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molecule.h
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Tue, Jul 30, 03:11

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
// number of atoms,bonds,etc in molecule
int natoms;
int nbonds,nangles,ndihedrals,nimpropers;
int ntypes;
int nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
// 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;
// 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;
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 *, char *, char *);
~Molecule();
void compute_center();
void compute_mass();
void compute_com();
void compute_inertia();
void check_attributes(int);
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
/* ERROR/WARNING messages:
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: No atom 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: 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 z coord must be 0.0 for 2d
Self-explanatory.
E: Invalid atom type in molecule file
Atom types must range from 1 to specified # of types.
E: Invalid atom diameter in molecule file
Diameters must be >= 0.0.
E: Invalid atom mass in molecule file
Masses must be > 0.0.
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 atom ID in Angles section of molecule file
Self-explanatory.
E: Invalid angle type in Angles section of 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 atom ID in impropers section of molecule file
Self-explanatory.
E: Invalid improper type in impropers section of 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: 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.
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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