sync Kokkos changes with current master

src/KOKKOS/atom_kokkos.cpp

@@ -257,48 +257,101 @@ void AtomKokkos::grow(unsigned int mask)
    return index in ivector or dvector of its location
 ------------------------------------------------------------------------- */
 
-int AtomKokkos::add_custom(const char *name, int flag)
+int AtomKokkos::add_custom(const char *name, int flag, int cols)
 {
   int index;
 
-  if (flag == 0) {
+  if (flag == 0 && cols == 0) {
     index = nivector;
     nivector++;
-    iname = (char **) memory->srealloc(iname, nivector * sizeof(char *), "atom:iname");
-    iname[index] = utils::strdup(name);
-    ivector = (int **) memory->srealloc(ivector, nivector * sizeof(int *), "atom:ivector");
-    memory->create(ivector[index], nmax, "atom:ivector");
-  } else {
+    ivname = (char **) memory->srealloc(ivname,nivector*sizeof(char *),
+					"atom:ivname");
+    int n = strlen(name) + 1;
+    ivname[index] = new char[n];
+    strcpy(ivname[index],name);
+    ivector = (int **) memory->srealloc(ivector,nivector*sizeof(int *),
+                                        "atom:ivector");
+    memory->create(ivector[index],nmax,"atom:ivector");
+    
+  } else if (flag == 1 && cols == 0) {
     index = ndvector;
     ndvector++;
-    dname = (char **) memory->srealloc(dname, ndvector * sizeof(char *), "atom:dname");
-    dname[index] = utils::strdup(name);
-    this->sync(Device, DVECTOR_MASK);
-    memoryKK->grow_kokkos(k_dvector, dvector, ndvector, nmax, "atom:dvector");
-    this->modified(Device, DVECTOR_MASK);
-  }
+    dvname = (char **) memory->srealloc(dvname,ndvector*sizeof(char *),
+					"atom:dvname");
+    int n = strlen(name) + 1;
+    dvname[index] = new char[n];
+    strcpy(dvname[index],name);
+    dvector = (double **) memory->srealloc(dvector,ndvector*sizeof(double *),
+                                           "atom:dvector");
+    this->sync(Device,DVECTOR_MASK);
+    memoryKK->grow_kokkos(k_dvector,dvector,ndvector,nmax,
+                        "atom:dvector");
+    this->modified(Device,DVECTOR_MASK);
 
+  } else if (flag == 0 && cols) {
+    index = niarray;
+    niarray++;
+    ianame = (char **) memory->srealloc(ianame,niarray*sizeof(char *),
+					"atom:ianame");
+    int n = strlen(name) + 1;
+    ianame[index] = new char[n];
+    strcpy(ianame[index],name);
+    iarray = (int ***) memory->srealloc(iarray,niarray*sizeof(int **),
+					"atom:iarray");
+    memory->create(iarray[index],nmax,cols,"atom:iarray");
+    
+    icols = (int *) memory->srealloc(icols,niarray*sizeof(int),"atom:icols");
+    icols[index] = cols;
+    
+  } else if (flag == 1 && cols) {
+    index = ndarray;
+    ndarray++;
+    daname = (char **) memory->srealloc(daname,ndarray*sizeof(char *),
+					"atom:daname");
+    int n = strlen(name) + 1;
+    daname[index] = new char[n];
+    strcpy(daname[index],name);
+    darray = (double ***) memory->srealloc(darray,ndarray*sizeof(double **),
+					   "atom:darray");
+    memory->create(darray[index],nmax,cols,"atom:darray");
+
+    dcols = (int *) memory->srealloc(dcols,ndarray*sizeof(int),"atom:dcols");
+    dcols[index] = cols;
+  }
+ 
   return index;
 }
 
 /* ----------------------------------------------------------------------
    remove a custom variable of type flag = 0/1 for int/double at index
-   free memory for vector and name and set ptrs to a null pointer
-   ivector/dvector and iname/dname lists never shrink
+   free memory for vector/array and name and set ptrs to a null pointer
+   these lists never shrink
 ------------------------------------------------------------------------- */
 
-void AtomKokkos::remove_custom(int flag, int index)
+void AtomKokkos::remove_custom(int index, int flag, int cols)
 {
-  if (flag == 0) {
+  if (flag == 0 && cols == 0) {
     memory->destroy(ivector[index]);
-    ivector[index] = nullptr;
-    delete[] iname[index];
-    iname[index] = nullptr;
-  } else {
-    //memoryKK->destroy_kokkos(dvector);
-    dvector[index] = nullptr;
-    delete[] dname[index];
-    dname[index] = nullptr;
+    ivector[index] = NULL;
+    delete [] ivname[index];
+    ivname[index] = NULL;
+    
+  } else if (flag == 1 && cols == 0) {
+    dvector[index] = NULL;
+    delete [] dvname[index];
+    dvname[index] = NULL;
+
+  } else if (flag == 0 && cols) {
+    memory->destroy(iarray[index]);
+    iarray[index] = NULL;
+    delete [] ianame[index];
+    ianame[index] = NULL;
+    
+  } else if (flag == 1 && cols) {
+    memory->destroy(darray[index]);
+    darray[index] = NULL;
+    delete [] daname[index];
+    daname[index] = NULL;
   }
 }
 

src/KOKKOS/atom_kokkos.h

@@ -111,8 +111,8 @@ class AtomKokkos : public Atom {
   void sync_overlapping_device(const ExecutionSpace space, unsigned int mask);
   virtual void sort();
   virtual void grow(unsigned int mask);
-  int add_custom(const char *, int);
-  void remove_custom(int, int);
+  int add_custom(const char *, int, int);
+  void remove_custom(int, int, int);
   virtual void deallocate_topology();
   void sync_modify(ExecutionSpace, unsigned int, unsigned int);
  private:

src/KOKKOS/pair_exp6_rx_kokkos.cpp

@@ -1788,7 +1788,7 @@ void PairExp6rxKokkos<DeviceType>::read_file(char *file)
     while ((words[nwords++] = strtok(nullptr," \t\n\r\f"))) continue;
 
     for (ispecies = 0; ispecies < nspecies; ispecies++)
-      if (strcmp(words[0],&atom->dname[ispecies][0]) == 0) break;
+      if (strcmp(words[0],&atom->dvname[ispecies][0]) == 0) break;
     if (ispecies == nspecies) continue;
 
     // load up parameter settings and error check their values
@@ -1801,8 +1801,9 @@ void PairExp6rxKokkos<DeviceType>::read_file(char *file)
     }
 
     params[nparams].ispecies = ispecies;
-    params[nparams].name = utils::strdup(&atom->dname[ispecies][0]);
+    params[nparams].name = utils::strdup(&atom->dvname[ispecies][0]);
     params[nparams].potential = utils::strdup(words[1]);
+
     if (strcmp(params[nparams].potential,"exp6") == 0) {
       params[nparams].alpha = atof(words[2]);
       params[nparams].epsilon = atof(words[3]);

src/KOKKOS/pair_table_rx_kokkos.cpp

@@ -1048,15 +1048,20 @@ void PairTableRXKokkos<DeviceType>::coeff(int narg, char **arg)
   site1 = utils::strdup(arg[4]);
 
   int ispecies;
-  for (ispecies = 0; ispecies < nspecies; ispecies++)
-    if (strcmp(site1,&atom->dname[ispecies][0]) == 0) break;
+  for (ispecies = 0; ispecies < nspecies; ispecies++) {
+    if (strcmp(site1,&atom->dvname[ispecies][0]) == 0) break;
+  }
 
   if (ispecies == nspecies && strcmp(site1,"1fluid") != 0)
     error->all(FLERR,"Site1 name not recognized in pair coefficients");
 
-  site2 = utils::strdup(arg[5]);
-  for (ispecies = 0; ispecies < nspecies; ispecies++)
-    if (strcmp(site2,&atom->dname[ispecies][0]) == 0) break;
+  n = strlen(arg[5]) + 1;
+  site2 = new char[n];
+  strcpy(site2,arg[5]);
+
+  for (ispecies = 0; ispecies < nspecies; ispecies++) {
+    if (strcmp(site2,&atom->dvname[ispecies][0]) == 0) break;
+  }
 
   if (ispecies == nspecies && strcmp(site2,"1fluid") != 0)
     error->all(FLERR,"Site2 name not recognized in pair coefficients");
@@ -1123,7 +1128,7 @@ void PairTableRXKokkos<DeviceType>::coeff(int narg, char **arg)
        isite1 = nspecies;
 
        for (int k = 0; k < nspecies; k++) {
-         if (strcmp(site1, atom->dname[k]) == 0) {
+         if (strcmp(site1, atom->dvname[k]) == 0) {
            isite1 = k;
            break;
          }
@@ -1138,7 +1143,7 @@ void PairTableRXKokkos<DeviceType>::coeff(int narg, char **arg)
        isite2 = nspecies;
 
        for (int k = 0; k < nspecies; k++) {
-         if (strcmp(site2, atom->dname[k]) == 0) {
+         if (strcmp(site2, atom->dvname[k]) == 0) {
            isite2 = ispecies;
            break;
          }