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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 348 by mmeineke, Fri Mar 14 21:33:10 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 +    pos = NULL;
16 +
17      index = theIndex;
18      offset = 3 * index;
19      offsetX = offset;
# Line 32 | Line 35 | class Atom{ (public)
35    virtual ~Atom() {}
36  
37    static void createArrays (int nElements) {
38 +    int i;
39 +    if( pos != NULL ) destroyArrays();
40 +    
41      pos = new double[nElements*3];
42      vel = new double[nElements*3];
43      frc = new double[nElements*3];
44      trq = new double[nElements*3];
45      Amat = new double[nElements*9];
46      mu = new double[nElements];
47 <    ul = new double[nElements];
47 >    ul = new double[nElements*3];
48  
49      // init directional values to zero
50      
51 <    trq[offsetX] = 0.0;
52 <    trq[offsetY] = 0.0;
53 <    trq[offsetZ] = 0.0;
54 <    
55 <    Amat[Axx] = 0.0;
56 <    Amat[Axy] = 0.0;
57 <    Amat[Axz] = 0.0;
58 <    
59 <    Amat[Ayx] = 0.0;
60 <    Amat[Ayy] = 0.0;
61 <    Amat[Ayz] = 0.0;
62 <
63 <    Amat[Azx] = 0.0;
64 <    Amat[Azy] = 0.0;
65 <    Amat[Azz] = 0.0;
66 <
67 <    mu[index] = 0.0;    
68 <
69 <    ul[offsetX] = 0.0;
70 <    ul[offsetY] = 0.0;
71 <    ul[offsetZ] = 0.0;
51 >    for( i=0; i<nElements; i++){
52 >      trq[i] = 0.0;
53 >      trq[i+1] = 0.0;
54 >      trq[i+2] = 0.0;
55 >      
56 >      Amat[i] = 1.0;
57 >      Amat[i+1] = 0.0;
58 >      Amat[i+2] = 0.0;
59 >      
60 >      Amat[i+3] = 0.0;
61 >      Amat[i+4] = 1.0;
62 >      Amat[i+5] = 0.0;
63 >      
64 >      Amat[i+6] = 0.0;
65 >      Amat[i+7] = 0.0;
66 >      Amat[i+8] = 1.0;
67 >      
68 >      mu[i] = 0.0;    
69 >      
70 >      ul[i] = 0.0;
71 >      ul[i+1] = 0.0;
72 >      ul[i+2] = 0.0;
73 >    }
74    }
75    static void destroyArrays(void) {
76      delete[] pos;
# Line 209 | Line 217 | class GeneralAtom : public Atom{ (public)
217  
218    int isDirectional( void ){ return 0; }
219    void zeroForces() {
220 <    frc[offsetX]   = 0.0;
220 >    frc[offsetX] = 0.0;
221      frc[offsetY] = 0.0;
222      frc[offsetZ] = 0.0;
223    }
# Line 221 | Line 229 | class DirectionalAtom : public Atom { (public)
229    DirectionalAtom(int theIndex) : Atom(theIndex)
230    {
231      ssdIdentity = 0;
232 <
232 >    sux = 0.0;
233 >    suy = 0.0;
234 >    suz = 0.0;
235    }
236    virtual ~DirectionalAtom() {}
237  
# Line 251 | Line 261 | class DirectionalAtom : public Atom { (public)
261    void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
262  
263    void zeroForces() {
264 <    frc[offsetX]   = 0.0;
264 >    frc[offsetX] = 0.0;
265      frc[offsetY] = 0.0;
266      frc[offsetZ] = 0.0;
267  
268 <    trq[offsetX]   = 0.0;
268 >    trq[offsetX] = 0.0;
269      trq[offsetY] = 0.0;
270      trq[offsetZ] = 0.0;
271    }
# Line 306 | Line 316 | class DirectionalAtom : public Atom { (public)
316  
317    void lab2Body( double r[3] );
318    void body2Lab( double r[3] );
319 +  void updateU( void );
320  
321   private:
322    int dIndex;

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