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; }

  void getRc(double theRc[3]);
  void setRc(double theRc[3]);

  double getMassRatio() { return *massRatio;}
  void setMassRatio(double theMassRatio) { *massRatio = theMassRatio;}

#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* rc; //the center of mass of the molecule
  double* massRatio; //the ratio of this atom to the total mass of the molecule

  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:	1136
Committed:	Tue Apr 27 16:26:44 2004 UTC (20 years, 4 months ago) by tim
File size:	2456 byte(s)
Log Message:	add center of mass of the molecule and massRation into atom class
#	User	Rev	Content
1	mmeineke	377	#ifndef _ATOM_H_
2			#define _ATOM_H_
3
4	gezelter	829	#include <string.h>
5			#include <stdlib.h>
6	mmeineke	377	#include <iostream>
7
8	mmeineke	670	#include "SimState.hpp"
9	gezelter	1097	#include "StuntDouble.hpp"
10	tim	1118	#include "BaseVisitor.hpp"
11	mmeineke	670
12	gezelter	1097	class Atom : public StuntDouble {
13	mmeineke	377	public:
14
15	mmeineke	670	Atom(int theIndex, SimState* theConfig );
16	gezelter	409	virtual ~Atom() {}
17	mmeineke	377
18	tim	689	virtual void setCoords(void);
19	mmeineke	377
20	mmeineke	599	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	gezelter	1097	virtual void zeroForces();
30	mmeineke	377
31	gezelter	1097	double getMass() {return c_mass;}
32	mmeineke	377	void setMass(double mass) {c_mass = mass;}
33
34			int getIndex() const {return index;}
35	gezelter	409	void setIndex(int theIndex);
36	gezelter	1097
37	mmeineke	377	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	tim	1136	void getRc(double theRc[3]);
44			void setRc(double theRc[3]);
45
46			double getMassRatio() { return *massRatio;}
47			void setMassRatio(double theMassRatio) { *massRatio = theMassRatio;}
48
49	mmeineke	377	#ifdef IS_MPI
50			int getGlobalIndex( void ) { return myGlobalIndex; }
51			void setGlobalIndex( int info ) { myGlobalIndex = info; }
52			#endif // is_mpi
53
54			void setHasDipole( int value ) { has_dipole = value; }
55			int hasDipole( void ) { return has_dipole; }
56
57	tim	1113	void setHasCharge(int value) {has_charge = value;}
58			int hasCharge(void) {return has_charge;}
59
60	tim	1118
61	tim	1126	virtual void accept(BaseVisitor* v) {v->visit(this);}
62	tim	1118
63	mmeineke	377	protected:
64
65	mmeineke	670	SimState* myConfig;
66
67			double* pos; // the position array
68			double* vel; // the velocity array
69			double* frc; // the forc array
70			double* trq; // the torque vector ( space fixed )
71			double* Amat; // the rotation matrix
72			double* mu; // the array of dipole moments
73			double* ul; // the lab frame unit directional vector
74	tim	1136	double* rc; //the center of mass of the molecule
75			double* massRatio; //the ratio of this atom to the total mass of the molecule
76	mmeineke	670
77	mmeineke	377	double c_mass; /* the mass of the atom in amu */
78
79			int index; /* set the atom's index */
80			int offset; // the atom's offset in the storage array
81			int offsetX, offsetY, offsetZ;
82
83			int Axx, Axy, Axz; // the rotational matrix indices
84			int Ayx, Ayy, Ayz;
85			int Azx, Azy, Azz;
86
87			char c_name[100]; /* it's name */
88			int ident; // it's unique numeric identity.
89
90			int has_dipole; // dipole boolean
91	tim	1113	int has_charge; // charge boolean
92	mmeineke	377
93	mmeineke	670	bool hasCoords;
94
95	mmeineke	377	#ifdef IS_MPI
96			int myGlobalIndex;
97			#endif
98
99			};
100
101			#endif