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
#	Content
1	#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	Atom(int theIndex);
12	virtual ~Atom() {}
13
14	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
23	static void createArrays (int the_nElements);
24	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
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	void setIndex(int theIndex);
75	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	void printAmatIndex( void );
158
159	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