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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 559 by mmeineke, Thu Jun 19 22:02:44 2003 UTC vs.
Revision 637 by gezelter, Thu Jul 17 21:50:01 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 | Integrator::Integrator( SimInfo* theInfo, ForceFields*
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 >    delete[] oldPos;
53    }
54    
55   }
# Line 71 | Line 72 | void Integrator::checkConstraints( void ){
72      for(int j=0; j<molecules[i].getNBonds(); j++){
73        
74        constrained = theArray[j]->is_constrained();
75 <      
75 >
76        if(constrained){
77 <        
77 >
78          dummy_plug = theArray[j]->get_constraint();
79          temp_con[nConstrained].set_a( dummy_plug->get_a() );
80          temp_con[nConstrained].set_b( dummy_plug->get_b() );
# Line 81 | Line 82 | void Integrator::checkConstraints( void ){
82          
83          nConstrained++;
84          constrained = 0;
85 <      }
85 >      }
86      }
87  
88      theArray = (SRI**) molecules[i].getMyBends();
# Line 136 | Line 137 | void Integrator::checkConstraints( void ){
137        constrainedA[i] = temp_con[i].get_a();
138        constrainedB[i] = temp_con[i].get_b();
139        constrainedDsqr[i] = temp_con[i].get_dsqr();
140 +
141      }
142  
143      
# Line 146 | Line 148 | void Integrator::checkConstraints( void ){
148      moving = new int[nAtoms];
149      moved  = new int[nAtoms];
150  
151 <    prePos = new double[nAtoms*3];
151 >    oldPos = new double[nAtoms*3];
152    }
153    
154    delete[] temp_con;
# Line 156 | Line 158 | void Integrator::integrate( void ){
158   void Integrator::integrate( void ){
159  
160    int i, j;                         // loop counters
159 –  double kE = 0.0;                  // the kinetic energy  
160 –  double rot_kE;
161 –  double trans_kE;
162 –  int tl;                        // the time loop conter
163 –  double dt2;                       // half the dt
161  
165 –  double vx, vy, vz;    // the velocities
166 –  double vx2, vy2, vz2; // the square of the velocities
167 –  double rx, ry, rz;    // the postitions
168 –  
169 –  double ji[3];   // the body frame angular momentum
170 –  double jx2, jy2, jz2; // the square of the angular momentums
171 –  double Tb[3];   // torque in the body frame
172 –  double angle;   // the angle through which to rotate the rotation matrix
173 –  double A[3][3]; // the rotation matrix
174 –  double press[9];
175 –
176 –  double dt          = info->dt;
162    double runTime     = info->run_time;
163    double sampleTime  = info->sampleTime;
164    double statusTime  = info->statusTime;
# Line 188 | Line 173 | void Integrator::integrate( void ){
173    int isError;
174  
175    tStats   = new Thermo( info );
176 <  e_out    = new StatWriter( info );
177 <  dump_out = new DumpWriter( info );
176 >  statOut  = new StatWriter( info );
177 >  dumpOut  = new DumpWriter( info );
178  
179 <  Atom** atoms = info->atoms;
179 >  atoms = info->atoms;
180    DirectionalAtom* dAtom;
181 +
182 +  dt = info->dt;
183    dt2 = 0.5 * dt;
184  
185    // initialize the forces before the first step
# Line 204 | Line 191 | void Integrator::integrate( void ){
191      tStats->velocitize();
192    }
193    
194 <  dump_out->writeDump( 0.0 );
195 <  e_out->writeStat( 0.0 );
194 >  dumpOut->writeDump( 0.0 );
195 >  statOut->writeStat( 0.0 );
196    
197    calcPot     = 0;
198    calcStress  = 0;
# Line 229 | Line 216 | void Integrator::integrate( void ){
216        calcPot = 1;
217        calcStress = 1;
218      }
219 <    
219 >
220      integrateStep( calcPot, calcStress );
221        
222      currTime += dt;
223 +    info->setTime(currTime);
224  
225      if( info->setTemp ){
226        if( currTime >= currThermal ){
# Line 242 | Line 230 | void Integrator::integrate( void ){
230      }
231  
232      if( currTime >= currSample ){
233 <      dump_out->writeDump( currTime );
233 >      dumpOut->writeDump( currTime );
234        currSample += sampleTime;
235      }
236  
237      if( currTime >= currStatus ){
238 <      e_out->writeStat( time * dt );
238 >      statOut->writeStat( currTime );
239        calcPot = 0;
240        calcStress = 0;
241        currStatus += statusTime;
# Line 261 | Line 249 | void Integrator::integrate( void ){
249  
250    }
251  
252 <  dump_out->writeFinal();
252 >  dumpOut->writeFinal(currTime);
253  
254 <  delete dump_out;
255 <  delete e_out;
254 >  delete dumpOut;
255 >  delete statOut;
256   }
257  
258   void Integrator::integrateStep( int calcPot, int calcStress ){
259  
260 +
261 +      
262    // Position full step, and velocity half step
263  
264 <  //preMove();
264 >  preMove();
265    moveA();
266    if( nConstrained ) constrainA();
267  
268 +  
269 + #ifdef IS_MPI
270 +  strcpy( checkPointMsg, "Succesful moveA\n" );
271 +  MPIcheckPoint();
272 + #endif // is_mpi
273 +  
274 +
275    // calc forces
276  
277    myFF->doForces(calcPot,calcStress);
278 +
279 + #ifdef IS_MPI
280 +  strcpy( checkPointMsg, "Succesful doForces\n" );
281 +  MPIcheckPoint();
282 + #endif // is_mpi
283 +  
284  
285    // finish the velocity  half step
286    
287    moveB();
288    if( nConstrained ) constrainB();
289 <  
289 >  
290 > #ifdef IS_MPI
291 >  strcpy( checkPointMsg, "Succesful moveB\n" );
292 >  MPIcheckPoint();
293 > #endif // is_mpi
294 >  
295 >
296   }
297  
298  
299   void Integrator::moveA( void ){
300    
301 <  int i,j,k;
293 <  int atomIndex, aMatIndex;
301 >  int i, j;
302    DirectionalAtom* dAtom;
303 <  double Tb[3];
304 <  double ji[3];
303 >  double Tb[3], ji[3];
304 >  double A[3][3], I[3][3];
305 >  double angle;
306 >  double vel[3], pos[3], frc[3];
307 >  double mass;
308  
309    for( i=0; i<nAtoms; i++ ){
299 –    atomIndex = i * 3;
300 –    aMatIndex = i * 9;
301 –    
302 –    // velocity half step
303 –    for( j=atomIndex; j<(atomIndex+3); j++ )
304 –      vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
310  
311 <    // position whole step    
312 <    for( j=atomIndex; j<(atomIndex+3); j++ )
311 >    atoms[i]->getVel( vel );
312 >    atoms[i]->getPos( pos );
313 >    atoms[i]->getFrc( frc );
314 >
315 >    mass = atoms[i]->getMass();
316 >
317 >    for (j=0; j < 3; j++) {
318 >      // velocity half step
319 >      vel[j] += ( dt2 * frc[j] / mass ) * eConvert;
320 >      // position whole step
321        pos[j] += dt * vel[j];
322 +    }
323  
324 <  
324 >    atoms[i]->setVel( vel );
325 >    atoms[i]->setPos( pos );
326 >
327      if( atoms[i]->isDirectional() ){
328  
329        dAtom = (DirectionalAtom *)atoms[i];
330            
331        // get and convert the torque to body frame
332        
333 <      Tb[0] = dAtom->getTx();
318 <      Tb[1] = dAtom->getTy();
319 <      Tb[2] = dAtom->getTz();
320 <      
333 >      dAtom->getTrq( Tb );
334        dAtom->lab2Body( Tb );
335 <      
335 >
336        // get the angular momentum, and propagate a half step
337 +
338 +      dAtom->getJ( ji );
339 +
340 +      for (j=0; j < 3; j++)
341 +        ji[j] += (dt2 * Tb[j]) * eConvert;
342        
325 –      ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
326 –      ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
327 –      ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
328 –      
343        // use the angular velocities to propagate the rotation matrix a
344        // full time step
345 <      
346 <      // rotate about the x-axis      
347 <      angle = dt2 * ji[0] / dAtom->getIxx();
348 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
349 <      
345 >
346 >      dAtom->getA(A);
347 >      dAtom->getI(I);
348 >    
349 >      // rotate about the x-axis      
350 >      angle = dt2 * ji[0] / I[0][0];
351 >      this->rotate( 1, 2, angle, ji, A );
352 >
353        // rotate about the y-axis
354 <      angle = dt2 * ji[1] / dAtom->getIyy();
355 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
354 >      angle = dt2 * ji[1] / I[1][1];
355 >      this->rotate( 2, 0, angle, ji, A );
356        
357        // rotate about the z-axis
358 <      angle = dt * ji[2] / dAtom->getIzz();
359 <      this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] );
358 >      angle = dt * ji[2] / I[2][2];
359 >      this->rotate( 0, 1, angle, ji, A);
360        
361        // rotate about the y-axis
362 <      angle = dt2 * ji[1] / dAtom->getIyy();
363 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
362 >      angle = dt2 * ji[1] / I[1][1];
363 >      this->rotate( 2, 0, angle, ji, A );
364        
365         // rotate about the x-axis
366 <      angle = dt2 * ji[0] / dAtom->getIxx();
367 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
366 >      angle = dt2 * ji[0] / I[0][0];
367 >      this->rotate( 1, 2, angle, ji, A );
368        
369 <      dAtom->setJx( ji[0] );
370 <      dAtom->setJy( ji[1] );
371 <      dAtom->setJz( ji[2] );
372 <    }
373 <    
369 >
370 >      dAtom->setJ( ji );
371 >      dAtom->setA( A  );
372 >          
373 >    }    
374    }
375   }
376  
377  
378   void Integrator::moveB( void ){
379 <  int i,j,k;
363 <  int atomIndex;
379 >  int i, j;
380    DirectionalAtom* dAtom;
381 <  double Tb[3];
382 <  double ji[3];
381 >  double Tb[3], ji[3];
382 >  double vel[3], frc[3];
383 >  double mass;
384  
385    for( i=0; i<nAtoms; i++ ){
386 <    atomIndex = i * 3;
386 >
387 >    atoms[i]->getVel( vel );
388 >    atoms[i]->getFrc( frc );
389  
390 <    // velocity half step
372 <    for( j=atomIndex; j<(atomIndex+3); j++ )
373 <      vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
390 >    mass = atoms[i]->getMass();
391  
392 +    // velocity half step
393 +    for (j=0; j < 3; j++)
394 +      vel[j] += ( dt2 * frc[j] / mass ) * eConvert;
395 +    
396 +    atoms[i]->setVel( vel );
397 +
398      if( atoms[i]->isDirectional() ){
399 <      
399 >
400        dAtom = (DirectionalAtom *)atoms[i];
401 <      
402 <      // get and convert the torque to body frame
403 <      
404 <      Tb[0] = dAtom->getTx();
382 <      Tb[1] = dAtom->getTy();
383 <      Tb[2] = dAtom->getTz();
384 <      
401 >
402 >      // get and convert the torque to body frame      
403 >
404 >      dAtom->getTrq( Tb );
405        dAtom->lab2Body( Tb );
406 +
407 +      // get the angular momentum, and propagate a half step
408 +
409 +      dAtom->getJ( ji );
410 +
411 +      for (j=0; j < 3; j++)
412 +        ji[j] += (dt2 * Tb[j]) * eConvert;
413        
414 <      // get the angular momentum, and complete the angular momentum
415 <      // half step
389 <      
390 <      ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
391 <      ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
392 <      ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
393 <      
394 <      jx2 = ji[0] * ji[0];
395 <      jy2 = ji[1] * ji[1];
396 <      jz2 = ji[2] * ji[2];
397 <      
398 <      dAtom->setJx( ji[0] );
399 <      dAtom->setJy( ji[1] );
400 <      dAtom->setJz( ji[2] );
414 >
415 >      dAtom->setJ( ji );
416      }
417    }
403 –
418   }
419  
420   void Integrator::preMove( void ){
421 <  int i;
421 >  int i, j;
422 >  double pos[3];
423  
424    if( nConstrained ){
425 <    if( oldAtoms != nAtoms ){
426 <      
427 <      // save oldAtoms to check for lode balanceing later on.
428 <      
429 <      oldAtoms = nAtoms;
430 <      
431 <      delete[] moving;
432 <      delete[] moved;
433 <      delete[] oldPos;
419 <      
420 <      moving = new int[nAtoms];
421 <      moved  = new int[nAtoms];
422 <      
423 <      oldPos = new double[nAtoms*3];
425 >
426 >    for(i=0; i < nAtoms; i++) {
427 >
428 >      atoms[i]->getPos( pos );
429 >
430 >      for (j = 0; j < 3; j++) {        
431 >        oldPos[3*i + j] = pos[j];
432 >      }
433 >
434      }
435 <  
436 <    for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i];
427 <  }
428 < }  
435 >  }  
436 > }
437  
438   void Integrator::constrainA(){
439  
440    int i,j,k;
441    int done;
442 <  double pxab, pyab, pzab;
443 <  double rxab, ryab, rzab;
444 <  int a, b;
442 >  double posA[3], posB[3];
443 >  double velA[3], velB[3];
444 >  double pab[3];
445 >  double rab[3];
446 >  int a, b, ax, ay, az, bx, by, bz;
447    double rma, rmb;
448    double dx, dy, dz;
449 +  double rpab;
450    double rabsq, pabsq, rpabsq;
451    double diffsq;
452    double gab;
453    int iteration;
454  
455 <
445 <  
446 <  for( i=0; i<nAtoms; i++){
447 <    
455 >  for( i=0; i<nAtoms; i++){    
456      moving[i] = 0;
457      moved[i]  = 1;
458    }
459 <  
452 <  
459 >
460    iteration = 0;
461    done = 0;
462    while( !done && (iteration < maxIteration )){
# Line 459 | Line 466 | void Integrator::constrainA(){
466  
467        a = constrainedA[i];
468        b = constrainedB[i];
469 <    
469 >      
470 >      ax = (a*3) + 0;
471 >      ay = (a*3) + 1;
472 >      az = (a*3) + 2;
473 >
474 >      bx = (b*3) + 0;
475 >      by = (b*3) + 1;
476 >      bz = (b*3) + 2;
477 >
478        if( moved[a] || moved[b] ){
479 <        
480 <        pxab = pos[3*a+0] - pos[3*b+0];
481 <        pyab = pos[3*a+1] - pos[3*b+1];
482 <        pzab = pos[3*a+2] - pos[3*b+2];
479 >        
480 >        atoms[a]->getPos( posA );
481 >        atoms[b]->getPos( posB );
482 >        
483 >        for (j = 0; j < 3; j++ )
484 >          pab[j] = posA[j] - posB[j];
485 >        
486 >        //periodic boundary condition
487  
488 <        //periodic boundary condition
470 <        pxab = pxab - info->box_x * copysign(1, pxab)
471 <          * int(pxab / info->box_x + 0.5);
472 <        pyab = pyab - info->box_y * copysign(1, pyab)
473 <          * int(pyab / info->box_y + 0.5);
474 <        pzab = pzab - info->box_z * copysign(1, pzab)
475 <          * int(pzab / info->box_z + 0.5);
476 <      
477 <        pabsq = pxab * pxab + pyab * pyab + pzab * pzab;
478 <        rabsq = constraintedDsqr[i];
479 <        diffsq = pabsq - rabsq;
488 >        info->wrapVector( pab );
489  
490 +        pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
491 +
492 +        rabsq = constrainedDsqr[i];
493 +        diffsq = rabsq - pabsq;
494 +
495          // the original rattle code from alan tidesley
496 <        if (fabs(diffsq) > tol*rabsq*2) {
497 <          rxab = oldPos[3*a+0] - oldPos[3*b+0];
498 <          ryab = oldPos[3*a+1] - oldPos[3*b+1];
499 <          rzab = oldPos[3*a+2] - oldPos[3*b+2];
486 <
487 <          rxab = rxab - info->box_x * copysign(1, rxab)
488 <            * int(rxab / info->box_x + 0.5);
489 <          ryab = ryab - info->box_y * copysign(1, ryab)
490 <            * int(ryab / info->box_y + 0.5);
491 <          rzab = rzab - info->box_z * copysign(1, rzab)
492 <            * int(rzab / info->box_z + 0.5);
496 >        if (fabs(diffsq) > (tol*rabsq*2)) {
497 >          rab[0] = oldPos[ax] - oldPos[bx];
498 >          rab[1] = oldPos[ay] - oldPos[by];
499 >          rab[2] = oldPos[az] - oldPos[bz];
500  
501 <          rpab = rxab * pxab + ryab * pyab + rzab * pzab;
501 >          info->wrapVector( rab );
502 >
503 >          rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
504 >
505            rpabsq = rpab * rpab;
506  
507  
508            if (rpabsq < (rabsq * -diffsq)){
509 +
510   #ifdef IS_MPI
511              a = atoms[a]->getGlobalIndex();
512              b = atoms[b]->getGlobalIndex();
513   #endif //is_mpi
514              sprintf( painCave.errMsg,
515 <                     "Constraint failure in constrainA at atom %d and %d\n.",
515 >                     "Constraint failure in constrainA at atom %d and %d.\n",
516                       a, b );
517              painCave.isFatal = 1;
518              simError();
# Line 509 | Line 520 | void Integrator::constrainA(){
520  
521            rma = 1.0 / atoms[a]->getMass();
522            rmb = 1.0 / atoms[b]->getMass();
523 <          
523 >
524            gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab );
514 –          dx = rxab * gab;
515 –          dy = ryab * gab;
516 –          dz = rzab * gab;
525  
526 <          pos[3*a+0] += rma * dx;
527 <          pos[3*a+1] += rma * dy;
528 <          pos[3*a+2] += rma * dz;
526 >          dx = rab[0] * gab;
527 >          dy = rab[1] * gab;
528 >          dz = rab[2] * gab;
529  
530 <          pos[3*b+0] -= rmb * dx;
531 <          pos[3*b+1] -= rmb * dy;
532 <          pos[3*b+2] -= rmb * dz;
530 >          posA[0] += rma * dx;
531 >          posA[1] += rma * dy;
532 >          posA[2] += rma * dz;
533  
534 +          atoms[a]->setPos( posA );
535 +
536 +          posB[0] -= rmb * dx;
537 +          posB[1] -= rmb * dy;
538 +          posB[2] -= rmb * dz;
539 +
540 +          atoms[b]->setPos( posB );
541 +
542            dx = dx / dt;
543            dy = dy / dt;
544            dz = dz / dt;
545  
546 <          vel[3*a+0] += rma * dx;
531 <          vel[3*a+1] += rma * dy;
532 <          vel[3*a+2] += rma * dz;
546 >          atoms[a]->getVel( velA );
547  
548 <          vel[3*b+0] -= rmb * dx;
549 <          vel[3*b+1] -= rmb * dy;
550 <          vel[3*b+2] -= rmb * dz;
548 >          velA[0] += rma * dx;
549 >          velA[1] += rma * dy;
550 >          velA[2] += rma * dz;
551  
552 +          atoms[a]->setVel( velA );
553 +
554 +          atoms[b]->getVel( velB );
555 +
556 +          velB[0] -= rmb * dx;
557 +          velB[1] -= rmb * dy;
558 +          velB[2] -= rmb * dz;
559 +
560 +          atoms[b]->setVel( velB );
561 +
562            moving[a] = 1;
563            moving[b] = 1;
564            done = 0;
# Line 553 | Line 577 | void Integrator::constrainA(){
577  
578    if( !done ){
579  
580 <    sprintf( painCae.errMsg,
580 >    sprintf( painCave.errMsg,
581               "Constraint failure in constrainA, too many iterations: %d\n",
582 <             iterations );
582 >             iteration );
583      painCave.isFatal = 1;
584      simError();
585    }
# Line 566 | Line 590 | void Integrator::constrainB( void ){
590    
591    int i,j,k;
592    int done;
593 +  double posA[3], posB[3];
594 +  double velA[3], velB[3];
595    double vxab, vyab, vzab;
596 <  double rxab, ryab, rzab;
597 <  int a, b;
596 >  double rab[3];
597 >  int a, b, ax, ay, az, bx, by, bz;
598    double rma, rmb;
599    double dx, dy, dz;
600    double rabsq, pabsq, rvab;
# Line 576 | Line 602 | void Integrator::constrainB( void ){
602    double gab;
603    int iteration;
604  
605 <  for(i=0; i<nAtom; i++){
605 >  for(i=0; i<nAtoms; i++){
606      moving[i] = 0;
607      moved[i] = 1;
608    }
609  
610    done = 0;
611 +  iteration = 0;
612    while( !done && (iteration < maxIteration ) ){
613  
614 +    done = 1;
615 +
616      for(i=0; i<nConstrained; i++){
617        
618        a = constrainedA[i];
619        b = constrainedB[i];
620  
621 +      ax = (a*3) + 0;
622 +      ay = (a*3) + 1;
623 +      az = (a*3) + 2;
624 +
625 +      bx = (b*3) + 0;
626 +      by = (b*3) + 1;
627 +      bz = (b*3) + 2;
628 +
629        if( moved[a] || moved[b] ){
593 –        
594 –        vxab = vel[3*a+0] - vel[3*b+0];
595 –        vyab = vel[3*a+1] - vel[3*b+1];
596 –        vzab = vel[3*a+2] - vel[3*b+2];
630  
631 <        rxab = pos[3*a+0] - pos[3*b+0];q
632 <        ryab = pos[3*a+1] - pos[3*b+1];
633 <        rzab = pos[3*a+2] - pos[3*b+2];
634 <        
635 <        rxab = rxab - info->box_x * copysign(1, rxab)
636 <          * int(rxab / info->box_x + 0.5);
604 <        ryab = ryab - info->box_y * copysign(1, ryab)
605 <          * int(ryab / info->box_y + 0.5);
606 <        rzab = rzab - info->box_z * copysign(1, rzab)
607 <          * int(rzab / info->box_z + 0.5);
631 >        atoms[a]->getVel( velA );
632 >        atoms[b]->getVel( velB );
633 >          
634 >        vxab = velA[0] - velB[0];
635 >        vyab = velA[1] - velB[1];
636 >        vzab = velA[2] - velB[2];
637  
638 +        atoms[a]->getPos( posA );
639 +        atoms[b]->getPos( posB );
640 +
641 +        for (j = 0; j < 3; j++)
642 +          rab[j] = posA[j] - posB[j];
643 +          
644 +        info->wrapVector( rab );
645 +        
646          rma = 1.0 / atoms[a]->getMass();
647          rmb = 1.0 / atoms[b]->getMass();
648  
649 <        rvab = rxab * vxab + ryab * vyab + rzab * vzab;
649 >        rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
650            
651 <        gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] );
651 >        gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] );
652  
653          if (fabs(gab) > tol) {
654            
655 <          dx = rxab * gab;
656 <          dy = ryab * gab;
657 <          dz = rzab * gab;
658 <          
659 <          vel[3*a+0] += rma * dx;
660 <          vel[3*a+1] += rma * dy;
661 <          vel[3*a+2] += rma * dz;
655 >          dx = rab[0] * gab;
656 >          dy = rab[1] * gab;
657 >          dz = rab[2] * gab;
658 >        
659 >          velA[0] += rma * dx;
660 >          velA[1] += rma * dy;
661 >          velA[2] += rma * dz;
662  
663 <          vel[3*b+0] -= rmb * dx;
664 <          vel[3*b+1] -= rmb * dy;
665 <          vel[3*b+2] -= rmb * dz;
663 >          atoms[a]->setVel( velA );
664 >
665 >          velB[0] -= rmb * dx;
666 >          velB[1] -= rmb * dy;
667 >          velB[2] -= rmb * dz;
668 >
669 >          atoms[b]->setVel( velB );
670            
671            moving[a] = 1;
672            moving[b] = 1;
# Line 641 | Line 682 | void Integrator::constrainB( void ){
682      
683      iteration++;
684    }
685 <
685 >  
686    if( !done ){
687  
688    
689 <    sprintf( painCae.errMsg,
689 >    sprintf( painCave.errMsg,
690               "Constraint failure in constrainB, too many iterations: %d\n",
691 <             iterations );
691 >             iteration );
692      painCave.isFatal = 1;
693      simError();
694    }
695  
696   }
697  
657 –
658 –
659 –
660 –
661 –
662 –
698   void Integrator::rotate( int axes1, int axes2, double angle, double ji[3],
699                           double A[3][3] ){
700  
# Line 728 | Line 763 | void Integrator::rotate( int axes1, int axes2, double
763    //            A[][] = A[][] * transpose(rot[][])
764  
765  
766 <  // NOte for as yet unknown reason, we are setting the performing the
766 >  // NOte for as yet unknown reason, we are performing the
767    // calculation as:
768    //                transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
769  

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