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molecule.h
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rLAMMPS lammps
molecule.h
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/* ----------------------------------------------------------------------
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_MOLEUCULE_H
#include "pointers.h"
namespace
LAMMPS_NS
{
class
Molecule
:
protected
Pointers
{
public:
char
*
id
;
// number of atoms,bonds,etc in molecule
int
natoms
;
int
nbonds
,
nangles
,
ndihedrals
,
nimpropers
;
// max bond,angle,etc per atom
int
maxtype
;
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
;
// 1 if attribute defined or computed, 0 if not
int
centerflag
,
massflag
,
comflag
,
inertiaflag
;
// 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
;
int
**
bond_atom
;
int
*
num_angle
;
int
**
angle_type
;
int
**
angle_atom1
,
**
angle_atom2
,
**
angle_atom3
;
int
*
num_dihedral
;
int
**
dihedral_type
;
int
**
dihedral_atom1
,
**
dihedral_atom2
,
**
dihedral_atom3
,
**
dihedral_atom4
;
int
*
num_improper
;
int
**
improper_type
;
int
**
improper_atom1
,
**
improper_atom2
,
**
improper_atom3
,
**
improper_atom4
;
int
**
nspecial
;
int
**
special
;
int
*
shake_flag
;
int
**
shake_atom
;
int
**
shake_type
;
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
molradius
;
// radius of molecule from COM,
// 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)
Molecule
(
class
LAMMPS
*
,
int
,
char
**
);
~
Molecule
();
void
compute_center
();
void
compute_mass
();
void
compute_com
();
void
compute_inertia
();
private:
int
me
;
FILE
*
fp
;
int
*
count
;
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
shakeflag_read
(
char
*
);
void
shakeatom_read
(
char
*
);
void
shaketype_read
(
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
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