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lammps/src/GPU/pair_born_coul_wolf_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 authors: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
#include "pair_born_coul_wolf_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "math_const.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include <cmath>
using namespace LAMMPS_NS;
using namespace MathConst;
// External functions from cuda library for atom decomposition
int borncw_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv, double **host_born1,
double **host_born2, double **host_born3, double **host_a, double **host_c,
double **host_d, double **sigma, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen, double **host_cut_ljsq,
double host_cut_coulsq, double *host_special_coul, const double qqrd2e,
const double alf, const double e_shift, const double f_shift);
void borncw_gpu_clear();
int **borncw_gpu_compute_n(const int ago, const int inum_full, 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, double *host_q,
double *boxlo, double *prd);
void borncw_gpu_compute(const int ago, const int inum_full, 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, double *host_q, const int nlocal,
double *boxlo, double *prd);
double borncw_gpu_bytes();
/* ---------------------------------------------------------------------- */
PairBornCoulWolfGPU::PairBornCoulWolfGPU(LAMMPS *lmp) : PairBornCoulWolf(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairBornCoulWolfGPU::~PairBornCoulWolfGPU()
{
borncw_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairBornCoulWolfGPU::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;
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 = borncw_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, atom->q, domain->boxlo, domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
borncw_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
}
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 PairBornCoulWolfGPU::init_style()
{
if (!atom->q_flag) error->all(FLERR, "Pair style born/coul/wolf/gpu requires atom attribute q");
// 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;
cut_coulsq = cut_coul * cut_coul;
double e_shift = erfc(alf * cut_coul) / cut_coul;
double f_shift =
-(e_shift + 2.0 * alf / MY_PIS * exp(-alf * alf * cut_coul * cut_coul)) / cut_coul;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
borncw_gpu_init(atom->ntypes + 1, cutsq, rhoinv, born1, born2, born3, a, c, d, sigma, offset,
force->special_lj, atom->nlocal, atom->nlocal + atom->nghost, mnf, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq, cut_coulsq, force->special_coul,
force->qqrd2e, alf, e_shift, f_shift);
GPU_EXTRA::check_flag(success, error, world);
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairBornCoulWolfGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + borncw_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairBornCoulWolfGPU::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 xtmp, ytmp, ztmp, qtmp, delx, dely, delz, evdwl, ecoul, fpair;
double rsq, r2inv, r6inv, forcecoul, forceborn, factor_coul, factor_lj;
double erfcc, erfcd, v_sh, dvdrr, e_self, qisq;
double prefactor;
double r, rexp;
int *jlist;
evdwl = ecoul = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
double e_shift = erfc(alf * cut_coul) / cut_coul;
double f_shift =
-(e_shift + 2.0 * alf / MY_PIS * exp(-alf * alf * cut_coul * cut_coul)) / cut_coul;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
qisq = qtmp * qtmp;
e_self = -(e_shift / 2.0 + alf / MY_PIS) * qisq * qqrd2e;
if (evflag) ev_tally(i, i, nlocal, 0, 0.0, e_self, 0.0, 0.0, 0.0, 0.0);
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[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]) {
r2inv = 1.0 / rsq;
if (rsq < cut_coulsq) {
r = sqrt(rsq);
prefactor = qqrd2e * qtmp * q[j] / r;
erfcc = erfc(alf * r);
erfcd = exp(-alf * alf * r * r);
v_sh = (erfcc - e_shift * r) * prefactor;
dvdrr = (erfcc / rsq + 2.0 * alf / MY_PIS * erfcd / r) + f_shift;
forcecoul = dvdrr * rsq * prefactor;
if (factor_coul < 1.0) forcecoul -= (1.0 - factor_coul) * prefactor;
} else
forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv * r2inv * r2inv;
r = sqrt(rsq);
rexp = exp((sigma[itype][jtype] - r) * rhoinv[itype][jtype]);
forceborn = born1[itype][jtype] * r * rexp - born2[itype][jtype] * r6inv +
born3[itype][jtype] * r2inv * r6inv;
} else
forceborn = 0.0;
fpair = (factor_coul * forcecoul + factor_lj * forceborn) * r2inv;
f[i][0] += delx * fpair;
f[i][1] += dely * fpair;
f[i][2] += delz * fpair;
if (eflag) {
if (rsq < cut_coulsq) {
ecoul = v_sh;
if (factor_coul < 1.0) ecoul -= (1.0 - factor_coul) * prefactor;
} else
ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = a[itype][jtype] * rexp - c[itype][jtype] * r6inv +
d[itype][jtype] * r6inv * r2inv - offset[itype][jtype];
evdwl *= factor_lj;
} else
evdwl = 0.0;
}
if (evflag) ev_tally_full(i, evdwl, ecoul, fpair, delx, dely, delz);
}
}
}
}
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