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root/OpenMD/trunk/src/constraints/ZconstraintForceManager.cpp
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Comparing trunk/src/constraints/ZconstraintForceManager.cpp (file contents):
Revision 1781 by gezelter, Fri Jul 9 19:29:05 2010 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

# Line 36 | Line 36
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).                        
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   #include <cmath>
# Line 45 | Line 46
46   #include "utils/simError.h"
47   #include "utils/PhysicalConstants.hpp"
48   #include "utils/StringUtils.hpp"
49 + #ifdef IS_MPI
50 + #include <mpi.h>
51 + #endif
52 +
53   namespace OpenMD {
54    ZconstraintForceManager::ZconstraintForceManager(SimInfo* info): ForceManager(info), infiniteTime(1e31) {
55      currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
# 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 326 | Line 334 | namespace OpenMD {
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 391 | Line 405 | namespace OpenMD {
405  
406      // apply negative to fixed z-constrained molecues;
407      for ( i = fixedZMols_.begin(); i !=  fixedZMols_.end(); ++i) {
408 +
409        mol = i->mol;
395 –      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
396 –          integrableObject = mol->nextIntegrableObject(ii)) {
410  
411 <        force[whichDirection] = -getZFOfFixedZMols(mol, integrableObject, i->fz);
412 <        integrableObject->addFrc(force);
411 >      for(sd = mol->beginIntegrableObject(ii); sd != NULL;
412 >          sd = mol->nextIntegrableObject(ii)) {
413 >
414 >        force[whichDirection] = -getZFOfFixedZMols(mol, sd, i->fz);
415 >        sd->addFrc(force);
416        }
417      }
418  
419      //modify the forces of moving z-constrained molecules
420      for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
421 +
422        mol = i->mol;
406 –      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
407 –          integrableObject = mol->nextIntegrableObject(ii)) {
423  
424 +      for(sd = mol->beginIntegrableObject(ii); sd != NULL;
425 +          sd = mol->nextIntegrableObject(ii)) {
426 +
427          force[whichDirection] = -getZFOfMovingMols(mol,totalFZ);
428 <        integrableObject->addFrc(force);
428 >        sd->addFrc(force);
429        }
430      }
431  
432      //modify the forces of unconstrained molecules
433      std::vector<Molecule*>::iterator j;
434      for ( j = unzconsMols_.begin(); j !=  unzconsMols_.end(); ++j) {
435 +
436        mol =*j;
418 –      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
419 –          integrableObject = mol->nextIntegrableObject(ii)) {
437  
438 +      for(sd = mol->beginIntegrableObject(ii); sd != NULL;
439 +          sd = mol->nextIntegrableObject(ii)) {
440 +
441          force[whichDirection] = -getZFOfMovingMols(mol, totalFZ);
442 <        integrableObject->addFrc(force);
442 >        sd->addFrc(force);
443        }
444      }
445  
# Line 431 | Line 451 | namespace OpenMD {
451      Vector3d force(0.0);
452      Vector3d com;
453      RealType totalFZ_local = 0;
454 +    RealType lrPot;
455      std::list<ZconstraintMol>::iterator i;
456 <    StuntDouble* integrableObject;
456 >    StuntDouble* sd;
457      Molecule::IntegrableObjectIterator ii;
458      Molecule* mol;
459      for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
# Line 441 | Line 462 | namespace OpenMD {
462        RealType resPos = usingSMD_? i->cantPos : i->param.zTargetPos;
463        RealType diff = com[whichDirection] - resPos;
464        RealType harmonicU = 0.5 * i->param.kz * diff * diff;
465 <      currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += harmonicU;
465 >      lrPot = currSnapshot_->getLongRangePotential();
466 >      lrPot += harmonicU;
467 >      currSnapshot_->setLongRangePotential(lrPot);
468        RealType harmonicF = -i->param.kz * diff;
469        totalFZ_local += harmonicF;
470  
471        //adjust force
472 <      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
473 <          integrableObject = mol->nextIntegrableObject(ii)) {
472 >      for(sd = mol->beginIntegrableObject(ii); sd != NULL;
473 >          sd = mol->nextIntegrableObject(ii)) {
474  
475 <        force[whichDirection] = getHFOfFixedZMols(mol, integrableObject, harmonicF);
476 <        integrableObject->addFrc(force);            
475 >        force[whichDirection] = getHFOfFixedZMols(mol, sd, harmonicF);
476 >        sd->addFrc(force);            
477        }
478      }
479  
# Line 463 | Line 486 | namespace OpenMD {
486      //modify the forces of unconstrained molecules
487      std::vector<Molecule*>::iterator j;
488      for ( j = unzconsMols_.begin(); j !=  unzconsMols_.end(); ++j) {
489 +
490        mol = *j;
467 –      for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
468 –          integrableObject = mol->nextIntegrableObject(ii)) {
491  
492 +      for(sd = mol->beginIntegrableObject(ii); sd != NULL;
493 +          sd = mol->nextIntegrableObject(ii)) {
494 +
495          force[whichDirection] = getHFOfUnconsMols(mol, totalFZ);
496 <        integrableObject->addFrc(force);            
496 >        sd->addFrc(force);            
497        }
498      }
499  

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