/* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://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 "domain.h" #include "dump_custom_gz.h" #include "error.h" #include "update.h" #include using namespace LAMMPS_NS; DumpCustomGZ::DumpCustomGZ(LAMMPS *lmp, int narg, char **arg) : DumpCustom(lmp, narg, arg) { if (!compressed) error->all(FLERR,"Dump custom/gz only writes compressed files"); } /* ---------------------------------------------------------------------- */ DumpCustomGZ::~DumpCustomGZ() { } /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped some derived classes override this function ------------------------------------------------------------------------- */ void DumpCustomGZ::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] = utils::strdup(filecurrent); ++numfiles; } else { if (remove(nameslist[fileidx]) != 0) { error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; } } } // each proc with filewriter = 1 opens a file if (filewriter) { try { writer.open(filecurrent, append_flag); } catch (FileWriterException &e) { error->one(FLERR, e.what()); } } // delete string with timestep replaced if (multifile) delete [] filecurrent; } void DumpCustomGZ::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 ATOMS\n{}\n", 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: ATOMS {}\n", columns); writer.write(header.c_str(), header.length()); } } /* ---------------------------------------------------------------------- */ void DumpCustomGZ::write_data(int n, double *mybuf) { if (buffer_flag == 1) { writer.write(mybuf, n); } else { constexpr size_t VBUFFER_SIZE = 256; char vbuffer[VBUFFER_SIZE]; int m = 0; for (int i = 0; i < n; i++) { for (int j = 0; j < nfield; j++) { int written = 0; if (vtype[j] == Dump::INT) { written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); } else if (vtype[j] == Dump::DOUBLE) { written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); } else if (vtype[j] == Dump::STRING) { written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]); } else if (vtype[j] == Dump::BIGINT) { written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); } if (written > 0) { writer.write(vbuffer, written); } else if (written < 0) { error->one(FLERR, "Error while writing dump custom/gz output"); } m++; } writer.write("\n", 1); } } } /* ---------------------------------------------------------------------- */ void DumpCustomGZ::write() { DumpCustom::write(); if (filewriter) { if (multifile) { writer.close(); } else { if (flush_flag && writer.isopen()) { writer.flush(); } } } } /* ---------------------------------------------------------------------- */ int DumpCustomGZ::modify_param(int narg, char **arg) { int consumed = DumpCustom::modify_param(narg, arg); if (consumed == 0) { try { if (strcmp(arg[0],"compression_level") == 0) { if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); int compression_level = utils::inumeric(FLERR, arg[1], false, lmp); writer.setCompressionLevel(compression_level); return 2; } } catch (FileWriterException &e) { error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; }