mdtools/headers/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;
  }
  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];
  }
  static void destroyArrays(void) {
    delete[] pos;
    delete[] vel;
    delete[] frc;
    delete[] trq;
  }
  
  double getX() const {return pos[offset];}
  double getY() const {return pos[offset+1];}
  double getZ() const {return pos[offset+2];}
  void setX(double x) {pos[offset]   = x;}
  void setY(double y) {pos[offset+1] = y;}
  void setZ(double z) {pos[offset+2] = z;}
  
  double get_vx() const  {return vel[offset];}
  double get_vy() const  {return vel[offset+1];}
  double get_vz() const  {return vel[offset+2];}
  void set_vx(double vx) {vel[offset]   = vx;}
  void set_vy(double vy) {vel[offset+1] = vy;}
  void set_vz(double vz) {vel[offset+2] = vz;}
  
  double getFx() const   {return frc[offset];}
  double getFy() const   {return frc[offset+1];}
  double getFz() const   {return frc[offset+2];}
  void addFx(double add) {frc[offset]   += add;}
  void addFy(double add) {frc[offset+1] += add;}
  void addFz(double add) {frc[offset+2] += 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;}
  
  char *getType() {return c_name;}
  void setType(char * name) {strcpy(c_name,name);}

  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 )

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

  char c_name[100]; /* it's name */

  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
  
};


class GeneralAtom : public Atom{

public:
  GeneralAtom(int theIndex): Atom(theIndex){}
  virtual ~GeneralAtom(){}

  int isDirectional( void ){ return 0; }
  void zeroForces() {
    frc[offset]   = 0.0; 
    frc[offset+1] = 0.0; 
    frc[offset+2] = 0.0;
  }
};

class DirectionalAtom : public Atom {
  
public:
  DirectionalAtom(int theIndex) : Atom(theIndex)
  { 
    ssdIdentity = 0; 
  }
  virtual ~DirectionalAtom() {}

  static void createDArrays(int nElements){
    trq = new double[nElements*3];
  }
  static void destroyDArrays(void){
    delete[] trq;
  }

  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[offset]   += the_tx;}
  void addTy( double the_ty ) { trq[offset+1] += the_ty;}
  void addTz( double the_tz ) { trq[offset+2] += the_tz;}

  void setMu( double the_mu ) { mu = the_mu; }

  void zeroForces() {
    frc[offset]   = 0.0; 
    frc[offset+1] = 0.0; 
    frc[offset+2] = 0.0;

    trq[offset]   = 0.0; 
    trq[offset+1] = 0.0; 
    trq[offset+2] = 0.0;
  }

  double getAxx( void ) { return Axx; } 
  double getAxy( void ) { return Axy; }
  double getAxz( void ) { return Axz; }
  
  double getAyx( void ) { return Ayx; } 
  double getAyy( void ) { return Ayy; }
  double getAyz( void ) { return Ayz; }
  
  double getAzx( void ) { return Azx; } 
  double getAzy( void ) { return Azy; }
  double getAzz( void ) { return 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 vector
  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[offset];} 
  double getTy( void ) { return trq[offset+1]; }
  double getTz( void ) { return trq[offset+2]; }

  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; }

  void lab2Body( double r[3] );
  void body2Lab( double r[3] );

private:
  int dIndex;

  double Axx, Axy, Axz; // the rotational matrix 
  double Ayx, Ayy, Ayz;
  double Azx, Azy, Azz;

  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;

  double mu; // the magnitude of the dipole moment
  
  int ssdIdentity; // boolean of whether atom is ssd

};

#endif
Revision:	189
Committed:	Tue Nov 26 21:04:43 2002 UTC (21 years, 8 months ago) by mmeineke
File size:	6732 byte(s)
Log Message:	* empty log message *
#	User	Rev	Content
1	mmeineke	10	#ifndef _ATOM_H_
2			#define _ATOM_H_
3
4			#include <cstring>
5			#include <iostream>
6
7			class Atom{
8			public:
9	mmeineke	143	Atom(int theIndex) {
10	mmeineke	10	c_n_hyd = 0;
11			has_dipole = 0;
12			is_VDW = 0;
13			is_LJ = 0;
14	mmeineke	143	index = theIndex;
15	mmeineke	189	offset = 3 * index;
16	mmeineke	10	}
17	mmeineke	117	virtual ~Atom() {}
18	mmeineke	143
19			static void createArrays (int nElements) {
20			pos = new double[nElements*3];
21			vel = new double[nElements*3];
22			frc = new double[nElements*3];
23			trq = new double[nElements*3];
24			}
25			static void destroyArrays(void) {
26			delete[] pos;
27			delete[] vel;
28			delete[] frc;
29			delete[] trq;
30			}
31	mmeineke	10
32	mmeineke	189	double getX() const {return pos[offset];}
33			double getY() const {return pos[offset+1];}
34			double getZ() const {return pos[offset+2];}
35			void setX(double x) {pos[offset] = x;}
36			void setY(double y) {pos[offset+1] = y;}
37			void setZ(double z) {pos[offset+2] = z;}
38	mmeineke	10
39	mmeineke	189	double get_vx() const {return vel[offset];}
40			double get_vy() const {return vel[offset+1];}
41			double get_vz() const {return vel[offset+2];}
42			void set_vx(double vx) {vel[offset] = vx;}
43			void set_vy(double vy) {vel[offset+1] = vy;}
44			void set_vz(double vz) {vel[offset+2] = vz;}
45	mmeineke	10
46	mmeineke	189	double getFx() const {return frc[offset];}
47			double getFy() const {return frc[offset+1];}
48			double getFz() const {return frc[offset+2];}
49			void addFx(double add) {frc[offset] += add;}
50			void addFy(double add) {frc[offset+1] += add;}
51			void addFz(double add) {frc[offset+2] += add;}
52	mmeineke	10	virtual void zeroForces() = 0;
53
54			double getMass() const {return c_mass;}
55			void setMass(double mass) {c_mass = mass;}
56
57			double getSigma() const {return c_sigma;}
58			void setSigma(double sigma) {c_sigma = sigma;}
59
60			double getEpslon() const {return c_epslon;}
61			void setEpslon(double epslon) {c_epslon = epslon;}
62
63			double getCovalent() const {return c_covalent;}
64			void setCovalent(double covalent) {c_covalent = covalent;}
65
66	mmeineke	143	int getIndex() const {return index;}
67	mmeineke	189	void setIndex(int theIndex) {index = theIndex; offset = index*3;}
68	mmeineke	10
69			char *getType() {return c_name;}
70			void setType(char * name) {strcpy(c_name,name);}
71
72			void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
73			int get_n_hydrogens() const {return c_n_hyd;}
74
75			void setHasDipole( int value ) { has_dipole = value; }
76	chuckv	134	int hasDipole( void ) { return has_dipole; }
77	mmeineke	10
78			void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
79	chuckv	134	int isLJ( void ) { return is_LJ; }
80	mmeineke	10
81			void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
82	chuckv	134	int isVDW( void ) { return is_VDW; }
83	mmeineke	10
84			virtual int isDirectional( void ) = 0;
85
86	mmeineke	143	static double* pos; // the position array
87			static double* vel; // the velocity array
88			static double* frc; // the forc array
89			static double* trq; // the torque vector ( space fixed )
90
91	mmeineke	184	protected:
92
93	mmeineke	10	double c_mass; /* the mass of the atom in amu */
94			double c_sigma; /* the sigma parameter for van der walls interactions */
95			double c_epslon; /* the esplon parameter for VDW interactions */
96			double c_covalent; // The covalent radius of the atom.
97
98	mmeineke	143	int index; /* set the atom's index */
99	mmeineke	189	int offset; // the atom's offset in the storage array
100	mmeineke	10
101			char c_name[100]; /* it's name */
102
103			int c_n_hyd; // the number of hydrogens bonded to the atom
104
105	chuckv	134	int has_dipole; // dipole boolean
106			int is_VDW; // VDW boolean
107			int is_LJ; // LJ boolean
108	mmeineke	10
109			};
110
111	mmeineke	184
112
113	mmeineke	10	class GeneralAtom : public Atom{
114
115			public:
116	mmeineke	143	GeneralAtom(int theIndex): Atom(theIndex){}
117	mmeineke	117	virtual ~GeneralAtom(){}
118	mmeineke	10
119			int isDirectional( void ){ return 0; }
120			void zeroForces() {
121	mmeineke	189	frc[offset] = 0.0;
122			frc[offset+1] = 0.0;
123			frc[offset+2] = 0.0;
124	mmeineke	10	}
125			};
126
127			class DirectionalAtom : public Atom {
128
129			public:
130	mmeineke	143	DirectionalAtom(int theIndex) : Atom(theIndex)
131			{
132			ssdIdentity = 0;
133			}
134	mmeineke	117	virtual ~DirectionalAtom() {}
135	mmeineke	10
136	mmeineke	143	static void createDArrays(int nElements){
137			trq = new double[nElements*3];
138			}
139			static void destroyDArrays(void){
140			delete[] trq;
141			}
142
143	mmeineke	10	int isDirectional(void) { return 1; }
144
145			void setSSD( int value) { ssdIdentity = value; }
146			int isSSD(void) {return ssdIdentity; }
147
148			void setA( double the_A[3][3] );
149
150			void setI( double the_I[3][3] );
151
152			void setQ( double the_q[4] );
153
154			void setEuler( double phi, double theta, double psi );
155
156			void setSUx( double the_sux ) { sux = the_sux; }
157			void setSUy( double the_suy ) { suy = the_suy; }
158			void setSUz( double the_suz ) { suz = the_suz; }
159
160			void setJx( double the_jx ) { jx = the_jx; }
161			void setJy( double the_jy ) { jy = the_jy; }
162			void setJz( double the_jz ) { jz = the_jz; }
163
164	mmeineke	189	void addTx( double the_tx ) { trq[offset] += the_tx;}
165			void addTy( double the_ty ) { trq[offset+1] += the_ty;}
166			void addTz( double the_tz ) { trq[offset+2] += the_tz;}
167	mmeineke	10
168			void setMu( double the_mu ) { mu = the_mu; }
169
170			void zeroForces() {
171	mmeineke	189	frc[offset] = 0.0;
172			frc[offset+1] = 0.0;
173			frc[offset+2] = 0.0;
174	mmeineke	143
175	mmeineke	189	trq[offset] = 0.0;
176			trq[offset+1] = 0.0;
177			trq[offset+2] = 0.0;
178	mmeineke	10	}
179
180			double getAxx( void ) { return Axx; }
181			double getAxy( void ) { return Axy; }
182			double getAxz( void ) { return Axz; }
183
184			double getAyx( void ) { return Ayx; }
185			double getAyy( void ) { return Ayy; }
186			double getAyz( void ) { return Ayz; }
187
188			double getAzx( void ) { return Azx; }
189			double getAzy( void ) { return Azy; }
190			double getAzz( void ) { return Azz; }
191
192	mmeineke	30	void getA( double the_A[3][3] ); // get the full rotation matrix
193
194	mmeineke	10	double getSUx( void ) { return sux; }
195			double getSUy( void ) { return suy; }
196			double getSUz( void ) { return suz; }
197
198			void getU( double the_u[3] ); // get the unit vector
199			void getQ( double the_q[4] ); // get the quanternions
200
201			double getJx( void ) { return jx; }
202			double getJy( void ) { return jy; }
203			double getJz( void ) { return jz; }
204
205	mmeineke	189	double getTx( void ) { return trq[offset];}
206			double getTy( void ) { return trq[offset+1]; }
207			double getTz( void ) { return trq[offset+2]; }
208	mmeineke	10
209			double getIxx( void ) { return Ixx; }
210			double getIxy( void ) { return Ixy; }
211			double getIxz( void ) { return Ixz; }
212
213			double getIyx( void ) { return Iyx; }
214			double getIyy( void ) { return Iyy; }
215			double getIyz( void ) { return Iyz; }
216
217			double getIzx( void ) { return Izx; }
218			double getIzy( void ) { return Izy; }
219			double getIzz( void ) { return Izz; }
220
221			double getMu( void ) { return mu; }
222
223			void lab2Body( double r[3] );
224			void body2Lab( double r[3] );
225
226			private:
227	mmeineke	143	int dIndex;
228	mmeineke	10
229	chuckv	134	double Axx, Axy, Axz; // the rotational matrix
230	mmeineke	10	double Ayx, Ayy, Ayz;
231			double Azx, Azy, Azz;
232
233	mmeineke	143	double sux, suy, suz; // the standard unit vector ( body fixed )
234			double jx, jy, jz; // the angular momentum vector ( body fixed )
235	mmeineke	10
236	mmeineke	143	double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
237	mmeineke	10	double Iyx, Iyy, Iyz;
238			double Izx, Izy, Izz;
239
240			double mu; // the magnitude of the dipole moment
241
242			int ssdIdentity; // boolean of whether atom is ssd
243
244			};
245
246			#endif