/* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, 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 "dump_cfg_zstd.h" #include "atom.h" #include "domain.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"); } /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or compressed 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) { filecurrent = utils::strdup(utils::star_subst(filecurrent, update->ntimestep, padflag)); if (maxfiles > 0) { if (numfiles < maxfiles) { nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { if (remove(nameslist[fileidx]) != 0) { error->warning(FLERR, "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) { 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 = {:g} Angstrom (basic length-scale)\n", scale); header += fmt::format("H0(1,1) = {: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) = {:g} A\n", domain->xy); header += fmt::format("H0(2,2) = {:g} A\n", domain->yprd); header += fmt::format("H0(2,3) = 0 A\n"); header += fmt::format("H0(3,1) = {:g} A\n", domain->xz); header += fmt::format("H0(3,2) = {:g} A\n", domain->yz); header += fmt::format("H0(3,3) = {: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) { if (buffer_flag) { writer.write(mybuf, n); } else { constexpr size_t VBUFFER_SIZE = 256; char vbuffer[VBUFFER_SIZE]; if (unwrapflag == 0) { int m = 0; for (int i = 0; i < n; i++) { for (int j = 0; j < size_one; j++) { int written = 0; if (j == 0) { written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]); } else if (j == 1) { written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]); } else if (j >= 2) { 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 cfg/gz output"); } m++; } writer.write("\n", 1); } } else if (unwrapflag == 1) { int m = 0; for (int i = 0; i < n; i++) { for (int j = 0; j < size_one; j++) { int written = 0; if (j == 0) { written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]); } else if (j == 1) { written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]); } else if (j >= 2 && j <= 4) { double unwrap_coord = (mybuf[m] - 0.5) / UNWRAPEXPAND + 0.5; written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], unwrap_coord); } else if (j >= 5) { 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 cfg/gz output"); } m++; } writer.write("\n", 1); } } } } /* ---------------------------------------------------------------------- */ 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"); writer.setChecksum(utils::logical(FLERR, arg[1], false, lmp) == 1); return 2; } else if (strcmp(arg[0], "compression_level") == 0) { if (narg < 2) error->all(FLERR, "Illegal dump_modify command"); writer.setCompressionLevel(utils::inumeric(FLERR, arg[1], false, lmp)); return 2; } } catch (FileWriterException &e) { error->one(FLERR, e.what()); } } return consumed; } #endif