Add optional TIME to binary dump atom format

src/dump_atom.cpp

@@ -217,6 +217,19 @@ void DumpAtom::header_columns_binary()
 
 /* ---------------------------------------------------------------------- */
 
+void DumpAtom::header_time_binary()
+{
+  char flag = time_flag ? 1 : 0;
+  fwrite(&flag, sizeof(char), 1, fp);
+
+  if (time_flag) {
+    double t = compute_time();
+    fwrite(&t, sizeof(double), 1, fp);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
 void DumpAtom::header_format_binary()
 {
   format_magic_string_binary();
@@ -243,6 +256,7 @@ void DumpAtom::header_binary(bigint ndump)
   fwrite(&size_one,sizeof(int),1,fp);
 
   header_unit_style_binary();
+  header_time_binary();
   header_columns_binary();
 
   if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);
@@ -271,6 +285,7 @@ void DumpAtom::header_binary_triclinic(bigint ndump)
   fwrite(&size_one,sizeof(int),1,fp);
 
   header_unit_style_binary();
+  header_time_binary();
   header_columns_binary();
 
   if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);

src/dump_atom.h

@@ -47,6 +47,7 @@ class DumpAtom : public Dump {
 
   void header_format_binary();
   void header_unit_style_binary();
+  void header_time_binary();
   void header_columns_binary();
   void format_magic_string_binary();
   void format_endian_binary();

tools/binary2txt.cpp

@@ -148,7 +148,8 @@ int main(int narg, char **arg)
       fread(&size_one,sizeof(int),1,fp);
 
       if (magic_string && revision > 0x0001) {
-        // newer format includes units and columns string
+        // newer format includes units string, columns string
+        // and time
         int len = 0;
         fread(&len, sizeof(int), 1, fp);
 
@@ -162,6 +163,15 @@ int main(int narg, char **arg)
           fprintf(fptxt, "%s\n", unit_style);
         }
 
+        char flag = 0;
+        fread(&flag, sizeof(char), 1, fp);
+
+        if (flag) {
+          double time;
+          fread(&time, sizeof(double), 1, fp);
+          fprintf(fptxt, "ITEM: TIME\n%.16g\n", time);
+        }
+
         fread(&len, sizeof(int), 1, fp);
         delete [] columns;
         columns = new char[len+1];

unittest/formats/test_dump_atom.cpp

@@ -267,6 +267,25 @@ TEST_F(DumpAtomTest, with_units_run0)
     delete_file("dump_with_units_run0.melt");
 }
 
+TEST_F(DumpAtomTest, with_time_run0)
+{
+    if (!verbose) ::testing::internal::CaptureStdout();
+    command("dump id all atom 1 dump_with_time_run0.melt");
+    command("dump_modify id scale no time yes");
+    command("run 0");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    ASSERT_FILE_EXISTS("dump_with_time_run0.melt");
+
+    auto lines = read_lines("dump_with_time_run0.melt");
+    ASSERT_EQ(lines.size(), 43);
+    ASSERT_STREQ(lines[0].c_str(), "ITEM: TIME");
+    ASSERT_STREQ(lines[10].c_str(), "ITEM: ATOMS id type x y z");
+    ASSERT_EQ(utils::split_words(lines[11]).size(), 5);
+
+    delete_file("dump_with_time_run0.melt");
+}
+
 TEST_F(DumpAtomTest, with_units_run1)
 {
     if (!verbose) ::testing::internal::CaptureStdout();
@@ -342,6 +361,61 @@ TEST_F(DumpAtomTest, binary_triclinic_with_units_run0)
     delete_file("dump_binary_tri_with_units_run0.melt.bin.txt");
 }
 
+TEST_F(DumpAtomTest, binary_with_time_run0)
+{
+    if(!BINARY2TXT_BINARY) GTEST_SKIP();
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    command("dump id0 all atom 1 dump_text_with_time_run0.melt");
+    command("dump id1 all atom 1 dump_binary_with_time_run0.melt.bin");
+    command("dump_modify id0 scale no time yes");
+    command("dump_modify id1 scale no time yes");
+    command("run 0");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    ASSERT_FILE_EXISTS("dump_text_with_time_run0.melt");
+    ASSERT_FILE_EXISTS("dump_binary_with_time_run0.melt.bin");
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    std::string cmdline = fmt::format("{} dump_binary_with_time_run0.melt.bin", BINARY2TXT_BINARY);
+    system(cmdline.c_str());
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    ASSERT_FILE_EXISTS("dump_binary_with_time_run0.melt.bin.txt");
+    ASSERT_FILE_EQUAL("dump_text_with_time_run0.melt", "dump_binary_with_time_run0.melt.bin.txt");
+    delete_file("dump_text_with_time_run0.melt");
+    delete_file("dump_binary_with_time_run0.melt.bin");
+    delete_file("dump_binary_with_time_run0.melt.bin.txt");
+}
+
+TEST_F(DumpAtomTest, binary_triclinic_with_time_run0)
+{
+    if(!BINARY2TXT_BINARY) GTEST_SKIP();
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    command("change_box all triclinic");
+    command("dump id0 all atom 1 dump_text_tri_with_time_run0.melt");
+    command("dump id1 all atom 1 dump_binary_tri_with_time_run0.melt.bin");
+    command("dump_modify id0 scale no time yes");
+    command("dump_modify id1 scale no time yes");
+    command("run 0");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    ASSERT_FILE_EXISTS("dump_text_tri_with_time_run0.melt");
+    ASSERT_FILE_EXISTS("dump_binary_tri_with_time_run0.melt.bin");
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    std::string cmdline = fmt::format("{} dump_binary_tri_with_time_run0.melt.bin", BINARY2TXT_BINARY);
+    system(cmdline.c_str());
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    ASSERT_FILE_EXISTS("dump_binary_tri_with_time_run0.melt.bin.txt");
+    ASSERT_FILE_EQUAL("dump_text_tri_with_time_run0.melt", "dump_binary_tri_with_time_run0.melt.bin.txt");
+    delete_file("dump_text_tri_with_time_run0.melt");
+    delete_file("dump_binary_tri_with_time_run0.melt.bin");
+    delete_file("dump_binary_tri_with_time_run0.melt.bin.txt");
+}
+
 TEST_F(DumpAtomTest, no_buffer_with_scale_and_image_run0)
 {
     if (!verbose) ::testing::internal::CaptureStdout();
@@ -401,6 +475,27 @@ TEST_F(DumpAtomTest, tricilinic_with_units_run0)
     delete_file("dump_triclinic_with_units_run0.melt");
 }
 
+TEST_F(DumpAtomTest, tricilinic_with_time_run0)
+{
+    if (!verbose) ::testing::internal::CaptureStdout();
+
+    command("change_box all triclinic");
+    command("dump id all atom 1 dump_triclinic_with_time_run0.melt");
+    command("dump_modify id time yes");
+    command("run 0");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    ASSERT_FILE_EXISTS("dump_triclinic_with_time_run0.melt");
+
+    auto lines = read_lines("dump_triclinic_with_time_run0.melt");
+    ASSERT_STREQ(lines[0].c_str(), "ITEM: TIME");
+    ASSERT_STREQ(lines[6].c_str(), "ITEM: BOX BOUNDS xy xz yz pp pp pp");
+    ASSERT_EQ(utils::split_words(lines[7]).size(), 3);
+
+    ASSERT_EQ(lines.size(), 43);
+    delete_file("dump_triclinic_with_time_run0.melt");
+}
+
 TEST_F(DumpAtomTest, triclinic_with_image_run0)
 {
     if (!verbose) ::testing::internal::CaptureStdout();