lammps-sys 0.6.0

/* ----------------------------------------------------------------------
   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 "pair_dpd_tstat_gpu.h"
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#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 "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;
  reinitflag = 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)
{
  ev_init(eflag,vflag);

  // 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,instance_me);
    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,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);
      }
    }
  }
}