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Revision 1616 by gezelter, Tue Aug 30 15:45:35 2011 UTC vs.
Revision 1767 by gezelter, Fri Jul 6 22:01:58 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   /**
# Line 109 | Line 110 | namespace OpenMD {
110      Globals* simParams_ = info_->getSimParams();
111      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112      int mdFileVersion;
113 +    rCut_ = 0.0; //Needs a value for a later max() call;  
114      
115      if (simParams_->haveMDfileVersion())
116        mdFileVersion = simParams_->getMDfileVersion();
# Line 200 | Line 202 | namespace OpenMD {
202          // electrostaticSummationMethod keyword.
203          
204          if (simParams_->haveElectrostaticSummationMethod()) {
205 <          std::string myMethod = simParams_->getElectrostaticSummationMethod();
205 >          string myMethod = simParams_->getElectrostaticSummationMethod();
206            toUpper(myMethod);
207          
208            if (myMethod == "SHIFTED_POTENTIAL") {
# Line 255 | Line 257 | namespace OpenMD {
257      stringToCutoffPolicy["MAX"] = MAX;
258      stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
259  
260 <    std::string cutPolicy;
260 >    string cutPolicy;
261      if (forceFieldOptions_.haveCutoffPolicy()){
262        cutPolicy = forceFieldOptions_.getCutoffPolicy();
263      }else if (simParams_->haveCutoffPolicy()) {
# Line 317 | Line 319 | namespace OpenMD {
319          simError();
320        }
321      } else {
322 <      if (simParams_->haveSwitchingRadius()) {
323 <        map<string, CutoffMethod>::const_iterator it;
324 <        string theMeth;
325 <        for (it = stringToCutoffMethod.begin();
326 <             it != stringToCutoffMethod.end(); ++it) {
327 <          if (it->second == cutoffMethod_) {
328 <            theMeth = it->first;
329 <            break;
322 >      if (mdFileVersion > 1) {
323 >        // throw an error if we define a switching radius and don't need one.
324 >        // older file versions should not do this.
325 >        if (simParams_->haveSwitchingRadius()) {
326 >          map<string, CutoffMethod>::const_iterator it;
327 >          string theMeth;
328 >          for (it = stringToCutoffMethod.begin();
329 >               it != stringToCutoffMethod.end(); ++it) {
330 >            if (it->second == cutoffMethod_) {
331 >              theMeth = it->first;
332 >              break;
333 >            }
334            }
335 +          sprintf(painCave.errMsg,
336 +                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
337 +                  "\tis not set to SWITCHED, so switchingRadius value\n"
338 +                  "\twill be ignored for this simulation\n", theMeth.c_str());
339 +          painCave.isFatal = 0;
340 +          painCave.severity = OPENMD_WARNING;
341 +          simError();
342          }
330 –        sprintf(painCave.errMsg,
331 –                "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
332 –                "\tis not set to SWITCHED, so switchingRadius value\n"
333 –                "\twill be ignored for this simulation\n", theMeth.c_str());
334 –        painCave.isFatal = 0;
335 –        painCave.severity = OPENMD_WARNING;
336 –        simError();
343        }
338 –
344        rSwitch_ = rCut_;
345      }
346      
# Line 384 | Line 389 | namespace OpenMD {
389        setupCutoffs();
390  
391        info_->prepareTopology();      
392 +
393 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
394 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
395 +      if (doHeatFlux_) doParticlePot_ = true;
396 +  
397      }
398  
399      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
# Line 439 | Line 449 | namespace OpenMD {
449      Molecule::CutoffGroupIterator ci;
450      CutoffGroup* cg;
451      
452 <    // forces are zeroed here, before any are accumulated.
452 >    // forces and potentials are zeroed here, before any are
453 >    // accumulated.
454      
455 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
456 +
457 +    snap->setBondPotential(0.0);
458 +    snap->setBendPotential(0.0);
459 +    snap->setTorsionPotential(0.0);
460 +    snap->setInversionPotential(0.0);
461 +
462 +    potVec zeroPot(0.0);
463 +    snap->setLongRangePotential(zeroPot);
464 +    snap->setExcludedPotentials(zeroPot);
465 +
466 +    snap->setRestraintPotential(0.0);
467 +    snap->setRawPotential(0.0);
468 +
469      for (mol = info_->beginMolecule(mi); mol != NULL;
470           mol = info_->nextMolecule(mi)) {
471        for(atom = mol->beginAtom(ai); atom != NULL;
# Line 464 | Line 489 | namespace OpenMD {
489      }
490      
491      // Zero out the stress tensor
492 <    tau *= 0.0;
493 <    
492 >    stressTensor *= 0.0;
493 >    // Zero out the heatFlux
494 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
495    }
496    
497    void ForceManager::shortRangeInteractions() {
# Line 498 | Line 524 | namespace OpenMD {
524  
525        for (bond = mol->beginBond(bondIter); bond != NULL;
526             bond = mol->nextBond(bondIter)) {
527 <        bond->calcForce();
527 >        bond->calcForce(doParticlePot_);
528          bondPotential += bond->getPotential();
529        }
530  
# Line 506 | Line 532 | namespace OpenMD {
532             bend = mol->nextBend(bendIter)) {
533          
534          RealType angle;
535 <        bend->calcForce(angle);
535 >        bend->calcForce(angle, doParticlePot_);
536          RealType currBendPot = bend->getPotential();          
537          
538          bendPotential += bend->getPotential();
# Line 531 | Line 557 | namespace OpenMD {
557        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
558             torsion = mol->nextTorsion(torsionIter)) {
559          RealType angle;
560 <        torsion->calcForce(angle);
560 >        torsion->calcForce(angle, doParticlePot_);
561          RealType currTorsionPot = torsion->getPotential();
562          torsionPotential += torsion->getPotential();
563          map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
# Line 555 | Line 581 | namespace OpenMD {
581             inversion != NULL;
582             inversion = mol->nextInversion(inversionIter)) {
583          RealType angle;
584 <        inversion->calcForce(angle);
584 >        inversion->calcForce(angle, doParticlePot_);
585          RealType currInversionPot = inversion->getPotential();
586          inversionPotential += inversion->getPotential();
587          map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
# Line 575 | Line 601 | namespace OpenMD {
601          }      
602        }      
603      }
604 <    
605 <    RealType  shortRangePotential = bondPotential + bendPotential +
606 <      torsionPotential +  inversionPotential;    
604 >
605 > #ifdef IS_MPI
606 >    // Collect from all nodes.  This should eventually be moved into a
607 >    // SystemDecomposition, but this is a better place than in
608 >    // Thermo to do the collection.
609 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
610 >                              MPI::SUM);
611 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
612 >                              MPI::SUM);
613 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
614 >                              MPI::REALTYPE, MPI::SUM);
615 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
616 >                              MPI::REALTYPE, MPI::SUM);
617 > #endif
618 >
619      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
620 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
621 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
622 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
623 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
624 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
620 >
621 >    curSnapshot->setBondPotential(bondPotential);
622 >    curSnapshot->setBendPotential(bendPotential);
623 >    curSnapshot->setTorsionPotential(torsionPotential);
624 >    curSnapshot->setInversionPotential(inversionPotential);
625 >    
626 >    // RealType shortRangePotential = bondPotential + bendPotential +
627 >    //   torsionPotential +  inversionPotential;    
628 >
629 >    // curSnapshot->setShortRangePotential(shortRangePotential);
630    }
631    
632    void ForceManager::longRangeInteractions() {
633  
634 +
635      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
636      DataStorage* config = &(curSnapshot->atomData);
637      DataStorage* cgConfig = &(curSnapshot->cgData);
# Line 611 | Line 655 | namespace OpenMD {
655        // center of mass of the group is the same as position of the atom  
656        // if cutoff group does not exist
657        cgConfig->position = config->position;
658 +      cgConfig->velocity = config->velocity;
659      }
660  
661      fDecomp_->zeroWorkArrays();
662      fDecomp_->distributeData();
663      
664      int cg1, cg2, atom1, atom2, topoDist;
665 <    Vector3d d_grp, dag, d;
665 >    Vector3d d_grp, dag, d, gvel2, vel2;
666      RealType rgrpsq, rgrp, r2, r;
667      RealType electroMult, vdwMult;
668      RealType vij;
# Line 630 | Line 675 | namespace OpenMD {
675      InteractionData idat;
676      SelfData sdat;
677      RealType mf;
633 –    RealType lrPot;
678      RealType vpair;
679 +    RealType dVdFQ1(0.0);
680 +    RealType dVdFQ2(0.0);
681      potVec longRangePotential(0.0);
682      potVec workPot(0.0);
683 +    potVec exPot(0.0);
684 +    vector<int>::iterator ia, jb;
685  
686      int loopStart, loopEnd;
687  
688      idat.vdwMult = &vdwMult;
689      idat.electroMult = &electroMult;
690      idat.pot = &workPot;
691 +    idat.excludedPot = &exPot;
692      sdat.pot = fDecomp_->getEmbeddingPotential();
693 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
694      idat.vpair = &vpair;
695 +    idat.dVdFQ1 = &dVdFQ1;
696 +    idat.dVdFQ2 = &dVdFQ2;
697      idat.f1 = &f1;
698      idat.sw = &sw;
699      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
700      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
701 +    idat.doParticlePot = doParticlePot_;
702 +    sdat.doParticlePot = doParticlePot_;
703      
704      loopEnd = PAIR_LOOP;
705      if (info_->requiresPrepair() ) {
# Line 653 | Line 707 | namespace OpenMD {
707      } else {
708        loopStart = PAIR_LOOP;
709      }
656 –  
710      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
711      
712        if (iLoop == loopStart) {
# Line 685 | Line 738 | namespace OpenMD {
738            
739            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
740                                                       rgrp);
741 <          
741 >
742            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
743            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
744  
745 <          for (vector<int>::iterator ia = atomListRow.begin();
745 >          if (doHeatFlux_)
746 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
747 >
748 >          for (ia = atomListRow.begin();
749                 ia != atomListRow.end(); ++ia) {            
750              atom1 = (*ia);
751 <            
752 <            for (vector<int>::iterator jb = atomListColumn.begin();
751 >
752 >            for (jb = atomListColumn.begin();
753                   jb != atomListColumn.end(); ++jb) {              
754                atom2 = (*jb);
755  
756 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
756 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
757 >
758                  vpair = 0.0;
759                  workPot = 0.0;
760 +                exPot = 0.0;
761                  f1 = V3Zero;
762 +                dVdFQ1 = 0.0;
763 +                dVdFQ2 = 0.0;
764  
765                  fDecomp_->fillInteractionData(idat, atom1, atom2);
766 <                
766 >
767                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
768                  vdwMult = vdwScale_[topoDist];
769                  electroMult = electrostaticScale_[topoDist];
# Line 711 | Line 771 | namespace OpenMD {
771                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
772                    idat.d = &d_grp;
773                    idat.r2 = &rgrpsq;
774 +                  if (doHeatFlux_)
775 +                    vel2 = gvel2;
776                  } else {
777                    d = fDecomp_->getInteratomicVector(atom1, atom2);
778                    curSnapshot->wrapVector( d );
779                    r2 = d.lengthSquare();
780                    idat.d = &d;
781                    idat.r2 = &r2;
782 +                  if (doHeatFlux_)
783 +                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
784                  }
785                
786                  r = sqrt( *(idat.r2) );
# Line 729 | Line 793 | namespace OpenMD {
793                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
794                    vij += vpair;
795                    fij += f1;
796 <                  tau -= outProduct( *(idat.d), f1);
796 >                  stressTensor -= outProduct( *(idat.d), f1);
797 >                  if (doHeatFlux_)
798 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
799                  }
800                }
801              }
# Line 742 | Line 808 | namespace OpenMD {
808                fij += fg;
809  
810                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
811 <                tau -= outProduct( *(idat.d), fg);
811 >                stressTensor -= outProduct( *(idat.d), fg);
812 >                if (doHeatFlux_)
813 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
814 >                
815                }
816            
817 <              for (vector<int>::iterator ia = atomListRow.begin();
817 >              for (ia = atomListRow.begin();
818                     ia != atomListRow.end(); ++ia) {            
819                  atom1 = (*ia);                
820                  mf = fDecomp_->getMassFactorRow(atom1);
# Line 758 | Line 827 | namespace OpenMD {
827                      // find the distance between the atom
828                      // and the center of the cutoff group:
829                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
830 <                    tau -= outProduct(dag, fg);
830 >                    stressTensor -= outProduct(dag, fg);
831 >                    if (doHeatFlux_)
832 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
833                    }
834                  }
835                }
836 <              for (vector<int>::iterator jb = atomListColumn.begin();
836 >              for (jb = atomListColumn.begin();
837                     jb != atomListColumn.end(); ++jb) {              
838                  atom2 = (*jb);
839                  mf = fDecomp_->getMassFactorColumn(atom2);
# Line 776 | Line 847 | namespace OpenMD {
847                      // find the distance between the atom
848                      // and the center of the cutoff group:
849                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
850 <                    tau -= outProduct(dag, fg);
850 >                    stressTensor -= outProduct(dag, fg);
851 >                    if (doHeatFlux_)
852 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
853                    }
854                  }
855                }
856              }
857              //if (!info_->usesAtomicVirial()) {
858 <            //  tau -= outProduct(d_grp, fij);
858 >            //  stressTensor -= outProduct(d_grp, fij);
859 >            //  if (doHeatFlux_)
860 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
861              //}
862            }
863          }
# Line 793 | Line 868 | namespace OpenMD {
868  
869            fDecomp_->collectIntermediateData();
870  
871 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
871 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
872              fDecomp_->fillSelfData(sdat, atom1);
873              interactionMan_->doPreForce(sdat);
874            }
# Line 804 | Line 879 | namespace OpenMD {
879        }
880      }
881      
882 +    // collects pairwise information
883      fDecomp_->collectData();
884          
885      if (info_->requiresSelfCorrection()) {
886 <
811 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
886 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
887          fDecomp_->fillSelfData(sdat, atom1);
888          interactionMan_->doSelfCorrection(sdat);
889        }
815 –
890      }
891  
892 +    // collects single-atom information
893 +    fDecomp_->collectSelfData();
894 +
895      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
896        *(fDecomp_->getPairwisePotential());
897  
898 <    lrPot = longRangePotential.sum();
898 >    curSnapshot->setLongRangePotential(longRangePotential);
899 >    
900 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
901 >                                         *(fDecomp_->getExcludedPotential()));
902  
823 –    //store the tau and long range potential    
824 –    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
825 –    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
826 –    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
903    }
904  
905    
# Line 833 | Line 909 | namespace OpenMD {
909      Molecule::RigidBodyIterator rbIter;
910      RigidBody* rb;
911      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
912 <    
912 >  
913      // collect the atomic forces onto rigid bodies
914      
915      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 841 | Line 917 | namespace OpenMD {
917        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
918             rb = mol->nextRigidBody(rbIter)) {
919          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
920 <        tau += rbTau;
920 >        stressTensor += rbTau;
921        }
922      }
923      
924   #ifdef IS_MPI
925 <    Mat3x3d tmpTau(tau);
926 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
851 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
925 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
926 >                              MPI::REALTYPE, MPI::SUM);
927   #endif
928 <    curSnapshot->statData.setTau(tau);
928 >    curSnapshot->setStressTensor(stressTensor);
929 >    
930    }
931  
932   } //end namespace OpenMD

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