forked from lijiext/lammps
Update dump local and local/gz
This commit is contained in:
Richard Berger
parent
d19cd8fb11
commit
cf41ea6faf
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@ -11,24 +11,18 @@
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "dump_local_gz.h"
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#include "domain.h"
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#include "dump_local_gz.h"
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#include "error.h"
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#include "update.h"
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#include <cstring>
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using namespace LAMMPS_NS;
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DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) :
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DumpLocal(lmp, narg, arg)
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{
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gzFp = nullptr;
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compression_level = Z_BEST_COMPRESSION;
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if (!compressed)
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error->all(FLERR,"Dump local/gz only writes compressed files");
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}
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@ -38,12 +32,8 @@ DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) :
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DumpLocalGZ::~DumpLocalGZ()
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{
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if (gzFp) gzclose(gzFp);
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gzFp = nullptr;
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fp = nullptr;
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}
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/* ----------------------------------------------------------------------
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generic opening of a dump file
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ASCII or binary or gzipped
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@ -93,17 +83,12 @@ void DumpLocalGZ::openfile()
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// each proc with filewriter = 1 opens a file
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if (filewriter) {
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std::string mode;
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if (append_flag) {
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mode = fmt::format("ab{}", compression_level);
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} else {
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mode = fmt::format("wb{}", compression_level);
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try {
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writer.open(filecurrent, append_flag);
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} catch (FileWriterException &e) {
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error->one(FLERR, e.what());
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}
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gzFp = gzopen(filecurrent, mode.c_str());
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if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file");
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} else gzFp = nullptr;
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}
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// delete string with timestep replaced
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@ -112,29 +97,34 @@ void DumpLocalGZ::openfile()
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void DumpLocalGZ::write_header(bigint ndump)
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{
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std::string header;
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if ((multiproc) || (!multiproc && me == 0)) {
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if (unit_flag && !unit_count) {
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++unit_count;
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gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);
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header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style);
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}
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if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time());
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gzprintf(gzFp,"ITEM: TIMESTEP\n");
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gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
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gzprintf(gzFp,"ITEM: NUMBER OF %s\n",label);
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gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
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if (domain->triclinic) {
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gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
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gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy);
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gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz);
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gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz);
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} else {
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gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
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gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi);
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gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi);
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gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi);
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if (time_flag) {
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header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
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}
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gzprintf(gzFp,"ITEM: %s %s\n",label,columns);
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header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
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header += fmt::format("ITEM: NUMBER OF {}\n{}\n", label, ndump);
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if (domain->triclinic == 0) {
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header += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr);
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header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxxlo, boxxhi);
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header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxylo, boxyhi);
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header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxzlo, boxzhi);
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} else {
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header += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr);
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header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxxlo, boxxhi, boxxy);
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header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxylo, boxyhi, boxxz);
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header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxzlo, boxzhi, boxyz);
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}
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header += fmt::format("ITEM: {} {}\n", label, columns);
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writer.write(header.c_str(), header.length());
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}
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}
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@ -143,19 +133,28 @@ void DumpLocalGZ::write_header(bigint ndump)
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void DumpLocalGZ::write_data(int n, double *mybuf)
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{
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if (buffer_flag == 1) {
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gzwrite(gzFp,mybuf,sizeof(char)*n);
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writer.write(mybuf, sizeof(char)*n);
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} else {
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int i,j;
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constexpr size_t VBUFFER_SIZE = 256;
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char vbuffer[VBUFFER_SIZE];
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int m = 0;
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for (i = 0; i < n; i++) {
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for (j = 0; j < size_one; j++) {
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if (vtype[j] == INT)
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gzprintf(gzFp,vformat[j],static_cast<int> (mybuf[m]));
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else gzprintf(gzFp,vformat[j],mybuf[m]);
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for (int i = 0; i < n; i++) {
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for (int j = 0; j < size_one; j++) {
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int written = 0;
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if (vtype[j] == Dump::INT) {
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written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
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} else {
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written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
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}
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if (written > 0) {
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writer.write(vbuffer, written);
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} else if (written < 0) {
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error->one(FLERR, "Error while writing dump local/gz output");
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}
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m++;
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}
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gzprintf(gzFp,"\n");
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writer.write("\n", 1);
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}
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}
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}
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@ -167,11 +166,11 @@ void DumpLocalGZ::write()
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DumpLocal::write();
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if (filewriter) {
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if (multifile) {
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gzclose(gzFp);
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gzFp = nullptr;
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writer.close();
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} else {
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if (flush_flag)
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gzflush(gzFp,Z_SYNC_FLUSH);
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if (flush_flag && writer.isopen()) {
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writer.flush();
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}
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}
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}
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}
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@ -182,14 +181,15 @@ int DumpLocalGZ::modify_param(int narg, char **arg)
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{
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int consumed = DumpLocal::modify_param(narg, arg);
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if (consumed == 0) {
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if (strcmp(arg[0],"compression_level") == 0) {
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if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
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int min_level = Z_DEFAULT_COMPRESSION;
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int max_level = Z_BEST_COMPRESSION;
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compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
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if (compression_level < min_level || compression_level > max_level)
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error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level));
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return 2;
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try {
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if (strcmp(arg[0],"compression_level") == 0) {
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if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
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int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
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writer.setCompressionLevel(compression_level);
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return 2;
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}
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} catch (FileWriterException &e) {
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error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what()));
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}
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}
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return consumed;
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@ -21,7 +21,7 @@ DumpStyle(local/gz,DumpLocalGZ)
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#define LMP_DUMP_LOCAL_GZ_H
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#include "dump_local.h"
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#include <zlib.h>
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#include "gz_file_writer.h"
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namespace LAMMPS_NS {
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@ -31,8 +31,7 @@ class DumpLocalGZ : public DumpLocal {
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virtual ~DumpLocalGZ();
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protected:
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int compression_level;
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gzFile gzFp; // file pointer for the compressed output stream
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GzFileWriter writer;
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virtual void openfile();
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virtual void write_header(bigint);
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@ -17,15 +17,13 @@
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#ifdef LAMMPS_ZSTD
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#include "dump_local_zstd.h"
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#include "domain.h"
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#include "dump_local_zstd.h"
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#include "error.h"
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#include "update.h"
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#include <cstring>
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using namespace LAMMPS_NS;
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DumpLocalZstd::DumpLocalZstd(LAMMPS *lmp, int narg, char **arg) :
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@ -42,7 +40,6 @@ DumpLocalZstd::~DumpLocalZstd()
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{
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}
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/* ----------------------------------------------------------------------
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generic opening of a dump file
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ASCII or binary or gzipped
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@ -145,7 +142,31 @@ void DumpLocalZstd::write_header(bigint ndump)
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void DumpLocalZstd::write_data(int n, double *mybuf)
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{
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writer.write(mybuf, sizeof(char)*n);
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if (buffer_flag == 1) {
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writer.write(mybuf, sizeof(char)*n);
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} else {
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constexpr size_t VBUFFER_SIZE = 256;
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char vbuffer[VBUFFER_SIZE];
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int m = 0;
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for (int i = 0; i < n; i++) {
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for (int j = 0; j < size_one; j++) {
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int written = 0;
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if (vtype[j] == Dump::INT) {
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written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
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} else {
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written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
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}
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if (written > 0) {
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writer.write(vbuffer, written);
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} else if (written < 0) {
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error->one(FLERR, "Error while writing dump local/gz output");
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}
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m++;
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}
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writer.write("\n", 1);
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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@ -184,7 +205,7 @@ int DumpLocalZstd::modify_param(int narg, char **arg)
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return 2;
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}
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} catch (FileWriterException &e) {
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error->one(FLERR, e.what());
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error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what()));
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}
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}
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return consumed;
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@ -93,6 +93,18 @@ TEST_F(DumpLocalTest, run0)
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delete_file(dump_file);
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}
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TEST_F(DumpLocalTest, label_run0)
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{
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auto dump_file = "dump_local_label_run0.melt";
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generate_dump(dump_file, "index c_comp[1]", "label ELEMENTS", 0);
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ASSERT_FILE_EXISTS(dump_file);
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auto lines = read_lines(dump_file);
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ASSERT_THAT(lines[2], Eq("ITEM: NUMBER OF ELEMENTS"));
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ASSERT_THAT(lines[8], Eq("ITEM: ELEMENTS index c_comp[1] "));
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delete_file(dump_file);
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}
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TEST_F(DumpLocalTest, format_line_run0)
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{
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auto dump_file = "dump_local_format_line_run0.melt";
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@ -170,6 +182,60 @@ TEST_F(DumpLocalTest, no_buffer_run0)
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delete_file(dump_file);
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}
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TEST_F(DumpLocalTest, with_units_run0)
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{
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auto dump_file = "dump_with_units_run0.melt";
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generate_dump(dump_file, "index c_comp[1]", "units yes", 0);
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ASSERT_FILE_EXISTS(dump_file);
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auto lines = read_lines(dump_file);
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ASSERT_EQ(lines.size(), 875);
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ASSERT_THAT(lines[0], Eq("ITEM: UNITS"));
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ASSERT_THAT(lines[1], Eq("lj"));
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ASSERT_THAT(lines[2], Eq("ITEM: TIMESTEP"));
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ASSERT_EQ(std::stoi(lines[3]), 0);
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ASSERT_THAT(lines[4], Eq("ITEM: NUMBER OF ENTRIES"));
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ASSERT_EQ(std::stoi(lines[5]), 864);
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}
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TEST_F(DumpLocalTest, with_time_run0)
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{
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auto dump_file = "dump_with_time_run0.melt";
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generate_dump(dump_file, "index c_comp[1]", "time yes", 0);
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ASSERT_FILE_EXISTS(dump_file);
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auto lines = read_lines(dump_file);
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ASSERT_EQ(lines.size(), 875);
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ASSERT_THAT(lines[0], Eq("ITEM: TIME"));
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ASSERT_THAT(std::stof(lines[1]), 0.0);
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ASSERT_THAT(lines[2], Eq("ITEM: TIMESTEP"));
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ASSERT_EQ(std::stoi(lines[3]), 0);
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ASSERT_THAT(lines[4], Eq("ITEM: NUMBER OF ENTRIES"));
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ASSERT_EQ(std::stoi(lines[5]), 864);
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}
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TEST_F(DumpLocalTest, triclinic_run0)
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{
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auto dump_file = "dump_local_triclinic_run0.melt";
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enable_triclinic();
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generate_dump(dump_file, "index c_comp[1]", "", 0);
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ASSERT_FILE_EXISTS(dump_file);
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auto lines = read_lines(dump_file);
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ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS xy xz yz pp pp pp"));
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ASSERT_EQ(utils::split_words(lines[5]).size(), 3);
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ASSERT_EQ(utils::split_words(lines[6]).size(), 3);
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ASSERT_EQ(utils::split_words(lines[7]).size(), 3);
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delete_file(dump_file);
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}
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int main(int argc, char **argv)
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{
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MPI_Init(&argc, &argv);
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@ -69,6 +69,135 @@ TEST_F(DumpLocalCompressTest, compressed_run0)
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delete_file(converted_file_0);
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}
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TEST_F(DumpLocalCompressTest, compressed_no_buffer_run0)
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{
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if (!COMPRESS_BINARY) GTEST_SKIP();
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auto base_name = "no_buffer_run*.melt.local";
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auto base_name_0 = "no_buffer_run0.melt.local";
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auto text_files = text_dump_filename(base_name);
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auto compressed_files = compressed_dump_filename(base_name);
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auto text_file_0 = text_dump_filename(base_name_0);
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auto compressed_file_0 = compressed_dump_filename(base_name_0);
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auto fields = "index c_comp[1]";
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if(compression_style == "local/zstd") {
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generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "buffer no", "buffer no checksum yes", 0);
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} else {
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generate_text_and_compressed_dump(text_files, compressed_files, fields, "buffer no", 0);
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}
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TearDown();
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ASSERT_FILE_EXISTS(text_file_0);
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ASSERT_FILE_EXISTS(compressed_file_0);
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auto converted_file_0 = convert_compressed_to_text(compressed_file_0);
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ASSERT_FILE_EXISTS(converted_file_0);
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ASSERT_FILE_EQUAL(text_file_0, converted_file_0);
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delete_file(text_file_0);
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delete_file(compressed_file_0);
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delete_file(converted_file_0);
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}
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TEST_F(DumpLocalCompressTest, compressed_with_time_run0)
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{
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if (!COMPRESS_BINARY) GTEST_SKIP();
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auto base_name = "with_time_run*.melt.local";
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auto base_name_0 = "with_time_run0.melt.local";
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auto text_files = text_dump_filename(base_name);
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auto compressed_files = compressed_dump_filename(base_name);
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auto text_file_0 = text_dump_filename(base_name_0);
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auto compressed_file_0 = compressed_dump_filename(base_name_0);
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auto fields = "index c_comp[1]";
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if(compression_style == "local/zstd") {
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generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "time yes", "time yes checksum yes", 0);
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} else {
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generate_text_and_compressed_dump(text_files, compressed_files, fields, "time yes", 0);
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}
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TearDown();
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ASSERT_FILE_EXISTS(text_file_0);
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ASSERT_FILE_EXISTS(compressed_file_0);
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auto converted_file_0 = convert_compressed_to_text(compressed_file_0);
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ASSERT_FILE_EXISTS(converted_file_0);
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ASSERT_FILE_EQUAL(text_file_0, converted_file_0);
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delete_file(text_file_0);
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delete_file(compressed_file_0);
|
||||
delete_file(converted_file_0);
|
||||
}
|
||||
|
||||
TEST_F(DumpLocalCompressTest, compressed_with_units_run0)
|
||||
{
|
||||
if (!COMPRESS_BINARY) GTEST_SKIP();
|
||||
|
||||
auto base_name = "with_units_run*.melt.local";
|
||||
auto base_name_0 = "with_units_run0.melt.local";
|
||||
auto text_files = text_dump_filename(base_name);
|
||||
auto compressed_files = compressed_dump_filename(base_name);
|
||||
auto text_file_0 = text_dump_filename(base_name_0);
|
||||
auto compressed_file_0 = compressed_dump_filename(base_name_0);
|
||||
auto fields = "index c_comp[1]";
|
||||
|
||||
if(compression_style == "local/zstd") {
|
||||
generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "units yes", "units yes checksum yes", 0);
|
||||
} else {
|
||||
generate_text_and_compressed_dump(text_files, compressed_files, fields, "units yes", 0);
|
||||
}
|
||||
|
||||
TearDown();
|
||||
|
||||
ASSERT_FILE_EXISTS(text_file_0);
|
||||
ASSERT_FILE_EXISTS(compressed_file_0);
|
||||
|
||||
auto converted_file_0 = convert_compressed_to_text(compressed_file_0);
|
||||
|
||||
ASSERT_FILE_EXISTS(converted_file_0);
|
||||
ASSERT_FILE_EQUAL(text_file_0, converted_file_0);
|
||||
delete_file(text_file_0);
|
||||
delete_file(compressed_file_0);
|
||||
delete_file(converted_file_0);
|
||||
}
|
||||
|
||||
TEST_F(DumpLocalCompressTest, compressed_triclinic_run0)
|
||||
{
|
||||
if (!COMPRESS_BINARY) GTEST_SKIP();
|
||||
enable_triclinic();
|
||||
|
||||
auto base_name = "triclinic_run*.melt.local";
|
||||
auto base_name_0 = "triclinic_run0.melt.local";
|
||||
auto text_files = text_dump_filename(base_name);
|
||||
auto compressed_files = compressed_dump_filename(base_name);
|
||||
auto text_file_0 = text_dump_filename(base_name_0);
|
||||
auto compressed_file_0 = compressed_dump_filename(base_name_0);
|
||||
auto fields = "index c_comp[1]";
|
||||
|
||||
if(compression_style == "local/zstd") {
|
||||
generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "", "checksum yes", 0);
|
||||
} else {
|
||||
generate_text_and_compressed_dump(text_files, compressed_files, fields, "", 0);
|
||||
}
|
||||
|
||||
TearDown();
|
||||
|
||||
ASSERT_FILE_EXISTS(text_file_0);
|
||||
ASSERT_FILE_EXISTS(compressed_file_0);
|
||||
|
||||
auto converted_file_0 = convert_compressed_to_text(compressed_file_0);
|
||||
|
||||
ASSERT_FILE_EXISTS(converted_file_0);
|
||||
ASSERT_FILE_EQUAL(text_file_0, converted_file_0);
|
||||
delete_file(text_file_0);
|
||||
delete_file(compressed_file_0);
|
||||
delete_file(converted_file_0);
|
||||
}
|
||||
|
||||
TEST_F(DumpLocalCompressTest, compressed_multi_file_run1)
|
||||
{
|
||||
if (!COMPRESS_BINARY) GTEST_SKIP();
|
||||
|
|
@ -209,7 +338,7 @@ TEST_F(DumpLocalCompressTest, compressed_modify_bad_param)
|
|||
command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.local"), fields));
|
||||
END_HIDE_OUTPUT();
|
||||
|
||||
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");
|
||||
);
|
||||
}
|
||||
|
|
@ -224,7 +353,7 @@ TEST_F(DumpLocalCompressTest, compressed_modify_multi_bad_param)
|
|||
command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.local"), fields));
|
||||
END_HIDE_OUTPUT();
|
||||
|
||||
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");
|
||||
);
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue