Unverified Commit fbcc9758 authored by Richard Berger's avatar Richard Berger
Browse files

Update binary format of dump custom

parent 71ec1408

src/dump_custom.cpp

+81 −1
Original line number Diff line number Diff line
@@ -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

+12 −0
Original line number Diff line number Diff line
@@ -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

+1 −0
Original line number Diff line number Diff line
@@ -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

+78 −14
Original line number Diff line number Diff line
@@ -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_STREQ(lines[4].c_str(), "ITEM: BOX BOUNDS pp pp pp");

    ASSERT_EQ(utils::split_words(lines[5]).size(), 2);

    ASSERT_STREQ(lines[8].c_str(), "ITEM: ATOMS id type x y vx fx");

    ASSERT_EQ(utils::split_words(lines[9]).size(), 6);

    ASSERT_EQ(lines.size(), 84);

    ASSERT_STREQ(lines[6].c_str(), "ITEM: BOX BOUNDS pp pp pp");

    ASSERT_EQ(utils::split_words(lines[7]).size(), 2);

    ASSERT_STREQ(lines[10].c_str(), "ITEM: ATOMS id type x y vx fx");

    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_EQ(utils::split_words(lines[5]).size(), 3);

    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(), 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)

{

CRA Git | Maintained and supported by SUSTech CRA and CCSE