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] = 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:	377
Committed:	Fri Mar 21 17:42:12 2003 UTC (21 years, 3 months ago) by mmeineke
Original Path:	*branches/mmeineke/OOPSE/libmdtools/Atom.hpp*
File size:	8651 byte(s)
Log Message:	New OOPSE Tree
#	User	Rev	Content
1	mmeineke	377	#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] = 0.0;
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