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root/group/trunk/OOPSE/libmdtools/Symplectic.cpp
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Comparing trunk/OOPSE/libmdtools/Symplectic.cpp (file contents):
Revision 423 by mmeineke, Thu Mar 27 20:12:15 2003 UTC vs.
Revision 468 by gezelter, Mon Apr 7 16:56:38 2003 UTC

# Line 5 | Line 5
5   #include "Thermo.hpp"
6   #include "ReadWrite.hpp"
7   #include "ForceFields.hpp"
8 + #include "ExtendedSystem.hpp"
9   #include "simError.h"
10  
11   extern "C"{
# Line 30 | Line 31 | extern "C"{
31  
32  
33  
34 < Symplectic::Symplectic( SimInfo* the_entry_plug, ForceFields* the_ff ){
34 > Symplectic::Symplectic( SimInfo* the_entry_plug, ForceFields* the_ff,
35 >                        ExtendedSystem* the_es ){
36    entry_plug = the_entry_plug;
37    myFF = the_ff;
38 +  myES = the_es;
39    isFirst = 1;
40  
41    molecules = entry_plug->molecules;
# Line 48 | Line 51 | Symplectic::Symplectic( SimInfo* the_entry_plug, Force
51    mass = new double[entry_plug->n_atoms];
52    for(int i = 0; i < entry_plug->n_atoms; i++){
53      mass[i] = entry_plug->atoms[i]->getMass();
54 <  }
52 <
53 <  
54 >  }  
55  
56    // check for constraints
57  
# Line 65 | Line 66 | Symplectic::Symplectic( SimInfo* the_entry_plug, Force
66    SRI** theArray;
67    for(int i = 0; i < nMols; i++){
68      
69 <    theArray = molecules[i].getMyBonds();
70 <    for(int j=0; j<molecules[i].getNbonds(); j++){
69 >    theArray = (SRI**) molecules[i].getMyBonds();
70 >    for(int j=0; j<molecules[i].getNBonds(); j++){
71        
72        constrained = theArray[j]->is_constrained();
73        
74        if(constrained){
75          
76          dummy_plug = theArray[j]->get_constraint();
77 <        temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
78 <        temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
79 <        temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
77 >        temp_con[n_constrained].set_a( dummy_plug->get_a() );
78 >        temp_con[n_constrained].set_b( dummy_plug->get_b() );
79 >        temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );
80          
81 <        c_n_constrained++;
81 >        n_constrained++;
82          constrained = 0;
83        }
84      }
85  
86 <    theArray = molecules[i].getMyBends();
87 <    for(int j=0; j<molecules[i].getNbends(); j++){
86 >    theArray = (SRI**) molecules[i].getMyBends();
87 >    for(int j=0; j<molecules[i].getNBends(); j++){
88        
89        constrained = theArray[j]->is_constrained();
90        
91        if(constrained){
92          
93          dummy_plug = theArray[j]->get_constraint();
94 <        temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
95 <        temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
96 <        temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
94 >        temp_con[n_constrained].set_a( dummy_plug->get_a() );
95 >        temp_con[n_constrained].set_b( dummy_plug->get_b() );
96 >        temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );
97          
98 <        c_n_constrained++;
98 >        n_constrained++;
99          constrained = 0;
100        }
101      }
102  
103 <    theArray = molecules[i].getMyTorsions();
104 <    for(int j=0; j<molecules[i].getNtorsions(); j++){
103 >    theArray = (SRI**) molecules[i].getMyTorsions();
104 >    for(int j=0; j<molecules[i].getNTorsions(); j++){
105        
106        constrained = theArray[j]->is_constrained();
107        
108        if(constrained){
109          
110          dummy_plug = theArray[j]->get_constraint();
111 <        temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
112 <        temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
113 <        temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
111 >        temp_con[n_constrained].set_a( dummy_plug->get_a() );
112 >        temp_con[n_constrained].set_b( dummy_plug->get_b() );
113 >        temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );
114          
115 <        c_n_constrained++;
115 >        n_constrained++;
116          constrained = 0;
117        }
118      }
# Line 183 | Line 184 | void Symplectic::integrate( void ){
184    int status_n = (int)( statusTime / dt );
185    int vel_n    = (int)( thermalTime / dt );
186  
187 <  int calcPot;
187 >  int calcPot, calcStress;
188  
189     Thermo *tStats = new Thermo( entry_plug );
190  
# Line 196 | Line 197 | void Symplectic::integrate( void ){
197  
198    // initialize the forces the before the first step
199  
200 <  myFF->doForces(1,0);
200 >  myFF->doForces(1,1);
201    
202    if( entry_plug->setTemp ){
203      
# Line 324 | Line 325 | void Symplectic::integrate( void ){
325        
326        // calculate the forces
327        
328 <      myFF->doForces(calcPot, 0);
328 >      myFF->doForces(calcPot, calcStress);
329        
330        // move b
331  
# Line 395 | Line 396 | void Symplectic::integrate( void ){
396          if( !(time % vel_n) ) tStats->velocitize();
397        }
398        if( !(time % sample_n) ) dump_out->writeDump( time * dt );
399 <      if( !((time+1) % status_n) ) calcPot = 1;
400 <      if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; }
399 >      if( !((time+1) % status_n) ) {
400 >        calcPot = 1;
401 >        calcStress = 1;
402 >      }
403 >      if( !(time % status_n) ){
404 >        e_out->writeStat( time * dt );
405 >        calcPot = 0;
406 >        calcStress = 0;
407 >      }
408      }
409    }
410    else{
# Line 494 | Line 502 | void Symplectic::integrate( void ){
502        
503        // calculate the forces
504        
505 <      myFF->doForces(calcPot,0);
505 >      myFF->doForces(calcPot,calcStress);
506        
507        for( i=0; i< nAtoms; i++ ){
508          
# Line 553 | Line 561 | void Symplectic::integrate( void ){
561          if( !(time % vel_n) ) tStats->velocitize();
562        }
563        if( !(time % sample_n) ) dump_out->writeDump( time * dt );
564 <      if( !((time+1) % status_n) ) calcPot = 1;
565 <      if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; }
564 >      if( !((time+1) % status_n) ) {
565 >        calcPot = 1;
566 >        calcStress = 1;
567 >      }
568 >      if( !(time % status_n) ){
569 >        e_out->writeStat( time * dt );
570 >        calcPot = 0;
571 >        calcStress = 0;
572 >      }      
573      }
574    }
575  
# Line 581 | Line 596 | void Symplectic::rotate( int axes1, int axes2, double
596  
597    for(i=0; i<3; i++){
598      for(j=0; j<3; j++){
599 <      tempA[i][j] = A[i][j];
599 >      tempA[j][i] = A[i][j];
600      }
601    }
602  
# Line 640 | Line 655 | void Symplectic::rotate( int axes1, int axes2, double
655      for(j=0; j<3; j++){
656        A[j][i] = 0.0;
657        for(k=0; k<3; k++){
658 <        A[j][i] += tempA[k][i] * rot[j][k];
658 >        A[j][i] += tempA[i][k] * rot[j][k];
659        }
660      }
661    }

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