git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12148 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/GPU/pair_coul_cut_gpu.cpp

@@ -0,0 +1,247 @@
+/* ----------------------------------------------------------------------
+   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
+------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdio.h"
+#include "stdlib.h"
+#include "pair_coul_cut_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 "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 coul_gpu_init(const int ntypes, double **host_scale, double **cutsq,
+                  double *special_coul, const int nlocal,
+                  const int nall, const int max_nbors, const int maxspecial,
+                  const double cell_size, int &gpu_mode, FILE *screen,
+                  const double qqrd2e);
+void coul_gpu_reinit(const int ntypes, double **host_scale);
+void coul_gpu_clear();
+int ** coul_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, double *host_q, double *boxlo,
+                         double *prd);
+void coul_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 *host_q, const int nlocal,
+                     double *boxlo, double *prd);
+double coul_gpu_bytes();
+
+/* ---------------------------------------------------------------------- */
+
+PairCoulCutGPU::PairCoulCutGPU(LAMMPS *lmp) : PairCoulCut(lmp), gpu_mode(GPU_FORCE)
+{
+  respa_enable = 0;
+  cpu_time = 0.0;
+  GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+}
+
+/* ----------------------------------------------------------------------
+   free all arrays
+------------------------------------------------------------------------- */
+
+PairCoulCutGPU::~PairCoulCutGPU()
+{
+  coul_gpu_clear();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairCoulCutGPU::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;
+
+  bool success = true;
+  int *ilist, *numneigh, **firstneigh;
+  if (gpu_mode != GPU_FORCE) {
+    inum = atom->nlocal;
+    firstneigh = coul_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->q, domain->boxlo,
+                                   domain->prd);
+  } else {
+    inum = list->inum;
+    ilist = list->ilist;
+    numneigh = list->numneigh;
+    firstneigh = list->firstneigh;
+    coul_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 (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 PairCoulCutGPU::init_style()
+{
+  if (!atom->q_flag)
+    error->all(FLERR,"Pair style coul/cut/gpu requires atom attribute q");
+
+  if (force->newton_pair)
+    error->all(FLERR,"Cannot use newton pair with coul/cut/gpu pair 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 maxspecial=0;
+  if (atom->molecular)
+    maxspecial=atom->maxspecial;
+  int success = coul_gpu_init(atom->ntypes+1, scale, cutsq,
+                             force->special_coul, atom->nlocal,
+                             atom->nlocal+atom->nghost, 300, maxspecial,
+                             cell_size, gpu_mode, screen, force->qqrd2e);
+  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;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairCoulCutGPU::reinit()
+{
+  Pair::reinit();
+  
+  coul_gpu_reinit(atom->ntypes+1, scale);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairCoulCutGPU::memory_usage()
+{
+  double bytes = Pair::memory_usage();
+  return bytes + coul_gpu_bytes();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairCoulCutGPU::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 qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
+  double rsq,r2inv,forcecoul,factor_coul;
+  int *jlist;
+
+  ecoul = 0.0;
+
+  double **x = atom->x;
+  double **f = atom->f;
+  double *q = atom->q;
+  int *type = atom->type;
+  double *special_coul = force->special_coul;
+  double qqrd2e = force->qqrd2e;
+
+  // 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];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      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;
+        forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
+        fpair = factor_coul*forcecoul * r2inv;
+
+        f[i][0] += delx*fpair;
+        f[i][1] += dely*fpair;
+        f[i][2] += delz*fpair;
+
+        if (eflag) {
+          ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
+        }
+
+        if (evflag) ev_tally_full(i,0.0,ecoul,fpair,delx,dely,delz);
+      }
+    }
+  }
+}

src/GPU/pair_coul_cut_gpu.h

@@ -0,0 +1,63 @@
+/* ----------------------------------------------------------------------
+   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(coul/cut/gpu,PairCoulCutGPU)
+
+#else
+
+#ifndef LMP_PAIR_COUL_CUT_GPU_H
+#define LMP_PAIR_COUL_CUT_GPU_H
+
+#include "pair_coul_cut.h"
+
+namespace LAMMPS_NS {
+
+class PairCoulCutGPU : public PairCoulCut {
+ public:
+  PairCoulCutGPU(LAMMPS *lmp);
+  ~PairCoulCutGPU();
+  void cpu_compute(int, int, int, int, int *, int *, int **);
+  void compute(int, int);
+  void init_style();
+  void reinit();
+  double memory_usage();
+
+ enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
+
+ private:
+  int gpu_mode;
+  double cpu_time;
+};
+
+}
+#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: Pair style lj/cut/coul/cut/gpu requires atom attribute q
+
+The atom style defined does not have this attribute.
+
+E: Cannot use newton pair with lj/cut/coul/cut/gpu pair style
+
+Self-explanatory.
+
+*/

src/GPU/pair_coul_debye_gpu.cpp

@@ -0,0 +1,256 @@
+/* ----------------------------------------------------------------------
+   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 (ndtrung@umich.edu)
+------------------------------------------------------------------------- */
+
+#include "lmptype.h"
+#include "math.h"
+#include "stdio.h"
+#include "stdlib.h"
+#include "pair_coul_debye_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 "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 cdebye_gpu_init(const int ntypes, double **host_scale, double **cutsq,
+                    double *special_coul, const int nlocal, const int nall,
+                    const int max_nbors, const int maxspecial,
+                    const double cell_size, int &gpu_mode, FILE *screen,
+                    const double qqrd2e, const double kappa);
+void cdebye_gpu_reinit(const int ntypes, double **host_scale);
+void cdebye_gpu_clear();
+int ** cdebye_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, double *host_q, double *boxlo,
+                          double *prd);
+void cdebye_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 *host_q, const int nlocal,
+                      double *boxlo, double *prd);
+double cdebye_gpu_bytes();
+
+/* ---------------------------------------------------------------------- */
+
+PairCoulDebyeGPU::PairCoulDebyeGPU(LAMMPS *lmp) : 
+  PairCoulDebye(lmp), gpu_mode(GPU_FORCE)
+{
+  respa_enable = 0;
+  cpu_time = 0.0;
+  GPU_EXTRA::gpu_ready(lmp->modify, lmp->error); 
+}
+
+/* ----------------------------------------------------------------------
+   free all arrays
+------------------------------------------------------------------------- */
+
+PairCoulDebyeGPU::~PairCoulDebyeGPU()
+{
+  cdebye_gpu_clear();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairCoulDebyeGPU::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;
+  
+  bool success = true;
+  int *ilist, *numneigh, **firstneigh;  
+  if (gpu_mode != GPU_FORCE) {
+    inum = atom->nlocal;
+    firstneigh = cdebye_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->q, domain->boxlo, 
+                                    domain->prd);
+  } else {
+    inum = list->inum;
+    ilist = list->ilist;
+    numneigh = list->numneigh;
+    firstneigh = list->firstneigh;
+    cdebye_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 (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 PairCoulDebyeGPU::init_style()
+{
+  if (!atom->q_flag)
+    error->all(FLERR,"Pair style coul/debye/gpu requires atom attribute q");
+
+  if (force->newton_pair) 
+    error->all(FLERR,"Cannot use newton pair with coul/debye/gpu pair 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 maxspecial=0;
+  if (atom->molecular)
+    maxspecial=atom->maxspecial;
+  int success = cdebye_gpu_init(atom->ntypes+1, scale, cutsq,
+                                force->special_coul, atom->nlocal,
+                                atom->nlocal+atom->nghost, 300, maxspecial,
+                                cell_size, gpu_mode, screen,
+                                force->qqrd2e, kappa);
+  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;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairCoulDebyeGPU::reinit()
+{
+  Pair::reinit();
+  
+  cdebye_gpu_reinit(atom->ntypes+1, scale);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairCoulDebyeGPU::memory_usage()
+{
+  double bytes = Pair::memory_usage();
+  return bytes + cdebye_gpu_bytes();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairCoulDebyeGPU::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 qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
+  double rsq,r2inv,forcecoul,factor_coul;
+  double r,rinv,screening;
+  int *jlist;
+
+  ecoul = 0.0;
+
+  double **x = atom->x;
+  double **f = atom->f;
+  double *q = atom->q;
+  int *type = atom->type;
+  double *special_coul = force->special_coul;
+  double qqrd2e = force->qqrd2e;
+
+  // 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];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      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;
+        r = sqrt(rsq);
+        rinv = 1.0/r;
+        screening = exp(-kappa*r);
+        forcecoul = qqrd2e * scale[itype][jtype] *
+          qtmp*q[j] * screening * (kappa + rinv);
+        fpair = factor_coul*forcecoul * r2inv;
+
+        f[i][0] += delx*fpair;
+        f[i][1] += dely*fpair;
+        f[i][2] += delz*fpair;
+
+        if (eflag) {
+          ecoul = factor_coul * qqrd2e * scale[itype][jtype] *
+            qtmp*q[j] * rinv * screening;
+        }
+
+        if (evflag) ev_tally_full(i,0.0,ecoul,fpair,delx,dely,delz);
+      }
+    }
+  }
+}

src/GPU/pair_coul_debye_gpu.h

@@ -0,0 +1,63 @@
+/* ----------------------------------------------------------------------
+   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(coul/debye/gpu,PairCoulDebyeGPU)
+
+#else
+
+#ifndef LMP_PAIR_COUL_DEBYE_GPU_H
+#define LMP_PAIR_COUL_DEBYE_GPU_H
+
+#include "pair_coul_debye.h"
+
+namespace LAMMPS_NS {
+
+class PairCoulDebyeGPU : public PairCoulDebye {
+ public:
+  PairCoulDebyeGPU(LAMMPS *lmp);
+  ~PairCoulDebyeGPU();
+  void cpu_compute(int, int, int, int, int *, int *, int **);
+  void compute(int, int);
+  void init_style();
+  void reinit();
+  double memory_usage();
+
+ enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
+
+ private:
+  int gpu_mode;
+  double cpu_time;
+};
+
+}
+#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: Pair style lj/cut/coul/debye/gpu requires atom attribute q
+
+The atom style defined does not have this attribute.
+
+E: Cannot use newton pair with lj/cut/coul/debye/gpu pair style
+
+Self-explanatory.
+
+*/