Add UNITS information to dump atom binary format (6d825dcb) · Commits · 郑智淋 / lammps

src/dump_atom.cpp

+26 −2

Original line number	Diff line number	Diff line
		@@ -204,6 +204,7 @@ void DumpAtom::header_format_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);
		@@ -216,10 +217,22 @@ void DumpAtom::header_binary(bigint ndump)
		fwrite(&boxzhi,sizeof(double),1,fp);
		fwrite(&size_one,sizeof(int),1,fp);

		int len = strlen(columns);
		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);
		}

		len = strlen(columns);
		fwrite(&len, sizeof(int), 1, fp);
		fwrite(columns, sizeof(char), len, fp);


		if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);
		else fwrite(&nprocs,sizeof(int),1,fp);
		}
		@@ -244,7 +257,18 @@ void DumpAtom::header_binary_triclinic(bigint ndump)
		fwrite(&boxyz,sizeof(double),1,fp);
		fwrite(&size_one,sizeof(int),1,fp);

		int len = strlen(columns);
		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);
		}

		len = strlen(columns);
		fwrite(&len, sizeof(int), 1, fp);
		fwrite(columns, sizeof(char), len, fp);

tools/binary2txt.cpp

+18 −2

Original line number	Diff line number	Diff line
		@@ -93,7 +93,7 @@ int main(int narg, char **arg)
		// detect newer format
		char * magic_string = nullptr;
		char * columns = nullptr;

		char * unit_style = nullptr;

		// loop over snapshots in file

		@@ -148,8 +148,20 @@ int main(int narg, char **arg)
		fread(&size_one,sizeof(int),1,fp);

		if (magic_string && revision > 0x0001) {
		// newer format includes columns string
		// newer format includes units and columns string
		int len = 0;
		fread(&len, sizeof(int), 1, fp);

		if (len > 0) {
		// has units
		delete [] unit_style;
		unit_style = new char[len+1];
		fread(unit_style, sizeof(char), len, fp);
		unit_style[len+1] = '\0';
		fprintf(fptxt, "ITEM: UNITS\n");
		fprintf(fptxt, "%s\n", unit_style);
		}

		fread(&len, sizeof(int), 1, fp);
		delete [] columns;
		columns = new char[len+1];
		@@ -229,6 +241,10 @@ int main(int narg, char **arg)
		printf("\n");
		delete [] columns;
		delete [] magic_string;
		delete [] unit_style;
		columns = nullptr;
		magic_string = nullptr;
		unit_style = nullptr;
		}

		if (buf) delete [] buf;

unittest/formats/test_dump.cpp

+77 −0

Original line number	Diff line number	Diff line
		@@ -270,6 +270,61 @@ TEST_F(DumpAtomTest, with_units_run1)
		delete_file("dump_with_units_run1.melt");
		}

		TEST_F(DumpAtomTest, binary_with_units_run0)
		{
		if(!BINARY2TXT_BINARY) GTEST_SKIP();

		if (!verbose) ::testing::internal::CaptureStdout();
		command("dump id0 all atom 1 dump_text_with_units_run0.melt");
		command("dump id1 all atom 1 dump_binary_with_units_run0.melt.bin");
		command("dump_modify id0 scale no units yes");
		command("dump_modify id1 scale no units yes");
		command("run 0");
		if (!verbose) ::testing::internal::GetCapturedStdout();

		ASSERT_FILE_EXISTS("dump_text_with_units_run0.melt");
		ASSERT_FILE_EXISTS("dump_binary_with_units_run0.melt.bin");

		if (!verbose) ::testing::internal::CaptureStdout();
		std::string cmdline = fmt::format("{} dump_binary_with_units_run0.melt.bin", BINARY2TXT_BINARY);
		system(cmdline.c_str());
		if (!verbose) ::testing::internal::GetCapturedStdout();

		ASSERT_FILE_EXISTS("dump_binary_with_units_run0.melt.bin.txt");
		ASSERT_FILE_EQUAL("dump_text_with_units_run0.melt", "dump_binary_with_units_run0.melt.bin.txt");
		delete_file("dump_text_with_units_run0.melt");
		delete_file("dump_binary_with_units_run0.melt.bin");
		delete_file("dump_binary_with_units_run0.melt.bin.txt");
		}

		TEST_F(DumpAtomTest, binary_triclinic_with_units_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_units_run0.melt");
		command("dump id1 all atom 1 dump_binary_tri_with_units_run0.melt.bin");
		command("dump_modify id0 scale no units yes");
		command("dump_modify id1 scale no units yes");
		command("run 0");
		if (!verbose) ::testing::internal::GetCapturedStdout();

		ASSERT_FILE_EXISTS("dump_text_tri_with_units_run0.melt");
		ASSERT_FILE_EXISTS("dump_binary_tri_with_units_run0.melt.bin");

		if (!verbose) ::testing::internal::CaptureStdout();
		std::string cmdline = fmt::format("{} dump_binary_tri_with_units_run0.melt.bin", BINARY2TXT_BINARY);
		system(cmdline.c_str());
		if (!verbose) ::testing::internal::GetCapturedStdout();

		ASSERT_FILE_EXISTS("dump_binary_tri_with_units_run0.melt.bin.txt");
		ASSERT_FILE_EQUAL("dump_text_tri_with_units_run0.melt", "dump_binary_tri_with_units_run0.melt.bin.txt");
		delete_file("dump_text_tri_with_units_run0.melt");
		delete_file("dump_binary_tri_with_units_run0.melt.bin");
		delete_file("dump_binary_tri_with_units_run0.melt.bin.txt");
		}

		TEST_F(DumpAtomTest, no_buffer_with_scale_and_image_run0)
		{
		if (!verbose) ::testing::internal::CaptureStdout();
		@@ -307,6 +362,28 @@ TEST_F(DumpAtomTest, tricilinic_run0)
		delete_file("dump_triclinic_run0.melt");
		}

		TEST_F(DumpAtomTest, tricilinic_with_units_run0)
		{
		if (!verbose) ::testing::internal::CaptureStdout();

		command("change_box all triclinic");
		command("dump id all atom 1 dump_triclinic_with_units_run0.melt");
		command("dump_modify id units yes");
		command("run 0");
		if (!verbose) ::testing::internal::GetCapturedStdout();

		ASSERT_FILE_EXISTS("dump_triclinic_with_units_run0.melt");

		auto lines = read_lines("dump_triclinic_with_units_run0.melt");
		ASSERT_STREQ(lines[0].c_str(), "ITEM: UNITS");
		ASSERT_STREQ(lines[1].c_str(), "lj");
		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_units_run0.melt");
		}

		TEST_F(DumpAtomTest, triclinic_with_image_run0)
		{
		if (!verbose) ::testing::internal::CaptureStdout();

Admin message