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lammps/src/GPU/pair_colloid_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: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
#include "pair_colloid_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_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 colloid_gpu_init(const int ntypes, double **cutsq, double **host_lj1, double **host_lj2,
double **host_lj3, double **host_lj4, double **offset, double *special_lj,
double **host_a12, double **host_a1, double **host_a2, double **host_d1,
double **host_d2, double **host_sigma3, double **host_sigma6, int **host_form,
const int nlocal, const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void colloid_gpu_clear();
int **colloid_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);
void colloid_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);
double colloid_gpu_bytes();
/* ---------------------------------------------------------------------- */
PairColloidGPU::PairColloidGPU(LAMMPS *lmp) : PairColloid(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
------------------------------------------------------------------------- */
PairColloidGPU::~PairColloidGPU()
{
colloid_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairColloidGPU::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 =
colloid_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);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
colloid_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success);
}
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 PairColloidGPU::init_style()
{
// 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 **_form = nullptr;
int n = atom->ntypes;
memory->create(_form, n + 1, n + 1, "colloid/gpu:_form");
for (int i = 1; i <= n; i++) {
for (int j = 1; j <= n; j++) {
if (form[i][j] == SMALL_SMALL)
_form[i][j] = 0;
else if (form[i][j] == SMALL_LARGE)
_form[i][j] = 1;
else if (form[i][j] == LARGE_LARGE)
_form[i][j] = 2;
}
}
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
colloid_gpu_init(atom->ntypes + 1, cutsq, lj1, lj2, lj3, lj4, offset, force->special_lj, a12,
a1, a2, d1, d2, sigma3, sigma6, _form, atom->nlocal,
atom->nlocal + atom->nghost, mnf, maxspecial, cell_size, gpu_mode, screen);
memory->destroy(_form);
GPU_EXTRA::check_flag(success, error, world);
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairColloidGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + colloid_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairColloidGPU::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, delx, dely, delz, evdwl, fpair;
double r, rsq, r2inv, r6inv, forcelj, factor_lj;
double c1, c2, fR, dUR, dUA;
double K[9], h[4], g[4];
int *jlist;
double **x = atom->x;
double **f = atom->f;
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];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[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]) continue;
switch (form[itype][jtype]) {
case SMALL_SMALL:
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
fpair = factor_lj * forcelj * r2inv;
if (eflag)
evdwl = r6inv * (r6inv * lj3[itype][jtype] - lj4[itype][jtype]) - offset[itype][jtype];
break;
case SMALL_LARGE:
c2 = a2[itype][jtype];
K[1] = c2 * c2;
K[2] = rsq;
K[0] = K[1] - rsq;
K[4] = rsq * rsq;
K[3] = K[1] - K[2];
K[3] *= K[3] * K[3];
K[6] = K[3] * K[3];
fR = sigma3[itype][jtype] * a12[itype][jtype] * c2 * K[1] / K[3];
fpair = 4.0 / 15.0 * fR * factor_lj *
(2.0 * (K[1] + K[2]) * (K[1] * (5.0 * K[1] + 22.0 * K[2]) + 5.0 * K[4]) *
sigma6[itype][jtype] / K[6] -
5.0) /
K[0];
if (eflag)
evdwl = 2.0 / 9.0 * fR *
(1.0 -
(K[1] * (K[1] * (K[1] / 3.0 + 3.0 * K[2]) + 4.2 * K[4]) + K[2] * K[4]) *
sigma6[itype][jtype] / K[6]) -
offset[itype][jtype];
if (rsq <= K[1]) error->one(FLERR, "Overlapping small/large in pair colloid");
break;
case LARGE_LARGE:
r = sqrt(rsq);
c1 = a1[itype][jtype];
c2 = a2[itype][jtype];
K[0] = c1 * c2;
K[1] = c1 + c2;
K[2] = c1 - c2;
K[3] = K[1] + r;
K[4] = K[1] - r;
K[5] = K[2] + r;
K[6] = K[2] - r;
K[7] = 1.0 / (K[3] * K[4]);
K[8] = 1.0 / (K[5] * K[6]);
g[0] = pow(K[3], -7.0);
g[1] = pow(K[4], -7.0);
g[2] = pow(K[5], -7.0);
g[3] = pow(K[6], -7.0);
h[0] = ((K[3] + 5.0 * K[1]) * K[3] + 30.0 * K[0]) * g[0];
h[1] = ((K[4] + 5.0 * K[1]) * K[4] + 30.0 * K[0]) * g[1];
h[2] = ((K[5] + 5.0 * K[2]) * K[5] - 30.0 * K[0]) * g[2];
h[3] = ((K[6] + 5.0 * K[2]) * K[6] - 30.0 * K[0]) * g[3];
g[0] *= 42.0 * K[0] / K[3] + 6.0 * K[1] + K[3];
g[1] *= 42.0 * K[0] / K[4] + 6.0 * K[1] + K[4];
g[2] *= -42.0 * K[0] / K[5] + 6.0 * K[2] + K[5];
g[3] *= -42.0 * K[0] / K[6] + 6.0 * K[2] + K[6];
fR = a12[itype][jtype] * sigma6[itype][jtype] / r / 37800.0;
evdwl = fR * (h[0] - h[1] - h[2] + h[3]);
dUR = evdwl / r + 5.0 * fR * (g[0] + g[1] - g[2] - g[3]);
dUA = -a12[itype][jtype] / 3.0 * r *
((2.0 * K[0] * K[7] + 1.0) * K[7] + (2.0 * K[0] * K[8] - 1.0) * K[8]);
fpair = factor_lj * (dUR + dUA) / r;
if (eflag)
evdwl += a12[itype][jtype] / 6.0 * (2.0 * K[0] * (K[7] + K[8]) - log(K[8] / K[7])) -
offset[itype][jtype];
if (r <= K[1]) error->one(FLERR, "Overlapping large/large in pair colloid");
break;
}
if (eflag) evdwl *= factor_lj;
f[i][0] += delx * fpair;
f[i][1] += dely * fpair;
f[i][2] += delz * fpair;
if (evflag) ev_tally_full(i, evdwl, 0.0, fpair, delx, dely, delz);
}
}
}
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