OOPSE/libmdtools/Atom.hpp

#ifndef _ATOM_H_
#define _ATOM_H_

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

#include "SimState.hpp"

class Atom{
public:

  Atom(int theIndex, SimState* theConfig );
  virtual ~Atom() {} 

  virtual void setCoords(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);

  void getPos( double theP[3] );
  void setPos( double theP[3] );

  void getVel( double theV[3] );
  void setVel( double theV[3] );

  void getFrc( double theF[3] );
  void addFrc( double theF[3] );

  virtual void zeroForces() = 0;

  double getMass() const {return c_mass;}
  void setMass(double mass) {c_mass = mass;}

  double getEamRcut() const {return myEamRcut;}
  void setEamRcut(double eamRcut) {myEamRcut = eamRcut;}
  
  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; }

  void setEAM( void ) { is_EAM = 1; }
  int  isEAM( void ) { return is_EAM; }

  virtual int isDirectional( void ) = 0;


protected:
  
  SimState* myConfig;

  double* pos; // the position array
  double* vel; // the velocity array
  double* frc; // the forc array
  double* trq; // the torque vector  ( space fixed )
  double* Amat; // the rotation matrix
  double* mu;   // the array of dipole moments
  double* ul;   // the lab frame unit directional vector

  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.

  double myEamRcut; // Atom rcut for eam defined by the forcefield.

  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
  int is_EAM; //EAM boolean

  bool hasCoords;

#ifdef IS_MPI
  int myGlobalIndex;
#endif
  
};

class GeneralAtom : public Atom{

public:
  GeneralAtom(int theIndex, SimState* theConfig): Atom(theIndex, theConfig){}
  virtual ~GeneralAtom(){}

  int isDirectional( void ){ return 0; }
  void zeroForces( void );
};

class DirectionalAtom : public Atom {
  
public:
  DirectionalAtom(int theIndex, SimState* theConfig) : Atom(theIndex, 
                                                            theConfig)
  { 
    ssdIdentity = 0; 
    sux = 0.0;
    suy = 0.0;
    suz = 0.0;
    myMu = 0.0;
  }
  virtual ~DirectionalAtom() {}

  virtual void setCoords(void);

  void printAmatIndex( void );

  int isDirectional(void) { return 1; }
  
  void setSSD( int value) { ssdIdentity = value; }
  int isSSD(void) {return ssdIdentity; }

  
  void setEuler( double phi, double theta, double psi );

  double getSUx( void ) { return sux; }
  double getSUy( void ) { return suy; }
  double getSUz( void ) { return suz; }
  
  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 zeroForces();

  void getA( double the_A[3][3] ); // get the full rotation matrix
  void setA( double the_A[3][3] );

  void getU( double the_u[3] ); // get the unit vetor
  void updateU( void );

  void getQ( double the_q[4] ); // get the quanternions
  void setQ( double the_q[4] );
 
  void getJ( double theJ[3] );
  void setJ( double theJ[3] );

  double getJx( void ) { return jx; } 
  double getJy( void ) { return jy; }
  double getJz( void ) { return jz; }

  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 getTrq( double theT[3] );
  void addTrq( double theT[3] );

  //  double getTx( void ) { return trq[offsetX];} 
  //  double getTy( void ) { return trq[offsetY]; }
  //  double getTz( void ) { return trq[offsetZ]; }

  void setI( double the_I[3][3] );
  void getI( double the_I[3][3] );
  
  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 );
  void setMu( double the_mu );

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


private:
  int dIndex;

  double myMu;

  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:	689
Committed:	Tue Aug 12 19:56:49 2003 UTC (20 years, 10 months ago) by tim
File size:	6185 byte(s)
Log Message:	debugging globals
#	Content
1	#ifndef _ATOM_H_
2	#define _ATOM_H_
3
4	#include <cstring>
5	#include <cstdlib>
6	#include <iostream>
7
8	#include "SimState.hpp"
9
10	class Atom{
11	public:
12
13	Atom(int theIndex, SimState* theConfig );
14	virtual ~Atom() {}
15
16	virtual void setCoords(void);
17
18	// void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
19	// double* Atrq, double* AAmat, double* Amu,
20	// double* Aul);
21	// void deleteAtom(int theIndex);
22	// void deleteRange(int startIndex, int stopIndex);
23
24	void getPos( double theP[3] );
25	void setPos( double theP[3] );
26
27	void getVel( double theV[3] );
28	void setVel( double theV[3] );
29
30	void getFrc( double theF[3] );
31	void addFrc( double theF[3] );
32
33	virtual void zeroForces() = 0;
34
35	double getMass() const {return c_mass;}
36	void setMass(double mass) {c_mass = mass;}
37
38	double getEamRcut() const {return myEamRcut;}
39	void setEamRcut(double eamRcut) {myEamRcut = eamRcut;}
40
41	double getSigma() const {return c_sigma;}
42	void setSigma(double sigma) {c_sigma = sigma;}
43
44	double getEpslon() const {return c_epslon;}
45	void setEpslon(double epslon) {c_epslon = epslon;}
46
47	double getCovalent() const {return c_covalent;}
48	void setCovalent(double covalent) {c_covalent = covalent;}
49
50	int getIndex() const {return index;}
51	void setIndex(int theIndex);
52	char *getType() {return c_name;}
53	void setType(char * name) {strcpy(c_name,name);}
54
55	int getIdent( void ) { return ident; }
56	void setIdent( int info ) { ident = info; }
57
58	#ifdef IS_MPI
59	int getGlobalIndex( void ) { return myGlobalIndex; }
60	void setGlobalIndex( int info ) { myGlobalIndex = info; }
61	#endif // is_mpi
62
63	void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
64	int get_n_hydrogens() const {return c_n_hyd;}
65
66	void setHasDipole( int value ) { has_dipole = value; }
67	int hasDipole( void ) { return has_dipole; }
68
69	void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
70	int isLJ( void ) { return is_LJ; }
71
72	void seVDW( void ) { is_VDW = 1; is_LJ = 0; }
73	int isVDW( void ) { return is_VDW; }
74
75	void setEAM( void ) { is_EAM = 1; }
76	int isEAM( void ) { return is_EAM; }
77
78	virtual int isDirectional( void ) = 0;
79
80
81	protected:
82
83	SimState* myConfig;
84
85	double* pos; // the position array
86	double* vel; // the velocity array
87	double* frc; // the forc array
88	double* trq; // the torque vector ( space fixed )
89	double* Amat; // the rotation matrix
90	double* mu; // the array of dipole moments
91	double* ul; // the lab frame unit directional vector
92
93	double c_mass; /* the mass of the atom in amu */
94	double c_sigma; /* the sigma parameter for van der walls interactions */
95	double c_epslon; /* the esplon parameter for VDW interactions */
96	double c_covalent; // The covalent radius of the atom.
97
98	double myEamRcut; // Atom rcut for eam defined by the forcefield.
99
100	int index; /* set the atom's index */
101	int offset; // the atom's offset in the storage array
102	int offsetX, offsetY, offsetZ;
103
104	int Axx, Axy, Axz; // the rotational matrix indices
105	int Ayx, Ayy, Ayz;
106	int Azx, Azy, Azz;
107
108	char c_name[100]; /* it's name */
109	int ident; // it's unique numeric identity.
110
111	int c_n_hyd; // the number of hydrogens bonded to the atom
112
113	int has_dipole; // dipole boolean
114	int is_VDW; // VDW boolean
115	int is_LJ; // LJ boolean
116	int is_EAM; //EAM boolean
117
118	bool hasCoords;
119
120	#ifdef IS_MPI
121	int myGlobalIndex;
122	#endif
123
124	};
125
126	class GeneralAtom : public Atom{
127
128	public:
129	GeneralAtom(int theIndex, SimState* theConfig): Atom(theIndex, theConfig){}
130	virtual ~GeneralAtom(){}
131
132	int isDirectional( void ){ return 0; }
133	void zeroForces( void );
134	};
135
136	class DirectionalAtom : public Atom {
137
138	public:
139	DirectionalAtom(int theIndex, SimState* theConfig) : Atom(theIndex,
140	theConfig)
141	{
142	ssdIdentity = 0;
143	sux = 0.0;
144	suy = 0.0;
145	suz = 0.0;
146	myMu = 0.0;
147	}
148	virtual ~DirectionalAtom() {}
149
150	virtual void setCoords(void);
151
152	void printAmatIndex( void );
153
154	int isDirectional(void) { return 1; }
155
156	void setSSD( int value) { ssdIdentity = value; }
157	int isSSD(void) {return ssdIdentity; }
158
159
160	void setEuler( double phi, double theta, double psi );
161
162	double getSUx( void ) { return sux; }
163	double getSUy( void ) { return suy; }
164	double getSUz( void ) { return suz; }
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 zeroForces();
171
172	void getA( double the_A[3][3] ); // get the full rotation matrix
173	void setA( double the_A[3][3] );
174
175	void getU( double the_u[3] ); // get the unit vetor
176	void updateU( void );
177
178	void getQ( double the_q[4] ); // get the quanternions
179	void setQ( double the_q[4] );
180
181	void getJ( double theJ[3] );
182	void setJ( double theJ[3] );
183
184	double getJx( void ) { return jx; }
185	double getJy( void ) { return jy; }
186	double getJz( void ) { return jz; }
187
188	void setJx( double the_jx ) { jx = the_jx; }
189	void setJy( double the_jy ) { jy = the_jy; }
190	void setJz( double the_jz ) { jz = the_jz; }
191
192	void getTrq( double theT[3] );
193	void addTrq( double theT[3] );
194
195	// double getTx( void ) { return trq[offsetX];}
196	// double getTy( void ) { return trq[offsetY]; }
197	// double getTz( void ) { return trq[offsetZ]; }
198
199	void setI( double the_I[3][3] );
200	void getI( double the_I[3][3] );
201
202	double getIxx( void ) { return Ixx; }
203	double getIxy( void ) { return Ixy; }
204	double getIxz( void ) { return Ixz; }
205
206	double getIyx( void ) { return Iyx; }
207	double getIyy( void ) { return Iyy; }
208	double getIyz( void ) { return Iyz; }
209
210	double getIzx( void ) { return Izx; }
211	double getIzy( void ) { return Izy; }
212	double getIzz( void ) { return Izz; }
213
214	double getMu( void );
215	void setMu( double the_mu );
216
217	void lab2Body( double r[3] );
218	void body2Lab( double r[3] );
219
220
221	private:
222	int dIndex;
223
224	double myMu;
225
226	double sux, suy, suz; // the standard unit vector ( body fixed )
227	double jx, jy, jz; // the angular momentum vector ( body fixed )
228
229	double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
230	double Iyx, Iyy, Iyz;
231	double Izx, Izy, Izz;
232
233	int ssdIdentity; // boolean of whether atom is ssd
234
235	};
236
237	#endif