpp: comm->forward_comm_compute(this); +compute_deprecated.cpp: if (lmp->comm->me == 0) +compute_erotate_sphere_atom.cpp: if (count > 1 && comm->me == 0) +compute_fragment_atom.cpp: if (count > 1 && comm->me == 0) +compute_fragment_atom.cpp: comm->forward_comm_compute(this); +compute_fragment_atom.cpp: comm->forward_comm_compute(this); +compute_group_group.cpp: if ((fabs(e_correction) > SMALL) && (comm->me == 0)) +compute_hexorder_atom.cpp: if (count > 1 && comm->me == 0) +compute_ke_atom.cpp: if (count > 1 && comm->me == 0) +compute_orientorder_atom.cpp: if (count > 1 && comm->me == 0) +compute_pe_atom.cpp: comm->reverse_comm_compute(this); +compute_property_atom.cpp: int me = comm->me; +compute_rdf.cpp: cutghost = MAX(force->pair->cutforce+skin,comm->cutghostuser); +compute_rdf.cpp: cutghost = comm->cutghostuser; +compute_rdf.cpp: if (comm->me == 0) +compute_stress_atom.cpp: comm->reverse_comm_compute(this); +compute_temp_deform.cpp: comm->me == 0) +compute_temp_deform.cpp: if (i == modify->nfix && comm->me == 0) +create_atoms.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +create_atoms.cpp: if (comm->myloc[0] == 0) sublo[0] -= epsilon[0]; +create_atoms.cpp: if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0]; +create_atoms.cpp: if (comm->myloc[1] == 0) sublo[1] -= epsilon[1]; +create_atoms.cpp: if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*epsilon[1]; +create_atoms.cpp: if (comm->myloc[2] == 0) sublo[2] -= epsilon[2]; +create_atoms.cpp: if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*epsilon[2]; +create_atoms.cpp: if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0]; +create_atoms.cpp: if (comm->mysplit[0][1] == 1.0) subhi[0] -= 2.0*epsilon[0]; +create_atoms.cpp: if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1]; +create_atoms.cpp: if (comm->mysplit[1][1] == 1.0) subhi[1] -= 2.0*epsilon[1]; +create_atoms.cpp: if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2]; +create_atoms.cpp: if (comm->mysplit[2][1] == 1.0) subhi[2] -= 2.0*epsilon[2]; +create_bonds.cpp: // init entire system since comm->borders and neighbor->build is done +create_bonds.cpp: if (rmax > neighbor->cutneighmin && comm->me == 0) +create_bonds.cpp: comm->setup(); +create_bonds.cpp: comm->exchange(); +create_bonds.cpp: comm->borders(); +create_bonds.cpp: if (comm->me == 0) +create_box.cpp: comm->set_proc_grid(); +delete_atoms.cpp: } else if (comm->me == 0) +delete_atoms.cpp: if (comm->me == 0) { +delete_atoms.cpp: if (comm->me == 0) utils::logmesg(lmp,"System init for delete_atoms ...\n"); +delete_atoms.cpp: // init entire system since comm->borders and neighbor->build is done +delete_atoms.cpp: if (cut > neighbor->cutneighmin && comm->me == 0) +delete_atoms.cpp: comm->setup(); +delete_atoms.cpp: comm->exchange(); +delete_atoms.cpp: comm->borders(); +delete_atoms.cpp: RanMars *random = new RanMars(lmp,seed + comm->me); +delete_atoms.cpp: // pass list to all other procs via comm->ring() +delete_atoms.cpp: comm->ring(n,sizeof(tagint),list,1,bondring,nullptr,(void *)this); +delete_atoms.cpp: // pass list to all other procs via comm->ring() +delete_atoms.cpp: comm->ring(n,sizeof(tagint),list,1,molring,nullptr,(void *)this); +delete_atoms.cpp: callback from comm->ring() in delete_bond() +delete_atoms.cpp: callback from comm->ring() in delete_molecule() +delete_bonds.cpp: // init entire system since comm->borders is done +delete_bonds.cpp: if (comm->me == 0) utils::logmesg(lmp,"System init for delete_bonds ...\n"); +delete_bonds.cpp: if (comm->me == 0) utils::logmesg(lmp,"Deleting bonds ...\n"); +delete_bonds.cpp: comm->setup(); +delete_bonds.cpp: comm->exchange(); +delete_bonds.cpp: comm->borders(); +delete_bonds.cpp: if (comm->me == 0) { +deprecated.cpp: if (lmp->comm->me == 0) +deprecated.cpp: if (lmp->comm->me == 0) +dihedral_charmm.cpp: if (comm->me == 0) { +dihedral_charmmfsw.cpp: if (comm->me == 0) { +dihedral.cpp: memory->create(eatom,comm->nthreads*maxeatom,"dihedral:eatom"); +dihedral.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"dihedral:vatom"); +dihedral.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"dihedral:cvatom"); +dihedral.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); +dihedral.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); +dihedral.cpp: bytes += comm->nthreads*maxcvatom*9 * sizeof(double); +dihedral_deprecated.cpp: if (lmp->comm->me == 0) +dihedral_harmonic.cpp: if (comm->me == 0) { +dihedral_helix.cpp: if (comm->me == 0) { +dihedral_hybrid.cpp: int me = comm->me; +dihedral_multi_harmonic.cpp: if (comm->me == 0) { +dihedral_opls.cpp: if (comm->me == 0) { +displace_atoms.cpp: if (comm->me == 0) utils::logmesg(lmp,"Displacing atoms ...\n"); +displace_atoms.cpp: if (natoms != atom->natoms && comm->me == 0) +domain.cpp: else if (comm->me == 0) +domain.cpp: uses comm->xyz_split or comm->mysplit +domain.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +domain.cpp: int *myloc = comm->myloc; +domain.cpp: double *xsplit = comm->xsplit; +domain.cpp: double *ysplit = comm->ysplit; +domain.cpp: double *zsplit = comm->zsplit; +domain.cpp: double (*mysplit)[2] = comm->mysplit; +domain.cpp: uses comm->xyz_split or comm->mysplit +domain.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +domain.cpp: int *myloc = comm->myloc; +domain.cpp: int *procgrid = comm->procgrid; +domain.cpp: double *xsplit = comm->xsplit; +domain.cpp: double *ysplit = comm->ysplit; +domain.cpp: double *zsplit = comm->zsplit; +domain.cpp: double (*mysplit)[2] = comm->mysplit; +domain.cpp: comm->forward_comm_array(3,unwrap); +domain.cpp: if (flagall && comm->me == 0) +domain.cpp: if (all && comm->me == 0) +domain.cpp: if (all && comm->me == 0) +domain.cpp: if (flagall && comm->me == 0) +domain.cpp: since may lead to lost atoms in comm->exchange() +domain.cpp: if (flagall && comm->me == 0) +domain.cpp: if ((flag_all > 0) && (comm->me == 0)) +domain.cpp: if (comm->me == 0) { +dump_deprecated.cpp: if (lmp->comm->me == 0) +dump_image.cpp: comm->forward_comm_dump(this); +dump_movie.cpp: if ((comm->me == 0) && (fp == nullptr)) { +finish.cpp: const int nthreads = comm->nthreads; +fix_balance.cpp: if (lbstyle == BISECTION && comm->style == 0) +fix_balance.cpp: compute final imbalance factor based on nlocal after comm->exchange() +fix_balance.cpp: // invoke balancer and reset comm->uniform flag +fix_balance.cpp: comm->layout = Comm::LAYOUT_NONUNIFORM; +fix_balance.cpp: comm->layout = Comm::LAYOUT_TILED; +fix_balance.cpp: // since may lead to lost atoms in comm->exchange() +fix_balance.cpp: // else allow caller's comm->exchange() to do it +fix_balance.cpp: // b/c atoms may migrate again in comm->exchange() +fix_balance.cpp: // can only be done after atoms migrate in comm->exchange() +fix_box_relax.cpp: if (temperature->igroup != 0 && comm->me == 0) +fix_cmap.cpp: if (comm->me == 0) { +fix_cmap.cpp: if (comm->me == 0) +fix_cmap.cpp: if (comm->me == 0) fclose(fp); +fix_cmap.cpp: if (comm->me == 0) { +fix_deform.cpp: if (comm->me == 0) { +fix_deprecated.cpp: if (lmp->comm->me == 0) +fix_deprecated.cpp: if (lmp->comm->me == 0) +fix_dt_reset.cpp: strcmp(output->dump[i]->style,"xtc") == 0) && comm->me == 0) +fix_group.cpp: if (warn && comm->me == 0) +fix_halt.cpp: if (comm->me == 0 && msgflag == YESMSG) error->message(FLERR,message); +fix_langevin.cpp: random = new RanMars(lmp,seed + comm->me); +fix_langevin.cpp: if (temperature->igroup != igroup && comm->me == 0) +fix_move.cpp: if (comm->me == 0) { +fix_neigh_history.cpp: int nmypage = comm->nthreads; +fix_neigh_history.cpp: comm->reverse_comm_fix(this,0); +fix_neigh_history.cpp: comm->reverse_comm_fix_variable(this); +fix_neigh_history.cpp: int nmypage = comm->nthreads; +fix_neigh_history.cpp: if (comm->me == 0) { +fix_nh.cpp: if (comm->me == 0) { +fix_nh.cpp: if (temperature->igroup != 0 && comm->me == 0) +fix_nve_limit.cpp: if (comm->me == 0) +fix_pour.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +fix_pour.cpp: if (comm->myloc[2] == comm->procgrid[2]-1 && +fix_pour.cpp: if (comm->mysplit[2][1] == 1.0 && +fix_pour.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +fix_pour.cpp: if (comm->myloc[1] == comm->procgrid[1]-1 && +fix_pour.cpp: if (comm->mysplit[1][1] == 1.0 && +fix_press_berendsen.cpp: if (temperature->igroup != 0 && comm->me == 0) +fix_property_atom.cpp: if (flag && comm->me == 0) +fix_recenter.cpp: if (flag && comm->me == 0) +fix_restrain.cpp: comm->me,update->ntimestep)); +fix_restrain.cpp: comm->me,update->ntimestep)); +fix_restrain.cpp: comm->me,update->ntimestep)); +fix_restrain.cpp: comm->me,update->ntimestep)); +fix_restrain.cpp: ids[m][2],comm->me,update->ntimestep)); +fix_restrain.cpp: ids[m][2],comm->me,update->ntimestep)); +fix_restrain.cpp: ids[m][2],ids[m][3],comm->me, +fix_restrain.cpp: ids[m][2],ids[m][3],comm->me, +fix_restrain.cpp: comm->me,x[i1][0],x[i1][1],x[i1][2], +fix_restrain.cpp: comm->me,x[i2][0],x[i2][1],x[i2][2], +fix_restrain.cpp: comm->me,x[i3][0],x[i3][1],x[i3][2], +fix_restrain.cpp: comm->me,x[i4][0],x[i4][1],x[i4][2]); +fix_spring_chunk.cpp: if (comm->me == 0) { +fix_spring_chunk.cpp: if (comm->me == 0) +fix_spring_rg.cpp: if (comm->me == 0) { +fix_store.cpp: // PERATOM may be comm->exchanged before filled by caller +fix_store.cpp: if (comm->me == 0) { +fix_temp_berendsen.cpp: if (temperature->igroup != igroup && comm->me == 0) +fix_temp_berendsen.cpp: if (comm->me == 0) { +fix_temp_csld.cpp: random = new RanMars(lmp,seed + comm->me); +fix_temp_csld.cpp: if (temperature->igroup != igroup && comm->me == 0) +fix_temp_csld.cpp: int nsize = PRNGSIZE*comm->nprocs+2; // pRNG state per proc + nprocs + energy +fix_temp_csld.cpp: if (comm->me == 0) { +fix_temp_csld.cpp: list[1] = comm->nprocs; +fix_temp_csld.cpp: if (comm->me == 0) { +fix_temp_csld.cpp: if (nprocs != comm->nprocs) { +fix_temp_csld.cpp: if (comm->me == 0) +fix_temp_csld.cpp: } else random->set_state(list+2+comm->me*103); +fix_temp_csvr.cpp: random = new RanMars(lmp,seed + comm->me); +fix_temp_csvr.cpp: if (comm->me == 0) { +fix_temp_csvr.cpp: if (temperature->igroup != igroup && comm->me == 0) +fix_temp_csvr.cpp: int nsize = PRNGSIZE*comm->nprocs+2; // pRNG state per proc + nprocs + energy +fix_temp_csvr.cpp: if (comm->me == 0) { +fix_temp_csvr.cpp: list[1] = comm->nprocs; +fix_temp_csvr.cpp: if (comm->me == 0) { +fix_temp_csvr.cpp: if (nprocs != comm->nprocs) { +fix_temp_csvr.cpp: if (comm->me == 0) +fix_temp_csvr.cpp: } else random->set_state(list+2+comm->me*103); +fix_temp_rescale.cpp: if (temperature->igroup != igroup && comm->me == 0) +fix_temp_rescale.cpp: if (comm->me == 0) { +fix_wall_gran_region.cpp: if (comm->me) return; +fix_wall_reflect.cpp: if (nrigid && comm->me == 0) +force.cpp: if (comm->me == 0) { +group.cpp: // pass list to all other procs via comm->ring() +group.cpp: comm->ring(n,sizeof(tagint),list,1,molring,nullptr,(void *)this); +group.cpp: callback from comm->ring() +imbalance_neigh.cpp: if (comm->me == 0 && !did_warn) +improper.cpp: memory->create(eatom,comm->nthreads*maxeatom,"improper:eatom"); +improper.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"improper:vatom"); +improper.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"improper:cvatom"); +improper.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); +improper.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); +improper_cvff.cpp: if (comm->me == 0) { +improper_deprecated.cpp: if (lmp->comm->me == 0) +improper_harmonic.cpp: if (comm->me == 0) { +improper_hybrid.cpp: int me = comm->me; +improper_umbrella.cpp: if (comm->me == 0) { +info.cpp: if (comm->me != 0) return; +info.cpp: commstyles[comm->style], commlayout[comm->layout], +info.cpp: comm->ghost_velocity ? "yes" : "no"); +info.cpp: if (comm->mode == 0) +info.cpp: comm->get_comm_cutoff()); +info.cpp: if (comm->mode == 1) { +info.cpp: if (comm->cutusermulti) cut = MAX(cut,comm->cutusermulti[i]); +info.cpp: fmt::print(out,"Nprocs = {}, Nthreads = {}\n",comm->nprocs,comm->nthreads); +info.cpp: fmt::print(out,"Processor grid = {} x {} x {}\n",comm->procgrid[0], +info.cpp: comm->procgrid[1], comm->procgrid[2]); +info.cpp: style = commstyles[comm->style]; +info.cpp: bytes += comm->memory_usage(); +input.cpp: comm->modify_params(narg,arg); +input.cpp: if (comm->style == 0) return; +input.cpp: if (comm->style == 1) return; +input.cpp: comm->set_processors(narg,arg); +irregular.cpp: can be used in place of comm->exchange() +irregular.cpp: if (!preassign) comm->coord2proc_setup(); +irregular.cpp: mproclist[nsendatom] = comm->coord2proc(x[i],igx,igy,igz); +irregular.cpp: if not, caller can decide to use comm->exchange() instead +irregular.cpp: if (comm->layout == Comm::LAYOUT_TILED) return 1; +irregular.cpp: // cannot check via comm->procneigh since it ignores PBC +irregular.cpp: int *myloc = comm->myloc; +irregular.cpp: int *procgrid = comm->procgrid; +irregular.cpp: comm->coord2proc(x[i],igx,igy,igz); +kspace.cpp: if ((qsqsum == 0.0) && (comm->me == 0) && warn_nocharge && warning_flag) { +kspace.cpp: if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message); +kspace.cpp: if (comm->me == 0) { +kspace.cpp: if ((table_accuracy > spr) && (comm->me == 0)) +kspace.cpp: if (slab_volfactor < 2.0 && comm->me == 0) +kspace_deprecated.cpp: if (lmp->comm->me == 0) +lammps.cpp: const int me = comm->me; +lammps.cpp: comm->init(); // comm must come after force, modify, neighbor, atom +lattice.cpp: if (comm->me == 0) +library.cpp: && (lmp->comm->me == 0)) { +library.cpp: && (lmp->comm->me == 0)) { +library.cpp: lmp->comm->set_proc_grid(); +library.cpp: if (strcmp(keyword,"world_rank") == 0) return lmp->comm->me; +library.cpp: if (strcmp(keyword,"world_size") == 0) return lmp->comm->nprocs; +library.cpp: if (strcmp(keyword,"nthreads") == 0) return lmp->comm->nthreads; +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: int nprocs = lmp->comm->nprocs; +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: int nprocs = lmp->comm->nprocs; +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) lmp->error->warning(FLERR,msg); +min.cpp: if (comm->me == 0) +min.cpp: if (comm->me == 0 && screen) { +min.cpp: if (comm->me == 0 && screen) +min.cpp: comm->setup(); +min.cpp: comm->exchange(); +min.cpp: comm->borders(); +min.cpp: // atoms may have migrated in comm->exchange() +min.cpp: if (force->newton) comm->reverse_comm(); +min.cpp: comm->setup(); +min.cpp: comm->exchange(); +min.cpp: comm->borders(); +min.cpp: // atoms may have migrated in comm->exchange() +min.cpp: if (force->newton) comm->reverse_comm(); +min.cpp: comm->forward_comm(); +min.cpp: comm->setup(); +min.cpp: comm->exchange(); +min.cpp: comm->borders(); +min.cpp: comm->reverse_comm(); +min_fire.cpp: if (comm->me == 0 && logfile) { +modify.cpp: if (comm->me == 0 && checkall) +modify.cpp: if (fix[ifix]->igroup != igroup && comm->me == 0) +modify.cpp: if (comm->me == 0) +modify.cpp: if (comm->me == 0) +modify.cpp: int me = comm->me; +modify.cpp: int me = comm->me; +modify.cpp: if (flag && comm->me == 0) { +modify.cpp: if (flag && comm->me == 0) { +molecule.cpp: me = comm->me; +nbin_multi.cpp: // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost +nbin_multi.cpp: // include dimension-dependent extension via comm->cutghost +nbin_multi.cpp: double *cutghost = comm->cutghost; +nbin_standard.cpp: // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost +nbin_standard.cpp: // include dimension-dependent extension via comm->cutghost +nbin_standard.cpp: double *cutghost = comm->cutghost; +neighbor.cpp: if (!same && comm->me == 0) print_pairwise_info(); +neighbor.cpp: if (comm->me == 0) printf("SAME flag %d\n",same); +neighbor.cpp: const double cutghost = MAX(cutneighmax,comm->cutghostuser); +neigh_list.cpp: int nmypage = comm->nthreads; +neigh_list.cpp: if (comm->me != 0) return; +neigh_list.cpp: int nmypage = comm->nthreads; +ntopo.cpp: me = comm->me; +ntopo.cpp: nprocs = comm->nprocs; +output.cpp: if (thermo->modified && comm->me == 0) +output.cpp: if (strchr(arg[1],'%')) multiproc = comm->nprocs; +output.cpp: mbavg /= comm->nprocs; +output.cpp: if (comm->me == 0) +pair_beck.cpp: int me = comm->me; +pair_beck.cpp: int me = comm->me; +pair_born_coul_dsf.cpp: int me = comm->me; +pair_born_coul_dsf.cpp: if (comm->me == 0) { +pair_born_coul_wolf.cpp: int me = comm->me; +pair_born_coul_wolf.cpp: if (comm->me == 0) { +pair_born.cpp: int me = comm->me; +pair_born.cpp: if (comm->me == 0) { +pair_brownian.cpp: random = new RanMars(lmp,seed + comm->me); +pair_brownian.cpp: if (force->newton_pair == 0 && comm->me == 0) +pair_brownian.cpp: int me = comm->me; +pair_brownian.cpp: int me = comm->me; +pair_brownian.cpp: random = new RanMars(lmp,seed + comm->me); +pair_buck_coul_cut.cpp: int me = comm->me; +pair_buck_coul_cut.cpp: if (comm->me == 0) { +pair_buck.cpp: int me = comm->me; +pair_buck.cpp: if (comm->me == 0) { +pair_colloid.cpp: if (comm->me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); +pair_colloid.cpp: if (comm->me == 0) { +pair_colloid.cpp: int me = comm->me; +pair_coul_cut.cpp: int me = comm->me; +pair_coul_cut.cpp: if (comm->me == 0) { +pair_coul_debye.cpp: if (comm->me == 0) { +pair_coul_dsf.cpp: int me = comm->me; +pair_coul_dsf.cpp: if (comm->me == 0) { +pair_coul_streitz.cpp: if (comm->me == 0) { +pair_coul_streitz.cpp: if (comm->me != 0) { +pair_coul_wolf.cpp: int me = comm->me; +pair_coul_wolf.cpp: if (comm->me == 0) { +pair.cpp: if (tail_flag && domain->nonperiodic && comm->me == 0) +pair.cpp: if (!compute_flag && tail_flag && comm->me == 0) +pair.cpp: if (!compute_flag && offset_flag && comm->me == 0) +pair.cpp: if (flag && comm->me == 0) +pair.cpp: if (comm->me == 0) +pair.cpp: if (comm->me == 0) +pair.cpp: memory->create(eatom,comm->nthreads*maxeatom,"pair:eatom"); +pair.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"pair:vatom"); +pair.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"pair:cvatom"); +pair.cpp: if (comm->me == 0) { +pair.cpp: if ((comm->me == 0) && (epair)) +pair.cpp: if (comm->me == 0) +pair.cpp: if (comm->me == 0) fprintf(fp,"%d %.15g %.15g %.15g\n",i+1,r,e,f); +pair.cpp: if (comm->me == 0) fclose(fp); +pair.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); +pair.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); +pair.cpp: bytes += comm->nthreads*maxcvatom*9 * sizeof(double); +pair_deprecated.cpp: if (lmp->comm->me == 0) +pair_deprecated.cpp: if (lmp->comm->me == 0) +pair_dpd.cpp: random = new RanMars(lmp,seed + comm->me); +pair_dpd.cpp: if (comm->ghost_velocity == 0) +pair_dpd.cpp: if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR, +pair_dpd.cpp: int me = comm->me; +pair_dpd.cpp: if (comm->me == 0) { +pair_dpd.cpp: random = new RanMars(lmp,seed + comm->me); +pair_dpd_tstat.cpp: random = new RanMars(lmp,seed + comm->me); +pair_dpd_tstat.cpp: int me = comm->me; +pair_dpd_tstat.cpp: if (comm->me == 0) { +pair_dpd_tstat.cpp: random = new RanMars(lmp,seed + comm->me); +pair_gauss.cpp: int me = comm->me; +pair_gauss.cpp: if (comm->me == 0) { +pair_gran_hertz_history.cpp: comm->forward_comm_pair(this); +pair_gran_hooke.cpp: comm->forward_comm_pair(this); +pair_gran_hooke_history.cpp: comm->forward_comm_pair(this); +pair_gran_hooke_history.cpp: if (comm->ghost_velocity == 0) +pair_gran_hooke_history.cpp: int me = comm->me; +pair_gran_hooke_history.cpp: if (comm->me == 0) { +pair_granular.cpp: comm->forward_comm_pair(this); +pair_granular.cpp: if (comm->ghost_velocity == 0) +pair_granular.cpp: int me = comm->me; +pair_hybrid.cpp: int me = comm->me; +pair_lj96_cut.cpp: int me = comm->me; +pair_lj96_cut.cpp: int me = comm->me; +pair_lj_charmm_coul_charmm.cpp: int me = comm->me; +pair_lj_charmm_coul_charmm.cpp: if (comm->me == 0) { +pair_lj_charmmfsw_coul_charmmfsh.cpp: if ((comm->me == 0) && (force->qqr2e != force->qqr2e_charmm_real)) +pair_lj_charmmfsw_coul_charmmfsh.cpp: if ((comm->me == 0) && (force->qqr2e == force->qqr2e_charmm_real)) +pair_lj_charmmfsw_coul_charmmfsh.cpp: int me = comm->me; +pair_lj_charmmfsw_coul_charmmfsh.cpp: if (comm->me == 0) { +pair_lj_cubic.cpp: int me = comm->me; +pair_lj_cubic.cpp: int me = comm->me; +pair_lj_cut_coul_cut.cpp: int me = comm->me; +pair_lj_cut_coul_cut.cpp: if (comm->me == 0) { +pair_lj_cut_coul_debye.cpp: if (comm->me == 0) { +pair_lj_cut_coul_dsf.cpp: int me = comm->me; +pair_lj_cut_coul_dsf.cpp: if (comm->me == 0) { +pair_lj_cut_coul_wolf.cpp: int me = comm->me; +pair_lj_cut_coul_wolf.cpp: int me = comm->me; +pair_lj_cut.cpp: int me = comm->me; +pair_lj_cut.cpp: int me = comm->me; +pair_lj_cut_tip4p_cut.cpp: int me = comm->me; +pair_lj_cut_tip4p_cut.cpp: if (comm->me == 0) { +pair_lj_expand.cpp: int me = comm->me; +pair_lj_expand.cpp: if (comm->me == 0) { +pair_lj_gromacs_coul_gromacs.cpp: int me = comm->me; +pair_lj_gromacs_coul_gromacs.cpp: if (comm->me == 0) { +pair_lj_gromacs.cpp: int me = comm->me; +pair_lj_gromacs.cpp: int me = comm->me; +pair_lj_smooth.cpp: int me = comm->me; +pair_lj_smooth.cpp: int me = comm->me; +pair_lj_smooth_linear.cpp: int me = comm->me; +pair_lj_smooth_linear.cpp: int me = comm->me; +pair_lubricate.cpp: // no need to do this if not shearing since comm->ghost_velocity is set +pair_lubricate.cpp: comm->forward_comm_pair(this); +pair_lubricate.cpp: if (comm->ghost_velocity == 0) +pair_lubricate.cpp: int me = comm->me; +pair_lubricate.cpp: int me = comm->me; +pair_lubricate_poly.cpp: // no need to do this if not shearing since comm->ghost_velocity is set +pair_lubricate_poly.cpp: comm->forward_comm_pair(this); +pair_lubricate_poly.cpp: if (comm->ghost_velocity == 0) +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU.cpp: comm->forward_comm_pair(this); +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU.cpp: comm->forward_comm_pair(this); +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU.cpp: comm->forward_comm_pair(this); +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU.cpp: comm->forward_comm_pair(this); +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU.cpp: comm->forward_comm_pair(this); +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU.cpp: comm->forward_comm_pair(this); +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); // not really needed +pair_lubricateU.cpp: if (comm->ghost_velocity == 0) +pair_lubricateU.cpp: int me = comm->me; +pair_lubricateU.cpp: int me = comm->me; +pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU_poly.cpp: comm->forward_comm_pair(this); +pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU_poly.cpp: comm->forward_comm_pair(this); +pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU_poly.cpp: comm->forward_comm_pair(this); +pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); // not really needed +pair_lubricateU_poly.cpp: if (comm->ghost_velocity == 0) +pair_lubricateU_poly.cpp: if (!comm->me) { +pair_mie_cut.cpp: int me = comm->me; +pair_mie_cut.cpp: int me = comm->me; +pair_morse.cpp: int me = comm->me; +pair_morse.cpp: if (comm->me == 0) { +pair_soft.cpp: int me = comm->me; +pair_soft.cpp: if (comm->me == 0) { +pair_table.cpp: if (comm->me == 0) { +pair_tip4p_cut.cpp: int me = comm->me; +pair_tip4p_cut.cpp: if (comm->me == 0) { +pair_ufm.cpp: int me = comm->me; +pair_ufm.cpp: int me = comm->me; +pair_yukawa.cpp: int me = comm->me; +pair_yukawa.cpp: if (comm->me == 0) { +pair_zbl.cpp: int me = comm->me; +pair_zbl.cpp: int me = comm->me; +pair_zero.cpp: int me = comm->me; +pair_zero.cpp: int me = comm->me; +potential_file_reader.cpp: if (comm->me != 0) { +random_mars.cpp: //if (comm->me == 0) printf("%d %ld %ld %g %ld\n", +read_data.cpp: if (comm->nprocs == 1) n = static_cast (atom->natoms); +read_data.cpp: else n = static_cast (LB_FACTOR * atom->natoms / comm->nprocs); +read_data.cpp: comm->set_proc_grid(); +read_data.cpp: comm->set_proc_grid(); +read_data.cpp: // do comm->init() but not comm->setup() b/c pair/neigh cutoffs not yet set +read_data.cpp: // need call to map_set() b/c comm->exchange clears atom map +read_data.cpp: if (comm->me == 0) +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf); +read_data.cpp: int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf); +read_data.cpp: int eof = comm->read_lines_from_file(fp,nsq,MAXLINE,buf); +read_data.cpp: int eof = comm->read_lines_from_file(fp,nbondtypes,MAXLINE,buf); +read_data.cpp: int eof = comm->read_lines_from_file(fp,nangletypes,MAXLINE,buf); +read_data.cpp: int eof = comm->read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf); +read_data.cpp: int eof = comm->read_lines_from_file(fp,nimpropertypes,MAXLINE,buf); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_dump.cpp: comm->set_proc_grid(0); +read_restart.cpp: comm->set_proc_grid(); +read_restart.cpp: if (comm->me == 0) +read_restart.cpp: if (nprocs_file != comm->nprocs && me == 0) +read_restart.cpp: comm->nprocs)); +read_restart.cpp: if (comm->user_procgrid[0] != 0 && +read_restart.cpp: procgrid[0] != comm->user_procgrid[0]) flag = 1; +read_restart.cpp: if (comm->user_procgrid[1] != 0 && +read_restart.cpp: procgrid[1] != comm->user_procgrid[1]) flag = 1; +read_restart.cpp: if (comm->user_procgrid[2] != 0 && +read_restart.cpp: procgrid[2] != comm->user_procgrid[2]) flag = 1; +read_restart.cpp: if (comm->me ==0) +read_restart.cpp: comm->mode = read_int(); +read_restart.cpp: comm->cutghostuser = read_double(); +read_restart.cpp: comm->ghost_velocity = read_int(); +read_restart.cpp: if (comm->me ==0) +read_restart.cpp: if (comm->me ==0) +read_restart.cpp: if (comm->me ==0) +read_restart.cpp: if (comm->me ==0) +read_restart.cpp: if (comm->me ==0) +read_restart.cpp: if (comm->me ==0) +region_deprecated.cpp: if (lmp->comm->me == 0) +replicate.cpp: int me = comm->me; +replicate.cpp: int nprocs = comm->nprocs; +replicate.cpp: if (comm->me == 0) +replicate.cpp: comm->set_proc_grid(); +replicate.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +replicate.cpp: if (comm->myloc[0] == 0) sublo[0] -= epsilon[0]; +replicate.cpp: if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += epsilon[0]; +replicate.cpp: if (comm->myloc[1] == 0) sublo[1] -= epsilon[1]; +replicate.cpp: if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += epsilon[1]; +replicate.cpp: if (comm->myloc[2] == 0) sublo[2] -= epsilon[2]; +replicate.cpp: if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += epsilon[2]; +replicate.cpp: if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0]; +replicate.cpp: if (comm->mysplit[0][1] == 1.0) subhi[0] += epsilon[0]; +replicate.cpp: if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1]; +replicate.cpp: if (comm->mysplit[1][1] == 1.0) subhi[1] += epsilon[1]; +replicate.cpp: if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2]; +replicate.cpp: if (comm->mysplit[2][1] == 1.0) subhi[2] += epsilon[2]; +reset_atom_ids.cpp: if (comm->me == 0) utils::logmesg(lmp,"Resetting atom IDs ...\n"); +reset_atom_ids.cpp: // initialize system since comm->borders() will be invoked +reset_atom_ids.cpp: comm->setup(); +reset_atom_ids.cpp: comm->exchange(); +reset_atom_ids.cpp: comm->borders(); +reset_atom_ids.cpp: comm->forward_comm_array(1,newIDs); +reset_atom_ids.cpp: int me = comm->me; +reset_atom_ids.cpp: int nprocs = comm->nprocs; +reset_atom_ids.cpp: int nreturn = comm->rendezvous(1,nlocal,(char *) atombuf,sizeof(AtomRvous), +reset_atom_ids.cpp: // rptr->comm->me,i,n,in[i].ibin,binlo,binhi); +reset_atom_ids.cpp: // pass outbuf of IDRvous datums back to comm->rendezvous +reset_mol_ids.cpp: if (comm->me == 0) utils::logmesg(lmp,"Resetting molecule IDs ...\n"); +reset_mol_ids.cpp: // initialize system since comm->borders() will be invoked +reset_mol_ids.cpp: comm->setup(); +reset_mol_ids.cpp: comm->exchange(); +reset_mol_ids.cpp: comm->borders(); +reset_mol_ids.cpp: if (comm->me == 0) { +respa.cpp: if (comm->me == 0) { +respa.cpp: if (flag && comm->me == 0) +respa.cpp: if (modify->nfix == 0 && comm->me == 0) +respa.cpp: if (comm->me == 0 && screen) { +respa.cpp: comm->setup(); +respa.cpp: comm->exchange(); +respa.cpp: comm->borders(); +respa.cpp: if (newton[ilevel]) comm->reverse_comm(); +respa.cpp: comm->setup(); +respa.cpp: comm->exchange(); +respa.cpp: comm->borders(); +respa.cpp: if (newton[ilevel]) comm->reverse_comm(); +respa.cpp: comm->setup(); +respa.cpp: comm->exchange(); +respa.cpp: comm->borders(); +respa.cpp: comm->forward_comm(); +respa.cpp: comm->forward_comm(); +respa.cpp: comm->reverse_comm(); +set.cpp: if (comm->me == 0) utils::logmesg(lmp,"Setting atom values ...\n"); +set.cpp: if (comm->me == 0) { +set.cpp: RanMars *ranmars = new RanMars(lmp,seed + comm->me); +set.cpp: // init entire system since comm->exchange is done +set.cpp: if (comm->me == 0) utils::logmesg(lmp," system init for set ...\n"); +set.cpp: comm->setup(); +set.cpp: comm->exchange(); +set.cpp: comm->borders(); +special.cpp: comm->rendezvous(RVOUS,nlocal,(char *) idbuf,sizeof(IDRvous),0,proclist, +special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), +special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), +special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), +special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), +special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), +special.cpp: if (comm->me == 0) diff --git a/src/nbin.cpp b/src/nbin.cpp index c28c22882c..1323a9042a 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -41,11 +41,8 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) bininvx_multi = nullptr; bininvy_multi = nullptr; bininvz_multi = nullptr; binhead_multi = nullptr; maxbins_multi = nullptr; - - map_type_multi = nullptr; - cutmultisq = nullptr; - maxgroups = 0; + maxcollections = 0; neighbor->last_setup_bins = -1; @@ -85,7 +82,7 @@ NBin::~NBin() memory->destroy(bininvy_multi); memory->destroy(bininvz_multi); - for (int n = 0; n < maxgroups; n++) { + for (int n = 0; n < maxcollections; n++) { memory->destroy(binhead_multi[n]); } delete [] binhead_multi; @@ -115,9 +112,8 @@ void NBin::copy_neighbor_info() bboxlo = neighbor->bboxlo; bboxhi = neighbor->bboxhi; - n_multi_groups = neighbor->n_multi_groups; - map_type_multi = neighbor->map_type_multi; - cutmultisq = neighbor->cutmultisq; + ncollections = neighbor->ncollections; + cutcollectionsq = neighbor->cutcollectionsq; // overwrite Neighbor cutoff with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -175,10 +171,10 @@ int NBin::coord2bin(double *x) /* ---------------------------------------------------------------------- - convert atom coords into local bin # for a particular grouping + convert atom coords into local bin # for a particular collection ------------------------------------------------------------------------- */ -int NBin::coord2bin_multi(double *x, int ig) +int NBin::coord2bin_multi(double *x, int ic) { int ix,iy,iz; int ibin; @@ -187,33 +183,33 @@ int NBin::coord2bin_multi(double *x, int ig) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ig]) + nbinx_multi[ig]; + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ic]) + nbinx_multi[ic]; else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]); - ix = MIN(ix,nbinx_multi[ig]-1); + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ic]); + ix = MIN(ix,nbinx_multi[ic]-1); } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]) - 1; + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ic]) - 1; if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ig]) + nbiny_multi[ig]; + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ic]) + nbiny_multi[ic]; else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]); - iy = MIN(iy,nbiny_multi[ig]-1); + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ic]); + iy = MIN(iy,nbiny_multi[ic]-1); } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]) - 1; + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ic]) - 1; if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ig]) + nbinz_multi[ig]; + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ic]) + nbinz_multi[ic]; else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]); - iz = MIN(iz,nbinz_multi[ig]-1); + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ic]); + iz = MIN(iz,nbinz_multi[ic]-1); } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]) - 1; + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ic]) - 1; - ibin = (iz-mbinzlo_multi[ig])*mbiny_multi[ig]*mbinx_multi[ig] - + (iy-mbinylo_multi[ig])*mbinx_multi[ig] - + (ix-mbinxlo_multi[ig]); + ibin = (iz-mbinzlo_multi[ic])*mbiny_multi[ic]*mbinx_multi[ic] + + (iy-mbinylo_multi[ic])*mbinx_multi[ic] + + (ix-mbinxlo_multi[ic]); return ibin; } diff --git a/src/nbin.h b/src/nbin.h index e31e5bab99..97299398fa 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -73,9 +73,8 @@ class NBin : protected Pointers { int binsizeflag; double binsize_user; double *bboxlo,*bboxhi; - int n_multi_groups; - int *map_type_multi; - double **cutmultisq; + int ncollections; + double **cutcollectionsq; // data common to all NBin variants @@ -89,7 +88,7 @@ class NBin : protected Pointers { // data for multi NBin - int maxgroups; // size of multi arrays + int maxcollections; // size of multi arrays int * maxbins_multi; // size of 2nd dimension of binhead_multi array // methods diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index 04756ff803..db1e8d5682 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -38,7 +38,7 @@ void NBinMulti::bin_atoms_setup(int nall) { // binhead_multi[n] = per-bin vector mbins in length mbins_multi[n] - for (int n = 0; n < maxgroups; n++) { + for (int n = 0; n < maxcollections; n++) { if (mbins_multi[n] > maxbins_multi[n]) { maxbins_multi[n] = mbins_multi[n]; memory->destroy(binhead_multi[n]); @@ -75,81 +75,80 @@ void NBinMulti::bin_atoms_setup(int nall) for triclinic boxes: tilted simulation box cannot contain integer # of bins stencil & neigh list built differently to account for this - mbinlo_multi = lowest global bin any of my ghost atoms could fall into for each grouping - mbinhi_multi = highest global bin any of my ghost atoms could fall into for each grouping - mbin_multi = number of bins I need in a dimension for each grouping + mbinlo_multi = lowest global bin any of my ghost atoms could fall into for each collection + mbinhi_multi = highest global bin any of my ghost atoms could fall into for each collection + mbin_multi = number of bins I need in a dimension for each collection ------------------------------------------------------------------------- */ -void NBinMulti::setup_bins(int style) +void NBinMulti::setup_bins(int /*style*/) { int n; // Initialize arrays - if (n_multi_groups > maxgroups) { + if (ncollections > maxcollections) { // Clear any/all memory for existing groupings - for (n = 0; n < maxgroups; n++) + for (n = 0; n < maxcollections; n++) memory->destroy(binhead_multi[n]); delete [] binhead_multi; - // Realloacte at updated maxgroups - maxgroups = n_multi_groups; + maxcollections = ncollections; - binhead_multi = new int*[maxgroups](); + binhead_multi = new int*[maxcollections](); memory->destroy(nbinx_multi); memory->destroy(nbiny_multi); memory->destroy(nbinz_multi); - memory->create(nbinx_multi, maxgroups, "neigh:nbinx_multi"); - memory->create(nbiny_multi, maxgroups, "neigh:nbiny_multi"); - memory->create(nbinz_multi, maxgroups, "neigh:nbinz_multi"); + memory->create(nbinx_multi, maxcollections, "neigh:nbinx_multi"); + memory->create(nbiny_multi, maxcollections, "neigh:nbiny_multi"); + memory->create(nbinz_multi, maxcollections, "neigh:nbinz_multi"); memory->destroy(mbins_multi); memory->destroy(mbinx_multi); memory->destroy(mbiny_multi); memory->destroy(mbinz_multi); - memory->create(mbins_multi, maxgroups, "neigh:mbins_multi"); - memory->create(mbinx_multi, maxgroups, "neigh:mbinx_multi"); - memory->create(mbiny_multi, maxgroups, "neigh:mbiny_multi"); - memory->create(mbinz_multi, maxgroups, "neigh:mbinz_multi"); + memory->create(mbins_multi, maxcollections, "neigh:mbins_multi"); + memory->create(mbinx_multi, maxcollections, "neigh:mbinx_multi"); + memory->create(mbiny_multi, maxcollections, "neigh:mbiny_multi"); + memory->create(mbinz_multi, maxcollections, "neigh:mbinz_multi"); memory->destroy(mbinxlo_multi); memory->destroy(mbinylo_multi); memory->destroy(mbinzlo_multi); - memory->create(mbinxlo_multi, maxgroups, "neigh:mbinxlo_multi"); - memory->create(mbinylo_multi, maxgroups, "neigh:mbinylo_multi"); - memory->create(mbinzlo_multi, maxgroups, "neigh:mbinzlo_multi"); + memory->create(mbinxlo_multi, maxcollections, "neigh:mbinxlo_multi"); + memory->create(mbinylo_multi, maxcollections, "neigh:mbinylo_multi"); + memory->create(mbinzlo_multi, maxcollections, "neigh:mbinzlo_multi"); memory->destroy(binsizex_multi); memory->destroy(binsizey_multi); memory->destroy(binsizez_multi); - memory->create(binsizex_multi, maxgroups, "neigh:binsizex_multi"); - memory->create(binsizey_multi, maxgroups, "neigh:binsizey_multi"); - memory->create(binsizez_multi, maxgroups, "neigh:binsizez_multi"); + memory->create(binsizex_multi, maxcollections, "neigh:binsizex_multi"); + memory->create(binsizey_multi, maxcollections, "neigh:binsizey_multi"); + memory->create(binsizez_multi, maxcollections, "neigh:binsizez_multi"); memory->destroy(bininvx_multi); memory->destroy(bininvy_multi); memory->destroy(bininvz_multi); - memory->create(bininvx_multi, maxgroups, "neigh:bininvx_multi"); - memory->create(bininvy_multi, maxgroups, "neigh:bininvy_multi"); - memory->create(bininvz_multi, maxgroups, "neigh:bininvz_multi"); + memory->create(bininvx_multi, maxcollections, "neigh:bininvx_multi"); + memory->create(bininvy_multi, maxcollections, "neigh:bininvy_multi"); + memory->create(bininvz_multi, maxcollections, "neigh:bininvz_multi"); memory->destroy(maxbins_multi); - memory->create(maxbins_multi, maxgroups, "neigh:maxbins_multi"); + memory->create(maxbins_multi, maxcollections, "neigh:maxbins_multi"); // ensure reallocation occurs in bin_atoms_setup() - for (n = 0; n < maxgroups; n++) { + for (n = 0; n < maxcollections; n++) { maxbins_multi[n] = 0; } maxatom = 0; } - // Identify smallest group - int igroupmin = 0; - for (n = 0; n < maxgroups; n++) - if (cutmultisq[n][n] < cutmultisq[igroupmin][igroupmin]) - igroupmin = n; + // Identify smallest collection + int icollectionmin = 0; + for (n = 0; n < maxcollections; n++) + if (cutcollectionsq[n][n] < cutcollectionsq[icollectionmin][icollectionmin]) + icollectionmin = n; // bbox = size of bbox of entire domain // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost @@ -189,13 +188,13 @@ void NBinMulti::setup_bins(int style) double binsize_optimal, binsizeinv, coord; int mbinxhi,mbinyhi,mbinzhi; - for (n = 0; n < maxgroups; n++) { - // binsize_user only relates to smallest group - // optimal bin size is roughly 1/2 the group-group cutoff + for (n = 0; n < maxcollections; n++) { + // binsize_user only relates to smallest collection + // optimal bin size is roughly 1/2 the collection-collection cutoff // special case of all cutoffs = 0.0, binsize = box size - if (n == igroupmin && binsizeflag) binsize_optimal = binsize_user; - else binsize_optimal = 0.5*sqrt(cutmultisq[n][n]); + if (n == icollectionmin && binsizeflag) binsize_optimal = binsize_user; + else binsize_optimal = 0.5*sqrt(cutcollectionsq[n][n]); if (binsize_optimal == 0.0) binsize_optimal = bbox[0]; binsizeinv = 1.0/binsize_optimal; @@ -296,16 +295,15 @@ void NBinMulti::bin_atoms() int i,ibin,n; last_bin = update->ntimestep; - for (n = 0; n < maxgroups; n++) { + for (n = 0; n < maxcollections; n++) { for (i = 0; i < mbins_multi[n]; i++) binhead_multi[n][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 + int *collection = neighbor->collection; double **x = atom->x; int *mask = atom->mask; - int *type = atom->type; int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; @@ -313,7 +311,7 @@ void NBinMulti::bin_atoms() int bitmask = group->bitmask[includegroup]; for (i = nall-1; i >= nlocal; i--) { if (mask[i] & bitmask) { - n = map_type_multi[type[i]]; + n = collection[i]; ibin = coord2bin_multi(x[i], n); atom2bin[i] = ibin; bins[i] = binhead_multi[n][ibin]; @@ -321,15 +319,15 @@ void NBinMulti::bin_atoms() } } for (i = atom->nfirst-1; i >= 0; i--) { - n = map_type_multi[type[i]]; + n = collection[i]; ibin = coord2bin_multi(x[i], n); atom2bin[i] = ibin; bins[i] = binhead_multi[n][ibin]; binhead_multi[n][ibin] = i; } } else { - for (i = nall-1; i >= 0; i--) { - n = map_type_multi[type[i]]; + for (i = nall-1; i >= 0; i--) { + n = collection[i]; ibin = coord2bin_multi(x[i], n); atom2bin[i] = ibin; bins[i] = binhead_multi[n][ibin]; @@ -343,7 +341,7 @@ void NBinMulti::bin_atoms() double NBinMulti::memory_usage() { double bytes = 0; - for (int m = 0; m < maxgroups; m++) + for (int m = 0; m < maxcollections; m++) bytes += maxbins_multi[m]*sizeof(int); bytes += 2*maxatom*sizeof(int); return bytes; diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 5a1255edbe..16aca434f1 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -43,6 +43,7 @@ #include "style_npair.h" #include "style_nstencil.h" #include "style_ntopo.h" +#include "tokenizer.h" #include "update.h" #include @@ -53,6 +54,7 @@ using namespace NeighConst; #define RQDELTA 1 #define EXDELTA 1 +#define DELTA_PERATOM 64 #define BIG 1.0e20 @@ -195,9 +197,13 @@ pairclass(nullptr), pairnames(nullptr), pairmasks(nullptr) // Multi data - map_type_multi = nullptr; - cutmultisq = nullptr; - multi_groups = 0; + type2collection = nullptr; + collection2cut = nullptr; + collection = nullptr; + cutcollectionsq = nullptr; + custom_collection_flag = 0; + interval_collection_flag = 0; + nmax_collection = 0; // Kokkos setting @@ -265,8 +271,10 @@ Neighbor::~Neighbor() delete [] ex_mol_bit; memory->destroy(ex_mol_intra); - memory->destroy(map_type_multi); - memory->destroy(cutmultisq); + memory->destroy(type2collection); + memory->destroy(collection2cut); + memory->destroy(collection); + memory->destroy(cutcollectionsq); } /* ---------------------------------------------------------------------- */ @@ -350,33 +358,96 @@ void Neighbor::init() } cutneighmaxsq = cutneighmax * cutneighmax; - // multi cutoffs + // Define cutoffs for multi if(style == Neighbor::MULTI){ - int igroup, jgroup; + int icollection, jcollection; - // If not defined from custom grouping, create default map - if(not map_type_multi) { - n_multi_groups = n; - memory->create(map_type_multi,n+1,"neigh:map_type_multi"); + // If collections not yet defined, create default map using types + if(not custom_collection_flag) { + ncollections = n; + interval_collection_flag = 0; + memory->create(type2collection,n+1,"neigh:type2collection"); for(i = 1; i <= n; i++) - map_type_multi[i] = i-1; + type2collection[i] = i-1; } - // Define maximum interaction distance for each pair of groups - memory->grow(cutmultisq, n_multi_groups, n_multi_groups, "neigh:cutmultisq"); - for(i = 0; i < n_multi_groups; i++) - for(j = 0; j < n_multi_groups; j++) - cutmultisq[i][j] = 0.0; + memory->grow(cutcollectionsq, ncollections, ncollections, "neigh:cutcollectionsq"); - for(i = 1; i <= n; i++){ - igroup = map_type_multi[i]; - for(j = 1; j <= n; j++){ - jgroup = map_type_multi[j]; - if(cutneighsq[i][j] > cutmultisq[igroup][jgroup]) { - cutmultisq[igroup][jgroup] = cutneighsq[i][j]; - cutmultisq[jgroup][igroup] = cutneighsq[i][j]; + // 3 possible ways of defining collections + // 1) Types are used to define collections + // Each collection loops through its owned types, and uses cutneighsq to calculate its cutoff + // 2) Collections are defined by intervals, point particles + // Types are first sorted into collections based on cutneighsq[i][i] + // Each collection loops through its owned types, and uses cutneighsq to calculate its cutoff + // 3) Collections are defined by intervals, finite particles + // + + // Define collection cutoffs + for(i = 0; i < ncollections; i++) + for(j = 0; j < ncollections; j++) + cutcollectionsq[i][j] = 0.0; + + if(not interval_collection_flag){ + finite_cut_flag = 0; + for(i = 1; i <= n; i++){ + icollection = type2collection[i]; + for(j = 1; j <= n; j++){ + jcollection = type2collection[j]; + if(cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { + cutcollectionsq[icollection][jcollection] = cutneighsq[i][j]; + cutcollectionsq[jcollection][icollection] = cutneighsq[i][j]; + } } } + } else { + if(force->pair->finitecutflag){ + finite_cut_flag = 1; + // If cutoffs depend on finite atom sizes, use radii of intervals to find cutoffs + double ri, rj, tmp; + for(i = 0; i < ncollections; i++){ + ri = collection2cut[i]*0.5; + for(j = 0; j < ncollections; j++){ + rj = collection2cut[j]*0.5; + tmp = force->pair->radii2cut(ri, rj); + cutcollectionsq[i][j] = tmp*tmp; + } + } + } else { + finite_cut_flag = 0; + + // Map types to collections + if(not type2collection) + memory->create(type2collection,n+1,"neigh:type2collection"); + + for(i = 1; i <= n; i++) + type2collection[i] = -1; + + double cuttmp; + for(i = 1; i <= n; i++){ + cuttmp = sqrt(cutneighsq[i][i]); + for(icollection = 0; icollection < ncollections; icollection ++){ + if(collection2cut[icollection] > cuttmp) { + type2collection[i] = icollection; + break; + } + } + + if(type2collection[i] == -1) + error->all(FLERR, "Pair cutoff exceeds interval cutoffs for multi"); + } + + // Define cutoffs + for(i = 1; i <= n; i++){ + icollection = type2collection[i]; + for(j = 1; j <= n; j++){ + jcollection = type2collection[j]; + if(cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { + cutcollectionsq[icollection][jcollection] = cutneighsq[i][j]; + cutcollectionsq[jcollection][icollection] = cutneighsq[i][j]; + } + } + } + } } } @@ -2100,6 +2171,8 @@ void Neighbor::build(int topoflag) int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; + // rebuild collection array from scratch + if(style == Neighbor::MULTI) build_collection(0); // check that using special bond flags will not overflow neigh lists @@ -2140,7 +2213,7 @@ void Neighbor::build(int topoflag) } } } - + // bin atoms for all NBin instances // not just NBin associated with perpetual lists, also occasional lists // b/c cannot wait to bin occasional lists in build_one() call @@ -2423,53 +2496,91 @@ void Neighbor::modify_params(int narg, char **arg) iarg += 2; } else error->all(FLERR,"Illegal neigh_modify command"); - } else if (strcmp(arg[iarg],"multi/custom") == 0) { + } else if (strcmp(arg[iarg],"collection/interval") == 0) { if(style != Neighbor::MULTI) - error->all(FLERR,"Cannot use multi/custom command without multi setting"); + error->all(FLERR,"Cannot use collection/interval command without multi setting"); if(iarg+2 > narg) - error->all(FLERR,"Invalid multi/custom command"); - int nextra = utils::inumeric(FLERR,arg[iarg+1],false,lmp); - if(iarg+1+nextra > narg) - error->all(FLERR,"Invalid multi/custom command"); + error->all(FLERR,"Invalid collection/interval command"); + ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if(iarg+1+ncollections > narg) + error->all(FLERR,"Invalid collection/interval command"); int ntypes = atom->ntypes; - int n, nlo, nhi, i, j, igroup, jgroup; + int n, nlo, nhi, i, j; + + interval_collection_flag = 1; + custom_collection_flag = 1; + if(not collection2cut) + memory->create(collection2cut,ncollections,"neigh:collection2cut"); - if(not map_type_multi) - memory->create(map_type_multi,ntypes+1,"neigh:map_type_multi"); + // Set upper cutoff for each collection + char *id; + double cut_interval; + for(i = 0; i < ncollections; i++){ + cut_interval = utils::numeric(FLERR,arg[iarg+2+i],false,lmp); + collection2cut[i] = cut_interval; + + if(i != 0) + if(collection2cut[i-1] >= collection2cut[i]) + error->all(FLERR,"Nonsequential interval cutoffs in collection/interval setting"); + } + + iarg += 2 + ncollections; + } else if (strcmp(arg[iarg],"collection/type") == 0) { + if(style != Neighbor::MULTI) + error->all(FLERR,"Cannot use collection/type command without multi setting"); + + if(iarg+2 > narg) + error->all(FLERR,"Invalid collection/type command"); + ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if(iarg+1+ncollections > narg) + error->all(FLERR,"Invalid collection/type command"); + + int ntypes = atom->ntypes; + int n, nlo, nhi, i, j, k; + + interval_collection_flag = 0; + custom_collection_flag = 1; + if(not type2collection) + memory->create(type2collection,ntypes+1,"neigh:type2collection"); // Erase previous mapping for(i = 1; i <= ntypes; i++) - map_type_multi[i] = -1; + type2collection[i] = -1; // For each custom range, define mapping for types in interval - n_multi_groups = 0; - char *id; - for(i = 0; i < nextra; i++){ + int nfield; + char *str; + for(i = 0; i < ncollections; i++){ n = strlen(arg[iarg+2+i]) + 1; - id = new char[n]; - strcpy(id,arg[iarg+2+i]); - utils::bounds(FLERR,id,1,ntypes,nlo,nhi,error); - delete [] id; + str = new char[n]; + strcpy(str,arg[iarg+2+i]); + std::vector words = Tokenizer(str, ",").as_vector(); + nfield = words.size(); + + for (j = 0; j < nfield; j++) { + const char * field = words[j].c_str(); + utils::bounds(FLERR,field,1,ntypes,nlo,nhi,error); - for (j = nlo; j <= nhi; j++) { - if(map_type_multi[j] != -1) - error->all(FLERR,"Type specified more than once in multi/custom commnd"); - map_type_multi[j] = n_multi_groups; + for (k = nlo; k <= nhi; k++) { + if(type2collection[k] != -1) + error->all(FLERR,"Type specified more than once in collection/type commnd"); + type2collection[k] = i; + } } - n_multi_groups += 1; + + delete [] str; } - // Create separate group for each undefined atom type + // Check for undefined atom type for(i = 1; i <= ntypes; i++){ - if(map_type_multi[i] == -1){ - map_type_multi[i] = n_multi_groups; - n_multi_groups += 1; + if(type2collection[i] == -1){ + error->all(FLERR,"Type missing in collection/type commnd"); } } - iarg += 2 + nextra; + iarg += 2 + ncollections; } else error->all(FLERR,"Illegal neigh_modify command"); } } @@ -2521,6 +2632,46 @@ int Neighbor::any_full() return any_full; } +/* ---------------------------------------------------------------------- + populate collection array for multi starting at the index istart +------------------------------------------------------------------------- */ + +void Neighbor::build_collection(int istart) +{ + if (style != Neighbor::MULTI) + error->all(FLERR, "Cannot define atom collections without neighbor style multi"); + + int nmax = atom->nlocal+atom->nghost; + if(nmax > nmax_collection){ + nmax_collection = nmax+DELTA_PERATOM; + memory->grow(collection, nmax_collection, "neigh:collection"); + } + + if(finite_cut_flag){ + double cut; + int icollection; + for(int i = istart; i < nmax; i++){ + cut = force->pair->atom2cut(i); + collection[i] = -1; + + for(icollection = 0; icollection < ncollections; icollection++){ + if(collection2cut[icollection] > cut) { + collection[i] = icollection; + break; + } + } + + if(collection[i] == -1) + error->one(FLERR, "Atom cutoff exceeds interval cutoffs for multi"); + } + } else { + int *type = atom->type; + for(int i = istart; i < nmax; i++){ + collection[i] = type2collection[type[i]]; + } + } +} + /* ---------------------------------------------------------------------- return # of bytes of allocated memory ------------------------------------------------------------------------- */ diff --git a/src/neighbor.h b/src/neighbor.h index b8e1189b35..7b6246dec7 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -104,11 +104,16 @@ class Neighbor : protected Pointers { // optional type grouping for multi - int multi_groups; // 1 if custom groupings are defined for multi - int n_multi_groups; // # of custom groupings - int *map_type_multi; // ntype array mapping types to custom groupings - double **cutmultisq; // cutoffs for each combination of custom groupings - + int custom_collection_flag; // 1 if custom collections are defined for multi + int interval_collection_flag; // 1 if custom collections use intervals + int finite_cut_flag; // 1 if multi considers finite atom size + int ncollections; // # of custom collections + int nmax_collection; // maximum atoms stored in collection array + int *type2collection; // ntype array mapping types to custom collections + double *collection2cut; // ncollection array with upper bounds on cutoff intervals + double **cutcollectionsq; // cutoffs for each combination of collections + int *collection; // local per-atom array to store collection id + // public methods Neighbor(class LAMMPS *); @@ -130,6 +135,7 @@ class Neighbor : protected Pointers { int exclude_setting(); // return exclude value to accelerator pkg class NeighRequest *find_request(void *); // find a neighbor request int any_full(); // Check if any old requests had full neighbor lists + void build_collection(int); // build peratom collection array starting at the given index double memory_usage(); diff --git a/src/npair.cpp b/src/npair.cpp index 95a61fbefa..eee8610958 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -97,9 +97,8 @@ void NPair::copy_neighbor_info() // multi info - n_multi_groups = neighbor->n_multi_groups; - map_type_multi = neighbor->map_type_multi; - cutmultisq = neighbor->cutmultisq; + ncollections = neighbor->ncollections; + cutcollectionsq = neighbor->cutcollectionsq; // overwrite per-type Neighbor cutoffs with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -184,9 +183,8 @@ void NPair::build_setup() { if (nb) copy_bin_info(); if (ns) copy_stencil_info(); - + // set here, since build_setup() always called before build() - last_build = update->ntimestep; } @@ -269,10 +267,10 @@ int NPair::coord2bin(double *x, int &ix, int &iy, int &iz) /* ---------------------------------------------------------------------- - multi version of coord2bin for a given grouping + multi version of coord2bin for a given collection ------------------------------------------------------------------------- */ -int NPair::coord2bin(double *x, int ig) +int NPair::coord2bin(double *x, int ic) { int ix,iy,iz; int ibin; @@ -281,32 +279,32 @@ int NPair::coord2bin(double *x, int ig) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ig]) + nbinx_multi[ig]; + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ic]) + nbinx_multi[ic]; else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]); - ix = MIN(ix,nbinx_multi[ig]-1); + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ic]); + ix = MIN(ix,nbinx_multi[ic]-1); } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]) - 1; + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ic]) - 1; if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ig]) + nbiny_multi[ig]; + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ic]) + nbiny_multi[ic]; else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]); - iy = MIN(iy,nbiny_multi[ig]-1); + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ic]); + iy = MIN(iy,nbiny_multi[ic]-1); } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]) - 1; + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ic]) - 1; if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ig]) + nbinz_multi[ig]; + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ic]) + nbinz_multi[ic]; else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]); - iz = MIN(iz,nbinz_multi[ig]-1); + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ic]); + iz = MIN(iz,nbinz_multi[ic]-1); } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]) - 1; + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ic]) - 1; - ix -= mbinxlo_multi[ig]; - iy -= mbinylo_multi[ig]; - iz -= mbinzlo_multi[ig]; - ibin = iz*mbiny_multi[ig]*mbinx_multi[ig] + iy*mbinx_multi[ig] + ix; + ix -= mbinxlo_multi[ic]; + iy -= mbinylo_multi[ic]; + iz -= mbinzlo_multi[ic]; + ibin = iz*mbiny_multi[ic]*mbinx_multi[ic] + iy*mbinx_multi[ic] + ix; return ibin; } diff --git a/src/npair.h b/src/npair.h index c857ec0924..b8416208ca 100644 --- a/src/npair.h +++ b/src/npair.h @@ -48,9 +48,8 @@ class NPair : protected Pointers { double cut_middle_sq; double cut_middle_inside_sq; double *bboxlo,*bboxhi; - int n_multi_groups; - int *map_type_multi; - double **cutmultisq; + int ncollections; + double **cutcollectionsq; // exclusion data from Neighbor class diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp index c78f7b2d1d..0ce717f722 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_full_multi.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -28,18 +29,19 @@ NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ void NPairFullMulti::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; int js; + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -68,7 +70,7 @@ void NPairFullMulti::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -80,22 +82,22 @@ void NPairFullMulti::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in surrounding bins in stencil including self // skip i = j - // use full stencil for all group combinations + // use full stencil for all collection combinations - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { if (i == j) continue; diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index 11bab91e6a..5f050429ac 100755 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newtoff.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -28,7 +29,7 @@ NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent 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) @@ -36,12 +37,13 @@ NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} void NPairHalfMultiNewtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; int js; + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -70,7 +72,7 @@ void NPairHalfMultiNewtoff::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -82,24 +84,24 @@ void NPairHalfMultiNewtoff::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // 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 - // use full stencil for all group combinations + // use full stencil for all collection combinations - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index aa8f606242..18e66d4adb 100755 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newton.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -28,19 +29,20 @@ NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfMultiNewton::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; int js; + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -69,7 +71,7 @@ void NPairHalfMultiNewton::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -81,29 +83,29 @@ void NPairHalfMultiNewton::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(igroup == jgroup) js = bins[i]; - else js = binhead_multi[jgroup][jbin]; + if(icollection == jcollection) js = bins[i]; + else js = binhead_multi[jcollection][jbin]; - // if same group, + // if same collection, // 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 - // if different groups, + // if different collections, // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(igroup != jgroup and j < i) continue; + if(icollection != jcollection and j < i) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -139,16 +141,16 @@ void NPairHalfMultiNewton::build(NeighList *list) } } - // for all groups, loop over all atoms in other bins in stencil, store every pair + // for all collections, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index 6969c9cfab..90c6cf714d 100755 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newton_tri.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -28,19 +29,20 @@ NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfMultiNewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; int js; - + + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -69,7 +71,7 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -81,12 +83,12 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil // stencil is empty if i larger than j @@ -97,15 +99,15 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { - // if same size (same group), use half stencil - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + // if same size (same collection), use half stencil + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index e361bbce76..77aa4f746b 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -13,6 +13,7 @@ es certain rights in this software. This software is distributed under #include #include "npair_half_size_multi_newtoff.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -28,7 +29,7 @@ NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) { /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent 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) @@ -36,12 +37,13 @@ NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) { void NPairHalfSizeMultiNewtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; int js; + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -65,7 +67,7 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -73,24 +75,24 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // 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 - // use full stencil for all group combinations + // use full stencil for all collection combinations - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index 84571a3b02..67715ebe68 100755 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_multi_newton.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -27,18 +28,19 @@ NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfSizeMultiNewton::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns,js; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -62,7 +64,7 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -70,29 +72,29 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(igroup == jgroup) js = bins[i]; - else js = binhead_multi[jgroup][jbin]; + if(icollection == jcollection) js = bins[i]; + else js = binhead_multi[jcollection][jbin]; - // if same group, + // if same collection, // 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 - // if different groups, + // if different collections, // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(igroup != jgroup and j < i) continue; + if(icollection != jcollection and j < i) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -121,16 +123,16 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) } } - // for all groups, loop over all atoms in other bins in stencil, store every pair + // for all collections, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 2000927c63..2bf033781e 100755 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_multi_newton_tri.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -27,18 +28,19 @@ NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lm /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns,js; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -62,7 +64,7 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -70,12 +72,12 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil // stencil is empty if i larger than j @@ -86,15 +88,15 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { - // if same size (same group), use half stencil - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + // if same size (same collection), use half stencil + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/npair_half_size_multi_old_newtoff.cpp b/src/npair_half_size_multi_old_newtoff.cpp index 35095b4856..fd22412f00 100644 --- a/src/npair_half_size_multi_old_newtoff.cpp +++ b/src/npair_half_size_multi_old_newtoff.cpp @@ -35,7 +35,7 @@ NPairHalfSizeMultiOldNewtoff::NPairHalfSizeMultiOldNewtoff(LAMMPS *lmp) : NPair( void NPairHalfSizeMultiOldNewtoff::build(NeighList *list) { - int i,j,k,m,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; diff --git a/src/npair_half_size_multi_old_newton.cpp b/src/npair_half_size_multi_old_newton.cpp index 0112c0593f..1f6918625b 100644 --- a/src/npair_half_size_multi_old_newton.cpp +++ b/src/npair_half_size_multi_old_newton.cpp @@ -34,7 +34,7 @@ NPairHalfSizeMultiOldNewton::NPairHalfSizeMultiOldNewton(LAMMPS *lmp) : NPair(lm void NPairHalfSizeMultiOldNewton::build(NeighList *list) { - int i,j,k,m,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; diff --git a/src/npair_half_size_multi_old_newton_tri.cpp b/src/npair_half_size_multi_old_newton_tri.cpp index f29c323944..e7477fada4 100644 --- a/src/npair_half_size_multi_old_newton_tri.cpp +++ b/src/npair_half_size_multi_old_newton_tri.cpp @@ -33,7 +33,7 @@ NPairHalfSizeMultiOldNewtonTri::NPairHalfSizeMultiOldNewtonTri(LAMMPS *lmp) : NP void NPairHalfSizeMultiOldNewtonTri::build(NeighList *list) { - int i,j,k,m,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 3d86b57b9e..c6ed76b6eb 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -52,14 +52,14 @@ using namespace LAMMPS_NS; cutoff is not cutneighmaxsq, but max cutoff for that atom type no versions that allow ghost on (any need for it?) for multi: - create one stencil for each igroup-jgroup pairing - the full/half stencil label refers to the same-group stencil - a half list with newton on has a half same-group stencil - a full list or half list with newton off has a full same-group stencil - cross group stencils are always full to allow small-to-large lookups + create one stencil for each icollection-jcollection pairing + the full/half stencil label refers to the same-collection stencil + a half list with newton on has a half same-collection stencil + a full list or half list with newton off has a full same-collection stencil + cross collection stencils are always full to allow small-to-large lookups for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above - cutoff is not cutneighmaxsq, but max cutoff for that atom group + cutoff is not cutneighmaxsq, but max cutoff for that atom collection no versions that allow ghost on (any need for it?) ------------------------------------------------------------------------- */ @@ -81,7 +81,7 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) flag_half_multi = nullptr; flag_skip_multi = nullptr; - bin_group_multi = nullptr; + bin_collection_multi = nullptr; dimension = domain->dimension; } @@ -107,7 +107,7 @@ NStencil::~NStencil() if (stencil_multi) { - int n = n_multi_groups; + int n = ncollections; memory->destroy(nstencil_multi); for (int i = 0; i < n; i++) { for (int j = 0; j < n; j++) { @@ -120,7 +120,7 @@ NStencil::~NStencil() memory->destroy(maxstencil_multi); memory->destroy(flag_half_multi); memory->destroy(flag_skip_multi); - memory->destroy(bin_group_multi); + memory->destroy(bin_collection_multi); memory->destroy(stencil_sx_multi); memory->destroy(stencil_sy_multi); @@ -156,9 +156,9 @@ void NStencil::copy_neighbor_info() cuttypesq = neighbor->cuttypesq; cutneighsq = neighbor->cutneighsq; - n_multi_groups = neighbor->n_multi_groups; - map_type_multi = neighbor->map_type_multi; - cutmultisq = neighbor->cutmultisq; + ncollections = neighbor->ncollections; + collection = neighbor->collection; + cutcollectionsq = neighbor->cutcollectionsq; // overwrite Neighbor cutoff with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -269,9 +269,9 @@ void NStencil::create_setup() } } } else { - int i, j, bin_group, smax; + int i, j, bin_collection, smax; double stencil_range; - int n = n_multi_groups; + int n = ncollections; if(nb) copy_bin_info_multi(); @@ -280,8 +280,8 @@ void NStencil::create_setup() "neighstencil:flag_half_multi"); memory->create(flag_skip_multi, n, n, "neighstencil:flag_skip_multi"); - memory->create(bin_group_multi, n, n, - "neighstencil:bin_group_multi"); + memory->create(bin_collection_multi, n, n, + "neighstencil:bin_collection_multi"); memory->create(stencil_sx_multi, n, n, "neighstencil:stencil_sx_multi"); @@ -335,25 +335,25 @@ void NStencil::create_setup() // Skip creation of unused stencils if (flag_skip_multi[i][j]) continue; - // Copy bin info for this pair of atom types - bin_group = bin_group_multi[i][j]; + // Copy bin info for this pair of atom collections + bin_collection = bin_collection_multi[i][j]; - stencil_binsizex_multi[i][j] = binsizex_multi[bin_group]; - stencil_binsizey_multi[i][j] = binsizey_multi[bin_group]; - stencil_binsizez_multi[i][j] = binsizez_multi[bin_group]; + stencil_binsizex_multi[i][j] = binsizex_multi[bin_collection]; + stencil_binsizey_multi[i][j] = binsizey_multi[bin_collection]; + stencil_binsizez_multi[i][j] = binsizez_multi[bin_collection]; - stencil_mbinx_multi[i][j] = mbinx_multi[bin_group]; - stencil_mbiny_multi[i][j] = mbiny_multi[bin_group]; - stencil_mbinz_multi[i][j] = mbinz_multi[bin_group]; + stencil_mbinx_multi[i][j] = mbinx_multi[bin_collection]; + stencil_mbiny_multi[i][j] = mbiny_multi[bin_collection]; + stencil_mbinz_multi[i][j] = mbinz_multi[bin_collection]; - stencil_range = sqrt(cutmultisq[i][j]); + stencil_range = sqrt(cutcollectionsq[i][j]); - sx = static_cast (stencil_range*bininvx_multi[bin_group]); - if (sx*binsizex_multi[bin_group] < stencil_range) sx++; - sy = static_cast (stencil_range*bininvy_multi[bin_group]); - if (sy*binsizey_multi[bin_group] < stencil_range) sy++; - sz = static_cast (stencil_range*bininvz_multi[bin_group]); - if (sz*binsizez_multi[bin_group] < stencil_range) sz++; + sx = static_cast (stencil_range*bininvx_multi[bin_collection]); + if (sx*binsizex_multi[bin_collection] < stencil_range) sx++; + sy = static_cast (stencil_range*bininvy_multi[bin_collection]); + if (sy*binsizey_multi[bin_collection] < stencil_range) sy++; + sz = static_cast (stencil_range*bininvz_multi[bin_collection]); + if (sz*binsizez_multi[bin_collection] < stencil_range) sz++; stencil_sx_multi[i][j] = sx; stencil_sy_multi[i][j] = sy; @@ -397,24 +397,24 @@ double NStencil::bin_distance(int i, int j, int k) /* ---------------------------------------------------------------------- - compute closest distance for a given atom grouping + compute closest distance for a given atom collection ------------------------------------------------------------------------- */ -double NStencil::bin_distance_multi(int i, int j, int k, int ig) +double NStencil::bin_distance_multi(int i, int j, int k, int ic) { double delx,dely,delz; - if (i > 0) delx = (i-1)*binsizex_multi[ig]; + if (i > 0) delx = (i-1)*binsizex_multi[ic]; else if (i == 0) delx = 0.0; - else delx = (i+1)*binsizex_multi[ig]; + else delx = (i+1)*binsizex_multi[ic]; - if (j > 0) dely = (j-1)*binsizey_multi[ig]; + if (j > 0) dely = (j-1)*binsizey_multi[ic]; else if (j == 0) dely = 0.0; - else dely = (j+1)*binsizey_multi[ig]; + else dely = (j+1)*binsizey_multi[ic]; - if (k > 0) delz = (k-1)*binsizez_multi[ig]; + if (k > 0) delz = (k-1)*binsizez_multi[ic]; else if (k == 0) delz = 0.0; - else delz = (k+1)*binsizez_multi[ig]; + else delz = (k+1)*binsizez_multi[ic]; return (delx*delx + dely*dely + delz*delz); } @@ -431,7 +431,7 @@ double NStencil::memory_usage() bytes += atom->ntypes*maxstencil_multi_old * sizeof(int); bytes += atom->ntypes*maxstencil_multi_old * sizeof(double); } else if (neighstyle == Neighbor::MULTI) { - int n = n_multi_groups; + int n = ncollections; for (int i = 0; i < n; i++) { for (int j = 0; j < n; j++) { bytes += maxstencil_multi[i][j] * sizeof(int); diff --git a/src/nstencil.h b/src/nstencil.h index b38276b45f..37cedec045 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -43,8 +43,8 @@ class NStencil : protected Pointers { // Arrays to store options for multi itype-jtype stencils bool **flag_half_multi; // flag creation of a half stencil for igroup-jgroup - bool **flag_skip_multi; // skip creation of igroup-jgroup stencils (for newton on) - int **bin_group_multi; // what group to use for bin information + bool **flag_skip_multi; // skip creation of icollection-jcollection stencils (for newton on) + int **bin_collection_multi; // what collection to use for bin information NStencil(class LAMMPS *); virtual ~NStencil(); @@ -66,9 +66,9 @@ class NStencil : protected Pointers { double cutneighmaxsq; double *cuttypesq; double **cutneighsq; - double **cutmultisq; - int n_multi_groups; - int *map_type_multi; + double **cutcollectionsq; + int ncollections; + int *collection; // data from NBin class @@ -112,7 +112,7 @@ class NStencil : protected Pointers { // methods for multi NStencil - double bin_distance_multi(int, int, int, int); // distance between bin corners for different types + double bin_distance_multi(int, int, int, int); // distance between bin corners for different collections void copy_bin_info_multi(); // copy multi info from NBin class virtual void set_stencil_properties(){} // determine which stencils to build and how }; diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index 4c96f41a56..b27e3c2a9c 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -29,7 +29,7 @@ NStencilFullMulti2d::NStencilFullMulti2d(LAMMPS *lmp) : NStencil(lmp) {} void NStencilFullMulti2d::set_stencil_properties() { - int n = n_multi_groups; + int n = ncollections; int i, j; // Always look up neighbor using full stencil and neighbor's bin @@ -38,7 +38,7 @@ void NStencilFullMulti2d::set_stencil_properties() for (j = 0; j < n; j++) { flag_half_multi[i][j] = 0; flag_skip_multi[i][j] = 0; - bin_group_multi[i][j] = j; + bin_collection_multi[i][j] = j; } } } @@ -49,33 +49,33 @@ void NStencilFullMulti2d::set_stencil_properties() void NStencilFullMulti2d::create() { - int igroup, jgroup, bin_group, i, j, k, ns; - int n = n_multi_groups; + int icollection, jcollection, bin_collection, i, j, k, ns; + int n = ncollections; double cutsq; - for (igroup = 0; igroup < n; igroup++) { - for (jgroup = 0; jgroup < n; jgroup++) { - if (flag_skip_multi[igroup][jgroup]) continue; + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - sx = stencil_sx_multi[igroup][jgroup]; - sy = stencil_sy_multi[igroup][jgroup]; + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; - mbinx = stencil_mbinx_multi[igroup][jgroup]; - mbiny = stencil_mbiny_multi[igroup][jgroup]; + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; - bin_group = bin_group_multi[igroup][jgroup]; + bin_collection = bin_collection_multi[icollection][jcollection]; - cutsq = cutmultisq[igroup][jgroup]; + cutsq = cutcollectionsq[icollection][jcollection]; for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; - nstencil_multi[igroup][jgroup] = ns; + nstencil_multi[icollection][jcollection] = ns; } } } diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp index bc76433723..3d97bc10ad 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -29,7 +29,7 @@ NStencilFullMulti3d::NStencilFullMulti3d(LAMMPS *lmp) : NStencil(lmp) {} void NStencilFullMulti3d::set_stencil_properties() { - int n = n_multi_groups; + int n = ncollections; int i, j; // Always look up neighbor using full stencil and neighbor's bin @@ -39,7 +39,7 @@ void NStencilFullMulti3d::set_stencil_properties() for (j = 0; j < n; j++) { flag_half_multi[i][j] = 0; flag_skip_multi[i][j] = 0; - bin_group_multi[i][j] = j; + bin_collection_multi[i][j] = j; } } } @@ -50,37 +50,37 @@ void NStencilFullMulti3d::set_stencil_properties() void NStencilFullMulti3d::create() { - int igroup, jgroup, bin_group, i, j, k, ns; - int n = n_multi_groups; + int icollection, jcollection, bin_collection, i, j, k, ns; + int n = ncollections; double cutsq; - for (igroup = 0; igroup < n; igroup++) { - for (jgroup = 0; jgroup < n; jgroup++) { - if (flag_skip_multi[igroup][jgroup]) continue; + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - sx = stencil_sx_multi[igroup][jgroup]; - sy = stencil_sy_multi[igroup][jgroup]; - sz = stencil_sz_multi[igroup][jgroup]; + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; + sz = stencil_sz_multi[icollection][jcollection]; - mbinx = stencil_mbinx_multi[igroup][jgroup]; - mbiny = stencil_mbiny_multi[igroup][jgroup]; - mbinz = stencil_mbinz_multi[igroup][jgroup]; + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; + mbinz = stencil_mbinz_multi[icollection][jcollection]; - bin_group = bin_group_multi[igroup][jgroup]; + bin_collection = bin_collection_multi[icollection][jcollection]; - cutsq = cutmultisq[igroup][jgroup]; + cutsq = cutcollectionsq[icollection][jcollection]; for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; - nstencil_multi[igroup][jgroup] = ns; + nstencil_multi[icollection][jcollection] = ns; } } } diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_2d.cpp index 8be8a1c151..57352c7c6f 100644 --- a/src/nstencil_half_multi_2d.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti2d::NStencilHalfMulti2d(LAMMPS *lmp) : void NStencilHalfMulti2d::set_stencil_properties() { - int n = n_multi_groups; + int n = ncollections; int i, j; - // Cross groups: use full stencil, looking one way through hierarchy + // Cross collections: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { - if(cutmultisq[i][i] > cutmultisq[j][j]) continue; + if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutmultisq[i][i] == cutmultisq[j][j]){ + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ flag_half_multi[i][j] = 1; - bin_group_multi[i][j] = i; + bin_collection_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_group_multi[i][j] = j; + bin_collection_multi[i][j] = j; } } } @@ -61,42 +61,42 @@ void NStencilHalfMulti2d::set_stencil_properties() void NStencilHalfMulti2d::create() { - int igroup, jgroup, bin_group, i, j, ns; - int n = n_multi_groups; + int icollection, jcollection, bin_collection, i, j, ns; + int n = ncollections; double cutsq; - for (igroup = 0; igroup < n; igroup++) { - for (jgroup = 0; jgroup < n; jgroup++) { - if (flag_skip_multi[igroup][jgroup]) continue; + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - sx = stencil_sx_multi[igroup][jgroup]; - sy = stencil_sy_multi[igroup][jgroup]; + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; - mbinx = stencil_mbinx_multi[igroup][jgroup]; - mbiny = stencil_mbiny_multi[igroup][jgroup]; + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; - bin_group = bin_group_multi[igroup][jgroup]; + bin_collection = bin_collection_multi[icollection][jcollection]; - cutsq = cutmultisq[igroup][jgroup]; + cutsq = cutcollectionsq[icollection][jcollection]; - if (flag_half_multi[igroup][jgroup]) { + if (flag_half_multi[icollection][jcollection]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) if (j > 0 || (j == 0 && i > 0)) { - if (bin_distance_multi(i,j,0,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; } } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; } - nstencil_multi[igroup][jgroup] = ns; + nstencil_multi[icollection][jcollection] = ns; } } } diff --git a/src/nstencil_half_multi_2d_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp index 4a4e74c4a0..6588248109 100755 --- a/src/nstencil_half_multi_2d_tri.cpp +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti2dTri::NStencilHalfMulti2dTri(LAMMPS *lmp) : void NStencilHalfMulti2dTri::set_stencil_properties() { - int n = n_multi_groups; + int n = ncollections; int i, j; - // Cross groups: use full stencil, looking one way through hierarchy + // Cross collections: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { - if(cutmultisq[i][i] > cutmultisq[j][j]) continue; + if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutmultisq[i][i] == cutmultisq[j][j]){ + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ flag_half_multi[i][j] = 1; - bin_group_multi[i][j] = i; + bin_collection_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_group_multi[i][j] = j; + bin_collection_multi[i][j] = j; } } } @@ -61,40 +61,40 @@ void NStencilHalfMulti2dTri::set_stencil_properties() void NStencilHalfMulti2dTri::create() { - int igroup, jgroup, bin_group, i, j, ns; - int n = n_multi_groups; + int icollection, jcollection, bin_collection, i, j, ns; + int n = ncollections; double cutsq; - for (igroup = 0; igroup < n; igroup++) { - for (jgroup = 0; jgroup < n; jgroup++) { - if (flag_skip_multi[igroup][jgroup]) continue; + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - sx = stencil_sx_multi[igroup][jgroup]; - sy = stencil_sy_multi[igroup][jgroup]; + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; - mbinx = stencil_mbinx_multi[igroup][jgroup]; - mbiny = stencil_mbiny_multi[igroup][jgroup]; + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; - bin_group = bin_group_multi[igroup][jgroup]; + bin_collection = bin_collection_multi[icollection][jcollection]; - cutsq = cutmultisq[igroup][jgroup]; + cutsq = cutcollectionsq[icollection][jcollection]; - if (flag_half_multi[igroup][jgroup]) { + if (flag_half_multi[icollection][jcollection]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; } - nstencil_multi[igroup][jgroup] = ns; + nstencil_multi[icollection][jcollection] = ns; } } } diff --git a/src/nstencil_half_multi_3d.cpp b/src/nstencil_half_multi_3d.cpp index ad4970603c..19cd051392 100644 --- a/src/nstencil_half_multi_3d.cpp +++ b/src/nstencil_half_multi_3d.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti3d::NStencilHalfMulti3d(LAMMPS *lmp) : void NStencilHalfMulti3d::set_stencil_properties() { - int n = n_multi_groups; + int n = ncollections; int i, j; - // Cross groups: use full stencil, looking one way through hierarchy + // Cross collections: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { - if(cutmultisq[i][i] > cutmultisq[j][j]) continue; + if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutmultisq[i][i] == cutmultisq[j][j]){ + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ flag_half_multi[i][j] = 1; - bin_group_multi[i][j] = i; + bin_collection_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_group_multi[i][j] = j; + bin_collection_multi[i][j] = j; } } } @@ -61,48 +61,48 @@ void NStencilHalfMulti3d::set_stencil_properties() void NStencilHalfMulti3d::create() { - int igroup, jgroup, bin_group, i, j, k, ns; - int n = n_multi_groups; + int icollection, jcollection, bin_collection, i, j, k, ns; + int n = ncollections; double cutsq; - for (igroup = 0; igroup < n; igroup++) { - for (jgroup = 0; jgroup < n; jgroup++) { - if (flag_skip_multi[igroup][jgroup]) continue; + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - sx = stencil_sx_multi[igroup][jgroup]; - sy = stencil_sy_multi[igroup][jgroup]; - sz = stencil_sz_multi[igroup][jgroup]; + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; + sz = stencil_sz_multi[icollection][jcollection]; - mbinx = stencil_mbinx_multi[igroup][jgroup]; - mbiny = stencil_mbiny_multi[igroup][jgroup]; - mbinz = stencil_mbinz_multi[igroup][jgroup]; + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; + mbinz = stencil_mbinz_multi[icollection][jcollection]; - bin_group = bin_group_multi[igroup][jgroup]; + bin_collection = bin_collection_multi[icollection][jcollection]; - cutsq = cutmultisq[igroup][jgroup]; + cutsq = cutcollectionsq[icollection][jcollection]; - if (flag_half_multi[igroup][jgroup]) { + if (flag_half_multi[icollection][jcollection]) { 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_multi(i,j,k,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; } } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; } - nstencil_multi[igroup][jgroup] = ns; + nstencil_multi[icollection][jcollection] = ns; } } } diff --git a/src/nstencil_half_multi_3d_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp index 779f0865a5..3c5efac463 100755 --- a/src/nstencil_half_multi_3d_tri.cpp +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti3dTri::NStencilHalfMulti3dTri(LAMMPS *lmp) : void NStencilHalfMulti3dTri::set_stencil_properties() { - int n = n_multi_groups; + int n = ncollections; int i, j; - // Cross groups: use full stencil, looking one way through hierarchy + // Cross collections: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { - if(cutmultisq[i][i] > cutmultisq[j][j]) continue; + if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutmultisq[i][i] == cutmultisq[j][j]){ + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ flag_half_multi[i][j] = 1; - bin_group_multi[i][j] = i; + bin_collection_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_group_multi[i][j] = j; + bin_collection_multi[i][j] = j; } } } @@ -61,46 +61,46 @@ void NStencilHalfMulti3dTri::set_stencil_properties() void NStencilHalfMulti3dTri::create() { - int igroup, jgroup, bin_group, i, j, k, ns; - int n = n_multi_groups; + int icollection, jcollection, bin_collection, i, j, k, ns; + int n = ncollections; double cutsq; - for (igroup = 0; igroup < n; igroup++) { - for (jgroup = 0; jgroup < n; jgroup++) { - if (flag_skip_multi[igroup][jgroup]) continue; + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - sx = stencil_sx_multi[igroup][jgroup]; - sy = stencil_sy_multi[igroup][jgroup]; - sz = stencil_sz_multi[igroup][jgroup]; + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; + sz = stencil_sz_multi[icollection][jcollection]; - mbinx = stencil_mbinx_multi[igroup][jgroup]; - mbiny = stencil_mbiny_multi[igroup][jgroup]; - mbinz = stencil_mbinz_multi[igroup][jgroup]; + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; + mbinz = stencil_mbinz_multi[icollection][jcollection]; - bin_group = bin_group_multi[igroup][jgroup]; + bin_collection = bin_collection_multi[icollection][jcollection]; - cutsq = cutmultisq[igroup][jgroup]; + cutsq = cutcollectionsq[icollection][jcollection]; - if (flag_half_multi[igroup][jgroup]) { + if (flag_half_multi[icollection][jcollection]) { for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; } - nstencil_multi[igroup][jgroup] = ns; + nstencil_multi[icollection][jcollection] = ns; } } } diff --git a/src/pair.cpp b/src/pair.cpp index afc5eb2785..04aafbe863 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -63,6 +63,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp) one_coeff = 0; no_virial_fdotr_compute = 0; writedata = 0; + finitecutflag = 0; ghostneigh = 0; unit_convert_flag = utils::NOCONVERT; diff --git a/src/pair.h b/src/pair.h index 5801941458..3c6710229e 100644 --- a/src/pair.h +++ b/src/pair.h @@ -56,6 +56,7 @@ class Pair : protected Pointers { int unit_convert_flag; // value != 0 indicates support for unit conversion. int no_virial_fdotr_compute; // 1 if does not invoke virial_fdotr_compute() int writedata; // 1 if writes coeffs to data file + int finitecutflag; // 1 if cut depends on finite atom size int ghostneigh; // 1 if pair style needs neighbors of ghosts double **cutghost; // cutoff for each ghost pair @@ -205,6 +206,8 @@ class Pair : protected Pointers { virtual void min_xf_get(int) {} virtual void min_x_set(int) {} virtual void transfer_history(double *, double*) {} + virtual double atom2cut(int) {return 0.0;} + virtual double radii2cut(double,double) {return 0.0;} // management of callbacks to be run from ev_tally() diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 3026c9c741..e559e81f84 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -401,6 +401,7 @@ void PairHybrid::flags() if (styles[m]->dispersionflag) dispersionflag = 1; if (styles[m]->tip4pflag) tip4pflag = 1; if (styles[m]->compute_flag) compute_flag = 1; + if (styles[m]->finitecutflag) finitecutflag = 1; } single_enable = (single_enable == nstyles) ? 1 : 0; respa_enable = (respa_enable == nstyles) ? 1 : 0; @@ -1072,6 +1073,42 @@ int PairHybrid::check_ijtype(int itype, int jtype, char *substyle) return 0; } +/* ---------------------------------------------------------------------- + check if substyles calculate self-interaction range of particle +------------------------------------------------------------------------- */ + +double PairHybrid::atom2cut(int i) +{ + double temp, cut; + + cut = 0.0; + for (int m = 0; m < nstyles; m++) { + if (styles[m]->finitecutflag){ + temp = styles[m]->atom2cut(i); + if(temp > cut) cut = temp; + } + } + return cut; +} + +/* ---------------------------------------------------------------------- + check if substyles calculate maximum interaction range for two finite particles +------------------------------------------------------------------------- */ + +double PairHybrid::radii2cut(double r1, double r2) +{ + double temp, cut; + + cut = 0.0; + for (int m = 0; m < nstyles; m++) { + if (styles[m]->finitecutflag){ + temp = styles[m]->radii2cut(r1,r2); + if(temp > cut) cut = temp; + } + } + return cut; +} + /* ---------------------------------------------------------------------- memory usage of each sub-style ------------------------------------------------------------------------- */ diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index 7717d1fd51..9d10e91684 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -58,6 +58,8 @@ class PairHybrid : public Pair { virtual void add_tally_callback(class Compute *); virtual void del_tally_callback(class Compute *); + double atom2cut(int); + double radii2cut(double,double); protected: int nstyles; // # of sub-styles From 0676c953c033a8be591cbc22e7d30e8f9d0ea7d7 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 2 Feb 2021 09:41:50 -0700 Subject: [PATCH 48/73] Removing stray file --- src/init | 789 ------------------------------------------------------- 1 file changed, 789 deletions(-) delete mode 100644 src/init diff --git a/src/init b/src/init deleted file mode 100644 index 617c9effa3..0000000000 --- a/src/init +++ /dev/null @@ -1,789 +0,0 @@ -angle_charmm.cpp: if (comm->me == 0) { -angle_cosine.cpp: if (comm->me == 0) utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,nullptr,error); -angle_cosine_periodic.cpp: if (comm->me == 0) { -angle_cosine_squared.cpp: if (comm->me == 0) { -angle.cpp: memory->create(eatom,comm->nthreads*maxeatom,"angle:eatom"); -angle.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"angle:vatom"); -angle.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"angle:cvatom"); -angle.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); -angle.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); -angle.cpp: bytes += comm->nthreads*maxcvatom*9 * sizeof(double); -angle_deprecated.cpp: if (lmp->comm->me == 0) -angle_harmonic.cpp: if (comm->me == 0) { -angle_hybrid.cpp: const int nthreads = comm->nthreads; -angle_hybrid.cpp: if (comm->nthreads > 1) { -angle_hybrid.cpp: int me = comm->me; -angle_table.cpp: if (comm->me == 0) { -angle_zero.cpp: if (comm->me == 0) { -atom.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -atom.cpp: if (comm->myloc[0] == 0) sublo[0] -= epsilon[0]; -atom.cpp: if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += epsilon[0]; -atom.cpp: if (comm->myloc[1] == 0) sublo[1] -= epsilon[1]; -atom.cpp: if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += epsilon[1]; -atom.cpp: if (comm->myloc[2] == 0) sublo[2] -= epsilon[2]; -atom.cpp: if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += epsilon[2]; -atom.cpp: if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0]; -atom.cpp: if (comm->mysplit[0][1] == 1.0) subhi[0] += epsilon[0]; -atom.cpp: if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1]; -atom.cpp: if (comm->mysplit[1][1] == 1.0) subhi[1] += epsilon[1]; -atom.cpp: if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2]; -atom.cpp: if (comm->mysplit[2][1] == 1.0) subhi[2] += epsilon[2]; -atom.cpp: if (comm->me == 0) { -atom.cpp: called by comm->exchange() if atom_modify first group is set -atom.cpp: always called between comm->exchange() and comm->borders() -atom.cpp: if (comm->me == 0) -atom_map.cpp: int nper = static_cast (natoms/comm->nprocs); -atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); -atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); -atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); -atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); -atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); -atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); -atom_vec.cpp: f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f"); -atom_vec.cpp: const int nthreads = threads[i] ? comm->nthreads : 1; -atom_vec.cpp: bytes += memory->usage(f,nmax*comm->nthreads,3); -atom_vec.cpp: const int nthreads = threads[i] ? comm->nthreads : 1; -atom_vec_hybrid.cpp: if (mass_pertype && mass_peratom && comm->me == 0) -atom_vec_hybrid.cpp: if ((ptr && strstr(ptr+1,dup)) && (comm->me == 0)) -atom_vec_line.cpp: //if (comm->me == 1 && update->ntimestep == 873) -atom_vec_line.cpp: printf("BAD vecline ptrs: %s: %d %d: %d\n",str,comm->me, -atom_vec_line.cpp: str,comm->me,update->ntimestep,count,nlocal_bonus); -balance.cpp: int *procgrid = comm->procgrid; -balance.cpp: if (style == BISECTION && comm->style == 0) -balance.cpp: // init entire system since comm->setup is done -balance.cpp: comm->setup(); -balance.cpp: comm->exchange(); -balance.cpp: if (comm->layout == Comm::LAYOUT_TILED && style != BISECTION) { -balance.cpp: if (comm->layout == Comm::LAYOUT_UNIFORM) { -balance.cpp: comm->layout = Comm::LAYOUT_NONUNIFORM; -balance.cpp: } else if (comm->layout == Comm::LAYOUT_NONUNIFORM) { -balance.cpp: comm->layout = Comm::LAYOUT_UNIFORM; -balance.cpp: } else if (comm->layout == Comm::LAYOUT_TILED) { -balance.cpp: comm->layout = Comm::LAYOUT_UNIFORM; -balance.cpp: else comm->layout = Comm::LAYOUT_NONUNIFORM; -balance.cpp: comm->xsplit[i] = i * 1.0/procgrid[0]; -balance.cpp: comm->xsplit[procgrid[0]] = 1.0; -balance.cpp: for (int i = 0; i <= procgrid[0]; i++) comm->xsplit[i] = user_xsplit[i]; -balance.cpp: comm->ysplit[i] = i * 1.0/procgrid[1]; -balance.cpp: comm->ysplit[procgrid[1]] = 1.0; -balance.cpp: for (int i = 0; i <= procgrid[1]; i++) comm->ysplit[i] = user_ysplit[i]; -balance.cpp: comm->zsplit[i] = i * 1.0/procgrid[2]; -balance.cpp: comm->zsplit[procgrid[2]] = 1.0; -balance.cpp: for (int i = 0; i <= procgrid[2]; i++) comm->zsplit[i] = user_zsplit[i]; -balance.cpp: comm->layout = Comm::LAYOUT_NONUNIFORM; -balance.cpp: comm->layout = Comm::LAYOUT_TILED; -balance.cpp: for (int i = 0; i <= comm->procgrid[0]; i++) -balance.cpp: mesg += fmt::format(" {:.8}",comm->xsplit[i]); -balance.cpp: for (int i = 0; i <= comm->procgrid[1]; i++) -balance.cpp: mesg += fmt::format(" {:.8}",comm->ysplit[i]); -balance.cpp: for (int i = 0; i <= comm->procgrid[2]; i++) -balance.cpp: mesg += fmt::format(" {:.8}",comm->zsplit[i]); -balance.cpp: if (outflag && comm->me == 0) { -balance.cpp: comm->rcbnew = 1; -balance.cpp: if (idim >= 0) comm->rcbcutfrac = (rcb->cut - boxlo[idim]) / prd[idim]; -balance.cpp: else comm->rcbcutfrac = 0.0; -balance.cpp: comm->rcbcutdim = idim; -balance.cpp: double (*mysplit)[2] = comm->mysplit; -balance.cpp: int max = MAX(comm->procgrid[0],comm->procgrid[1]); -balance.cpp: max = MAX(max,comm->procgrid[2]); -balance.cpp: if (comm->layout == Comm::LAYOUT_TILED) { -balance.cpp: int *procgrid = comm->procgrid; -balance.cpp: double *xsplit = comm->xsplit; -balance.cpp: double *ysplit = comm->ysplit; -balance.cpp: double *zsplit = comm->zsplit; -balance.cpp: int *procgrid = comm->procgrid; -balance.cpp: split = comm->xsplit; -balance.cpp: split = comm->ysplit; -balance.cpp: split = comm->zsplit; -balance.cpp: double *xsplit = comm->xsplit; -balance.cpp: double *ysplit = comm->ysplit; -balance.cpp: double *zsplit = comm->zsplit; -balance.cpp: int nx = comm->procgrid[0]; -balance.cpp: int ny = comm->procgrid[1]; -balance.cpp: int nz = comm->procgrid[2]; -bond.cpp: memory->create(eatom,comm->nthreads*maxeatom,"bond:eatom"); -bond.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"bond:vatom"); -bond.cpp: if (comm->me == 0) { -bond.cpp: if (comm->me == 0) { -bond.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); -bond.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); -bond_deprecated.cpp: if (lmp->comm->me == 0) -bond_fene.cpp: if (comm->me == 0) -bond_fene.cpp: if (comm->me == 0) { -bond_fene_expand.cpp: if (comm->me == 0) -bond_fene_expand.cpp: if (comm->me == 0) { -bond_gromos.cpp: if (comm->me == 0) { -bond_harmonic.cpp: if (comm->me == 0) { -bond_hybrid.cpp: const int nthreads = comm->nthreads; -bond_hybrid.cpp: int me = comm->me; -bond_morse.cpp: if (comm->me == 0) { -bond_nonlinear.cpp: if (comm->me == 0) { -bond_quartic.cpp: if (comm->me == 0) { -bond_table.cpp: if (comm->me == 0) { -bond_zero.cpp: if (comm->me == 0) { -change_box.cpp: if (comm->me == 0) utils::logmesg(lmp,"Changing box ...\n"); -change_box.cpp: if (natoms != atom->natoms && comm->me == 0) -comm_brick.cpp: if (oldcomm->layout == Comm::LAYOUT_TILED) -comm_brick.cpp: layout = oldcomm->layout; -comm.cpp: if (oldcomm->grid2proc) { -comm.cpp: memcpy(&grid2proc[0][0][0],&oldcomm->grid2proc[0][0][0], -comm.cpp: memcpy(xsplit,oldcomm->xsplit,(procgrid[0]+1)*sizeof(double)); -comm.cpp: memcpy(ysplit,oldcomm->ysplit,(procgrid[1]+1)*sizeof(double)); -comm.cpp: memcpy(zsplit,oldcomm->zsplit,(procgrid[2]+1)*sizeof(double)); -comm.cpp: if (oldcomm->cutusermulti) { -comm.cpp: memcpy(cutusermulti,oldcomm->cutusermulti,ncollections); -comm.cpp: if (oldcomm->cutusermultiold) { -comm.cpp: memcpy(cutusermultiold,oldcomm->cutusermultiold,atom->ntypes+1); -comm.cpp: int n = strlen(oldcomm->customfile) + 1; -comm.cpp: strcpy(customfile,oldcomm->customfile); -comm.cpp: int n = strlen(oldcomm->outfile) + 1; -comm.cpp: strcpy(outfile,oldcomm->outfile); -comm_tiled.cpp: layout = oldcomm->layout; -compute_adf.cpp: if (mycutneigh > comm->cutghostuser) -compute_aggregate_atom.cpp: if (count > 1 && comm->me == 0) -compute_aggregate_atom.cpp: comm->forward_comm_compute(this); -compute_aggregate_atom.cpp: comm->forward_comm_compute(this); -compute_aggregate_atom.cpp: comm->reverse_comm_compute(this); -compute_bond_local.cpp: if (velflag && !comm->ghost_velocity) ghostvelflag = 1; -compute_bond_local.cpp: if (ghostvelflag && !initflag) comm->forward_comm_compute(this); -compute_centro_atom.cpp: if (count > 1 && comm->me == 0) -compute_centroid_stress_atom.cpp: comm->reverse_comm_compute(this); -compute_chunk_atom.cpp: int nprocs = comm->nprocs; -compute_chunk_atom.cpp: comm->ring(n,sizeof(int),list,1,idring,nullptr,(void *)this,0); -compute_chunk_atom.cpp: callback from comm->ring() -compute_chunk_atom.cpp: if (flagall && comm->me == 0) -compute_cluster_atom.cpp: if (count > 1 && comm->me == 0) -compute_cluster_atom.cpp: comm->forward_comm_compute(this); -compute_cluster_atom.cpp: comm->forward_comm_compute(this); -compute_cluster_atom.cpp: comm->forward_comm_compute(this); -compute_cna_atom.cpp: comm->me == 0) -compute_cna_atom.cpp: if (count > 1 && comm->me == 0) -compute_cna_atom.cpp: if (nerrorall && comm->me == 0) -compute_cna_atom.cpp: if (nerrorall && comm->me == 0) -compute_contact_atom.cpp: if (count > 1 && comm->me == 0) -compute_contact_atom.cpp: if (force->newton_pair) comm->reverse_comm_compute(this); -compute_coord_atom.cpp: comm->forward_comm_compute(this); -compute_deprecated.cpp: if (lmp->comm->me == 0) -compute_erotate_sphere_atom.cpp: if (count > 1 && comm->me == 0) -compute_fragment_atom.cpp: if (count > 1 && comm->me == 0) -compute_fragment_atom.cpp: comm->forward_comm_compute(this); -compute_fragment_atom.cpp: comm->forward_comm_compute(this); -compute_group_group.cpp: if ((fabs(e_correction) > SMALL) && (comm->me == 0)) -compute_hexorder_atom.cpp: if (count > 1 && comm->me == 0) -compute_ke_atom.cpp: if (count > 1 && comm->me == 0) -compute_orientorder_atom.cpp: if (count > 1 && comm->me == 0) -compute_pe_atom.cpp: comm->reverse_comm_compute(this); -compute_property_atom.cpp: int me = comm->me; -compute_rdf.cpp: cutghost = MAX(force->pair->cutforce+skin,comm->cutghostuser); -compute_rdf.cpp: cutghost = comm->cutghostuser; -compute_rdf.cpp: if (comm->me == 0) -compute_stress_atom.cpp: comm->reverse_comm_compute(this); -compute_temp_deform.cpp: comm->me == 0) -compute_temp_deform.cpp: if (i == modify->nfix && comm->me == 0) -create_atoms.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -create_atoms.cpp: if (comm->myloc[0] == 0) sublo[0] -= epsilon[0]; -create_atoms.cpp: if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0]; -create_atoms.cpp: if (comm->myloc[1] == 0) sublo[1] -= epsilon[1]; -create_atoms.cpp: if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*epsilon[1]; -create_atoms.cpp: if (comm->myloc[2] == 0) sublo[2] -= epsilon[2]; -create_atoms.cpp: if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*epsilon[2]; -create_atoms.cpp: if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0]; -create_atoms.cpp: if (comm->mysplit[0][1] == 1.0) subhi[0] -= 2.0*epsilon[0]; -create_atoms.cpp: if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1]; -create_atoms.cpp: if (comm->mysplit[1][1] == 1.0) subhi[1] -= 2.0*epsilon[1]; -create_atoms.cpp: if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2]; -create_atoms.cpp: if (comm->mysplit[2][1] == 1.0) subhi[2] -= 2.0*epsilon[2]; -create_bonds.cpp: // init entire system since comm->borders and neighbor->build is done -create_bonds.cpp: if (rmax > neighbor->cutneighmin && comm->me == 0) -create_bonds.cpp: comm->setup(); -create_bonds.cpp: comm->exchange(); -create_bonds.cpp: comm->borders(); -create_bonds.cpp: if (comm->me == 0) -create_box.cpp: comm->set_proc_grid(); -delete_atoms.cpp: } else if (comm->me == 0) -delete_atoms.cpp: if (comm->me == 0) { -delete_atoms.cpp: if (comm->me == 0) utils::logmesg(lmp,"System init for delete_atoms ...\n"); -delete_atoms.cpp: // init entire system since comm->borders and neighbor->build is done -delete_atoms.cpp: if (cut > neighbor->cutneighmin && comm->me == 0) -delete_atoms.cpp: comm->setup(); -delete_atoms.cpp: comm->exchange(); -delete_atoms.cpp: comm->borders(); -delete_atoms.cpp: RanMars *random = new RanMars(lmp,seed + comm->me); -delete_atoms.cpp: // pass list to all other procs via comm->ring() -delete_atoms.cpp: comm->ring(n,sizeof(tagint),list,1,bondring,nullptr,(void *)this); -delete_atoms.cpp: // pass list to all other procs via comm->ring() -delete_atoms.cpp: comm->ring(n,sizeof(tagint),list,1,molring,nullptr,(void *)this); -delete_atoms.cpp: callback from comm->ring() in delete_bond() -delete_atoms.cpp: callback from comm->ring() in delete_molecule() -delete_bonds.cpp: // init entire system since comm->borders is done -delete_bonds.cpp: if (comm->me == 0) utils::logmesg(lmp,"System init for delete_bonds ...\n"); -delete_bonds.cpp: if (comm->me == 0) utils::logmesg(lmp,"Deleting bonds ...\n"); -delete_bonds.cpp: comm->setup(); -delete_bonds.cpp: comm->exchange(); -delete_bonds.cpp: comm->borders(); -delete_bonds.cpp: if (comm->me == 0) { -deprecated.cpp: if (lmp->comm->me == 0) -deprecated.cpp: if (lmp->comm->me == 0) -dihedral_charmm.cpp: if (comm->me == 0) { -dihedral_charmmfsw.cpp: if (comm->me == 0) { -dihedral.cpp: memory->create(eatom,comm->nthreads*maxeatom,"dihedral:eatom"); -dihedral.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"dihedral:vatom"); -dihedral.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"dihedral:cvatom"); -dihedral.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); -dihedral.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); -dihedral.cpp: bytes += comm->nthreads*maxcvatom*9 * sizeof(double); -dihedral_deprecated.cpp: if (lmp->comm->me == 0) -dihedral_harmonic.cpp: if (comm->me == 0) { -dihedral_helix.cpp: if (comm->me == 0) { -dihedral_hybrid.cpp: int me = comm->me; -dihedral_multi_harmonic.cpp: if (comm->me == 0) { -dihedral_opls.cpp: if (comm->me == 0) { -displace_atoms.cpp: if (comm->me == 0) utils::logmesg(lmp,"Displacing atoms ...\n"); -displace_atoms.cpp: if (natoms != atom->natoms && comm->me == 0) -domain.cpp: else if (comm->me == 0) -domain.cpp: uses comm->xyz_split or comm->mysplit -domain.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -domain.cpp: int *myloc = comm->myloc; -domain.cpp: double *xsplit = comm->xsplit; -domain.cpp: double *ysplit = comm->ysplit; -domain.cpp: double *zsplit = comm->zsplit; -domain.cpp: double (*mysplit)[2] = comm->mysplit; -domain.cpp: uses comm->xyz_split or comm->mysplit -domain.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -domain.cpp: int *myloc = comm->myloc; -domain.cpp: int *procgrid = comm->procgrid; -domain.cpp: double *xsplit = comm->xsplit; -domain.cpp: double *ysplit = comm->ysplit; -domain.cpp: double *zsplit = comm->zsplit; -domain.cpp: double (*mysplit)[2] = comm->mysplit; -domain.cpp: comm->forward_comm_array(3,unwrap); -domain.cpp: if (flagall && comm->me == 0) -domain.cpp: if (all && comm->me == 0) -domain.cpp: if (all && comm->me == 0) -domain.cpp: if (flagall && comm->me == 0) -domain.cpp: since may lead to lost atoms in comm->exchange() -domain.cpp: if (flagall && comm->me == 0) -domain.cpp: if ((flag_all > 0) && (comm->me == 0)) -domain.cpp: if (comm->me == 0) { -dump_deprecated.cpp: if (lmp->comm->me == 0) -dump_image.cpp: comm->forward_comm_dump(this); -dump_movie.cpp: if ((comm->me == 0) && (fp == nullptr)) { -finish.cpp: const int nthreads = comm->nthreads; -fix_balance.cpp: if (lbstyle == BISECTION && comm->style == 0) -fix_balance.cpp: compute final imbalance factor based on nlocal after comm->exchange() -fix_balance.cpp: // invoke balancer and reset comm->uniform flag -fix_balance.cpp: comm->layout = Comm::LAYOUT_NONUNIFORM; -fix_balance.cpp: comm->layout = Comm::LAYOUT_TILED; -fix_balance.cpp: // since may lead to lost atoms in comm->exchange() -fix_balance.cpp: // else allow caller's comm->exchange() to do it -fix_balance.cpp: // b/c atoms may migrate again in comm->exchange() -fix_balance.cpp: // can only be done after atoms migrate in comm->exchange() -fix_box_relax.cpp: if (temperature->igroup != 0 && comm->me == 0) -fix_cmap.cpp: if (comm->me == 0) { -fix_cmap.cpp: if (comm->me == 0) -fix_cmap.cpp: if (comm->me == 0) fclose(fp); -fix_cmap.cpp: if (comm->me == 0) { -fix_deform.cpp: if (comm->me == 0) { -fix_deprecated.cpp: if (lmp->comm->me == 0) -fix_deprecated.cpp: if (lmp->comm->me == 0) -fix_dt_reset.cpp: strcmp(output->dump[i]->style,"xtc") == 0) && comm->me == 0) -fix_group.cpp: if (warn && comm->me == 0) -fix_halt.cpp: if (comm->me == 0 && msgflag == YESMSG) error->message(FLERR,message); -fix_langevin.cpp: random = new RanMars(lmp,seed + comm->me); -fix_langevin.cpp: if (temperature->igroup != igroup && comm->me == 0) -fix_move.cpp: if (comm->me == 0) { -fix_neigh_history.cpp: int nmypage = comm->nthreads; -fix_neigh_history.cpp: comm->reverse_comm_fix(this,0); -fix_neigh_history.cpp: comm->reverse_comm_fix_variable(this); -fix_neigh_history.cpp: int nmypage = comm->nthreads; -fix_neigh_history.cpp: if (comm->me == 0) { -fix_nh.cpp: if (comm->me == 0) { -fix_nh.cpp: if (temperature->igroup != 0 && comm->me == 0) -fix_nve_limit.cpp: if (comm->me == 0) -fix_pour.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -fix_pour.cpp: if (comm->myloc[2] == comm->procgrid[2]-1 && -fix_pour.cpp: if (comm->mysplit[2][1] == 1.0 && -fix_pour.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -fix_pour.cpp: if (comm->myloc[1] == comm->procgrid[1]-1 && -fix_pour.cpp: if (comm->mysplit[1][1] == 1.0 && -fix_press_berendsen.cpp: if (temperature->igroup != 0 && comm->me == 0) -fix_property_atom.cpp: if (flag && comm->me == 0) -fix_recenter.cpp: if (flag && comm->me == 0) -fix_restrain.cpp: comm->me,update->ntimestep)); -fix_restrain.cpp: comm->me,update->ntimestep)); -fix_restrain.cpp: comm->me,update->ntimestep)); -fix_restrain.cpp: comm->me,update->ntimestep)); -fix_restrain.cpp: ids[m][2],comm->me,update->ntimestep)); -fix_restrain.cpp: ids[m][2],comm->me,update->ntimestep)); -fix_restrain.cpp: ids[m][2],ids[m][3],comm->me, -fix_restrain.cpp: ids[m][2],ids[m][3],comm->me, -fix_restrain.cpp: comm->me,x[i1][0],x[i1][1],x[i1][2], -fix_restrain.cpp: comm->me,x[i2][0],x[i2][1],x[i2][2], -fix_restrain.cpp: comm->me,x[i3][0],x[i3][1],x[i3][2], -fix_restrain.cpp: comm->me,x[i4][0],x[i4][1],x[i4][2]); -fix_spring_chunk.cpp: if (comm->me == 0) { -fix_spring_chunk.cpp: if (comm->me == 0) -fix_spring_rg.cpp: if (comm->me == 0) { -fix_store.cpp: // PERATOM may be comm->exchanged before filled by caller -fix_store.cpp: if (comm->me == 0) { -fix_temp_berendsen.cpp: if (temperature->igroup != igroup && comm->me == 0) -fix_temp_berendsen.cpp: if (comm->me == 0) { -fix_temp_csld.cpp: random = new RanMars(lmp,seed + comm->me); -fix_temp_csld.cpp: if (temperature->igroup != igroup && comm->me == 0) -fix_temp_csld.cpp: int nsize = PRNGSIZE*comm->nprocs+2; // pRNG state per proc + nprocs + energy -fix_temp_csld.cpp: if (comm->me == 0) { -fix_temp_csld.cpp: list[1] = comm->nprocs; -fix_temp_csld.cpp: if (comm->me == 0) { -fix_temp_csld.cpp: if (nprocs != comm->nprocs) { -fix_temp_csld.cpp: if (comm->me == 0) -fix_temp_csld.cpp: } else random->set_state(list+2+comm->me*103); -fix_temp_csvr.cpp: random = new RanMars(lmp,seed + comm->me); -fix_temp_csvr.cpp: if (comm->me == 0) { -fix_temp_csvr.cpp: if (temperature->igroup != igroup && comm->me == 0) -fix_temp_csvr.cpp: int nsize = PRNGSIZE*comm->nprocs+2; // pRNG state per proc + nprocs + energy -fix_temp_csvr.cpp: if (comm->me == 0) { -fix_temp_csvr.cpp: list[1] = comm->nprocs; -fix_temp_csvr.cpp: if (comm->me == 0) { -fix_temp_csvr.cpp: if (nprocs != comm->nprocs) { -fix_temp_csvr.cpp: if (comm->me == 0) -fix_temp_csvr.cpp: } else random->set_state(list+2+comm->me*103); -fix_temp_rescale.cpp: if (temperature->igroup != igroup && comm->me == 0) -fix_temp_rescale.cpp: if (comm->me == 0) { -fix_wall_gran_region.cpp: if (comm->me) return; -fix_wall_reflect.cpp: if (nrigid && comm->me == 0) -force.cpp: if (comm->me == 0) { -group.cpp: // pass list to all other procs via comm->ring() -group.cpp: comm->ring(n,sizeof(tagint),list,1,molring,nullptr,(void *)this); -group.cpp: callback from comm->ring() -imbalance_neigh.cpp: if (comm->me == 0 && !did_warn) -improper.cpp: memory->create(eatom,comm->nthreads*maxeatom,"improper:eatom"); -improper.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"improper:vatom"); -improper.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"improper:cvatom"); -improper.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); -improper.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); -improper_cvff.cpp: if (comm->me == 0) { -improper_deprecated.cpp: if (lmp->comm->me == 0) -improper_harmonic.cpp: if (comm->me == 0) { -improper_hybrid.cpp: int me = comm->me; -improper_umbrella.cpp: if (comm->me == 0) { -info.cpp: if (comm->me != 0) return; -info.cpp: commstyles[comm->style], commlayout[comm->layout], -info.cpp: comm->ghost_velocity ? "yes" : "no"); -info.cpp: if (comm->mode == 0) -info.cpp: comm->get_comm_cutoff()); -info.cpp: if (comm->mode == 1) { -info.cpp: if (comm->cutusermulti) cut = MAX(cut,comm->cutusermulti[i]); -info.cpp: fmt::print(out,"Nprocs = {}, Nthreads = {}\n",comm->nprocs,comm->nthreads); -info.cpp: fmt::print(out,"Processor grid = {} x {} x {}\n",comm->procgrid[0], -info.cpp: comm->procgrid[1], comm->procgrid[2]); -info.cpp: style = commstyles[comm->style]; -info.cpp: bytes += comm->memory_usage(); -input.cpp: comm->modify_params(narg,arg); -input.cpp: if (comm->style == 0) return; -input.cpp: if (comm->style == 1) return; -input.cpp: comm->set_processors(narg,arg); -irregular.cpp: can be used in place of comm->exchange() -irregular.cpp: if (!preassign) comm->coord2proc_setup(); -irregular.cpp: mproclist[nsendatom] = comm->coord2proc(x[i],igx,igy,igz); -irregular.cpp: if not, caller can decide to use comm->exchange() instead -irregular.cpp: if (comm->layout == Comm::LAYOUT_TILED) return 1; -irregular.cpp: // cannot check via comm->procneigh since it ignores PBC -irregular.cpp: int *myloc = comm->myloc; -irregular.cpp: int *procgrid = comm->procgrid; -irregular.cpp: comm->coord2proc(x[i],igx,igy,igz); -kspace.cpp: if ((qsqsum == 0.0) && (comm->me == 0) && warn_nocharge && warning_flag) { -kspace.cpp: if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message); -kspace.cpp: if (comm->me == 0) { -kspace.cpp: if ((table_accuracy > spr) && (comm->me == 0)) -kspace.cpp: if (slab_volfactor < 2.0 && comm->me == 0) -kspace_deprecated.cpp: if (lmp->comm->me == 0) -lammps.cpp: const int me = comm->me; -lammps.cpp: comm->init(); // comm must come after force, modify, neighbor, atom -lattice.cpp: if (comm->me == 0) -library.cpp: && (lmp->comm->me == 0)) { -library.cpp: && (lmp->comm->me == 0)) { -library.cpp: lmp->comm->set_proc_grid(); -library.cpp: if (strcmp(keyword,"world_rank") == 0) return lmp->comm->me; -library.cpp: if (strcmp(keyword,"world_size") == 0) return lmp->comm->nprocs; -library.cpp: if (strcmp(keyword,"nthreads") == 0) return lmp->comm->nthreads; -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: int nprocs = lmp->comm->nprocs; -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: int nprocs = lmp->comm->nprocs; -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) lmp->error->warning(FLERR,msg); -min.cpp: if (comm->me == 0) -min.cpp: if (comm->me == 0 && screen) { -min.cpp: if (comm->me == 0 && screen) -min.cpp: comm->setup(); -min.cpp: comm->exchange(); -min.cpp: comm->borders(); -min.cpp: // atoms may have migrated in comm->exchange() -min.cpp: if (force->newton) comm->reverse_comm(); -min.cpp: comm->setup(); -min.cpp: comm->exchange(); -min.cpp: comm->borders(); -min.cpp: // atoms may have migrated in comm->exchange() -min.cpp: if (force->newton) comm->reverse_comm(); -min.cpp: comm->forward_comm(); -min.cpp: comm->setup(); -min.cpp: comm->exchange(); -min.cpp: comm->borders(); -min.cpp: comm->reverse_comm(); -min_fire.cpp: if (comm->me == 0 && logfile) { -modify.cpp: if (comm->me == 0 && checkall) -modify.cpp: if (fix[ifix]->igroup != igroup && comm->me == 0) -modify.cpp: if (comm->me == 0) -modify.cpp: if (comm->me == 0) -modify.cpp: int me = comm->me; -modify.cpp: int me = comm->me; -modify.cpp: if (flag && comm->me == 0) { -modify.cpp: if (flag && comm->me == 0) { -molecule.cpp: me = comm->me; -nbin_multi.cpp: // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost -nbin_multi.cpp: // include dimension-dependent extension via comm->cutghost -nbin_multi.cpp: double *cutghost = comm->cutghost; -nbin_standard.cpp: // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost -nbin_standard.cpp: // include dimension-dependent extension via comm->cutghost -nbin_standard.cpp: double *cutghost = comm->cutghost; -neighbor.cpp: if (!same && comm->me == 0) print_pairwise_info(); -neighbor.cpp: if (comm->me == 0) printf("SAME flag %d\n",same); -neighbor.cpp: const double cutghost = MAX(cutneighmax,comm->cutghostuser); -neigh_list.cpp: int nmypage = comm->nthreads; -neigh_list.cpp: if (comm->me != 0) return; -neigh_list.cpp: int nmypage = comm->nthreads; -ntopo.cpp: me = comm->me; -ntopo.cpp: nprocs = comm->nprocs; -output.cpp: if (thermo->modified && comm->me == 0) -output.cpp: if (strchr(arg[1],'%')) multiproc = comm->nprocs; -output.cpp: mbavg /= comm->nprocs; -output.cpp: if (comm->me == 0) -pair_beck.cpp: int me = comm->me; -pair_beck.cpp: int me = comm->me; -pair_born_coul_dsf.cpp: int me = comm->me; -pair_born_coul_dsf.cpp: if (comm->me == 0) { -pair_born_coul_wolf.cpp: int me = comm->me; -pair_born_coul_wolf.cpp: if (comm->me == 0) { -pair_born.cpp: int me = comm->me; -pair_born.cpp: if (comm->me == 0) { -pair_brownian.cpp: random = new RanMars(lmp,seed + comm->me); -pair_brownian.cpp: if (force->newton_pair == 0 && comm->me == 0) -pair_brownian.cpp: int me = comm->me; -pair_brownian.cpp: int me = comm->me; -pair_brownian.cpp: random = new RanMars(lmp,seed + comm->me); -pair_buck_coul_cut.cpp: int me = comm->me; -pair_buck_coul_cut.cpp: if (comm->me == 0) { -pair_buck.cpp: int me = comm->me; -pair_buck.cpp: if (comm->me == 0) { -pair_colloid.cpp: if (comm->me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); -pair_colloid.cpp: if (comm->me == 0) { -pair_colloid.cpp: int me = comm->me; -pair_coul_cut.cpp: int me = comm->me; -pair_coul_cut.cpp: if (comm->me == 0) { -pair_coul_debye.cpp: if (comm->me == 0) { -pair_coul_dsf.cpp: int me = comm->me; -pair_coul_dsf.cpp: if (comm->me == 0) { -pair_coul_streitz.cpp: if (comm->me == 0) { -pair_coul_streitz.cpp: if (comm->me != 0) { -pair_coul_wolf.cpp: int me = comm->me; -pair_coul_wolf.cpp: if (comm->me == 0) { -pair.cpp: if (tail_flag && domain->nonperiodic && comm->me == 0) -pair.cpp: if (!compute_flag && tail_flag && comm->me == 0) -pair.cpp: if (!compute_flag && offset_flag && comm->me == 0) -pair.cpp: if (flag && comm->me == 0) -pair.cpp: if (comm->me == 0) -pair.cpp: if (comm->me == 0) -pair.cpp: memory->create(eatom,comm->nthreads*maxeatom,"pair:eatom"); -pair.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"pair:vatom"); -pair.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"pair:cvatom"); -pair.cpp: if (comm->me == 0) { -pair.cpp: if ((comm->me == 0) && (epair)) -pair.cpp: if (comm->me == 0) -pair.cpp: if (comm->me == 0) fprintf(fp,"%d %.15g %.15g %.15g\n",i+1,r,e,f); -pair.cpp: if (comm->me == 0) fclose(fp); -pair.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); -pair.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); -pair.cpp: bytes += comm->nthreads*maxcvatom*9 * sizeof(double); -pair_deprecated.cpp: if (lmp->comm->me == 0) -pair_deprecated.cpp: if (lmp->comm->me == 0) -pair_dpd.cpp: random = new RanMars(lmp,seed + comm->me); -pair_dpd.cpp: if (comm->ghost_velocity == 0) -pair_dpd.cpp: if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR, -pair_dpd.cpp: int me = comm->me; -pair_dpd.cpp: if (comm->me == 0) { -pair_dpd.cpp: random = new RanMars(lmp,seed + comm->me); -pair_dpd_tstat.cpp: random = new RanMars(lmp,seed + comm->me); -pair_dpd_tstat.cpp: int me = comm->me; -pair_dpd_tstat.cpp: if (comm->me == 0) { -pair_dpd_tstat.cpp: random = new RanMars(lmp,seed + comm->me); -pair_gauss.cpp: int me = comm->me; -pair_gauss.cpp: if (comm->me == 0) { -pair_gran_hertz_history.cpp: comm->forward_comm_pair(this); -pair_gran_hooke.cpp: comm->forward_comm_pair(this); -pair_gran_hooke_history.cpp: comm->forward_comm_pair(this); -pair_gran_hooke_history.cpp: if (comm->ghost_velocity == 0) -pair_gran_hooke_history.cpp: int me = comm->me; -pair_gran_hooke_history.cpp: if (comm->me == 0) { -pair_granular.cpp: comm->forward_comm_pair(this); -pair_granular.cpp: if (comm->ghost_velocity == 0) -pair_granular.cpp: int me = comm->me; -pair_hybrid.cpp: int me = comm->me; -pair_lj96_cut.cpp: int me = comm->me; -pair_lj96_cut.cpp: int me = comm->me; -pair_lj_charmm_coul_charmm.cpp: int me = comm->me; -pair_lj_charmm_coul_charmm.cpp: if (comm->me == 0) { -pair_lj_charmmfsw_coul_charmmfsh.cpp: if ((comm->me == 0) && (force->qqr2e != force->qqr2e_charmm_real)) -pair_lj_charmmfsw_coul_charmmfsh.cpp: if ((comm->me == 0) && (force->qqr2e == force->qqr2e_charmm_real)) -pair_lj_charmmfsw_coul_charmmfsh.cpp: int me = comm->me; -pair_lj_charmmfsw_coul_charmmfsh.cpp: if (comm->me == 0) { -pair_lj_cubic.cpp: int me = comm->me; -pair_lj_cubic.cpp: int me = comm->me; -pair_lj_cut_coul_cut.cpp: int me = comm->me; -pair_lj_cut_coul_cut.cpp: if (comm->me == 0) { -pair_lj_cut_coul_debye.cpp: if (comm->me == 0) { -pair_lj_cut_coul_dsf.cpp: int me = comm->me; -pair_lj_cut_coul_dsf.cpp: if (comm->me == 0) { -pair_lj_cut_coul_wolf.cpp: int me = comm->me; -pair_lj_cut_coul_wolf.cpp: int me = comm->me; -pair_lj_cut.cpp: int me = comm->me; -pair_lj_cut.cpp: int me = comm->me; -pair_lj_cut_tip4p_cut.cpp: int me = comm->me; -pair_lj_cut_tip4p_cut.cpp: if (comm->me == 0) { -pair_lj_expand.cpp: int me = comm->me; -pair_lj_expand.cpp: if (comm->me == 0) { -pair_lj_gromacs_coul_gromacs.cpp: int me = comm->me; -pair_lj_gromacs_coul_gromacs.cpp: if (comm->me == 0) { -pair_lj_gromacs.cpp: int me = comm->me; -pair_lj_gromacs.cpp: int me = comm->me; -pair_lj_smooth.cpp: int me = comm->me; -pair_lj_smooth.cpp: int me = comm->me; -pair_lj_smooth_linear.cpp: int me = comm->me; -pair_lj_smooth_linear.cpp: int me = comm->me; -pair_lubricate.cpp: // no need to do this if not shearing since comm->ghost_velocity is set -pair_lubricate.cpp: comm->forward_comm_pair(this); -pair_lubricate.cpp: if (comm->ghost_velocity == 0) -pair_lubricate.cpp: int me = comm->me; -pair_lubricate.cpp: int me = comm->me; -pair_lubricate_poly.cpp: // no need to do this if not shearing since comm->ghost_velocity is set -pair_lubricate_poly.cpp: comm->forward_comm_pair(this); -pair_lubricate_poly.cpp: if (comm->ghost_velocity == 0) -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU.cpp: comm->forward_comm_pair(this); -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU.cpp: comm->forward_comm_pair(this); -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU.cpp: comm->forward_comm_pair(this); -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU.cpp: comm->forward_comm_pair(this); -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU.cpp: comm->forward_comm_pair(this); -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU.cpp: comm->forward_comm_pair(this); -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); // not really needed -pair_lubricateU.cpp: if (comm->ghost_velocity == 0) -pair_lubricateU.cpp: int me = comm->me; -pair_lubricateU.cpp: int me = comm->me; -pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU_poly.cpp: comm->forward_comm_pair(this); -pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU_poly.cpp: comm->forward_comm_pair(this); -pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU_poly.cpp: comm->forward_comm_pair(this); -pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); // not really needed -pair_lubricateU_poly.cpp: if (comm->ghost_velocity == 0) -pair_lubricateU_poly.cpp: if (!comm->me) { -pair_mie_cut.cpp: int me = comm->me; -pair_mie_cut.cpp: int me = comm->me; -pair_morse.cpp: int me = comm->me; -pair_morse.cpp: if (comm->me == 0) { -pair_soft.cpp: int me = comm->me; -pair_soft.cpp: if (comm->me == 0) { -pair_table.cpp: if (comm->me == 0) { -pair_tip4p_cut.cpp: int me = comm->me; -pair_tip4p_cut.cpp: if (comm->me == 0) { -pair_ufm.cpp: int me = comm->me; -pair_ufm.cpp: int me = comm->me; -pair_yukawa.cpp: int me = comm->me; -pair_yukawa.cpp: if (comm->me == 0) { -pair_zbl.cpp: int me = comm->me; -pair_zbl.cpp: int me = comm->me; -pair_zero.cpp: int me = comm->me; -pair_zero.cpp: int me = comm->me; -potential_file_reader.cpp: if (comm->me != 0) { -random_mars.cpp: //if (comm->me == 0) printf("%d %ld %ld %g %ld\n", -read_data.cpp: if (comm->nprocs == 1) n = static_cast (atom->natoms); -read_data.cpp: else n = static_cast (LB_FACTOR * atom->natoms / comm->nprocs); -read_data.cpp: comm->set_proc_grid(); -read_data.cpp: comm->set_proc_grid(); -read_data.cpp: // do comm->init() but not comm->setup() b/c pair/neigh cutoffs not yet set -read_data.cpp: // need call to map_set() b/c comm->exchange clears atom map -read_data.cpp: if (comm->me == 0) -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf); -read_data.cpp: int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf); -read_data.cpp: int eof = comm->read_lines_from_file(fp,nsq,MAXLINE,buf); -read_data.cpp: int eof = comm->read_lines_from_file(fp,nbondtypes,MAXLINE,buf); -read_data.cpp: int eof = comm->read_lines_from_file(fp,nangletypes,MAXLINE,buf); -read_data.cpp: int eof = comm->read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf); -read_data.cpp: int eof = comm->read_lines_from_file(fp,nimpropertypes,MAXLINE,buf); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_dump.cpp: comm->set_proc_grid(0); -read_restart.cpp: comm->set_proc_grid(); -read_restart.cpp: if (comm->me == 0) -read_restart.cpp: if (nprocs_file != comm->nprocs && me == 0) -read_restart.cpp: comm->nprocs)); -read_restart.cpp: if (comm->user_procgrid[0] != 0 && -read_restart.cpp: procgrid[0] != comm->user_procgrid[0]) flag = 1; -read_restart.cpp: if (comm->user_procgrid[1] != 0 && -read_restart.cpp: procgrid[1] != comm->user_procgrid[1]) flag = 1; -read_restart.cpp: if (comm->user_procgrid[2] != 0 && -read_restart.cpp: procgrid[2] != comm->user_procgrid[2]) flag = 1; -read_restart.cpp: if (comm->me ==0) -read_restart.cpp: comm->mode = read_int(); -read_restart.cpp: comm->cutghostuser = read_double(); -read_restart.cpp: comm->ghost_velocity = read_int(); -read_restart.cpp: if (comm->me ==0) -read_restart.cpp: if (comm->me ==0) -read_restart.cpp: if (comm->me ==0) -read_restart.cpp: if (comm->me ==0) -read_restart.cpp: if (comm->me ==0) -read_restart.cpp: if (comm->me ==0) -region_deprecated.cpp: if (lmp->comm->me == 0) -replicate.cpp: int me = comm->me; -replicate.cpp: int nprocs = comm->nprocs; -replicate.cpp: if (comm->me == 0) -replicate.cpp: comm->set_proc_grid(); -replicate.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -replicate.cpp: if (comm->myloc[0] == 0) sublo[0] -= epsilon[0]; -replicate.cpp: if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += epsilon[0]; -replicate.cpp: if (comm->myloc[1] == 0) sublo[1] -= epsilon[1]; -replicate.cpp: if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += epsilon[1]; -replicate.cpp: if (comm->myloc[2] == 0) sublo[2] -= epsilon[2]; -replicate.cpp: if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += epsilon[2]; -replicate.cpp: if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0]; -replicate.cpp: if (comm->mysplit[0][1] == 1.0) subhi[0] += epsilon[0]; -replicate.cpp: if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1]; -replicate.cpp: if (comm->mysplit[1][1] == 1.0) subhi[1] += epsilon[1]; -replicate.cpp: if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2]; -replicate.cpp: if (comm->mysplit[2][1] == 1.0) subhi[2] += epsilon[2]; -reset_atom_ids.cpp: if (comm->me == 0) utils::logmesg(lmp,"Resetting atom IDs ...\n"); -reset_atom_ids.cpp: // initialize system since comm->borders() will be invoked -reset_atom_ids.cpp: comm->setup(); -reset_atom_ids.cpp: comm->exchange(); -reset_atom_ids.cpp: comm->borders(); -reset_atom_ids.cpp: comm->forward_comm_array(1,newIDs); -reset_atom_ids.cpp: int me = comm->me; -reset_atom_ids.cpp: int nprocs = comm->nprocs; -reset_atom_ids.cpp: int nreturn = comm->rendezvous(1,nlocal,(char *) atombuf,sizeof(AtomRvous), -reset_atom_ids.cpp: // rptr->comm->me,i,n,in[i].ibin,binlo,binhi); -reset_atom_ids.cpp: // pass outbuf of IDRvous datums back to comm->rendezvous -reset_mol_ids.cpp: if (comm->me == 0) utils::logmesg(lmp,"Resetting molecule IDs ...\n"); -reset_mol_ids.cpp: // initialize system since comm->borders() will be invoked -reset_mol_ids.cpp: comm->setup(); -reset_mol_ids.cpp: comm->exchange(); -reset_mol_ids.cpp: comm->borders(); -reset_mol_ids.cpp: if (comm->me == 0) { -respa.cpp: if (comm->me == 0) { -respa.cpp: if (flag && comm->me == 0) -respa.cpp: if (modify->nfix == 0 && comm->me == 0) -respa.cpp: if (comm->me == 0 && screen) { -respa.cpp: comm->setup(); -respa.cpp: comm->exchange(); -respa.cpp: comm->borders(); -respa.cpp: if (newton[ilevel]) comm->reverse_comm(); -respa.cpp: comm->setup(); -respa.cpp: comm->exchange(); -respa.cpp: comm->borders(); -respa.cpp: if (newton[ilevel]) comm->reverse_comm(); -respa.cpp: comm->setup(); -respa.cpp: comm->exchange(); -respa.cpp: comm->borders(); -respa.cpp: comm->forward_comm(); -respa.cpp: comm->forward_comm(); -respa.cpp: comm->reverse_comm(); -set.cpp: if (comm->me == 0) utils::logmesg(lmp,"Setting atom values ...\n"); -set.cpp: if (comm->me == 0) { -set.cpp: RanMars *ranmars = new RanMars(lmp,seed + comm->me); -set.cpp: // init entire system since comm->exchange is done -set.cpp: if (comm->me == 0) utils::logmesg(lmp," system init for set ...\n"); -set.cpp: comm->setup(); -set.cpp: comm->exchange(); -set.cpp: comm->borders(); -special.cpp: comm->rendezvous(RVOUS,nlocal,(char *) idbuf,sizeof(IDRvous),0,proclist, -special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), -special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), -special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), -special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), -special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), -special.cpp: if (comm->me == 0) From 852e4efc6f5f9e3601d67b9742ebdab90cef983e Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 2 Feb 2021 14:50:30 -0700 Subject: [PATCH 49/73] Updating documentation/examples, patching comm_modify cutoff/multi command --- doc/src/comm_modify.rst | 54 ++++++++++++++++++++++++-------------- doc/src/neigh_modify.rst | 38 ++++++++++++++++++--------- doc/src/neighbor.rst | 6 ++--- examples/multi/in.colloid | 4 +-- examples/multi/in.granular | 2 +- src/comm.cpp | 20 +++++--------- src/comm.h | 2 ++ src/comm_brick.cpp | 26 +++++++++++++----- src/comm_tiled.cpp | 23 ++++++++++++---- 9 files changed, 113 insertions(+), 62 deletions(-) diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index a3f7dba4eb..489ab407ee 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -15,12 +15,15 @@ Syntax .. parsed-literal:: - *mode* value = *single* or *multi* = communicate atoms within a single or multiple distances + *mode* value = *single*, *multi*, or *multi/old* = communicate atoms within a single or multiple distances *cutoff* value = Rcut (distance units) = communicate atoms from this far away - *cutoff/multi* type value + *cutoff/multi* collection value + collection = atom collection or collection range (supports asterisk notation) + value = Rcut (distance units) = communicate atoms for selected types from this far away + *reduce/multi* arg = none = reduce number of communicated ghost atoms for multi style + *cutoff/multi/old* type value type = atom type or type range (supports asterisk notation) value = Rcut (distance units) = communicate atoms for selected types from this far away - *multi/reduce* arg = none = reduce number of communicated ghost atoms for multi style *group* value = group-ID = only communicate atoms in the group *vel* value = *yes* or *no* = do or do not communicate velocity info with ghost atoms @@ -29,7 +32,7 @@ Examples .. code-block:: LAMMPS - comm_modify mode multi + comm_modify mode multi reduce/multi comm_modify mode multi group solvent comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0 comm_modify vel yes @@ -63,13 +66,18 @@ sub-domain. The distance is by default the maximum of the neighbor cutoff across all atom type pairs. For many systems this is an efficient algorithm, but for systems with -widely varying cutoffs for different type pairs, the *multi* mode can -be faster. In this case, each atom type is assigned its own distance +widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can +be faster. In *multi*, each atom is assigned to a collection which should +correspond to a set of atoms with similar interaction cutoffs. +In this case, each atom collection is assigned its own distance cutoff for communication purposes, and fewer atoms will be -communicated. See the :doc:`neighbor multi ` command for a -neighbor list construction option that may also be beneficial for -simulations of this kind. The *multi* mode is compatable with both the -*multi* and *multi/old* neighbor styles. +communicated. in *multi/old*, a similar technique is used but atoms +are grouped by atom type. See the :doc:`neighbor multi ` and +:doc:`neighbor multi/old ` commands for +neighbor list construction options that may also be beneficial for +simulations of this kind. The *multi* communiction mode is only compatable +with the *multi* neighbor style. The *multi/old* communication mode is compatble +with both the *multi* and *multi/old* neighbor styles. The *cutoff* keyword allows you to extend the ghost cutoff distance for communication mode *single*\ , which is the distance from the borders @@ -89,18 +97,24 @@ warning is printed, if this bond based estimate is larger than the communication cutoff used. The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to -communication mode *multi* instead. Since in this case the communication -cutoffs are determined per atom type, a type specifier is needed and -cutoff for one or multiple types can be extended. Also ranges of types -using the usual asterisk notation can be given. For granular pair styles, -the default cutoff is set to the sum of the current maximum atomic radii -for each type. +communication mode *multi* instead. Since the communication +cutoffs are determined per atom collections, a collection specifier is needed and +cutoff for one or multiple collections can be extended. Also ranges of collections +using the usual asterisk notation can be given. +Note that the arguments for *cutoff/multi* are parsed right before each +simulation to account for potential changes in the number of collections. +Custom cutoffs are preserved between runs but if collections are redefined, +one may want to respecify communication cutoffs. +For granular pair styles,the default cutoff is set to the sum of the +current maximum atomic radii for each collection. +The *cutoff/multi/old* option is similar to *cutoff/multi* except it +operates on atom types as opposed to collections. -The *multi/reduce* option applies to *multi* and sets communication -cutoffs for different sized particles based on the largest interaction distance -between two particles in the same multi grouping. This reduces the number of +The *reduce/multi* option applies to *multi* and sets the communication +cutoff for a particle equal to the maximum interaction distance between particles +in the same collection. This reduces the number of ghost atoms that need to be communicated. This method is only compatible with the -*multi* neighbor style and requires only half neighbor lists and Newton on. +*multi* neighbor style and requires a half neighbor list and Newton on. See the :doc:`neighbor multi ` command for more information. These are simulation scenarios in which it may be useful or even diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index c6f573ef08..6ee21d7419 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -14,7 +14,7 @@ Syntax .. parsed-literal:: - keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *multi/custom* + keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *collection/type* or *collection/interval* *delay* value = N N = delay building until this many steps since last build *every* value = M @@ -47,9 +47,12 @@ Syntax N = max number of neighbors of one atom *binsize* value = size size = bin size for neighbor list construction (distance units) - *multi/custom* values = N arg1 ... argN - N = number of custom groups - arg = N separate types or ranges of types (see below) + *collection/type* values = N arg1 ... argN + N = number of custom collections + arg = N separate lists of types (see below) + *collection/interval* values = N arg1 ... argN + N = number of custom collections + arg = N separate cutoffs for intervals (see below) Examples """""""" @@ -61,7 +64,8 @@ Examples neigh_modify exclude group frozen frozen check no neigh_modify exclude group residue1 chain3 neigh_modify exclude molecule/intra rigid - neigh_modify multi/custom 2 1*2 3*4 + neigh_modify collection/type 2 1*2,5 3*4 + neigh_modify collection/interval 2 1.0 10.0 Description """"""""""" @@ -192,8 +196,9 @@ atom can have. The *binsize* option allows you to specify what size of bins will be used in neighbor list construction to sort and find neighboring atoms. By default, for :doc:`neighbor style bin `, LAMMPS uses bins -that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi `, the bins are 1/2 the size of the minimum pair -cutoff. Typically these are good values for minimizing the time for +that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi `, +the bins are 1/2 the size of the collection interaction cutoff. +Typically these are good values for minimizing the time for neighbor list construction. This setting overrides the default. If you make it too big, there is little overhead due to looping over bins, but more atoms are checked. If you make it too @@ -201,19 +206,28 @@ small, the optimal number of atoms is checked, but bin overhead goes up. If you set the binsize to 0.0, LAMMPS will use the default binsize of 1/2 the cutoff. -The *multi/custom* option allows you to define custom groups of atom +The *collection/type* option allows you to define custom collections of atom types for the *multi* neighbor mode. By grouping atom types with similar cutoffs, one may be able to improve performance by reducing -overhead. You must first specify the number of custom groups N to be -defined followed by N ranges of types. The range can be specified as a +overhead. You must first specify the number of custom collections N to be +defined followed by N lists of types. Each list consists of a series of type +ranges separated by commas. The range can be specified as a single numeric value, or a wildcard asterisk can be used to specify a range of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For example, if M = the number of atom types, then an asterisk with no numeric values means all types from 1 to M. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to M (inclusive). A middle asterisk means all types from m to n (inclusive). -Note that any atom types not included in a custom group will be automatically -placed within a separate group. +Note that all atom types must be included in a custom collection. + +The *collection/interval* option provides a similar capability. +This command allows a user to define custom collections by specifying a +series of cutoff intervals. LAMMPS will automatically sort atoms into these intervals +based on their type-dependent cutoffs or their finite size. +You must first specify the number of custom collections N to be +defined followed by N values representing the upper cutoff of each interval. +This command is particularly useful for granular pairstyles where the interaction distance +of particles depends on their radius and may not depend on their atom type. Restrictions """""""""""" diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index 52d59dae75..bd58f7045d 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -56,13 +56,13 @@ the largest cutoff distance between any pair of atom types and a single set of bins is defined to search over for all atom types. This can be inefficient if one pair of types has a very long cutoff, but other type pairs have a much shorter cutoff. The *multi* style uses -different sized bins for groups of different sized particles. Different +different sized bins for collections of different sized particles. Different sets of bins are then used to construct the neighbor lists as as further described by Shire, Hanley, and Stratford :ref:`(Shire) `. This imposes some extra setup overhead, but the searches themselves -may be much faster. By default, separate groups of particles are defined +may be much faster. By default, separate collections of particles are defined for each atom type. For systems with two or more types with similar -cutoffs, one can reduce the extra overhead by defining custom groupings +cutoffs, one can reduce the extra overhead by defining custom collections using the :doc:`neigh_modify ` command. See the :doc:`comm_modify mode bytype ` command for compatible communication options that may be beneficial for simulations of this kind. diff --git a/examples/multi/in.colloid b/examples/multi/in.colloid index b332560777..835032f2e2 100644 --- a/examples/multi/in.colloid +++ b/examples/multi/in.colloid @@ -30,8 +30,8 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency neighbor 1 multi #multi/old -neigh_modify delay 0 multi/custom 2 1*4 5 -comm_modify mode multi multi/reduce +neigh_modify delay 0 collection/type 2 1*4 5 +comm_modify mode multi reduce/multi # colloid potential diff --git a/examples/multi/in.granular b/examples/multi/in.granular index 8f1743f90d..f43e9505e4 100644 --- a/examples/multi/in.granular +++ b/examples/multi/in.granular @@ -29,7 +29,7 @@ velocity all create 1.44 87287 loop geom neighbor 1 multi #multi/old neigh_modify delay 0 -comm_modify mode multi vel yes multi/reduce +comm_modify mode multi vel yes reduce/multi # colloid potential diff --git a/src/comm.cpp b/src/comm.cpp index 3f2d4ecde6..c84f0249ef 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -35,7 +35,7 @@ #include "update.h" #include - +#include #ifdef _OPENMP #include #endif @@ -59,6 +59,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) cutghostuser = 0.0; cutusermulti = nullptr; cutusermultiold = nullptr; + ncollections_prior = 0; ghost_velocity = 0; user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0; @@ -339,24 +340,17 @@ void Comm::modify_params(int narg, char **arg) error->all(FLERR,"Use cutoff keyword to set cutoff in single mode"); if (mode == Comm::MULTIOLD) error->all(FLERR,"Use cutoff/multi/old keyword to set cutoff in multi/old mode"); - if (domain->box_exist == 0) + if (domain->box_exist == 0) error->all(FLERR, "Cannot set cutoff/multi before simulation box is defined"); - ncollections = neighbor->ncollections; - if (iarg+3 > narg) - error->all(FLERR,"Illegal comm_modify command"); - if (cutusermulti == nullptr) { - memory->create(cutusermulti,ncollections,"comm:cutusermulti"); - for (i=0; i < ncollections; ++i) - cutusermulti[i] = -1.0; - } - utils::bounds(FLERR,arg[iarg+1],1,ncollections,nlo,nhi,error); + + // save arguments so they can be parsed in comm->setup() + // ncollections can be changed by neigh_modify commands cut = utils::numeric(FLERR,arg[iarg+2],false,lmp); cutghostuser = MAX(cutghostuser,cut); if (cut < 0.0) error->all(FLERR,"Invalid cutoff in comm_modify command"); - for (i=nlo; i<=nhi; ++i) - cutusermulti[i] = cut; + usermultiargs.emplace_back(arg[iarg+1], cut); iarg += 3; } else if (strcmp(arg[iarg],"cutoff/multi/old") == 0) { int i,nlo,nhi; diff --git a/src/comm.h b/src/comm.h index 877941523c..2afdfd8765 100644 --- a/src/comm.h +++ b/src/comm.h @@ -33,6 +33,8 @@ class Comm : protected Pointers { double cutghost[3]; // cutoffs used for acquiring ghost atoms double cutghostuser; // user-specified ghost cutoff (mode == 0) double *cutusermulti; // per collection user ghost cutoff (mode == 1) + std::vector> usermultiargs; + // collection args for custom ghost cutoffs double *cutusermultiold; // per type user ghost cutoff (mode == 2) int recv_from_partition; // recv proc layout from this partition int send_to_partition; // send my proc layout to this partition diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index ca0fea8757..3cb841d20f 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -30,6 +30,7 @@ #include #include +#include using namespace LAMMPS_NS; @@ -194,12 +195,9 @@ void CommBrick::setup() if (mode == Comm::MULTI) { // build initial collection array - neighbor->build_collection(0); - - if(cutusermulti and ncollections != neighbor->ncollections) - error->all(FLERR, "Cannot change number of collections after defining comm_modify multi/cutoff"); - else ncollections = neighbor->ncollections; - + neighbor->build_collection(0); + ncollections = neighbor->ncollections; + // reallocate memory for multi-style communication at setup if ncollections change if(ncollections_prior != ncollections){ if(multilo) free_multi(); @@ -207,8 +205,24 @@ void CommBrick::setup() allocate_multi(maxswap); memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); + memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); + for(i = ncollections_prior; i < ncollections; i++) + cutusermulti[i] = -1.0; + ncollections_prior = ncollections; } + + // parse any cutoff/multi commands + int nhi, nlo; + for(auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { + utils::bounds(FLERR,it->first,1,ncollections,nlo,nhi,error); + if(nhi >= ncollections) + error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); + for (j=nlo; j<=nhi; ++j) + cutusermulti[j] = it->second; + } + usermultiargs.clear(); + double **cutcollectionsq = neighbor->cutcollectionsq; // If using multi/reduce, communicate particles a distance equal diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index accdbf7b04..c06ad52d6c 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -31,6 +31,7 @@ #include #include +#include using namespace LAMMPS_NS; @@ -182,12 +183,8 @@ void CommTiled::setup() if (mode == Comm::MULTI) { // build collection from scratch as it is needed for atom exchange neighbor->build_collection(0); - - if(cutusermulti and ncollections != neighbor->ncollections) - error->all(FLERR, "Cannot change number of collections after defining comm_modify multi/cutoff"); - ncollections = neighbor->ncollections; - + // allocate memory for multi-style communication at setup as ncollections can change if(ncollections_prior != ncollections){ memory->destroy(cutghostmulti); @@ -197,8 +194,24 @@ void CommTiled::setup() for(i = 0; i < maxswap; i ++) grow_swap_send_multi(i,DELTA_PROCS); + memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); + for(i = ncollections_prior; i < ncollections; i++) + cutusermulti[i] = -1.0; + ncollections_prior = ncollections; + } + + // parse any cutoff/multi commands + int nhi, nlo; + for(auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { + utils::bounds(FLERR,it->first,1,ncollections,nlo,nhi,error); + if(nhi >= ncollections) + error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); + + for (j=nlo; j<=nhi; ++j) + cutusermulti[j] = it->second; } + usermultiargs.clear(); double **cutcollectionsq = neighbor->cutcollectionsq; // If using multi/reduce, communicate particles a distance equal From 56841ba9123635e2da4302f4afb8ee7390231d39 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 2 Feb 2021 18:05:19 -0700 Subject: [PATCH 50/73] Fixing typo in pair gran, fixing bugs in communication and neighbor --- src/GRANULAR/pair_granular.cpp | 6 +++--- src/comm.cpp | 7 +++++++ src/neighbor.cpp | 2 +- src/nstencil.cpp | 1 + 4 files changed, 12 insertions(+), 4 deletions(-) diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 0f1fbd49f3..e9da16c760 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -1831,9 +1831,9 @@ double PairGranular::atom2cut(int i) cut = atom->radius[i]*2; if(beyond_contact) { - int itype = atom->type[i] + int itype = atom->type[i]; if(normal_model[itype][itype] == JKR) { - cut += pulloffdistance(cut, cut, itype, itype); + cut += pulloff_distance(cut, cut, itype, itype); } } @@ -1856,7 +1856,7 @@ double PairGranular::radii2cut(double r1, double r2) for(int i = 0; i < n; i++){ for(int j = 0; j < n; j++){ if(normal_model[i][j] == JKR) { - temp = pulloffdistance(r1, r2, i, j); + temp = pulloff_distance(r1, r2, i, j); if(temp > cut) cut = temp; } } diff --git a/src/comm.cpp b/src/comm.cpp index c84f0249ef..33e4b894d5 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -735,6 +735,13 @@ double Comm::get_comm_cutoff() maxcommcutoff)); } + // Check maximum interval size for neighbor multi + if(neighbor->interval_collection_flag){ + for(int i = 0; i < neighbor->ncollections; i++){ + maxcommcutoff = MAX(maxcommcutoff, neighbor->collection2cut[i]); + } + } + return maxcommcutoff; } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 16aca434f1..2671553a07 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -2655,7 +2655,7 @@ void Neighbor::build_collection(int istart) collection[i] = -1; for(icollection = 0; icollection < ncollections; icollection++){ - if(collection2cut[icollection] > cut) { + if(collection2cut[icollection] >= cut) { collection[i] = icollection; break; } diff --git a/src/nstencil.cpp b/src/nstencil.cpp index c6ed76b6eb..ca8c3156e3 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -354,6 +354,7 @@ void NStencil::create_setup() if (sy*binsizey_multi[bin_collection] < stencil_range) sy++; sz = static_cast (stencil_range*bininvz_multi[bin_collection]); if (sz*binsizez_multi[bin_collection] < stencil_range) sz++; + if (dimension == 2) sz = 0; stencil_sx_multi[i][j] = sx; stencil_sy_multi[i][j] = sy; From c94a740b4e5c3c800c0c30a6a26279c7cc0390c9 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Fri, 5 Feb 2021 16:43:52 -0700 Subject: [PATCH 51/73] Updating examples --- doc/src/Examples.rst | 2 + examples/multi/data.powerlaw | 20015 ++++++++++++++++ examples/multi/in.colloid | 2 +- examples/multi/in.granular | 16 +- examples/multi/in.powerlaw | 33 + examples/multi/log.30Nov20.colloid.intel.1 | 32 +- examples/multi/log.30Nov20.colloid.intel.4 | 30 +- .../multi/log.30Nov20.colloid.old.intel.1 | 30 +- .../multi/log.30Nov20.colloid.old.intel.4 | 32 +- examples/multi/log.30Nov20.granular.intel.1 | 142 +- examples/multi/log.30Nov20.granular.intel.4 | 150 +- .../multi/log.30Nov20.granular.old.intel.1 | 32 +- .../multi/log.30Nov20.granular.old.intel.4 | 34 +- examples/multi/log.30Nov20.powerlaw.intel.1 | 191 + examples/multi/log.30Nov20.powerlaw.intel.4 | 191 + src/nbin_multi.cpp | 5 +- 16 files changed, 20681 insertions(+), 256 deletions(-) create mode 100755 examples/multi/data.powerlaw create mode 100755 examples/multi/in.powerlaw create mode 100644 examples/multi/log.30Nov20.powerlaw.intel.1 create mode 100644 examples/multi/log.30Nov20.powerlaw.intel.4 diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 8a76dca66e..8bfc4ad573 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -108,6 +108,8 @@ Lowercase directories +-------------+------------------------------------------------------------------+ | msst | MSST shock dynamics | +-------------+------------------------------------------------------------------+ +| multi | multi neighboring for systems with large interaction disparities | ++-------------+------------------------------------------------------------------+ | nb3b | use of non-bonded 3-body harmonic pair style | +-------------+------------------------------------------------------------------+ | neb | nudged elastic band (NEB) calculation for barrier finding | diff --git a/examples/multi/data.powerlaw b/examples/multi/data.powerlaw new file mode 100755 index 0000000000..8d1239f18b --- /dev/null +++ b/examples/multi/data.powerlaw @@ -0,0 +1,20015 @@ +LAMMPS data file via write_data, version 24 Dec 2020, timestep = 400000 + +10000 atoms +1 atom types + +9.95143358025075 331.8139610404791 xlo xhi +9.95143358025075 331.8139610404791 ylo yhi +0 1 zlo zhi +0 0 0 xy xz yz + +Atoms # sphere + +5 1 53.3452 1 24.11983771564243 68.3864105656564 0 0 0 0 +16 1 27.0148 1 44.452300814629524 34.553717084559324 0 0 0 0 +17 1 25.5929 1 68.38354504971392 54.06475170935992 0 0 0 0 +37 1 16.0333 1 21.245215917793043 25.77572727368242 0 0 0 0 +8263 1 1.097 1 11.708192742157616 17.87628382394025 0 1 0 0 +3384 1 1.72 1 50.90886093789832 62.30285871322583 0 0 0 0 +1246 1 2.857 1 48.42720785177107 19.125614604813737 0 0 1 0 +163 1 7.4543 1 52.92059018138831 11.758077886663509 0 0 0 0 +166 1 7.4036 1 52.22842193013173 57.14032835838031 0 0 0 0 +168 1 7.3782 1 67.8997369874434 37.71308832601801 0 0 0 0 +6557 1 1.2369 1 11.295799175061966 44.30117186186906 0 1 0 0 +208 1 6.6527 1 61.1259176496811 36.19196224734089 0 0 0 0 +336 1 5.417 1 65.06953771853591 21.29750437142649 0 0 0 0 +346 1 5.3618 1 22.215439365950207 37.0147208031179 0 0 0 0 +5513 1 1.3496 1 57.12033179181392 10.64220332754185 0 0 0 0 +412 1 4.8776 1 17.672010595684508 40.11493119326499 0 0 0 0 +439 1 4.6882 1 71.11713930089661 21.10972952271469 0 0 0 0 +511 1 4.3207 1 61.99786200551653 15.7285378811011 0 0 0 0 +527 1 4.2767 1 51.578706654445845 20.727968822288982 0 0 0 0 +4272 1 1.5377 1 57.071595881584244 19.179812412376158 0 0 1 0 +543 1 4.2317 1 27.26359333718018 39.94157599264931 0 0 0 0 +562 1 4.1677 1 59.81433643375789 66.07528891967839 0 0 0 0 +567 1 4.1383 1 16.49975368111738 34.647919218460544 0 0 0 0 +569 1 4.1329 1 29.01334056124924 32.03678406685905 0 0 0 0 +600 1 4.0221 1 54.27815300580397 62.3600853316132 0 0 0 0 +5108 1 1.4029 1 73.73125627225376 19.677797581451607 0 0 0 0 +617 1 3.975 1 55.98574134419896 67.02182364027037 0 0 0 0 +629 1 3.9339 1 70.33990954744172 31.235263322465816 0 0 0 0 +632 1 3.927 1 59.10259779677181 20.90661579877451 0 0 0 0 +675 1 3.8345 1 67.43217050972282 25.075831741614678 0 0 0 0 +7224 1 1.1762 1 60.56971642466663 73.63795194238719 0 0 0 0 +781 1 3.6204 1 65.88843570308798 16.951378069907122 0 0 0 0 +816 1 3.5492 1 29.47255639818249 36.989781506165265 0 0 0 0 +818 1 3.5444 1 71.07247296695553 25.216862431845435 0 0 0 0 +826 1 3.5256 1 56.16977635130581 23.054438891951555 0 0 0 0 +839 1 3.4855 1 59.32150307446647 31.552032584430012 0 0 0 0 +844 1 3.4658 1 63.84742712072895 29.721610754958064 0 0 0 0 +848 1 3.4621 1 30.529974422317608 23.147962676957526 0 0 0 0 +917 1 3.3207 1 37.49425767354572 19.137889093582253 0 0 0 0 +924 1 3.3086 1 61.362409489439216 27.55964246321922 0 0 0 0 +936 1 3.2842 1 25.72506969645315 34.50534872289077 0 0 0 0 +980 1 3.2089 1 66.77355321573 31.18937461590332 0 0 0 0 +3643 1 1.6639 1 29.605676776639253 20.209519255093625 0 0 0 0 +7408 1 1.1605 1 13.145943365896626 22.862344767769148 0 1 0 0 +731 1 3.7184 1 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-3.0467620168779193e-05 +9094 0.000744625343311001 -0.00031967382357756246 0 0 0 2.526728571228735e-05 +2199 0.00042321437699091 2.592987440383578e-05 0 0 0 -8.18072673517025e-06 +1655 0.0007916395866808383 -0.00035457576070874246 0 0 0 -2.377735842840034e-05 +7207 0.0007452629981695557 -0.00015036527011953076 0 0 0 -0.00010872542216077849 +7875 0.0006585619246582422 3.7484154374812544e-05 0 0 0 0.00016718166745976926 +645 0.0006822356766865151 -0.00030148060339422317 0 0 0 9.296688489967334e-05 +9972 0.00036547266030541705 0.00014472173048552157 0 0 0 -3.0834187318466155e-05 +2113 0.0007081949702739137 -0.0007224063339711531 0 0 0 -3.8479080361991125e-05 +1412 -1.2039149567225154e-05 0.00010147738508380671 0 0 0 -0.00014286610388043424 +5701 0.0004761925580242084 5.147696238223329e-05 0 0 0 -0.00015663562454425414 +5800 0.0008450331921778463 -0.00033908595153051745 0 0 0 -3.0708573661039805e-05 diff --git a/examples/multi/in.colloid b/examples/multi/in.colloid index 835032f2e2..71987acbd6 100644 --- a/examples/multi/in.colloid +++ b/examples/multi/in.colloid @@ -31,7 +31,7 @@ velocity all create 1.44 87287 loop geom neighbor 1 multi #multi/old neigh_modify delay 0 collection/type 2 1*4 5 -comm_modify mode multi reduce/multi +comm_modify mode multi reduce/multi #multi/old # colloid potential diff --git a/examples/multi/in.granular b/examples/multi/in.granular index f43e9505e4..99e9ddfb33 100644 --- a/examples/multi/in.granular +++ b/examples/multi/in.granular @@ -1,4 +1,4 @@ -# Bidisperse set of grains +# Big colloid particles and small LJ particles units lj atom_style sphere @@ -28,10 +28,10 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency neighbor 1 multi #multi/old -neigh_modify delay 0 -comm_modify mode multi vel yes reduce/multi +neigh_modify delay 0 collection/interval 2 1 20 +comm_modify mode multi vel yes reduce/multi #multi/old -# colloid potential +# granular potential pair_style granular pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity @@ -42,14 +42,6 @@ fix 3 all deform 1 xy erate 1e-3 #dump 1 all custom 1000 dump.granular id x y z radius -#dump 2 all image 1000 image.*.jpg type type & -# zoom 1.5 center d 0.5 0.5 0.5 -#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 - -#dump 3 all movie 1000 movie.mpg type type & -# zoom 1.5 center d 0.5 0.5 0.5 -#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 - thermo_style custom step temp epair etotal press vol thermo 1000 diff --git a/examples/multi/in.powerlaw b/examples/multi/in.powerlaw new file mode 100755 index 0000000000..90fc7aae3c --- /dev/null +++ b/examples/multi/in.powerlaw @@ -0,0 +1,33 @@ +# Shear power-law distributed granular particles + +units lj +atom_style sphere +dimension 2 +read_data data.powerlaw +change_box all triclinic + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 +comm_modify mode multi vel yes reduce/multi + +# granular potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +# fixes + +fix 1 all nve/sphere +fix 2 all enforce2d +fix 3 all deform 1 xy erate 2e-4 + +# dump 1 all custom 2000 dump.granular id x y z radius + +thermo_style custom step temp epair etotal press vol pxy +thermo 1000 + +timestep 0.005 + +run 100000 diff --git a/examples/multi/log.30Nov20.colloid.intel.1 b/examples/multi/log.30Nov20.colloid.intel.1 index 2bc82eaab0..5dcb8c3bf1 100644 --- a/examples/multi/log.30Nov20.colloid.intel.1 +++ b/examples/multi/log.30Nov20.colloid.intel.1 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -53,9 +53,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi #/old -neigh_modify delay 0 multi/custom 2 1*4 5 -comm_modify mode multi multi/reduce +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/type 2 1*4 5 +comm_modify mode multi reduce/multi #multi/old # colloid potential @@ -72,7 +72,7 @@ pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 fix 2 all enforce2d -dump 1 all atom 1000 dump.colloid +#dump 1 all atom 1000 dump.colloid #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -98,7 +98,7 @@ Neighbor list info ... pair build: half/multi/newton stencil: half/multi/2d bin: multi -Per MPI rank memory allocation (min/avg/max) = 5.538 | 5.538 | 5.538 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.385 | 4.385 | 4.385 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395241 0.121 36000 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 @@ -151,20 +151,20 @@ Step Temp E_pair TotEng Press Volume 48000 2.0109636 -0.78968551 1.2206135 0.89458323 9496.7246 49000 2.0131059 -0.79687252 1.2155681 0.91239613 9418.3093 50000 2.0073361 -0.79981468 1.206858 0.98524334 9289.4715 -Loop time of 20.4651 on 1 procs for 50000 steps with 3026 atoms +Loop time of 19.7532 on 1 procs for 50000 steps with 3026 atoms -Performance: 1055453.279 tau/day, 2443.179 timesteps/s +Performance: 1093493.133 tau/day, 2531.234 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 11.099 | 11.099 | 11.099 | 0.0 | 54.23 -Neigh | 2.7536 | 2.7536 | 2.7536 | 0.0 | 13.46 -Comm | 0.53353 | 0.53353 | 0.53353 | 0.0 | 2.61 -Output | 0.11209 | 0.11209 | 0.11209 | 0.0 | 0.55 -Modify | 5.1627 | 5.1627 | 5.1627 | 0.0 | 25.23 -Other | | 0.8046 | | | 3.93 +Pair | 10.789 | 10.789 | 10.789 | 0.0 | 54.62 +Neigh | 2.6848 | 2.6848 | 2.6848 | 0.0 | 13.59 +Comm | 0.53244 | 0.53244 | 0.53244 | 0.0 | 2.70 +Output | 0.0010482 | 0.0010482 | 0.0010482 | 0.0 | 0.01 +Modify | 4.9599 | 4.9599 | 4.9599 | 0.0 | 25.11 +Other | | 0.7856 | | | 3.98 Nlocal: 3026.00 ave 3026 max 3026 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -180,4 +180,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:20 +Total wall time: 0:00:19 diff --git a/examples/multi/log.30Nov20.colloid.intel.4 b/examples/multi/log.30Nov20.colloid.intel.4 index 48a5846a09..906400df66 100644 --- a/examples/multi/log.30Nov20.colloid.intel.4 +++ b/examples/multi/log.30Nov20.colloid.intel.4 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -53,9 +53,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi #/old -neigh_modify delay 0 multi/custom 2 1*4 5 -comm_modify mode multi multi/reduce +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/type 2 1*4 5 +comm_modify mode multi reduce/multi #multi/old # colloid potential @@ -72,7 +72,7 @@ pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 fix 2 all enforce2d -dump 1 all atom 1000 dump.colloid +#dump 1 all atom 1000 dump.colloid #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -98,7 +98,7 @@ Neighbor list info ... pair build: half/multi/newton stencil: half/multi/2d bin: multi -Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.382 | 5.384 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.327 | 4.329 | 4.330 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395241 0.121 36000 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 @@ -151,20 +151,20 @@ Step Temp E_pair TotEng Press Volume 48000 2.0108204 -0.76655178 1.2436041 0.95379465 9633.6453 49000 1.9868193 -0.76613798 1.2200247 0.88790224 9504.2918 50000 2.0141467 -0.80029827 1.2131829 1.0064263 9346.3268 -Loop time of 7.28248 on 4 procs for 50000 steps with 3026 atoms +Loop time of 6.98615 on 4 procs for 50000 steps with 3026 atoms -Performance: 2966022.789 tau/day, 6865.793 timesteps/s +Performance: 3091831.080 tau/day, 7157.016 timesteps/s 99.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.1624 | 2.5918 | 2.9227 | 17.4 | 35.59 -Neigh | 0.62508 | 0.7436 | 0.83321 | 9.2 | 10.21 -Comm | 1.1035 | 1.5265 | 2.0746 | 29.3 | 20.96 -Output | 0.050094 | 0.050233 | 0.05062 | 0.1 | 0.69 -Modify | 1.8164 | 1.8966 | 1.9583 | 4.2 | 26.04 -Other | | 0.4737 | | | 6.50 +Pair | 2.2795 | 2.5856 | 2.9414 | 17.4 | 37.01 +Neigh | 0.62273 | 0.70156 | 0.76736 | 7.4 | 10.04 +Comm | 1.0765 | 1.4945 | 1.8884 | 28.6 | 21.39 +Output | 0.00076496 | 0.0008953 | 0.0012832 | 0.0 | 0.01 +Modify | 1.718 | 1.7755 | 1.827 | 3.7 | 25.41 +Other | | 0.4281 | | | 6.13 Nlocal: 756.500 ave 839 max 673 min Histogram: 1 0 1 0 0 0 0 1 0 1 diff --git a/examples/multi/log.30Nov20.colloid.old.intel.1 b/examples/multi/log.30Nov20.colloid.old.intel.1 index 291e8f89df..70c7db2afd 100644 --- a/examples/multi/log.30Nov20.colloid.old.intel.1 +++ b/examples/multi/log.30Nov20.colloid.old.intel.1 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -53,9 +53,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi/old +neighbor 1 multi/old #multi neigh_modify delay 0 #multi/custom 2 1*4 5 -comm_modify mode multi #multi/reduce +comm_modify mode multi/old #multi multi/reduce # colloid potential @@ -72,7 +72,7 @@ pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 fix 2 all enforce2d -dump 1 all atom 1000 dump.colloid +#dump 1 all atom 1000 dump.colloid #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -98,7 +98,7 @@ Neighbor list info ... pair build: half/multi/old/newton stencil: half/multi/old/2d bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.611 | 5.611 | 5.611 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.496 | 4.496 | 4.496 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395241 0.121 36000 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 @@ -151,20 +151,20 @@ Step Temp E_pair TotEng Press Volume 48000 2.0283587 -0.79063641 1.237052 0.83617499 9610.9933 49000 2.0051919 -0.79078067 1.2137485 0.95651813 9411.7165 50000 2.0140985 -0.81796958 1.1954634 0.93791038 9296.069 -Loop time of 29.8066 on 1 procs for 50000 steps with 3026 atoms +Loop time of 28.5339 on 1 procs for 50000 steps with 3026 atoms -Performance: 724671.093 tau/day, 1677.479 timesteps/s +Performance: 756994.490 tau/day, 1752.302 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 11.698 | 11.698 | 11.698 | 0.0 | 39.25 -Neigh | 10.292 | 10.292 | 10.292 | 0.0 | 34.53 -Comm | 1.405 | 1.405 | 1.405 | 0.0 | 4.71 -Output | 0.11474 | 0.11474 | 0.11474 | 0.0 | 0.38 -Modify | 5.3019 | 5.3019 | 5.3019 | 0.0 | 17.79 -Other | | 0.9947 | | | 3.34 +Pair | 10.918 | 10.918 | 10.918 | 0.0 | 38.26 +Neigh | 10.375 | 10.375 | 10.375 | 0.0 | 36.36 +Comm | 1.2856 | 1.2856 | 1.2856 | 0.0 | 4.51 +Output | 0.0010955 | 0.0010955 | 0.0010955 | 0.0 | 0.00 +Modify | 5.0132 | 5.0132 | 5.0132 | 0.0 | 17.57 +Other | | 0.9412 | | | 3.30 Nlocal: 3026.00 ave 3026 max 3026 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -180,4 +180,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:29 +Total wall time: 0:00:28 diff --git a/examples/multi/log.30Nov20.colloid.old.intel.4 b/examples/multi/log.30Nov20.colloid.old.intel.4 index 0eae8cc8e7..6d159d9405 100644 --- a/examples/multi/log.30Nov20.colloid.old.intel.4 +++ b/examples/multi/log.30Nov20.colloid.old.intel.4 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -53,9 +53,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi/old +neighbor 1 multi/old #multi neigh_modify delay 0 #multi/custom 2 1*4 5 -comm_modify mode multi #multi/reduce +comm_modify mode multi/old #multi multi/reduce # colloid potential @@ -72,7 +72,7 @@ pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 fix 2 all enforce2d -dump 1 all atom 1000 dump.colloid +#dump 1 all atom 1000 dump.colloid #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -98,7 +98,7 @@ Neighbor list info ... pair build: half/multi/old/newton stencil: half/multi/old/2d bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.438 | 5.441 | 5.444 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.404 | 4.406 | 4.410 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395241 0.121 36000 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 @@ -151,20 +151,20 @@ Step Temp E_pair TotEng Press Volume 48000 1.9977505 -0.77207122 1.225019 0.92107083 9647.1543 49000 2.0000901 -0.76254934 1.2368798 1.0320945 9536.2823 50000 2.0150929 -0.80463979 1.2097872 0.99556424 9324.0277 -Loop time of 11.239 on 4 procs for 50000 steps with 3026 atoms +Loop time of 10.7578 on 4 procs for 50000 steps with 3026 atoms -Performance: 1921872.705 tau/day, 4448.779 timesteps/s -98.0% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 2007847.166 tau/day, 4647.794 timesteps/s +98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.3936 | 2.7411 | 3.1078 | 16.7 | 24.39 -Neigh | 2.2948 | 2.6755 | 3.1013 | 18.5 | 23.81 -Comm | 2.522 | 3.3135 | 4.0361 | 31.7 | 29.48 -Output | 0.040863 | 0.041031 | 0.041456 | 0.1 | 0.37 -Modify | 1.844 | 1.9014 | 1.9701 | 3.4 | 16.92 -Other | | 0.5666 | | | 5.04 +Pair | 2.3814 | 2.6878 | 2.9507 | 15.2 | 24.98 +Neigh | 2.3959 | 2.6615 | 2.9677 | 16.2 | 24.74 +Comm | 2.4113 | 2.9894 | 3.5621 | 29.6 | 27.79 +Output | 0.00077024 | 0.00091029 | 0.0012971 | 0.0 | 0.01 +Modify | 1.7966 | 1.8497 | 1.907 | 3.8 | 17.19 +Other | | 0.5686 | | | 5.29 Nlocal: 756.500 ave 838 max 693 min Histogram: 2 0 0 0 0 0 0 1 0 1 @@ -180,4 +180,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:11 +Total wall time: 0:00:10 diff --git a/examples/multi/log.30Nov20.granular.intel.1 b/examples/multi/log.30Nov20.granular.intel.1 index 2e313231ca..06d02b8531 100644 --- a/examples/multi/log.30Nov20.granular.intel.1 +++ b/examples/multi/log.30Nov20.granular.intel.1 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -51,9 +51,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi #/old -neigh_modify delay 0 -comm_modify mode multi vel yes +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/interval 2 1 20 +comm_modify mode multi vel yes reduce/multi #multi/old # colloid potential @@ -64,7 +64,7 @@ fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 fix 2 all enforce2d fix 3 all deform 1 xy erate 1e-3 -dump 1 all custom 1000 dump.granular id x y z radius +#dump 1 all custom 1000 dump.granular id x y z radius #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -90,86 +90,86 @@ Neighbor list info ... pair build: half/size/multi/newton/tri stencil: half/multi/2d/tri bin: multi -Per MPI rank memory allocation (min/avg/max) = 11.78 | 11.78 | 11.78 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.29 | 10.29 | 10.29 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395623 0.66837658 7200 - 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 - 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 - 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 - 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 - 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 - 6000 0.025856 0 0.025848141 0.021241317 7603.5534 - 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 - 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 - 9000 0.016370159 0 0.016365184 0.020261904 6515.3445 - 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 - 11000 0.014156551 0 0.014152248 0.021324815 5815.4665 - 12000 0.013725406 0 0.013721235 0.021159958 5483.6304 - 13000 0.013215746 0 0.013211729 0.021685712 5165.4758 - 14000 0.012398153 0 0.012394384 0.024155434 4862.8657 - 15000 0.011842796 0 0.011839196 0.028503991 4577.9008 - 16000 0.011433182 0 0.011429706 0.033564839 4309.8792 - 17000 0.011166574 0 0.01116318 0.040592677 4058.9964 - 18000 0.01100067 0 0.010997326 0.04899206 3825.155 - 19000 0.010224474 0 0.010221366 0.063670337 3607.6577 - 20000 0.0091360559 0 0.0091332789 0.088230111 3408.5658 - 21000 0.007733647 0 0.0077312964 0.11769368 3227.7002 - 22000 0.0060202358 0 0.0060184059 0.15272491 3064.3986 - 23000 0.004670574 0 0.0046691543 0.19450724 2918.0014 - 24000 0.0040248313 0 0.004023608 0.24161742 2788.4113 - 25000 0.0032075275 0 0.0032065526 0.2897693 2674.5604 - 26000 0.0021358024 0 0.0021351532 0.33635617 2574.9564 - 27000 0.0016902752 0 0.0016897614 0.37624266 2487.2379 - 28000 0.0014038218 0 0.0014033951 0.41492104 2409.2461 - 29000 0.00090262506 0 0.0009023507 0.45392905 2340.0308 - 30000 0.00049466342 0 0.00049451306 0.49295072 2279.2316 - 31000 0.00056998139 0 0.00056980815 0.53299515 2226.5683 - 32000 0.00057326945 0 0.0005730952 0.56856537 2181.7092 - 33000 0.00044845112 0 0.00044831481 0.59623471 2142.7573 - 34000 0.00059840183 0 0.00059821994 0.61758983 2107.1253 - 35000 0.00075310993 0 0.00075288103 0.63756827 2072.7217 - 36000 0.00053774066 0 0.00053757721 0.66026064 2039.1655 - 37000 0.00030440106 0 0.00030430853 0.69059102 2007.7903 - 38000 0.00034436264 0 0.00034425797 0.72166344 1980.7137 - 39000 0.00039693498 0 0.00039681433 0.74680327 1957.9531 - 40000 0.00035425567 0 0.000354148 0.76604186 1937.3834 - 41000 0.0003094733 0 0.00030937924 0.78323163 1916.7027 - 42000 0.00027259246 0 0.0002725096 0.80315535 1895.0714 - 43000 0.00020659817 0 0.00020653538 0.8274603 1873.5407 - 44000 0.00016023333 0 0.00016018463 0.85418969 1853.8674 - 45000 0.00016111931 0 0.00016107034 0.87913944 1837.1141 - 46000 0.00016130888 0 0.00016125985 0.89921705 1822.7354 - 47000 0.00015755049 0 0.0001575026 0.91653538 1809.0285 - 48000 0.00017794781 0 0.00017789372 0.93582908 1794.7041 - 49000 0.00018878437 0 0.00018872699 0.95775203 1780.032 - 50000 0.0001778042 0 0.00017775016 0.97893714 1765.9439 -Loop time of 77.4487 on 1 procs for 50000 steps with 3290 atoms + 1000 0.32604952 0 0.32595042 0.17341597 7862.5013 + 2000 0.12631038 0 0.12627198 0.069126477 8216.6956 + 3000 0.069351715 0 0.069330635 0.040799593 8344.1931 + 4000 0.045023755 0 0.04501007 0.029184795 8239.1832 + 5000 0.032735149 0 0.0327252 0.025640841 7943.5691 + 6000 0.026205227 0 0.026197262 0.021206924 7617.6672 + 7000 0.02165475 0 0.021648168 0.018789365 7255.2897 + 8000 0.018299317 0 0.018293755 0.019272158 6887.3386 + 9000 0.016283763 0 0.016278813 0.020434892 6524.0274 + 10000 0.015148918 0 0.015144313 0.021650465 6168.4941 + 11000 0.014180465 0 0.014176155 0.022320009 5823.98 + 12000 0.013505744 0 0.013501639 0.023978674 5492.4853 + 13000 0.013009585 0 0.01300563 0.024391329 5175.7455 + 14000 0.012494373 0 0.012490576 0.027331543 4874.3212 + 15000 0.012057669 0 0.012054004 0.030561239 4589.518 + 16000 0.011510988 0 0.01150749 0.034613772 4321.1694 + 17000 0.011198594 0 0.01119519 0.042263536 4070.0115 + 18000 0.010978603 0 0.010975266 0.053637275 3836.0304 + 19000 0.010768789 0 0.010765516 0.069472547 3619.75 + 20000 0.0102256 0 0.010222492 0.085332898 3420.2738 + 21000 0.0089630315 0 0.0089603072 0.11199196 3236.9821 + 22000 0.006565581 0 0.0065635854 0.14807426 3071.3012 + 23000 0.0050916998 0 0.0050901522 0.1903446 2923.4162 + 24000 0.0040345997 0 0.0040333734 0.237983 2792.2658 + 25000 0.0032995328 0 0.0032985299 0.29120001 2677.7475 + 26000 0.0024157863 0 0.002415052 0.33851944 2578.4972 + 27000 0.0020664445 0 0.0020658164 0.37561848 2491.0264 + 28000 0.0017843883 0 0.0017838459 0.41119961 2412.3871 + 29000 0.0011813262 0 0.0011809672 0.44749341 2341.7208 + 30000 0.00063084711 0 0.00063065536 0.4879202 2279.0452 + 31000 0.00056027405 0 0.00056010376 0.52932126 2224.9456 + 32000 0.00053304715 0 0.00053288513 0.56822504 2179.1224 + 33000 0.00052245707 0 0.00052229826 0.60025509 2140.5345 + 34000 0.00073726189 0 0.0007370378 0.62001489 2106.3045 + 35000 0.00075804791 0 0.0007578175 0.6359631 2072.525 + 36000 0.00052579203 0 0.00052563222 0.65678516 2038.1907 + 37000 0.00036977909 0 0.0003696667 0.68784389 2005.5831 + 38000 0.00036252798 0 0.00036241779 0.72116044 1977.7441 + 39000 0.00036254566 0 0.00036243547 0.74720837 1954.9127 + 40000 0.00036237175 0 0.00036226161 0.76605408 1934.6006 + 41000 0.00032453104 0 0.00032443239 0.78424188 1914.1939 + 42000 0.00025394755 0 0.00025387036 0.80529272 1893.064 + 43000 0.00021067821 0 0.00021061418 0.82962095 1872.365 + 44000 0.00017927684 0 0.00017922235 0.85522899 1853.531 + 45000 0.0001464225 0 0.000146378 0.87925998 1837.2423 + 46000 0.00012922979 0 0.00012919051 0.8986549 1822.9227 + 47000 0.0001643557 0 0.00016430575 0.91743602 1809.0605 + 48000 0.00020154753 0 0.00020148627 0.93686779 1794.9227 + 49000 0.00017742528 0 0.00017737135 0.94988773 1780.3811 + 50000 0.00015150521 0 0.00015145916 0.97929588 1764.7507 +Loop time of 54.9135 on 1 procs for 50000 steps with 3290 atoms -Performance: 278894.354 tau/day, 645.589 timesteps/s +Performance: 393345.914 tau/day, 910.523 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 60.017 | 60.017 | 60.017 | 0.0 | 77.49 -Neigh | 0.47 | 0.47 | 0.47 | 0.0 | 0.61 -Comm | 6.6765 | 6.6765 | 6.6765 | 0.0 | 8.62 -Output | 0.24799 | 0.24799 | 0.24799 | 0.0 | 0.32 -Modify | 8.8677 | 8.8677 | 8.8677 | 0.0 | 11.45 -Other | | 1.17 | | | 1.51 +Pair | 44.691 | 44.691 | 44.691 | 0.0 | 81.38 +Neigh | 0.21653 | 0.21653 | 0.21653 | 0.0 | 0.39 +Comm | 0.75388 | 0.75388 | 0.75388 | 0.0 | 1.37 +Output | 0.0011999 | 0.0011999 | 0.0011999 | 0.0 | 0.00 +Modify | 8.4718 | 8.4718 | 8.4718 | 0.0 | 15.43 +Other | | 0.7794 | | | 1.42 Nlocal: 3290.00 ave 3290 max 3290 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 6295.00 ave 6295 max 6295 min +Nghost: 525.000 ave 525 max 525 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 53729.0 ave 53729 max 53729 min +Neighs: 26732.0 ave 26732 max 26732 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 53729 -Ave neighs/atom = 16.331003 -Neighbor list builds = 348 +Total # of neighbors = 26732 +Ave neighs/atom = 8.1252280 +Neighbor list builds = 342 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:01:17 +Total wall time: 0:00:54 diff --git a/examples/multi/log.30Nov20.granular.intel.4 b/examples/multi/log.30Nov20.granular.intel.4 index d53684c596..3aa05d79c7 100644 --- a/examples/multi/log.30Nov20.granular.intel.4 +++ b/examples/multi/log.30Nov20.granular.intel.4 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -52,8 +52,8 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency neighbor 1 multi #multi/old -neigh_modify delay 0 -comm_modify mode multi vel yes multi/reduce +neigh_modify delay 0 collection/interval 2 1 20 +comm_modify mode multi vel yes reduce/multi #multi/old # colloid potential @@ -64,7 +64,7 @@ fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 fix 2 all enforce2d fix 3 all deform 1 xy erate 1e-3 -dump 1 all custom 1000 dump.granular id x y z radius +#dump 1 all custom 1000 dump.granular id x y z radius #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -90,86 +90,86 @@ Neighbor list info ... pair build: half/size/multi/newton/tri stencil: half/multi/2d/tri bin: multi -Per MPI rank memory allocation (min/avg/max) = 11.33 | 11.33 | 11.33 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.09 | 10.10 | 10.10 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395623 0.66837658 7200 - 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 - 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 - 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 - 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 - 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 - 6000 0.025856 0 0.025848141 0.021241317 7603.5534 - 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 - 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 - 9000 0.01637016 0 0.016365184 0.020261904 6515.3445 - 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 - 11000 0.014156553 0 0.01415225 0.021324818 5815.4665 - 12000 0.013725412 0 0.01372124 0.021159958 5483.6304 - 13000 0.013215733 0 0.013211716 0.021685624 5165.4758 - 14000 0.012398179 0 0.012394411 0.024155572 4862.8657 - 15000 0.01184269 0 0.01183909 0.028504106 4577.901 - 16000 0.01143291 0 0.011429435 0.033564204 4309.88 - 17000 0.011166204 0 0.01116281 0.040588854 4058.9972 - 18000 0.011000875 0 0.010997532 0.048998904 3825.1569 - 19000 0.010225905 0 0.010222797 0.063669586 3607.6622 - 20000 0.0091390249 0 0.0091362471 0.088165396 3408.567 - 21000 0.0077382016 0 0.0077358496 0.11770473 3227.6936 - 22000 0.0060173113 0 0.0060154823 0.15261992 3064.3873 - 23000 0.0046667554 0 0.004665337 0.19453813 2917.9782 - 24000 0.0040425764 0 0.0040413476 0.24145834 2788.3897 - 25000 0.0031933187 0 0.0031923481 0.28989732 2674.5164 - 26000 0.0021139018 0 0.0021132592 0.33598721 2574.9313 - 27000 0.0017005052 0 0.0016999884 0.37665029 2487.1628 - 28000 0.001443434 0 0.0014429952 0.41572112 2409.3271 - 29000 0.00089885805 0 0.00089858484 0.45343123 2340.2314 - 30000 0.00048558336 0 0.00048543577 0.49175966 2279.2156 - 31000 0.00058132898 0 0.00058115228 0.53236819 2226.2347 - 32000 0.00057751441 0 0.00057733887 0.56915062 2181.2736 - 33000 0.00044720497 0 0.00044706904 0.59696122 2142.5709 - 34000 0.00060927898 0 0.00060909379 0.61734988 2107.128 - 35000 0.00077422577 0 0.00077399045 0.63696024 2072.6004 - 36000 0.00055753008 0 0.00055736062 0.65981839 2038.8237 - 37000 0.0003140158 0 0.00031392035 0.69018918 2007.323 - 38000 0.00034970199 0 0.0003495957 0.72155094 1980.1702 - 39000 0.00041435514 0 0.00041422919 0.7468053 1957.3837 - 40000 0.00037229543 0 0.00037218227 0.76581519 1936.8032 - 41000 0.00031027679 0 0.00031018248 0.78321128 1916.1103 - 42000 0.00026621832 0 0.00026613741 0.80267694 1894.4646 - 43000 0.00020544063 0 0.00020537818 0.82714181 1872.768 - 44000 0.00015635243 0 0.00015630491 0.85496512 1853.0303 - 45000 0.00014985611 0 0.00014981056 0.87924561 1836.4779 - 46000 0.00015645346 0 0.00015640591 0.89896131 1822.2004 - 47000 0.00016007816 0 0.00016002951 0.91662026 1808.4601 - 48000 0.00017439363 0 0.00017434063 0.93565314 1794.1244 - 49000 0.00018647711 0 0.00018642043 0.95733125 1779.401 - 50000 0.00018463414 0 0.00018457802 0.96449755 1765.1506 -Loop time of 22.3987 on 4 procs for 50000 steps with 3290 atoms + 1000 0.32605303 0 0.32595393 0.17341558 7862.5037 + 2000 0.12631567 0 0.12627728 0.069188881 8216.7174 + 3000 0.069373812 0 0.069352726 0.040740832 8344.2982 + 4000 0.045084633 0 0.045070929 0.029328609 8239.3656 + 5000 0.032681746 0 0.032671813 0.025416741 7943.7831 + 6000 0.026301239 0 0.026293245 0.021418793 7617.8426 + 7000 0.021666723 0 0.021660138 0.018961011 7255.9338 + 8000 0.018141337 0 0.018135823 0.019306113 6887.4963 + 9000 0.015922309 0 0.015917469 0.020033398 6524.016 + 10000 0.014744547 0 0.014740066 0.020959503 6168.1945 + 11000 0.013872852 0 0.013868636 0.021708943 5823.3153 + 12000 0.013321594 0 0.013317545 0.02332141 5491.4979 + 13000 0.01269964 0 0.012695779 0.024796428 5174.6263 + 14000 0.01227055 0 0.012266821 0.027785072 4873.4516 + 15000 0.012120508 0 0.012116824 0.029656636 4588.8603 + 16000 0.011612027 0 0.011608498 0.034695109 4320.4674 + 17000 0.011216697 0 0.011213288 0.042746966 4069.4275 + 18000 0.010950166 0 0.010946838 0.053528994 3835.5439 + 19000 0.010887635 0 0.010884325 0.069684492 3619.562 + 20000 0.010563449 0 0.010560238 0.08654561 3420.2636 + 21000 0.0092336323 0 0.0092308257 0.11286068 3237.1408 + 22000 0.006929086 0 0.0069269799 0.15018917 3072.0438 + 23000 0.0052239156 0 0.0052223277 0.19067193 2924.441 + 24000 0.0044210081 0 0.0044196644 0.23908686 2793.2426 + 25000 0.0034916086 0 0.0034905473 0.29112824 2678.7912 + 26000 0.002549072 0 0.0025482972 0.33567824 2579.3738 + 27000 0.0020890726 0 0.0020884377 0.37328514 2491.0502 + 28000 0.001772982 0 0.0017724431 0.41079958 2411.9111 + 29000 0.001127719 0 0.0011273762 0.44752241 2341.1888 + 30000 0.00053266563 0 0.00053250373 0.48791815 2278.5611 + 31000 0.00050278646 0 0.00050263364 0.52896525 2224.5328 + 32000 0.00051880956 0 0.00051865187 0.56884574 2178.6674 + 33000 0.00054908167 0 0.00054891477 0.6016387 2140.3696 + 34000 0.00075213884 0 0.00075191023 0.62070188 2106.6504 + 35000 0.00081295162 0 0.00081270452 0.63492031 2073.0077 + 36000 0.00056699821 0 0.00056682587 0.65608409 2038.3251 + 37000 0.0003540723 0 0.00035396468 0.68803919 2005.497 + 38000 0.00031139738 0 0.00031130273 0.72103717 1977.7345 + 39000 0.00034087822 0 0.00034077461 0.74697975 1954.8979 + 40000 0.00035452426 0 0.0003544165 0.76682035 1934.5695 + 41000 0.00030882258 0 0.00030872871 0.78390763 1914.3326 + 42000 0.00025492799 0 0.00025485051 0.80439795 1893.1474 + 43000 0.00021545017 0 0.00021538468 0.82803644 1872.073 + 44000 0.00017293257 0 0.00017288 0.85436769 1852.6548 + 45000 0.00014097725 0 0.0001409344 0.8796181 1836.0087 + 46000 0.0001139199 0 0.00011388527 0.90006173 1821.7977 + 47000 0.00012678598 0 0.00012674745 0.90876359 1808.4913 + 48000 0.00013796773 0 0.00013792579 0.93661523 1793.8082 + 49000 0.00014723144 0 0.00014718669 0.95869417 1779.1875 + 50000 0.00013610653 0 0.00013606516 0.97777198 1765.3247 +Loop time of 17.7405 on 4 procs for 50000 steps with 3290 atoms -Performance: 964340.770 tau/day, 2232.270 timesteps/s -99.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 1217551.996 tau/day, 2818.407 timesteps/s +100.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 8.5158 | 12.318 | 15.836 | 92.1 | 54.99 -Neigh | 0.092527 | 0.11392 | 0.13595 | 5.6 | 0.51 -Comm | 2.7127 | 6.2337 | 10.096 | 131.0 | 27.83 -Output | 0.088027 | 0.088284 | 0.088812 | 0.1 | 0.39 -Modify | 2.8544 | 3.0435 | 3.2034 | 9.2 | 13.59 -Other | | 0.6017 | | | 2.69 +Pair | 6.6629 | 9.6168 | 12.444 | 76.6 | 54.21 +Neigh | 0.049771 | 0.055182 | 0.06133 | 2.0 | 0.31 +Comm | 1.7883 | 4.6306 | 7.6179 | 111.5 | 26.10 +Output | 0.00085342 | 0.0010606 | 0.0015425 | 0.9 | 0.01 +Modify | 2.7244 | 2.895 | 3.0436 | 8.2 | 16.32 +Other | | 0.5419 | | | 3.05 -Nlocal: 822.500 ave 859 max 785 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Nghost: 395.750 ave 424 max 368 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Neighs: 13439.5 ave 14346 max 12017 min -Histogram: 1 0 0 0 0 1 0 0 0 2 +Nlocal: 822.500 ave 897 max 779 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 190.500 ave 211 max 179 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Neighs: 6665.75 ave 7329 max 6104 min +Histogram: 1 0 0 1 1 0 0 0 0 1 -Total # of neighbors = 53758 -Ave neighs/atom = 16.339818 -Neighbor list builds = 348 +Total # of neighbors = 26663 +Ave neighs/atom = 8.1042553 +Neighbor list builds = 342 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:22 +Total wall time: 0:00:17 diff --git a/examples/multi/log.30Nov20.granular.old.intel.1 b/examples/multi/log.30Nov20.granular.old.intel.1 index ad827423c5..f928621824 100644 --- a/examples/multi/log.30Nov20.granular.old.intel.1 +++ b/examples/multi/log.30Nov20.granular.old.intel.1 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -51,9 +51,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi/old -neigh_modify delay 0 -comm_modify mode multi vel yes +neighbor 1 multi/old #multi +neigh_modify delay 0 #collection/interval 2 1 20 +comm_modify mode multi/old vel yes #reduce/multi # colloid potential @@ -64,7 +64,7 @@ fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 fix 2 all enforce2d fix 3 all deform 1 xy erate 1e-3 -dump 1 all custom 1000 dump.granular id x y z radius +#dump 1 all custom 1000 dump.granular id x y z radius #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -90,7 +90,7 @@ Neighbor list info ... pair build: half/size/multi/old/newton/tri stencil: half/multi/old/2d/tri bin: standard -Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.75 | 11.75 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.38 | 10.38 | 10.38 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395623 0.66837658 7200 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 @@ -143,20 +143,20 @@ Step Temp E_pair TotEng Press Volume 48000 0.00017794764 0 0.00017789356 0.93582953 1794.7043 49000 0.00018879338 0 0.000188736 0.95775166 1780.0323 50000 0.00017781117 0 0.00017775712 0.97893641 1765.9442 -Loop time of 80.8597 on 1 procs for 50000 steps with 3290 atoms +Loop time of 74.6636 on 1 procs for 50000 steps with 3290 atoms -Performance: 267129.375 tau/day, 618.355 timesteps/s +Performance: 289297.713 tau/day, 669.671 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 61.524 | 61.524 | 61.524 | 0.0 | 76.09 -Neigh | 2.2021 | 2.2021 | 2.2021 | 0.0 | 2.72 -Comm | 6.748 | 6.748 | 6.748 | 0.0 | 8.35 -Output | 0.25904 | 0.25904 | 0.25904 | 0.0 | 0.32 -Modify | 8.9408 | 8.9408 | 8.9408 | 0.0 | 11.06 -Other | | 1.186 | | | 1.47 +Pair | 56.696 | 56.696 | 56.696 | 0.0 | 75.93 +Neigh | 2.2232 | 2.2232 | 2.2232 | 0.0 | 2.98 +Comm | 6.1867 | 6.1867 | 6.1867 | 0.0 | 8.29 +Output | 0.0012016 | 0.0012016 | 0.0012016 | 0.0 | 0.00 +Modify | 8.432 | 8.432 | 8.432 | 0.0 | 11.29 +Other | | 1.125 | | | 1.51 Nlocal: 3290.00 ave 3290 max 3290 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -172,4 +172,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:01:20 +Total wall time: 0:01:14 diff --git a/examples/multi/log.30Nov20.granular.old.intel.4 b/examples/multi/log.30Nov20.granular.old.intel.4 index e41741b536..507de22119 100644 --- a/examples/multi/log.30Nov20.granular.old.intel.4 +++ b/examples/multi/log.30Nov20.granular.old.intel.4 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -15,7 +15,7 @@ Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.8528 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 3600 atoms - create_atoms CPU = 0.001 seconds + create_atoms CPU = 0.063 seconds change_box all triclinic Changing box ... triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) @@ -51,9 +51,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi/old -neigh_modify delay 0 -comm_modify mode multi vel yes #multi/reduce +neighbor 1 multi/old #multi +neigh_modify delay 0 #collection/interval 2 1 20 +comm_modify mode multi/old vel yes #reduce/multi # colloid potential @@ -64,7 +64,7 @@ fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 fix 2 all enforce2d fix 3 all deform 1 xy erate 1e-3 -dump 1 all custom 1000 dump.granular id x y z radius +#dump 1 all custom 1000 dump.granular id x y z radius #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -90,7 +90,7 @@ Neighbor list info ... pair build: half/size/multi/old/newton/tri stencil: half/multi/old/2d/tri bin: standard -Per MPI rank memory allocation (min/avg/max) = 11.48 | 11.48 | 11.49 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.20 | 10.20 | 10.20 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395623 0.66837658 7200 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 @@ -143,20 +143,20 @@ Step Temp E_pair TotEng Press Volume 48000 0.00017437702 0 0.00017432402 0.93565475 1794.1258 49000 0.00018645903 0 0.00018640235 0.95733183 1779.4032 50000 0.00018469122 0 0.00018463508 0.96446925 1765.1534 -Loop time of 30.9351 on 4 procs for 50000 steps with 3290 atoms +Loop time of 30.1448 on 4 procs for 50000 steps with 3290 atoms -Performance: 698235.574 tau/day, 1616.286 timesteps/s -89.8% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 716540.413 tau/day, 1658.658 timesteps/s +90.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 9.3702 | 12.796 | 16.045 | 84.3 | 41.36 -Neigh | 0.43499 | 0.55158 | 0.64861 | 12.8 | 1.78 -Comm | 10.183 | 13.476 | 16.961 | 83.7 | 43.56 -Output | 0.088474 | 0.088715 | 0.089272 | 0.1 | 0.29 -Modify | 3.0446 | 3.1809 | 3.3227 | 7.4 | 10.28 -Other | | 0.8418 | | | 2.72 +Pair | 8.7565 | 12.704 | 16.036 | 89.8 | 42.14 +Neigh | 0.4494 | 0.56436 | 0.66263 | 11.8 | 1.87 +Comm | 9.5962 | 12.989 | 17.006 | 90.8 | 43.09 +Output | 0.00088467 | 0.0011022 | 0.0015811 | 0.9 | 0.00 +Modify | 2.9732 | 3.0944 | 3.2463 | 7.0 | 10.27 +Other | | 0.7918 | | | 2.63 Nlocal: 822.500 ave 859 max 785 min Histogram: 1 0 1 0 0 0 0 0 1 1 diff --git a/examples/multi/log.30Nov20.powerlaw.intel.1 b/examples/multi/log.30Nov20.powerlaw.intel.1 new file mode 100644 index 0000000000..81b116ddd4 --- /dev/null +++ b/examples/multi/log.30Nov20.powerlaw.intel.1 @@ -0,0 +1,191 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 +read_data data +Reading data file ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10000 atoms + reading velocities ... + 10000 velocities + read_data CPU = 0.027 seconds +change_box all triclinic +Changing box ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 +comm_modify mode multi vel yes reduce/multi + +# granular potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +# fixes + +fix 1 all nve/sphere +fix 2 all enforce2d +fix 3 all deform 1 xy erate 2e-4 + +# dump 1 all custom 2000 dump.granular id x y z radius + +thermo_style custom step temp epair etotal press vol pxy +thermo 1000 + +timestep 0.005 + +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 164.7888 + ghost atom cutoff = 164.7888 + binsize = 82.3944, bins = 4 4 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 14.76 | 14.76 | 14.76 Mbytes +Step Temp E_pair TotEng Press Volume Pxy + 0 0.00014649953 0 0.00014648488 0.027643657 103595.49 -0.0014952693 + 1000 0.00014726802 0 0.00014725329 0.029388139 103595.49 -0.00172238 + 2000 0.00014880425 0 0.00014878937 0.029608995 103595.49 -0.0023614491 + 3000 0.00015154766 0 0.0001515325 0.029668747 103595.49 -0.0029243775 + 4000 0.00015547813 0 0.00015546258 0.029662951 103595.49 -0.0034433688 + 5000 0.00015919808 0 0.00015918216 0.02988062 103595.49 -0.0037443111 + 6000 0.00016272902 0 0.00016271275 0.029776943 103595.49 -0.0042445445 + 7000 0.00016666322 0 0.00016664655 0.029919286 103595.49 -0.0045231987 + 8000 0.00017137531 0 0.00017135817 0.029849078 103595.49 -0.0049023441 + 9000 0.00017774522 0 0.00017772744 0.029925275 103595.49 -0.0051437804 + 10000 0.00018294048 0 0.00018292219 0.030166956 103595.49 -0.0052769381 + 11000 0.00019030719 0 0.00019028816 0.02988594 103595.49 -0.0058095975 + 12000 0.00019806568 0 0.00019804587 0.029852302 103595.49 -0.0060925449 + 13000 0.00020800749 0 0.00020798669 0.029927995 103595.49 -0.0062667347 + 14000 0.00021854888 0 0.00021852703 0.029984135 103595.49 -0.0064949797 + 15000 0.00022975749 0 0.00022973451 0.030063358 103595.49 -0.0065788835 + 16000 0.00024074076 0 0.00024071668 0.03006058 103595.49 -0.006757928 + 17000 0.00025363768 0 0.00025361232 0.030138053 103595.49 -0.0068153904 + 18000 0.00026618156 0 0.00026615494 0.030621109 103595.49 -0.0067026865 + 19000 0.00028000661 0 0.00027997861 0.030520699 103595.49 -0.0067126187 + 20000 0.00029472369 0 0.00029469422 0.030182866 103595.49 -0.0071232374 + 21000 0.00031065822 0 0.00031062716 0.030417926 103595.49 -0.0070815254 + 22000 0.00032789694 0 0.00032786415 0.030434044 103595.49 -0.007044194 + 23000 0.00034491703 0 0.00034488253 0.031195478 103595.49 -0.006895101 + 24000 0.00036262497 0 0.00036258871 0.030348688 103595.49 -0.0073503964 + 25000 0.00038232332 0 0.00038228509 0.030429549 103595.49 -0.0073043833 + 26000 0.00040292952 0 0.00040288922 0.030277517 103595.49 -0.0074475354 + 27000 0.00042260162 0 0.00042255936 0.030270875 103595.49 -0.0074037511 + 28000 0.00044296255 0 0.00044291826 0.030568983 103595.49 -0.0070827585 + 29000 0.00046164594 0 0.00046159978 0.030392129 103595.49 -0.0070495682 + 30000 0.00048018966 0 0.00048014164 0.03027035 103595.49 -0.0071339757 + 31000 0.00049904958 0 0.00049899968 0.030278024 103595.49 -0.0070690708 + 32000 0.00051586592 0 0.00051581433 0.030105498 103595.49 -0.007134143 + 33000 0.000533257 0 0.00053320367 0.029788452 103595.49 -0.0072245811 + 34000 0.00054849405 0 0.0005484392 0.029873916 103595.49 -0.0069597013 + 35000 0.00056356221 0 0.00056350586 0.029706011 103595.49 -0.00704387 + 36000 0.00057701153 0 0.00057695383 0.029584377 103595.49 -0.006959137 + 37000 0.00058975804 0 0.00058969906 0.029510998 103595.49 -0.0069205813 + 38000 0.00060106815 0 0.00060100804 0.029866588 103595.49 -0.006493655 + 39000 0.00061178223 0 0.00061172105 0.0294686 103595.49 -0.0066809721 + 40000 0.00062087616 0 0.00062081407 0.029305512 103595.49 -0.0067040127 + 41000 0.00062938061 0 0.00062931767 0.029313523 103595.49 -0.0065943738 + 42000 0.0006366437 0 0.00063658004 0.029294719 103595.49 -0.0065039414 + 43000 0.00064403805 0 0.00064397364 0.029169615 103595.49 -0.0065453715 + 44000 0.00064990286 0 0.00064983787 0.029173689 103595.49 -0.0064757302 + 45000 0.00065485285 0 0.00065478736 0.02911295 103595.49 -0.0065336599 + 46000 0.00065918851 0 0.00065912259 0.029664657 103595.49 -0.0060618092 + 47000 0.00066143867 0 0.00066137253 0.029672077 103595.49 -0.0061605571 + 48000 0.00066260774 0 0.00066254148 0.029356515 103595.49 -0.0063944326 + 49000 0.0006641111 0 0.00066404469 0.029771162 103595.49 -0.0061440485 + 50000 0.00066562386 0 0.0006655573 0.02944773 103595.49 -0.0063912951 + 51000 0.00066744319 0 0.00066737645 0.029507067 103595.49 -0.00636767 + 52000 0.00066927675 0 0.00066920982 0.029773443 103595.49 -0.0062192673 + 53000 0.00066999455 0 0.00066992755 0.029626747 103595.49 -0.0062819185 + 54000 0.00067204697 0 0.00067197976 0.029608834 103595.49 -0.0063047897 + 55000 0.00067089926 0 0.00067083217 0.029778336 103595.49 -0.006198876 + 56000 0.00067044673 0 0.00067037969 0.029707087 103595.49 -0.0062920606 + 57000 0.00066987451 0 0.00066980752 0.029751879 103595.49 -0.0062887511 + 58000 0.00066781462 0 0.00066774784 0.029673932 103595.49 -0.0063301658 + 59000 0.00065347402 0 0.00065340867 0.029540521 103595.49 -0.0064527808 + 60000 0.00065304518 0 0.00065297988 0.029801357 103595.49 -0.0062633754 + 61000 0.00065183192 0 0.00065176673 0.029786145 103595.49 -0.0063152956 + 62000 0.00065242331 0 0.00065235807 0.030461931 103595.49 -0.0060591261 + 63000 0.00065491938 0 0.00065485389 0.029715839 103595.49 -0.0065344894 + 64000 0.00065769719 0 0.00065763142 0.02977148 103595.49 -0.0065105553 + 65000 0.00066125407 0 0.00066118795 0.029534462 103595.49 -0.0066901883 + 66000 0.00066433913 0 0.0006642727 0.029949304 103595.49 -0.0064367129 + 67000 0.00066819344 0 0.00066812662 0.029629692 103595.49 -0.0067136218 + 68000 0.00067300953 0 0.00067294223 0.029793673 103595.49 -0.0065898421 + 69000 0.00067875538 0 0.0006786875 0.029651968 103595.49 -0.0067198512 + 70000 0.00068416104 0 0.00068409262 0.030125821 103595.49 -0.0063225262 + 71000 0.00068728347 0 0.00068721475 0.02958142 103595.49 -0.0066417995 + 72000 0.00068926082 0 0.00068919189 0.02976018 103595.49 -0.0063898599 + 73000 0.00068953168 0 0.00068946272 0.029574927 103595.49 -0.0065193167 + 74000 0.00069104787 0 0.00069097876 0.030209247 103595.49 -0.0060666707 + 75000 0.00069606779 0 0.00069599818 0.029636657 103595.49 -0.006387635 + 76000 0.00070399158 0 0.00070392118 0.029585803 103595.49 -0.0063291939 + 77000 0.00070284473 0 0.00070277445 0.029936591 103595.49 -0.0060359763 + 78000 0.00070619015 0 0.00070611953 0.029554333 103595.49 -0.0062453302 + 79000 0.00070892936 0 0.00070885847 0.029853506 103595.49 -0.0060833753 + 80000 0.00071125368 0 0.00071118255 0.029625268 103595.49 -0.0062046031 + 81000 0.00070944317 0 0.00070937223 0.029629542 103595.49 -0.0062343125 + 82000 0.00070892851 0 0.00070885762 0.029664456 103595.49 -0.006250692 + 83000 0.00070946812 0 0.00070939718 0.029964177 103595.49 -0.006159583 + 84000 0.00071198659 0 0.00071191539 0.029813631 103595.49 -0.0062607732 + 85000 0.00071266579 0 0.00071259453 0.029645729 103595.49 -0.0064004319 + 86000 0.00071461592 0 0.00071454446 0.029700002 103595.49 -0.0063398759 + 87000 0.00071781454 0 0.00071774276 0.029748726 103595.49 -0.0063600357 + 88000 0.00072016268 0 0.00072009067 0.029772487 103595.49 -0.0063655529 + 89000 0.00072272254 0 0.00072265027 0.030006837 103595.49 -0.0063122612 + 90000 0.00072122914 0 0.00072115701 0.029982109 103595.49 -0.006439831 + 91000 0.00072443479 0 0.00072436235 0.029830121 103595.49 -0.0065202831 + 92000 0.00072738733 0 0.00072731459 0.030194727 103595.49 -0.0062808688 + 93000 0.00072899838 0 0.00072892548 0.030175295 103595.49 -0.0062914883 + 94000 0.00072984304 0 0.00072977006 0.029844017 103595.49 -0.0064737335 + 95000 0.00073206475 0 0.00073199154 0.029798899 103595.49 -0.0064644006 + 96000 0.00073374806 0 0.00073367468 0.030226823 103595.49 -0.0061626549 + 97000 0.00073388886 0 0.00073381547 0.029993629 103595.49 -0.0063710254 + 98000 0.00073534207 0 0.00073526854 0.030245848 103595.49 -0.0063407392 + 99000 0.00073805531 0 0.0007379815 0.030287955 103595.49 -0.0063646707 + 100000 0.0007385798 0 0.00073850594 0.030172948 103595.49 -0.0064654963 +Loop time of 233.709 on 1 procs for 100000 steps with 10000 atoms + +Performance: 184845.371 tau/day, 427.883 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 193.18 | 193.18 | 193.18 | 0.0 | 82.66 +Neigh | 1.1138 | 1.1138 | 1.1138 | 0.0 | 0.48 +Comm | 2.3652 | 2.3652 | 2.3652 | 0.0 | 1.01 +Output | 0.0092981 | 0.0092981 | 0.0092981 | 0.0 | 0.00 +Modify | 32.407 | 32.407 | 32.407 | 0.0 | 13.87 +Other | | 4.628 | | | 1.98 + +Nlocal: 10000.0 ave 10000 max 10000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 446.000 ave 446 max 446 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 34464.0 ave 34464 max 34464 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 34464 +Ave neighs/atom = 3.4464000 +Neighbor list builds = 153 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:03:53 diff --git a/examples/multi/log.30Nov20.powerlaw.intel.4 b/examples/multi/log.30Nov20.powerlaw.intel.4 new file mode 100644 index 0000000000..34d3b85c1b --- /dev/null +++ b/examples/multi/log.30Nov20.powerlaw.intel.4 @@ -0,0 +1,191 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 +read_data data +Reading data file ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 10000 atoms + reading velocities ... + 10000 velocities + read_data CPU = 0.024 seconds +change_box all triclinic +Changing box ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 +comm_modify mode multi vel yes reduce/multi + +# granular potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +# fixes + +fix 1 all nve/sphere +fix 2 all enforce2d +fix 3 all deform 1 xy erate 2e-4 + +# dump 1 all custom 2000 dump.granular id x y z radius + +thermo_style custom step temp epair etotal press vol pxy +thermo 1000 + +timestep 0.005 + +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 164.7888 + ghost atom cutoff = 164.7888 + binsize = 82.3944, bins = 4 4 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.67 | 12.68 Mbytes +Step Temp E_pair TotEng Press Volume Pxy + 0 0.00014649953 0 0.00014648488 0.027643657 103595.49 -0.0014952693 + 1000 0.00014726802 0 0.00014725329 0.029388139 103595.49 -0.00172238 + 2000 0.00014880425 0 0.00014878937 0.029608995 103595.49 -0.0023614491 + 3000 0.00015154766 0 0.0001515325 0.029668747 103595.49 -0.0029243775 + 4000 0.00015547813 0 0.00015546258 0.029662951 103595.49 -0.0034433688 + 5000 0.00015919808 0 0.00015918216 0.02988062 103595.49 -0.0037443111 + 6000 0.00016272902 0 0.00016271275 0.029776943 103595.49 -0.0042445445 + 7000 0.00016666322 0 0.00016664655 0.029919286 103595.49 -0.0045231987 + 8000 0.00017137531 0 0.00017135817 0.029849078 103595.49 -0.0049023441 + 9000 0.00017774522 0 0.00017772744 0.029925275 103595.49 -0.0051437804 + 10000 0.00018294048 0 0.00018292219 0.030166956 103595.49 -0.0052769381 + 11000 0.00019030719 0 0.00019028816 0.02988594 103595.49 -0.0058095975 + 12000 0.00019806568 0 0.00019804587 0.029852302 103595.49 -0.0060925449 + 13000 0.00020800749 0 0.00020798669 0.029927995 103595.49 -0.0062667347 + 14000 0.00021854888 0 0.00021852703 0.029984135 103595.49 -0.0064949797 + 15000 0.00022975749 0 0.00022973451 0.030063358 103595.49 -0.0065788835 + 16000 0.00024074076 0 0.00024071668 0.03006058 103595.49 -0.006757928 + 17000 0.00025363768 0 0.00025361232 0.030138053 103595.49 -0.0068153904 + 18000 0.00026618156 0 0.00026615494 0.030621109 103595.49 -0.0067026865 + 19000 0.00028000661 0 0.00027997861 0.030520699 103595.49 -0.0067126187 + 20000 0.00029472369 0 0.00029469422 0.030182866 103595.49 -0.0071232374 + 21000 0.00031065822 0 0.00031062716 0.030417926 103595.49 -0.0070815254 + 22000 0.00032789694 0 0.00032786415 0.030434044 103595.49 -0.007044194 + 23000 0.00034491703 0 0.00034488253 0.031195478 103595.49 -0.006895101 + 24000 0.00036262497 0 0.00036258871 0.030348688 103595.49 -0.0073503964 + 25000 0.00038232332 0 0.00038228509 0.030429549 103595.49 -0.0073043833 + 26000 0.00040292952 0 0.00040288922 0.030277517 103595.49 -0.0074475354 + 27000 0.00042260162 0 0.00042255936 0.030270875 103595.49 -0.0074037511 + 28000 0.00044296255 0 0.00044291826 0.030568983 103595.49 -0.0070827585 + 29000 0.00046164594 0 0.00046159978 0.030392129 103595.49 -0.0070495682 + 30000 0.00048018966 0 0.00048014164 0.03027035 103595.49 -0.0071339757 + 31000 0.00049904958 0 0.00049899968 0.030278024 103595.49 -0.0070690709 + 32000 0.00051586592 0 0.00051581433 0.030105498 103595.49 -0.007134143 + 33000 0.000533257 0 0.00053320367 0.029788452 103595.49 -0.0072245811 + 34000 0.00054849405 0 0.0005484392 0.029873916 103595.49 -0.0069597013 + 35000 0.00056356221 0 0.00056350586 0.029706011 103595.49 -0.00704387 + 36000 0.00057701153 0 0.00057695383 0.029584377 103595.49 -0.006959137 + 37000 0.00058975804 0 0.00058969906 0.029510998 103595.49 -0.0069205813 + 38000 0.00060106815 0 0.00060100804 0.029866588 103595.49 -0.006493655 + 39000 0.0006117822 0 0.00061172102 0.029468049 103595.49 -0.0066810094 + 40000 0.00062087615 0 0.00062081406 0.02930398 103595.49 -0.0067044715 + 41000 0.00062938044 0 0.0006293175 0.029314381 103595.49 -0.0065941361 + 42000 0.00063664289 0 0.00063657923 0.029294787 103595.49 -0.0065039202 + 43000 0.00064404027 0 0.00064397587 0.029224232 103595.49 -0.0065035306 + 44000 0.00064990723 0 0.00064984224 0.029142324 103595.49 -0.0065034116 + 45000 0.00065485343 0 0.00065478795 0.029121173 103595.49 -0.0065214973 + 46000 0.00065918796 0 0.00065912204 0.029651005 103595.49 -0.0060509446 + 47000 0.00066144517 0 0.00066137903 0.029234729 103595.49 -0.0064672274 + 48000 0.00066261185 0 0.00066254559 0.029229845 103595.49 -0.0065053596 + 49000 0.00066414215 0 0.00066407574 0.029562705 103595.49 -0.0062441985 + 50000 0.0006656453 0 0.00066557874 0.029728174 103595.49 -0.0062147051 + 51000 0.00066738973 0 0.00066732299 0.029928822 103595.49 -0.0060118516 + 52000 0.00066929756 0 0.00066923063 0.029886551 103595.49 -0.0061374389 + 53000 0.00067003172 0 0.00066996472 0.029567015 103595.49 -0.0063482821 + 54000 0.00067198511 0 0.00067191791 0.029833698 103595.49 -0.0061879264 + 55000 0.00067091193 0 0.00067084484 0.029711467 103595.49 -0.006233379 + 56000 0.00067046578 0 0.00067039873 0.030035238 103595.49 -0.0060959401 + 57000 0.00066988234 0 0.00066981535 0.030055225 103595.49 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0.0006872347 0.029970497 103595.49 -0.0063646358 + 72000 0.00068930016 0 0.00068923123 0.029602044 103595.49 -0.0064953597 + 73000 0.00068953092 0 0.00068946197 0.029671751 103595.49 -0.0064422021 + 74000 0.00069106659 0 0.00069099748 0.029918321 103595.49 -0.0062634576 + 75000 0.00069609345 0 0.00069602384 0.029666179 103595.49 -0.0063552778 + 76000 0.00070399534 0 0.00070392494 0.029599912 103595.49 -0.0063251165 + 77000 0.00070284669 0 0.00070277641 0.029658992 103595.49 -0.0061988379 + 78000 0.00070619715 0 0.00070612653 0.029578035 103595.49 -0.0062153063 + 79000 0.00070895477 0 0.00070888388 0.029617734 103595.49 -0.0062090554 + 80000 0.00071127424 0 0.00071120311 0.029539347 103595.49 -0.0062883775 + 81000 0.00070945256 0 0.00070938162 0.029515493 103595.49 -0.0063350852 + 82000 0.00070895167 0 0.00070888078 0.029537389 103595.49 -0.0063819074 + 83000 0.00070948858 0 0.00070941763 0.02998589 103595.49 -0.0061284544 + 84000 0.00071197606 0 0.00071190486 0.030005566 103595.49 -0.0061829926 + 85000 0.00071266684 0 0.00071259557 0.029675137 103595.49 -0.0063804963 + 86000 0.00071465352 0 0.00071458205 0.029762675 103595.49 -0.0062924985 + 87000 0.00071779428 0 0.0007177225 0.029712831 103595.49 -0.0063812951 + 88000 0.00072016431 0 0.0007200923 0.029932619 103595.49 -0.0063145709 + 89000 0.00072271727 0 0.000722645 0.029818327 103595.49 -0.0064025621 + 90000 0.00072122834 0 0.00072115622 0.029829495 103595.49 -0.0065870713 + 91000 0.00072441206 0 0.00072433962 0.029939415 103595.49 -0.0064224045 + 92000 0.00072735846 0 0.00072728572 0.02991447 103595.49 -0.0064256019 + 93000 0.00072898882 0 0.00072891592 0.030230938 103595.49 -0.0061929729 + 94000 0.00072985209 0 0.00072977911 0.030145973 103595.49 -0.0062797016 + 95000 0.0007320685 0 0.0007319953 0.030113809 103595.49 -0.0062765142 + 96000 0.0007337917 0 0.00073371832 0.029919191 103595.49 -0.0063350801 + 97000 0.00073385417 0 0.00073378078 0.030184207 103595.49 -0.0062855982 + 98000 0.00073531629 0 0.00073524276 0.029974905 103595.49 -0.0064826333 + 99000 0.0007380024 0 0.0007379286 0.030678507 103595.49 -0.0060867823 + 100000 0.00073858055 0 0.00073850669 0.030048209 103595.49 -0.0065772058 +Loop time of 77.8133 on 4 procs for 100000 steps with 10000 atoms + +Performance: 555175.163 tau/day, 1285.128 timesteps/s +100.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 28.939 | 48.992 | 61.808 | 189.4 | 62.96 +Neigh | 0.22765 | 0.31872 | 0.38751 | 10.9 | 0.41 +Comm | 3.53 | 16.362 | 36.515 | 328.8 | 21.03 +Output | 0.0046275 | 0.0064601 | 0.008626 | 1.8 | 0.01 +Modify | 5.0862 | 8.3128 | 10.255 | 74.1 | 10.68 +Other | | 3.821 | | | 4.91 + +Nlocal: 2500.00 ave 3016 max 1605 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 221.500 ave 273 max 176 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 8616.00 ave 10377 max 5447 min +Histogram: 1 0 0 0 0 1 0 0 0 2 + +Total # of neighbors = 34464 +Ave neighs/atom = 3.4464000 +Neighbor list builds = 153 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:17 diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index db1e8d5682..46829a2720 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -232,8 +232,9 @@ void NBinMulti::setup_bins(int /*style*/) bininvz_multi[n] = 1.0 / binsizez_multi[n]; if (binsize_optimal*bininvx_multi[n] > CUT2BIN_RATIO || - binsize_optimal*bininvy_multi[n] > CUT2BIN_RATIO || - binsize_optimal*bininvz_multi[n] > CUT2BIN_RATIO) + binsize_optimal*bininvy_multi[n] > CUT2BIN_RATIO) + error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); + if(dimension == 3 and binsize_optimal*bininvz_multi[n] > 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 From 65a82bb5858080214b77ecede4ab93ddc021de30 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 6 Feb 2021 12:57:19 -0700 Subject: [PATCH 52/73] Adding new example --- examples/multi/data.powerlaw | 40000 +++++++++--------- examples/multi/in.powerlaw | 8 +- examples/multi/log.30Nov20.powerlaw.intel.1 | 344 +- examples/multi/log.30Nov20.powerlaw.intel.4 | 348 +- 4 files changed, 20450 insertions(+), 20250 deletions(-) diff --git a/examples/multi/data.powerlaw b/examples/multi/data.powerlaw index 8d1239f18b..2ce54cf4a6 100755 --- a/examples/multi/data.powerlaw +++ b/examples/multi/data.powerlaw @@ -10,20006 +10,20006 @@ LAMMPS data file via write_data, version 24 Dec 2020, timestep = 400000 Atoms # sphere -5 1 53.3452 1 24.11983771564243 68.3864105656564 0 0 0 0 -16 1 27.0148 1 44.452300814629524 34.553717084559324 0 0 0 0 -17 1 25.5929 1 68.38354504971392 54.06475170935992 0 0 0 0 -37 1 16.0333 1 21.245215917793043 25.77572727368242 0 0 0 0 -8263 1 1.097 1 11.708192742157616 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b/examples/multi/in.powerlaw index 90fc7aae3c..213aa3544e 100755 --- a/examples/multi/in.powerlaw +++ b/examples/multi/in.powerlaw @@ -15,19 +15,19 @@ comm_modify mode multi vel yes reduce/multi # granular potential pair_style granular -pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity +pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity # fixes fix 1 all nve/sphere fix 2 all enforce2d -fix 3 all deform 1 xy erate 2e-4 +fix 3 all deform 1 xy erate 1e-4 -# dump 1 all custom 2000 dump.granular id x y z radius +# dump 1 all custom 20000 dump.granular id x y z radius thermo_style custom step temp epair etotal press vol pxy thermo 1000 timestep 0.005 -run 100000 +run 200000 diff --git a/examples/multi/log.30Nov20.powerlaw.intel.1 b/examples/multi/log.30Nov20.powerlaw.intel.1 index 81b116ddd4..d0ed6e2685 100644 --- a/examples/multi/log.30Nov20.powerlaw.intel.1 +++ b/examples/multi/log.30Nov20.powerlaw.intel.1 @@ -1,12 +1,12 @@ LAMMPS (24 Dec 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task -# Big colloid particles and small LJ particles +# Shear power-law distributed granular particles units lj atom_style sphere dimension 2 -read_data data +read_data data.powerlaw Reading data file ... triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) 1 by 1 by 1 MPI processor grid @@ -28,22 +28,22 @@ comm_modify mode multi vel yes reduce/multi # granular potential pair_style granular -pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity +pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity # fixes fix 1 all nve/sphere fix 2 all enforce2d -fix 3 all deform 1 xy erate 2e-4 +fix 3 all deform 1 xy erate 1e-4 -# dump 1 all custom 2000 dump.granular id x y z radius +# dump 1 all custom 20000 dump.granular id x y z radius thermo_style custom step temp epair etotal press vol pxy thermo 1000 timestep 0.005 -run 100000 +run 200000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -56,136 +56,236 @@ Neighbor list info ... pair build: half/size/multi/newton/tri stencil: half/multi/2d/tri bin: multi -Per MPI rank memory allocation (min/avg/max) = 14.76 | 14.76 | 14.76 Mbytes +Per MPI rank memory allocation (min/avg/max) = 14.77 | 14.77 | 14.77 Mbytes Step Temp E_pair TotEng Press Volume Pxy - 0 0.00014649953 0 0.00014648488 0.027643657 103595.49 -0.0014952693 - 1000 0.00014726802 0 0.00014725329 0.029388139 103595.49 -0.00172238 - 2000 0.00014880425 0 0.00014878937 0.029608995 103595.49 -0.0023614491 - 3000 0.00015154766 0 0.0001515325 0.029668747 103595.49 -0.0029243775 - 4000 0.00015547813 0 0.00015546258 0.029662951 103595.49 -0.0034433688 - 5000 0.00015919808 0 0.00015918216 0.02988062 103595.49 -0.0037443111 - 6000 0.00016272902 0 0.00016271275 0.029776943 103595.49 -0.0042445445 - 7000 0.00016666322 0 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0.55477696 103595.49 -0.094417347 + 194000 0.00075725781 0 0.00075718208 0.55457687 103595.49 -0.094241721 + 195000 0.0007434693 0 0.00074339496 0.55471575 103595.49 -0.094102015 + 196000 0.00073792493 0 0.00073785114 0.55463671 103595.49 -0.094452279 + 197000 0.00074673445 0 0.00074665978 0.55459327 103595.49 -0.09463863 + 198000 0.00072734835 0 0.00072727561 0.55514628 103595.49 -0.094622434 + 199000 0.00071846919 0 0.00071839734 0.55501969 103595.49 -0.094414887 + 200000 0.00072384651 0 0.00072377412 0.55533335 103595.49 -0.094159469 +Loop time of 443.321 on 1 procs for 200000 steps with 10000 atoms -Performance: 184845.371 tau/day, 427.883 timesteps/s +Performance: 194892.839 tau/day, 451.141 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 193.18 | 193.18 | 193.18 | 0.0 | 82.66 -Neigh | 1.1138 | 1.1138 | 1.1138 | 0.0 | 0.48 -Comm | 2.3652 | 2.3652 | 2.3652 | 0.0 | 1.01 -Output | 0.0092981 | 0.0092981 | 0.0092981 | 0.0 | 0.00 -Modify | 32.407 | 32.407 | 32.407 | 0.0 | 13.87 -Other | | 4.628 | | | 1.98 +Pair | 362.28 | 362.28 | 362.28 | 0.0 | 81.72 +Neigh | 1.737 | 1.737 | 1.737 | 0.0 | 0.39 +Comm | 5.0082 | 5.0082 | 5.0082 | 0.0 | 1.13 +Output | 0.01774 | 0.01774 | 0.01774 | 0.0 | 0.00 +Modify | 64.992 | 64.992 | 64.992 | 0.0 | 14.66 +Other | | 9.286 | | | 2.09 Nlocal: 10000.0 ave 10000 max 10000 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 446.000 ave 446 max 446 min +Nghost: 487.000 ave 487 max 487 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 34464.0 ave 34464 max 34464 min +Neighs: 34427.0 ave 34427 max 34427 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 34464 -Ave neighs/atom = 3.4464000 -Neighbor list builds = 153 +Total # of neighbors = 34427 +Ave neighs/atom = 3.4427000 +Neighbor list builds = 244 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:03:53 +Total wall time: 0:07:23 diff --git a/examples/multi/log.30Nov20.powerlaw.intel.4 b/examples/multi/log.30Nov20.powerlaw.intel.4 index 34d3b85c1b..109b4582db 100644 --- a/examples/multi/log.30Nov20.powerlaw.intel.4 +++ b/examples/multi/log.30Nov20.powerlaw.intel.4 @@ -1,12 +1,12 @@ LAMMPS (24 Dec 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task -# Big colloid particles and small LJ particles +# Shear power-law distributed granular particles units lj atom_style sphere dimension 2 -read_data data +read_data data.powerlaw Reading data file ... triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) 2 by 2 by 1 MPI processor grid @@ -14,7 +14,7 @@ Reading data file ... 10000 atoms reading velocities ... 10000 velocities - read_data CPU = 0.024 seconds + read_data CPU = 0.114 seconds change_box all triclinic Changing box ... triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) @@ -28,22 +28,22 @@ comm_modify mode multi vel yes reduce/multi # granular potential pair_style granular -pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity +pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity # fixes fix 1 all nve/sphere fix 2 all enforce2d -fix 3 all deform 1 xy erate 2e-4 +fix 3 all deform 1 xy erate 1e-4 -# dump 1 all custom 2000 dump.granular id x y z radius +# dump 1 all custom 20000 dump.granular id x y z radius thermo_style custom step temp epair etotal press vol pxy thermo 1000 timestep 0.005 -run 100000 +run 200000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -58,134 +58,234 @@ Neighbor list info ... bin: multi Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.67 | 12.68 Mbytes Step Temp E_pair TotEng Press Volume Pxy - 0 0.00014649953 0 0.00014648488 0.027643657 103595.49 -0.0014952693 - 1000 0.00014726802 0 0.00014725329 0.029388139 103595.49 -0.00172238 - 2000 0.00014880425 0 0.00014878937 0.029608995 103595.49 -0.0023614491 - 3000 0.00015154766 0 0.0001515325 0.029668747 103595.49 -0.0029243775 - 4000 0.00015547813 0 0.00015546258 0.029662951 103595.49 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0.00068923123 0.029602044 103595.49 -0.0064953597 - 73000 0.00068953092 0 0.00068946197 0.029671751 103595.49 -0.0064422021 - 74000 0.00069106659 0 0.00069099748 0.029918321 103595.49 -0.0062634576 - 75000 0.00069609345 0 0.00069602384 0.029666179 103595.49 -0.0063552778 - 76000 0.00070399534 0 0.00070392494 0.029599912 103595.49 -0.0063251165 - 77000 0.00070284669 0 0.00070277641 0.029658992 103595.49 -0.0061988379 - 78000 0.00070619715 0 0.00070612653 0.029578035 103595.49 -0.0062153063 - 79000 0.00070895477 0 0.00070888388 0.029617734 103595.49 -0.0062090554 - 80000 0.00071127424 0 0.00071120311 0.029539347 103595.49 -0.0062883775 - 81000 0.00070945256 0 0.00070938162 0.029515493 103595.49 -0.0063350852 - 82000 0.00070895167 0 0.00070888078 0.029537389 103595.49 -0.0063819074 - 83000 0.00070948858 0 0.00070941763 0.02998589 103595.49 -0.0061284544 - 84000 0.00071197606 0 0.00071190486 0.030005566 103595.49 -0.0061829926 - 85000 0.00071266684 0 0.00071259557 0.029675137 103595.49 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0.0007379286 0.030678507 103595.49 -0.0060867823 - 100000 0.00073858055 0 0.00073850669 0.030048209 103595.49 -0.0065772058 -Loop time of 77.8133 on 4 procs for 100000 steps with 10000 atoms + 0 4.9204851e-05 0 4.9199931e-05 0.61204991 103595.49 -0.00083309917 + 1000 0.00038076464 0 0.00038072657 0.58694623 103595.49 -0.0066712806 + 2000 0.00027986478 0 0.00027983679 0.5845274 103595.49 -0.008880933 + 3000 0.00022105227 0 0.00022103017 0.58295464 103595.49 -0.011327442 + 4000 0.00020888366 0 0.00020886277 0.5826542 103595.49 -0.014147424 + 5000 0.00019912663 0 0.00019910672 0.58175837 103595.49 -0.015685634 + 6000 0.0001989441 0 0.00019892421 0.58170841 103595.49 -0.017379973 + 7000 0.00019307783 0 0.00019305852 0.58133913 103595.49 -0.019556709 + 8000 0.00018132444 0 0.00018130631 0.58134077 103595.49 -0.021609399 + 9000 0.00017909088 0 0.00017907297 0.58117179 103595.49 -0.023603514 + 10000 0.00018391928 0 0.00018390089 0.58070675 103595.49 -0.026026784 + 11000 0.00018985439 0 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0.56401103 103595.49 -0.090443168 + 123000 0.0005456223 0 0.00054556773 0.56376875 103595.49 -0.090277114 + 124000 0.00054080131 0 0.00054074723 0.563306 103595.49 -0.091297668 + 125000 0.00054597 0 0.0005459154 0.56387718 103595.49 -0.091522394 + 126000 0.000544669 0 0.00054461453 0.56318185 103595.49 -0.091100523 + 127000 0.00054592361 0 0.00054586902 0.56328758 103595.49 -0.091299714 + 128000 0.00056246325 0 0.000562407 0.56296852 103595.49 -0.091491356 + 129000 0.00057655488 0 0.00057649723 0.56242057 103595.49 -0.091474584 + 130000 0.00060363901 0 0.00060357864 0.56182729 103595.49 -0.091367782 + 131000 0.00060590757 0 0.00060584698 0.56115572 103595.49 -0.090594163 + 132000 0.00061689139 0 0.0006168297 0.56029248 103595.49 -0.089857939 + 133000 0.00063288773 0 0.00063282444 0.55971427 103595.49 -0.08954619 + 134000 0.00064153654 0 0.00064147238 0.55929877 103595.49 -0.089860563 + 135000 0.00065473169 0 0.00065466622 0.5590797 103595.49 -0.089932375 + 136000 0.0006814182 0 0.00068135006 0.55797116 103595.49 -0.08929097 + 137000 0.00068344911 0 0.00068338077 0.55796657 103595.49 -0.089644888 + 138000 0.00071510067 0 0.00071502916 0.55752379 103595.49 -0.089734088 + 139000 0.00074772787 0 0.0007476531 0.55740054 103595.49 -0.089968295 + 140000 0.00072706311 0 0.0007269904 0.55659113 103595.49 -0.090370844 + 141000 0.0007179286 0 0.00071785681 0.55659012 103595.49 -0.089976688 + 142000 0.00072587657 0 0.00072580399 0.55589037 103595.49 -0.090532153 + 143000 0.00074470967 0 0.0007446352 0.55553128 103595.49 -0.091019969 + 144000 0.00071737422 0 0.00071730248 0.55555994 103595.49 -0.090926005 + 145000 0.00070363824 0 0.00070356787 0.55548936 103595.49 -0.0912353 + 146000 0.00069604487 0 0.00069597527 0.55540516 103595.49 -0.091656715 + 147000 0.00070047196 0 0.00070040191 0.55466746 103595.49 -0.092101291 + 148000 0.00069764904 0 0.00069757927 0.55460283 103595.49 -0.092334573 + 149000 0.00068884707 0 0.00068877819 0.55462796 103595.49 -0.0928736 + 150000 0.00067704593 0 0.00067697823 0.55520015 103595.49 -0.093512131 + 151000 0.00067702275 0 0.00067695505 0.55530068 103595.49 -0.094127311 + 152000 0.000690717 0 0.00069064792 0.55432538 103595.49 -0.094248615 + 153000 0.00067758953 0 0.00067752177 0.55460446 103595.49 -0.094839924 + 154000 0.00067748542 0 0.00067741767 0.55532529 103595.49 -0.095832411 + 155000 0.00068723442 0 0.0006871657 0.55637763 103595.49 -0.096838207 + 156000 0.00071590663 0 0.00071583504 0.5569485 103595.49 -0.097686166 + 157000 0.00078378647 0 0.0007837081 0.55755381 103595.49 -0.097968527 + 158000 0.00080144334 0 0.00080136319 0.55741023 103595.49 -0.098119361 + 159000 0.00079183165 0 0.00079175247 0.55756142 103595.49 -0.097925888 + 160000 0.00081212358 0 0.00081204237 0.55669124 103595.49 -0.098171108 + 161000 0.00082903843 0 0.00082895553 0.55608918 103595.49 -0.097827206 + 162000 0.00084257416 0 0.0008424899 0.5560239 103595.49 -0.096775743 + 163000 0.00086279615 0 0.00086270987 0.55550215 103595.49 -0.095981927 + 164000 0.00092139657 0 0.00092130443 0.55395137 103595.49 -0.095215338 + 165000 0.00095519936 0 0.00095510384 0.55376787 103595.49 -0.0945666 + 166000 0.00092201276 0 0.00092192056 0.55373794 103595.49 -0.093531233 + 167000 0.0008525194 0 0.00085243415 0.55375862 103595.49 -0.09389901 + 168000 0.00081977785 0 0.00081969587 0.5536646 103595.49 -0.093829746 + 169000 0.00079692467 0 0.00079684497 0.55416599 103595.49 -0.094433271 + 170000 0.00077787798 0 0.0007778002 0.55416629 103595.49 -0.095043413 + 171000 0.0007651362 0 0.00076505969 0.55418872 103595.49 -0.095212376 + 172000 0.00074631438 0 0.00074623975 0.55403881 103595.49 -0.095463949 + 173000 0.00074431288 0 0.00074423845 0.55415801 103595.49 -0.095319615 + 174000 0.00073924649 0 0.00073917257 0.55373682 103595.49 -0.094724272 + 175000 0.00070973165 0 0.00070966068 0.55393569 103595.49 -0.094201112 + 176000 0.00069820766 0 0.00069813784 0.55341229 103595.49 -0.093530469 + 177000 0.00070922657 0 0.00070915564 0.55282781 103595.49 -0.093282587 + 178000 0.00073688566 0 0.00073681197 0.55223248 103595.49 -0.092190554 + 179000 0.00072455886 0 0.0007244864 0.55244288 103595.49 -0.09182393 + 180000 0.00071894558 0 0.00071887369 0.55281517 103595.49 -0.092177032 + 181000 0.00071752475 0 0.000717453 0.55297293 103595.49 -0.09230934 + 182000 0.00072247421 0 0.00072240196 0.55287294 103595.49 -0.092465908 + 183000 0.00070596821 0 0.00070589761 0.5526242 103595.49 -0.092013313 + 184000 0.00072460909 0 0.00072453663 0.55230817 103595.49 -0.092211243 + 185000 0.00072499917 0 0.00072492667 0.55273387 103595.49 -0.092920761 + 186000 0.00072852698 0 0.00072845413 0.55358929 103595.49 -0.093428623 + 187000 0.00072515668 0 0.00072508417 0.55336733 103595.49 -0.093440126 + 188000 0.00071355728 0 0.00071348593 0.55408468 103595.49 -0.094819333 + 189000 0.00071703212 0 0.00071696042 0.55424355 103595.49 -0.096198144 + 190000 0.00071808849 0 0.00071801668 0.55504118 103595.49 -0.097199842 + 191000 0.00072458142 0 0.00072450896 0.55493515 103595.49 -0.097564772 + 192000 0.00071472504 0 0.00071465357 0.55572657 103595.49 -0.097663072 + 193000 0.00070803966 0 0.00070796886 0.55546116 103595.49 -0.097306162 + 194000 0.00068236077 0 0.00068229254 0.55581155 103595.49 -0.097141594 + 195000 0.00067304613 0 0.00067297882 0.55559507 103595.49 -0.096646489 + 196000 0.00066680808 0 0.0006667414 0.55512029 103595.49 -0.096241456 + 197000 0.00065829161 0 0.00065822578 0.55545375 103595.49 -0.095808778 + 198000 0.0006617611 0 0.00066169492 0.55551074 103595.49 -0.095423531 + 199000 0.00066805655 0 0.00066798975 0.55581298 103595.49 -0.095287337 + 200000 0.00067263902 0 0.00067257175 0.55601669 103595.49 -0.095551006 +Loop time of 145.127 on 4 procs for 200000 steps with 10000 atoms -Performance: 555175.163 tau/day, 1285.128 timesteps/s +Performance: 595339.507 tau/day, 1378.101 timesteps/s 100.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 28.939 | 48.992 | 61.808 | 189.4 | 62.96 -Neigh | 0.22765 | 0.31872 | 0.38751 | 10.9 | 0.41 -Comm | 3.53 | 16.362 | 36.515 | 328.8 | 21.03 -Output | 0.0046275 | 0.0064601 | 0.008626 | 1.8 | 0.01 -Modify | 5.0862 | 8.3128 | 10.255 | 74.1 | 10.68 -Other | | 3.821 | | | 4.91 +Pair | 57.89 | 91.946 | 113.82 | 229.7 | 63.36 +Neigh | 0.34276 | 0.48607 | 0.56708 | 13.1 | 0.33 +Comm | 6.569 | 28.916 | 63.505 | 417.0 | 19.92 +Output | 0.0087178 | 0.011935 | 0.01563 | 2.3 | 0.01 +Modify | 10.432 | 16.495 | 20.378 | 97.7 | 11.37 +Other | | 7.272 | | | 5.01 -Nlocal: 2500.00 ave 3016 max 1605 min +Nlocal: 2500.00 ave 2990 max 1652 min Histogram: 1 0 0 0 0 1 0 0 0 2 -Nghost: 221.500 ave 273 max 176 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Neighs: 8616.00 ave 10377 max 5447 min +Nghost: 228.000 ave 254 max 198 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 8611.25 ave 10364 max 5676 min Histogram: 1 0 0 0 0 1 0 0 0 2 -Total # of neighbors = 34464 -Ave neighs/atom = 3.4464000 -Neighbor list builds = 153 +Total # of neighbors = 34445 +Ave neighs/atom = 3.4445000 +Neighbor list builds = 241 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:01:17 +Total wall time: 0:02:25 From 880b40e10465d7292d4987302b7a49ab86042a64 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 7 Feb 2021 10:44:51 -0700 Subject: [PATCH 53/73] Adding setup_bins() method to nbin_intel.cpp --- src/USER-INTEL/nbin_intel.cpp | 161 ++++++++++++++++++++++++++++++++++ src/USER-INTEL/nbin_intel.h | 1 + 2 files changed, 162 insertions(+) diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp index 31b53e3462..848ac6edd8 100644 --- a/src/USER-INTEL/nbin_intel.cpp +++ b/src/USER-INTEL/nbin_intel.cpp @@ -21,11 +21,15 @@ #include "comm.h" #include "error.h" #include "group.h" +#include "domain.h" #include "modify.h" #include "update.h" using namespace LAMMPS_NS; +#define SMALL 1.0e-6 +#define CUT2BIN_RATIO 100 + /* ---------------------------------------------------------------------- */ NBinIntel::NBinIntel(LAMMPS *lmp) : NBinStandard(lmp) { @@ -132,6 +136,163 @@ void NBinIntel::bin_atoms_setup(int nall) } } + +/* ---------------------------------------------------------------------- + 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 NBinIntel::setup_bins(int style) +{ + // 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_OLD 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 == Neighbor::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 (bbox[0]*binsizeinv); + nbiny = static_cast (bbox[1]*binsizeinv); + if (dimension == 3) nbinz = static_cast (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 ((coord-bboxlo[0])*bininvx); + if (coord < bboxlo[0]) mbinxlo = mbinxlo - 1; + coord = bsubboxhi[0] + SMALL*bbox[0]; + mbinxhi = static_cast ((coord-bboxlo[0])*bininvx); + + coord = bsubboxlo[1] - SMALL*bbox[1]; + mbinylo = static_cast ((coord-bboxlo[1])*bininvy); + if (coord < bboxlo[1]) mbinylo = mbinylo - 1; + coord = bsubboxhi[1] + SMALL*bbox[1]; + mbinyhi = static_cast ((coord-bboxlo[1])*bininvy); + + if (dimension == 3) { + coord = bsubboxlo[2] - SMALL*bbox[2]; + mbinzlo = static_cast ((coord-bboxlo[2])*bininvz); + if (coord < bboxlo[2]) mbinzlo = mbinzlo - 1; + coord = bsubboxhi[2] + SMALL*bbox[2]; + mbinzhi = static_cast ((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 ------------------------------------------------------------------------- */ diff --git a/src/USER-INTEL/nbin_intel.h b/src/USER-INTEL/nbin_intel.h index a7a28010ba..e49f332392 100644 --- a/src/USER-INTEL/nbin_intel.h +++ b/src/USER-INTEL/nbin_intel.h @@ -33,6 +33,7 @@ class NBinIntel : public NBinStandard { NBinIntel(class LAMMPS *); ~NBinIntel(); void bin_atoms_setup(int); + void setup_bins(int); void bin_atoms(); int * get_binpacked() { return _binpacked; } From 05f02fbc32230222900853b675be015fd77de018 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 7 Feb 2021 12:40:59 -0700 Subject: [PATCH 54/73] Removing setup method and adding correct nbin bitmask --- src/USER-INTEL/nbin_intel.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-INTEL/nbin_intel.h b/src/USER-INTEL/nbin_intel.h index e49f332392..b2b3d5d0ca 100644 --- a/src/USER-INTEL/nbin_intel.h +++ b/src/USER-INTEL/nbin_intel.h @@ -15,7 +15,7 @@ NBinStyle(intel, NBinIntel, - NB_INTEL) + NB_STANDARD | NB_INTEL) #else From 5a4c45f2ea98867af95ac1dc90a600f48ee2c2d6 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 7 Feb 2021 13:02:45 -0700 Subject: [PATCH 55/73] Fixing bitmasks and removing method again --- src/USER-INTEL/nbin_intel.cpp | 161 ---------------------------------- src/USER-INTEL/nbin_intel.h | 1 - 2 files changed, 162 deletions(-) diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp index 848ac6edd8..31b53e3462 100644 --- a/src/USER-INTEL/nbin_intel.cpp +++ b/src/USER-INTEL/nbin_intel.cpp @@ -21,15 +21,11 @@ #include "comm.h" #include "error.h" #include "group.h" -#include "domain.h" #include "modify.h" #include "update.h" using namespace LAMMPS_NS; -#define SMALL 1.0e-6 -#define CUT2BIN_RATIO 100 - /* ---------------------------------------------------------------------- */ NBinIntel::NBinIntel(LAMMPS *lmp) : NBinStandard(lmp) { @@ -136,163 +132,6 @@ void NBinIntel::bin_atoms_setup(int nall) } } - -/* ---------------------------------------------------------------------- - 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 NBinIntel::setup_bins(int style) -{ - // 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_OLD 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 == Neighbor::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 (bbox[0]*binsizeinv); - nbiny = static_cast (bbox[1]*binsizeinv); - if (dimension == 3) nbinz = static_cast (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 ((coord-bboxlo[0])*bininvx); - if (coord < bboxlo[0]) mbinxlo = mbinxlo - 1; - coord = bsubboxhi[0] + SMALL*bbox[0]; - mbinxhi = static_cast ((coord-bboxlo[0])*bininvx); - - coord = bsubboxlo[1] - SMALL*bbox[1]; - mbinylo = static_cast ((coord-bboxlo[1])*bininvy); - if (coord < bboxlo[1]) mbinylo = mbinylo - 1; - coord = bsubboxhi[1] + SMALL*bbox[1]; - mbinyhi = static_cast ((coord-bboxlo[1])*bininvy); - - if (dimension == 3) { - coord = bsubboxlo[2] - SMALL*bbox[2]; - mbinzlo = static_cast ((coord-bboxlo[2])*bininvz); - if (coord < bboxlo[2]) mbinzlo = mbinzlo - 1; - coord = bsubboxhi[2] + SMALL*bbox[2]; - mbinzhi = static_cast ((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 ------------------------------------------------------------------------- */ diff --git a/src/USER-INTEL/nbin_intel.h b/src/USER-INTEL/nbin_intel.h index b2b3d5d0ca..fef1bf0f26 100644 --- a/src/USER-INTEL/nbin_intel.h +++ b/src/USER-INTEL/nbin_intel.h @@ -33,7 +33,6 @@ class NBinIntel : public NBinStandard { NBinIntel(class LAMMPS *); ~NBinIntel(); void bin_atoms_setup(int); - void setup_bins(int); void bin_atoms(); int * get_binpacked() { return _binpacked; } From 952216033ee551769611e0d31cfe059856405baf Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 7 Feb 2021 13:33:11 -0700 Subject: [PATCH 56/73] Adding correct masks to kokks/user-dpd nbin classes --- src/KOKKOS/nbin_kokkos.h | 4 ++-- src/KOKKOS/nbin_ssa_kokkos.h | 4 ++-- src/USER-DPD/nbin_ssa.h | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/KOKKOS/nbin_kokkos.h b/src/KOKKOS/nbin_kokkos.h index bf2ccc5908..7297489d4a 100644 --- a/src/KOKKOS/nbin_kokkos.h +++ b/src/KOKKOS/nbin_kokkos.h @@ -15,11 +15,11 @@ NBinStyle(kk/host, NBinKokkos, - NB_KOKKOS_HOST) + NB_STANDARD | NB_KOKKOS_HOST) NBinStyle(kk/device, NBinKokkos, - NB_KOKKOS_DEVICE) + NB_STANDARD | NB_KOKKOS_DEVICE) #else diff --git a/src/KOKKOS/nbin_ssa_kokkos.h b/src/KOKKOS/nbin_ssa_kokkos.h index c9a389bed4..b094bf8ae6 100644 --- a/src/KOKKOS/nbin_ssa_kokkos.h +++ b/src/KOKKOS/nbin_ssa_kokkos.h @@ -15,11 +15,11 @@ NBinStyle(ssa/kk/host, NBinSSAKokkos, - NB_SSA | NB_KOKKOS_HOST) + NB_STANDARD | NB_SSA | NB_KOKKOS_HOST) NBinStyle(ssa/kk/device, NBinSSAKokkos, - NB_SSA | NB_KOKKOS_DEVICE) + NB_STANDARD | NB_SSA | NB_KOKKOS_DEVICE) #else diff --git a/src/USER-DPD/nbin_ssa.h b/src/USER-DPD/nbin_ssa.h index eb4b2db24c..7c6bf4325b 100644 --- a/src/USER-DPD/nbin_ssa.h +++ b/src/USER-DPD/nbin_ssa.h @@ -15,7 +15,7 @@ NBinStyle(ssa, NBinSSA, - NB_SSA) + NB_STANDARD | NB_SSA) #else From de1205c5a9e3aa80e6958135169902d22f9afbac Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 7 Feb 2021 20:38:24 -0700 Subject: [PATCH 57/73] Fixing misc valgrind issues, particularly with resizing ncollections --- src/comm.cpp | 2 + src/comm.h | 1 + src/comm_brick.cpp | 11 +-- src/comm_tiled.cpp | 15 ++-- src/nbin_multi.cpp | 6 +- src/neighbor.cpp | 9 ++- src/nstencil.cpp | 121 ++++++++++++++++++++------------- src/nstencil.h | 3 +- src/nstencil_half_multi_2d.cpp | 2 +- 9 files changed, 105 insertions(+), 65 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index 33e4b894d5..d729545dba 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -58,6 +58,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) bordergroup = 0; cutghostuser = 0.0; cutusermulti = nullptr; + cutusermultiflag = 0; cutusermultiold = nullptr; ncollections_prior = 0; ghost_velocity = 0; @@ -348,6 +349,7 @@ void Comm::modify_params(int narg, char **arg) // ncollections can be changed by neigh_modify commands cut = utils::numeric(FLERR,arg[iarg+2],false,lmp); cutghostuser = MAX(cutghostuser,cut); + cutusermultiflag = 1; if (cut < 0.0) error->all(FLERR,"Invalid cutoff in comm_modify command"); usermultiargs.emplace_back(arg[iarg+1], cut); diff --git a/src/comm.h b/src/comm.h index 2afdfd8765..418983b6e6 100644 --- a/src/comm.h +++ b/src/comm.h @@ -33,6 +33,7 @@ class Comm : protected Pointers { double cutghost[3]; // cutoffs used for acquiring ghost atoms double cutghostuser; // user-specified ghost cutoff (mode == 0) double *cutusermulti; // per collection user ghost cutoff (mode == 1) + int cutusermultiflag; std::vector> usermultiargs; // collection args for custom ghost cutoffs double *cutusermultiold; // per type user ghost cutoff (mode == 2) diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 58c6a65837..160ecf2c3d 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -142,6 +142,7 @@ void CommBrick::init() // allocate in setup if (mode == Comm::MULTI && multilo == nullptr) { + ncollections = neighbor->ncollections; allocate_multi(maxswap); memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); ncollections_prior = ncollections; @@ -205,10 +206,12 @@ void CommBrick::setup() allocate_multi(maxswap); memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); - for(i = ncollections_prior; i < ncollections; i++) - cutusermulti[i] = -1.0; - + if(cutusermultiflag) { + memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); + for(i = ncollections_prior; i < ncollections; i++) + cutusermulti[i] = -1.0; + } + ncollections_prior = ncollections; } diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index c06ad52d6c..0a09dc830d 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -104,6 +104,11 @@ void CommTiled::init_buffers() cutghostmultiold = nullptr; sendbox_multi = nullptr; sendbox_multiold = nullptr; + + // initialize ncollections so grow_swap_send_multi() will not + // construct arrays in init() but will wait for setup() + ncollections = 0; + ncollections_prior = 0; maxswap = 6; allocate_swap(maxswap); @@ -194,10 +199,12 @@ void CommTiled::setup() for(i = 0; i < maxswap; i ++) grow_swap_send_multi(i,DELTA_PROCS); - memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); - for(i = ncollections_prior; i < ncollections; i++) - cutusermulti[i] = -1.0; - + if(cutusermultiflag){ + memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); + for(i = ncollections_prior; i < ncollections; i++) + cutusermulti[i] = -1.0; + } + ncollections_prior = ncollections; } diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index bbc69dc2d6..a39f10d074 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -146,7 +146,7 @@ void NBinMulti::setup_bins(int /*style*/) // Identify smallest collection int icollectionmin = 0; - for (n = 0; n < maxcollections; n++) + for (n = 0; n < ncollections; n++) if (cutcollectionsq[n][n] < cutcollectionsq[icollectionmin][icollectionmin]) icollectionmin = n; @@ -188,7 +188,7 @@ void NBinMulti::setup_bins(int /*style*/) double binsize_optimal, binsizeinv, coord; int mbinxhi,mbinyhi,mbinzhi; - for (n = 0; n < maxcollections; n++) { + for (n = 0; n < ncollections; n++) { // binsize_user only relates to smallest collection // optimal bin size is roughly 1/2 the collection-collection cutoff // special case of all cutoffs = 0.0, binsize = box size @@ -296,7 +296,7 @@ void NBinMulti::bin_atoms() int i,ibin,n; last_bin = update->ntimestep; - for (n = 0; n < maxcollections; n++) { + for (n = 0; n < ncollections; n++) { for (i = 0; i < mbins_multi[n]; i++) binhead_multi[n][i] = -1; } // bin in reverse order so linked list will be in forward order diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 2671553a07..e8f9798df8 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -426,7 +426,7 @@ void Neighbor::init() for(i = 1; i <= n; i++){ cuttmp = sqrt(cutneighsq[i][i]); for(icollection = 0; icollection < ncollections; icollection ++){ - if(collection2cut[icollection] > cuttmp) { + if(collection2cut[icollection] >= cuttmp) { type2collection[i] = icollection; break; } @@ -2503,6 +2503,8 @@ void Neighbor::modify_params(int narg, char **arg) if(iarg+2 > narg) error->all(FLERR,"Invalid collection/interval command"); ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if(ncollections < 1) + error->all(FLERR,"Invalid collection/interval command"); if(iarg+1+ncollections > narg) error->all(FLERR,"Invalid collection/interval command"); @@ -2511,8 +2513,7 @@ void Neighbor::modify_params(int narg, char **arg) interval_collection_flag = 1; custom_collection_flag = 1; - if(not collection2cut) - memory->create(collection2cut,ncollections,"neigh:collection2cut"); + memory->grow(collection2cut,ncollections,"neigh:collection2cut"); // Set upper cutoff for each collection char *id; @@ -2534,6 +2535,8 @@ void Neighbor::modify_params(int narg, char **arg) if(iarg+2 > narg) error->all(FLERR,"Invalid collection/type command"); ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if(ncollections < 1) + error->all(FLERR,"Invalid collection/interval command"); if(iarg+1+ncollections > narg) error->all(FLERR,"Invalid collection/type command"); diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 3cf75d8d68..ba7259a9fc 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -82,6 +82,8 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) flag_half_multi = nullptr; flag_skip_multi = nullptr; bin_collection_multi = nullptr; + + maxcollections = 0; dimension = domain->dimension; } @@ -105,15 +107,12 @@ NStencil::~NStencil() delete [] distsq_multi_old; } - if (stencil_multi) { + if (maxstencil_multi) { - int n = ncollections; memory->destroy(nstencil_multi); - for (int i = 0; i < n; i++) { - for (int j = 0; j < n; j++) { - if (! flag_skip_multi[i][j]) - memory->destroy(stencil_multi[i][j]); - } + for (int i = 0; i < maxcollections; i++) { + for (int j = 0; j < maxcollections; j++) + memory->destroy(stencil_multi[i][j]); delete [] stencil_multi[i]; } delete [] stencil_multi; @@ -275,47 +274,60 @@ void NStencil::create_setup() if(nb) copy_bin_info_multi(); - // Allocate arrays to store stencil information - memory->create(flag_half_multi, n, n, - "neighstencil:flag_half_multi"); - memory->create(flag_skip_multi, n, n, - "neighstencil:flag_skip_multi"); - memory->create(bin_collection_multi, n, n, - "neighstencil:bin_collection_multi"); - - memory->create(stencil_sx_multi, n, n, - "neighstencil:stencil_sx_multi"); - memory->create(stencil_sy_multi, n, n, - "neighstencil:stencil_sy_multi"); - memory->create(stencil_sz_multi, n, n, - "neighstencil:stencil_sz_multi"); - - memory->create(stencil_binsizex_multi, n, n, - "neighstencil:stencil_binsizex_multi"); - memory->create(stencil_binsizey_multi, n, n, - "neighstencil:stencil_binsizey_multi"); - memory->create(stencil_binsizez_multi, n, n, - "neighstencil:stencil_binsizez_multi"); - - memory->create(stencil_mbinx_multi, n, n, - "neighstencil:stencil_mbinx_multi"); - memory->create(stencil_mbiny_multi, n, n, - "neighstencil:stencil_mbiny_multi"); - memory->create(stencil_mbinz_multi, n, n, - "neighstencil:stencil_mbinz_multi"); - - // Skip all stencils by default, initialize smax - for (i = 0; i < n; i++) { - for (j = 0; j < n; j++) { - flag_skip_multi[i][j] = 1; + // Deallocate arrays if previously allocated + if(n > maxcollections and stencil_multi){ + memory->destroy(nstencil_multi); + for (i = 0; i < maxcollections; i++) { + for (j = 0; j < maxcollections; j++) + memory->destroy(stencil_multi[i][j]); + delete [] stencil_multi[i]; } - } + delete [] stencil_multi; + memory->destroy(maxstencil_multi); + memory->destroy(flag_half_multi); + memory->destroy(flag_skip_multi); + memory->destroy(bin_collection_multi); + memory->destroy(stencil_sx_multi); + memory->destroy(stencil_sy_multi); + memory->destroy(stencil_sz_multi); + memory->destroy(stencil_binsizex_multi); + memory->destroy(stencil_binsizey_multi); + memory->destroy(stencil_binsizez_multi); + memory->destroy(stencil_mbinx_multi); + memory->destroy(stencil_mbiny_multi); + memory->destroy(stencil_mbinz_multi); + } - // Determine which stencils need to be built - set_stencil_properties(); - - // Allocate arrays to store stencils - if (!maxstencil_multi) { + // Allocate arrays + if(!maxstencil_multi) { + memory->create(flag_half_multi, n, n, + "neighstencil:flag_half_multi"); + memory->create(flag_skip_multi, n, n, + "neighstencil:flag_skip_multi"); + memory->create(bin_collection_multi, n, n, + "neighstencil:bin_collection_multi"); + + memory->create(stencil_sx_multi, n, n, + "neighstencil:stencil_sx_multi"); + memory->create(stencil_sy_multi, n, n, + "neighstencil:stencil_sy_multi"); + memory->create(stencil_sz_multi, n, n, + "neighstencil:stencil_sz_multi"); + + memory->create(stencil_binsizex_multi, n, n, + "neighstencil:stencil_binsizex_multi"); + memory->create(stencil_binsizey_multi, n, n, + "neighstencil:stencil_binsizey_multi"); + memory->create(stencil_binsizez_multi, n, n, + "neighstencil:stencil_binsizez_multi"); + + memory->create(stencil_mbinx_multi, n, n, + "neighstencil:stencil_mbinx_multi"); + memory->create(stencil_mbiny_multi, n, n, + "neighstencil:stencil_mbiny_multi"); + memory->create(stencil_mbinz_multi, n, n, + "neighstencil:stencil_mbinz_multi"); + memory->create(maxstencil_multi, n, n, "neighstencil::maxstencil_multi"); memory->create(nstencil_multi, n, n, "neighstencil::nstencil_multi"); stencil_multi = new int**[n](); @@ -326,12 +338,22 @@ void NStencil::create_setup() nstencil_multi[i][j] = 0; stencil_multi[i][j] = nullptr; } + } + maxcollections = n; + } + + // Skip all stencils by default, initialize smax + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + flag_skip_multi[i][j] = 1; } - } + } + + // Determine which stencils need to be built + set_stencil_properties(); for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { - // Skip creation of unused stencils if (flag_skip_multi[i][j]) continue; @@ -364,7 +386,8 @@ void NStencil::create_setup() if (smax > maxstencil_multi[i][j]) { maxstencil_multi[i][j] = smax; - memory->destroy(stencil_multi[i][j]); + if(stencil_multi[i][j]) + memory->destroy(stencil_multi[i][j]); memory->create(stencil_multi[i][j], smax, "neighstencil::stencil_multi"); } diff --git a/src/nstencil.h b/src/nstencil.h index 37cedec045..6e8c2da97c 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -33,6 +33,7 @@ class NStencil : protected Pointers { int ** nstencil_multi; // # bins bins in each igroup-jgroup multi stencil int *** stencil_multi; // list of bin offsets in each multi stencil int ** maxstencil_multi; // max stencil size for each multi stencil + int maxcollections; // size of multi arrays int sx,sy,sz; // extent of stencil in each dim int **stencil_sx_multi; // analogs for each multi stencil @@ -42,7 +43,7 @@ class NStencil : protected Pointers { double cutoff_custom; // cutoff set by requestor // Arrays to store options for multi itype-jtype stencils - bool **flag_half_multi; // flag creation of a half stencil for igroup-jgroup + bool **flag_half_multi; // flag creation of a half stencil for icollection-jcollection bool **flag_skip_multi; // skip creation of icollection-jcollection stencils (for newton on) int **bin_collection_multi; // what collection to use for bin information diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_2d.cpp index 57352c7c6f..32ee0297ff 100644 --- a/src/nstencil_half_multi_2d.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -71,7 +71,7 @@ void NStencilHalfMulti2d::create() if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - + sx = stencil_sx_multi[icollection][jcollection]; sy = stencil_sy_multi[icollection][jcollection]; From 58e4938b0f5e6c1006404f0bf9c8718bb87ce371 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 8 Feb 2021 10:50:57 -0700 Subject: [PATCH 58/73] Updating examples, updating multi in info, fixing memory issues in comm/neighbor --- src/comm.cpp | 18 ++++++++++++++++-- src/comm_brick.cpp | 24 +++++++++++++++++++++++- src/comm_tiled.cpp | 6 +++--- src/info.cpp | 17 ++++++++++++++++- src/neighbor.cpp | 3 ++- 5 files changed, 60 insertions(+), 8 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index d729545dba..f41f046e63 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -298,18 +298,32 @@ void Comm::modify_params(int narg, char **arg) // need to reset cutghostuser when switching comm mode if (mode == Comm::MULTI) cutghostuser = 0.0; if (mode == Comm::MULTIOLD) cutghostuser = 0.0; - memory->destroy(cutusermulti); - cutusermulti = nullptr; + if(cutusermulti){ + memory->destroy(cutusermulti); + cutusermulti = nullptr; + } + if(cutusermultiold){ + memory->destroy(cutusermultiold); + cutusermultiold = nullptr; + } mode = Comm::SINGLE; } else if (strcmp(arg[iarg+1],"multi") == 0) { // need to reset cutghostuser when switching comm mode if (mode == Comm::SINGLE) cutghostuser = 0.0; if (mode == Comm::MULTIOLD) cutghostuser = 0.0; + if(cutusermultiold){ + memory->destroy(cutusermultiold); + cutusermultiold = nullptr; + } mode = Comm::MULTI; } else if (strcmp(arg[iarg+1],"multi/old") == 0) { // need to reset cutghostuser when switching comm mode if (mode == Comm::SINGLE) cutghostuser = 0.0; if (mode == Comm::MULTI) cutghostuser = 0.0; + if(cutusermulti){ + memory->destroy(cutusermulti); + cutusermulti = nullptr; + } mode = Comm::MULTIOLD; } else error->all(FLERR,"Illegal comm_modify command"); iarg += 2; diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 160ecf2c3d..50c18e5fe7 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -145,6 +145,12 @@ void CommBrick::init() ncollections = neighbor->ncollections; allocate_multi(maxswap); memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); + if(cutusermultiflag) { + memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); + for(int i = ncollections_prior; i < ncollections; i++) + cutusermulti[i] = -1.0; + } + ncollections_prior = ncollections; } if ((mode == Comm::SINGLE or mode == Comm::MULTIOLD) && multilo) { @@ -218,7 +224,7 @@ void CommBrick::setup() // parse any cutoff/multi commands int nhi, nlo; for(auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { - utils::bounds(FLERR,it->first,1,ncollections,nlo,nhi,error); + utils::bounds(FLERR,it->first,0,ncollections,nlo,nhi,error); if(nhi >= ncollections) error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); for (j=nlo; j<=nhi; ++j) @@ -898,6 +904,22 @@ void CommBrick::borders() if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); sendlist[iswap][nsend++] = i; } + } else if (mode == Comm::MULTI) { + ngroup = atom->nfirst; + for (i = 0; i < ngroup; i++) { + icollection = collection[i]; + if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) { + if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); + sendlist[iswap][nsend++] = i; + } + } + for (i = atom->nlocal; i < nlast; i++) { + icollection = collection[i]; + if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) { + if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); + sendlist[iswap][nsend++] = i; + } + } } else { ngroup = atom->nfirst; for (i = 0; i < ngroup; i++) { diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 0a09dc830d..27f630f720 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -198,7 +198,6 @@ void CommTiled::setup() for(i = 0; i < maxswap; i ++) grow_swap_send_multi(i,DELTA_PROCS); - if(cutusermultiflag){ memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); for(i = ncollections_prior; i < ncollections; i++) @@ -211,10 +210,10 @@ void CommTiled::setup() // parse any cutoff/multi commands int nhi, nlo; for(auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { - utils::bounds(FLERR,it->first,1,ncollections,nlo,nhi,error); + utils::bounds(FLERR,it->first,0,ncollections,nlo,nhi,error); if(nhi >= ncollections) error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); - + for (j=nlo; j<=nhi; ++j) cutusermulti[j] = it->second; } @@ -224,6 +223,7 @@ void CommTiled::setup() // If using multi/reduce, communicate particles a distance equal // to the max cutoff with equally sized or smaller collections // If not, communicate the maximum cutoff of the entire collection + for (i = 0; i < ncollections; i++) { if (cutusermulti) { cutghostmulti[i][0] = cutusermulti[i]; diff --git a/src/info.cpp b/src/info.cpp index bf6f14a48a..0d3c47efa8 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -414,9 +414,24 @@ void Info::command(int narg, char **arg) if (comm->mode == 1) { fputs("Communication mode = multi\n",out); double cut; + for (int i=0; i < neighbor->ncollections; ++i) { + if (comm->cutusermulti) cut = comm->cutusermulti[i]; + else cut = 0.0; + for (int j=0; j < neighbor->ncollections; ++j) { + cut = MAX(cut,sqrt(neighbor->cutcollectionsq[i][j])); + } + + if (comm->cutusermulti) cut = MAX(cut,comm->cutusermulti[i]); + fmt::print(out,"Communication cutoff for collection {} = {:.8}\n", i, cut); + } + } + + if (comm->mode == 2) { + fputs("Communication mode = multi/old\n",out); + double cut; for (int i=1; i <= atom->ntypes && neighbor->cuttype; ++i) { cut = neighbor->cuttype[i]; - if (comm->cutusermulti) cut = MAX(cut,comm->cutusermulti[i]); + if (comm->cutusermultiold) cut = MAX(cut,comm->cutusermultiold[i]); fmt::print(out,"Communication cutoff for type {} = {:.8}\n", i, cut); } } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index e8f9798df8..c33345f88d 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -366,7 +366,8 @@ void Neighbor::init() if(not custom_collection_flag) { ncollections = n; interval_collection_flag = 0; - memory->create(type2collection,n+1,"neigh:type2collection"); + if(not type2collection) + memory->create(type2collection,n+1,"neigh:type2collection"); for(i = 1; i <= n; i++) type2collection[i] = i-1; } From 039ed4c7503858bd93ecb091f83e804597d2c9b6 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 16 Feb 2021 10:24:15 -0700 Subject: [PATCH 59/73] Fixing example input scripts with mode multi --- doc/src/comm_modify.rst | 3 ++- examples/granregion/in.granregion.funnel | 2 +- examples/granregion/in.granregion.mixer | 2 +- examples/srd/in.srd.mixture | 2 +- 4 files changed, 5 insertions(+), 4 deletions(-) diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 489ab407ee..06087bd9a2 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -34,7 +34,7 @@ Examples comm_modify mode multi reduce/multi comm_modify mode multi group solvent - comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0 + comm_modift mode multi cutoff/multi 0 10.0 cutoff/multi 2*4 15.0 comm_modify vel yes comm_modify mode single cutoff 5.0 vel yes comm_modify cutoff/multi * 0.0 @@ -101,6 +101,7 @@ communication mode *multi* instead. Since the communication cutoffs are determined per atom collections, a collection specifier is needed and cutoff for one or multiple collections can be extended. Also ranges of collections using the usual asterisk notation can be given. +Collections are indexed from 0 to N-1 where N is the total number of collections. Note that the arguments for *cutoff/multi* are parsed right before each simulation to account for potential changes in the number of collections. Custom cutoffs are preserved between runs but if collections are redefined, diff --git a/examples/granregion/in.granregion.funnel b/examples/granregion/in.granregion.funnel index 63e79a7114..ef74ce5109 100644 --- a/examples/granregion/in.granregion.funnel +++ b/examples/granregion/in.granregion.funnel @@ -86,7 +86,7 @@ pair_style gran/hertz/history & ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 pair_coeff * * -neighbor ${skin} bin +neighbor ${skin} multi thermo ${logfreq} comm_style brick diff --git a/examples/granregion/in.granregion.mixer b/examples/granregion/in.granregion.mixer index f9a9d04cbe..383f51f074 100644 --- a/examples/granregion/in.granregion.mixer +++ b/examples/granregion/in.granregion.mixer @@ -49,7 +49,7 @@ pair_style gran/hertz/history & ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 pair_coeff * * -neighbor ${skin} bin +neighbor ${skin} multi thermo ${logfreq} comm_style brick diff --git a/examples/srd/in.srd.mixture b/examples/srd/in.srd.mixture index ff6e6f5b72..6a0100d800 100644 --- a/examples/srd/in.srd.mixture +++ b/examples/srd/in.srd.mixture @@ -62,7 +62,7 @@ delete_atoms overlap 0.5 small big reset_timestep 0 -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes From d9d5d3a36a175a492c4c617a4d67a4fa5b7ab68a Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Fri, 19 Mar 2021 09:29:47 -0600 Subject: [PATCH 60/73] Correcting skin distance calculation for collection/interval --- src/neighbor.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index c33345f88d..13f5c9f958 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -409,7 +409,7 @@ void Neighbor::init() ri = collection2cut[i]*0.5; for(j = 0; j < ncollections; j++){ rj = collection2cut[j]*0.5; - tmp = force->pair->radii2cut(ri, rj); + tmp = force->pair->radii2cut(ri, rj) + skin; cutcollectionsq[i][j] = tmp*tmp; } } @@ -425,7 +425,8 @@ void Neighbor::init() double cuttmp; for(i = 1; i <= n; i++){ - cuttmp = sqrt(cutneighsq[i][i]); + // Remove skin added to cutneighsq + cuttmp = sqrt(cutneighsq[i][i]) - skin; for(icollection = 0; icollection < ncollections; icollection ++){ if(collection2cut[icollection] >= cuttmp) { type2collection[i] = icollection; From bd6dd658d6b037c03203d413fdff71f358cbc15b Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Wed, 7 Apr 2021 17:21:16 -0600 Subject: [PATCH 61/73] Updating to master, misc style changes --- src/USER-OMP/npair_full_multi_omp.cpp | 2 +- src/USER-OMP/npair_half_multi_newtoff_omp.cpp | 4 +- src/USER-OMP/npair_half_multi_newton_omp.cpp | 8 +- .../npair_half_multi_newton_tri_omp.cpp | 4 +- src/comm.cpp | 18 ++-- src/comm_brick.cpp | 26 ++--- src/comm_tiled.cpp | 22 ++--- src/nbin_multi.cpp | 2 +- src/neighbor.cpp | 98 +++++++++---------- src/npair_half_multi_newtoff.cpp | 4 +- src/npair_half_multi_newton.cpp | 4 +- src/npair_half_multi_newton_tri.cpp | 2 +- src/npair_half_size_multi_newtoff.cpp | 4 +- src/npair_half_size_multi_newton.cpp | 8 +- src/npair_half_size_multi_newton_tri.cpp | 4 +- src/nstencil.cpp | 6 +- src/pair_hybrid.cpp | 8 +- 17 files changed, 112 insertions(+), 112 deletions(-) diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index 4fc6fb4a68..a6df0c6dbe 100755 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -98,7 +98,7 @@ void NPairFullMultiOmp::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in surrounding bins in stencil including self diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp index ed0e770b2f..bf5d5efa69 100755 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -100,7 +100,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in other bins in stencil including self @@ -114,7 +114,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; - for (j = js; j >=0; j = bins[j]) { + for (j = js; j >= 0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index 13d286ab5b..00e4b6c624 100755 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -99,13 +99,13 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin - if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(icollection == jcollection) js = bins[i]; + if (icollection == jcollection) js = bins[i]; else js = binhead_multi[jcollection][jbin]; // if same collection, @@ -117,7 +117,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(icollection != jcollection and j < i) continue; + if ((icollection != jcollection) && (j < i)) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index cb758673d4..31e7635414 100755 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -100,7 +100,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil @@ -120,7 +120,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) for (j = js; j >= 0; j = bins[j]) { // if same size (same collection), use half stencil - if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/comm.cpp b/src/comm.cpp index 7e3d6d839b..dc6d75dd79 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -246,15 +246,15 @@ void Comm::init() for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; - if(mode == Comm::MULTI and neighbor->style != Neighbor::MULTI) + if ((mode == Comm::MULTI) && (neighbor->style != Neighbor::MULTI)) error->all(FLERR,"Cannot use comm mode multi without multi-style neighbor lists"); - if(multi_reduce){ + if (multi_reduce) { if (force->newton == 0) error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); if (neighbor->any_full()) error->all(FLERR,"Cannot use multi/reduce communication with a full neighbor list"); - if(mode != Comm::MULTI) + if (mode != Comm::MULTI) error->all(FLERR,"Cannot use multi/reduce communication without mode multi"); } } @@ -293,11 +293,11 @@ void Comm::modify_params(int narg, char **arg) // need to reset cutghostuser when switching comm mode if (mode == Comm::MULTI) cutghostuser = 0.0; if (mode == Comm::MULTIOLD) cutghostuser = 0.0; - if(cutusermulti){ + if (cutusermulti) { memory->destroy(cutusermulti); cutusermulti = nullptr; } - if(cutusermultiold){ + if (cutusermultiold) { memory->destroy(cutusermultiold); cutusermultiold = nullptr; } @@ -306,7 +306,7 @@ void Comm::modify_params(int narg, char **arg) // need to reset cutghostuser when switching comm mode if (mode == Comm::SINGLE) cutghostuser = 0.0; if (mode == Comm::MULTIOLD) cutghostuser = 0.0; - if(cutusermultiold){ + if (cutusermultiold) { memory->destroy(cutusermultiold); cutusermultiold = nullptr; } @@ -315,7 +315,7 @@ void Comm::modify_params(int narg, char **arg) // need to reset cutghostuser when switching comm mode if (mode == Comm::SINGLE) cutghostuser = 0.0; if (mode == Comm::MULTI) cutghostuser = 0.0; - if(cutusermulti){ + if (cutusermulti) { memory->destroy(cutusermulti); cutusermulti = nullptr; } @@ -743,8 +743,8 @@ double Comm::get_comm_cutoff() } // Check maximum interval size for neighbor multi - if(neighbor->interval_collection_flag){ - for(int i = 0; i < neighbor->ncollections; i++){ + if (neighbor->interval_collection_flag) { + for (int i = 0; i < neighbor->ncollections; i++){ maxcommcutoff = MAX(maxcommcutoff, neighbor->collection2cut[i]); } } diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 50c18e5fe7..b6306eb042 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -145,9 +145,9 @@ void CommBrick::init() ncollections = neighbor->ncollections; allocate_multi(maxswap); memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - if(cutusermultiflag) { + if (cutusermultiflag) { memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); - for(int i = ncollections_prior; i < ncollections; i++) + for (int i = ncollections_prior; i < ncollections; i++) cutusermulti[i] = -1.0; } @@ -206,15 +206,15 @@ void CommBrick::setup() ncollections = neighbor->ncollections; // reallocate memory for multi-style communication at setup if ncollections change - if(ncollections_prior != ncollections){ - if(multilo) free_multi(); - if(cutghostmulti) memory->destroy(cutghostmulti); + if (ncollections_prior != ncollections) { + if (multilo) free_multi(); + if (cutghostmulti) memory->destroy(cutghostmulti); allocate_multi(maxswap); memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - if(cutusermultiflag) { + if (cutusermultiflag) { memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); - for(i = ncollections_prior; i < ncollections; i++) + for (i = ncollections_prior; i < ncollections; i++) cutusermulti[i] = -1.0; } @@ -223,11 +223,11 @@ void CommBrick::setup() // parse any cutoff/multi commands int nhi, nlo; - for(auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { + for (auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { utils::bounds(FLERR,it->first,0,ncollections,nlo,nhi,error); - if(nhi >= ncollections) + if (nhi >= ncollections) error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); - for (j=nlo; j<=nhi; ++j) + for (j = nlo; j<=nhi; ++j) cutusermulti[j] = it->second; } usermultiargs.clear(); @@ -249,7 +249,7 @@ void CommBrick::setup() } for (j = 0; j < ncollections; j++){ - if(multi_reduce and cutcollectionsq[j][j] > cutcollectionsq[i][i]) continue; + if (multi_reduce && (cutcollectionsq[j][j] > cutcollectionsq[i][i])) continue; cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j])); cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j])); cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j])); @@ -815,7 +815,7 @@ void CommBrick::borders() AtomVec *avec = atom->avec; // After exchanging/sorting, need to reconstruct collection array for border communication - if(mode == Comm::MULTI) neighbor->build_collection(0); + if (mode == Comm::MULTI) neighbor->build_collection(0); // do swaps over all 3 dimensions @@ -989,7 +989,7 @@ void CommBrick::borders() firstrecv[iswap] = atom->nlocal + atom->nghost; nprior = atom->nlocal + atom->nghost; atom->nghost += nrecv; - if(neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); + if (neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); iswap++; } diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 27f630f720..da3bb3a65f 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -191,16 +191,16 @@ void CommTiled::setup() ncollections = neighbor->ncollections; // allocate memory for multi-style communication at setup as ncollections can change - if(ncollections_prior != ncollections){ + if (ncollections_prior != ncollections) { memory->destroy(cutghostmulti); if (mode == Comm::MULTI) memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - for(i = 0; i < maxswap; i ++) + for (i = 0; i < maxswap; i ++) grow_swap_send_multi(i,DELTA_PROCS); - if(cutusermultiflag){ + if (cutusermultiflag) { memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); - for(i = ncollections_prior; i < ncollections; i++) + for (i = ncollections_prior; i < ncollections; i++) cutusermulti[i] = -1.0; } @@ -209,12 +209,12 @@ void CommTiled::setup() // parse any cutoff/multi commands int nhi, nlo; - for(auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { + for (auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { utils::bounds(FLERR,it->first,0,ncollections,nlo,nhi,error); - if(nhi >= ncollections) + if (nhi >= ncollections) error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); - for (j=nlo; j<=nhi; ++j) + for (j = nlo; j <= nhi; ++j) cutusermulti[j] = it->second; } usermultiargs.clear(); @@ -236,7 +236,7 @@ void CommTiled::setup() } for (j = 0; j < ncollections; j++){ - if(multi_reduce and cutcollectionsq[j][j] > cutcollectionsq[i][i]) continue; + if (multi_reduce && (cutcollectionsq[j][j] > cutcollectionsq[i][i])) continue; cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j])); cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j])); cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j])); @@ -1066,7 +1066,7 @@ void CommTiled::borders() AtomVec *avec = atom->avec; // After exchanging, need to reconstruct collection array for border communication - if(mode == Comm::MULTI) neighbor->build_collection(0); + if (mode == Comm::MULTI) neighbor->build_collection(0); // send/recv max one = max # of atoms in single send/recv for any swap // send/recv max all = max # of atoms in all sends/recvs within any swap @@ -1357,7 +1357,7 @@ void CommTiled::borders() if (n) { nprior = atom->nghost + atom->nlocal; atom->nghost += forward_recv_offset[iswap][n-1] + recvnum[iswap][n-1]; - if(neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); + if (neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); } } @@ -2405,7 +2405,7 @@ void CommTiled::grow_swap_send_multi(int i, int n) { memory->destroy(sendbox_multi[i]); - if(ncollections > 0) + if (ncollections > 0) memory->create(sendbox_multi[i],n,ncollections,6,"comm:sendbox_multi"); } diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index a39f10d074..3bfe26239b 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -234,7 +234,7 @@ void NBinMulti::setup_bins(int /*style*/) if (binsize_optimal*bininvx_multi[n] > CUT2BIN_RATIO || binsize_optimal*bininvy_multi[n] > CUT2BIN_RATIO) error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); - if(dimension == 3 and binsize_optimal*bininvz_multi[n] > CUT2BIN_RATIO) + if ((dimension == 3) && (binsize_optimal*bininvz_multi[n] > 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 diff --git a/src/neighbor.cpp b/src/neighbor.cpp index def4cbd228..5a4c574ce9 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -359,16 +359,16 @@ void Neighbor::init() cutneighmaxsq = cutneighmax * cutneighmax; // Define cutoffs for multi - if(style == Neighbor::MULTI){ + if (style == Neighbor::MULTI) { int icollection, jcollection; // If collections not yet defined, create default map using types - if(not custom_collection_flag) { + if (not custom_collection_flag) { ncollections = n; interval_collection_flag = 0; - if(not type2collection) + if (not type2collection) memory->create(type2collection,n+1,"neigh:type2collection"); - for(i = 1; i <= n; i++) + for (i = 1; i <= n; i++) type2collection[i] = i-1; } @@ -384,30 +384,30 @@ void Neighbor::init() // // Define collection cutoffs - for(i = 0; i < ncollections; i++) - for(j = 0; j < ncollections; j++) + for (i = 0; i < ncollections; i++) + for (j = 0; j < ncollections; j++) cutcollectionsq[i][j] = 0.0; - if(not interval_collection_flag){ + if (not interval_collection_flag) { finite_cut_flag = 0; - for(i = 1; i <= n; i++){ + for (i = 1; i <= n; i++){ icollection = type2collection[i]; - for(j = 1; j <= n; j++){ + for (j = 1; j <= n; j++){ jcollection = type2collection[j]; - if(cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { + if (cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { cutcollectionsq[icollection][jcollection] = cutneighsq[i][j]; cutcollectionsq[jcollection][icollection] = cutneighsq[i][j]; } } } } else { - if(force->pair->finitecutflag){ + if (force->pair->finitecutflag) { finite_cut_flag = 1; // If cutoffs depend on finite atom sizes, use radii of intervals to find cutoffs double ri, rj, tmp; - for(i = 0; i < ncollections; i++){ + for (i = 0; i < ncollections; i++){ ri = collection2cut[i]*0.5; - for(j = 0; j < ncollections; j++){ + for (j = 0; j < ncollections; j++){ rj = collection2cut[j]*0.5; tmp = force->pair->radii2cut(ri, rj) + skin; cutcollectionsq[i][j] = tmp*tmp; @@ -417,33 +417,33 @@ void Neighbor::init() finite_cut_flag = 0; // Map types to collections - if(not type2collection) + if (not type2collection) memory->create(type2collection,n+1,"neigh:type2collection"); - for(i = 1; i <= n; i++) + for (i = 1; i <= n; i++) type2collection[i] = -1; double cuttmp; - for(i = 1; i <= n; i++){ + for (i = 1; i <= n; i++){ // Remove skin added to cutneighsq cuttmp = sqrt(cutneighsq[i][i]) - skin; - for(icollection = 0; icollection < ncollections; icollection ++){ - if(collection2cut[icollection] >= cuttmp) { + for (icollection = 0; icollection < ncollections; icollection ++){ + if (collection2cut[icollection] >= cuttmp) { type2collection[i] = icollection; break; } } - if(type2collection[i] == -1) + if (type2collection[i] == -1) error->all(FLERR, "Pair cutoff exceeds interval cutoffs for multi"); } // Define cutoffs - for(i = 1; i <= n; i++){ + for (i = 1; i <= n; i++){ icollection = type2collection[i]; - for(j = 1; j <= n; j++){ + for (j = 1; j <= n; j++){ jcollection = type2collection[j]; - if(cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { + if (cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { cutcollectionsq[icollection][jcollection] = cutneighsq[i][j]; cutcollectionsq[jcollection][icollection] = cutneighsq[i][j]; } @@ -2175,7 +2175,7 @@ void Neighbor::build(int topoflag) int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; // rebuild collection array from scratch - if(style == Neighbor::MULTI) build_collection(0); + if (style == Neighbor::MULTI) build_collection(0); // check that using special bond flags will not overflow neigh lists @@ -2500,15 +2500,15 @@ void Neighbor::modify_params(int narg, char **arg) } else error->all(FLERR,"Illegal neigh_modify command"); } else if (strcmp(arg[iarg],"collection/interval") == 0) { - if(style != Neighbor::MULTI) + if (style != Neighbor::MULTI) error->all(FLERR,"Cannot use collection/interval command without multi setting"); - if(iarg+2 > narg) + if (iarg+2 > narg) error->all(FLERR,"Invalid collection/interval command"); ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); - if(ncollections < 1) + if (ncollections < 1) error->all(FLERR,"Invalid collection/interval command"); - if(iarg+1+ncollections > narg) + if (iarg+1+ncollections > narg) error->all(FLERR,"Invalid collection/interval command"); int ntypes = atom->ntypes; @@ -2521,26 +2521,26 @@ void Neighbor::modify_params(int narg, char **arg) // Set upper cutoff for each collection char *id; double cut_interval; - for(i = 0; i < ncollections; i++){ + for (i = 0; i < ncollections; i++){ cut_interval = utils::numeric(FLERR,arg[iarg+2+i],false,lmp); collection2cut[i] = cut_interval; - if(i != 0) - if(collection2cut[i-1] >= collection2cut[i]) + if (i != 0) + if (collection2cut[i-1] >= collection2cut[i]) error->all(FLERR,"Nonsequential interval cutoffs in collection/interval setting"); } iarg += 2 + ncollections; } else if (strcmp(arg[iarg],"collection/type") == 0) { - if(style != Neighbor::MULTI) + if (style != Neighbor::MULTI) error->all(FLERR,"Cannot use collection/type command without multi setting"); - if(iarg+2 > narg) + if (iarg+2 > narg) error->all(FLERR,"Invalid collection/type command"); ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); - if(ncollections < 1) + if (ncollections < 1) error->all(FLERR,"Invalid collection/interval command"); - if(iarg+1+ncollections > narg) + if (iarg+1+ncollections > narg) error->all(FLERR,"Invalid collection/type command"); int ntypes = atom->ntypes; @@ -2548,17 +2548,17 @@ void Neighbor::modify_params(int narg, char **arg) interval_collection_flag = 0; custom_collection_flag = 1; - if(not type2collection) + if (not type2collection) memory->create(type2collection,ntypes+1,"neigh:type2collection"); // Erase previous mapping - for(i = 1; i <= ntypes; i++) + for (i = 1; i <= ntypes; i++) type2collection[i] = -1; // For each custom range, define mapping for types in interval int nfield; char *str; - for(i = 0; i < ncollections; i++){ + for (i = 0; i < ncollections; i++){ n = strlen(arg[iarg+2+i]) + 1; str = new char[n]; strcpy(str,arg[iarg+2+i]); @@ -2570,7 +2570,7 @@ void Neighbor::modify_params(int narg, char **arg) utils::bounds(FLERR,field,1,ntypes,nlo,nhi,error); for (k = nlo; k <= nhi; k++) { - if(type2collection[k] != -1) + if (type2collection[k] != -1) error->all(FLERR,"Type specified more than once in collection/type commnd"); type2collection[k] = i; } @@ -2580,8 +2580,8 @@ void Neighbor::modify_params(int narg, char **arg) } // Check for undefined atom type - for(i = 1; i <= ntypes; i++){ - if(type2collection[i] == -1){ + for (i = 1; i <= ntypes; i++){ + if (type2collection[i] == -1) { error->all(FLERR,"Type missing in collection/type commnd"); } } @@ -2632,8 +2632,8 @@ int Neighbor::exclude_setting() int Neighbor::any_full() { int any_full = 0; - for(int i = 0; i < old_nrequest; i++) { - if(old_requests[i]->full) any_full = 1; + for (int i = 0; i < old_nrequest; i++) { + if (old_requests[i]->full) any_full = 1; } return any_full; } @@ -2648,31 +2648,31 @@ void Neighbor::build_collection(int istart) error->all(FLERR, "Cannot define atom collections without neighbor style multi"); int nmax = atom->nlocal+atom->nghost; - if(nmax > nmax_collection){ + if (nmax > nmax_collection) { nmax_collection = nmax+DELTA_PERATOM; memory->grow(collection, nmax_collection, "neigh:collection"); } - if(finite_cut_flag){ + if (finite_cut_flag) { double cut; int icollection; - for(int i = istart; i < nmax; i++){ + for (int i = istart; i < nmax; i++){ cut = force->pair->atom2cut(i); collection[i] = -1; - for(icollection = 0; icollection < ncollections; icollection++){ - if(collection2cut[icollection] >= cut) { + for (icollection = 0; icollection < ncollections; icollection++){ + if (collection2cut[icollection] >= cut) { collection[i] = icollection; break; } } - if(collection[i] == -1) + if (collection[i] == -1) error->one(FLERR, "Atom cutoff exceeds interval cutoffs for multi"); } } else { int *type = atom->type; - for(int i = istart; i < nmax; i++){ + for (int i = istart; i < nmax; i++){ collection[i] = type2collection[type[i]]; } } diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index 5f050429ac..e1f66800dc 100755 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -88,7 +88,7 @@ void NPairHalfMultiNewtoff::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in other bins in stencil including self @@ -102,7 +102,7 @@ void NPairHalfMultiNewtoff::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; - for (j = js; j >=0; j = bins[j]) { + for (j = js; j >= 0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index 18e66d4adb..4cf30f0ce5 100755 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -93,7 +93,7 @@ void NPairHalfMultiNewton::build(NeighList *list) // if same size: uses half stencil so check central bin if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(icollection == jcollection) js = bins[i]; + if (icollection == jcollection) js = bins[i]; else js = binhead_multi[jcollection][jbin]; // if same collection, @@ -105,7 +105,7 @@ void NPairHalfMultiNewton::build(NeighList *list) // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(icollection != jcollection and j < i) continue; + if((icollection != jcollection) && (j < i)) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index 90c6cf714d..556529eba6 100755 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -87,7 +87,7 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index 77aa4f746b..23ea27b209 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -79,7 +79,7 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in other bins in stencil including self @@ -93,7 +93,7 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; - for (j = js; j >=0; j = bins[j]) { + for (j = js; j >= 0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index 67715ebe68..50db6c19ec 100755 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -76,13 +76,13 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin - if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(icollection == jcollection) js = bins[i]; + if (icollection == jcollection) js = bins[i]; else js = binhead_multi[jcollection][jbin]; // if same collection, @@ -94,7 +94,7 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(icollection != jcollection and j < i) continue; + if ((icollection != jcollection) && (j < i)) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 2bf033781e..290c8c76f4 100755 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -76,7 +76,7 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil @@ -96,7 +96,7 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) for (j = js; j >= 0; j = bins[j]) { // if same size (same collection), use half stencil - if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/nstencil.cpp b/src/nstencil.cpp index ba7259a9fc..729b690ba1 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -272,10 +272,10 @@ void NStencil::create_setup() double stencil_range; int n = ncollections; - if(nb) copy_bin_info_multi(); + if (nb) copy_bin_info_multi(); // Deallocate arrays if previously allocated - if(n > maxcollections and stencil_multi){ + if((n > maxcollections) && stencil_multi){ memory->destroy(nstencil_multi); for (i = 0; i < maxcollections; i++) { for (j = 0; j < maxcollections; j++) @@ -299,7 +299,7 @@ void NStencil::create_setup() } // Allocate arrays - if(!maxstencil_multi) { + if (!maxstencil_multi) { memory->create(flag_half_multi, n, n, "neighstencil:flag_half_multi"); memory->create(flag_skip_multi, n, n, diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 6e8b55fd67..075290ef38 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -1083,9 +1083,9 @@ double PairHybrid::atom2cut(int i) cut = 0.0; for (int m = 0; m < nstyles; m++) { - if (styles[m]->finitecutflag){ + if (styles[m]->finitecutflag) { temp = styles[m]->atom2cut(i); - if(temp > cut) cut = temp; + if (temp > cut) cut = temp; } } return cut; @@ -1101,9 +1101,9 @@ double PairHybrid::radii2cut(double r1, double r2) cut = 0.0; for (int m = 0; m < nstyles; m++) { - if (styles[m]->finitecutflag){ + if (styles[m]->finitecutflag) { temp = styles[m]->radii2cut(r1,r2); - if(temp > cut) cut = temp; + if (temp > cut) cut = temp; } } return cut; From fa386c0e9652b38b5cbe2ec707229371024ece58 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 4 May 2021 17:12:17 -0600 Subject: [PATCH 62/73] Changing how multi/cutoff works, changing collection indexing in user args --- src/GRANULAR/pair_gran_hooke_history.cpp | 2 +- src/comm.cpp | 22 +++++--- src/comm.h | 7 +-- src/comm_brick.cpp | 71 +++++++++--------------- src/comm_tiled.cpp | 67 +++++++++------------- src/neighbor.cpp | 4 ++ src/nstencil_full_multi_2d.cpp | 5 +- src/nstencil_full_multi_3d.cpp | 5 +- src/nstencil_half_multi_2d.cpp | 5 +- src/nstencil_half_multi_2d_tri.cpp | 5 +- src/nstencil_half_multi_3d.cpp | 5 +- src/nstencil_half_multi_3d_tri.cpp | 5 +- 12 files changed, 100 insertions(+), 103 deletions(-) diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 510d0713b1..95cfaad3e0 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -824,4 +824,4 @@ double PairGranHookeHistory::radii2cut(double r1, double r2) { double cut = r1+r2; return cut; -} \ No newline at end of file +} diff --git a/src/comm.cpp b/src/comm.cpp index dc6d75dd79..ca09af2238 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -35,7 +35,6 @@ #include "update.h" #include -#include #ifdef _OPENMP #include #endif @@ -58,9 +57,8 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) bordergroup = 0; cutghostuser = 0.0; cutusermulti = nullptr; - cutusermultiflag = 0; cutusermultiold = nullptr; - ncollections_prior = 0; + ncollections = 0; ghost_velocity = 0; user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0; @@ -149,6 +147,7 @@ void Comm::copy_arrays(Comm *oldcomm) memcpy(zsplit,oldcomm->zsplit,(procgrid[2]+1)*sizeof(double)); } + ncollections = oldcomm->ncollections; if (oldcomm->cutusermulti) { memory->create(cutusermulti,ncollections,"comm:cutusermulti"); memcpy(cutusermulti,oldcomm->cutusermulti,ncollections); @@ -354,14 +353,23 @@ void Comm::modify_params(int narg, char **arg) error->all(FLERR, "Cannot set cutoff/multi before simulation box is defined"); - // save arguments so they can be parsed in comm->setup() - // ncollections can be changed by neigh_modify commands + // Check if # of collections has changed, if so erase any previously defined cutoffs + // Neighbor will reset ncollections if collections are redefined + if (ncollections_cutoff != neighbor->ncollections) { + ncollections_cutoff = neighbor->ncollections; + if (cutusermulti) memory->destroy(cutusermulti); + memory->create(cutusermulti,ncollections_cutoff,"comm:cutusermulti"); + for (i=0; i < ncollections_cutoff; ++i) + cutusermulti[i] = -1.0; + } + utils::bounds(FLERR,arg[iarg+1],1,ncollections_cutoff+1,nlo,nhi,error); cut = utils::numeric(FLERR,arg[iarg+2],false,lmp); cutghostuser = MAX(cutghostuser,cut); - cutusermultiflag = 1; if (cut < 0.0) error->all(FLERR,"Invalid cutoff in comm_modify command"); - usermultiargs.emplace_back(arg[iarg+1], cut); + // collections use 1-based indexing externally and 0-based indexing internally + for (i=nlo; i<=nhi; ++i) + cutusermulti[i-1] = cut; iarg += 3; } else if (strcmp(arg[iarg],"cutoff/multi/old") == 0) { int i,nlo,nhi; diff --git a/src/comm.h b/src/comm.h index 418983b6e6..5d3d0b3d53 100644 --- a/src/comm.h +++ b/src/comm.h @@ -33,10 +33,9 @@ class Comm : protected Pointers { double cutghost[3]; // cutoffs used for acquiring ghost atoms double cutghostuser; // user-specified ghost cutoff (mode == 0) double *cutusermulti; // per collection user ghost cutoff (mode == 1) - int cutusermultiflag; - std::vector> usermultiargs; - // collection args for custom ghost cutoffs double *cutusermultiold; // per type user ghost cutoff (mode == 2) + int ncollections; // # of collections known by comm, used to test if # has changed + int ncollections_cutoff; // # of collections stored b cutoff/multi int recv_from_partition; // recv proc layout from this partition int send_to_partition; // send my proc layout to this partition // -1 if no recv or send @@ -157,8 +156,6 @@ class Comm : protected Pointers { int coregrid[3]; // 3d grid of cores within a node int user_coregrid[3]; // user request for cores in each dim int multi_reduce; // 1 if multi cutoff is intra-collection cutoff - int ncollections; // number of collection cutoffs defined for multi - int ncollections_prior; // value of ncollections at last setup void init_exchange(); int rendezvous_irregular(int, char *, int, int, int *, diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index b6306eb042..184babccd2 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -141,19 +141,30 @@ void CommBrick::init() // memory for multi style communication // allocate in setup - if (mode == Comm::MULTI && multilo == nullptr) { - ncollections = neighbor->ncollections; - allocate_multi(maxswap); - memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - if (cutusermultiflag) { - memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); - for (int i = ncollections_prior; i < ncollections; i++) - cutusermulti[i] = -1.0; - } + if (mode == Comm::MULTI) { + // If inconsitent # of collections, destroy any preexisting arrays (may be missized) + if (ncollections != neighbor->ncollections) { + ncollections = neighbor->ncollections; + if (multilo != nullptr) { + free_multi(); + memory->destroy(cutghostmulti); + } + } - ncollections_prior = ncollections; + // delete any old user cutoffs if # of collections chanaged + if (cutusermulti && ncollections != ncollections_cutoff) { + if(me == 0) error->warning(FLERR, "cutoff/multi settings discarded, must be defined" + " after customizing collections in neigh_modify"); + memory->destroy(cutusermulti); + cutusermulti = nullptr; + } + + if (multilo == nullptr) { + allocate_multi(maxswap); + memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); + } } - if ((mode == Comm::SINGLE or mode == Comm::MULTIOLD) && multilo) { + if ((mode == Comm::SINGLE || mode == Comm::MULTIOLD) && multilo) { free_multi(); memory->destroy(cutghostmulti); } @@ -164,7 +175,7 @@ void CommBrick::init() allocate_multiold(maxswap); memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold"); } - if ((mode == Comm::SINGLE or mode == Comm::MULTI) && multioldlo) { + if ((mode == Comm::SINGLE || mode == Comm::MULTI) && multioldlo) { free_multiold(); memory->destroy(cutghostmultiold); } @@ -201,39 +212,11 @@ void CommBrick::setup() "will be generated. Atoms may get lost."); if (mode == Comm::MULTI) { - // build initial collection array - neighbor->build_collection(0); - ncollections = neighbor->ncollections; - - // reallocate memory for multi-style communication at setup if ncollections change - if (ncollections_prior != ncollections) { - if (multilo) free_multi(); - if (cutghostmulti) memory->destroy(cutghostmulti); - - allocate_multi(maxswap); - memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - if (cutusermultiflag) { - memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); - for (i = ncollections_prior; i < ncollections; i++) - cutusermulti[i] = -1.0; - } - - ncollections_prior = ncollections; - } - - // parse any cutoff/multi commands - int nhi, nlo; - for (auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { - utils::bounds(FLERR,it->first,0,ncollections,nlo,nhi,error); - if (nhi >= ncollections) - error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); - for (j = nlo; j<=nhi; ++j) - cutusermulti[j] = it->second; - } - usermultiargs.clear(); - - double **cutcollectionsq = neighbor->cutcollectionsq; + + // build collection array for atom exchange + neighbor->build_collection(0); + // If using multi/reduce, communicate particles a distance equal // to the max cutoff with equally sized or smaller collections // If not, communicate the maximum cutoff of the entire collection diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index da3bb3a65f..277228522b 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -104,12 +104,8 @@ void CommTiled::init_buffers() cutghostmultiold = nullptr; sendbox_multi = nullptr; sendbox_multiold = nullptr; - - // initialize ncollections so grow_swap_send_multi() will not - // construct arrays in init() but will wait for setup() - ncollections = 0; - ncollections_prior = 0; + // Note this may skip growing multi arrays, will call again in init() maxswap = 6; allocate_swap(maxswap); } @@ -125,11 +121,32 @@ void CommTiled::init() nswap = 2*domain->dimension; + memory->destroy(cutghostmulti); + if (mode == Comm::MULTI) { + // If inconsitent # of collections, destroy any preexisting arrays (may be missized) + if (ncollections != neighbor->ncollections) { + ncollections = neighbor->ncollections; + } + + // delete any old user cutoffs if # of collections chanaged + if (cutusermulti && ncollections != ncollections_cutoff) { + if(me == 0) error->warning(FLERR, "cutoff/multi settings discarded, must be defined" + " after customizing collections in neigh_modify"); + memory->destroy(cutusermulti); + cutusermulti = nullptr; + } + + // grow sendbox_multi now that ncollections is known + for (int i = 0; i < maxswap; i ++) + grow_swap_send_multi(i,DELTA_PROCS); + + memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); + } + memory->destroy(cutghostmultiold); if (mode == Comm::MULTIOLD) memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold"); - int bufextra_old = bufextra; init_exchange(); if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2); @@ -186,44 +203,14 @@ void CommTiled::setup() // check that cutoff < any periodic box length if (mode == Comm::MULTI) { - // build collection from scratch as it is needed for atom exchange - neighbor->build_collection(0); - ncollections = neighbor->ncollections; - - // allocate memory for multi-style communication at setup as ncollections can change - if (ncollections_prior != ncollections) { - memory->destroy(cutghostmulti); - if (mode == Comm::MULTI) - memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - - for (i = 0; i < maxswap; i ++) - grow_swap_send_multi(i,DELTA_PROCS); - if (cutusermultiflag) { - memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); - for (i = ncollections_prior; i < ncollections; i++) - cutusermulti[i] = -1.0; - } - - ncollections_prior = ncollections; - } - - // parse any cutoff/multi commands - int nhi, nlo; - for (auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { - utils::bounds(FLERR,it->first,0,ncollections,nlo,nhi,error); - if (nhi >= ncollections) - error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); - - for (j = nlo; j <= nhi; ++j) - cutusermulti[j] = it->second; - } - usermultiargs.clear(); - double **cutcollectionsq = neighbor->cutcollectionsq; + + // build collection array for atom exchange + neighbor->build_collection(0); + // If using multi/reduce, communicate particles a distance equal // to the max cutoff with equally sized or smaller collections // If not, communicate the maximum cutoff of the entire collection - for (i = 0; i < ncollections; i++) { if (cutusermulti) { cutghostmulti[i][0] = cutusermulti[i]; diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 5a4c574ce9..ab63a6874b 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -2514,6 +2514,8 @@ void Neighbor::modify_params(int narg, char **arg) int ntypes = atom->ntypes; int n, nlo, nhi, i, j; + // Invalidate old user cutoffs + comm->ncollections_cutoff = 0; interval_collection_flag = 1; custom_collection_flag = 1; memory->grow(collection2cut,ncollections,"neigh:collection2cut"); @@ -2546,6 +2548,8 @@ void Neighbor::modify_params(int narg, char **arg) int ntypes = atom->ntypes; int n, nlo, nhi, i, j, k; + // Invalidate old user cutoffs + comm->ncollections_cutoff = 0; interval_collection_flag = 0; custom_collection_flag = 1; if (not type2collection) diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index b27e3c2a9c..c3b0472c26 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -56,7 +56,10 @@ void NStencilFullMulti2d::create() for (icollection = 0; icollection < n; icollection++) { for (jcollection = 0; jcollection < n; jcollection++) { - if (flag_skip_multi[icollection][jcollection]) continue; + if (flag_skip_multi[icollection][jcollection]) { + nstencil_multi[icollection][jcollection] = 0; + continue; + } ns = 0; diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp index 3d97bc10ad..194afa408c 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -57,7 +57,10 @@ void NStencilFullMulti3d::create() for (icollection = 0; icollection < n; icollection++) { for (jcollection = 0; jcollection < n; jcollection++) { - if (flag_skip_multi[icollection][jcollection]) continue; + if (flag_skip_multi[icollection][jcollection]) { + nstencil_multi[icollection][jcollection] = 0; + continue; + } ns = 0; diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_2d.cpp index 32ee0297ff..0c8cd775e1 100644 --- a/src/nstencil_half_multi_2d.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -68,7 +68,10 @@ void NStencilHalfMulti2d::create() for (icollection = 0; icollection < n; icollection++) { for (jcollection = 0; jcollection < n; jcollection++) { - if (flag_skip_multi[icollection][jcollection]) continue; + if (flag_skip_multi[icollection][jcollection]) { + nstencil_multi[icollection][jcollection] = 0; + continue; + } ns = 0; diff --git a/src/nstencil_half_multi_2d_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp index 6588248109..974f5611df 100755 --- a/src/nstencil_half_multi_2d_tri.cpp +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -68,7 +68,10 @@ void NStencilHalfMulti2dTri::create() for (icollection = 0; icollection < n; icollection++) { for (jcollection = 0; jcollection < n; jcollection++) { - if (flag_skip_multi[icollection][jcollection]) continue; + if (flag_skip_multi[icollection][jcollection]) { + nstencil_multi[icollection][jcollection] = 0; + continue; + } ns = 0; diff --git a/src/nstencil_half_multi_3d.cpp b/src/nstencil_half_multi_3d.cpp index 19cd051392..070daa75da 100644 --- a/src/nstencil_half_multi_3d.cpp +++ b/src/nstencil_half_multi_3d.cpp @@ -68,7 +68,10 @@ void NStencilHalfMulti3d::create() for (icollection = 0; icollection < n; icollection++) { for (jcollection = 0; jcollection < n; jcollection++) { - if (flag_skip_multi[icollection][jcollection]) continue; + if (flag_skip_multi[icollection][jcollection]) { + nstencil_multi[icollection][jcollection] = 0; + continue; + } ns = 0; diff --git a/src/nstencil_half_multi_3d_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp index 3c5efac463..f1dfe2a78f 100755 --- a/src/nstencil_half_multi_3d_tri.cpp +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -68,7 +68,10 @@ void NStencilHalfMulti3dTri::create() for (icollection = 0; icollection < n; icollection++) { for (jcollection = 0; jcollection < n; jcollection++) { - if (flag_skip_multi[icollection][jcollection]) continue; + if (flag_skip_multi[icollection][jcollection]) { + nstencil_multi[icollection][jcollection] = 0; + continue; + } ns = 0; From 350ec7cc077b1c5a7db68e3f17e2266ee2f13995 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 4 May 2021 17:22:35 -0600 Subject: [PATCH 63/73] Updating documentation --- doc/src/comm_modify.rst | 4 ++-- doc/src/neigh_modify.rst | 15 ++++++++------- doc/src/neighbor.rst | 25 ++++++++++++++++--------- 3 files changed, 26 insertions(+), 18 deletions(-) diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 06087bd9a2..e11a75ed12 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -34,7 +34,7 @@ Examples comm_modify mode multi reduce/multi comm_modify mode multi group solvent - comm_modift mode multi cutoff/multi 0 10.0 cutoff/multi 2*4 15.0 + comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0 comm_modify vel yes comm_modify mode single cutoff 5.0 vel yes comm_modify cutoff/multi * 0.0 @@ -101,7 +101,7 @@ communication mode *multi* instead. Since the communication cutoffs are determined per atom collections, a collection specifier is needed and cutoff for one or multiple collections can be extended. Also ranges of collections using the usual asterisk notation can be given. -Collections are indexed from 0 to N-1 where N is the total number of collections. +Collections are indexed from 1 to N where N is the total number of collections. Note that the arguments for *cutoff/multi* are parsed right before each simulation to account for potential changes in the number of collections. Custom cutoffs are preserved between runs but if collections are redefined, diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 6ee21d7419..6e2d1bee2c 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -206,10 +206,11 @@ small, the optimal number of atoms is checked, but bin overhead goes up. If you set the binsize to 0.0, LAMMPS will use the default binsize of 1/2 the cutoff. -The *collection/type* option allows you to define custom collections of atom -types for the *multi* neighbor mode. By grouping atom types with -similar cutoffs, one may be able to improve performance by reducing -overhead. You must first specify the number of custom collections N to be +The *collection/type* option allows you to define collections of atom +types, used by the *multi* neighbor mode. By grouping atom types with +similar physical size or interaction cutoff lengths, one may be able +to improve performance by reducing +overhead. You must first specify the number of collections N to be defined followed by N lists of types. Each list consists of a series of type ranges separated by commas. The range can be specified as a single numeric value, or a wildcard asterisk can be used to specify a range @@ -218,13 +219,13 @@ example, if M = the number of atom types, then an asterisk with no numeric values means all types from 1 to M. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to M (inclusive). A middle asterisk means all types from m to n (inclusive). -Note that all atom types must be included in a custom collection. +Note that all atom types must be included in exactly one of the N collections. The *collection/interval* option provides a similar capability. -This command allows a user to define custom collections by specifying a +This command allows a user to define collections by specifying a series of cutoff intervals. LAMMPS will automatically sort atoms into these intervals based on their type-dependent cutoffs or their finite size. -You must first specify the number of custom collections N to be +You must first specify the number of collections N to be defined followed by N values representing the upper cutoff of each interval. This command is particularly useful for granular pairstyles where the interaction distance of particles depends on their radius and may not depend on their atom type. diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index bd58f7045d..80497d57cd 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -56,23 +56,30 @@ the largest cutoff distance between any pair of atom types and a single set of bins is defined to search over for all atom types. This can be inefficient if one pair of types has a very long cutoff, but other type pairs have a much shorter cutoff. The *multi* style uses -different sized bins for collections of different sized particles. Different +different sized bins for collections of different sized particles, where +"size" may mean the physical size of the particle or its cutoff +distance for interacting with other particles. Different sets of bins are then used to construct the neighbor lists as as further described by Shire, Hanley, and Stratford :ref:`(Shire) `. This imposes some extra setup overhead, but the searches themselves -may be much faster. By default, separate collections of particles are defined -for each atom type. For systems with two or more types with similar -cutoffs, one can reduce the extra overhead by defining custom collections -using the :doc:`neigh_modify ` command. See the -:doc:`comm_modify mode bytype ` command for compatible -communication options that may be beneficial for simulations of this kind. +may be much faster. By default, each atom type defines a separate +collection of particles. For systems where two or more atom types +have the same size (either physical size or cutoff distance), the +definition of collections can be customized, which can result in less +overhead and faster performance. See the :doc:`neigh_modify ` +command for how to define custom collections. Whether the collection +definition is customized or not, also see the +:doc:`comm_modify mode multi ` command for communication +options that further improve performance in a manner consistent with +neighbor style multi. An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest cutoff distance and multiple sets of bins are defined to search over for different atom types. This algorithm used to be the default *multi* algorithm in LAMMPS but was found to be significantly slower than the new -approach. Although, there may be instances where the *multi/old* style -could outperform the new style. +approach. For now we are keeping the old option in case there are use cases +where multi/old outperforms the new multi style. + The :doc:`neigh_modify ` command has additional options that control how often neighbor lists are built and which pairs are From 24075b3281e9708f01936f95d77cd97cc053aa2e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 May 2021 06:24:19 -0400 Subject: [PATCH 64/73] remove unused variable declarations --- src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp | 2 +- src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp | 2 +- src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp | 2 +- src/neighbor.cpp | 5 ++--- src/nstencil_full_multi_2d.cpp | 2 +- 5 files changed, 6 insertions(+), 7 deletions(-) diff --git a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp index 48fe1a8102..22128b29df 100644 --- a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp @@ -48,7 +48,7 @@ void NPairHalfSizeMultiOldNewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,m,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp index 104ba2477c..6747778dd6 100644 --- a/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp @@ -47,7 +47,7 @@ void NPairHalfSizeMultiOldNewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,m,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp index 41f6f764e4..73c36681f1 100644 --- a/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp @@ -47,7 +47,7 @@ void NPairHalfSizeMultiOldNewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,m,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; diff --git a/src/neighbor.cpp b/src/neighbor.cpp index bc4349f9fc..8088629295 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -2511,8 +2511,7 @@ void Neighbor::modify_params(int narg, char **arg) if (iarg+1+ncollections > narg) error->all(FLERR,"Invalid collection/interval command"); - int ntypes = atom->ntypes; - int n, nlo, nhi, i, j; + int i; // Invalidate old user cutoffs comm->ncollections_cutoff = 0; @@ -2521,7 +2520,7 @@ void Neighbor::modify_params(int narg, char **arg) memory->grow(collection2cut,ncollections,"neigh:collection2cut"); // Set upper cutoff for each collection - char *id; + double cut_interval; for (i = 0; i < ncollections; i++){ cut_interval = utils::numeric(FLERR,arg[iarg+2+i],false,lmp); diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index 7236d2bb5a..f106b6c8af 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -49,7 +49,7 @@ void NStencilFullMulti2d::set_stencil_properties() void NStencilFullMulti2d::create() { - int icollection, jcollection, bin_collection, i, j, k, ns; + int icollection, jcollection, bin_collection, i, j, ns; int n = ncollections; double cutsq; From 9ef039531318f22649b046014e5df5bfa4c16610 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 May 2021 06:30:52 -0400 Subject: [PATCH 65/73] whitespace fixes --- doc/src/comm_modify.rst | 18 +-- doc/src/neigh_modify.rst | 24 ++-- doc/src/neighbor.rst | 36 +++--- src/GRANULAR/pair_granular.cpp | 16 +-- src/USER-OMP/npair_full_multi_omp.cpp | 14 +-- src/USER-OMP/npair_half_multi_newtoff_omp.cpp | 20 +-- src/USER-OMP/npair_half_multi_newton_omp.cpp | 44 +++---- .../npair_half_multi_newton_tri_omp.cpp | 22 ++-- .../npair_half_size_multi_newtoff_omp.cpp | 22 ++-- .../npair_half_size_multi_newton_omp.cpp | 46 +++---- .../npair_half_size_multi_newton_tri_omp.cpp | 24 ++-- src/comm.cpp | 4 +- src/comm_brick.cpp | 50 ++++---- src/comm_tiled.cpp | 30 ++--- src/info.cpp | 4 +- src/nbin.cpp | 10 +- src/nbin.h | 10 +- src/nbin_multi.cpp | 16 +-- src/nbin_standard.h | 2 +- src/neighbor.cpp | 96 +++++++------- src/neighbor.h | 4 +- src/npair.cpp | 4 +- src/npair.h | 4 +- src/npair_full_multi.cpp | 12 +- src/npair_half_multi_newtoff.cpp | 20 +-- src/npair_half_multi_newton.cpp | 46 +++---- src/npair_half_multi_newton_tri.cpp | 26 ++-- src/npair_half_size_multi_newtoff.cpp | 20 +-- src/npair_half_size_multi_newton.cpp | 48 +++---- src/npair_half_size_multi_newton.h | 2 +- src/npair_half_size_multi_newton_tri.cpp | 20 +-- src/npair_half_size_multi_newton_tri.h | 2 +- src/npair_half_size_multi_old_newton.cpp | 6 +- src/npair_half_size_multi_old_newton_tri.cpp | 2 +- src/nstencil.cpp | 118 +++++++++--------- src/nstencil.h | 26 ++-- src/nstencil_full_multi_2d.cpp | 20 +-- src/nstencil_full_multi_3d.cpp | 24 ++-- src/nstencil_half_multi_2d.cpp | 24 ++-- src/nstencil_half_multi_2d_tri.cpp | 20 +-- src/nstencil_half_multi_3d.cpp | 26 ++-- src/nstencil_half_multi_3d_tri.cpp | 26 ++-- src/pair_hybrid.cpp | 4 +- 43 files changed, 505 insertions(+), 507 deletions(-) diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index e11a75ed12..4e9e6325c1 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -67,7 +67,7 @@ cutoff across all atom type pairs. For many systems this is an efficient algorithm, but for systems with widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can -be faster. In *multi*, each atom is assigned to a collection which should +be faster. In *multi*, each atom is assigned to a collection which should correspond to a set of atoms with similar interaction cutoffs. In this case, each atom collection is assigned its own distance cutoff for communication purposes, and fewer atoms will be @@ -100,22 +100,22 @@ The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to communication mode *multi* instead. Since the communication cutoffs are determined per atom collections, a collection specifier is needed and cutoff for one or multiple collections can be extended. Also ranges of collections -using the usual asterisk notation can be given. +using the usual asterisk notation can be given. Collections are indexed from 1 to N where N is the total number of collections. Note that the arguments for *cutoff/multi* are parsed right before each simulation to account for potential changes in the number of collections. -Custom cutoffs are preserved between runs but if collections are redefined, +Custom cutoffs are preserved between runs but if collections are redefined, one may want to respecify communication cutoffs. -For granular pair styles,the default cutoff is set to the sum of the -current maximum atomic radii for each collection. +For granular pair styles,the default cutoff is set to the sum of the +current maximum atomic radii for each collection. The *cutoff/multi/old* option is similar to *cutoff/multi* except it operates on atom types as opposed to collections. -The *reduce/multi* option applies to *multi* and sets the communication -cutoff for a particle equal to the maximum interaction distance between particles +The *reduce/multi* option applies to *multi* and sets the communication +cutoff for a particle equal to the maximum interaction distance between particles in the same collection. This reduces the number of -ghost atoms that need to be communicated. This method is only compatible with the -*multi* neighbor style and requires a half neighbor list and Newton on. +ghost atoms that need to be communicated. This method is only compatible with the +*multi* neighbor style and requires a half neighbor list and Newton on. See the :doc:`neighbor multi ` command for more information. These are simulation scenarios in which it may be useful or even diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 6e2d1bee2c..208eca22ec 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -196,8 +196,8 @@ atom can have. The *binsize* option allows you to specify what size of bins will be used in neighbor list construction to sort and find neighboring atoms. By default, for :doc:`neighbor style bin `, LAMMPS uses bins -that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi `, -the bins are 1/2 the size of the collection interaction cutoff. +that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi `, +the bins are 1/2 the size of the collection interaction cutoff. Typically these are good values for minimizing the time for neighbor list construction. This setting overrides the default. If you make it too big, there is little overhead due to @@ -206,23 +206,23 @@ small, the optimal number of atoms is checked, but bin overhead goes up. If you set the binsize to 0.0, LAMMPS will use the default binsize of 1/2 the cutoff. -The *collection/type* option allows you to define collections of atom -types, used by the *multi* neighbor mode. By grouping atom types with -similar physical size or interaction cutoff lengths, one may be able +The *collection/type* option allows you to define collections of atom +types, used by the *multi* neighbor mode. By grouping atom types with +similar physical size or interaction cutoff lengths, one may be able to improve performance by reducing overhead. You must first specify the number of collections N to be defined followed by N lists of types. Each list consists of a series of type -ranges separated by commas. The range can be specified as a +ranges separated by commas. The range can be specified as a single numeric value, or a wildcard asterisk can be used to specify a range of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For -example, if M = the number of atom types, then an asterisk with no numeric -values means all types from 1 to M. A leading asterisk means all types -from 1 to n (inclusive). A trailing asterisk means all types from n to M -(inclusive). A middle asterisk means all types from m to n (inclusive). +example, if M = the number of atom types, then an asterisk with no numeric +values means all types from 1 to M. A leading asterisk means all types +from 1 to n (inclusive). A trailing asterisk means all types from n to M +(inclusive). A middle asterisk means all types from m to n (inclusive). Note that all atom types must be included in exactly one of the N collections. -The *collection/interval* option provides a similar capability. -This command allows a user to define collections by specifying a +The *collection/interval* option provides a similar capability. +This command allows a user to define collections by specifying a series of cutoff intervals. LAMMPS will automatically sort atoms into these intervals based on their type-dependent cutoffs or their finite size. You must first specify the number of collections N to be diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index 80497d57cd..1b10ec8998 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -56,28 +56,28 @@ the largest cutoff distance between any pair of atom types and a single set of bins is defined to search over for all atom types. This can be inefficient if one pair of types has a very long cutoff, but other type pairs have a much shorter cutoff. The *multi* style uses -different sized bins for collections of different sized particles, where -"size" may mean the physical size of the particle or its cutoff +different sized bins for collections of different sized particles, where +"size" may mean the physical size of the particle or its cutoff distance for interacting with other particles. Different -sets of bins are then used to construct the neighbor lists as as further -described by Shire, Hanley, and Stratford :ref:`(Shire) `. +sets of bins are then used to construct the neighbor lists as as further +described by Shire, Hanley, and Stratford :ref:`(Shire) `. This imposes some extra setup overhead, but the searches themselves -may be much faster. By default, each atom type defines a separate -collection of particles. For systems where two or more atom types -have the same size (either physical size or cutoff distance), the -definition of collections can be customized, which can result in less -overhead and faster performance. See the :doc:`neigh_modify ` -command for how to define custom collections. Whether the collection -definition is customized or not, also see the -:doc:`comm_modify mode multi ` command for communication -options that further improve performance in a manner consistent with -neighbor style multi. +may be much faster. By default, each atom type defines a separate +collection of particles. For systems where two or more atom types +have the same size (either physical size or cutoff distance), the +definition of collections can be customized, which can result in less +overhead and faster performance. See the :doc:`neigh_modify ` +command for how to define custom collections. Whether the collection +definition is customized or not, also see the +:doc:`comm_modify mode multi ` command for communication +options that further improve performance in a manner consistent with +neighbor style multi. -An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest -cutoff distance and multiple sets of bins are defined to search over for -different atom types. This algorithm used to be the default *multi* +An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest +cutoff distance and multiple sets of bins are defined to search over for +different atom types. This algorithm used to be the default *multi* algorithm in LAMMPS but was found to be significantly slower than the new -approach. For now we are keeping the old option in case there are use cases +approach. For now we are keeping the old option in case there are use cases where multi/old outperforms the new multi style. diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 798664ba39..318656fc42 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -1846,7 +1846,7 @@ void PairGranular::transfer_history(double* source, double* target) double PairGranular::atom2cut(int i) { double cut; - + cut = atom->radius[i]*2; if(beyond_contact) { int itype = atom->type[i]; @@ -1854,7 +1854,7 @@ double PairGranular::atom2cut(int i) cut += pulloff_distance(cut, cut, itype, itype); } } - + return cut; } @@ -1865,11 +1865,11 @@ double PairGranular::atom2cut(int i) double PairGranular::radii2cut(double r1, double r2) { double cut = 0.0; - + if(beyond_contact) { int n = atom->ntypes; double temp; - + // Check all combinations of i and j to find theoretical maximum pull off distance for(int i = 0; i < n; i++){ for(int j = 0; j < n; j++){ @@ -1877,11 +1877,11 @@ double PairGranular::radii2cut(double r1, double r2) temp = pulloff_distance(r1, r2, i, j); if(temp > cut) cut = temp; } - } + } } - } - + } + cut += r1 + r2; - + return cut; } diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index 30279c787f..f1eeae6453 100755 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -31,7 +31,7 @@ NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi stencil is icollection-jcollection dependent + multi stencil is icollection-jcollection dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ @@ -51,7 +51,7 @@ void NPairFullMultiOmp::build(NeighList *list) tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; - int js; + int js; // loop over each atom, storing neighbors @@ -82,7 +82,7 @@ void NPairFullMultiOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - icollection = collection[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -93,7 +93,7 @@ void NPairFullMultiOmp::build(NeighList *list) } ibin = atom2bin[i]; - + // loop through stencils for all collections for (jcollection = 0; jcollection < ncollections; jcollection++) { @@ -107,12 +107,12 @@ void NPairFullMultiOmp::build(NeighList *list) s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { if (i == j) continue; - + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; @@ -120,7 +120,7 @@ void NPairFullMultiOmp::build(NeighList *list) dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - + if (rsq <= cutneighsq[itype][jtype]) { if (molecular != Atom::ATOMIC) { if (!moltemplate) diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp index 77eb3304ee..d1d3ba6808 100755 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -31,7 +31,7 @@ NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi stencil is icollection-jcollection dependent + multi stencil is icollection-jcollection dependent 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) @@ -95,36 +95,36 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) } ibin = atom2bin[i]; - - // loop through stencils for all collections + + // loop through stencils for all collections for (jcollection = 0; jcollection < ncollections; jcollection++) { - + // if same collection use own bin if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); - + // 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 + // stores own/ghost pairs on both procs // use full stencil for all collection combinations s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; 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 != Atom::ATOMIC) { if (!moltemplate) diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index b097571dcc..124b3d7c55 100755 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -94,31 +94,31 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) } ibin = atom2bin[i]; - + // loop through stencils for all collections for (jcollection = 0; jcollection < ncollections; jcollection++) { - + // if same collection use own bin if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - + if (icollection == jcollection) js = bins[i]; else js = binhead_multi[jcollection][jbin]; - - // if same collection, + + // if same collection, // 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 - + // if j is ghost, only store if j coords are "above and to the right" of i + // if different collections, // if j is owned atom, store it if j > i - // if j is ghost, only store if j coords are "above and to the right" of i - + // if j is ghost, only store if j coords are "above and to the right" of i + for (j = js; j >= 0; j = bins[j]) { - if ((icollection != jcollection) && (j < i)) continue; - + if ((icollection != jcollection) && (j < i)) continue; + if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -126,15 +126,15 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) 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) @@ -150,29 +150,29 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; } - } + } } - - // for all collections, loop over all atoms in other bins in stencil, store every pair + + // for all collections, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - + s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; 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 != Atom::ATOMIC) { if (!moltemplate) diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index 976011c9d2..c023d801cd 100755 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -32,7 +32,7 @@ NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi stencil is icollection-jcollection dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -95,14 +95,14 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) } ibin = atom2bin[i]; - + // loop through stencils for all collections for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); - + // loop over all atoms in bins in stencil // stencil is empty if i larger than j // stencil is half if i same size as j @@ -114,12 +114,12 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { - - // if same size (same collection), use half stencil + + // if same size (same collection), use half stencil if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -128,17 +128,17 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) 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 != Atom::ATOMIC) { if (!moltemplate) diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp index 04634c34c2..c6af398548 100755 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp @@ -31,7 +31,7 @@ NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : NPair( /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi stencil is icollection-jcollection dependent + multi stencil is icollection-jcollection dependent 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) @@ -59,7 +59,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) int *collection = neighbor->collection; double **x = atom->x; - double *radius = atom->radius; + double *radius = atom->radius; int *type = atom->type; int *mask = atom->mask; tagint *molecule = atom->molecule; @@ -85,31 +85,31 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) radi = radius[i]; ibin = atom2bin[i]; - - // loop through stencils for all collections + + // loop through stencils for all collections for (jcollection = 0; jcollection < ncollections; jcollection++) { - + // if same collection use own bin if(icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); - + // 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 + // stores own/ghost pairs on both procs // use full stencil for all collection combinations s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; 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]; @@ -118,7 +118,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) cutdistsq = (radsum+skin) * (radsum+skin); if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; else neighptr[n++] = j; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index 2c96027c48..cf69668424 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -58,7 +58,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) int *collection = neighbor->collection; double **x = atom->x; - double *radius = atom->radius; + double *radius = atom->radius; int *type = atom->type; int *mask = atom->mask; tagint *molecule = atom->molecule; @@ -84,10 +84,10 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) radi = radius[i]; ibin = atom2bin[i]; - + // loop through stencils for all collections for (jcollection = 0; jcollection < ncollections; jcollection++) { - + // if same collection use own bin if(icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); @@ -97,18 +97,18 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) if(icollection == jcollection) js = bins[i]; else js = binhead_multi[jcollection][jbin]; - - // if same collection, + + // if same collection, // 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 - + // if j is ghost, only store if j coords are "above and to the right" of i + // if different collections, // if j is owned atom, store it if j > i - // if j is ghost, only store if j coords are "above and to the right" of i - + // if j is ghost, only store if j coords are "above and to the right" of i + for (j = js; j >= 0; j = bins[j]) { - if(icollection != jcollection and j < i) continue; - + if(icollection != jcollection and j < i) continue; + if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -116,38 +116,38 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) 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; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); - + if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; - else + else neighptr[n++] = j; } } - } + } - // for all collections, loop over all atoms in other bins in stencil, store every pair + // for all collections, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - + s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { - + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; @@ -157,9 +157,9 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) rsq = delx*delx + dely*dely + delz*delz; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); - + if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; else neighptr[n++] = j; diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp index 5d032f40d7..1084b8b453 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp @@ -32,14 +32,14 @@ NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi stencil is icollection-jcollection dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) { - const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; const int mask_history = 3 << SBBITS; @@ -59,7 +59,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) int *collection = neighbor->collection; double **x = atom->x; - double *radius = atom->radius; + double *radius = atom->radius; int *type = atom->type; int *mask = atom->mask; tagint *molecule = atom->molecule; @@ -105,12 +105,12 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { - - // if same size (same collection), use half stencil + + // if same size (same collection), use half stencil if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -119,21 +119,21 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) 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; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); - + if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; else neighptr[n++] = j; diff --git a/src/comm.cpp b/src/comm.cpp index 9954e578a7..e60c538ed2 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -361,7 +361,7 @@ void Comm::modify_params(int narg, char **arg) memory->create(cutusermulti,ncollections_cutoff,"comm:cutusermulti"); for (i=0; i < ncollections_cutoff; ++i) cutusermulti[i] = -1.0; - } + } utils::bounds(FLERR,arg[iarg+1],1,ncollections_cutoff+1,nlo,nhi,error); cut = utils::numeric(FLERR,arg[iarg+2],false,lmp); cutghostuser = MAX(cutghostuser,cut); @@ -752,7 +752,7 @@ double Comm::get_comm_cutoff() if (neighbor->interval_collection_flag) { for (int i = 0; i < neighbor->ncollections; i++){ maxcommcutoff = MAX(maxcommcutoff, neighbor->collection2cut[i]); - } + } } return maxcommcutoff; diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 184babccd2..3d80bfceb0 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -43,13 +43,11 @@ using namespace LAMMPS_NS; CommBrick::CommBrick(LAMMPS *lmp) : Comm(lmp), sendnum(nullptr), recvnum(nullptr), sendproc(nullptr), recvproc(nullptr), - size_forward_recv(nullptr), - size_reverse_send(nullptr), size_reverse_recv(nullptr), + size_forward_recv(nullptr), size_reverse_send(nullptr), size_reverse_recv(nullptr), slablo(nullptr), slabhi(nullptr), multilo(nullptr), multihi(nullptr), - cutghostmulti(nullptr), pbc_flag(nullptr), pbc(nullptr), firstrecv(nullptr), - multioldlo(nullptr), multioldhi(nullptr), cutghostmultiold(nullptr), - sendlist(nullptr), localsendlist(nullptr), maxsendlist(nullptr), - buf_send(nullptr), buf_recv(nullptr) + multioldlo(nullptr), multioldhi(nullptr), cutghostmulti(nullptr), cutghostmultiold(nullptr), + pbc_flag(nullptr), pbc(nullptr), firstrecv(nullptr), sendlist(nullptr), + localsendlist(nullptr), maxsendlist(nullptr), buf_send(nullptr), buf_recv(nullptr) { style = 0; layout = Comm::LAYOUT_UNIFORM; @@ -141,44 +139,44 @@ void CommBrick::init() // memory for multi style communication // allocate in setup - if (mode == Comm::MULTI) { + if (mode == Comm::MULTI) { // If inconsitent # of collections, destroy any preexisting arrays (may be missized) if (ncollections != neighbor->ncollections) { ncollections = neighbor->ncollections; if (multilo != nullptr) { free_multi(); memory->destroy(cutghostmulti); - } + } } - + // delete any old user cutoffs if # of collections chanaged if (cutusermulti && ncollections != ncollections_cutoff) { if(me == 0) error->warning(FLERR, "cutoff/multi settings discarded, must be defined" " after customizing collections in neigh_modify"); memory->destroy(cutusermulti); cutusermulti = nullptr; - } - + } + if (multilo == nullptr) { allocate_multi(maxswap); - memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); + memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); } - } + } if ((mode == Comm::SINGLE || mode == Comm::MULTIOLD) && multilo) { free_multi(); memory->destroy(cutghostmulti); } - + // memory for multi/old-style communication if (mode == Comm::MULTIOLD && multioldlo == nullptr) { allocate_multiold(maxswap); memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold"); - } + } if ((mode == Comm::SINGLE || mode == Comm::MULTI) && multioldlo) { free_multiold(); memory->destroy(cutghostmultiold); - } + } } /* ---------------------------------------------------------------------- @@ -201,7 +199,7 @@ void CommBrick::setup() // cutghostmulti = same as cutghost, only for each atom collection // for multi/old: // cutghostmultiold = same as cutghost, only for each atom type - + int i,j; int ntypes = atom->ntypes; double *prd,*sublo,*subhi; @@ -213,10 +211,10 @@ void CommBrick::setup() if (mode == Comm::MULTI) { double **cutcollectionsq = neighbor->cutcollectionsq; - - // build collection array for atom exchange - neighbor->build_collection(0); - + + // build collection array for atom exchange + neighbor->build_collection(0); + // If using multi/reduce, communicate particles a distance equal // to the max cutoff with equally sized or smaller collections // If not, communicate the maximum cutoff of the entire collection @@ -230,7 +228,7 @@ void CommBrick::setup() cutghostmulti[i][1] = 0.0; cutghostmulti[i][2] = 0.0; } - + for (j = 0; j < ncollections; j++){ if (multi_reduce && (cutcollectionsq[j][j] > cutcollectionsq[i][i])) continue; cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j])); @@ -239,7 +237,7 @@ void CommBrick::setup() } } } - + if (mode == Comm::MULTIOLD) { double *cuttype = neighbor->cuttype; for (i = 1; i <= ntypes; i++) { @@ -275,7 +273,7 @@ void CommBrick::setup() cutghostmulti[i][2] *= length2; } } - + if (mode == Comm::MULTIOLD) { for (i = 1; i <= ntypes; i++) { cutghostmultiold[i][0] *= length0; @@ -902,7 +900,7 @@ void CommBrick::borders() if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); sendlist[iswap][nsend++] = i; } - } + } } else { ngroup = atom->nfirst; for (i = 0; i < ngroup; i++) { @@ -973,7 +971,7 @@ void CommBrick::borders() nprior = atom->nlocal + atom->nghost; atom->nghost += nrecv; if (neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); - + iswap++; } } diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 277228522b..d5c2244424 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -122,24 +122,24 @@ void CommTiled::init() nswap = 2*domain->dimension; memory->destroy(cutghostmulti); - if (mode == Comm::MULTI) { + if (mode == Comm::MULTI) { // If inconsitent # of collections, destroy any preexisting arrays (may be missized) if (ncollections != neighbor->ncollections) { ncollections = neighbor->ncollections; } - + // delete any old user cutoffs if # of collections chanaged if (cutusermulti && ncollections != ncollections_cutoff) { if(me == 0) error->warning(FLERR, "cutoff/multi settings discarded, must be defined" " after customizing collections in neigh_modify"); memory->destroy(cutusermulti); cutusermulti = nullptr; - } - + } + // grow sendbox_multi now that ncollections is known for (int i = 0; i < maxswap; i ++) - grow_swap_send_multi(i,DELTA_PROCS); - + grow_swap_send_multi(i,DELTA_PROCS); + memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); } @@ -201,13 +201,13 @@ void CommTiled::setup() // set cutoff for comm forward and comm reverse // check that cutoff < any periodic box length - + if (mode == Comm::MULTI) { double **cutcollectionsq = neighbor->cutcollectionsq; // build collection array for atom exchange - neighbor->build_collection(0); - + neighbor->build_collection(0); + // If using multi/reduce, communicate particles a distance equal // to the max cutoff with equally sized or smaller collections // If not, communicate the maximum cutoff of the entire collection @@ -221,7 +221,7 @@ void CommTiled::setup() cutghostmulti[i][1] = 0.0; cutghostmulti[i][2] = 0.0; } - + for (j = 0; j < ncollections; j++){ if (multi_reduce && (cutcollectionsq[j][j] > cutcollectionsq[i][i])) continue; cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j])); @@ -230,7 +230,7 @@ void CommTiled::setup() } } } - + if (mode == Comm::MULTIOLD) { double *cuttype = neighbor->cuttype; for (i = 1; i <= ntypes; i++) { @@ -264,7 +264,7 @@ void CommTiled::setup() cutghostmulti[i][2] *= length2; } } - + if (mode == Comm::MULTIOLD) { for (i = 1; i <= ntypes; i++) { cutghostmultiold[i][0] *= length0; @@ -1051,9 +1051,9 @@ void CommTiled::borders() double *bbox; double **x; AtomVec *avec = atom->avec; - + // After exchanging, need to reconstruct collection array for border communication - if (mode == Comm::MULTI) neighbor->build_collection(0); + if (mode == Comm::MULTI) neighbor->build_collection(0); // send/recv max one = max # of atoms in single send/recv for any swap // send/recv max all = max # of atoms in all sends/recvs within any swap @@ -2391,7 +2391,7 @@ void CommTiled::grow_swap_recv(int i, int n) void CommTiled::grow_swap_send_multi(int i, int n) { memory->destroy(sendbox_multi[i]); - + if (ncollections > 0) memory->create(sendbox_multi[i],n,ncollections,6,"comm:sendbox_multi"); } diff --git a/src/info.cpp b/src/info.cpp index 9b8ef48115..b9c320bf2e 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -373,12 +373,12 @@ void Info::command(int narg, char **arg) for (int j=0; j < neighbor->ncollections; ++j) { cut = MAX(cut,sqrt(neighbor->cutcollectionsq[i][j])); } - + if (comm->cutusermulti) cut = MAX(cut,comm->cutusermulti[i]); fmt::print(out,"Communication cutoff for collection {} = {:.8}\n", i, cut); } } - + if (comm->mode == 2) { fputs("Communication mode = multi/old\n",out); double cut; diff --git a/src/nbin.cpp b/src/nbin.cpp index 1323a9042a..7b604ca29d 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -61,9 +61,9 @@ NBin::~NBin() memory->destroy(binhead); memory->destroy(bins); memory->destroy(atom2bin); - + if (!binhead_multi) return; - + memory->destroy(nbinx_multi); memory->destroy(nbiny_multi); memory->destroy(nbinz_multi); @@ -87,7 +87,7 @@ NBin::~NBin() } delete [] binhead_multi; - memory->destroy(maxbins_multi); + memory->destroy(maxbins_multi); } /* ---------------------------------------------------------------------- */ @@ -111,7 +111,7 @@ void NBin::copy_neighbor_info() binsize_user = neighbor->binsize_user; bboxlo = neighbor->bboxlo; bboxhi = neighbor->bboxhi; - + ncollections = neighbor->ncollections; cutcollectionsq = neighbor->cutcollectionsq; @@ -206,7 +206,7 @@ int NBin::coord2bin_multi(double *x, int ic) } else iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ic]) - 1; - + ibin = (iz-mbinzlo_multi[ic])*mbiny_multi[ic]*mbinx_multi[ic] + (iy-mbinylo_multi[ic])*mbinx_multi[ic] + (ix-mbinxlo_multi[ic]); diff --git a/src/nbin.h b/src/nbin.h index ade98002c6..06b5f189be 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -22,7 +22,7 @@ class NBin : protected Pointers { public: int istyle; // 1-N index into binnames bigint last_bin; // last timestep atoms were binned - double cutoff_custom; // cutoff set by requestor + double cutoff_custom; // cutoff set by requestor // Variables for NBinStandard @@ -39,7 +39,7 @@ class NBin : protected Pointers { int *atom2bin; // bin assignment for each atom (local+ghost) // Analogues for NBinMultimulti - + int *nbinx_multi, *nbiny_multi, *nbinz_multi; int *mbins_multi; int *mbinx_multi, *mbiny_multi, *mbinz_multi; @@ -48,7 +48,7 @@ class NBin : protected Pointers { double *bininvx_multi, *bininvy_multi, *bininvz_multi; int **binhead_multi; - + NBin(class LAMMPS *); ~NBin(); void post_constructor(class NeighRequest *); @@ -82,7 +82,7 @@ class NBin : protected Pointers { int triclinic; // data for standard NBin - + int maxatom; // size of bins array int maxbin; // size of binhead array @@ -94,7 +94,7 @@ class NBin : protected Pointers { // methods int coord2bin(double *); - int coord2bin_multi(double *, int); + int coord2bin_multi(double *, int); }; } diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index a0c1fa270a..14ea62200c 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -34,10 +34,10 @@ NBinMulti::NBinMulti(LAMMPS *lmp) : NBin(lmp) {} setup for bin_atoms() ------------------------------------------------------------------------- */ -void NBinMulti::bin_atoms_setup(int nall) +void NBinMulti::bin_atoms_setup(int nall) { // binhead_multi[n] = per-bin vector mbins in length mbins_multi[n] - + for (int n = 0; n < maxcollections; n++) { if (mbins_multi[n] > maxbins_multi[n]) { maxbins_multi[n] = mbins_multi[n]; @@ -90,7 +90,7 @@ void NBinMulti::setup_bins(int /*style*/) // Clear any/all memory for existing groupings for (n = 0; n < maxcollections; n++) memory->destroy(binhead_multi[n]); - + delete [] binhead_multi; maxcollections = ncollections; @@ -136,7 +136,7 @@ void NBinMulti::setup_bins(int /*style*/) memory->destroy(maxbins_multi); memory->create(maxbins_multi, maxcollections, "neigh:maxbins_multi"); - + // ensure reallocation occurs in bin_atoms_setup() for (n = 0; n < maxcollections; n++) { maxbins_multi[n] = 0; @@ -147,7 +147,7 @@ void NBinMulti::setup_bins(int /*style*/) // Identify smallest collection int icollectionmin = 0; for (n = 0; n < ncollections; n++) - if (cutcollectionsq[n][n] < cutcollectionsq[icollectionmin][icollectionmin]) + if (cutcollectionsq[n][n] < cutcollectionsq[icollectionmin][icollectionmin]) icollectionmin = n; // bbox = size of bbox of entire domain @@ -279,7 +279,7 @@ void NBinMulti::setup_bins(int /*style*/) } else mbinzlo_multi[n] = mbinzhi = 0; mbinz_multi[n] = mbinzhi - mbinzlo_multi[n] + 1; - bigint bbin = ((bigint) mbinx_multi[n]) + bigint bbin = ((bigint) mbinx_multi[n]) * ((bigint) mbiny_multi[n]) * ((bigint) mbinz_multi[n]) + 1; if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins"); mbins_multi[n] = bbin; @@ -327,7 +327,7 @@ void NBinMulti::bin_atoms() binhead_multi[n][ibin] = i; } } else { - for (i = nall-1; i >= 0; i--) { + for (i = nall-1; i >= 0; i--) { n = collection[i]; ibin = coord2bin_multi(x[i], n); atom2bin[i] = ibin; @@ -344,6 +344,6 @@ double NBinMulti::memory_usage() double bytes = 0; for (int m = 0; m < maxcollections; m++) bytes += (double)maxbins_multi[m]*sizeof(int); - bytes += (double)2*maxatom*sizeof(int); + bytes += (double)2*maxatom*sizeof(int); return bytes; } diff --git a/src/nbin_standard.h b/src/nbin_standard.h index b81d4ef0ed..54a6cf8358 100644 --- a/src/nbin_standard.h +++ b/src/nbin_standard.h @@ -30,7 +30,7 @@ class NBinStandard : public NBin { public: NBinStandard(class LAMMPS *); ~NBinStandard() {} - void bin_atoms_setup(int); + void bin_atoms_setup(int); void setup_bins(int); void bin_atoms(); double memory_usage(); diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 8088629295..13d12fde81 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -88,7 +88,7 @@ static const char cite_neigh_multi[] = "@article{Stratford2018,\n" " author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin},\n" " title = {Implementation of multi-level contact detection in LAMMPS},\n" - " year = {2018}\n" + " year = {2018}\n" "}\n\n" "@article{Shire2020,\n" " author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},\n" @@ -196,7 +196,7 @@ pairclass(nullptr), pairnames(nullptr), pairmasks(nullptr) ex_mol_group = ex_mol_bit = ex_mol_intra = nullptr; // Multi data - + type2collection = nullptr; collection2cut = nullptr; collection = nullptr; @@ -270,7 +270,7 @@ Neighbor::~Neighbor() memory->destroy(ex_mol_group); delete [] ex_mol_bit; memory->destroy(ex_mol_intra); - + memory->destroy(type2collection); memory->destroy(collection2cut); memory->destroy(collection); @@ -361,19 +361,19 @@ void Neighbor::init() // Define cutoffs for multi if (style == Neighbor::MULTI) { int icollection, jcollection; - + // If collections not yet defined, create default map using types if (not custom_collection_flag) { ncollections = n; interval_collection_flag = 0; if (not type2collection) - memory->create(type2collection,n+1,"neigh:type2collection"); + memory->create(type2collection,n+1,"neigh:type2collection"); for (i = 1; i <= n; i++) type2collection[i] = i-1; - } + } memory->grow(cutcollectionsq, ncollections, ncollections, "neigh:cutcollectionsq"); - + // 3 possible ways of defining collections // 1) Types are used to define collections // Each collection loops through its owned types, and uses cutneighsq to calculate its cutoff @@ -381,14 +381,14 @@ void Neighbor::init() // Types are first sorted into collections based on cutneighsq[i][i] // Each collection loops through its owned types, and uses cutneighsq to calculate its cutoff // 3) Collections are defined by intervals, finite particles - // - - // Define collection cutoffs + // + + // Define collection cutoffs for (i = 0; i < ncollections; i++) for (j = 0; j < ncollections; j++) - cutcollectionsq[i][j] = 0.0; - - if (not interval_collection_flag) { + cutcollectionsq[i][j] = 0.0; + + if (not interval_collection_flag) { finite_cut_flag = 0; for (i = 1; i <= n; i++){ icollection = type2collection[i]; @@ -403,26 +403,26 @@ void Neighbor::init() } else { if (force->pair->finitecutflag) { finite_cut_flag = 1; - // If cutoffs depend on finite atom sizes, use radii of intervals to find cutoffs + // If cutoffs depend on finite atom sizes, use radii of intervals to find cutoffs double ri, rj, tmp; for (i = 0; i < ncollections; i++){ ri = collection2cut[i]*0.5; for (j = 0; j < ncollections; j++){ rj = collection2cut[j]*0.5; tmp = force->pair->radii2cut(ri, rj) + skin; - cutcollectionsq[i][j] = tmp*tmp; + cutcollectionsq[i][j] = tmp*tmp; } - } + } } else { finite_cut_flag = 0; - + // Map types to collections if (not type2collection) - memory->create(type2collection,n+1,"neigh:type2collection"); - + memory->create(type2collection,n+1,"neigh:type2collection"); + for (i = 1; i <= n; i++) type2collection[i] = -1; - + double cuttmp; for (i = 1; i <= n; i++){ // Remove skin added to cutneighsq @@ -433,11 +433,11 @@ void Neighbor::init() break; } } - + if (type2collection[i] == -1) error->all(FLERR, "Pair cutoff exceeds interval cutoffs for multi"); - } - + } + // Define cutoffs for (i = 1; i <= n; i++){ icollection = type2collection[i]; @@ -448,7 +448,7 @@ void Neighbor::init() cutcollectionsq[jcollection][icollection] = cutneighsq[i][j]; } } - } + } } } } @@ -2216,7 +2216,7 @@ void Neighbor::build(int topoflag) } } } - + // bin atoms for all NBin instances // not just NBin associated with perpetual lists, also occasional lists // b/c cannot wait to bin occasional lists in build_one() call @@ -2497,12 +2497,12 @@ void Neighbor::modify_params(int narg, char **arg) } else if (strcmp(arg[iarg+1],"none") == 0) { nex_type = nex_group = nex_mol = 0; iarg += 2; - + } else error->all(FLERR,"Illegal neigh_modify command"); } else if (strcmp(arg[iarg],"collection/interval") == 0) { if (style != Neighbor::MULTI) error->all(FLERR,"Cannot use collection/interval command without multi setting"); - + if (iarg+2 > narg) error->all(FLERR,"Invalid collection/interval command"); ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); @@ -2512,12 +2512,12 @@ void Neighbor::modify_params(int narg, char **arg) error->all(FLERR,"Invalid collection/interval command"); int i; - + // Invalidate old user cutoffs comm->ncollections_cutoff = 0; interval_collection_flag = 1; custom_collection_flag = 1; - memory->grow(collection2cut,ncollections,"neigh:collection2cut"); + memory->grow(collection2cut,ncollections,"neigh:collection2cut"); // Set upper cutoff for each collection @@ -2525,34 +2525,34 @@ void Neighbor::modify_params(int narg, char **arg) for (i = 0; i < ncollections; i++){ cut_interval = utils::numeric(FLERR,arg[iarg+2+i],false,lmp); collection2cut[i] = cut_interval; - + if (i != 0) if (collection2cut[i-1] >= collection2cut[i]) error->all(FLERR,"Nonsequential interval cutoffs in collection/interval setting"); - } - + } + iarg += 2 + ncollections; } else if (strcmp(arg[iarg],"collection/type") == 0) { if (style != Neighbor::MULTI) error->all(FLERR,"Cannot use collection/type command without multi setting"); - + if (iarg+2 > narg) error->all(FLERR,"Invalid collection/type command"); ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); if (ncollections < 1) - error->all(FLERR,"Invalid collection/interval command"); + error->all(FLERR,"Invalid collection/interval command"); if (iarg+1+ncollections > narg) error->all(FLERR,"Invalid collection/type command"); int ntypes = atom->ntypes; int n, nlo, nhi, i, j, k; - + // Invalidate old user cutoffs comm->ncollections_cutoff = 0; interval_collection_flag = 0; custom_collection_flag = 1; if (not type2collection) - memory->create(type2collection,ntypes+1,"neigh:type2collection"); + memory->create(type2collection,ntypes+1,"neigh:type2collection"); // Erase previous mapping for (i = 1; i <= ntypes; i++) @@ -2567,28 +2567,28 @@ void Neighbor::modify_params(int narg, char **arg) strcpy(str,arg[iarg+2+i]); std::vector words = Tokenizer(str, ",").as_vector(); nfield = words.size(); - + for (j = 0; j < nfield; j++) { - const char * field = words[j].c_str(); + const char * field = words[j].c_str(); utils::bounds(FLERR,field,1,ntypes,nlo,nhi,error); for (k = nlo; k <= nhi; k++) { if (type2collection[k] != -1) error->all(FLERR,"Type specified more than once in collection/type commnd"); type2collection[k] = i; - } + } } - - delete [] str; - } - // Check for undefined atom type + delete [] str; + } + + // Check for undefined atom type for (i = 1; i <= ntypes; i++){ if (type2collection[i] == -1) { error->all(FLERR,"Type missing in collection/type commnd"); } } - + iarg += 2 + ncollections; } else error->all(FLERR,"Illegal neigh_modify command"); } @@ -2671,21 +2671,21 @@ void Neighbor::build_collection(int istart) nmax_collection = nmax+DELTA_PERATOM; memory->grow(collection, nmax_collection, "neigh:collection"); } - + if (finite_cut_flag) { double cut; int icollection; for (int i = istart; i < nmax; i++){ cut = force->pair->atom2cut(i); collection[i] = -1; - + for (icollection = 0; icollection < ncollections; icollection++){ if (collection2cut[icollection] >= cut) { collection[i] = icollection; break; } } - + if (collection[i] == -1) error->one(FLERR, "Atom cutoff exceeds interval cutoffs for multi"); } @@ -2693,7 +2693,7 @@ void Neighbor::build_collection(int istart) int *type = atom->type; for (int i = istart; i < nmax; i++){ collection[i] = type2collection[type[i]]; - } + } } } diff --git a/src/neighbor.h b/src/neighbor.h index 09cbe0e850..2aa1f203c4 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -103,7 +103,7 @@ class Neighbor : protected Pointers { int **improperlist; // optional type grouping for multi - + int custom_collection_flag; // 1 if custom collections are defined for multi int interval_collection_flag; // 1 if custom collections use intervals int finite_cut_flag; // 1 if multi considers finite atom size @@ -113,7 +113,7 @@ class Neighbor : protected Pointers { double *collection2cut; // ncollection array with upper bounds on cutoff intervals double **cutcollectionsq; // cutoffs for each combination of collections int *collection; // local per-atom array to store collection id - + // public methods Neighbor(class LAMMPS *); diff --git a/src/npair.cpp b/src/npair.cpp index eee8610958..1472da512a 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -96,7 +96,7 @@ void NPair::copy_neighbor_info() special_flag = neighbor->special_flag; // multi info - + ncollections = neighbor->ncollections; cutcollectionsq = neighbor->cutcollectionsq; @@ -183,7 +183,7 @@ void NPair::build_setup() { if (nb) copy_bin_info(); if (ns) copy_stencil_info(); - + // set here, since build_setup() always called before build() last_build = update->ntimestep; } diff --git a/src/npair.h b/src/npair.h index 4061fd683f..5324eea406 100644 --- a/src/npair.h +++ b/src/npair.h @@ -50,7 +50,7 @@ class NPair : protected Pointers { double *bboxlo,*bboxhi; int ncollections; double **cutcollectionsq; - + // exclusion data from Neighbor class int nex_type; // # of entries in type exclusion list @@ -99,7 +99,7 @@ class NPair : protected Pointers { int ** nstencil_multi; int *** stencil_multi; - + // data common to all NPair variants int molecular; diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp index 42198e8e7c..c99d6f7a6b 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi.cpp @@ -30,7 +30,7 @@ NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi stencil is icollection-jcollection dependent + multi stencil is icollection-jcollection dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ @@ -82,7 +82,7 @@ void NPairFullMulti::build(NeighList *list) } ibin = atom2bin[i]; - + // loop through stencils for all collections for (jcollection = 0; jcollection < ncollections; jcollection++) { @@ -96,20 +96,20 @@ void NPairFullMulti::build(NeighList *list) s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; 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 != Atom::ATOMIC) { if (!moltemplate) diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index eb680311ba..1efcfe447d 100755 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -30,7 +30,7 @@ NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi stencil is icollection-jcollection dependent + multi stencil is icollection-jcollection dependent 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) @@ -84,36 +84,36 @@ void NPairHalfMultiNewtoff::build(NeighList *list) } ibin = atom2bin[i]; - - // loop through stencils for all collections + + // loop through stencils for all collections for (jcollection = 0; jcollection < ncollections; jcollection++) { - + // if same collection use own bin if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); - + // 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 + // stores own/ghost pairs on both procs // use full stencil for all collection combinations s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; 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 != Atom::ATOMIC) { if (!moltemplate) diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index 5292dfc813..a1a0aa07ca 100755 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -83,31 +83,31 @@ void NPairHalfMultiNewton::build(NeighList *list) } ibin = atom2bin[i]; - + // loop through stencils for all collections for (jcollection = 0; jcollection < ncollections; jcollection++) { - + // if same collection use own bin if(icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - + if (icollection == jcollection) js = bins[i]; else js = binhead_multi[jcollection][jbin]; - - // if same collection, + + // if same collection, // 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 - + // if j is ghost, only store if j coords are "above and to the right" of i + // if different collections, // if j is owned atom, store it if j > i - // if j is ghost, only store if j coords are "above and to the right" of i - + // if j is ghost, only store if j coords are "above and to the right" of i + for (j = js; j >= 0; j = bins[j]) { - if((icollection != jcollection) && (j < i)) continue; - + if((icollection != jcollection) && (j < i)) continue; + if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -115,15 +115,15 @@ void NPairHalfMultiNewton::build(NeighList *list) 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) @@ -139,29 +139,29 @@ void NPairHalfMultiNewton::build(NeighList *list) else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; } - } + } } - - // for all collections, loop over all atoms in other bins in stencil, store every pair + + // for all collections, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - + s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; 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 != Atom::ATOMIC) { if (!moltemplate) @@ -180,7 +180,7 @@ void NPairHalfMultiNewton::build(NeighList *list) } } } - + ilist[inum++] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index 83b54ff56e..eb01a91f28 100755 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -30,7 +30,7 @@ NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi stencil is icollection-jcollection dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -42,7 +42,7 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; int js; - + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; @@ -83,14 +83,14 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) } ibin = atom2bin[i]; - + // loop through stencils for all collections for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); - + // loop over all atoms in bins in stencil // stencil is empty if i larger than j // stencil is half if i same size as j @@ -102,12 +102,12 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { - - // if same size (same collection), use half stencil + + // if same size (same collection), use half stencil if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -116,17 +116,17 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) 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 != Atom::ATOMIC) { if (!moltemplate) @@ -145,7 +145,7 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) } } } - + ilist[inum++] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index c073739d58..ec1f512fc0 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -29,7 +29,7 @@ NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) { /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi stencil is icollection-jcollection dependent + multi stencil is icollection-jcollection dependent 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) @@ -74,31 +74,31 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) radi = radius[i]; ibin = atom2bin[i]; - - // loop through stencils for all collections + + // loop through stencils for all collections for (jcollection = 0; jcollection < ncollections; jcollection++) { - + // if same collection use own bin if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); - + // 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 + // stores own/ghost pairs on both procs // use full stencil for all collection combinations s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; 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]; @@ -107,7 +107,7 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) cutdistsq = (radsum+skin) * (radsum+skin); if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; else neighptr[n++] = j; diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index 651b39a36d..95f31e1c52 100755 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -71,10 +71,10 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) radi = radius[i]; ibin = atom2bin[i]; - + // loop through stencils for all collections for (jcollection = 0; jcollection < ncollections; jcollection++) { - + // if same collection use own bin if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); @@ -84,18 +84,18 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) if (icollection == jcollection) js = bins[i]; else js = binhead_multi[jcollection][jbin]; - - // if same collection, + + // if same collection, // 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 - + // if j is ghost, only store if j coords are "above and to the right" of i + // if different collections, // if j is owned atom, store it if j > i - // if j is ghost, only store if j coords are "above and to the right" of i - + // if j is ghost, only store if j coords are "above and to the right" of i + for (j = js; j >= 0; j = bins[j]) { - if ((icollection != jcollection) && (j < i)) continue; - + if ((icollection != jcollection) && (j < i)) continue; + if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -103,50 +103,50 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) 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; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); - + if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; - else + else neighptr[n++] = j; } } - } + } - // for all collections, loop over all atoms in other bins in stencil, store every pair + // for all collections, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - + s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; 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; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); - + if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; else neighptr[n++] = j; @@ -154,7 +154,7 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) } } } - + ilist[inum++] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/npair_half_size_multi_newton.h b/src/npair_half_size_multi_newton.h index cb4b4f1f9f..ad20d2acf3 100755 --- a/src/npair_half_size_multi_newton.h +++ b/src/npair_half_size_multi_newton.h @@ -44,4 +44,4 @@ E: Neighbor list overflow, boost neigh_modify one UNDOCUMENTED -*/ \ No newline at end of file +*/ diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 250f48c84d..904321b697 100755 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -28,7 +28,7 @@ NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lm /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi stencil is icollection-jcollection dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -90,12 +90,12 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) s = stencil_multi[icollection][jcollection]; ns = nstencil_multi[icollection][jcollection]; - + for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { - - // if same size (same collection), use half stencil + + // if same size (same collection), use half stencil if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -104,21 +104,21 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) 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; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); - + if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; else neighptr[n++] = j; diff --git a/src/npair_half_size_multi_newton_tri.h b/src/npair_half_size_multi_newton_tri.h index 56842555fa..bac776627a 100755 --- a/src/npair_half_size_multi_newton_tri.h +++ b/src/npair_half_size_multi_newton_tri.h @@ -44,4 +44,4 @@ E: Neighbor list overflow, boost neigh_modify one UNDOCUMENTED -*/ \ No newline at end of file +*/ diff --git a/src/npair_half_size_multi_old_newton.cpp b/src/npair_half_size_multi_old_newton.cpp index 01cb5bc69a..68d4133d7d 100644 --- a/src/npair_half_size_multi_old_newton.cpp +++ b/src/npair_half_size_multi_old_newton.cpp @@ -94,9 +94,9 @@ void NPairHalfSizeMultiOldNewton::build(NeighList *list) cutdistsq = (radsum+skin) * (radsum+skin); if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; - else + else neighptr[n++] = j; } } @@ -124,7 +124,7 @@ void NPairHalfSizeMultiOldNewton::build(NeighList *list) cutdistsq = (radsum+skin) * (radsum+skin); if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; else neighptr[n++] = j; diff --git a/src/npair_half_size_multi_old_newton_tri.cpp b/src/npair_half_size_multi_old_newton_tri.cpp index 7a8cc079c6..45576899bc 100644 --- a/src/npair_half_size_multi_old_newton_tri.cpp +++ b/src/npair_half_size_multi_old_newton_tri.cpp @@ -106,7 +106,7 @@ void NPairHalfSizeMultiOldNewtonTri::build(NeighList *list) cutdistsq = (radsum+skin) * (radsum+skin); if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; else neighptr[n++] = j; diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 729b690ba1..0648f0e3b1 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -31,7 +31,7 @@ using namespace LAMMPS_NS; 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 full list or half list with newton off + for full list or half list with newton off use a full stencil stencil is all surrounding bins including self regardless of triclinic @@ -57,7 +57,7 @@ using namespace LAMMPS_NS; a half list with newton on has a half same-collection stencil a full list or half list with newton off has a full same-collection stencil cross collection stencils are always full to allow small-to-large lookups - for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin + for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above cutoff is not cutneighmaxsq, but max cutoff for that atom collection no versions that allow ghost on (any need for it?) @@ -74,15 +74,15 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) nstencil_multi_old = nullptr; stencil_multi_old = nullptr; distsq_multi_old = nullptr; - + nstencil_multi = nullptr; stencil_multi = nullptr; maxstencil_multi = nullptr; - + flag_half_multi = nullptr; flag_skip_multi = nullptr; bin_collection_multi = nullptr; - + maxcollections = 0; dimension = domain->dimension; @@ -106,9 +106,9 @@ NStencil::~NStencil() delete [] stencil_multi_old; delete [] distsq_multi_old; } - + if (maxstencil_multi) { - + memory->destroy(nstencil_multi); for (int i = 0; i < maxcollections; i++) { for (int j = 0; j < maxcollections; j++) @@ -120,7 +120,7 @@ NStencil::~NStencil() memory->destroy(flag_half_multi); memory->destroy(flag_skip_multi); memory->destroy(bin_collection_multi); - + memory->destroy(stencil_sx_multi); memory->destroy(stencil_sy_multi); memory->destroy(stencil_sz_multi); @@ -128,7 +128,7 @@ NStencil::~NStencil() memory->destroy(stencil_mbinx_multi); memory->destroy(stencil_mbiny_multi); memory->destroy(stencil_mbinz_multi); - + memory->destroy(stencil_binsizex_multi); memory->destroy(stencil_binsizey_multi); memory->destroy(stencil_binsizez_multi); @@ -154,7 +154,7 @@ void NStencil::copy_neighbor_info() cutneighmaxsq = neighbor->cutneighmaxsq; cuttypesq = neighbor->cuttypesq; cutneighsq = neighbor->cutneighsq; - + ncollections = neighbor->ncollections; collection = neighbor->collection; cutcollectionsq = neighbor->cutcollectionsq; @@ -209,15 +209,15 @@ void NStencil::copy_bin_info_multi() void NStencil::create_setup() { - + if (neighstyle != Neighbor::MULTI){ if (nb) copy_bin_info(); last_stencil = 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 (cutneighmax*bininvx); if (sx*binsizex < cutneighmax) sx++; sy = static_cast (cutneighmax*bininvy); @@ -225,12 +225,12 @@ void NStencil::create_setup() sz = static_cast (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_OLD styles - + if (neighstyle == Neighbor::BIN) { if (smax > maxstencil) { maxstencil = smax; @@ -241,7 +241,7 @@ void NStencil::create_setup() memory->create(stencilxyz,maxstencil,3,"neighstencil:stencilxyz"); } } - + } else { int i; int n = atom->ntypes; @@ -271,19 +271,19 @@ void NStencil::create_setup() int i, j, bin_collection, smax; double stencil_range; int n = ncollections; - + if (nb) copy_bin_info_multi(); // Deallocate arrays if previously allocated - if((n > maxcollections) && stencil_multi){ + if((n > maxcollections) && stencil_multi){ memory->destroy(nstencil_multi); for (i = 0; i < maxcollections; i++) { for (j = 0; j < maxcollections; j++) memory->destroy(stencil_multi[i][j]); delete [] stencil_multi[i]; } - delete [] stencil_multi; - memory->destroy(maxstencil_multi); + delete [] stencil_multi; + memory->destroy(maxstencil_multi); memory->destroy(flag_half_multi); memory->destroy(flag_skip_multi); memory->destroy(bin_collection_multi); @@ -295,39 +295,39 @@ void NStencil::create_setup() memory->destroy(stencil_binsizez_multi); memory->destroy(stencil_mbinx_multi); memory->destroy(stencil_mbiny_multi); - memory->destroy(stencil_mbinz_multi); - } - - // Allocate arrays - if (!maxstencil_multi) { - memory->create(flag_half_multi, n, n, + memory->destroy(stencil_mbinz_multi); + } + + // Allocate arrays + if (!maxstencil_multi) { + memory->create(flag_half_multi, n, n, "neighstencil:flag_half_multi"); - memory->create(flag_skip_multi, n, n, + memory->create(flag_skip_multi, n, n, "neighstencil:flag_skip_multi"); - memory->create(bin_collection_multi, n, n, + memory->create(bin_collection_multi, n, n, "neighstencil:bin_collection_multi"); - - memory->create(stencil_sx_multi, n, n, - "neighstencil:stencil_sx_multi"); - memory->create(stencil_sy_multi, n, n, + + memory->create(stencil_sx_multi, n, n, + "neighstencil:stencil_sx_multi"); + memory->create(stencil_sy_multi, n, n, "neighstencil:stencil_sy_multi"); - memory->create(stencil_sz_multi, n, n, + memory->create(stencil_sz_multi, n, n, "neighstencil:stencil_sz_multi"); - - memory->create(stencil_binsizex_multi, n, n, + + memory->create(stencil_binsizex_multi, n, n, "neighstencil:stencil_binsizex_multi"); - memory->create(stencil_binsizey_multi, n, n, + memory->create(stencil_binsizey_multi, n, n, "neighstencil:stencil_binsizey_multi"); - memory->create(stencil_binsizez_multi, n, n, + memory->create(stencil_binsizez_multi, n, n, "neighstencil:stencil_binsizez_multi"); - - memory->create(stencil_mbinx_multi, n, n, + + memory->create(stencil_mbinx_multi, n, n, "neighstencil:stencil_mbinx_multi"); - memory->create(stencil_mbiny_multi, n, n, + memory->create(stencil_mbiny_multi, n, n, "neighstencil:stencil_mbiny_multi"); - memory->create(stencil_mbinz_multi, n, n, + memory->create(stencil_mbinz_multi, n, n, "neighstencil:stencil_mbinz_multi"); - + memory->create(maxstencil_multi, n, n, "neighstencil::maxstencil_multi"); memory->create(nstencil_multi, n, n, "neighstencil::nstencil_multi"); stencil_multi = new int**[n](); @@ -338,38 +338,38 @@ void NStencil::create_setup() nstencil_multi[i][j] = 0; stencil_multi[i][j] = nullptr; } - } - maxcollections = n; + } + maxcollections = n; } - + // Skip all stencils by default, initialize smax for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { - flag_skip_multi[i][j] = 1; + flag_skip_multi[i][j] = 1; } } - + // Determine which stencils need to be built - set_stencil_properties(); - + set_stencil_properties(); + for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { - // Skip creation of unused stencils + // Skip creation of unused stencils if (flag_skip_multi[i][j]) continue; - + // Copy bin info for this pair of atom collections bin_collection = bin_collection_multi[i][j]; - + stencil_binsizex_multi[i][j] = binsizex_multi[bin_collection]; stencil_binsizey_multi[i][j] = binsizey_multi[bin_collection]; stencil_binsizez_multi[i][j] = binsizez_multi[bin_collection]; - + stencil_mbinx_multi[i][j] = mbinx_multi[bin_collection]; stencil_mbiny_multi[i][j] = mbiny_multi[bin_collection]; stencil_mbinz_multi[i][j] = mbinz_multi[bin_collection]; - + stencil_range = sqrt(cutcollectionsq[i][j]); - + sx = static_cast (stencil_range*bininvx_multi[bin_collection]); if (sx*binsizex_multi[bin_collection] < stencil_range) sx++; sy = static_cast (stencil_range*bininvy_multi[bin_collection]); @@ -377,13 +377,13 @@ void NStencil::create_setup() sz = static_cast (stencil_range*bininvz_multi[bin_collection]); if (sz*binsizez_multi[bin_collection] < stencil_range) sz++; if (dimension == 2) sz = 0; - + stencil_sx_multi[i][j] = sx; stencil_sy_multi[i][j] = sy; stencil_sz_multi[i][j] = sz; - smax = ((2*sx+1) * (2*sy+1) * (2*sz+1)); - + smax = ((2*sx+1) * (2*sy+1) * (2*sz+1)); + if (smax > maxstencil_multi[i][j]) { maxstencil_multi[i][j] = smax; if(stencil_multi[i][j]) diff --git a/src/nstencil.h b/src/nstencil.h index 18a8442894..821f9a7e55 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -34,17 +34,17 @@ class NStencil : protected Pointers { int *** stencil_multi; // list of bin offsets in each multi stencil int ** maxstencil_multi; // max stencil size for each multi stencil int maxcollections; // size of multi arrays - + int sx,sy,sz; // extent of stencil in each dim int **stencil_sx_multi; // analogs for each multi stencil int **stencil_sy_multi; int **stencil_sz_multi; - double cutoff_custom; // cutoff set by requestor - + double cutoff_custom; // cutoff set by requestor + // Arrays to store options for multi itype-jtype stencils bool **flag_half_multi; // flag creation of a half stencil for icollection-jcollection - bool **flag_skip_multi; // skip creation of icollection-jcollection stencils (for newton on) + bool **flag_skip_multi; // skip creation of icollection-jcollection stencils (for newton on) int **bin_collection_multi; // what collection to use for bin information NStencil(class LAMMPS *); @@ -70,15 +70,15 @@ class NStencil : protected Pointers { double **cutcollectionsq; int ncollections; int *collection; - + // data from NBin class int mbinx,mbiny,mbinz; double binsizex,binsizey,binsizez; double bininvx,bininvy,bininvz; - + // data from NBin class for multi - + int *mbinx_multi; int *mbiny_multi; int *mbinz_multi; @@ -88,16 +88,16 @@ class NStencil : protected Pointers { double *bininvx_multi; double *bininvy_multi; double *bininvz_multi; - + // Stored bin information for each stencil - + int **stencil_mbinx_multi; int **stencil_mbiny_multi; int **stencil_mbinz_multi; double **stencil_binsizex_multi; double **stencil_binsizey_multi; - double **stencil_binsizez_multi; - + double **stencil_binsizez_multi; + // data common to all NStencil variants int xyzflag; // 1 if stencilxyz is allocated @@ -113,9 +113,9 @@ class NStencil : protected Pointers { // methods for multi NStencil - double bin_distance_multi(int, int, int, int); // distance between bin corners for different collections + double bin_distance_multi(int, int, int, int); // distance between bin corners for different collections void copy_bin_info_multi(); // copy multi info from NBin class - virtual void set_stencil_properties(){} // determine which stencils to build and how + virtual void set_stencil_properties(){} // determine which stencils to build and how }; } diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index f106b6c8af..ae7bcad52e 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -31,7 +31,7 @@ void NStencilFullMulti2d::set_stencil_properties() { int n = ncollections; int i, j; - + // Always look up neighbor using full stencil and neighbor's bin for (i = 0; i < n; i++) { @@ -52,32 +52,32 @@ void NStencilFullMulti2d::create() int icollection, jcollection, bin_collection, i, j, ns; int n = ncollections; double cutsq; - - + + for (icollection = 0; icollection < n; icollection++) { for (jcollection = 0; jcollection < n; jcollection++) { if (flag_skip_multi[icollection][jcollection]) { nstencil_multi[icollection][jcollection] = 0; continue; } - + ns = 0; - + sx = stencil_sx_multi[icollection][jcollection]; sy = stencil_sy_multi[icollection][jcollection]; - + mbinx = stencil_mbinx_multi[icollection][jcollection]; mbiny = stencil_mbiny_multi[icollection][jcollection]; - + bin_collection = bin_collection_multi[icollection][jcollection]; - + cutsq = cutcollectionsq[icollection][jcollection]; - + for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance_multi(i,j,0,bin_collection) < cutsq) stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; - + nstencil_multi[icollection][jcollection] = ns; } } diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp index 390b30c8bd..7bdf9561f1 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -31,7 +31,7 @@ void NStencilFullMulti3d::set_stencil_properties() { int n = ncollections; int i, j; - + // Always look up neighbor using full stencil and neighbor's bin // Stencil cutoff set by i-j cutoff @@ -53,36 +53,36 @@ void NStencilFullMulti3d::create() int icollection, jcollection, bin_collection, i, j, k, ns; int n = ncollections; double cutsq; - - + + for (icollection = 0; icollection < n; icollection++) { for (jcollection = 0; jcollection < n; jcollection++) { if (flag_skip_multi[icollection][jcollection]) { nstencil_multi[icollection][jcollection] = 0; continue; } - + ns = 0; - + sx = stencil_sx_multi[icollection][jcollection]; sy = stencil_sy_multi[icollection][jcollection]; sz = stencil_sz_multi[icollection][jcollection]; - + mbinx = stencil_mbinx_multi[icollection][jcollection]; mbiny = stencil_mbiny_multi[icollection][jcollection]; - mbinz = stencil_mbinz_multi[icollection][jcollection]; - + mbinz = stencil_mbinz_multi[icollection][jcollection]; + bin_collection = bin_collection_multi[icollection][jcollection]; - + cutsq = cutcollectionsq[icollection][jcollection]; - + for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance_multi(i,j,k,bin_collection) < cutsq) - stencil_multi[icollection][jcollection][ns++] = + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; - + nstencil_multi[icollection][jcollection] = ns; } } diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_2d.cpp index 2b1ce83425..6754ddb658 100644 --- a/src/nstencil_half_multi_2d.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -43,7 +43,7 @@ void NStencilHalfMulti2d::set_stencil_properties() if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; flag_skip_multi[i][j] = 0; - + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ flag_half_multi[i][j] = 1; bin_collection_multi[i][j] = i; @@ -64,31 +64,31 @@ void NStencilHalfMulti2d::create() int icollection, jcollection, bin_collection, i, j, ns; int n = ncollections; double cutsq; - - + + for (icollection = 0; icollection < n; icollection++) { for (jcollection = 0; jcollection < n; jcollection++) { if (flag_skip_multi[icollection][jcollection]) { nstencil_multi[icollection][jcollection] = 0; continue; } - + ns = 0; - + sx = stencil_sx_multi[icollection][jcollection]; sy = stencil_sy_multi[icollection][jcollection]; - + mbinx = stencil_mbinx_multi[icollection][jcollection]; mbiny = stencil_mbiny_multi[icollection][jcollection]; - - bin_collection = bin_collection_multi[icollection][jcollection]; - + + bin_collection = bin_collection_multi[icollection][jcollection]; + cutsq = cutcollectionsq[icollection][jcollection]; - + if (flag_half_multi[icollection][jcollection]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (j > 0 || (j == 0 && i > 0)) { + if (j > 0 || (j == 0 && i > 0)) { if (bin_distance_multi(i,j,0,bin_collection) < cutsq) stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; } @@ -98,7 +98,7 @@ void NStencilHalfMulti2d::create() if (bin_distance_multi(i,j,0,bin_collection) < cutsq) stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; } - + nstencil_multi[icollection][jcollection] = ns; } } diff --git a/src/nstencil_half_multi_2d_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp index 35b6267854..cd215ee384 100755 --- a/src/nstencil_half_multi_2d_tri.cpp +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -43,7 +43,7 @@ void NStencilHalfMulti2dTri::set_stencil_properties() if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; flag_skip_multi[i][j] = 0; - + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ flag_half_multi[i][j] = 1; bin_collection_multi[i][j] = i; @@ -64,27 +64,27 @@ void NStencilHalfMulti2dTri::create() int icollection, jcollection, bin_collection, i, j, ns; int n = ncollections; double cutsq; - - + + for (icollection = 0; icollection < n; icollection++) { for (jcollection = 0; jcollection < n; jcollection++) { if (flag_skip_multi[icollection][jcollection]) { nstencil_multi[icollection][jcollection] = 0; continue; } - + ns = 0; - + sx = stencil_sx_multi[icollection][jcollection]; sy = stencil_sy_multi[icollection][jcollection]; - + mbinx = stencil_mbinx_multi[icollection][jcollection]; mbiny = stencil_mbiny_multi[icollection][jcollection]; - + bin_collection = bin_collection_multi[icollection][jcollection]; - + cutsq = cutcollectionsq[icollection][jcollection]; - + if (flag_half_multi[icollection][jcollection]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) @@ -96,7 +96,7 @@ void NStencilHalfMulti2dTri::create() if (bin_distance_multi(i,j,0,bin_collection) < cutsq) stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; } - + nstencil_multi[icollection][jcollection] = ns; } } diff --git a/src/nstencil_half_multi_3d.cpp b/src/nstencil_half_multi_3d.cpp index dd35befd3d..6e60c34343 100644 --- a/src/nstencil_half_multi_3d.cpp +++ b/src/nstencil_half_multi_3d.cpp @@ -43,7 +43,7 @@ void NStencilHalfMulti3d::set_stencil_properties() if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; flag_skip_multi[i][j] = 0; - + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ flag_half_multi[i][j] = 1; bin_collection_multi[i][j] = i; @@ -64,36 +64,36 @@ void NStencilHalfMulti3d::create() int icollection, jcollection, bin_collection, i, j, k, ns; int n = ncollections; double cutsq; - - + + for (icollection = 0; icollection < n; icollection++) { for (jcollection = 0; jcollection < n; jcollection++) { if (flag_skip_multi[icollection][jcollection]) { nstencil_multi[icollection][jcollection] = 0; continue; } - + ns = 0; - + sx = stencil_sx_multi[icollection][jcollection]; sy = stencil_sy_multi[icollection][jcollection]; sz = stencil_sz_multi[icollection][jcollection]; - + mbinx = stencil_mbinx_multi[icollection][jcollection]; mbiny = stencil_mbiny_multi[icollection][jcollection]; mbinz = stencil_mbinz_multi[icollection][jcollection]; - + bin_collection = bin_collection_multi[icollection][jcollection]; - + cutsq = cutcollectionsq[icollection][jcollection]; - + if (flag_half_multi[icollection][jcollection]) { 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 (k > 0 || j > 0 || (j == 0 && i > 0)) { if (bin_distance_multi(i,j,k,bin_collection) < cutsq) - stencil_multi[icollection][jcollection][ns++] = + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; } } else { @@ -101,10 +101,10 @@ void NStencilHalfMulti3d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance_multi(i,j,k,bin_collection) < cutsq) - stencil_multi[icollection][jcollection][ns++] = + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; } - + nstencil_multi[icollection][jcollection] = ns; } } diff --git a/src/nstencil_half_multi_3d_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp index fb83a24d28..632ca5f0ed 100755 --- a/src/nstencil_half_multi_3d_tri.cpp +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -32,7 +32,7 @@ void NStencilHalfMulti3dTri::set_stencil_properties() { int n = ncollections; int i, j; - + // Cross collections: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required @@ -43,7 +43,7 @@ void NStencilHalfMulti3dTri::set_stencil_properties() if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; flag_skip_multi[i][j] = 0; - + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ flag_half_multi[i][j] = 1; bin_collection_multi[i][j] = i; @@ -64,45 +64,45 @@ void NStencilHalfMulti3dTri::create() int icollection, jcollection, bin_collection, i, j, k, ns; int n = ncollections; double cutsq; - - + + for (icollection = 0; icollection < n; icollection++) { for (jcollection = 0; jcollection < n; jcollection++) { if (flag_skip_multi[icollection][jcollection]) { nstencil_multi[icollection][jcollection] = 0; continue; } - + ns = 0; - + sx = stencil_sx_multi[icollection][jcollection]; sy = stencil_sy_multi[icollection][jcollection]; sz = stencil_sz_multi[icollection][jcollection]; - + mbinx = stencil_mbinx_multi[icollection][jcollection]; mbiny = stencil_mbiny_multi[icollection][jcollection]; mbinz = stencil_mbinz_multi[icollection][jcollection]; - + bin_collection = bin_collection_multi[icollection][jcollection]; - + cutsq = cutcollectionsq[icollection][jcollection]; - + if (flag_half_multi[icollection][jcollection]) { for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance_multi(i,j,k,bin_collection) < cutsq) - stencil_multi[icollection][jcollection][ns++] = + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance_multi(i,j,k,bin_collection) < cutsq) - stencil_multi[icollection][jcollection][ns++] = + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; } - + nstencil_multi[icollection][jcollection] = ns; } } diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 61a9cadd44..14d58f9414 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -1090,7 +1090,7 @@ double PairHybrid::atom2cut(int i) for (int m = 0; m < nstyles; m++) { if (styles[m]->finitecutflag) { temp = styles[m]->atom2cut(i); - if (temp > cut) cut = temp; + if (temp > cut) cut = temp; } } return cut; @@ -1108,7 +1108,7 @@ double PairHybrid::radii2cut(double r1, double r2) for (int m = 0; m < nstyles; m++) { if (styles[m]->finitecutflag) { temp = styles[m]->radii2cut(r1,r2); - if (temp > cut) cut = temp; + if (temp > cut) cut = temp; } } return cut; From 986a72ff6eb8f841bf5b7f082967cdc5832e5de9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 May 2021 06:32:58 -0400 Subject: [PATCH 66/73] remove executable permissions on non-executable files --- examples/multi/data.powerlaw | 0 examples/multi/in.powerlaw | 0 src/USER-OMP/npair_full_multi_omp.cpp | 0 src/USER-OMP/npair_full_multi_omp.h | 0 src/USER-OMP/npair_half_multi_newtoff_omp.cpp | 0 src/USER-OMP/npair_half_multi_newtoff_omp.h | 0 src/USER-OMP/npair_half_multi_newton_omp.cpp | 0 src/USER-OMP/npair_half_multi_newton_omp.h | 0 src/USER-OMP/npair_half_multi_newton_tri_omp.cpp | 0 src/USER-OMP/npair_half_multi_newton_tri_omp.h | 0 src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp | 0 src/USER-OMP/npair_half_size_multi_newtoff_omp.h | 0 src/USER-OMP/npair_half_size_multi_newton_omp.cpp | 0 src/USER-OMP/npair_half_size_multi_newton_omp.h | 0 src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp | 0 src/USER-OMP/npair_half_size_multi_newton_tri_omp.h | 0 src/npair_half_multi_newtoff.cpp | 0 src/npair_half_multi_newtoff.h | 0 src/npair_half_multi_newton.cpp | 0 src/npair_half_multi_newton.h | 0 src/npair_half_multi_newton_tri.cpp | 0 src/npair_half_multi_newton_tri.h | 0 src/npair_half_size_multi_newton.cpp | 0 src/npair_half_size_multi_newton.h | 0 src/npair_half_size_multi_newton_tri.cpp | 0 src/npair_half_size_multi_newton_tri.h | 0 src/nstencil_half_multi_2d_tri.cpp | 0 src/nstencil_half_multi_2d_tri.h | 0 src/nstencil_half_multi_3d_tri.cpp | 0 src/nstencil_half_multi_3d_tri.h | 0 30 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 examples/multi/data.powerlaw mode change 100755 => 100644 examples/multi/in.powerlaw mode change 100755 => 100644 src/USER-OMP/npair_full_multi_omp.cpp mode change 100755 => 100644 src/USER-OMP/npair_full_multi_omp.h mode change 100755 => 100644 src/USER-OMP/npair_half_multi_newtoff_omp.cpp mode change 100755 => 100644 src/USER-OMP/npair_half_multi_newtoff_omp.h mode change 100755 => 100644 src/USER-OMP/npair_half_multi_newton_omp.cpp mode change 100755 => 100644 src/USER-OMP/npair_half_multi_newton_omp.h mode change 100755 => 100644 src/USER-OMP/npair_half_multi_newton_tri_omp.cpp mode change 100755 => 100644 src/USER-OMP/npair_half_multi_newton_tri_omp.h mode change 100755 => 100644 src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp mode change 100755 => 100644 src/USER-OMP/npair_half_size_multi_newtoff_omp.h mode change 100755 => 100644 src/USER-OMP/npair_half_size_multi_newton_omp.cpp mode change 100755 => 100644 src/USER-OMP/npair_half_size_multi_newton_omp.h mode change 100755 => 100644 src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp mode change 100755 => 100644 src/USER-OMP/npair_half_size_multi_newton_tri_omp.h mode change 100755 => 100644 src/npair_half_multi_newtoff.cpp mode change 100755 => 100644 src/npair_half_multi_newtoff.h mode change 100755 => 100644 src/npair_half_multi_newton.cpp mode change 100755 => 100644 src/npair_half_multi_newton.h mode change 100755 => 100644 src/npair_half_multi_newton_tri.cpp mode change 100755 => 100644 src/npair_half_multi_newton_tri.h mode change 100755 => 100644 src/npair_half_size_multi_newton.cpp mode change 100755 => 100644 src/npair_half_size_multi_newton.h mode change 100755 => 100644 src/npair_half_size_multi_newton_tri.cpp mode change 100755 => 100644 src/npair_half_size_multi_newton_tri.h mode change 100755 => 100644 src/nstencil_half_multi_2d_tri.cpp mode change 100755 => 100644 src/nstencil_half_multi_2d_tri.h mode change 100755 => 100644 src/nstencil_half_multi_3d_tri.cpp mode change 100755 => 100644 src/nstencil_half_multi_3d_tri.h diff --git a/examples/multi/data.powerlaw b/examples/multi/data.powerlaw old mode 100755 new mode 100644 diff --git a/examples/multi/in.powerlaw b/examples/multi/in.powerlaw old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_full_multi_omp.h b/src/USER-OMP/npair_full_multi_omp.h old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.h b/src/USER-OMP/npair_half_multi_newtoff_omp.h old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_half_multi_newton_omp.h b/src/USER-OMP/npair_half_multi_newton_omp.h old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.h b/src/USER-OMP/npair_half_multi_newton_tri_omp.h old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.h b/src/USER-OMP/npair_half_size_multi_newtoff_omp.h old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.h b/src/USER-OMP/npair_half_size_multi_newton_omp.h old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp old mode 100755 new mode 100644 diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h old mode 100755 new mode 100644 diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp old mode 100755 new mode 100644 diff --git a/src/npair_half_multi_newtoff.h b/src/npair_half_multi_newtoff.h old mode 100755 new mode 100644 diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp old mode 100755 new mode 100644 diff --git a/src/npair_half_multi_newton.h b/src/npair_half_multi_newton.h old mode 100755 new mode 100644 diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp old mode 100755 new mode 100644 diff --git a/src/npair_half_multi_newton_tri.h b/src/npair_half_multi_newton_tri.h old mode 100755 new mode 100644 diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp old mode 100755 new mode 100644 diff --git a/src/npair_half_size_multi_newton.h b/src/npair_half_size_multi_newton.h old mode 100755 new mode 100644 diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp old mode 100755 new mode 100644 diff --git a/src/npair_half_size_multi_newton_tri.h b/src/npair_half_size_multi_newton_tri.h old mode 100755 new mode 100644 diff --git a/src/nstencil_half_multi_2d_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp old mode 100755 new mode 100644 diff --git a/src/nstencil_half_multi_2d_tri.h b/src/nstencil_half_multi_2d_tri.h old mode 100755 new mode 100644 diff --git a/src/nstencil_half_multi_3d_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp old mode 100755 new mode 100644 diff --git a/src/nstencil_half_multi_3d_tri.h b/src/nstencil_half_multi_3d_tri.h old mode 100755 new mode 100644 From b49d91fa8effffe01bdd7ab5287143f933abb20b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 May 2021 07:00:47 -0400 Subject: [PATCH 67/73] add contributing author and citation DOIs --- src/neighbor.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 13d12fde81..e2296b6115 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -13,6 +13,7 @@ /* ---------------------------------------------------------------------- Contributing author (triclinic and multi-neigh) : Pieter in 't Veld (SNL) + Contributing author (improved multi-neigh) : Joel Clemmer (SNL) ------------------------------------------------------------------------- */ #include "neighbor.h" @@ -61,7 +62,7 @@ using namespace NeighConst; enum{NONE,ALL,PARTIAL,TEMPLATE}; static const char cite_neigh_multi_old[] = - "neighbor multi/old command:\n\n" + "neighbor multi/old command: doi:10.1016/j.cpc.2008.03.005\n\n" "@Article{Intveld08,\n" " author = {P.{\\,}J.~in{\\,}'t~Veld and S.{\\,}J.~Plimpton" " and G.{\\,}S.~Grest},\n" @@ -74,7 +75,7 @@ static const char cite_neigh_multi_old[] = "}\n\n"; static const char cite_neigh_multi[] = - "neighbor multi command:\n\n" + "neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2\n\n" "@Article{Intveld08,\n" " author = {P.{\\,}J.~in{\\,}'t~Veld and S.{\\,}J.~Plimpton" " and G.{\\,}S.~Grest},\n" From 1d10147cb66bdd75caa0b9af454f683b8907d62f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 May 2021 07:53:18 -0400 Subject: [PATCH 68/73] reformat and shorten new example inputs --- examples/multi/in.colloid | 70 +++++++++++++++++++------------------- examples/multi/in.granular | 38 ++++++++++----------- examples/multi/in.powerlaw | 24 ++++++------- 3 files changed, 66 insertions(+), 66 deletions(-) diff --git a/examples/multi/in.colloid b/examples/multi/in.colloid index 71987acbd6..9f9883f61a 100644 --- a/examples/multi/in.colloid +++ b/examples/multi/in.colloid @@ -1,18 +1,18 @@ # Big colloid particles and small LJ particles -units lj -atom_style sphere -dimension 2 +units lj +atom_style sphere +dimension 2 -lattice sq 0.1 -region box block 0 60 0 60 -0.5 0.5 -create_box 5 box +lattice sq 0.1 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box create_atoms 1 box #Roughly equally partition atoms between types 1-4 -set group all type/fraction 2 0.500 23984 -set group all type/fraction 3 0.333 43684 -set group all type/fraction 4 0.250 87811 +set group all type/fraction 2 0.500 23984 +set group all type/fraction 3 0.333 43684 +set group all type/fraction 4 0.250 87811 # remove two spheres of small particles and add large particles in the voids region sphere1 sphere 60.0 60.0 0.0 30.0 units box @@ -22,46 +22,46 @@ delete_atoms region sphere2 create_atoms 5 single 60.0 60.0 0.0 units box create_atoms 5 single 130.0 130.0 0.0 units box -set type 1 mass 400 -set type 2 mass 1 +set type 1 mass 400 +set type 2 mass 1 -velocity all create 1.44 87287 loop geom +velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi #multi/old -neigh_modify delay 0 collection/type 2 1*4 5 +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/type 2 1*4 5 comm_modify mode multi reduce/multi #multi/old # colloid potential -pair_style colloid 20.0 -pair_coeff * * 144.0 1.0 0.0 0.0 3.0 -pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 -pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 -pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 -pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 -pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 -fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 & - mtk no pchain 0 tchain 1 -fix 2 all enforce2d +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 & + mtk no pchain 0 tchain 1 +fix 2 all enforce2d -#dump 1 all atom 1000 dump.colloid +#dump 1 all atom 1000 dump.colloid -#dump 2 all image 1000 image.*.jpg type type & -# zoom 1.5 center d 0.5 0.5 0.5 -#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 +#dump 2 all image 1000 image.*.jpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 -#dump 3 all movie 1000 movie.mpg type type & -# zoom 1.5 center d 0.5 0.5 0.5 -#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 +#dump 3 all movie 1000 movie.mpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 -thermo_style custom step temp epair etotal press vol -thermo 1000 +thermo_style custom step temp epair etotal press vol +thermo 100 -timestep 0.005 +timestep 0.005 -run 50000 +run 2000 diff --git a/examples/multi/in.granular b/examples/multi/in.granular index 99e9ddfb33..468d0dcbf1 100644 --- a/examples/multi/in.granular +++ b/examples/multi/in.granular @@ -1,13 +1,13 @@ # Big colloid particles and small LJ particles -units lj -atom_style sphere -dimension 2 +units lj +atom_style sphere +dimension 2 -lattice sq 0.5 -region box block 0 60 0 60 -0.5 0.5 -create_box 2 box -create_atoms 1 box +lattice sq 0.5 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +create_atoms 1 box change_box all triclinic # remove two spheres of small particles and add large particles in the voids @@ -18,17 +18,17 @@ delete_atoms region sphere2 create_atoms 2 single 20.0 20.0 0.0 units box create_atoms 2 single 60.0 60.0 0.0 units box -set type 2 mass 400 -set type 1 mass 1 +set type 2 mass 400 +set type 1 mass 1 set type 2 diameter 20 set type 1 diameter 1 -velocity all create 1.44 87287 loop geom +velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi #multi/old -neigh_modify delay 0 collection/interval 2 1 20 +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/interval 2 1 20 comm_modify mode multi vel yes reduce/multi #multi/old # granular potential @@ -36,15 +36,15 @@ comm_modify mode multi vel yes reduce/multi #multi/old pair_style granular pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity -fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 -fix 2 all enforce2d +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d fix 3 all deform 1 xy erate 1e-3 -#dump 1 all custom 1000 dump.granular id x y z radius +#dump 1 all custom 1000 dump.granular id x y z radius -thermo_style custom step temp epair etotal press vol -thermo 1000 +thermo_style custom step temp epair etotal press vol +thermo 100 -timestep 0.005 +timestep 0.005 -run 50000 +run 2000 diff --git a/examples/multi/in.powerlaw b/examples/multi/in.powerlaw index 213aa3544e..b69e6a56a3 100644 --- a/examples/multi/in.powerlaw +++ b/examples/multi/in.powerlaw @@ -1,15 +1,15 @@ # Shear power-law distributed granular particles -units lj -atom_style sphere -dimension 2 +units lj +atom_style sphere +dimension 2 read_data data.powerlaw change_box all triclinic # multi neighbor and comm for efficiency -neighbor 1 multi -neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 +neighbor 1 multi +neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 comm_modify mode multi vel yes reduce/multi # granular potential @@ -19,15 +19,15 @@ pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping # fixes -fix 1 all nve/sphere -fix 2 all enforce2d +fix 1 all nve/sphere +fix 2 all enforce2d fix 3 all deform 1 xy erate 1e-4 -# dump 1 all custom 20000 dump.granular id x y z radius +# dump 1 all custom 20000 dump.granular id x y z radius -thermo_style custom step temp epair etotal press vol pxy -thermo 1000 +thermo_style custom step temp epair etotal press vol pxy +thermo 100 -timestep 0.005 +timestep 0.005 -run 200000 +run 1000 From 6b45f9052f1a6552f1189a1907557b92352f7b33 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 May 2021 08:55:00 -0400 Subject: [PATCH 69/73] small fixed and error checking --- src/MOLECULE/bond_fene_expand.h | 2 +- src/comm.cpp | 38 +++++++++++---------------------- src/comm.h | 6 +++--- src/nstencil.cpp | 8 +++---- 4 files changed, 21 insertions(+), 33 deletions(-) diff --git a/src/MOLECULE/bond_fene_expand.h b/src/MOLECULE/bond_fene_expand.h index 6c79b1cfd0..49a8b8ab8e 100644 --- a/src/MOLECULE/bond_fene_expand.h +++ b/src/MOLECULE/bond_fene_expand.h @@ -13,7 +13,7 @@ #ifdef BOND_CLASS -BondStyle(fene / expand, BondFENEExpand) +BondStyle(fene/expand, BondFENEExpand) #else diff --git a/src/comm.cpp b/src/comm.cpp index e60c538ed2..513349f6eb 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -292,32 +292,24 @@ void Comm::modify_params(int narg, char **arg) // need to reset cutghostuser when switching comm mode if (mode == Comm::MULTI) cutghostuser = 0.0; if (mode == Comm::MULTIOLD) cutghostuser = 0.0; - if (cutusermulti) { - memory->destroy(cutusermulti); - cutusermulti = nullptr; - } - if (cutusermultiold) { - memory->destroy(cutusermultiold); - cutusermultiold = nullptr; - } + memory->destroy(cutusermulti); + memory->destroy(cutusermultiold); mode = Comm::SINGLE; } else if (strcmp(arg[iarg+1],"multi") == 0) { + if (neighbor->style != Neighbor::MULTI) + error->all(FLERR,"Cannot use comm mode 'multi' without 'multi' style neighbor lists"); // need to reset cutghostuser when switching comm mode if (mode == Comm::SINGLE) cutghostuser = 0.0; if (mode == Comm::MULTIOLD) cutghostuser = 0.0; - if (cutusermultiold) { - memory->destroy(cutusermultiold); - cutusermultiold = nullptr; - } + memory->destroy(cutusermultiold); mode = Comm::MULTI; } else if (strcmp(arg[iarg+1],"multi/old") == 0) { + if (neighbor->style == Neighbor::MULTI) + error->all(FLERR,"Cannot use comm mode 'multi/old' with 'multi' style neighbor lists"); // need to reset cutghostuser when switching comm mode if (mode == Comm::SINGLE) cutghostuser = 0.0; if (mode == Comm::MULTI) cutghostuser = 0.0; - if (cutusermulti) { - memory->destroy(cutusermulti); - cutusermulti = nullptr; - } + memory->destroy(cutusermulti); mode = Comm::MULTIOLD; } else error->all(FLERR,"Illegal comm_modify command"); iarg += 2; @@ -333,11 +325,9 @@ void Comm::modify_params(int narg, char **arg) } else if (strcmp(arg[iarg],"cutoff") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command"); if (mode == Comm::MULTI) - error->all(FLERR, - "Use cutoff/multi keyword to set cutoff in multi mode"); + error->all(FLERR, "Use cutoff/multi keyword to set cutoff in multi mode"); if (mode == Comm::MULTIOLD) - error->all(FLERR, - "Use cutoff/multi/old keyword to set cutoff in multi mode"); + error->all(FLERR, "Use cutoff/multi/old keyword to set cutoff in multi mode"); cutghostuser = utils::numeric(FLERR,arg[iarg+1],false,lmp); if (cutghostuser < 0.0) error->all(FLERR,"Invalid cutoff in comm_modify command"); @@ -350,14 +340,13 @@ void Comm::modify_params(int narg, char **arg) if (mode == Comm::MULTIOLD) error->all(FLERR,"Use cutoff/multi/old keyword to set cutoff in multi/old mode"); if (domain->box_exist == 0) - error->all(FLERR, - "Cannot set cutoff/multi before simulation box is defined"); + error->all(FLERR, "Cannot set cutoff/multi before simulation box is defined"); // Check if # of collections has changed, if so erase any previously defined cutoffs // Neighbor will reset ncollections if collections are redefined if (ncollections_cutoff != neighbor->ncollections) { ncollections_cutoff = neighbor->ncollections; - if (cutusermulti) memory->destroy(cutusermulti); + memory->destroy(cutusermulti); memory->create(cutusermulti,ncollections_cutoff,"comm:cutusermulti"); for (i=0; i < ncollections_cutoff; ++i) cutusermulti[i] = -1.0; @@ -379,8 +368,7 @@ void Comm::modify_params(int narg, char **arg) if (mode == Comm::MULTI) error->all(FLERR,"Use cutoff/multi keyword to set cutoff in multi mode"); if (domain->box_exist == 0) - error->all(FLERR, - "Cannot set cutoff/multi before simulation box is defined"); + error->all(FLERR, "Cannot set cutoff/multi before simulation box is defined"); const int ntypes = atom->ntypes; if (iarg+3 > narg) error->all(FLERR,"Illegal comm_modify command"); diff --git a/src/comm.h b/src/comm.h index 414b9414bc..df016c0b72 100644 --- a/src/comm.h +++ b/src/comm.h @@ -31,9 +31,9 @@ class Comm : protected Pointers { int me,nprocs; // proc info int ghost_velocity; // 1 if ghost atoms have velocity, 0 if not double cutghost[3]; // cutoffs used for acquiring ghost atoms - double cutghostuser; // user-specified ghost cutoff (mode == 0) - double *cutusermulti; // per collection user ghost cutoff (mode == 1) - double *cutusermultiold; // per type user ghost cutoff (mode == 2) + double cutghostuser; // user-specified ghost cutoff (mode == SINGLE) + double *cutusermulti; // per collection user ghost cutoff (mode == MULTI) + double *cutusermultiold; // per type user ghost cutoff (mode == MULTIOLD) int ncollections; // # of collections known by comm, used to test if # has changed int ncollections_cutoff; // # of collections stored b cutoff/multi int recv_from_partition; // recv proc layout from this partition diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 0648f0e3b1..c412c280ef 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -210,7 +210,7 @@ void NStencil::copy_bin_info_multi() void NStencil::create_setup() { - if (neighstyle != Neighbor::MULTI){ + if (neighstyle != Neighbor::MULTI) { if (nb) copy_bin_info(); last_stencil = update->ntimestep; @@ -218,11 +218,11 @@ void NStencil::create_setup() // smax = max possible size of entire 3d stencil // stencil will be empty if cutneighmax = 0.0 - sx = static_cast (cutneighmax*bininvx); + sx = static_cast(cutneighmax*bininvx); if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); + sy = static_cast(cutneighmax*bininvy); if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); + sz = static_cast(cutneighmax*bininvz); if (sz*binsizez < cutneighmax) sz++; if (dimension == 2) sz = 0; From 7f94712839b3ef9537228fb1849884e7b254c99a Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Wed, 12 May 2021 08:17:14 -0600 Subject: [PATCH 70/73] Explicitly defining default ncollections --- src/comm.cpp | 1 + src/neighbor.cpp | 6 ++++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index 513349f6eb..8e69f18a35 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -303,6 +303,7 @@ void Comm::modify_params(int narg, char **arg) if (mode == Comm::MULTIOLD) cutghostuser = 0.0; memory->destroy(cutusermultiold); mode = Comm::MULTI; + ncollections_cutoff = 0; } else if (strcmp(arg[iarg+1],"multi/old") == 0) { if (neighbor->style == Neighbor::MULTI) error->all(FLERR,"Cannot use comm mode 'multi/old' with 'multi' style neighbor lists"); diff --git a/src/neighbor.cpp b/src/neighbor.cpp index e2296b6115..3a9b7289e8 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -2349,8 +2349,10 @@ void Neighbor::set(int narg, char **arg) if (strcmp(arg[1],"nsq") == 0) style = Neighbor::NSQ; else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN; - else if (strcmp(arg[1],"multi") == 0) style = Neighbor::MULTI; - else if (strcmp(arg[1],"multi/old") == 0) style = Neighbor::MULTI_OLD; + else if (strcmp(arg[1],"multi") == 0) { + style = Neighbor::MULTI; + ncollections = atom->ntypes; + } else if (strcmp(arg[1],"multi/old") == 0) style = Neighbor::MULTI_OLD; else error->all(FLERR,"Illegal neighbor command"); if (style == Neighbor::MULTI_OLD && lmp->citeme) lmp->citeme->add(cite_neigh_multi_old); From cac634076d9d68246161800eee8a3d2cf7709c63 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Wed, 12 May 2021 08:59:12 -0600 Subject: [PATCH 71/73] ensuring cutusermulti always created --- src/comm.cpp | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index 8e69f18a35..650c39bac3 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -59,6 +59,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) cutusermulti = nullptr; cutusermultiold = nullptr; ncollections = 0; + ncollections_cutoff = 0; ghost_velocity = 0; user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0; @@ -148,9 +149,10 @@ void Comm::copy_arrays(Comm *oldcomm) } ncollections = oldcomm->ncollections; + ncollections_cutoff = oldcomm->ncollections_cutoff; if (oldcomm->cutusermulti) { - memory->create(cutusermulti,ncollections,"comm:cutusermulti"); - memcpy(cutusermulti,oldcomm->cutusermulti,ncollections); + memory->create(cutusermulti,ncollections_cutoff,"comm:cutusermulti"); + memcpy(cutusermulti,oldcomm->cutusermulti,ncollections_cutoff); } if (oldcomm->cutusermultiold) { @@ -303,7 +305,6 @@ void Comm::modify_params(int narg, char **arg) if (mode == Comm::MULTIOLD) cutghostuser = 0.0; memory->destroy(cutusermultiold); mode = Comm::MULTI; - ncollections_cutoff = 0; } else if (strcmp(arg[iarg+1],"multi/old") == 0) { if (neighbor->style == Neighbor::MULTI) error->all(FLERR,"Cannot use comm mode 'multi/old' with 'multi' style neighbor lists"); @@ -345,14 +346,14 @@ void Comm::modify_params(int narg, char **arg) // Check if # of collections has changed, if so erase any previously defined cutoffs // Neighbor will reset ncollections if collections are redefined - if (ncollections_cutoff != neighbor->ncollections) { + if (! cutusermulti || ncollections_cutoff != neighbor->ncollections) { ncollections_cutoff = neighbor->ncollections; memory->destroy(cutusermulti); memory->create(cutusermulti,ncollections_cutoff,"comm:cutusermulti"); for (i=0; i < ncollections_cutoff; ++i) cutusermulti[i] = -1.0; } - utils::bounds(FLERR,arg[iarg+1],1,ncollections_cutoff+1,nlo,nhi,error); + utils::bounds(FLERR,arg[iarg+1],1,ncollections_cutoff,nlo,nhi,error); cut = utils::numeric(FLERR,arg[iarg+2],false,lmp); cutghostuser = MAX(cutghostuser,cut); if (cut < 0.0) From 4ccb17ab6273efc6463133f8cf81d5aeacf89db0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 May 2021 13:49:41 -0400 Subject: [PATCH 72/73] whitespace --- src/neighbor.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 3a9b7289e8..357784927b 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -2351,7 +2351,7 @@ void Neighbor::set(int narg, char **arg) else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN; else if (strcmp(arg[1],"multi") == 0) { style = Neighbor::MULTI; - ncollections = atom->ntypes; + ncollections = atom->ntypes; } else if (strcmp(arg[1],"multi/old") == 0) style = Neighbor::MULTI_OLD; else error->all(FLERR,"Illegal neighbor command"); From 0ee7bc6e01160b4d1be31dfac8f1444ce8c05421 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 11 May 2021 21:22:29 -0400 Subject: [PATCH 73/73] Update remaining variable names after refactor --- python/lammps/core.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/python/lammps/core.py b/python/lammps/core.py index 6761f9502c..1e8f739943 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -911,14 +911,14 @@ class lammps(object): else: return None if ctype == LMP_TYPE_SCALAR: - if style == LMP_STYLE_GLOBAL: + if cstyle == LMP_STYLE_GLOBAL: self.lib.lammps_extract_compute.restype = POINTER(c_double) with ExceptionCheck(self): ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype) return ptr[0] - elif style == LMP_STYLE_ATOM: + elif cstyle == LMP_STYLE_ATOM: return None - elif style == LMP_STYLE_LOCAL: + elif cstyle == LMP_STYLE_LOCAL: self.lib.lammps_extract_compute.restype = POINTER(c_int) with ExceptionCheck(self): ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)