mdtools/libmdCode/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;
  }

  static double* getPosArray( void ) { return pos; }
  static double* getVelArray( void ) { return vel; }
  static double* getFrcArray( void ) { return frc; }
  static double* getTrqArray( void ) { return 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);}
  
  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;

  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 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; 
  }
  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:	270
Committed:	Fri Feb 14 17:08:46 2003 UTC (21 years, 6 months ago) by mmeineke
File size:	7446 byte(s)
Log Message:	added libmdCode and a couple help scripts
#	User	Rev	Content
1	mmeineke	270	#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			static double* getPosArray( void ) { return pos; }
36			static double* getVelArray( void ) { return vel; }
37			static double* getFrcArray( void ) { return frc; }
38			static double* getTrqArray( void ) { return trq; }
39
40
41			double getX() const {return pos[offsetX];}
42			double getY() const {return pos[offsetY];}
43			double getZ() const {return pos[offsetZ];}
44			void setX(double x) {pos[offsetX] = x;}
45			void setY(double y) {pos[offsetY] = y;}
46			void setZ(double z) {pos[offsetZ] = z;}
47
48			double get_vx() const {return vel[offsetX];}
49			double get_vy() const {return vel[offsetY];}
50			double get_vz() const {return vel[offsetZ];}
51			void set_vx(double vx) {vel[offsetX] = vx;}
52			void set_vy(double vy) {vel[offsetY] = vy;}
53			void set_vz(double vz) {vel[offsetZ] = vz;}
54
55			double getFx() const {return frc[offsetX];}
56			double getFy() const {return frc[offsetY];}
57			double getFz() const {return frc[offsetZ];}
58			void addFx(double add) {frc[offsetX] += add;}
59			void addFy(double add) {frc[offsetY] += add;}
60			void addFz(double add) {frc[offsetZ] += add;}
61			virtual void zeroForces() = 0;
62
63			double getMass() const {return c_mass;}
64			void setMass(double mass) {c_mass = mass;}
65
66			double getSigma() const {return c_sigma;}
67			void setSigma(double sigma) {c_sigma = sigma;}
68
69			double getEpslon() const {return c_epslon;}
70			void setEpslon(double epslon) {c_epslon = epslon;}
71
72			double getCovalent() const {return c_covalent;}
73			void setCovalent(double covalent) {c_covalent = covalent;}
74
75			int getIndex() const {return index;}
76			void setIndex(int theIndex) {
77			index = theIndex;
78			offset = index*3;
79			offsetX = offset;
80			offsetY = offset+1;
81			offsetZ = offset+2;
82			}
83
84			char *getType() {return c_name;}
85			void setType(char * name) {strcpy(c_name,name);}
86
87			int getIdent( void ) { return ident; }
88			void setIdent( int info ) { ident = info; }
89
90			#ifdef IS_MPI
91			int getGlobalIndex( void ) { return myGlobalIndex; }
92			void setGlobalIndex( int info ) { myGlobalIndex = info; }
93			#endif // is_mpi
94
95			void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
96			int get_n_hydrogens() const {return c_n_hyd;}
97
98			void setHasDipole( int value ) { has_dipole = value; }
99			int hasDipole( void ) { return has_dipole; }
100
101			void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
102			int isLJ( void ) { return is_LJ; }
103
104			void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
105			int isVDW( void ) { return is_VDW; }
106
107			virtual int isDirectional( void ) = 0;
108
109			static double* pos; // the position array
110			static double* vel; // the velocity array
111			static double* frc; // the forc array
112			static double* trq; // the torque vector ( space fixed )
113
114			protected:
115
116			double c_mass; /* the mass of the atom in amu */
117			double c_sigma; /* the sigma parameter for van der walls interactions */
118			double c_epslon; /* the esplon parameter for VDW interactions */
119			double c_covalent; // The covalent radius of the atom.
120
121			int index; /* set the atom's index */
122			int offset; // the atom's offset in the storage array
123			int offsetX, offsetY, offsetZ;
124
125			char c_name[100]; /* it's name */
126			int ident; // it's unique numeric identity.
127
128			int c_n_hyd; // the number of hydrogens bonded to the atom
129
130			int has_dipole; // dipole boolean
131			int is_VDW; // VDW boolean
132			int is_LJ; // LJ boolean
133
134			#ifdef IS_MPI
135			int myGlobalIndex;
136			#endif
137
138			};
139
140
141
142			class GeneralAtom : public Atom{
143
144			public:
145			GeneralAtom(int theIndex): Atom(theIndex){}
146			virtual ~GeneralAtom(){}
147
148			int isDirectional( void ){ return 0; }
149			void zeroForces() {
150			frc[offsetX] = 0.0;
151			frc[offsetY] = 0.0;
152			frc[offsetZ] = 0.0;
153			}
154			};
155
156			class DirectionalAtom : public Atom {
157
158			public:
159			DirectionalAtom(int theIndex) : Atom(theIndex)
160			{
161			ssdIdentity = 0;
162			}
163			virtual ~DirectionalAtom() {}
164
165			static void createDArrays(int nElements){
166			trq = new double[nElements*3];
167			}
168			static void destroyDArrays(void){
169			delete[] trq;
170			}
171
172			int isDirectional(void) { return 1; }
173
174			void setSSD( int value) { ssdIdentity = value; }
175			int isSSD(void) {return ssdIdentity; }
176
177			void setA( double the_A[3][3] );
178
179			void setI( double the_I[3][3] );
180
181			void setQ( double the_q[4] );
182
183			void setEuler( double phi, double theta, double psi );
184
185			void setSUx( double the_sux ) { sux = the_sux; }
186			void setSUy( double the_suy ) { suy = the_suy; }
187			void setSUz( double the_suz ) { suz = the_suz; }
188
189			void setJx( double the_jx ) { jx = the_jx; }
190			void setJy( double the_jy ) { jy = the_jy; }
191			void setJz( double the_jz ) { jz = the_jz; }
192
193			void addTx( double the_tx ) { trq[offsetX] += the_tx;}
194			void addTy( double the_ty ) { trq[offsetY] += the_ty;}
195			void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
196
197			void setMu( double the_mu ) { mu = the_mu; }
198
199			void zeroForces() {
200			frc[offsetX] = 0.0;
201			frc[offsetY] = 0.0;
202			frc[offsetZ] = 0.0;
203
204			trq[offsetX] = 0.0;
205			trq[offsetY] = 0.0;
206			trq[offsetZ] = 0.0;
207			}
208
209			double getAxx( void ) { return Axx; }
210			double getAxy( void ) { return Axy; }
211			double getAxz( void ) { return Axz; }
212
213			double getAyx( void ) { return Ayx; }
214			double getAyy( void ) { return Ayy; }
215			double getAyz( void ) { return Ayz; }
216
217			double getAzx( void ) { return Azx; }
218			double getAzy( void ) { return Azy; }
219			double getAzz( void ) { return Azz; }
220
221			void getA( double the_A[3][3] ); // get the full rotation matrix
222
223			double getSUx( void ) { return sux; }
224			double getSUy( void ) { return suy; }
225			double getSUz( void ) { return suz; }
226
227			void getU( double the_u[3] ); // get the unit vector
228			void getQ( double the_q[4] ); // get the quanternions
229
230			double getJx( void ) { return jx; }
231			double getJy( void ) { return jy; }
232			double getJz( void ) { return jz; }
233
234			double getTx( void ) { return trq[offsetX];}
235			double getTy( void ) { return trq[offsetY]; }
236			double getTz( void ) { return trq[offsetZ]; }
237
238			double getIxx( void ) { return Ixx; }
239			double getIxy( void ) { return Ixy; }
240			double getIxz( void ) { return Ixz; }
241
242			double getIyx( void ) { return Iyx; }
243			double getIyy( void ) { return Iyy; }
244			double getIyz( void ) { return Iyz; }
245
246			double getIzx( void ) { return Izx; }
247			double getIzy( void ) { return Izy; }
248			double getIzz( void ) { return Izz; }
249
250			double getMu( void ) { return mu; }
251
252			void lab2Body( double r[3] );
253			void body2Lab( double r[3] );
254
255			private:
256			int dIndex;
257
258			double Axx, Axy, Axz; // the rotational matrix
259			double Ayx, Ayy, Ayz;
260			double Azx, Azy, Azz;
261
262			double sux, suy, suz; // the standard unit vector ( body fixed )
263			double jx, jy, jz; // the angular momentum vector ( body fixed )
264
265			double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
266			double Iyx, Iyy, Iyz;
267			double Izx, Izy, Izz;
268
269			double mu; // the magnitude of the dipole moment
270
271			int ssdIdentity; // boolean of whether atom is ssd
272
273			};
274
275			#endif