mdtools/libmdCode/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;
    pos = NULL;

    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;
    if( pos != NULL ) destroyArrays();
    
    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] = 0.0;
      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:	348
Committed:	Fri Mar 14 21:33:10 2003 UTC (21 years, 4 months ago) by mmeineke
File size:	8710 byte(s)
Log Message:	mostly compiles. interface twixt c and fortran is broken. (c needs to be brought up to date with fortran.)
#	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	pos = NULL;
16
17	index = theIndex;
18	offset = 3 * index;
19	offsetX = offset;
20	offsetY = offset+1;
21	offsetZ = offset+2;
22
23	Axx = index*9;
24	Axy = Axx+1;
25	Axz = Axx+2;
26
27	Ayx = Axx+3;
28	Ayy = Axx+4;
29	Ayz = Axx+5;
30
31	Azx = Axx+6;
32	Azy = Axx+7;
33	Azz = Axx+8;
34	}
35	virtual ~Atom() {}
36
37	static void createArrays (int nElements) {
38	int i;
39	if( pos != NULL ) destroyArrays();
40
41	pos = new double[nElements*3];
42	vel = new double[nElements*3];
43	frc = new double[nElements*3];
44	trq = new double[nElements*3];
45	Amat = new double[nElements*9];
46	mu = new double[nElements];
47	ul = new double[nElements*3];
48
49	// init directional values to zero
50
51	for( i=0; i<nElements; i++){
52	trq[i] = 0.0;
53	trq[i+1] = 0.0;
54	trq[i+2] = 0.0;
55
56	Amat[i] = 1.0;
57	Amat[i+1] = 0.0;
58	Amat[i+2] = 0.0;
59
60	Amat[i+3] = 0.0;
61	Amat[i+4] = 1.0;
62	Amat[i+5] = 0.0;
63
64	Amat[i+6] = 0.0;
65	Amat[i+7] = 0.0;
66	Amat[i+8] = 1.0;
67
68	mu[i] = 0.0;
69
70	ul[i] = 0.0;
71	ul[i+1] = 0.0;
72	ul[i+2] = 0.0;
73	}
74	}
75	static void destroyArrays(void) {
76	delete[] pos;
77	delete[] vel;
78	delete[] frc;
79	delete[] trq;
80	delete[] Amat;
81	delete[] mu;
82	}
83
84	static double* getPosArray( void ) { return pos; }
85	static double* getVelArray( void ) { return vel; }
86	static double* getFrcArray( void ) { return frc; }
87	static double* getTrqArray( void ) { return trq; }
88	static double* getAmatArray( void ) { return Amat; }
89	static double* getMuArray( void ) { return mu; }
90	static double* getUlArray( void ) { return ul; }
91
92	double getX() const {return pos[offsetX];}
93	double getY() const {return pos[offsetY];}
94	double getZ() const {return pos[offsetZ];}
95	void setX(double x) {pos[offsetX] = x;}
96	void setY(double y) {pos[offsetY] = y;}
97	void setZ(double z) {pos[offsetZ] = z;}
98
99	double get_vx() const {return vel[offsetX];}
100	double get_vy() const {return vel[offsetY];}
101	double get_vz() const {return vel[offsetZ];}
102	void set_vx(double vx) {vel[offsetX] = vx;}
103	void set_vy(double vy) {vel[offsetY] = vy;}
104	void set_vz(double vz) {vel[offsetZ] = vz;}
105
106	double getFx() const {return frc[offsetX];}
107	double getFy() const {return frc[offsetY];}
108	double getFz() const {return frc[offsetZ];}
109	void addFx(double add) {frc[offsetX] += add;}
110	void addFy(double add) {frc[offsetY] += add;}
111	void addFz(double add) {frc[offsetZ] += add;}
112	virtual void zeroForces() = 0;
113
114	double getMass() const {return c_mass;}
115	void setMass(double mass) {c_mass = mass;}
116
117	double getSigma() const {return c_sigma;}
118	void setSigma(double sigma) {c_sigma = sigma;}
119
120	double getEpslon() const {return c_epslon;}
121	void setEpslon(double epslon) {c_epslon = epslon;}
122
123	double getCovalent() const {return c_covalent;}
124	void setCovalent(double covalent) {c_covalent = covalent;}
125
126	int getIndex() const {return index;}
127	void setIndex(int theIndex) {
128	index = theIndex;
129	offset = index*3;
130	offsetX = offset;
131	offsetY = offset+1;
132	offsetZ = offset+2;
133
134	Axx = index*9;
135	Axy = Axx+1;
136	Axz = Axx+2;
137
138	Ayx = Axx+3;
139	Ayy = Axx+4;
140	Ayz = Axx+5;
141
142	Azx = Axx+6;
143	Azy = Axx+7;
144	Azz = Axx+8;
145	}
146
147	char *getType() {return c_name;}
148	void setType(char * name) {strcpy(c_name,name);}
149
150	int getIdent( void ) { return ident; }
151	void setIdent( int info ) { ident = info; }
152
153	#ifdef IS_MPI
154	int getGlobalIndex( void ) { return myGlobalIndex; }
155	void setGlobalIndex( int info ) { myGlobalIndex = info; }
156	#endif // is_mpi
157
158	void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
159	int get_n_hydrogens() const {return c_n_hyd;}
160
161	void setHasDipole( int value ) { has_dipole = value; }
162	int hasDipole( void ) { return has_dipole; }
163
164	void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
165	int isLJ( void ) { return is_LJ; }
166
167	void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
168	int isVDW( void ) { return is_VDW; }
169
170	virtual int isDirectional( void ) = 0;
171
172	static double* pos; // the position array
173	static double* vel; // the velocity array
174	static double* frc; // the forc array
175	static double* trq; // the torque vector ( space fixed )
176	static double* Amat; // the rotation matrix
177	static double* mu; // the dipole moment array
178	static double* ul; // the lab frame unit directional vector
179
180	protected:
181
182	double c_mass; /* the mass of the atom in amu */
183	double c_sigma; /* the sigma parameter for van der walls interactions */
184	double c_epslon; /* the esplon parameter for VDW interactions */
185	double c_covalent; // The covalent radius of the atom.
186
187	int index; /* set the atom's index */
188	int offset; // the atom's offset in the storage array
189	int offsetX, offsetY, offsetZ;
190
191	int Axx, Axy, Axz; // the rotational matrix indices
192	int Ayx, Ayy, Ayz;
193	int Azx, Azy, Azz;
194
195	char c_name[100]; /* it's name */
196	int ident; // it's unique numeric identity.
197
198	int c_n_hyd; // the number of hydrogens bonded to the atom
199
200	int has_dipole; // dipole boolean
201	int is_VDW; // VDW boolean
202	int is_LJ; // LJ boolean
203
204	#ifdef IS_MPI
205	int myGlobalIndex;
206	#endif
207
208	};
209
210
211
212	class GeneralAtom : public Atom{
213
214	public:
215	GeneralAtom(int theIndex): Atom(theIndex){}
216	virtual ~GeneralAtom(){}
217
218	int isDirectional( void ){ return 0; }
219	void zeroForces() {
220	frc[offsetX] = 0.0;
221	frc[offsetY] = 0.0;
222	frc[offsetZ] = 0.0;
223	}
224	};
225
226	class DirectionalAtom : public Atom {
227
228	public:
229	DirectionalAtom(int theIndex) : Atom(theIndex)
230	{
231	ssdIdentity = 0;
232	sux = 0.0;
233	suy = 0.0;
234	suz = 0.0;
235	}
236	virtual ~DirectionalAtom() {}
237
238	int isDirectional(void) { return 1; }
239
240	void setSSD( int value) { ssdIdentity = value; }
241	int isSSD(void) {return ssdIdentity; }
242
243	void setA( double the_A[3][3] );
244
245	void setI( double the_I[3][3] );
246
247	void setQ( double the_q[4] );
248
249	void setEuler( double phi, double theta, double psi );
250
251	void setSUx( double the_sux ) { sux = the_sux; }
252	void setSUy( double the_suy ) { suy = the_suy; }
253	void setSUz( double the_suz ) { suz = the_suz; }
254
255	void setJx( double the_jx ) { jx = the_jx; }
256	void setJy( double the_jy ) { jy = the_jy; }
257	void setJz( double the_jz ) { jz = the_jz; }
258
259	void addTx( double the_tx ) { trq[offsetX] += the_tx;}
260	void addTy( double the_ty ) { trq[offsetY] += the_ty;}
261	void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
262
263	void zeroForces() {
264	frc[offsetX] = 0.0;
265	frc[offsetY] = 0.0;
266	frc[offsetZ] = 0.0;
267
268	trq[offsetX] = 0.0;
269	trq[offsetY] = 0.0;
270	trq[offsetZ] = 0.0;
271	}
272
273	double getAxx( void ) { return Amat[Axx]; }
274	double getAxy( void ) { return Amat[Axy]; }
275	double getAxz( void ) { return Amat[Axz]; }
276
277	double getAyx( void ) { return Amat[Ayx]; }
278	double getAyy( void ) { return Amat[Ayy]; }
279	double getAyz( void ) { return Amat[Ayz]; }
280
281	double getAzx( void ) { return Amat[Azx]; }
282	double getAzy( void ) { return Amat[Azy]; }
283	double getAzz( void ) { return Amat[Azz]; }
284
285	void getA( double the_A[3][3] ); // get the full rotation matrix
286
287	double getSUx( void ) { return sux; }
288	double getSUy( void ) { return suy; }
289	double getSUz( void ) { return suz; }
290
291	void getU( double the_u[3] ); // get the unit vetor
292	void getQ( double the_q[4] ); // get the quanternions
293
294	double getJx( void ) { return jx; }
295	double getJy( void ) { return jy; }
296	double getJz( void ) { return jz; }
297
298	double getTx( void ) { return trq[offsetX];}
299	double getTy( void ) { return trq[offsetY]; }
300	double getTz( void ) { return trq[offsetZ]; }
301
302	double getIxx( void ) { return Ixx; }
303	double getIxy( void ) { return Ixy; }
304	double getIxz( void ) { return Ixz; }
305
306	double getIyx( void ) { return Iyx; }
307	double getIyy( void ) { return Iyy; }
308	double getIyz( void ) { return Iyz; }
309
310	double getIzx( void ) { return Izx; }
311	double getIzy( void ) { return Izy; }
312	double getIzz( void ) { return Izz; }
313
314	double getMu( void ) { return mu[index]; }
315	void setMu( double the_mu ) { mu[index] = the_mu; }
316
317	void lab2Body( double r[3] );
318	void body2Lab( double r[3] );
319	void updateU( void );
320
321	private:
322	int dIndex;
323
324	double sux, suy, suz; // the standard unit vector ( body fixed )
325	double jx, jy, jz; // the angular momentum vector ( body fixed )
326
327	double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
328	double Iyx, Iyy, Iyz;
329	double Izx, Izy, Izz;
330
331	int ssdIdentity; // boolean of whether atom is ssd
332
333	};
334
335	#endif