OOPSE/libmdtools/Atom.hpp

#ifndef _ATOM_H_
#define _ATOM_H_

#include <cstring>
#include <cstdlib>
#include <iostream>

class Atom{
public:

  Atom(int theIndex);
  virtual ~Atom() {} 

  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 )
  static double* Amat; // the rotation matrix
  static double* mu; // the dipole moment array
  static double* ul; // the lab frame unit directional vector
  static int nElements;

  static void createArrays (int the_nElements);
  static void destroyArrays(void);
  void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, 
                double* Atrq, double* AAmat, double* Amu, 
                double* Aul);
  void deleteAtom(int theIndex);
  void deleteRange(int startIndex, int stopIndex);

  static double* getPosArray( void ) { return pos; }
  static double* getVelArray( void ) { return vel; }
  static double* getFrcArray( void ) { return frc; }
  static double* getTrqArray( void ) { return trq; }
  static double* getAmatArray( void ) { return Amat; }
  static double* getMuArray( void ) { return mu; }
  static double* getUlArray( void ) { return ul; }
  
  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);
  char *getType() {return c_name;}
  void setType(char * name) {strcpy(c_name,name);}
  
  int getIdent( void ) { return ident; }
  void setIdent( int info ) { ident = info; }

#ifdef IS_MPI
  int getGlobalIndex( void ) { return myGlobalIndex; }
  void setGlobalIndex( int info ) { myGlobalIndex = info; }
#endif // is_mpi

  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:
  
  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;

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

  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

#ifdef IS_MPI
  int myGlobalIndex;
#endif
  
};

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; 
    sux = 0.0;
    suy = 0.0;
    suz = 0.0;
  }
  virtual ~DirectionalAtom() {}

  void printAmatIndex( void );

  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 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;
  }

  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 vetor
  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[index]; }
  void setMu( double the_mu ) { mu[index] = the_mu; }

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

private:
  int dIndex;

  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;

  int ssdIdentity; // boolean of whether atom is ssd

};

#endif
Revision:	597
Committed:	Mon Jul 14 21:28:54 2003 UTC (20 years, 11 months ago) by mmeineke
File size:	7048 byte(s)
Log Message:	found a bug. Unit vectors were not being updated
#	User	Rev	Content
1	mmeineke	377	#ifndef _ATOM_H_
2			#define _ATOM_H_
3
4			#include <cstring>
5			#include <cstdlib>
6			#include <iostream>
7
8			class Atom{
9			public:
10
11	gezelter	409	Atom(int theIndex);
12			virtual ~Atom() {}
13	mmeineke	377
14	gezelter	409	static double* pos; // the position array
15			static double* vel; // the velocity array
16			static double* frc; // the forc array
17			static double* trq; // the torque vector ( space fixed )
18			static double* Amat; // the rotation matrix
19			static double* mu; // the dipole moment array
20			static double* ul; // the lab frame unit directional vector
21			static int nElements;
22	mmeineke	377
23	mmeineke	413	static void createArrays (int the_nElements);
24	gezelter	409	static void destroyArrays(void);
25			void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
26			double* Atrq, double* AAmat, double* Amu,
27			double* Aul);
28			void deleteAtom(int theIndex);
29			void deleteRange(int startIndex, int stopIndex);
30	mmeineke	377
31			static double* getPosArray( void ) { return pos; }
32			static double* getVelArray( void ) { return vel; }
33			static double* getFrcArray( void ) { return frc; }
34			static double* getTrqArray( void ) { return trq; }
35			static double* getAmatArray( void ) { return Amat; }
36			static double* getMuArray( void ) { return mu; }
37			static double* getUlArray( void ) { return ul; }
38
39			double getX() const {return pos[offsetX];}
40			double getY() const {return pos[offsetY];}
41			double getZ() const {return pos[offsetZ];}
42			void setX(double x) {pos[offsetX] = x;}
43			void setY(double y) {pos[offsetY] = y;}
44			void setZ(double z) {pos[offsetZ] = z;}
45
46			double get_vx() const {return vel[offsetX];}
47			double get_vy() const {return vel[offsetY];}
48			double get_vz() const {return vel[offsetZ];}
49			void set_vx(double vx) {vel[offsetX] = vx;}
50			void set_vy(double vy) {vel[offsetY] = vy;}
51			void set_vz(double vz) {vel[offsetZ] = vz;}
52
53			double getFx() const {return frc[offsetX];}
54			double getFy() const {return frc[offsetY];}
55			double getFz() const {return frc[offsetZ];}
56			void addFx(double add) {frc[offsetX] += add;}
57			void addFy(double add) {frc[offsetY] += add;}
58			void addFz(double add) {frc[offsetZ] += add;}
59			virtual void zeroForces() = 0;
60
61			double getMass() const {return c_mass;}
62			void setMass(double mass) {c_mass = mass;}
63
64			double getSigma() const {return c_sigma;}
65			void setSigma(double sigma) {c_sigma = sigma;}
66
67			double getEpslon() const {return c_epslon;}
68			void setEpslon(double epslon) {c_epslon = epslon;}
69
70			double getCovalent() const {return c_covalent;}
71			void setCovalent(double covalent) {c_covalent = covalent;}
72
73			int getIndex() const {return index;}
74	gezelter	409	void setIndex(int theIndex);
75	mmeineke	377	char *getType() {return c_name;}
76			void setType(char * name) {strcpy(c_name,name);}
77
78			int getIdent( void ) { return ident; }
79			void setIdent( int info ) { ident = info; }
80
81			#ifdef IS_MPI
82			int getGlobalIndex( void ) { return myGlobalIndex; }
83			void setGlobalIndex( int info ) { myGlobalIndex = info; }
84			#endif // is_mpi
85
86			void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
87			int get_n_hydrogens() const {return c_n_hyd;}
88
89			void setHasDipole( int value ) { has_dipole = value; }
90			int hasDipole( void ) { return has_dipole; }
91
92			void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
93			int isLJ( void ) { return is_LJ; }
94
95			void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
96			int isVDW( void ) { return is_VDW; }
97
98			virtual int isDirectional( void ) = 0;
99
100
101			protected:
102
103			double c_mass; /* the mass of the atom in amu */
104			double c_sigma; /* the sigma parameter for van der walls interactions */
105			double c_epslon; /* the esplon parameter for VDW interactions */
106			double c_covalent; // The covalent radius of the atom.
107
108			int index; /* set the atom's index */
109			int offset; // the atom's offset in the storage array
110			int offsetX, offsetY, offsetZ;
111
112			int Axx, Axy, Axz; // the rotational matrix indices
113			int Ayx, Ayy, Ayz;
114			int Azx, Azy, Azz;
115
116			char c_name[100]; /* it's name */
117			int ident; // it's unique numeric identity.
118
119			int c_n_hyd; // the number of hydrogens bonded to the atom
120
121			int has_dipole; // dipole boolean
122			int is_VDW; // VDW boolean
123			int is_LJ; // LJ boolean
124
125			#ifdef IS_MPI
126			int myGlobalIndex;
127			#endif
128
129			};
130
131			class GeneralAtom : public Atom{
132
133			public:
134			GeneralAtom(int theIndex): Atom(theIndex){}
135			virtual ~GeneralAtom(){}
136
137			int isDirectional( void ){ return 0; }
138			void zeroForces() {
139			frc[offsetX] = 0.0;
140			frc[offsetY] = 0.0;
141			frc[offsetZ] = 0.0;
142			}
143			};
144
145			class DirectionalAtom : public Atom {
146
147			public:
148			DirectionalAtom(int theIndex) : Atom(theIndex)
149			{
150			ssdIdentity = 0;
151			sux = 0.0;
152			suy = 0.0;
153			suz = 0.0;
154			}
155			virtual ~DirectionalAtom() {}
156
157	mmeineke	597	void printAmatIndex( void );
158
159	mmeineke	377	int isDirectional(void) { return 1; }
160
161			void setSSD( int value) { ssdIdentity = value; }
162			int isSSD(void) {return ssdIdentity; }
163
164			void setA( double the_A[3][3] );
165
166			void setI( double the_I[3][3] );
167
168			void setQ( double the_q[4] );
169
170			void setEuler( double phi, double theta, double psi );
171
172			void setSUx( double the_sux ) { sux = the_sux; }
173			void setSUy( double the_suy ) { suy = the_suy; }
174			void setSUz( double the_suz ) { suz = the_suz; }
175
176			void setJx( double the_jx ) { jx = the_jx; }
177			void setJy( double the_jy ) { jy = the_jy; }
178			void setJz( double the_jz ) { jz = the_jz; }
179
180			void addTx( double the_tx ) { trq[offsetX] += the_tx;}
181			void addTy( double the_ty ) { trq[offsetY] += the_ty;}
182			void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
183
184			void zeroForces() {
185			frc[offsetX] = 0.0;
186			frc[offsetY] = 0.0;
187			frc[offsetZ] = 0.0;
188
189			trq[offsetX] = 0.0;
190			trq[offsetY] = 0.0;
191			trq[offsetZ] = 0.0;
192			}
193
194			void getA( double the_A[3][3] ); // get the full rotation matrix
195
196			double getSUx( void ) { return sux; }
197			double getSUy( void ) { return suy; }
198			double getSUz( void ) { return suz; }
199
200			void getU( double the_u[3] ); // get the unit vetor
201			void getQ( double the_q[4] ); // get the quanternions
202
203			double getJx( void ) { return jx; }
204			double getJy( void ) { return jy; }
205			double getJz( void ) { return jz; }
206
207			double getTx( void ) { return trq[offsetX];}
208			double getTy( void ) { return trq[offsetY]; }
209			double getTz( void ) { return trq[offsetZ]; }
210
211			double getIxx( void ) { return Ixx; }
212			double getIxy( void ) { return Ixy; }
213			double getIxz( void ) { return Ixz; }
214
215			double getIyx( void ) { return Iyx; }
216			double getIyy( void ) { return Iyy; }
217			double getIyz( void ) { return Iyz; }
218
219			double getIzx( void ) { return Izx; }
220			double getIzy( void ) { return Izy; }
221			double getIzz( void ) { return Izz; }
222
223			double getMu( void ) { return mu[index]; }
224			void setMu( double the_mu ) { mu[index] = the_mu; }
225
226			void lab2Body( double r[3] );
227			void body2Lab( double r[3] );
228			void updateU( void );
229
230			private:
231			int dIndex;
232
233			double sux, suy, suz; // the standard unit vector ( body fixed )
234			double jx, jy, jz; // the angular momentum vector ( body fixed )
235
236			double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
237			double Iyx, Iyy, Iyz;
238			double Izx, Izy, Izz;
239
240			int ssdIdentity; // boolean of whether atom is ssd
241
242			};
243
244			#endif