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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 558 by mmeineke, Thu Jun 19 19:21:23 2003 UTC vs.
Revision 601 by gezelter, Mon Jul 14 23:06:09 2003 UTC

# Line 1 | Line 1
1   #include <iostream>
2   #include <cstdlib>
3 + #include <cmath>
4  
5   #ifdef IS_MPI
6   #include "mpiSimulation.hpp"
# Line 10 | Line 11
11   #include "simError.h"
12  
13  
14 < Integrator::Integrator( SimInfo* theInfo, ForceFields* the_ff ){
14 > Integrator::Integrator( SimInfo *theInfo, ForceFields* the_ff ){
15    
16    info = theInfo;
17    myFF = the_ff;
# Line 33 | Line 34 | Integrator::Integrator( SimInfo* theInfo, ForceFields*
34    constrainedDsqr = NULL;
35    moving          = NULL;
36    moved           = NULL;
37 <  prePos          = NULL;
37 >  oldPos          = NULL;
38    
39    nConstrained = 0;
40  
# Line 48 | Line 49 | Integrator::~Integrator() {
49      delete[] constrainedDsqr;
50      delete[] moving;
51      delete[] moved;
52 <    delete[] prePos;
52 < k
52 >    delete[] oldPos;
53    }
54    
55   }
# Line 72 | Line 72 | void Integrator::checkConstraints( void ){
72      for(int j=0; j<molecules[i].getNBonds(); j++){
73        
74        constrained = theArray[j]->is_constrained();
75 +
76 +      std::cerr << "Is the folowing bond constrained \n";
77 +      theArray[j]->printMe();
78        
79        if(constrained){
80          
81 +        std::cerr << "Yes\n";
82 +
83          dummy_plug = theArray[j]->get_constraint();
84          temp_con[nConstrained].set_a( dummy_plug->get_a() );
85          temp_con[nConstrained].set_b( dummy_plug->get_b() );
# Line 82 | Line 87 | void Integrator::checkConstraints( void ){
87          
88          nConstrained++;
89          constrained = 0;
90 <      }
90 >      }
91 >      else std::cerr << "No.\n";
92      }
93  
94      theArray = (SRI**) molecules[i].getMyBends();
# Line 137 | Line 143 | void Integrator::checkConstraints( void ){
143        constrainedA[i] = temp_con[i].get_a();
144        constrainedB[i] = temp_con[i].get_b();
145        constrainedDsqr[i] = temp_con[i].get_dsqr();
146 +
147      }
148  
149      
# Line 147 | Line 154 | void Integrator::checkConstraints( void ){
154      moving = new int[nAtoms];
155      moved  = new int[nAtoms];
156  
157 <    prePos = new double[nAtoms*3];
157 >    oldPos = new double[nAtoms*3];
158    }
159    
160    delete[] temp_con;
# Line 157 | Line 164 | void Integrator::integrate( void ){
164   void Integrator::integrate( void ){
165  
166    int i, j;                         // loop counters
160 –  double kE = 0.0;                  // the kinetic energy  
161 –  double rot_kE;
162 –  double trans_kE;
163 –  int tl;                        // the time loop conter
164 –  double dt2;                       // half the dt
167  
166 –  double vx, vy, vz;    // the velocities
167 –  double vx2, vy2, vz2; // the square of the velocities
168 –  double rx, ry, rz;    // the postitions
169 –  
170 –  double ji[3];   // the body frame angular momentum
171 –  double jx2, jy2, jz2; // the square of the angular momentums
172 –  double Tb[3];   // torque in the body frame
173 –  double angle;   // the angle through which to rotate the rotation matrix
174 –  double A[3][3]; // the rotation matrix
175 –  double press[9];
176 –
177 –  double dt          = info->dt;
168    double runTime     = info->run_time;
169    double sampleTime  = info->sampleTime;
170    double statusTime  = info->statusTime;
# Line 189 | Line 179 | void Integrator::integrate( void ){
179    int isError;
180  
181    tStats   = new Thermo( info );
182 <  e_out    = new StatWriter( info );
183 <  dump_out = new DumpWriter( info );
184 <
185 <  Atom** atoms = info->atoms;
182 >  statOut  = new StatWriter( info );
183 >  dumpOut  = new DumpWriter( info );
184 >
185 >  atoms = info->atoms;
186    DirectionalAtom* dAtom;
187 +
188 +  dt = info->dt;
189    dt2 = 0.5 * dt;
190  
191    // initialize the forces before the first step
# Line 205 | Line 197 | void Integrator::integrate( void ){
197      tStats->velocitize();
198    }
199    
200 <  dump_out->writeDump( 0.0 );
201 <  e_out->writeStat( 0.0 );
200 >  dumpOut->writeDump( 0.0 );
201 >  statOut->writeStat( 0.0 );
202    
203    calcPot     = 0;
204    calcStress  = 0;
# Line 215 | Line 207 | void Integrator::integrate( void ){
207    currStatus  = statusTime;
208    currTime    = 0.0;;
209  
210 +
211 +  readyCheck();
212 +
213 + #ifdef IS_MPI
214 +  strcpy( checkPointMsg,
215 +          "The integrator is ready to go." );
216 +  MPIcheckPoint();
217 + #endif // is_mpi
218 +
219    while( currTime < runTime ){
220  
221      if( (currTime+dt) >= currStatus ){
222        calcPot = 1;
223        calcStress = 1;
224      }
225 <    
225 >
226      integrateStep( calcPot, calcStress );
227        
228      currTime += dt;
# Line 234 | Line 235 | void Integrator::integrate( void ){
235      }
236  
237      if( currTime >= currSample ){
238 <      dump_out->writeDump( currTime );
238 >      dumpOut->writeDump( currTime );
239        currSample += sampleTime;
240      }
241  
242      if( currTime >= currStatus ){
243 <      e_out->writeStat( time * dt );
243 >      statOut->writeStat( currTime );
244        calcPot = 0;
245        calcStress = 0;
246        currStatus += statusTime;
247      }
248 +
249 + #ifdef IS_MPI
250 +    strcpy( checkPointMsg,
251 +            "successfully took a time step." );
252 +    MPIcheckPoint();
253 + #endif // is_mpi
254 +
255    }
256  
257 <  dump_out->writeFinal();
257 >  dumpOut->writeFinal(currTime);
258  
259 <  delete dump_out;
260 <  delete e_out;
259 >  delete dumpOut;
260 >  delete statOut;
261   }
262  
263   void Integrator::integrateStep( int calcPot, int calcStress ){
264  
265 +
266 +      
267    // Position full step, and velocity half step
268  
269 <  //preMove();
269 >  preMove();
270    moveA();
271    if( nConstrained ) constrainA();
272  
# Line 274 | Line 284 | void Integrator::moveA( void ){
284  
285   void Integrator::moveA( void ){
286    
287 <  int i,j,k;
278 <  int atomIndex, aMatIndex;
287 >  int i, j;
288    DirectionalAtom* dAtom;
289 <  double Tb[3];
290 <  double ji[3];
289 >  double Tb[3], ji[3];
290 >  double A[3][3], I[3][3];
291 >  double angle;
292 >  double vel[3], pos[3], frc[3];
293 >  double mass;
294  
295    for( i=0; i<nAtoms; i++ ){
284 –    atomIndex = i * 3;
285 –    aMatIndex = i * 9;
286 –    
287 –    // velocity half step
288 –    for( j=atomIndex; j<(atomIndex+3); j++ )
289 –      vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
296  
297 <    // position whole step    
298 <    for( j=atomIndex; j<(atomIndex+3); j++ )
297 >    atoms[i]->getVel( vel );
298 >    atoms[i]->getPos( pos );
299 >    atoms[i]->getFrc( frc );
300 >
301 >    mass = atoms[i]->getMass();
302 >
303 >    for (j=0; j < 3; j++) {
304 >      // velocity half step
305 >      vel[j] += ( dt2 * frc[j] / mass ) * eConvert;
306 >      // position whole step
307        pos[j] += dt * vel[j];
308 +    }
309  
310 <  
310 >    atoms[i]->setVel( vel );
311 >    atoms[i]->setPos( pos );
312 >
313      if( atoms[i]->isDirectional() ){
314  
315        dAtom = (DirectionalAtom *)atoms[i];
316            
317        // get and convert the torque to body frame
318        
319 <      Tb[0] = dAtom->getTx();
303 <      Tb[1] = dAtom->getTy();
304 <      Tb[2] = dAtom->getTz();
305 <      
319 >      dAtom->getTrq( Tb );
320        dAtom->lab2Body( Tb );
321 <      
321 >
322        // get the angular momentum, and propagate a half step
323 +
324 +      dAtom->getJ( ji );
325 +
326 +      for (j=0; j < 3; j++)
327 +        ji[j] += (dt2 * Tb[j]) * eConvert;
328        
310 –      ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
311 –      ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
312 –      ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
313 –      
329        // use the angular velocities to propagate the rotation matrix a
330        // full time step
331 <      
331 >
332 >      dAtom->getA(A);
333 >      dAtom->getI(I);
334 >    
335        // rotate about the x-axis      
336 <      angle = dt2 * ji[0] / dAtom->getIxx();
337 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
338 <      
336 >      angle = dt2 * ji[0] / I[0][0];
337 >      this->rotate( 1, 2, angle, ji, A );
338 >
339        // rotate about the y-axis
340 <      angle = dt2 * ji[1] / dAtom->getIyy();
341 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
340 >      angle = dt2 * ji[1] / I[1][1];
341 >      this->rotate( 2, 0, angle, ji, A );
342        
343        // rotate about the z-axis
344 <      angle = dt * ji[2] / dAtom->getIzz();
345 <      this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] );
344 >      angle = dt * ji[2] / I[2][2];
345 >      this->rotate( 0, 1, angle, ji, A);
346        
347        // rotate about the y-axis
348 <      angle = dt2 * ji[1] / dAtom->getIyy();
349 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
348 >      angle = dt2 * ji[1] / I[1][1];
349 >      this->rotate( 2, 0, angle, ji, A );
350        
351         // rotate about the x-axis
352 <      angle = dt2 * ji[0] / dAtom->getIxx();
353 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
352 >      angle = dt2 * ji[0] / I[0][0];
353 >      this->rotate( 1, 2, angle, ji, A );
354        
355 <      dAtom->setJx( ji[0] );
356 <      dAtom->setJy( ji[1] );
357 <      dAtom->setJz( ji[2] );
358 <    }
359 <    
355 >
356 >      dAtom->setJ( ji );
357 >      dAtom->setA( A  );
358 >          
359 >    }    
360    }
361   }
362  
363  
364   void Integrator::moveB( void ){
365 <  int i,j,k;
348 <  int atomIndex;
365 >  int i, j;
366    DirectionalAtom* dAtom;
367 <  double Tb[3];
368 <  double ji[3];
367 >  double Tb[3], ji[3];
368 >  double vel[3], frc[3];
369 >  double mass;
370  
371    for( i=0; i<nAtoms; i++ ){
372 <    atomIndex = i * 3;
372 >
373 >    atoms[i]->getVel( vel );
374 >    atoms[i]->getFrc( frc );
375  
376 <    // velocity half step
357 <    for( j=atomIndex; j<(atomIndex+3); j++ )
358 <      vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
376 >    mass = atoms[i]->getMass();
377  
378 +    // velocity half step
379 +    for (j=0; j < 3; j++)
380 +      vel[j] += ( dt2 * frc[j] / mass ) * eConvert;
381 +    
382 +    atoms[i]->setVel( vel );
383 +
384      if( atoms[i]->isDirectional() ){
385 <      
385 >
386        dAtom = (DirectionalAtom *)atoms[i];
387 <      
388 <      // get and convert the torque to body frame
389 <      
390 <      Tb[0] = dAtom->getTx();
367 <      Tb[1] = dAtom->getTy();
368 <      Tb[2] = dAtom->getTz();
369 <      
387 >
388 >      // get and convert the torque to body frame      
389 >
390 >      dAtom->getTrq( Tb );
391        dAtom->lab2Body( Tb );
392 +
393 +      // get the angular momentum, and propagate a half step
394 +
395 +      dAtom->getJ( ji );
396 +
397 +      for (j=0; j < 3; j++)
398 +        ji[j] += (dt2 * Tb[j]) * eConvert;
399        
400 <      // get the angular momentum, and complete the angular momentum
401 <      // half step
374 <      
375 <      ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
376 <      ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
377 <      ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
378 <      
379 <      jx2 = ji[0] * ji[0];
380 <      jy2 = ji[1] * ji[1];
381 <      jz2 = ji[2] * ji[2];
382 <      
383 <      dAtom->setJx( ji[0] );
384 <      dAtom->setJy( ji[1] );
385 <      dAtom->setJz( ji[2] );
400 >
401 >      dAtom->setJ( ji );
402      }
403    }
388 –
404   }
405  
406   void Integrator::preMove( void ){
407 <  int i;
407 >  int i, j;
408 >  double pos[3];
409  
410    if( nConstrained ){
411 <    if( oldAtoms != nAtoms ){
412 <      
413 <      // save oldAtoms to check for lode balanceing later on.
414 <      
415 <      oldAtoms = nAtoms;
416 <      
417 <      delete[] moving;
418 <      delete[] moved;
419 <      delete[] oldPos;
404 <      
405 <      moving = new int[nAtoms];
406 <      moved  = new int[nAtoms];
407 <      
408 <      oldPos = new double[nAtoms*3];
411 >
412 >    for(i=0; i < nAtoms; i++) {
413 >
414 >      atoms[i]->getPos( pos );
415 >
416 >      for (j = 0; j < 3; j++) {        
417 >        oldPos[3*i + j] = pos[j];
418 >      }
419 >
420      }
421 <  
422 <    for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i];
412 <  }
413 < }  
421 >  }  
422 > }
423  
424   void Integrator::constrainA(){
425  
426    int i,j,k;
427    int done;
428 <  double pxab, pyab, pzab;
429 <  double rxab, ryab, rzab;
430 <  int a, b;
428 >  double posA[3], posB[3];
429 >  double velA[3], velB[3];
430 >  double pab[3];
431 >  double rab[3];
432 >  int a, b, ax, ay, az, bx, by, bz;
433    double rma, rmb;
434    double dx, dy, dz;
435 +  double rpab;
436    double rabsq, pabsq, rpabsq;
437    double diffsq;
438    double gab;
439    int iteration;
440  
441 <
430 <  
431 <  for( i=0; i<nAtoms; i++){
432 <    
441 >  for( i=0; i<nAtoms; i++){    
442      moving[i] = 0;
443      moved[i]  = 1;
444    }
445 <  
437 <  
445 >
446    iteration = 0;
447    done = 0;
448    while( !done && (iteration < maxIteration )){
# Line 444 | Line 452 | void Integrator::constrainA(){
452  
453        a = constrainedA[i];
454        b = constrainedB[i];
455 <    
455 >      
456 >      ax = (a*3) + 0;
457 >      ay = (a*3) + 1;
458 >      az = (a*3) + 2;
459 >
460 >      bx = (b*3) + 0;
461 >      by = (b*3) + 1;
462 >      bz = (b*3) + 2;
463 >
464        if( moved[a] || moved[b] ){
465 <        
466 <        pxab = pos[3*a+0] - pos[3*b+0];
467 <        pyab = pos[3*a+1] - pos[3*b+1];
468 <        pzab = pos[3*a+2] - pos[3*b+2];
465 >        
466 >        atoms[a]->getPos( posA );
467 >        atoms[b]->getPos( posB );
468 >        
469 >        for (j = 0; j < 3; j++ )
470 >          pab[j] = posA[j] - posB[j];
471 >        
472 >        //periodic boundary condition
473  
474 <        //periodic boundary condition
455 <        pxab = pxab - info->box_x * copysign(1, pxab)
456 <          * int(pxab / info->box_x + 0.5);
457 <        pyab = pyab - info->box_y * copysign(1, pyab)
458 <          * int(pyab / info->box_y + 0.5);
459 <        pzab = pzab - info->box_z * copysign(1, pzab)
460 <          * int(pzab / info->box_z + 0.5);
461 <      
462 <        pabsq = pxab * pxab + pyab * pyab + pzab * pzab;
463 <        rabsq = constraintedDsqr[i];
464 <        diffsq = pabsq - rabsq;
474 >        info->wrapVector( pab );
475  
476 +        pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
477 +
478 +        rabsq = constrainedDsqr[i];
479 +        diffsq = rabsq - pabsq;
480 +
481          // the original rattle code from alan tidesley
482 <        if (fabs(diffsq) > tol*rabsq*2) {
483 <          rxab = oldPos[3*a+0] - oldPos[3*b+0];
484 <          ryab = oldPos[3*a+1] - oldPos[3*b+1];
485 <          rzab = oldPos[3*a+2] - oldPos[3*b+2];
471 <
472 <          rxab = rxab - info->box_x * copysign(1, rxab)
473 <            * int(rxab / info->box_x + 0.5);
474 <          ryab = ryab - info->box_y * copysign(1, ryab)
475 <            * int(ryab / info->box_y + 0.5);
476 <          rzab = rzab - info->box_z * copysign(1, rzab)
477 <            * int(rzab / info->box_z + 0.5);
482 >        if (fabs(diffsq) > (tol*rabsq*2)) {
483 >          rab[0] = oldPos[ax] - oldPos[bx];
484 >          rab[1] = oldPos[ay] - oldPos[by];
485 >          rab[2] = oldPos[az] - oldPos[bz];
486  
487 <          rpab = rxab * pxab + ryab * pyab + rzab * pzab;
487 >          info->wrapVector( rab );
488 >
489 >          rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
490 >
491            rpabsq = rpab * rpab;
492  
493  
494            if (rpabsq < (rabsq * -diffsq)){
495 +
496   #ifdef IS_MPI
497              a = atoms[a]->getGlobalIndex();
498              b = atoms[b]->getGlobalIndex();
499   #endif //is_mpi
500              sprintf( painCave.errMsg,
501 <                     "Constraint failure in constrainA at atom %d and %d\n.",
501 >                     "Constraint failure in constrainA at atom %d and %d.\n",
502                       a, b );
503              painCave.isFatal = 1;
504              simError();
# Line 494 | Line 506 | void Integrator::constrainA(){
506  
507            rma = 1.0 / atoms[a]->getMass();
508            rmb = 1.0 / atoms[b]->getMass();
509 <          
509 >
510            gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab );
499 –          dx = rxab * gab;
500 –          dy = ryab * gab;
501 –          dz = rzab * gab;
511  
512 <          pos[3*a+0] += rma * dx;
513 <          pos[3*a+1] += rma * dy;
514 <          pos[3*a+2] += rma * dz;
512 >          dx = rab[0] * gab;
513 >          dy = rab[1] * gab;
514 >          dz = rab[2] * gab;
515  
516 <          pos[3*b+0] -= rmb * dx;
517 <          pos[3*b+1] -= rmb * dy;
518 <          pos[3*b+2] -= rmb * dz;
516 >          posA[0] += rma * dx;
517 >          posA[1] += rma * dy;
518 >          posA[2] += rma * dz;
519  
520 +          atoms[a]->setPos( posA );
521 +
522 +          posB[0] -= rmb * dx;
523 +          posB[1] -= rmb * dy;
524 +          posB[2] -= rmb * dz;
525 +
526 +          atoms[b]->setPos( posB );
527 +
528            dx = dx / dt;
529            dy = dy / dt;
530            dz = dz / dt;
531  
532 <          vel[3*a+0] += rma * dx;
516 <          vel[3*a+1] += rma * dy;
517 <          vel[3*a+2] += rma * dz;
532 >          atoms[a]->getVel( velA );
533  
534 <          vel[3*b+0] -= rmb * dx;
535 <          vel[3*b+1] -= rmb * dy;
536 <          vel[3*b+2] -= rmb * dz;
534 >          velA[0] += rma * dx;
535 >          velA[1] += rma * dy;
536 >          velA[2] += rma * dz;
537  
538 +          atoms[a]->setVel( velA );
539 +
540 +          atoms[b]->getVel( velB );
541 +
542 +          velB[0] -= rmb * dx;
543 +          velB[1] -= rmb * dy;
544 +          velB[2] -= rmb * dz;
545 +
546 +          atoms[b]->setVel( velB );
547 +
548            moving[a] = 1;
549            moving[b] = 1;
550            done = 0;
# Line 538 | Line 563 | void Integrator::constrainA(){
563  
564    if( !done ){
565  
566 <    sprintf( painCae.errMsg,
566 >    sprintf( painCave.errMsg,
567               "Constraint failure in constrainA, too many iterations: %d\n",
568 <             iterations );
568 >             iteration );
569      painCave.isFatal = 1;
570      simError();
571    }
# Line 551 | Line 576 | void Integrator::constrainB( void ){
576    
577    int i,j,k;
578    int done;
579 +  double posA[3], posB[3];
580 +  double velA[3], velB[3];
581    double vxab, vyab, vzab;
582 <  double rxab, ryab, rzab;
583 <  int a, b;
582 >  double rab[3];
583 >  int a, b, ax, ay, az, bx, by, bz;
584    double rma, rmb;
585    double dx, dy, dz;
586    double rabsq, pabsq, rvab;
# Line 561 | Line 588 | void Integrator::constrainB( void ){
588    double gab;
589    int iteration;
590  
591 <  for(i=0; i<nAtom; i++){
591 >  for(i=0; i<nAtoms; i++){
592      moving[i] = 0;
593      moved[i] = 1;
594    }
595  
596    done = 0;
597 +  iteration = 0;
598    while( !done && (iteration < maxIteration ) ){
599  
600 +    done = 1;
601 +
602      for(i=0; i<nConstrained; i++){
603        
604        a = constrainedA[i];
605        b = constrainedB[i];
606  
607 +      ax = (a*3) + 0;
608 +      ay = (a*3) + 1;
609 +      az = (a*3) + 2;
610 +
611 +      bx = (b*3) + 0;
612 +      by = (b*3) + 1;
613 +      bz = (b*3) + 2;
614 +
615        if( moved[a] || moved[b] ){
578 –        
579 –        vxab = vel[3*a+0] - vel[3*b+0];
580 –        vyab = vel[3*a+1] - vel[3*b+1];
581 –        vzab = vel[3*a+2] - vel[3*b+2];
616  
617 <        rxab = pos[3*a+0] - pos[3*b+0];q
618 <        ryab = pos[3*a+1] - pos[3*b+1];
619 <        rzab = pos[3*a+2] - pos[3*b+2];
620 <        
621 <        rxab = rxab - info->box_x * copysign(1, rxab)
622 <          * int(rxab / info->box_x + 0.5);
589 <        ryab = ryab - info->box_y * copysign(1, ryab)
590 <          * int(ryab / info->box_y + 0.5);
591 <        rzab = rzab - info->box_z * copysign(1, rzab)
592 <          * int(rzab / info->box_z + 0.5);
617 >        atoms[a]->getVel( velA );
618 >        atoms[b]->getVel( velB );
619 >          
620 >        vxab = velA[0] - velB[0];
621 >        vyab = velA[1] - velB[1];
622 >        vzab = velA[2] - velB[2];
623  
624 +        atoms[a]->getPos( posA );
625 +        atoms[b]->getPos( posB );
626 +
627 +        for (j = 0; j < 3; j++)
628 +          rab[j] = posA[j] - posB[j];
629 +          
630 +        info->wrapVector( rab );
631 +        
632          rma = 1.0 / atoms[a]->getMass();
633          rmb = 1.0 / atoms[b]->getMass();
634  
635 <        rvab = rxab * vxab + ryab * vyab + rzab * vzab;
635 >        rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
636            
637 <        gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] );
637 >        gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] );
638  
639          if (fabs(gab) > tol) {
640            
641 <          dx = rxab * gab;
642 <          dy = ryab * gab;
643 <          dz = rzab * gab;
644 <          
645 <          vel[3*a+0] += rma * dx;
646 <          vel[3*a+1] += rma * dy;
647 <          vel[3*a+2] += rma * dz;
641 >          dx = rab[0] * gab;
642 >          dy = rab[1] * gab;
643 >          dz = rab[2] * gab;
644 >        
645 >          velA[0] += rma * dx;
646 >          velA[1] += rma * dy;
647 >          velA[2] += rma * dz;
648  
649 <          vel[3*b+0] -= rmb * dx;
650 <          vel[3*b+1] -= rmb * dy;
651 <          vel[3*b+2] -= rmb * dz;
649 >          atoms[a]->setVel( velA );
650 >
651 >          velB[0] -= rmb * dx;
652 >          velB[1] -= rmb * dy;
653 >          velB[2] -= rmb * dz;
654 >
655 >          atoms[b]->setVel( velB );
656            
657            moving[a] = 1;
658            moving[b] = 1;
# Line 626 | Line 668 | void Integrator::constrainB( void ){
668      
669      iteration++;
670    }
671 <
671 >  
672    if( !done ){
673  
674    
675 <    sprintf( painCae.errMsg,
675 >    sprintf( painCave.errMsg,
676               "Constraint failure in constrainB, too many iterations: %d\n",
677 <             iterations );
677 >             iteration );
678      painCave.isFatal = 1;
679      simError();
680    }
681  
682   }
683  
642 –
643 –
644 –
645 –
646 –
647 –
684   void Integrator::rotate( int axes1, int axes2, double angle, double ji[3],
685                           double A[3][3] ){
686  
# Line 713 | Line 749 | void Integrator::rotate( int axes1, int axes2, double
749    //            A[][] = A[][] * transpose(rot[][])
750  
751  
752 <  // NOte for as yet unknown reason, we are setting the performing the
752 >  // NOte for as yet unknown reason, we are performing the
753    // calculation as:
754    //                transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
755  

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