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root/group/trunk/OOPSE/libmdtools/Atom.hpp
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Comparing trunk/OOPSE/libmdtools/Atom.hpp (file contents):
Revision 393 by mmeineke, Mon Mar 24 18:33:51 2003 UTC vs.
Revision 409 by gezelter, Wed Mar 26 21:04:38 2003 UTC

# Line 7 | Line 7 | class Atom{ (public)
7  
8   class Atom{
9   public:
10 –  Atom(int theIndex) {
11 –    c_n_hyd = 0;
12 –    has_dipole = 0;
13 –    is_VDW = 0;
14 –    is_LJ = 0;
10  
11 <    index = theIndex;
12 <    offset = 3 * index;
18 <    offsetX = offset;
19 <    offsetY = offset+1;
20 <    offsetZ = offset+2;
11 >  Atom(int theIndex);
12 >  virtual ~Atom() {}
13  
14 <    Axx = index*9;
15 <    Axy = Axx+1;
16 <    Axz = Axx+2;
17 <    
18 <    Ayx = Axx+3;
19 <    Ayy = Axx+4;
20 <    Ayz = Axx+5;
14 >  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;
22  
23 <    Azx = Axx+6;
24 <    Azy = Axx+7;
25 <    Azz = Axx+8;
26 <  }
27 <  virtual ~Atom() {}
28 <
29 <  static void createArrays (int nElements) {
37 <    int i;
38 <    
39 <    pos = new double[nElements*3];
40 <    vel = new double[nElements*3];
41 <    frc = new double[nElements*3];
42 <    trq = new double[nElements*3];
43 <    Amat = new double[nElements*9];
44 <    mu = new double[nElements];
45 <    ul = new double[nElements*3];
46 <
47 <    // init directional values to zero
48 <    
49 <    for( i=0; i<nElements; i++){
50 <      trq[i] = 0.0;
51 <      trq[i+1] = 0.0;
52 <      trq[i+2] = 0.0;
53 <      
54 <      Amat[i] = 1.0;
55 <      Amat[i+1] = 0.0;
56 <      Amat[i+2] = 0.0;
57 <      
58 <      Amat[i+3] = 0.0;
59 <      Amat[i+4] = 1.0;
60 <      Amat[i+5] = 0.0;
61 <      
62 <      Amat[i+6] = 0.0;
63 <      Amat[i+7] = 0.0;
64 <      Amat[i+8] = 1.0;
65 <      
66 <      mu[i] = 0.0;    
67 <      
68 <      ul[i] = 1.0;
69 <      ul[i+1] = 0.0;
70 <      ul[i+2] = 0.0;
71 <    }
72 <  }
73 <  static void destroyArrays(void) {
74 <    delete[] pos;
75 <    delete[] vel;
76 <    delete[] frc;
77 <    delete[] trq;
78 <    delete[] Amat;
79 <    delete[] mu;
80 <  }
23 >  static void createArrays (int 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; }
# Line 122 | Line 71 | class Atom{ (public)
71    void setCovalent(double covalent) {c_covalent = covalent;}
72    
73    int getIndex() const {return index;}
74 <  void setIndex(int theIndex) {
126 <    index = theIndex;
127 <    offset = index*3;
128 <    offsetX = offset;
129 <    offsetY = offset+1;
130 <    offsetZ = offset+2;
131 <
132 <    Axx = index*9;
133 <    Axy = Axx+1;
134 <    Axz = Axx+2;
135 <    
136 <    Ayx = Axx+3;
137 <    Ayy = Axx+4;
138 <    Ayz = Axx+5;
139 <
140 <    Azx = Axx+6;
141 <    Azy = Axx+7;
142 <    Azz = Axx+8;
143 <  }
144 <
74 >  void setIndex(int theIndex);
75    char *getType() {return c_name;}
76    void setType(char * name) {strcpy(c_name,name);}
77    
# Line 167 | Line 97 | class Atom{ (public)
97  
98    virtual int isDirectional( void ) = 0;
99  
170 –  static double* pos; // the position array
171 –  static double* vel; // the velocity array
172 –  static double* frc; // the forc array
173 –  static double* trq; // the torque vector  ( space fixed )
174 –  static double* Amat; // the rotation matrix
175 –  static double* mu; // the dipole moment array
176 –  static double* ul; // the lab frame unit directional vector
100  
101   protected:
102    
# Line 205 | Line 128 | class Atom{ (public)
128    
129   };
130  
208 –
209 –
131   class GeneralAtom : public Atom{
132  
133   public:

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