fold native binary reader class in to native reader class
This commit is contained in:
Axel Kohlmeyer
@ -25,11 +25,13 @@ using namespace LAMMPS_NS;
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Reader::Reader(LAMMPS *lmp) : Pointers(lmp)
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{
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fp = nullptr;
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binary = false;
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compressed = false;
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}
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/* ----------------------------------------------------------------------
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try to open given file
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generic version for ASCII files that may be compressed
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generic version for ASCII files that may be compressed or native binary dumps
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------------------------------------------------------------------------- */
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void Reader::open_file(const std::string &file)
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@ -37,12 +39,18 @@ void Reader::open_file(const std::string &file)
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if (fp != nullptr) close_file();
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if (platform::has_compress_extension(file)) {
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compressed = 1;
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compressed = true;
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fp = platform::compressed_read(file);
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if (!fp) error->one(FLERR,"Cannot open compressed file for reading");
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} else {
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compressed = 0;
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fp = fopen(file.c_str(),"r");
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compressed = false;
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if (utils::strmatch(file, "\\.bin$")) {
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binary = true;
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fp = fopen(file.c_str(),"rb");
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} else {
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fp = fopen(file.c_str(),"r");
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binary = false;
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}
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}
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if (!fp) error->one(FLERR,"Cannot open file {}: {}", file, utils::getsyserror());
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@ -38,7 +38,8 @@ class Reader : protected Pointers {
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protected:
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FILE *fp; // pointer to opened file or pipe
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int compressed; // flag for dump file compression
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bool compressed; // flag for dump file compression
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bool binary; // flag for (native) binary files
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};
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} // namespace LAMMPS_NS
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@ -36,14 +36,17 @@ ReaderNative::ReaderNative(LAMMPS *lmp) : Reader(lmp)
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{
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line = new char[MAXLINE];
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fieldindex = nullptr;
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maxbuf = 0;
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databuf = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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ReaderNative::~ReaderNative()
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{
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delete [] line;
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delete[] line;
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memory->destroy(fieldindex);
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memory->destroy(databuf);
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}
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/* ----------------------------------------------------------------------
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@ -54,25 +57,56 @@ ReaderNative::~ReaderNative()
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int ReaderNative::read_time(bigint &ntimestep)
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{
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char *eof = fgets(line,MAXLINE,fp);
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if (eof == nullptr) return 1;
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if (binary) {
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int 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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// skip over unit and time information, if present.
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fread(&ntimestep, sizeof(bigint), 1, fp);
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if (utils::strmatch(line,"^\\s*ITEM: UNITS\\s*$"))
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read_lines(2);
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// detect end-of-file
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if (feof(fp)) return 1;
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if (utils::strmatch(line,"^\\s*ITEM: TIME\\s*$"))
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read_lines(2);
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// detect newer format
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if (ntimestep < 0) {
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// first bigint encodes negative format name length
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bigint magic_string_len = -ntimestep;
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if (!utils::strmatch(line,"^\\s*ITEM: TIMESTEP\\s*$"))
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error->one(FLERR,"Dump file is incorrectly formatted");
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delete[] magic_string;
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magic_string = new char[magic_string_len + 1];
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read_buf(magic_string, sizeof(char), magic_string_len);
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magic_string[magic_string_len] = '\0';
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read_lines(1);
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int rv = sscanf(line,BIGINT_FORMAT,&ntimestep);
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if (rv != 1)
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error->one(FLERR,"Dump file is incorrectly formatted");
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// read endian flag
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read_buf(&endian, sizeof(int), 1);
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// read revision number
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read_buf(&revision, sizeof(int), 1);
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// read the real ntimestep
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read_buf(&ntimestep, sizeof(bigint), 1);
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}
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} else {
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char *eof = fgets(line,MAXLINE,fp);
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if (eof == nullptr) return 1;
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// skip over unit and time information, if present.
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if (utils::strmatch(line,"^\\s*ITEM: UNITS\\s*$"))
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read_lines(2);
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if (utils::strmatch(line,"^\\s*ITEM: TIME\\s*$"))
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read_lines(2);
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if (!utils::strmatch(line,"^\\s*ITEM: TIMESTEP\\s*$"))
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error->one(FLERR,"Dump file is incorrectly formatted");
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read_lines(1);
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int rv = sscanf(line,BIGINT_FORMAT,&ntimestep);
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if (rv != 1)
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error->one(FLERR,"Dump file is incorrectly formatted");
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}
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return 0;
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}
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@ -83,22 +117,73 @@ int ReaderNative::read_time(bigint &ntimestep)
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void ReaderNative::skip()
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{
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read_lines(2);
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bigint natoms;
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int rv = sscanf(line,BIGINT_FORMAT,&natoms);
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if (rv != 1)
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error->one(FLERR,"Dump file is incorrectly formatted");
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if (binary) {
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bigint natoms;
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int triclinic;
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skip_buf(sizeof(bigint));
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read_buf(&triclinic, sizeof(int), 1);
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skip_buf((sizeof(int)+sizeof(double))*6);
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if (triclinic) {
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skip_buf(sizeof(double)*3);
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}
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skip_buf(sizeof(int));
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read_lines(5);
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skip_reading_magic_str();
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// invoke read_lines() in chunks no larger than MAXSMALLINT
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// read chunk and skip them
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int nchunk;
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bigint nremain = natoms;
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while (nremain) {
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nchunk = MIN(nremain,MAXSMALLINT);
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read_lines(nchunk);
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nremain -= nchunk;
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int nchunk;
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read_buf(&nchunk, sizeof(int), 1);
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int n;
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for (int i = 0; i < nchunk; i++) {
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read_buf(&n, sizeof(int), 1);
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read_double_chunk(n);
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}
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delete[] magic_string;
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delete[] unit_style;
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} else {
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read_lines(2);
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bigint natoms;
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int rv = sscanf(line,BIGINT_FORMAT,&natoms);
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if (rv != 1)
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error->one(FLERR,"Dump file is incorrectly formatted");
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read_lines(5);
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// invoke read_lines() in chunks no larger than MAXSMALLINT
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int nchunk;
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bigint nremain = natoms;
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while (nremain) {
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nchunk = MIN(nremain,MAXSMALLINT);
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read_lines(nchunk);
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nremain -= nchunk;
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}
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}
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}
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void ReaderNative::skip_reading_magic_str()
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{
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if (magic_string && revision > 0x0001) {
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int len;
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read_buf(&len, sizeof(int), 1);
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if (len > 0) {
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// has units
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skip_buf(sizeof(char)*len);
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}
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char flag = 0;
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read_buf(&flag, sizeof(char), 1);
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if (flag) {
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skip_buf(sizeof(double));
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}
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read_buf(&len, sizeof(int), 1);
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skip_buf(sizeof(char)*len);
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}
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}
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@ -123,45 +208,103 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
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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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int rv;
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bigint natoms = 0;
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int len = 0;
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char *labelline;
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read_lines(2);
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rv = sscanf(line,BIGINT_FORMAT,&natoms);
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if (rv != 1)
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error->one(FLERR,"Dump file is incorrectly formatted");
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if (binary) {
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read_buf(&natoms, sizeof(bigint), 1);
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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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read_lines(1);
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if (line[strlen("ITEM: BOX BOUNDS ")] == 'x') triclinic = 1;
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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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read_lines(1);
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if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[0][0],&box[0][1]);
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else rv = 3 - sscanf(line,"%lg %lg %lg",&box[0][0],&box[0][1],&box[0][2]);
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if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
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int boundary[3][2];
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read_buf(&triclinic, sizeof(int), 1);
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read_buf(&boundary[0][0], sizeof(int), 6);
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read_buf(box[0], sizeof(double), 2);
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read_buf(box[1], sizeof(double), 2);
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read_buf(box[2], sizeof(double), 2);
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if (triclinic) {
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read_buf(&box[0][2], sizeof(double), 1);
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read_buf(&box[1][2], sizeof(double), 1);
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read_buf(&box[2][2], sizeof(double), 1);
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}
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read_lines(1);
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if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[1][0],&box[1][1]);
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else rv = 3 - sscanf(line,"%lg %lg %lg",&box[1][0],&box[1][1],&box[1][2]);
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if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
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// extract column labels and match to requested fields
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read_buf(&size_one, sizeof(int), 1);
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read_lines(1);
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if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[2][0],&box[2][1]);
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else rv = 3 - sscanf(line,"%lg %lg %lg",&box[2][0],&box[2][1],&box[2][2]);
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if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
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if (!fieldinfo) {
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skip_reading_magic_str();
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return natoms;
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}
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read_lines(1);
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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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read_buf(&len, sizeof(int), 1);
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labelline = new char[len + 1];
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// if no field info requested, just return
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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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read_buf(unit_style, sizeof(char), len);
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unit_style[len] = '\0';
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}
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if (!fieldinfo) return natoms;
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char flag = 0;
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read_buf(&flag, sizeof(char), 1);
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// exatract column labels and match to requested fields
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if (flag) {
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double time;
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read_buf(&time, sizeof(double), 1);
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}
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char *labelline = &line[strlen("ITEM: ATOMS ")];
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read_buf(&len, sizeof(int), 1);
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read_buf(labelline, sizeof(char), len);
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labelline[len] = '\0';
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}
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} else {
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int rv;
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read_lines(2);
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rv = sscanf(line,BIGINT_FORMAT,&natoms);
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if (rv != 1)
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error->one(FLERR,"Dump file is incorrectly formatted");
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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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read_lines(1);
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if (line[strlen("ITEM: BOX BOUNDS ")] == 'x') triclinic = 1;
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read_lines(1);
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if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[0][0],&box[0][1]);
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else rv = 3 - sscanf(line,"%lg %lg %lg",&box[0][0],&box[0][1],&box[0][2]);
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if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
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read_lines(1);
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if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[1][0],&box[1][1]);
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else rv = 3 - sscanf(line,"%lg %lg %lg",&box[1][0],&box[1][1],&box[1][2]);
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if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
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read_lines(1);
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if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[2][0],&box[2][1]);
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else rv = 3 - sscanf(line,"%lg %lg %lg",&box[2][0],&box[2][1],&box[2][2]);
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if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
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read_lines(1);
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// if no field info requested, just return
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if (!fieldinfo) return natoms;
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// extract column labels and match to requested fields
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labelline = &line[strlen("ITEM: ATOMS ")];
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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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@ -174,8 +317,9 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
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return 1;
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}
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match_fields(nfield, xflag, yflag, zflag, fieldtype, fieldlabel, scaleflag, wrapflag, fieldflag, labels);
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match_fields(nfield, xflag, yflag, zflag, fieldtype, fieldlabel,
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scaleflag, wrapflag, fieldflag, labels);
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return natoms;
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}
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@ -323,22 +467,52 @@ void ReaderNative::match_fields(int nfield,
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void ReaderNative::read_atoms(int n, int nfield, double **fields)
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{
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int i,m;
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char *eof;
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if (binary) {
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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 (i = 0; i < n; i++) {
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eof = fgets(line,MAXLINE,fp);
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if (eof == nullptr) error->one(FLERR,"Unexpected end of dump file");
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int i_atom = 0;
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int nchunk;
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read_buf(&nchunk, sizeof(int), 1);
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for (int i = 0; i < nchunk; i++) {
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// tokenize the line
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std::vector<std::string> words = Tokenizer(line).as_vector();
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read_buf(&n, sizeof(int), 1);
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if ((int)words.size() < nwords) error->one(FLERR,"Insufficient columns in dump file");
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// read chunk and write as size_one values per line
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read_double_chunk(n);
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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 = &databuf[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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// convert selected fields to floats
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} else {
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int i,m;
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char *eof;
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for (m = 0; m < nfield; m++)
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fields[i][m] = atof(words[fieldindex[m]].c_str());
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for (i = 0; i < n; i++) {
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eof = fgets(line,MAXLINE,fp);
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if (eof == nullptr) error->one(FLERR,"Unexpected end of dump file");
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// tokenize the line
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std::vector<std::string> words = Tokenizer(line).as_vector();
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if ((int)words.size() < nwords) error->one(FLERR,"Insufficient columns in dump file");
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// convert selected fields to floats
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for (m = 0; m < nfield; m++)
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fields[i][m] = atof(words[fieldindex[m]].c_str());
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}
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}
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}
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@ -369,3 +543,28 @@ void ReaderNative::read_lines(int n)
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for (int i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp);
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if (eof == nullptr) error->one(FLERR,"Unexpected end of dump file");
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}
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void ReaderNative::read_buf(void * ptr, size_t size, size_t count)
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{
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fread(ptr, size, count, fp);
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// detect end-of-file
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if (feof(fp)) error->one(FLERR,"Unexpected end of dump file");
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}
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void ReaderNative::read_double_chunk(size_t count)
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{
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// extend buffer to fit chunk size
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if (count > maxbuf) {
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memory->grow(databuf,count,"reader:databuf");
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maxbuf = count;
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}
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read_buf(databuf, sizeof(double), count);
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}
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void ReaderNative::skip_buf(size_t size)
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{
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bigint pos = platform::ftell(fp);
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pos += size;
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platform::fseek(fp,pos);
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}
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@ -39,18 +39,30 @@ class ReaderNative : public Reader {
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int &, int &);
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void read_atoms(int, int, double **);
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protected:
|
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int *fieldindex; //
|
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private:
|
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int revision;
|
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|
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char *magic_string;
|
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char *unit_style;
|
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int *fieldindex;
|
||||
|
||||
char *line; // line read from dump file
|
||||
double *databuf; // buffer for binary data
|
||||
int nwords; // # of per-atom columns in dump file
|
||||
|
||||
int size_one; // number of double for one atom
|
||||
int maxbuf; // maximum buffer size
|
||||
|
||||
void match_fields(int, int &, int &, int &, int *, char **, int, int, int &,
|
||||
std::map<std::string, int>);
|
||||
|
||||
private:
|
||||
char *line; // line read from dump file
|
||||
|
||||
int nwords; // # of per-atom columns in dump file
|
||||
|
||||
int find_label(const std::string &label, const std::map<std::string, int> &labels);
|
||||
void read_lines(int);
|
||||
|
||||
void read_buf(void *, size_t, size_t);
|
||||
void read_double_chunk(size_t);
|
||||
void skip_buf(size_t);
|
||||
void skip_reading_magic_str();
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -1,320 +0,0 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "reader_native_bin.h"
|
||||
|
||||
#include "error.h"
|
||||
#include "memory.h"
|
||||
#include "tokenizer.h"
|
||||
|
||||
#include <cstring>
|
||||
#include <utility>
|
||||
#include <iostream>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
enum{ID,TYPE,X,Y,Z,VX,VY,VZ,Q,IX,IY,IZ,FX,FY,FZ};
|
||||
enum{UNSET,NOSCALE_NOWRAP,NOSCALE_WRAP,SCALE_NOWRAP,SCALE_WRAP};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ReaderNativeBin::ReaderNativeBin(LAMMPS *lmp) : ReaderNative(lmp)
|
||||
{
|
||||
fieldindex = nullptr;
|
||||
buf = new double[maxbuf];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ReaderNativeBin::~ReaderNativeBin()
|
||||
{
|
||||
delete [] buf;
|
||||
memory->destroy(fieldindex);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
overload the open_file function to open the binary file
|
||||
------------------------------------------------------------------------- */
|
||||
void ReaderNativeBin::open_file(const std::string &file)
|
||||
{
|
||||
if (fp != nullptr) close_file();
|
||||
|
||||
if (platform::has_compress_extension(file)) {
|
||||
error->one(FLERR,"Compressed binary files are not supported");
|
||||
} else {
|
||||
compressed = 0;
|
||||
fp = fopen(file.c_str(), "rb");
|
||||
}
|
||||
|
||||
if (!fp) error->one(FLERR,"Cannot open file {}: {}", file, utils::getsyserror());
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
read and return time stamp from dump file
|
||||
if first read reaches end-of-file, return 1 so caller can open next file
|
||||
only called by proc 0
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int ReaderNativeBin::read_time(bigint &ntimestep)
|
||||
{
|
||||
|
||||
int endian = 0x0001;
|
||||
revision = 0x0001;
|
||||
magic_string = nullptr;
|
||||
unit_style = nullptr;
|
||||
|
||||
fread(&ntimestep, sizeof(bigint), 1, fp);
|
||||
|
||||
// detect end-of-file
|
||||
if (feof(fp)) return 1;
|
||||
|
||||
// detect newer format
|
||||
if (ntimestep < 0) {
|
||||
// first bigint encodes negative format name length
|
||||
bigint magic_string_len = -ntimestep;
|
||||
|
||||
delete[] magic_string;
|
||||
magic_string = new char[magic_string_len + 1];
|
||||
read_buf(magic_string, sizeof(char), magic_string_len);
|
||||
magic_string[magic_string_len] = '\0';
|
||||
|
||||
// read endian flag
|
||||
read_buf(&endian, sizeof(int), 1);
|
||||
|
||||
// read revision number
|
||||
read_buf(&revision, sizeof(int), 1);
|
||||
|
||||
// read the real ntimestep
|
||||
read_buf(&ntimestep, sizeof(bigint), 1);
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
skip snapshot from timestamp onward
|
||||
only called by proc 0
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ReaderNativeBin::skip()
|
||||
{
|
||||
bigint natoms;
|
||||
int triclinic;
|
||||
skip_buf(sizeof(bigint));
|
||||
read_buf(&triclinic, sizeof(int), 1);
|
||||
skip_buf((sizeof(int)+sizeof(double))*6);
|
||||
if (triclinic) {
|
||||
skip_buf(sizeof(double)*3);
|
||||
}
|
||||
skip_buf(sizeof(int));
|
||||
|
||||
skip_reading_magic_str();
|
||||
|
||||
// read chunk and skip them
|
||||
|
||||
int nchunk;
|
||||
read_buf(&nchunk, sizeof(int), 1);
|
||||
|
||||
int n;
|
||||
for (int i = 0; i < nchunk; i++) {
|
||||
read_buf(&n, sizeof(int), 1);
|
||||
read_double_chunk(n);
|
||||
}
|
||||
|
||||
delete[] magic_string;
|
||||
delete[] unit_style;
|
||||
}
|
||||
|
||||
void ReaderNativeBin::skip_reading_magic_str()
|
||||
{
|
||||
if (magic_string && revision > 0x0001) {
|
||||
int len;
|
||||
read_buf(&len, sizeof(int), 1);
|
||||
|
||||
if (len > 0) {
|
||||
// has units
|
||||
skip_buf(sizeof(char)*len);
|
||||
}
|
||||
|
||||
char flag = 0;
|
||||
read_buf(&flag, sizeof(char), 1);
|
||||
|
||||
if (flag) {
|
||||
skip_buf(sizeof(double));
|
||||
}
|
||||
|
||||
read_buf(&len, sizeof(int), 1);
|
||||
skip_buf(sizeof(char)*len);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
read remaining header info:
|
||||
return natoms
|
||||
box bounds, triclinic (inferred), fieldflag (1 if any fields not found),
|
||||
xyz flags = UNSET (not a requested field), SCALE/WRAP as in enum
|
||||
if fieldflag set:
|
||||
match Nfield fields to per-atom column labels
|
||||
allocate and set fieldindex = which column each field maps to
|
||||
fieldtype = X,VX,IZ etc
|
||||
fieldlabel = user-specified label or nullptr if use fieldtype default
|
||||
xyz flags = scaleflag+wrapflag if has fieldlabel name,
|
||||
else set by x,xs,xu,xsu
|
||||
only called by proc 0
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
bigint ReaderNativeBin::read_header(double box[3][3], int &boxinfo, int &triclinic,
|
||||
int fieldinfo, int nfield,
|
||||
int *fieldtype, char **fieldlabel,
|
||||
int scaleflag, int wrapflag, int &fieldflag,
|
||||
int &xflag, int &yflag, int &zflag)
|
||||
{
|
||||
bigint natoms;
|
||||
|
||||
read_buf(&natoms, sizeof(bigint), 1);
|
||||
|
||||
boxinfo = 1;
|
||||
triclinic = 0;
|
||||
box[0][2] = box[1][2] = box[2][2] = 0.0;
|
||||
|
||||
int boundary[3][2];
|
||||
read_buf(&triclinic, sizeof(int), 1);
|
||||
read_buf(&boundary[0][0], sizeof(int), 6);
|
||||
read_buf(box[0], sizeof(double), 2);
|
||||
read_buf(box[1], sizeof(double), 2);
|
||||
read_buf(box[2], sizeof(double), 2);
|
||||
if (triclinic) {
|
||||
read_buf(&box[0][2], sizeof(double), 1);
|
||||
read_buf(&box[1][2], sizeof(double), 1);
|
||||
read_buf(&box[2][2], sizeof(double), 1);
|
||||
}
|
||||
|
||||
// exatract column labels and match to requested fields
|
||||
read_buf(&size_one, sizeof(int), 1);
|
||||
|
||||
if (!fieldinfo) {
|
||||
skip_reading_magic_str();
|
||||
return natoms;
|
||||
}
|
||||
|
||||
int len = 0;
|
||||
char *labelline;
|
||||
|
||||
if (magic_string && revision > 0x0001) {
|
||||
// newer format includes units string, columns string
|
||||
// and time
|
||||
read_buf(&len, sizeof(int), 1);
|
||||
labelline = new char[len + 1];
|
||||
|
||||
if (len > 0) {
|
||||
// has units
|
||||
delete[] unit_style;
|
||||
unit_style = new char[len + 1];
|
||||
read_buf(unit_style, sizeof(char), len);
|
||||
unit_style[len] = '\0';
|
||||
}
|
||||
|
||||
char flag = 0;
|
||||
read_buf(&flag, sizeof(char), 1);
|
||||
|
||||
if (flag) {
|
||||
double time;
|
||||
read_buf(&time, sizeof(double), 1);
|
||||
}
|
||||
|
||||
read_buf(&len, sizeof(int), 1);
|
||||
read_buf(labelline, sizeof(char), len);
|
||||
labelline[len] = '\0';
|
||||
}
|
||||
|
||||
std::map<std::string, int> labels;
|
||||
Tokenizer tokens(labelline);
|
||||
int nwords = 0;
|
||||
|
||||
while (tokens.has_next()) {
|
||||
labels[tokens.next()] = nwords++;
|
||||
}
|
||||
|
||||
if (nwords == 0) {
|
||||
return 1;
|
||||
}
|
||||
|
||||
match_fields(nfield, xflag, yflag, zflag, fieldtype, fieldlabel, scaleflag, wrapflag, fieldflag, labels);
|
||||
|
||||
|
||||
return natoms;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
read N atom lines from dump file
|
||||
stores appropriate values in fields array
|
||||
return 0 if success, 1 if error
|
||||
only called by proc 0
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ReaderNativeBin::read_atoms(int n, int nfield, double **fields)
|
||||
{
|
||||
if (feof(fp)) {
|
||||
error->one(FLERR,"Unexpected end of dump file");
|
||||
}
|
||||
|
||||
int i_atom = 0;
|
||||
int nchunk;
|
||||
read_buf(&nchunk, sizeof(int), 1);
|
||||
for (int i = 0; i < nchunk; i++) {
|
||||
|
||||
read_buf(&n, sizeof(int), 1);
|
||||
|
||||
// read chunk and write as size_one values per line
|
||||
read_double_chunk(n);
|
||||
n /= size_one;
|
||||
int m = 0;
|
||||
for (int j = 0; j < n; j++)
|
||||
{
|
||||
double *words = &buf[m];
|
||||
for (int k = 0; k < nfield; k++)
|
||||
fields[i_atom][k] = words[fieldindex[k]];
|
||||
i_atom += 1;
|
||||
m+=size_one;
|
||||
}
|
||||
}
|
||||
|
||||
delete[] magic_string;
|
||||
delete[] unit_style;
|
||||
}
|
||||
|
||||
void ReaderNativeBin::read_buf(void * ptr, size_t size, size_t count)
|
||||
{
|
||||
fread(ptr, size, count, fp);
|
||||
|
||||
// detect end-of-file
|
||||
if (feof(fp)) error->one(FLERR,"Unexpected end of dump file");
|
||||
}
|
||||
|
||||
void ReaderNativeBin::read_double_chunk(size_t count)
|
||||
{
|
||||
// extend buffer to fit chunk size
|
||||
if (count > maxbuf) {
|
||||
if (buf) delete[] buf;
|
||||
buf = new double[count];
|
||||
maxbuf = count;
|
||||
}
|
||||
read_buf(buf, sizeof(double), count);
|
||||
}
|
||||
|
||||
void ReaderNativeBin::skip_buf(size_t size)
|
||||
{
|
||||
char tmp[size];
|
||||
read_buf(tmp, 1, size);
|
||||
}
|
||||
@ -1,73 +0,0 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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.
|
||||
|
||||
Contributed by Lixin Sun
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef READER_CLASS
|
||||
// clang-format off
|
||||
ReaderStyle(native/bin,ReaderNativeBin);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_READER_NATIVE_BIN_H
|
||||
#define LMP_READER_NATIVE_BIN_H
|
||||
|
||||
#include "reader_native.h"
|
||||
|
||||
#include <map>
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ReaderNativeBin : public ReaderNative {
|
||||
public:
|
||||
ReaderNativeBin(class LAMMPS *);
|
||||
~ReaderNativeBin();
|
||||
|
||||
int read_time(bigint &);
|
||||
void skip();
|
||||
bigint read_header(double[3][3], int &, int &, int, int, int *, char **, int, int, int &, int &,
|
||||
int &, int &);
|
||||
void read_atoms(int, int, double **);
|
||||
void open_file(const std::string &);
|
||||
|
||||
private:
|
||||
int revision;
|
||||
char *magic_string;
|
||||
char *unit_style;
|
||||
|
||||
int size_one; // number of double for one atom
|
||||
double *buf;
|
||||
int maxbuf = 1; // maximum buffer size
|
||||
|
||||
void read_buf(void *, size_t, size_t);
|
||||
void read_double_chunk(size_t);
|
||||
void skip_buf(size_t);
|
||||
void skip_reading_magic_str();
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Dump file is incorrectly formatted
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Unexpected end of dump file
|
||||
|
||||
A read operation from the file failed.
|
||||
|
||||
*/
|
||||
Reference in New Issue
Block a user