Merge pull request #12 from lammps/master

rebase

doc/src/fix_restrain.txt

@@ -187,10 +187,17 @@ added forces to be included in the total potential energy of the
 system (the quantity being minimized), you MUST enable the
 "fix_modify"_fix_modify.html {energy} option for this fix.
 
-This fix computes a global scalar, which can be accessed by various
-"output commands"_Section_howto.html#howto_15.  The scalar is the
-potential energy for all the restraints as discussed above. The scalar
-value calculated by this fix is "extensive".
+This fix computes a global scalar and a global vector of length 3, which
+can be accessed by various "output commands"_Section_howto.html#howto_15.
+The scalar is the total potential energy for {all} the restraints as
+discussed above. The vector values are the sum of contributions to the
+following individual categories:
+
+1 = bond energy
+2 = angle energy
+3 = dihedral energy :ul
+
+The scalar and vector values calculated by this fix are "extensive".
 
 No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.

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/Array.h

@@ -4,7 +4,7 @@
 #include <cstdlib>
 #include <iostream>
 #include <string>
-#include <stdio.h>
+#include <cstdio>
 
 // for macros
 #include "MatrixDef.h"

lib/atc/Array2D.h

@@ -2,10 +2,9 @@
 #define ARRAY2D_H
 
 #include <cstdlib>
+#include <cstdio>
 #include <string>
 #include <iostream>
-#include <cstdlib>
-#include <stdio.h>
 
 #include "Array.h"
 

lib/atc/ElectronPhononExchange.cpp

@@ -5,7 +5,7 @@
 
 #include <iostream>
 #include <vector>
-#include <math.h>
+#include <cmath>
 
 using ATC_Utility::command_line;
 using ATC_Utility::str2dbl;

lib/atc/FE_Element.cpp

@@ -8,7 +8,7 @@
 #include "Utility.h"
 
 // Other headers
-#include "math.h"
+#include <cmath>
 
 using ATC_Utility::dbl_geq;
 using ATC_Utility::det3;

lib/atc/FE_Engine.cpp

@@ -7,8 +7,8 @@
 #include "KernelFunction.h"
 #include "Utility.h"
 #include "MPI_Wrappers.h"
-#include <stdio.h>
-#include <stdlib.h>
+#include <cstdio>
+#include <cstdlib>
 #include <map>
 #include <string>
 
@@ -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/FE_Interpolate.cpp

@@ -5,7 +5,7 @@
 #include "FE_Quadrature.h"
 
 // Other headers
-#include "math.h"
+#include <cmath>
 
 using std::map;
 using std::vector;

lib/atc/FE_Mesh.cpp

@@ -6,7 +6,7 @@
 #include "OutputManager.h"
 #include "Utility.h"
 #include <sstream>
-#include <assert.h>
+#include <cassert>
 #include <algorithm>
 #include <cmath>
 #include <functional>

lib/atc/FE_Mesh.h

@@ -12,7 +12,7 @@
 #include <map>
 #include <set>
 #include <utility>
-#include <float.h>
+#include <cfloat>
 #include <string>
 #include <vector>
 #include "mpi.h"

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/Function.h

@@ -1,7 +1,7 @@
 #ifndef XT_FUNCTION_H
 #define XT_FUNCTION_H
 
-#include <math.h>
+#include <cmath>
 #include <string>
 #include <set>
 #include <cstdlib>

lib/atc/GMRES.h

@@ -19,7 +19,7 @@
 //  
 //*****************************************************************
 
-#include <math.h>
+#include <cmath>
 
 
 template<class Real>

lib/atc/InterscaleOperators.h

@@ -279,7 +279,7 @@ namespace ATC {
       typename std::map<std::string,data * >::iterator it = list.find(tag);
       if (it==list.end()) return NULL;
       return it->second;
-    };
+    }
 
     /** helper function to add a data entry to a list */
     template <typename data>
@@ -290,7 +290,7 @@ namespace ATC {
         throw ATC_Error("Tried to add another Quantity with tag "+tag+" in InterscaleManager::add_quantity");
       typename std::template pair<std::string,data * > myPair(tag,quantity);
       list.insert(myPair);
-    };
+    }
 
     /** helper function to add a data entry to a list when it requires neighbor communication*/
     template <typename data>
@@ -302,7 +302,7 @@ namespace ATC {
       if (quantity->atom_type() == PROC_GHOST) {
         commList.push_back(quantity);
       }
-    };
+    }
 
      /** helper function to fina a data entry in a list */
     template <typename data>
@@ -311,7 +311,7 @@ namespace ATC {
       typename std::map<std::string,data * >::iterator it = list.find(tag);
       if (it!=list.end()) return it->second;
       return NULL;
-    };
+    }
 
     /** helper function to force the reset of all data in a list */
     template <typename data>
@@ -319,7 +319,7 @@ namespace ATC {
     {
       for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
         (it->second)->force_reset();
-    };
+    }
 
     /** helper function to set the memory type to temporary of a list */
     template <typename data>
@@ -327,7 +327,7 @@ namespace ATC {
     {
       for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
         (it->second)->set_memory_type(TEMPORARY);
-    };
+    }
 
     /** helper function to perform intialization for dfs of a list */
     template <typename data>
@@ -336,7 +336,7 @@ namespace ATC {
       for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
         (it->second)->dfsFound_ = false;
       }
-    };
+    }
 
     /** helper function to start the dfs visit for list */
     template <typename data>
@@ -349,7 +349,7 @@ namespace ATC {
         if ((it->second)->memory_type()==TEMPORARY) list.erase(it++);
         else ++it;
       }
-    };
+    }
 
     // PAQ helper functions
     /** helper function to adjust local atom count for all data in a list before exchange, only valid with quantities that do that are aware of atom counts */
@@ -359,7 +359,7 @@ namespace ATC {
       for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
         (it->second)->reset_nlocal();
       }
-    };
+    }
 
     /** helper function to indicate lammps data is stale for all data in a list before exchange, only valid with PAQs */
     template <typename data>
@@ -367,7 +367,7 @@ namespace ATC {
     {
       for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
         (it->second)->lammps_force_reset();
-    };
+    }
 
     /** helper function to size all data in a list, only valid with comm lists */
     template <typename data>
@@ -375,7 +375,7 @@ namespace ATC {
     {
       for (typename std::vector<data* >::iterator it = list.begin(); it != list.end(); ++it)
         (*it)->quantity();
-    };
+    }
 
     /** helper function to pack all data in a list before exchange, only valid with quantities that do work before parallel communication */
     template <typename data>
@@ -384,7 +384,7 @@ namespace ATC {
       for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
         (it->second)->prepare_exchange();
       }
-    };
+    }
 
     /** helper function to extract all data in a list after exchange, only valid with quantities that do work after parallel communication */
     template <typename data>
@@ -393,7 +393,7 @@ namespace ATC {
       for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
         (it->second)->post_exchange();
       }
-    };
+    }
 
     /** helper function to determine memory usage of all data in a list, only valid with PAQs */
     template <typename data>
@@ -401,7 +401,7 @@ namespace ATC {
     {
       for (typename std::map<std::string,data* >::const_iterator it = list.begin(); it != list.end(); ++it)
         usage += (it->second)->memory_usage();
-    };
+    }
 
     /** helper function to pack arrays of all data before exchange in a list, only valid with PAQs */
     template <typename data>
@@ -410,7 +410,7 @@ namespace ATC {
       for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
         index += (it->second)->pack_exchange(i,&buffer[index]);
       }
-    };
+    }
 
     /** helper function to unpack arrays of all data after exchange in a list, only valid with PAQs */
     template <typename data>
@@ -418,7 +418,7 @@ namespace ATC {
     {
       for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
         index += (it->second)->unpack_exchange(i,&buffer[index]);
-    };
+    }
 
     /** helper function to pack arrays of all data in a list, only valid with comm lists */
     template <typename data>
@@ -427,7 +427,7 @@ namespace ATC {
     {
       for (typename std::vector<data* >::iterator it = list.begin(); it != list.end(); ++it)
         size += (*it)->pack_comm(index,&buf[size],pbc_flag,pbc);
-    };
+    }
 
     /** helper function to unpack arrays of all data in a list, only valid with comm lists */
     template <typename data>
@@ -435,7 +435,7 @@ namespace ATC {
     {
       for (typename std::vector<data* >::iterator it = list.begin(); it != list.end(); ++it)
         size += (*it)->unpack_comm(index,&buf[size]);
-    };
+    }
 
     /** helper function to grow arrays of all data in a list, only valid with PAQs */
     template <typename data>
@@ -443,7 +443,7 @@ namespace ATC {
     {
       for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
         (it->second)->grow_lammps_array(nmax,prefix_+it->first);
-    };
+    }
 
     /** helper function to copy arrays of all data in a list, only valid with PAQs */
     template <typename data>

lib/atc/KD_Tree.cpp

@@ -1,5 +1,5 @@
 #include "KD_Tree.h"
-#include <assert.h>
+#include <cassert>
 
 using std::vector;
 

lib/atc/KD_Tree.h

@@ -4,7 +4,7 @@
 #include "Array2D.h"
 #include "MatrixDef.h"
 #include "MatrixLibrary.h"
-#include <math.h>
+#include <cmath>
 #include <vector>
 #include <utility>
 

lib/atc/KernelFunction.cpp

@@ -1,5 +1,5 @@
 #include "KernelFunction.h"
-#include "math.h"
+#include <cmath>
 #include <vector>
 #include "ATC_Error.h"
 #include "Quadrature.h"

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

@@ -2,7 +2,7 @@
 #define LAMMPS_INTERFACE_H
 
 #include <iostream>
-#include <stdlib.h>
+#include <cstdlib>
 #include <map>
 #include <iostream>
 #include <string>
@@ -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/OutputManager.cpp

@@ -1,6 +1,6 @@
 #include <string>
 #include <fstream>
-#include <stdio.h>
+#include <cstdio>
 #include <sstream>
 #include "OutputManager.h"
 #include "ATC_Error.h"

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;
     }
 
     /** */

lib/atc/ShapeFunction.h

@@ -5,10 +5,10 @@
 
 #include "DependencyManager.h"
 #include "PaqAtcUtility.h"
-#include <map.h>
-#include <vector.h>
-#include <set.h>
-#include <pair.h>
+#include <map>
+#include <vector>
+#include <set>
+#include <pair>
 
 namespace ATC {
 

lib/atc/Utility.h

@@ -13,7 +13,7 @@
 #include <sstream>
 #include <iomanip>
 #include <algorithm>
-#include "math.h"
+#include <cmath>
 
 #include "ATC_Error.h"
 

lib/awpmd/ivutils/include/cerf.h

@@ -42,11 +42,6 @@ Software Foundation, 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 //
 
 
-//#include <math.h>
-//#include <octave/oct.h>
-
-//#include "f77-fcn.h"
-
 //
 // Abramowitz and Stegun: (eqn: 7.1.14) gives this continued
 // fraction for erfc(z)

lib/awpmd/ivutils/include/logexc.h

@@ -1,9 +1,9 @@
 # ifndef LOGEXC_H
 # define LOGEXC_H
 
-#include <stdio.h>
-#include <stdlib.h>
-#include <stdarg.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstdarg>
 #include <stdexcept>
 #include <string>
 

lib/awpmd/ivutils/include/vector_3.h

@@ -84,7 +84,7 @@
 # include <iostream>
 # include <cmath>
 # include <limits>
-# include <stdlib.h>
+# include <cstdlib>
 
 // some compilers don't define PI!
 # ifndef M_PI

lib/colvars/colvar_UIestimator.h

@@ -731,6 +731,6 @@ namespace UIestimator {
             }
         }
     };
-};
+}
 
 #endif

lib/colvars/colvarmodule.cpp

@@ -8,7 +8,7 @@
 // Colvars repository at GitHub.
 
 #include <sstream>
-#include <string.h>
+#include <cstring>
 
 #include "colvarmodule.h"
 #include "colvarparse.h"

lib/colvars/colvarproxy.cpp

@@ -8,7 +8,7 @@
 // Colvars repository at GitHub.
 
 #include <sstream>
-#include <string.h>
+#include <cstring>
 
 #if defined(_OPENMP)
 #include <omp.h>

lib/colvars/colvarscript.cpp

@@ -8,8 +8,7 @@
 // Colvars repository at GitHub.
 
 #include <cstdlib>
-#include <stdlib.h>
-#include <string.h>
+#include <cstring>
 
 #define COLVARSCRIPT_CPP
 #include "colvarscript.h"

lib/colvars/colvartypes.cpp

@@ -7,8 +7,8 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
 
 #include "colvarmodule.h"
 #include "colvartypes.h"

lib/gpu/Makefile.linux_opencl

@@ -6,10 +6,10 @@
 
 EXTRAMAKE = Makefile.lammps.opencl
 
-OCL_TUNE = -DFERMI_OCL       # -- Uncomment for NVIDIA Fermi
+# OCL_TUNE = -DFERMI_OCL       # -- Uncomment for NVIDIA Fermi
 # OCL_TUNE = -DKEPLER_OCL    # -- Uncomment for NVIDIA Kepler
 # OCL_TUNE = -DCYPRESS_OCL   # -- Uncomment for AMD Cypress
-# OCL_TUNE = -DGENERIC_OCL   # -- Uncomment for generic device
+OCL_TUNE = -DGENERIC_OCL   # -- Uncomment for generic device
 
 # this setting should match LAMMPS Makefile
 # one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL

lib/gpu/cudpp_mini/cudpp.h

@@ -300,7 +300,7 @@
 #ifndef __CUDPP_H__
 #define __CUDPP_H__
 
-#include <stdlib.h> // for size_t
+#include <cstdlib> // for size_t
 
 #ifdef __cplusplus
 extern "C" {

lib/gpu/cudpp_mini/cudpp_plan.cpp

@@ -16,7 +16,7 @@
 //#include "cudpp_spmvmult.h"
 #include "cudpp_radixsort.h"
 
-#include <assert.h>
+#include <cassert>
 
 CUDPPPlanManager* CUDPPPlanManager::m_instance = NULL;
 

lib/gpu/cudpp_mini/cudpp_util.h

@@ -25,7 +25,7 @@
 #include <cuda.h>
 #include <cudpp.h>
 #include <limits.h>
-#include <float.h>
+#include <cfloat>
 
 #if (CUDA_VERSION >= 3000)
 #define LAUNCH_BOUNDS(x) __launch_bounds__((x))

lib/gpu/geryon/nvd_macros.h

@@ -1,7 +1,7 @@
 #ifndef NVD_MACROS_H
 #define NVD_MACROS_H
 
-#include <stdio.h>
+#include <cstdio>
 #include <cassert>
 #include <cuda.h>
 

lib/gpu/geryon/ocl_device.h

@@ -353,7 +353,7 @@ int UCL_Device::set_platform(int pid) {
     _num_devices=0;
     return UCL_ERROR;
   }
-  cl_device_id device_list[_num_devices];
+  cl_device_id *device_list = new cl_device_id[_num_devices];
   CL_SAFE_CALL(clGetDeviceIDs(_cl_platform,CL_DEVICE_TYPE_ALL,n,device_list,
                               &n));
 
@@ -362,7 +362,7 @@ int UCL_Device::set_platform(int pid) {
     _cl_devices.push_back(device_list[i]);
     add_properties(device_list[i]);
   }
-
+  delete[] device_list;
   return UCL_SUCCESS;
 }
 
@@ -518,13 +518,14 @@ int UCL_Device::device_type(const int i) {
 int UCL_Device::set(int num) {
   clear();
 
-  cl_device_id device_list[_num_devices];
+  cl_device_id *device_list = new cl_device_id[_num_devices];
   cl_uint n;
   CL_SAFE_CALL(clGetDeviceIDs(_cl_platform,CL_DEVICE_TYPE_ALL,_num_devices,
                                device_list,&n));
 
   _device=num;
   _cl_device=device_list[_device];
+  delete[] device_list;
   return create_context();
 }
 

lib/gpu/geryon/ocl_kernel.h

@@ -111,7 +111,7 @@ class UCL_Program {
       size_t ms;
       CL_SAFE_CALL(clGetProgramBuildInfo(_program,_device,CL_PROGRAM_BUILD_LOG,0,
                                          NULL, &ms));
-      char build_log[ms];
+      char *build_log = new char[ms];
       CL_SAFE_CALL(clGetProgramBuildInfo(_program,_device,CL_PROGRAM_BUILD_LOG,ms,
                                          build_log, NULL));
 
@@ -127,8 +127,9 @@ class UCL_Program {
                   << "----------------------------------------------------------\n";
         std::cerr << build_log << std::endl;
         #endif
+        delete[] build_log;
         return UCL_COMPILE_ERROR;
-      }
+      } else delete[] build_log;
     }
 
     return UCL_SUCCESS;

lib/gpu/geryon/ocl_macros.h

@@ -1,7 +1,7 @@
 #ifndef OCL_MACROS_H
 #define OCL_MACROS_H
 
-#include <stdio.h>
+#include <cstdio>
 #include <cassert>
 
 #ifdef __APPLE__

lib/gpu/geryon/ocl_memory.h

@@ -407,7 +407,7 @@ inline void _ocl_build(cl_program &program, cl_device_id &device,
   size_t ms;
   CL_SAFE_CALL(clGetProgramBuildInfo(program, device,CL_PROGRAM_BUILD_LOG, 0,
                                      NULL, &ms));
-  char build_log[ms];
+  char *build_log = new char[ms];
   CL_SAFE_CALL(clGetProgramBuildInfo(program,device,CL_PROGRAM_BUILD_LOG,ms,
                                      build_log, NULL));
 
@@ -416,6 +416,7 @@ inline void _ocl_build(cl_program &program, cl_device_id &device,
             << " Error compiling OpenCL Program...\n"
             << "----------------------------------------------------------\n";
   std::cerr << build_log << std::endl;
+  delete[] build_log;
 }
 
 inline void _ocl_kernel_from_source(cl_context &context, cl_device_id &device,

lib/gpu/lal_answer.h

@@ -16,7 +16,7 @@
 #ifndef LAL_ANSWER_H
 #define LAL_ANSWER_H
 
-#include <math.h>
+#include <cmath>
 #include "mpi.h"
 
 #if defined(USE_OPENCL)

lib/gpu/lal_atom.h

@@ -16,7 +16,7 @@
 #ifndef PAIR_GPU_ATOM_H
 #define PAIR_GPU_ATOM_H
 
-#include <math.h>
+#include <cmath>
 #include "mpi.h"
 
 #if defined(USE_OPENCL)

lib/gpu/lal_balance.h

@@ -17,7 +17,7 @@
 #define LAL_BALANCE_H
 
 #include "lal_device.h"
-#include <math.h>
+#include <cmath>
 
 #define _HD_BALANCE_EVERY 25
 #define _HD_BALANCE_WEIGHT 0.5

lib/gpu/lal_beck_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_beck.h"
 

lib/gpu/lal_born_coul_long_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_born_coul_long.h"
 

lib/gpu/lal_born_coul_wolf_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_born_coul_wolf.h"
 

lib/gpu/lal_born_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_born.h"
 

lib/gpu/lal_buck_coul_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_buck_coul.h"
 

lib/gpu/lal_buck_coul_long_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_buck_coul_long.h"
 

lib/gpu/lal_buck_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_buck.h"
 

lib/gpu/lal_charmm_long_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_charmm_long.h"
 

lib/gpu/lal_colloid_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_colloid.h"
 

lib/gpu/lal_coul_debye_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_coul_debye.h"
 

lib/gpu/lal_coul_dsf_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_coul_dsf.h"
 

lib/gpu/lal_coul_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_coul.h"
 

lib/gpu/lal_coul_long_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_coul_long.h"
 

lib/gpu/lal_device.cpp

@@ -16,7 +16,7 @@
 #include "lal_device.h"
 #include "lal_precision.h"
 #include <map>
-#include <math.h>
+#include <cmath>
 #ifdef _OPENMP
 #include <omp.h>
 #endif
@@ -78,7 +78,7 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu,
   // Get the names of all nodes
   int name_length;
   char node_name[MPI_MAX_PROCESSOR_NAME];
-  char node_names[MPI_MAX_PROCESSOR_NAME*_world_size];
+  char *node_names = new char[MPI_MAX_PROCESSOR_NAME*_world_size];
   MPI_Get_processor_name(node_name,&name_length);
   MPI_Allgather(&node_name,MPI_MAX_PROCESSOR_NAME,MPI_CHAR,&node_names,
                 MPI_MAX_PROCESSOR_NAME,MPI_CHAR,_comm_world);
@@ -104,6 +104,7 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu,
       split_id=split_num;
     split_num++;
   }
+  delete[] node_names;
 
   // Set up a per node communicator and find rank within
   MPI_Comm node_comm;

lib/gpu/lal_device.h

@@ -22,7 +22,7 @@
 #include "lal_pppm.h"
 #include "mpi.h"
 #include <sstream>
-#include "stdio.h"
+#include <cstdio>
 #include <string>
 #include <queue>
 

lib/gpu/lal_dipole_lj_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_dipole_lj.h"
 

lib/gpu/lal_dipole_lj_sf_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_dipole_lj_sf.h"
 

lib/gpu/lal_dpd_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_dpd.h"
 

lib/gpu/lal_eam_alloy_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_eam.h"
 

lib/gpu/lal_eam_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_eam.h"
 

lib/gpu/lal_eam_fs_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_eam.h"
 

lib/gpu/lal_gauss_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_gauss.h"
 

lib/gpu/lal_gayberne_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_gayberne.h"
 

lib/gpu/lal_lj96_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_lj96.h"
 

lib/gpu/lal_lj_class2_long_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_lj_class2_long.h"
 

lib/gpu/lal_lj_coul_debye_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_lj_coul_debye.h"
 

lib/gpu/lal_lj_coul_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_lj_coul.h"
 

lib/gpu/lal_lj_coul_long_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_lj_coul_long.h"
 

lib/gpu/lal_lj_coul_msm_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_lj_coul_msm.h"
 

lib/gpu/lal_lj_cubic_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_lj_cubic.h"
 

lib/gpu/lal_lj_dsf_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_lj_dsf.h"
 

lib/gpu/lal_lj_expand_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_lj_expand.h"
 

lib/gpu/lal_lj_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_lj.h"
 

lib/gpu/lal_lj_gromacs_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_lj_gromacs.h"
 

lib/gpu/lal_lj_sdk_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_lj_sdk.h"
 

lib/gpu/lal_lj_sdk_long_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_lj_sdk_long.h"
 

lib/gpu/lal_mie_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_mie.h"
 

lib/gpu/lal_morse_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_morse.h"
 

lib/gpu/lal_neighbor.cpp

@@ -17,7 +17,7 @@
 #include "lal_precision.h"
 #include "lal_neighbor.h"
 #include "lal_device.h"
-#include "math.h"
+#include <cmath>
 using namespace LAMMPS_AL;
 
 int Neighbor::bytes_per_atom(const int max_nbors) const {

lib/gpu/lal_pppm_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_pppm.h"
 

lib/gpu/lal_re_squared_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_re_squared.h"
 

lib/gpu/lal_soft_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_soft.h"
 

lib/gpu/lal_sw_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_sw.h"
 

lib/gpu/lal_table_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_table.h"
 

lib/gpu/lal_tersoff_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_tersoff.h"
 

lib/gpu/lal_tersoff_mod_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_tersoff_mod.h"
 

lib/gpu/lal_tersoff_zbl_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_tersoff_zbl.h"
 

lib/gpu/lal_ufm_ext.cpp

@@ -17,7 +17,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_ufm.h"
 

lib/gpu/lal_vashishta_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_vashishta.h"
 using namespace LAMMPS_AL;

lib/gpu/lal_yukawa_colloid_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_yukawa_colloid.h"
 

lib/gpu/lal_yukawa_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_yukawa.h"
 

lib/gpu/lal_zbl_ext.cpp

@@ -15,7 +15,7 @@
 
 #include <iostream>
 #include <cassert>
-#include <math.h>
+#include <cmath>
 
 #include "lal_zbl.h"
 

lib/poems/eulerparameters.cpp

@@ -16,7 +16,7 @@
  *_________________________________________________________________________*/
 
 #include "eulerparameters.h"
-#include "math.h"
+#include <cmath>
 
 using namespace std;
 

lib/poems/fastmatrixops.cpp

@@ -262,7 +262,7 @@ void FastLU(Matrix& A, Matrix& LU, int *indx){ // LU is the LU decomposition of
     for (j=0;j<n;j++){
       temp=fabs(LU.rows[i][j]);
       if (temp > big) big=temp;
-      }
+    }
     vv[i]=1.0/big;
   }
   for (j=0;j<n;j++){
@@ -276,8 +276,8 @@ void FastLU(Matrix& A, Matrix& LU, int *indx){ // LU is the LU decomposition of
       sum=LU.rows[i][j];
       for (k=0;k<j;k++)
         sum -= LU.rows[i][k]*LU.rows[k][j];
-        LU.rows[i][j]=sum;
-        if ((dum=vv[i]*fabs(sum)) >= big) {
+      LU.rows[i][j]=sum;
+      if ((dum=vv[i]*fabs(sum)) >= big) {
         big=dum;
         imax=i;
       }
@@ -311,7 +311,7 @@ void FastLU(Mat3x3& A, Mat3x3& LU, int *indx){ // LU is the LU decomposition of
     for (j=0;j<3;j++){
       temp=fabs(LU.BasicGet(i,j));
       if (temp > big) big=temp;
-      }
+    }
     vv[i]=1.0/big;
   }
   for (j=0;j<3;j++){
@@ -325,8 +325,8 @@ void FastLU(Mat3x3& A, Mat3x3& LU, int *indx){ // LU is the LU decomposition of
       sum=LU.BasicGet(i,j);
       for (k=0;k<j;k++)
         sum -= LU.BasicGet(i,k)*LU.BasicGet(k,j);
-        LU.BasicSet(i,j,sum);
-        if ((dum=vv[i]*fabs(sum)) >= big) {
+      LU.BasicSet(i,j,sum);
+      if ((dum=vv[i]*fabs(sum)) >= big) {
         big=dum;
         imax=i;
       }
@@ -373,8 +373,8 @@ void FastLU(Mat4x4& A, Mat4x4& LU, int *indx){ // LU is the LU decomposition of
       sum=LU.BasicGet(i,j);
       for (k=0;k<j;k++)
         sum -= LU.BasicGet(i,k)*LU.BasicGet(k,j);
-        LU.BasicSet(i,j,sum);
-        if ((dum=vv[i]*fabs(sum)) >= big) {
+      LU.BasicSet(i,j,sum);
+      if ((dum=vv[i]*fabs(sum)) >= big) {
         big=dum;
         imax=i;
       }
@@ -421,8 +421,8 @@ void FastLU(Mat6x6& A, Mat6x6& LU, int *indx){ // LU is the LU decomposition of
       sum=LU.BasicGet(i,j);
       for (k=0;k<j;k++)
         sum -= LU.BasicGet(i,k)*LU.BasicGet(k,j);
-        LU.BasicSet(i,j,sum);
-        if ((dum=vv[i]*fabs(sum)) >= big) {
+      LU.BasicSet(i,j,sum);
+      if ((dum=vv[i]*fabs(sum)) >= big) {
         big=dum;
         imax=i;
       }
@@ -1030,4 +1030,3 @@ void FastAssignT(Mat4x4& A, Mat4x4& C){
   C.elements[2][3] = A.elements[3][2];
   C.elements[3][2] = A.elements[2][3];
 }
-