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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 594 by mmeineke, Fri Jul 11 22:34:48 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 26 | 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 33 | Line 36 | Integrator::Integrator( SimInfo* theInfo, ForceFields*
36    constrainedDsqr = NULL;
37    moving          = NULL;
38    moved           = NULL;
39 <  prePos          = NULL;
39 >  oldPos          = NULL;
40    
41    nConstrained = 0;
42  
# Line 48 | Line 51 | Integrator::~Integrator() {
51      delete[] constrainedDsqr;
52      delete[] moving;
53      delete[] moved;
54 <    delete[] prePos;
52 < k
54 >    delete[] oldPos;
55    }
56    
57   }
# 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 137 | Line 145 | void Integrator::checkConstraints( void ){
145        constrainedA[i] = temp_con[i].get_a();
146        constrainedB[i] = temp_con[i].get_b();
147        constrainedDsqr[i] = temp_con[i].get_dsqr();
148 +
149      }
150  
151      
# Line 147 | Line 156 | void Integrator::checkConstraints( void ){
156      moving = new int[nAtoms];
157      moved  = new int[nAtoms];
158  
159 <    prePos = new double[nAtoms*3];
159 >    oldPos = new double[nAtoms*3];
160    }
161    
162    delete[] temp_con;
# Line 157 | Line 166 | void Integrator::integrate( void ){
166   void Integrator::integrate( void ){
167  
168    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
169  
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;
170    double runTime     = info->run_time;
171    double sampleTime  = info->sampleTime;
172    double statusTime  = info->statusTime;
# Line 188 | Line 180 | void Integrator::integrate( void ){
180    int calcPot, calcStress;
181    int isError;
182  
183 +
184 +
185    tStats   = new Thermo( info );
186 <  e_out    = new StatWriter( info );
187 <  dump_out = new DumpWriter( info );
186 >  statOut  = new StatWriter( info );
187 >  dumpOut  = new DumpWriter( info );
188  
189 <  Atom** atoms = info->atoms;
189 >  atoms = info->atoms;
190    DirectionalAtom* dAtom;
191 +
192 +  dt = info->dt;
193    dt2 = 0.5 * dt;
194  
195    // initialize the forces before the first step
# Line 205 | Line 201 | void Integrator::integrate( void ){
201      tStats->velocitize();
202    }
203    
204 <  dump_out->writeDump( 0.0 );
205 <  e_out->writeStat( 0.0 );
204 >  dumpOut->writeDump( 0.0 );
205 >  statOut->writeStat( 0.0 );
206    
207    calcPot     = 0;
208    calcStress  = 0;
# Line 215 | Line 211 | void Integrator::integrate( void ){
211    currStatus  = statusTime;
212    currTime    = 0.0;;
213  
214 +
215 +  readyCheck();
216 +
217 + #ifdef IS_MPI
218 +  strcpy( checkPointMsg,
219 +          "The integrator is ready to go." );
220 +  MPIcheckPoint();
221 + #endif // is_mpi
222 +
223 +
224 +  pos  = Atom::getPosArray();
225 +  vel  = Atom::getVelArray();
226 +  frc  = Atom::getFrcArray();
227 +  trq  = Atom::getTrqArray();
228 +  Amat = Atom::getAmatArray();
229 +
230    while( currTime < runTime ){
231  
232      if( (currTime+dt) >= currStatus ){
233        calcPot = 1;
234        calcStress = 1;
235      }
236 <    
236 >
237 >    std::cerr << "calcPot = " << calcPot << "; calcStress = "
238 >              << calcStress << "\n";
239 >
240      integrateStep( calcPot, calcStress );
241        
242      currTime += dt;
# Line 234 | Line 249 | void Integrator::integrate( void ){
249      }
250  
251      if( currTime >= currSample ){
252 <      dump_out->writeDump( currTime );
252 >      dumpOut->writeDump( currTime );
253        currSample += sampleTime;
254      }
255  
256      if( currTime >= currStatus ){
257 <      e_out->writeStat( time * dt );
257 >      statOut->writeStat( currTime );
258        calcPot = 0;
259        calcStress = 0;
260        currStatus += statusTime;
261      }
262 +
263 + #ifdef IS_MPI
264 +    strcpy( checkPointMsg,
265 +            "successfully took a time step." );
266 +    MPIcheckPoint();
267 + #endif // is_mpi
268 +
269    }
270  
271 <  dump_out->writeFinal();
271 >  dumpOut->writeFinal(currTime);
272  
273 <  delete dump_out;
274 <  delete e_out;
273 >  delete dumpOut;
274 >  delete statOut;
275   }
276  
277   void Integrator::integrateStep( int calcPot, int calcStress ){
278 +
279  
280 +      
281    // Position full step, and velocity half step
282  
283 <  //preMove();
283 >  preMove();
284    moveA();
285    if( nConstrained ) constrainA();
286  
# Line 279 | Line 303 | void Integrator::moveA( void ){
303    DirectionalAtom* dAtom;
304    double Tb[3];
305    double ji[3];
306 +  double angle;
307 +  double A[3][3];
308  
309 +
310    for( i=0; i<nAtoms; i++ ){
311      atomIndex = i * 3;
312      aMatIndex = i * 9;
313 <    
313 >
314      // velocity half step
315      for( j=atomIndex; j<(atomIndex+3); j++ )
316        vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
317  
318 +    std::cerr<< "MoveA vel[" << i << "] = "
319 +             << vel[atomIndex] << "\t"
320 +             << vel[atomIndex+1]<< "\t"
321 +             << vel[atomIndex+2]<< "\n";
322 +
323      // position whole step    
324 <    for( j=atomIndex; j<(atomIndex+3); j++ )
325 <      pos[j] += dt * vel[j];
324 >    for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j];
325 >    
326  
327 <  
327 >    std::cerr<< "MoveA pos[" << i << "] = "
328 >             << pos[atomIndex] << "\t"
329 >             << pos[atomIndex+1]<< "\t"
330 >             << pos[atomIndex+2]<< "\n";
331 >
332      if( atoms[i]->isDirectional() ){
333  
334        dAtom = (DirectionalAtom *)atoms[i];
# Line 314 | Line 350 | void Integrator::moveA( void ){
350        // use the angular velocities to propagate the rotation matrix a
351        // full time step
352        
353 +          // get the atom's rotation matrix
354 +          
355 +      A[0][0] = dAtom->getAxx();
356 +      A[0][1] = dAtom->getAxy();
357 +      A[0][2] = dAtom->getAxz();
358 +      
359 +      A[1][0] = dAtom->getAyx();
360 +      A[1][1] = dAtom->getAyy();
361 +      A[1][2] = dAtom->getAyz();
362 +      
363 +      A[2][0] = dAtom->getAzx();
364 +      A[2][1] = dAtom->getAzy();
365 +      A[2][2] = dAtom->getAzz();
366 +      
367        // rotate about the x-axis      
368        angle = dt2 * ji[0] / dAtom->getIxx();
369 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
369 >      this->rotate( 1, 2, angle, ji, A );
370        
371        // rotate about the y-axis
372        angle = dt2 * ji[1] / dAtom->getIyy();
373 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
373 >      this->rotate( 2, 0, angle, ji, A );
374        
375        // rotate about the z-axis
376        angle = dt * ji[2] / dAtom->getIzz();
377 <      this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] );
377 >      this->rotate( 0, 1, angle, ji, A );
378        
379        // rotate about the y-axis
380        angle = dt2 * ji[1] / dAtom->getIyy();
381 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
381 >      this->rotate( 2, 0, angle, ji, A );
382        
383         // rotate about the x-axis
384        angle = dt2 * ji[0] / dAtom->getIxx();
385 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
385 >      this->rotate( 1, 2, angle, ji, A );
386        
387        dAtom->setJx( ji[0] );
388        dAtom->setJy( ji[1] );
# Line 357 | Line 407 | void Integrator::moveB( void ){
407      for( j=atomIndex; j<(atomIndex+3); j++ )
408        vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
409  
410 +    std::cerr<< "MoveB vel[" << i << "] = "
411 +             << vel[atomIndex] << "\t"
412 +             << vel[atomIndex+1]<< "\t"
413 +             << vel[atomIndex+2]<< "\n";
414 +
415 +
416      if( atoms[i]->isDirectional() ){
417        
418        dAtom = (DirectionalAtom *)atoms[i];
# Line 376 | Line 432 | void Integrator::moveB( void ){
432        ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
433        ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
434        
379 –      jx2 = ji[0] * ji[0];
380 –      jy2 = ji[1] * ji[1];
381 –      jz2 = ji[2] * ji[2];
382 –      
435        dAtom->setJx( ji[0] );
436        dAtom->setJy( ji[1] );
437        dAtom->setJz( ji[2] );
# Line 392 | Line 444 | void Integrator::preMove( void ){
444    int i;
445  
446    if( nConstrained ){
447 <    if( oldAtoms != nAtoms ){
396 <      
397 <      // save oldAtoms to check for lode balanceing later on.
398 <      
399 <      oldAtoms = nAtoms;
400 <      
401 <      delete[] moving;
402 <      delete[] moved;
403 <      delete[] oldPos;
404 <      
405 <      moving = new int[nAtoms];
406 <      moved  = new int[nAtoms];
407 <      
408 <      oldPos = new double[nAtoms*3];
409 <    }
410 <  
447 >
448      for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i];
449    }
450   }  
# Line 416 | Line 453 | void Integrator::constrainA(){
453  
454    int i,j,k;
455    int done;
456 <  double pxab, pyab, pzab;
457 <  double rxab, ryab, rzab;
458 <  int a, b;
456 >  double pab[3];
457 >  double rab[3];
458 >  int a, b, ax, ay, az, bx, by, bz;
459    double rma, rmb;
460    double dx, dy, dz;
461 +  double rpab;
462    double rabsq, pabsq, rpabsq;
463    double diffsq;
464    double gab;
465    int iteration;
466  
429 –
430 –  
467    for( i=0; i<nAtoms; i++){
468      
469      moving[i] = 0;
470      moved[i]  = 1;
471    }
472 <  
437 <  
472 >
473    iteration = 0;
474    done = 0;
475    while( !done && (iteration < maxIteration )){
# Line 444 | Line 479 | void Integrator::constrainA(){
479  
480        a = constrainedA[i];
481        b = constrainedB[i];
482 <    
482 >      
483 >      ax = (a*3) + 0;
484 >      ay = (a*3) + 1;
485 >      az = (a*3) + 2;
486 >
487 >      bx = (b*3) + 0;
488 >      by = (b*3) + 1;
489 >      bz = (b*3) + 2;
490 >
491        if( moved[a] || moved[b] ){
492          
493 <        pxab = pos[3*a+0] - pos[3*b+0];
494 <        pyab = pos[3*a+1] - pos[3*b+1];
495 <        pzab = pos[3*a+2] - pos[3*b+2];
493 >        pab[0] = pos[ax] - pos[bx];
494 >        pab[1] = pos[ay] - pos[by];
495 >        pab[2] = pos[az] - pos[bz];
496  
497 <        //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;
497 >        //periodic boundary condition
498  
499 +        info->wrapVector( pab );
500 +
501 +        pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
502 +
503 +        rabsq = constrainedDsqr[i];
504 +        diffsq = rabsq - pabsq;
505 +
506          // the original rattle code from alan tidesley
507 <        if (fabs(diffsq) > tol*rabsq*2) {
508 <          rxab = oldPos[3*a+0] - oldPos[3*b+0];
509 <          ryab = oldPos[3*a+1] - oldPos[3*b+1];
510 <          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);
507 >        if (fabs(diffsq) > (tol*rabsq*2)) {
508 >          rab[0] = oldPos[ax] - oldPos[bx];
509 >          rab[1] = oldPos[ay] - oldPos[by];
510 >          rab[2] = oldPos[az] - oldPos[bz];
511  
512 <          rpab = rxab * pxab + ryab * pyab + rzab * pzab;
512 >          info->wrapVector( rab );
513 >
514 >          rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
515 >
516            rpabsq = rpab * rpab;
517  
518  
519            if (rpabsq < (rabsq * -diffsq)){
520 +
521   #ifdef IS_MPI
522              a = atoms[a]->getGlobalIndex();
523              b = atoms[b]->getGlobalIndex();
524   #endif //is_mpi
525              sprintf( painCave.errMsg,
526 <                     "Constraint failure in constrainA at atom %d and %d\n.",
526 >                     "Constraint failure in constrainA at atom %d and %d.\n",
527                       a, b );
528              painCave.isFatal = 1;
529              simError();
# Line 494 | Line 531 | void Integrator::constrainA(){
531  
532            rma = 1.0 / atoms[a]->getMass();
533            rmb = 1.0 / atoms[b]->getMass();
534 <          
534 >
535            gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab );
499 –          dx = rxab * gab;
500 –          dy = ryab * gab;
501 –          dz = rzab * gab;
536  
537 <          pos[3*a+0] += rma * dx;
538 <          pos[3*a+1] += rma * dy;
539 <          pos[3*a+2] += rma * dz;
537 >          dx = rab[0] * gab;
538 >          dy = rab[1] * gab;
539 >          dz = rab[2] * gab;
540  
541 <          pos[3*b+0] -= rmb * dx;
542 <          pos[3*b+1] -= rmb * dy;
543 <          pos[3*b+2] -= rmb * dz;
541 >          pos[ax] += rma * dx;
542 >          pos[ay] += rma * dy;
543 >          pos[az] += rma * dz;
544  
545 +          pos[bx] -= rmb * dx;
546 +          pos[by] -= rmb * dy;
547 +          pos[bz] -= rmb * dz;
548 +
549            dx = dx / dt;
550            dy = dy / dt;
551            dz = dz / dt;
552  
553 <          vel[3*a+0] += rma * dx;
554 <          vel[3*a+1] += rma * dy;
555 <          vel[3*a+2] += rma * dz;
553 >          vel[ax] += rma * dx;
554 >          vel[ay] += rma * dy;
555 >          vel[az] += rma * dz;
556  
557 <          vel[3*b+0] -= rmb * dx;
558 <          vel[3*b+1] -= rmb * dy;
559 <          vel[3*b+2] -= rmb * dz;
557 >          vel[bx] -= rmb * dx;
558 >          vel[by] -= rmb * dy;
559 >          vel[bz] -= rmb * dz;
560  
561            moving[a] = 1;
562            moving[b] = 1;
# Line 538 | 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 552 | Line 590 | void Integrator::constrainB( void ){
590    int i,j,k;
591    int done;
592    double vxab, vyab, vzab;
593 <  double rxab, ryab, rzab;
594 <  int a, b;
593 >  double rab[3];
594 >  int a, b, ax, ay, az, bx, by, bz;
595    double rma, rmb;
596    double dx, dy, dz;
597    double rabsq, pabsq, rvab;
# Line 561 | Line 599 | void Integrator::constrainB( void ){
599    double gab;
600    int iteration;
601  
602 <  for(i=0; i<nAtom; i++){
602 >  for(i=0; i<nAtoms; i++){
603      moving[i] = 0;
604      moved[i] = 1;
605    }
606  
607    done = 0;
608 +  iteration = 0;
609    while( !done && (iteration < maxIteration ) ){
610  
611 +    done = 1;
612 +
613      for(i=0; i<nConstrained; i++){
614        
615        a = constrainedA[i];
616        b = constrainedB[i];
617  
618 +      ax = (a*3) + 0;
619 +      ay = (a*3) + 1;
620 +      az = (a*3) + 2;
621 +
622 +      bx = (b*3) + 0;
623 +      by = (b*3) + 1;
624 +      bz = (b*3) + 2;
625 +
626        if( moved[a] || moved[b] ){
627          
628 <        vxab = vel[3*a+0] - vel[3*b+0];
629 <        vyab = vel[3*a+1] - vel[3*b+1];
630 <        vzab = vel[3*a+2] - vel[3*b+2];
628 >        vxab = vel[ax] - vel[bx];
629 >        vyab = vel[ay] - vel[by];
630 >        vzab = vel[az] - vel[bz];
631  
632 <        rxab = pos[3*a+0] - pos[3*b+0];q
633 <        ryab = pos[3*a+1] - pos[3*b+1];
634 <        rzab = pos[3*a+2] - pos[3*b+2];
632 >        rab[0] = pos[ax] - pos[bx];
633 >        rab[1] = pos[ay] - pos[by];
634 >        rab[2] = pos[az] - pos[bz];
635          
636 <        rxab = rxab - info->box_x * copysign(1, rxab)
637 <          * 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);
593 <
636 >        info->wrapVector( rab );
637 >        
638          rma = 1.0 / atoms[a]->getMass();
639          rmb = 1.0 / atoms[b]->getMass();
640  
641 <        rvab = rxab * vxab + ryab * vyab + rzab * vzab;
641 >        rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
642            
643 <        gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] );
643 >        gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] );
644  
645          if (fabs(gab) > tol) {
646            
647 <          dx = rxab * gab;
648 <          dy = ryab * gab;
649 <          dz = rzab * gab;
647 >          dx = rab[0] * gab;
648 >          dy = rab[1] * gab;
649 >          dz = rab[2] * gab;
650            
651 <          vel[3*a+0] += rma * dx;
652 <          vel[3*a+1] += rma * dy;
653 <          vel[3*a+2] += rma * dz;
651 >          vel[ax] += rma * dx;
652 >          vel[ay] += rma * dy;
653 >          vel[az] += rma * dz;
654  
655 <          vel[3*b+0] -= rmb * dx;
656 <          vel[3*b+1] -= rmb * dy;
657 <          vel[3*b+2] -= rmb * dz;
655 >          vel[bx] -= rmb * dx;
656 >          vel[by] -= rmb * dy;
657 >          vel[bz] -= rmb * dz;
658            
659            moving[a] = 1;
660            moving[b] = 1;
# Line 630 | Line 674 | void Integrator::constrainB( void ){
674    if( !done ){
675  
676    
677 <    sprintf( painCae.errMsg,
677 >    sprintf( painCave.errMsg,
678               "Constraint failure in constrainB, too many iterations: %d\n",
679 <             iterations );
679 >             iteration );
680      painCave.isFatal = 1;
681      simError();
682    }
# Line 713 | Line 757 | void Integrator::rotate( int axes1, int axes2, double
757    //            A[][] = A[][] * transpose(rot[][])
758  
759  
760 <  // NOte for as yet unknown reason, we are setting the performing the
760 >  // NOte for as yet unknown reason, we are performing the
761    // calculation as:
762    //                transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
763  

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