git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8258 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/reader_native.cpp
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323
src/reader_native.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, 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 "string.h"
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#include "stdlib.h"
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#include "reader_native.h"
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#include "atom.h"
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#include "memory.h"
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#include "error.h"
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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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enum{ID,TYPE,X,Y,Z,VX,VY,VZ,IX,IY,IZ};
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enum{UNSET,UNSCALED,SCALED};
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/* ---------------------------------------------------------------------- */
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ReaderNative::ReaderNative(LAMMPS *lmp) : Reader(lmp)
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{
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line = new char[MAXLINE];
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words = NULL;
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fieldindex = NULL;
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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 [] words;
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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 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 == NULL) return 1;
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if (strstr(line,"ITEM: TIMESTEP") != line)
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error->one(FLERR,"Dump file is incorrectly formatted");
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read_lines(1);
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sscanf(line,BIGINT_FORMAT,&ntimestep);
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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 ReaderNative::skip()
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{
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read_lines(2);
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bigint natoms;
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sscanf(line,BIGINT_FORMAT,&natoms);
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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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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 flag = UNSET (not a requested field), SCALED, UNSCALED
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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 NULL if use fieldtype default
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xyz flag = scaledflag if has fieldlabel name, 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 ReaderNative::read_header(double box[3][3], int &triclinic,
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int fieldinfo, int nfield,
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int *fieldtype, char **fieldlabel,
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int scaledflag, 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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read_lines(2);
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sscanf(line,BIGINT_FORMAT,&natoms);
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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) sscanf(line,"%lg %lg",&box[0][0],&box[0][1]);
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else sscanf(line,"%lg %lg %lg",&box[0][0],&box[0][1],&box[0][2]);
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read_lines(1);
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if (!triclinic) sscanf(line,"%lg %lg",&box[1][0],&box[1][1]);
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else sscanf(line,"%lg %lg %lg",&box[1][0],&box[1][1],&box[1][2]);
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read_lines(1);
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if (!triclinic) sscanf(line,"%lg %lg",&box[2][0],&box[2][1]);
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else sscanf(line,"%lg %lg %lg",&box[2][0],&box[2][1],&box[2][2]);
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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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// exatract column labels and match to requested fields
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char *labelline = &line[strlen("ITEM: ATOMS ")];
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nwords = atom->count_words(labelline);
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char **labels = new char*[nwords];
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labels[0] = strtok(labelline," \t\n\r\f");
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if (labels[0] == NULL) return 1;
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for (int m = 1; m < nwords; m++) {
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labels[m] = strtok(NULL," \t\n\r\f");
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if (labels[m] == NULL) return 1;
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}
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// match each field with a column of per-atom data
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// if fieldlabel set, match with explicit column
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// else infer one or more column matches from fieldtype
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// xyz flag set by scaledflag (if fieldlabel set) or column label
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memory->create(fieldindex,nfield,"read_dump:fieldindex");
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int s_index,u_index,su_index;
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xflag = UNSET;
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yflag = UNSET;
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zflag = UNSET;
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for (int i = 0; i < nfield; i++) {
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if (fieldlabel[i]) {
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fieldindex[i] = find_label(fieldlabel[i],nwords,labels);
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if (fieldtype[i] == X) xflag = scaledflag;
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else if (fieldtype[i] == Y) yflag = scaledflag;
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else if (fieldtype[i] == Z) zflag = scaledflag;
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}
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else if (fieldtype[i] == ID)
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fieldindex[i] = find_label("id",nwords,labels);
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else if (fieldtype[i] == TYPE)
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fieldindex[i] = find_label("type",nwords,labels);
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else if (fieldtype[i] == X) {
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fieldindex[i] = find_label("x",nwords,labels);
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xflag = UNSCALED;
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if (fieldindex[i] < 0) {
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fieldindex[i] = nwords;
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s_index = find_label("xs",nwords,labels);
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u_index = find_label("xu",nwords,labels);
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su_index = find_label("xsu",nwords,labels);
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if (s_index >= 0 && s_index < fieldindex[i]) {
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fieldindex[i] = s_index;
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xflag = SCALED;
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}
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if (u_index >= 0 && u_index < fieldindex[i]) {
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fieldindex[i] = u_index;
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xflag = UNSCALED;
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}
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if (su_index >= 0 && su_index < fieldindex[i]) {
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fieldindex[i] = su_index;
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xflag = SCALED;
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}
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}
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if (fieldindex[i] == nwords) fieldindex[i] = -1;
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} else if (fieldtype[i] == Y) {
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fieldindex[i] = find_label("y",nwords,labels);
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yflag = UNSCALED;
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if (fieldindex[i] < 0) {
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fieldindex[i] = nwords;
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s_index = find_label("ys",nwords,labels);
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u_index = find_label("yu",nwords,labels);
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su_index = find_label("ysu",nwords,labels);
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if (s_index >= 0 && s_index < fieldindex[i]) {
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fieldindex[i] = s_index;
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yflag = SCALED;
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}
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if (u_index >= 0 && u_index < fieldindex[i]) {
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fieldindex[i] = u_index;
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yflag = UNSCALED;
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}
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if (su_index >= 0 && su_index < fieldindex[i]) {
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fieldindex[i] = su_index;
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yflag = SCALED;
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}
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}
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if (fieldindex[i] == nwords) fieldindex[i] = -1;
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} else if (fieldtype[i] == Z) {
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fieldindex[i] = find_label("z",nwords,labels);
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zflag = UNSCALED;
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if (fieldindex[i] < 0) {
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fieldindex[i] = nwords;
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s_index = find_label("zs",nwords,labels);
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u_index = find_label("zu",nwords,labels);
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su_index = find_label("zsu",nwords,labels);
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if (s_index >= 0 && s_index < fieldindex[i]) {
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fieldindex[i] = s_index;
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zflag = SCALED;
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}
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if (u_index >= 0 && u_index < fieldindex[i]) {
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fieldindex[i] = u_index;
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zflag = UNSCALED;
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}
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if (su_index >= 0 && su_index < fieldindex[i]) {
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fieldindex[i] = su_index;
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zflag = SCALED;
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}
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}
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if (fieldindex[i] == nwords) fieldindex[i] = -1;
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} else if (fieldtype[i] == VX)
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fieldindex[i] = find_label("vx",nwords,labels);
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else if (fieldtype[i] == VY)
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fieldindex[i] = find_label("vy",nwords,labels);
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else if (fieldtype[i] == VZ)
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fieldindex[i] = find_label("vz",nwords,labels);
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else if (fieldtype[i] == IX)
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fieldindex[i] = find_label("ix",nwords,labels);
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else if (fieldtype[i] == IY)
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fieldindex[i] = find_label("iy",nwords,labels);
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else if (fieldtype[i] == IZ)
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fieldindex[i] = find_label("iz",nwords,labels);
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}
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delete [] labels;
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// set fieldflag = 1 if any unfound fields
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fieldflag = 0;
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for (int i = 0; i < nfield; i++)
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if (fieldindex[i] < 0) fieldflag = 1;
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// create internal vector of word ptrs for future parsing of per-atom lines
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words = new char*[nwords];
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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 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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for (int i = 0; i < n; i++) {
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eof = fgets(line,MAXLINE,fp);
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if (eof == NULL) error->one(FLERR,"Unexpected end of dump file");
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// tokenize the line
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words[0] = strtok(line," \t\n\r\f");
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for (m = 1; m < nwords; m++)
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words[m] = strtok(NULL," \t\n\r\f");
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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]]);
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}
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}
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/* ----------------------------------------------------------------------
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match label to any of N labels
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return index of match or -1 if no match
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------------------------------------------------------------------------- */
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int ReaderNative::find_label(const char *label, int n, char **labels)
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{
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for (int i = 0; i < n; i++)
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if (strcmp(label,labels[i]) == 0) return i;
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return -1;
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}
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/* ----------------------------------------------------------------------
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read N lines from dump file
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only last one is saved in line
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return NULL if end-of-file error, else non-NULL
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only called by proc 0
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------------------------------------------------------------------------- */
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void ReaderNative::read_lines(int n)
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{
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char *eof;
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for (int i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp);
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if (eof == NULL) error->all(FLERR,"Unexpected end of dump file");
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}
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