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, 5 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.)
#	User	Rev	Content
1	mmeineke	270	#ifndef _ATOM_H_
2			#define _ATOM_H_
3
4			#include <cstring>
5	mmeineke	299	#include <cstdlib>
6	mmeineke	270	#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	mmeineke	299	pos = NULL;
16
17	mmeineke	270	index = theIndex;
18			offset = 3 * index;
19			offsetX = offset;
20			offsetY = offset+1;
21			offsetZ = offset+2;
22	mmeineke	296
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	mmeineke	270	}
35			virtual ~Atom() {}
36
37			static void createArrays (int nElements) {
38	mmeineke	348	int i;
39	mmeineke	299	if( pos != NULL ) destroyArrays();
40
41	mmeineke	270	pos = new double[nElements*3];
42			vel = new double[nElements*3];
43			frc = new double[nElements*3];
44			trq = new double[nElements*3];
45	mmeineke	296	Amat = new double[nElements*9];
46			mu = new double[nElements];
47	mmeineke	348	ul = new double[nElements*3];
48	mmeineke	296
49			// init directional values to zero
50
51	mmeineke	348	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	mmeineke	270	}
75			static void destroyArrays(void) {
76			delete[] pos;
77			delete[] vel;
78			delete[] frc;
79			delete[] trq;
80	mmeineke	296	delete[] Amat;
81			delete[] mu;
82	mmeineke	270	}
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	mmeineke	296	static double* getAmatArray( void ) { return Amat; }
89			static double* getMuArray( void ) { return mu; }
90			static double* getUlArray( void ) { return ul; }
91	mmeineke	270
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	mmeineke	296
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	mmeineke	270	}
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	mmeineke	296	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	mmeineke	270
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	mmeineke	296	int Axx, Axy, Axz; // the rotational matrix indices
192			int Ayx, Ayy, Ayz;
193			int Azx, Azy, Azz;
194
195	mmeineke	270	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	mmeineke	299	frc[offsetX] = 0.0;
221	mmeineke	270	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	mmeineke	299	sux = 0.0;
233			suy = 0.0;
234			suz = 0.0;
235	mmeineke	270	}
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	mmeineke	296	void addTx( double the_tx ) { trq[offsetX] += the_tx;}
260	mmeineke	270	void addTy( double the_ty ) { trq[offsetY] += the_ty;}
261			void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
262
263			void zeroForces() {
264	mmeineke	299	frc[offsetX] = 0.0;
265	mmeineke	270	frc[offsetY] = 0.0;
266			frc[offsetZ] = 0.0;
267
268	mmeineke	299	trq[offsetX] = 0.0;
269	mmeineke	270	trq[offsetY] = 0.0;
270			trq[offsetZ] = 0.0;
271			}
272
273	mmeineke	296	double getAxx( void ) { return Amat[Axx]; }
274			double getAxy( void ) { return Amat[Axy]; }
275			double getAxz( void ) { return Amat[Axz]; }
276	mmeineke	270
277	mmeineke	296	double getAyx( void ) { return Amat[Ayx]; }
278			double getAyy( void ) { return Amat[Ayy]; }
279			double getAyz( void ) { return Amat[Ayz]; }
280	mmeineke	270
281	mmeineke	296	double getAzx( void ) { return Amat[Azx]; }
282			double getAzy( void ) { return Amat[Azy]; }
283			double getAzz( void ) { return Amat[Azz]; }
284	mmeineke	270
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	mmeineke	296	void getU( double the_u[3] ); // get the unit vetor
292	mmeineke	270	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	mmeineke	296	double getMu( void ) { return mu[index]; }
315			void setMu( double the_mu ) { mu[index] = the_mu; }
316	mmeineke	270
317			void lab2Body( double r[3] );
318			void body2Lab( double r[3] );
319	mmeineke	299	void updateU( void );
320	mmeineke	270
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