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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1587 by gezelter, Fri Jul 8 20:25:32 2011 UTC vs.
Revision 1760 by gezelter, Thu Jun 21 19:26:46 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 86 | Line 87 | namespace OpenMD {
87     *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
88     *      Use the maximum suggested value that was found.
89     *
90 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
90 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
91 >   *                        or SHIFTED_POTENTIAL)
92     *      If cutoffMethod was explicitly set, use that choice.
93     *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
94     *
# Line 107 | 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 165 | 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 179 | 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 241 | 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          }
254 –        sprintf(painCave.errMsg,
255 –                "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
256 –                "\tis not set to SWITCHED, so switchingRadius value\n"
257 –                "\twill be ignored for this simulation\n", theMeth.c_str());
258 –        painCave.isFatal = 0;
259 –        painCave.severity = OPENMD_WARNING;
260 –        simError();
343        }
262 –
344        rSwitch_ = rCut_;
345      }
346      
# Line 290 | Line 371 | namespace OpenMD {
371      switcher_->setSwitch(rSwitch_, rCut_);
372      interactionMan_->setSwitchingRadius(rSwitch_);
373    }
374 +
375 +
376 +
377    
378    void ForceManager::initialize() {
379  
380      if (!info_->isTopologyDone()) {
381 +
382        info_->update();
383        interactionMan_->setSimInfo(info_);
384        interactionMan_->initialize();
# Line 301 | Line 386 | namespace OpenMD {
386        // We want to delay the cutoffs until after the interaction
387        // manager has set up the atom-atom interactions so that we can
388        // query them for suggested cutoff values
304 –
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();
400      
401 <    // Force fields can set options on how to scale van der Waals and electrostatic
402 <    // interactions for atoms connected via bonds, bends and torsions
403 <    // in this case the topological distance between atoms is:
401 >    // Force fields can set options on how to scale van der Waals and
402 >    // electrostatic interactions for atoms connected via bonds, bends
403 >    // and torsions in this case the topological distance between
404 >    // atoms is:
405      // 0 = topologically unconnected
406      // 1 = bonded together
407      // 2 = connected via a bend
# Line 363 | Line 453 | namespace OpenMD {
453      
454      for (mol = info_->beginMolecule(mi); mol != NULL;
455           mol = info_->nextMolecule(mi)) {
456 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
456 >      for(atom = mol->beginAtom(ai); atom != NULL;
457 >          atom = mol->nextAtom(ai)) {
458          atom->zeroForcesAndTorques();
459        }
460 <          
460 >      
461        //change the positions of atoms which belong to the rigidbodies
462        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
463             rb = mol->nextRigidBody(rbIter)) {
464          rb->zeroForcesAndTorques();
465        }        
466 <
466 >      
467        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
468          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
469              cg = mol->nextCutoffGroup(ci)) {
# Line 381 | Line 472 | namespace OpenMD {
472          }
473        }      
474      }
384 –  
385 –    // Zero out the stress tensor
386 –    tau *= 0.0;
475      
476 +    // Zero out the stress tensor
477 +    stressTensor *= 0.0;
478 +    // Zero out the heatFlux
479 +    fDecomp_->setHeatFlux( Vector3d(0.0) );    
480    }
481    
482    void ForceManager::shortRangeInteractions() {
# Line 417 | Line 509 | namespace OpenMD {
509  
510        for (bond = mol->beginBond(bondIter); bond != NULL;
511             bond = mol->nextBond(bondIter)) {
512 <        bond->calcForce();
512 >        bond->calcForce(doParticlePot_);
513          bondPotential += bond->getPotential();
514        }
515  
# Line 425 | Line 517 | namespace OpenMD {
517             bend = mol->nextBend(bendIter)) {
518          
519          RealType angle;
520 <        bend->calcForce(angle);
520 >        bend->calcForce(angle, doParticlePot_);
521          RealType currBendPot = bend->getPotential();          
522          
523          bendPotential += bend->getPotential();
# Line 435 | Line 527 | namespace OpenMD {
527            dataSet.prev.angle = dataSet.curr.angle = angle;
528            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
529            dataSet.deltaV = 0.0;
530 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
530 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
531 >                                                                  dataSet));
532          }else {
533            i->second.prev.angle = i->second.curr.angle;
534            i->second.prev.potential = i->second.curr.potential;
# Line 449 | Line 542 | namespace OpenMD {
542        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
543             torsion = mol->nextTorsion(torsionIter)) {
544          RealType angle;
545 <        torsion->calcForce(angle);
545 >        torsion->calcForce(angle, doParticlePot_);
546          RealType currTorsionPot = torsion->getPotential();
547          torsionPotential += torsion->getPotential();
548          map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
# Line 473 | Line 566 | namespace OpenMD {
566             inversion != NULL;
567             inversion = mol->nextInversion(inversionIter)) {
568          RealType angle;
569 <        inversion->calcForce(angle);
569 >        inversion->calcForce(angle, doParticlePot_);
570          RealType currInversionPot = inversion->getPotential();
571          inversionPotential += inversion->getPotential();
572          map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
# Line 493 | Line 586 | namespace OpenMD {
586          }      
587        }      
588      }
589 +
590 + #ifdef IS_MPI
591 +    // Collect from all nodes.  This should eventually be moved into a
592 +    // SystemDecomposition, but this is a better place than in
593 +    // Thermo to do the collection.
594 +    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
595 +                              MPI::SUM);
596 +    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
597 +                              MPI::SUM);
598 +    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
599 +                              MPI::REALTYPE, MPI::SUM);
600 +    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
601 +                              MPI::REALTYPE, MPI::SUM);
602 + #endif
603 +
604 +    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
605 +
606 +    curSnapshot->setBondPotential(bondPotential);
607 +    curSnapshot->setBendPotential(bendPotential);
608 +    curSnapshot->setTorsionPotential(torsionPotential);
609 +    curSnapshot->setInversionPotential(inversionPotential);
610      
611 <    RealType  shortRangePotential = bondPotential + bendPotential +
611 >    RealType shortRangePotential = bondPotential + bendPotential +
612        torsionPotential +  inversionPotential;    
613 <    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
614 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
501 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
502 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
503 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
504 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
613 >
614 >    curSnapshot->setShortRangePotential(shortRangePotential);
615    }
616    
617    void ForceManager::longRangeInteractions() {
618  
619 +
620      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
621      DataStorage* config = &(curSnapshot->atomData);
622      DataStorage* cgConfig = &(curSnapshot->cgData);
# Line 529 | Line 640 | namespace OpenMD {
640        // center of mass of the group is the same as position of the atom  
641        // if cutoff group does not exist
642        cgConfig->position = config->position;
643 +      cgConfig->velocity = config->velocity;
644      }
645  
646      fDecomp_->zeroWorkArrays();
647      fDecomp_->distributeData();
648      
649      int cg1, cg2, atom1, atom2, topoDist;
650 <    Vector3d d_grp, dag, d;
650 >    Vector3d d_grp, dag, d, gvel2, vel2;
651      RealType rgrpsq, rgrp, r2, r;
652      RealType electroMult, vdwMult;
653      RealType vij;
# Line 550 | Line 662 | namespace OpenMD {
662      RealType mf;
663      RealType lrPot;
664      RealType vpair;
665 +    RealType dVdFQ1(0.0);
666 +    RealType dVdFQ2(0.0);
667      potVec longRangePotential(0.0);
668      potVec workPot(0.0);
669 +    potVec exPot(0.0);
670 +    vector<int>::iterator ia, jb;
671  
672      int loopStart, loopEnd;
673  
674      idat.vdwMult = &vdwMult;
675      idat.electroMult = &electroMult;
676      idat.pot = &workPot;
677 +    idat.excludedPot = &exPot;
678      sdat.pot = fDecomp_->getEmbeddingPotential();
679      idat.vpair = &vpair;
680 +    idat.dVdFQ1 = &dVdFQ1;
681 +    idat.dVdFQ2 = &dVdFQ2;
682      idat.f1 = &f1;
683      idat.sw = &sw;
684      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
685      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
686 +    idat.doParticlePot = doParticlePot_;
687 +    sdat.doParticlePot = doParticlePot_;
688      
689      loopEnd = PAIR_LOOP;
690      if (info_->requiresPrepair() ) {
# Line 571 | Line 692 | namespace OpenMD {
692      } else {
693        loopStart = PAIR_LOOP;
694      }
574 –  
695      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
696      
697        if (iLoop == loopStart) {
698          bool update_nlist = fDecomp_->checkNeighborList();
699          if (update_nlist)
700            neighborList = fDecomp_->buildNeighborList();
701 <      }      
702 <        
701 >      }            
702 >
703        for (vector<pair<int, int> >::iterator it = neighborList.begin();
704               it != neighborList.end(); ++it) {
705                  
# Line 589 | Line 709 | namespace OpenMD {
709          cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
710  
711          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
712 +
713          curSnapshot->wrapVector(d_grp);        
714          rgrpsq = d_grp.lengthSquare();
594 –
715          rCutSq = cuts.second;
716  
717          if (rgrpsq < rCutSq) {
# Line 603 | Line 723 | namespace OpenMD {
723            
724            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
725                                                       rgrp);
726 <              
726 >
727            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
728            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
729  
730 <          for (vector<int>::iterator ia = atomListRow.begin();
730 >          if (doHeatFlux_)
731 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
732 >
733 >          for (ia = atomListRow.begin();
734                 ia != atomListRow.end(); ++ia) {            
735              atom1 = (*ia);
736 <            
737 <            for (vector<int>::iterator jb = atomListColumn.begin();
736 >
737 >            for (jb = atomListColumn.begin();
738                   jb != atomListColumn.end(); ++jb) {              
739                atom2 = (*jb);
740 <            
741 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
740 >
741 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
742 >
743                  vpair = 0.0;
744                  workPot = 0.0;
745 +                exPot = 0.0;
746                  f1 = V3Zero;
747 +                dVdFQ1 = 0.0;
748 +                dVdFQ2 = 0.0;
749  
750                  fDecomp_->fillInteractionData(idat, atom1, atom2);
751 <                
751 >
752                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
753                  vdwMult = vdwScale_[topoDist];
754                  electroMult = electrostaticScale_[topoDist];
# Line 629 | Line 756 | namespace OpenMD {
756                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
757                    idat.d = &d_grp;
758                    idat.r2 = &rgrpsq;
759 +                  if (doHeatFlux_)
760 +                    vel2 = gvel2;
761                  } else {
762                    d = fDecomp_->getInteratomicVector(atom1, atom2);
763                    curSnapshot->wrapVector( d );
764                    r2 = d.lengthSquare();
765                    idat.d = &d;
766                    idat.r2 = &r2;
767 +                  if (doHeatFlux_)
768 +                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
769                  }
770 <                
770 >              
771                  r = sqrt( *(idat.r2) );
772                  idat.rij = &r;
773                
# Line 647 | Line 778 | namespace OpenMD {
778                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
779                    vij += vpair;
780                    fij += f1;
781 <                  tau -= outProduct( *(idat.d), f1);
781 >                  stressTensor -= outProduct( *(idat.d), f1);
782 >                  if (doHeatFlux_)
783 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
784                  }
785                }
786              }
# Line 660 | Line 793 | namespace OpenMD {
793                fij += fg;
794  
795                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
796 <                tau -= outProduct( *(idat.d), fg);
796 >                stressTensor -= outProduct( *(idat.d), fg);
797 >                if (doHeatFlux_)
798 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
799 >                
800                }
801            
802 <              for (vector<int>::iterator ia = atomListRow.begin();
802 >              for (ia = atomListRow.begin();
803                     ia != atomListRow.end(); ++ia) {            
804                  atom1 = (*ia);                
805                  mf = fDecomp_->getMassFactorRow(atom1);
# Line 671 | Line 807 | namespace OpenMD {
807                  // presence in switching region
808                  fg = swderiv * d_grp * mf;
809                  fDecomp_->addForceToAtomRow(atom1, fg);
674 –
810                  if (atomListRow.size() > 1) {
811                    if (info_->usesAtomicVirial()) {
812                      // find the distance between the atom
813                      // and the center of the cutoff group:
814                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
815 <                    tau -= outProduct(dag, fg);
815 >                    stressTensor -= outProduct(dag, fg);
816 >                    if (doHeatFlux_)
817 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
818                    }
819                  }
820                }
821 <              for (vector<int>::iterator jb = atomListColumn.begin();
821 >              for (jb = atomListColumn.begin();
822                     jb != atomListColumn.end(); ++jb) {              
823                  atom2 = (*jb);
824                  mf = fDecomp_->getMassFactorColumn(atom2);
# Line 695 | Line 832 | namespace OpenMD {
832                      // find the distance between the atom
833                      // and the center of the cutoff group:
834                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
835 <                    tau -= outProduct(dag, fg);
835 >                    stressTensor -= outProduct(dag, fg);
836 >                    if (doHeatFlux_)
837 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
838                    }
839                  }
840                }
841              }
842 <            //if (!SIM_uses_AtomicVirial) {
843 <            //  tau -= outProduct(d_grp, fij);
842 >            //if (!info_->usesAtomicVirial()) {
843 >            //  stressTensor -= outProduct(d_grp, fij);
844 >            //  if (doHeatFlux_)
845 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
846              //}
847            }
848          }
849        }
850  
851        if (iLoop == PREPAIR_LOOP) {
852 <        if (info_->requiresPrepair()) {            
852 >        if (info_->requiresPrepair()) {
853 >
854            fDecomp_->collectIntermediateData();
855  
856            for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
857              fDecomp_->fillSelfData(sdat, atom1);
858              interactionMan_->doPreForce(sdat);
859            }
860 <          
861 <          
862 <          fDecomp_->distributeIntermediateData();        
860 >
861 >          fDecomp_->distributeIntermediateData();
862 >
863          }
864        }
723 –
865      }
866      
867 +    // collects pairwise information
868      fDecomp_->collectData();
869          
870      if (info_->requiresSelfCorrection()) {
871 <
730 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
871 >      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
872          fDecomp_->fillSelfData(sdat, atom1);
873          interactionMan_->doSelfCorrection(sdat);
874        }
734 –
875      }
876  
877 +    // collects single-atom information
878 +    fDecomp_->collectSelfData();
879 +
880      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
881        *(fDecomp_->getPairwisePotential());
882  
883 +    curSnapshot->setLongRangePotentialFamilies(longRangePotential);
884 +
885      lrPot = longRangePotential.sum();
886  
887 <    //store the tau and long range potential    
888 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
889 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
890 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
887 >    //store the long range potential  
888 >    curSnapshot->setLongRangePotential(lrPot);
889 >
890 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedPotential()));
891 >
892    }
893  
894    
# Line 760 | Line 906 | namespace OpenMD {
906        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
907             rb = mol->nextRigidBody(rbIter)) {
908          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
909 <        tau += rbTau;
909 >        stressTensor += rbTau;
910        }
911      }
912      
913   #ifdef IS_MPI
914 <    Mat3x3d tmpTau(tau);
915 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
770 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
914 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
915 >                              MPI::REALTYPE, MPI::SUM);
916   #endif
917 <    curSnapshot->statData.setTau(tau);
917 >    curSnapshot->setStressTensor(stressTensor);
918 >    
919    }
920  
921   } //end namespace OpenMD

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