fold native binary reader class in to native reader class
This commit is contained in:
Axel Kohlmeyer
@ -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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