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lammps/src/GPU/pair_gayberne_gpu.cpp
W. Michael Brown 37f22c8627 Misc Improvements to GPU Package 
- Optimizations for molecular systems
-   Improved kernel performance and greater CPU overlap
- Reduced GPU to CPU communications for discrete devices
- Switch classic Intel makefiles to use LLVM-based compilers
- Prefetch optimizations supported for OpenCL
- Optimized data repack for quaternions
2023-03-05 21:03:12 -08:00

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/* ----------------------------------------------------------------------
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: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "pair_gayberne_gpu.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "math_extra.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include <cmath>
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int gb_gpu_init(const int ntypes, const double gamma, const double upsilon,
const double mu, double **shape, double **well, double **cutsq,
double **sigma, double **epsilon, double *host_lshape,
int **form, double **host_lj1, double **host_lj2,
double **host_lj3, double **host_lj4, double **offset,
double *special_lj, const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void gb_gpu_clear();
int **gb_gpu_compute_n(const int ago, const int inum, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, const int *ellipsoid,
const void *bonus);
int *gb_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, const int *ellipsoid,
const void *bonus);
double gb_gpu_bytes();
enum { SPHERE_SPHERE, SPHERE_ELLIPSE, ELLIPSE_SPHERE, ELLIPSE_ELLIPSE };
/* ---------------------------------------------------------------------- */
PairGayBerneGPU::PairGayBerneGPU(LAMMPS *lmp) : PairGayBerne(lmp),
gpu_mode(GPU_FORCE)
{
reinitflag = 0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairGayBerneGPU::~PairGayBerneGPU()
{
gb_gpu_clear();
cpu_time = 0.0;
}
/* ---------------------------------------------------------------------- */
void PairGayBerneGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
if (gpu_mode != GPU_FORCE) {
double sublo[3], subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
sublo[2] = domain->sublo[2];
subhi[0] = domain->subhi[0];
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh =
gb_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, sublo,
subhi, atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time, success,
ellipsoid, bonus);
} else {
inum = list->inum;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ilist = gb_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
list->ilist, numneigh, firstneigh, eflag, vflag,
eflag_atom, vflag_atom, host_start, cpu_time,
success, ellipsoid, bonus);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
if (host_start < inum) {
cpu_time = platform::walltime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = platform::walltime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairGayBerneGPU::init_style()
{
avec = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
if (!avec) error->all(FLERR, "Pair gayberne/gpu requires atom style ellipsoid");
if (!atom->ellipsoid_flag) error->all(FLERR, "Pair gayberne/gpu requires atom style ellipsoid");
// per-type shape precalculations
// require that atom shapes are identical within each type
// if shape = 0 for point particle, set shape = 1 as required by Gay-Berne
for (int i = 1; i <= atom->ntypes; i++) {
if (!atom->shape_consistency(i, shape1[i][0], shape1[i][1], shape1[i][2]))
error->all(FLERR, "Pair gayberne/gpu requires atoms with same type have same shape");
if (shape1[i][0] == 0.0) shape1[i][0] = shape1[i][1] = shape1[i][2] = 1.0;
shape2[i][0] = shape1[i][0] * shape1[i][0];
shape2[i][1] = shape1[i][1] * shape1[i][1];
shape2[i][2] = shape1[i][2] * shape1[i][2];
lshape[i] = (shape1[i][0] * shape1[i][1] + shape1[i][2] * shape1[i][2]) *
sqrt(shape1[i][0] * shape1[i][1]);
}
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i, j);
cut *= cut;
if (cut > maxcut) maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
gb_gpu_init(atom->ntypes + 1, gamma, upsilon, mu, shape2, well, cutsq,
sigma, epsilon, lshape, form, lj1, lj2, lj3, lj4, offset,
force->special_lj, atom->nlocal, atom->nlocal + atom->nghost,
mnf, maxspecial, cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success, error, world);
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairGayBerneGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + gb_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairGayBerneGPU::cpu_compute(int start, int inum, int eflag,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i, j, ii, jj, jnum, itype, jtype;
double evdwl, one_eng, rsq, r2inv, r6inv, forcelj, factor_lj;
double fforce[3], ttor[3], rtor[3], r12[3];
double a1[3][3], b1[3][3], g1[3][3], a2[3][3], b2[3][3], g2[3][3], temp[3][3];
int *jlist;
double *iquat, *jquat;
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
double **x = atom->x;
double **f = atom->f;
double **tor = atom->torque;
int *type = atom->type;
double *special_lj = force->special_lj;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
itype = type[i];
if (form[itype][itype] == ELLIPSE_ELLIPSE) {
iquat = bonus[ellipsoid[i]].quat;
MathExtra::quat_to_mat_trans(iquat, a1);
MathExtra::diag_times3(well[itype], a1, temp);
MathExtra::transpose_times3(a1, temp, b1);
MathExtra::diag_times3(shape2[itype], a1, temp);
MathExtra::transpose_times3(a1, temp, g1);
}
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
// r12 = center to center vector
r12[0] = x[j][0] - x[i][0];
r12[1] = x[j][1] - x[i][1];
r12[2] = x[j][2] - x[i][2];
rsq = MathExtra::dot3(r12, r12);
jtype = type[j];
// compute if less than cutoff
if (rsq < cutsq[itype][jtype]) {
switch (form[itype][jtype]) {
case SPHERE_SPHERE:
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
forcelj *= -r2inv;
if (eflag)
one_eng =
r6inv * (r6inv * lj3[itype][jtype] - lj4[itype][jtype]) - offset[itype][jtype];
fforce[0] = r12[0] * forcelj;
fforce[1] = r12[1] * forcelj;
fforce[2] = r12[2] * forcelj;
ttor[0] = ttor[1] = ttor[2] = 0.0;
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
case SPHERE_ELLIPSE:
jquat = bonus[ellipsoid[j]].quat;
MathExtra::quat_to_mat_trans(jquat, a2);
MathExtra::diag_times3(well[jtype], a2, temp);
MathExtra::transpose_times3(a2, temp, b2);
MathExtra::diag_times3(shape2[jtype], a2, temp);
MathExtra::transpose_times3(a2, temp, g2);
one_eng = gayberne_lj(j, i, a2, b2, g2, r12, rsq, fforce, rtor);
ttor[0] = ttor[1] = ttor[2] = 0.0;
break;
case ELLIPSE_SPHERE:
one_eng = gayberne_lj(i, j, a1, b1, g1, r12, rsq, fforce, ttor);
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
default:
jquat = bonus[ellipsoid[j]].quat;
MathExtra::quat_to_mat_trans(jquat, a2);
MathExtra::diag_times3(well[jtype], a2, temp);
MathExtra::transpose_times3(a2, temp, b2);
MathExtra::diag_times3(shape2[jtype], a2, temp);
MathExtra::transpose_times3(a2, temp, g2);
one_eng = gayberne_analytic(i, j, a1, a2, b1, b2, g1, g2, r12, rsq, fforce, ttor, rtor);
break;
}
fforce[0] *= factor_lj;
fforce[1] *= factor_lj;
fforce[2] *= factor_lj;
ttor[0] *= factor_lj;
ttor[1] *= factor_lj;
ttor[2] *= factor_lj;
f[i][0] += fforce[0];
f[i][1] += fforce[1];
f[i][2] += fforce[2];
tor[i][0] += ttor[0];
tor[i][1] += ttor[1];
tor[i][2] += ttor[2];
if (eflag) evdwl = factor_lj * one_eng;
if (evflag)
ev_tally_xyz_full(i, evdwl, 0.0, fforce[0], fforce[1], fforce[2], -r12[0], -r12[1],
-r12[2]);
}
}
}
}
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