Migrate changes to dump custom/gz and add tests (e9fd8b3e) · Commits · 郑智淋 / lammps

src/COMPRESS/dump_custom_gz.cpp

+32 −8

Original line number	Diff line number	Diff line
		@@ -15,8 +15,10 @@
		#include "domain.h"
		#include "error.h"
		#include "update.h"
		#include "force.h"

		#include <cstring>
		#include <fmt/format.h>

		using namespace LAMMPS_NS;

		@@ -25,6 +27,8 @@ DumpCustomGZ::DumpCustomGZ(LAMMPS lmp, int narg, char *arg) :
		{
		gzFp = NULL;

		compression_level = Z_BEST_COMPRESSION;

		if (!compressed)
		error->all(FLERR,"Dump custom/gz only writes compressed files");
		}
		@@ -91,12 +95,15 @@ void DumpCustomGZ::openfile()
		// each proc with filewriter = 1 opens a file

		if (filewriter) {
		std::string mode;
		if (append_flag) {
		gzFp = gzopen(filecurrent,"ab9");
		mode = fmt::format("ab{}", compression_level);
		} else {
		gzFp = gzopen(filecurrent,"wb9");
		mode = fmt::format("wb{}", compression_level);
		}

		gzFp = gzopen(filecurrent, mode.c_str());

		if (gzFp == NULL) error->one(FLERR,"Cannot open dump file");
		} else gzFp = NULL;

		@@ -120,14 +127,14 @@ void DumpCustomGZ::write_header(bigint ndump)
		gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
		if (domain->triclinic == 0) {
		gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
		gzprintf(gzFp,"%-1.16g %-1.16g\n",boxxlo,boxxhi);
		gzprintf(gzFp,"%-1.16g %-1.16g\n",boxylo,boxyhi);
		gzprintf(gzFp,"%-1.16g %-1.16g\n",boxzlo,boxzhi);
		gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi);
		gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi);
		gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi);
		} else {
		gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
		gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy);
		gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz);
		gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz);
		gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy);
		gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz);
		gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz);
		}
		gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
		}
		@@ -156,3 +163,20 @@ void DumpCustomGZ::write()
		}
		}

		/* ---------------------------------------------------------------------- */

		int DumpCustomGZ::modify_param(int narg, char **arg)
		{
		int consumed = DumpCustom::modify_param(narg, arg);
		if(consumed == 0) {
		if (strcmp(arg[0],"compression_level") == 0) {
		if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
		int min_level = Z_DEFAULT_COMPRESSION;
		int max_level = Z_BEST_COMPRESSION;
		if (compression_level < 0 \|\| compression_level > max_level)
		error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level));
		return 2;
		}
		}
		return consumed;
		}

src/COMPRESS/dump_custom_gz.h

+3 −0

Original line number	Diff line number	Diff line
		@@ -31,12 +31,15 @@ class DumpCustomGZ : public DumpCustom {
		virtual ~DumpCustomGZ();

		protected:
		int compression_level;
		gzFile gzFp; // file pointer for the compressed output stream

		virtual void openfile();
		virtual void write_header(bigint);
		virtual void write_data(int, double *);
		virtual void write();

		virtual int modify_param(int, char **);
		};

		}

unittest/formats/CMakeLists.txt

+7 −0

Original line number	Diff line number	Diff line
		@@ -31,12 +31,19 @@ set_tests_properties(DumpAtom PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS

		if (PKG_COMPRESS)
		find_program(GZIP_BINARY NAMES gzip REQUIRED)

		add_executable(test_dump_atom_gz test_dump_atom_gz.cpp)
		target_link_libraries(test_dump_atom_gz PRIVATE lammps GTest::GMock GTest::GTest)
		add_test(NAME DumpAtomGZ COMMAND test_dump_atom_gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
		set_tests_properties(DumpAtomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
		set_tests_properties(DumpAtomGZ PROPERTIES ENVIRONMENT "GZIP_BINARY=${GZIP_BINARY}")

		add_executable(test_dump_custom_gz test_dump_custom_gz.cpp)
		target_link_libraries(test_dump_custom_gz PRIVATE lammps GTest::GMock GTest::GTest)
		add_test(NAME DumpCustomGZ COMMAND test_dump_custom_gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
		set_tests_properties(DumpCustomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
		set_tests_properties(DumpCustomGZ PROPERTIES ENVIRONMENT "GZIP_BINARY=${GZIP_BINARY}")

		find_program(ZSTD_BINARY NAMES zstd)

		if (ZSTD_BINARY)

unittest/formats/test_dump_custom_gz.cpp

0 → 100644

+140 −0

Original line number	Diff line number	Diff line
		/* ----------------------------------------------------------------------
		LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
		http://lammps.sandia.gov, Sandia National Laboratories
		Steve Plimpton, sjplimp@sandia.gov

		Copyright (2003) Sandia Corporation. Under the terms of Contract
		DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
		certain rights in this software. This software is distributed under
		the GNU General Public License.

		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		#include "gtest/gtest.h"
		#include "gmock/gmock.h"
		#include "fmt/format.h"
		#include "utils.h"
		#include "../testing/core.h"
		#include "../testing/systems/melt.h"
		#include "../testing/utils.h"

		using ::testing::Eq;

		char * GZIP_BINARY = nullptr;

		class DumpCustomGZTest : public MeltTest {
		std::string dump_style = "custom";
		public:
		void enable_triclinic() {
		if (!verbose) ::testing::internal::CaptureStdout();
		command("change_box all triclinic");
		if (!verbose) ::testing::internal::GetCapturedStdout();
		}

		void generate_dump(std::string dump_file, std::string fields, std::string dump_modify_options, int ntimesteps) {
		if (!verbose) ::testing::internal::CaptureStdout();
		command(fmt::format("dump id all {} 1 {} {}", dump_style, dump_file, fields));

		if (!dump_modify_options.empty()) {
		command(fmt::format("dump_modify id {}", dump_modify_options));
		}

		command(fmt::format("run {}", ntimesteps));
		if (!verbose) ::testing::internal::GetCapturedStdout();
		}

		void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, std::string compression_style,
		std::string fields, std::string dump_modify_options, int ntimesteps) {
		if (!verbose) ::testing::internal::CaptureStdout();
		command(fmt::format("dump id0 all {} 1 {} {}", dump_style, text_file, fields));
		command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_file, fields));

		if (!dump_modify_options.empty()) {
		command(fmt::format("dump_modify id0 {}", dump_modify_options));
		command(fmt::format("dump_modify id1 {}", dump_modify_options));
		}

		command(fmt::format("run {}", ntimesteps));
		if (!verbose) ::testing::internal::GetCapturedStdout();
		}

		std::string convert_compressed_to_text(std::string compressed_file) {
		if (!verbose) ::testing::internal::CaptureStdout();
		std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.'));
		std::string cmdline = fmt::format("{} -d -c {} > {}", GZIP_BINARY, compressed_file, converted_file);
		system(cmdline.c_str());
		if (!verbose) ::testing::internal::GetCapturedStdout();
		return converted_file;
		}
		};

		TEST_F(DumpCustomGZTest, compressed_run1)
		{
		if(!GZIP_BINARY) GTEST_SKIP();

		auto text_file = "dump_custom_text_run1.melt";
		auto compressed_file = "dump_custom_compressed_run1.melt.gz";
		auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz";

		generate_text_and_compressed_dump(text_file, compressed_file, "custom/gz", fields, "units yes", 1);

		ASSERT_FILE_EXISTS(text_file);
		ASSERT_FILE_EXISTS(compressed_file);

		auto converted_file = convert_compressed_to_text(compressed_file);

		ASSERT_FILE_EXISTS(converted_file);
		ASSERT_FILE_EQUAL(text_file, converted_file);
		delete_file(text_file);
		delete_file(compressed_file);
		delete_file(converted_file);
		}

		TEST_F(DumpCustomGZTest, compressed_triclinic_run1)
		{
		if(!GZIP_BINARY) GTEST_SKIP();

		auto text_file = "dump_custom_tri_text_run1.melt";
		auto compressed_file = "dump_custom_tri_compressed_run1.melt.gz";
		auto fields = "id type proc x y z xs ys zs xsu ysu zsu vx vy vz fx fy fz";

		enable_triclinic();

		generate_text_and_compressed_dump(text_file, compressed_file, "custom/gz", fields, "units yes", 1);

		ASSERT_FILE_EXISTS(text_file);
		ASSERT_FILE_EXISTS(compressed_file);

		auto converted_file = convert_compressed_to_text(compressed_file);

		ASSERT_FILE_EXISTS(converted_file);
		ASSERT_FILE_EQUAL(text_file, converted_file);
		delete_file(text_file);
		delete_file(compressed_file);
		delete_file(converted_file);
		}

		int main(int argc, char **argv)
		{
		MPI_Init(&argc, &argv);
		::testing::InitGoogleMock(&argc, argv);

		// handle arguments passed via environment variable
		if (const char *var = getenv("TEST_ARGS")) {
		std::vector<std::string> env = utils::split_words(var);
		for (auto arg : env) {
		if (arg == "-v") {
		verbose = true;
		}
		}
		}

		GZIP_BINARY = getenv("GZIP_BINARY");

		if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;

		int rv = RUN_ALL_TESTS();
		MPI_Finalize();
		return rv;
		}

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