Update binary format of dump custom

src/dump_custom.cpp

@@ -302,7 +302,7 @@ void DumpCustom::init_style()
       strcpy(vformat[i],ptr);
     }
 
-    vformat[i] = strcat(vformat[i]," ");
+    if (i+1 < size_one) vformat[i] = strcat(vformat[i]," ");
   }
 
   // setup boundary string
@@ -381,8 +381,83 @@ void DumpCustom::write_header(bigint ndump)
 
 /* ---------------------------------------------------------------------- */
 
+void DumpCustom::format_magic_string_binary()
+{
+  // use negative ntimestep as marker for new format
+  bigint fmtlen = strlen(MAGIC_STRING);
+  bigint marker = -fmtlen;
+  fwrite(&marker, sizeof(bigint), 1, fp);
+  fwrite(MAGIC_STRING, sizeof(char), fmtlen, fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpCustom::format_endian_binary()
+{
+  int endian = ENDIAN;
+  fwrite(&endian, sizeof(int), 1, fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpCustom::format_revision_binary()
+{
+  int revision = FORMAT_REVISION;
+  fwrite(&revision, sizeof(int), 1, fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpCustom::header_unit_style_binary()
+{
+  int len = 0;
+  if (unit_flag && !unit_count) {
+    ++unit_count;
+    len = strlen(update->unit_style);
+    fwrite(&len, sizeof(int), 1, fp);
+    fwrite(update->unit_style, sizeof(char), len, fp);
+  } else {
+    fwrite(&len, sizeof(int), 1, fp);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpCustom::header_columns_binary()
+{
+  int len = strlen(columns);
+  fwrite(&len, sizeof(int), 1, fp);
+  fwrite(columns, sizeof(char), len, fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpCustom::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 DumpCustom::header_format_binary()
+{
+  format_magic_string_binary();
+  format_endian_binary();
+  format_revision_binary();
+}
+
+/* ---------------------------------------------------------------------- */
+
 void DumpCustom::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);
@@ -394,6 +469,11 @@ void DumpCustom::header_binary(bigint ndump)
   fwrite(&boxzlo,sizeof(double),1,fp);
   fwrite(&boxzhi,sizeof(double),1,fp);
   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);
   else fwrite(&nprocs,sizeof(int),1,fp);
 }

src/dump_custom.h

@@ -29,6 +29,10 @@ class DumpCustom : public Dump {
   DumpCustom(class LAMMPS *, int, char **);
   virtual ~DumpCustom();
 
+  const char * MAGIC_STRING = "DUMPCUSTOM";
+  const int    FORMAT_REVISION = 0x0002;
+  const int    ENDIAN = 0x0001;
+
  protected:
   int nevery;                // dump frequency for output
   int iregion;               // -1 if no region, else which region
@@ -107,6 +111,14 @@ class DumpCustom : public Dump {
   int add_custom(char *, int);
   virtual int modify_param(int, char **);
 
+  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();
+  void format_revision_binary();
+
   typedef void (DumpCustom::*FnPtrHeader)(bigint);
   FnPtrHeader header_choice;           // ptr to write header functions
   void header_binary(bigint);

unittest/formats/CMakeLists.txt

@@ -36,4 +36,5 @@ set_tests_properties(DumpCustom PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMM
 
 if (BUILD_TOOLS)
     set_tests_properties(DumpAtom PROPERTIES ENVIRONMENT "BINARY2TXT_BINARY=$<TARGET_FILE:binary2txt>")
+    set_tests_properties(DumpCustom PROPERTIES ENVIRONMENT "BINARY2TXT_BINARY=$<TARGET_FILE:binary2txt>")
 endif()

unittest/formats/test_dump_custom.cpp

@@ -24,46 +24,110 @@ char * BINARY2TXT_BINARY = nullptr;
 class DumpCustomTest : public MeltTest {
 };
 
-TEST_F(DumpCustomTest, run0)
+TEST_F(DumpCustomTest, run1)
 {
-    auto dump_file = "dump_custom_run0.melt";
+    auto dump_file = "dump_custom_run1.melt";
 
     if (!verbose) ::testing::internal::CaptureStdout();
     command(fmt::format("dump id all custom 1 {} id type x y vx fx", dump_file));
-    command("run 0");
+    command("dump_modify id units yes");
+    command("run 1");
     if (!verbose) ::testing::internal::GetCapturedStdout();
 
 
     ASSERT_FILE_EXISTS(dump_file);
     auto lines = read_lines(dump_file);
-    ASSERT_EQ(lines.size(), 41);
+    ASSERT_EQ(lines.size(), 84);
-    ASSERT_STREQ(lines[4].c_str(), "ITEM: BOX BOUNDS pp pp pp");
+    ASSERT_STREQ(lines[6].c_str(), "ITEM: BOX BOUNDS pp pp pp");
-    ASSERT_EQ(utils::split_words(lines[5]).size(), 2);
+    ASSERT_EQ(utils::split_words(lines[7]).size(), 2);
-    ASSERT_STREQ(lines[8].c_str(), "ITEM: ATOMS id type x y vx fx");
+    ASSERT_STREQ(lines[10].c_str(), "ITEM: ATOMS id type x y vx fx");
-    ASSERT_EQ(utils::split_words(lines[9]).size(), 6);
+    ASSERT_EQ(utils::split_words(lines[11]).size(), 6);
     delete_file(dump_file);
 }
 
-TEST_F(DumpCustomTest, triclinic_run0)
+TEST_F(DumpCustomTest, binary_run1)
 {
-    auto dump_file = "dump_custom_tri_run0.melt";
+    auto text_file = "dump_custom_text_run1.melt";
+    auto binary_file = "dump_custom_binary_run1.melt.bin";
+    auto converted_file = fmt::format("{}.txt", binary_file);
+
+    if(!BINARY2TXT_BINARY) GTEST_SKIP();
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    command(fmt::format("dump id0 all custom 1 {} id type x y vx fx", text_file));
+    command(fmt::format("dump id1 all custom 1 {} id type x y vx fx", binary_file));
+    command("dump_modify id0 units yes");
+    command("dump_modify id1 units yes");
+    command("run 1");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    ASSERT_FILE_EXISTS(text_file);
+    ASSERT_FILE_EXISTS(binary_file);
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    std::string cmdline = fmt::format("{} {}", BINARY2TXT_BINARY, binary_file);
+    system(cmdline.c_str());
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    ASSERT_FILE_EXISTS(converted_file);
+    ASSERT_FILE_EQUAL(text_file, converted_file);
+    delete_file(text_file);
+    delete_file(binary_file);
+    delete_file(converted_file);
+}
+
+TEST_F(DumpCustomTest, triclinic_run1)
+{
+    auto dump_file = "dump_custom_tri_run1.melt";
     if (!verbose) ::testing::internal::CaptureStdout();
 
     command("change_box all triclinic");
     command(fmt::format("dump id all custom 1 {} id type x y vx fx", dump_file));
-    command("run 0");
+    command("dump_modify id units yes");
+    command("run 1");
     if (!verbose) ::testing::internal::GetCapturedStdout();
 
     ASSERT_FILE_EXISTS(dump_file);
 
     auto lines = read_lines(dump_file);
-    ASSERT_STREQ(lines[4].c_str(), "ITEM: BOX BOUNDS xy xz yz pp pp pp");
+    ASSERT_STREQ(lines[6].c_str(), "ITEM: BOX BOUNDS xy xz yz pp pp pp");
-    ASSERT_EQ(utils::split_words(lines[5]).size(), 3);
+    ASSERT_EQ(utils::split_words(lines[7]).size(), 3);
 
-    ASSERT_EQ(lines.size(), 41);
+    ASSERT_EQ(lines.size(), 84);
     delete_file(dump_file);
 }
 
+TEST_F(DumpCustomTest, binary_triclinic_run1)
+{
+    auto text_file = "dump_custom_tri_text_run1.melt";
+    auto binary_file = "dump_custom_tri_binary_run1.melt.bin";
+    auto converted_file = fmt::format("{}.txt", binary_file);
+
+    if(!BINARY2TXT_BINARY) GTEST_SKIP();
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    command(fmt::format("dump id0 all custom 1 {} id type x y vx fx", text_file));
+    command(fmt::format("dump id1 all custom 1 {} id type x y vx fx", binary_file));
+    command("dump_modify id0 units yes");
+    command("dump_modify id1 units yes");
+    command("run 1");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    ASSERT_FILE_EXISTS(text_file);
+    ASSERT_FILE_EXISTS(binary_file);
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    std::string cmdline = fmt::format("{} {}", BINARY2TXT_BINARY, binary_file);
+    system(cmdline.c_str());
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    ASSERT_FILE_EXISTS(converted_file);
+    ASSERT_FILE_EQUAL(text_file, converted_file);
+    delete_file(text_file);
+    delete_file(binary_file);
+    delete_file(converted_file);
+}
+
 
 int main(int argc, char **argv)
 {