git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2648 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/dump.cpp

@@ -135,6 +135,9 @@ void Dump::write()
     boxyhi = domain->boxhi_bound[1];
     boxzlo = domain->boxlo_bound[2];
     boxzhi = domain->boxhi_bound[2];
+    boxxy = domain->xy;
+    boxxz = domain->xz;
+    boxyz = domain->yz;
   }
 
   // nme = # of dump lines this proc will contribute to dump

src/dump.h

@@ -52,8 +52,9 @@ class Dump : protected Pointers {
 
  protected:
   double boxxlo,boxxhi;      // local copies of domain values
-  double boxylo,boxyhi;      // adjusted to be bounding box for triclinic
+  double boxylo,boxyhi;      // lo/hi are bounding box for triclinic
   double boxzlo,boxzhi;
+  double boxxy,boxxz,boxyz;
 
   virtual void openfile();
   virtual int modify_param(int, char **) {return 0;}

src/dump_atom.cpp

@@ -61,10 +61,27 @@ void DumpAtom::init()
     strcat(format,"\n");
   }
 
+  // setup column string
+
+  if (scale_flag == 0 && image_flag == 0)
+    columns = "id type x y z";
+  else if (scale_flag == 0 && image_flag == 1)
+    columns = "id type x y z ix iy iz";
+  else if (scale_flag == 1 && image_flag == 0)
+    columns = "id type xs ys zs";
+  else if (scale_flag == 1 && image_flag == 1)
+    columns = "id type xs ys zs ix iy iz";
+
   // setup function ptrs
 
-  if (binary) header_choice = &DumpAtom::header_binary;
+  if (binary && domain->triclinic == 0)
-  else header_choice = &DumpAtom::header_item;
+    header_choice = &DumpAtom::header_binary;
+  else if (binary && domain->triclinic == 1)
+    header_choice = &DumpAtom::header_binary_triclinic;
+  else if (!binary && domain->triclinic == 0)
+    header_choice = &DumpAtom::header_item;
+  else if (!binary && domain->triclinic == 1)
+    header_choice = &DumpAtom::header_item_triclinic;
 
   if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 0)
     pack_choice = &DumpAtom::pack_scale_noimage;
@@ -146,6 +163,7 @@ void DumpAtom::header_binary(int ndump)
 {
   fwrite(&update->ntimestep,sizeof(int),1,fp);
   fwrite(&ndump,sizeof(int),1,fp);
+  fwrite(&domain->triclinic,sizeof(int),1,fp);
   fwrite(&boxxlo,sizeof(double),1,fp);
   fwrite(&boxxhi,sizeof(double),1,fp);
   fwrite(&boxylo,sizeof(double),1,fp);
@@ -161,6 +179,29 @@ void DumpAtom::header_binary(int ndump)
 
 /* ---------------------------------------------------------------------- */
 
+void DumpAtom::header_binary_triclinic(int ndump)
+{
+  fwrite(&update->ntimestep,sizeof(int),1,fp);
+  fwrite(&ndump,sizeof(int),1,fp);
+  fwrite(&domain->triclinic,sizeof(int),1,fp);
+  fwrite(&boxxlo,sizeof(double),1,fp);
+  fwrite(&boxxhi,sizeof(double),1,fp);
+  fwrite(&boxylo,sizeof(double),1,fp);
+  fwrite(&boxyhi,sizeof(double),1,fp);
+  fwrite(&boxzlo,sizeof(double),1,fp);
+  fwrite(&boxzhi,sizeof(double),1,fp);
+  fwrite(&boxxy,sizeof(double),1,fp);
+  fwrite(&boxxz,sizeof(double),1,fp);
+  fwrite(&boxyz,sizeof(double),1,fp);
+  fwrite(&size_one,sizeof(int),1,fp);
+  if (multiproc) {
+    int one = 1;
+    fwrite(&one,sizeof(int),1,fp);
+  } else fwrite(&nprocs,sizeof(int),1,fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
 void DumpAtom::header_item(int ndump)
 {
   fprintf(fp,"ITEM: TIMESTEP\n");
@@ -171,7 +212,22 @@ void DumpAtom::header_item(int ndump)
   fprintf(fp,"%g %g\n",boxxlo,boxxhi);
   fprintf(fp,"%g %g\n",boxylo,boxyhi);
   fprintf(fp,"%g %g\n",boxzlo,boxzhi);
-  fprintf(fp,"ITEM: ATOMS\n");
+  fprintf(fp,"ITEM: ATOMS %s\n",columns);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpAtom::header_item_triclinic(int ndump)
+{
+  fprintf(fp,"ITEM: TIMESTEP\n");
+  fprintf(fp,"%d\n",update->ntimestep);
+  fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
+  fprintf(fp,"%d\n",ndump);
+  fprintf(fp,"ITEM: BOX BOUNDS xy xz yz\n");
+  fprintf(fp,"%g %g %g\n",boxxlo,boxxhi,boxxy);
+  fprintf(fp,"%g %g %g\n",boxylo,boxyhi,boxxz);
+  fprintf(fp,"%g %g %g\n",boxzlo,boxzhi,boxyz);
+  fprintf(fp,"ITEM: ATOMS %s\n",columns);
 }
 
 /* ---------------------------------------------------------------------- */

src/dump_atom.h

@@ -27,6 +27,8 @@ class DumpAtom : public Dump {
   int scale_flag;            // 1 if atom coords are scaled, 0 if no
   int image_flag;            // 1 if append box count to atom coords, 0 if no
 
+  char *columns;             // column labels
+
   int modify_param(int, char **);
   void write_header(int);
   int count();
@@ -36,7 +38,9 @@ class DumpAtom : public Dump {
   typedef void (DumpAtom::*FnPtrHeader)(int);
   FnPtrHeader header_choice;           // ptr to write header functions
   void header_binary(int);
+  void header_binary_triclinic(int);
   void header_item(int);
+  void header_item_triclinic(int);
 
   typedef int (DumpAtom::*FnPtrPack)();
   FnPtrPack pack_choice;               // ptr to pack functions

src/dump_custom.cpp

@@ -61,7 +61,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
   thresh_op = NULL;
   thresh_value = NULL;
 
-  // compute, fix, variables the dump accesses
+  // computes, fixes, variables which the dump accesses
 
   field2index = (int *) memory->smalloc(nfield*sizeof(int),"dump:field2index");
   argindex = (int *) memory->smalloc(nfield*sizeof(int),"dump:argindex");
@@ -102,6 +102,17 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
     vformat[i] = NULL;
   }
 
+  // setup column string
+
+  int n = 0;
+  for (int iarg = 5; iarg < narg; iarg++) n += strlen(arg[iarg]) + 2;
+  columns = new char[n];
+  columns[0] = '\0';
+  for (int iarg = 5; iarg < narg; iarg++) {
+    strcat(columns,arg[iarg]);
+    strcat(columns," ");
+  }
+
   // one-time file open
 
   if (multifile == 0) openfile();
@@ -140,6 +151,8 @@ DumpCustom::~DumpCustom()
 
   for (int i = 0; i < size_one; i++) delete [] vformat[i];
   delete [] vformat;
+
+  delete [] columns;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -169,8 +182,14 @@ void DumpCustom::init()
 
   // setup function ptrs
 
-  if (binary) header_choice = &DumpCustom::header_binary;
+  if (binary && domain->triclinic == 0)
-  else header_choice = &DumpCustom::header_item;
+    header_choice = &DumpCustom::header_binary;
+  else if (binary && domain->triclinic == 1)
+    header_choice = &DumpCustom::header_binary_triclinic;
+  else if (!binary && domain->triclinic == 0)
+    header_choice = &DumpCustom::header_item;
+  else if (!binary && domain->triclinic == 1)
+    header_choice = &DumpCustom::header_item_triclinic;
 
   if (binary) write_choice = &DumpCustom::write_binary;
   else write_choice = &DumpCustom::write_text;
@@ -215,6 +234,7 @@ void DumpCustom::header_binary(int ndump)
 {
   fwrite(&update->ntimestep,sizeof(int),1,fp);
   fwrite(&ndump,sizeof(int),1,fp);
+  fwrite(&domain->triclinic,sizeof(int),1,fp);
   fwrite(&boxxlo,sizeof(double),1,fp);
   fwrite(&boxxhi,sizeof(double),1,fp);
   fwrite(&boxylo,sizeof(double),1,fp);
@@ -230,6 +250,29 @@ void DumpCustom::header_binary(int ndump)
 
 /* ---------------------------------------------------------------------- */
 
+void DumpCustom::header_binary_triclinic(int ndump)
+{
+  fwrite(&update->ntimestep,sizeof(int),1,fp);
+  fwrite(&ndump,sizeof(int),1,fp);
+  fwrite(&domain->triclinic,sizeof(int),1,fp);
+  fwrite(&boxxlo,sizeof(double),1,fp);
+  fwrite(&boxxhi,sizeof(double),1,fp);
+  fwrite(&boxylo,sizeof(double),1,fp);
+  fwrite(&boxyhi,sizeof(double),1,fp);
+  fwrite(&boxzlo,sizeof(double),1,fp);
+  fwrite(&boxzhi,sizeof(double),1,fp);
+  fwrite(&boxxy,sizeof(double),1,fp);
+  fwrite(&boxxz,sizeof(double),1,fp);
+  fwrite(&boxyz,sizeof(double),1,fp);
+  fwrite(&size_one,sizeof(int),1,fp);
+  if (multiproc) {
+    int one = 1;
+    fwrite(&one,sizeof(int),1,fp);
+  } else fwrite(&nprocs,sizeof(int),1,fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
 void DumpCustom::header_item(int ndump)
 {
   fprintf(fp,"ITEM: TIMESTEP\n");
@@ -240,7 +283,22 @@ void DumpCustom::header_item(int ndump)
   fprintf(fp,"%g %g\n",boxxlo,boxxhi);
   fprintf(fp,"%g %g\n",boxylo,boxyhi);
   fprintf(fp,"%g %g\n",boxzlo,boxzhi);
-  fprintf(fp,"ITEM: ATOMS\n");
+  fprintf(fp,"ITEM: ATOMS %s\n",columns);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpCustom::header_item_triclinic(int ndump)
+{
+  fprintf(fp,"ITEM: TIMESTEP\n");
+  fprintf(fp,"%d\n",update->ntimestep);
+  fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
+  fprintf(fp,"%d\n",ndump);
+  fprintf(fp,"ITEM: BOX BOUNDS xy xz yz\n");
+  fprintf(fp,"%g %g %g\n",boxxlo,boxxhi,boxxy);
+  fprintf(fp,"%g %g %g\n",boxylo,boxyhi,boxxz);
+  fprintf(fp,"%g %g %g\n",boxzlo,boxzhi,boxyz);
+  fprintf(fp,"ITEM: ATOMS %s\n",columns);
 }
 
 /* ---------------------------------------------------------------------- */

src/dump_custom.h

@@ -37,6 +37,8 @@ class DumpCustom : public Dump {
   int *vtype;                // type of each vector (INT, DOUBLE)
   char **vformat;            // format string for each vector element
 
+  char *columns;             // column labels
+
   int maxlocal;              // size of atom selection and variable arrays
   int *choose;               // 1 if output this atom, 0 if no
   double *dchoose;           // value for each atom to threshhold against
@@ -76,7 +78,9 @@ class DumpCustom : public Dump {
   typedef void (DumpCustom::*FnPtrHeader)(int);
   FnPtrHeader header_choice;           // ptr to write header functions
   void header_binary(int);
+  void header_binary_triclinic(int);
   void header_item(int);
+  void header_item_triclinic(int);
 
   typedef void (DumpCustom::*FnPtrData)(int, double *);
   FnPtrData write_choice;              // ptr to write data functions

src/group.cpp

@@ -84,7 +84,7 @@ void Group::assign(int narg, char **arg)
   if (narg < 2) error->all("Illegal group command");
 
   // find group in existing list
-  // igroup = -1 is a new group name, add it
+  // igroup = -1 requires a new group, add it
 
   int igroup = find(arg[0]);
 
@@ -329,7 +329,7 @@ void Group::create(char *name, int *flag)
   int i;
 
   // find group in existing list
-  // igroup = -1 is a new group name, add it
+  // igroup = -1 requires a new group, add it
 
   int igroup = find(name);