Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F77549370
read_data.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
Thu, Aug 15, 03:09
Size
12 KB
Mime Type
text/x-c
Expires
Sat, Aug 17, 03:09 (1 d, 21 h)
Engine
blob
Format
Raw Data
Handle
19881595
Attached To
rLAMMPS lammps
read_data.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.
------------------------------------------------------------------------- */
#ifdef COMMAND_CLASS
CommandStyle
(
read_data
,
ReadData
)
#else
#ifndef LMP_READ_DATA_H
#define LMP_READ_DATA_H
#include "stdio.h"
#include "pointers.h"
namespace
LAMMPS_NS
{
class
ReadData
:
protected
Pointers
{
public:
ReadData
(
class
LAMMPS
*
);
~
ReadData
();
void
command
(
int
,
char
**
);
private:
int
me
,
compressed
;
char
*
line
,
*
keyword
,
*
buffer
,
*
style
;
FILE
*
fp
;
char
**
arg
;
int
narg
,
maxarg
;
char
argoffset1
[
8
],
argoffset2
[
8
];
bigint
id_offset
;
bigint
natoms
;
bigint
nbonds
,
nangles
,
ndihedrals
,
nimpropers
;
int
ntypes
;
int
nbondtypes
,
nangletypes
,
ndihedraltypes
,
nimpropertypes
;
bigint
nellipsoids
;
class
AtomVecEllipsoid
*
avec_ellipsoid
;
bigint
nlines
;
class
AtomVecLine
*
avec_line
;
bigint
ntris
;
class
AtomVecTri
*
avec_tri
;
bigint
nbodies
;
class
AtomVecBody
*
avec_body
;
// box info
double
boxlo
[
3
],
boxhi
[
3
];
double
xy
,
xz
,
yz
;
int
triclinic
;
// optional args
int
addflag
,
offsetflag
,
shiftflag
;
tagint
addvalue
;
int
toffset
,
boffset
,
aoffset
,
doffset
,
ioffset
;
double
shift
[
3
];
int
extra_atom_types
,
extra_bond_types
,
extra_angle_types
;
int
extra_dihedral_types
,
extra_improper_types
;
int
groupbit
;
int
nfix
;
int
*
fix_index
;
char
**
fix_header
;
char
**
fix_section
;
// methods
void
open
(
char
*
);
void
scan
(
int
&
,
int
&
,
int
&
,
int
&
);
int
reallocate
(
int
**
,
int
,
int
);
void
header
();
void
parse_keyword
(
int
);
void
skip_lines
(
bigint
);
void
parse_coeffs
(
char
*
,
const
char
*
,
int
,
int
,
int
);
int
style_match
(
const
char
*
,
const
char
*
);
void
atoms
();
void
velocities
();
void
bonds
(
int
);
void
bond_scan
(
int
,
char
*
,
int
*
);
void
angles
(
int
);
void
dihedrals
(
int
);
void
impropers
(
int
);
void
bonus
(
bigint
,
class
AtomVec
*
,
const
char
*
);
void
bodies
(
int
);
void
mass
();
void
paircoeffs
();
void
pairIJcoeffs
();
void
bondcoeffs
();
void
anglecoeffs
(
int
);
void
dihedralcoeffs
(
int
);
void
impropercoeffs
(
int
);
void
fix
(
int
,
char
*
);
};
}
#endif
#endif
/* ERROR/WARNING messages:
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: Fix ID for read_data does not exist
Self-explanatory.
E: Cannot read_data after simulation box is defined
The read_data command cannot be used after a read_data,
read_restart, or create_box command.
E: Cannot read_data add and merge
These options are not yet supported.
E: Cannot use non-zero z offset in read_data for 2d simulation
The offset option is not yet supported.
E: Cannot run 2d simulation with nonperiodic Z dimension
Use the boundary command to make the z dimension periodic in order to
run a 2d simulation.
W: Atom style in data file differs from currently defined atom style
Self-explanatory.
E: Must read Atoms before Velocities
The Atoms section of a data file must come before a Velocities
section.
E: Invalid data file section: Bonds
Atom style does not allow bonds.
E: Must read Atoms before Bonds
The Atoms section of a data file must come before a Bonds section.
E: Invalid data file section: Angles
Atom style does not allow angles.
E: Must read Atoms before Angles
The Atoms section of a data file must come before an Angles section.
E: Invalid data file section: Dihedrals
Atom style does not allow dihedrals.
E: Must read Atoms before Dihedrals
The Atoms section of a data file must come before a Dihedrals section.
E: Invalid data file section: Impropers
Atom style does not allow impropers.
E: Must read Atoms before Impropers
The Atoms section of a data file must come before an Impropers
section.
E: Invalid data file section: Ellipsoids
Atom style does not allow ellipsoids.
E: Must read Atoms before Ellipsoids
The Atoms section of a data file must come before a Ellipsoids
section.
E: Invalid data file section: Lines
Atom style does not allow lines.
E: Must read Atoms before Lines
The Atoms section of a data file must come before a Lines section.
E: Invalid data file section: Triangles
Atom style does not allow triangles.
E: Must read Atoms before Triangles
The Atoms section of a data file must come before a Triangles section.
E: Invalid data file section: Bodies
Atom style does not allow bodies.
E: Must read Atoms before Bodies
The Atoms section of a data file must come before a Bodies section.
E: Must define pair_style before Pair Coeffs
Must use a pair_style command before reading a data file that defines
Pair Coeffs.
W: Pair style in data file differs from currently defined pair style
Self-explanatory.
E: Must define pair_style before PairIJ Coeffs
Must use a pair_style command before reading a data file that defines
PairIJ Coeffs.
E: Invalid data file section: Bond Coeffs
Atom style does not allow bonds.
E: Must define bond_style before Bond Coeffs
Must use a bond_style command before reading a data file that
defines Bond Coeffs.
W: Bond style in data file differs from currently defined bond style
Self-explanatory.
E: Invalid data file section: Angle Coeffs
Atom style does not allow angles.
E: Must define angle_style before Angle Coeffs
Must use an angle_style command before reading a data file that
defines Angle Coeffs.
W: Angle style in data file differs from currently defined angle style
Self-explanatory.
E: Invalid data file section: Dihedral Coeffs
Atom style does not allow dihedrals.
E: Must define dihedral_style before Dihedral Coeffs
Must use a dihedral_style command before reading a data file that
defines Dihedral Coeffs.
W: Dihedral style in data file differs from currently defined dihedral style
Self-explanatory.
E: Invalid data file section: Improper Coeffs
Atom style does not allow impropers.
E: Must define improper_style before Improper Coeffs
Must use an improper_style command before reading a data file that
defines Improper Coeffs.
W: Improper style in data file differs from currently defined improper style
Self-explanatory.
E: Invalid data file section: BondBond Coeffs
Atom style does not allow angles.
E: Must define angle_style before BondBond Coeffs
Must use an angle_style command before reading a data file that
defines Angle Coeffs.
E: Invalid data file section: BondAngle Coeffs
Atom style does not allow angles.
E: Must define angle_style before BondAngle Coeffs
Must use an angle_style command before reading a data file that
defines Angle Coeffs.
E: Invalid data file section: MiddleBondTorsion Coeffs
Atom style does not allow dihedrals.
E: Must define dihedral_style before MiddleBondTorsion Coeffs
Must use a dihedral_style command before reading a data file that
defines MiddleBondTorsion Coeffs.
E: Invalid data file section: EndBondTorsion Coeffs
Atom style does not allow dihedrals.
E: Must define dihedral_style before EndBondTorsion Coeffs
Must use a dihedral_style command before reading a data file that
defines EndBondTorsion Coeffs.
E: Invalid data file section: AngleTorsion Coeffs
Atom style does not allow dihedrals.
E: Must define dihedral_style before AngleTorsion Coeffs
Must use a dihedral_style command before reading a data file that
defines AngleTorsion Coeffs.
E: Invalid data file section: AngleAngleTorsion Coeffs
Atom style does not allow dihedrals.
E: Must define dihedral_style before AngleAngleTorsion Coeffs
Must use a dihedral_style command before reading a data file that
defines AngleAngleTorsion Coeffs.
E: Invalid data file section: BondBond13 Coeffs
Atom style does not allow dihedrals.
E: Must define dihedral_style before BondBond13 Coeffs
Must use a dihedral_style command before reading a data file that
defines BondBond13 Coeffs.
E: Invalid data file section: AngleAngle Coeffs
Atom style does not allow impropers.
E: Must define improper_style before AngleAngle Coeffs
Must use an improper_style command before reading a data file that
defines AngleAngle Coeffs.
E: Unknown identifier in data file: %s
A section of the data file cannot be read by LAMMPS.
E: No atoms in data file
The header of the data file indicated that atoms would be included,
but they are not present.
E: Needed molecular topology not in data file
The header of the data file indicated bonds, angles, etc would be
included, but they are not present.
E: Needed bonus data not in data file
Some atom styles require bonus data. See the read_data doc page for
details.
E: Read_data shrink wrap did not assign all atoms correctly
This is typically because the box-size specified in the data file is
large compared to the actual extent of atoms in a shrink-wrapped
dimension. When LAMMPS shrink-wraps the box atoms will be lost if the
processor they are re-assigned to is too far away. Choose a box
size closer to the actual extent of the atoms.
E: Unexpected end of data file
LAMMPS hit the end of the data file while attempting to read a
section. Something is wrong with the format of the data file.
E: No ellipsoids allowed with this atom style
Self-explanatory. Check data file.
E: No lines allowed with this atom style
Self-explanatory. Check data file.
E: No triangles allowed with this atom style
Self-explanatory. Check data file.
E: No bodies allowed with this atom style
Self-explanatory. Check data file.
E: System in data file is too big
See the setting for bigint in the src/lmptype.h file.
E: No bonds allowed with this atom style
Self-explanatory.
E: No angles allowed with this atom style
Self-explanatory.
E: No dihedrals allowed with this atom style
Self-explanatory.
E: No impropers allowed with this atom style
Self-explanatory.
E: Bonds defined but no bond types
The data file header lists bonds but no bond types.
E: Angles defined but no angle types
The data file header lists angles but no angle types.
E: Dihedrals defined but no dihedral types
The data file header lists dihedrals but no dihedral types.
E: Impropers defined but no improper types
The data file header lists improper but no improper types.
E: No molecule topology allowed with atom style template
The data file cannot specify the number of bonds, angles, etc,
because this info if inferred from the molecule templates.
E: Did not assign all atoms correctly
Atoms read in from a data file were not assigned correctly to
processors. This is likely due to some atom coordinates being
outside a non-periodic simulation box.
E: Bonds assigned incorrectly
Bonds read in from the data file were not assigned correctly to atoms.
This means there is something invalid about the topology definitions.
E: Angles assigned incorrectly
Angles read in from the data file were not assigned correctly to
atoms. This means there is something invalid about the topology
definitions.
E: Dihedrals assigned incorrectly
Dihedrals read in from the data file were not assigned correctly to
atoms. This means there is something invalid about the topology
definitions.
E: Impropers assigned incorrectly
Impropers read in from the data file were not assigned correctly to
atoms. This means there is something invalid about the topology
definitions.
E: Too many lines in one body in data file - boost MAXBODY
MAXBODY is a setting at the top of the src/read_data.cpp file.
Set it larger and re-compile the code.
E: Unexpected end of PairCoeffs section
Read a blank line.
E: Unexpected end of BondCoeffs section
Read a blank line.
E: Unexpected end of AngleCoeffs section
Read a blank line.
E: Unexpected end of DihedralCoeffs section
Read a blank line.
E: Unexpected end of ImproperCoeffs section
Read a blank line.
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 file %s
The specified file cannot be opened. Check that the path and name are
correct. If the file is a compressed file, also check that the gzip
executable can be found and run.
*/
Event Timeline
Log In to Comment