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;
    offsetX = offset;
    offsetY = offset+1;
    offsetZ = offset+2;
  }
  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[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;
  }

  char *getType() {return c_name;}
  void setType(char * name) {strcpy(c_name,name);}
  
  int getIdent( void ) { return ident; }
  void setIdent( int info ) { ident = info; }

  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
  int offsetX, offsetY, offsetZ;

  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
  
};


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; 
  }
  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[offsetX]   += the_tx;}
  void addTy( double the_ty ) { trq[offsetY] += the_ty;}
  void addTz( double the_tz ) { trq[offsetZ] += the_tz;}

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

  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 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[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; }

  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:	225
Committed:	Wed Jan 8 21:54:20 2003 UTC (21 years, 8 months ago) by mmeineke
File size:	7042 byte(s)
Log Message:	fixed up LJ_FF
#	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	190	offsetX = offset;
17			offsetY = offset+1;
18			offsetZ = offset+2;
19	mmeineke	10	}
20	mmeineke	117	virtual ~Atom() {}
21	mmeineke	143
22			static void createArrays (int nElements) {
23			pos = new double[nElements*3];
24			vel = new double[nElements*3];
25			frc = new double[nElements*3];
26			trq = new double[nElements*3];
27			}
28			static void destroyArrays(void) {
29			delete[] pos;
30			delete[] vel;
31			delete[] frc;
32			delete[] trq;
33			}
34	mmeineke	10
35	mmeineke	190	double getX() const {return pos[offsetX];}
36			double getY() const {return pos[offsetY];}
37			double getZ() const {return pos[offsetZ];}
38			void setX(double x) {pos[offsetX] = x;}
39			void setY(double y) {pos[offsetY] = y;}
40			void setZ(double z) {pos[offsetZ] = z;}
41	mmeineke	10
42	mmeineke	190	double get_vx() const {return vel[offsetX];}
43			double get_vy() const {return vel[offsetY];}
44			double get_vz() const {return vel[offsetZ];}
45			void set_vx(double vx) {vel[offsetX] = vx;}
46			void set_vy(double vy) {vel[offsetY] = vy;}
47			void set_vz(double vz) {vel[offsetZ] = vz;}
48	mmeineke	10
49	mmeineke	190	double getFx() const {return frc[offsetX];}
50			double getFy() const {return frc[offsetY];}
51			double getFz() const {return frc[offsetZ];}
52			void addFx(double add) {frc[offsetX] += add;}
53			void addFy(double add) {frc[offsetY] += add;}
54			void addFz(double add) {frc[offsetZ] += add;}
55	mmeineke	10	virtual void zeroForces() = 0;
56
57			double getMass() const {return c_mass;}
58			void setMass(double mass) {c_mass = mass;}
59
60			double getSigma() const {return c_sigma;}
61			void setSigma(double sigma) {c_sigma = sigma;}
62
63			double getEpslon() const {return c_epslon;}
64			void setEpslon(double epslon) {c_epslon = epslon;}
65
66			double getCovalent() const {return c_covalent;}
67			void setCovalent(double covalent) {c_covalent = covalent;}
68
69	mmeineke	143	int getIndex() const {return index;}
70	mmeineke	190	void setIndex(int theIndex) {
71			index = theIndex;
72			offset = index*3;
73			offsetX = offset;
74			offsetY = offset+1;
75			offsetZ = offset+2;
76			}
77
78	mmeineke	10	char *getType() {return c_name;}
79			void setType(char * name) {strcpy(c_name,name);}
80	mmeineke	225
81			int getIdent( void ) { return ident; }
82			void setIdent( int info ) { ident = info; }
83	mmeineke	10
84			void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
85			int get_n_hydrogens() const {return c_n_hyd;}
86
87			void setHasDipole( int value ) { has_dipole = value; }
88	chuckv	134	int hasDipole( void ) { return has_dipole; }
89	mmeineke	10
90			void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
91	chuckv	134	int isLJ( void ) { return is_LJ; }
92	mmeineke	10
93			void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
94	chuckv	134	int isVDW( void ) { return is_VDW; }
95	mmeineke	10
96			virtual int isDirectional( void ) = 0;
97
98	mmeineke	143	static double* pos; // the position array
99			static double* vel; // the velocity array
100			static double* frc; // the forc array
101			static double* trq; // the torque vector ( space fixed )
102
103	mmeineke	184	protected:
104
105	mmeineke	10	double c_mass; /* the mass of the atom in amu */
106			double c_sigma; /* the sigma parameter for van der walls interactions */
107			double c_epslon; /* the esplon parameter for VDW interactions */
108			double c_covalent; // The covalent radius of the atom.
109
110	mmeineke	143	int index; /* set the atom's index */
111	mmeineke	189	int offset; // the atom's offset in the storage array
112	mmeineke	213	int offsetX, offsetY, offsetZ;
113	mmeineke	10
114			char c_name[100]; /* it's name */
115	mmeineke	225	int ident; // it's unique numeric identity.
116	mmeineke	10
117			int c_n_hyd; // the number of hydrogens bonded to the atom
118
119	chuckv	134	int has_dipole; // dipole boolean
120			int is_VDW; // VDW boolean
121			int is_LJ; // LJ boolean
122	mmeineke	10
123			};
124
125	mmeineke	184
126
127	mmeineke	10	class GeneralAtom : public Atom{
128
129			public:
130	mmeineke	143	GeneralAtom(int theIndex): Atom(theIndex){}
131	mmeineke	117	virtual ~GeneralAtom(){}
132	mmeineke	10
133			int isDirectional( void ){ return 0; }
134			void zeroForces() {
135	mmeineke	190	frc[offsetX] = 0.0;
136			frc[offsetY] = 0.0;
137			frc[offsetZ] = 0.0;
138	mmeineke	10	}
139			};
140
141			class DirectionalAtom : public Atom {
142
143			public:
144	mmeineke	143	DirectionalAtom(int theIndex) : Atom(theIndex)
145			{
146			ssdIdentity = 0;
147			}
148	mmeineke	117	virtual ~DirectionalAtom() {}
149	mmeineke	10
150	mmeineke	143	static void createDArrays(int nElements){
151			trq = new double[nElements*3];
152			}
153			static void destroyDArrays(void){
154			delete[] trq;
155			}
156
157	mmeineke	10	int isDirectional(void) { return 1; }
158
159			void setSSD( int value) { ssdIdentity = value; }
160			int isSSD(void) {return ssdIdentity; }
161
162			void setA( double the_A[3][3] );
163
164			void setI( double the_I[3][3] );
165
166			void setQ( double the_q[4] );
167
168			void setEuler( double phi, double theta, double psi );
169
170			void setSUx( double the_sux ) { sux = the_sux; }
171			void setSUy( double the_suy ) { suy = the_suy; }
172			void setSUz( double the_suz ) { suz = the_suz; }
173
174			void setJx( double the_jx ) { jx = the_jx; }
175			void setJy( double the_jy ) { jy = the_jy; }
176			void setJz( double the_jz ) { jz = the_jz; }
177
178	mmeineke	190	void addTx( double the_tx ) { trq[offsetX] += the_tx;}
179			void addTy( double the_ty ) { trq[offsetY] += the_ty;}
180			void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
181	mmeineke	10
182			void setMu( double the_mu ) { mu = the_mu; }
183
184			void zeroForces() {
185	mmeineke	190	frc[offsetX] = 0.0;
186			frc[offsetY] = 0.0;
187			frc[offsetZ] = 0.0;
188	mmeineke	143
189	mmeineke	190	trq[offsetX] = 0.0;
190			trq[offsetY] = 0.0;
191			trq[offsetZ] = 0.0;
192	mmeineke	10	}
193
194			double getAxx( void ) { return Axx; }
195			double getAxy( void ) { return Axy; }
196			double getAxz( void ) { return Axz; }
197
198			double getAyx( void ) { return Ayx; }
199			double getAyy( void ) { return Ayy; }
200			double getAyz( void ) { return Ayz; }
201
202			double getAzx( void ) { return Azx; }
203			double getAzy( void ) { return Azy; }
204			double getAzz( void ) { return Azz; }
205
206	mmeineke	30	void getA( double the_A[3][3] ); // get the full rotation matrix
207
208	mmeineke	10	double getSUx( void ) { return sux; }
209			double getSUy( void ) { return suy; }
210			double getSUz( void ) { return suz; }
211
212			void getU( double the_u[3] ); // get the unit vector
213			void getQ( double the_q[4] ); // get the quanternions
214
215			double getJx( void ) { return jx; }
216			double getJy( void ) { return jy; }
217			double getJz( void ) { return jz; }
218
219	mmeineke	190	double getTx( void ) { return trq[offsetX];}
220			double getTy( void ) { return trq[offsetY]; }
221			double getTz( void ) { return trq[offsetZ]; }
222	mmeineke	10
223			double getIxx( void ) { return Ixx; }
224			double getIxy( void ) { return Ixy; }
225			double getIxz( void ) { return Ixz; }
226
227			double getIyx( void ) { return Iyx; }
228			double getIyy( void ) { return Iyy; }
229			double getIyz( void ) { return Iyz; }
230
231			double getIzx( void ) { return Izx; }
232			double getIzy( void ) { return Izy; }
233			double getIzz( void ) { return Izz; }
234
235			double getMu( void ) { return mu; }
236
237			void lab2Body( double r[3] );
238			void body2Lab( double r[3] );
239
240			private:
241	mmeineke	143	int dIndex;
242	mmeineke	10
243	chuckv	134	double Axx, Axy, Axz; // the rotational matrix
244	mmeineke	10	double Ayx, Ayy, Ayz;
245			double Azx, Azy, Azz;
246
247	mmeineke	143	double sux, suy, suz; // the standard unit vector ( body fixed )
248			double jx, jy, jz; // the angular momentum vector ( body fixed )
249	mmeineke	10
250	mmeineke	143	double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
251	mmeineke	10	double Iyx, Iyy, Iyz;
252			double Izx, Izy, Izz;
253
254			double mu; // the magnitude of the dipole moment
255
256			int ssdIdentity; // boolean of whether atom is ssd
257
258			};
259
260			#endif