jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Update dump custom/gz

This commit is contained in:
Richard Berger 2021-04-09 16:36:30 -04:00
parent c17ee12989
commit 511f64fde4
No known key found for this signature in database
GPG Key ID: A9E83994E0BA0CAB
12 changed files with 106 additions and 70 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
src/COMPRESS/dump_atom_gz.cpp
View File

@ -71,7 +71,9 @@ void DumpAtomGZ::openfile()
nameslist[numfiles] = utils::strdup(filecurrent);
++numfiles;
} else {
remove(nameslist[fileidx]);
if (remove(nameslist[fileidx]) != 0) {
error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
}
delete[] nameslist[fileidx];
nameslist[fileidx] = utils::strdup(filecurrent);
fileidx = (fileidx + 1) % maxfiles;

4
src/COMPRESS/dump_atom_zstd.cpp
View File

@ -79,7 +79,9 @@ void DumpAtomZstd::openfile()
nameslist[numfiles] = utils::strdup(filecurrent);
++numfiles;
} else {
remove(nameslist[fileidx]);
if (remove(nameslist[fileidx]) != 0) {
error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
}
delete[] nameslist[fileidx];
nameslist[fileidx] = utils::strdup(filecurrent);
fileidx = (fileidx + 1) % maxfiles;

4
src/COMPRESS/dump_cfg_gz.cpp
View File

@ -73,7 +73,9 @@ void DumpCFGGZ::openfile()
nameslist[numfiles] = utils::strdup(filecurrent);
++numfiles;
} else {
remove(nameslist[fileidx]);
if (remove(nameslist[fileidx]) != 0) {
error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
}
delete[] nameslist[fileidx];
nameslist[fileidx] = utils::strdup(filecurrent);
fileidx = (fileidx + 1) % maxfiles;

4
src/COMPRESS/dump_cfg_zstd.cpp
View File

@ -81,7 +81,9 @@ void DumpCFGZstd::openfile()
nameslist[numfiles] = utils::strdup(filecurrent);
++numfiles;
} else {
remove(nameslist[fileidx]);
if (remove(nameslist[fileidx]) != 0) {
error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
}
delete[] nameslist[fileidx];
nameslist[fileidx] = utils::strdup(filecurrent);
fileidx = (fileidx + 1) % maxfiles;

98
src/COMPRESS/dump_custom_gz.cpp
View File

@ -11,39 +11,28 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "dump_custom_gz.h"
#include "domain.h"
#include "dump_custom_gz.h"
#include "error.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
DumpCustomGZ::DumpCustomGZ(LAMMPS *lmp, int narg, char **arg) :
DumpCustom(lmp, narg, arg)
{
gzFp = nullptr;
compression_level = Z_BEST_COMPRESSION;
if (!compressed)
error->all(FLERR,"Dump custom/gz only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpCustomGZ::~DumpCustomGZ()
{
if (gzFp) gzclose(gzFp);
gzFp = nullptr;
fp = nullptr;
}
/* ----------------------------------------------------------------------
generic opening of a dump file
ASCII or binary or gzipped
@ -82,7 +71,9 @@ void DumpCustomGZ::openfile()
nameslist[numfiles] = utils::strdup(filecurrent);
++numfiles;
} else {
remove(nameslist[fileidx]);
if (remove(nameslist[fileidx]) != 0) {
error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
}
delete[] nameslist[fileidx];
nameslist[fileidx] = utils::strdup(filecurrent);
fileidx = (fileidx + 1) % maxfiles;
@ -93,17 +84,12 @@ void DumpCustomGZ::openfile()
// each proc with filewriter = 1 opens a file
if (filewriter) {
std::string mode;
if (append_flag) {
mode = fmt::format("ab{}", compression_level);
} else {
mode = fmt::format("wb{}", compression_level);
try {
writer.open(filecurrent, append_flag);
} catch (FileWriterException &e) {
error->one(FLERR, e.what());
}
gzFp = gzopen(filecurrent, mode.c_str());
if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file");
} else gzFp = nullptr;
}
// delete string with timestep replaced
@ -112,29 +98,34 @@ void DumpCustomGZ::openfile()
void DumpCustomGZ::write_header(bigint ndump)
{
std::string header;
if ((multiproc) || (!multiproc && me == 0)) {
if (unit_flag && !unit_count) {
++unit_count;
gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);
header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style);
}
if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time());
gzprintf(gzFp,"ITEM: TIMESTEP\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
if (domain->triclinic == 0) {
gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
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,"%-1.16e %-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);
if (time_flag) {
header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
}
gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
if (domain->triclinic == 0) {
header += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr);
header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxxlo, boxxhi);
header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxylo, boxyhi);
header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxzlo, boxzhi);
} else {
header += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr);
header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxxlo, boxxhi, boxxy);
header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxylo, boxyhi, boxxz);
header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxzlo, boxzhi, boxyz);
}
header += fmt::format("ITEM: ATOMS {}\n", columns);
writer.write(header.c_str(), header.length());
}
}
@ -142,7 +133,7 @@ void DumpCustomGZ::write_header(bigint ndump)
void DumpCustomGZ::write_data(int n, double *mybuf)
{
gzwrite(gzFp,mybuf,sizeof(char)*n);
writer.write(mybuf, n);
}
/* ---------------------------------------------------------------------- */
@ -152,11 +143,11 @@ void DumpCustomGZ::write()
DumpCustom::write();
if (filewriter) {
if (multifile) {
gzclose(gzFp);
gzFp = nullptr;
writer.close();
} else {
if (flush_flag)
gzflush(gzFp,Z_SYNC_FLUSH);
if (flush_flag && writer.isopen()) {
writer.flush();
}
}
}
}
@ -167,14 +158,15 @@ 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;
compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
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],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
writer.setCompressionLevel(compression_level);
return 2;
}
} catch (FileWriterException &e) {
error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what()));
}
}
return consumed;

5
src/COMPRESS/dump_custom_gz.h
View File

@ -21,7 +21,7 @@ DumpStyle(custom/gz,DumpCustomGZ)
#define LMP_DUMP_CUSTOM_GZ_H
#include "dump_custom.h"
#include <zlib.h>
#include "gz_file_writer.h"
namespace LAMMPS_NS {
@ -31,8 +31,7 @@ class DumpCustomGZ : public DumpCustom {
virtual ~DumpCustomGZ();
protected:
int compression_level;
gzFile gzFp; // file pointer for the compressed output stream
GzFileWriter writer;
virtual void openfile();
virtual void write_header(bigint);

7
src/COMPRESS/dump_custom_zstd.cpp
View File

@ -20,7 +20,6 @@
#include "domain.h"
#include "dump_custom_zstd.h"
#include "error.h"
#include "file_writer.h"
#include "update.h"
#include <cstring>
@ -79,7 +78,9 @@ void DumpCustomZstd::openfile()
nameslist[numfiles] = utils::strdup(filecurrent);
++numfiles;
} else {
remove(nameslist[fileidx]);
if (remove(nameslist[fileidx]) != 0) {
error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
}
delete[] nameslist[fileidx];
nameslist[fileidx] = utils::strdup(filecurrent);
fileidx = (fileidx + 1) % maxfiles;
@ -184,7 +185,7 @@ int DumpCustomZstd::modify_param(int narg, char **arg)
return 2;
}
} catch (FileWriterException &e) {
error->one(FLERR, e.what());
error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what()));
}
}
return consumed;

5
src/COMPRESS/dump_local_gz.cpp
View File

@ -27,7 +27,6 @@ DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Dump local/gz only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpLocalGZ::~DumpLocalGZ()
@ -72,7 +71,9 @@ void DumpLocalGZ::openfile()
nameslist[numfiles] = utils::strdup(filecurrent);
++numfiles;
} else {
remove(nameslist[fileidx]);
if (remove(nameslist[fileidx]) != 0) {
error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
}
delete[] nameslist[fileidx];
nameslist[fileidx] = utils::strdup(filecurrent);
fileidx = (fileidx + 1) % maxfiles;

4
src/COMPRESS/dump_local_zstd.cpp
View File

@ -78,7 +78,9 @@ void DumpLocalZstd::openfile()
nameslist[numfiles] = utils::strdup(filecurrent);
++numfiles;
} else {
remove(nameslist[fileidx]);
if (remove(nameslist[fileidx]) != 0) {
error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
}
delete[] nameslist[fileidx];
nameslist[fileidx] = utils::strdup(filecurrent);
fileidx = (fileidx + 1) % maxfiles;

4
src/COMPRESS/dump_xyz_gz.cpp
View File

@ -71,7 +71,9 @@ void DumpXYZGZ::openfile()
nameslist[numfiles] = utils::strdup(filecurrent);
++numfiles;
} else {
remove(nameslist[fileidx]);
if (remove(nameslist[fileidx]) != 0) {
error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
}
delete[] nameslist[fileidx];
nameslist[fileidx] = utils::strdup(filecurrent);
fileidx = (fileidx + 1) % maxfiles;

4
src/COMPRESS/dump_xyz_zstd.cpp
View File

@ -78,7 +78,9 @@ void DumpXYZZstd::openfile()
nameslist[numfiles] = utils::strdup(filecurrent);
++numfiles;
} else {
remove(nameslist[fileidx]);
if (remove(nameslist[fileidx]) != 0) {
error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
}
delete[] nameslist[fileidx];
nameslist[fileidx] = utils::strdup(filecurrent);
fileidx = (fileidx + 1) % maxfiles;

33
unittest/formats/test_dump_custom_compressed.cpp
View File

@ -58,6 +58,35 @@ TEST_F(DumpCustomCompressTest, compressed_run1)
delete_file(converted_file);
}
TEST_F(DumpCustomCompressTest, compressed_with_time_run1)
{
if (!COMPRESS_BINARY) GTEST_SKIP();
auto base_name = "with_time_custom_run1.melt";
auto text_file = text_dump_filename(base_name);
auto compressed_file = compressed_dump_filename(base_name);
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";
if(compression_style == "custom/zstd") {
generate_text_and_compressed_dump(text_file, compressed_file, fields, fields, "time yes", "time yes checksum yes", 1);
} else {
generate_text_and_compressed_dump(text_file, compressed_file, fields, "time yes", 1);
}
TearDown();
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(DumpCustomCompressTest, compressed_triclinic_run1)
{
if (!COMPRESS_BINARY) GTEST_SKIP();
@ -222,7 +251,7 @@ TEST_F(DumpCustomCompressTest, compressed_modify_bad_param)
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";
command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.custom"), fields));
TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*",
TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*",
command("dump_modify id1 compression_level 12");
);
}
@ -234,7 +263,7 @@ TEST_F(DumpCustomCompressTest, compressed_modify_multi_bad_param)
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";
command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.custom"), fields));
TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*",
TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*",
command("dump_modify id1 pad 3 compression_level 12");
);
}