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rLAMMPS lammps
dump.h
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/* -*- 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)
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
();
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
/* 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.
*/
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