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Migrate changes to dump custom/gz and add tests

This commit is contained in:
Richard Berger 2020-08-26 19:44:55 -04:00
parent 78a1b92503
commit e9fd8b3ec6
No known key found for this signature in database
GPG Key ID: A9E83994E0BA0CAB
4 changed files with 182 additions and 8 deletions
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40
src/COMPRESS/dump_custom_gz.cpp
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@ -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;
}

3
src/COMPRESS/dump_custom_gz.h
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@ -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 **);
};
}

7
unittest/formats/CMakeLists.txt
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@ -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)

140
unittest/formats/test_dump_custom_gz.cpp Normal file
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@ -0,0 +1,140 @@
/* ----------------------------------------------------------------------
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;
}