Add Zstd variants of dump local and xyz (c5a2e50b) · Commits · 郑智淋 / lammps

src/COMPRESS/dump_cfg_zstd.cpp

+4 −0

Original line number	Diff line number	Diff line
		@@ -11,6 +11,10 @@
		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		/* ----------------------------------------------------------------------
		Contributing author: Richard Berger (Temple U)
		------------------------------------------------------------------------- */

		#include "dump_cfg_zstd.h"
		#include "atom.h"
		#include "domain.h"

src/COMPRESS/dump_cfg_zstd.h

+4 −0

Original line number	Diff line number	Diff line
		@@ -11,6 +11,10 @@
		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		/* ----------------------------------------------------------------------
		Contributing author: Richard Berger (Temple U)
		------------------------------------------------------------------------- */

		#ifdef DUMP_CLASS

		DumpStyle(cfg/zstd,DumpCFGZstd)

src/COMPRESS/dump_local_gz.cpp

+7 −7

Original line number	Diff line number	Diff line
		@@ -122,18 +122,18 @@ void DumpLocalGZ::write_header(bigint ndump)

		gzprintf(gzFp,"ITEM: TIMESTEP\n");
		gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
		gzprintf(gzFp,"ITEM: NUMBER OF ENTRIES\n");
		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,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy);
		gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz);
		gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz);
		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,"%-1.16g %-1.16g\n",boxxlo,boxxhi);
		gzprintf(gzFp,"%-1.16g %-1.16g\n",boxylo,boxyhi);
		gzprintf(gzFp,"%-1.16g %-1.16g\n",boxzlo,boxzhi);
		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);
		}
		gzprintf(gzFp,"ITEM: %s %s\n",label,columns);
		}

src/COMPRESS/dump_local_zstd.cpp

0 → 100644

+191 −0

Original line number	Diff line number	Diff line
		/* ----------------------------------------------------------------------
		LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
		http://lammps.sandia.gov, Sandia National Laboratories
		Steve Plimpton, sjplimp@sandia.gov

		Copyright (2003) Sandia Corporation. Under the terms of Contract
		DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
		certain rights in this software. This software is distributed under
		the GNU General Public License.

		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		/* ----------------------------------------------------------------------
		Contributing author: Richard Berger (Temple U)
		------------------------------------------------------------------------- */

		#include "dump_local_zstd.h"
		#include "domain.h"
		#include "error.h"
		#include "update.h"
		#include "force.h"

		#include <cstring>
		#include <fmt/format.h>

		using namespace LAMMPS_NS;

		DumpLocalZstd::DumpLocalZstd(LAMMPS lmp, int narg, char *arg) :
		DumpLocal(lmp, narg, arg)
		{
		if (!compressed)
		error->all(FLERR,"Dump local/zstd only writes compressed files");
		}


		/* ---------------------------------------------------------------------- */

		DumpLocalZstd::~DumpLocalZstd()
		{
		}


		/* ----------------------------------------------------------------------
		generic opening of a dump file
		ASCII or binary or gzipped
		some derived classes override this function
		------------------------------------------------------------------------- */

		void DumpLocalZstd::openfile()
		{
		// single file, already opened, so just return

		if (singlefile_opened) return;
		if (multifile == 0) singlefile_opened = 1;

		// if one file per timestep, replace '*' with current timestep

		char *filecurrent = filename;
		if (multiproc) filecurrent = multiname;

		if (multifile) {
		char *filestar = filecurrent;
		filecurrent = new char[strlen(filestar) + 16];
		char ptr = strchr(filestar,'');
		*ptr = '\0';
		if (padflag == 0)
		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 DumpLocalZstd::write_header(bigint ndump)
		{
		std::string header;

		if ((multiproc) \|\| (!multiproc && me == 0)) {
		if (unit_flag && !unit_count) {
		++unit_count;
		header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style);
		}

		if (time_flag) {
		header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
		}

		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());
		}
		}

		/* ---------------------------------------------------------------------- */

		void DumpLocalZstd::write_data(int n, double *mybuf)
		{
		writer.write(mybuf, sizeof(char)*n);
		}

		/* ---------------------------------------------------------------------- */

		void DumpLocalZstd::write()
		{
		DumpLocal::write();
		if (filewriter) {
		if (multifile) {
		writer.close();
		} else {
		if (flush_flag && writer.isopen()) {
		writer.flush();
		}
		}
		}
		}

		/* ---------------------------------------------------------------------- */

		int DumpLocalZstd::modify_param(int narg, char **arg)
		{
		int consumed = DumpLocal::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;
		}

src/COMPRESS/dump_local_zstd.h

0 → 100644

+63 −0

Original line number	Diff line number	Diff line
		/* -- 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(local/zstd,DumpLocalZstd)

		#else

		#ifndef LMP_DUMP_LOCAL_ZSTD_H
		#define LMP_DUMP_LOCAL_ZSTD_H

		#include "dump_local.h"
		#include "zstd_file_writer.h"

		namespace LAMMPS_NS {

		class DumpLocalZstd : public DumpLocal {
		public:
		DumpLocalZstd(class LAMMPS , int, char *);
		virtual ~DumpLocalZstd();

		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 local/zstd only writes compressed files

		The dump local/zstd output file name must have a .zst suffix.

		E: Cannot open dump file

		Self-explanatory.

		*/

Admin message