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This commit is contained in:
Axel Kohlmeyer
2021-05-12 00:17:12 -04:00
parent d5c7ef113d
commit 8dad40ea49
2 changed files with 82 additions and 98 deletions
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165
src/GPU/pair_lj_smooth_gpu.cpp
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@ -16,58 +16,51 @@
------------------------------------------------------------------------- */
#include "pair_lj_smooth_gpu.h"
#include <cmath>
#include <cstdio>
#include <cstring>
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "gpu_extra.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "suffix.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "gpu_extra.h"
#include "suffix.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
// External functions from gpu library for atom decomposition
int ljsmt_gpu_init(const int ntypes, double **cutsq, 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,
double **host_ljsw0, double **host_ljsw1, double **host_ljsw2,
double **host_ljsw3, double **host_ljsw4,
double **cut_inner, double **cut_innersq);
int ljsmt_gpu_init(const int ntypes, double **cutsq, 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, double **host_ljsw0,
double **host_ljsw1, double **host_ljsw2, double **host_ljsw3,
double **host_ljsw4, double **cut_inner, double **cut_innersq);
void ljsmt_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset,
double **host_ljsw0, double **host_ljsw1, double **host_ljsw2,
double **host_ljsw3, double **host_ljsw4,
double **cut_inner, double **cut_innersq);
void ljsmt_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1, double **host_lj2,
double **host_lj3, double **host_lj4, double **offset, double **host_ljsw0,
double **host_ljsw1, double **host_ljsw2, double **host_ljsw3,
double **host_ljsw4, double **cut_inner, double **cut_innersq);
void ljsmt_gpu_clear();
int ** ljsmt_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,
int **ljsmt_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 ljsmt_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,
void ljsmt_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 ljsmt_gpu_bytes();
@ -94,7 +87,7 @@ PairLJSmoothGPU::~PairLJSmoothGPU()
void PairLJSmoothGPU::compute(int eflag, int vflag)
{
ev_init(eflag,vflag);
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
@ -102,7 +95,7 @@ void PairLJSmoothGPU::compute(int eflag, int vflag)
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
double sublo[3],subhi[3];
double sublo[3], subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
@ -111,28 +104,24 @@ void PairLJSmoothGPU::compute(int eflag, int vflag)
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda,domain->subhi_lamda,sublo,subhi);
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh = ljsmt_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);
firstneigh =
ljsmt_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;
ljsmt_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
ljsmt_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 (!success) error->one(FLERR, "Insufficient memory on accelerator");
if (host_start<inum) {
if (host_start < inum) {
cpu_time = MPI_Wtime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = MPI_Wtime() - cpu_time;
@ -148,8 +137,7 @@ void PairLJSmoothGPU::init_style()
{
//cut_respa = nullptr;
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/smooth/gpu pair style");
if (force->newton_pair) error->all(FLERR, "Cannot use newton pair with lj/smooth/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
@ -157,10 +145,9 @@ void PairLJSmoothGPU::init_style()
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 = init_one(i, j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
if (cut > maxcut) maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
@ -168,19 +155,17 @@ void PairLJSmoothGPU::init_style()
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int maxspecial = 0;
if (atom->molecular) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = ljsmt_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, mnf, maxspecial,
cell_size, gpu_mode, screen, ljsw0, ljsw1, ljsw2,
ljsw3, ljsw4, cut_inner, cut_inner_sq);
GPU_EXTRA::check_flag(success,error,world);
int success =
ljsmt_gpu_init(atom->ntypes + 1, cutsq, lj1, lj2, lj3, lj4, offset, force->special_lj,
atom->nlocal, atom->nlocal + atom->nghost, mnf, maxspecial, cell_size,
gpu_mode, screen, ljsw0, ljsw1, ljsw2, ljsw3, ljsw4, cut_inner, cut_inner_sq);
GPU_EXTRA::check_flag(success, error, world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this,instance_me);
int irequest = neighbor->request(this, instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
@ -192,7 +177,8 @@ void PairLJSmoothGPU::reinit()
{
Pair::reinit();
ljsmt_gpu_reinit(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, offset, ljsw0, ljsw1, ljsw2, ljsw3, ljsw4, cut_inner, cut_inner_sq);
ljsmt_gpu_reinit(atom->ntypes + 1, cutsq, lj1, lj2, lj3, lj4, offset, ljsw0, ljsw1, ljsw2, ljsw3,
ljsw4, cut_inner, cut_inner_sq);
}
/* ---------------------------------------------------------------------- */
@ -205,12 +191,13 @@ double PairLJSmoothGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJSmoothGPU::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 rsq,r2inv,r6inv,forcelj,factor_lj;
double r,t,tsq,fskin;
void PairLJSmoothGPU::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 rsq, r2inv, r6inv, forcelj, factor_lj;
double r, t, tsq, fskin;
int *jlist;
double **x = atom->x;
@ -237,43 +224,41 @@ void PairLJSmoothGPU::cpu_compute(int start, int inum, int eflag, int /* vflag *
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
rsq = delx * delx + dely * dely + delz * delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r2inv = 1.0 / rsq;
if (rsq < cut_inner_sq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
r6inv = r2inv * r2inv * r2inv;
forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
} else {
r = sqrt(rsq);
t = r - cut_inner[itype][jtype];
tsq = t*t;
fskin = ljsw1[itype][jtype] + ljsw2[itype][jtype]*t +
ljsw3[itype][jtype]*tsq + ljsw4[itype][jtype]*tsq*t;
forcelj = fskin*r;
tsq = t * t;
fskin = ljsw1[itype][jtype] + ljsw2[itype][jtype] * t + ljsw3[itype][jtype] * tsq +
ljsw4[itype][jtype] * tsq * t;
forcelj = fskin * r;
}
fpair = factor_lj*forcelj*r2inv;
fpair = factor_lj * forcelj * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[i][0] += delx * fpair;
f[i][1] += dely * fpair;
f[i][2] += delz * fpair;
if (eflag) {
if (rsq < cut_inner_sq[itype][jtype])
evdwl = r6inv * (lj3[itype][jtype]*r6inv -
lj4[itype][jtype]) - offset[itype][jtype];
evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
else
evdwl = ljsw0[itype][jtype] - ljsw1[itype][jtype]*t -
ljsw2[itype][jtype]*tsq/2.0 - ljsw3[itype][jtype]*tsq*t/3.0 -
ljsw4[itype][jtype]*tsq*tsq/4.0 - offset[itype][jtype];
evdwl = ljsw0[itype][jtype] - ljsw1[itype][jtype] * t -
ljsw2[itype][jtype] * tsq / 2.0 - ljsw3[itype][jtype] * tsq * t / 3.0 -
ljsw4[itype][jtype] * tsq * tsq / 4.0 - offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally_full(i, evdwl, 0.0, fpair, delx, dely, delz);
}
}
}
}

9
src/GPU/pair_lj_smooth_gpu.h
View File

@ -12,9 +12,9 @@
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(lj/smooth/gpu,PairLJSmoothGPU)
// clang-format off
PairStyle(lj/smooth/gpu, PairLJSmoothGPU);
// clang-format on
#else
#ifndef LMP_PAIR_LJ_SMOOTH_GPU_H
@ -41,7 +41,7 @@ class PairLJSmoothGPU : public PairLJSmooth {
double cpu_time;
};
}
} // namespace LAMMPS_NS
#endif
#endif
@ -57,4 +57,3 @@ E: Cannot use newton pair with lj/smooth/gpu pair style
Self-explanatory.
*/