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root/group/trunk/OOPSE/libmdtools/Verlet.cpp
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Comparing trunk/OOPSE/libmdtools/Verlet.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 423 by mmeineke, Thu Mar 27 20:12:15 2003 UTC

# Line 36 | Line 36 | Verlet::Verlet( SimInfo &info, ForceFields* the_ff ){
36    entry_plug = &info;
37    myFF = the_ff;
38  
39 <
39 >  
40    c_natoms = info.n_atoms;
41    c_atoms = info.atoms;
42 <  c_sr_interactions = info.sr_interactions;
43 <  c_n_SRI = info.n_SRI;
42 >  nMols = info.n_mol;
43 >  molecules = info.molecules;
44    c_is_constrained = 0;
45    c_box_x = info.box_x;
46    c_box_y = info.box_y;
# Line 67 | Line 67 | Verlet::Verlet( SimInfo &info, ForceFields* the_ff ){
67  
68    Constraint *temp_con;
69    Constraint *dummy_plug;
70 <  temp_con = new Constraint[c_n_SRI];
70 >  temp_con = new Constraint[info.n_SRI];
71  
72    c_n_constrained = 0;
73    int constrained = 0;
74 <  
75 <  for(int i = 0; i < c_n_SRI; i++){
74 >  SRI** theArray;
75 >  for(int i = 0; i < nMols; i++){
76      
77 <    constrained = c_sr_interactions[i]->is_constrained();
78 <
79 <    if(constrained){
77 >    theArray = molecules[i].getMyBonds();
78 >    for(int j=0; j<molecules[i].getNbonds(); j++){
79        
80 <      dummy_plug = c_sr_interactions[i]->get_constraint();
81 <      temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
82 <      temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
83 <      temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
80 >      constrained = theArray[j]->is_constrained();
81 >      
82 >      if(constrained){
83 >        
84 >        dummy_plug = theArray[j]->get_constraint();
85 >        temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
86 >        temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
87 >        temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
88 >        
89 >        c_n_constrained++;
90 >        constrained = 0;
91 >      }
92 >    }
93  
94 <      c_n_constrained++;
95 <      constrained = 0;
94 >    theArray = molecules[i].getMyBends();
95 >    for(int j=0; j<molecules[i].getNbends(); j++){
96 >      
97 >      constrained = theArray[j]->is_constrained();
98 >      
99 >      if(constrained){
100 >        
101 >        dummy_plug = theArray[j]->get_constraint();
102 >        temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
103 >        temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
104 >        temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
105 >        
106 >        c_n_constrained++;
107 >        constrained = 0;
108 >      }
109 >    }
110 >
111 >    theArray = molecules[i].getMyTorsions();
112 >    for(int j=0; j<molecules[i].getNtorsions(); j++){
113 >      
114 >      constrained = theArray[j]->is_constrained();
115 >      
116 >      if(constrained){
117 >        
118 >        dummy_plug = theArray[j]->get_constraint();
119 >        temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
120 >        temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
121 >        temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
122 >        
123 >        c_n_constrained++;
124 >        constrained = 0;
125 >      }
126      }
127 +
128 +
129    }
130  
131    if(c_n_constrained > 0){
# Line 94 | Line 134 | Verlet::Verlet( SimInfo &info, ForceFields* the_ff ){
134      c_constrained_i = new int[c_n_constrained];
135      c_constrained_j = new int[c_n_constrained];
136      c_constrained_dsqr = new double[c_n_constrained];
137 <
137 >    
138      for( int i = 0; i < c_n_constrained; i++){
139        
140        /* add 1 to the index for the fortran arrays. */
141 <
141 >      
142        c_constrained_i[i] = temp_con[i].get_a() + 1;
143        c_constrained_j[i] = temp_con[i].get_b() + 1;
144        c_constrained_dsqr[i] = temp_con[i].get_dsqr();

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