diff --git a/src/DPD-BASIC/pair_dpd_ext.h b/src/DPD-BASIC/pair_dpd_ext.h index da779a131b..1d025d74c0 100644 --- a/src/DPD-BASIC/pair_dpd_ext.h +++ b/src/DPD-BASIC/pair_dpd_ext.h @@ -50,7 +50,6 @@ class PairDPDExt : public Pair { double **sigma, **sigmaT; double **ws, **wsT; class RanMars *random; - virtual void allocate(); }; diff --git a/src/DPD-BASIC/pair_dpd_ext_tstat.h b/src/DPD-BASIC/pair_dpd_ext_tstat.h index d1bb8c53de..daae388aa6 100644 --- a/src/DPD-BASIC/pair_dpd_ext_tstat.h +++ b/src/DPD-BASIC/pair_dpd_ext_tstat.h @@ -40,8 +40,6 @@ class PairDPDExtTstat : public PairDPDExt { protected: double t_start, t_stop; }; - } // namespace LAMMPS_NS - #endif #endif diff --git a/src/OPENMP/pair_dpd_ext_omp.cpp b/src/OPENMP/pair_dpd_ext_omp.cpp new file mode 100644 index 0000000000..dda677154d --- /dev/null +++ b/src/OPENMP/pair_dpd_ext_omp.cpp @@ -0,0 +1,273 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + This software is distributed under the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include "pair_dpd_ext_omp.h" + +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "update.h" +#include "random_mars.h" +#include "suffix.h" + +#include + +#include "omp_compat.h" +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-10 + +/* ---------------------------------------------------------------------- */ + +PairDPDExtOMP::PairDPDExtOMP(LAMMPS *lmp) : + PairDPDExt(lmp), ThrOMP(lmp, THR_PAIR) +{ + suffix_flag |= Suffix::OMP; + respa_enable = 0; + random_thr = nullptr; + nthreads = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairDPDExtOMP::~PairDPDExtOMP() +{ + if (random_thr) { + for (int i=1; i < nthreads; ++i) + delete random_thr[i]; + + delete[] random_thr; + random_thr = nullptr; + } +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDExtOMP::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); + + const int nall = atom->nlocal + atom->nghost; + const int inum = list->inum; + + // number of threads has changed. reallocate pool of pRNGs + if (nthreads != comm->nthreads) { + if (random_thr) { + for (int i=1; i < nthreads; ++i) + delete random_thr[i]; + + delete[] random_thr; + } + + nthreads = comm->nthreads; + random_thr = new RanMars*[nthreads]; + for (int i=1; i < nthreads; ++i) + random_thr[i] = nullptr; + + // to ensure full compatibility with the serial DPD style + // we use the serial random number generator instance for thread 0 + random_thr[0] = random; + } + +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag) +#endif + { + int ifrom, ito, tid; + + loop_setup_thr(ifrom, ito, tid, inum, nthreads); + ThrData *thr = fix->get_thr(tid); + thr->timer(Timer::START); + ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr); + + // generate a random number generator instance for + // all threads != 0. make sure we use unique seeds. + if ((tid > 0) && (random_thr[tid] == nullptr)) + random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me + + comm->nprocs*tid); + + if (evflag) { + if (eflag) { + if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr); + else eval<1,1,0>(ifrom, ito, thr); + } else { + if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr); + else eval<1,0,0>(ifrom, ito, thr); + } + } else { + if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr); + else eval<0,0,0>(ifrom, ito, thr); + } + + thr->timer(Timer::PAIR); + reduce_thr(this, eflag, vflag, thr); + } // end of omp parallel region +} + +template +void PairDPDExtOMP::eval(int iifrom, int iito, ThrData * const thr) +{ + int i,j,ii,jj,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpairx,fpairy,fpairz,fpair; + double vxtmp,vytmp,vztmp,delvx,delvy,delvz; + double rsq,r,rinv,dot,wd,wdPar,wdPerp,randnum,randnumx,randnumy,randnumz,factor_dpd; + double P[3][3]; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + + const auto * _noalias const x = (dbl3_t *) atom->x[0]; + const auto * _noalias const v = (dbl3_t *) atom->v[0]; + auto * _noalias const f = (dbl3_t *) thr->get_f()[0]; + const int * _noalias const type = atom->type; + const int nlocal = atom->nlocal; + const double *special_lj = force->special_lj; + const double dtinvsqrt = 1.0/sqrt(update->dt); + double fxtmp,fytmp,fztmp; + RanMars &rng = *random_thr[thr->get_tid()]; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = iifrom; ii < iito; ++ii) { + + i = ilist[ii]; + xtmp = x[i].x; + ytmp = x[i].y; + ztmp = x[i].z; + vxtmp = v[i].x; + vytmp = v[i].y; + vztmp = v[i].z; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + fxtmp=fytmp=fztmp=0.0; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j].x; + dely = ytmp - x[j].y; + delz = ztmp - x[j].z; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in DPD systems + rinv = 1.0/r; + delvx = vxtmp - v[j].x; + delvy = vytmp - v[j].y; + delvz = vztmp - v[j].z; + dot = delx*delvx + dely*delvy + delz*delvz; + + P[0][0] = 1.0 - delx*delx*rinv*rinv; + P[0][1] = - delx*dely*rinv*rinv; + P[0][2] = - delx*delz*rinv*rinv; + + P[1][0] = P[0][1]; + P[1][1] = 1.0 - dely*dely*rinv*rinv; + P[1][2] = - dely*delz*rinv*rinv; + + P[2][0] = P[0][2]; + P[2][1] = P[1][2]; + P[2][2] = 1.0 - delz*delz*rinv*rinv; + + wd = 1.0 - r/cut[itype][jtype]; + wdPar = pow(wd,ws[itype][jtype]); + wdPerp = pow(wd,wsT[itype][jtype]); + + randnum = rng.gaussian(); + randnumx = rng.gaussian(); + randnumy = rng.gaussian(); + randnumz = rng.gaussian(); + + // conservative force + fpair = a0[itype][jtype]*wd; + + // drag force - parallel + fpair -= gamma[itype][jtype]*wdPar*wdPar*dot*rinv; + + // random force - parallel + fpair += sigma[itype][jtype]*wdPar*randnum*dtinvsqrt; + + fpairx = fpair*rinv*delx; + fpairy = fpair*rinv*dely; + fpairz = fpair*rinv*delz; + + // drag force - perpendicular + fpairx -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[0][0]*delvx + P[0][1]*delvy + P[0][2]*delvz); + fpairy -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[1][0]*delvx + P[1][1]*delvy + P[1][2]*delvz); + fpairz -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[2][0]*delvx + P[2][1]*delvy + P[2][2]*delvz); + + // random force - perpendicular + fpairx += sigmaT[itype][jtype]*wdPerp* + (P[0][0]*randnumx + P[0][1]*randnumy + P[0][2]*randnumz)*dtinvsqrt; + fpairy += sigmaT[itype][jtype]*wdPerp* + (P[1][0]*randnumx + P[1][1]*randnumy + P[1][2]*randnumz)*dtinvsqrt; + fpairz += sigmaT[itype][jtype]*wdPerp* + (P[2][0]*randnumx + P[2][1]*randnumy + P[2][2]*randnumz)*dtinvsqrt; + + fpairx *= factor_dpd; + fpairy *= factor_dpd; + fpairz *= factor_dpd; + + fxtmp += fpairx; + fytmp += fpairy; + fztmp += fpairz; + if (NEWTON_PAIR || j < nlocal) { + f[j].x -= fpairx; + f[j].y -= fpairy; + f[j].z -= fpairz; + } + + if (EFLAG) { + // unshifted eng of conservative term: + // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]); + // eng shifted to 0.0 at cutoff + evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd; + evdwl *= factor_dpd; + } + + if (EVFLAG) ev_tally_xyz_thr(this, i,j,nlocal,NEWTON_PAIR,evdwl,0.0, + fpairx,fpairy,fpairz,delx,dely,delz,thr); + } + } + f[i].x += fxtmp; + f[i].y += fytmp; + f[i].z += fztmp; + } +} + +/* ---------------------------------------------------------------------- */ + +double PairDPDExtOMP::memory_usage() +{ + double bytes = memory_usage_thr(); + bytes += PairDPDExt::memory_usage(); + bytes += (double)comm->nthreads * sizeof(RanMars*); + bytes += (double)comm->nthreads * sizeof(RanMars); + + return bytes; +} diff --git a/src/OPENMP/pair_dpd_ext_omp.h b/src/OPENMP/pair_dpd_ext_omp.h new file mode 100644 index 0000000000..4ea82bbef5 --- /dev/null +++ b/src/OPENMP/pair_dpd_ext_omp.h @@ -0,0 +1,51 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(dpd/ext/omp,PairDPDExtOMP); +// clang-format on +#else + +#ifndef LMP_PAIR_DPD_EXT_OMP_H +#define LMP_PAIR_DPD_EXT_OMP_H + +#include "pair_dpd_ext.h" +#include "thr_omp.h" + +namespace LAMMPS_NS { + +class PairDPDExtOMP : public PairDPDExt, public ThrOMP { + + public: + PairDPDExtOMP(class LAMMPS *); + ~PairDPDExtOMP() override; + + void compute(int, int) override; + double memory_usage() override; + + protected: + class RanMars **random_thr; + int nthreads; + + private: + template + void eval(int ifrom, int ito, ThrData *const thr); +}; +} // namespace LAMMPS_NS +#endif +#endif diff --git a/src/OPENMP/pair_dpd_ext_tstat_omp.cpp b/src/OPENMP/pair_dpd_ext_tstat_omp.cpp new file mode 100644 index 0000000000..d1bd134645 --- /dev/null +++ b/src/OPENMP/pair_dpd_ext_tstat_omp.cpp @@ -0,0 +1,275 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + This software is distributed under the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include "pair_dpd_ext_tstat_omp.h" + +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "update.h" +#include "random_mars.h" +#include "suffix.h" + +#include + +#include "omp_compat.h" +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-10 + +/* ---------------------------------------------------------------------- */ + +PairDPDExtTstatOMP::PairDPDExtTstatOMP(LAMMPS *lmp) : + PairDPDExtTstat(lmp), ThrOMP(lmp, THR_PAIR) +{ + suffix_flag |= Suffix::OMP; + respa_enable = 0; + random_thr = nullptr; + nthreads = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairDPDExtTstatOMP::~PairDPDExtTstatOMP() +{ + if (random_thr) { + for (int i=1; i < nthreads; ++i) + delete random_thr[i]; + + delete[] random_thr; + random_thr = nullptr; + } +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDExtTstatOMP::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); + + const int nall = atom->nlocal + atom->nghost; + const int inum = list->inum; + + // number of threads has changed. reallocate pool of pRNGs + if (nthreads != comm->nthreads) { + if (random_thr) { + for (int i=1; i < nthreads; ++i) + delete random_thr[i]; + + delete[] random_thr; + } + + nthreads = comm->nthreads; + random_thr = new RanMars*[nthreads]; + for (int i=1; i < nthreads; ++i) + random_thr[i] = nullptr; + + // to ensure full compatibility with the serial DPD style + // we use the serial random number generator instance for thread 0 + random_thr[0] = random; + } + + // adjust sigma if target T is changing + + if (t_start != t_stop) { + double delta = update->ntimestep - update->beginstep; + if (delta != 0.0) delta /= update->endstep - update->beginstep; + temperature = t_start + delta * (t_stop-t_start); + double boltz = force->boltz; + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = i; j <= atom->ntypes; j++) { + sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]); + sigmaT[i][j] = sigmaT[j][i] = sqrt(2.0*boltz*temperature*gammaT[i][j]); + } + } + } + +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag) +#endif + { + int ifrom, ito, tid; + + loop_setup_thr(ifrom, ito, tid, inum, nthreads); + ThrData *thr = fix->get_thr(tid); + thr->timer(Timer::START); + ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr); + + // generate a random number generator instance for + // all threads != 0. make sure we use unique seeds. + if ((tid > 0) && (random_thr[tid] == nullptr)) + random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me + + comm->nprocs*tid); + + if (evflag) { + if (eflag) { + if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr); + else eval<1,1,0>(ifrom, ito, thr); + } else { + if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr); + else eval<1,0,0>(ifrom, ito, thr); + } + } else { + if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr); + else eval<0,0,0>(ifrom, ito, thr); + } + + thr->timer(Timer::PAIR); + reduce_thr(this, eflag, vflag, thr); + } // end of omp parallel region +} + +template +void PairDPDExtTstatOMP::eval(int iifrom, int iito, ThrData * const thr) +{ + int i,j,ii,jj,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,fpairx,fpairy,fpairz,fpair; + double vxtmp,vytmp,vztmp,delvx,delvy,delvz; + double rsq,r,rinv,dot,wd,wdPar,wdPerp,randnum,randnumx,randnumy,randnumz,factor_dpd; + double P[3][3]; + int *ilist,*jlist,*numneigh,**firstneigh; + + const auto * _noalias const x = (dbl3_t *) atom->x[0]; + const auto * _noalias const v = (dbl3_t *) atom->v[0]; + auto * _noalias const f = (dbl3_t *) thr->get_f()[0]; + const int * _noalias const type = atom->type; + const int nlocal = atom->nlocal; + const double *special_lj = force->special_lj; + const double dtinvsqrt = 1.0/sqrt(update->dt); + double fxtmp,fytmp,fztmp; + RanMars &rng = *random_thr[thr->get_tid()]; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = iifrom; ii < iito; ++ii) { + + i = ilist[ii]; + xtmp = x[i].x; + ytmp = x[i].y; + ztmp = x[i].z; + vxtmp = v[i].x; + vytmp = v[i].y; + vztmp = v[i].z; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + fxtmp=fytmp=fztmp=0.0; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j].x; + dely = ytmp - x[j].y; + delz = ztmp - x[j].z; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in DPD systems + rinv = 1.0/r; + delvx = vxtmp - v[j].x; + delvy = vytmp - v[j].y; + delvz = vztmp - v[j].z; + dot = delx*delvx + dely*delvy + delz*delvz; + + P[0][0] = 1.0 - delx*delx*rinv*rinv; + P[0][1] = - delx*dely*rinv*rinv; + P[0][2] = - delx*delz*rinv*rinv; + + P[1][0] = P[0][1]; + P[1][1] = 1.0 - dely*dely*rinv*rinv; + P[1][2] = - dely*delz*rinv*rinv; + + P[2][0] = P[0][2]; + P[2][1] = P[1][2]; + P[2][2] = 1.0 - delz*delz*rinv*rinv; + + wd = 1.0 - r/cut[itype][jtype]; + wdPar = pow(wd,ws[itype][jtype]); + wdPerp = pow(wd,wsT[itype][jtype]); + + randnum = rng.gaussian(); + randnumx = rng.gaussian(); + randnumy = rng.gaussian(); + randnumz = rng.gaussian(); + + // drag force - parallel + fpair = -gamma[itype][jtype]*wdPar*wdPar*dot*rinv; + + // random force - parallel + fpair += sigma[itype][jtype]*wdPar*randnum*dtinvsqrt; + + fpairx = fpair*rinv*delx; + fpairy = fpair*rinv*dely; + fpairz = fpair*rinv*delz; + + // drag force - perpendicular + fpairx -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[0][0]*delvx + P[0][1]*delvy + P[0][2]*delvz); + fpairy -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[1][0]*delvx + P[1][1]*delvy + P[1][2]*delvz); + fpairz -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[2][0]*delvx + P[2][1]*delvy + P[2][2]*delvz); + + // random force - perpendicular + fpairx += sigmaT[itype][jtype]*wdPerp* + (P[0][0]*randnumx + P[0][1]*randnumy + P[0][2]*randnumz)*dtinvsqrt; + fpairy += sigmaT[itype][jtype]*wdPerp* + (P[1][0]*randnumx + P[1][1]*randnumy + P[1][2]*randnumz)*dtinvsqrt; + fpairz += sigmaT[itype][jtype]*wdPerp* + (P[2][0]*randnumx + P[2][1]*randnumy + P[2][2]*randnumz)*dtinvsqrt; + + fpairx *= factor_dpd; + fpairy *= factor_dpd; + fpairz *= factor_dpd; + + fxtmp += fpairx; + fytmp += fpairy; + fztmp += fpairz; + if (NEWTON_PAIR || j < nlocal) { + f[j].x -= fpairx; + f[j].y -= fpairy; + f[j].z -= fpairz; + } + + if (EVFLAG) ev_tally_xyz_thr(this, i,j,nlocal,NEWTON_PAIR,0.0,0.0, + fpairx,fpairy,fpairz,delx,dely,delz,thr); + } + } + f[i].x += fxtmp; + f[i].y += fytmp; + f[i].z += fztmp; + } +} + +/* ---------------------------------------------------------------------- */ + +double PairDPDExtTstatOMP::memory_usage() +{ + double bytes = memory_usage_thr(); + bytes += PairDPDExtTstat::memory_usage(); + bytes += (double)comm->nthreads * sizeof(RanMars*); + bytes += (double)comm->nthreads * sizeof(RanMars); + + return bytes; +} diff --git a/src/OPENMP/pair_dpd_ext_tstat_omp.h b/src/OPENMP/pair_dpd_ext_tstat_omp.h new file mode 100644 index 0000000000..ef6d0494be --- /dev/null +++ b/src/OPENMP/pair_dpd_ext_tstat_omp.h @@ -0,0 +1,51 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(dpd/ext/tstat/omp,PairDPDExtTstatOMP); +// clang-format on +#else + +#ifndef LMP_PAIR_DPD_EXT_TSTAT_OMP_H +#define LMP_PAIR_DPD_EXT_TSTAT_OMP_H + +#include "pair_dpd_ext_tstat.h" +#include "thr_omp.h" + +namespace LAMMPS_NS { + +class PairDPDExtTstatOMP : public PairDPDExtTstat, public ThrOMP { + + public: + PairDPDExtTstatOMP(class LAMMPS *); + ~PairDPDExtTstatOMP() override; + + void compute(int, int) override; + double memory_usage() override; + + protected: + class RanMars **random_thr; + int nthreads; + + private: + template + void eval(int ifrom, int ito, ThrData *const thr); +}; +} // namespace LAMMPS_NS +#endif +#endif