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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 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

# Line 44 | Line 44
44   * @file ForceManager.cpp
45   * @author tlin
46   * @date 11/09/2004
47 – * @time 10:39am
47   * @version 1.0
48   */
49  
# Line 58 | Line 57
57   #include "primitives/Torsion.hpp"
58   #include "primitives/Inversion.hpp"
59   #include "nonbonded/NonBondedInteraction.hpp"
60 + #include "perturbations/ElectricField.hpp"
61   #include "parallel/ForceMatrixDecomposition.hpp"
62  
63   #include <cstdio>
# Line 369 | Line 369 | namespace OpenMD {
369      }
370      switcher_->setSwitchType(sft_);
371      switcher_->setSwitch(rSwitch_, rCut_);
372 –    interactionMan_->setSwitchingRadius(rSwitch_);
372    }
373  
374  
# Line 393 | Line 392 | namespace OpenMD {
392        doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
393        doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
394        if (doHeatFlux_) doParticlePot_ = true;
395 +
396 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
397    
398      }
399  
# Line 423 | Line 424 | namespace OpenMD {
424      electrostaticScale_[2] = fopts.getelectrostatic13scale();
425      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
426      
427 +    if (info_->getSimParams()->haveElectricField()) {
428 +      ElectricField* eField = new ElectricField(info_);
429 +      perturbations_.push_back(eField);
430 +    }
431 +
432      fDecomp_->distributeInitialData();
433  
434      initialized_ = true;
# Line 449 | Line 455 | namespace OpenMD {
455      Molecule::CutoffGroupIterator ci;
456      CutoffGroup* cg;
457      
458 <    // forces are zeroed here, before any are accumulated.
458 >    // forces and potentials are zeroed here, before any are
459 >    // accumulated.
460      
461 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
462 +
463 +    snap->setBondPotential(0.0);
464 +    snap->setBendPotential(0.0);
465 +    snap->setTorsionPotential(0.0);
466 +    snap->setInversionPotential(0.0);
467 +
468 +    potVec zeroPot(0.0);
469 +    snap->setLongRangePotential(zeroPot);
470 +    snap->setExcludedPotentials(zeroPot);
471 +
472 +    snap->setRestraintPotential(0.0);
473 +    snap->setRawPotential(0.0);
474 +
475      for (mol = info_->beginMolecule(mi); mol != NULL;
476           mol = info_->nextMolecule(mi)) {
477        for(atom = mol->beginAtom(ai); atom != NULL;
# Line 608 | Line 629 | namespace OpenMD {
629      curSnapshot->setTorsionPotential(torsionPotential);
630      curSnapshot->setInversionPotential(inversionPotential);
631      
632 <    RealType shortRangePotential = bondPotential + bendPotential +
633 <      torsionPotential +  inversionPotential;    
632 >    // RealType shortRangePotential = bondPotential + bendPotential +
633 >    //   torsionPotential +  inversionPotential;    
634  
635 <    curSnapshot->setShortRangePotential(shortRangePotential);
635 >    // curSnapshot->setShortRangePotential(shortRangePotential);
636    }
637    
638    void ForceManager::longRangeInteractions() {
# Line 660 | Line 681 | namespace OpenMD {
681      InteractionData idat;
682      SelfData sdat;
683      RealType mf;
663 –    RealType lrPot;
684      RealType vpair;
685      RealType dVdFQ1(0.0);
686      RealType dVdFQ2(0.0);
687      potVec longRangePotential(0.0);
688      potVec workPot(0.0);
689      potVec exPot(0.0);
690 +    Vector3d eField1(0.0);
691 +    Vector3d eField2(0.0);
692      vector<int>::iterator ia, jb;
693  
694      int loopStart, loopEnd;
# Line 680 | Line 702 | namespace OpenMD {
702      idat.vpair = &vpair;
703      idat.dVdFQ1 = &dVdFQ1;
704      idat.dVdFQ2 = &dVdFQ2;
705 +    idat.eField1 = &eField1;
706 +    idat.eField2 = &eField2;  
707      idat.f1 = &f1;
708      idat.sw = &sw;
709      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
710      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
711      idat.doParticlePot = doParticlePot_;
712 +    idat.doElectricField = doElectricField_;
713      sdat.doParticlePot = doParticlePot_;
714      
715      loopEnd = PAIR_LOOP;
# Line 854 | Line 879 | namespace OpenMD {
879  
880            fDecomp_->collectIntermediateData();
881  
882 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
882 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
883              fDecomp_->fillSelfData(sdat, atom1);
884              interactionMan_->doPreForce(sdat);
885            }
# Line 869 | Line 894 | namespace OpenMD {
894      fDecomp_->collectData();
895          
896      if (info_->requiresSelfCorrection()) {
897 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
897 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
898          fDecomp_->fillSelfData(sdat, atom1);
899          interactionMan_->doSelfCorrection(sdat);
900        }
# Line 881 | Line 906 | namespace OpenMD {
906      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
907        *(fDecomp_->getPairwisePotential());
908  
909 <    curSnapshot->setLongRangePotentialFamilies(longRangePotential);
909 >    curSnapshot->setLongRangePotential(longRangePotential);
910  
911 <    lrPot = longRangePotential.sum();
911 >    // collects single-atom information
912 >    fDecomp_->collectSelfData();
913  
914 <    //store the long range potential  
915 <    curSnapshot->setLongRangePotential(lrPot);
914 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
915 >      *(fDecomp_->getPairwisePotential());
916 >
917 >    curSnapshot->setLongRangePotential(longRangePotential);
918      
919      curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
920                                           *(fDecomp_->getExcludedPotential()));
# Line 895 | Line 923 | namespace OpenMD {
923  
924    
925    void ForceManager::postCalculation() {
926 +
927 +    vector<Perturbation*>::iterator pi;
928 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
929 +      (*pi)->applyPerturbation();
930 +    }
931 +
932      SimInfo::MoleculeIterator mi;
933      Molecule* mol;
934      Molecule::RigidBodyIterator rbIter;
935      RigidBody* rb;
936      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
937 <    
937 >  
938      // collect the atomic forces onto rigid bodies
939      
940      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 919 | Line 953 | namespace OpenMD {
953      curSnapshot->setStressTensor(stressTensor);
954      
955    }
922 –
956   } //end namespace OpenMD

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