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rLAMMPS lammps
molecule.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_ONE_MOLECULE_H
#define LMP_ONE_MOLECULE_H
#include "pointers.h"
namespace
LAMMPS_NS
{
class
Molecule
:
protected
Pointers
{
public:
char
*
id
;
// template id of this molecule, same for all molecules in set
int
nset
;
// if first in set, # of molecules in this set
// else 0 if not first in set
int
last
;
// 1 if last molecule in set, else 0
// number of atoms,bonds,etc in molecule
// nibody,ndbody = # of integer/double fields in body
int
natoms
;
int
nbonds
,
nangles
,
ndihedrals
,
nimpropers
;
int
ntypes
;
int
nbondtypes
,
nangletypes
,
ndihedraltypes
,
nimpropertypes
;
int
nibody
,
ndbody
;
// max bond,angle,etc per atom
int
bond_per_atom
,
angle_per_atom
,
dihedral_per_atom
,
improper_per_atom
;
int
maxspecial
;
// 1 if attribute defined in file, 0 if not
int
xflag
,
typeflag
,
qflag
,
radiusflag
,
rmassflag
;
int
bondflag
,
angleflag
,
dihedralflag
,
improperflag
;
int
nspecialflag
,
specialflag
;
int
shakeflag
,
shakeflagflag
,
shakeatomflag
,
shaketypeflag
;
int
bodyflag
,
ibodyflag
,
dbodyflag
;
// 1 if attribute defined or computed, 0 if not
int
centerflag
,
massflag
,
comflag
,
inertiaflag
;
// 1 if molecule fields require atom IDs
int
tag_require
;
// attributes
double
**
x
;
// displacement of each atom from origin
int
*
type
;
// type of each atom
double
*
q
;
// charge on each atom
double
*
radius
;
// radius of each atom
double
*
rmass
;
// mass of each atom
int
*
num_bond
;
// bonds, angles, dihedrals, impropers for each atom
int
**
bond_type
;
tagint
**
bond_atom
;
int
*
num_angle
;
int
**
angle_type
;
tagint
**
angle_atom1
,
**
angle_atom2
,
**
angle_atom3
;
int
*
num_dihedral
;
int
**
dihedral_type
;
tagint
**
dihedral_atom1
,
**
dihedral_atom2
,
**
dihedral_atom3
,
**
dihedral_atom4
;
int
*
num_improper
;
int
**
improper_type
;
tagint
**
improper_atom1
,
**
improper_atom2
,
**
improper_atom3
,
**
improper_atom4
;
int
**
nspecial
;
tagint
**
special
;
int
*
shake_flag
;
tagint
**
shake_atom
;
int
**
shake_type
;
class
AtomVecBody
*
avec_body
;
int
*
ibodyparams
;
// integer and double body params
double
*
dbodyparams
;
double
center
[
3
];
// geometric center of molecule
double
masstotal
;
// total mass of molecule
double
com
[
3
];
// center of mass of molecule
double
itensor
[
6
];
// moments of inertia of molecule
double
inertia
[
3
];
// principal moments of inertia of molecule
double
ex
[
3
],
ey
[
3
],
ez
[
3
];
// principal axes of molecule in space coords
double
quat
[
4
];
// quaternion for orientation of molecule
double
maxradius
;
// max radius of any atom in molecule
double
molradius
;
// radius of molecule from geometric center
// including finite-size particle radii
int
comatom
;
// index (1-Natom) of atom closest to COM
double
maxextent
;
// furthest any atom in molecule is from comatom
double
**
dx
;
// displacement of each atom relative to center
double
**
dxcom
;
// displacement of each atom relative to COM
double
**
dxbody
;
// displacement of each atom relative to COM
// in body frame (diagonalized interia tensor)
double
*
quat_external
;
// orientation imposed by external class
// e.g. FixPour or CreateAtoms
Molecule
(
class
LAMMPS
*
,
int
,
char
**
,
int
&
);
~
Molecule
();
void
compute_center
();
void
compute_mass
();
void
compute_com
();
void
compute_inertia
();
void
check_attributes
(
int
);
private:
int
me
;
FILE
*
fp
;
int
*
count
;
int
toffset
,
boffset
,
aoffset
,
doffset
,
ioffset
;
int
autospecial
;
double
sizescale
;
void
read
(
int
);
void
coords
(
char
*
);
void
types
(
char
*
);
void
charges
(
char
*
);
void
diameters
(
char
*
);
void
masses
(
char
*
);
void
bonds
(
int
,
char
*
);
void
angles
(
int
,
char
*
);
void
dihedrals
(
int
,
char
*
);
void
impropers
(
int
,
char
*
);
void
nspecial_read
(
int
,
char
*
);
void
special_read
(
char
*
);
void
special_generate
();
void
shakeflag_read
(
char
*
);
void
shakeatom_read
(
char
*
);
void
shaketype_read
(
char
*
);
void
body
(
int
,
int
,
char
*
);
void
initialize
();
void
allocate
();
void
deallocate
();
void
open
(
char
*
);
void
readline
(
char
*
);
void
parse_keyword
(
int
,
char
*
,
char
*
);
void
skip_lines
(
int
,
char
*
);
int
parse
(
char
*
,
char
**
,
int
);
// void print();
};
}
#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: Molecule template ID must be alphanumeric or underscore characters
Self-explanatory.
E: Insufficient Jacobi rotations for rigid molecule
Eigensolve for rigid body was not sufficiently accurate.
E: Unexpected end of molecule file
Self-explanatory.
E: Molecule file z center-of-mass must be 0.0 for 2d
Self-explanatory.
E: Molecule file requires atom style body
Self-explanatory.
E: No count or invalid atom count in molecule file
The number of atoms must be specified.
E: Invalid bond count in molecule file
Self-explanatory.
E: Invalid angle count in molecule file
Self-explanatory.
E: Invalid dihedral count in molecule file
Self-explanatory.
E: Invalid improper count in molecule file
Self-explanatory.
E: Molecule file has bonds but no nbonds setting
Self-explanatory.
E: Molecule file has angles but no nangles setting
Self-explanatory.
E: Molecule file has dihedrals but no ndihedrals setting
Self-explanatory.
E: Molecule file has impropers but no nimpropers setting
Self-explanatory.
E: Molecule file shake flags not before shake atoms
The order of the two sections is important.
E: Molecule file shake flags not before shake bonds
The order of the two sections is important.
E: Molecule file has body params but no setting for them
Self-explanatory.
E: Unknown section in molecule file
Self-explanatory.
E: Molecule file needs both Special Bond sections
Self-explanatory.
E: Molecule file has special flags but no bonds
Self-explanatory.
E: Molecule file shake info is incomplete
All 3 SHAKE sections are needed.
E: Molecule file has no Body Integers section
Self-explanatory.
E: Molecule file has no Body Doubles section
Self-explanatory.
E: Molecule natoms must be 1 for body particle
Self-explanatory.
E: Molecule sizescale must be 1.0 for body particle
Self-explanatory.
E: Invalid Coords section in molecule file
Self-explanatory.
E: Molecule file z coord must be 0.0 for 2d
Self-explanatory.
E: Invalid Types section in molecule file
Self-explanatory.
E: Invalid atom type in molecule file
Atom types must range from 1 to specified # of types.
E: Invalid Charges section in molecule file
Self-explanatory.
E: Invalid Diameters section in molecule file
Self-explanatory.
E: Invalid atom diameter in molecule file
Diameters must be >= 0.0.
E: Invalid Masses section in molecule file
Self-explanatory.
E: Invalid atom mass in molecule file
Masses must be > 0.0.
E: Invalid Bonds section in molecule file
Self-explanatory.
E: Invalid atom ID in Bonds section of molecule file
Self-explanatory.
E: Invalid bond type in Bonds section of molecule file
Self-explanatory.
E: Invalid Angles section in molecule file
Self-explanatory.
E: Invalid atom ID in Angles section of molecule file
Self-explanatory.
E: Invalid angle type in Angles section of molecule file
Self-explanatory.
E: Invalid Dihedrals section in molecule file
Self-explanatory.
E: Invalid atom ID in dihedrals section of molecule file
Self-explanatory.
E: Invalid dihedral type in dihedrals section of molecule file
Self-explanatory.
E: Invalid Impropers section in molecule file
Self-explanatory.
E: Invalid atom ID in impropers section of molecule file
Self-explanatory.
E: Invalid improper type in impropers section of molecule file
Self-explanatory.
E: Invalid Special Bond Counts section in molecule file
Self-explanatory.
E: Molecule file special list does not match special count
The number of values in an atom's special list does not match count.
E: Invalid special atom index in molecule file
Self-explanatory.
E: Molecule auto special bond generation overflow
Counts exceed maxspecial setting for other atoms in system.
E: Invalid shake flag in molecule file
Self-explanatory.
E: Invalid shake atom in molecule file
Self-explanatory.
E: Invalid shake bond type in molecule file
Self-explanatory.
E: Invalid shake angle type in molecule file
Self-explanatory.
E: Too few values in body section of molecule file
Self-explanatory.
E: Too many values in body section of molecule file
Self-explanatory.
W: Molecule attributes do not match system attributes
An attribute is specified (e.g. diameter, charge) that is
not defined for the specified atom style.
E: Molecule topology type exceeds system topology type
The number of bond, angle, etc types in the molecule exceeds the
system setting. See the create_box command for how to specify these
values.
E: Molecule toplogy/atom exceeds system topology/atom
The number of bonds, angles, etc per-atom in the molecule exceeds the
system setting. See the create_box command for how to specify these
values.
W: Molecule has bond topology but no special bond settings
This means the bonded atoms will not be excluded in pair-wise
interactions.
E: Cannot open molecule file %s
The specified file cannot be opened. Check that the path and name are
correct.
*/
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