From 560c29a0e1d100679bbaf7c29a16dd4a1015ac32 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Tue, 11 Aug 2020 17:37:46 -0400
Subject: [PATCH] Extends header of new binary format of dump atom

---
 src/dump_atom.cpp    | 45 +++++++++++++++++++++++++++++++++++---------
 src/dump_atom.h      |  9 +++++++++
 tools/binary2txt.cpp | 24 +++++++++++++++--------
 3 files changed, 61 insertions(+), 17 deletions(-)

diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp
index 188dc1676f..4b2ee96b69 100644
--- a/src/dump_atom.cpp
+++ b/src/dump_atom.cpp
@@ -166,13 +166,44 @@ void DumpAtom::write_data(int n, double *mybuf)
 
 /* ---------------------------------------------------------------------- */
 
-void DumpAtom::header_binary(bigint ndump)
+void DumpAtom::format_magic_string_binary()
 {
   // use negative ntimestep as marker for new format
-  bigint fmtlen = strlen("DUMPATOM");
+  bigint fmtlen = strlen(MAGIC_STRING);
   bigint marker = -fmtlen;
-  fwrite(&marker,sizeof(bigint),1,fp);
-  fwrite("DUMPATOM",sizeof(char),fmtlen,fp);
+  fwrite(&marker, sizeof(bigint), 1, fp);
+  fwrite(MAGIC_STRING, sizeof(char), fmtlen, fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpAtom::format_endian_binary()
+{
+  int endian = ENDIAN;
+  fwrite(&endian, sizeof(int), 1, fp);
+}
+/* ---------------------------------------------------------------------- */
+
+void DumpAtom::format_revision_binary()
+{
+  int revision = FORMAT_REVISION;
+  fwrite(&revision, sizeof(int), 1, fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpAtom::header_format_binary()
+{
+  format_magic_string_binary();
+  format_endian_binary();
+  format_revision_binary();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpAtom::header_binary(bigint ndump)
+{
+  header_format_binary();
   fwrite(&update->ntimestep,sizeof(bigint),1,fp);
   fwrite(&ndump,sizeof(bigint),1,fp);
   fwrite(&domain->triclinic,sizeof(int),1,fp);
@@ -197,11 +228,7 @@ void DumpAtom::header_binary(bigint ndump)
 
 void DumpAtom::header_binary_triclinic(bigint ndump)
 {
-  // use negative ntimestep as marker for new format
-  bigint fmtlen = strlen("DUMPATOM");
-  bigint marker = -fmtlen;
-  fwrite(&marker,sizeof(bigint),1,fp);
-  fwrite("DUMPATOM",sizeof(char),fmtlen,fp);
+  header_format_binary();
   fwrite(&update->ntimestep,sizeof(bigint),1,fp);
   fwrite(&ndump,sizeof(bigint),1,fp);
   fwrite(&domain->triclinic,sizeof(int),1,fp);
diff --git a/src/dump_atom.h b/src/dump_atom.h
index ce317fea4f..4431a67bc0 100644
--- a/src/dump_atom.h
+++ b/src/dump_atom.h
@@ -28,6 +28,10 @@ class DumpAtom : public Dump {
  public:
   DumpAtom(LAMMPS *, int, char**);
 
+  const char * MAGIC_STRING = "DUMPATOM";
+  const int    FORMAT_REVISION = 0x0002;
+  const int    ENDIAN = 0x0001;
+
  protected:
   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
@@ -41,6 +45,11 @@ class DumpAtom : public Dump {
   int convert_string(int, double *);
   void write_data(int, double *);
 
+  void header_format_binary();
+  void format_magic_string_binary();
+  void format_endian_binary();
+  void format_revision_binary();
+
   typedef void (DumpAtom::*FnPtrHeader)(bigint);
   FnPtrHeader header_choice;           // ptr to write header functions
   void header_binary(bigint);
diff --git a/tools/binary2txt.cpp b/tools/binary2txt.cpp
index 6e243ccc94..d65e74b0d1 100644
--- a/tools/binary2txt.cpp
+++ b/tools/binary2txt.cpp
@@ -91,13 +91,15 @@ int main(int narg, char **arg)
     delete [] filetxt;
 
     // detect newer format
-    char * formatname = nullptr;
+    char * magic_string = nullptr;
     char * columns = nullptr;
 
 
     // loop over snapshots in file
 
     while (1) {
+      int endian = 0x0001;
+      int revision = 0x0001;
 
       fread(&ntimestep,sizeof(bigint),1,fp);
 
@@ -112,12 +114,18 @@ int main(int narg, char **arg)
       // detect newer format
       if (ntimestep < 0) {
         // first bigint encodes negative format name length
-        bigint formatlen = -ntimestep;
+        bigint magic_string_len = -ntimestep;
 
-        delete [] formatname;
-        formatname = new char[formatlen + 1];
-        fread(formatname, sizeof(char), formatlen, fp);
-        formatname[formatlen] = '\0';
+        delete [] magic_string;
+        magic_string = new char[magic_string_len + 1];
+        fread(magic_string, sizeof(char), magic_string_len, fp);
+        magic_string[magic_string_len] = '\0';
+
+        // read endian flag
+        fread(&endian, sizeof(int), 1, fp);
+
+        // read revision number
+        fread(&revision, sizeof(int), 1, fp);
 
         // read the real ntimestep
         fread(&ntimestep,sizeof(bigint),1,fp);
@@ -139,7 +147,7 @@ int main(int narg, char **arg)
       }
       fread(&size_one,sizeof(int),1,fp);
 
-      if (formatname) {
+      if (magic_string && revision > 0x0001) {
         // newer format includes columns string
         int len = 0;
         fread(&len, sizeof(int), 1, fp);
@@ -220,7 +228,7 @@ int main(int narg, char **arg)
     }
     printf("\n");
     delete [] columns;
-    delete [] formatname;
+    delete [] magic_string;
   }
 
   if (buf) delete [] buf;