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 zAngle; // the rotation about the z-axis ( body-fixed )

  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:	1187
Committed:	Sat May 22 18:16:18 2004 UTC (20 years, 3 months ago) by chrisfen
File size:	2210 byte(s)
Log Message:	Fixed Thermodynamic integration code.
#	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			#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	tim	1113	void setHasCharge(int value) {has_charge = value;}
52			int hasCharge(void) {return has_charge;}
53
54	tim	1118
55	tim	1126	virtual void accept(BaseVisitor* v) {v->visit(this);}
56	tim	1118
57	mmeineke	377	protected:
58
59	mmeineke	670	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	chrisfen	1187	double zAngle; // the rotation about the z-axis ( body-fixed )
70
71	mmeineke	377	double c_mass; /* the mass of the atom in amu */
72
73			int index; /* set the atom's index */
74			int offset; // the atom's offset in the storage array
75			int offsetX, offsetY, offsetZ;
76
77			int Axx, Axy, Axz; // the rotational matrix indices
78			int Ayx, Ayy, Ayz;
79			int Azx, Azy, Azz;
80
81			char c_name[100]; /* it's name */
82			int ident; // it's unique numeric identity.
83
84			int has_dipole; // dipole boolean
85	tim	1113	int has_charge; // charge boolean
86	mmeineke	377
87	mmeineke	670	bool hasCoords;
88
89	mmeineke	377	#ifdef IS_MPI
90			int myGlobalIndex;
91			#endif
92
93			};
94
95			#endif