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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 296 by mmeineke, Thu Mar 6 20:05:39 2003 UTC vs.
Revision 368 by chuckv, Thu Mar 20 00:02:39 2003 UTC

# Line 2 | Line 2
2   #define _ATOM_H_
3  
4   #include <cstring>
5 + #include <cstdlib>
6   #include <iostream>
7  
8   class Atom{
# Line 11 | Line 12 | class Atom{ (public)
12      has_dipole = 0;
13      is_VDW = 0;
14      is_LJ = 0;
15 +
16      index = theIndex;
17      offset = 3 * index;
18      offsetX = offset;
# Line 32 | Line 34 | class Atom{ (public)
34    virtual ~Atom() {}
35  
36    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];
45 >    ul = new double[nElements*3];
46  
47      // init directional values to zero
48      
49 <    trq[offsetX] = 0.0;
50 <    trq[offsetY] = 0.0;
51 <    trq[offsetZ] = 0.0;
52 <    
53 <    Amat[Axx] = 0.0;
54 <    Amat[Axy] = 0.0;
55 <    Amat[Axz] = 0.0;
56 <    
57 <    Amat[Ayx] = 0.0;
58 <    Amat[Ayy] = 0.0;
59 <    Amat[Ayz] = 0.0;
60 <
61 <    Amat[Azx] = 0.0;
62 <    Amat[Azy] = 0.0;
63 <    Amat[Azz] = 0.0;
64 <
65 <    mu[index] = 0.0;    
66 <
67 <    ul[offsetX] = 0.0;
68 <    ul[offsetY] = 0.0;
69 <    ul[offsetZ] = 0.0;
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] = 0.0;
69 >      ul[i+1] = 0.0;
70 >      ul[i+2] = 0.0;
71 >    }
72    }
73    static void destroyArrays(void) {
74      delete[] pos;
# Line 209 | Line 215 | class GeneralAtom : public Atom{ (public)
215  
216    int isDirectional( void ){ return 0; }
217    void zeroForces() {
218 <    frc[offsetX]   = 0.0;
218 >    frc[offsetX] = 0.0;
219      frc[offsetY] = 0.0;
220      frc[offsetZ] = 0.0;
221    }
# Line 221 | Line 227 | class DirectionalAtom : public Atom { (public)
227    DirectionalAtom(int theIndex) : Atom(theIndex)
228    {
229      ssdIdentity = 0;
230 <
230 >    sux = 0.0;
231 >    suy = 0.0;
232 >    suz = 0.0;
233    }
234    virtual ~DirectionalAtom() {}
235  
# Line 251 | Line 259 | class DirectionalAtom : public Atom { (public)
259    void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
260  
261    void zeroForces() {
262 <    frc[offsetX]   = 0.0;
262 >    frc[offsetX] = 0.0;
263      frc[offsetY] = 0.0;
264      frc[offsetZ] = 0.0;
265  
266 <    trq[offsetX]   = 0.0;
266 >    trq[offsetX] = 0.0;
267      trq[offsetY] = 0.0;
268      trq[offsetZ] = 0.0;
269    }
# Line 306 | Line 314 | class DirectionalAtom : public Atom { (public)
314  
315    void lab2Body( double r[3] );
316    void body2Lab( double r[3] );
317 +  void updateU( void );
318  
319   private:
320    int dIndex;

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