git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6817 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/GPU/pair_omp_gpu.cpp

@@ -42,14 +42,14 @@ PairOMPGPU::PairOMPGPU(LAMMPS *lmp) : Pointers(lmp)
 
 PairOMPGPU::~PairOMPGPU()
 {
-  mem_free();
+  free_mem();
 }
 
 /* ----------------------------------------------------------------------
    free any allocated memory
 ------------------------------------------------------------------------- */
 
-void PairOMPGPU::mem_free() {
+void PairOMPGPU::free_mem() {
   memory->sfree(eng_vdwl_thr);
   memory->sfree(eng_coul_thr);
   memory->destroy(virial_thr);
@@ -71,7 +71,7 @@ void PairOMPGPU::mem_free() {
 
 void PairOMPGPU::init_style()
 {
-  mem_free();
+  free_mem();
   
   #pragma omp parallel
   {

src/GPU/pair_omp_gpu.h

@@ -52,7 +52,7 @@ class PairOMPGPU : protected Pointers {
   PairOMPGPU(LAMMPS *);
   ~PairOMPGPU();
 
-  void mem_free();
+  void free_mem();
   void init_style();
   double memory_usage();
  

src/KSPACE/pair_coul_long.h

@@ -28,19 +28,19 @@ class PairCoulLong : public Pair {
  public:
   PairCoulLong(class LAMMPS *);
   ~PairCoulLong();
-  void compute(int, int);
-  void settings(int, char **);
+  virtual void compute(int, int);
+  virtual void settings(int, char **);
   void coeff(int, char **);
-  void init_style();
+  virtual void init_style();
   double init_one(int, int);
   void write_restart(FILE *);
   void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  double single(int, int, int, int, double, double, double, double &);
+  virtual void write_restart_settings(FILE *);
+  virtual void read_restart_settings(FILE *);
+  virtual double single(int, int, int, int, double, double, double, double &);
   void *extract(char *, int &);
 
- private:
+ protected:
   double cut_coul,cut_coulsq;
   double *cut_respa;
   double g_ewald;

src/finish.cpp

@@ -18,6 +18,7 @@
 #include "finish.h"
 #include "timer.h"
 #include "atom.h"
+#include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
@@ -82,7 +83,22 @@ void Finish::end(int flag)
     time_loop = tmp/nprocs;
 
     // overall loop time
-    
+
+#if defined(_OPENMP)    
+    if (me == 0) {
+      int ntasks = nprocs * comm->nthreads;
+      if (screen) fprintf(screen,
+			  "Loop time of %g on %d procs (%d MPI x %d OpenMP) "
+			  "for %d steps with " BIGINT_FORMAT " atoms\n",
+			  time_loop,ntasks,nprocs,comm->nthreads,
+			  update->nsteps,atom->natoms);
+      if (logfile) fprintf(logfile,
+			  "Loop time of %g on %d procs (%d MPI x %d OpenMP) "
+			  "for %d steps with " BIGINT_FORMAT " atoms\n",
+			  time_loop,ntasks,nprocs,comm->nthreads,
+			  update->nsteps,atom->natoms);
+    }
+#else
     if (me == 0) {
       if (screen) fprintf(screen,
 			  "Loop time of %g on %d procs for %d steps with " 
@@ -92,7 +108,8 @@ void Finish::end(int flag)
 			   "Loop time of %g on %d procs for %d steps with " 
 			   BIGINT_FORMAT " atoms\n",
 			   time_loop,nprocs,update->nsteps,atom->natoms);
-  }
+    }
+#endif
 
     if (time_loop == 0.0) time_loop = 1.0;
   }

src/min.cpp

@@ -515,9 +515,10 @@ void Min::force_clear()
   int nall;
   if (force->newton) nall = atom->nlocal + atom->nghost;
   else nall = atom->nlocal;
+  int ntot = nall * comm->nthreads;
 
   double **f = atom->f;
-  for (i = 0; i < nall; i++) {
+  for (i = 0; i < ntot; i++) {
     f[i][0] = 0.0;
     f[i][1] = 0.0;
     f[i][2] = 0.0;
@@ -534,8 +535,7 @@ void Min::force_clear()
 
   if (erforceflag) {
     double *erforce = atom->erforce;
-    for (i = 0; i < nall; i++)
-      erforce[i] = 0.0;
+    for (i = 0; i < nall; i++) erforce[i] = 0.0;
   }
 }
 

src/respa.cpp

@@ -601,9 +601,10 @@ void Respa::force_clear(int newtonflag)
   int nall;
   if (newtonflag) nall = atom->nlocal + atom->nghost;
   else nall = atom->nlocal;
+  int ntot = nall * comm->nthreads;
 
   double **f = atom->f;
-  for (i = 0; i < nall; i++) {
+  for (i = 0; i < ntot; i++) {
     f[i][0] = 0.0;
     f[i][1] = 0.0;
     f[i][2] = 0.0;
@@ -620,8 +621,7 @@ void Respa::force_clear(int newtonflag)
 
   if (erforceflag) {
     double *erforce = atom->erforce;
-    for (i = 0; i < nall; i++)
-      erforce[i] = 0.0;
+    for (i = 0; i < nall; i++) erforce[i] = 0.0;
   }
 }
 

src/verlet.cpp

@@ -311,9 +311,10 @@ void Verlet::force_clear()
     int nall;
     if (force->newton) nall = atom->nlocal + atom->nghost;
     else nall = atom->nlocal;
+    int ntot = nall * comm->nthreads;
 
     double **f = atom->f;
-    for (i = 0; i < nall; i++) {
+    for (i = 0; i < ntot; i++) {
       f[i][0] = 0.0;
       f[i][1] = 0.0;
       f[i][2] = 0.0;
@@ -330,8 +331,7 @@ void Verlet::force_clear()
 
     if (erforceflag) {
       double *erforce = atom->erforce;
-      for (i = 0; i < nall; i++)
-	erforce[i] = 0.0;
+      for (i = 0; i < nall; i++) erforce[i] = 0.0;
     }
 
   // neighbor includegroup flag is set
@@ -359,8 +359,7 @@ void Verlet::force_clear()
 
     if (erforceflag) {
       double *erforce = atom->erforce;
-      for (i = 0; i < nall; i++)
-	erforce[i] = 0.0;
+      for (i = 0; i < nall; i++) erforce[i] = 0.0;
     }
 
     if (force->newton) {
@@ -383,8 +382,7 @@ void Verlet::force_clear()
 
       if (erforceflag) {
 	double *erforce = atom->erforce;
-	for (i = atom->nlocal; i < nall; i++)
-	  erforce[i] = 0.0;
+	for (i = atom->nlocal; i < nall; i++) erforce[i] = 0.0;
       }
     }
   }