template for smooth/spu

src/GPU/Install.sh

@@ -101,6 +101,8 @@ action pair_lj_cut_coul_msm_gpu.cpp pair_lj_cut_coul_msm.cpp
 action pair_lj_cut_coul_msm_gpu.h pair_lj_cut_coul_msm.h
 action pair_lj_cut_gpu.cpp
 action pair_lj_cut_gpu.h
+action pair_lj_smooth_gpu.cpp
+action pair_lj_smooth_gpu.h
 action pair_lj_expand_gpu.cpp
 action pair_lj_expand_gpu.h
 action pair_lj_expand_coul_long_gpu.cpp pair_lj_expand_coul_long.cpp

src/GPU/pair_lj_smooth_gpu.cpp

@@ -0,0 +1,255 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://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: Mike Brown (SNL)
+------------------------------------------------------------------------- */
+
+#include "pair_lj_smooth_gpu.h"
+#include <cmath>
+#include <cstdio>
+
+#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 "universe.h"
+#include "update.h"
+#include "domain.h"
+#include "gpu_extra.h"
+#include "suffix.h"
+
+using namespace LAMMPS_NS;
+
+// External functions from cuda library for atom decomposition
+
+int ljl_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);
+
+void ljl_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
+                   double **host_lj2, double **host_lj3, double **host_lj4,
+                   double **offset);
+
+void ljl_gpu_clear();
+int ** ljl_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 ljl_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 ljl_gpu_bytes();
+
+/* ---------------------------------------------------------------------- */
+
+PairLJSmoothGPU::PairLJSmoothGPU(LAMMPS *lmp) : PairLJCut(lmp), gpu_mode(GPU_FORCE)
+{
+  respa_enable = 0;
+  cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
+  GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+}
+
+/* ----------------------------------------------------------------------
+   free all arrays
+------------------------------------------------------------------------- */
+
+PairLJSmoothGPU::~PairLJSmoothGPU()
+{
+  ljl_gpu_clear();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJSmoothGPU::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 = ljl_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;
+    ljl_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 (host_start<inum) {
+    cpu_time = MPI_Wtime();
+    cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
+    cpu_time = MPI_Wtime() - cpu_time;
+  }
+  //fprintf("LJ_SMOOTH_GPU");
+}
+
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairLJSmoothGPU::init_style()
+{
+  cut_respa = nullptr;
+
+  if (force->newton_pair)
+    error->all(FLERR,"Cannot use newton pair with lj/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 = ljl_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
+                             offset, force->special_lj, 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;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJSmoothGPU::reinit()
+{
+  Pair::reinit();
+
+  ljl_gpu_reinit(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, offset);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairLJSmoothGPU::memory_usage()
+{
+  double bytes = Pair::memory_usage();
+  return bytes + ljl_gpu_bytes();
+}
+
+/* ---------------------------------------------------------------------- */
+
+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;
+  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]) {
+        r2inv = 1.0/rsq;
+        r6inv = r2inv*r2inv*r2inv;
+        forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+        fpair = factor_lj*forcelj*r2inv;
+
+        f[i][0] += delx*fpair;
+        f[i][1] += dely*fpair;
+        f[i][2] += delz*fpair;
+
+        if (eflag) {
+          evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+            offset[itype][jtype];
+          evdwl *= factor_lj;
+        }
+
+        if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
+      }
+    }
+  }
+}
+

src/GPU/pair_lj_smooth_gpu.h

@@ -0,0 +1,60 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   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(lj/smooth/gpu,PairLJSmoothGPU)
+
+#else
+
+#ifndef LMP_PAIR_LJ_SMOOTH_GPU_H
+#define LMP_PAIR_LJ_SMOOTH_GPU_H
+
+#include "pair_lj_cut.h"
+
+namespace LAMMPS_NS {
+
+class PairLJSmoothGPU : public PairLJCut {
+ public:
+  PairLJSmoothGPU(LAMMPS *lmp);
+  ~PairLJSmoothGPU();
+  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: Cannot use newton pair with lj/cut/gpu pair style
+
+Self-explanatory.
+
+*/
+