mdtools/libmdCode/Atom.hpp

#ifndef _ATOM_H_
#define _ATOM_H_

#include <cstring>
#include <iostream>

class Atom{
public:
  Atom(int theIndex) {
    c_n_hyd = 0; 
    has_dipole = 0;
    is_VDW = 0;
    is_LJ = 0;
    index = theIndex;
    offset = 3 * index;
    offsetX = offset;
    offsetY = offset+1;
    offsetZ = offset+2;

    Axx = index*9;
    Axy = Axx+1;
    Axz = Axx+2;
    
    Ayx = Axx+3;
    Ayy = Axx+4;
    Ayz = Axx+5;

    Azx = Axx+6;
    Azy = Axx+7;
    Azz = Axx+8;
  }
  virtual ~Atom() {}

  static void createArrays (int nElements) {
    pos = new double[nElements*3];
    vel = new double[nElements*3];
    frc = new double[nElements*3];
    trq = new double[nElements*3];
    Amat = new double[nElements*9];
    mu = new double[nElements];
    ul = new double[nElements];

    // init directional values to zero
    
    trq[offsetX] = 0.0;
    trq[offsetY] = 0.0;
    trq[offsetZ] = 0.0;
    
    Amat[Axx] = 0.0;
    Amat[Axy] = 0.0;
    Amat[Axz] = 0.0;
    
    Amat[Ayx] = 0.0;
    Amat[Ayy] = 0.0;
    Amat[Ayz] = 0.0;

    Amat[Azx] = 0.0;
    Amat[Azy] = 0.0;
    Amat[Azz] = 0.0;

    mu[index] = 0.0;    

    ul[offsetX] = 0.0;
    ul[offsetY] = 0.0;
    ul[offsetZ] = 0.0;
  }
  static void destroyArrays(void) {
    delete[] pos;
    delete[] vel;
    delete[] frc;
    delete[] trq;
    delete[] Amat;
    delete[] mu;
  }

  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; }
  
  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;}
  
  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;}
  
  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) {
    index = theIndex; 
    offset = index*3;
    offsetX = offset;
    offsetY = offset+1;
    offsetZ = offset+2;

    Axx = index*9;
    Axy = Axx+1;
    Axz = Axx+2;
    
    Ayx = Axx+3;
    Ayy = Axx+4;
    Ayz = Axx+5;

    Azx = Axx+6;
    Azy = Axx+7;
    Azz = Axx+8;
  }

  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; }

  virtual int isDirectional( void ) = 0;

  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

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

#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; 

  }
  virtual ~DirectionalAtom() {}

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

  void setA( double the_A[3][3] );

  void setI( double the_I[3][3] );

  void setQ( double the_q[4] );
  
  void setEuler( double phi, double theta, double psi );
  
  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 setJx( double the_jx ) { jx = the_jx; }
  void setJy( double the_jy ) { jy = the_jy; }
  void setJz( double the_jz ) { jz = the_jz; }
    
  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 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;
  }

  double getAxx( void ) { return Amat[Axx]; } 
  double getAxy( void ) { return Amat[Axy]; }
  double getAxz( void ) { return Amat[Axz]; }
  
  double getAyx( void ) { return Amat[Ayx]; } 
  double getAyy( void ) { return Amat[Ayy]; }
  double getAyz( void ) { return Amat[Ayz]; }
  
  double getAzx( void ) { return Amat[Azx]; } 
  double getAzy( void ) { return Amat[Azy]; }
  double getAzz( void ) { return Amat[Azz]; }

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

  double getSUx( void ) { return sux; }
  double getSUy( void ) { return suy; }
  double getSUz( void ) { return suz; }

  void getU( double the_u[3] ); // get the unit vetor
  void getQ( double the_q[4] ); // get the quanternions
 
  double getJx( void ) { return jx; } 
  double getJy( void ) { return jy; }
  double getJz( void ) { return jz; }

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

  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:	296
Committed:	Thu Mar 6 20:05:39 2003 UTC (21 years, 6 months ago) by mmeineke
File size:	8496 byte(s)
Log Message:	dded more static arrays to the Atom class;
#	Content
1	#ifndef _ATOM_H_
2	#define _ATOM_H_
3
4	#include <cstring>
5	#include <iostream>
6
7	class Atom{
8	public:
9	Atom(int theIndex) {
10	c_n_hyd = 0;
11	has_dipole = 0;
12	is_VDW = 0;
13	is_LJ = 0;
14	index = theIndex;
15	offset = 3 * index;
16	offsetX = offset;
17	offsetY = offset+1;
18	offsetZ = offset+2;
19
20	Axx = index*9;
21	Axy = Axx+1;
22	Axz = Axx+2;
23
24	Ayx = Axx+3;
25	Ayy = Axx+4;
26	Ayz = Axx+5;
27
28	Azx = Axx+6;
29	Azy = Axx+7;
30	Azz = Axx+8;
31	}
32	virtual ~Atom() {}
33
34	static void createArrays (int nElements) {
35	pos = new double[nElements*3];
36	vel = new double[nElements*3];
37	frc = new double[nElements*3];
38	trq = new double[nElements*3];
39	Amat = new double[nElements*9];
40	mu = new double[nElements];
41	ul = new double[nElements];
42
43	// init directional values to zero
44
45	trq[offsetX] = 0.0;
46	trq[offsetY] = 0.0;
47	trq[offsetZ] = 0.0;
48
49	Amat[Axx] = 0.0;
50	Amat[Axy] = 0.0;
51	Amat[Axz] = 0.0;
52
53	Amat[Ayx] = 0.0;
54	Amat[Ayy] = 0.0;
55	Amat[Ayz] = 0.0;
56
57	Amat[Azx] = 0.0;
58	Amat[Azy] = 0.0;
59	Amat[Azz] = 0.0;
60
61	mu[index] = 0.0;
62
63	ul[offsetX] = 0.0;
64	ul[offsetY] = 0.0;
65	ul[offsetZ] = 0.0;
66	}
67	static void destroyArrays(void) {
68	delete[] pos;
69	delete[] vel;
70	delete[] frc;
71	delete[] trq;
72	delete[] Amat;
73	delete[] mu;
74	}
75
76	static double* getPosArray( void ) { return pos; }
77	static double* getVelArray( void ) { return vel; }
78	static double* getFrcArray( void ) { return frc; }
79	static double* getTrqArray( void ) { return trq; }
80	static double* getAmatArray( void ) { return Amat; }
81	static double* getMuArray( void ) { return mu; }
82	static double* getUlArray( void ) { return ul; }
83
84	double getX() const {return pos[offsetX];}
85	double getY() const {return pos[offsetY];}
86	double getZ() const {return pos[offsetZ];}
87	void setX(double x) {pos[offsetX] = x;}
88	void setY(double y) {pos[offsetY] = y;}
89	void setZ(double z) {pos[offsetZ] = z;}
90
91	double get_vx() const {return vel[offsetX];}
92	double get_vy() const {return vel[offsetY];}
93	double get_vz() const {return vel[offsetZ];}
94	void set_vx(double vx) {vel[offsetX] = vx;}
95	void set_vy(double vy) {vel[offsetY] = vy;}
96	void set_vz(double vz) {vel[offsetZ] = vz;}
97
98	double getFx() const {return frc[offsetX];}
99	double getFy() const {return frc[offsetY];}
100	double getFz() const {return frc[offsetZ];}
101	void addFx(double add) {frc[offsetX] += add;}
102	void addFy(double add) {frc[offsetY] += add;}
103	void addFz(double add) {frc[offsetZ] += add;}
104	virtual void zeroForces() = 0;
105
106	double getMass() const {return c_mass;}
107	void setMass(double mass) {c_mass = mass;}
108
109	double getSigma() const {return c_sigma;}
110	void setSigma(double sigma) {c_sigma = sigma;}
111
112	double getEpslon() const {return c_epslon;}
113	void setEpslon(double epslon) {c_epslon = epslon;}
114
115	double getCovalent() const {return c_covalent;}
116	void setCovalent(double covalent) {c_covalent = covalent;}
117
118	int getIndex() const {return index;}
119	void setIndex(int theIndex) {
120	index = theIndex;
121	offset = index*3;
122	offsetX = offset;
123	offsetY = offset+1;
124	offsetZ = offset+2;
125
126	Axx = index*9;
127	Axy = Axx+1;
128	Axz = Axx+2;
129
130	Ayx = Axx+3;
131	Ayy = Axx+4;
132	Ayz = Axx+5;
133
134	Azx = Axx+6;
135	Azy = Axx+7;
136	Azz = Axx+8;
137	}
138
139	char *getType() {return c_name;}
140	void setType(char * name) {strcpy(c_name,name);}
141
142	int getIdent( void ) { return ident; }
143	void setIdent( int info ) { ident = info; }
144
145	#ifdef IS_MPI
146	int getGlobalIndex( void ) { return myGlobalIndex; }
147	void setGlobalIndex( int info ) { myGlobalIndex = info; }
148	#endif // is_mpi
149
150	void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
151	int get_n_hydrogens() const {return c_n_hyd;}
152
153	void setHasDipole( int value ) { has_dipole = value; }
154	int hasDipole( void ) { return has_dipole; }
155
156	void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
157	int isLJ( void ) { return is_LJ; }
158
159	void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
160	int isVDW( void ) { return is_VDW; }
161
162	virtual int isDirectional( void ) = 0;
163
164	static double* pos; // the position array
165	static double* vel; // the velocity array
166	static double* frc; // the forc array
167	static double* trq; // the torque vector ( space fixed )
168	static double* Amat; // the rotation matrix
169	static double* mu; // the dipole moment array
170	static double* ul; // the lab frame unit directional vector
171
172	protected:
173
174	double c_mass; /* the mass of the atom in amu */
175	double c_sigma; /* the sigma parameter for van der walls interactions */
176	double c_epslon; /* the esplon parameter for VDW interactions */
177	double c_covalent; // The covalent radius of the atom.
178
179	int index; /* set the atom's index */
180	int offset; // the atom's offset in the storage array
181	int offsetX, offsetY, offsetZ;
182
183	int Axx, Axy, Axz; // the rotational matrix indices
184	int Ayx, Ayy, Ayz;
185	int Azx, Azy, Azz;
186
187	char c_name[100]; /* it's name */
188	int ident; // it's unique numeric identity.
189
190	int c_n_hyd; // the number of hydrogens bonded to the atom
191
192	int has_dipole; // dipole boolean
193	int is_VDW; // VDW boolean
194	int is_LJ; // LJ boolean
195
196	#ifdef IS_MPI
197	int myGlobalIndex;
198	#endif
199
200	};
201
202
203
204	class GeneralAtom : public Atom{
205
206	public:
207	GeneralAtom(int theIndex): Atom(theIndex){}
208	virtual ~GeneralAtom(){}
209
210	int isDirectional( void ){ return 0; }
211	void zeroForces() {
212	frc[offsetX] = 0.0;
213	frc[offsetY] = 0.0;
214	frc[offsetZ] = 0.0;
215	}
216	};
217
218	class DirectionalAtom : public Atom {
219
220	public:
221	DirectionalAtom(int theIndex) : Atom(theIndex)
222	{
223	ssdIdentity = 0;
224
225	}
226	virtual ~DirectionalAtom() {}
227
228	int isDirectional(void) { return 1; }
229
230	void setSSD( int value) { ssdIdentity = value; }
231	int isSSD(void) {return ssdIdentity; }
232
233	void setA( double the_A[3][3] );
234
235	void setI( double the_I[3][3] );
236
237	void setQ( double the_q[4] );
238
239	void setEuler( double phi, double theta, double psi );
240
241	void setSUx( double the_sux ) { sux = the_sux; }
242	void setSUy( double the_suy ) { suy = the_suy; }
243	void setSUz( double the_suz ) { suz = the_suz; }
244
245	void setJx( double the_jx ) { jx = the_jx; }
246	void setJy( double the_jy ) { jy = the_jy; }
247	void setJz( double the_jz ) { jz = the_jz; }
248
249	void addTx( double the_tx ) { trq[offsetX] += the_tx;}
250	void addTy( double the_ty ) { trq[offsetY] += the_ty;}
251	void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
252
253	void zeroForces() {
254	frc[offsetX] = 0.0;
255	frc[offsetY] = 0.0;
256	frc[offsetZ] = 0.0;
257
258	trq[offsetX] = 0.0;
259	trq[offsetY] = 0.0;
260	trq[offsetZ] = 0.0;
261	}
262
263	double getAxx( void ) { return Amat[Axx]; }
264	double getAxy( void ) { return Amat[Axy]; }
265	double getAxz( void ) { return Amat[Axz]; }
266
267	double getAyx( void ) { return Amat[Ayx]; }
268	double getAyy( void ) { return Amat[Ayy]; }
269	double getAyz( void ) { return Amat[Ayz]; }
270
271	double getAzx( void ) { return Amat[Azx]; }
272	double getAzy( void ) { return Amat[Azy]; }
273	double getAzz( void ) { return Amat[Azz]; }
274
275	void getA( double the_A[3][3] ); // get the full rotation matrix
276
277	double getSUx( void ) { return sux; }
278	double getSUy( void ) { return suy; }
279	double getSUz( void ) { return suz; }
280
281	void getU( double the_u[3] ); // get the unit vetor
282	void getQ( double the_q[4] ); // get the quanternions
283
284	double getJx( void ) { return jx; }
285	double getJy( void ) { return jy; }
286	double getJz( void ) { return jz; }
287
288	double getTx( void ) { return trq[offsetX];}
289	double getTy( void ) { return trq[offsetY]; }
290	double getTz( void ) { return trq[offsetZ]; }
291
292	double getIxx( void ) { return Ixx; }
293	double getIxy( void ) { return Ixy; }
294	double getIxz( void ) { return Ixz; }
295
296	double getIyx( void ) { return Iyx; }
297	double getIyy( void ) { return Iyy; }
298	double getIyz( void ) { return Iyz; }
299
300	double getIzx( void ) { return Izx; }
301	double getIzy( void ) { return Izy; }
302	double getIzz( void ) { return Izz; }
303
304	double getMu( void ) { return mu[index]; }
305	void setMu( double the_mu ) { mu[index] = the_mu; }
306
307	void lab2Body( double r[3] );
308	void body2Lab( double r[3] );
309
310	private:
311	int dIndex;
312
313	double sux, suy, suz; // the standard unit vector ( body fixed )
314	double jx, jy, jz; // the angular momentum vector ( body fixed )
315
316	double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
317	double Iyx, Iyy, Iyz;
318	double Izx, Izy, Izz;
319
320	int ssdIdentity; // boolean of whether atom is ssd
321
322	};
323
324	#endif