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root/group/trunk/OOPSE/libmdtools/Atom.hpp
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Comparing trunk/OOPSE/libmdtools/Atom.hpp (file contents):
Revision 631 by chuckv, Thu Jul 17 19:25:51 2003 UTC vs.
Revision 829 by gezelter, Tue Oct 28 16:03:37 2003 UTC

# Line 1 | Line 1
1   #ifndef _ATOM_H_
2   #define _ATOM_H_
3  
4 < #include <cstring>
5 < #include <cstdlib>
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);
13 >  Atom(int theIndex, SimState* theConfig );
14    virtual ~Atom() {}
15  
16 <  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;
16 >  virtual void setCoords(void);
17  
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 –  
18    void getPos( double theP[3] );
19    void setPos( double theP[3] );
20  
42 –  double getX() const {return pos[offsetX];}
43 –  double getY() const {return pos[offsetY];}
44 –  double getZ() const {return pos[offsetZ];}
45 –  void setX(double x) {pos[offsetX] = x;}
46 –  void setY(double y) {pos[offsetY] = y;}
47 –  void setZ(double z) {pos[offsetZ] = z;}
48 –  
21    void getVel( double theV[3] );
22    void setVel( double theV[3] );
23  
52 –  double get_vx() const  {return vel[offsetX];}
53 –  double get_vy() const  {return vel[offsetY];}
54 –  double get_vz() const  {return vel[offsetZ];}
55 –  void set_vx(double vx) {vel[offsetX] = vx;}
56 –  void set_vy(double vy) {vel[offsetY] = vy;}
57 –  void set_vz(double vz) {vel[offsetZ] = vz;}
58 –  
59 –
24    void getFrc( double theF[3] );
25    void addFrc( double theF[3] );
26  
63 –  double getFx() const   {return frc[offsetX];}
64 –  double getFy() const   {return frc[offsetY];}
65 –  double getFz() const   {return frc[offsetZ];}
66 –  void addFx(double add) {frc[offsetX] += add;}
67 –  void addFy(double add) {frc[offsetY] += add;}
68 –  void addFz(double add) {frc[offsetZ] += add;}
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;}
# Line 113 | Line 74 | class Atom{ (protected)
74  
75   protected:
76    
77 +  SimState* myConfig;
78 +
79 +  double* pos; // the position array
80 +  double* vel; // the velocity array
81 +  double* frc; // the forc array
82 +  double* trq; // the torque vector  ( space fixed )
83 +  double* Amat; // the rotation matrix
84 +  double* mu;   // the array of dipole moments
85 +  double* ul;   // the lab frame unit directional vector
86 +
87    double c_mass; /* the mass of the atom in amu */
88    double c_sigma; /* the sigma parameter for van der walls interactions */
89    double c_epslon; /* the esplon parameter for VDW interactions */
90    double c_covalent; // The covalent radius of the atom.
91  
92 +  double myEamRcut; // Atom rcut for eam defined by the forcefield.
93 +
94    int index; /* set the atom's index */
95    int offset; // the atom's offset in the storage array
96    int offsetX, offsetY, offsetZ;
# Line 136 | Line 109 | class Atom{ (protected)
109    int is_LJ;    // LJ boolean
110    int is_EAM; //EAM boolean
111  
112 +  bool hasCoords;
113 +
114   #ifdef IS_MPI
115    int myGlobalIndex;
116   #endif
# Line 145 | Line 120 | class GeneralAtom : public Atom{ (public)
120   class GeneralAtom : public Atom{
121  
122   public:
123 <  GeneralAtom(int theIndex): Atom(theIndex){}
123 >  GeneralAtom(int theIndex, SimState* theConfig): Atom(theIndex, theConfig){}
124    virtual ~GeneralAtom(){}
125  
126    int isDirectional( void ){ return 0; }
127 <  void zeroForces() {
153 <    frc[offsetX] = 0.0;
154 <    frc[offsetY] = 0.0;
155 <    frc[offsetZ] = 0.0;
156 <  }
127 >  void zeroForces( void );
128   };
129  
130   class DirectionalAtom : public Atom {
131    
132   public:
133 <  DirectionalAtom(int theIndex) : Atom(theIndex)
133 >  DirectionalAtom(int theIndex, SimState* theConfig) : Atom(theIndex,
134 >                                                            theConfig)
135    {
136      ssdIdentity = 0;
137      sux = 0.0;
138      suy = 0.0;
139      suz = 0.0;
140 +    myMu = 0.0;
141    }
142    virtual ~DirectionalAtom() {}
143  
144 +  virtual void setCoords(void);
145 +
146    void printAmatIndex( void );
147  
148    int isDirectional(void) { return 1; }
# Line 186 | Line 161 | class DirectionalAtom : public Atom { (public)
161    void setSUy( double the_suy ) { suy = the_suy; }
162    void setSUz( double the_suz ) { suz = the_suz; }
163  
164 <  void zeroForces() {
190 <    frc[offsetX] = 0.0;
191 <    frc[offsetY] = 0.0;
192 <    frc[offsetZ] = 0.0;
164 >  void zeroForces();
165  
194 –    trq[offsetX] = 0.0;
195 –    trq[offsetY] = 0.0;
196 –    trq[offsetZ] = 0.0;
197 –  }
198 –
166    void getA( double the_A[3][3] ); // get the full rotation matrix
167    void setA( double the_A[3][3] );
168  
# Line 223 | Line 190 | class DirectionalAtom : public Atom { (public)
190    //  double getTy( void ) { return trq[offsetY]; }
191    //  double getTz( void ) { return trq[offsetZ]; }
192  
226 –  void addTx( double the_tx ) { trq[offsetX] += the_tx;}
227 –  void addTy( double the_ty ) { trq[offsetY] += the_ty;}
228 –  void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
229 –
193    void setI( double the_I[3][3] );
194    void getI( double the_I[3][3] );
195    
# Line 241 | Line 204 | class DirectionalAtom : public Atom { (public)
204    double getIzx( void ) { return Izx; }
205    double getIzy( void ) { return Izy; }
206    double getIzz( void ) { return Izz; }
244 –  
207  
208 <  double getMu( void ) { return mu[index]; }
209 <  void setMu( double the_mu ) { mu[index] = the_mu; }
208 >  double getMu( void );
209 >  void setMu( double the_mu );
210  
211    void lab2Body( double r[3] );
212    void body2Lab( double r[3] );
# Line 253 | Line 215 | class DirectionalAtom : public Atom { (public)
215   private:
216    int dIndex;
217  
218 +  double myMu;
219 +
220    double sux, suy, suz; // the standard unit vector    ( body fixed )
221    double jx, jy, jz;    // the angular momentum vector ( body fixed )
222    

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