diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index 676df07b6..52287d586 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -1,836 +1,837 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- Contributing authors: James Larentzos (U.S. Army Research Laboratory) and Timothy I. Mattox (Engility Corporation) Martin Lisal (Institute of Chemical Process Fundamentals of the Czech Academy of Sciences and J. E. Purkinje University) John Brennan, Joshua Moore and William Mattson (Army Research Lab) Please cite the related publications: J. P. Larentzos, J. K. Brennan, J. D. Moore, M. Lisal, W. D. Mattson, "Parallel implementation of isothermal and isoenergetic Dissipative Particle Dynamics using Shardlow-like splitting algorithms", Computer Physics Communications, 2014, 185, pp 1987--1998. M. Lisal, J. K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms", Journal of Chemical Physics, 2011, 135, 204105. ------------------------------------------------------------------------- */ #include #include #include #include "fix_shardlow_kokkos.h" #include "atom.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" #include #include "atom_vec.h" #include "comm.h" #include "neighbor.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" #include "memory.h" #include "domain.h" #include "modify.h" // #include "pair_dpd_fdt.h" #include "pair_dpd_fdt_energy_kokkos.h" #include "pair.h" #include "npair_ssa_kokkos.h" #include "citeme.h" using namespace LAMMPS_NS; using namespace FixConst; #define EPSILON 1.0e-10 #define EPSILON_SQUARED ((EPSILON) * (EPSILON)) /* ---------------------------------------------------------------------- */ template FixShardlowKokkos::FixShardlowKokkos(LAMMPS *lmp, int narg, char **arg) : FixShardlow(lmp, narg, arg), k_pairDPDE(NULL), ghostmax(0), nlocal(0) , nghost(0) { kokkosable = 1; // atomKK = (AtomKokkos *) atom; // execution_space = ExecutionSpaceFromDevice::space; // datamask_read = X_MASK | V_MASK | F_MASK | MASK_MASK | Q_MASK | TYPE_MASK; // datamask_modify = Q_MASK | X_MASK; if (narg != 3) error->all(FLERR,"Illegal fix shardlow command"); // k_pairDPD = NULL; k_pairDPDE = NULL; // k_pairDPD = (PairDPDfdtKokkos *) force->pair_match("dpd/fdt",1); k_pairDPDE = dynamic_cast *>(force->pair_match("dpd/fdt/energy",0)); // if(k_pairDPDE){ comm_forward = 3; comm_reverse = 5; maxRNG = 0; #ifdef DPD_USE_RAN_MARS pp_random = NULL; #endif // } else { // comm_forward = 3; // comm_reverse = 3; // } if(/* k_pairDPD == NULL &&*/ k_pairDPDE == NULL) error->all(FLERR,"Must use pair_style "/*"dpd/fdt/kk or "*/"dpd/fdt/energy/kk with fix shardlow/kk"); #ifdef DEBUG_PAIR_CT d_counters = typename AT::t_int_2d("FixShardlowKokkos::d_counters", 2, 3); d_hist = typename AT::t_int_1d("FixShardlowKokkos::d_hist", 32); #ifndef KOKKOS_USE_CUDA_UVM h_counters = Kokkos::create_mirror_view(d_counters); h_hist = Kokkos::create_mirror_view(d_hist); #else h_counters = d_counters; h_hist = d_hist; #endif #endif } /* ---------------------------------------------------------------------- */ template FixShardlowKokkos::~FixShardlowKokkos() { ghostmax = 0; #ifdef DPD_USE_RAN_MARS if (pp_random) { for (int i = 1; i < maxRNG; ++i) delete pp_random[i]; delete[] pp_random; pp_random = NULL; } #endif } /* ---------------------------------------------------------------------- */ template int FixShardlowKokkos::setmask() { int mask = 0; mask |= INITIAL_INTEGRATE | PRE_NEIGHBOR; return mask; } /* ---------------------------------------------------------------------- */ template void FixShardlowKokkos::init() { FixShardlow::init(); int irequest = neighbor->nrequest - 1; neighbor->requests[irequest]-> kokkos_host = Kokkos::Impl::is_same::value && !Kokkos::Impl::is_same::value; neighbor->requests[irequest]-> kokkos_device = Kokkos::Impl::is_same::value; // neighbor->requests[irequest]->pair = 0; // neighbor->requests[irequest]->fix = 1; // neighbor->requests[irequest]->ghost= 1; // neighbor->requests[irequest]->ssa = 1; int ntypes = atom->ntypes; k_params = Kokkos::DualView ("FixShardlowKokkos::params",ntypes+1,ntypes+1); params = k_params.template view(); //FIXME either create cutsq and fill it in, or just point to pairDPD's... // memory->destroy(cutsq); //FIXME // memory->create_kokkos(k_cutsq,cutsq,ntypes+1,ntypes+1,"FixShardlowKokkos:cutsq"); d_cutsq = k_pairDPDE->k_cutsq.template view(); //FIXME const double boltz2 = 2.0*force->boltz; for (int i = 1; i <= ntypes; i++) { for (int j = i; j <= ntypes; j++) { F_FLOAT cutone = k_pairDPDE->cut[i][j]; // k_cutsq.h_view(i,j) = k_cutsq.h_view(j,i) = cutone*cutone; //FIXME if (cutone > EPSILON) k_params.h_view(i,j).cutinv = 1.0/cutone; else k_params.h_view(i,j).cutinv = FLT_MAX; k_params.h_view(i,j).halfsigma = 0.5*k_pairDPDE->sigma[i][j]; k_params.h_view(i,j).kappa = k_pairDPDE->kappa[i][j]; k_params.h_view(i,j).alpha = sqrt(boltz2*k_pairDPDE->kappa[i][j]); k_params.h_view(j,i) = k_params.h_view(i,j); if(ik_cutsq.h_view(i,j); } } } // k_cutsq.template modify(); k_params.template modify(); } /* ---------------------------------------------------------------------- */ template void FixShardlowKokkos::init_list(int id, NeighList *ptr) { FixShardlow::init_list(id, ptr); k_list = static_cast*>(ptr); } /* ---------------------------------------------------------------------- */ template void FixShardlowKokkos::pre_neighbor() { // NOTE: this logic is specific to orthogonal boxes, not triclinic // Enforce the constraint that ghosts must be contained in the nearest sub-domains double bbx = domain->subhi[0] - domain->sublo[0]; double bby = domain->subhi[1] - domain->sublo[1]; double bbz = domain->subhi[2] - domain->sublo[2]; double rcut = 2.0*neighbor->cutneighmax; if (domain->triclinic) error->all(FLERR,"Fix shardlow does not yet support triclinic geometries"); if(rcut >= bbx || rcut >= bby || rcut>= bbz ) { char fmt[] = {"Shardlow algorithm requires sub-domain length > 2*(rcut+skin). Either reduce the number of processors requested, or change the cutoff/skin: rcut= %e bbx= %e bby= %e bbz= %e\n"}; char *msg = (char *) malloc(sizeof(fmt) + 4*15); sprintf(msg, fmt, rcut, bbx, bby, bbz); error->one(FLERR, msg); } nlocal = atomKK->nlocal; nghost = atomKK->nghost; // Allocate memory for h_v_t0 to hold the initial velocities for the ghosts if (nghost > ghostmax) { ghostmax = nghost; k_v_t0 = DAT::tdual_v_array("FixShardlowKokkos:v_t0", ghostmax); // d_v_t0 = k_v_t0.template view(); h_v_t0 = k_v_t0.h_view; } // Setup views of relevant data x = atomKK->k_x.template view(); v = atomKK->k_v.template view(); h_v = atomKK->k_v.h_view; uCond = atomKK->k_uCond.template view(); h_uCond = atomKK->k_uCond.h_view; uMech = atomKK->k_uMech.template view(); h_uMech = atomKK->k_uMech.h_view; type = atomKK->k_type.view(); if (atomKK->rmass) { massPerI = true; masses = atomKK->k_rmass.view(); } else { massPerI = false; masses = atomKK->k_mass.view(); } // if(k_pairDPDE){ dpdTheta = atomKK->k_dpdTheta.view(); //} else { //} } template void FixShardlowKokkos::setup_pre_neighbor() { pre_neighbor(); } /* ---------------------------------------------------------------------- */ #ifdef NOTNOW /* ---------------------------------------------------------------------- Perform the stochastic integration and Shardlow update for constant temperature Allow for both per-type and per-atom mass NOTE: only implemented for orthogonal boxes, not triclinic ------------------------------------------------------------------------- */ template template void FixShardlowKokkos::ssa_update_dpd( int start_ii, int count, int id ) { #ifdef DPD_USE_RAN_MARS class RanMars *pRNG = pp_random[id]; #else rand_type rand_gen = rand_pool.get_state(id); #endif const double theta_ij_inv = 1.0/k_pairDPD->temperature; // independent of i,j const double boltz_inv = 1.0/force->boltz; const double ftm2v = force->ftm2v; const double dt = update->dt; int ct = count; int ii = start_ii; while (ct-- > 0) { const int i = d_ilist(ii); const int jlen = d_numneigh(ii); const double xtmp = x(i, 0); const double ytmp = x(i, 1); const double ztmp = x(i, 2); // load velocity for i from memory double vxi = v(i, 0); double vyi = v(i, 1); double vzi = v(i, 2); const int itype = type(i); const double mass_i = masses(massPerI ? i : itype); const double massinv_i = 1.0 / mass_i; // Loop over Directional Neighbors only for (int jj = 0; jj < jlen; jj++) { const int j = d_neighbors(ii,jj) & NEIGHMASK; int jtype = type[j]; const X_FLOAT delx = xtmp - x(j, 0); const X_FLOAT dely = ytmp - x(j, 1); const X_FLOAT delz = ztmp - x(j, 2); const F_FLOAT rsq = delx*delx + dely*dely + delz*delz; #ifdef DEBUG_PAIR_CT if ((i < nlocal) && (j < nlocal)) Kokkos::atomic_increment(&(d_counters(0, 0))); else Kokkos::atomic_increment(&(d_counters(0, 1))); Kokkos::atomic_increment(&(d_counters(0, 2))); int rsqi = rsq / 8; if (rsqi < 0) rsqi = 0; else if (rsqi > 31) rsqi = 31; Kokkos::atomic_increment(&(d_hist(rsqi))); #endif // NOTE: r can be 0.0 in DPD systems, so do EPSILON_SQUARED test if ((rsq < (STACKPARAMS?m_cutsq[itype][jtype]:d_cutsq(itype,jtype))) && (rsq >= EPSILON_SQUARED)) { #ifdef DEBUG_PAIR_CT if ((i < nlocal) && (j < nlocal)) Kokkos::atomic_increment(&(d_counters(1, 0))); else Kokkos::atomic_increment(&(d_counters(1, 1))); Kokkos::atomic_increment(&(d_counters(1, 2))); #endif double r = sqrt(rsq); double rinv = 1.0/r; double delx_rinv = delx*rinv; double dely_rinv = dely*rinv; double delz_rinv = delz*rinv; double wr = 1.0 - r*(STACKPARAMS?m_params[itype][jtype].cutinv:params(itype,jtype).cutinv); double wdt = wr*wr*dt; double halfsigma_ij = STACKPARAMS?m_params[itype][jtype].halfsigma:params(itype,jtype).halfsigma; double halfgamma_ij = halfsigma_ij*halfsigma_ij*boltz_inv*theta_ij_inv; double sigmaRand = halfsigma_ij*wr*dtsqrt*ftm2v * #ifdef DPD_USE_RAN_MARS pRNG->gaussian(); #else rand_gen.normal(); #endif const double mass_j = masses(massPerI ? j : jtype); double massinv_j = 1.0 / mass_j; double gammaFactor = halfgamma_ij*wdt*ftm2v; double inv_1p_mu_gammaFactor = 1.0/(1.0 + (massinv_i + massinv_j)*gammaFactor); double vxj = v(j, 0); double vyj = v(j, 1); double vzj = v(j, 2); // Compute the initial velocity difference between atom i and atom j double delvx = vxi - vxj; double delvy = vyi - vyj; double delvz = vzi - vzj; double dot_rinv = (delx_rinv*delvx + dely_rinv*delvy + delz_rinv*delvz); // Compute momentum change between t and t+dt double factorA = sigmaRand - gammaFactor*dot_rinv; // Update the velocity on i vxi += delx_rinv*factorA*massinv_i; vyi += dely_rinv*factorA*massinv_i; vzi += delz_rinv*factorA*massinv_i; // Update the velocity on j vxj -= delx_rinv*factorA*massinv_j; vyj -= dely_rinv*factorA*massinv_j; vzj -= delz_rinv*factorA*massinv_j; //ii. Compute the new velocity diff delvx = vxi - vxj; delvy = vyi - vyj; delvz = vzi - vzj; dot_rinv = delx_rinv*delvx + dely_rinv*delvy + delz_rinv*delvz; // Compute the new momentum change between t and t+dt double factorB = (sigmaRand - gammaFactor*dot_rinv)*inv_1p_mu_gammaFactor; // Update the velocity on i vxi += delx_rinv*factorB*massinv_i; vyi += dely_rinv*factorB*massinv_i; vzi += delz_rinv*factorB*massinv_i; // Update the velocity on j vxj -= delx_rinv*factorB*massinv_j; vyj -= dely_rinv*factorB*massinv_j; vzj -= delz_rinv*factorB*massinv_j; // Store updated velocity for j v(j, 0) = vxj; v(j, 1) = vyj; v(j, 2) = vzj; } } // store updated velocity for i v(i, 0) = vxi; v(i, 1) = vyi; v(i, 2) = vzi; } #ifndef DPD_USE_RAN_MARS rand_pool.free_state(rand_gen); #endif } #endif /* ---------------------------------------------------------------------- Perform the stochastic integration and Shardlow update for constant energy Allow for both per-type and per-atom mass NOTE: only implemented for orthogonal boxes, not triclinic ------------------------------------------------------------------------- */ template template KOKKOS_INLINE_FUNCTION void FixShardlowKokkos::ssa_update_dpde( int start_ii, int count, int id ) { #ifdef DPD_USE_RAN_MARS class RanMars *pRNG = pp_random[id]; #else rand_type rand_gen = rand_pool.get_state(id); #endif const double boltz_inv = 1.0/force->boltz; const double ftm2v = force->ftm2v; const double dt = update->dt; int ct = count; int ii = start_ii; while (ct-- > 0) { const int i = d_ilist(ii); const int jlen = d_numneigh(ii); const double xtmp = x(i, 0); const double ytmp = x(i, 1); const double ztmp = x(i, 2); // load velocity for i from memory double vxi = v(i, 0); double vyi = v(i, 1); double vzi = v(i, 2); double uMech_i = uMech(i); double uCond_i = uCond(i); const int itype = type(i); const double theta_i_inv = 1.0/dpdTheta(i); const double mass_i = masses(massPerI ? i : itype); const double massinv_i = 1.0 / mass_i; const double mass_i_div_neg4_ftm2v = mass_i*(-0.25)/ftm2v; // Loop over Directional Neighbors only for (int jj = 0; jj < jlen; jj++) { const int j = d_neighbors(ii,jj) & NEIGHMASK; const int jtype = type(j); const X_FLOAT delx = xtmp - x(j, 0); const X_FLOAT dely = ytmp - x(j, 1); const X_FLOAT delz = ztmp - x(j, 2); const F_FLOAT rsq = delx*delx + dely*dely + delz*delz; #ifdef DEBUG_PAIR_CT if ((i < nlocal) && (j < nlocal)) Kokkos::atomic_increment(&(d_counters(0, 0))); else Kokkos::atomic_increment(&(d_counters(0, 1))); Kokkos::atomic_increment(&(d_counters(0, 2))); int rsqi = rsq / 8; if (rsqi < 0) rsqi = 0; else if (rsqi > 31) rsqi = 31; Kokkos::atomic_increment(&(d_hist(rsqi))); #endif // NOTE: r can be 0.0 in DPD systems, so do EPSILON_SQUARED test if ((rsq < (STACKPARAMS?m_cutsq[itype][jtype]:d_cutsq(itype,jtype))) && (rsq >= EPSILON_SQUARED)) { #ifdef DEBUG_PAIR_CT if ((i < nlocal) && (j < nlocal)) Kokkos::atomic_increment(&(d_counters(1, 0))); else Kokkos::atomic_increment(&(d_counters(1, 1))); Kokkos::atomic_increment(&(d_counters(1, 2))); #endif double r = sqrt(rsq); double rinv = 1.0/r; double delx_rinv = delx*rinv; double dely_rinv = dely*rinv; double delz_rinv = delz*rinv; double wr = 1.0 - r*(STACKPARAMS?m_params[itype][jtype].cutinv:params(itype,jtype).cutinv); double wdt = wr*wr*dt; // Compute the current temperature double theta_j_inv = 1.0/dpdTheta(j); double theta_ij_inv = 0.5*(theta_i_inv + theta_j_inv); double halfsigma_ij = STACKPARAMS?m_params[itype][jtype].halfsigma:params(itype,jtype).halfsigma; double halfgamma_ij = halfsigma_ij*halfsigma_ij*boltz_inv*theta_ij_inv; double sigmaRand = halfsigma_ij*wr*dtsqrt*ftm2v * #ifdef DPD_USE_RAN_MARS pRNG->gaussian(); #else rand_gen.normal(); #endif const double mass_j = masses(massPerI ? j : jtype); double mass_ij_div_neg4_ftm2v = mass_j*mass_i_div_neg4_ftm2v; double massinv_j = 1.0 / mass_j; // Compute uCond double kappa_ij = STACKPARAMS?m_params[itype][jtype].kappa:params(itype,jtype).kappa; double alpha_ij = STACKPARAMS?m_params[itype][jtype].alpha:params(itype,jtype).alpha; double del_uCond = alpha_ij*wr*dtsqrt * #ifdef DPD_USE_RAN_MARS pRNG->gaussian(); #else rand_gen.normal(); #endif del_uCond += kappa_ij*(theta_i_inv - theta_j_inv)*wdt; uCond[j] -= del_uCond; uCond_i += del_uCond; double gammaFactor = halfgamma_ij*wdt*ftm2v; double inv_1p_mu_gammaFactor = 1.0/(1.0 + (massinv_i + massinv_j)*gammaFactor); double vxj = v(j, 0); double vyj = v(j, 1); double vzj = v(j, 2); double dot4 = vxj*vxj + vyj*vyj + vzj*vzj; double dot3 = vxi*vxi + vyi*vyi + vzi*vzi; // Compute the initial velocity difference between atom i and atom j double delvx = vxi - vxj; double delvy = vyi - vyj; double delvz = vzi - vzj; double dot_rinv = (delx_rinv*delvx + dely_rinv*delvy + delz_rinv*delvz); // Compute momentum change between t and t+dt double factorA = sigmaRand - gammaFactor*dot_rinv; // Update the velocity on i vxi += delx_rinv*factorA*massinv_i; vyi += dely_rinv*factorA*massinv_i; vzi += delz_rinv*factorA*massinv_i; // Update the velocity on j vxj -= delx_rinv*factorA*massinv_j; vyj -= dely_rinv*factorA*massinv_j; vzj -= delz_rinv*factorA*massinv_j; //ii. Compute the new velocity diff delvx = vxi - vxj; delvy = vyi - vyj; delvz = vzi - vzj; dot_rinv = delx_rinv*delvx + dely_rinv*delvy + delz_rinv*delvz; // Compute the new momentum change between t and t+dt double factorB = (sigmaRand - gammaFactor*dot_rinv)*inv_1p_mu_gammaFactor; // Update the velocity on i vxi += delx_rinv*factorB*massinv_i; vyi += dely_rinv*factorB*massinv_i; vzi += delz_rinv*factorB*massinv_i; double partial_uMech = (vxi*vxi + vyi*vyi + vzi*vzi - dot3)*massinv_j; // Update the velocity on j vxj -= delx_rinv*factorB*massinv_j; vyj -= dely_rinv*factorB*massinv_j; vzj -= delz_rinv*factorB*massinv_j; partial_uMech += (vxj*vxj + vyj*vyj + vzj*vzj - dot4)*massinv_i; // Store updated velocity for j v(j, 0) = vxj; v(j, 1) = vyj; v(j, 2) = vzj; // Compute uMech double del_uMech = partial_uMech*mass_ij_div_neg4_ftm2v; uMech_i += del_uMech; uMech(j) += del_uMech; } } // store updated velocity for i v(i, 0) = vxi; v(i, 1) = vyi; v(i, 2) = vzi; // store updated uMech and uCond for i uMech(i) = uMech_i; uCond(i) = uCond_i; ii++; } #ifndef DPD_USE_RAN_MARS rand_pool.free_state(rand_gen); #endif } template void FixShardlowKokkos::initial_integrate(int vflag) { d_numneigh = k_list->d_numneigh; d_neighbors = k_list->d_neighbors; d_ilist = k_list->d_ilist; copymode = 1; dtsqrt = sqrt(update->dt); NPairSSAKokkos *np_ssa = dynamic_cast*>(list->np); if (!np_ssa) error->one(FLERR, "NPair wasn't a NPairSSAKokkos object"); ssa_phaseCt = np_ssa->ssa_phaseCt; ssa_phaseLen = np_ssa->ssa_phaseLen; ssa_itemLoc = np_ssa->ssa_itemLoc; ssa_itemLen = np_ssa->ssa_itemLen; ssa_gphaseCt = np_ssa->ssa_gphaseCt; ssa_gphaseLen = np_ssa->ssa_gphaseLen; ssa_gitemLoc = np_ssa->ssa_gitemLoc; ssa_gitemLen = np_ssa->ssa_gitemLen; int maxWorkItemCt = (int) ssa_itemLoc.dimension_1(); if (maxWorkItemCt < (int) ssa_gitemLoc.dimension_1()) { maxWorkItemCt = (int) ssa_gitemLoc.dimension_1(); } if (maxWorkItemCt > maxRNG) { #ifdef DPD_USE_RAN_MARS if (pp_random) { for (int i = 1; i < maxRNG; ++i) delete pp_random[i]; delete[] pp_random; pp_random = NULL; } pp_random = new RanMars*[maxWorkItemCt]; for (int i = 1; i < maxWorkItemCt; ++i) { pp_random[i] = new RanMars(lmp, k_pairDPDE->seed + comm->me + comm->nprocs*i); } pp_random[0] = k_pairDPDE->random; #else rand_pool.init(k_pairDPDE->seed + comm->me, maxWorkItemCt); #endif maxRNG = maxWorkItemCt; } #ifdef DEBUG_PAIR_CT for (int i = 0; i < 2; ++i) for (int j = 0; j < 3; ++j) h_counters(i,j) = 0; for (int i = 0; i < 32; ++i) h_hist[i] = 0; deep_copy(d_counters, h_counters); deep_copy(d_hist, h_hist); #endif // process neighbors in the local AIR for (int workPhase = 0; workPhase < ssa_phaseCt; ++workPhase) { int workItemCt = ssa_phaseLen[workPhase]; if(atom->ntypes > MAX_TYPES_STACKPARAMS) { Kokkos::parallel_for(workItemCt, LAMMPS_LAMBDA (const int workItem ) { int ct = ssa_itemLen(workPhase, workItem); int ii = ssa_itemLoc(workPhase, workItem); ssa_update_dpde(ii, ct, workItem); }); } else { Kokkos::parallel_for(workItemCt, LAMMPS_LAMBDA (const int workItem ) { int ct = ssa_itemLen(workPhase, workItem); int ii = ssa_itemLoc(workPhase, workItem); ssa_update_dpde(ii, ct, workItem); }); } } //Loop over all 13 outward directions (7 stages) for (int workPhase = 0; workPhase < ssa_gphaseCt; ++workPhase) { // int airnum = workPhase + 1; int workItemCt = ssa_gphaseLen[workPhase]; // Communicate the updated velocities to all nodes comm->forward_comm_fix(this); if(k_pairDPDE){ // Zero out the ghosts' uCond & uMech to be used as delta accumulators // memset(&(atom->uCond[nlocal]), 0, sizeof(double)*nghost); // memset(&(atom->uMech[nlocal]), 0, sizeof(double)*nghost); Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+nghost), LAMMPS_LAMBDA (const int i) { uCond(i) = 0.0; uMech(i) = 0.0; }); DeviceType::fence(); } // process neighbors in this AIR if(atom->ntypes > MAX_TYPES_STACKPARAMS) { Kokkos::parallel_for(workItemCt, LAMMPS_LAMBDA (const int workItem ) { int ct = ssa_gitemLen(workPhase, workItem); int ii = ssa_gitemLoc(workPhase, workItem); ssa_update_dpde(ii, ct, workItem); }); } else { Kokkos::parallel_for(workItemCt, LAMMPS_LAMBDA (const int workItem ) { int ct = ssa_gitemLen(workPhase, workItem); int ii = ssa_gitemLoc(workPhase, workItem); ssa_update_dpde(ii, ct, workItem); }); } // Communicate the ghost deltas to the atom owners comm->reverse_comm_fix(this); } //End Loop over all directions For airnum = Top, Top-Right, Right, Bottom-Right, Back #ifdef DEBUG_PAIR_CT deep_copy(h_counters, d_counters); deep_copy(h_hist, d_hist); for (int i = 0; i < 32; ++i) fprintf(stdout, "%8d", h_hist[i]); fprintf(stdout, "\n%6d %6d,%6d %6d: " ,h_counters(0, 2) ,h_counters(1, 2) ,h_counters(0, 1) ,h_counters(1, 1) ); #endif + copymode = 0; } /* ---------------------------------------------------------------------- */ template int FixShardlowKokkos::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { int ii,jj,m; m = 0; for (ii = 0; ii < n; ii++) { jj = list[ii]; buf[m++] = h_v(jj, 0); buf[m++] = h_v(jj, 1); buf[m++] = h_v(jj, 2); } return m; } /* ---------------------------------------------------------------------- */ template void FixShardlowKokkos::unpack_forward_comm(int n, int first, double *buf) { int ii,m,last; m = 0; last = first + n ; for (ii = first; ii < last; ii++) { h_v_t0(ii - nlocal, 0) = h_v(ii, 0) = buf[m++]; h_v_t0(ii - nlocal, 1) = h_v(ii, 1) = buf[m++]; h_v_t0(ii - nlocal, 2) = h_v(ii, 2) = buf[m++]; } } /* ---------------------------------------------------------------------- */ template int FixShardlowKokkos::pack_reverse_comm(int n, int first, double *buf) { int i,m,last; m = 0; last = first + n; for (i = first; i < last; i++) { buf[m++] = h_v(i, 0) - h_v_t0(i - nlocal, 0); buf[m++] = h_v(i, 1) - h_v_t0(i - nlocal, 1); buf[m++] = h_v(i, 2) - h_v_t0(i - nlocal, 2); if(k_pairDPDE){ buf[m++] = h_uCond(i); // for ghosts, this is an accumulated delta buf[m++] = h_uMech(i); // for ghosts, this is an accumulated delta } } return m; } /* ---------------------------------------------------------------------- */ template void FixShardlowKokkos::unpack_reverse_comm(int n, int *list, double *buf) { int i,j,m; m = 0; for (i = 0; i < n; i++) { j = list[i]; h_v(j, 0) += buf[m++]; h_v(j, 1) += buf[m++]; h_v(j, 2) += buf[m++]; if(k_pairDPDE){ h_uCond(j) += buf[m++]; // add in the accumulated delta h_uMech(j) += buf[m++]; // add in the accumulated delta } } } /* ---------------------------------------------------------------------- */ template double FixShardlowKokkos::memory_usage() { double bytes = 0.0; bytes += sizeof(double)*3*ghostmax; // v_t0[] return bytes; } namespace LAMMPS_NS { template class FixShardlowKokkos; #ifdef KOKKOS_HAVE_CUDA template class FixShardlowKokkos; #endif }