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root/group/trunk/OOPSE_old/src/mdtools/libmdCode/Atom.hpp
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Comparing trunk/OOPSE_old/src/mdtools/libmdCode/Atom.hpp (file contents):
Revision 295 by mmeineke, Fri Feb 14 17:08:46 2003 UTC vs.
Revision 296 by mmeineke, Thu Mar 6 20:05:39 2003 UTC

# Line 16 | Line 16 | class Atom{ (public)
16      offsetX = offset;
17      offsetY = offset+1;
18      offsetZ = offset+2;
19 +
20 +    Axx = index*9;
21 +    Axy = Axx+1;
22 +    Axz = Axx+2;
23 +    
24 +    Ayx = Axx+3;
25 +    Ayy = Axx+4;
26 +    Ayz = Axx+5;
27 +
28 +    Azx = Axx+6;
29 +    Azy = Axx+7;
30 +    Azz = Axx+8;
31    }
32    virtual ~Atom() {}
33  
# Line 24 | Line 36 | class Atom{ (public)
36      vel = new double[nElements*3];
37      frc = new double[nElements*3];
38      trq = new double[nElements*3];
39 +    Amat = new double[nElements*9];
40 +    mu = new double[nElements];
41 +    ul = new double[nElements];
42 +
43 +    // init directional values to zero
44 +    
45 +    trq[offsetX] = 0.0;
46 +    trq[offsetY] = 0.0;
47 +    trq[offsetZ] = 0.0;
48 +    
49 +    Amat[Axx] = 0.0;
50 +    Amat[Axy] = 0.0;
51 +    Amat[Axz] = 0.0;
52 +    
53 +    Amat[Ayx] = 0.0;
54 +    Amat[Ayy] = 0.0;
55 +    Amat[Ayz] = 0.0;
56 +
57 +    Amat[Azx] = 0.0;
58 +    Amat[Azy] = 0.0;
59 +    Amat[Azz] = 0.0;
60 +
61 +    mu[index] = 0.0;    
62 +
63 +    ul[offsetX] = 0.0;
64 +    ul[offsetY] = 0.0;
65 +    ul[offsetZ] = 0.0;
66    }
67    static void destroyArrays(void) {
68      delete[] pos;
69      delete[] vel;
70      delete[] frc;
71      delete[] trq;
72 +    delete[] Amat;
73 +    delete[] mu;
74    }
75  
76    static double* getPosArray( void ) { return pos; }
77    static double* getVelArray( void ) { return vel; }
78    static double* getFrcArray( void ) { return frc; }
79    static double* getTrqArray( void ) { return trq; }
80 +  static double* getAmatArray( void ) { return Amat; }
81 +  static double* getMuArray( void ) { return mu; }
82 +  static double* getUlArray( void ) { return ul; }
83    
40 –  
84    double getX() const {return pos[offsetX];}
85    double getY() const {return pos[offsetY];}
86    double getZ() const {return pos[offsetZ];}
# Line 79 | Line 122 | class Atom{ (public)
122      offsetX = offset;
123      offsetY = offset+1;
124      offsetZ = offset+2;
125 +
126 +    Axx = index*9;
127 +    Axy = Axx+1;
128 +    Axz = Axx+2;
129 +    
130 +    Ayx = Axx+3;
131 +    Ayy = Axx+4;
132 +    Ayz = Axx+5;
133 +
134 +    Azx = Axx+6;
135 +    Azy = Axx+7;
136 +    Azz = Axx+8;
137    }
138  
139    char *getType() {return c_name;}
# Line 110 | Line 165 | class Atom{ (public)
165    static double* vel; // the velocity array
166    static double* frc; // the forc array
167    static double* trq; // the torque vector  ( space fixed )
168 +  static double* Amat; // the rotation matrix
169 +  static double* mu; // the dipole moment array
170 +  static double* ul; // the lab frame unit directional vector
171  
172   protected:
173    
# Line 122 | Line 180 | class Atom{ (public)
180    int offset; // the atom's offset in the storage array
181    int offsetX, offsetY, offsetZ;
182  
183 +  int Axx, Axy, Axz; // the rotational matrix indices
184 +  int Ayx, Ayy, Ayz;
185 +  int Azx, Azy, Azz;
186 +
187    char c_name[100]; /* it's name */
188    int ident;  // it's unique numeric identity.
189  
# Line 159 | Line 221 | class DirectionalAtom : public Atom { (public)
221    DirectionalAtom(int theIndex) : Atom(theIndex)
222    {
223      ssdIdentity = 0;
224 +
225    }
226    virtual ~DirectionalAtom() {}
227  
165 –  static void createDArrays(int nElements){
166 –    trq = new double[nElements*3];
167 –  }
168 –  static void destroyDArrays(void){
169 –    delete[] trq;
170 –  }
171 –
228    int isDirectional(void) { return 1; }
229    
230    void setSSD( int value) { ssdIdentity = value; }
# Line 190 | Line 246 | class DirectionalAtom : public Atom { (public)
246    void setJy( double the_jy ) { jy = the_jy; }
247    void setJz( double the_jz ) { jz = the_jz; }
248      
249 <  void addTx( double the_tx ) { trq[offsetX]   += the_tx;}
249 >  void addTx( double the_tx ) { trq[offsetX] += the_tx;}
250    void addTy( double the_ty ) { trq[offsetY] += the_ty;}
251    void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
252  
197 –  void setMu( double the_mu ) { mu = the_mu; }
198 –
253    void zeroForces() {
254      frc[offsetX]   = 0.0;
255      frc[offsetY] = 0.0;
# Line 206 | Line 260 | class DirectionalAtom : public Atom { (public)
260      trq[offsetZ] = 0.0;
261    }
262  
263 <  double getAxx( void ) { return Axx; }
264 <  double getAxy( void ) { return Axy; }
265 <  double getAxz( void ) { return Axz; }
263 >  double getAxx( void ) { return Amat[Axx]; }
264 >  double getAxy( void ) { return Amat[Axy]; }
265 >  double getAxz( void ) { return Amat[Axz]; }
266    
267 <  double getAyx( void ) { return Ayx; }
268 <  double getAyy( void ) { return Ayy; }
269 <  double getAyz( void ) { return Ayz; }
267 >  double getAyx( void ) { return Amat[Ayx]; }
268 >  double getAyy( void ) { return Amat[Ayy]; }
269 >  double getAyz( void ) { return Amat[Ayz]; }
270    
271 <  double getAzx( void ) { return Azx; }
272 <  double getAzy( void ) { return Azy; }
273 <  double getAzz( void ) { return Azz; }
271 >  double getAzx( void ) { return Amat[Azx]; }
272 >  double getAzy( void ) { return Amat[Azy]; }
273 >  double getAzz( void ) { return Amat[Azz]; }
274  
275    void getA( double the_A[3][3] ); // get the full rotation matrix
276  
# Line 224 | Line 278 | class DirectionalAtom : public Atom { (public)
278    double getSUy( void ) { return suy; }
279    double getSUz( void ) { return suz; }
280  
281 <  void getU( double the_u[3] ); // get the unit vector
281 >  void getU( double the_u[3] ); // get the unit vetor
282    void getQ( double the_q[4] ); // get the quanternions
283  
284    double getJx( void ) { return jx; }
# Line 247 | Line 301 | class DirectionalAtom : public Atom { (public)
301    double getIzy( void ) { return Izy; }
302    double getIzz( void ) { return Izz; }
303  
304 <  double getMu( void ) { return mu; }
304 >  double getMu( void ) { return mu[index]; }
305 >  void setMu( double the_mu ) { mu[index] = the_mu; }
306  
307    void lab2Body( double r[3] );
308    void body2Lab( double r[3] );
# Line 255 | Line 310 | class DirectionalAtom : public Atom { (public)
310   private:
311    int dIndex;
312  
258 –  double Axx, Axy, Axz; // the rotational matrix
259 –  double Ayx, Ayy, Ayz;
260 –  double Azx, Azy, Azz;
261 –
313    double sux, suy, suz; // the standard unit vector    ( body fixed )
314    double jx, jy, jz;    // the angular momentum vector ( body fixed )
315    
# Line 266 | Line 317 | class DirectionalAtom : public Atom { (public)
317    double Iyx, Iyy, Iyz;
318    double Izx, Izy, Izz;
319  
269 –  double mu; // the magnitude of the dipole moment
270 –  
320    int ssdIdentity; // boolean of whether atom is ssd
321  
322   };

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