git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15418 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_reduce.cpp

@@ -82,7 +82,7 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
   arghold = arg;
   arg = earg;
 
-  // parse remaining values until one isn't recognized
+  // parse values until one isn't recognized
 
   which = new int[nargnew];
   argindex = new int[nargnew];

src/fix_ave_chunk.cpp

@@ -57,15 +57,25 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
   global_freq = nfreq;
   no_change_box = 1;
 
+  // expand args if any have wildcard character "*"
+
+  int expand = 0;
+  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
 
-  int iarg = 7;
+  which = new int[nargnew];
-  which = new int[narg-iarg];
+  argindex = new int[nargnew];
-  argindex = new int[narg-iarg];
+  ids = new char*[nargnew];
-  ids = new char*[narg-iarg];
+  value2index = new int[nargnew];
-  value2index = new int[narg-iarg];
   nvalues = 0;
 
+  int iarg = 7;
   while (iarg < narg) {
     ids[nvalues] = NULL;
 
@@ -152,7 +162,7 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
   char *title2 = NULL;
   char *title3 = NULL;
 
-  while (iarg < narg) {
+  while (iarg < nargnew) {
     if (strcmp(arg[iarg],"norm") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
       if (strcmp(arg[iarg+1],"all") == 0) {
@@ -349,7 +359,7 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
         else if (ncoord == 3)
           fprintf(fp,"# Chunk OrigID Coord1 Coord2 Coord3 Ncount");
       }
-      for (int i = 0; i < nvalues; i++) fprintf(fp," %s",arg[7+i]);
+      for (int i = 0; i < nvalues; i++) fprintf(fp," %s",earg[i]);
       fprintf(fp,"\n");
     }
     if (ferror(fp))
@@ -362,6 +372,15 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
   delete [] title2;
   delete [] title3;
 
+  // if wildcard expansion occurred, free earg memory from expand_args()
+  // wait to do this until after file comment lines are printed
+
+  if (expand) {
+    for (int i = 0; i < nvalues; i++) delete [] earg[i];
+    memory->sfree(earg);
+    arg = arghold;
+  }
+
   // this fix produces a global array
   // size_array_rows is variable and set by allocate()
 

src/fix_ave_correlate.cpp

@@ -56,16 +56,26 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
 
   global_freq = nfreq;
 
+  // expand args if any have wildcard character "*"
+
+  int expand = 0;
+  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
 
-  which = new int[narg-6];
+  which = new int[nargnew];
-  argindex = new int[narg-6];
+  argindex = new int[nargnew];
-  ids = new char*[narg-6];
+  ids = new char*[nargnew];
-  value2index = new int[narg-6];
+  value2index = new int[nargnew];
   nvalues = 0;
 
-  int iarg = 6;
+  int iarg = 0;
-  while (iarg < narg) {
+  while (iarg < nargnew) {
     if (strncmp(arg[iarg],"c_",2) == 0 ||
         strncmp(arg[iarg],"f_",2) == 0 ||
         strncmp(arg[iarg],"v_",2) == 0) {
@@ -107,7 +117,7 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
   char *title2 = NULL;
   char *title3 = NULL;
 
-  while (iarg < narg) {
+  while (iarg < nargnew) {
     if (strcmp(arg[iarg],"type") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command");
       if (strcmp(arg[iarg+1],"auto") == 0) type = AUTO;
@@ -245,27 +255,27 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
       fprintf(fp,"# Index TimeDelta Ncount");
       if (type == AUTO)
         for (int i = 0; i < nvalues; i++)
-          fprintf(fp," %s*%s",arg[6+i],arg[6+i]);
+          fprintf(fp," %s*%s",earg[i],earg[i]);
       else if (type == UPPER)
         for (int i = 0; i < nvalues; i++)
           for (int j = i+1; j < nvalues; j++)
-            fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
+            fprintf(fp," %s*%s",earg[i],earg[j]);
       else if (type == LOWER)
         for (int i = 0; i < nvalues; i++)
           for (int j = 0; j < i-1; j++)
-            fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
+            fprintf(fp," %s*%s",earg[i],earg[j]);
       else if (type == AUTOUPPER)
         for (int i = 0; i < nvalues; i++)
           for (int j = i; j < nvalues; j++)
-            fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
+            fprintf(fp," %s*%s",earg[i],earg[j]);
       else if (type == AUTOLOWER)
         for (int i = 0; i < nvalues; i++)
           for (int j = 0; j < i; j++)
-            fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
+            fprintf(fp," %s*%s",earg[i],earg[j]);
       else if (type == FULL)
         for (int i = 0; i < nvalues; i++)
           for (int j = 0; j < nvalues; j++)
-            fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
+            fprintf(fp," %s*%s",earg[i],earg[j]);
       fprintf(fp,"\n");
     }
     if (ferror(fp))
@@ -278,6 +288,15 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
   delete [] title2;
   delete [] title3;
 
+  // if wildcard expansion occurred, free earg memory from expand_args()
+  // wait to do this until after file comment lines are printed
+
+  if (expand) {
+    for (int i = 0; i < nvalues; i++) delete [] earg[i];
+    memory->sfree(earg);
+    arg = arghold;
+  }
+
   // allocate and initialize memory for averaging
   // set count and corr to zero since they accumulate
   // also set save versions to zero in case accessed via compute_array()

src/fix_ave_histo.cpp

@@ -92,146 +92,108 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
     } else break;
   }
 
-  options(narg,arg);
+  if (nvalues == 0) error->all(FLERR,"No values in fix ave/histo command");
 
-  // parse values until one isn't recognized
+  options(iarg,narg,arg);
-  // if mode = VECTOR and value is a global array:
+
-  //   expand it as if columns listed one by one
+  // expand args if any have wildcard character "*"
-  //   adjust nvalues accordingly via maxvalues
+  // this can reset nvalues
+
+  int expand = 0;
+  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 = argindex = value2index = NULL;
   ids = NULL;
-  int maxvalues = nvalues;
+  allocate_values(nvalues);
-  allocate_values(maxvalues);
-  nvalues = 0;
 
-  iarg = 9;
+  for (int i = 0; i < nvalues; i++) {
-  while (iarg < narg) {
+    if (strcmp(arg[i],"x") == 0) {
-    if (strcmp(arg[iarg],"x") == 0) {
+      which[i] = X;
-      which[nvalues] = X;
+      argindex[i] = 0;
-      argindex[nvalues] = 0;
+      ids[i] = NULL;
-      ids[nvalues] = NULL;
-      nvalues++;
       iarg++;
-    } else if (strcmp(arg[iarg],"y") == 0) {
+    } else if (strcmp(arg[i],"y") == 0) {
-      which[nvalues] = X;
+      which[i] = X;
-      argindex[nvalues] = 1;
+      argindex[i] = 1;
-      ids[nvalues] = NULL;
+      ids[i] = NULL;
-      nvalues++;
       iarg++;
-    } else if (strcmp(arg[iarg],"z") == 0) {
+    } else if (strcmp(arg[i],"z") == 0) {
-      which[nvalues] = X;
+      which[i] = X;
-      argindex[nvalues] = 2;
+      argindex[i] = 2;
-      ids[nvalues] = NULL;
+      ids[i] = NULL;
-      nvalues++;
       iarg++;
 
-    } else if (strcmp(arg[iarg],"vx") == 0) {
+    } else if (strcmp(arg[i],"vx") == 0) {
-      which[nvalues] = V;
+      which[i] = V;
-      argindex[nvalues] = 0;
+      argindex[i] = 0;
-      ids[nvalues] = NULL;
+      ids[i] = NULL;
-      nvalues++;
       iarg++;
-    } else if (strcmp(arg[iarg],"vy") == 0) {
+    } else if (strcmp(arg[i],"vy") == 0) {
-      which[nvalues] = V;
+      which[i] = V;
-      argindex[nvalues] = 1;
+      argindex[i] = 1;
-      ids[nvalues] = NULL;
+      ids[i] = NULL;
-      nvalues++;
       iarg++;
-    } else if (strcmp(arg[iarg],"vz") == 0) {
+    } else if (strcmp(arg[i],"vz") == 0) {
-      which[nvalues] = V;
+      which[i] = V;
-      argindex[nvalues] = 2;
+      argindex[i] = 2;
-      ids[nvalues] = NULL;
+      ids[i] = NULL;
-      nvalues++;
       iarg++;
 
-    } else if (strcmp(arg[iarg],"fx") == 0) {
+    } else if (strcmp(arg[i],"fx") == 0) {
-      which[nvalues] = F;
+      which[i] = F;
-      argindex[nvalues] = 0;
+      argindex[i] = 0;
-      ids[nvalues] = NULL;
+      ids[i] = NULL;
-      nvalues++;
       iarg++;
-    } else if (strcmp(arg[iarg],"fy") == 0) {
+    } else if (strcmp(arg[i],"fy") == 0) {
-      which[nvalues] = F;
+      which[i] = F;
-      argindex[nvalues] = 1;
+      argindex[i] = 1;
-      ids[nvalues] = NULL;
+      ids[i] = NULL;
-      nvalues++;
       iarg++;
-    } else if (strcmp(arg[iarg],"fz") == 0) {
+    } else if (strcmp(arg[i],"fz") == 0) {
-      which[nvalues] = F;
+      which[i] = F;
-      argindex[nvalues] = 2;
+      argindex[i] = 2;
-      ids[nvalues] = NULL;
+      ids[i] = NULL;
-      nvalues++;
       iarg++;
 
-    } else if ((strncmp(arg[iarg],"c_",2) == 0) ||
+    } else if ((strncmp(arg[i],"c_",2) == 0) ||
-        (strncmp(arg[iarg],"f_",2) == 0) ||
+        (strncmp(arg[i],"f_",2) == 0) ||
-        (strncmp(arg[iarg],"v_",2) == 0)) {
+        (strncmp(arg[i],"v_",2) == 0)) {
-      if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
+      if (arg[i][0] == 'c') which[i] = COMPUTE;
-      else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
+      else if (arg[i][0] == 'f') which[i] = FIX;
-      else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
+      else if (arg[i][0] == 'v') which[i] = VARIABLE;
 
-      int n = strlen(arg[iarg]);
+      int n = strlen(arg[i]);
       char *suffix = new char[n];
-      strcpy(suffix,&arg[iarg][2]);
+      strcpy(suffix,&arg[i][2]);
 
       char *ptr = strchr(suffix,'[');
       if (ptr) {
         if (suffix[strlen(suffix)-1] != ']')
           error->all(FLERR,"Illegal fix ave/histo command");
-        argindex[nvalues] = atoi(ptr+1);
+        argindex[i] = atoi(ptr+1);
         *ptr = '\0';
-      } else argindex[nvalues] = 0;
+      } else argindex[i] = 0;
 
       n = strlen(suffix) + 1;
-      ids[nvalues] = new char[n];
+      ids[i] = new char[n];
-      strcpy(ids[nvalues],suffix);
+      strcpy(ids[i],suffix);
       delete [] suffix;
+    }
+  }
 
-      if (mode == VECTOR && which[nvalues] == COMPUTE &&
+  // if wildcard expansion occurred, free earg memory from expand_args()
-          argindex[nvalues] == 0) {
-        int icompute = modify->find_compute(ids[nvalues]);
-        if (icompute < 0)
-          error->all(FLERR,"Compute ID for fix ave/histo does not exist");
-        if (modify->compute[icompute]->array_flag) {
-          int ncols = modify->compute[icompute]->size_array_cols;
-          maxvalues += ncols-1;
-          allocate_values(maxvalues);
-          argindex[nvalues] = 1;
-          for (int icol = 1; icol < ncols; icol++) {
-            which[nvalues+icol] = which[nvalues];
-            argindex[nvalues+icol] = icol+1;
-            n = strlen(ids[nvalues]) + 1;
-            ids[nvalues+icol] = new char[n];
-            strcpy(ids[nvalues+icol],ids[nvalues]);
-          }
-          nvalues += ncols-1;
-        }
 
-      } else if (mode == VECTOR && which[nvalues] == FIX &&
+  if (expand) {
-                 argindex[nvalues] == 0) {
+    for (int i = 0; i < nvalues; i++) delete [] earg[i];
-        int ifix = modify->find_fix(ids[nvalues]);
+    memory->sfree(earg);
-        if (ifix < 0)
+    arg = arghold;
-          error->all(FLERR,"Fix ID for fix ave/histo does not exist");
-        if (modify->fix[ifix]->array_flag) {
-          int ncols = modify->fix[ifix]->size_array_cols;
-          maxvalues += ncols-1;
-          allocate_values(maxvalues);
-          argindex[nvalues] = 1;
-          for (int icol = 1; icol < ncols; icol++) {
-            which[nvalues+icol] = which[nvalues];
-            argindex[nvalues+icol] = icol+1;
-            n = strlen(ids[nvalues]) + 1;
-            ids[nvalues+icol] = new char[n];
-            strcpy(ids[nvalues+icol],ids[nvalues]);
-          }
-          nvalues += ncols-1;
-        }
-      }
-
-      nvalues++;
-      iarg++;
-    } else break;
   }
 
   // setup and error check
@@ -955,7 +917,7 @@ void FixAveHisto::bin_atoms(double *values, int stride)
    parse optional args
 ------------------------------------------------------------------------- */
 
-void FixAveHisto::options(int narg, char **arg)
+void FixAveHisto::options(int iarg, int narg, char **arg)
 {
   // option defaults
 
@@ -971,7 +933,6 @@ void FixAveHisto::options(int narg, char **arg)
 
   // optional args
 
-  int iarg = 9 + nvalues;
   while (iarg < narg) {
     if (strcmp(arg[iarg],"file") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command");

src/fix_ave_histo.h

@@ -65,7 +65,7 @@ class FixAveHisto : public Fix {
   void bin_one(double);
   void bin_vector(int, double *, int);
   void bin_atoms(double *, int);
-  void options(int, char **);
+  void options(int, int, char **);
   void allocate_values(int);
   bigint nextvalid();
 };

src/fix_ave_time.cpp

@@ -288,7 +288,7 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
   delete [] title3;
 
   // if wildcard expansion occurred, free earg memory from expand_args()
-  // wait to do this after file comment lines are printed
+  // wait to do this until after file comment lines are printed
 
   if (expand) {
     for (int i = 0; i < nvalues; i++) delete [] earg[i];