OOPSE/libmdtools/Atom.hpp

#ifndef _ATOM_H_
#define _ATOM_H_

#include <cstring>
#include <cstdlib>
#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) {
    int i;
    
    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*3];

    // init directional values to zero
    
    for( i=0; i<nElements; i++){
      trq[i] = 0.0;
      trq[i+1] = 0.0;
      trq[i+2] = 0.0;
      
      Amat[i] = 1.0;
      Amat[i+1] = 0.0;
      Amat[i+2] = 0.0;
      
      Amat[i+3] = 0.0;
      Amat[i+4] = 1.0;
      Amat[i+5] = 0.0;
      
      Amat[i+6] = 0.0;
      Amat[i+7] = 0.0;
      Amat[i+8] = 1.0;
      
      mu[i] = 0.0;    
      
      ul[i] = 1.0;
      ul[i+1] = 0.0;
      ul[i+2] = 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; 
    sux = 0.0;
    suy = 0.0;
    suz = 0.0;
  }
  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] );
  void updateU( void );

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:	393
Committed:	Mon Mar 24 18:33:51 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	8651 byte(s)
Log Message:	little bug fixes here and there
#	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	Atom(int theIndex) {
11	c_n_hyd = 0;
12	has_dipole = 0;
13	is_VDW = 0;
14	is_LJ = 0;
15
16	index = theIndex;
17	offset = 3 * index;
18	offsetX = offset;
19	offsetY = offset+1;
20	offsetZ = offset+2;
21
22	Axx = index*9;
23	Axy = Axx+1;
24	Axz = Axx+2;
25
26	Ayx = Axx+3;
27	Ayy = Axx+4;
28	Ayz = Axx+5;
29
30	Azx = Axx+6;
31	Azy = Axx+7;
32	Azz = Axx+8;
33	}
34	virtual ~Atom() {}
35
36	static void createArrays (int nElements) {
37	int i;
38
39	pos = new double[nElements*3];
40	vel = new double[nElements*3];
41	frc = new double[nElements*3];
42	trq = new double[nElements*3];
43	Amat = new double[nElements*9];
44	mu = new double[nElements];
45	ul = new double[nElements*3];
46
47	// init directional values to zero
48
49	for( i=0; i<nElements; i++){
50	trq[i] = 0.0;
51	trq[i+1] = 0.0;
52	trq[i+2] = 0.0;
53
54	Amat[i] = 1.0;
55	Amat[i+1] = 0.0;
56	Amat[i+2] = 0.0;
57
58	Amat[i+3] = 0.0;
59	Amat[i+4] = 1.0;
60	Amat[i+5] = 0.0;
61
62	Amat[i+6] = 0.0;
63	Amat[i+7] = 0.0;
64	Amat[i+8] = 1.0;
65
66	mu[i] = 0.0;
67
68	ul[i] = 1.0;
69	ul[i+1] = 0.0;
70	ul[i+2] = 0.0;
71	}
72	}
73	static void destroyArrays(void) {
74	delete[] pos;
75	delete[] vel;
76	delete[] frc;
77	delete[] trq;
78	delete[] Amat;
79	delete[] mu;
80	}
81
82	static double* getPosArray( void ) { return pos; }
83	static double* getVelArray( void ) { return vel; }
84	static double* getFrcArray( void ) { return frc; }
85	static double* getTrqArray( void ) { return trq; }
86	static double* getAmatArray( void ) { return Amat; }
87	static double* getMuArray( void ) { return mu; }
88	static double* getUlArray( void ) { return ul; }
89
90	double getX() const {return pos[offsetX];}
91	double getY() const {return pos[offsetY];}
92	double getZ() const {return pos[offsetZ];}
93	void setX(double x) {pos[offsetX] = x;}
94	void setY(double y) {pos[offsetY] = y;}
95	void setZ(double z) {pos[offsetZ] = z;}
96
97	double get_vx() const {return vel[offsetX];}
98	double get_vy() const {return vel[offsetY];}
99	double get_vz() const {return vel[offsetZ];}
100	void set_vx(double vx) {vel[offsetX] = vx;}
101	void set_vy(double vy) {vel[offsetY] = vy;}
102	void set_vz(double vz) {vel[offsetZ] = vz;}
103
104	double getFx() const {return frc[offsetX];}
105	double getFy() const {return frc[offsetY];}
106	double getFz() const {return frc[offsetZ];}
107	void addFx(double add) {frc[offsetX] += add;}
108	void addFy(double add) {frc[offsetY] += add;}
109	void addFz(double add) {frc[offsetZ] += add;}
110	virtual void zeroForces() = 0;
111
112	double getMass() const {return c_mass;}
113	void setMass(double mass) {c_mass = mass;}
114
115	double getSigma() const {return c_sigma;}
116	void setSigma(double sigma) {c_sigma = sigma;}
117
118	double getEpslon() const {return c_epslon;}
119	void setEpslon(double epslon) {c_epslon = epslon;}
120
121	double getCovalent() const {return c_covalent;}
122	void setCovalent(double covalent) {c_covalent = covalent;}
123
124	int getIndex() const {return index;}
125	void setIndex(int theIndex) {
126	index = theIndex;
127	offset = index*3;
128	offsetX = offset;
129	offsetY = offset+1;
130	offsetZ = offset+2;
131
132	Axx = index*9;
133	Axy = Axx+1;
134	Axz = Axx+2;
135
136	Ayx = Axx+3;
137	Ayy = Axx+4;
138	Ayz = Axx+5;
139
140	Azx = Axx+6;
141	Azy = Axx+7;
142	Azz = Axx+8;
143	}
144
145	char *getType() {return c_name;}
146	void setType(char * name) {strcpy(c_name,name);}
147
148	int getIdent( void ) { return ident; }
149	void setIdent( int info ) { ident = info; }
150
151	#ifdef IS_MPI
152	int getGlobalIndex( void ) { return myGlobalIndex; }
153	void setGlobalIndex( int info ) { myGlobalIndex = info; }
154	#endif // is_mpi
155
156	void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
157	int get_n_hydrogens() const {return c_n_hyd;}
158
159	void setHasDipole( int value ) { has_dipole = value; }
160	int hasDipole( void ) { return has_dipole; }
161
162	void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
163	int isLJ( void ) { return is_LJ; }
164
165	void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
166	int isVDW( void ) { return is_VDW; }
167
168	virtual int isDirectional( void ) = 0;
169
170	static double* pos; // the position array
171	static double* vel; // the velocity array
172	static double* frc; // the forc array
173	static double* trq; // the torque vector ( space fixed )
174	static double* Amat; // the rotation matrix
175	static double* mu; // the dipole moment array
176	static double* ul; // the lab frame unit directional vector
177
178	protected:
179
180	double c_mass; /* the mass of the atom in amu */
181	double c_sigma; /* the sigma parameter for van der walls interactions */
182	double c_epslon; /* the esplon parameter for VDW interactions */
183	double c_covalent; // The covalent radius of the atom.
184
185	int index; /* set the atom's index */
186	int offset; // the atom's offset in the storage array
187	int offsetX, offsetY, offsetZ;
188
189	int Axx, Axy, Axz; // the rotational matrix indices
190	int Ayx, Ayy, Ayz;
191	int Azx, Azy, Azz;
192
193	char c_name[100]; /* it's name */
194	int ident; // it's unique numeric identity.
195
196	int c_n_hyd; // the number of hydrogens bonded to the atom
197
198	int has_dipole; // dipole boolean
199	int is_VDW; // VDW boolean
200	int is_LJ; // LJ boolean
201
202	#ifdef IS_MPI
203	int myGlobalIndex;
204	#endif
205
206	};
207
208
209
210	class GeneralAtom : public Atom{
211
212	public:
213	GeneralAtom(int theIndex): Atom(theIndex){}
214	virtual ~GeneralAtom(){}
215
216	int isDirectional( void ){ return 0; }
217	void zeroForces() {
218	frc[offsetX] = 0.0;
219	frc[offsetY] = 0.0;
220	frc[offsetZ] = 0.0;
221	}
222	};
223
224	class DirectionalAtom : public Atom {
225
226	public:
227	DirectionalAtom(int theIndex) : Atom(theIndex)
228	{
229	ssdIdentity = 0;
230	sux = 0.0;
231	suy = 0.0;
232	suz = 0.0;
233	}
234	virtual ~DirectionalAtom() {}
235
236	int isDirectional(void) { return 1; }
237
238	void setSSD( int value) { ssdIdentity = value; }
239	int isSSD(void) {return ssdIdentity; }
240
241	void setA( double the_A[3][3] );
242
243	void setI( double the_I[3][3] );
244
245	void setQ( double the_q[4] );
246
247	void setEuler( double phi, double theta, double psi );
248
249	void setSUx( double the_sux ) { sux = the_sux; }
250	void setSUy( double the_suy ) { suy = the_suy; }
251	void setSUz( double the_suz ) { suz = the_suz; }
252
253	void setJx( double the_jx ) { jx = the_jx; }
254	void setJy( double the_jy ) { jy = the_jy; }
255	void setJz( double the_jz ) { jz = the_jz; }
256
257	void addTx( double the_tx ) { trq[offsetX] += the_tx;}
258	void addTy( double the_ty ) { trq[offsetY] += the_ty;}
259	void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
260
261	void zeroForces() {
262	frc[offsetX] = 0.0;
263	frc[offsetY] = 0.0;
264	frc[offsetZ] = 0.0;
265
266	trq[offsetX] = 0.0;
267	trq[offsetY] = 0.0;
268	trq[offsetZ] = 0.0;
269	}
270
271	double getAxx( void ) { return Amat[Axx]; }
272	double getAxy( void ) { return Amat[Axy]; }
273	double getAxz( void ) { return Amat[Axz]; }
274
275	double getAyx( void ) { return Amat[Ayx]; }
276	double getAyy( void ) { return Amat[Ayy]; }
277	double getAyz( void ) { return Amat[Ayz]; }
278
279	double getAzx( void ) { return Amat[Azx]; }
280	double getAzy( void ) { return Amat[Azy]; }
281	double getAzz( void ) { return Amat[Azz]; }
282
283	void getA( double the_A[3][3] ); // get the full rotation matrix
284
285	double getSUx( void ) { return sux; }
286	double getSUy( void ) { return suy; }
287	double getSUz( void ) { return suz; }
288
289	void getU( double the_u[3] ); // get the unit vetor
290	void getQ( double the_q[4] ); // get the quanternions
291
292	double getJx( void ) { return jx; }
293	double getJy( void ) { return jy; }
294	double getJz( void ) { return jz; }
295
296	double getTx( void ) { return trq[offsetX];}
297	double getTy( void ) { return trq[offsetY]; }
298	double getTz( void ) { return trq[offsetZ]; }
299
300	double getIxx( void ) { return Ixx; }
301	double getIxy( void ) { return Ixy; }
302	double getIxz( void ) { return Ixz; }
303
304	double getIyx( void ) { return Iyx; }
305	double getIyy( void ) { return Iyy; }
306	double getIyz( void ) { return Iyz; }
307
308	double getIzx( void ) { return Izx; }
309	double getIzy( void ) { return Izy; }
310	double getIzz( void ) { return Izz; }
311
312	double getMu( void ) { return mu[index]; }
313	void setMu( double the_mu ) { mu[index] = the_mu; }
314
315	void lab2Body( double r[3] );
316	void body2Lab( double r[3] );
317	void updateU( void );
318
319	private:
320	int dIndex;
321
322	double sux, suy, suz; // the standard unit vector ( body fixed )
323	double jx, jy, jz; // the angular momentum vector ( body fixed )
324
325	double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
326	double Iyx, Iyy, Iyz;
327	double Izx, Izy, Izz;
328
329	int ssdIdentity; // boolean of whether atom is ssd
330
331	};
332
333	#endif