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Update dump local and local/gz

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This commit is contained in:
Richard Berger
2021-04-09 15:42:28 -04:00
parent d19cd8fb11
commit cf41ea6faf
5 changed files with 285 additions and 70 deletions
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118
src/COMPRESS/dump_local_gz.cpp
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@ -11,24 +11,18 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "dump_local_gz.h"
#include "domain.h"
#include "dump_local_gz.h"
#include "error.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) :
DumpLocal(lmp, narg, arg)
{
gzFp = nullptr;
compression_level = Z_BEST_COMPRESSION;
if (!compressed)
error->all(FLERR,"Dump local/gz only writes compressed files");
}
@ -38,12 +32,8 @@ DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) :
DumpLocalGZ::~DumpLocalGZ()
{
if (gzFp) gzclose(gzFp);
gzFp = nullptr;
fp = nullptr;
}
/* ----------------------------------------------------------------------
generic opening of a dump file
ASCII or binary or gzipped
@ -93,17 +83,12 @@ void DumpLocalGZ::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 +97,34 @@ void DumpLocalGZ::openfile()
void DumpLocalGZ::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 %s\n",label);
gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
if (domain->triclinic) {
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);
} else {
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);
if (time_flag) {
header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
}
gzprintf(gzFp,"ITEM: %s %s\n",label,columns);
header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
header += fmt::format("ITEM: NUMBER OF {}\n{}\n", label, 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: {} {}\n", label, columns);
writer.write(header.c_str(), header.length());
}
}
@ -143,19 +133,28 @@ void DumpLocalGZ::write_header(bigint ndump)
void DumpLocalGZ::write_data(int n, double *mybuf)
{
if (buffer_flag == 1) {
gzwrite(gzFp,mybuf,sizeof(char)*n);
writer.write(mybuf, sizeof(char)*n);
} else {
int i,j;
constexpr size_t VBUFFER_SIZE = 256;
char vbuffer[VBUFFER_SIZE];
int m = 0;
for (i = 0; i < n; i++) {
for (j = 0; j < size_one; j++) {
if (vtype[j] == INT)
gzprintf(gzFp,vformat[j],static_cast<int> (mybuf[m]));
else gzprintf(gzFp,vformat[j],mybuf[m]);
for (int i = 0; i < n; i++) {
for (int j = 0; j < size_one; j++) {
int written = 0;
if (vtype[j] == Dump::INT) {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
} else {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
}
if (written > 0) {
writer.write(vbuffer, written);
} else if (written < 0) {
error->one(FLERR, "Error while writing dump local/gz output");
}
m++;
}
gzprintf(gzFp,"\n");
writer.write("\n", 1);
}
}
}
@ -167,11 +166,11 @@ void DumpLocalGZ::write()
DumpLocal::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();
}
}
}
}
@ -182,14 +181,15 @@ int DumpLocalGZ::modify_param(int narg, char **arg)
{
int consumed = DumpLocal::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;