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;
  }
  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[3*index];}
  double getY() const {return pos[3*index+1];}
  double getZ() const {return pos[3*index+2];}
  void setX(double x) {pos[3*index]   = x;}
  void setY(double y) {pos[3*index+1] = y;}
  void setZ(double z) {pos[3*index+2] = z;}
  
  double get_vx() const  {return vel[3*index];}
  double get_vy() const  {return vel[3*index+1];}
  double get_vz() const  {return vel[3*index+2];}
  void set_vx(double vx) {vel[3*index]   = vx;}
  void set_vy(double vy) {vel[3*index+1] = vy;}
  void set_vz(double vz) {vel[3*index+2] = vz;}
  
  double getFx() const   {return frc[3*index];}
  double getFy() const   {return frc[3*index+1];}
  double getFz() const   {return frc[3*index+2];}
  void addFx(double add) {frc[3*index]   += add;}
  void addFy(double add) {frc[3*index+1] += add;}
  void addFz(double add) {frc[3*index+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;}
  
  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;

protected:
  
  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 )

  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 */

  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[3*index]   = 0.0; 
    frc[3*index+1] = 0.0; 
    frc[3*index+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[3*index]   += the_tx;}
  void addTy( double the_ty ) { trq[3*index+1] += the_ty;}
  void addTz( double the_tz ) { trq[3*index+2] += the_tz;}

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

  void zeroForces() {
    frc[3*index]   = 0.0; 
    frc[3*index+1] = 0.0; 
    frc[3*index+2] = 0.0;

    trq[3*index]   = 0.0; 
    trq[3*index+1] = 0.0; 
    trq[3*index+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[3*index];} 
  double getTy( void ) { return trq[3*index+1]; }
  double getTz( void ) { return trq[3*index+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:	143
Committed:	Thu Oct 17 21:58:55 2002 UTC (21 years, 9 months ago) by mmeineke
File size:	6665 byte(s)
Log Message:	Changing internal storage of positions, torqes, forces, velocities, etc.
#	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	10	}
16	mmeineke	117	virtual ~Atom() {}
17	mmeineke	143
18			static void createArrays (int nElements) {
19			pos = new double[nElements*3];
20			vel = new double[nElements*3];
21			frc = new double[nElements*3];
22			trq = new double[nElements*3];
23			}
24			static void destroyArrays(void) {
25			delete[] pos;
26			delete[] vel;
27			delete[] frc;
28			delete[] trq;
29			}
30	mmeineke	10
31	mmeineke	143	double getX() const {return pos[3*index];}
32			double getY() const {return pos[3*index+1];}
33			double getZ() const {return pos[3*index+2];}
34			void setX(double x) {pos[3*index] = x;}
35			void setY(double y) {pos[3*index+1] = y;}
36			void setZ(double z) {pos[3*index+2] = z;}
37	mmeineke	10
38	mmeineke	143	double get_vx() const {return vel[3*index];}
39			double get_vy() const {return vel[3*index+1];}
40			double get_vz() const {return vel[3*index+2];}
41			void set_vx(double vx) {vel[3*index] = vx;}
42			void set_vy(double vy) {vel[3*index+1] = vy;}
43			void set_vz(double vz) {vel[3*index+2] = vz;}
44	mmeineke	10
45	mmeineke	143	double getFx() const {return frc[3*index];}
46			double getFy() const {return frc[3*index+1];}
47			double getFz() const {return frc[3*index+2];}
48			void addFx(double add) {frc[3*index] += add;}
49			void addFy(double add) {frc[3*index+1] += add;}
50			void addFz(double add) {frc[3*index+2] += add;}
51	mmeineke	10	virtual void zeroForces() = 0;
52
53			double getMass() const {return c_mass;}
54			void setMass(double mass) {c_mass = mass;}
55
56			double getSigma() const {return c_sigma;}
57			void setSigma(double sigma) {c_sigma = sigma;}
58
59			double getEpslon() const {return c_epslon;}
60			void setEpslon(double epslon) {c_epslon = epslon;}
61
62			double getCovalent() const {return c_covalent;}
63			void setCovalent(double covalent) {c_covalent = covalent;}
64
65	mmeineke	143	int getIndex() const {return index;}
66			void setIndex(int theIndex) {index = theIndex;}
67	mmeineke	10
68			char *getType() {return c_name;}
69			void setType(char * name) {strcpy(c_name,name);}
70
71			void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
72			int get_n_hydrogens() const {return c_n_hyd;}
73
74			void setHasDipole( int value ) { has_dipole = value; }
75	chuckv	134	int hasDipole( void ) { return has_dipole; }
76	mmeineke	10
77			void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
78	chuckv	134	int isLJ( void ) { return is_LJ; }
79	mmeineke	10
80			void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
81	chuckv	134	int isVDW( void ) { return is_VDW; }
82	mmeineke	10
83			virtual int isDirectional( void ) = 0;
84
85			protected:
86
87	mmeineke	143	static double* pos; // the position array
88			static double* vel; // the velocity array
89			static double* frc; // the forc array
90			static double* trq; // the torque vector ( space fixed )
91
92	mmeineke	10	double c_mass; /* the mass of the atom in amu */
93			double c_sigma; /* the sigma parameter for van der walls interactions */
94			double c_epslon; /* the esplon parameter for VDW interactions */
95			double c_covalent; // The covalent radius of the atom.
96
97	mmeineke	143	int index; /* set the atom's index */
98	mmeineke	10
99			char c_name[100]; /* it's name */
100
101			int c_n_hyd; // the number of hydrogens bonded to the atom
102
103	chuckv	134	int has_dipole; // dipole boolean
104			int is_VDW; // VDW boolean
105			int is_LJ; // LJ boolean
106	mmeineke	10
107			};
108
109			class GeneralAtom : public Atom{
110
111			public:
112	mmeineke	143	GeneralAtom(int theIndex): Atom(theIndex){}
113	mmeineke	117	virtual ~GeneralAtom(){}
114	mmeineke	10
115			int isDirectional( void ){ return 0; }
116			void zeroForces() {
117	mmeineke	143	frc[3*index] = 0.0;
118			frc[3*index+1] = 0.0;
119			frc[3*index+2] = 0.0;
120	mmeineke	10	}
121			};
122
123			class DirectionalAtom : public Atom {
124
125			public:
126	mmeineke	143	DirectionalAtom(int theIndex) : Atom(theIndex)
127			{
128			ssdIdentity = 0;
129			}
130	mmeineke	117	virtual ~DirectionalAtom() {}
131	mmeineke	10
132	mmeineke	143	static void createDArrays(int nElements){
133			trq = new double[nElements*3];
134			}
135			static void destroyDArrays(void){
136			delete[] trq;
137			}
138
139	mmeineke	10	int isDirectional(void) { return 1; }
140
141			void setSSD( int value) { ssdIdentity = value; }
142			int isSSD(void) {return ssdIdentity; }
143
144			void setA( double the_A[3][3] );
145
146			void setI( double the_I[3][3] );
147
148			void setQ( double the_q[4] );
149
150			void setEuler( double phi, double theta, double psi );
151
152			void setSUx( double the_sux ) { sux = the_sux; }
153			void setSUy( double the_suy ) { suy = the_suy; }
154			void setSUz( double the_suz ) { suz = the_suz; }
155
156			void setJx( double the_jx ) { jx = the_jx; }
157			void setJy( double the_jy ) { jy = the_jy; }
158			void setJz( double the_jz ) { jz = the_jz; }
159
160	mmeineke	143	void addTx( double the_tx ) { trq[3*index] += the_tx;}
161			void addTy( double the_ty ) { trq[3*index+1] += the_ty;}
162			void addTz( double the_tz ) { trq[3*index+2] += the_tz;}
163	mmeineke	10
164			void setMu( double the_mu ) { mu = the_mu; }
165
166			void zeroForces() {
167	mmeineke	143	frc[3*index] = 0.0;
168			frc[3*index+1] = 0.0;
169			frc[3*index+2] = 0.0;
170
171			trq[3*index] = 0.0;
172			trq[3*index+1] = 0.0;
173			trq[3*index+2] = 0.0;
174	mmeineke	10	}
175
176			double getAxx( void ) { return Axx; }
177			double getAxy( void ) { return Axy; }
178			double getAxz( void ) { return Axz; }
179
180			double getAyx( void ) { return Ayx; }
181			double getAyy( void ) { return Ayy; }
182			double getAyz( void ) { return Ayz; }
183
184			double getAzx( void ) { return Azx; }
185			double getAzy( void ) { return Azy; }
186			double getAzz( void ) { return Azz; }
187
188	mmeineke	30	void getA( double the_A[3][3] ); // get the full rotation matrix
189
190	mmeineke	10	double getSUx( void ) { return sux; }
191			double getSUy( void ) { return suy; }
192			double getSUz( void ) { return suz; }
193
194			void getU( double the_u[3] ); // get the unit vector
195			void getQ( double the_q[4] ); // get the quanternions
196
197			double getJx( void ) { return jx; }
198			double getJy( void ) { return jy; }
199			double getJz( void ) { return jz; }
200
201	mmeineke	143	double getTx( void ) { return trq[3*index];}
202			double getTy( void ) { return trq[3*index+1]; }
203			double getTz( void ) { return trq[3*index+2]; }
204	mmeineke	10
205			double getIxx( void ) { return Ixx; }
206			double getIxy( void ) { return Ixy; }
207			double getIxz( void ) { return Ixz; }
208
209			double getIyx( void ) { return Iyx; }
210			double getIyy( void ) { return Iyy; }
211			double getIyz( void ) { return Iyz; }
212
213			double getIzx( void ) { return Izx; }
214			double getIzy( void ) { return Izy; }
215			double getIzz( void ) { return Izz; }
216
217			double getMu( void ) { return mu; }
218
219			void lab2Body( double r[3] );
220			void body2Lab( double r[3] );
221
222			private:
223	mmeineke	143	int dIndex;
224	mmeineke	10
225	chuckv	134	double Axx, Axy, Axz; // the rotational matrix
226	mmeineke	10	double Ayx, Ayy, Ayz;
227			double Azx, Azy, Azz;
228
229	mmeineke	143	double sux, suy, suz; // the standard unit vector ( body fixed )
230			double jx, jy, jz; // the angular momentum vector ( body fixed )
231	mmeineke	10
232	mmeineke	143	double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
233	mmeineke	10	double Iyx, Iyy, Iyz;
234			double Izx, Izy, Izz;
235
236			double mu; // the magnitude of the dipole moment
237
238			int ssdIdentity; // boolean of whether atom is ssd
239
240			};
241
242			#endif