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Refactor Zstd dump styles

This commit is contained in:
Richard Berger 2020-08-27 11:59:57 -04:00
parent ced78a72eb
commit 2f629db3d4
No known key found for this signature in database
GPG Key ID: A9E83994E0BA0CAB
11 changed files with 400 additions and 262 deletions
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131
src/COMPRESS/dump_atom_zstd.cpp
View File

@ -11,29 +11,24 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Richard Berger (Temple U)
------------------------------------------------------------------------- */
#include "dump_atom_zstd.h"
#include "domain.h"
#include "error.h"
#include "update.h"
#include "force.h"
#include <fmt/format.h>
#include <cstring>
#include <fmt/format.h>
using namespace LAMMPS_NS;
DumpAtomZstd::DumpAtomZstd(LAMMPS *lmp, int narg, char **arg) :
DumpAtom(lmp, narg, arg)
{
cctx = nullptr;
zstdFp = nullptr;
fp = nullptr;
out_buffer_size = ZSTD_CStreamOutSize();
out_buffer = new char[out_buffer_size];
checksum_flag = 1;
compression_level = 0; // = default
if (!compressed)
error->all(FLERR,"Dump atom/zstd only writes compressed files");
}
@ -42,11 +37,6 @@ DumpAtomZstd::DumpAtomZstd(LAMMPS *lmp, int narg, char **arg) :
DumpAtomZstd::~DumpAtomZstd()
{
if(cctx && zstdFp) zstd_close();
delete [] out_buffer;
out_buffer = nullptr;
out_buffer_size = 0;
}
/* ----------------------------------------------------------------------
@ -101,19 +91,15 @@ void DumpAtomZstd::openfile()
if (filewriter) {
if (append_flag) {
zstdFp = fopen(filecurrent,"ab");
} else {
zstdFp = fopen(filecurrent,"wb");
error->one(FLERR, "dump/zstd currently doesn't support append");
}
if (zstdFp == nullptr) error->one(FLERR,"Cannot open dump file");
cctx = ZSTD_createCCtx();
ZSTD_CCtx_setParameter(cctx, ZSTD_c_compressionLevel, compression_level);
ZSTD_CCtx_setParameter(cctx, ZSTD_c_checksumFlag, checksum_flag);
if (cctx == nullptr) error->one(FLERR,"Cannot create Zstd context");
} else zstdFp = nullptr;
try {
writer.open(filecurrent);
} catch (FileWriterException & e) {
error->one(FLERR, e.what());
}
}
// delete string with timestep replaced
@ -151,7 +137,7 @@ void DumpAtomZstd::write_header(bigint ndump)
}
header += fmt::format("ITEM: ATOMS {}\n", columns);
zstd_write(header.c_str(), header.length());
writer.write(header.c_str(), header.length());
}
}
@ -159,14 +145,7 @@ void DumpAtomZstd::write_header(bigint ndump)
void DumpAtomZstd::write_data(int n, double *mybuf)
{
ZSTD_inBuffer input = { mybuf, (size_t)n, 0 };
ZSTD_EndDirective mode = ZSTD_e_continue;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
size_t const remaining = ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, zstdFp);
} while(input.pos < input.size);
writer.write(mybuf, n);
}
/* ---------------------------------------------------------------------- */
@ -176,11 +155,10 @@ void DumpAtomZstd::write()
DumpAtom::write();
if (filewriter) {
if (multifile) {
zstd_close();
writer.close();
} else {
if (flush_flag && zstdFp) {
zstd_flush();
fflush(zstdFp);
if (flush_flag && writer.isopen()) {
writer.flush();
}
}
}
@ -192,67 +170,22 @@ int DumpAtomZstd::modify_param(int narg, char **arg)
{
int consumed = DumpAtom::modify_param(narg, arg);
if(consumed == 0) {
if (strcmp(arg[0],"checksum") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) checksum_flag = 1;
else if (strcmp(arg[1],"no") == 0) checksum_flag = 0;
else error->all(FLERR,"Illegal dump_modify command");
return 2;
} else if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
compression_level = force->inumeric(FLERR,arg[1]);
int min_level = ZSTD_minCLevel();
int max_level = ZSTD_maxCLevel();
if (compression_level < min_level || 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;
try {
if (strcmp(arg[0],"checksum") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) writer.setChecksum(true);
else if (strcmp(arg[1],"no") == 0) writer.setChecksum(false);
else error->all(FLERR,"Illegal dump_modify command");
return 2;
} else if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
int compression_level = force->inumeric(FLERR,arg[1]);
writer.setCompressionLevel(compression_level);
return 2;
}
} catch (FileWriterException & e) {
error->one(FLERR, e.what());
}
}
return consumed;
}
/* ---------------------------------------------------------------------- */
void DumpAtomZstd::zstd_write(const void * buffer, size_t length)
{
ZSTD_inBuffer input = { buffer, length, 0 };
ZSTD_EndDirective mode = ZSTD_e_continue;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
size_t const remaining = ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, zstdFp);
} while(input.pos < input.size);
}
void DumpAtomZstd::zstd_flush() {
size_t remaining;
ZSTD_inBuffer input = { nullptr, 0, 0 };
ZSTD_EndDirective mode = ZSTD_e_flush;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
remaining = ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, zstdFp);
} while(remaining);
}
/* ---------------------------------------------------------------------- */
void DumpAtomZstd::zstd_close()
{
size_t remaining;
ZSTD_inBuffer input = { nullptr, 0, 0 };
ZSTD_EndDirective mode = ZSTD_e_end;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
remaining = ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, zstdFp);
} while(remaining);
ZSTD_freeCCtx(cctx);
cctx = nullptr;
if (zstdFp) fclose(zstdFp);
zstdFp = nullptr;
}

19
src/COMPRESS/dump_atom_zstd.h
View File

@ -11,6 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Richard Berger (Temple U)
------------------------------------------------------------------------- */
#ifdef DUMP_CLASS
DumpStyle(atom/zstd,DumpAtomZstd)
@ -21,8 +25,7 @@ DumpStyle(atom/zstd,DumpAtomZstd)
#define LMP_DUMP_ATOM_ZSTD_H
#include "dump_atom.h"
#include <zstd.h>
#include <stdio.h>
#include "zstd_file_writer.h"
namespace LAMMPS_NS {
@ -32,13 +35,7 @@ class DumpAtomZstd : public DumpAtom {
virtual ~DumpAtomZstd();
protected:
int compression_level;
int checksum_flag;
ZSTD_CCtx * cctx;
FILE * zstdFp;
char * out_buffer;
size_t out_buffer_size;
ZstdFileWriter writer;
virtual void openfile();
virtual void write_header(bigint);
@ -46,10 +43,6 @@ class DumpAtomZstd : public DumpAtom {
virtual void write();
virtual int modify_param(int, char **);
void zstd_write(const void * buffer, size_t length);
void zstd_flush();
void zstd_close();
};
}

133
src/COMPRESS/dump_custom_zstd.cpp
View File

@ -11,6 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Richard Berger (Temple U)
------------------------------------------------------------------------- */
#include "dump_custom_zstd.h"
#include "domain.h"
#include "error.h"
@ -25,32 +29,16 @@ using namespace LAMMPS_NS;
DumpCustomZstd::DumpCustomZstd(LAMMPS *lmp, int narg, char **arg) :
DumpCustom(lmp, narg, arg)
{
cctx = nullptr;
zstdFp = nullptr;
fp = nullptr;
out_buffer_size = ZSTD_CStreamOutSize();
out_buffer = new char[out_buffer_size];
checksum_flag = 1;
compression_level = 0; // = default
if (!compressed)
error->all(FLERR,"Dump custom/zstd only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpCustomZstd::~DumpCustomZstd()
{
if(cctx && zstdFp) zstd_close();
delete [] out_buffer;
out_buffer = nullptr;
out_buffer_size = 0;
}
/* ----------------------------------------------------------------------
generic opening of a dump file
ASCII or binary or gzipped
@ -103,25 +91,23 @@ void DumpCustomZstd::openfile()
if (filewriter) {
if (append_flag) {
zstdFp = fopen(filecurrent,"ab");
} else {
zstdFp = fopen(filecurrent,"wb");
error->one(FLERR, "dump/zstd currently doesn't support append");
}
if (zstdFp == nullptr) error->one(FLERR,"Cannot open dump file");
cctx = ZSTD_createCCtx();
ZSTD_CCtx_setParameter(cctx, ZSTD_c_compressionLevel, compression_level);
ZSTD_CCtx_setParameter(cctx, ZSTD_c_checksumFlag, checksum_flag);
if (cctx == nullptr) error->one(FLERR,"Cannot create Zstd context");
} else zstdFp = nullptr;
try {
writer.open(filecurrent);
} catch (FileWriterException & e) {
error->one(FLERR, e.what());
}
}
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
}
/* ---------------------------------------------------------------------- */
void DumpCustomZstd::write_header(bigint ndump)
{
std::string header;
@ -151,7 +137,7 @@ void DumpCustomZstd::write_header(bigint ndump)
}
header += fmt::format("ITEM: ATOMS {}\n", columns);
zstd_write(header.c_str(), header.length());
writer.write(header.c_str(), header.length());
}
}
@ -159,14 +145,7 @@ void DumpCustomZstd::write_header(bigint ndump)
void DumpCustomZstd::write_data(int n, double *mybuf)
{
ZSTD_inBuffer input = { mybuf, (size_t)n, 0 };
ZSTD_EndDirective mode = ZSTD_e_continue;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
size_t const remaining = ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, zstdFp);
} while(input.pos < input.size);
writer.write(mybuf, n);
}
/* ---------------------------------------------------------------------- */
@ -176,11 +155,10 @@ void DumpCustomZstd::write()
DumpCustom::write();
if (filewriter) {
if (multifile) {
zstd_close();
writer.close();
} else {
if (flush_flag && zstdFp) {
zstd_flush();
fflush(zstdFp);
if (flush_flag && writer.isopen()) {
writer.flush();
}
}
}
@ -192,67 +170,22 @@ int DumpCustomZstd::modify_param(int narg, char **arg)
{
int consumed = DumpCustom::modify_param(narg, arg);
if(consumed == 0) {
if (strcmp(arg[0],"checksum") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) checksum_flag = 1;
else if (strcmp(arg[1],"no") == 0) checksum_flag = 0;
else error->all(FLERR,"Illegal dump_modify command");
return 2;
} else if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
compression_level = force->inumeric(FLERR,arg[1]);
int min_level = ZSTD_minCLevel();
int max_level = ZSTD_maxCLevel();
if (compression_level < min_level || 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;
try {
if (strcmp(arg[0],"checksum") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) writer.setChecksum(true);
else if (strcmp(arg[1],"no") == 0) writer.setChecksum(false);
else error->all(FLERR,"Illegal dump_modify command");
return 2;
} else if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
int compression_level = force->inumeric(FLERR,arg[1]);
writer.setCompressionLevel(compression_level);
return 2;
}
} catch (FileWriterException & e) {
error->one(FLERR, e.what());
}
}
return consumed;
}
/* ---------------------------------------------------------------------- */
void DumpCustomZstd::zstd_write(const void * buffer, size_t length)
{
ZSTD_inBuffer input = { buffer, length, 0 };
ZSTD_EndDirective mode = ZSTD_e_continue;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
size_t const remaining = ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, zstdFp);
} while(input.pos < input.size);
}
void DumpCustomZstd::zstd_flush() {
size_t remaining;
ZSTD_inBuffer input = { nullptr, 0, 0 };
ZSTD_EndDirective mode = ZSTD_e_flush;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
remaining = ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, zstdFp);
} while(remaining);
}
/* ---------------------------------------------------------------------- */
void DumpCustomZstd::zstd_close()
{
size_t remaining;
ZSTD_inBuffer input = { nullptr, 0, 0 };
ZSTD_EndDirective mode = ZSTD_e_end;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
remaining = ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, zstdFp);
} while(remaining);
ZSTD_freeCCtx(cctx);
cctx = nullptr;
if (zstdFp) fclose(zstdFp);
zstdFp = nullptr;
}

18
src/COMPRESS/dump_custom_zstd.h
View File

@ -11,6 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Richard Berger (Temple U)
------------------------------------------------------------------------- */
#ifdef DUMP_CLASS
DumpStyle(custom/zstd,DumpCustomZstd)
@ -21,7 +25,7 @@ DumpStyle(custom/zstd,DumpCustomZstd)
#define LMP_DUMP_CUSTOM_ZSTD_H
#include "dump_custom.h"
#include <zstd.h>
#include "zstd_file_writer.h"
#include <stdio.h>
namespace LAMMPS_NS {
@ -32,13 +36,7 @@ class DumpCustomZstd : public DumpCustom {
virtual ~DumpCustomZstd();
protected:
int compression_level;
int checksum_flag;
ZSTD_CCtx * cctx;
FILE * zstdFp;
char * out_buffer;
size_t out_buffer_size;
ZstdFileWriter writer;
virtual void openfile();
virtual void write_header(bigint);
@ -46,10 +44,6 @@ class DumpCustomZstd : public DumpCustom {
virtual void write();
virtual int modify_param(int, char **);
void zstd_write(const void * buffer, size_t length);
void zstd_flush();
void zstd_close();
};
}

158
src/COMPRESS/zstd_file_writer.cpp Normal file
View File

@ -0,0 +1,158 @@
/* -*- c++ -*- ----------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Richard Berger (Temple U)
------------------------------------------------------------------------- */
#include "zstd_file_writer.h"
#include <stdio.h>
#include <fmt/format.h>
using namespace LAMMPS_NS;
ZstdFileWriter::ZstdFileWriter() : FileWriter(),
fp(nullptr),
cctx(nullptr),
compression_level(0),
checksum_flag(1)
{
out_buffer_size = ZSTD_CStreamOutSize();
out_buffer = new char[out_buffer_size];
}
/* ---------------------------------------------------------------------- */
ZstdFileWriter::~ZstdFileWriter()
{
close();
delete [] out_buffer;
out_buffer = nullptr;
out_buffer_size = 0;
}
/* ---------------------------------------------------------------------- */
void ZstdFileWriter::open(const std::string & path)
{
if(isopen()) return;
fp = fopen(path.c_str(), "wb");
if (!fp) {
throw FileWriterException(fmt::format("Could not open file '{}'", path));
}
cctx = ZSTD_createCCtx();
if (!cctx) {
fclose(fp);
fp = nullptr;
throw FileWriterException("Could not create Zstd context");
}
ZSTD_CCtx_setParameter(cctx, ZSTD_c_compressionLevel, compression_level);
ZSTD_CCtx_setParameter(cctx, ZSTD_c_checksumFlag, checksum_flag);
}
/* ---------------------------------------------------------------------- */
size_t ZstdFileWriter::write(const void * buffer, size_t length)
{
if(!isopen()) return 0;
ZSTD_inBuffer input = { buffer, length, 0 };
ZSTD_EndDirective mode = ZSTD_e_continue;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
size_t const remaining = ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, fp);
} while(input.pos < input.size);
return length;
}
/* ---------------------------------------------------------------------- */
void ZstdFileWriter::flush()
{
if(!isopen()) return;
size_t remaining;
ZSTD_inBuffer input = { nullptr, 0, 0 };
ZSTD_EndDirective mode = ZSTD_e_flush;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
remaining = ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, fp);
} while(remaining);
fflush(fp);
}
/* ---------------------------------------------------------------------- */
void ZstdFileWriter::close()
{
if(!isopen()) return;
size_t remaining;
ZSTD_inBuffer input = { nullptr, 0, 0 };
ZSTD_EndDirective mode = ZSTD_e_end;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
remaining = ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, fp);
} while(remaining);
ZSTD_freeCCtx(cctx);
cctx = nullptr;
fclose(fp);
fp = nullptr;
}
/* ---------------------------------------------------------------------- */
bool ZstdFileWriter::isopen() const
{
return fp && cctx;
}
/* ---------------------------------------------------------------------- */
void ZstdFileWriter::setCompressionLevel(int level)
{
if (isopen())
throw FileWriterException("Compression level can not be changed while file is open");
const int min_level = ZSTD_minCLevel();
const int max_level = ZSTD_maxCLevel();
if(level < min_level || level > max_level)
throw FileWriterException(fmt::format("Compression level must in the range of [{}, {}]", min_level, max_level));
compression_level = level;
}
/* ---------------------------------------------------------------------- */
void ZstdFileWriter::setChecksum(bool enabled)
{
if (isopen())
throw FileWriterException("Checksum flag can not be changed while file is open");
checksum_flag = enabled ? 1 : 0;
}

52
src/COMPRESS/zstd_file_writer.h Normal file
View File

@ -0,0 +1,52 @@
/* -*- c++ -*- ----------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Richard Berger (Temple U)
------------------------------------------------------------------------- */
#ifndef LMP_ZSTD_FILE_WRITER_H
#define LMP_ZSTD_FILE_WRITER_H
#include "file_writer.h"
#include <string>
#include <zstd.h>
#include <exception>
namespace LAMMPS_NS {
class ZstdFileWriter : public FileWriter {
int compression_level;
int checksum_flag;
ZSTD_CCtx * cctx;
FILE * fp;
char * out_buffer;
size_t out_buffer_size;
public:
ZstdFileWriter();
virtual ~ZstdFileWriter();
virtual void open(const std::string & path) override;
virtual void close() override;
virtual void flush() override;
virtual size_t write(const void * buffer, size_t length) override;
virtual bool isopen() const override;
void setCompressionLevel(int level);
void setChecksum(bool enabled);
};
}
#endif

53
src/file_writer.h Normal file
View File

@ -0,0 +1,53 @@
/* -*- c++ -*- ----------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Richard Berger (Temple U)
------------------------------------------------------------------------- */
#ifndef LMP_FILE_WRITER_H
#define LMP_FILE_WRITER_H
#include <string>
namespace LAMMPS_NS {
class FileWriter {
public:
FileWriter() = default;
virtual ~FileWriter() = default;
virtual void open(const std::string & path) = 0;
virtual void close() = 0;
virtual void flush() = 0;
virtual size_t write(const void * buffer, size_t length) = 0;
virtual bool isopen() const = 0;
};
class FileWriterException : public std::exception {
std::string message;
public:
FileWriterException(const std::string & msg) : message(msg) {
}
~FileWriterException() throw() {
}
virtual const char * what() const throw() {
return message.c_str();
}
};
}
#endif

44
unittest/formats/test_dump_atom_gz.cpp
View File

@ -79,17 +79,19 @@ TEST_F(DumpAtomGZTest, compressed_run0)
{
if(!GZIP_BINARY) GTEST_SKIP();
auto text_file = "dump_text_run0.melt";
auto compressed_file = "dump_compressed_run0.melt.gz";
auto text_file = "dump_gz_text_run0.melt";
auto compressed_file = "dump_gz_compressed_run0.melt.gz";
generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "", 0);
TearDown();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(compressed_file);
auto converted_file = convert_compressed_to_text(compressed_file);
ASSERT_THAT(converted_file, Eq("dump_compressed_run0.melt"));
ASSERT_THAT(converted_file, Eq("dump_gz_compressed_run0.melt"));
ASSERT_FILE_EXISTS(converted_file);
ASSERT_FILE_EQUAL(text_file, converted_file);
delete_file(text_file);
@ -101,11 +103,13 @@ TEST_F(DumpAtomGZTest, compressed_with_units_run0)
{
if(!GZIP_BINARY) GTEST_SKIP();
auto text_file = "dump_text_with_units_run0.melt";
auto compressed_file = "dump_compressed_with_units_run0.melt.gz";
auto text_file = "dump_gz_text_with_units_run0.melt";
auto compressed_file = "dump_gz_compressed_with_units_run0.melt.gz";
generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "scale no units yes", 0);
TearDown();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(compressed_file);
@ -122,11 +126,13 @@ TEST_F(DumpAtomGZTest, compressed_with_time_run0)
{
if(!GZIP_BINARY) GTEST_SKIP();
auto text_file = "dump_text_with_time_run0.melt";
auto compressed_file = "dump_compressed_with_time_run0.melt.gz";
auto text_file = "dump_gz_text_with_time_run0.melt";
auto compressed_file = "dump_gz_compressed_with_time_run0.melt.gz";
generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "scale no time yes", 0);
TearDown();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(compressed_file);
@ -143,12 +149,14 @@ TEST_F(DumpAtomGZTest, compressed_triclinic_run0)
{
if(!GZIP_BINARY) GTEST_SKIP();
auto text_file = "dump_text_tri_run0.melt";
auto compressed_file = "dump_compressed_tri_run0.melt.gz";
auto text_file = "dump_gz_text_tri_run0.melt";
auto compressed_file = "dump_gz_compressed_tri_run0.melt.gz";
enable_triclinic();
generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "", 0);
TearDown();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(compressed_file);
@ -165,12 +173,14 @@ TEST_F(DumpAtomGZTest, compressed_triclinic_with_units_run0)
{
if(!GZIP_BINARY) GTEST_SKIP();
auto text_file = "dump_text_tri_with_units_run0.melt";
auto compressed_file = "dump_compressed_tri_with_units_run0.melt.gz";
auto text_file = "dump_gz_text_tri_with_units_run0.melt";
auto compressed_file = "dump_gz_compressed_tri_with_units_run0.melt.gz";
enable_triclinic();
generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "scale no units yes", 0);
TearDown();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(compressed_file);
@ -187,12 +197,14 @@ TEST_F(DumpAtomGZTest, compressed_triclinic_with_time_run0)
{
if(!GZIP_BINARY) GTEST_SKIP();
auto text_file = "dump_text_tri_with_time_run0.melt";
auto compressed_file = "dump_compressed_tri_with_time_run0.melt.gz";
auto text_file = "dump_gz_text_tri_with_time_run0.melt";
auto compressed_file = "dump_gz_compressed_tri_with_time_run0.melt.gz";
enable_triclinic();
generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "scale no time yes", 0);
TearDown();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(compressed_file);
@ -209,12 +221,14 @@ TEST_F(DumpAtomGZTest, compressed_triclinic_with_image_run0)
{
if(!GZIP_BINARY) GTEST_SKIP();
auto text_file = "dump_text_tri_with_image_run0.melt";
auto compressed_file = "dump_compressed_tri_with_image_run0.melt.gz";
auto text_file = "dump_gz_text_tri_with_image_run0.melt";
auto compressed_file = "dump_gz_compressed_tri_with_image_run0.melt.gz";
enable_triclinic();
generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "image yes", 0);
TearDown();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(compressed_file);

30
unittest/formats/test_dump_atom_zstd.cpp
View File

@ -79,8 +79,8 @@ TEST_F(DumpAtomZSTDTest, compressed_run0)
{
if(!ZSTD_BINARY) GTEST_SKIP();
auto text_file = "dump_text_run0.melt";
auto compressed_file = "dump_compressed_run0.melt.zst";
auto text_file = "dump_zstd_text_run0.melt";
auto compressed_file = "dump_zstd_compressed_run0.melt.zst";
generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "", 0);
@ -92,7 +92,7 @@ TEST_F(DumpAtomZSTDTest, compressed_run0)
auto converted_file = convert_compressed_to_text(compressed_file);
ASSERT_THAT(converted_file, Eq("dump_compressed_run0.melt"));
ASSERT_THAT(converted_file, Eq("dump_zstd_compressed_run0.melt"));
ASSERT_FILE_EXISTS(converted_file);
ASSERT_FILE_EQUAL(text_file, converted_file);
delete_file(text_file);
@ -104,8 +104,8 @@ TEST_F(DumpAtomZSTDTest, compressed_with_units_run0)
{
if(!ZSTD_BINARY) GTEST_SKIP();
auto text_file = "dump_text_with_units_run0.melt";
auto compressed_file = "dump_compressed_with_units_run0.melt.zst";
auto text_file = "dump_zstd_text_with_units_run0.melt";
auto compressed_file = "dump_zstd_compressed_with_units_run0.melt.zst";
generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "scale no units yes", 0);
@ -128,8 +128,8 @@ TEST_F(DumpAtomZSTDTest, compressed_with_time_run0)
{
if(!ZSTD_BINARY) GTEST_SKIP();
auto text_file = "dump_text_with_time_run0.melt";
auto compressed_file = "dump_compressed_with_time_run0.melt.zst";
auto text_file = "dump_zstd_text_with_time_run0.melt";
auto compressed_file = "dump_zstd_compressed_with_time_run0.melt.zst";
generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "scale no time yes", 0);
@ -152,8 +152,8 @@ TEST_F(DumpAtomZSTDTest, compressed_triclinic_run0)
{
if(!ZSTD_BINARY) GTEST_SKIP();
auto text_file = "dump_text_tri_run0.melt";
auto compressed_file = "dump_compressed_tri_run0.melt.zst";
auto text_file = "dump_zstd_text_tri_run0.melt";
auto compressed_file = "dump_zstd_compressed_tri_run0.melt.zst";
enable_triclinic();
generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "", 0);
@ -177,8 +177,8 @@ TEST_F(DumpAtomZSTDTest, compressed_triclinic_with_units_run0)
{
if(!ZSTD_BINARY) GTEST_SKIP();
auto text_file = "dump_text_tri_with_units_run0.melt";
auto compressed_file = "dump_compressed_tri_with_units_run0.melt.zst";
auto text_file = "dump_zstd_text_tri_with_units_run0.melt";
auto compressed_file = "dump_zstd_compressed_tri_with_units_run0.melt.zst";
enable_triclinic();
generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "scale no units yes", 0);
@ -202,8 +202,8 @@ TEST_F(DumpAtomZSTDTest, compressed_triclinic_with_time_run0)
{
if(!ZSTD_BINARY) GTEST_SKIP();
auto text_file = "dump_text_tri_with_time_run0.melt";
auto compressed_file = "dump_compressed_tri_with_time_run0.melt.zst";
auto text_file = "dump_zstd_text_tri_with_time_run0.melt";
auto compressed_file = "dump_zstd_compressed_tri_with_time_run0.melt.zst";
enable_triclinic();
generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "scale no time yes", 0);
@ -227,8 +227,8 @@ TEST_F(DumpAtomZSTDTest, compressed_triclinic_with_image_run0)
{
if(!ZSTD_BINARY) GTEST_SKIP();
auto text_file = "dump_text_tri_with_image_run0.melt";
auto compressed_file = "dump_compressed_tri_with_image_run0.melt.zst";
auto text_file = "dump_zstd_text_tri_with_image_run0.melt";
auto compressed_file = "dump_zstd_compressed_tri_with_image_run0.melt.zst";
enable_triclinic();
generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "image yes", 0);

12
unittest/formats/test_dump_custom_gz.cpp
View File

@ -73,12 +73,14 @@ 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 text_file = "dump_custom_gz_text_run1.melt";
auto compressed_file = "dump_custom_gz_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);
TearDown();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(compressed_file);
@ -95,14 +97,16 @@ 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 text_file = "dump_custom_gz_tri_text_run1.melt";
auto compressed_file = "dump_custom_gz_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);
TearDown();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(compressed_file);

12
unittest/formats/test_dump_custom_zstd.cpp
View File

@ -73,12 +73,14 @@ TEST_F(DumpCustomZstdTest, compressed_run1)
{
if(!ZSTD_BINARY) GTEST_SKIP();
auto text_file = "dump_custom_text_run1.melt";
auto compressed_file = "dump_custom_compressed_run1.melt.zst";
auto text_file = "dump_custom_zstd_text_run1.melt";
auto compressed_file = "dump_custom_zstd_compressed_run1.melt.zst";
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/zstd", fields, "units yes", 1);
TearDown();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(compressed_file);
@ -95,14 +97,16 @@ TEST_F(DumpCustomZstdTest, compressed_triclinic_run1)
{
if(!ZSTD_BINARY) GTEST_SKIP();
auto text_file = "dump_custom_tri_text_run1.melt";
auto compressed_file = "dump_custom_tri_compressed_run1.melt.zst";
auto text_file = "dump_custom_zstd_tri_text_run1.melt";
auto compressed_file = "dump_custom_zstd_tri_compressed_run1.melt.zst";
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/zstd", fields, "units yes", 1);
TearDown();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(compressed_file);