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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1584 by gezelter, Fri Jun 17 20:16:35 2011 UTC vs.
Revision 1755 by gezelter, Thu Jun 14 01:58:35 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 75 | Line 76 | namespace OpenMD {
76    /**
77     * setupCutoffs
78     *
79 <   * Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
79 >   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
80 >   * and cutoffPolicy
81     *
82     * cutoffRadius : realType
83     *  If the cutoffRadius was explicitly set, use that value.
# Line 85 | 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     *
95     * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
96     *      If cutoffPolicy was explicitly set, use that choice.
97     *      If cutoffPolicy was not explicitly set, use TRADITIONAL
98 +   *
99 +   * switchingRadius : realType
100 +   *  If the cutoffMethod was set to SWITCHED:
101 +   *      If the switchingRadius was explicitly set, use that value
102 +   *          (but do a sanity check first).
103 +   *      If the switchingRadius was not explicitly set: use 0.85 *
104 +   *      cutoffRadius_
105 +   *  If the cutoffMethod was not set to SWITCHED:
106 +   *      Set switchingRadius equal to cutoffRadius for safety.
107     */
108    void ForceManager::setupCutoffs() {
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 155 | 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 169 | 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 202 | Line 290 | namespace OpenMD {
290        simError();
291        cutoffPolicy_ = TRADITIONAL;        
292      }
205 –    fDecomp_->setCutoffPolicy(cutoffPolicy_);
206 –  }
293  
294 <  /**
295 <   * setupSwitching
210 <   *
211 <   * Sets the values of switchingRadius and
212 <   *  If the switchingRadius was explicitly set, use that value (but check it)
213 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
214 <   */
215 <  void ForceManager::setupSwitching() {
216 <    Globals* simParams_ = info_->getSimParams();
217 <
294 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
295 >        
296      // create the switching function object:
297 +
298      switcher_ = new SwitchingFunction();
299 <    
300 <    if (simParams_->haveSwitchingRadius()) {
301 <      rSwitch_ = simParams_->getSwitchingRadius();
302 <      if (rSwitch_ > rCut_) {        
299 >  
300 >    if (cutoffMethod_ == SWITCHED) {
301 >      if (simParams_->haveSwitchingRadius()) {
302 >        rSwitch_ = simParams_->getSwitchingRadius();
303 >        if (rSwitch_ > rCut_) {        
304 >          sprintf(painCave.errMsg,
305 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
306 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
307 >          painCave.isFatal = 1;
308 >          painCave.severity = OPENMD_ERROR;
309 >          simError();
310 >        }
311 >      } else {      
312 >        rSwitch_ = 0.85 * rCut_;
313          sprintf(painCave.errMsg,
314 <                "ForceManager::setupSwitching: switchingRadius (%f) is larger "
315 <                "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
316 <        painCave.isFatal = 1;
317 <        painCave.severity = OPENMD_ERROR;
314 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
315 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
316 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
317 >        painCave.isFatal = 0;
318 >        painCave.severity = OPENMD_WARNING;
319          simError();
320        }
321 <    } else {      
322 <      rSwitch_ = 0.85 * rCut_;
323 <      sprintf(painCave.errMsg,
324 <              "ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
325 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
326 <              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
327 <      painCave.isFatal = 0;
328 <      painCave.severity = OPENMD_WARNING;
329 <      simError();
330 <    }          
321 >    } else {
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 >        }
343 >      }
344 >      rSwitch_ = rCut_;
345 >    }
346      
347      // Default to cubic switching function.
348      sft_ = cubic;
# Line 266 | 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 277 | 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
280 –
389        setupCutoffs();
282 –      setupSwitching();
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 340 | 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 358 | Line 472 | namespace OpenMD {
472          }
473        }      
474      }
361 –  
362 –    // Zero out the stress tensor
363 –    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 394 | 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 402 | 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 412 | 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 426 | 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 450 | 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 483 | Line 599 | namespace OpenMD {
599    
600    void ForceManager::longRangeInteractions() {
601  
602 +
603      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
604      DataStorage* config = &(curSnapshot->atomData);
605      DataStorage* cgConfig = &(curSnapshot->cgData);
# Line 506 | Line 623 | namespace OpenMD {
623        // center of mass of the group is the same as position of the atom  
624        // if cutoff group does not exist
625        cgConfig->position = config->position;
626 +      cgConfig->velocity = config->velocity;
627      }
628  
629      fDecomp_->zeroWorkArrays();
630      fDecomp_->distributeData();
631      
632      int cg1, cg2, atom1, atom2, topoDist;
633 <    Vector3d d_grp, dag, d;
633 >    Vector3d d_grp, dag, d, gvel2, vel2;
634      RealType rgrpsq, rgrp, r2, r;
635      RealType electroMult, vdwMult;
636      RealType vij;
# Line 527 | Line 645 | namespace OpenMD {
645      RealType mf;
646      RealType lrPot;
647      RealType vpair;
648 +    RealType dVdFQ1(0.0);
649 +    RealType dVdFQ2(0.0);
650      potVec longRangePotential(0.0);
651      potVec workPot(0.0);
652 +    vector<int>::iterator ia, jb;
653  
654      int loopStart, loopEnd;
655  
# Line 537 | Line 658 | namespace OpenMD {
658      idat.pot = &workPot;
659      sdat.pot = fDecomp_->getEmbeddingPotential();
660      idat.vpair = &vpair;
661 +    idat.dVdFQ1 = &dVdFQ1;
662 +    idat.dVdFQ2 = &dVdFQ2;
663      idat.f1 = &f1;
664      idat.sw = &sw;
665      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
666      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
667 +    idat.doParticlePot = doParticlePot_;
668 +    sdat.doParticlePot = doParticlePot_;
669      
670      loopEnd = PAIR_LOOP;
671      if (info_->requiresPrepair() ) {
# Line 548 | Line 673 | namespace OpenMD {
673      } else {
674        loopStart = PAIR_LOOP;
675      }
551 –  
676      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
677      
678        if (iLoop == loopStart) {
679          bool update_nlist = fDecomp_->checkNeighborList();
680          if (update_nlist)
681            neighborList = fDecomp_->buildNeighborList();
682 <      }      
683 <        
682 >      }            
683 >
684        for (vector<pair<int, int> >::iterator it = neighborList.begin();
685               it != neighborList.end(); ++it) {
686                  
# Line 566 | Line 690 | namespace OpenMD {
690          cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
691  
692          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
693 +
694          curSnapshot->wrapVector(d_grp);        
695          rgrpsq = d_grp.lengthSquare();
571 –
696          rCutSq = cuts.second;
697  
698          if (rgrpsq < rCutSq) {
699            idat.rcut = &cuts.first;
700            if (iLoop == PAIR_LOOP) {
701 <            vij *= 0.0;
701 >            vij = 0.0;
702              fij = V3Zero;
703            }
704            
705            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
706                                                       rgrp);
583 –              
707            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
708            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
709  
710 <          for (vector<int>::iterator ia = atomListRow.begin();
710 >          if (doHeatFlux_)
711 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
712 >
713 >          for (ia = atomListRow.begin();
714                 ia != atomListRow.end(); ++ia) {            
715              atom1 = (*ia);
716 <            
717 <            for (vector<int>::iterator jb = atomListColumn.begin();
716 >
717 >            for (jb = atomListColumn.begin();
718                   jb != atomListColumn.end(); ++jb) {              
719                atom2 = (*jb);
720 <            
720 >
721                if (!fDecomp_->skipAtomPair(atom1, atom2)) {
722                  vpair = 0.0;
723                  workPot = 0.0;
724                  f1 = V3Zero;
725 +                dVdFQ1 = 0.0;
726 +                dVdFQ2 = 0.0;
727  
728                  fDecomp_->fillInteractionData(idat, atom1, atom2);
729 <                
729 >
730                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
731                  vdwMult = vdwScale_[topoDist];
732                  electroMult = electrostaticScale_[topoDist];
# Line 606 | Line 734 | namespace OpenMD {
734                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
735                    idat.d = &d_grp;
736                    idat.r2 = &rgrpsq;
737 +                  if (doHeatFlux_)
738 +                    vel2 = gvel2;
739                  } else {
740                    d = fDecomp_->getInteratomicVector(atom1, atom2);
741                    curSnapshot->wrapVector( d );
742                    r2 = d.lengthSquare();
743                    idat.d = &d;
744                    idat.r2 = &r2;
745 +                  if (doHeatFlux_)
746 +                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
747                  }
748 <                
748 >              
749                  r = sqrt( *(idat.r2) );
750                  idat.rij = &r;
751                
# Line 624 | Line 756 | namespace OpenMD {
756                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
757                    vij += vpair;
758                    fij += f1;
759 <                  tau -= outProduct( *(idat.d), f1);
759 >                  stressTensor -= outProduct( *(idat.d), f1);
760 >                  if (doHeatFlux_)
761 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
762                  }
763                }
764              }
# Line 634 | Line 768 | namespace OpenMD {
768              if (in_switching_region) {
769                swderiv = vij * dswdr / rgrp;
770                fg = swderiv * d_grp;
637 –
771                fij += fg;
772  
773                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
774 <                tau -= outProduct( *(idat.d), fg);
774 >                stressTensor -= outProduct( *(idat.d), fg);
775 >                if (doHeatFlux_)
776 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
777 >                
778                }
779            
780 <              for (vector<int>::iterator ia = atomListRow.begin();
780 >              for (ia = atomListRow.begin();
781                     ia != atomListRow.end(); ++ia) {            
782                  atom1 = (*ia);                
783                  mf = fDecomp_->getMassFactorRow(atom1);
# Line 649 | Line 785 | namespace OpenMD {
785                  // presence in switching region
786                  fg = swderiv * d_grp * mf;
787                  fDecomp_->addForceToAtomRow(atom1, fg);
652 –
788                  if (atomListRow.size() > 1) {
789                    if (info_->usesAtomicVirial()) {
790                      // find the distance between the atom
791                      // and the center of the cutoff group:
792                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
793 <                    tau -= outProduct(dag, fg);
793 >                    stressTensor -= outProduct(dag, fg);
794 >                    if (doHeatFlux_)
795 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
796                    }
797                  }
798                }
799 <              for (vector<int>::iterator jb = atomListColumn.begin();
799 >              for (jb = atomListColumn.begin();
800                     jb != atomListColumn.end(); ++jb) {              
801                  atom2 = (*jb);
802                  mf = fDecomp_->getMassFactorColumn(atom2);
# Line 673 | Line 810 | namespace OpenMD {
810                      // find the distance between the atom
811                      // and the center of the cutoff group:
812                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
813 <                    tau -= outProduct(dag, fg);
813 >                    stressTensor -= outProduct(dag, fg);
814 >                    if (doHeatFlux_)
815 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
816                    }
817                  }
818                }
819              }
820 <            //if (!SIM_uses_AtomicVirial) {
821 <            //  tau -= outProduct(d_grp, fij);
820 >            //if (!info_->usesAtomicVirial()) {
821 >            //  stressTensor -= outProduct(d_grp, fij);
822 >            //  if (doHeatFlux_)
823 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
824              //}
825            }
826          }
827        }
828  
829        if (iLoop == PREPAIR_LOOP) {
830 <        if (info_->requiresPrepair()) {            
830 >        if (info_->requiresPrepair()) {
831 >
832            fDecomp_->collectIntermediateData();
833  
834            for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
835              fDecomp_->fillSelfData(sdat, atom1);
836              interactionMan_->doPreForce(sdat);
837            }
696 –          
697 –          
698 –          fDecomp_->distributeIntermediateData();        
699 –        }
700 –      }
838  
839 <    }
703 <    
704 <    fDecomp_->collectData();
705 <    
706 <    if ( info_->requiresSkipCorrection() ) {
707 <      
708 <      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
839 >          fDecomp_->distributeIntermediateData();
840  
710 –        vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 );
711 –        
712 –        for (vector<int>::iterator jb = skipList.begin();
713 –             jb != skipList.end(); ++jb) {        
714 –    
715 –          atom2 = (*jb);
716 –          fDecomp_->fillSkipData(idat, atom1, atom2);
717 –          interactionMan_->doSkipCorrection(idat);
718 –          fDecomp_->unpackSkipData(idat, atom1, atom2);
719 –
841          }
842        }
843      }
844      
845 +    fDecomp_->collectData();
846 +        
847      if (info_->requiresSelfCorrection()) {
848  
849        for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
# Line 735 | Line 858 | namespace OpenMD {
858  
859      lrPot = longRangePotential.sum();
860  
861 <    //store the tau and long range potential    
861 >    //store the stressTensor and long range potential    
862      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
863      curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
864      curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
# Line 756 | Line 879 | namespace OpenMD {
879        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
880             rb = mol->nextRigidBody(rbIter)) {
881          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
882 <        tau += rbTau;
882 >        stressTensor += rbTau;
883        }
884      }
885      
886   #ifdef IS_MPI
887 <    Mat3x3d tmpTau(tau);
888 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
889 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
887 >
888 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
889 >                              MPI::REALTYPE, MPI::SUM);
890   #endif
891 <    curSnapshot->statData.setTau(tau);
891 >    curSnapshot->setStressTensor(stressTensor);
892 >    
893    }
894  
895   } //end namespace OpenMD

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