apply clang-format

src/GPU/pair_lj_smooth_gpu.cpp

@@ -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 "gpu_extra.h"
-#include "neigh_list.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 <cmath>
-#include "suffix.h"
+#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,
+int ljsmt_gpu_init(const int ntypes, double **cutsq, double **host_lj1, double **host_lj2,
-                 double **host_lj2, double **host_lj3, double **host_lj4,
+                   double **host_lj3, double **host_lj4, double **offset, double *special_lj,
-                 double **offset, double *special_lj, const int nlocal,
+                   const int nlocal, const int nall, const int max_nbors, const int maxspecial,
-                 const int nall, const int max_nbors, const int maxspecial,
+                   const double cell_size, int &gpu_mode, FILE *screen, double **host_ljsw0,
-                 const double cell_size, int &gpu_mode, FILE *screen,
+                   double **host_ljsw1, double **host_ljsw2, double **host_ljsw3,
-                 double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, 
+                   double **host_ljsw4, double **cut_inner, double **cut_innersq);
-                 double **host_ljsw3, double **host_ljsw4,
-                 double **cut_inner, double **cut_innersq);
 
-void ljsmt_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
+void ljsmt_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1, double **host_lj2,
-                   double **host_lj2, double **host_lj3, double **host_lj4,
+                      double **host_lj3, double **host_lj4, double **offset, double **host_ljsw0,
-                   double **offset,
+                      double **host_ljsw1, double **host_ljsw2, double **host_ljsw3,
-                   double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, 
+                      double **host_ljsw4, double **cut_inner, double **cut_innersq);
-                   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,
+int **ljsmt_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x,
-                         const int nall, double **host_x, int *host_type,
+                          int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial,
-                         double *sublo, double *subhi, tagint *tag, int **nspecial,
+                          tagint **special, const bool eflag, const bool vflag, const bool eatom,
-                         tagint **special, const bool eflag, const bool vflag,
+                          const bool vatom, int &host_start, int **ilist, int **jnum,
-                         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,
+void ljsmt_gpu_compute(const int ago, const int inum, const int nall, double **host_x,
-                     double **host_x, int *host_type, int *ilist, int *numj,
+                       int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag,
-                     int **firstneigh, const bool eflag, const bool vflag,
+                       const bool vflag, const bool eatom, const bool vatom, int &host_start,
-                     const bool eatom, const bool vatom, int &host_start,
                        const double cpu_time, bool &success);
 double ljsmt_gpu_bytes();
 
@@ -114,23 +107,19 @@ void PairLJSmoothGPU::compute(int eflag, int vflag)
       domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
     }
     inum = atom->nlocal;
-    firstneigh = ljsmt_gpu_compute_n(neighbor->ago, inum, nall,
+    firstneigh =
-                                   atom->x, atom->type, sublo,
+        ljsmt_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag,
-                                   subhi, atom->tag, atom->nspecial,
+                            atom->nspecial, atom->special, eflag, vflag, eflag_atom, vflag_atom,
-                                   atom->special, eflag, vflag, eflag_atom,
+                            host_start, &ilist, &numneigh, cpu_time, success);
-                                   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,
+    ljsmt_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
-                    ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+                      eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success);
-                    vflag_atom, host_start, cpu_time, success);
   }
-  if (!success)
+  if (!success) error->one(FLERR, "Insufficient memory on accelerator");
-    error->one(FLERR,"Insufficient memory on accelerator");
 
   if (host_start < inum) {
     cpu_time = MPI_Wtime();
@@ -148,8 +137,7 @@ void PairLJSmoothGPU::init_style()
 {
   //cut_respa = nullptr;
 
-  if (force->newton_pair)
+  if (force->newton_pair) error->all(FLERR, "Cannot use newton pair with lj/smooth/gpu pair style");
-    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;
@@ -159,8 +147,7 @@ void PairLJSmoothGPU::init_style()
       if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
         cut = init_one(i, j);
         cut *= cut;
-        if (cut > maxcut)
+        if (cut > maxcut) maxcut = cut;
-          maxcut = cut;
         cutsq[i][j] = cutsq[j][i] = cut;
       } else
         cutsq[i][j] = cutsq[j][i] = 0.0;
@@ -169,14 +156,12 @@ void PairLJSmoothGPU::init_style()
   double cell_size = sqrt(maxcut) + neighbor->skin;
 
   int maxspecial = 0;
-  if (atom->molecular)
+  if (atom->molecular) maxspecial = atom->maxspecial;
-    maxspecial=atom->maxspecial;
   int mnf = 5e-2 * neighbor->oneatom;
-  int success = ljsmt_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
+  int success =
-                             offset, force->special_lj, atom->nlocal,
+      ljsmt_gpu_init(atom->ntypes + 1, cutsq, lj1, lj2, lj3, lj4, offset, force->special_lj,
-                             atom->nlocal+atom->nghost, mnf, maxspecial,
+                     atom->nlocal, atom->nlocal + atom->nghost, mnf, maxspecial, cell_size,
-                             cell_size, gpu_mode, screen, ljsw0, ljsw1, ljsw2,
+                     gpu_mode, screen, ljsw0, ljsw1, ljsw2, ljsw3, ljsw4, cut_inner, cut_inner_sq);
-                             ljsw3, ljsw4, cut_inner, cut_inner_sq);
   GPU_EXTRA::check_flag(success, error, world);
 
   if (gpu_mode == GPU_FORCE) {
@@ -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);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -205,8 +191,9 @@ double PairLJSmoothGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void PairLJSmoothGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */,
+void PairLJSmoothGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist,
-                               int *ilist, int *numneigh, int **firstneigh) {
+                                  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;
@@ -249,8 +236,8 @@ void PairLJSmoothGPU::cpu_compute(int start, int inum, int eflag, int /* vflag *
           r = sqrt(rsq);
           t = r - cut_inner[itype][jtype];
           tsq = t * t;
-          fskin = ljsw1[itype][jtype] + ljsw2[itype][jtype]*t +
+          fskin = ljsw1[itype][jtype] + ljsw2[itype][jtype] * t + ljsw3[itype][jtype] * tsq +
-            ljsw3[itype][jtype]*tsq + ljsw4[itype][jtype]*tsq*t;
+              ljsw4[itype][jtype] * tsq * t;
           forcelj = fskin * r;
         }
 
@@ -262,8 +249,7 @@ void PairLJSmoothGPU::cpu_compute(int start, int inum, int eflag, int /* vflag *
 
         if (eflag) {
           if (rsq < cut_inner_sq[itype][jtype])
-            evdwl = r6inv * (lj3[itype][jtype]*r6inv -
+            evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
-                             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 -
@@ -276,4 +262,3 @@ void PairLJSmoothGPU::cpu_compute(int start, int inum, int eflag, int /* vflag *
     }
   }
 }
-

src/GPU/pair_lj_smooth_gpu.h

@@ -12,9 +12,9 @@
 ------------------------------------------------------------------------- */
 
 #ifdef PAIR_CLASS
-
+// clang-format off
-PairStyle(lj/smooth/gpu,PairLJSmoothGPU)
+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.
 
 */
-