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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC vs.
Revision 1812 by gezelter, Fri Nov 16 21:18:42 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 675 | Line 681 | namespace OpenMD {
681      InteractionData idat;
682      SelfData sdat;
683      RealType mf;
678 –    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 695 | 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 809 | Line 819 | namespace OpenMD {
819                fij += fg;
820  
821                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
822 <                stressTensor -= outProduct( *(idat.d), fg);
823 <                if (doHeatFlux_)
824 <                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
825 <                
822 >                if (!fDecomp_->skipAtomPair(atomListRow[0],
823 >                                            atomListColumn[0],
824 >                                            cg1, cg2)) {
825 >                  stressTensor -= outProduct( *(idat.d), fg);
826 >                  if (doHeatFlux_)
827 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
828 >                }                
829                }
830            
831                for (ia = atomListRow.begin();
# Line 869 | Line 882 | namespace OpenMD {
882  
883            fDecomp_->collectIntermediateData();
884  
885 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
885 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
886              fDecomp_->fillSelfData(sdat, atom1);
887              interactionMan_->doPreForce(sdat);
888            }
# Line 884 | Line 897 | namespace OpenMD {
897      fDecomp_->collectData();
898          
899      if (info_->requiresSelfCorrection()) {
900 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
900 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
901          fDecomp_->fillSelfData(sdat, atom1);
902          interactionMan_->doSelfCorrection(sdat);
903        }
# Line 898 | Line 911 | namespace OpenMD {
911  
912      curSnapshot->setLongRangePotential(longRangePotential);
913  
914 <    // lrPot = longRangePotential.sum();
914 >    // collects single-atom information
915 >    fDecomp_->collectSelfData();
916  
917 <    // //store the long range potential  
918 <    // curSnapshot->setLongRangePotential(lrPot);
917 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
918 >      *(fDecomp_->getPairwisePotential());
919 >
920 >    curSnapshot->setLongRangePotential(longRangePotential);
921      
922      curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
923                                           *(fDecomp_->getExcludedPotential()));
# Line 910 | Line 926 | namespace OpenMD {
926  
927    
928    void ForceManager::postCalculation() {
929 +
930 +    vector<Perturbation*>::iterator pi;
931 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
932 +      (*pi)->applyPerturbation();
933 +    }
934 +
935      SimInfo::MoleculeIterator mi;
936      Molecule* mol;
937      Molecule::RigidBodyIterator rbIter;
# Line 934 | Line 956 | namespace OpenMD {
956      curSnapshot->setStressTensor(stressTensor);
957      
958    }
937 –
959   } //end namespace OpenMD

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