Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F78329706
dump.h
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Mon, Aug 19, 20:59
Size
7 KB
Mime Type
text/x-c
Expires
Wed, Aug 21, 20:59 (2 d)
Engine
blob
Format
Raw Data
Handle
20028756
Attached To
rLAMMPS lammps
dump.h
View Options
/* -*- c++ -*- ----------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifndef LMP_DUMP_H
#define LMP_DUMP_H
#include <mpi.h>
#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
class Dump : protected Pointers {
public:
char *id; // user-defined name of Dump
char *style; // style of Dump
char *filename; // user-specified file
int igroup,groupbit; // group that Dump is performed on
int first_flag; // 0 if no initial dump, 1 if yes initial dump
int clearstep; // 1 if dump invokes computes, 0 if not
int comm_forward; // size of forward communication (0 if none)
int comm_reverse; // size of reverse communication (0 if none)
#if defined(LMP_QSORT)
// static variable across all Dump objects
static Dump *dumpptr; // holds a ptr to Dump currently being used
#endif
Dump(class LAMMPS *, int, char **);
virtual ~Dump();
void init();
virtual void write();
virtual int pack_forward_comm(int, int *, double *, int, int *) {return 0;}
virtual void unpack_forward_comm(int, int, double *) {}
virtual int pack_reverse_comm(int, int, double *) {return 0;}
virtual void unpack_reverse_comm(int, int *, double *) {}
void modify_params(int, char **);
virtual bigint memory_usage();
protected:
int me,nprocs; // proc info
int compressed; // 1 if dump file is written compressed, 0 no
int binary; // 1 if dump file is written binary, 0 no
int multifile; // 0 = one big file, 1 = one file per timestep
int multiproc; // 0 = proc 0 writes for all,
// else # of procs writing files
int nclusterprocs; // # of procs in my cluster that write to one file
int filewriter; // 1 if this proc writes a file, else 0
int fileproc; // ID of proc in my cluster who writes to file
char *multiname; // filename with % converted to cluster ID
MPI_Comm clustercomm; // MPI communicator within my cluster of procs
int header_flag; // 0 = item, 2 = xyz
int flush_flag; // 0 if no flush, 1 if flush every dump
int sort_flag; // 1 if sorted output
int append_flag; // 1 if open file in append mode, 0 if not
int buffer_allow; // 1 if style allows for buffer_flag, 0 if not
int buffer_flag; // 1 if buffer output as one big string, 0 if not
int padflag; // timestep padding in filename
int pbcflag; // 1 if remap dumped atoms via PBC, 0 if not
int singlefile_opened; // 1 = one big file, already opened, else 0
int sortcol; // 0 to sort on ID, 1-N on columns
int sortcolm1; // sortcol - 1
int sortorder; // ASCEND or DESCEND
char boundstr[9]; // encoding of boundary flags
char *format; // format string for the file write
char *format_default; // default format string
char *format_line_user; // user-specified format strings
char *format_float_user;
char *format_int_user;
char *format_bigint_user;
char **format_column_user;
FILE *fp; // file to write dump to
int size_one; // # of quantities for one atom
int nme; // # of atoms in this dump from me
int nsme; // # of chars in string output from me
double boxxlo,boxxhi; // local copies of domain values
double boxylo,boxyhi; // lo/hi are bounding box for triclinic
double boxzlo,boxzhi;
double boxxy,boxxz,boxyz;
bigint ntotal; // total # of per-atom lines in snapshot
int reorderflag; // 1 if OK to reorder instead of sort
int ntotal_reorder; // # of atoms that must be in snapshot
int nme_reorder; // # of atoms I must own in snapshot
tagint idlo; // lowest ID I own when reordering
int maxbuf; // size of buf
double *buf; // memory for atom quantities
int maxsbuf; // size of sbuf
char *sbuf; // memory for atom quantities in string format
int maxids; // size of ids
int maxsort; // size of bufsort, idsort, index
int maxproc; // size of proclist
tagint *ids; // list of atom IDs, if sorting on IDs
double *bufsort;
tagint *idsort;
int *index,*proclist;
double **xpbc,**vpbc;
imageint *imagepbc;
int maxpbc;
class Irregular *irregular;
virtual void init_style() = 0;
virtual void openfile();
virtual int modify_param(int, char **) {return 0;}
virtual void write_header(bigint) = 0;
virtual int count();
virtual void pack(tagint *) = 0;
virtual int convert_string(int, double *) {return 0;}
virtual void write_data(int, double *) = 0;
void pbc_allocate();
void sort();
#if defined(LMP_QSORT)
static int idcompare(const void *, const void *);
static int bufcompare(const void *, const void *);
static int bufcompare_reverse(const void *, const void *);
#else
static int idcompare(const int, const int, void *);
static int bufcompare(const int, const int, void *);
static int bufcompare_reverse(const int, const int, void *);
#endif
};
}
#endif
/* ERROR/WARNING messages:
E: Dump file MPI-IO output not allowed with % in filename
This is because a % signifies one file per processor and MPI-IO
creates one large file for all processors.
E: Cannot dump sort when multiple dump files are written
In this mode, each processor dumps its atoms to a file, so
no sorting is allowed.
E: Cannot dump sort on atom IDs with no atom IDs defined
Self-explanatory.
E: Dump sort column is invalid
Self-explanatory.
E: Too many atoms to dump sort
Cannot sort when running with more than 2^31 atoms.
E: Too much per-proc info for dump
Number of local atoms times number of columns must fit in a 32-bit
integer for dump.
E: Too much buffered per-proc info for dump
The size of the buffered string must fit in a 32-bit integer for a
dump.
E: Cannot open gzipped file
LAMMPS was compiled without support for reading and writing gzipped
files through a pipeline to the gzip program with -DLAMMPS_GZIP.
E: Cannot open dump file
Self-explanatory.
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Dump_modify buffer yes not allowed for this style
Self-explanatory.
E: Cannot use dump_modify fileper without % in dump file name
Self-explanatory.
E: Cannot use dump_modify nfile without % in dump file name
Self-explanatory.
*/
Event Timeline
Log In to Comment