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root/OpenMD/branches/development/src/brains/ForceManager.cpp
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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1761 by gezelter, Fri Jun 22 20:01:37 2012 UTC vs.
Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

# Line 58 | Line 58
58   #include "primitives/Torsion.hpp"
59   #include "primitives/Inversion.hpp"
60   #include "nonbonded/NonBondedInteraction.hpp"
61 + #include "perturbations/ElectricField.hpp"
62   #include "parallel/ForceMatrixDecomposition.hpp"
63  
64   #include <cstdio>
# Line 369 | Line 370 | namespace OpenMD {
370      }
371      switcher_->setSwitchType(sft_);
372      switcher_->setSwitch(rSwitch_, rCut_);
372 –    interactionMan_->setSwitchingRadius(rSwitch_);
373    }
374  
375  
# Line 393 | Line 393 | namespace OpenMD {
393        doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
394        doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
395        if (doHeatFlux_) doParticlePot_ = true;
396 +
397 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
398    
399      }
400  
# Line 423 | Line 425 | namespace OpenMD {
425      electrostaticScale_[2] = fopts.getelectrostatic13scale();
426      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
427      
428 +    if (info_->getSimParams()->haveElectricField()) {
429 +      ElectricField* eField = new ElectricField(info_);
430 +      perturbations_.push_back(eField);
431 +    }
432 +
433      fDecomp_->distributeInitialData();
434  
435      initialized_ = true;
# Line 449 | Line 456 | namespace OpenMD {
456      Molecule::CutoffGroupIterator ci;
457      CutoffGroup* cg;
458      
459 <    // forces are zeroed here, before any are accumulated.
459 >    // forces and potentials are zeroed here, before any are
460 >    // accumulated.
461      
462 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
463 +
464 +    snap->setBondPotential(0.0);
465 +    snap->setBendPotential(0.0);
466 +    snap->setTorsionPotential(0.0);
467 +    snap->setInversionPotential(0.0);
468 +
469 +    potVec zeroPot(0.0);
470 +    snap->setLongRangePotential(zeroPot);
471 +    snap->setExcludedPotentials(zeroPot);
472 +
473 +    snap->setRestraintPotential(0.0);
474 +    snap->setRawPotential(0.0);
475 +
476      for (mol = info_->beginMolecule(mi); mol != NULL;
477           mol = info_->nextMolecule(mi)) {
478        for(atom = mol->beginAtom(ai); atom != NULL;
# Line 608 | Line 630 | namespace OpenMD {
630      curSnapshot->setTorsionPotential(torsionPotential);
631      curSnapshot->setInversionPotential(inversionPotential);
632      
633 <    RealType shortRangePotential = bondPotential + bendPotential +
634 <      torsionPotential +  inversionPotential;    
633 >    // RealType shortRangePotential = bondPotential + bendPotential +
634 >    //   torsionPotential +  inversionPotential;    
635  
636 <    curSnapshot->setShortRangePotential(shortRangePotential);
636 >    // curSnapshot->setShortRangePotential(shortRangePotential);
637    }
638    
639    void ForceManager::longRangeInteractions() {
# Line 660 | Line 682 | namespace OpenMD {
682      InteractionData idat;
683      SelfData sdat;
684      RealType mf;
663 –    RealType lrPot;
685      RealType vpair;
686      RealType dVdFQ1(0.0);
687      RealType dVdFQ2(0.0);
688      potVec longRangePotential(0.0);
689      potVec workPot(0.0);
690      potVec exPot(0.0);
691 +    Vector3d eField1(0.0);
692 +    Vector3d eField2(0.0);
693      vector<int>::iterator ia, jb;
694  
695      int loopStart, loopEnd;
# Line 680 | Line 703 | namespace OpenMD {
703      idat.vpair = &vpair;
704      idat.dVdFQ1 = &dVdFQ1;
705      idat.dVdFQ2 = &dVdFQ2;
706 +    idat.eField1 = &eField1;
707 +    idat.eField2 = &eField2;  
708      idat.f1 = &f1;
709      idat.sw = &sw;
710      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
711      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
712      idat.doParticlePot = doParticlePot_;
713 +    idat.doElectricField = doElectricField_;
714      sdat.doParticlePot = doParticlePot_;
715      
716      loopEnd = PAIR_LOOP;
# Line 854 | Line 880 | namespace OpenMD {
880  
881            fDecomp_->collectIntermediateData();
882  
883 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
883 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
884              fDecomp_->fillSelfData(sdat, atom1);
885              interactionMan_->doPreForce(sdat);
886            }
# Line 869 | Line 895 | namespace OpenMD {
895      fDecomp_->collectData();
896          
897      if (info_->requiresSelfCorrection()) {
898 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
898 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
899          fDecomp_->fillSelfData(sdat, atom1);
900          interactionMan_->doSelfCorrection(sdat);
901        }
# Line 880 | Line 906 | namespace OpenMD {
906  
907      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
908        *(fDecomp_->getPairwisePotential());
883 –
884 –    curSnapshot->setLongRangePotentialFamilies(longRangePotential);
909  
910 <    lrPot = longRangePotential.sum();
887 <
888 <    //store the long range potential  
889 <    curSnapshot->setLongRangePotential(lrPot);
910 >    curSnapshot->setLongRangePotential(longRangePotential);
911      
912      curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
913                                           *(fDecomp_->getExcludedPotential()));
# Line 895 | Line 916 | namespace OpenMD {
916  
917    
918    void ForceManager::postCalculation() {
919 +
920 +    vector<Perturbation*>::iterator pi;
921 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
922 +      (*pi)->applyPerturbation();
923 +    }
924 +
925      SimInfo::MoleculeIterator mi;
926      Molecule* mol;
927      Molecule::RigidBodyIterator rbIter;
928      RigidBody* rb;
929      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
930 <    
930 >  
931      // collect the atomic forces onto rigid bodies
932      
933      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 919 | Line 946 | namespace OpenMD {
946      curSnapshot->setStressTensor(stressTensor);
947      
948    }
922 –
949   } //end namespace OpenMD

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