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);}

  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[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:	190
Committed:	Tue Nov 26 21:12:04 2002 UTC (21 years, 8 months ago) by mmeineke
File size:	6872 byte(s)
Log Message:	some quick optimizations to the indexing in the storage arrays
#	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
81			void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
82			int get_n_hydrogens() const {return c_n_hyd;}
83
84			void setHasDipole( int value ) { has_dipole = value; }
85	chuckv	134	int hasDipole( void ) { return has_dipole; }
86	mmeineke	10
87			void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
88	chuckv	134	int isLJ( void ) { return is_LJ; }
89	mmeineke	10
90			void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
91	chuckv	134	int isVDW( void ) { return is_VDW; }
92	mmeineke	10
93			virtual int isDirectional( void ) = 0;
94
95	mmeineke	143	static double* pos; // the position array
96			static double* vel; // the velocity array
97			static double* frc; // the forc array
98			static double* trq; // the torque vector ( space fixed )
99
100	mmeineke	184	protected:
101
102	mmeineke	10	double c_mass; /* the mass of the atom in amu */
103			double c_sigma; /* the sigma parameter for van der walls interactions */
104			double c_epslon; /* the esplon parameter for VDW interactions */
105			double c_covalent; // The covalent radius of the atom.
106
107	mmeineke	143	int index; /* set the atom's index */
108	mmeineke	189	int offset; // the atom's offset in the storage array
109	mmeineke	10
110			char c_name[100]; /* it's name */
111
112			int c_n_hyd; // the number of hydrogens bonded to the atom
113
114	chuckv	134	int has_dipole; // dipole boolean
115			int is_VDW; // VDW boolean
116			int is_LJ; // LJ boolean
117	mmeineke	10
118			};
119
120	mmeineke	184
121
122	mmeineke	10	class GeneralAtom : public Atom{
123
124			public:
125	mmeineke	143	GeneralAtom(int theIndex): Atom(theIndex){}
126	mmeineke	117	virtual ~GeneralAtom(){}
127	mmeineke	10
128			int isDirectional( void ){ return 0; }
129			void zeroForces() {
130	mmeineke	190	frc[offsetX] = 0.0;
131			frc[offsetY] = 0.0;
132			frc[offsetZ] = 0.0;
133	mmeineke	10	}
134			};
135
136			class DirectionalAtom : public Atom {
137
138			public:
139	mmeineke	143	DirectionalAtom(int theIndex) : Atom(theIndex)
140			{
141			ssdIdentity = 0;
142			}
143	mmeineke	117	virtual ~DirectionalAtom() {}
144	mmeineke	10
145	mmeineke	143	static void createDArrays(int nElements){
146			trq = new double[nElements*3];
147			}
148			static void destroyDArrays(void){
149			delete[] trq;
150			}
151
152	mmeineke	10	int isDirectional(void) { return 1; }
153
154			void setSSD( int value) { ssdIdentity = value; }
155			int isSSD(void) {return ssdIdentity; }
156
157			void setA( double the_A[3][3] );
158
159			void setI( double the_I[3][3] );
160
161			void setQ( double the_q[4] );
162
163			void setEuler( double phi, double theta, double psi );
164
165			void setSUx( double the_sux ) { sux = the_sux; }
166			void setSUy( double the_suy ) { suy = the_suy; }
167			void setSUz( double the_suz ) { suz = the_suz; }
168
169			void setJx( double the_jx ) { jx = the_jx; }
170			void setJy( double the_jy ) { jy = the_jy; }
171			void setJz( double the_jz ) { jz = the_jz; }
172
173	mmeineke	190	void addTx( double the_tx ) { trq[offsetX] += the_tx;}
174			void addTy( double the_ty ) { trq[offsetY] += the_ty;}
175			void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
176	mmeineke	10
177			void setMu( double the_mu ) { mu = the_mu; }
178
179			void zeroForces() {
180	mmeineke	190	frc[offsetX] = 0.0;
181			frc[offsetY] = 0.0;
182			frc[offsetZ] = 0.0;
183	mmeineke	143
184	mmeineke	190	trq[offsetX] = 0.0;
185			trq[offsetY] = 0.0;
186			trq[offsetZ] = 0.0;
187	mmeineke	10	}
188
189			double getAxx( void ) { return Axx; }
190			double getAxy( void ) { return Axy; }
191			double getAxz( void ) { return Axz; }
192
193			double getAyx( void ) { return Ayx; }
194			double getAyy( void ) { return Ayy; }
195			double getAyz( void ) { return Ayz; }
196
197			double getAzx( void ) { return Azx; }
198			double getAzy( void ) { return Azy; }
199			double getAzz( void ) { return Azz; }
200
201	mmeineke	30	void getA( double the_A[3][3] ); // get the full rotation matrix
202
203	mmeineke	10	double getSUx( void ) { return sux; }
204			double getSUy( void ) { return suy; }
205			double getSUz( void ) { return suz; }
206
207			void getU( double the_u[3] ); // get the unit vector
208			void getQ( double the_q[4] ); // get the quanternions
209
210			double getJx( void ) { return jx; }
211			double getJy( void ) { return jy; }
212			double getJz( void ) { return jz; }
213
214	mmeineke	190	double getTx( void ) { return trq[offsetX];}
215			double getTy( void ) { return trq[offsetY]; }
216			double getTz( void ) { return trq[offsetZ]; }
217	mmeineke	10
218			double getIxx( void ) { return Ixx; }
219			double getIxy( void ) { return Ixy; }
220			double getIxz( void ) { return Ixz; }
221
222			double getIyx( void ) { return Iyx; }
223			double getIyy( void ) { return Iyy; }
224			double getIyz( void ) { return Iyz; }
225
226			double getIzx( void ) { return Izx; }
227			double getIzy( void ) { return Izy; }
228			double getIzz( void ) { return Izz; }
229
230			double getMu( void ) { return mu; }
231
232			void lab2Body( double r[3] );
233			void body2Lab( double r[3] );
234
235			private:
236	mmeineke	143	int dIndex;
237	mmeineke	10
238	chuckv	134	double Axx, Axy, Axz; // the rotational matrix
239	mmeineke	10	double Ayx, Ayy, Ayz;
240			double Azx, Azy, Azz;
241
242	mmeineke	143	double sux, suy, suz; // the standard unit vector ( body fixed )
243			double jx, jy, jz; // the angular momentum vector ( body fixed )
244	mmeineke	10
245	mmeineke	143	double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
246	mmeineke	10	double Iyx, Iyy, Iyz;
247			double Izx, Izy, Izz;
248
249			double mu; // the magnitude of the dipole moment
250
251			int ssdIdentity; // boolean of whether atom is ssd
252
253			};
254
255			#endif