OOPSE/libmdtools/Atom.hpp

#ifndef _ATOM_H_
#define _ATOM_H_

#include <string.h>
#include <stdlib.h>
#include <iostream>

#include "SimState.hpp"
#include "StuntDouble.hpp"
#include "BaseVisitor.hpp"

class Atom : public StuntDouble {
public:

  Atom(int theIndex, SimState* theConfig );
  virtual ~Atom() {} 

  virtual void setCoords(void);

  void getPos( double theP[3] );
  void setPos( double theP[3] );

  void getVel( double theV[3] );
  void setVel( double theV[3] );

  void getFrc( double theF[3] );
  void addFrc( double theF[3] );

  virtual void zeroForces();

  double getMass() {return c_mass;}
  void setMass(double mass) {c_mass = mass;}
  
  int getIndex() const {return index;}
  void setIndex(int theIndex);

  char *getType() {return c_name;}
  void setType(char * name) {strcpy(c_name,name);}
  
  int getIdent( void ) { return ident; }
  void setIdent( int info ) { ident = info; }

#ifdef IS_MPI
  int getGlobalIndex( void ) { return myGlobalIndex; }
  void setGlobalIndex( int info ) { myGlobalIndex = info; }
#endif // is_mpi

  void setHasDipole( int value ) { has_dipole = value; }
  int hasDipole( void ) { return has_dipole; }

  void setHasCharge(int value) {has_charge = value;}
  int hasCharge(void) {return has_charge;}


  virtual void accept(BaseVisitor* v) {v->visit(this);}
  
protected:
  
  SimState* myConfig;

  double* pos; // the position array
  double* vel; // the velocity array
  double* frc; // the forc array
  double* trq; // the torque vector  ( space fixed )
  double* Amat; // the rotation matrix
  double* mu;   // the array of dipole moments
  double* ul;   // the lab frame unit directional vector

  double c_mass; /* the mass of the atom in amu */

  int index; /* set the atom's index */
  int offset; // the atom's offset in the storage array
  int offsetX, offsetY, offsetZ;

  int Axx, Axy, Axz; // the rotational matrix indices
  int Ayx, Ayy, Ayz;
  int Azx, Azy, Azz;

  char c_name[100]; /* it's name */
  int ident;  // it's unique numeric identity.
  
  int has_dipole; // dipole boolean
  int has_charge; // charge boolean

  bool hasCoords;

#ifdef IS_MPI
  int myGlobalIndex;
#endif
  
};

#endif
Revision:	1167
Committed:	Wed May 12 16:38:45 2004 UTC (20 years, 11 months ago) by tim
File size:	2144 byte(s)
Log Message:	get rid of rc and massratio from simState, creat cutoff group forevery atom which does not belong to cutoff group defined at mdl file
#	Content
1	#ifndef _ATOM_H_
2	#define _ATOM_H_
3
4	#include <string.h>
5	#include <stdlib.h>
6	#include <iostream>
7
8	#include "SimState.hpp"
9	#include "StuntDouble.hpp"
10	#include "BaseVisitor.hpp"
11
12	class Atom : public StuntDouble {
13	public:
14
15	Atom(int theIndex, SimState* theConfig );
16	virtual ~Atom() {}
17
18	virtual void setCoords(void);
19
20	void getPos( double theP[3] );
21	void setPos( double theP[3] );
22
23	void getVel( double theV[3] );
24	void setVel( double theV[3] );
25
26	void getFrc( double theF[3] );
27	void addFrc( double theF[3] );
28
29	virtual void zeroForces();
30
31	double getMass() {return c_mass;}
32	void setMass(double mass) {c_mass = mass;}
33
34	int getIndex() const {return index;}
35	void setIndex(int theIndex);
36
37	char *getType() {return c_name;}
38	void setType(char * name) {strcpy(c_name,name);}
39
40	int getIdent( void ) { return ident; }
41	void setIdent( int info ) { ident = info; }
42
43	#ifdef IS_MPI
44	int getGlobalIndex( void ) { return myGlobalIndex; }
45	void setGlobalIndex( int info ) { myGlobalIndex = info; }
46	#endif // is_mpi
47
48	void setHasDipole( int value ) { has_dipole = value; }
49	int hasDipole( void ) { return has_dipole; }
50
51	void setHasCharge(int value) {has_charge = value;}
52	int hasCharge(void) {return has_charge;}
53
54
55	virtual void accept(BaseVisitor* v) {v->visit(this);}
56
57	protected:
58
59	SimState* myConfig;
60
61	double* pos; // the position array
62	double* vel; // the velocity array
63	double* frc; // the forc array
64	double* trq; // the torque vector ( space fixed )
65	double* Amat; // the rotation matrix
66	double* mu; // the array of dipole moments
67	double* ul; // the lab frame unit directional vector
68
69	double c_mass; /* the mass of the atom in amu */
70
71	int index; /* set the atom's index */
72	int offset; // the atom's offset in the storage array
73	int offsetX, offsetY, offsetZ;
74
75	int Axx, Axy, Axz; // the rotational matrix indices
76	int Ayx, Ayy, Ayz;
77	int Azx, Azy, Azz;
78
79	char c_name[100]; /* it's name */
80	int ident; // it's unique numeric identity.
81
82	int has_dipole; // dipole boolean
83	int has_charge; // charge boolean
84
85	bool hasCoords;
86
87	#ifdef IS_MPI
88	int myGlobalIndex;
89	#endif
90
91	};
92
93	#endif