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root/group/trunk/OOPSE/libmdtools/Atom.hpp
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Comparing trunk/OOPSE/libmdtools/Atom.hpp (file contents):
Revision 599 by mmeineke, Mon Jul 14 21:48:43 2003 UTC vs.
Revision 689 by tim, Tue Aug 12 19:56:49 2003 UTC

# Line 5 | Line 5 | class Atom{
5   #include <cstdlib>
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  
18 <  static void createArrays (int the_nElements);
19 <  static void destroyArrays(void);
20 <  void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
21 <                double* Atrq, double* AAmat, double* Amu,
22 <                double* Aul);
28 <  void deleteAtom(int theIndex);
29 <  void deleteRange(int startIndex, int stopIndex);
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  
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 –  
24    void getPos( double theP[3] );
25    void setPos( double theP[3] );
26  
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 –  
27    void getVel( double theV[3] );
28    void setVel( double theV[3] );
29  
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 –
30    void getFrc( double theF[3] );
31    void addFrc( double theF[3] );
32  
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;}
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;}
# Line 105 | Line 72 | class Atom{ (public)
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;
# Line 131 | Line 113 | class Atom{ (public)
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
# Line 141 | Line 126 | class GeneralAtom : public Atom{ (public)
126   class GeneralAtom : public Atom{
127  
128   public:
129 <  GeneralAtom(int theIndex): Atom(theIndex){}
129 >  GeneralAtom(int theIndex, SimState* theConfig): Atom(theIndex, theConfig){}
130    virtual ~GeneralAtom(){}
131  
132    int isDirectional( void ){ return 0; }
133 <  void zeroForces() {
149 <    frc[offsetX] = 0.0;
150 <    frc[offsetY] = 0.0;
151 <    frc[offsetZ] = 0.0;
152 <  }
133 >  void zeroForces( void );
134   };
135  
136   class DirectionalAtom : public Atom {
137    
138   public:
139 <  DirectionalAtom(int theIndex) : Atom(theIndex)
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; }
# Line 182 | Line 167 | class DirectionalAtom : public Atom { (public)
167    void setSUy( double the_suy ) { suy = the_suy; }
168    void setSUz( double the_suz ) { suz = the_suz; }
169  
170 <  void zeroForces() {
186 <    frc[offsetX] = 0.0;
187 <    frc[offsetY] = 0.0;
188 <    frc[offsetZ] = 0.0;
170 >  void zeroForces();
171  
190 –    trq[offsetX] = 0.0;
191 –    trq[offsetY] = 0.0;
192 –    trq[offsetZ] = 0.0;
193 –  }
194 –
172    void getA( double the_A[3][3] ); // get the full rotation matrix
173    void setA( double the_A[3][3] );
174  
# Line 215 | Line 192 | class DirectionalAtom : public Atom { (public)
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]; }
195 >  //  double getTx( void ) { return trq[offsetX];}
196 >  //  double getTy( void ) { return trq[offsetY]; }
197 >  //  double getTz( void ) { return trq[offsetZ]; }
198  
222 –  void addTx( double the_tx ) { trq[offsetX] += the_tx;}
223 –  void addTy( double the_ty ) { trq[offsetY] += the_ty;}
224 –  void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
225 –
199    void setI( double the_I[3][3] );
200    void getI( double the_I[3][3] );
201    
# Line 237 | Line 210 | class DirectionalAtom : public Atom { (public)
210    double getIzx( void ) { return Izx; }
211    double getIzy( void ) { return Izy; }
212    double getIzz( void ) { return Izz; }
240 –  
213  
214 <  double getMu( void ) { return mu[index]; }
215 <  void setMu( double the_mu ) { mu[index] = the_mu; }
214 >  double getMu( void );
215 >  void setMu( double the_mu );
216  
217    void lab2Body( double r[3] );
218    void body2Lab( double r[3] );
# Line 249 | Line 221 | class DirectionalAtom : public Atom { (public)
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    

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