add parallel file read capability to ReadDump

src/read_dump.h

@@ -22,6 +22,7 @@ CommandStyle(read_dump,ReadDump)
 #ifndef LMP_READ_DUMP_H
 #define LMP_READ_DUMP_H
 
+#include <mpi.h>
 #include <cstdio>
 #include "pointers.h"
 
@@ -43,15 +44,26 @@ class ReadDump : protected Pointers {
 
 private:
   int me,nprocs;
-  FILE *fp;
 
-  int dimension;
+  char **files;            // list of input dump files to process
+  int nfile;               // # of dump files to process (each may be parallel)
+  int currentfile;         // current open file (0 to nfile-1)
+
+  MPI_Comm clustercomm;    // comm for proc cluster that reads/shares a file
+  int me_cluster,nprocs_cluster;  // proc ID and count for my read cluster
+
+  int multiproc;           // 0 = each dump file is a single file
+                           // 1 = each dump file is parallel (multiple files)
+  int multiproc_nfile;     // number of parallel files in one dump file
+
+  int nreader;             // # of parallel dump files read by my cluster
+  int firstfile;           // index of 1st dump file my cluster reads
+                           //   (0 to multiproc_nfile-1)
+  int filereader;          // 1 if this proc reads from a dump file(s)
+
+  int dimension;           // same as in Domain
   int triclinic;
 
-  int nfile;               // # of dump files to process
-  char **files;            // list of file names
-  int currentfile;         // currently open file
-
   int boxflag;             // overwrite simulation with dump file box params
   int replaceflag,addflag; // flags for processing dump snapshot atoms
   int trimflag,purgeflag;
@@ -59,10 +71,13 @@ private:
   int wrapflag;            // user 0/1 if dump file coords are unwrapped/wrapped
   char *readerstyle;       // style of dump files to read
 
+  int nnew;                // # of dump file atoms this proc owns
   int nfield;              // # of fields to extract from dump file
   int *fieldtype;          // type of each field = X,VY,IZ,etc
   char **fieldlabel;       // user specified label for field
   double **fields;         // per-atom field values
+  int maxnew;              // allocation size of fields array
+  double **buf;            // read buffer
 
   int scaled;              // 0/1 if dump file coords are unscaled/scaled
   int wrapped;             // 0/1 if dump file coords are unwrapped/wrapped
@@ -71,20 +86,26 @@ private:
   double xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz;  // dump snapshot box params
   double xprd,yprd,zprd;
 
-  bigint nsnapatoms;        // # of atoms in dump file shapshot
+  bigint *nsnapatoms;       // # of atoms in one snapshot from 
+                            //   one (parallel) dump file
+                            // nreader-length vector b/c a reader proc
+                            //   may read from multiple parallel dump files
 
   int npurge,nreplace,ntrim,nadd;     // stats on processed atoms
-  int addproc;                        // proc that should add next atom
   int yindex,zindex;                  // field index for Y,Z coords
 
-  int *uflag;               // set to 1 if snapshot atom matches owned atom
-  int *ucflag,*ucflag_all;  // set to 1 if snapshot chunk atom was processed
+  class Reader **readers;   // class that reads a dump file
+                            // nreader-length list of readers if proc reads
+                            //   from multiple parallel dump files
 
-  class Reader *reader;           // class that reads dump file
+  void read_atoms();
+  void process_atoms();
+  void migrate_old_atoms();
+  void migrate_new_atoms();
+  void migrate_atoms_by_coords();
 
+  void setup_multiproc();
   int whichtype(char *);
-  void process_atoms(int);
-  void delete_atoms();
 
   double xfield(int, int);
   double yfield(int, int);

src/rerun.cpp

@@ -57,7 +57,7 @@ void Rerun::command(int narg, char **arg)
   if (nfile == 0 || nfile == narg) error->all(FLERR,"Illegal rerun command");
 
   // parse optional args up until "dump"
-  // user MAXBIGINT -1 so Output can add 1 to it and still be a big int
+  // use MAXBIGINT -1 so Output can add 1 to it and still be a big int
 
   bigint first = 0;
   bigint last = MAXBIGINT - 1;