/* ---------------------------------------------------------------------- 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 "dump_atom_gz.h" #include "domain.h" #include "error.h" #include "update.h" #include "force.h" #include #include "fmt/format.h" using namespace LAMMPS_NS; DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) : DumpAtom(lmp, narg, arg) { gzFp = NULL; compression_level = Z_BEST_COMPRESSION; if (!compressed) error->all(FLERR,"Dump atom/gz only writes compressed files"); } /* ---------------------------------------------------------------------- */ DumpAtomGZ::~DumpAtomGZ() { if (gzFp) gzclose(gzFp); gzFp = NULL; fp = NULL; } /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped some derived classes override this function ------------------------------------------------------------------------- */ void DumpAtomGZ::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) { std::string mode; if (append_flag) { mode = fmt::format("ab{}", compression_level); } else { mode = fmt::format("wb{}", compression_level); } gzFp = gzopen(filecurrent, mode.c_str()); if (gzFp == NULL) error->one(FLERR,"Cannot open dump file"); } else gzFp = NULL; // delete string with timestep replaced if (multifile) delete [] filecurrent; } /* ---------------------------------------------------------------------- */ void DumpAtomGZ::write_header(bigint ndump) { if ((multiproc) || (!multiproc && me == 0)) { if (unit_flag && !unit_count) { ++unit_count; gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style); } if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time()); gzprintf(gzFp,"ITEM: TIMESTEP\n"); gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); if (domain->triclinic == 0) { gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr); gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi); gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi); gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi); } else { gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy); gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz); gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz); } gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); } } /* ---------------------------------------------------------------------- */ void DumpAtomGZ::write_data(int n, double *mybuf) { gzwrite(gzFp,mybuf,sizeof(char)*n); } /* ---------------------------------------------------------------------- */ void DumpAtomGZ::write() { DumpAtom::write(); if (filewriter) { if (multifile) { gzclose(gzFp); gzFp = NULL; } else { if (flush_flag) gzflush(gzFp,Z_SYNC_FLUSH); } } } /* ---------------------------------------------------------------------- */ int DumpAtomGZ::modify_param(int narg, char **arg) { int consumed = DumpAtom::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 = force->inumeric(FLERR,arg[1]); 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; } } return consumed; }