git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8159 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/dump_xyz.cpp

@@ -17,6 +17,7 @@
 #include "group.h"
 #include "error.h"
 #include "memory.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 
@@ -31,10 +32,30 @@ DumpXYZ::DumpXYZ(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
   sort_flag = 1;
   sortcol = 0;
 
-  char *str = (char *) "%d %g %g %g";
+  if (format_default) delete [] format_default;
+
+  char *str = (char *) "%s %g %g %g";
   int n = strlen(str) + 1;
   format_default = new char[n];
   strcpy(format_default,str);
+
+  ntypes = atom->ntypes;
+  typenames = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+DumpXYZ::~DumpXYZ()
+{
+  delete[] format_default;
+  format_default = NULL;
+
+  if (typenames) {
+    for (int i = 1; i <= ntypes; i++)
+      delete [] typenames[i];
+    delete [] typenames;
+    typenames = NULL;
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -51,6 +72,17 @@ void DumpXYZ::init_style()
   strcpy(format,str);
   strcat(format,"\n");
 
+  // initialize typenames array to be backward compatible by default
+  // a 32-bit int can be maximally 10 digits plus sign
+
+  if (typenames == NULL) {
+    typenames = new char*[ntypes+1];
+    for (int itype = 1; itype <= ntypes; itype++) {
+      typenames[itype] = new char[12];
+      sprintf(typenames[itype],"%d",itype);
+    }
+  }
+
   // open single file, one time only
 
   if (multifile == 0) openfile();
@@ -58,31 +90,45 @@ void DumpXYZ::init_style()
 
 /* ---------------------------------------------------------------------- */
 
+int DumpXYZ::modify_param(int narg, char **arg)
+{
+  if (strcmp(arg[0],"element") == 0) {
+    if (narg < ntypes+1)
+      error->all(FLERR, "Dump modify element names do not match atom types");
+
+    if (typenames) {
+      for (int i = 1; i <= ntypes; i++)
+	delete [] typenames[i];
+
+      delete [] typenames;
+      typenames = NULL;
+    }
+
+    typenames = new char*[ntypes+1];
+    for (int itype = 1; itype <= ntypes; itype++) {
+      int n = strlen(arg[itype]) + 1;
+      typenames[itype] = new char[n];
+      strcpy(typenames[itype],arg[itype]);
+    }
+
+    return ntypes+1;
+  }
+
+  return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
 void DumpXYZ::write_header(bigint n)
 {
   if (me == 0) {
     fprintf(fp,BIGINT_FORMAT "\n",n);
-    fprintf(fp,"Atoms\n");
+    fprintf(fp,"Atoms. Timestep: " BIGINT_FORMAT "\n",update->ntimestep);
   }
 }
 
 /* ---------------------------------------------------------------------- */
 
-int DumpXYZ::count()
-{
-  if (igroup == 0) return atom->nlocal;
-
-  int *mask = atom->mask;
-  int nlocal = atom->nlocal;
-
-  int m = 0;
-  for (int i = 0; i < nlocal; i++)
-    if (mask[i] & groupbit) m++;
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
 void DumpXYZ::pack(int *ids)
 {
   int m,n;
@@ -112,7 +158,8 @@ void DumpXYZ::write_data(int n, double *mybuf)
   int m = 0;
   for (int i = 0; i < n; i++) {
     fprintf(fp,format,
-	    static_cast<int> (mybuf[m+1]),mybuf[m+2],mybuf[m+3],mybuf[m+4]);
+	    typenames[static_cast<int> (mybuf[m+1])],
+	    mybuf[m+2],mybuf[m+3],mybuf[m+4]);
     m += size_one;
   }
 }