OOPSE/libmdtools/Atom.hpp

#ifndef _ATOM_H_
#define _ATOM_H_

#include <cstring>
#include <cstdlib>
#include <iostream>

#include "SimState.hpp"

class Atom{
public:

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

  void setCoords(void);

//   void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, 
//                 double* Atrq, double* AAmat, double* Amu, 
//                 double* Aul);
//   void deleteAtom(int theIndex);
//   void deleteRange(int startIndex, int stopIndex);

  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() = 0;

  double getMass() const {return c_mass;}
  void setMass(double mass) {c_mass = mass;}

  double getEamRcut() const {return myEamRcut;}
  void setEamRcut(double eamRcut) {myEamRcut = eamRcut;}
  
  double getSigma() const {return c_sigma;}
  void setSigma(double sigma) {c_sigma = sigma;}

  double getEpslon() const {return c_epslon;}
  void setEpslon(double epslon) {c_epslon = epslon;}
  
  double getCovalent() const {return c_covalent;}
  void setCovalent(double covalent) {c_covalent = covalent;}
  
  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 set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
  int get_n_hydrogens() const {return c_n_hyd;}

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

  void setLJ( void )        { is_LJ = 1; is_VDW = 0; }
  int isLJ( void )    { return is_LJ; }

  void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
  int isVDW( void )    { return is_VDW; }

  void setEAM( void ) { is_EAM = 1; }
  int  isEAM( void ) { return is_EAM; }

  virtual int isDirectional( void ) = 0;


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 */
  double c_sigma; /* the sigma parameter for van der walls interactions */
  double c_epslon; /* the esplon parameter for VDW interactions */
  double c_covalent; // The covalent radius of the atom.

  double myEamRcut; // Atom rcut for eam defined by the forcefield.

  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 c_n_hyd; // the number of hydrogens bonded to the atom 
  
  int has_dipole; // dipole boolean
  int is_VDW;    // VDW boolean
  int is_LJ;    // LJ boolean
  int is_EAM; //EAM boolean

  bool hasCoords;

#ifdef IS_MPI
  int myGlobalIndex;
#endif
  
};

class GeneralAtom : public Atom{

public:
  GeneralAtom(int theIndex, SimState* theConfig): Atom(theIndex, theConfig){}
  virtual ~GeneralAtom(){}

  int isDirectional( void ){ return 0; }
  void zeroForces( void );
};

class DirectionalAtom : public Atom {
  
public:
  DirectionalAtom(int theIndex, SimState* theConfig) : Atom(theIndex, 
                                                            theConfig)
  { 
    ssdIdentity = 0; 
    sux = 0.0;
    suy = 0.0;
    suz = 0.0;
  }
  virtual ~DirectionalAtom() {}

  void printAmatIndex( void );

  int isDirectional(void) { return 1; }
  
  void setSSD( int value) { ssdIdentity = value; }
  int isSSD(void) {return ssdIdentity; }

  
  void setEuler( double phi, double theta, double psi );

  double getSUx( void ) { return sux; }
  double getSUy( void ) { return suy; }
  double getSUz( void ) { return suz; }
  
  void setSUx( double the_sux ) { sux = the_sux; }
  void setSUy( double the_suy ) { suy = the_suy; }
  void setSUz( double the_suz ) { suz = the_suz; }

  void zeroForces();

  void getA( double the_A[3][3] ); // get the full rotation matrix
  void setA( double the_A[3][3] );

  void getU( double the_u[3] ); // get the unit vetor
  void updateU( void );

  void getQ( double the_q[4] ); // get the quanternions
  void setQ( double the_q[4] );
 
  void getJ( double theJ[3] );
  void setJ( double theJ[3] );

  double getJx( void ) { return jx; } 
  double getJy( void ) { return jy; }
  double getJz( void ) { return jz; }

  void setJx( double the_jx ) { jx = the_jx; }
  void setJy( double the_jy ) { jy = the_jy; }
  void setJz( double the_jz ) { jz = the_jz; }

  void getTrq( double theT[3] );
  void addTrq( double theT[3] );

  //  double getTx( void ) { return trq[offsetX];} 
  //  double getTy( void ) { return trq[offsetY]; }
  //  double getTz( void ) { return trq[offsetZ]; }

  void setI( double the_I[3][3] );
  void getI( double the_I[3][3] );
  
  double getIxx( void ) { return Ixx; } 
  double getIxy( void ) { return Ixy; }
  double getIxz( void ) { return Ixz; }
  
  double getIyx( void ) { return Iyx; } 
  double getIyy( void ) { return Iyy; }
  double getIyz( void ) { return Iyz; }
  
  double getIzx( void ) { return Izx; } 
  double getIzy( void ) { return Izy; }
  double getIzz( void ) { return Izz; }

  double getMu( void );
  void setMu( double the_mu );

  void lab2Body( double r[3] );
  void body2Lab( double r[3] );


private:
  int dIndex;

  double sux, suy, suz; // the standard unit vector    ( body fixed )
  double jx, jy, jz;    // the angular momentum vector ( body fixed )
  
  double Ixx, Ixy, Ixz; // the inertial tensor matrix  ( body fixed )
  double Iyx, Iyy, Iyz;
  double Izx, Izy, Izz;

  int ssdIdentity; // boolean of whether atom is ssd

};

#endif
Revision:	670
Committed:	Thu Aug 7 21:47:18 2003 UTC (20 years, 11 months ago) by mmeineke
File size:	6112 byte(s)
Log Message:	switched SimInfo to use a system configuration from SimState rather than arrays from Atom
#	User	Rev	Content
1	mmeineke	377	#ifndef _ATOM_H_
2			#define _ATOM_H_
3
4			#include <cstring>
5			#include <cstdlib>
6			#include <iostream>
7
8	mmeineke	670	#include "SimState.hpp"
9
10	mmeineke	377	class Atom{
11			public:
12
13	mmeineke	670	Atom(int theIndex, SimState* theConfig );
14	gezelter	409	virtual ~Atom() {}
15	mmeineke	377
16	mmeineke	670	void setCoords(void);
17	mmeineke	377
18	mmeineke	670	// void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
19			// double* Atrq, double* AAmat, double* Amu,
20			// double* Aul);
21			// void deleteAtom(int theIndex);
22			// void deleteRange(int startIndex, int stopIndex);
23	mmeineke	377
24	mmeineke	599	void getPos( double theP[3] );
25			void setPos( double theP[3] );
26
27			void getVel( double theV[3] );
28			void setVel( double theV[3] );
29
30			void getFrc( double theF[3] );
31			void addFrc( double theF[3] );
32
33	mmeineke	377	virtual void zeroForces() = 0;
34
35			double getMass() const {return c_mass;}
36			void setMass(double mass) {c_mass = mass;}
37	chuckv	669
38			double getEamRcut() const {return myEamRcut;}
39			void setEamRcut(double eamRcut) {myEamRcut = eamRcut;}
40	mmeineke	377
41			double getSigma() const {return c_sigma;}
42			void setSigma(double sigma) {c_sigma = sigma;}
43
44			double getEpslon() const {return c_epslon;}
45			void setEpslon(double epslon) {c_epslon = epslon;}
46
47			double getCovalent() const {return c_covalent;}
48			void setCovalent(double covalent) {c_covalent = covalent;}
49
50			int getIndex() const {return index;}
51	gezelter	409	void setIndex(int theIndex);
52	mmeineke	377	char *getType() {return c_name;}
53			void setType(char * name) {strcpy(c_name,name);}
54
55			int getIdent( void ) { return ident; }
56			void setIdent( int info ) { ident = info; }
57
58			#ifdef IS_MPI
59			int getGlobalIndex( void ) { return myGlobalIndex; }
60			void setGlobalIndex( int info ) { myGlobalIndex = info; }
61			#endif // is_mpi
62
63			void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
64			int get_n_hydrogens() const {return c_n_hyd;}
65
66			void setHasDipole( int value ) { has_dipole = value; }
67			int hasDipole( void ) { return has_dipole; }
68
69			void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
70			int isLJ( void ) { return is_LJ; }
71
72			void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
73			int isVDW( void ) { return is_VDW; }
74
75	chuckv	631	void setEAM( void ) { is_EAM = 1; }
76			int isEAM( void ) { return is_EAM; }
77
78	mmeineke	377	virtual int isDirectional( void ) = 0;
79
80
81			protected:
82
83	mmeineke	670	SimState* myConfig;
84
85			double* pos; // the position array
86			double* vel; // the velocity array
87			double* frc; // the forc array
88			double* trq; // the torque vector ( space fixed )
89			double* Amat; // the rotation matrix
90			double* mu; // the array of dipole moments
91			double* ul; // the lab frame unit directional vector
92
93	mmeineke	377	double c_mass; /* the mass of the atom in amu */
94			double c_sigma; /* the sigma parameter for van der walls interactions */
95			double c_epslon; /* the esplon parameter for VDW interactions */
96			double c_covalent; // The covalent radius of the atom.
97
98	chuckv	669	double myEamRcut; // Atom rcut for eam defined by the forcefield.
99
100	mmeineke	377	int index; /* set the atom's index */
101			int offset; // the atom's offset in the storage array
102			int offsetX, offsetY, offsetZ;
103
104			int Axx, Axy, Axz; // the rotational matrix indices
105			int Ayx, Ayy, Ayz;
106			int Azx, Azy, Azz;
107
108			char c_name[100]; /* it's name */
109			int ident; // it's unique numeric identity.
110
111			int c_n_hyd; // the number of hydrogens bonded to the atom
112
113			int has_dipole; // dipole boolean
114			int is_VDW; // VDW boolean
115			int is_LJ; // LJ boolean
116	chuckv	631	int is_EAM; //EAM boolean
117	mmeineke	377
118	mmeineke	670	bool hasCoords;
119
120	mmeineke	377	#ifdef IS_MPI
121			int myGlobalIndex;
122			#endif
123
124			};
125
126			class GeneralAtom : public Atom{
127
128			public:
129	mmeineke	670	GeneralAtom(int theIndex, SimState* theConfig): Atom(theIndex, theConfig){}
130	mmeineke	377	virtual ~GeneralAtom(){}
131
132			int isDirectional( void ){ return 0; }
133	mmeineke	670	void zeroForces( void );
134	mmeineke	377	};
135
136			class DirectionalAtom : public Atom {
137
138			public:
139	mmeineke	670	DirectionalAtom(int theIndex, SimState* theConfig) : Atom(theIndex,
140			theConfig)
141	mmeineke	377	{
142			ssdIdentity = 0;
143			sux = 0.0;
144			suy = 0.0;
145			suz = 0.0;
146			}
147			virtual ~DirectionalAtom() {}
148
149	mmeineke	597	void printAmatIndex( void );
150
151	mmeineke	377	int isDirectional(void) { return 1; }
152
153			void setSSD( int value) { ssdIdentity = value; }
154			int isSSD(void) {return ssdIdentity; }
155
156
157			void setEuler( double phi, double theta, double psi );
158	mmeineke	599
159			double getSUx( void ) { return sux; }
160			double getSUy( void ) { return suy; }
161			double getSUz( void ) { return suz; }
162	mmeineke	377
163			void setSUx( double the_sux ) { sux = the_sux; }
164			void setSUy( double the_suy ) { suy = the_suy; }
165			void setSUz( double the_suz ) { suz = the_suz; }
166
167	mmeineke	670	void zeroForces();
168	mmeineke	377
169			void getA( double the_A[3][3] ); // get the full rotation matrix
170	mmeineke	599	void setA( double the_A[3][3] );
171	mmeineke	377
172	mmeineke	599	void getU( double the_u[3] ); // get the unit vetor
173			void updateU( void );
174	mmeineke	377
175			void getQ( double the_q[4] ); // get the quanternions
176	mmeineke	599	void setQ( double the_q[4] );
177	mmeineke	377
178	mmeineke	599	void getJ( double theJ[3] );
179			void setJ( double theJ[3] );
180
181	mmeineke	377	double getJx( void ) { return jx; }
182			double getJy( void ) { return jy; }
183			double getJz( void ) { return jz; }
184
185	mmeineke	599	void setJx( double the_jx ) { jx = the_jx; }
186			void setJy( double the_jy ) { jy = the_jy; }
187			void setJz( double the_jz ) { jz = the_jz; }
188
189			void getTrq( double theT[3] );
190			void addTrq( double theT[3] );
191
192	gezelter	611	// double getTx( void ) { return trq[offsetX];}
193			// double getTy( void ) { return trq[offsetY]; }
194			// double getTz( void ) { return trq[offsetZ]; }
195	mmeineke	377
196	mmeineke	599	void setI( double the_I[3][3] );
197			void getI( double the_I[3][3] );
198
199	mmeineke	377	double getIxx( void ) { return Ixx; }
200			double getIxy( void ) { return Ixy; }
201			double getIxz( void ) { return Ixz; }
202
203			double getIyx( void ) { return Iyx; }
204			double getIyy( void ) { return Iyy; }
205			double getIyz( void ) { return Iyz; }
206
207			double getIzx( void ) { return Izx; }
208			double getIzy( void ) { return Izy; }
209			double getIzz( void ) { return Izz; }
210
211	mmeineke	670	double getMu( void );
212			void setMu( double the_mu );
213	mmeineke	377
214			void lab2Body( double r[3] );
215			void body2Lab( double r[3] );
216
217	mmeineke	599
218	mmeineke	377	private:
219			int dIndex;
220
221			double sux, suy, suz; // the standard unit vector ( body fixed )
222			double jx, jy, jz; // the angular momentum vector ( body fixed )
223
224			double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
225			double Iyx, Iyy, Iyz;
226			double Izx, Izy, Izz;
227
228			int ssdIdentity; // boolean of whether atom is ssd
229
230			};
231
232			#endif