Add optional TIME to binary dump atom format (f9697bd9) · Commits · 郑智淋 / lammps

src/dump_atom.cpp

+15 −0

Original line number	Diff line number	Diff line
		@@ -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

+1 −0

Original line number	Diff line number	Diff line
		@@ -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

+11 −1

Original line number	Diff line number	Diff line
		@@ -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

+95 −0

Original line number	Diff line number	Diff line
		@@ -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();

Admin message