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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 572 by mmeineke, Wed Jul 2 21:26:55 2003 UTC vs.
Revision 597 by mmeineke, Mon Jul 14 21:28:54 2003 UTC

# Line 27 | Line 27 | Integrator::Integrator( SimInfo *theInfo, ForceFields*
27  
28    nAtoms = info->n_atoms;
29  
30 +  std::cerr << "integ nAtoms = "  << nAtoms << "\n";
31 +
32    // check for constraints
33    
34    constrainedA    = NULL;
# Line 72 | Line 74 | void Integrator::checkConstraints( void ){
74      for(int j=0; j<molecules[i].getNBonds(); j++){
75        
76        constrained = theArray[j]->is_constrained();
77 +
78 +      std::cerr << "Is the folowing bond constrained \n";
79 +      theArray[j]->printMe();
80        
81        if(constrained){
82          
83 +        std::cerr << "Yes\n";
84 +
85          dummy_plug = theArray[j]->get_constraint();
86          temp_con[nConstrained].set_a( dummy_plug->get_a() );
87          temp_con[nConstrained].set_b( dummy_plug->get_b() );
# Line 82 | Line 89 | void Integrator::checkConstraints( void ){
89          
90          nConstrained++;
91          constrained = 0;
92 <      }
92 >      }
93 >      else std::cerr << "No.\n";
94      }
95  
96      theArray = (SRI**) molecules[i].getMyBends();
# Line 216 | Line 224 | void Integrator::integrate( void ){
224    pos  = Atom::getPosArray();
225    vel  = Atom::getVelArray();
226    frc  = Atom::getFrcArray();
219 –  trq  = Atom::getTrqArray();
220 –  Amat = Atom::getAmatArray();
227  
228    while( currTime < runTime ){
229  
# Line 226 | Line 232 | void Integrator::integrate( void ){
232        calcStress = 1;
233      }
234  
235 +    std::cerr << currTime << "\n";
236 +
237      integrateStep( calcPot, calcStress );
238        
239      currTime += dt;
# Line 271 | Line 279 | void Integrator::integrateStep( int calcPot, int calcS
279  
280    preMove();
281    moveA();
282 <  if( nConstrained ) constrainA();
282 >  //if( nConstrained ) constrainA();
283  
284    // calc forces
285  
# Line 293 | Line 301 | void Integrator::moveA( void ){
301    double Tb[3];
302    double ji[3];
303    double angle;
304 <
304 >  double A[3][3], At[3][3];
305  
306  
307    for( i=0; i<nAtoms; i++ ){
# Line 304 | Line 312 | void Integrator::moveA( void ){
312      for( j=atomIndex; j<(atomIndex+3); j++ )
313        vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
314  
315 +
316      // position whole step    
317      for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j];
318      
319 +
320      if( atoms[i]->isDirectional() ){
321  
322        dAtom = (DirectionalAtom *)atoms[i];
# Line 316 | Line 326 | void Integrator::moveA( void ){
326        Tb[0] = dAtom->getTx();
327        Tb[1] = dAtom->getTy();
328        Tb[2] = dAtom->getTz();
329 <      
329 >
330        dAtom->lab2Body( Tb );
331 <      
331 >
332        // get the angular momentum, and propagate a half step
333        
334        ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
# Line 331 | Line 341 | void Integrator::moveA( void ){
341        // rotate about the x-axis      
342        angle = dt2 * ji[0] / dAtom->getIxx();
343        this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
344 <      
344 >
345        // rotate about the y-axis
346        angle = dt2 * ji[1] / dAtom->getIyy();
347        this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
# Line 351 | Line 361 | void Integrator::moveA( void ){
361        dAtom->setJx( ji[0] );
362        dAtom->setJy( ji[1] );
363        dAtom->setJz( ji[2] );
364 +
365 +      std::cerr << "Amat[" << i << "]\n";
366 +      info->printMat9( &Amat[aMatIndex] );
367 +          
368 +      std::cerr << "ji[" << i << "]\t"
369 +                << ji[0] << "\t"
370 +                << ji[1] << "\t"
371 +                << ji[2] << "\n";
372 +          
373      }
374      
375    }
# Line 359 | Line 378 | void Integrator::moveB( void ){
378  
379   void Integrator::moveB( void ){
380    int i,j,k;
381 <  int atomIndex;
381 >  int atomIndex, aMatIndex;
382    DirectionalAtom* dAtom;
383    double Tb[3];
384    double ji[3];
385  
386    for( i=0; i<nAtoms; i++ ){
387      atomIndex = i * 3;
388 +    aMatIndex = i * 9;
389  
390      // velocity half step
391      for( j=atomIndex; j<(atomIndex+3); j++ )
392        vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
393  
394 +
395      if( atoms[i]->isDirectional() ){
396        
397        dAtom = (DirectionalAtom *)atoms[i];
# Line 381 | Line 402 | void Integrator::moveB( void ){
402        Tb[1] = dAtom->getTy();
403        Tb[2] = dAtom->getTz();
404        
405 +      std::cerr << "TrqB[" << i << "]\t"
406 +                << Tb[0] << "\t"
407 +                << Tb[1] << "\t"
408 +                << Tb[2] << "\n";
409 +
410        dAtom->lab2Body( Tb );
411        
412        // get the angular momentum, and complete the angular momentum
# Line 393 | Line 419 | void Integrator::moveB( void ){
419        dAtom->setJx( ji[0] );
420        dAtom->setJy( ji[1] );
421        dAtom->setJz( ji[2] );
422 +
423 +
424 +      std::cerr << "Amat[" << i << "]\n";
425 +      info->printMat9( &Amat[aMatIndex] );
426 +          
427 +      std::cerr << "ji[" << i << "]\t"
428 +                << ji[0] << "\t"
429 +                << ji[1] << "\t"
430 +                << ji[2] << "\n";
431      }
432    }
433  
# Line 422 | Line 457 | void Integrator::constrainA(){
457    double gab;
458    int iteration;
459  
425 –
426 –  
460    for( i=0; i<nAtoms; i++){
461      
462      moving[i] = 0;
# Line 662 | Line 695 | void Integrator::rotate( int axes1, int axes2, double
695    double tempA[3][3];
696    double tempJ[3];
697  
698 +
699    // initialize the tempA
700  
701    for(i=0; i<3; i++){
702      for(j=0; j<3; j++){
703 <      tempA[j][i] = A[3*i + j];
703 >      tempA[j][i] = A[3*i+j];
704      }
705    }
706  
# Line 723 | Line 757 | void Integrator::rotate( int axes1, int axes2, double
757  
758    for(i=0; i<3; i++){
759      for(j=0; j<3; j++){
760 <      A[3*j + i] = 0.0;
760 >      A[3*j+i] = 0.0;
761        for(k=0; k<3; k++){
762 <        A[3*j + i] += tempA[i][k] * rot[j][k];
762 >        A[3*j+i] += tempA[i][k] * rot[j][k];
763        }
764      }
765    }

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