git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8334 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/reader_xyz.cpp

@@ -0,0 +1,215 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Axel Kohlmeyer (Temple U)
+------------------------------------------------------------------------- */
+
+#include "string.h"
+#include "stdlib.h"
+#include "reader_xyz.h"
+#include "atom.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define MAXLINE 1024        // max line length in dump file
+
+enum{ID,TYPE,X,Y,Z};
+
+/* ---------------------------------------------------------------------- */
+
+ReaderXYZ::ReaderXYZ(LAMMPS *lmp) : Reader(lmp)
+{
+  line = new char[MAXLINE];
+  fieldindex = NULL;
+  nstep = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ReaderXYZ::~ReaderXYZ()
+{
+  delete [] line;
+  memory->destroy(fieldindex);
+}
+
+/* ----------------------------------------------------------------------
+   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 ReaderXYZ::read_time(bigint &ntimestep)
+{
+  char *eof = fgets(line,MAXLINE,fp);
+  if (eof == NULL) return 1;
+
+  // first line has to have the number of atoms
+
+  natoms = ATOBIGINT(line);
+  if (natoms < 1)
+    error->one(FLERR,"Dump file is incorrectly formatted");
+
+  // skip over comment/title line
+
+  read_lines(1);
+
+  // fake time step numbers
+
+  ntimestep = nstep;
+
+  // count this frame
+
+  ++nstep;
+  return 0;
+}
+
+/* ----------------------------------------------------------------------
+   skip snapshot from timestamp onward
+   only called by proc 0
+------------------------------------------------------------------------- */
+
+void ReaderXYZ::skip()
+{
+  // invoke read_lines() in chunks no larger than MAXSMALLINT
+
+  int nchunk;
+  bigint nremain = natoms;
+  while (nremain) {
+    nchunk = MIN(nremain,MAXSMALLINT);
+    read_lines(nchunk);
+    nremain -= nchunk;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   read remaining header info:
+     return natoms
+     box bounds, triclinic (inferred), fieldflag (1 if any fields not found),
+     xyz flag = UNSET (not a requested field), SCALED, UNSCALED
+   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 NULL if use fieldtype default
+   xyz flag = scaledflag if has fieldlabel name, else set by x,xs,xu,xsu
+   only called by proc 0
+------------------------------------------------------------------------- */
+
+bigint ReaderXYZ::read_header(double box[3][3], int &triclinic,
+                              int fieldinfo, int nfield,
+                              int *fieldtype, char **fieldlabel,
+                              int scaledflag, int &fieldflag,
+                              int &xflag, int &yflag, int &zflag)
+{
+
+  nid = 0;
+
+  // signal that we have no box info at all
+
+  triclinic = -1;
+
+  // if no field info requested, just return
+
+  if (!fieldinfo) return natoms;
+
+  memory->create(fieldindex,nfield,"read_dump:fieldindex");
+
+  // for xyz we know nothing about the style of coordinates, 
+  // so the caller has to set the proper flag.
+
+  xflag = scaledflag;
+  yflag = scaledflag;
+  zflag = scaledflag;
+
+  // copy fieldtype list for supported fields
+
+  fieldflag = 0;
+  for (int i = 0; i < nfield; i++) {
+    if ( (fieldtype[i] == X) ||
+         (fieldtype[i] == Y) ||
+         (fieldtype[i] == Z) ||
+         (fieldtype[i] == ID) ||
+         (fieldtype[i] == TYPE) ) {
+      fieldindex[i] = fieldtype[i];
+    } else {
+      fieldflag = 1;
+    }
+  }
+  
+  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 ReaderXYZ::read_atoms(int n, int nfield, double **fields)
+{
+  int i,m;
+  char *eof;
+  int mytype;
+  double myx, myy, myz;
+
+  for (i = 0; i < n; i++) {
+    eof = fgets(line,MAXLINE,fp);
+    if (eof == NULL) error->one(FLERR,"Unexpected end of dump file");
+
+    ++nid;
+    sscanf(line,"%*s%lg%lg%lg", &myx, &myy, &myz);
+
+    // XXX: we could insert an element2type translation here
+    // XXX: for now we flag unrecognized types as type 0,
+    // XXX: which should trigger an error, if LAMMPS uses it.
+    mytype = atoi(line);
+
+    for (m = 0; m < nfield; m++) {
+      switch (fieldindex[m]) {
+      case X:
+        fields[i][m] = myx;
+        break;
+      case Y:
+        fields[i][m] = myy;
+        break;
+      case Z:
+        fields[i][m] = myz;
+        break;
+      case ID:
+        fields[i][m] = nid;
+        break;
+      case TYPE:
+        fields[i][m] = mytype;
+        break;
+      }
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   read N lines from dump file
+   only last one is saved in line
+   return NULL if end-of-file error, else non-NULL
+   only called by proc 0
+------------------------------------------------------------------------- */
+
+void ReaderXYZ::read_lines(int n)
+{
+  char *eof;
+  for (int i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp);
+  if (eof == NULL) error->all(FLERR,"Unexpected end of dump file");
+}