304 lines
10 KiB
C++
304 lines
10 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Mike Brown (SNL)
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------------------------------------------------------------------------- */
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#include "pair_resquared_gpu.h"
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#include "atom.h"
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#include "atom_vec_ellipsoid.h"
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#include "domain.h"
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#include "error.h"
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#include "force.h"
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#include "gpu_extra.h"
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#include "math_extra.h"
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#include "memory.h"
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#include "neigh_list.h"
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#include "neighbor.h"
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#include "suffix.h"
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#include <cmath>
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using namespace LAMMPS_NS;
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// External functions from cuda library for atom decomposition
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int re_gpu_init(const int ntypes, double **shape, double **well, double **cutsq, double **sigma,
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double **epsilon, int **form, double **host_lj1, double **host_lj2,
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double **host_lj3, double **host_lj4, double **offset, double *special_lj,
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const int nlocal, const int nall, const int max_nbors, const int maxspecial,
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const double cell_size, int &gpu_mode, FILE *screen);
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void re_gpu_clear();
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int **re_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x,
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int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial,
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tagint **special, const bool eflag, const bool vflag, const bool eatom,
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const bool vatom, int &host_start, int **ilist, int **jnum,
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const double cpu_time, bool &success, double **host_quat);
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int *re_gpu_compute(const int ago, const int inum, const int nall, double **host_x, int *host_type,
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int *ilist, int *numj, int **firstneigh, const bool eflag, const bool vflag,
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const bool eatom, const bool vatom, int &host_start, const double cpu_time,
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bool &success, double **host_quat);
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double re_gpu_bytes();
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enum { SPHERE_SPHERE, SPHERE_ELLIPSE, ELLIPSE_SPHERE, ELLIPSE_ELLIPSE };
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/* ---------------------------------------------------------------------- */
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PairRESquaredGPU::PairRESquaredGPU(LAMMPS *lmp) : PairRESquared(lmp), gpu_mode(GPU_FORCE)
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{
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reinitflag = 0;
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avec = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
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if (!avec) error->all(FLERR, "Pair resquared/gpu requires atom style ellipsoid");
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quat_nmax = 0;
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quat = nullptr;
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suffix_flag |= Suffix::GPU;
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GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
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}
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/* ----------------------------------------------------------------------
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free all arrays
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------------------------------------------------------------------------- */
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PairRESquaredGPU::~PairRESquaredGPU()
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{
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re_gpu_clear();
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cpu_time = 0.0;
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memory->destroy(quat);
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}
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/* ---------------------------------------------------------------------- */
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void PairRESquaredGPU::compute(int eflag, int vflag)
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{
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ev_init(eflag, vflag);
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int nall = atom->nlocal + atom->nghost;
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int inum, host_start;
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bool success = true;
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int *ilist, *numneigh, **firstneigh;
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if (nall > quat_nmax) {
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quat_nmax = static_cast<int>(1.1 * nall);
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memory->grow(quat, quat_nmax, 4, "pair:quat");
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}
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AtomVecEllipsoid::Bonus *bonus = avec->bonus;
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int *ellipsoid = atom->ellipsoid;
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for (int i = 0; i < nall; i++) {
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int qi = ellipsoid[i];
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if (qi > -1) {
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quat[i][0] = bonus[qi].quat[0];
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quat[i][1] = bonus[qi].quat[1];
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quat[i][2] = bonus[qi].quat[2];
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quat[i][3] = bonus[qi].quat[3];
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}
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}
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if (gpu_mode != GPU_FORCE) {
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double sublo[3], subhi[3];
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if (domain->triclinic == 0) {
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sublo[0] = domain->sublo[0];
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sublo[1] = domain->sublo[1];
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sublo[2] = domain->sublo[2];
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subhi[0] = domain->subhi[0];
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subhi[1] = domain->subhi[1];
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subhi[2] = domain->subhi[2];
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} else {
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domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
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}
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inum = atom->nlocal;
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firstneigh =
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re_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag,
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atom->nspecial, atom->special, eflag, vflag, eflag_atom, vflag_atom,
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host_start, &ilist, &numneigh, cpu_time, success, quat);
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} else {
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inum = list->inum;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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ilist = re_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, list->ilist, numneigh,
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firstneigh, eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time,
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success, quat);
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}
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if (!success) error->one(FLERR, "Insufficient memory on accelerator");
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if (host_start < inum) {
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cpu_time = platform::walltime();
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cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
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cpu_time = platform::walltime() - cpu_time;
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}
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairRESquaredGPU::init_style()
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{
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if (!atom->ellipsoid_flag) error->all(FLERR, "Pair resquared/gpu requires atom style ellipsoid");
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// per-type shape precalculations
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// require that atom shapes are identical within each type
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// if shape = 0 for point particle, set shape = 1 as required by Gay-Berne
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for (int i = 1; i <= atom->ntypes; i++) {
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if (!atom->shape_consistency(i, shape1[i][0], shape1[i][1], shape1[i][2]))
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error->all(FLERR, "Pair resquared/gpu requires atoms with same type have same shape");
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if (setwell[i]) {
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shape2[i][0] = shape1[i][0] * shape1[i][0];
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shape2[i][1] = shape1[i][1] * shape1[i][1];
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shape2[i][2] = shape1[i][2] * shape1[i][2];
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lshape[i] = shape1[i][0] * shape1[i][1] * shape1[i][2];
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}
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}
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// Repeat cutsq calculation because done after call to init_style
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double maxcut = -1.0;
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double cut;
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for (int i = 1; i <= atom->ntypes; i++) {
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for (int j = i; j <= atom->ntypes; j++) {
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if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
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cut = init_one(i, j);
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cut *= cut;
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if (cut > maxcut) maxcut = cut;
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cutsq[i][j] = cutsq[j][i] = cut;
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} else
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cutsq[i][j] = cutsq[j][i] = 0.0;
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}
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}
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double cell_size = sqrt(maxcut) + neighbor->skin;
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int maxspecial = 0;
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if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
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int mnf = 5e-2 * neighbor->oneatom;
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int success =
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re_gpu_init(atom->ntypes + 1, shape1, well, cutsq, sigma, epsilon, form, lj1, lj2, lj3, lj4,
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offset, force->special_lj, atom->nlocal, atom->nlocal + atom->nghost, mnf,
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maxspecial, cell_size, gpu_mode, screen);
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GPU_EXTRA::check_flag(success, error, world);
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if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
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quat_nmax = static_cast<int>(1.1 * (atom->nlocal + atom->nghost));
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memory->grow(quat, quat_nmax, 4, "pair:quat");
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}
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/* ---------------------------------------------------------------------- */
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double PairRESquaredGPU::memory_usage()
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{
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double bytes = Pair::memory_usage();
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return bytes + memory->usage(quat, quat_nmax) + re_gpu_bytes();
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}
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/* ---------------------------------------------------------------------- */
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void PairRESquaredGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist,
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int *numneigh, int **firstneigh)
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{
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int i, j, ii, jj, jnum, itype, jtype;
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double evdwl, one_eng, rsq, r2inv, r6inv, forcelj, factor_lj;
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double fforce[3], ttor[3], rtor[3], r12[3];
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int *jlist;
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RE2Vars wi, wj;
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double **x = atom->x;
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double **f = atom->f;
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double **tor = atom->torque;
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int *type = atom->type;
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double *special_lj = force->special_lj;
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// loop over neighbors of my atoms
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for (ii = start; ii < inum; ii++) {
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i = ilist[ii];
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itype = type[i];
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// not a LJ sphere
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if (lshape[itype] != 0.0) precompute_i(i, wi);
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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factor_lj = special_lj[sbmask(j)];
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j &= NEIGHMASK;
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// r12 = center to center vector
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r12[0] = x[j][0] - x[i][0];
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r12[1] = x[j][1] - x[i][1];
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r12[2] = x[j][2] - x[i][2];
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rsq = MathExtra::dot3(r12, r12);
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jtype = type[j];
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// compute if less than cutoff
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if (rsq < cutsq[itype][jtype]) {
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switch (form[itype][jtype]) {
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case SPHERE_SPHERE:
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r2inv = 1.0 / rsq;
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r6inv = r2inv * r2inv * r2inv;
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forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
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forcelj *= -r2inv;
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if (eflag)
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one_eng =
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r6inv * (r6inv * lj3[itype][jtype] - lj4[itype][jtype]) - offset[itype][jtype];
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fforce[0] = r12[0] * forcelj;
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fforce[1] = r12[1] * forcelj;
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fforce[2] = r12[2] * forcelj;
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break;
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case SPHERE_ELLIPSE:
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precompute_i(j, wj);
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one_eng = resquared_lj(j, i, wj, r12, rsq, fforce, rtor, false);
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break;
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case ELLIPSE_SPHERE:
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one_eng = resquared_lj(i, j, wi, r12, rsq, fforce, ttor, true);
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tor[i][0] += ttor[0] * factor_lj;
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tor[i][1] += ttor[1] * factor_lj;
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tor[i][2] += ttor[2] * factor_lj;
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break;
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default:
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precompute_i(j, wj);
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one_eng = resquared_analytic(i, j, wi, wj, r12, rsq, fforce, ttor, rtor);
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tor[i][0] += ttor[0] * factor_lj;
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tor[i][1] += ttor[1] * factor_lj;
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tor[i][2] += ttor[2] * factor_lj;
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break;
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}
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fforce[0] *= factor_lj;
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fforce[1] *= factor_lj;
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fforce[2] *= factor_lj;
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f[i][0] += fforce[0];
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f[i][1] += fforce[1];
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f[i][2] += fforce[2];
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if (eflag) evdwl = factor_lj * one_eng;
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if (evflag)
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ev_tally_xyz_full(i, evdwl, 0.0, fforce[0], fforce[1], fforce[2], -r12[0], -r12[1],
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-r12[2]);
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}
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}
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}
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}
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