mirror of https://github.com/lammps/lammps.git
Add Zstd variants of dump local and xyz
This commit is contained in:
Richard Berger
parent
a0f82a4b18
commit
c5a2e50bf5
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@ -11,6 +11,10 @@
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See the README file in the top-level LAMMPS directory.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Richard Berger (Temple U)
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------------------------------------------------------------------------- */
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#include "dump_cfg_zstd.h"
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#include "dump_cfg_zstd.h"
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#include "atom.h"
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#include "atom.h"
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#include "domain.h"
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#include "domain.h"
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@ -11,6 +11,10 @@
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See the README file in the top-level LAMMPS directory.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Richard Berger (Temple U)
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------------------------------------------------------------------------- */
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#ifdef DUMP_CLASS
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#ifdef DUMP_CLASS
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DumpStyle(cfg/zstd,DumpCFGZstd)
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DumpStyle(cfg/zstd,DumpCFGZstd)
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@ -122,18 +122,18 @@ void DumpLocalGZ::write_header(bigint ndump)
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gzprintf(gzFp,"ITEM: TIMESTEP\n");
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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,BIGINT_FORMAT "\n",update->ntimestep);
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gzprintf(gzFp,"ITEM: NUMBER OF ENTRIES\n");
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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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gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
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if (domain->triclinic) {
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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,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
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gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy);
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gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy);
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gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz);
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gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz);
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gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz);
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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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} else {
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gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
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gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
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gzprintf(gzFp,"%-1.16g %-1.16g\n",boxxlo,boxxhi);
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gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi);
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gzprintf(gzFp,"%-1.16g %-1.16g\n",boxylo,boxyhi);
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gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi);
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gzprintf(gzFp,"%-1.16g %-1.16g\n",boxzlo,boxzhi);
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gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi);
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}
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}
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gzprintf(gzFp,"ITEM: %s %s\n",label,columns);
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gzprintf(gzFp,"ITEM: %s %s\n",label,columns);
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}
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}
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@ -0,0 +1,191 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Richard Berger (Temple U)
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------------------------------------------------------------------------- */
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#include "dump_local_zstd.h"
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#include "domain.h"
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#include "error.h"
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#include "update.h"
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#include "force.h"
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#include <cstring>
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#include <fmt/format.h>
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using namespace LAMMPS_NS;
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DumpLocalZstd::DumpLocalZstd(LAMMPS *lmp, int narg, char **arg) :
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DumpLocal(lmp, narg, arg)
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{
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if (!compressed)
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error->all(FLERR,"Dump local/zstd only writes compressed files");
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}
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/* ---------------------------------------------------------------------- */
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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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some derived classes override this function
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------------------------------------------------------------------------- */
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void DumpLocalZstd::openfile()
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{
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// single file, already opened, so just return
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if (singlefile_opened) return;
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if (multifile == 0) singlefile_opened = 1;
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// if one file per timestep, replace '*' with current timestep
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char *filecurrent = filename;
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if (multiproc) filecurrent = multiname;
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if (multifile) {
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char *filestar = filecurrent;
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filecurrent = new char[strlen(filestar) + 16];
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char *ptr = strchr(filestar,'*');
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*ptr = '\0';
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if (padflag == 0)
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sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
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filestar,update->ntimestep,ptr+1);
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else {
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char bif[8],pad[16];
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strcpy(bif,BIGINT_FORMAT);
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sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
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sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
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}
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*ptr = '*';
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if (maxfiles > 0) {
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if (numfiles < maxfiles) {
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nameslist[numfiles] = new char[strlen(filecurrent)+1];
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strcpy(nameslist[numfiles],filecurrent);
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++numfiles;
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} else {
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remove(nameslist[fileidx]);
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delete[] nameslist[fileidx];
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nameslist[fileidx] = new char[strlen(filecurrent)+1];
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strcpy(nameslist[fileidx],filecurrent);
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fileidx = (fileidx + 1) % maxfiles;
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}
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}
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}
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// each proc with filewriter = 1 opens a file
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if (filewriter) {
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if (append_flag) {
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error->one(FLERR, "dump cfg/zstd currently doesn't support append");
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}
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try {
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writer.open(filecurrent);
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} catch (FileWriterException & e) {
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error->one(FLERR, e.what());
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}
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}
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// delete string with timestep replaced
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if (multifile) delete [] filecurrent;
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}
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void DumpLocalZstd::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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header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style);
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}
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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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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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/* ---------------------------------------------------------------------- */
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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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}
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/* ---------------------------------------------------------------------- */
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void DumpLocalZstd::write()
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{
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DumpLocal::write();
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if (filewriter) {
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if (multifile) {
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writer.close();
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} else {
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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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/* ---------------------------------------------------------------------- */
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int DumpLocalZstd::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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try {
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if (strcmp(arg[0],"checksum") == 0) {
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if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
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if (strcmp(arg[1],"yes") == 0) writer.setChecksum(true);
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else if (strcmp(arg[1],"no") == 0) writer.setChecksum(false);
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else error->all(FLERR,"Illegal dump_modify command");
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return 2;
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} else 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 = force->inumeric(FLERR,arg[1]);
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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, e.what());
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}
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}
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return consumed;
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}
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@ -0,0 +1,63 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Richard Berger (Temple U)
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------------------------------------------------------------------------- */
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#ifdef DUMP_CLASS
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DumpStyle(local/zstd,DumpLocalZstd)
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#else
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#ifndef LMP_DUMP_LOCAL_ZSTD_H
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#define LMP_DUMP_LOCAL_ZSTD_H
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#include "dump_local.h"
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#include "zstd_file_writer.h"
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namespace LAMMPS_NS {
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class DumpLocalZstd : public DumpLocal {
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public:
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DumpLocalZstd(class LAMMPS *, int, char **);
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virtual ~DumpLocalZstd();
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protected:
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ZstdFileWriter writer;
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virtual void openfile();
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virtual void write_header(bigint);
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virtual void write_data(int, double *);
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virtual void write();
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virtual int modify_param(int, char **);
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Dump local/zstd only writes compressed files
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The dump local/zstd output file name must have a .zst suffix.
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E: Cannot open dump file
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Self-explanatory.
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*/
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@ -0,0 +1,166 @@
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/* ----------------------------------------------------------------------
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||||||
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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|
http://lammps.sandia.gov, Sandia National Laboratories
|
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|
Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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||||||
|
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.
|
||||||
|
------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Richard Berger (Temple U)
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------------------------------------------------------------------------- */
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#include "dump_xyz_zstd.h"
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#include "error.h"
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#include "update.h"
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#include "force.h"
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#include <cstring>
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#include <fmt/format.h>
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using namespace LAMMPS_NS;
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DumpXYZZstd::DumpXYZZstd(LAMMPS *lmp, int narg, char **arg) :
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DumpXYZ(lmp, narg, arg)
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{
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if (!compressed)
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error->all(FLERR,"Dump xyz/zstd only writes compressed files");
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}
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/* ---------------------------------------------------------------------- */
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DumpXYZZstd::~DumpXYZZstd()
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{
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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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||||||
|
some derived classes override this function
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------------------------------------------------------------------------- */
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void DumpXYZZstd::openfile()
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{
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// single file, already opened, so just return
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if (singlefile_opened) return;
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if (multifile == 0) singlefile_opened = 1;
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// if one file per timestep, replace '*' with current timestep
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char *filecurrent = filename;
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if (multiproc) filecurrent = multiname;
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if (multifile) {
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char *filestar = filecurrent;
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filecurrent = new char[strlen(filestar) + 16];
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char *ptr = strchr(filestar,'*');
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*ptr = '\0';
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if (padflag == 0)
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||||||
|
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
|
||||||
|
filestar,update->ntimestep,ptr+1);
|
||||||
|
else {
|
||||||
|
char bif[8],pad[16];
|
||||||
|
strcpy(bif,BIGINT_FORMAT);
|
||||||
|
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
|
||||||
|
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
|
||||||
|
}
|
||||||
|
*ptr = '*';
|
||||||
|
if (maxfiles > 0) {
|
||||||
|
if (numfiles < maxfiles) {
|
||||||
|
nameslist[numfiles] = new char[strlen(filecurrent)+1];
|
||||||
|
strcpy(nameslist[numfiles],filecurrent);
|
||||||
|
++numfiles;
|
||||||
|
} else {
|
||||||
|
remove(nameslist[fileidx]);
|
||||||
|
delete[] nameslist[fileidx];
|
||||||
|
nameslist[fileidx] = new char[strlen(filecurrent)+1];
|
||||||
|
strcpy(nameslist[fileidx],filecurrent);
|
||||||
|
fileidx = (fileidx + 1) % maxfiles;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// each proc with filewriter = 1 opens a file
|
||||||
|
|
||||||
|
if (filewriter) {
|
||||||
|
if (append_flag) {
|
||||||
|
error->one(FLERR, "dump cfg/zstd currently doesn't support append");
|
||||||
|
}
|
||||||
|
|
||||||
|
try {
|
||||||
|
writer.open(filecurrent);
|
||||||
|
} catch (FileWriterException & e) {
|
||||||
|
error->one(FLERR, e.what());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// delete string with timestep replaced
|
||||||
|
|
||||||
|
if (multifile) delete [] filecurrent;
|
||||||
|
}
|
||||||
|
|
||||||
|
void DumpXYZZstd::write_header(bigint ndump)
|
||||||
|
{
|
||||||
|
if (me == 0) {
|
||||||
|
std::string header = fmt::format("{}\n", ndump);
|
||||||
|
header += fmt::format("Atoms. Timestep: {}\n", update->ntimestep);
|
||||||
|
writer.write(header.c_str(), header.length());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void DumpXYZZstd::write_data(int n, double *mybuf)
|
||||||
|
{
|
||||||
|
writer.write(mybuf, n);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void DumpXYZZstd::write()
|
||||||
|
{
|
||||||
|
DumpXYZ::write();
|
||||||
|
if (filewriter) {
|
||||||
|
if (multifile) {
|
||||||
|
writer.close();
|
||||||
|
} else {
|
||||||
|
if (flush_flag && writer.isopen()) {
|
||||||
|
writer.flush();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
int DumpXYZZstd::modify_param(int narg, char **arg)
|
||||||
|
{
|
||||||
|
int consumed = DumpXYZ::modify_param(narg, arg);
|
||||||
|
if(consumed == 0) {
|
||||||
|
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;
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,63 @@
|
||||||
|
/* -*- 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)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef DUMP_CLASS
|
||||||
|
|
||||||
|
DumpStyle(xyz/zstd,DumpXYZZstd)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_DUMP_XYZ_ZSTD_H
|
||||||
|
#define LMP_DUMP_XYZ_ZSTD_H
|
||||||
|
|
||||||
|
#include "dump_xyz.h"
|
||||||
|
#include "zstd_file_writer.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class DumpXYZZstd : public DumpXYZ {
|
||||||
|
public:
|
||||||
|
DumpXYZZstd(class LAMMPS *, int, char **);
|
||||||
|
virtual ~DumpXYZZstd();
|
||||||
|
|
||||||
|
protected:
|
||||||
|
ZstdFileWriter writer;
|
||||||
|
|
||||||
|
virtual void openfile();
|
||||||
|
virtual void write_header(bigint);
|
||||||
|
virtual void write_data(int, double *);
|
||||||
|
virtual void write();
|
||||||
|
|
||||||
|
virtual int modify_param(int, char **);
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Dump xyz/zstd only writes compressed files
|
||||||
|
|
||||||
|
The dump xyz/zstd output file name must have a .zst suffix.
|
||||||
|
|
||||||
|
E: Cannot open dump file
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
*/
|
||||||
|
|
@ -268,14 +268,14 @@ void DumpLocal::write_header(bigint ndump)
|
||||||
fprintf(fp,BIGINT_FORMAT "\n",ndump);
|
fprintf(fp,BIGINT_FORMAT "\n",ndump);
|
||||||
if (domain->triclinic) {
|
if (domain->triclinic) {
|
||||||
fprintf(fp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
|
fprintf(fp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
|
||||||
fprintf(fp,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy);
|
fprintf(fp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy);
|
||||||
fprintf(fp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz);
|
fprintf(fp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz);
|
||||||
fprintf(fp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz);
|
fprintf(fp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz);
|
||||||
} else {
|
} else {
|
||||||
fprintf(fp,"ITEM: BOX BOUNDS %s\n",boundstr);
|
fprintf(fp,"ITEM: BOX BOUNDS %s\n",boundstr);
|
||||||
fprintf(fp,"%-1.16g %-1.16g\n",boxxlo,boxxhi);
|
fprintf(fp,"%-1.16e %-1.16e\n",boxxlo,boxxhi);
|
||||||
fprintf(fp,"%-1.16g %-1.16g\n",boxylo,boxyhi);
|
fprintf(fp,"%-1.16e %-1.16e\n",boxylo,boxyhi);
|
||||||
fprintf(fp,"%-1.16g %-1.16g\n",boxzlo,boxzhi);
|
fprintf(fp,"%-1.16e %-1.16e\n",boxzlo,boxzhi);
|
||||||
}
|
}
|
||||||
fprintf(fp,"ITEM: %s %s\n",label,columns);
|
fprintf(fp,"ITEM: %s %s\n",label,columns);
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -82,6 +82,18 @@ if (PKG_COMPRESS)
|
||||||
add_test(NAME DumpCfgZstd COMMAND test_dump_cfg_zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
add_test(NAME DumpCfgZstd COMMAND test_dump_cfg_zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
||||||
set_tests_properties(DumpCfgZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
|
set_tests_properties(DumpCfgZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
|
||||||
set_tests_properties(DumpCfgZstd PROPERTIES ENVIRONMENT "ZSTD_BINARY=${ZSTD_BINARY}")
|
set_tests_properties(DumpCfgZstd PROPERTIES ENVIRONMENT "ZSTD_BINARY=${ZSTD_BINARY}")
|
||||||
|
|
||||||
|
add_executable(test_dump_xyz_zstd test_dump_xyz_zstd.cpp)
|
||||||
|
target_link_libraries(test_dump_xyz_zstd PRIVATE lammps GTest::GMock GTest::GTest)
|
||||||
|
add_test(NAME DumpXYZZstd COMMAND test_dump_xyz_zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
||||||
|
set_tests_properties(DumpXYZZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
|
||||||
|
set_tests_properties(DumpXYZZstd PROPERTIES ENVIRONMENT "ZSTD_BINARY=${ZSTD_BINARY}")
|
||||||
|
|
||||||
|
add_executable(test_dump_local_zstd test_dump_local_zstd.cpp)
|
||||||
|
target_link_libraries(test_dump_local_zstd PRIVATE lammps GTest::GMock GTest::GTest)
|
||||||
|
add_test(NAME DumpLocalZstd COMMAND test_dump_local_zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
||||||
|
set_tests_properties(DumpLocalZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
|
||||||
|
set_tests_properties(DumpLocalZstd PROPERTIES ENVIRONMENT "ZSTD_BINARY=${ZSTD_BINARY}")
|
||||||
endif()
|
endif()
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,106 @@
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
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"
|
||||||
|
|
||||||
|
char * ZSTD_BINARY = nullptr;
|
||||||
|
|
||||||
|
using ::testing::Eq;
|
||||||
|
|
||||||
|
class DumpLocalGZTest : public MeltTest {
|
||||||
|
std::string dump_style = "local";
|
||||||
|
public:
|
||||||
|
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 {} > {}", ZSTD_BINARY, compressed_file, converted_file);
|
||||||
|
system(cmdline.c_str());
|
||||||
|
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||||
|
return converted_file;
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
TEST_F(DumpLocalGZTest, compressed_run0)
|
||||||
|
{
|
||||||
|
if(!ZSTD_BINARY) GTEST_SKIP();
|
||||||
|
|
||||||
|
if (!verbose) ::testing::internal::CaptureStdout();
|
||||||
|
command("compute comp all pair/local dist eng");
|
||||||
|
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||||
|
|
||||||
|
auto text_files = "dump_local_zstd_text_run*.melt.local";
|
||||||
|
auto compressed_files = "dump_local_zstd_compressed_run*.melt.local.zst";
|
||||||
|
auto text_file = "dump_local_zstd_text_run0.melt.local";
|
||||||
|
auto compressed_file = "dump_local_zstd_compressed_run0.melt.local.zst";
|
||||||
|
auto fields = "index c_comp[1]";
|
||||||
|
|
||||||
|
generate_text_and_compressed_dump(text_files, compressed_files, "local/zstd", fields, "", 0);
|
||||||
|
|
||||||
|
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);
|
||||||
|
}
|
||||||
|
|
||||||
|
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;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ZSTD_BINARY = getenv("ZSTD_BINARY");
|
||||||
|
|
||||||
|
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
|
||||||
|
|
||||||
|
int rv = RUN_ALL_TESTS();
|
||||||
|
MPI_Finalize();
|
||||||
|
return rv;
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,101 @@
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
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"
|
||||||
|
|
||||||
|
char * ZSTD_BINARY = nullptr;
|
||||||
|
|
||||||
|
using ::testing::Eq;
|
||||||
|
|
||||||
|
class DumpXYZGZTest : public MeltTest {
|
||||||
|
std::string dump_style = "xyz";
|
||||||
|
public:
|
||||||
|
void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, std::string compression_style,
|
||||||
|
std::string dump_modify_options, int ntimesteps) {
|
||||||
|
if (!verbose) ::testing::internal::CaptureStdout();
|
||||||
|
command(fmt::format("dump id0 all {} 1 {}", dump_style, text_file));
|
||||||
|
command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_file));
|
||||||
|
|
||||||
|
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 {} > {}", ZSTD_BINARY, compressed_file, converted_file);
|
||||||
|
system(cmdline.c_str());
|
||||||
|
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||||
|
return converted_file;
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
TEST_F(DumpXYZGZTest, compressed_run0)
|
||||||
|
{
|
||||||
|
if(!ZSTD_BINARY) GTEST_SKIP();
|
||||||
|
|
||||||
|
auto text_files = "dump_xyz_zstd_text_run*.melt.xyz";
|
||||||
|
auto compressed_files = "dump_xyz_zstd_compressed_run*.melt.xyz.zst";
|
||||||
|
auto text_file = "dump_xyz_zstd_text_run0.melt.xyz";
|
||||||
|
auto compressed_file = "dump_xyz_zstd_compressed_run0.melt.xyz.zst";
|
||||||
|
|
||||||
|
generate_text_and_compressed_dump(text_files, compressed_files, "xyz/zstd", "", 0);
|
||||||
|
|
||||||
|
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);
|
||||||
|
}
|
||||||
|
|
||||||
|
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;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ZSTD_BINARY = getenv("ZSTD_BINARY");
|
||||||
|
|
||||||
|
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
|
||||||
|
|
||||||
|
int rv = RUN_ALL_TESTS();
|
||||||
|
MPI_Finalize();
|
||||||
|
return rv;
|
||||||
|
}
|
||||||
Loading…
Reference in New Issue