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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 567 by mmeineke, Wed Jun 25 21:12:14 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 257 | Line 265 | void Integrator::integrate( void ){
265  
266    }
267  
268 <  dumpOut->writeFinal();
268 >  dumpOut->writeFinal(currTime);
269  
270    delete dumpOut;
271    delete statOut;
# 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 +  double A[3][3], At[3][3];
305  
306  
298 –
307    for( i=0; i<nAtoms; i++ ){
308      atomIndex = i * 3;
309      aMatIndex = i * 9;
# 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 411 | Line 446 | void Integrator::constrainA(){
446  
447    int i,j,k;
448    int done;
449 <  double pxab, pyab, pzab;
450 <  double rxab, ryab, rzab;
449 >  double pab[3];
450 >  double rab[3];
451    int a, b, ax, ay, az, bx, by, bz;
452    double rma, rmb;
453    double dx, dy, dz;
# 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 450 | Line 483 | void Integrator::constrainA(){
483  
484        if( moved[a] || moved[b] ){
485          
486 <        pxab = pos[ax] - pos[bx];
487 <        pyab = pos[ay] - pos[by];
488 <        pzab = pos[az] - pos[bz];
486 >        pab[0] = pos[ax] - pos[bx];
487 >        pab[1] = pos[ay] - pos[by];
488 >        pab[2] = pos[az] - pos[bz];
489  
490          //periodic boundary condition
458 –        pxab = pxab - info->box_x * copysign(1, pxab)
459 –          * (int)( fabs(pxab / info->box_x) + 0.5);
460 –        pyab = pyab - info->box_y * copysign(1, pyab)
461 –          * (int)( fabs(pyab / info->box_y) + 0.5);
462 –        pzab = pzab - info->box_z * copysign(1, pzab)
463 –          * (int)( fabs(pzab / info->box_z) + 0.5);
491  
492 <        pabsq = pxab * pxab + pyab * pyab + pzab * pzab;
492 >        info->wrapVector( pab );
493  
494 +        pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
495 +
496          rabsq = constrainedDsqr[i];
497          diffsq = rabsq - pabsq;
498  
499          // the original rattle code from alan tidesley
500          if (fabs(diffsq) > (tol*rabsq*2)) {
501 <          rxab = oldPos[ax] - oldPos[bx];
502 <          ryab = oldPos[ay] - oldPos[by];
503 <          rzab = oldPos[az] - oldPos[bz];
501 >          rab[0] = oldPos[ax] - oldPos[bx];
502 >          rab[1] = oldPos[ay] - oldPos[by];
503 >          rab[2] = oldPos[az] - oldPos[bz];
504  
505 <          rxab = rxab - info->box_x * copysign(1, rxab)
477 <            * (int)( fabs(rxab / info->box_x) + 0.5);
478 <          ryab = ryab - info->box_y * copysign(1, ryab)
479 <            * (int)( fabs(ryab / info->box_y) + 0.5);
480 <          rzab = rzab - info->box_z * copysign(1, rzab)
481 <            * (int)( fabs(rzab / info->box_z) + 0.5);
505 >          info->wrapVector( rab );
506  
507 <          rpab = rxab * pxab + ryab * pyab + rzab * pzab;
507 >          rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
508  
509            rpabsq = rpab * rpab;
510  
# Line 503 | Line 527 | void Integrator::constrainA(){
527  
528            gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab );
529  
530 <          dx = rxab * gab;
531 <          dy = ryab * gab;
532 <          dz = rzab * gab;
530 >          dx = rab[0] * gab;
531 >          dy = rab[1] * gab;
532 >          dz = rab[2] * gab;
533  
534            pos[ax] += rma * dx;
535            pos[ay] += rma * dy;
# Line 559 | Line 583 | void Integrator::constrainB( void ){
583    int i,j,k;
584    int done;
585    double vxab, vyab, vzab;
586 <  double rxab, ryab, rzab;
586 >  double rab[3];
587    int a, b, ax, ay, az, bx, by, bz;
588    double rma, rmb;
589    double dx, dy, dz;
# Line 598 | Line 622 | void Integrator::constrainB( void ){
622          vyab = vel[ay] - vel[by];
623          vzab = vel[az] - vel[bz];
624  
625 <        rxab = pos[ax] - pos[bx];
626 <        ryab = pos[ay] - pos[by];
627 <        rzab = pos[az] - pos[bz];
625 >        rab[0] = pos[ax] - pos[bx];
626 >        rab[1] = pos[ay] - pos[by];
627 >        rab[2] = pos[az] - pos[bz];
628          
629 <
606 <        rxab = rxab - info->box_x * copysign(1, rxab)
607 <          * (int)( fabs(rxab / info->box_x) + 0.5);
608 <        ryab = ryab - info->box_y * copysign(1, ryab)
609 <          * (int)( fabs(ryab / info->box_y) + 0.5);
610 <        rzab = rzab - info->box_z * copysign(1, rzab)
611 <          * (int)( fabs(rzab / info->box_z) + 0.5);
629 >        info->wrapVector( rab );
630          
631          rma = 1.0 / atoms[a]->getMass();
632          rmb = 1.0 / atoms[b]->getMass();
633  
634 <        rvab = rxab * vxab + ryab * vyab + rzab * vzab;
634 >        rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
635            
636          gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] );
637  
638          if (fabs(gab) > tol) {
639            
640 <          dx = rxab * gab;
641 <          dy = ryab * gab;
642 <          dz = rzab * gab;
640 >          dx = rab[0] * gab;
641 >          dy = rab[1] * gab;
642 >          dz = rab[2] * gab;
643            
644            vel[ax] += rma * dx;
645            vel[ay] += rma * dy;
# Line 677 | 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 738 | 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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