OOPSE/libmdtools/Atom.hpp

#ifndef _ATOM_H_
#define _ATOM_H_

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

class Atom{
public:

  Atom(int theIndex);
  virtual ~Atom() {} 

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

  static void createArrays (int the_nElements);
  static void destroyArrays(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);

  static double* getPosArray( void ) { return pos; }
  static double* getVelArray( void ) { return vel; }
  static double* getFrcArray( void ) { return frc; }
  static double* getTrqArray( void ) { return trq; }
  static double* getAmatArray( void ) { return Amat; }
  static double* getMuArray( void ) { return mu; }
  static double* getUlArray( void ) { return ul; }
  
  void getPos( double theP[3] );
  void setPos( double theP[3] );

  double getX() const {return pos[offsetX];}
  double getY() const {return pos[offsetY];}
  double getZ() const {return pos[offsetZ];}
  void setX(double x) {pos[offsetX] = x;}
  void setY(double y) {pos[offsetY] = y;}
  void setZ(double z) {pos[offsetZ] = z;}
  
  void getVel( double theV[3] );
  void setVel( double theV[3] );

  double get_vx() const  {return vel[offsetX];}
  double get_vy() const  {return vel[offsetY];}
  double get_vz() const  {return vel[offsetZ];}
  void set_vx(double vx) {vel[offsetX] = vx;}
  void set_vy(double vy) {vel[offsetY] = vy;}
  void set_vz(double vz) {vel[offsetZ] = vz;}
  

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

  double getFx() const   {return frc[offsetX];}
  double getFy() const   {return frc[offsetY];}
  double getFz() const   {return frc[offsetZ];}
  void addFx(double add) {frc[offsetX] += add;}
  void addFy(double add) {frc[offsetY] += add;}
  void addFz(double add) {frc[offsetZ] += add;}
  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:
  
  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

#ifdef IS_MPI
  int myGlobalIndex;
#endif
  
};

class GeneralAtom : public Atom{

public:
  GeneralAtom(int theIndex): Atom(theIndex){}
  virtual ~GeneralAtom(){}

  int isDirectional( void ){ return 0; }
  void zeroForces() {
    frc[offsetX] = 0.0; 
    frc[offsetY] = 0.0; 
    frc[offsetZ] = 0.0;
  }
};

class DirectionalAtom : public Atom {
  
public:
  DirectionalAtom(int theIndex) : Atom(theIndex)
  { 
    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() {
    frc[offsetX] = 0.0; 
    frc[offsetY] = 0.0; 
    frc[offsetZ] = 0.0;

    trq[offsetX] = 0.0; 
    trq[offsetY] = 0.0; 
    trq[offsetZ] = 0.0;
  }

  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 addTx( double the_tx ) { trq[offsetX] += the_tx;}
  void addTy( double the_ty ) { trq[offsetY] += the_ty;}
  void addTz( double the_tz ) { trq[offsetZ] += the_tz;}

  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 ) { return mu[index]; }
  void setMu( double the_mu ) { mu[index] = 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:	669
Committed:	Thu Aug 7 00:47:33 2003 UTC (20 years, 11 months ago) by chuckv
File size:	7711 byte(s)
Log Message:	Bug fixes for eam...
#	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			class Atom{
9			public:
10
11	gezelter	409	Atom(int theIndex);
12			virtual ~Atom() {}
13	mmeineke	377
14	gezelter	409	static double* pos; // the position array
15			static double* vel; // the velocity array
16			static double* frc; // the forc array
17			static double* trq; // the torque vector ( space fixed )
18			static double* Amat; // the rotation matrix
19			static double* mu; // the dipole moment array
20			static double* ul; // the lab frame unit directional vector
21			static int nElements;
22	mmeineke	377
23	mmeineke	413	static void createArrays (int the_nElements);
24	gezelter	409	static void destroyArrays(void);
25			void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
26			double* Atrq, double* AAmat, double* Amu,
27			double* Aul);
28			void deleteAtom(int theIndex);
29			void deleteRange(int startIndex, int stopIndex);
30	mmeineke	377
31			static double* getPosArray( void ) { return pos; }
32			static double* getVelArray( void ) { return vel; }
33			static double* getFrcArray( void ) { return frc; }
34			static double* getTrqArray( void ) { return trq; }
35			static double* getAmatArray( void ) { return Amat; }
36			static double* getMuArray( void ) { return mu; }
37			static double* getUlArray( void ) { return ul; }
38
39	mmeineke	599	void getPos( double theP[3] );
40			void setPos( double theP[3] );
41
42	mmeineke	377	double getX() const {return pos[offsetX];}
43			double getY() const {return pos[offsetY];}
44			double getZ() const {return pos[offsetZ];}
45			void setX(double x) {pos[offsetX] = x;}
46			void setY(double y) {pos[offsetY] = y;}
47			void setZ(double z) {pos[offsetZ] = z;}
48
49	mmeineke	599	void getVel( double theV[3] );
50			void setVel( double theV[3] );
51
52	mmeineke	377	double get_vx() const {return vel[offsetX];}
53			double get_vy() const {return vel[offsetY];}
54			double get_vz() const {return vel[offsetZ];}
55			void set_vx(double vx) {vel[offsetX] = vx;}
56			void set_vy(double vy) {vel[offsetY] = vy;}
57			void set_vz(double vz) {vel[offsetZ] = vz;}
58
59	mmeineke	599
60			void getFrc( double theF[3] );
61			void addFrc( double theF[3] );
62
63	mmeineke	377	double getFx() const {return frc[offsetX];}
64			double getFy() const {return frc[offsetY];}
65			double getFz() const {return frc[offsetZ];}
66			void addFx(double add) {frc[offsetX] += add;}
67			void addFy(double add) {frc[offsetY] += add;}
68			void addFz(double add) {frc[offsetZ] += add;}
69			virtual void zeroForces() = 0;
70
71			double getMass() const {return c_mass;}
72			void setMass(double mass) {c_mass = mass;}
73	chuckv	669
74			double getEamRcut() const {return myEamRcut;}
75			void setEamRcut(double eamRcut) {myEamRcut = eamRcut;}
76	mmeineke	377
77			double getSigma() const {return c_sigma;}
78			void setSigma(double sigma) {c_sigma = sigma;}
79
80			double getEpslon() const {return c_epslon;}
81			void setEpslon(double epslon) {c_epslon = epslon;}
82
83			double getCovalent() const {return c_covalent;}
84			void setCovalent(double covalent) {c_covalent = covalent;}
85
86			int getIndex() const {return index;}
87	gezelter	409	void setIndex(int theIndex);
88	mmeineke	377	char *getType() {return c_name;}
89			void setType(char * name) {strcpy(c_name,name);}
90
91			int getIdent( void ) { return ident; }
92			void setIdent( int info ) { ident = info; }
93
94			#ifdef IS_MPI
95			int getGlobalIndex( void ) { return myGlobalIndex; }
96			void setGlobalIndex( int info ) { myGlobalIndex = info; }
97			#endif // is_mpi
98
99			void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
100			int get_n_hydrogens() const {return c_n_hyd;}
101
102			void setHasDipole( int value ) { has_dipole = value; }
103			int hasDipole( void ) { return has_dipole; }
104
105			void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
106			int isLJ( void ) { return is_LJ; }
107
108			void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
109			int isVDW( void ) { return is_VDW; }
110
111	chuckv	631	void setEAM( void ) { is_EAM = 1; }
112			int isEAM( void ) { return is_EAM; }
113
114	mmeineke	377	virtual int isDirectional( void ) = 0;
115
116
117			protected:
118
119			double c_mass; /* the mass of the atom in amu */
120			double c_sigma; /* the sigma parameter for van der walls interactions */
121			double c_epslon; /* the esplon parameter for VDW interactions */
122			double c_covalent; // The covalent radius of the atom.
123
124	chuckv	669	double myEamRcut; // Atom rcut for eam defined by the forcefield.
125
126	mmeineke	377	int index; /* set the atom's index */
127			int offset; // the atom's offset in the storage array
128			int offsetX, offsetY, offsetZ;
129
130			int Axx, Axy, Axz; // the rotational matrix indices
131			int Ayx, Ayy, Ayz;
132			int Azx, Azy, Azz;
133
134			char c_name[100]; /* it's name */
135			int ident; // it's unique numeric identity.
136
137			int c_n_hyd; // the number of hydrogens bonded to the atom
138
139			int has_dipole; // dipole boolean
140			int is_VDW; // VDW boolean
141			int is_LJ; // LJ boolean
142	chuckv	631	int is_EAM; //EAM boolean
143	mmeineke	377
144			#ifdef IS_MPI
145			int myGlobalIndex;
146			#endif
147
148			};
149
150			class GeneralAtom : public Atom{
151
152			public:
153			GeneralAtom(int theIndex): Atom(theIndex){}
154			virtual ~GeneralAtom(){}
155
156			int isDirectional( void ){ return 0; }
157			void zeroForces() {
158			frc[offsetX] = 0.0;
159			frc[offsetY] = 0.0;
160			frc[offsetZ] = 0.0;
161			}
162			};
163
164			class DirectionalAtom : public Atom {
165
166			public:
167			DirectionalAtom(int theIndex) : Atom(theIndex)
168			{
169			ssdIdentity = 0;
170			sux = 0.0;
171			suy = 0.0;
172			suz = 0.0;
173			}
174			virtual ~DirectionalAtom() {}
175
176	mmeineke	597	void printAmatIndex( void );
177
178	mmeineke	377	int isDirectional(void) { return 1; }
179
180			void setSSD( int value) { ssdIdentity = value; }
181			int isSSD(void) {return ssdIdentity; }
182
183
184			void setEuler( double phi, double theta, double psi );
185	mmeineke	599
186			double getSUx( void ) { return sux; }
187			double getSUy( void ) { return suy; }
188			double getSUz( void ) { return suz; }
189	mmeineke	377
190			void setSUx( double the_sux ) { sux = the_sux; }
191			void setSUy( double the_suy ) { suy = the_suy; }
192			void setSUz( double the_suz ) { suz = the_suz; }
193
194			void zeroForces() {
195			frc[offsetX] = 0.0;
196			frc[offsetY] = 0.0;
197			frc[offsetZ] = 0.0;
198
199			trq[offsetX] = 0.0;
200			trq[offsetY] = 0.0;
201			trq[offsetZ] = 0.0;
202			}
203
204			void getA( double the_A[3][3] ); // get the full rotation matrix
205	mmeineke	599	void setA( double the_A[3][3] );
206	mmeineke	377
207	mmeineke	599	void getU( double the_u[3] ); // get the unit vetor
208			void updateU( void );
209	mmeineke	377
210			void getQ( double the_q[4] ); // get the quanternions
211	mmeineke	599	void setQ( double the_q[4] );
212	mmeineke	377
213	mmeineke	599	void getJ( double theJ[3] );
214			void setJ( double theJ[3] );
215
216	mmeineke	377	double getJx( void ) { return jx; }
217			double getJy( void ) { return jy; }
218			double getJz( void ) { return jz; }
219
220	mmeineke	599	void setJx( double the_jx ) { jx = the_jx; }
221			void setJy( double the_jy ) { jy = the_jy; }
222			void setJz( double the_jz ) { jz = the_jz; }
223
224			void getTrq( double theT[3] );
225			void addTrq( double theT[3] );
226
227	gezelter	611	// double getTx( void ) { return trq[offsetX];}
228			// double getTy( void ) { return trq[offsetY]; }
229			// double getTz( void ) { return trq[offsetZ]; }
230	mmeineke	377
231	mmeineke	599	void addTx( double the_tx ) { trq[offsetX] += the_tx;}
232			void addTy( double the_ty ) { trq[offsetY] += the_ty;}
233			void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
234
235			void setI( double the_I[3][3] );
236			void getI( double the_I[3][3] );
237
238	mmeineke	377	double getIxx( void ) { return Ixx; }
239			double getIxy( void ) { return Ixy; }
240			double getIxz( void ) { return Ixz; }
241
242			double getIyx( void ) { return Iyx; }
243			double getIyy( void ) { return Iyy; }
244			double getIyz( void ) { return Iyz; }
245
246			double getIzx( void ) { return Izx; }
247			double getIzy( void ) { return Izy; }
248			double getIzz( void ) { return Izz; }
249	mmeineke	599
250	mmeineke	377
251			double getMu( void ) { return mu[index]; }
252			void setMu( double the_mu ) { mu[index] = the_mu; }
253
254			void lab2Body( double r[3] );
255			void body2Lab( double r[3] );
256
257	mmeineke	599
258	mmeineke	377	private:
259			int dIndex;
260
261			double sux, suy, suz; // the standard unit vector ( body fixed )
262			double jx, jy, jz; // the angular momentum vector ( body fixed )
263
264			double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
265			double Iyx, Iyy, Iyz;
266			double Izx, Izy, Izz;
267
268			int ssdIdentity; // boolean of whether atom is ssd
269
270			};
271
272			#endif