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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 614 by mmeineke, Tue Jul 15 17:57:04 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 >    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;
# Line 242 | Line 229 | void Integrator::integrate( void ){
229      }
230  
231      if( currTime >= currSample ){
232 <      dump_out->writeDump( currTime );
232 >      dumpOut->writeDump( currTime );
233        currSample += sampleTime;
234      }
235  
236      if( currTime >= currStatus ){
237 <      e_out->writeStat( time * dt );
237 >      statOut->writeStat( currTime );
238        calcPot = 0;
239        calcStress = 0;
240        currStatus += statusTime;
# Line 261 | Line 248 | void Integrator::integrate( void ){
248  
249    }
250  
251 <  dump_out->writeFinal();
251 >  dumpOut->writeFinal(currTime);
252  
253 <  delete dump_out;
254 <  delete e_out;
253 >  delete dumpOut;
254 >  delete statOut;
255   }
256  
257   void Integrator::integrateStep( int calcPot, int calcStress ){
258  
259 +
260 +      
261    // Position full step, and velocity half step
262  
263 <  //preMove();
263 >  preMove();
264    moveA();
265    if( nConstrained ) constrainA();
266  
267 +  
268 + #ifdef IS_MPI
269 +  strcpy( checkPointMsg, "Succesful moveA\n" );
270 +  MPIcheckPoint();
271 + #endif // is_mpi
272 +  
273 +
274    // calc forces
275  
276    myFF->doForces(calcPot,calcStress);
277  
278 + #ifdef IS_MPI
279 +  strcpy( checkPointMsg, "Succesful doForces\n" );
280 +  MPIcheckPoint();
281 + #endif // is_mpi
282 +  
283 +
284    // finish the velocity  half step
285    
286    moveB();
287    if( nConstrained ) constrainB();
288 <  
288 >  
289 > #ifdef IS_MPI
290 >  strcpy( checkPointMsg, "Succesful moveB\n" );
291 >  MPIcheckPoint();
292 > #endif // is_mpi
293 >  
294 >
295   }
296  
297  
298   void Integrator::moveA( void ){
299    
300 <  int i,j,k;
293 <  int atomIndex, aMatIndex;
300 >  int i, j;
301    DirectionalAtom* dAtom;
302 <  double Tb[3];
303 <  double ji[3];
302 >  double Tb[3], ji[3];
303 >  double A[3][3], I[3][3];
304 >  double angle;
305 >  double vel[3], pos[3], frc[3];
306 >  double mass;
307  
308    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;
309  
310 <    // position whole step    
311 <    for( j=atomIndex; j<(atomIndex+3); j++ )
310 >    atoms[i]->getVel( vel );
311 >    atoms[i]->getPos( pos );
312 >    atoms[i]->getFrc( frc );
313 >
314 >    mass = atoms[i]->getMass();
315 >
316 >    for (j=0; j < 3; j++) {
317 >      // velocity half step
318 >      vel[j] += ( dt2 * frc[j] / mass ) * eConvert;
319 >      // position whole step
320        pos[j] += dt * vel[j];
321 +    }
322  
323 <  
323 >    atoms[i]->setVel( vel );
324 >    atoms[i]->setPos( pos );
325 >
326      if( atoms[i]->isDirectional() ){
327  
328        dAtom = (DirectionalAtom *)atoms[i];
329            
330        // get and convert the torque to body frame
331        
332 <      Tb[0] = dAtom->getTx();
318 <      Tb[1] = dAtom->getTy();
319 <      Tb[2] = dAtom->getTz();
320 <      
332 >      dAtom->getTrq( Tb );
333        dAtom->lab2Body( Tb );
334 <      
334 >
335        // get the angular momentum, and propagate a half step
336 +
337 +      dAtom->getJ( ji );
338 +
339 +      for (j=0; j < 3; j++)
340 +        ji[j] += (dt2 * Tb[j]) * eConvert;
341        
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 –      
342        // use the angular velocities to propagate the rotation matrix a
343        // full time step
344 <      
344 >
345 >      dAtom->getA(A);
346 >      dAtom->getI(I);
347 >    
348        // rotate about the x-axis      
349 <      angle = dt2 * ji[0] / dAtom->getIxx();
350 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
351 <      
349 >      angle = dt2 * ji[0] / I[0][0];
350 >      this->rotate( 1, 2, angle, ji, A );
351 >
352        // rotate about the y-axis
353 <      angle = dt2 * ji[1] / dAtom->getIyy();
354 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
353 >      angle = dt2 * ji[1] / I[1][1];
354 >      this->rotate( 2, 0, angle, ji, A );
355        
356        // rotate about the z-axis
357 <      angle = dt * ji[2] / dAtom->getIzz();
358 <      this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] );
357 >      angle = dt * ji[2] / I[2][2];
358 >      this->rotate( 0, 1, angle, ji, A);
359        
360        // rotate about the y-axis
361 <      angle = dt2 * ji[1] / dAtom->getIyy();
362 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
361 >      angle = dt2 * ji[1] / I[1][1];
362 >      this->rotate( 2, 0, angle, ji, A );
363        
364         // rotate about the x-axis
365 <      angle = dt2 * ji[0] / dAtom->getIxx();
366 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
365 >      angle = dt2 * ji[0] / I[0][0];
366 >      this->rotate( 1, 2, angle, ji, A );
367        
368 <      dAtom->setJx( ji[0] );
369 <      dAtom->setJy( ji[1] );
370 <      dAtom->setJz( ji[2] );
371 <    }
372 <    
368 >
369 >      dAtom->setJ( ji );
370 >      dAtom->setA( A  );
371 >          
372 >    }    
373    }
374   }
375  
376  
377   void Integrator::moveB( void ){
378 <  int i,j,k;
363 <  int atomIndex;
378 >  int i, j;
379    DirectionalAtom* dAtom;
380 <  double Tb[3];
381 <  double ji[3];
380 >  double Tb[3], ji[3];
381 >  double vel[3], frc[3];
382 >  double mass;
383  
384    for( i=0; i<nAtoms; i++ ){
385 <    atomIndex = i * 3;
385 >
386 >    atoms[i]->getVel( vel );
387 >    atoms[i]->getFrc( frc );
388  
389 <    // velocity half step
372 <    for( j=atomIndex; j<(atomIndex+3); j++ )
373 <      vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
389 >    mass = atoms[i]->getMass();
390  
391 +    // velocity half step
392 +    for (j=0; j < 3; j++)
393 +      vel[j] += ( dt2 * frc[j] / mass ) * eConvert;
394 +    
395 +    atoms[i]->setVel( vel );
396 +
397      if( atoms[i]->isDirectional() ){
398 <      
398 >
399        dAtom = (DirectionalAtom *)atoms[i];
400 <      
401 <      // get and convert the torque to body frame
402 <      
403 <      Tb[0] = dAtom->getTx();
382 <      Tb[1] = dAtom->getTy();
383 <      Tb[2] = dAtom->getTz();
384 <      
400 >
401 >      // get and convert the torque to body frame      
402 >
403 >      dAtom->getTrq( Tb );
404        dAtom->lab2Body( Tb );
405 +
406 +      // get the angular momentum, and propagate a half step
407 +
408 +      dAtom->getJ( ji );
409 +
410 +      for (j=0; j < 3; j++)
411 +        ji[j] += (dt2 * Tb[j]) * eConvert;
412        
413 <      // get the angular momentum, and complete the angular momentum
414 <      // 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] );
413 >
414 >      dAtom->setJ( ji );
415      }
416    }
403 –
417   }
418  
419   void Integrator::preMove( void ){
420 <  int i;
420 >  int i, j;
421 >  double pos[3];
422  
423    if( nConstrained ){
424 <    if( oldAtoms != nAtoms ){
425 <      
426 <      // save oldAtoms to check for lode balanceing later on.
427 <      
428 <      oldAtoms = nAtoms;
429 <      
430 <      delete[] moving;
431 <      delete[] moved;
432 <      delete[] oldPos;
419 <      
420 <      moving = new int[nAtoms];
421 <      moved  = new int[nAtoms];
422 <      
423 <      oldPos = new double[nAtoms*3];
424 >
425 >    for(i=0; i < nAtoms; i++) {
426 >
427 >      atoms[i]->getPos( pos );
428 >
429 >      for (j = 0; j < 3; j++) {        
430 >        oldPos[3*i + j] = pos[j];
431 >      }
432 >
433      }
434 <  
435 <    for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i];
427 <  }
428 < }  
434 >  }  
435 > }
436  
437   void Integrator::constrainA(){
438  
439    int i,j,k;
440    int done;
441 <  double pxab, pyab, pzab;
442 <  double rxab, ryab, rzab;
443 <  int a, b;
441 >  double posA[3], posB[3];
442 >  double velA[3], velB[3];
443 >  double pab[3];
444 >  double rab[3];
445 >  int a, b, ax, ay, az, bx, by, bz;
446    double rma, rmb;
447    double dx, dy, dz;
448 +  double rpab;
449    double rabsq, pabsq, rpabsq;
450    double diffsq;
451    double gab;
452    int iteration;
453  
454 <
445 <  
446 <  for( i=0; i<nAtoms; i++){
447 <    
454 >  for( i=0; i<nAtoms; i++){    
455      moving[i] = 0;
456      moved[i]  = 1;
457    }
458 <  
452 <  
458 >
459    iteration = 0;
460    done = 0;
461    while( !done && (iteration < maxIteration )){
# Line 459 | Line 465 | void Integrator::constrainA(){
465  
466        a = constrainedA[i];
467        b = constrainedB[i];
468 <    
468 >      
469 >      ax = (a*3) + 0;
470 >      ay = (a*3) + 1;
471 >      az = (a*3) + 2;
472 >
473 >      bx = (b*3) + 0;
474 >      by = (b*3) + 1;
475 >      bz = (b*3) + 2;
476 >
477        if( moved[a] || moved[b] ){
478 <        
479 <        pxab = pos[3*a+0] - pos[3*b+0];
480 <        pyab = pos[3*a+1] - pos[3*b+1];
481 <        pzab = pos[3*a+2] - pos[3*b+2];
478 >        
479 >        atoms[a]->getPos( posA );
480 >        atoms[b]->getPos( posB );
481 >        
482 >        for (j = 0; j < 3; j++ )
483 >          pab[j] = posA[j] - posB[j];
484 >        
485 >        //periodic boundary condition
486  
487 <        //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;
487 >        info->wrapVector( pab );
488  
489 +        pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
490 +
491 +        rabsq = constrainedDsqr[i];
492 +        diffsq = rabsq - pabsq;
493 +
494          // the original rattle code from alan tidesley
495 <        if (fabs(diffsq) > tol*rabsq*2) {
496 <          rxab = oldPos[3*a+0] - oldPos[3*b+0];
497 <          ryab = oldPos[3*a+1] - oldPos[3*b+1];
498 <          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);
495 >        if (fabs(diffsq) > (tol*rabsq*2)) {
496 >          rab[0] = oldPos[ax] - oldPos[bx];
497 >          rab[1] = oldPos[ay] - oldPos[by];
498 >          rab[2] = oldPos[az] - oldPos[bz];
499  
500 <          rpab = rxab * pxab + ryab * pyab + rzab * pzab;
500 >          info->wrapVector( rab );
501 >
502 >          rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
503 >
504            rpabsq = rpab * rpab;
505  
506  
507            if (rpabsq < (rabsq * -diffsq)){
508 +
509   #ifdef IS_MPI
510              a = atoms[a]->getGlobalIndex();
511              b = atoms[b]->getGlobalIndex();
512   #endif //is_mpi
513              sprintf( painCave.errMsg,
514 <                     "Constraint failure in constrainA at atom %d and %d\n.",
514 >                     "Constraint failure in constrainA at atom %d and %d.\n",
515                       a, b );
516              painCave.isFatal = 1;
517              simError();
# Line 509 | Line 519 | void Integrator::constrainA(){
519  
520            rma = 1.0 / atoms[a]->getMass();
521            rmb = 1.0 / atoms[b]->getMass();
522 <          
522 >
523            gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab );
514 –          dx = rxab * gab;
515 –          dy = ryab * gab;
516 –          dz = rzab * gab;
524  
525 <          pos[3*a+0] += rma * dx;
526 <          pos[3*a+1] += rma * dy;
527 <          pos[3*a+2] += rma * dz;
525 >          dx = rab[0] * gab;
526 >          dy = rab[1] * gab;
527 >          dz = rab[2] * gab;
528  
529 <          pos[3*b+0] -= rmb * dx;
530 <          pos[3*b+1] -= rmb * dy;
531 <          pos[3*b+2] -= rmb * dz;
529 >          posA[0] += rma * dx;
530 >          posA[1] += rma * dy;
531 >          posA[2] += rma * dz;
532  
533 +          atoms[a]->setPos( posA );
534 +
535 +          posB[0] -= rmb * dx;
536 +          posB[1] -= rmb * dy;
537 +          posB[2] -= rmb * dz;
538 +
539 +          atoms[b]->setPos( posB );
540 +
541            dx = dx / dt;
542            dy = dy / dt;
543            dz = dz / dt;
544  
545 <          vel[3*a+0] += rma * dx;
531 <          vel[3*a+1] += rma * dy;
532 <          vel[3*a+2] += rma * dz;
545 >          atoms[a]->getVel( velA );
546  
547 <          vel[3*b+0] -= rmb * dx;
548 <          vel[3*b+1] -= rmb * dy;
549 <          vel[3*b+2] -= rmb * dz;
547 >          velA[0] += rma * dx;
548 >          velA[1] += rma * dy;
549 >          velA[2] += rma * dz;
550  
551 +          atoms[a]->setVel( velA );
552 +
553 +          atoms[b]->getVel( velB );
554 +
555 +          velB[0] -= rmb * dx;
556 +          velB[1] -= rmb * dy;
557 +          velB[2] -= rmb * dz;
558 +
559 +          atoms[b]->setVel( velB );
560 +
561            moving[a] = 1;
562            moving[b] = 1;
563            done = 0;
# Line 553 | Line 576 | void Integrator::constrainA(){
576  
577    if( !done ){
578  
579 <    sprintf( painCae.errMsg,
579 >    sprintf( painCave.errMsg,
580               "Constraint failure in constrainA, too many iterations: %d\n",
581 <             iterations );
581 >             iteration );
582      painCave.isFatal = 1;
583      simError();
584    }
# Line 566 | Line 589 | void Integrator::constrainB( void ){
589    
590    int i,j,k;
591    int done;
592 +  double posA[3], posB[3];
593 +  double velA[3], velB[3];
594    double vxab, vyab, vzab;
595 <  double rxab, ryab, rzab;
596 <  int a, b;
595 >  double rab[3];
596 >  int a, b, ax, ay, az, bx, by, bz;
597    double rma, rmb;
598    double dx, dy, dz;
599    double rabsq, pabsq, rvab;
# Line 576 | Line 601 | void Integrator::constrainB( void ){
601    double gab;
602    int iteration;
603  
604 <  for(i=0; i<nAtom; i++){
604 >  for(i=0; i<nAtoms; i++){
605      moving[i] = 0;
606      moved[i] = 1;
607    }
608  
609    done = 0;
610 +  iteration = 0;
611    while( !done && (iteration < maxIteration ) ){
612  
613 +    done = 1;
614 +
615      for(i=0; i<nConstrained; i++){
616        
617        a = constrainedA[i];
618        b = constrainedB[i];
619  
620 +      ax = (a*3) + 0;
621 +      ay = (a*3) + 1;
622 +      az = (a*3) + 2;
623 +
624 +      bx = (b*3) + 0;
625 +      by = (b*3) + 1;
626 +      bz = (b*3) + 2;
627 +
628        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];
629  
630 <        rxab = pos[3*a+0] - pos[3*b+0];q
631 <        ryab = pos[3*a+1] - pos[3*b+1];
632 <        rzab = pos[3*a+2] - pos[3*b+2];
633 <        
634 <        rxab = rxab - info->box_x * copysign(1, rxab)
635 <          * 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);
630 >        atoms[a]->getVel( velA );
631 >        atoms[b]->getVel( velB );
632 >          
633 >        vxab = velA[0] - velB[0];
634 >        vyab = velA[1] - velB[1];
635 >        vzab = velA[2] - velB[2];
636  
637 +        atoms[a]->getPos( posA );
638 +        atoms[b]->getPos( posB );
639 +
640 +        for (j = 0; j < 3; j++)
641 +          rab[j] = posA[j] - posB[j];
642 +          
643 +        info->wrapVector( rab );
644 +        
645          rma = 1.0 / atoms[a]->getMass();
646          rmb = 1.0 / atoms[b]->getMass();
647  
648 <        rvab = rxab * vxab + ryab * vyab + rzab * vzab;
648 >        rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
649            
650 <        gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] );
650 >        gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] );
651  
652          if (fabs(gab) > tol) {
653            
654 <          dx = rxab * gab;
655 <          dy = ryab * gab;
656 <          dz = rzab * gab;
657 <          
658 <          vel[3*a+0] += rma * dx;
659 <          vel[3*a+1] += rma * dy;
660 <          vel[3*a+2] += rma * dz;
654 >          dx = rab[0] * gab;
655 >          dy = rab[1] * gab;
656 >          dz = rab[2] * gab;
657 >        
658 >          velA[0] += rma * dx;
659 >          velA[1] += rma * dy;
660 >          velA[2] += rma * dz;
661  
662 <          vel[3*b+0] -= rmb * dx;
663 <          vel[3*b+1] -= rmb * dy;
664 <          vel[3*b+2] -= rmb * dz;
662 >          atoms[a]->setVel( velA );
663 >
664 >          velB[0] -= rmb * dx;
665 >          velB[1] -= rmb * dy;
666 >          velB[2] -= rmb * dz;
667 >
668 >          atoms[b]->setVel( velB );
669            
670            moving[a] = 1;
671            moving[b] = 1;
# Line 641 | Line 681 | void Integrator::constrainB( void ){
681      
682      iteration++;
683    }
684 <
684 >  
685    if( !done ){
686  
687    
688 <    sprintf( painCae.errMsg,
688 >    sprintf( painCave.errMsg,
689               "Constraint failure in constrainB, too many iterations: %d\n",
690 <             iterations );
690 >             iteration );
691      painCave.isFatal = 1;
692      simError();
693    }
694  
695   }
696  
657 –
658 –
659 –
660 –
661 –
662 –
697   void Integrator::rotate( int axes1, int axes2, double angle, double ji[3],
698                           double A[3][3] ){
699  
# Line 728 | Line 762 | void Integrator::rotate( int axes1, int axes2, double
762    //            A[][] = A[][] * transpose(rot[][])
763  
764  
765 <  // NOte for as yet unknown reason, we are setting the performing the
765 >  // NOte for as yet unknown reason, we are performing the
766    // calculation as:
767    //                transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
768  

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