OOPSE/libmdtools/Atom.hpp

#ifndef _ATOM_H_
#define _ATOM_H_

#include <string.h>
#include <stdlib.h>
#include <iostream>

#include "SimState.hpp"

class Atom{
public:

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

  virtual void setCoords(void);

  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 setVDW( 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; }

  void setCharged( void ) { is_charged = 1; }
  int isCharged( void ) { return is_charged; }

  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
  int is_charged;   // isCharge 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] );


  // Four functions added for derivatives with respect to Euler Angles:
  // (Needed for minimization routines):

  void getGrad(double gradient[6] );
  void getEulerAngles( double myEuler[3] );

  double max(double x, double y);
  double min(double x, double y);
  

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:	999
Committed:	Fri Jan 30 15:01:09 2004 UTC (20 years, 5 months ago) by chrisfen
File size:	6338 byte(s)
Log Message:	Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser. This involved changes to WATER.cpp and ForceFields amoung other files. One important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on the next commit...
#	Content
1	#ifndef _ATOM_H_
2	#define _ATOM_H_
3
4	#include <string.h>
5	#include <stdlib.h>
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 getPos( double theP[3] );
19	void setPos( double theP[3] );
20
21	void getVel( double theV[3] );
22	void setVel( double theV[3] );
23
24	void getFrc( double theF[3] );
25	void addFrc( double theF[3] );
26
27	virtual void zeroForces() = 0;
28
29	double getMass() const {return c_mass;}
30	void setMass(double mass) {c_mass = mass;}
31
32	double getEamRcut() const {return myEamRcut;}
33	void setEamRcut(double eamRcut) {myEamRcut = eamRcut;}
34
35	double getSigma() const {return c_sigma;}
36	void setSigma(double sigma) {c_sigma = sigma;}
37
38	double getEpslon() const {return c_epslon;}
39	void setEpslon(double epslon) {c_epslon = epslon;}
40
41	double getCovalent() const {return c_covalent;}
42	void setCovalent(double covalent) {c_covalent = covalent;}
43
44	int getIndex() const {return index;}
45	void setIndex(int theIndex);
46	char *getType() {return c_name;}
47	void setType(char * name) {strcpy(c_name,name);}
48
49	int getIdent( void ) { return ident; }
50	void setIdent( int info ) { ident = info; }
51
52	#ifdef IS_MPI
53	int getGlobalIndex( void ) { return myGlobalIndex; }
54	void setGlobalIndex( int info ) { myGlobalIndex = info; }
55	#endif // is_mpi
56
57	void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
58	int get_n_hydrogens() const {return c_n_hyd;}
59
60	void setHasDipole( int value ) { has_dipole = value; }
61	int hasDipole( void ) { return has_dipole; }
62
63	void setLJ( void ) { is_LJ = 1; is_VDW = 0; }
64	int isLJ( void ) { return is_LJ; }
65
66	void setVDW( void ) { is_VDW = 1; is_LJ = 0; }
67	int isVDW( void ) { return is_VDW; }
68
69	void setEAM( void ) { is_EAM = 1; }
70	int isEAM( void ) { return is_EAM; }
71
72	void setCharged( void ) { is_charged = 1; }
73	int isCharged( void ) { return is_charged; }
74
75	virtual int isDirectional( void ) = 0;
76
77
78	protected:
79
80	SimState* myConfig;
81
82	double* pos; // the position array
83	double* vel; // the velocity array
84	double* frc; // the forc array
85	double* trq; // the torque vector ( space fixed )
86	double* Amat; // the rotation matrix
87	double* mu; // the array of dipole moments
88	double* ul; // the lab frame unit directional vector
89
90	double c_mass; /* the mass of the atom in amu */
91	double c_sigma; /* the sigma parameter for van der walls interactions */
92	double c_epslon; /* the esplon parameter for VDW interactions */
93	double c_covalent; // The covalent radius of the atom.
94
95	double myEamRcut; // Atom rcut for eam defined by the forcefield.
96
97	int index; /* set the atom's index */
98	int offset; // the atom's offset in the storage array
99	int offsetX, offsetY, offsetZ;
100
101	int Axx, Axy, Axz; // the rotational matrix indices
102	int Ayx, Ayy, Ayz;
103	int Azx, Azy, Azz;
104
105	char c_name[100]; /* it's name */
106	int ident; // it's unique numeric identity.
107
108	int c_n_hyd; // the number of hydrogens bonded to the atom
109
110	int has_dipole; // dipole boolean
111	int is_VDW; // VDW boolean
112	int is_LJ; // LJ boolean
113	int is_EAM; // EAM boolean
114	int is_charged; // isCharge boolean
115
116	bool hasCoords;
117
118	#ifdef IS_MPI
119	int myGlobalIndex;
120	#endif
121
122	};
123
124	class GeneralAtom : public Atom{
125
126	public:
127	GeneralAtom(int theIndex, SimState* theConfig): Atom(theIndex, theConfig){}
128	virtual ~GeneralAtom(){}
129
130	int isDirectional( void ){ return 0; }
131	void zeroForces( void );
132	};
133
134	class DirectionalAtom : public Atom {
135
136	public:
137	DirectionalAtom(int theIndex, SimState* theConfig) : Atom(theIndex,
138	theConfig)
139	{
140	ssdIdentity = 0;
141	sux = 0.0;
142	suy = 0.0;
143	suz = 0.0;
144	myMu = 0.0;
145	}
146	virtual ~DirectionalAtom() {}
147
148	virtual void setCoords(void);
149
150	void printAmatIndex( void );
151
152	int isDirectional(void) { return 1; }
153
154	void setSSD( int value) { ssdIdentity = value; }
155	int isSSD(void) {return ssdIdentity; }
156
157
158	void setEuler( double phi, double theta, double psi );
159
160	double getSUx( void ) { return sux; }
161	double getSUy( void ) { return suy; }
162	double getSUz( void ) { return suz; }
163
164	void setSUx( double the_sux ) { sux = the_sux; }
165	void setSUy( double the_suy ) { suy = the_suy; }
166	void setSUz( double the_suz ) { suz = the_suz; }
167
168	void zeroForces();
169
170	void getA( double the_A[3][3] ); // get the full rotation matrix
171	void setA( double the_A[3][3] );
172
173	void getU( double the_u[3] ); // get the unit vetor
174	void updateU( void );
175
176	void getQ( double the_q[4] ); // get the quanternions
177	void setQ( double the_q[4] );
178
179	void getJ( double theJ[3] );
180	void setJ( double theJ[3] );
181
182	double getJx( void ) { return jx; }
183	double getJy( void ) { return jy; }
184	double getJz( void ) { return jz; }
185
186	void setJx( double the_jx ) { jx = the_jx; }
187	void setJy( double the_jy ) { jy = the_jy; }
188	void setJz( double the_jz ) { jz = the_jz; }
189
190	void getTrq( double theT[3] );
191	void addTrq( double theT[3] );
192
193	// double getTx( void ) { return trq[offsetX];}
194	// double getTy( void ) { return trq[offsetY]; }
195	// double getTz( void ) { return trq[offsetZ]; }
196
197	void setI( double the_I[3][3] );
198	void getI( double the_I[3][3] );
199
200	double getIxx( void ) { return Ixx; }
201	double getIxy( void ) { return Ixy; }
202	double getIxz( void ) { return Ixz; }
203
204	double getIyx( void ) { return Iyx; }
205	double getIyy( void ) { return Iyy; }
206	double getIyz( void ) { return Iyz; }
207
208	double getIzx( void ) { return Izx; }
209	double getIzy( void ) { return Izy; }
210	double getIzz( void ) { return Izz; }
211
212	double getMu( void );
213	void setMu( double the_mu );
214
215	void lab2Body( double r[3] );
216	void body2Lab( double r[3] );
217
218
219	// Four functions added for derivatives with respect to Euler Angles:
220	// (Needed for minimization routines):
221
222	void getGrad(double gradient[6] );
223	void getEulerAngles( double myEuler[3] );
224
225	double max(double x, double y);
226	double min(double x, double y);
227
228
229	private:
230	int dIndex;
231
232	double myMu;
233
234	double sux, suy, suz; // the standard unit vector ( body fixed )
235	double jx, jy, jz; // the angular momentum vector ( body fixed )
236
237	double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
238	double Iyx, Iyy, Iyz;
239	double Izx, Izy, Izz;
240
241	int ssdIdentity; // boolean of whether atom is ssd
242
243	};
244
245	#endif