/* ---------------------------------------------------------------------- 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. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- Contributing author: Richard Berger (Temple U) ------------------------------------------------------------------------- */ #ifdef LAMMPS_ZSTD #include "atom.h" #include "domain.h" #include "dump_cfg_zstd.h" #include "error.h" #include "file_writer.h" #include "update.h" #include using namespace LAMMPS_NS; #define UNWRAPEXPAND 10.0 DumpCFGZstd::DumpCFGZstd(LAMMPS *lmp, int narg, char **arg) : DumpCFG(lmp, narg, arg) { if (!compressed) error->all(FLERR,"Dump cfg/zstd only writes compressed files"); } /* ---------------------------------------------------------------------- */ DumpCFGZstd::~DumpCFGZstd() { } /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or zstdipped some derived classes override this function ------------------------------------------------------------------------- */ void DumpCFGZstd::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 DumpCFGZstd::write_header(bigint n) { // set scale factor used by AtomEye for CFG viz // default = 1.0 // for peridynamics, set to pre-computed PD scale factor // so PD particles mimic C atoms // for unwrapped coords, set to UNWRAPEXPAND (10.0) // so molecules are not split across periodic box boundaries double scale = 1.0; if (atom->peri_flag) scale = atom->pdscale; else if (unwrapflag == 1) scale = UNWRAPEXPAND; std::string header = fmt::format("Number of particles = {}\n", n); header += fmt::format("A = {0:g} Angstrom (basic length-scale)\n", scale); header += fmt::format("H0(1,1) = {0:g} A\n",domain->xprd); header += fmt::format("H0(1,2) = 0 A \n"); header += fmt::format("H0(1,3) = 0 A \n"); header += fmt::format("H0(2,1) = {0:g} A \n",domain->xy); header += fmt::format("H0(2,2) = {0:g} A\n",domain->yprd); header += fmt::format("H0(2,3) = 0 A \n"); header += fmt::format("H0(3,1) = {0:g} A \n",domain->xz); header += fmt::format("H0(3,2) = {0:g} A \n",domain->yz); header += fmt::format("H0(3,3) = {0:g} A\n",domain->zprd); header += fmt::format(".NO_VELOCITY.\n"); header += fmt::format("entry_count = {}\n",nfield-2); for (int i = 0; i < nfield-5; i++) header += fmt::format("auxiliary[{}] = {}\n",i,auxname[i]); writer.write(header.c_str(), header.length()); } /* ---------------------------------------------------------------------- */ void DumpCFGZstd::write_data(int n, double *mybuf) { writer.write(mybuf, n); } /* ---------------------------------------------------------------------- */ void DumpCFGZstd::write() { DumpCFG::write(); if (filewriter) { if (multifile) { writer.close(); } else { if (flush_flag && writer.isopen()) { writer.flush(); } } } } /* ---------------------------------------------------------------------- */ int DumpCFGZstd::modify_param(int narg, char **arg) { int consumed = DumpCFG::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 = utils::inumeric(FLERR, arg[1], false, lmp); writer.setCompressionLevel(compression_level); return 2; } } catch (FileWriterException &e) { error->one(FLERR, e.what()); } } return consumed; } #endif