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 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.

  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:	631
Committed:	Thu Jul 17 19:25:51 2003 UTC (22 years, 3 months ago) by chuckv
File size:	7536 byte(s)
Log Message:	Added massive changes for eam....
#	Content
1	#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	Atom(int theIndex);
12	virtual ~Atom() {}
13
14	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
23	static void createArrays (int the_nElements);
24	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
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	void getPos( double theP[3] );
40	void setPos( double theP[3] );
41
42	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	void getVel( double theV[3] );
50	void setVel( double theV[3] );
51
52	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
60	void getFrc( double theF[3] );
61	void addFrc( double theF[3] );
62
63	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
74	double getSigma() const {return c_sigma;}
75	void setSigma(double sigma) {c_sigma = sigma;}
76
77	double getEpslon() const {return c_epslon;}
78	void setEpslon(double epslon) {c_epslon = epslon;}
79
80	double getCovalent() const {return c_covalent;}
81	void setCovalent(double covalent) {c_covalent = covalent;}
82
83	int getIndex() const {return index;}
84	void setIndex(int theIndex);
85	char *getType() {return c_name;}
86	void setType(char * name) {strcpy(c_name,name);}
87
88	int getIdent( void ) { return ident; }
89	void setIdent( int info ) { ident = info; }
90
91	#ifdef IS_MPI
92	int getGlobalIndex( void ) { return myGlobalIndex; }
93	void setGlobalIndex( int info ) { myGlobalIndex = info; }
94	#endif // is_mpi
95
96	void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
97	int get_n_hydrogens() const {return c_n_hyd;}
98
99	void setHasDipole( int value ) { has_dipole = value; }
100	int hasDipole( void ) { return has_dipole; }
101
102	void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
103	int isLJ( void ) { return is_LJ; }
104
105	void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
106	int isVDW( void ) { return is_VDW; }
107
108	void setEAM( void ) { is_EAM = 1; }
109	int isEAM( void ) { return is_EAM; }
110
111	virtual int isDirectional( void ) = 0;
112
113
114	protected:
115
116	double c_mass; /* the mass of the atom in amu */
117	double c_sigma; /* the sigma parameter for van der walls interactions */
118	double c_epslon; /* the esplon parameter for VDW interactions */
119	double c_covalent; // The covalent radius of the atom.
120
121	int index; /* set the atom's index */
122	int offset; // the atom's offset in the storage array
123	int offsetX, offsetY, offsetZ;
124
125	int Axx, Axy, Axz; // the rotational matrix indices
126	int Ayx, Ayy, Ayz;
127	int Azx, Azy, Azz;
128
129	char c_name[100]; /* it's name */
130	int ident; // it's unique numeric identity.
131
132	int c_n_hyd; // the number of hydrogens bonded to the atom
133
134	int has_dipole; // dipole boolean
135	int is_VDW; // VDW boolean
136	int is_LJ; // LJ boolean
137	int is_EAM; //EAM boolean
138
139	#ifdef IS_MPI
140	int myGlobalIndex;
141	#endif
142
143	};
144
145	class GeneralAtom : public Atom{
146
147	public:
148	GeneralAtom(int theIndex): Atom(theIndex){}
149	virtual ~GeneralAtom(){}
150
151	int isDirectional( void ){ return 0; }
152	void zeroForces() {
153	frc[offsetX] = 0.0;
154	frc[offsetY] = 0.0;
155	frc[offsetZ] = 0.0;
156	}
157	};
158
159	class DirectionalAtom : public Atom {
160
161	public:
162	DirectionalAtom(int theIndex) : Atom(theIndex)
163	{
164	ssdIdentity = 0;
165	sux = 0.0;
166	suy = 0.0;
167	suz = 0.0;
168	}
169	virtual ~DirectionalAtom() {}
170
171	void printAmatIndex( void );
172
173	int isDirectional(void) { return 1; }
174
175	void setSSD( int value) { ssdIdentity = value; }
176	int isSSD(void) {return ssdIdentity; }
177
178
179	void setEuler( double phi, double theta, double psi );
180
181	double getSUx( void ) { return sux; }
182	double getSUy( void ) { return suy; }
183	double getSUz( void ) { return suz; }
184
185	void setSUx( double the_sux ) { sux = the_sux; }
186	void setSUy( double the_suy ) { suy = the_suy; }
187	void setSUz( double the_suz ) { suz = the_suz; }
188
189	void zeroForces() {
190	frc[offsetX] = 0.0;
191	frc[offsetY] = 0.0;
192	frc[offsetZ] = 0.0;
193
194	trq[offsetX] = 0.0;
195	trq[offsetY] = 0.0;
196	trq[offsetZ] = 0.0;
197	}
198
199	void getA( double the_A[3][3] ); // get the full rotation matrix
200	void setA( double the_A[3][3] );
201
202	void getU( double the_u[3] ); // get the unit vetor
203	void updateU( void );
204
205	void getQ( double the_q[4] ); // get the quanternions
206	void setQ( double the_q[4] );
207
208	void getJ( double theJ[3] );
209	void setJ( double theJ[3] );
210
211	double getJx( void ) { return jx; }
212	double getJy( void ) { return jy; }
213	double getJz( void ) { return jz; }
214
215	void setJx( double the_jx ) { jx = the_jx; }
216	void setJy( double the_jy ) { jy = the_jy; }
217	void setJz( double the_jz ) { jz = the_jz; }
218
219	void getTrq( double theT[3] );
220	void addTrq( double theT[3] );
221
222	// double getTx( void ) { return trq[offsetX];}
223	// double getTy( void ) { return trq[offsetY]; }
224	// double getTz( void ) { return trq[offsetZ]; }
225
226	void addTx( double the_tx ) { trq[offsetX] += the_tx;}
227	void addTy( double the_ty ) { trq[offsetY] += the_ty;}
228	void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
229
230	void setI( double the_I[3][3] );
231	void getI( double the_I[3][3] );
232
233	double getIxx( void ) { return Ixx; }
234	double getIxy( void ) { return Ixy; }
235	double getIxz( void ) { return Ixz; }
236
237	double getIyx( void ) { return Iyx; }
238	double getIyy( void ) { return Iyy; }
239	double getIyz( void ) { return Iyz; }
240
241	double getIzx( void ) { return Izx; }
242	double getIzy( void ) { return Izy; }
243	double getIzz( void ) { return Izz; }
244
245
246	double getMu( void ) { return mu[index]; }
247	void setMu( double the_mu ) { mu[index] = the_mu; }
248
249	void lab2Body( double r[3] );
250	void body2Lab( double r[3] );
251
252
253	private:
254	int dIndex;
255
256	double sux, suy, suz; // the standard unit vector ( body fixed )
257	double jx, jy, jz; // the angular momentum vector ( body fixed )
258
259	double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
260	double Iyx, Iyy, Iyz;
261	double Izx, Izy, Izz;
262
263	int ssdIdentity; // boolean of whether atom is ssd
264
265	};
266
267	#endif