119 lines
4.2 KiB
C++
119 lines
4.2 KiB
C++
/* -*- c++ -*- ----------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
https://www.lammps.org/, Sandia National Laboratories
|
|
LAMMPS development team: developers@lammps.org
|
|
|
|
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 Timothy Sirk
|
|
------------------------------------------------------------------------- */
|
|
|
|
#ifdef COMMAND_CLASS
|
|
// clang-format off
|
|
CommandStyle(read_dump,ReadDump);
|
|
// clang-format on
|
|
#else
|
|
|
|
#ifndef LMP_READ_DUMP_H
|
|
#define LMP_READ_DUMP_H
|
|
|
|
#include "command.h"
|
|
|
|
namespace LAMMPS_NS {
|
|
|
|
class ReadDump : public Command {
|
|
public:
|
|
ReadDump(class LAMMPS *);
|
|
~ReadDump() override;
|
|
void command(int, char **) override;
|
|
|
|
void store_files(int, char **);
|
|
void setup_reader(int, char **);
|
|
bigint seek(bigint, int);
|
|
void header(int);
|
|
bigint next(bigint, bigint, int, int);
|
|
void atoms();
|
|
int fields_and_keywords(int, char **);
|
|
|
|
private:
|
|
int me, nprocs;
|
|
|
|
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 parallel; // 1 if parallel reading (e.g. via ADIOS2)
|
|
|
|
int dimension; // same as in Domain
|
|
int triclinic;
|
|
|
|
int boxflag; // overwrite simulation box with dump file box params
|
|
int timestepflag; // overwrite simulation timestep with dump file timestep
|
|
int replaceflag, addflag; // flags for processing dump snapshot atoms
|
|
int trimflag, purgeflag;
|
|
int scaleflag; // user 0/1 if dump file coords are unscaled/scaled
|
|
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
|
|
|
|
double box[3][3]; // dump file box parameters
|
|
double xlo, xhi, ylo, yhi, zlo, zhi, xy, xz, yz; // dump snapshot box params
|
|
double xprd, yprd, zprd;
|
|
|
|
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 yindex, zindex; // field index for Y,Z coords
|
|
|
|
class Reader **readers; // class that reads a dump file
|
|
// nreader-length list of readers if proc reads
|
|
// from multiple parallel dump files
|
|
|
|
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 *);
|
|
|
|
double xfield(int, int);
|
|
double yfield(int, int);
|
|
double zfield(int, int);
|
|
};
|
|
|
|
} // namespace LAMMPS_NS
|
|
|
|
#endif
|
|
#endif
|