mdtools/headers/Atom.hpp

#ifndef _ATOM_H_
#define _ATOM_H_

#include <cstring>
#include <iostream>

class Atom{
public:
  Atom() {
    c_n_hyd = 0; 
    has_dipole = 0;
    is_VDW = 0;
    is_LJ = 0;
  }
  virtual ~Atom() {}
  
  double getX() const {return c_x;}
  double getY() const {return c_y;}
  double getZ() const {return c_z;}
  void setX(double x) {c_x = x;}
  void setY(double y) {c_y = y;}
  void setZ(double z) {c_z = z;}
  
  double get_vx() const {return c_vx;}
  double get_vy() const {return c_vy;}
  double get_vz() const {return c_vz;}
  void set_vx(double vx) {c_vx = vx;}
  void set_vy(double vy) {c_vy = vy;}
  void set_vz(double vz) {c_vz = vz;}
  
  double getFx() const {return c_Fx;}
  double getFy() const {return c_Fy;}
  double getFz() const {return c_Fz;}
  void addFx(double add) {c_Fx += add;}
  void addFy(double add) {c_Fy += add;}
  void addFz(double add) {c_Fz += 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 c_index;}
  void setIndex(int index) {c_index = index;}
  
  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; }
  short int hasDipole( void ) { return has_dipole; }

  void setLJ( void )        { is_LJ = 1; is_VDW = 0; }
  short int isLJ( void )    { return is_LJ; }

  void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
  short int isVDW( void )    { return is_VDW; }

  virtual int isDirectional( void ) = 0;

protected:
  double c_x; /*the atom's position */
  double c_y;
  double c_z;
            
  double c_vx; /*the atom's velocity */
  double c_vy;
  double c_vz;
            
  double c_Fx; /* the atom's forces */
  double c_Fy;
  double c_Fz;
  
  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 c_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 
  
  short int has_dipole; // dipole boolean
  short int is_VDW;    // VDW boolean
  short int is_LJ;    // LJ boolean
  
};

class GeneralAtom : public Atom{

public:
  GeneralAtom(){}
  virtual ~GeneralAtom(){}

  int isDirectional( void ){ return 0; }
  void zeroForces() {
    c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0;
  }
};

class DirectionalAtom : public Atom {
  
public:
  DirectionalAtom() { ssdIdentity = 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 ) { tx += the_tx;}
  void addTy( double the_ty ) { ty += the_ty;}
  void addTz( double the_tz ) { tz += the_tz;}

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

  void zeroForces() {
    c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0;
    tx = 0.0; ty = 0.0; tz = 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 tx; } 
  double getTy( void ) { return ty; }
  double getTz( void ) { return tz; }

  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:

  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 tx, ty, tz; // the torque vector           ( space 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:	117
Committed:	Tue Sep 24 22:10:55 2002 UTC (21 years, 9 months ago) by mmeineke
File size:	5852 byte(s)
Log Message:	fixed allot of warnings, and adde the molecule
#	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			Atom() {
10			c_n_hyd = 0;
11			has_dipole = 0;
12			is_VDW = 0;
13			is_LJ = 0;
14			}
15	mmeineke	117	virtual ~Atom() {}
16	mmeineke	10
17			double getX() const {return c_x;}
18			double getY() const {return c_y;}
19			double getZ() const {return c_z;}
20			void setX(double x) {c_x = x;}
21			void setY(double y) {c_y = y;}
22			void setZ(double z) {c_z = z;}
23
24			double get_vx() const {return c_vx;}
25			double get_vy() const {return c_vy;}
26			double get_vz() const {return c_vz;}
27			void set_vx(double vx) {c_vx = vx;}
28			void set_vy(double vy) {c_vy = vy;}
29			void set_vz(double vz) {c_vz = vz;}
30
31			double getFx() const {return c_Fx;}
32			double getFy() const {return c_Fy;}
33			double getFz() const {return c_Fz;}
34			void addFx(double add) {c_Fx += add;}
35			void addFy(double add) {c_Fy += add;}
36			void addFz(double add) {c_Fz += add;}
37			virtual void zeroForces() = 0;
38
39			double getMass() const {return c_mass;}
40			void setMass(double mass) {c_mass = mass;}
41
42			double getSigma() const {return c_sigma;}
43			void setSigma(double sigma) {c_sigma = sigma;}
44
45			double getEpslon() const {return c_epslon;}
46			void setEpslon(double epslon) {c_epslon = epslon;}
47
48			double getCovalent() const {return c_covalent;}
49			void setCovalent(double covalent) {c_covalent = covalent;}
50
51			int getIndex() const {return c_index;}
52			void setIndex(int index) {c_index = index;}
53
54			char *getType() {return c_name;}
55			void setType(char * name) {strcpy(c_name,name);}
56
57			void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
58			int get_n_hydrogens() const {return c_n_hyd;}
59
60			void setHasDipole( int value ) { has_dipole = value; }
61			short int hasDipole( void ) { return has_dipole; }
62
63			void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
64			short int isLJ( void ) { return is_LJ; }
65
66			void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
67			short int isVDW( void ) { return is_VDW; }
68
69			virtual int isDirectional( void ) = 0;
70
71			protected:
72			double c_x; /the atom's position /
73			double c_y;
74			double c_z;
75
76			double c_vx; /the atom's velocity /
77			double c_vy;
78			double c_vz;
79
80			double c_Fx; /* the atom's forces */
81			double c_Fy;
82			double c_Fz;
83
84			double c_mass; /* the mass of the atom in amu */
85			double c_sigma; /* the sigma parameter for van der walls interactions */
86			double c_epslon; /* the esplon parameter for VDW interactions */
87			double c_covalent; // The covalent radius of the atom.
88
89			int c_index; /* set the atom's index */
90
91			char c_name[100]; /* it's name */
92
93			int c_n_hyd; // the number of hydrogens bonded to the atom
94
95			short int has_dipole; // dipole boolean
96			short int is_VDW; // VDW boolean
97			short int is_LJ; // LJ boolean
98
99			};
100
101			class GeneralAtom : public Atom{
102
103			public:
104			GeneralAtom(){}
105	mmeineke	117	virtual ~GeneralAtom(){}
106	mmeineke	10
107			int isDirectional( void ){ return 0; }
108			void zeroForces() {
109			c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0;
110			}
111			};
112
113			class DirectionalAtom : public Atom {
114
115			public:
116			DirectionalAtom() { ssdIdentity = 0; }
117	mmeineke	117	virtual ~DirectionalAtom() {}
118	mmeineke	10
119			int isDirectional(void) { return 1; }
120
121			void setSSD( int value) { ssdIdentity = value; }
122			int isSSD(void) {return ssdIdentity; }
123
124			void setA( double the_A[3][3] );
125
126			void setI( double the_I[3][3] );
127
128			void setQ( double the_q[4] );
129
130			void setEuler( double phi, double theta, double psi );
131
132			void setSUx( double the_sux ) { sux = the_sux; }
133			void setSUy( double the_suy ) { suy = the_suy; }
134			void setSUz( double the_suz ) { suz = the_suz; }
135
136			void setJx( double the_jx ) { jx = the_jx; }
137			void setJy( double the_jy ) { jy = the_jy; }
138			void setJz( double the_jz ) { jz = the_jz; }
139
140			void addTx( double the_tx ) { tx += the_tx;}
141			void addTy( double the_ty ) { ty += the_ty;}
142			void addTz( double the_tz ) { tz += the_tz;}
143
144			void setMu( double the_mu ) { mu = the_mu; }
145
146			void zeroForces() {
147			c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0;
148			tx = 0.0; ty = 0.0; tz = 0.0;
149			}
150
151			double getAxx( void ) { return Axx; }
152			double getAxy( void ) { return Axy; }
153			double getAxz( void ) { return Axz; }
154
155			double getAyx( void ) { return Ayx; }
156			double getAyy( void ) { return Ayy; }
157			double getAyz( void ) { return Ayz; }
158
159			double getAzx( void ) { return Azx; }
160			double getAzy( void ) { return Azy; }
161			double getAzz( void ) { return Azz; }
162
163	mmeineke	30	void getA( double the_A[3][3] ); // get the full rotation matrix
164
165	mmeineke	10	double getSUx( void ) { return sux; }
166			double getSUy( void ) { return suy; }
167			double getSUz( void ) { return suz; }
168
169			void getU( double the_u[3] ); // get the unit vector
170			void getQ( double the_q[4] ); // get the quanternions
171
172			double getJx( void ) { return jx; }
173			double getJy( void ) { return jy; }
174			double getJz( void ) { return jz; }
175
176			double getTx( void ) { return tx; }
177			double getTy( void ) { return ty; }
178			double getTz( void ) { return tz; }
179
180			double getIxx( void ) { return Ixx; }
181			double getIxy( void ) { return Ixy; }
182			double getIxz( void ) { return Ixz; }
183
184			double getIyx( void ) { return Iyx; }
185			double getIyy( void ) { return Iyy; }
186			double getIyz( void ) { return Iyz; }
187
188			double getIzx( void ) { return Izx; }
189			double getIzy( void ) { return Izy; }
190			double getIzz( void ) { return Izz; }
191
192			double getMu( void ) { return mu; }
193
194			void lab2Body( double r[3] );
195			void body2Lab( double r[3] );
196
197			private:
198
199			double Axx, Axy, Axz;; // the rotational matrix
200			double Ayx, Ayy, Ayz;
201			double Azx, Azy, Azz;
202
203			double sux, suy, suz; // the standard unit vector ( body fixed )
204			double jx, jy, jz; // the angular momentum vector ( body fixed )
205			double tx, ty, tz; // the torque vector ( space fixed )
206
207			double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
208			double Iyx, Iyy, Iyz;
209			double Izx, Izy, Izz;
210
211			double mu; // the magnitude of the dipole moment
212
213			int ssdIdentity; // boolean of whether atom is ssd
214
215			};
216
217			#endif