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Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
44   * @file ForceManager.cpp
45   * @author tlin
46   * @date 11/09/2004
46 – * @time 10:39am
47   * @version 1.0
48   */
49  
# Line 57 | Line 57
57   #include "primitives/Torsion.hpp"
58   #include "primitives/Inversion.hpp"
59   #include "nonbonded/NonBondedInteraction.hpp"
60 + #include "perturbations/ElectricField.hpp"
61   #include "parallel/ForceMatrixDecomposition.hpp"
62  
63   #include <cstdio>
# Line 66 | Line 67 | namespace OpenMD {
67   using namespace std;
68   namespace OpenMD {
69    
70 <  ForceManager::ForceManager(SimInfo * info) : info_(info) {
70 >  ForceManager::ForceManager(SimInfo * info) : info_(info), switcher_(NULL),
71 >                                               initialized_(false) {
72      forceField_ = info_->getForceField();
73      interactionMan_ = new InteractionManager();
74      fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
75 +    thermo = new Thermo(info_);
76    }
77  
78 +  ForceManager::~ForceManager() {
79 +    perturbations_.clear();
80 +    
81 +    delete switcher_;
82 +    delete interactionMan_;
83 +    delete fDecomp_;
84 +    delete thermo;
85 +  }
86 +  
87    /**
88     * setupCutoffs
89     *
# Line 109 | Line 121 | namespace OpenMD {
121      Globals* simParams_ = info_->getSimParams();
122      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
123      int mdFileVersion;
124 +    rCut_ = 0.0; //Needs a value for a later max() call;  
125      
126      if (simParams_->haveMDfileVersion())
127        mdFileVersion = simParams_->getMDfileVersion();
128      else
129        mdFileVersion = 0;
130    
131 +    // We need the list of simulated atom types to figure out cutoffs
132 +    // as well as long range corrections.
133  
134 +    set<AtomType*>::iterator i;
135 +    set<AtomType*> atomTypes_;
136 +    atomTypes_ = info_->getSimulatedAtomTypes();
137 +
138      if (simParams_->haveCutoffRadius()) {
139        rCut_ = simParams_->getCutoffRadius();
140      } else {      
# Line 130 | Line 149 | namespace OpenMD {
149          rCut_ = 12.0;
150        } else {
151          RealType thisCut;
152 <        set<AtomType*>::iterator i;
134 <        set<AtomType*> atomTypes;
135 <        atomTypes = info_->getSimulatedAtomTypes();        
136 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
152 >        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
153            thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
154            rCut_ = max(thisCut, rCut_);
155          }
# Line 173 | Line 189 | namespace OpenMD {
189          cutoffMethod_ = i->second;
190        }
191      } else {
192 <      sprintf(painCave.errMsg,
193 <              "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
194 <              "\tOpenMD will use SHIFTED_FORCE.\n");
195 <      painCave.isFatal = 0;
196 <      painCave.severity = OPENMD_INFO;
197 <      simError();
198 <      cutoffMethod_ = SHIFTED_FORCE;        
192 >      if (mdFileVersion > 1) {
193 >        sprintf(painCave.errMsg,
194 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
195 >                "\tOpenMD will use SHIFTED_FORCE.\n");
196 >        painCave.isFatal = 0;
197 >        painCave.severity = OPENMD_INFO;
198 >        simError();
199 >        cutoffMethod_ = SHIFTED_FORCE;        
200 >      } else {
201 >        // handle the case where the old file version was in play
202 >        // (there should be no cutoffMethod, so we have to deduce it
203 >        // from other data).        
204 >
205 >        sprintf(painCave.errMsg,
206 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
207 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
208 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
209 >                "\tbehavior of the older (version 1) code.  To remove this\n"
210 >                "\twarning, add an explicit cutoffMethod and change the top\n"
211 >                "\tof the file so that it begins with <OpenMD version=2>\n");
212 >        painCave.isFatal = 0;
213 >        painCave.severity = OPENMD_WARNING;
214 >        simError();            
215 >                
216 >        // The old file version tethered the shifting behavior to the
217 >        // electrostaticSummationMethod keyword.
218 >        
219 >        if (simParams_->haveElectrostaticSummationMethod()) {
220 >          string myMethod = simParams_->getElectrostaticSummationMethod();
221 >          toUpper(myMethod);
222 >        
223 >          if (myMethod == "SHIFTED_POTENTIAL") {
224 >            cutoffMethod_ = SHIFTED_POTENTIAL;
225 >          } else if (myMethod == "SHIFTED_FORCE") {
226 >            cutoffMethod_ = SHIFTED_FORCE;
227 >          }
228 >        
229 >          if (simParams_->haveSwitchingRadius())
230 >            rSwitch_ = simParams_->getSwitchingRadius();
231 >
232 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
233 >            if (simParams_->haveSwitchingRadius()){
234 >              sprintf(painCave.errMsg,
235 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
236 >                      "\tA value was set for the switchingRadius\n"
237 >                      "\teven though the electrostaticSummationMethod was\n"
238 >                      "\tset to %s\n", myMethod.c_str());
239 >              painCave.severity = OPENMD_WARNING;
240 >              painCave.isFatal = 1;
241 >              simError();            
242 >            }
243 >          }
244 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
245 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
246 >              sprintf(painCave.errMsg,
247 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
248 >                      "\tcutoffRadius and switchingRadius are set to the\n"
249 >                      "\tsame value.  OpenMD will use shifted force\n"
250 >                      "\tpotentials instead of switching functions.\n");
251 >              painCave.isFatal = 0;
252 >              painCave.severity = OPENMD_WARNING;
253 >              simError();            
254 >            } else {
255 >              cutoffMethod_ = SHIFTED_POTENTIAL;
256 >              sprintf(painCave.errMsg,
257 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
258 >                      "\tcutoffRadius and switchingRadius are set to the\n"
259 >                      "\tsame value.  OpenMD will use shifted potentials\n"
260 >                      "\tinstead of switching functions.\n");
261 >              painCave.isFatal = 0;
262 >              painCave.severity = OPENMD_WARNING;
263 >              simError();            
264 >            }
265 >          }
266 >        }
267 >      }
268      }
269  
270      map<string, CutoffPolicy> stringToCutoffPolicy;
# Line 187 | Line 272 | namespace OpenMD {
272      stringToCutoffPolicy["MAX"] = MAX;
273      stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
274  
275 <    std::string cutPolicy;
275 >    string cutPolicy;
276      if (forceFieldOptions_.haveCutoffPolicy()){
277        cutPolicy = forceFieldOptions_.getCutoffPolicy();
278      }else if (simParams_->haveCutoffPolicy()) {
# Line 249 | Line 334 | namespace OpenMD {
334          simError();
335        }
336      } else {
337 <      if (simParams_->haveSwitchingRadius()) {
338 <        map<string, CutoffMethod>::const_iterator it;
339 <        string theMeth;
340 <        for (it = stringToCutoffMethod.begin();
341 <             it != stringToCutoffMethod.end(); ++it) {
342 <          if (it->second == cutoffMethod_) {
343 <            theMeth = it->first;
344 <            break;
337 >      if (mdFileVersion > 1) {
338 >        // throw an error if we define a switching radius and don't need one.
339 >        // older file versions should not do this.
340 >        if (simParams_->haveSwitchingRadius()) {
341 >          map<string, CutoffMethod>::const_iterator it;
342 >          string theMeth;
343 >          for (it = stringToCutoffMethod.begin();
344 >               it != stringToCutoffMethod.end(); ++it) {
345 >            if (it->second == cutoffMethod_) {
346 >              theMeth = it->first;
347 >              break;
348 >            }
349            }
350 +          sprintf(painCave.errMsg,
351 +                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
352 +                  "\tis not set to SWITCHED, so switchingRadius value\n"
353 +                  "\twill be ignored for this simulation\n", theMeth.c_str());
354 +          painCave.isFatal = 0;
355 +          painCave.severity = OPENMD_WARNING;
356 +          simError();
357          }
262 –        sprintf(painCave.errMsg,
263 –                "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
264 –                "\tis not set to SWITCHED, so switchingRadius value\n"
265 –                "\twill be ignored for this simulation\n", theMeth.c_str());
266 –        painCave.isFatal = 0;
267 –        painCave.severity = OPENMD_WARNING;
268 –        simError();
358        }
270 –
359        rSwitch_ = rCut_;
360      }
361      
# Line 296 | Line 384 | namespace OpenMD {
384      }
385      switcher_->setSwitchType(sft_);
386      switcher_->setSwitch(rSwitch_, rCut_);
299 –    interactionMan_->setSwitchingRadius(rSwitch_);
387    }
388 +
389 +
390 +
391    
392    void ForceManager::initialize() {
393  
# Line 313 | Line 403 | namespace OpenMD {
403        setupCutoffs();
404  
405        info_->prepareTopology();      
406 +
407 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
408 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
409 +      if (doHeatFlux_) doParticlePot_ = true;
410 +
411 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
412 +  
413      }
414  
415      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
# Line 342 | Line 439 | namespace OpenMD {
439      electrostaticScale_[2] = fopts.getelectrostatic13scale();
440      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
441      
442 +    if (info_->getSimParams()->haveElectricField()) {
443 +      ElectricField* eField = new ElectricField(info_);
444 +      perturbations_.push_back(eField);
445 +    }
446 +
447 +    usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
448 +    
449      fDecomp_->distributeInitialData();
450 <
450 >    
451      initialized_ = true;
452 <
452 >    
453    }
454 <
454 >  
455    void ForceManager::calcForces() {
456      
457      if (!initialized_) initialize();
458 <
458 >    
459      preCalculation();  
460      shortRangeInteractions();
461      longRangeInteractions();
# Line 368 | Line 472 | namespace OpenMD {
472      Molecule::CutoffGroupIterator ci;
473      CutoffGroup* cg;
474      
475 <    // forces are zeroed here, before any are accumulated.
475 >    // forces and potentials are zeroed here, before any are
476 >    // accumulated.
477      
478 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
479 +
480 +    snap->setBondPotential(0.0);
481 +    snap->setBendPotential(0.0);
482 +    snap->setTorsionPotential(0.0);
483 +    snap->setInversionPotential(0.0);
484 +
485 +    potVec zeroPot(0.0);
486 +    snap->setLongRangePotential(zeroPot);
487 +    snap->setExcludedPotentials(zeroPot);
488 +
489 +    snap->setRestraintPotential(0.0);
490 +    snap->setRawPotential(0.0);
491 +
492      for (mol = info_->beginMolecule(mi); mol != NULL;
493           mol = info_->nextMolecule(mi)) {
494        for(atom = mol->beginAtom(ai); atom != NULL;
# Line 393 | Line 512 | namespace OpenMD {
512      }
513      
514      // Zero out the stress tensor
515 <    tau *= 0.0;
516 <    
515 >    stressTensor *= 0.0;
516 >    // Zero out the heatFlux
517 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
518    }
519    
520    void ForceManager::shortRangeInteractions() {
# Line 427 | Line 547 | namespace OpenMD {
547  
548        for (bond = mol->beginBond(bondIter); bond != NULL;
549             bond = mol->nextBond(bondIter)) {
550 <        bond->calcForce();
550 >        bond->calcForce(doParticlePot_);
551          bondPotential += bond->getPotential();
552        }
553  
# Line 435 | Line 555 | namespace OpenMD {
555             bend = mol->nextBend(bendIter)) {
556          
557          RealType angle;
558 <        bend->calcForce(angle);
558 >        bend->calcForce(angle, doParticlePot_);
559          RealType currBendPot = bend->getPotential();          
560          
561          bendPotential += bend->getPotential();
# Line 460 | Line 580 | namespace OpenMD {
580        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
581             torsion = mol->nextTorsion(torsionIter)) {
582          RealType angle;
583 <        torsion->calcForce(angle);
583 >        torsion->calcForce(angle, doParticlePot_);
584          RealType currTorsionPot = torsion->getPotential();
585          torsionPotential += torsion->getPotential();
586          map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
# Line 484 | Line 604 | namespace OpenMD {
604             inversion != NULL;
605             inversion = mol->nextInversion(inversionIter)) {
606          RealType angle;
607 <        inversion->calcForce(angle);
607 >        inversion->calcForce(angle, doParticlePot_);
608          RealType currInversionPot = inversion->getPotential();
609          inversionPotential += inversion->getPotential();
610          map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
# Line 504 | Line 624 | namespace OpenMD {
624          }      
625        }      
626      }
627 <    
628 <    RealType  shortRangePotential = bondPotential + bendPotential +
629 <      torsionPotential +  inversionPotential;    
627 >
628 > #ifdef IS_MPI
629 >    // Collect from all nodes.  This should eventually be moved into a
630 >    // SystemDecomposition, but this is a better place than in
631 >    // Thermo to do the collection.
632 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
633 >                              MPI::SUM);
634 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
635 >                              MPI::SUM);
636 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
637 >                              MPI::REALTYPE, MPI::SUM);
638 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
639 >                              MPI::REALTYPE, MPI::SUM);
640 > #endif
641 >
642      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
643 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
644 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
645 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
646 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
647 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
643 >
644 >    curSnapshot->setBondPotential(bondPotential);
645 >    curSnapshot->setBendPotential(bendPotential);
646 >    curSnapshot->setTorsionPotential(torsionPotential);
647 >    curSnapshot->setInversionPotential(inversionPotential);
648 >    
649 >    // RealType shortRangePotential = bondPotential + bendPotential +
650 >    //   torsionPotential +  inversionPotential;    
651 >
652 >    // curSnapshot->setShortRangePotential(shortRangePotential);
653    }
654    
655    void ForceManager::longRangeInteractions() {
656  
657 +
658      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
659      DataStorage* config = &(curSnapshot->atomData);
660      DataStorage* cgConfig = &(curSnapshot->cgData);
# Line 540 | Line 678 | namespace OpenMD {
678        // center of mass of the group is the same as position of the atom  
679        // if cutoff group does not exist
680        cgConfig->position = config->position;
681 +      cgConfig->velocity = config->velocity;
682      }
683  
684      fDecomp_->zeroWorkArrays();
685      fDecomp_->distributeData();
686      
687      int cg1, cg2, atom1, atom2, topoDist;
688 <    Vector3d d_grp, dag, d;
688 >    Vector3d d_grp, dag, d, gvel2, vel2;
689      RealType rgrpsq, rgrp, r2, r;
690      RealType electroMult, vdwMult;
691      RealType vij;
# Line 555 | Line 694 | namespace OpenMD {
694      RealType rCutSq;
695      bool in_switching_region;
696      RealType sw, dswdr, swderiv;
697 <    vector<int> atomListColumn, atomListRow, atomListLocal;
697 >    vector<int> atomListColumn, atomListRow;
698      InteractionData idat;
699      SelfData sdat;
700      RealType mf;
562 –    RealType lrPot;
701      RealType vpair;
702 +    RealType dVdFQ1(0.0);
703 +    RealType dVdFQ2(0.0);
704      potVec longRangePotential(0.0);
705      potVec workPot(0.0);
706 +    potVec exPot(0.0);
707 +    Vector3d eField1(0.0);
708 +    Vector3d eField2(0.0);
709 +    vector<int>::iterator ia, jb;
710  
711      int loopStart, loopEnd;
712  
713      idat.vdwMult = &vdwMult;
714      idat.electroMult = &electroMult;
715      idat.pot = &workPot;
716 +    idat.excludedPot = &exPot;
717      sdat.pot = fDecomp_->getEmbeddingPotential();
718 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
719      idat.vpair = &vpair;
720 +    idat.dVdFQ1 = &dVdFQ1;
721 +    idat.dVdFQ2 = &dVdFQ2;
722 +    idat.eField1 = &eField1;
723 +    idat.eField2 = &eField2;  
724      idat.f1 = &f1;
725      idat.sw = &sw;
726      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
727      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
728 +    idat.doParticlePot = doParticlePot_;
729 +    idat.doElectricField = doElectricField_;
730 +    sdat.doParticlePot = doParticlePot_;
731      
732      loopEnd = PAIR_LOOP;
733      if (info_->requiresPrepair() ) {
# Line 582 | Line 735 | namespace OpenMD {
735      } else {
736        loopStart = PAIR_LOOP;
737      }
585 –  
738      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
739      
740        if (iLoop == loopStart) {
741          bool update_nlist = fDecomp_->checkNeighborList();
742 <        if (update_nlist)
742 >        if (update_nlist) {
743 >          if (!usePeriodicBoundaryConditions_)
744 >            Mat3x3d bbox = thermo->getBoundingBox();
745            neighborList = fDecomp_->buildNeighborList();
746 <      }            
746 >        }
747 >      }
748  
749        for (vector<pair<int, int> >::iterator it = neighborList.begin();
750               it != neighborList.end(); ++it) {
# Line 610 | Line 765 | namespace OpenMD {
765            if (iLoop == PAIR_LOOP) {
766              vij = 0.0;
767              fij = V3Zero;
768 +            eField1 = V3Zero;
769 +            eField2 = V3Zero;
770            }
771            
772            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
773                                                       rgrp);
774 <              
774 >
775            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
776            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
620 –                      
777  
778 <          for (vector<int>::iterator ia = atomListRow.begin();
778 >          if (doHeatFlux_)
779 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
780 >
781 >          for (ia = atomListRow.begin();
782                 ia != atomListRow.end(); ++ia) {            
783              atom1 = (*ia);
784 <            
785 <            for (vector<int>::iterator jb = atomListColumn.begin();
784 >
785 >            for (jb = atomListColumn.begin();
786                   jb != atomListColumn.end(); ++jb) {              
787                atom2 = (*jb);
788  
789 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
789 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
790 >
791                  vpair = 0.0;
792                  workPot = 0.0;
793 +                exPot = 0.0;
794                  f1 = V3Zero;
795 +                dVdFQ1 = 0.0;
796 +                dVdFQ2 = 0.0;
797  
798                  fDecomp_->fillInteractionData(idat, atom1, atom2);
799 <                
799 >
800                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
801                  vdwMult = vdwScale_[topoDist];
802                  electroMult = electrostaticScale_[topoDist];
# Line 641 | Line 804 | namespace OpenMD {
804                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
805                    idat.d = &d_grp;
806                    idat.r2 = &rgrpsq;
807 +                  if (doHeatFlux_)
808 +                    vel2 = gvel2;
809                  } else {
810                    d = fDecomp_->getInteratomicVector(atom1, atom2);
811                    curSnapshot->wrapVector( d );
812                    r2 = d.lengthSquare();
813                    idat.d = &d;
814                    idat.r2 = &r2;
815 +                  if (doHeatFlux_)
816 +                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
817                  }
818                
819                  r = sqrt( *(idat.r2) );
# Line 657 | Line 824 | namespace OpenMD {
824                  } else {
825                    interactionMan_->doPair(idat);
826                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
660 –
827                    vij += vpair;
828                    fij += f1;
829 <                  tau -= outProduct( *(idat.d), f1);
829 >                  stressTensor -= outProduct( *(idat.d), f1);
830 >                  if (doHeatFlux_)
831 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
832                  }
833                }
834              }
# Line 673 | Line 841 | namespace OpenMD {
841                fij += fg;
842  
843                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
844 <                tau -= outProduct( *(idat.d), fg);
844 >                if (!fDecomp_->skipAtomPair(atomListRow[0],
845 >                                            atomListColumn[0],
846 >                                            cg1, cg2)) {
847 >                  stressTensor -= outProduct( *(idat.d), fg);
848 >                  if (doHeatFlux_)
849 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
850 >                }                
851                }
852            
853 <              for (vector<int>::iterator ia = atomListRow.begin();
853 >              for (ia = atomListRow.begin();
854                     ia != atomListRow.end(); ++ia) {            
855                  atom1 = (*ia);                
856                  mf = fDecomp_->getMassFactorRow(atom1);
# Line 684 | Line 858 | namespace OpenMD {
858                  // presence in switching region
859                  fg = swderiv * d_grp * mf;
860                  fDecomp_->addForceToAtomRow(atom1, fg);
687 –
861                  if (atomListRow.size() > 1) {
862                    if (info_->usesAtomicVirial()) {
863                      // find the distance between the atom
864                      // and the center of the cutoff group:
865                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
866 <                    tau -= outProduct(dag, fg);
866 >                    stressTensor -= outProduct(dag, fg);
867 >                    if (doHeatFlux_)
868 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
869                    }
870                  }
871                }
872 <              for (vector<int>::iterator jb = atomListColumn.begin();
872 >              for (jb = atomListColumn.begin();
873                     jb != atomListColumn.end(); ++jb) {              
874                  atom2 = (*jb);
875                  mf = fDecomp_->getMassFactorColumn(atom2);
# Line 708 | Line 883 | namespace OpenMD {
883                      // find the distance between the atom
884                      // and the center of the cutoff group:
885                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
886 <                    tau -= outProduct(dag, fg);
886 >                    stressTensor -= outProduct(dag, fg);
887 >                    if (doHeatFlux_)
888 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
889                    }
890                  }
891                }
892              }
893              //if (!info_->usesAtomicVirial()) {
894 <            //  tau -= outProduct(d_grp, fij);
894 >            //  stressTensor -= outProduct(d_grp, fij);
895 >            //  if (doHeatFlux_)
896 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
897              //}
898            }
899          }
# Line 725 | Line 904 | namespace OpenMD {
904  
905            fDecomp_->collectIntermediateData();
906  
907 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
907 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
908              fDecomp_->fillSelfData(sdat, atom1);
909              interactionMan_->doPreForce(sdat);
910            }
# Line 736 | Line 915 | namespace OpenMD {
915        }
916      }
917      
918 +    // collects pairwise information
919      fDecomp_->collectData();
920          
921      if (info_->requiresSelfCorrection()) {
922 <
743 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
922 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
923          fDecomp_->fillSelfData(sdat, atom1);
924          interactionMan_->doSelfCorrection(sdat);
925        }
747 –
926      }
927  
928 +    // collects single-atom information
929 +    fDecomp_->collectSelfData();
930 +
931      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
932        *(fDecomp_->getPairwisePotential());
933  
934 <    lrPot = longRangePotential.sum();
934 >    curSnapshot->setLongRangePotential(longRangePotential);
935 >    
936 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
937 >                                         *(fDecomp_->getExcludedPotential()));
938  
755 –    //store the tau and long range potential    
756 –    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
757 –    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
758 –    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
939    }
940  
941    
942    void ForceManager::postCalculation() {
943 +
944 +    vector<Perturbation*>::iterator pi;
945 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
946 +      (*pi)->applyPerturbation();
947 +    }
948 +
949      SimInfo::MoleculeIterator mi;
950      Molecule* mol;
951      Molecule::RigidBodyIterator rbIter;
952      RigidBody* rb;
953      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
954 <    
954 >  
955      // collect the atomic forces onto rigid bodies
956      
957      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 773 | Line 959 | namespace OpenMD {
959        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
960             rb = mol->nextRigidBody(rbIter)) {
961          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
962 <        tau += rbTau;
962 >        stressTensor += rbTau;
963        }
964      }
965      
966   #ifdef IS_MPI
967 <    Mat3x3d tmpTau(tau);
968 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
783 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
967 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
968 >                              MPI::REALTYPE, MPI::SUM);
969   #endif
970 <    curSnapshot->statData.setTau(tau);
971 <  }
970 >    curSnapshot->setStressTensor(stressTensor);
971 >    
972 >    if (info_->getSimParams()->getUseLongRangeCorrections()) {
973 >      /*
974 >      RealType vol = curSnapshot->getVolume();
975 >      RealType Elrc(0.0);
976 >      RealType Wlrc(0.0);
977  
978 < } //end namespace OpenMD
978 >      set<AtomType*>::iterator i;
979 >      set<AtomType*>::iterator j;
980 >    
981 >      RealType n_i, n_j;
982 >      RealType rho_i, rho_j;
983 >      pair<RealType, RealType> LRI;
984 >      
985 >      for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
986 >        n_i = RealType(info_->getGlobalCountOfType(*i));
987 >        rho_i = n_i /  vol;
988 >        for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
989 >          n_j = RealType(info_->getGlobalCountOfType(*j));
990 >          rho_j = n_j / vol;
991 >          
992 >          LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
993 >
994 >          Elrc += n_i   * rho_j * LRI.first;
995 >          Wlrc -= rho_i * rho_j * LRI.second;
996 >        }
997 >      }
998 >      Elrc *= 2.0 * NumericConstant::PI;
999 >      Wlrc *= 2.0 * NumericConstant::PI;
1000 >
1001 >      RealType lrp = curSnapshot->getLongRangePotential();
1002 >      curSnapshot->setLongRangePotential(lrp + Elrc);
1003 >      stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1004 >      curSnapshot->setStressTensor(stressTensor);
1005 >      */
1006 >    
1007 >    }
1008 >  }
1009 > }

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