git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7644 f3b2605a-c512-4ea7-a41b-209d697bcdaa

lib/gpu/lal_table.cpp

@@ -122,7 +122,7 @@ int TableT::init(const int ntypes,
       host_write[ix*lj_types+iy].w = (numtyp)0.0;
   }
   ucl_copy(coeff2,host_write,false);
-  
+
   // Allocate tablength arrays
   UCL_H_Vec<numtyp4> host_write2(_ntables*_tablength,*(this->ucl_device),
                                UCL_WRITE_OPTIMIZED);
@@ -307,29 +307,29 @@ void TableT::loop(const bool _eflag, const bool _vflag) {
                             &this->ans->dev_engv.begin(), &eflag, &vflag,
                             &ainum, &nbor_pitch, &this->_threads_per_atom, 
                             &_tablength);
-    }
+    } 
   } else {
     if (_tabstyle == LOOKUP) {
       this->k_pair.set_size(GX,BX);
       this->k_pair.run(&this->atom->dev_x.begin(), &tabindex.begin(),
-                     &coeff2.begin(), &coeff3.begin(), &coeff4.begin(), &cutsq.begin(),
+                     &coeff2.begin(), &coeff3.begin(), &coeff4.begin(), &_lj_types, 
-                     &_lj_types, &sp_lj.begin(), &this->nbor->dev_nbor.begin(),
+                     &cutsq.begin(), &sp_lj.begin(), &this->nbor->dev_nbor.begin(),
                      &this->_nbor_data->begin(), &this->ans->dev_ans.begin(),
                      &this->ans->dev_engv.begin(), &eflag, &vflag, &ainum,
                      &nbor_pitch, &this->_threads_per_atom, &_tablength);
     } else if (_tabstyle == LINEAR) {
       this->k_pair_linear.set_size(GX,BX);
       this->k_pair_linear.run(&this->atom->dev_x.begin(), &tabindex.begin(),
-                     &coeff2.begin(), &coeff3.begin(), &coeff4.begin(), &cutsq.begin(),
+                     &coeff2.begin(), &coeff3.begin(), &coeff4.begin(), &_lj_types, 
-                     &_lj_types, &sp_lj.begin(), &this->nbor->dev_nbor.begin(),
+                     &cutsq.begin(), &sp_lj.begin(), &this->nbor->dev_nbor.begin(),
                      &this->_nbor_data->begin(), &this->ans->dev_ans.begin(),
                      &this->ans->dev_engv.begin(), &eflag, &vflag, &ainum,
                      &nbor_pitch, &this->_threads_per_atom, &_tablength);
     } else if (_tabstyle == SPLINE) {
       this->k_pair_spline.set_size(GX,BX);
       this->k_pair_spline.run(&this->atom->dev_x.begin(), &tabindex.begin(),
-                     &coeff2.begin(), &coeff3.begin(), &coeff4.begin(), &cutsq.begin(),
+                     &coeff2.begin(), &coeff3.begin(), &coeff4.begin(), &_lj_types, 
-                     &_lj_types, &sp_lj.begin(), &this->nbor->dev_nbor.begin(),
+                     &cutsq.begin(), &sp_lj.begin(), &this->nbor->dev_nbor.begin(),
                      &this->_nbor_data->begin(), &this->ans->dev_ans.begin(),
                      &this->ans->dev_engv.begin(), &eflag, &vflag, &ainum,
                      &nbor_pitch, &this->_threads_per_atom, &_tablength);
@@ -337,8 +337,8 @@ void TableT::loop(const bool _eflag, const bool _vflag) {
       this->k_pair_bitmap.set_size(GX,BX);
       this->k_pair_bitmap.run(&this->atom->dev_x.begin(), &tabindex.begin(),
                      &nshiftbits.begin(), &nmask.begin(), 
-                     &coeff2.begin(), &coeff3.begin(), &coeff4.begin(), &cutsq.begin(),
+                     &coeff2.begin(), &coeff3.begin(), &coeff4.begin(), &_lj_types, 
-                     &_lj_types, &sp_lj.begin(), &this->nbor->dev_nbor.begin(),
+                     &cutsq.begin(), &sp_lj.begin(), &this->nbor->dev_nbor.begin(),
                      &this->_nbor_data->begin(), &this->ans->dev_ans.begin(),
                      &this->ans->dev_engv.begin(), &eflag, &vflag, &ainum,
                      &nbor_pitch, &this->_threads_per_atom, &_tablength);

src/GPU/pair_buck_coul_long_gpu.cpp

@@ -248,7 +248,7 @@ void PairBuckCoulLongGPU::cpu_compute(int start, int inum, int eflag,
 
       if (rsq < cutsq[itype][jtype]) {
 	r2inv = 1.0/rsq;
-
+	r = sqrt(rsq);
 	if (rsq < cut_coulsq) {
 	  grij = g_ewald * r;
 	  expm2 = exp(-grij*grij);

src/STUBS/mpi.c

@@ -125,6 +125,15 @@ int MPI_Send(void *buf, int count, MPI_Datatype datatype,
 
 /* ---------------------------------------------------------------------- */
 
+int MPI_Isend(void *buf, int count, MPI_Datatype datatype,
+              int source, int tag, MPI_Comm comm, MPI_Request *request)
+{
+  printf("MPI Stub WARNING: Should not send message to self\n");
+  return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
 int MPI_Rsend(void *buf, int count, MPI_Datatype datatype,
               int dest, int tag, MPI_Comm comm)
 {

src/STUBS/mpi.h

@@ -73,6 +73,8 @@ int MPI_Type_size(int, int *);
 
 int MPI_Send(void *buf, int count, MPI_Datatype datatype,
              int dest, int tag, MPI_Comm comm);
+int MPI_Isend(void *buf, int count, MPI_Datatype datatype,
+              int source, int tag, MPI_Comm comm, MPI_Request *request);
 int MPI_Rsend(void *buf, int count, MPI_Datatype datatype,
               int dest, int tag, MPI_Comm comm);
 int MPI_Recv(void *buf, int count, MPI_Datatype datatype,

src/USER-MISC/dihedral_table.h

@@ -36,15 +36,15 @@ namespace LAMMPS_NS {
 class DihedralTable : public Dihedral {
  public:
   DihedralTable(class LAMMPS *);
-  ~DihedralTable();
+  virtual ~DihedralTable();
-  void compute(int, int);
+  virtual void compute(int, int);
   void settings(int, char **);
   void coeff(int, char **);
   void write_restart(FILE *);
   void read_restart(FILE *);
   double single(int type, int i1, int i2, int i3, int i4);
 
- private:
+ protected:
   int tabstyle,tablength;
   // double *phi0;       <- equilibrium angles not supported
 

src/USER-OMP/bond_fene_expand_omp.cpp

@@ -81,6 +81,7 @@ void BondFENEExpandOMP::eval(int nfrom, int nto, ThrData * const thr)
   double * const * const f = thr->get_f();
   const int * const * const bondlist = neighbor->bondlist;
   const int nlocal = atom->nlocal;
+  const int tid = thr->get_tid();
 
   for (n = nfrom; n < nto; n++) {
     i1 = bondlist[n][0];
@@ -105,10 +106,14 @@ void BondFENEExpandOMP::eval(int nfrom, int nto, ThrData * const thr)
 
     if (rlogarg < 0.1) {
       char str[128];
+
       sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %d %d %g",
 	      update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
       error->warning(FLERR,str,0);
-      if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
+
+      if (check_error_thr((rlogarg <= -3.0),tid,FLERR,"Bad FENE bond"))
+	return;
+
       rlogarg = 0.1;
     }
 

src/USER-OMP/bond_fene_omp.cpp

@@ -80,6 +80,7 @@ void BondFENEOMP::eval(int nfrom, int nto, ThrData * const thr)
   double * const * const f = thr->get_f();
   const int * const * const bondlist = neighbor->bondlist;
   const int nlocal = atom->nlocal;
+  const int tid = thr->get_tid();
 
   for (n = nfrom; n < nto; n++) {
     i1 = bondlist[n][0];
@@ -101,10 +102,14 @@ void BondFENEOMP::eval(int nfrom, int nto, ThrData * const thr)
 
     if (rlogarg < 0.1) {
       char str[128];
+
       sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %d %d %g",
 	      update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
       error->warning(FLERR,str,0);
-      if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
+
+      if (check_error_thr((rlogarg <= -3.0),tid,FLERR,"Bad FENE bond"))
+	return;
+
       rlogarg = 0.1;
     }
 

src/USER-OMP/neigh_derive_omp.cpp

@@ -86,8 +86,8 @@ void Neighbor::half_from_full_no_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = inum_full;
@@ -175,8 +175,8 @@ void Neighbor::half_from_full_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = inum_full;

src/USER-OMP/neigh_full_omp.cpp

@@ -105,8 +105,8 @@ void Neighbor::full_nsq_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;
@@ -213,8 +213,8 @@ void Neighbor::full_nsq_ghost_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;
@@ -314,8 +314,8 @@ void Neighbor::full_bin_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;
@@ -324,7 +324,7 @@ void Neighbor::full_bin_omp(NeighList *list)
 
 /* ----------------------------------------------------------------------
    binned neighbor list construction for all neighbors
-   include neighbors of ghost atoms (no "special neighbors" for ghosts)
+   include neighbors of ghost atoms, but no "special neighbors" for ghosts
    every neighbor pair appears in list of both atoms i and j
 ------------------------------------------------------------------------- */
 
@@ -446,8 +446,8 @@ void Neighbor::full_bin_ghost_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;
@@ -555,8 +555,8 @@ void Neighbor::full_multi_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;

src/USER-OMP/neigh_gran_omp.cpp

@@ -163,8 +163,8 @@ void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
       firstshear[i] = shearptr;
     }
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;
@@ -266,8 +266,8 @@ void Neighbor::granular_nsq_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;
@@ -427,8 +427,8 @@ void Neighbor::granular_bin_no_newton_omp(NeighList *list)
       firstshear[i] = shearptr;
     }
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;
@@ -544,8 +544,8 @@ void Neighbor::granular_bin_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;
@@ -649,8 +649,8 @@ void Neighbor::granular_bin_newton_tri_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;

src/USER-OMP/neigh_half_bin_omp.cpp

@@ -118,8 +118,8 @@ void Neighbor::half_bin_no_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;
@@ -245,8 +245,8 @@ void Neighbor::half_bin_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;
@@ -356,8 +356,8 @@ void Neighbor::half_bin_newton_tri_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;

src/USER-OMP/neigh_half_multi_omp.cpp

@@ -126,8 +126,8 @@ void Neighbor::half_multi_no_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;
@@ -263,8 +263,8 @@ void Neighbor::half_multi_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;
@@ -384,8 +384,8 @@ void Neighbor::half_multi_newton_tri_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;

src/USER-OMP/neigh_half_nsq_omp.cpp

@@ -105,8 +105,8 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;
@@ -214,8 +214,8 @@ void Neighbor::half_nsq_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
   NEIGH_OMP_CLOSE;
   list->inum = nlocal;

src/USER-OMP/neigh_respa_omp.cpp

@@ -52,7 +52,7 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
 #endif
   NEIGH_OMP_SETUP(nlocal);
 
-  int i,j,n,itype,jtype,which,n_inner,n_middle;
+  int i,j,n,itype,jtype,n_inner,n_middle;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
   int *neighptr,*neighptr_inner,*neighptr_middle;
 
@@ -91,6 +91,8 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
   int npage_middle = tid;
   int npnt_middle = 0;
 
+  int which = 0;
+
   for (i = ifrom; i < ito; i++) {
 
 #if defined(_OPENMP)
@@ -168,23 +170,23 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
 
     ilist_inner[i] = i;
     firstneigh_inner[i] = neighptr_inner;
     numneigh_inner[i] = n_inner;
     npnt_inner += n_inner;
-    if (npnt_inner >= pgsize)
+    if (n_inner > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
 
     if (respamiddle) {
       ilist_middle[i] = i;
       firstneigh_middle[i] = neighptr_middle;
       numneigh_middle[i] = n_middle;
       npnt_middle += n_middle;
-      if (npnt_middle >= pgsize)
+      if (n_middle > oneatom)
-	error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+	error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
     }
   }
   NEIGH_OMP_CLOSE;
@@ -225,7 +227,7 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
 #endif
   NEIGH_OMP_SETUP(nlocal);
 
-  int i,j,n,itype,jtype,itag,jtag,which,n_inner,n_middle;
+  int i,j,n,itype,jtype,itag,jtag,n_inner,n_middle;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
   int *neighptr,*neighptr_inner,*neighptr_middle;
 
@@ -264,6 +266,8 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
   int npage_middle = tid;
   int npnt_middle = 0;
 
+  int which = 0;
+
   for (i = ifrom; i < ito; i++) {
 
 #if defined(_OPENMP)
@@ -359,23 +363,23 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
 
     ilist_inner[i] = i;
     firstneigh_inner[i] = neighptr_inner;
     numneigh_inner[i] = n_inner;
     npnt_inner += n_inner;
-    if (npnt_inner >= pgsize)
+    if (n_inner > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
 
     if (respamiddle) {
       ilist_middle[i] = i;
       firstneigh_middle[i] = neighptr_middle;
       numneigh_middle[i] = n_middle;
       npnt_middle += n_middle;
-      if (npnt_middle >= pgsize)
+      if (n_middle > oneatom)
-	error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+	error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
     }
   }
   NEIGH_OMP_CLOSE;
@@ -419,7 +423,7 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
 #endif
   NEIGH_OMP_SETUP(nlocal);
 
-  int i,j,k,n,itype,jtype,ibin,which,n_inner,n_middle;
+  int i,j,k,n,itype,jtype,ibin,n_inner,n_middle;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
   int *neighptr,*neighptr_inner,*neighptr_middle;
 
@@ -459,6 +463,8 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
   int npage_middle = tid;
   int npnt_middle = 0;
 
+  int which = 0;
+
   for (i = ifrom; i < ito; i++) {
 
 #if defined(_OPENMP)
@@ -545,23 +551,23 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
 
     ilist_inner[i] = i;
     firstneigh_inner[i] = neighptr_inner;
     numneigh_inner[i] = n_inner;
     npnt_inner += n_inner;
-    if (npnt_inner >= pgsize)
+    if (n_inner > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
 
     if (respamiddle) {
       ilist_middle[i] = i;
       firstneigh_middle[i] = neighptr_middle;
       numneigh_middle[i] = n_middle;
       npnt_middle += n_middle;
-      if (npnt_middle >= pgsize)
+      if (n_middle > oneatom)
-	error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+	error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
     }
   }
   NEIGH_OMP_CLOSE;
@@ -604,7 +610,7 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
 #endif
   NEIGH_OMP_SETUP(nlocal);
 
-  int i,j,k,n,itype,jtype,ibin,which,n_inner,n_middle;
+  int i,j,k,n,itype,jtype,ibin,n_inner,n_middle;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
   int *neighptr,*neighptr_inner,*neighptr_middle;
 
@@ -644,6 +650,8 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
   int npage_middle = tid;
   int npnt_middle = 0;
 
+  int which = 0;
+
   for (i = ifrom; i < ito; i++) {
 
 #if defined(_OPENMP)
@@ -766,23 +774,23 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
 
     ilist_inner[i] = i;
     firstneigh_inner[i] = neighptr_inner;
     numneigh_inner[i] = n_inner;
     npnt_inner += n_inner;
-    if (npnt_inner >= pgsize)
+    if (n_inner > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
 
     if (respamiddle) {
       ilist_middle[i] = i;
       firstneigh_middle[i] = neighptr_middle;
       numneigh_middle[i] = n_middle;
       npnt_middle += n_middle;
-      if (npnt_middle >= pgsize)
+      if (n_middle > oneatom)
-	error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+	error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
     }
   }
   NEIGH_OMP_CLOSE;
@@ -825,7 +833,7 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
 #endif
   NEIGH_OMP_SETUP(nlocal);
 
-  int i,j,k,n,itype,jtype,ibin,which,n_inner,n_middle;
+  int i,j,k,n,itype,jtype,ibin,n_inner,n_middle;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
   int *neighptr,*neighptr_inner,*neighptr_middle;
 
@@ -865,6 +873,8 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
   int npage_middle = tid;
   int npnt_middle = 0;
 
+  int which = 0;
+
   for (i = ifrom; i < ito; i++) {
 
 #if defined(_OPENMP)
@@ -959,23 +969,23 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     npnt += n;
-    if (n > oneatom || npnt >= pgsize)
+    if (n > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
 
     ilist_inner[i] = i;
     firstneigh_inner[i] = neighptr_inner;
     numneigh_inner[i] = n_inner;
     npnt_inner += n_inner;
-    if (npnt_inner >= pgsize)
+    if (n_inner > oneatom)
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
 
     if (respamiddle) {
       ilist_middle[i] = i;
       firstneigh_middle[i] = neighptr_middle;
       numneigh_middle[i] = n_middle;
       npnt_middle += n_middle;
-      if (npnt_middle >= pgsize)
+      if (n_middle > oneatom)
-	error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
+	error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
     }
   }
   NEIGH_OMP_CLOSE;

src/USER-OMP/neighbor_omp.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
@@ -35,9 +35,8 @@ namespace LAMMPS_NS {
     const int tid = omp_get_thread_num();		\
     const int idelta = 1 + num/nthreads;		\
     const int ifrom = tid*idelta;			\
-    int ito   = ifrom + idelta;				\
+    const int ito   = ((ifrom + idelta) > num)		\
-    if (ito > num)					\
+      ? num : (ifrom+idelta);				\
-      ito = num
 
 #define NEIGH_OMP_CLOSE }
 

src/USER-OMP/pair_airebo_omp.cpp

@@ -2653,7 +2653,6 @@ void PairAIREBOOMP::TORSION_thr(int ifrom, int ito,
 void PairAIREBOOMP::REBO_neigh_thr()
 {
   const int nlocal = atom->nlocal;
-  const int nall = nlocal + atom->nghost;
   const int nthreads = comm->nthreads;
 
   if (atom->nmax > maxlocal) {
@@ -2697,9 +2696,7 @@ void PairAIREBOOMP::REBO_neigh_thr()
 
     const int iidelta = 1 + allnum/nthreads;
     const int iifrom = tid*iidelta;
-    int iito   = iifrom + iidelta;
+    const int iito = ((iifrom+iidelta)>allnum) ? allnum : (iifrom+iidelta);
-    if (iito > allnum)
-      iito = allnum;
 
     // store all REBO neighs of owned and ghost atoms
     // scan full neighbor list of I
@@ -2757,6 +2754,7 @@ void PairAIREBOOMP::REBO_neigh_thr()
   }
 }
 
+
 /* ---------------------------------------------------------------------- */
 
 double PairAIREBOOMP::memory_usage()

src/USER-OMP/pair_colloid_omp.cpp

@@ -85,6 +85,7 @@ void PairColloidOMP::eval(int iifrom, int iito, ThrData * const thr)
   double * const * const f = thr->get_f();
   const int * const type = atom->type;
   const int nlocal = atom->nlocal;
+  const int tid = thr->get_tid();
   const double * const special_lj = force->special_lj;
   double fxtmp,fytmp,fztmp;
 
@@ -146,7 +147,11 @@ void PairColloidOMP::eval(int iifrom, int iito, ThrData * const thr)
 	  evdwl = 2.0/9.0*fR * 
 	    (1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
 	     sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
-	if (rsq <= K[1]) error->one(FLERR,"Overlapping small/large in pair colloid");
+
+	if (check_error_thr((rsq <= K[1]),tid,FLERR,
+			    "Overlapping small/large in pair colloid"))
+	  return;
+
 	break;
 
       case LARGE_LARGE:

src/USER-OMP/pair_comb_omp.cpp

@@ -22,12 +22,10 @@
 #include "neighbor.h"
 #include "neigh_list.h"
 
-#if defined(_OPENMP)
-#include <omp.h>
-#endif
-
 using namespace LAMMPS_NS;
 
+#define MAXNEIGH 24
+
 /* ---------------------------------------------------------------------- */
 
 PairCombOMP::PairCombOMP(LAMMPS *lmp) :
@@ -48,17 +46,8 @@ void PairCombOMP::compute(int eflag, int vflag)
   const int nthreads = comm->nthreads;
   const int inum = list->inum;
 
-  // grow coordination array if necessary
-
-  if (atom->nmax > nmax) {
-    memory->destroy(NCo);
-    memory->destroy(bbij);
-    nmax = atom->nmax;
-    memory->create(NCo,nmax,"pair:NCo");
-    memory->create(bbij,nmax,nmax,"pair:bbij");
-  }
-
   // Build short range neighbor list
+
   Short_neigh_thr();
 
 #if defined(_OPENMP)
@@ -102,7 +91,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
   double yaself;
   double potal,fac11,fac11e;
   double vionij,fvionij,sr1,sr2,sr3,Eov,Fov;
-  int sht_jnum, *sht_jlist;
+  int sht_jnum, *sht_jlist, nj;
 
   evdwl = ecoul = 0.0;
 
@@ -139,7 +128,8 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
     fxtmp = fytmp = fztmp = 0.0;
 
     iq = q[i];
-    NCo[i] = 0;  
+    NCo[i] = 0;
+    nj = 0;
     iparam_i = elem2param[itype][itype][itype];
 
     // self energy, only on i atom
@@ -242,7 +232,6 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
       int numcoor = 0;
       for (jj = 0; jj < sht_jnum; jj++) {
         j = sht_jlist[jj];
-	j &= NEIGHMASK;
 	jtype = map[type[j]];
 	iparam_ij = elem2param[itype][jtype][jtype];
 	
@@ -264,7 +253,6 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
 
     for (jj = 0; jj < sht_jnum; jj++) {
       j = sht_jlist[jj];
-      j &= NEIGHMASK;
 
       jtype = map[type[j]];
       iparam_ij = elem2param[itype][jtype][jtype];
@@ -279,6 +267,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
       rsq1 = vec3_dot(delr1,delr1);
 
       if (rsq1 > params[iparam_ij].cutsq) continue;
+      nj ++;
 
       // accumulate bondorder zeta for each i-j interaction via loop over k
 
@@ -289,7 +278,6 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
       for (kk = 0; kk < sht_jnum; kk++) {
 	k = sht_jlist[kk];
 	if (j == k) continue;
-	k &= NEIGHMASK;
 	ktype = map[type[k]];
 	iparam_ijk = elem2param[itype][jtype][ktype];
 
@@ -309,7 +297,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
       if (cuo_flag1 && cuo_flag2) cuo_flag = 1;
       else cuo_flag = 0;
 
-      force_zeta(&params[iparam_ij],EFLAG,i,j,rsq1,zeta_ij,
+      force_zeta(&params[iparam_ij],EFLAG,i,nj,rsq1,zeta_ij,
 		 iq,jq,fpair,prefactor,evdwl);
 
       // over-coordination correction for HfO2
@@ -334,7 +322,6 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
       for (kk = 0; kk < sht_jnum; kk++) {
 	k = sht_jlist[kk];
 	if (j == k) continue;
-	k &= NEIGHMASK;
 	ktype = map[type[k]];
 	iparam_ijk = elem2param[itype][jtype][ktype];
 
@@ -429,6 +416,7 @@ double PairCombOMP::yasu_char(double *qf_fix, int &igroup)
 
     const int i = ilist[ii];
     const int itag = tag[i];
+    int nj = 0;
 
     if (mask[i] & groupbit) {
       fqi = fqj = fqij = fqji = fqjj = 0.0; // should not be needed.
@@ -511,10 +499,11 @@ double PairCombOMP::yasu_char(double *qf_fix, int &igroup)
         const int iparam_ij = elem2param[itype][jtype][jtype];
 
         if (rsq1 > params[iparam_ij].cutsq) continue;
+	nj ++;
 
         // charge force in Aij and Bij
 
-        qfo_short(&params[iparam_ij],i,j,rsq1,iq,jq,fqij,fqjj);
+        qfo_short(&params[iparam_ij],i,nj,rsq1,iq,jq,fqij,fqjj);
         fqi += fqij;  
 #if defined(_OPENMP)
 #pragma omp atomic
@@ -522,7 +511,7 @@ double PairCombOMP::yasu_char(double *qf_fix, int &igroup)
 	qf[j] += fqjj;
       }
 
-#if defined(_OPENMP) && 0
+#if defined(_OPENMP)
 #pragma omp atomic
 #endif
       qf[i] += fqi;
@@ -559,12 +548,13 @@ void PairCombOMP::Short_neigh_thr()
 {
 
   if (atom->nmax > nmax) {
-    nmax = int(1.0 * atom->nmax);
+    nmax = atom->nmax;
-    memory->sfree(sht_num);
     memory->sfree(sht_first);
-    memory->create(sht_num,nmax,"pair:sht_num");
     sht_first = (int **) memory->smalloc(nmax*sizeof(int *),
 	    "pair:sht_first");
+    memory->grow(sht_num,nmax,"pair:sht_num");
+    memory->grow(NCo,nmax,"pair:NCo");
+    memory->grow(bbij,nmax,nmax,"pair:bbij");
   }
 
   const int nthreads = comm->nthreads;
@@ -602,46 +592,47 @@ void PairCombOMP::Short_neigh_thr()
     int npage = tid;
     npntj = 0;
 
-    for (ii = iifrom; ii < iito; ii++) {
+    if (iifrom < inum) {
-      i = ilist[ii];
+      for (ii = iifrom; ii < iito; ii++) {
-      itype = type[i];
+	i = ilist[ii];
+	itype = type[i];
 
 #if defined(_OPENMP)
 #pragma omp critical
 #endif
-      if(pgsize - npntj < oneatom) {
+	if(pgsize - npntj < oneatom) {
-	npntj = 0;
+	  npntj = 0;
-	npage++;
+	  npage += nthreads;
-	if (npage == maxpage) add_pages(nthreads);
+	  if (npage >= maxpage) add_pages(nthreads);
-      }
+	}
  
-      neighptrj = &pages[npage][npntj];
+	neighptrj = &pages[npage][npntj];
-      nj = 0;
+	nj = 0;
 
-      xtmp = x[i][0];
+	xtmp = x[i][0];
-      ytmp = x[i][1];
+	ytmp = x[i][1];
-      ztmp = x[i][2];
+	ztmp = x[i][2];
 
-      jlist = firstneigh[i];
+	jlist = firstneigh[i];
-      jnum = numneigh[i];
+	jnum = numneigh[i];
 
-      for (jj = 0; jj < jnum; jj++) {
+	for (jj = 0; jj < jnum; jj++) {
-	j = jlist[jj];
+	  j = jlist[jj];
-	j &= NEIGHMASK;
+	  j &= NEIGHMASK;
-	jtype = type[j];
+	  jtype = type[j];
-	iparam_ij = elem2param[itype][jtype][jtype];
 
-	delrj[0] = xtmp - x[j][0];
+	  delrj[0] = xtmp - x[j][0];
-	delrj[1] = ytmp - x[j][1];
+	  delrj[1] = ytmp - x[j][1];
-	delrj[2] = ztmp - x[j][2];
+	  delrj[2] = ztmp - x[j][2];
-	rsq = vec3_dot(delrj,delrj);
+	  rsq = vec3_dot(delrj,delrj);
       
-	if (rsq > cutmin) continue;
+	  if (rsq > cutmin) continue;
-	neighptrj[nj++] = j;
+	  neighptrj[nj++] = j;
+	}
+	sht_first[i] = neighptrj;
+	sht_num[i] = nj;
+	npntj += nj;
       }
-      sht_first[i] = neighptrj;
-      sht_num[i] = nj;
-      npntj += nj;
     }
   }
 }

src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.cpp

@@ -151,6 +151,7 @@ void PairLJCutCoulLongTIP4POMP::eval(int iifrom, int iito, ThrData * const thr)
   const double * const q = atom->q;
   const int * const type = atom->type;
   const int nlocal = atom->nlocal;
+  const int tid = thr->get_tid();
   const double * const special_coul = force->special_coul;
   const double * const special_lj = force->special_lj;
   const double qqrd2e = force->qqrd2e;
@@ -221,8 +222,11 @@ void PairLJCutCoulLongTIP4POMP::eval(int iifrom, int iito, ThrData * const thr)
 	  x2 = mpos[j];
 	  jH1 = h1idx[j];
 	  jH2 = h2idx[j];
-	  if (jtype == typeO  && ( jH1 < 0 || jH2 < 0 ))
+
-	    error->one(FLERR,"TIP4P hydrogen is missing");
+	  if (check_error_thr((jtype == typeO  && ( jH1 < 0 || jH2 < 0 )),
+			      tid, FLERR,"TIP4P hydrogen is missing"))
+	    return;
+
 	  delx = x1[0] - x2[0];
 	  dely = x1[1] - x2[1];
 	  delz = x1[2] - x2[2];

src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.cpp

@@ -179,6 +179,7 @@ void PairLJCutCoulPPPMTIP4POMP::eval(int iifrom, int iito, ThrData * const thr)
   const double * const q = atom->q;
   const int * const type = atom->type;
   const int nlocal = atom->nlocal;
+  const int tid = thr->get_tid();
   const double * const special_coul = force->special_coul;
   const double * const special_lj = force->special_lj;
   const double qqrd2e = force->qqrd2e;
@@ -249,8 +250,11 @@ void PairLJCutCoulPPPMTIP4POMP::eval(int iifrom, int iito, ThrData * const thr)
 	  x2 = mpos[j];
 	  jH1 = h1idx[j];
 	  jH2 = h2idx[j];
-	  if (jtype == typeO  && ( jH1 < 0 || jH2 < 0 ))
+
-	    error->one(FLERR,"TIP4P hydrogen is missing");
+	  if (check_error_thr((jtype == typeO  && ( jH1 < 0 || jH2 < 0 )),
+			      tid, FLERR,"TIP4P hydrogen is missing"))
+	    return;
+
 	  delx = x1[0] - x2[0];
 	  dely = x1[1] - x2[1];
 	  delz = x1[2] - x2[2];

src/USER-OMP/pair_peri_lps_omp.cpp

@@ -213,16 +213,15 @@ void PairPeriLPSOMP::eval(int iifrom, int iito, ThrData * const thr)
   // each thread works on a fixed chunk of atoms.
   const int idelta = 1 + nlocal/comm->nthreads;
   iifrom = thr->get_tid()*idelta;
-  iito   = iifrom + idelta;
+  iito   = ((iifrom + idelta) > nlocal) ? nlocal : (iifrom + idelta);
-  if (iito > nlocal)
-    iito = nlocal;
 #else 
   iifrom = 0;
   iito = nlocal;
 #endif
 
   // Compute the dilatation on each particle
-  compute_dilatation_thr(iifrom, iito);
+  if (iifrom < nlocal)
+    compute_dilatation_thr(iifrom, iito);
 
   // wait until all threads are done before communication
   sync_threads();
@@ -350,7 +349,8 @@ void PairPeriLPSOMP::eval(int iifrom, int iito, ThrData * const thr)
   sync_threads();
 
   // store new s0 (in parallel)
-  for (i = iifrom; i < iito; i++) s0[i] = s0_new[i]; 
+  if (iifrom < nlocal)
+    for (i = iifrom; i < iito; i++) s0[i] = s0_new[i];
 }
 
 /* ---------------------------------------------------------------------- */

src/USER-OMP/pair_peri_pmb_omp.cpp

@@ -203,9 +203,7 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr)
   // each thread works on a fixed chunk of atoms.
   const int idelta = 1 + nlocal/comm->nthreads;
   iifrom = thr->get_tid()*idelta;
-  iito   = iifrom + idelta;
+  iito   = ((iifrom + idelta) > nlocal) ? nlocal : (iifrom + idelta);
-  if (iito > nlocal)
-    iito = nlocal;
 #else 
   iifrom = 0;
   iito = nlocal;
@@ -234,8 +232,8 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr)
       // check if lost a partner without first breaking bond
 
       if (j < 0) {
-        partner[i][jj] = 0;
+	partner[i][jj] = 0;
-        continue;
+	continue;
       }
 
       // compute force density, add to PD equation of motion
@@ -257,7 +255,7 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr)
       // scale vfrac[j] if particle j near the horizon
 
       if ((fabs(r0[i][jj] - delta)) <= half_lc)
-        vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) + 
+	vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) + 
 	  (1.0 + ((delta - half_lc)/(2*half_lc) ) );
       else vfrac_scale = 1.0;
 
@@ -285,9 +283,9 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr)
       // update s0 for next timestep
 
       if (first)
-         s0_new[i] = s00[itype][jtype] - (alpha[itype][jtype] * stretch);
+	s0_new[i] = s00[itype][jtype] - (alpha[itype][jtype] * stretch);
       else
-         s0_new[i] = MAX(s0_new[i],s00[itype][jtype] - (alpha[itype][jtype] * stretch));
+	s0_new[i] = MAX(s0_new[i],s00[itype][jtype] - (alpha[itype][jtype] * stretch));
 
       first = false;
     }
@@ -296,7 +294,8 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr)
   sync_threads();
 
   // store new s0 (in parallel)
-  for (i = iifrom; i < iito; i++) s0[i] = s0_new[i]; 
+  if (iifrom < nlocal)
+    for (i = iifrom; i < iito; i++) s0[i] = s0_new[i]; 
 }
 
 /* ---------------------------------------------------------------------- */

src/USER-OMP/pair_table_omp.cpp

@@ -88,6 +88,7 @@ void PairTableOMP::eval(int iifrom, int iito, ThrData * const thr)
   double * const * const f = thr->get_f();
   const int * const type = atom->type;
   const int nlocal = atom->nlocal;
+  const int tid = thr->get_tid();
   const double * const special_lj = force->special_lj;
   double fxtmp,fytmp,fztmp;
 
@@ -121,25 +122,36 @@ void PairTableOMP::eval(int iifrom, int iito, ThrData * const thr)
 
       if (rsq < cutsq[itype][jtype]) {
 	tb = &tables[tabindex[itype][jtype]];
-	if (rsq < tb->innersq)
+
-	  error->one(FLERR,"Pair distance < table inner cutoff");
+	if (check_error_thr((rsq < tb->innersq),tid,
+			    FLERR,"Pair distance < table inner cutoff"))
+	  return;
  
 	if (tabstyle == LOOKUP) {
 	  itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
-	  if (itable >= tlm1)
+
-	    error->one(FLERR,"Pair distance > table outer cutoff");
+	  if (check_error_thr((itable >= tlm1),tid,
+			      FLERR,"Pair distance > table outer cutoff"))
+	    return;
+
 	  fpair = factor_lj * tb->f[itable];
 	} else if (tabstyle == LINEAR) {
 	  itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
-	  if (itable >= tlm1)
+
-	    error->one(FLERR,"Pair distance > table outer cutoff");
+	  if (check_error_thr((itable >= tlm1),tid,
+			      FLERR,"Pair distance > table outer cutoff"))
+	    return;
+
 	  fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
 	  value = tb->f[itable] + fraction*tb->df[itable];
 	  fpair = factor_lj * value;
 	} else if (tabstyle == SPLINE) {
 	  itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
-	  if (itable >= tlm1)
+
-	    error->one(FLERR,"Pair distance > table outer cutoff");
+	  if (check_error_thr((itable >= tlm1),tid,
+			      FLERR,"Pair distance > table outer cutoff"))
+	    return;
+
 	  b = (rsq - tb->rsq[itable]) * tb->invdelta;
 	  a = 1.0 - b;
 	  value = a * tb->f[itable] + b * tb->f[itable+1] + 

src/USER-OMP/pair_tersoff_table_omp.cpp

@@ -16,6 +16,7 @@
 #include "pair_tersoff_table_omp.h"
 #include "atom.h"
 #include "comm.h"
+#include "error.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
@@ -89,6 +90,7 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr)
   double * const * const f = thr->get_f();
   const int * const type = atom->type;
   const int nlocal = atom->nlocal;
+  const int tid = thr->get_tid();
 
   inum = list->inum;
   ilist = list->ilist;
@@ -108,6 +110,12 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr)
     jlist = firstneigh[i];
     jnum = numneigh[i];
 
+    if (check_error_thr((jnum > leadingDimensionInteractionList), tid,
+			FLERR,"Too many neighbors for interaction list.\n"
+			"Check your system or increase 'leadingDimension"
+			"InteractionList'"))
+      return;
+
     // Pre-calculate gteta and cutoff function
     for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) {
 

src/USER-OMP/thr_omp.cpp

@@ -42,7 +42,8 @@ using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
-ThrOMP::ThrOMP(LAMMPS *ptr, int style) : lmp(ptr), fix(NULL), thr_style(style)
+ThrOMP::ThrOMP(LAMMPS *ptr, int style) : lmp(ptr), fix(NULL),
+					 thr_style(style), thr_error(0)
 {
   // register fix omp with this class
   int ifix = lmp->modify->find_fix("package_omp");
@@ -66,6 +67,7 @@ void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
 			  double **vatom, ThrData *thr)
 {
   const int tid = thr->get_tid();
+  if (tid == 0) thr_error = 0;
   
   if (thr_style & THR_PAIR) {
     if (eflag & 2) {
@@ -171,6 +173,9 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
   double **f = lmp->atom->f;
   double **x = lmp->atom->x;
 
+  if (evflag)
+    sync_threads();
+
   switch (thr_style) {
 
   case THR_PAIR: {
@@ -201,11 +206,9 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
 	  }
       }
       if (eflag & 2) {
-	sync_threads();
 	data_reduce_thr(&(pair->eatom[0]), nall, nthreads, 1, tid);
       }
       if (vflag & 4) {
-	sync_threads();
 	data_reduce_thr(&(pair->vatom[0][0]), nall, nthreads, 6, tid);
       }
     }
@@ -248,11 +251,9 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
 	}
       }
       if (eflag & 2) {
-	sync_threads();
 	data_reduce_thr(&(pair->eatom[0]), nall, nthreads, 1, tid);
       }
       if (vflag & 4) {
-	sync_threads();
 	data_reduce_thr(&(pair->vatom[0][0]), nall, nthreads, 6, tid);
       }
     }
@@ -272,11 +273,9 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
 	  bond->virial[i] += thr->virial_bond[i];
       }
       if (eflag & 2) {
-	sync_threads();
 	data_reduce_thr(&(bond->eatom[0]), nall, nthreads, 1, tid);
       }
       if (vflag & 4) {
-	sync_threads();
 	data_reduce_thr(&(bond->vatom[0][0]), nall, nthreads, 6, tid);
       }
     }
@@ -295,11 +294,9 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
 	  angle->virial[i] += thr->virial_angle[i];
       }
       if (eflag & 2) {
-	sync_threads();
 	data_reduce_thr(&(angle->eatom[0]), nall, nthreads, 1, tid);
       }
       if (vflag & 4) {
-	sync_threads();
 	data_reduce_thr(&(angle->vatom[0][0]), nall, nthreads, 6, tid);
       }
     }
@@ -318,11 +315,9 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
 	  dihedral->virial[i] += thr->virial_dihed[i];
       }
       if (eflag & 2) {
-	sync_threads();
 	data_reduce_thr(&(dihedral->eatom[0]), nall, nthreads, 1, tid);
       }
       if (vflag & 4) {
-	sync_threads();
 	data_reduce_thr(&(dihedral->vatom[0][0]), nall, nthreads, 6, tid);
       }
     }
@@ -351,12 +346,10 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
 	}
       }
       if (eflag & 2) {
-	sync_threads();
 	data_reduce_thr(&(dihedral->eatom[0]), nall, nthreads, 1, tid);
 	data_reduce_thr(&(pair->eatom[0]), nall, nthreads, 1, tid);
       }
       if (vflag & 4) {
-	sync_threads();
 	data_reduce_thr(&(dihedral->vatom[0][0]), nall, nthreads, 6, tid);
 	data_reduce_thr(&(pair->vatom[0][0]), nall, nthreads, 6, tid);
       }
@@ -376,11 +369,9 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
 	  improper->virial[i] += thr->virial_imprp[i];
       }
       if (eflag & 2) {
-	sync_threads();
 	data_reduce_thr(&(improper->eatom[0]), nall, nthreads, 1, tid);
       }
       if (vflag & 4) {
-	sync_threads();
 	data_reduce_thr(&(improper->vatom[0][0]), nall, nthreads, 6, tid);
       }
     }
@@ -401,11 +392,9 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
 	  kspace->virial[i] += thr->virial_kspce[i];
       }
       if (eflag & 2) {
-	sync_threads();
 	data_reduce_thr(&(kspace->eatom[0]), nall, nthreads, 1, tid);
       }
       if (vflag & 4) {
-	sync_threads();
 	data_reduce_thr(&(kspace->vatom[0][0]), nall, nthreads, 6, tid);
       }
     }
@@ -418,7 +407,6 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
   }
     
     if (style == fix->last_omp_style) {
-    sync_threads();
     data_reduce_thr(&(f[0][0]), nall, nthreads, 3, tid);
     if (lmp->atom->torque)
       data_reduce_thr(&(lmp->atom->torque[0][0]), nall, nthreads, 3, tid);

src/USER-OMP/thr_omp.h

@@ -19,6 +19,7 @@
 #define LMP_THR_OMP_H
 
 #include "pointers.h"
+#include "error.h"
 #include "fix_omp.h"
 #include "thr_data.h"
 
@@ -40,6 +41,7 @@ class ThrOMP {
   FixOMP *fix; // pointer to fix_omp;
 
   const int thr_style;
+  int thr_error;
 
  public:
   ThrOMP(LAMMPS *, int);
@@ -68,7 +70,34 @@ class ThrOMP {
 				const int, const int, const int);
 
   // reduce per thread data as needed
-  void reduce_thr(void * const style, const int eflag, const int vflag, ThrData * const thr, const int nproxy=0);
+  void reduce_thr(void * const style, const int eflag, const int vflag,
+		  ThrData * const thr, const int nproxy=0);
+
+  // thread safe variant error abort support.
+  // signals an error condition in any thread by making
+  // thr_error > 0, if condition "cond" is true.
+  // will abort from thread 0 if thr_error is > 0
+  // otherwise return true.
+  // returns false if no error found on any thread.
+  // use return value to jump/return to end of threaded region.
+
+  bool check_error_thr(const bool cond, const int tid, const char *fname,
+		       const int line, const char *errmsg) {
+    if (cond) {
+#if defined(_OPENMP)
+#pragma omp atomic
+      ++thr_error;
+#endif
+      if (tid > 0) return true;
+      else lmp->error->one(fname,line,errmsg);
+    } else {
+      if (thr_error > 0) {
+	if (tid == 0) lmp->error->one(fname,line,errmsg);
+	else return true;
+      } else return false;
+    }
+    return false;
+  };
 
  protected:
 

src/memory.cpp

@@ -34,7 +34,8 @@ void *Memory::smalloc(bigint nbytes, const char *name)
 
 #if defined(LAMMPS_MEMALIGN)
   void *ptr;
-  posix_memalign(&ptr, LAMMPS_MEMALIGN, nbytes);
+  int retval = posix_memalign(&ptr, LAMMPS_MEMALIGN, nbytes);
+  if (retval) ptr = NULL;
 #else
   void *ptr = malloc(nbytes);
 #endif

tools/restart2data.cpp

@@ -475,7 +475,7 @@ int main (int narg, char **arg)
 
 void header(FILE *fp, Data &data)
 {
-  const char *version = "5 Jan 2012";
+  const char *version = "31 Jan 2012";
 
   data.triclinic = 0;
 
@@ -1506,6 +1506,8 @@ void pair(FILE *fp, Data &data, char *style, int flag)
 	}
       }
 
+  } else if (strcmp(style,"comb") == 0) {
+
   } else if (strcmp(style,"coul/diel") == 0) {
     m = 1;
     double cut_coul = read_double(fp);
@@ -2534,6 +2536,16 @@ void angle(FILE *fp, Data &data)
   } else if ((strcmp(data.angle_style,"cg/cmm") == 0) ||
 	     (strcmp(data.angle_style,"sdk") == 0)) {
 
+    data.angle_harmonic_k = new double[data.nangletypes+1];
+    data.angle_harmonic_theta0 = new double[data.nangletypes+1];
+    data.angle_cg_cmm_epsilon = new double[data.nangletypes+1];
+
+    fread(&data.angle_harmonic_k[1],sizeof(double),data.nangletypes,fp);
+    fread(&data.angle_harmonic_theta0[1],sizeof(double),data.nangletypes,fp);
+    fread(&data.angle_cg_cmm_epsilon[1],sizeof(double),data.nangletypes,fp);
+
+  } else if (strcmp(data.angle_style,"cg/cmm/old") == 0) {
+
     data.angle_harmonic_k = new double[data.nangletypes+1];
     data.angle_harmonic_theta0 = new double[data.nangletypes+1];
     data.angle_cg_cmm_epsilon = new double[data.nangletypes+1];
@@ -3046,6 +3058,7 @@ void Data::write(FILE *fp, FILE *fp2)
 	(strcmp(pair_style,"adp") != 0) &&
 	(strcmp(pair_style,"airebo") != 0) &&
 	(strcmp(pair_style,"brownian") != 0) &&
+	(strcmp(pair_style,"comb") != 0) &&
 	(strcmp(pair_style,"coul/cut") != 0) &&
 	(strcmp(pair_style,"coul/debye") != 0) &&
 	(strcmp(pair_style,"coul/diel") != 0) &&
@@ -3181,7 +3194,7 @@ void Data::write(FILE *fp, FILE *fp2)
                (strcmp(pair_style,"cg/cmm/coul/long") == 0) ||
                (strcmp(pair_style,"lj/sdk") == 0) ||
                (strcmp(pair_style,"lj/sdk/coul/long") == 0)) {
-      printf("ERROR: Cannot write pair_style %s to data file\n",
+      printf("ERROR: Cannot write pair_style %s to data file alone. please provide an input file, too.\n",
 	     pair_style);
       exit(1);
     }
@@ -3351,7 +3364,13 @@ void Data::write(FILE *fp, FILE *fp2)
 	fprintf(fp,"%d %g %g\n",i,
 		angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0);
 
-    } else if (strcmp(angle_style,"cg/cmm") == 0) {
+    } else if ((strcmp(angle_style,"cg/cmm") == 0) ||
+	       (strcmp(angle_style,"sdk") == 0)) {
+      for (int i = 1; i <= nangletypes; i++)
+	fprintf(fp,"%d %g %g %g\n",i,angle_harmonic_k[i],
+		angle_harmonic_theta0[i]/PI*180.0,angle_cg_cmm_epsilon[i]);
+
+    } else if (strcmp(angle_style,"cg/cmm/old") == 0) {
       for (int i = 1; i <= nangletypes; i++)
 	fprintf(fp,"%d %g %g %s %g %g\n",i,
 		angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0,
@@ -3376,7 +3395,13 @@ void Data::write(FILE *fp, FILE *fp2)
 	fprintf(fp2,"angle_coeffs  %d %g %g\n",i,
 		angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0);
 
-    } else if (strcmp(angle_style,"cg/cmm") == 0) {
+    } else if ((strcmp(angle_style,"cg/cmm") == 0) ||
+	       (strcmp(angle_style,"sdk") == 0)) {
+      for (int i = 1; i <= nangletypes; i++)
+	fprintf(fp2,"angle_coeffs  %d %g %g %g\n",i,angle_harmonic_k[i],
+		angle_harmonic_theta0[i]/PI*180.0,angle_cg_cmm_epsilon[i]);
+
+    } else if (strcmp(angle_style,"cg/cmm/old") == 0) {
       for (int i = 1; i <= nangletypes; i++)
 	fprintf(fp2,"angle_coeffs  %d %g %g %s %g %g\n",i,
 		angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0,