git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15462 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_reduce.cpp

@@ -75,10 +75,11 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
   // expand args if any have wildcard character "*"
 
   int expand = 0;
-  char **earg;
+  char **earg,**arghold;
   int nargnew = input->expand_args(narg-iarg,&arg[iarg],1,earg);
 
   if (earg != &arg[iarg]) expand = 1;
+  arghold = arg;
   arg = earg;
 
   // parse values until one isn't recognized
@@ -189,8 +190,9 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
   // if wildcard expansion occurred, free earg memory from expand_args()
 
   if (expand) {
-    for (int i = 0; i < nargnew; i++) delete [] earg[i];
+    for (int i = 0; i < nvalues; i++) delete [] earg[i];
     memory->sfree(earg);
+    arg = arghold;
   }
 
   // setup and error check

src/dump_custom.cpp

@@ -68,15 +68,13 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
   // nfield may be shrunk below if extra optional args exist
 
   expand = 0;
-  nfield = nargnew = input->expand_args(narg-5,&arg[5],1,earg);
+  nfield = input->expand_args(narg-5,&arg[5],1,earg);
   if (earg != &arg[5]) expand = 1;
 
   // allocate field vectors
 
   pack_choice = new FnPtrPack[nfield];
   vtype = new int[nfield];
-  field2index = new int[nfield];
-  argindex = new int[nfield];
 
   buffer_allow = 1;
   buffer_flag = 1;
@@ -89,6 +87,9 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
 
   // computes, fixes, variables which the dump accesses
 
+  memory->create(field2index,nfield,"dump:field2index");
+  memory->create(argindex,nfield,"dump:argindex");
+
   ncompute = 0;
   id_compute = NULL;
   compute = NULL;
@@ -180,14 +181,14 @@ DumpCustom::~DumpCustom()
   // could not do in constructor, b/c some derived classes process earg
 
   if (expand) {
-    for (int i = 0; i < nargnew; i++) delete [] earg[i];
+    for (int i = 0; i < nfield; i++) delete [] earg[i];
     memory->sfree(earg);
   }
 
   delete [] pack_choice;
   delete [] vtype;
-  delete [] field2index;
+  memory->destroy(field2index);
-  delete [] argindex;
+  memory->destroy(argindex);
 
   delete [] idregion;
   memory->destroy(thresh_array);

src/dump_custom.h

@@ -40,7 +40,6 @@ class DumpCustom : public Dump {
 
   int expand;                // flag for whether field args were expanded
   char **earg;               // field names with wildcard expansion
-  int nargnew;               // size of earg
 
   int *vtype;                // type of each vector (INT, DOUBLE)
   char **vformat;            // format string for each vector element

src/fix_ave_atom.cpp

@@ -49,10 +49,11 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
   // this can reset nvalues
 
   int expand = 0;
-  char **earg;
+  char **earg,**arghold;
   nvalues = input->expand_args(nvalues,&arg[6],1,earg);
 
   if (earg != &arg[6]) expand = 1;
+  arghold = arg;
   arg = earg;
 
   // parse values
@@ -127,6 +128,7 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
   if (expand) {
     for (int i = 0; i < nvalues; i++) delete [] earg[i];
     memory->sfree(earg);
+    arg = arghold;
   }
 
   // setup and error check

src/fix_ave_chunk.cpp

@@ -60,10 +60,11 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
   // expand args if any have wildcard character "*"
 
   int expand = 0;
-  char **earg;
+  char **earg,**arghold;
   int nargnew = input->expand_args(narg-7,&arg[7],1,earg);
 
   if (earg != &arg[7]) expand = 1;
+  arghold = arg;
   arg = earg;
 
   // parse values until one isn't recognized
@@ -74,9 +75,8 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
   value2index = new int[nargnew];
   nvalues = 0;
 
-  int iarg = 0;
+  int iarg = 7;
   while (iarg < narg) {
-
     ids[nvalues] = NULL;
 
     if (strcmp(arg[iarg],"vx") == 0) {
@@ -376,8 +376,9 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
   // wait to do this until after file comment lines are printed
 
   if (expand) {
-    for (int i = 0; i < nargnew; i++) delete [] earg[i];
+    for (int i = 0; i < nvalues; i++) delete [] earg[i];
     memory->sfree(earg);
+    arg = arghold;
   }
 
   // this fix produces a global array

src/fix_ave_correlate.cpp

@@ -59,10 +59,11 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
   // expand args if any have wildcard character "*"
 
   int expand = 0;
-  char **earg;
+  char **earg,**arghold;
   int nargnew = input->expand_args(narg-6,&arg[6],0,earg);
 
   if (earg != &arg[6]) expand = 1;
+  arghold = arg;
   arg = earg;
 
   // parse values until one isn't recognized
@@ -291,8 +292,9 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
   // wait to do this until after file comment lines are printed
 
   if (expand) {
-    for (int i = 0; i < nargnew; i++) delete [] earg[i];
+    for (int i = 0; i < nvalues; i++) delete [] earg[i];
     memory->sfree(earg);
+    arg = arghold;
   }
 
   // allocate and initialize memory for averaging

src/fix_ave_histo.cpp

@@ -100,58 +100,67 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
   // this can reset nvalues
 
   int expand = 0;
-  char **earg;
+  char **earg,**arghold;
   nvalues = input->expand_args(nvalues,&arg[9],mode,earg);
 
   if (earg != &arg[9]) expand = 1;
+  arghold = arg;
   arg = earg;
 
   // parse values
 
-  which = new int[nvalues];
+  which = argindex = value2index = NULL;
-  argindex = new int[nvalues];
+  ids = NULL;
-  value2index = new int[nvalues];
+  allocate_values(nvalues);
-  ids = new char*[nvalues];
 
   for (int i = 0; i < nvalues; i++) {
     if (strcmp(arg[i],"x") == 0) {
       which[i] = X;
       argindex[i] = 0;
       ids[i] = NULL;
+      iarg++;
     } else if (strcmp(arg[i],"y") == 0) {
       which[i] = X;
       argindex[i] = 1;
       ids[i] = NULL;
+      iarg++;
     } else if (strcmp(arg[i],"z") == 0) {
       which[i] = X;
       argindex[i] = 2;
       ids[i] = NULL;
+      iarg++;
 
     } else if (strcmp(arg[i],"vx") == 0) {
       which[i] = V;
       argindex[i] = 0;
       ids[i] = NULL;
+      iarg++;
     } else if (strcmp(arg[i],"vy") == 0) {
       which[i] = V;
       argindex[i] = 1;
       ids[i] = NULL;
+      iarg++;
     } else if (strcmp(arg[i],"vz") == 0) {
       which[i] = V;
       argindex[i] = 2;
       ids[i] = NULL;
+      iarg++;
 
     } else if (strcmp(arg[i],"fx") == 0) {
       which[i] = F;
       argindex[i] = 0;
       ids[i] = NULL;
+      iarg++;
     } else if (strcmp(arg[i],"fy") == 0) {
       which[i] = F;
       argindex[i] = 1;
       ids[i] = NULL;
+      iarg++;
     } else if (strcmp(arg[i],"fz") == 0) {
       which[i] = F;
       argindex[i] = 2;
       ids[i] = NULL;
+      iarg++;
 
     } else if ((strncmp(arg[i],"c_",2) == 0) ||
         (strncmp(arg[i],"f_",2) == 0) ||
@@ -184,6 +193,7 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
   if (expand) {
     for (int i = 0; i < nvalues; i++) delete [] earg[i];
     memory->sfree(earg);
+    arg = arghold;
   }
 
   // setup and error check
@@ -486,11 +496,11 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
 
 FixAveHisto::~FixAveHisto()
 {
-  delete [] which;
+  memory->destroy(which);
-  delete [] argindex;
+  memory->destroy(argindex);
-  delete [] value2index;
+  memory->destroy(value2index);
   for (int i = 0; i < nvalues; i++) delete [] ids[i];
-  delete [] ids;
+  memory->sfree(ids);
 
   if (fp && me == 0) fclose(fp);
 
@@ -993,6 +1003,18 @@ void FixAveHisto::options(int iarg, int narg, char **arg)
   }
 }
 
+/* ----------------------------------------------------------------------
+   reallocate vectors for each input value, of length N
+------------------------------------------------------------------------- */
+
+void FixAveHisto::allocate_values(int n)
+{
+  memory->grow(which,n,"ave/hsito:which");
+  memory->grow(argindex,n,"ave/histo:argindex");
+  memory->grow(value2index,n,"ave/histo:value2index");
+  ids = (char **) memory->srealloc(ids,n*sizeof(char *),"ave/histo:ids");
+}
+
 /* ----------------------------------------------------------------------
    calculate nvalid = next step on which end_of_step does something
    can be this timestep if multiple of nfreq and nrepeat = 1

src/fix_ave_histo.h

@@ -66,6 +66,7 @@ class FixAveHisto : public Fix {
   void bin_vector(int, double *, int);
   void bin_atoms(double *, int);
   void options(int, int, char **);
+  void allocate_values(int);
   bigint nextvalid();
 };
 

src/fix_ave_time.cpp

@@ -79,20 +79,18 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
   // this can reset nvalues
 
   int expand = 0;
-  char **earg;
+  char **earg,**arghold;
   nvalues = input->expand_args(nvalues,&arg[6],mode,earg);
 
   if (earg != &arg[6]) expand = 1;
+  arghold = arg;
   arg = earg;
 
   // parse values
 
-  which = new int[nvalues];
+  which = argindex = value2index = offcol = varlen = NULL;
-  argindex = new int[nvalues];
+  ids = NULL;
-  value2index = new int[nvalues];
+  allocate_values(nvalues);
-  offcol = new int[nvalues];
-  varlen = new int[nvalues];
-  ids = new char*[nvalues];
 
   for (int i = 0; i < nvalues; i++) {
     if (arg[i][0] == 'c') which[i] = COMPUTE;
@@ -295,6 +293,7 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
   if (expand) {
     for (int i = 0; i < nvalues; i++) delete [] earg[i];
     memory->sfree(earg);
+    arg = arghold;
   }
 
   // allocate memory for averaging
@@ -456,13 +455,13 @@ FixAveTime::~FixAveTime()
 
   delete [] format_user;
 
-  delete [] which;
+  memory->destroy(which);
-  delete [] argindex;
+  memory->destroy(argindex);
-  delete [] value2index;
+  memory->destroy(value2index);
-  delete [] offcol;
+  memory->destroy(offcol);
-  delete [] varlen;
+  memory->destroy(varlen);
   for (int i = 0; i < nvalues; i++) delete [] ids[i];
-  delete [] ids;
+  memory->sfree(ids);
 
   delete [] extlist;
 
@@ -1106,6 +1105,20 @@ void FixAveTime::options(int iarg, int narg, char **arg)
   }
 }
 
+/* ----------------------------------------------------------------------
+   reallocate vectors for N input values
+------------------------------------------------------------------------- */
+
+void FixAveTime::allocate_values(int n)
+{
+  memory->grow(which,n,"ave/time:which");
+  memory->grow(argindex,n,"ave/time:argindex");
+  memory->grow(value2index,n,"ave/time:value2index");
+  memory->grow(offcol,n,"ave/time:offcol");
+  memory->grow(varlen,n,"ave/time:varlen");
+  ids = (char **) memory->srealloc(ids,n*sizeof(char *),"ave/time:ids");
+}
+
 /* ----------------------------------------------------------------------
    reallocate arrays for mode = VECTOR of size Nrows x Nvalues
 ------------------------------------------------------------------------- */

src/fix_ave_time.h

@@ -70,6 +70,7 @@ class FixAveTime : public Fix {
   void invoke_scalar(bigint);
   void invoke_vector(bigint);
   void options(int, int, char **);
+  void allocate_values(int);
   void allocate_arrays();
   bigint nextvalid();
 };

src/thermo.cpp

@@ -569,7 +569,7 @@ void Thermo::modify_params(int narg, char **arg)
         format_int_user = NULL;
         format_bigint_user = NULL;
         format_float_user = NULL;
-        for (int i = 0; i < nfield_initial+1; i++) {
+        for (int i = 0; i < nfield_initial; i++) {
           delete [] format_column_user[i];
           format_column_user[i] = NULL;
         }
@@ -610,7 +610,7 @@ void Thermo::modify_params(int narg, char **arg)
         strcpy(format_float_user,arg[iarg+2]);
       } else {
         int i = force->inumeric(FLERR,arg[iarg+1]) - 1;
-        if (i < 0 || i >= nfield_initial+1)
+        if (i < 0 || i >= nfield_initial)
           error->all(FLERR,"Illegal thermo_modify command");
         if (format_column_user[i]) delete [] format_column_user[i];
         int n = strlen(arg[iarg+2]) + 1;