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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1581 by gezelter, Mon Jun 13 22:13:12 2011 UTC vs.
Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 59 | Line 60
60   #include "nonbonded/NonBondedInteraction.hpp"
61   #include "parallel/ForceMatrixDecomposition.hpp"
62  
63 + #include <cstdio>
64 + #include <iostream>
65 + #include <iomanip>
66 +
67   using namespace std;
68   namespace OpenMD {
69    
# Line 71 | 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 81 | 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 123 | Line 146 | namespace OpenMD {
146          painCave.severity = OPENMD_INFO;
147          simError();
148        }
126 –      fDecomp_->setUserCutoff(rCut_);
149      }
150  
151 +    fDecomp_->setUserCutoff(rCut_);
152 +    interactionMan_->setCutoffRadius(rCut_);
153 +
154      map<string, CutoffMethod> stringToCutoffMethod;
155      stringToCutoffMethod["HARD"] = HARD;
156      stringToCutoffMethod["SWITCHED"] = SWITCHED;
# Line 149 | 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 163 | 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 196 | Line 290 | namespace OpenMD {
290        simError();
291        cutoffPolicy_ = TRADITIONAL;        
292      }
199 –    fDecomp_->setCutoffPolicy(cutoffPolicy_);
200 –  }
293  
294 <  /**
295 <   * setupSwitching
204 <   *
205 <   * Sets the values of switchingRadius and
206 <   *  If the switchingRadius was explicitly set, use that value (but check it)
207 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
208 <   */
209 <  void ForceManager::setupSwitching() {
210 <    Globals* simParams_ = info_->getSimParams();
211 <
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 258 | Line 369 | namespace OpenMD {
369      }
370      switcher_->setSwitchType(sft_);
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 270 | 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
273 –
389        setupCutoffs();
275 –      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 329 | Line 449 | namespace OpenMD {
449      Molecule::CutoffGroupIterator ci;
450      CutoffGroup* cg;
451      
452 <    // forces are zeroed here, before any are accumulated.
452 >    // forces and potentials are zeroed here, before any are
453 >    // accumulated.
454      
455 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
456 +
457 +    snap->setBondPotential(0.0);
458 +    snap->setBendPotential(0.0);
459 +    snap->setTorsionPotential(0.0);
460 +    snap->setInversionPotential(0.0);
461 +
462 +    potVec zeroPot(0.0);
463 +    snap->setLongRangePotential(zeroPot);
464 +    snap->setExcludedPotentials(zeroPot);
465 +
466 +    snap->setRestraintPotential(0.0);
467 +    snap->setRawPotential(0.0);
468 +
469      for (mol = info_->beginMolecule(mi); mol != NULL;
470           mol = info_->nextMolecule(mi)) {
471 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
471 >      for(atom = mol->beginAtom(ai); atom != NULL;
472 >          atom = mol->nextAtom(ai)) {
473          atom->zeroForcesAndTorques();
474        }
475 <          
475 >      
476        //change the positions of atoms which belong to the rigidbodies
477        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
478             rb = mol->nextRigidBody(rbIter)) {
479          rb->zeroForcesAndTorques();
480        }        
481 <
481 >      
482        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
483          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
484              cg = mol->nextCutoffGroup(ci)) {
# Line 351 | Line 487 | namespace OpenMD {
487          }
488        }      
489      }
354 –  
355 –    // Zero out the stress tensor
356 –    tau *= 0.0;
490      
491 +    // Zero out the stress tensor
492 +    stressTensor *= 0.0;
493 +    // Zero out the heatFlux
494 +    fDecomp_->setHeatFlux( Vector3d(0.0) );    
495    }
496    
497    void ForceManager::shortRangeInteractions() {
# Line 387 | Line 524 | namespace OpenMD {
524  
525        for (bond = mol->beginBond(bondIter); bond != NULL;
526             bond = mol->nextBond(bondIter)) {
527 <        bond->calcForce();
527 >        bond->calcForce(doParticlePot_);
528          bondPotential += bond->getPotential();
529        }
530  
# Line 395 | Line 532 | namespace OpenMD {
532             bend = mol->nextBend(bendIter)) {
533          
534          RealType angle;
535 <        bend->calcForce(angle);
535 >        bend->calcForce(angle, doParticlePot_);
536          RealType currBendPot = bend->getPotential();          
537          
538          bendPotential += bend->getPotential();
# Line 405 | Line 542 | namespace OpenMD {
542            dataSet.prev.angle = dataSet.curr.angle = angle;
543            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
544            dataSet.deltaV = 0.0;
545 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
545 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
546 >                                                                  dataSet));
547          }else {
548            i->second.prev.angle = i->second.curr.angle;
549            i->second.prev.potential = i->second.curr.potential;
# Line 419 | Line 557 | namespace OpenMD {
557        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
558             torsion = mol->nextTorsion(torsionIter)) {
559          RealType angle;
560 <        torsion->calcForce(angle);
560 >        torsion->calcForce(angle, doParticlePot_);
561          RealType currTorsionPot = torsion->getPotential();
562          torsionPotential += torsion->getPotential();
563          map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
# Line 443 | Line 581 | namespace OpenMD {
581             inversion != NULL;
582             inversion = mol->nextInversion(inversionIter)) {
583          RealType angle;
584 <        inversion->calcForce(angle);
584 >        inversion->calcForce(angle, doParticlePot_);
585          RealType currInversionPot = inversion->getPotential();
586          inversionPotential += inversion->getPotential();
587          map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
# Line 463 | Line 601 | namespace OpenMD {
601          }      
602        }      
603      }
604 <    
605 <    RealType  shortRangePotential = bondPotential + bendPotential +
606 <      torsionPotential +  inversionPotential;    
604 >
605 > #ifdef IS_MPI
606 >    // Collect from all nodes.  This should eventually be moved into a
607 >    // SystemDecomposition, but this is a better place than in
608 >    // Thermo to do the collection.
609 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
610 >                              MPI::SUM);
611 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
612 >                              MPI::SUM);
613 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
614 >                              MPI::REALTYPE, MPI::SUM);
615 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
616 >                              MPI::REALTYPE, MPI::SUM);
617 > #endif
618 >
619      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
620 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
621 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
622 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
623 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
624 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
620 >
621 >    curSnapshot->setBondPotential(bondPotential);
622 >    curSnapshot->setBendPotential(bendPotential);
623 >    curSnapshot->setTorsionPotential(torsionPotential);
624 >    curSnapshot->setInversionPotential(inversionPotential);
625 >    
626 >    // RealType shortRangePotential = bondPotential + bendPotential +
627 >    //   torsionPotential +  inversionPotential;    
628 >
629 >    // curSnapshot->setShortRangePotential(shortRangePotential);
630    }
631    
632    void ForceManager::longRangeInteractions() {
633  
634 +
635      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
636      DataStorage* config = &(curSnapshot->atomData);
637      DataStorage* cgConfig = &(curSnapshot->cgData);
# Line 499 | Line 655 | namespace OpenMD {
655        // center of mass of the group is the same as position of the atom  
656        // if cutoff group does not exist
657        cgConfig->position = config->position;
658 +      cgConfig->velocity = config->velocity;
659      }
660  
661      fDecomp_->zeroWorkArrays();
662      fDecomp_->distributeData();
663      
664      int cg1, cg2, atom1, atom2, topoDist;
665 <    Vector3d d_grp, dag, d;
665 >    Vector3d d_grp, dag, d, gvel2, vel2;
666      RealType rgrpsq, rgrp, r2, r;
667      RealType electroMult, vdwMult;
668      RealType vij;
# Line 518 | Line 675 | namespace OpenMD {
675      InteractionData idat;
676      SelfData sdat;
677      RealType mf;
521 –    potVec pot(0.0);
522 –    potVec longRangePotential(0.0);
523 –    RealType lrPot;
678      RealType vpair;
679 +    RealType dVdFQ1(0.0);
680 +    RealType dVdFQ2(0.0);
681 +    potVec longRangePotential(0.0);
682 +    potVec workPot(0.0);
683 +    potVec exPot(0.0);
684 +    vector<int>::iterator ia, jb;
685  
686      int loopStart, loopEnd;
687  
688      idat.vdwMult = &vdwMult;
689      idat.electroMult = &electroMult;
690 <    idat.pot = &pot;
690 >    idat.pot = &workPot;
691 >    idat.excludedPot = &exPot;
692 >    sdat.pot = fDecomp_->getEmbeddingPotential();
693 >    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
694      idat.vpair = &vpair;
695 +    idat.dVdFQ1 = &dVdFQ1;
696 +    idat.dVdFQ2 = &dVdFQ2;
697      idat.f1 = &f1;
698      idat.sw = &sw;
699 <
699 >    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
700 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
701 >    idat.doParticlePot = doParticlePot_;
702 >    sdat.doParticlePot = doParticlePot_;
703 >    
704      loopEnd = PAIR_LOOP;
705      if (info_->requiresPrepair() ) {
706        loopStart = PREPAIR_LOOP;
707      } else {
708        loopStart = PAIR_LOOP;
709      }
541 –    
710      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
711      
712        if (iLoop == loopStart) {
713          bool update_nlist = fDecomp_->checkNeighborList();
714          if (update_nlist)
715            neighborList = fDecomp_->buildNeighborList();
716 <      }      
717 <        
716 >      }            
717 >
718        for (vector<pair<int, int> >::iterator it = neighborList.begin();
719               it != neighborList.end(); ++it) {
720                  
# Line 556 | Line 724 | namespace OpenMD {
724          cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
725  
726          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
727 +
728          curSnapshot->wrapVector(d_grp);        
729          rgrpsq = d_grp.lengthSquare();
561 –
730          rCutSq = cuts.second;
731  
732          if (rgrpsq < rCutSq) {
733            idat.rcut = &cuts.first;
734            if (iLoop == PAIR_LOOP) {
735 <            vij *= 0.0;
735 >            vij = 0.0;
736              fij = V3Zero;
737            }
738            
739            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
740                                                       rgrp);
741 <              
741 >
742            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
743            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
744  
745 <          for (vector<int>::iterator ia = atomListRow.begin();
745 >          if (doHeatFlux_)
746 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
747 >
748 >          for (ia = atomListRow.begin();
749                 ia != atomListRow.end(); ++ia) {            
750              atom1 = (*ia);
751 <            
752 <            for (vector<int>::iterator jb = atomListColumn.begin();
751 >
752 >            for (jb = atomListColumn.begin();
753                   jb != atomListColumn.end(); ++jb) {              
754                atom2 = (*jb);
755 <              
756 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
757 <                
755 >
756 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
757 >
758                  vpair = 0.0;
759 +                workPot = 0.0;
760 +                exPot = 0.0;
761                  f1 = V3Zero;
762 +                dVdFQ1 = 0.0;
763 +                dVdFQ2 = 0.0;
764  
765                  fDecomp_->fillInteractionData(idat, atom1, atom2);
766 <                
766 >
767                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
768                  vdwMult = vdwScale_[topoDist];
769                  electroMult = electrostaticScale_[topoDist];
# Line 596 | Line 771 | namespace OpenMD {
771                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
772                    idat.d = &d_grp;
773                    idat.r2 = &rgrpsq;
774 +                  if (doHeatFlux_)
775 +                    vel2 = gvel2;
776                  } else {
777                    d = fDecomp_->getInteratomicVector(atom1, atom2);
778                    curSnapshot->wrapVector( d );
779                    r2 = d.lengthSquare();
780                    idat.d = &d;
781                    idat.r2 = &r2;
782 +                  if (doHeatFlux_)
783 +                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
784                  }
785 <                
785 >              
786                  r = sqrt( *(idat.r2) );
787                  idat.rij = &r;
788                
# Line 614 | Line 793 | namespace OpenMD {
793                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
794                    vij += vpair;
795                    fij += f1;
796 <                  tau -= outProduct( *(idat.d), f1);
796 >                  stressTensor -= outProduct( *(idat.d), f1);
797 >                  if (doHeatFlux_)
798 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
799                  }
800                }
801              }
# Line 624 | Line 805 | namespace OpenMD {
805              if (in_switching_region) {
806                swderiv = vij * dswdr / rgrp;
807                fg = swderiv * d_grp;
627 –
808                fij += fg;
809  
810                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
811 <                tau -= outProduct( *(idat.d), fg);
811 >                stressTensor -= outProduct( *(idat.d), fg);
812 >                if (doHeatFlux_)
813 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
814 >                
815                }
816            
817 <              for (vector<int>::iterator ia = atomListRow.begin();
817 >              for (ia = atomListRow.begin();
818                     ia != atomListRow.end(); ++ia) {            
819                  atom1 = (*ia);                
820                  mf = fDecomp_->getMassFactorRow(atom1);
# Line 639 | Line 822 | namespace OpenMD {
822                  // presence in switching region
823                  fg = swderiv * d_grp * mf;
824                  fDecomp_->addForceToAtomRow(atom1, fg);
642 –
825                  if (atomListRow.size() > 1) {
826                    if (info_->usesAtomicVirial()) {
827                      // find the distance between the atom
828                      // and the center of the cutoff group:
829                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
830 <                    tau -= outProduct(dag, fg);
830 >                    stressTensor -= outProduct(dag, fg);
831 >                    if (doHeatFlux_)
832 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
833                    }
834                  }
835                }
836 <              for (vector<int>::iterator jb = atomListColumn.begin();
836 >              for (jb = atomListColumn.begin();
837                     jb != atomListColumn.end(); ++jb) {              
838                  atom2 = (*jb);
839                  mf = fDecomp_->getMassFactorColumn(atom2);
# Line 663 | Line 847 | namespace OpenMD {
847                      // find the distance between the atom
848                      // and the center of the cutoff group:
849                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
850 <                    tau -= outProduct(dag, fg);
850 >                    stressTensor -= outProduct(dag, fg);
851 >                    if (doHeatFlux_)
852 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
853                    }
854                  }
855                }
856              }
857 <            //if (!SIM_uses_AtomicVirial) {
858 <            //  tau -= outProduct(d_grp, fij);
857 >            //if (!info_->usesAtomicVirial()) {
858 >            //  stressTensor -= outProduct(d_grp, fij);
859 >            //  if (doHeatFlux_)
860 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
861              //}
862            }
863          }
864        }
865  
866        if (iLoop == PREPAIR_LOOP) {
867 <        if (info_->requiresPrepair()) {            
867 >        if (info_->requiresPrepair()) {
868 >
869            fDecomp_->collectIntermediateData();
870  
871 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
871 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
872              fDecomp_->fillSelfData(sdat, atom1);
873              interactionMan_->doPreForce(sdat);
874            }
875  
876 <          fDecomp_->distributeIntermediateData();        
876 >          fDecomp_->distributeIntermediateData();
877 >
878          }
879        }
690 –
880      }
881      
882 +    // collects pairwise information
883      fDecomp_->collectData();
694 –    
695 –    if ( info_->requiresSkipCorrection() ) {
696 –      
697 –      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
698 –
699 –        vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 );
884          
701 –        for (vector<int>::iterator jb = skipList.begin();
702 –             jb != skipList.end(); ++jb) {        
703 –    
704 –          atom2 = (*jb);
705 –          fDecomp_->fillSkipData(idat, atom1, atom2);
706 –          interactionMan_->doSkipCorrection(idat);
707 –
708 –        }
709 –      }
710 –    }
711 –    
885      if (info_->requiresSelfCorrection()) {
886 <
714 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
886 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
887          fDecomp_->fillSelfData(sdat, atom1);
888          interactionMan_->doSelfCorrection(sdat);
889        }
718 –
890      }
891  
892 <    longRangePotential = fDecomp_->getLongRangePotential();
893 <    lrPot = longRangePotential.sum();
892 >    // collects single-atom information
893 >    fDecomp_->collectSelfData();
894  
895 <    //store the tau and long range potential    
896 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
897 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
898 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
895 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
896 >      *(fDecomp_->getPairwisePotential());
897 >
898 >    curSnapshot->setLongRangePotential(longRangePotential);
899 >    
900 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
901 >                                         *(fDecomp_->getExcludedPotential()));
902 >
903    }
904  
905    
# Line 734 | Line 909 | namespace OpenMD {
909      Molecule::RigidBodyIterator rbIter;
910      RigidBody* rb;
911      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
912 <    
912 >  
913      // collect the atomic forces onto rigid bodies
914      
915      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 742 | Line 917 | namespace OpenMD {
917        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
918             rb = mol->nextRigidBody(rbIter)) {
919          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
920 <        tau += rbTau;
920 >        stressTensor += rbTau;
921        }
922      }
923      
924   #ifdef IS_MPI
925 <    Mat3x3d tmpTau(tau);
926 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
752 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
925 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
926 >                              MPI::REALTYPE, MPI::SUM);
927   #endif
928 <    curSnapshot->statData.setTau(tau);
928 >    curSnapshot->setStressTensor(stressTensor);
929 >    
930    }
931  
932   } //end namespace OpenMD

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