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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1597 by gezelter, Tue Jul 26 15:49:24 2011 UTC vs.
Revision 1808 by gezelter, Mon Oct 22 20:42:10 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   /**
44   * @file ForceManager.cpp
45   * @author tlin
46   * @date 11/09/2004
46 – * @time 10:39am
47   * @version 1.0
48   */
49  
# Line 57 | 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 108 | Line 109 | namespace OpenMD {
109      
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();
117 +    else
118 +      mdFileVersion = 0;
119 +  
120      if (simParams_->haveCutoffRadius()) {
121        rCut_ = simParams_->getCutoffRadius();
122      } else {      
# Line 166 | Line 174 | namespace OpenMD {
174          cutoffMethod_ = i->second;
175        }
176      } else {
177 <      sprintf(painCave.errMsg,
178 <              "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
179 <              "\tOpenMD will use SHIFTED_FORCE.\n");
180 <      painCave.isFatal = 0;
181 <      painCave.severity = OPENMD_INFO;
182 <      simError();
183 <      cutoffMethod_ = SHIFTED_FORCE;        
177 >      if (mdFileVersion > 1) {
178 >        sprintf(painCave.errMsg,
179 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
180 >                "\tOpenMD will use SHIFTED_FORCE.\n");
181 >        painCave.isFatal = 0;
182 >        painCave.severity = OPENMD_INFO;
183 >        simError();
184 >        cutoffMethod_ = SHIFTED_FORCE;        
185 >      } else {
186 >        // handle the case where the old file version was in play
187 >        // (there should be no cutoffMethod, so we have to deduce it
188 >        // from other data).        
189 >
190 >        sprintf(painCave.errMsg,
191 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
192 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
193 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
194 >                "\tbehavior of the older (version 1) code.  To remove this\n"
195 >                "\twarning, add an explicit cutoffMethod and change the top\n"
196 >                "\tof the file so that it begins with <OpenMD version=2>\n");
197 >        painCave.isFatal = 0;
198 >        painCave.severity = OPENMD_WARNING;
199 >        simError();            
200 >                
201 >        // The old file version tethered the shifting behavior to the
202 >        // electrostaticSummationMethod keyword.
203 >        
204 >        if (simParams_->haveElectrostaticSummationMethod()) {
205 >          string myMethod = simParams_->getElectrostaticSummationMethod();
206 >          toUpper(myMethod);
207 >        
208 >          if (myMethod == "SHIFTED_POTENTIAL") {
209 >            cutoffMethod_ = SHIFTED_POTENTIAL;
210 >          } else if (myMethod == "SHIFTED_FORCE") {
211 >            cutoffMethod_ = SHIFTED_FORCE;
212 >          }
213 >        
214 >          if (simParams_->haveSwitchingRadius())
215 >            rSwitch_ = simParams_->getSwitchingRadius();
216 >
217 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
218 >            if (simParams_->haveSwitchingRadius()){
219 >              sprintf(painCave.errMsg,
220 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
221 >                      "\tA value was set for the switchingRadius\n"
222 >                      "\teven though the electrostaticSummationMethod was\n"
223 >                      "\tset to %s\n", myMethod.c_str());
224 >              painCave.severity = OPENMD_WARNING;
225 >              painCave.isFatal = 1;
226 >              simError();            
227 >            }
228 >          }
229 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
230 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
231 >              sprintf(painCave.errMsg,
232 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
233 >                      "\tcutoffRadius and switchingRadius are set to the\n"
234 >                      "\tsame value.  OpenMD will use shifted force\n"
235 >                      "\tpotentials instead of switching functions.\n");
236 >              painCave.isFatal = 0;
237 >              painCave.severity = OPENMD_WARNING;
238 >              simError();            
239 >            } else {
240 >              cutoffMethod_ = SHIFTED_POTENTIAL;
241 >              sprintf(painCave.errMsg,
242 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
243 >                      "\tcutoffRadius and switchingRadius are set to the\n"
244 >                      "\tsame value.  OpenMD will use shifted potentials\n"
245 >                      "\tinstead of switching functions.\n");
246 >              painCave.isFatal = 0;
247 >              painCave.severity = OPENMD_WARNING;
248 >              simError();            
249 >            }
250 >          }
251 >        }
252 >      }
253      }
254  
255      map<string, CutoffPolicy> stringToCutoffPolicy;
# Line 180 | 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 242 | 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          }
255 –        sprintf(painCave.errMsg,
256 –                "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
257 –                "\tis not set to SWITCHED, so switchingRadius value\n"
258 –                "\twill be ignored for this simulation\n", theMeth.c_str());
259 –        painCave.isFatal = 0;
260 –        painCave.severity = OPENMD_WARNING;
261 –        simError();
343        }
263 –
344        rSwitch_ = rCut_;
345      }
346      
# Line 289 | Line 369 | namespace OpenMD {
369      }
370      switcher_->setSwitchType(sft_);
371      switcher_->setSwitch(rSwitch_, rCut_);
292 –    interactionMan_->setSwitchingRadius(rSwitch_);
372    }
373 +
374 +
375 +
376    
377    void ForceManager::initialize() {
378  
# Line 306 | Line 388 | namespace OpenMD {
388        setupCutoffs();
389  
390        info_->prepareTopology();      
391 +
392 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
393 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
394 +      if (doHeatFlux_) doParticlePot_ = true;
395 +
396 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
397 +  
398      }
399  
400      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
# Line 335 | 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 361 | 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;
478            atom = mol->nextAtom(ai)) {
479          atom->zeroForcesAndTorques();
371 –        cerr << "apos = " << atom->getPos() << "\n";
480        }
481        
482        //change the positions of atoms which belong to the rigidbodies
# Line 382 | Line 490 | namespace OpenMD {
490              cg = mol->nextCutoffGroup(ci)) {
491            //calculate the center of mass of cutoff group
492            cg->updateCOM();
385 –          cerr << "cgpos = " << cg->getPos() << "\n";
493          }
494        }      
495      }
496      
497      // Zero out the stress tensor
498 <    tau *= 0.0;
499 <    
498 >    stressTensor *= 0.0;
499 >    // Zero out the heatFlux
500 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
501    }
502    
503    void ForceManager::shortRangeInteractions() {
# Line 422 | Line 530 | namespace OpenMD {
530  
531        for (bond = mol->beginBond(bondIter); bond != NULL;
532             bond = mol->nextBond(bondIter)) {
533 <        bond->calcForce();
533 >        bond->calcForce(doParticlePot_);
534          bondPotential += bond->getPotential();
535        }
536  
# Line 430 | Line 538 | namespace OpenMD {
538             bend = mol->nextBend(bendIter)) {
539          
540          RealType angle;
541 <        bend->calcForce(angle);
541 >        bend->calcForce(angle, doParticlePot_);
542          RealType currBendPot = bend->getPotential();          
543          
544          bendPotential += bend->getPotential();
# Line 455 | Line 563 | namespace OpenMD {
563        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
564             torsion = mol->nextTorsion(torsionIter)) {
565          RealType angle;
566 <        torsion->calcForce(angle);
566 >        torsion->calcForce(angle, doParticlePot_);
567          RealType currTorsionPot = torsion->getPotential();
568          torsionPotential += torsion->getPotential();
569          map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
# Line 479 | Line 587 | namespace OpenMD {
587             inversion != NULL;
588             inversion = mol->nextInversion(inversionIter)) {
589          RealType angle;
590 <        inversion->calcForce(angle);
590 >        inversion->calcForce(angle, doParticlePot_);
591          RealType currInversionPot = inversion->getPotential();
592          inversionPotential += inversion->getPotential();
593          map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
# Line 499 | Line 607 | namespace OpenMD {
607          }      
608        }      
609      }
610 <    
611 <    RealType  shortRangePotential = bondPotential + bendPotential +
612 <      torsionPotential +  inversionPotential;    
610 >
611 > #ifdef IS_MPI
612 >    // Collect from all nodes.  This should eventually be moved into a
613 >    // SystemDecomposition, but this is a better place than in
614 >    // Thermo to do the collection.
615 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
616 >                              MPI::SUM);
617 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
618 >                              MPI::SUM);
619 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
620 >                              MPI::REALTYPE, MPI::SUM);
621 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
622 >                              MPI::REALTYPE, MPI::SUM);
623 > #endif
624 >
625      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
626 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
627 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
628 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
629 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
630 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
626 >
627 >    curSnapshot->setBondPotential(bondPotential);
628 >    curSnapshot->setBendPotential(bendPotential);
629 >    curSnapshot->setTorsionPotential(torsionPotential);
630 >    curSnapshot->setInversionPotential(inversionPotential);
631 >    
632 >    // RealType shortRangePotential = bondPotential + bendPotential +
633 >    //   torsionPotential +  inversionPotential;    
634 >
635 >    // curSnapshot->setShortRangePotential(shortRangePotential);
636    }
637    
638    void ForceManager::longRangeInteractions() {
639  
640 +
641      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
642      DataStorage* config = &(curSnapshot->atomData);
643      DataStorage* cgConfig = &(curSnapshot->cgData);
# Line 528 | Line 654 | namespace OpenMD {
654             mol = info_->nextMolecule(mi)) {
655          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
656              cg = mol->nextCutoffGroup(ci)) {
531 –          cerr << "branch1\n";
532 –          cerr << "globind = " << cg->getGlobalIndex() << "\n";
657            cg->updateCOM();
658          }
659        }      
660      } else {
661        // center of mass of the group is the same as position of the atom  
662        // if cutoff group does not exist
539 –      cerr << "branch2\n";
663        cgConfig->position = config->position;
664 +      cgConfig->velocity = config->velocity;
665      }
666  
667      fDecomp_->zeroWorkArrays();
668      fDecomp_->distributeData();
669      
670      int cg1, cg2, atom1, atom2, topoDist;
671 <    Vector3d d_grp, dag, d;
671 >    Vector3d d_grp, dag, d, gvel2, vel2;
672      RealType rgrpsq, rgrp, r2, r;
673      RealType electroMult, vdwMult;
674      RealType vij;
# Line 557 | Line 681 | namespace OpenMD {
681      InteractionData idat;
682      SelfData sdat;
683      RealType mf;
560 –    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;
695  
696      idat.vdwMult = &vdwMult;
697      idat.electroMult = &electroMult;
698      idat.pot = &workPot;
699 +    idat.excludedPot = &exPot;
700      sdat.pot = fDecomp_->getEmbeddingPotential();
701 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
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;
716      if (info_->requiresPrepair() ) {
# Line 580 | Line 718 | namespace OpenMD {
718      } else {
719        loopStart = PAIR_LOOP;
720      }
583 –  
721      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
722      
723        if (iLoop == loopStart) {
724          bool update_nlist = fDecomp_->checkNeighborList();
725          if (update_nlist)
726            neighborList = fDecomp_->buildNeighborList();
727 <      }      
728 <        
727 >      }            
728 >
729        for (vector<pair<int, int> >::iterator it = neighborList.begin();
730               it != neighborList.end(); ++it) {
731                  
# Line 598 | Line 735 | namespace OpenMD {
735          cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
736  
737          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
738 +
739          curSnapshot->wrapVector(d_grp);        
740          rgrpsq = d_grp.lengthSquare();
603 –
741          rCutSq = cuts.second;
742  
743          if (rgrpsq < rCutSq) {
# Line 612 | Line 749 | namespace OpenMD {
749            
750            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
751                                                       rgrp);
752 <              
752 >
753            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
754            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
755  
756 <          for (vector<int>::iterator ia = atomListRow.begin();
756 >          if (doHeatFlux_)
757 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
758 >
759 >          for (ia = atomListRow.begin();
760                 ia != atomListRow.end(); ++ia) {            
761              atom1 = (*ia);
762 <            
763 <            for (vector<int>::iterator jb = atomListColumn.begin();
762 >
763 >            for (jb = atomListColumn.begin();
764                   jb != atomListColumn.end(); ++jb) {              
765                atom2 = (*jb);
766  
767 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
767 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
768 >
769                  vpair = 0.0;
770                  workPot = 0.0;
771 +                exPot = 0.0;
772                  f1 = V3Zero;
773 +                dVdFQ1 = 0.0;
774 +                dVdFQ2 = 0.0;
775  
776                  fDecomp_->fillInteractionData(idat, atom1, atom2);
777 <                
777 >
778                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
779                  vdwMult = vdwScale_[topoDist];
780                  electroMult = electrostaticScale_[topoDist];
# Line 638 | Line 782 | namespace OpenMD {
782                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
783                    idat.d = &d_grp;
784                    idat.r2 = &rgrpsq;
785 <                  cerr << "dgrp = " << d_grp << "\n";
785 >                  if (doHeatFlux_)
786 >                    vel2 = gvel2;
787                  } else {
788                    d = fDecomp_->getInteratomicVector(atom1, atom2);
789                    curSnapshot->wrapVector( d );
790                    r2 = d.lengthSquare();
646 –                  cerr << "datm = " << d<< "\n";
791                    idat.d = &d;
792                    idat.r2 = &r2;
793 +                  if (doHeatFlux_)
794 +                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
795                  }
796 <                
651 <                cerr << "idat.d = " << *(idat.d) << "\n";
796 >              
797                  r = sqrt( *(idat.r2) );
798                  idat.rij = &r;
799                
# Line 657 | Line 802 | namespace OpenMD {
802                  } else {
803                    interactionMan_->doPair(idat);
804                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
660 –
661 –                  cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
805                    vij += vpair;
806                    fij += f1;
807 <                  tau -= outProduct( *(idat.d), f1);
807 >                  stressTensor -= outProduct( *(idat.d), f1);
808 >                  if (doHeatFlux_)
809 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
810                  }
811                }
812              }
# Line 674 | Line 819 | namespace OpenMD {
819                fij += fg;
820  
821                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
822 <                tau -= outProduct( *(idat.d), fg);
822 >                stressTensor -= outProduct( *(idat.d), fg);
823 >                if (doHeatFlux_)
824 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
825 >                
826                }
827            
828 <              for (vector<int>::iterator ia = atomListRow.begin();
828 >              for (ia = atomListRow.begin();
829                     ia != atomListRow.end(); ++ia) {            
830                  atom1 = (*ia);                
831                  mf = fDecomp_->getMassFactorRow(atom1);
# Line 685 | Line 833 | namespace OpenMD {
833                  // presence in switching region
834                  fg = swderiv * d_grp * mf;
835                  fDecomp_->addForceToAtomRow(atom1, fg);
688 –
836                  if (atomListRow.size() > 1) {
837                    if (info_->usesAtomicVirial()) {
838                      // find the distance between the atom
839                      // and the center of the cutoff group:
840                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
841 <                    tau -= outProduct(dag, fg);
841 >                    stressTensor -= outProduct(dag, fg);
842 >                    if (doHeatFlux_)
843 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
844                    }
845                  }
846                }
847 <              for (vector<int>::iterator jb = atomListColumn.begin();
847 >              for (jb = atomListColumn.begin();
848                     jb != atomListColumn.end(); ++jb) {              
849                  atom2 = (*jb);
850                  mf = fDecomp_->getMassFactorColumn(atom2);
# Line 709 | Line 858 | namespace OpenMD {
858                      // find the distance between the atom
859                      // and the center of the cutoff group:
860                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
861 <                    tau -= outProduct(dag, fg);
861 >                    stressTensor -= outProduct(dag, fg);
862 >                    if (doHeatFlux_)
863 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
864                    }
865                  }
866                }
867              }
868 <            //if (!SIM_uses_AtomicVirial) {
869 <            //  tau -= outProduct(d_grp, fij);
868 >            //if (!info_->usesAtomicVirial()) {
869 >            //  stressTensor -= outProduct(d_grp, fij);
870 >            //  if (doHeatFlux_)
871 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
872              //}
873            }
874          }
# Line 726 | 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 735 | Line 888 | namespace OpenMD {
888  
889          }
890        }
738 –
891      }
892      
893 +    // collects pairwise information
894      fDecomp_->collectData();
895          
896      if (info_->requiresSelfCorrection()) {
897 <
745 <      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        }
749 –
901      }
902  
903 +    // collects single-atom information
904 +    fDecomp_->collectSelfData();
905 +
906      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
907        *(fDecomp_->getPairwisePotential());
908  
909 <    lrPot = longRangePotential.sum();
909 >    curSnapshot->setLongRangePotential(longRangePotential);
910  
911 <    //store the tau and long range potential    
912 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
913 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
914 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
911 >    // collects single-atom information
912 >    fDecomp_->collectSelfData();
913 >
914 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
915 >      *(fDecomp_->getPairwisePotential());
916 >
917 >    curSnapshot->setLongRangePotential(longRangePotential);
918 >    
919 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
920 >                                         *(fDecomp_->getExcludedPotential()));
921 >
922    }
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 775 | Line 942 | namespace OpenMD {
942        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
943             rb = mol->nextRigidBody(rbIter)) {
944          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
945 <        tau += rbTau;
945 >        stressTensor += rbTau;
946        }
947      }
948      
949   #ifdef IS_MPI
950 <    Mat3x3d tmpTau(tau);
951 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
785 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
950 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
951 >                              MPI::REALTYPE, MPI::SUM);
952   #endif
953 <    curSnapshot->statData.setTau(tau);
953 >    curSnapshot->setStressTensor(stressTensor);
954 >    
955    }
789 –
956   } //end namespace OpenMD

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