add new ReaderNativeBin class
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nw13slx
271
src/reader_native_bin.cpp
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271
src/reader_native_bin.cpp
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "reader_native_bin.h"
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#include "error.h"
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#include "memory.h"
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#include "tokenizer.h"
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#include <cstring>
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#include <utility>
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using namespace LAMMPS_NS;
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#define MAXLINE 1024 // max line length in dump file
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// also in read_dump.cpp
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enum{ID,TYPE,X,Y,Z,VX,VY,VZ,Q,IX,IY,IZ,FX,FY,FZ};
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enum{UNSET,NOSCALE_NOWRAP,NOSCALE_WRAP,SCALE_NOWRAP,SCALE_WRAP};
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/* ---------------------------------------------------------------------- */
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ReaderNativeBin::ReaderNativeBin(LAMMPS *lmp) : ReaderNative(lmp)
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{
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line = new char[MAXLINE];
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fieldindex = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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ReaderNativeBin::~ReaderNativeBin()
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{
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delete [] line;
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memory->destroy(fieldindex);
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}
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/* ----------------------------------------------------------------------
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read and return time stamp from dump file
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if first read reaches end-of-file, return 1 so caller can open next file
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only called by proc 0
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------------------------------------------------------------------------- */
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int ReaderNativeBin::read_time(bigint &ntimestep)
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{
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endian = 0x0001;
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revision = 0x0001;
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magic_string = nullptr;
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unit_style = nullptr;
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fread(&ntimestep, sizeof(bigint), 1, fp);
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// detect end-of-file
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if (feof(fp)) return 1;
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// detect newer format
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if (ntimestep < 0) {
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// first bigint encodes negative format name length
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bigint magic_string_len = -ntimestep;
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delete[] magic_string;
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magic_string = new char[magic_string_len + 1];
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fread(magic_string, sizeof(char), magic_string_len, fp);
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magic_string[magic_string_len] = '\0';
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// read endian flag
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fread(&endian, sizeof(int), 1, fp);
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// read revision number
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fread(&revision, sizeof(int), 1, fp);
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// read the real ntimestep
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fread(&ntimestep, sizeof(bigint), 1, fp);
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}
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return 0;
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}
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/* ----------------------------------------------------------------------
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skip snapshot from timestamp onward
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only called by proc 0
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------------------------------------------------------------------------- */
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void ReaderNativeBin::skip()
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{
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int nchunk;
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fread(&nchunk, sizeof(int), 1, fp);
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if (feof(fp)) {
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error->one(FLERR,"Unexpected end of dump file");
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}
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for (int i = 0; i < nchunk; i++) {
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int n;
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fread(&n, sizeof(int), 1, fp);
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// extend buffer to fit chunk size
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if (n > maxbuf) {
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if (buf) delete[] buf;
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buf = new double[n];
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maxbuf = n;
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}
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// read chunk and write as size_one values per line
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fread(buf, sizeof(double), n, fp);
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if (feof(fp)) {
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error->one(FLERR,"Unexpected end of dump file");
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}
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}
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delete[] magic_string;
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delete[] unit_style;
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magic_string = nullptr;
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unit_style = nullptr;
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}
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/* ----------------------------------------------------------------------
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read remaining header info:
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return natoms
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box bounds, triclinic (inferred), fieldflag (1 if any fields not found),
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xyz flags = UNSET (not a requested field), SCALE/WRAP as in enum
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if fieldflag set:
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match Nfield fields to per-atom column labels
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allocate and set fieldindex = which column each field maps to
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fieldtype = X,VX,IZ etc
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fieldlabel = user-specified label or nullptr if use fieldtype default
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xyz flags = scaleflag+wrapflag if has fieldlabel name,
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else set by x,xs,xu,xsu
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only called by proc 0
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------------------------------------------------------------------------- */
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bigint ReaderNativeBin::read_header(double box[3][3], int &boxinfo, int &triclinic,
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int fieldinfo, int nfield,
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int *fieldtype, char **fieldlabel,
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int scaleflag, int wrapflag, int &fieldflag,
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int &xflag, int &yflag, int &zflag)
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{
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bigint natoms;
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fread(&natoms, sizeof(bigint), 1, fp);
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boxinfo = 1;
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triclinic = 0;
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box[0][2] = box[1][2] = box[2][2] = 0.0;
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int boundary[3][2];
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fread(&triclinic, sizeof(int), 1, fp);
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fread(&boundary[0][0], 6 * sizeof(int), 1, fp);
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fread(&box[0][0], sizeof(double), 1, fp);
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fread(&box[0][1], sizeof(double), 1, fp);
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fread(&box[1][0], sizeof(double), 1, fp);
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fread(&box[1][1], sizeof(double), 1, fp);
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fread(&box[2][0], sizeof(double), 1, fp);
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fread(&box[2][1], sizeof(double), 1, fp);
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if (triclinic) {
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fread(&box[0][2], sizeof(double), 1, fp);
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fread(&box[1][2], sizeof(double), 1, fp);
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fread(&box[2][2], sizeof(double), 1, fp);
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}
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if (!fieldinfo) return natoms;
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// exatract column labels and match to requested fields
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fread(&size_one, sizeof(int), 1, fp);
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int len = 0;
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char *labelline;
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if (magic_string && revision > 0x0001) {
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// newer format includes units string, columns string
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// and time
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fread(&len, sizeof(int), 1, fp);
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labelline = new char[len + 1];
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if (len > 0) {
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// has units
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delete[] unit_style;
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unit_style = new char[len + 1];
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fread(unit_style, sizeof(char), len, fp);
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unit_style[len] = '\0';
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}
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char flag = 0;
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fread(&flag, sizeof(char), 1, fp);
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if (flag) {
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double time;
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fread(&time, sizeof(double), 1, fp);
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}
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fread(&len, sizeof(int), 1, fp);
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fread(labelline, sizeof(char), len, fp);
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labelline[len] = '\0';
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}
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std::map<std::string, int> labels;
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Tokenizer tokens(labelline);
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nwords = 0;
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while (tokens.has_next()) {
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labels[tokens.next()] = nwords++;
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}
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if (nwords == 0) {
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return 1;
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}
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match_field(nfield, xflag, yflag, zflag, fieldtype, fieldlabel, scaleflag, wrapflag, fieldflag, labels);
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return natoms;
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}
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/* ----------------------------------------------------------------------
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read N atom lines from dump file
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stores appropriate values in fields array
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return 0 if success, 1 if error
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only called by proc 0
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------------------------------------------------------------------------- */
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void ReaderNativeBin::read_atoms(int n, int nfield, double **fields)
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{
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if (feof(fp)) {
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error->one(FLERR,"Unexpected end of dump file");
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}
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int i_atom = 0;
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int nchunk;
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fread(&nchunk, sizeof(int), 1, fp);
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for (int i = 0; i < nchunk; i++) {
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fread(&n, sizeof(int), 1, fp);
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// extend buffer to fit chunk size
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if (n > maxbuf) {
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if (buf) delete[] buf;
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buf = new double[n];
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maxbuf = n;
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}
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// read chunk and write as size_one values per line
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fread(buf, sizeof(double), n, fp);
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n /= size_one;
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int m = 0;
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for (int j = 0; j < n; j++)
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{
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double *words = &buf[m];
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for (int k = 0; k < nfield; k++)
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fields[i_atom][k] = words[fieldindex[k]];
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i_atom += 1;
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m+=size_one;
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}
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}
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delete[] magic_string;
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delete[] unit_style;
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magic_string = nullptr;
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unit_style = nullptr;
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}
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