Merge pull request #1672 from akohlmey/dump-with-unit

Add ITEM: UNITS line to native text format dumps

doc/src/dump.txt

@@ -21,7 +21,8 @@ dump ID group-ID style N file args :pre
 
 ID = user-assigned name for the dump :ulb,l
 group-ID = ID of the group of atoms to be dumped :l
-style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
+style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or
+{cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {local/gz} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
 N = dump every this many timesteps :l
 file = name of file to write dump info to :l
 args = list of arguments for a particular style :l

doc/src/dump_modify.txt

@@ -50,6 +50,7 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
   {sfactor} arg = coordinate scaling factor (> 0.0)
   {thermo} arg = {yes} or {no}
   {tfactor} arg = time scaling factor (> 0.0)
+  {units} arg = {yes} or {no}
   {sort} arg = {off} or {id} or N or -N
      off = no sorting of per-atom lines within a snapshot
      id = sort per-atom lines by atom ID
@@ -620,6 +621,21 @@ threshold criterion is met.  Otherwise it is not met.
 
 :line
 
+The {units} keyword only applies to the dump {atom}, {custom}, and
+{local} styles (and their COMPRESS package versions {atom/gz},
+{custom/gz} and {local/gz}). If set to {yes}, each individual dump
+file will contain two extra lines at the very beginning with:
+
+ITEM: UNITS
+\<units style\> :pre
+
+This will output the current selected "units"_units.html style
+to the dump file and thus allows visualization and post-processing
+tools to determine the choice of units of the data in the dump file.
+The default setting is {no}.
+
+:line
+
 The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles.
 If set to {yes}, coordinates will be written "unwrapped" by the image
 flags for each atom.  Unwrapped means that if the atom has passed through
@@ -924,6 +940,7 @@ scale = yes
 sort = off for dump styles {atom}, {custom}, {cfg}, and {local}
 sort = id for dump styles {dcd}, {xtc}, and {xyz}
 thresh = none
+units = no
 unwrap = no :ul
 
 acolor = * red/green/blue/yellow/aqua/cyan

src/COMPRESS/dump_atom_gz.cpp

@@ -108,27 +108,26 @@ void DumpAtomGZ::openfile()
 void DumpAtomGZ::write_header(bigint ndump)
 {
   if ((multiproc) || (!multiproc && me == 0)) {
+    if (unit_flag && !unit_count) {
+      ++unit_count;
+      gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);
+    }
+    gzprintf(gzFp,"ITEM: TIMESTEP\n");
+    gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
+    gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
+    gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
     if (domain->triclinic == 0) {
-      gzprintf(gzFp,"ITEM: TIMESTEP\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
-      gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
       gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
       gzprintf(gzFp,"%g %g\n",boxxlo,boxxhi);
       gzprintf(gzFp,"%g %g\n",boxylo,boxyhi);
       gzprintf(gzFp,"%g %g\n",boxzlo,boxzhi);
-      gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
     } else {
-      gzprintf(gzFp,"ITEM: TIMESTEP\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
-      gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
       gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
       gzprintf(gzFp,"%g %g %g\n",boxxlo,boxxhi,boxxy);
       gzprintf(gzFp,"%g %g %g\n",boxylo,boxyhi,boxxz);
       gzprintf(gzFp,"%g %g %g\n",boxzlo,boxzhi,boxyz);
-      gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
     }
+    gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
   }
 }
 

src/COMPRESS/dump_custom_gz.cpp

@@ -108,27 +108,26 @@ void DumpCustomGZ::openfile()
 void DumpCustomGZ::write_header(bigint ndump)
 {
   if ((multiproc) || (!multiproc && me == 0)) {
+    if (unit_flag && !unit_count) {
+      ++unit_count;
+      gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);
+    }
+    gzprintf(gzFp,"ITEM: TIMESTEP\n");
+    gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
+    gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
+    gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
     if (domain->triclinic == 0) {
-      gzprintf(gzFp,"ITEM: TIMESTEP\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
-      gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
       gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
       gzprintf(gzFp,"%-1.16g %-1.16g\n",boxxlo,boxxhi);
       gzprintf(gzFp,"%-1.16g %-1.16g\n",boxylo,boxyhi);
       gzprintf(gzFp,"%-1.16g %-1.16g\n",boxzlo,boxzhi);
-      gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
     } else {
-      gzprintf(gzFp,"ITEM: TIMESTEP\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
-      gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
       gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
       gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy);
       gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz);
       gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz);
-      gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
     }
+    gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
   }
 }
 

src/COMPRESS/dump_local_gz.cpp

@@ -0,0 +1,171 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "dump_local_gz.h"
+#include "domain.h"
+#include "error.h"
+#include "update.h"
+
+#include <cstring>
+
+using namespace LAMMPS_NS;
+
+DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) :
+  DumpLocal(lmp, narg, arg)
+{
+  gzFp = NULL;
+
+  if (!compressed)
+    error->all(FLERR,"Dump local/gz only writes compressed files");
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+DumpLocalGZ::~DumpLocalGZ()
+{
+  if (gzFp) gzclose(gzFp);
+  gzFp = NULL;
+  fp = NULL;
+}
+
+
+/* ----------------------------------------------------------------------
+   generic opening of a dump file
+   ASCII or binary or gzipped
+   some derived classes override this function
+------------------------------------------------------------------------- */
+
+void DumpLocalGZ::openfile()
+{
+  // single file, already opened, so just return
+
+  if (singlefile_opened) return;
+  if (multifile == 0) singlefile_opened = 1;
+
+  // if one file per timestep, replace '*' with current timestep
+
+  char *filecurrent = filename;
+  if (multiproc) filecurrent = multiname;
+
+  if (multifile) {
+    char *filestar = filecurrent;
+    filecurrent = new char[strlen(filestar) + 16];
+    char *ptr = strchr(filestar,'*');
+    *ptr = '\0';
+    if (padflag == 0)
+      sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
+              filestar,update->ntimestep,ptr+1);
+    else {
+      char bif[8],pad[16];
+      strcpy(bif,BIGINT_FORMAT);
+      sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
+      sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
+    }
+    *ptr = '*';
+    if (maxfiles > 0) {
+      if (numfiles < maxfiles) {
+        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[numfiles],filecurrent);
+        ++numfiles;
+      } else {
+        remove(nameslist[fileidx]);
+        delete[] nameslist[fileidx];
+        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[fileidx],filecurrent);
+        fileidx = (fileidx + 1) % maxfiles;
+      }
+    }
+  }
+
+  // each proc with filewriter = 1 opens a file
+
+  if (filewriter) {
+    if (append_flag) {
+      gzFp = gzopen(filecurrent,"ab9");
+    } else {
+      gzFp = gzopen(filecurrent,"wb9");
+    }
+
+    if (gzFp == NULL) error->one(FLERR,"Cannot open dump file");
+  } else gzFp = NULL;
+
+  // delete string with timestep replaced
+
+  if (multifile) delete [] filecurrent;
+}
+
+void DumpLocalGZ::write_header(bigint ndump)
+{
+  if ((multiproc) || (!multiproc && me == 0)) {
+    if (unit_flag && !unit_count) {
+      ++unit_count;
+      gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);
+    }
+    gzprintf(gzFp,"ITEM: TIMESTEP\n");
+    gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
+    gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
+    gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
+    if (domain->triclinic == 0) {
+      gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
+      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxxlo,boxxhi);
+      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxylo,boxyhi);
+      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxzlo,boxzhi);
+    } else {
+      gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
+      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy);
+      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz);
+      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz);
+    }
+    gzprintf(gzFp,"ITEM: %s %s\n",label,columns);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpLocalGZ::write_data(int n, double *mybuf)
+{
+  if (buffer_flag == 1) {
+    gzwrite(gzFp,mybuf,sizeof(char)*n);
+
+  } else {
+    int i,j;
+    int m = 0;
+    for (i = 0; i < n; i++) {
+      for (j = 0; j < size_one; j++) {
+        if (vtype[j] == INT)
+          gzprintf(gzFp,vformat[j],static_cast<int> (mybuf[m]));
+        else gzprintf(gzFp,vformat[j],mybuf[m]);
+        m++;
+      }
+      gzprintf(gzFp,"\n");
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpLocalGZ::write()
+{
+  DumpLocal::write();
+  if (filewriter) {
+    if (multifile) {
+      gzclose(gzFp);
+      gzFp = NULL;
+    } else {
+      if (flush_flag)
+        gzflush(gzFp,Z_SYNC_FLUSH);
+    }
+  }
+}
+

src/COMPRESS/dump_local_gz.h

@@ -0,0 +1,57 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef DUMP_CLASS
+
+DumpStyle(local/gz,DumpLocalGZ)
+
+#else
+
+#ifndef LMP_DUMP_LOCAL_GZ_H
+#define LMP_DUMP_LOCAL_GZ_H
+
+#include "dump_local.h"
+#include <zlib.h>
+
+namespace LAMMPS_NS {
+
+class DumpLocalGZ : public DumpLocal {
+ public:
+  DumpLocalGZ(class LAMMPS *, int, char **);
+  virtual ~DumpLocalGZ();
+
+ protected:
+  gzFile gzFp;  // file pointer for the compressed output stream
+
+  virtual void openfile();
+  virtual void write_header(bigint);
+  virtual void write_data(int, double *);
+  virtual void write();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Dump local/gz only writes compressed files
+
+The dump local/gz output file name must have a .gz suffix.
+
+E: Cannot open dump file
+
+Self-explanatory.
+
+*/

src/dump.cpp

@@ -87,6 +87,8 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   buffer_flag = 0;
   padflag = 0;
   pbcflag = 0;
+  unit_flag = 0;
+  unit_count = 0;
   delay_flag = 0;
 
   maxfiles = -1;
@@ -545,6 +547,8 @@ void Dump::openfile()
   if (singlefile_opened) return;
   if (multifile == 0) singlefile_opened = 1;
 
+  unit_count = 0;
+
   // if one file per timestep, replace '*' with current timestep
 
   char *filecurrent = filename;
@@ -1119,6 +1123,13 @@ void Dump::modify_params(int narg, char **arg)
       }
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"units") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
+      if (strcmp(arg[iarg+1],"yes") == 0) unit_flag = 1;
+      else if (strcmp(arg[iarg+1],"no") == 0) unit_flag = 0;
+      else error->all(FLERR,"Illegal dump_modify command");
+      iarg += 2;
+
     } else {
       int n = modify_param(narg-iarg,&arg[iarg]);
       if (n == 0) error->all(FLERR,"Illegal dump_modify command");

src/dump.h

@@ -75,6 +75,8 @@ class Dump : protected Pointers {
   int sortcol;               // 0 to sort on ID, 1-N on columns
   int sortcolm1;             // sortcol - 1
   int sortorder;             // ASCEND or DESCEND
+  int unit_flag;             // 1 if dump should contain unit information
+  int unit_count;            // # of times the unit information was written
   int delay_flag;            // 1 if delay output until delaystep
   bigint delaystep;
 

src/dump_atom.cpp

@@ -209,6 +209,10 @@ void DumpAtom::header_binary_triclinic(bigint ndump)
 
 void DumpAtom::header_item(bigint ndump)
 {
+  if (unit_flag && !unit_count) {
+    ++unit_count;
+    fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
+  }
   fprintf(fp,"ITEM: TIMESTEP\n");
   fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
   fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
@@ -224,6 +228,10 @@ void DumpAtom::header_item(bigint ndump)
 
 void DumpAtom::header_item_triclinic(bigint ndump)
 {
+  if (unit_flag && !unit_count) {
+    ++unit_count;
+    fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
+  }
   fprintf(fp,"ITEM: TIMESTEP\n");
   fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
   fprintf(fp,"ITEM: NUMBER OF ATOMS\n");

src/dump_custom.cpp

@@ -420,6 +420,10 @@ void DumpCustom::header_binary_triclinic(bigint ndump)
 
 void DumpCustom::header_item(bigint ndump)
 {
+  if (unit_flag && !unit_count) {
+    ++unit_count;
+    fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
+  }
   fprintf(fp,"ITEM: TIMESTEP\n");
   fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
   fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
@@ -435,6 +439,10 @@ void DumpCustom::header_item(bigint ndump)
 
 void DumpCustom::header_item_triclinic(bigint ndump)
 {
+  if (unit_flag && !unit_count) {
+    ++unit_count;
+    fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
+  }
   fprintf(fp,"ITEM: TIMESTEP\n");
   fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
   fprintf(fp,"ITEM: NUMBER OF ATOMS\n");

src/dump_local.cpp

@@ -256,6 +256,10 @@ int DumpLocal::modify_param(int narg, char **arg)
 void DumpLocal::write_header(bigint ndump)
 {
   if (me == 0) {
+    if (unit_flag && !unit_count) {
+      ++unit_count;
+      fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
+    }
     fprintf(fp,"ITEM: TIMESTEP\n");
     fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
     fprintf(fp,"ITEM: NUMBER OF %s\n",label);

src/dump_local.h

@@ -29,7 +29,7 @@ class DumpLocal : public Dump {
   DumpLocal(LAMMPS *, int, char **);
   virtual ~DumpLocal();
 
- private:
+ protected:
   int nevery;                // dump frequency to check Fix against
   char *label;               // string for dump file header
 
@@ -55,11 +55,11 @@ class DumpLocal : public Dump {
 
   void init_style();
   int modify_param(int, char **);
-  void write_header(bigint);
+  virtual void write_header(bigint);
   int count();
   void pack(tagint *);
   int convert_string(int, double *);
-  void write_data(int, double *);
+  virtual void write_data(int, double *);
 
   void parse_fields(int, char **);
   int add_compute(char *);

src/reader_native.cpp

@@ -56,12 +56,19 @@ int ReaderNative::read_time(bigint &ntimestep)
   char *eof = fgets(line,MAXLINE,fp);
   if (eof == NULL) return 1;
 
+  // skip over unit information, if present.
+
+  if (strstr(line,"ITEM: UNITS") == line)
+    read_lines(2);
+
   if (strstr(line,"ITEM: TIMESTEP") != line)
     error->one(FLERR,"Dump file is incorrectly formatted");
+
   read_lines(1);
   int rv = sscanf(line,BIGINT_FORMAT,&ntimestep);
   if (rv != 1)
     error->one(FLERR,"Dump file is incorrectly formatted");
+
   return 0;
 }
 

tools/binary2txt.cpp

@@ -99,9 +99,9 @@ int main(int narg, char **arg)
       // detect end-of-file
 
       if (feof(fp)) {
-	fclose(fp);
+        fclose(fp);
-	fclose(fptxt);
+        fclose(fptxt);
-	break;
+        break;
       }
 
       fread(&natoms,sizeof(bigint),1,fp);
@@ -114,13 +114,13 @@ int main(int narg, char **arg)
       fread(&zlo,sizeof(double),1,fp);
       fread(&zhi,sizeof(double),1,fp);
       if (triclinic) {
-	fread(&xy,sizeof(double),1,fp);
+        fread(&xy,sizeof(double),1,fp);
-	fread(&xz,sizeof(double),1,fp);
+        fread(&xz,sizeof(double),1,fp);
-	fread(&yz,sizeof(double),1,fp);
+        fread(&yz,sizeof(double),1,fp);
       }
       fread(&size_one,sizeof(int),1,fp);
       fread(&nchunk,sizeof(int),1,fp);
-      
+
       fprintf(fptxt,"ITEM: TIMESTEP\n");
       fprintf(fptxt,BIGINT_FORMAT "\n",ntimestep);
       fprintf(fptxt,"ITEM: NUMBER OF ATOMS\n");
@@ -128,26 +128,26 @@ int main(int narg, char **arg)
 
       m = 0;
       for (int idim = 0; idim < 3; idim++) {
-	for (int iside = 0; iside < 2; iside++) {
+        for (int iside = 0; iside < 2; iside++) {
-	  if (boundary[idim][iside] == 0) boundstr[m++] = 'p';
+          if (boundary[idim][iside] == 0) boundstr[m++] = 'p';
-	  else if (boundary[idim][iside] == 1) boundstr[m++] = 'f';
+          else if (boundary[idim][iside] == 1) boundstr[m++] = 'f';
-	  else if (boundary[idim][iside] == 2) boundstr[m++] = 's';
+          else if (boundary[idim][iside] == 2) boundstr[m++] = 's';
-	  else if (boundary[idim][iside] == 3) boundstr[m++] = 'm';
+          else if (boundary[idim][iside] == 3) boundstr[m++] = 'm';
-	}
+        }
-	boundstr[m++] = ' ';
+        boundstr[m++] = ' ';
       }
       boundstr[8] = '\0';
-      
+
       if (!triclinic) {
-	fprintf(fptxt,"ITEM: BOX BOUNDS %s\n",boundstr);
+        fprintf(fptxt,"ITEM: BOX BOUNDS %s\n",boundstr);
-	fprintf(fptxt,"%g %g\n",xlo,xhi);
+        fprintf(fptxt,"%g %g\n",xlo,xhi);
-	fprintf(fptxt,"%g %g\n",ylo,yhi);
+        fprintf(fptxt,"%g %g\n",ylo,yhi);
-	fprintf(fptxt,"%g %g\n",zlo,zhi);
+        fprintf(fptxt,"%g %g\n",zlo,zhi);
       } else {
-	fprintf(fptxt,"ITEM: BOX BOUNDS %s xy xz yz\n",boundstr);
+        fprintf(fptxt,"ITEM: BOX BOUNDS %s xy xz yz\n",boundstr);
-	fprintf(fptxt,"%g %g %g\n",xlo,xhi,xy);
+        fprintf(fptxt,"%g %g %g\n",xlo,xhi,xy);
-	fprintf(fptxt,"%g %g %g\n",ylo,yhi,xz);
+        fprintf(fptxt,"%g %g %g\n",ylo,yhi,xz);
-	fprintf(fptxt,"%g %g %g\n",zlo,zhi,yz);
+        fprintf(fptxt,"%g %g %g\n",zlo,zhi,yz);
       }
       fprintf(fptxt,"ITEM: ATOMS\n");
 
@@ -156,25 +156,25 @@ int main(int narg, char **arg)
       // loop over processor chunks in file
 
       for (i = 0; i < nchunk; i++) {
-	fread(&n,sizeof(int),1,fp);
+        fread(&n,sizeof(int),1,fp);
 
-	// extend buffer to fit chunk size
+        // extend buffer to fit chunk size
-	
-	if (n > maxbuf) {
-	  if (buf) delete [] buf;
-	  buf = new double[n];
-	  maxbuf = n;
-	}
 
-	// read chunk and write as size_one values per line
+        if (n > maxbuf) {
+          if (buf) delete [] buf;
+          buf = new double[n];
+          maxbuf = n;
+        }
 
-	fread(buf,sizeof(double),n,fp);
+        // read chunk and write as size_one values per line
-	n /= size_one;
+
-	m = 0;
+        fread(buf,sizeof(double),n,fp);
-	for (j = 0; j < n; j++) {
+        n /= size_one;
-	  for (k = 0; k < size_one; k++) fprintf(fptxt,"%g ",buf[m++]);
+        m = 0;
-	  fprintf(fptxt,"\n");
+        for (j = 0; j < n; j++) {
-	}
+          for (k = 0; k < size_one; k++) fprintf(fptxt,"%g ",buf[m++]);
+          fprintf(fptxt,"\n");
+        }
       }
 
       printf(" " BIGINT_FORMAT,ntimestep);