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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 1780 by jmarr, Mon Aug 20 18:28:22 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 57 | Line 58
58   #include "primitives/Torsion.hpp"
59   #include "primitives/Inversion.hpp"
60   #include "nonbonded/NonBondedInteraction.hpp"
61 + #include "perturbations/ElectricField.hpp"
62   #include "parallel/ForceMatrixDecomposition.hpp"
63  
64   #include <cstdio>
# Line 86 | Line 88 | namespace OpenMD {
88     *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
89     *      Use the maximum suggested value that was found.
90     *
91 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
91 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
92 >   *                        or SHIFTED_POTENTIAL)
93     *      If cutoffMethod was explicitly set, use that choice.
94     *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
95     *
# Line 107 | Line 110 | namespace OpenMD {
110      
111      Globals* simParams_ = info_->getSimParams();
112      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
113 +    int mdFileVersion;
114 +    rCut_ = 0.0; //Needs a value for a later max() call;  
115      
116 +    if (simParams_->haveMDfileVersion())
117 +      mdFileVersion = simParams_->getMDfileVersion();
118 +    else
119 +      mdFileVersion = 0;
120 +  
121      if (simParams_->haveCutoffRadius()) {
122        rCut_ = simParams_->getCutoffRadius();
123      } else {      
# Line 165 | Line 175 | namespace OpenMD {
175          cutoffMethod_ = i->second;
176        }
177      } else {
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;        
178 >      if (mdFileVersion > 1) {
179 >        sprintf(painCave.errMsg,
180 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
181 >                "\tOpenMD will use SHIFTED_FORCE.\n");
182 >        painCave.isFatal = 0;
183 >        painCave.severity = OPENMD_INFO;
184 >        simError();
185 >        cutoffMethod_ = SHIFTED_FORCE;        
186 >      } else {
187 >        // handle the case where the old file version was in play
188 >        // (there should be no cutoffMethod, so we have to deduce it
189 >        // from other data).        
190 >
191 >        sprintf(painCave.errMsg,
192 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
193 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
194 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
195 >                "\tbehavior of the older (version 1) code.  To remove this\n"
196 >                "\twarning, add an explicit cutoffMethod and change the top\n"
197 >                "\tof the file so that it begins with <OpenMD version=2>\n");
198 >        painCave.isFatal = 0;
199 >        painCave.severity = OPENMD_WARNING;
200 >        simError();            
201 >                
202 >        // The old file version tethered the shifting behavior to the
203 >        // electrostaticSummationMethod keyword.
204 >        
205 >        if (simParams_->haveElectrostaticSummationMethod()) {
206 >          string myMethod = simParams_->getElectrostaticSummationMethod();
207 >          toUpper(myMethod);
208 >        
209 >          if (myMethod == "SHIFTED_POTENTIAL") {
210 >            cutoffMethod_ = SHIFTED_POTENTIAL;
211 >          } else if (myMethod == "SHIFTED_FORCE") {
212 >            cutoffMethod_ = SHIFTED_FORCE;
213 >          }
214 >        
215 >          if (simParams_->haveSwitchingRadius())
216 >            rSwitch_ = simParams_->getSwitchingRadius();
217 >
218 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
219 >            if (simParams_->haveSwitchingRadius()){
220 >              sprintf(painCave.errMsg,
221 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
222 >                      "\tA value was set for the switchingRadius\n"
223 >                      "\teven though the electrostaticSummationMethod was\n"
224 >                      "\tset to %s\n", myMethod.c_str());
225 >              painCave.severity = OPENMD_WARNING;
226 >              painCave.isFatal = 1;
227 >              simError();            
228 >            }
229 >          }
230 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
231 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
232 >              sprintf(painCave.errMsg,
233 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
234 >                      "\tcutoffRadius and switchingRadius are set to the\n"
235 >                      "\tsame value.  OpenMD will use shifted force\n"
236 >                      "\tpotentials instead of switching functions.\n");
237 >              painCave.isFatal = 0;
238 >              painCave.severity = OPENMD_WARNING;
239 >              simError();            
240 >            } else {
241 >              cutoffMethod_ = SHIFTED_POTENTIAL;
242 >              sprintf(painCave.errMsg,
243 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
244 >                      "\tcutoffRadius and switchingRadius are set to the\n"
245 >                      "\tsame value.  OpenMD will use shifted potentials\n"
246 >                      "\tinstead of switching functions.\n");
247 >              painCave.isFatal = 0;
248 >              painCave.severity = OPENMD_WARNING;
249 >              simError();            
250 >            }
251 >          }
252 >        }
253 >      }
254      }
255  
256      map<string, CutoffPolicy> stringToCutoffPolicy;
# Line 179 | Line 258 | namespace OpenMD {
258      stringToCutoffPolicy["MAX"] = MAX;
259      stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
260  
261 <    std::string cutPolicy;
261 >    string cutPolicy;
262      if (forceFieldOptions_.haveCutoffPolicy()){
263        cutPolicy = forceFieldOptions_.getCutoffPolicy();
264      }else if (simParams_->haveCutoffPolicy()) {
# Line 241 | Line 320 | namespace OpenMD {
320          simError();
321        }
322      } else {
323 <      if (simParams_->haveSwitchingRadius()) {
324 <        map<string, CutoffMethod>::const_iterator it;
325 <        string theMeth;
326 <        for (it = stringToCutoffMethod.begin();
327 <             it != stringToCutoffMethod.end(); ++it) {
328 <          if (it->second == cutoffMethod_) {
329 <            theMeth = it->first;
330 <            break;
323 >      if (mdFileVersion > 1) {
324 >        // throw an error if we define a switching radius and don't need one.
325 >        // older file versions should not do this.
326 >        if (simParams_->haveSwitchingRadius()) {
327 >          map<string, CutoffMethod>::const_iterator it;
328 >          string theMeth;
329 >          for (it = stringToCutoffMethod.begin();
330 >               it != stringToCutoffMethod.end(); ++it) {
331 >            if (it->second == cutoffMethod_) {
332 >              theMeth = it->first;
333 >              break;
334 >            }
335            }
336 +          sprintf(painCave.errMsg,
337 +                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
338 +                  "\tis not set to SWITCHED, so switchingRadius value\n"
339 +                  "\twill be ignored for this simulation\n", theMeth.c_str());
340 +          painCave.isFatal = 0;
341 +          painCave.severity = OPENMD_WARNING;
342 +          simError();
343          }
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();
344        }
262 –
345        rSwitch_ = rCut_;
346      }
347      
# Line 290 | Line 372 | namespace OpenMD {
372      switcher_->setSwitch(rSwitch_, rCut_);
373      interactionMan_->setSwitchingRadius(rSwitch_);
374    }
375 +
376 +
377 +
378    
379    void ForceManager::initialize() {
380  
381      if (!info_->isTopologyDone()) {
382 +
383        info_->update();
384        interactionMan_->setSimInfo(info_);
385        interactionMan_->initialize();
# Line 301 | Line 387 | namespace OpenMD {
387        // We want to delay the cutoffs until after the interaction
388        // manager has set up the atom-atom interactions so that we can
389        // query them for suggested cutoff values
304 –
390        setupCutoffs();
391  
392        info_->prepareTopology();      
393 +
394 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
395 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
396 +      if (doHeatFlux_) doParticlePot_ = true;
397 +  
398      }
399  
400      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
401      
402 <    // Force fields can set options on how to scale van der Waals and electrostatic
403 <    // interactions for atoms connected via bonds, bends and torsions
404 <    // in this case the topological distance between atoms is:
402 >    // Force fields can set options on how to scale van der Waals and
403 >    // electrostatic interactions for atoms connected via bonds, bends
404 >    // and torsions in this case the topological distance between
405 >    // atoms is:
406      // 0 = topologically unconnected
407      // 1 = bonded together
408      // 2 = connected via a bend
# Line 333 | 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 359 | 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; atom = mol->nextAtom(ai)) {
477 >      for(atom = mol->beginAtom(ai); atom != NULL;
478 >          atom = mol->nextAtom(ai)) {
479          atom->zeroForcesAndTorques();
480        }
481 <          
481 >      
482        //change the positions of atoms which belong to the rigidbodies
483        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
484             rb = mol->nextRigidBody(rbIter)) {
485          rb->zeroForcesAndTorques();
486        }        
487 <
487 >      
488        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
489          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
490              cg = mol->nextCutoffGroup(ci)) {
# Line 381 | Line 493 | namespace OpenMD {
493          }
494        }      
495      }
496 <  
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 417 | 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 425 | 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 435 | Line 548 | namespace OpenMD {
548            dataSet.prev.angle = dataSet.curr.angle = angle;
549            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
550            dataSet.deltaV = 0.0;
551 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
551 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
552 >                                                                  dataSet));
553          }else {
554            i->second.prev.angle = i->second.curr.angle;
555            i->second.prev.potential = i->second.curr.potential;
# Line 449 | 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 473 | 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 493 | 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 529 | Line 661 | namespace OpenMD {
661        // center of mass of the group is the same as position of the atom  
662        // if cutoff group does not exist
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 548 | Line 681 | namespace OpenMD {
681      InteractionData idat;
682      SelfData sdat;
683      RealType mf;
551 –    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 +    vector<int>::iterator ia, jb;
691  
692      int loopStart, loopEnd;
693  
694      idat.vdwMult = &vdwMult;
695      idat.electroMult = &electroMult;
696      idat.pot = &workPot;
697 +    idat.excludedPot = &exPot;
698      sdat.pot = fDecomp_->getEmbeddingPotential();
699 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
700      idat.vpair = &vpair;
701 +    idat.dVdFQ1 = &dVdFQ1;
702 +    idat.dVdFQ2 = &dVdFQ2;
703      idat.f1 = &f1;
704      idat.sw = &sw;
705      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
706      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
707 +    idat.doParticlePot = doParticlePot_;
708 +    sdat.doParticlePot = doParticlePot_;
709      
710      loopEnd = PAIR_LOOP;
711      if (info_->requiresPrepair() ) {
# Line 571 | Line 713 | namespace OpenMD {
713      } else {
714        loopStart = PAIR_LOOP;
715      }
574 –  
716      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
717      
718        if (iLoop == loopStart) {
719          bool update_nlist = fDecomp_->checkNeighborList();
720          if (update_nlist)
721            neighborList = fDecomp_->buildNeighborList();
722 <      }      
723 <        
722 >      }            
723 >
724        for (vector<pair<int, int> >::iterator it = neighborList.begin();
725               it != neighborList.end(); ++it) {
726                  
# Line 589 | Line 730 | namespace OpenMD {
730          cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
731  
732          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
733 +
734          curSnapshot->wrapVector(d_grp);        
735          rgrpsq = d_grp.lengthSquare();
594 –
736          rCutSq = cuts.second;
737  
738          if (rgrpsq < rCutSq) {
# Line 603 | Line 744 | namespace OpenMD {
744            
745            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
746                                                       rgrp);
747 <              
747 >
748            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
749            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
750  
751 <          for (vector<int>::iterator ia = atomListRow.begin();
751 >          if (doHeatFlux_)
752 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
753 >
754 >          for (ia = atomListRow.begin();
755                 ia != atomListRow.end(); ++ia) {            
756              atom1 = (*ia);
757 <            
758 <            for (vector<int>::iterator jb = atomListColumn.begin();
757 >
758 >            for (jb = atomListColumn.begin();
759                   jb != atomListColumn.end(); ++jb) {              
760                atom2 = (*jb);
761 <            
762 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
761 >
762 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
763 >
764                  vpair = 0.0;
765                  workPot = 0.0;
766 +                exPot = 0.0;
767                  f1 = V3Zero;
768 +                dVdFQ1 = 0.0;
769 +                dVdFQ2 = 0.0;
770  
771                  fDecomp_->fillInteractionData(idat, atom1, atom2);
772 <                
772 >
773                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
774                  vdwMult = vdwScale_[topoDist];
775                  electroMult = electrostaticScale_[topoDist];
# Line 629 | Line 777 | namespace OpenMD {
777                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
778                    idat.d = &d_grp;
779                    idat.r2 = &rgrpsq;
780 +                  if (doHeatFlux_)
781 +                    vel2 = gvel2;
782                  } else {
783                    d = fDecomp_->getInteratomicVector(atom1, atom2);
784                    curSnapshot->wrapVector( d );
785                    r2 = d.lengthSquare();
786                    idat.d = &d;
787                    idat.r2 = &r2;
788 +                  if (doHeatFlux_)
789 +                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
790                  }
791 <                
791 >              
792                  r = sqrt( *(idat.r2) );
793                  idat.rij = &r;
794                
# Line 647 | Line 799 | namespace OpenMD {
799                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
800                    vij += vpair;
801                    fij += f1;
802 <                  tau -= outProduct( *(idat.d), f1);
802 >                  stressTensor -= outProduct( *(idat.d), f1);
803 >                  if (doHeatFlux_)
804 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
805                  }
806                }
807              }
# Line 660 | Line 814 | namespace OpenMD {
814                fij += fg;
815  
816                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
817 <                tau -= outProduct( *(idat.d), fg);
817 >                stressTensor -= outProduct( *(idat.d), fg);
818 >                if (doHeatFlux_)
819 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
820 >                
821                }
822            
823 <              for (vector<int>::iterator ia = atomListRow.begin();
823 >              for (ia = atomListRow.begin();
824                     ia != atomListRow.end(); ++ia) {            
825                  atom1 = (*ia);                
826                  mf = fDecomp_->getMassFactorRow(atom1);
# Line 671 | Line 828 | namespace OpenMD {
828                  // presence in switching region
829                  fg = swderiv * d_grp * mf;
830                  fDecomp_->addForceToAtomRow(atom1, fg);
674 –
831                  if (atomListRow.size() > 1) {
832                    if (info_->usesAtomicVirial()) {
833                      // find the distance between the atom
834                      // and the center of the cutoff group:
835                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
836 <                    tau -= outProduct(dag, fg);
836 >                    stressTensor -= outProduct(dag, fg);
837 >                    if (doHeatFlux_)
838 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
839                    }
840                  }
841                }
842 <              for (vector<int>::iterator jb = atomListColumn.begin();
842 >              for (jb = atomListColumn.begin();
843                     jb != atomListColumn.end(); ++jb) {              
844                  atom2 = (*jb);
845                  mf = fDecomp_->getMassFactorColumn(atom2);
# Line 695 | Line 853 | namespace OpenMD {
853                      // find the distance between the atom
854                      // and the center of the cutoff group:
855                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
856 <                    tau -= outProduct(dag, fg);
856 >                    stressTensor -= outProduct(dag, fg);
857 >                    if (doHeatFlux_)
858 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
859                    }
860                  }
861                }
862              }
863 <            //if (!SIM_uses_AtomicVirial) {
864 <            //  tau -= outProduct(d_grp, fij);
863 >            //if (!info_->usesAtomicVirial()) {
864 >            //  stressTensor -= outProduct(d_grp, fij);
865 >            //  if (doHeatFlux_)
866 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
867              //}
868            }
869          }
870        }
871  
872        if (iLoop == PREPAIR_LOOP) {
873 <        if (info_->requiresPrepair()) {            
873 >        if (info_->requiresPrepair()) {
874 >
875            fDecomp_->collectIntermediateData();
876  
877 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
877 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
878              fDecomp_->fillSelfData(sdat, atom1);
879              interactionMan_->doPreForce(sdat);
880            }
881 <          
882 <          
883 <          fDecomp_->distributeIntermediateData();        
881 >
882 >          fDecomp_->distributeIntermediateData();
883 >
884          }
885        }
723 –
886      }
887      
888 +    // collects pairwise information
889      fDecomp_->collectData();
890          
891      if (info_->requiresSelfCorrection()) {
892 <
730 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
892 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
893          fDecomp_->fillSelfData(sdat, atom1);
894          interactionMan_->doSelfCorrection(sdat);
895        }
734 –
896      }
897  
898 +    // collects single-atom information
899 +    fDecomp_->collectSelfData();
900 +
901      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
902        *(fDecomp_->getPairwisePotential());
903  
904 <    lrPot = longRangePotential.sum();
904 >    curSnapshot->setLongRangePotential(longRangePotential);
905 >    
906 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
907 >                                         *(fDecomp_->getExcludedPotential()));
908  
742 –    //store the tau and long range potential    
743 –    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
744 –    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
745 –    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
909    }
910  
911    
912    void ForceManager::postCalculation() {
913 +
914 +    vector<Perturbation*>::iterator pi;
915 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
916 +      (*pi)->applyPerturbation();
917 +    }
918 +
919      SimInfo::MoleculeIterator mi;
920      Molecule* mol;
921      Molecule::RigidBodyIterator rbIter;
922      RigidBody* rb;
923      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
924 <    
924 >  
925      // collect the atomic forces onto rigid bodies
926      
927      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 760 | Line 929 | namespace OpenMD {
929        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
930             rb = mol->nextRigidBody(rbIter)) {
931          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
932 <        tau += rbTau;
932 >        stressTensor += rbTau;
933        }
934      }
935      
936   #ifdef IS_MPI
937 <    Mat3x3d tmpTau(tau);
938 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
770 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
937 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
938 >                              MPI::REALTYPE, MPI::SUM);
939   #endif
940 <    curSnapshot->statData.setTau(tau);
940 >    curSnapshot->setStressTensor(stressTensor);
941 >    
942    }
774 –
943   } //end namespace OpenMD

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