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read_data.h
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read_data.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.
------------------------------------------------------------------------- */
#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,*copy,*keyword,*buffer,*style;
FILE *fp;
char **arg;
int narg,maxarg;
char argoffset1[8],argoffset2[8];
bigint id_offset;
int nlocal_previous;
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,coeffflag;
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(int);
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: Read data add offset is too big
It cannot be larger than the size of atom IDs, e.g. the maximum 32-bit
integer.
E: Non-zero read_data shift z value for 2d simulation
Self-explanatory.
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: Fix ID for read_data does not exist
Self-explanatory.
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.
E: Cannot read_data without add keyword after simulation box is defined
Self-explanatory.
E: Cannot use read_data add before simulation box is defined
Self-explanatory.
E: Cannot use read_data offset without add flag
Self-explanatory.
E: Cannot use read_data shift without add flag
Self-explanatory.
E: Cannot use read_data extra with add flag
Self-explanatory.
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: 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: Subsequent read data induced too many bonds per atom
See the create_box extra/bond/per/atom or read_data "extra bond per
atom" header value to set this limit larger.
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: Subsequent read data induced too many angles per atom
See the create_box extra/angle/per/atom or read_data "extra angle per
atom" header value to set this limit larger.
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: Subsequent read data induced too many dihedrals per atom
See the create_box extra/dihedral/per/atom or read_data "extra
dihedral per atom" header value to set this limit larger.
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: Subsequent read data induced too many impropers per atom
See the create_box extra/improper/per/atom or read_data "extra
improper per atom" header value to set this limit larger.
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 few values in body lines in data file
Self-explanatory.
E: Too many values in body lines in data file
Self-explanatory.
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.
*/

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