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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 468 by gezelter, Mon Apr 7 16:56:38 2003 UTC

# Line 7 | Line 7
7   #include "SimInfo.hpp"
8   #include "Thermo.hpp"
9   #include "ReadWrite.hpp"
10 + #include "ExtendedSystem.hpp"
11  
12   extern "C"{
13    
# Line 29 | Line 30 | Verlet::Verlet( SimInfo &info, ForceFields* the_ff ){
30   }
31  
32    
33 < Verlet::Verlet( SimInfo &info, ForceFields* the_ff ){
33 > Verlet::Verlet( SimInfo &info, ForceFields* the_ff, ExtendedSystem* the_es ){
34    
35    // get what information we need from the SimInfo object
36  
37    entry_plug = &info;
38    myFF = the_ff;
39 <
40 <
39 >  myES = the_es;
40 >  
41    c_natoms = info.n_atoms;
42    c_atoms = info.atoms;
43 <  c_sr_interactions = info.sr_interactions;
44 <  c_n_SRI = info.n_SRI;
43 >  nMols = info.n_mol;
44 >  molecules = info.molecules;
45    c_is_constrained = 0;
46    c_box_x = info.box_x;
47    c_box_y = info.box_y;
# Line 67 | Line 68 | Verlet::Verlet( SimInfo &info, ForceFields* the_ff ){
68  
69    Constraint *temp_con;
70    Constraint *dummy_plug;
71 <  temp_con = new Constraint[c_n_SRI];
71 >  temp_con = new Constraint[info.n_SRI];
72  
73    c_n_constrained = 0;
74    int constrained = 0;
75 <  
76 <  for(int i = 0; i < c_n_SRI; i++){
75 >  SRI** theArray;
76 >  for(int i = 0; i < nMols; i++){
77      
78 <    constrained = c_sr_interactions[i]->is_constrained();
79 <
79 <    if(constrained){
78 >    theArray = (SRI**) molecules[i].getMyBonds();
79 >    for(int j=0; j<molecules[i].getNBonds(); j++){
80        
81 <      dummy_plug = c_sr_interactions[i]->get_constraint();
82 <      temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
83 <      temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
84 <      temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
81 >      constrained = theArray[j]->is_constrained();
82 >      
83 >      if(constrained){
84 >        
85 >        dummy_plug = theArray[j]->get_constraint();
86 >        temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
87 >        temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
88 >        temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
89 >        
90 >        c_n_constrained++;
91 >        constrained = 0;
92 >      }
93 >    }
94  
95 <      c_n_constrained++;
96 <      constrained = 0;
95 >    theArray = (SRI**) molecules[i].getMyBends();
96 >    for(int j=0; j<molecules[i].getNBends(); j++){
97 >      
98 >      constrained = theArray[j]->is_constrained();
99 >      
100 >      if(constrained){
101 >        
102 >        dummy_plug = theArray[j]->get_constraint();
103 >        temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
104 >        temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
105 >        temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
106 >        
107 >        c_n_constrained++;
108 >        constrained = 0;
109 >      }
110      }
111 +
112 +    theArray = (SRI**) molecules[i].getMyTorsions();
113 +    for(int j=0; j<molecules[i].getNTorsions(); j++){
114 +      
115 +      constrained = theArray[j]->is_constrained();
116 +      
117 +      if(constrained){
118 +        
119 +        dummy_plug = theArray[j]->get_constraint();
120 +        temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
121 +        temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
122 +        temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
123 +        
124 +        c_n_constrained++;
125 +        constrained = 0;
126 +      }
127 +    }
128 +
129 +
130    }
131  
132    if(c_n_constrained > 0){
# Line 94 | Line 135 | Verlet::Verlet( SimInfo &info, ForceFields* the_ff ){
135      c_constrained_i = new int[c_n_constrained];
136      c_constrained_j = new int[c_n_constrained];
137      c_constrained_dsqr = new double[c_n_constrained];
138 <
138 >    
139      for( int i = 0; i < c_n_constrained; i++){
140        
141        /* add 1 to the index for the fortran arrays. */
142 <
142 >      
143        c_constrained_i[i] = temp_con[i].get_a() + 1;
144        c_constrained_j[i] = temp_con[i].get_b() + 1;
145        c_constrained_dsqr[i] = temp_con[i].get_dsqr();
# Line 126 | Line 167 | void Verlet::integrate( void ){
167   void Verlet::integrate( void ){
168    
169    int i, j; /* loop counters */
170 <  int calcPot;
170 >  int calcPot, calcStress;
171  
172    double kE;
173  
# Line 163 | Line 204 | void Verlet::integrate( void ){
204    // the first time integrate is called, the forces need to be initialized
205  
206    
207 <  myFF->doForces(1,0);
207 >  myFF->doForces(1,1);
208    
209    if( entry_plug->setTemp ){
210      tStats->velocitize();
# Line 174 | Line 215 | void Verlet::integrate( void ){
215    e_out->writeStat( 0.0 );
216  
217    calcPot = 0;
218 +  calcStress = 0;
219  
220    if( c_is_constrained ){
221      for(i = 0; i < n_loops; i++){
# Line 215 | Line 257 | void Verlet::integrate( void ){
257  
258        // calculate the forces
259        
260 <      myFF->doForces(calcPot,0);
260 >      myFF->doForces(calcPot,calcStress);
261        
262        // finish the constrain move ( same as above. )
263  
# Line 257 | Line 299 | void Verlet::integrate( void ){
299          if( !(time % vel_n) ) tStats->velocitize();
300        }
301        if( !(time % sample_n) ) dump_out->writeDump( time * dt );
302 <      if( !((time+1) % status_n) ) calcPot = 1;
303 <      if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; }
302 >      if( !((time+1) % status_n) ) {
303 >        calcPot = 1;
304 >        calcStress = 1;
305 >      }
306 >      if( !(time % status_n) ){
307 >        e_out->writeStat( time * dt );
308 >        calcPot = 0;
309 >        calcStress = 0;
310 >      }
311      }
312    }
313    else{
# Line 268 | Line 317 | void Verlet::integrate( void ){
317        
318        // calculate the forces
319        
320 <      myFF->doForces(calcPot,0);
320 >      myFF->doForces(calcPot,calcStress);
321              
322        // complete the verlet move
323        
# Line 280 | Line 329 | void Verlet::integrate( void ){
329          if( !(time % vel_n) ) tStats->velocitize();
330        }
331        if( !(time % sample_n) )  dump_out->writeDump( time * dt );
332 <      if( !((time+1) % status_n) ) calcPot = 1;
333 <      if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; }
332 >      if( !((time+1) % status_n) ) {
333 >        calcPot = 1;
334 >        calcStress = 1;
335 >      }
336 >      if( !(time % status_n) ){
337 >        e_out->writeStat( time * dt );
338 >        calcPot = 0;
339 >        calcStress = 0;
340 >      }
341      }
342    }
343    

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