git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6253 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/dump.h

@@ -87,7 +87,6 @@ class Dump : protected Pointers {
   double *bufsort;
   int *idsort,*index,*proclist;
 
-
   class Irregular *irregular;
 
   virtual void init_style() = 0;

src/dump_cfg.cpp

@@ -45,8 +45,7 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
       strcmp(arg[5],"id") != 0 || strcmp(arg[6],"type") != 0 ||
       (strcmp(arg[7],"xs") != 0 && strcmp(arg[7],"xsu") != 0) || 
       (strcmp(arg[8],"ys") != 0 && strcmp(arg[8],"ysu") != 0) ||
-      (strcmp(arg[9],"zs") != 0 && strcmp(arg[9],"zsu") != 0)
-      )
+      (strcmp(arg[9],"zs") != 0 && strcmp(arg[9],"zsu") != 0))
     error->all("Dump cfg arguments must start with "
 	       "'id type xs ys zs' or 'id type xsu ysu zsu'");
 
@@ -120,71 +119,7 @@ void DumpCFG::init_style()
 {
   if (multifile == 0) error->all("Dump cfg requires one snapshot per file");
 
-  // setup format strings
-
-  delete [] format;
-  char *str;
-  if (format_user) str = format_user;
-  else str = format_default;
-
-  int n = strlen(str) + 1;
-  format = new char[n];
-  strcpy(format,str);
-
-  // default for element names = C
-
-  if (typenames == NULL) {
-    typenames = new char*[ntypes+1];
-    for (int itype = 1; itype <= ntypes; itype++) {
-      typenames[itype] = new char[2];
-      strcpy(typenames[itype],"C");
-    }
-  }
-
-  // tokenize the format string and add space at end of each format element
-
-  char *ptr;
-  for (int i = 0; i < size_one; i++) {
-    if (i == 0) ptr = strtok(format," \0");
-    else ptr = strtok(NULL," \0");
-    delete [] vformat[i];
-    vformat[i] = new char[strlen(ptr) + 2];
-    strcpy(vformat[i],ptr);
-    vformat[i] = strcat(vformat[i]," ");
-  }
-
-  // find current ptr for each compute,fix,variable
-  // check that fix frequency is acceptable
-
-  int icompute;
-  for (int i = 0; i < ncompute; i++) {
-    icompute = modify->find_compute(id_compute[i]);
-    if (icompute < 0) error->all("Could not find dump cfg compute ID");
-    compute[i] = modify->compute[icompute];
-  }
-
-  int ifix;
-  for (int i = 0; i < nfix; i++) {
-    ifix = modify->find_fix(id_fix[i]);
-    if (ifix < 0) error->all("Could not find dump cfg fix ID");
-    fix[i] = modify->fix[ifix];
-    if (nevery % modify->fix[ifix]->peratom_freq)
-      error->all("Dump cfg and fix not computed at compatible times");
-  }
-
-  int ivariable;
-  for (int i = 0; i < nvariable; i++) {
-    ivariable = input->variable->find(id_variable[i]);
-    if (ivariable < 0) error->all("Could not find dump cfg variable name");
-    variable[i] = ivariable;
-  }
-
-  // set index and check validity of region
-
-  if (iregion >= 0) {
-    iregion = domain->find_region(idregion);
-    if (iregion == -1) error->all("Region ID for dump cfg does not exist");
-  }
+  DumpCustom::init_style();
 }
 
 /* ---------------------------------------------------------------------- */
@@ -194,8 +129,7 @@ void DumpCFG::write_header(bigint n)
   // special handling for atom style peri
   //   use average volume of particles to scale particles to mimic C atoms
   //   scale box dimension to sc lattice for C with sigma = 1.44 Angstroms  
-
-  // Special handling for unwrapped coordinates
+  // special handling for unwrapped coordinates
 
   double scale;
   if (atom->peri_flag) {
@@ -254,8 +188,6 @@ void DumpCFG::write_data(int n, double *mybuf)
 
   double *rmass = atom->rmass;
   double *mass = atom->mass;
-  int *type = atom->type;
-  int nlocal = atom->nlocal;
 
   // transfer data from buf to rbuf
   // if write by proc 0, transfer chunk by chunk

src/dump_custom.h

@@ -44,11 +44,13 @@ class DumpCustom : public Dump {
 
   char *columns;             // column labels
 
+  int nchoose;               // # of selected atoms
   int maxlocal;              // size of atom selection and variable arrays
-  int *choose;               // 1 if output this atom, 0 if no
+  int *choose;               // local indices of selected atoms
   double *dchoose;           // value for each atom to threshhold against
 
   int nfield;                // # of keywords listed by user
+  int ioptional;             // index of start of optional args
 
   int *field2index;          // which compute,fix,variable calcs this field
   int *argindex;             // index into compute,fix scalar_atom,vector_atom
@@ -79,12 +81,11 @@ class DumpCustom : public Dump {
   virtual void write_data(int, double *);
   bigint memory_usage();
 
-  void parse_fields(int, char **);
+  int parse_fields(int, char **);
   int add_compute(char *);
   int add_fix(char *);
   int add_variable(char *);
-  int modify_param(int, char **);
-  virtual int modify_param2(int, char **) {return 0;}
+  virtual int modify_param(int, char **);
 
   typedef void (DumpCustom::*FnPtrHeader)(bigint);
   FnPtrHeader header_choice;           // ptr to write header functions