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root/OpenMD/trunk/src/constraints/ZconstraintForceManager.cpp
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Comparing trunk/src/constraints/ZconstraintForceManager.cpp (file contents):
Revision 1464 by gezelter, Fri Jul 9 19:29:05 2010 UTC vs.
Revision 2067 by gezelter, Thu Mar 5 15:35:37 2015 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43 + #ifdef IS_MPI
44 + #include <mpi.h>
45 + #endif
46   #include <cmath>
47   #include "constraints/ZconstraintForceManager.hpp"
48   #include "integrators/Integrator.hpp"
49   #include "utils/simError.h"
50   #include "utils/PhysicalConstants.hpp"
51   #include "utils/StringUtils.hpp"
52 +
53   namespace OpenMD {
54    ZconstraintForceManager::ZconstraintForceManager(SimInfo* info): ForceManager(info), infiniteTime(1e31) {
55      currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
# Line 156 | Line 161 | namespace OpenMD {
161   #ifndef IS_MPI
162      totMassUnconsMols_ = totMassUnconsMols_local;
163   #else
164 <    MPI_Allreduce(&totMassUnconsMols_local, &totMassUnconsMols_, 1, MPI_REALTYPE,
165 <                  MPI_SUM, MPI_COMM_WORLD);  
164 >    MPI_Allreduce(&totMassUnconsMols_local, &totMassUnconsMols_, 1,
165 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
166   #endif
167  
168      // creat zconsWriter  
# Line 282 | Line 287 | namespace OpenMD {
287      Vector3d vel;
288      std::list<ZconstraintMol>::iterator i;
289      Molecule* mol;
290 <    StuntDouble* integrableObject;
290 >    StuntDouble* sd;
291      Molecule::IntegrableObjectIterator ii;
292  
293      //zero out the velocities of center of mass of fixed z-constrained molecules
294      for(i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) {
295 +
296        mol = i->mol;
297        comVel = mol->getComVel();
298 <      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
299 <          integrableObject = mol->nextIntegrableObject(ii)) {
300 <        vel = integrableObject->getVel();  
298 >
299 >      for(sd = mol->beginIntegrableObject(ii); sd != NULL;
300 >          sd = mol->nextIntegrableObject(ii)) {
301 >
302 >        vel = sd->getVel();  
303          vel[whichDirection] -= comVel[whichDirection];
304 <        integrableObject->setVel(vel);
304 >        sd->setVel(vel);
305        }
306      }
307  
# Line 318 | Line 326 | namespace OpenMD {
326   #ifndef IS_MPI
327      pzMovingMols = pzMovingMols_local;
328   #else
329 <    MPI_Allreduce(&pzMovingMols_local, &pzMovingMols, 1, MPI_REALTYPE,
330 <                  MPI_SUM, MPI_COMM_WORLD);
329 >    MPI_Allreduce(&pzMovingMols_local, &pzMovingMols, 1,
330 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
331   #endif
332  
333      RealType vzMovingMols = pzMovingMols / (totMassMovingZMols_ + totMassUnconsMols_);
334  
335      //modify the velocities of moving z-constrained molecuels
336      for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
337 +
338        mol = i->mol;
330 –      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
331 –          integrableObject = mol->nextIntegrableObject(ii)) {
339  
340 <        vel = integrableObject->getVel();
340 >      for(sd = mol->beginIntegrableObject(ii); sd != NULL;
341 >          sd = mol->nextIntegrableObject(ii)) {
342 >
343 >        vel = sd->getVel();
344          vel[whichDirection] -= vzMovingMols;
345 <        integrableObject->setVel(vel);
345 >        sd->setVel(vel);
346        }
347      }
348  
349      //modify the velocites of unconstrained molecules  
350      for ( j = unzconsMols_.begin(); j !=  unzconsMols_.end(); ++j) {
351 +
352        mol =*j;
342 –      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
343 –          integrableObject = mol->nextIntegrableObject(ii)) {
353  
354 <        vel = integrableObject->getVel();
354 >      for(sd = mol->beginIntegrableObject(ii); sd != NULL;
355 >          sd = mol->nextIntegrableObject(ii)) {
356 >
357 >        vel = sd->getVel();
358          vel[whichDirection] -= vzMovingMols;
359 <        integrableObject->setVel(vel);
359 >        sd->setVel(vel);
360        }
361      }
362      
# Line 366 | Line 378 | namespace OpenMD {
378      //calculate the total z-contrained force of fixed z-contrained molecules
379      std::list<ZconstraintMol>::iterator i;
380      Molecule* mol;
381 <    StuntDouble* integrableObject;
381 >    StuntDouble* sd;
382      Molecule::IntegrableObjectIterator ii;
383  
384      for ( i = fixedZMols_.begin(); i !=  fixedZMols_.end(); ++i) {
385 +
386        mol = i->mol;
387        i->fz = 0.0;
375 –      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
376 –          integrableObject = mol->nextIntegrableObject(ii)) {
388  
389 <        force = integrableObject->getFrc();    
389 >      for( sd = mol->beginIntegrableObject(ii); sd != NULL;
390 >           sd = mol->nextIntegrableObject(ii)) {
391 >
392 >        force = sd->getFrc();    
393          i->fz += force[whichDirection];
394        }
395        totalFZ_local += i->fz;
# Line 383 | Line 397 | namespace OpenMD {
397  
398      //calculate total z-constraint force
399   #ifdef IS_MPI
400 <    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
400 >    MPI_Allreduce(&totalFZ_local, &totalFZ, 1,
401 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
402   #else
403      totalFZ = totalFZ_local;
404   #endif
# Line 391 | Line 406 | namespace OpenMD {
406  
407      // apply negative to fixed z-constrained molecues;
408      for ( i = fixedZMols_.begin(); i !=  fixedZMols_.end(); ++i) {
409 <      mol = i->mol;
410 <      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
396 <          integrableObject = mol->nextIntegrableObject(ii)) {
409 >
410 >      mol = i->mol;
411  
412 <        force[whichDirection] = -getZFOfFixedZMols(mol, integrableObject, i->fz);
413 <        integrableObject->addFrc(force);
412 >      for(sd = mol->beginIntegrableObject(ii); sd != NULL;
413 >          sd = mol->nextIntegrableObject(ii)) {
414 >
415 >        force[whichDirection] = -getZFOfFixedZMols(mol, sd, i->fz);
416 >        sd->addFrc(force);
417        }
418      }
419  
420      //modify the forces of moving z-constrained molecules
421      for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
422 +
423        mol = i->mol;
406 –      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
407 –          integrableObject = mol->nextIntegrableObject(ii)) {
424  
425 +      for(sd = mol->beginIntegrableObject(ii); sd != NULL;
426 +          sd = mol->nextIntegrableObject(ii)) {
427 +
428          force[whichDirection] = -getZFOfMovingMols(mol,totalFZ);
429 <        integrableObject->addFrc(force);
429 >        sd->addFrc(force);
430        }
431      }
432  
433      //modify the forces of unconstrained molecules
434      std::vector<Molecule*>::iterator j;
435      for ( j = unzconsMols_.begin(); j !=  unzconsMols_.end(); ++j) {
436 +
437        mol =*j;
418 –      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
419 –          integrableObject = mol->nextIntegrableObject(ii)) {
438  
439 +      for(sd = mol->beginIntegrableObject(ii); sd != NULL;
440 +          sd = mol->nextIntegrableObject(ii)) {
441 +
442          force[whichDirection] = -getZFOfMovingMols(mol, totalFZ);
443 <        integrableObject->addFrc(force);
443 >        sd->addFrc(force);
444        }
445      }
446  
# Line 431 | Line 452 | namespace OpenMD {
452      Vector3d force(0.0);
453      Vector3d com;
454      RealType totalFZ_local = 0;
455 +    RealType lrPot;
456      std::list<ZconstraintMol>::iterator i;
457 <    StuntDouble* integrableObject;
457 >    StuntDouble* sd;
458      Molecule::IntegrableObjectIterator ii;
459      Molecule* mol;
460      for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
# Line 441 | Line 463 | namespace OpenMD {
463        RealType resPos = usingSMD_? i->cantPos : i->param.zTargetPos;
464        RealType diff = com[whichDirection] - resPos;
465        RealType harmonicU = 0.5 * i->param.kz * diff * diff;
466 <      currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += harmonicU;
466 >      lrPot = currSnapshot_->getLongRangePotential();
467 >      lrPot += harmonicU;
468 >      currSnapshot_->setLongRangePotential(lrPot);
469        RealType harmonicF = -i->param.kz * diff;
470        totalFZ_local += harmonicF;
471  
472        //adjust force
473 <      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
474 <          integrableObject = mol->nextIntegrableObject(ii)) {
473 >      for(sd = mol->beginIntegrableObject(ii); sd != NULL;
474 >          sd = mol->nextIntegrableObject(ii)) {
475  
476 <        force[whichDirection] = getHFOfFixedZMols(mol, integrableObject, harmonicF);
477 <        integrableObject->addFrc(force);            
476 >        force[whichDirection] = getHFOfFixedZMols(mol, sd, harmonicF);
477 >        sd->addFrc(force);            
478        }
479      }
480  
481   #ifndef IS_MPI
482      totalFZ = totalFZ_local;
483   #else
484 <    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);  
484 >    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_REALTYPE,
485 >                  MPI_SUM, MPI_COMM_WORLD);
486   #endif
487  
488      //modify the forces of unconstrained molecules
489      std::vector<Molecule*>::iterator j;
490      for ( j = unzconsMols_.begin(); j !=  unzconsMols_.end(); ++j) {
491 +
492        mol = *j;
467 –      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
468 –          integrableObject = mol->nextIntegrableObject(ii)) {
493  
494 +      for(sd = mol->beginIntegrableObject(ii); sd != NULL;
495 +          sd = mol->nextIntegrableObject(ii)) {
496 +
497          force[whichDirection] = getHFOfUnconsMols(mol, totalFZ);
498 <        integrableObject->addFrc(force);            
498 >        sd->addFrc(force);            
499        }
500      }
501  
# Line 540 | Line 567 | namespace OpenMD {
567   #ifndef IS_MPI
568      havingFixed = havingFixed_local;
569   #else
570 <    MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM,
571 <                  MPI_COMM_WORLD);
570 >    MPI_Allreduce(&havingFixed_local, &havingFixed, 1,
571 >                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
572   #endif
573  
574      return havingFixed > 0;
# Line 557 | Line 584 | namespace OpenMD {
584   #ifndef IS_MPI
585      havingMoving = havingMoving_local;
586   #else
587 <    MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM,
588 <                  MPI_COMM_WORLD);
587 >    MPI_Allreduce(&havingMoving_local, &havingMoving, 1,
588 >                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
589   #endif
590  
591      return havingMoving > 0;
# Line 573 | Line 600 | namespace OpenMD {
600      }
601      
602   #ifdef IS_MPI
603 <    MPI_Allreduce(&totMassMovingZMols_local, &totMassMovingZMols_, 1, MPI_REALTYPE,
604 <                  MPI_SUM, MPI_COMM_WORLD);
603 >    MPI_Allreduce(&totMassMovingZMols_local, &totMassMovingZMols_,
604 >                  1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
605   #else
606      totMassMovingZMols_ = totMassMovingZMols_local;
607   #endif
# Line 598 | Line 625 | namespace OpenMD {
625    }
626  
627    void ZconstraintForceManager::updateZPos(){
601 –    RealType curTime = currSnapshot_->getTime();
628      std::list<ZconstraintMol>::iterator i;
629      for ( i = fixedZMols_.begin(); i !=  fixedZMols_.end(); ++i) {
630        i->param.zTargetPos += zconsGap_;    

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