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
  int offsetX, offsetY, offsetZ;

  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:	213
Committed:	Mon Dec 16 21:42:11 2002 UTC (21 years, 6 months ago) by mmeineke
File size:	6905 byte(s)
Log Message:	finishing work on making DumpWriter parrallel
#	Content
1	#ifndef _ATOM_H_
2	#define _ATOM_H_
3
4	#include <cstring>
5	#include <iostream>
6
7	class Atom{
8	public:
9	Atom(int theIndex) {
10	c_n_hyd = 0;
11	has_dipole = 0;
12	is_VDW = 0;
13	is_LJ = 0;
14	index = theIndex;
15	offset = 3 * index;
16	offsetX = offset;
17	offsetY = offset+1;
18	offsetZ = offset+2;
19	}
20	virtual ~Atom() {}
21
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
35	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
42	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
49	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	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	int getIndex() const {return index;}
70	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	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	int hasDipole( void ) { return has_dipole; }
86
87	void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
88	int isLJ( void ) { return is_LJ; }
89
90	void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
91	int isVDW( void ) { return is_VDW; }
92
93	virtual int isDirectional( void ) = 0;
94
95	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	protected:
101
102	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	int index; /* set the atom's index */
108	int offset; // the atom's offset in the storage array
109	int offsetX, offsetY, offsetZ;
110
111	char c_name[100]; /* it's name */
112
113	int c_n_hyd; // the number of hydrogens bonded to the atom
114
115	int has_dipole; // dipole boolean
116	int is_VDW; // VDW boolean
117	int is_LJ; // LJ boolean
118
119	};
120
121
122
123	class GeneralAtom : public Atom{
124
125	public:
126	GeneralAtom(int theIndex): Atom(theIndex){}
127	virtual ~GeneralAtom(){}
128
129	int isDirectional( void ){ return 0; }
130	void zeroForces() {
131	frc[offsetX] = 0.0;
132	frc[offsetY] = 0.0;
133	frc[offsetZ] = 0.0;
134	}
135	};
136
137	class DirectionalAtom : public Atom {
138
139	public:
140	DirectionalAtom(int theIndex) : Atom(theIndex)
141	{
142	ssdIdentity = 0;
143	}
144	virtual ~DirectionalAtom() {}
145
146	static void createDArrays(int nElements){
147	trq = new double[nElements*3];
148	}
149	static void destroyDArrays(void){
150	delete[] trq;
151	}
152
153	int isDirectional(void) { return 1; }
154
155	void setSSD( int value) { ssdIdentity = value; }
156	int isSSD(void) {return ssdIdentity; }
157
158	void setA( double the_A[3][3] );
159
160	void setI( double the_I[3][3] );
161
162	void setQ( double the_q[4] );
163
164	void setEuler( double phi, double theta, double psi );
165
166	void setSUx( double the_sux ) { sux = the_sux; }
167	void setSUy( double the_suy ) { suy = the_suy; }
168	void setSUz( double the_suz ) { suz = the_suz; }
169
170	void setJx( double the_jx ) { jx = the_jx; }
171	void setJy( double the_jy ) { jy = the_jy; }
172	void setJz( double the_jz ) { jz = the_jz; }
173
174	void addTx( double the_tx ) { trq[offsetX] += the_tx;}
175	void addTy( double the_ty ) { trq[offsetY] += the_ty;}
176	void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
177
178	void setMu( double the_mu ) { mu = the_mu; }
179
180	void zeroForces() {
181	frc[offsetX] = 0.0;
182	frc[offsetY] = 0.0;
183	frc[offsetZ] = 0.0;
184
185	trq[offsetX] = 0.0;
186	trq[offsetY] = 0.0;
187	trq[offsetZ] = 0.0;
188	}
189
190	double getAxx( void ) { return Axx; }
191	double getAxy( void ) { return Axy; }
192	double getAxz( void ) { return Axz; }
193
194	double getAyx( void ) { return Ayx; }
195	double getAyy( void ) { return Ayy; }
196	double getAyz( void ) { return Ayz; }
197
198	double getAzx( void ) { return Azx; }
199	double getAzy( void ) { return Azy; }
200	double getAzz( void ) { return Azz; }
201
202	void getA( double the_A[3][3] ); // get the full rotation matrix
203
204	double getSUx( void ) { return sux; }
205	double getSUy( void ) { return suy; }
206	double getSUz( void ) { return suz; }
207
208	void getU( double the_u[3] ); // get the unit vector
209	void getQ( double the_q[4] ); // get the quanternions
210
211	double getJx( void ) { return jx; }
212	double getJy( void ) { return jy; }
213	double getJz( void ) { return jz; }
214
215	double getTx( void ) { return trq[offsetX];}
216	double getTy( void ) { return trq[offsetY]; }
217	double getTz( void ) { return trq[offsetZ]; }
218
219	double getIxx( void ) { return Ixx; }
220	double getIxy( void ) { return Ixy; }
221	double getIxz( void ) { return Ixz; }
222
223	double getIyx( void ) { return Iyx; }
224	double getIyy( void ) { return Iyy; }
225	double getIyz( void ) { return Iyz; }
226
227	double getIzx( void ) { return Izx; }
228	double getIzy( void ) { return Izy; }
229	double getIzz( void ) { return Izz; }
230
231	double getMu( void ) { return mu; }
232
233	void lab2Body( double r[3] );
234	void body2Lab( double r[3] );
235
236	private:
237	int dIndex;
238
239	double Axx, Axy, Axz; // the rotational matrix
240	double Ayx, Ayy, Ayz;
241	double Azx, Azy, Azz;
242
243	double sux, suy, suz; // the standard unit vector ( body fixed )
244	double jx, jy, jz; // the angular momentum vector ( body fixed )
245
246	double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
247	double Iyx, Iyy, Iyz;
248	double Izx, Izy, Izz;
249
250	double mu; // the magnitude of the dipole moment
251
252	int ssdIdentity; // boolean of whether atom is ssd
253
254	};
255
256	#endif