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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11662 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-03-20 15:00:59 +00:00
parent 8d9e3945dd
commit 1ce84626f2
6 changed files with 957 additions and 1 deletions
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4
src/GPU/Install.sh
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@ -47,6 +47,10 @@ action pair_coul_dsf_gpu.cpp
action pair_coul_dsf_gpu.h
action pair_coul_long_gpu.cpp pair_coul_long.cpp
action pair_coul_long_gpu.h pair_coul_long.cpp
action pair_dpd_gpu.cpp
action pair_dpd_gpu.h
action pair_dpd_tstat_gpu.cpp
action pair_dpd_tstat_gpu.h
action pair_lj_cut_dipole_cut_gpu.cpp pair_lj_cut_dipole_cut.cpp
action pair_lj_cut_dipole_cut_gpu.h pair_lj_cut_dipole_cut.cpp
action pair_lj_sf_dipole_sf_gpu.cpp pair_lj_sf_dipole_sf.cpp

10
src/GPU/fix_gpu.cpp
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@ -46,7 +46,7 @@ extern double lmp_gpu_forces(double **f, double **tor, double *eatom,
double **vatom, double *virial, double &ecoul);
static const char cite_gpu_package[] =
"GPU package (short-range and long-range):\n\n"
"GPU package (short-range, long-range and three-body potentials):\n\n"
"@Article{Brown11,\n"
" author = {W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington},\n"
" title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces},\n"
@ -62,6 +62,14 @@ static const char cite_gpu_package[] =
" year = 2012,\n"
" volume = 183,\n"
" pages = {449--459}\n"
"}\n\n"
"@Article{Brown13,\n"
" author = {W. M. Brown, Y. Masako},\n"
" title = {Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" year = 2013,\n"
" volume = 184,\n"
" pages = {2785--2793}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */

409
src/GPU/pair_dpd_gpu.cpp Normal file
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@ -0,0 +1,409 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_dpd_gpu.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "random_mars.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#include "gpu_extra.h"
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int dpd_gpu_init(const int ntypes, double **cutsq, double **host_a0,
double **host_gamma, double **host_sigma, double **host_cut,
double *special_lj, bool tstat_only, const int inum,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void dpd_gpu_clear();
int ** dpd_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_v, const double dtinvsqrt,
const int seed, const int timestep,
double *boxlo, double *prd);
void dpd_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, tagint *tag,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
const int nlocal, double *boxlo, double *prd);
double dpd_gpu_bytes();
#define EPSILON 1.0e-10
//#define _USE_UNIFORM_SARU_LCG
//#define _USE_UNIFORM_SARU_TEA8
//#define _USE_GAUSSIAN_SARU_LCG
#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && !defined(_USE_GAUSSIAN_SARU_LCG)
#define _USE_UNIFORM_SARU_LCG
#endif
// References:
// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
#define LCGA 0x4beb5d59 // Full period 32 bit LCG
#define LCGC 0x2600e1f7
#define oWeylPeriod 0xda879add // Prime period 3666320093
#define oWeylOffset 0x8009d14b
#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0]
// using the inherent LCG, then multiply u with sqrt(3) to "match"
// with a normal random distribution.
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
// Curly brackets to make variables local to the scope.
#ifdef _USE_UNIFORM_SARU_LCG
#define numtyp double
#define SQRT3 (numtyp)1.7320508075688772935274463
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
// then multiply u with sqrt(3) to "match" with a normal random distribution
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
#ifdef _USE_UNIFORM_SARU_TEA8
#define numtyp double
#define SQRT3 (numtyp)1.7320508075688772935274463
#define k0 0xA341316C
#define k1 0xC8013EA4
#define k2 0xAD90777D
#define k3 0x7E95761E
#define delta 0x9e3779b9
#define rounds 8
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int sum = 0; \
for (int i=0; i < rounds; i++) { \
sum += delta; \
state += ((wstate<<4) + k0)^(wstate + sum)^((wstate>>5) + k1); \
wstate += ((state<<4) + k2)^(state + sum)^((state>>5) + k3); \
} \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
// and uses the polar method (Marsaglia's) to transform to a normal random value
// This is used to compared with CPU DPD using RandMars::gaussian()
#ifdef _USE_GAUSSIAN_SARU_LCG
#define numtyp double
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state=0x12345678; \
unsigned int wstate=12345678; \
state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int v, s; \
numtyp r1, r2, rsq; \
while (1) { \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r1 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r2 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
rsq = r1 * r1 + r2 * r2; \
if (rsq < (numtyp)1.0) break; \
} \
numtyp fac = sqrt((numtyp)-2.0*log(rsq)/rsq); \
randnum = r2*fac; \
}
#endif
/* ---------------------------------------------------------------------- */
PairDPDGPU::PairDPDGPU(LAMMPS *lmp) : PairDPD(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairDPDGPU::~PairDPDGPU()
{
dpd_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairDPDGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
double dtinvsqrt = 1.0/sqrt(update->dt);
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = dpd_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->v, dtinvsqrt, seed,
update->ntimestep,
domain->boxlo, domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
dpd_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->tag, atom->v, dtinvsqrt, seed,
update->ntimestep,
atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
if (host_start<inum) {
cpu_time = MPI_Wtime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairDPDGPU::init_style()
{
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with dpd/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double mcut;
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)) {
mcut = init_one(i,j);
mcut *= mcut;
if (mcut > maxcut)
maxcut = mcut;
cutsq[i][j] = cutsq[j][i] = mcut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = dpd_gpu_init(atom->ntypes+1, cutsq, a0, gamma, sigma,
cut, force->special_lj, false, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairDPDGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + dpd_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairDPDGPU::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 vxtmp,vytmp,vztmp,delvx,delvy,delvz;
double rsq,r,rinv,dot,wd,randnum,factor_dpd;
int *jlist;
tagint itag,jtag;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
int *type = atom->type;
tagint *tag = atom->tag;
double *special_lj = force->special_lj;
double dtinvsqrt = 1.0/sqrt(update->dt);
int timestep = (int)update->ntimestep;
// 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];
vxtmp = v[i][0];
vytmp = v[i][1];
vztmp = v[i][2];
itype = type[i];
itag = tag[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_dpd = 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];
jtag = tag[j];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
if (r < EPSILON) continue; // r can be 0.0 in DPD systems
rinv = 1.0/r;
delvx = vxtmp - v[j][0];
delvy = vytmp - v[j][1];
delvz = vztmp - v[j][2];
dot = delx*delvx + dely*delvy + delz*delvz;
wd = 1.0 - r/cut[itype][jtype];
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
randnum = 0.0;
saru(tag1, tag2, seed, timestep, randnum);
// conservative force = a0 * wd
// drag force = -gamma * wd^2 * (delx dot delv) / r
// random force = sigma * wd * rnd * dtinvsqrt;
fpair = a0[itype][jtype]*wd;
fpair -= gamma[itype][jtype]*wd*wd*dot*rinv;
fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
fpair *= factor_dpd*rinv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
// unshifted eng of conservative term:
// evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
// eng shifted to 0.0 at cutoff
evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd;
evdwl *= factor_dpd;
}
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}

59
src/GPU/pair_dpd_gpu.h Normal file
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@ -0,0 +1,59 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(dpd/gpu,PairDPDGPU)
#else
#ifndef LMP_PAIR_DPD_GPU_H
#define LMP_PAIR_DPD_GPU_H
#include "pair_dpd.h"
namespace LAMMPS_NS {
class PairDPDGPU : public PairDPD {
public:
PairDPDGPU(LAMMPS *lmp);
~PairDPDGPU();
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int);
void init_style();
double memory_usage();
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
int *gpulist;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Insufficient memory on accelerator
There is insufficient memory on one of the devices specified for the gpu
package
E: Cannot use newton pair with lj/cut/gpu pair style
Self-explanatory.
*/

417
src/GPU/pair_dpd_tstat_gpu.cpp Normal file
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@ -0,0 +1,417 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_dpd_tstat_gpu.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "random_mars.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#include "gpu_extra.h"
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int dpd_gpu_init(const int ntypes, double **cutsq, double **host_a0,
double **host_gamma, double **host_sigma, double **host_cut,
double *special_lj, bool tstat_only, const int inum,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void dpd_gpu_clear();
int ** dpd_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_v, const double dtinvsqrt,
const int seed, const int timestep,
double *boxlo, double *prd);
void dpd_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, tagint *tag,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
const int nlocal, double *boxlo, double *prd);
void dpd_gpu_update_coeff(int ntypes, double **host_a0, double **host_gamma,
double **host_sigma, double **host_cut);
double dpd_gpu_bytes();
#define EPSILON 1.0e-10
//#define _USE_UNIFORM_SARU_LCG
//#define _USE_UNIFORM_SARU_TEA8
//#define _USE_GAUSSIAN_SARU_LCG
#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && !defined(_USE_GAUSSIAN_SARU_LCG)
#define _USE_UNIFORM_SARU_LCG
#endif
// References:
// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
#define LCGA 0x4beb5d59 // Full period 32 bit LCG
#define LCGC 0x2600e1f7
#define oWeylPeriod 0xda879add // Prime period 3666320093
#define oWeylOffset 0x8009d14b
#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0]
// using the inherent LCG, then multiply u with sqrt(3) to "match"
// with a normal random distribution.
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
// Curly brackets to make variables local to the scope.
#ifdef _USE_UNIFORM_SARU_LCG
#define numtyp double
#define SQRT3 (numtyp)1.7320508075688772935274463
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
// then multiply u with sqrt(3) to "match" with a normal random distribution
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
#ifdef _USE_UNIFORM_SARU_TEA8
#define numtyp double
#define SQRT3 (numtyp)1.7320508075688772935274463
#define k0 0xA341316C
#define k1 0xC8013EA4
#define k2 0xAD90777D
#define k3 0x7E95761E
#define delta 0x9e3779b9
#define rounds 8
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int sum = 0; \
for (int i=0; i < rounds; i++) { \
sum += delta; \
state += ((wstate<<4) + k0)^(wstate + sum)^((wstate>>5) + k1); \
wstate += ((state<<4) + k2)^(state + sum)^((state>>5) + k3); \
} \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
// and uses the polar method (Marsaglia's) to transform to a normal random value
// This is used to compared with CPU DPD using RandMars::gaussian()
#ifdef _USE_GAUSSIAN_SARU_LCG
#define numtyp double
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state=0x12345678; \
unsigned int wstate=12345678; \
state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int v, s; \
numtyp r1, r2, rsq; \
while (1) { \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r1 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r2 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
rsq = r1 * r1 + r2 * r2; \
if (rsq < (numtyp)1.0) break; \
} \
numtyp fac = sqrt((numtyp)-2.0*log(rsq)/rsq); \
randnum = r2*fac; \
}
#endif
/* ---------------------------------------------------------------------- */
PairDPDTstatGPU::PairDPDTstatGPU(LAMMPS *lmp) : PairDPDTstat(lmp),
gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairDPDTstatGPU::~PairDPDTstatGPU()
{
dpd_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairDPDTstatGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
// adjust sigma if target T is changing
if (t_start != t_stop) {
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
temperature = t_start + delta * (t_stop-t_start);
double boltz = force->boltz;
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]);
dpd_gpu_update_coeff(atom->ntypes+1, a0, gamma, sigma, cut);
}
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
double dtinvsqrt = 1.0/sqrt(update->dt);
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = dpd_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->v, dtinvsqrt, seed,
update->ntimestep,
domain->boxlo, domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
dpd_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->tag, atom->v, dtinvsqrt, seed,
update->ntimestep,
atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
if (host_start<inum) {
cpu_time = MPI_Wtime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairDPDTstatGPU::init_style()
{
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with dpd/tstat/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double mcut;
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)) {
mcut = init_one(i,j);
mcut *= mcut;
if (mcut > maxcut)
maxcut = mcut;
cutsq[i][j] = cutsq[j][i] = mcut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = dpd_gpu_init(atom->ntypes+1, cutsq, a0, gamma, sigma,
cut, force->special_lj, true, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairDPDTstatGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + dpd_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairDPDTstatGPU::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 vxtmp,vytmp,vztmp,delvx,delvy,delvz;
double rsq,r,rinv,dot,wd,randnum,factor_dpd;
int *jlist;
tagint itag,jtag;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
int *type = atom->type;
tagint *tag = atom->tag;
double *special_lj = force->special_lj;
double dtinvsqrt = 1.0/sqrt(update->dt);
int timestep = (int)update->ntimestep;
// 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];
vxtmp = v[i][0];
vytmp = v[i][1];
vztmp = v[i][2];
itype = type[i];
itag = tag[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_dpd = 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];
jtag = tag[j];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
if (r < EPSILON) continue; // r can be 0.0 in DPD systems
rinv = 1.0/r;
delvx = vxtmp - v[j][0];
delvy = vytmp - v[j][1];
delvz = vztmp - v[j][2];
dot = delx*delvx + dely*delvy + delz*delvz;
wd = 1.0 - r/cut[itype][jtype];
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
randnum = 0.0;
saru(tag1, tag2, seed, timestep, randnum);
// conservative force = a0 * wd
// drag force = -gamma * wd^2 * (delx dot delv) / r
// random force = sigma * wd * rnd * dtinvsqrt;
fpair = -gamma[itype][jtype]*wd*wd*dot*rinv;
fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
fpair *= factor_dpd*rinv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (evflag) ev_tally_full(i,0.0,0.0,fpair,delx,dely,delz);
}
}
}
}

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(dpd/tstat/gpu,PairDPDTstatGPU)
#else
#ifndef LMP_PAIR_DPD_TSTAT_GPU_H
#define LMP_PAIR_DPD_TSTAT_GPU_H
#include "pair_dpd_tstat.h"
namespace LAMMPS_NS {
class PairDPDTstatGPU : public PairDPDTstat {
public:
PairDPDTstatGPU(LAMMPS *lmp);
~PairDPDTstatGPU();
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int);
void init_style();
double memory_usage();
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
int *gpulist;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Insufficient memory on accelerator
There is insufficient memory on one of the devices specified for the gpu
package
E: Cannot use newton pair with lj/cut/gpu pair style
Self-explanatory.
*/