git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15459 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_reduce.cpp

@@ -75,11 +75,10 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
   // expand args if any have wildcard character "*"
 
   int expand = 0;
-  char **earg,**arghold;
+  char **earg;
   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
@@ -190,9 +189,8 @@ 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 < nvalues; i++) delete [] earg[i];
+    for (int i = 0; i < nargnew; i++) delete [] earg[i];
     memory->sfree(earg);
-    arg = arghold;
   }
 
   // setup and error check

src/dump_custom.cpp

@@ -68,13 +68,15 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
   // nfield may be shrunk below if extra optional args exist
 
   expand = 0;
-  nfield = input->expand_args(narg-5,&arg[5],1,earg);
+  nfield = nargnew = 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;
@@ -87,9 +89,6 @@ 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;
@@ -181,14 +180,14 @@ DumpCustom::~DumpCustom()
   // could not do in constructor, b/c some derived classes process earg
 
   if (expand) {
-    for (int i = 0; i < nfield; i++) delete [] earg[i];
+    for (int i = 0; i < nargnew; i++) delete [] earg[i];
     memory->sfree(earg);
   }
 
   delete [] pack_choice;
   delete [] vtype;
-  memory->destroy(field2index);
+  delete [] field2index;
-  memory->destroy(argindex);
+  delete [] argindex;
 
   delete [] idregion;
   memory->destroy(thresh_array);

src/dump_custom.h

@@ -40,6 +40,7 @@ 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

@@ -49,11 +49,10 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
   // this can reset nvalues
 
   int expand = 0;
-  char **earg,**arghold;
+  char **earg;
   nvalues = input->expand_args(nvalues,&arg[6],1,earg);
 
   if (earg != &arg[6]) expand = 1;
-  arghold = arg;
   arg = earg;
 
   // parse values
@@ -128,7 +127,6 @@ 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

@@ -60,11 +60,10 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
   // expand args if any have wildcard character "*"
 
   int expand = 0;
-  char **earg,**arghold;
+  char **earg;
   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
@@ -377,9 +376,8 @@ 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 < nvalues; i++) delete [] earg[i];
+    for (int i = 0; i < nargnew; i++) delete [] earg[i];
     memory->sfree(earg);
-    arg = arghold;
   }
 
   // this fix produces a global array

src/fix_ave_correlate.cpp

@@ -59,11 +59,10 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
   // expand args if any have wildcard character "*"
 
   int expand = 0;
-  char **earg,**arghold;
+  char **earg;
   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
@@ -292,9 +291,8 @@ 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 < nvalues; i++) delete [] earg[i];
+    for (int i = 0; i < nargnew; i++) delete [] earg[i];
     memory->sfree(earg);
-    arg = arghold;
   }
 
   // allocate and initialize memory for averaging

src/fix_ave_histo.cpp

@@ -100,67 +100,58 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
   // this can reset nvalues
 
   int expand = 0;
-  char **earg,**arghold;
+  char **earg;
   nvalues = input->expand_args(nvalues,&arg[9],mode,earg);
 
   if (earg != &arg[9]) expand = 1;
-  arghold = arg;
   arg = earg;
 
   // parse values
 
-  which = argindex = value2index = NULL;
+  which = new int[nvalues];
-  ids = NULL;
+  argindex = new int[nvalues];
-  allocate_values(nvalues);
+  value2index = new int[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) ||
@@ -193,7 +184,6 @@ 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
@@ -496,11 +486,11 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
 
 FixAveHisto::~FixAveHisto()
 {
-  memory->destroy(which);
+  delete [] which;
-  memory->destroy(argindex);
+  delete [] argindex;
-  memory->destroy(value2index);
+  delete [] value2index;
   for (int i = 0; i < nvalues; i++) delete [] ids[i];
-  memory->sfree(ids);
+  delete [] ids;
 
   if (fp && me == 0) fclose(fp);
 
@@ -1003,18 +993,6 @@ 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

@@ -66,7 +66,6 @@ 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

@@ -79,18 +79,20 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
   // this can reset nvalues
 
   int expand = 0;
-  char **earg,**arghold;
+  char **earg;
   nvalues = input->expand_args(nvalues,&arg[6],mode,earg);
 
   if (earg != &arg[6]) expand = 1;
-  arghold = arg;
   arg = earg;
 
   // parse values
 
-  which = argindex = value2index = offcol = varlen = NULL;
+  which = new int[nvalues];
-  ids = NULL;
+  argindex = new int[nvalues];
-  allocate_values(nvalues);
+  value2index = new int[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;
@@ -293,7 +295,6 @@ 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
@@ -455,13 +456,13 @@ FixAveTime::~FixAveTime()
 
   delete [] format_user;
 
-  memory->destroy(which);
+  delete [] which;
-  memory->destroy(argindex);
+  delete [] argindex;
-  memory->destroy(value2index);
+  delete [] value2index;
-  memory->destroy(offcol);
+  delete [] offcol;
-  memory->destroy(varlen);
+  delete [] varlen;
   for (int i = 0; i < nvalues; i++) delete [] ids[i];
-  memory->sfree(ids);
+  delete [] ids;
 
   delete [] extlist;
 
@@ -1105,20 +1106,6 @@ 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

@@ -70,7 +70,6 @@ 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; i++) {
+        for (int i = 0; i < nfield_initial+1; 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)
+        if (i < 0 || i >= nfield_initial+1)
           error->all(FLERR,"Illegal thermo_modify command");
         if (format_column_user[i]) delete [] format_column_user[i];
         int n = strlen(arg[iarg+2]) + 1;