eliminate variable length arrays from AtC lib for C++ standard compliance

lib/atc/ATC_Method.cpp

@@ -2015,8 +2015,8 @@ pecified
       LammpsInterface::instance()->int_allmax(&send_size,&max_size);
 
       if (comm_rank == 0) {
-        int intbuf[max_size];
-        double buf[max_size];
+        int *intbuf = new int[max_size];
+        double *buf = new double[max_size];
         for (int iproc = 1; iproc < nprocs; iproc++) {
           LammpsInterface::instance()->int_recv(intbuf,max_size,iproc);
           LammpsInterface::instance()->recv(buf,max_size,iproc);
@@ -2024,15 +2024,19 @@ pecified
             out << intbuf[i] << "  " << buf[i] << "\n";
           }  
         }
+        delete[] intbuf;
+        delete[] buf;
       } else {
-        int intbuf[send_size];
-        double buf[send_size];
+        int *intbuf = new int[send_size];
+        double *buf = new double[send_size];
         for (int i = 0; i < send_size; i++) {
           intbuf[i] = id2tag[i];
           buf[i] = atomicVolumeMatrix(i,i);
         }
         LammpsInterface::instance()->int_send(intbuf,send_size);
         LammpsInterface::instance()->send(buf,send_size);
+        delete[] intbuf;
+        delete[] buf;
       }
     }
                 

lib/atc/FE_Engine.cpp

@@ -352,8 +352,9 @@ namespace ATC{
     // each segment of the piecewise funcion is length-normalized separately
     else if (strcmp(arg[argIdx],"position-number-density")==0) { 
       argIdx++;
-      double y[nx],w[nx];
-      int n[nx];
+      double *y = new double[nx];
+      double *w = new double[nx];
+      int *n = new int[nx];
       int nn = 0;
       while (argIdx < narg) { 
         if (! is_numeric(arg[argIdx])) break;
@@ -369,7 +370,7 @@ namespace ATC{
         double w0 = w[i-1];
         double dw = w[i]-w0;
         double lx = 0;
-        double l[dn];
+        double *l = new double[dn];
         for (int j = 0; j < dn; ++j) {
           double x = (j+0.5)/dn; 
           double dl = w0+x*dw;
@@ -380,7 +381,11 @@ namespace ATC{
         for (int j = 0; j < dn; ++j) {
           dx(k++) = scale*l[j];
         }
+        delete[] l;
       }
+      delete[] y;
+      delete[] w;
+      delete[] n;
     }
     // construct relative values from a density function
     // evaluate for a domain (0,1)

lib/atc/Function.cpp

@@ -1,3 +1,4 @@
+#include <alloca.h>
 #include "Function.h"
 #include "ATC_Error.h"
 #include "LammpsInterface.h"
@@ -58,7 +59,7 @@ namespace ATC {
   {
     string type = args[0];
     int narg = nargs -1;
-    double dargs[narg];
+    double *dargs = alloca(sizeof(double) * narg);
     for (int i = 0; i < narg; ++i) dargs[i] = atof(args[i+1]);
   
     return function(type, narg, dargs);
@@ -192,7 +193,7 @@ XT_Function_Mgr * XT_Function_Mgr::myInstance_ = NULL;
   {
     string type = args[0];
     int narg = nargs -1;
-    double dargs[narg];
+    double *dargs = alloca(sizeof(double) * narg);
     for (int i = 0; i < narg; ++i) dargs[i] = atof(args[i+1]);
   
     return function(type, narg, dargs);

lib/atc/LammpsInterface.cpp

@@ -131,15 +131,15 @@ void LammpsInterface::sparse_allsum(SparseMatrix<double> &toShare) const
   if (error != MPI_SUCCESS) throw ATC_Error("error in sparse_allsum_numrows "+to_string(error));
 
   // adjust row sendcounts because recRowsCRS is off by one
-  int rowCounts[nProcs];
-  int sizeCounts[nProcs];
+  int *rowCounts = new int[nProcs];
+  int *sizeCounts = new int[nProcs];
   // set up total size of receive buffers for Allgatherv calls
   int totalRowsCRS = 0;
   int totalSize = 0;
   // set up array of displacements for Allgatherv calls
-  int rowOffsets[nProcs];
+  int *rowOffsets = new int[nProcs];
   rowOffsets[0] = 0;
-  int sizeOffsets[nProcs];
+  int *sizeOffsets = new int[nProcs];
   sizeOffsets[0] = 0;
   for (int i = 0; i < nProcs; i++) {
     // find the total number of entries to share in the mpi calls below
@@ -156,8 +156,8 @@ void LammpsInterface::sparse_allsum(SparseMatrix<double> &toShare) const
   // get actual rows
   INDEX *rec_ia = new INDEX[totalRowsCRS];
   if (toShare.size() == 0) {
-    double dummy[0];
-    error = MPI_Allgatherv(dummy, 0, MPI_INT,
+    double dummy;
+    error = MPI_Allgatherv(&dummy, 0, MPI_INT,
                            rec_ia, rowCounts, rowOffsets, MPI_INT, lammps_->world);
   }
   else
@@ -211,6 +211,10 @@ void LammpsInterface::sparse_allsum(SparseMatrix<double> &toShare) const
       toShare += tempMat;
     }
   }
+  delete[] rowCounts;
+  delete[] sizeCounts;
+  delete[] rowOffsets;
+  delete[] sizeOffsets;
 
   delete[] recInfo;
   delete[] rec_ia;

lib/atc/LammpsInterface.h

@@ -315,7 +315,7 @@ class LammpsInterface {
     } 
     else {
       int commSize = comm_size();
-      double recv[commSize];
+      double *recv = new double[commSize];
       MPI_Wrappers::gather(lammps_->world,data,recv);
       if (rank_zero()) {
         full_msg << " ATC:" << tag;
@@ -324,6 +324,7 @@ class LammpsInterface {
         }
         full_msg << "\n";
       }
+      delete[] recv;
     }
     if (rank_zero()) {
       std::string mesg = full_msg.str();
@@ -577,13 +578,13 @@ class LammpsInterface {
   void destroy_2d_int_array(int **i) const;
   int ** grow_2d_int_array(int **array, int n1, int n2, const char *name) const;
   template <typename T>
-    T * grow_array(T *&array, int n, const char *name) const {return lammps_->memory->grow(array,n,name);};
+    T * grow_array(T *&array, int n, const char *name) const {return lammps_->memory->grow(array,n,name);}
   template <typename T>
-    void destroy_array(T * array) {lammps_->memory->destroy(array);};
+    void destroy_array(T * array) {lammps_->memory->destroy(array);}
   template <typename T>
-    T ** grow_array(T **&array, int n1, int n2, const char *name) const {return lammps_->memory->grow(array,n1,n2,name);};
+    T ** grow_array(T **&array, int n1, int n2, const char *name) const {return lammps_->memory->grow(array,n1,n2,name);}
   template <typename T>
-    void destroy_array(T ** array) const {lammps_->memory->destroy(array);};
+    void destroy_array(T ** array) const {lammps_->memory->destroy(array);}
   /*@}*/
 
   /** \name Methods that interface with Update class */

lib/atc/MPI_Wrappers.cpp

@@ -94,7 +94,8 @@ namespace MPI_Wrappers {
   {
     int myRank;
     MPI_Comm_rank(MPI_COMM_WORLD, &myRank);
-    DOUBLE_RANK in[count],out[count];
+    DOUBLE_RANK *in = new DOUBLE_RANK[count];
+    DOUBLE_RANK *out = new DOUBLE_RANK[count];
     for (int i = 0; i < count; i++) {
       in[i].val = send_buf[i];
       in[i].rank = myRank;
@@ -105,6 +106,8 @@ namespace MPI_Wrappers {
     for (int i = 0; i < count; i++) {
       rec_buf[i] = out[i].val;
     }
+    delete[] in;
+    delete[] out;
     return out[0].rank;
   }
 
@@ -154,14 +157,16 @@ namespace MPI_Wrappers {
   {
     int error;
     int numprocs = size(comm);
-    int sizes[numprocs];
-    int displacements[numprocs];
+    int *sizes = new int[numprocs];
+    int *displacements = new int[numprocs];
     for (int i = 0; i < numprocs; ++i) {
       sizes[i] = 1;
       displacements[i] = i;
     }
     error = MPI_Scatterv(send_buf, sizes, displacements, MPI_INT, rec_buf, count, MPI_INT, 0, comm);
     if (error != MPI_SUCCESS) throw ATC_Error("error in int_scatter "+to_string(error));
+    delete[] sizes;
+    delete[] displacements;
   }
 
   void allgatherv(MPI_Comm comm, double *send_buf, int send_count,

lib/atc/Makefile.mpi

@@ -52,4 +52,4 @@ fastdep.exe: ../../src/DEPEND/fastdep.c
 clean:
 	-rm -f *.o *~ .depend $(LIB) fastdep.exe
 
-sinclude $(DEPENDS)
+sinclude .depend

lib/atc/Makefile.mpic++

@@ -1 +0,0 @@
-Makefile.mpi

lib/atc/PrescribedDataManager.h

@@ -154,7 +154,7 @@ namespace ATC {
       std::set<int> fluxes;
       //list of nodes to insert. 
       //1 for nodes to insert, 0 for nodes not to insert.
-      int toInsert[nNodes_];
+      int *toInsert = new int[nNodes_];
       for (int i = 0; i < nNodes_; ++i) toInsert[i] = 0;
 
       const std::map < std::pair <int, int>, Array < XT_Function * > > & sources = faceSources_.find(thisField)->second;
@@ -178,6 +178,7 @@ namespace ATC {
       for (int node = 0; node < nNodes_; ++node) {
         if (toInsert[node]) fluxes.insert(node);
       }
+      delete[] toInsert;
       return fluxes;
     }
 
@@ -189,7 +190,7 @@ namespace ATC {
     {
       //list of nodes to insert. 
       //1 for nodes to insert, 0 for nodes not to insert.
-      int toInsert[nNodes_];
+      int *toInsert = new int[nNodes_];
       for (int i = 0; i < nNodes_; ++i) toInsert[i] = 0;
 
       const std::map < std::pair <int, int>, Array < XT_Function * > > & sources = faceSources_.find(thisField)->second;
@@ -213,6 +214,7 @@ namespace ATC {
       for (int node = 0; node < nNodes_; ++node) {
         if (toInsert[node]) fluxes.insert(node);
       }
+      delete[] toInsert;
     }
 
     /** */
@@ -223,7 +225,7 @@ namespace ATC {
       std::set<int> fluxes;
       //list of nodes to insert. 
       //1 for nodes to insert, 0 for nodes not to insert.
-      int toInsert[nNodes_];
+      int *toInsert = new int[nNodes_];
       for (int i = 0; i < nNodes_; ++i) toInsert[i] = 0;
 
       const Array2D < XT_Function *> & sources = elementSources_.find(thisField)->second;
@@ -244,6 +246,7 @@ namespace ATC {
       for (int node = 0; node < nNodes_; ++node) {
         if (toInsert[node]) fluxes.insert(node);
       }
+      delete[] toInsert;
       return fluxes;
     }
 
@@ -255,7 +258,7 @@ namespace ATC {
     {
       //list of nodes to insert. 
       //1 for nodes to insert, 0 for nodes not to insert.
-      int toInsert[nNodes_];
+      int *toInsert = new int[nNodes_];
       for (int i = 0; i < nNodes_; ++i) toInsert[i] = 0;
 
       const Array2D < XT_Function *> & sources = elementSources_.find(thisField)->second;
@@ -276,6 +279,7 @@ namespace ATC {
       for (int node = 0; node < nNodes_; ++node) {
         if (toInsert[node]) fluxes.insert(node);
       }
+      delete[] toInsert;
     }
 
     /** */