ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/brains/ForceManager.cpp
(Generate patch)

Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
Revision 1616 by gezelter, Tue Aug 30 15:45:35 2011 UTC

# Line 59 | Line 59
59   #include "nonbonded/NonBondedInteraction.hpp"
60   #include "parallel/ForceMatrixDecomposition.hpp"
61  
62 + #include <cstdio>
63 + #include <iostream>
64 + #include <iomanip>
65 +
66   using namespace std;
67   namespace OpenMD {
68    
69    ForceManager::ForceManager(SimInfo * info) : info_(info) {
70      forceField_ = info_->getForceField();
71 <    fDecomp_ = new ForceMatrixDecomposition(info_);
71 >    interactionMan_ = new InteractionManager();
72 >    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
73    }
74  
75    /**
76     * setupCutoffs
77     *
78 <   * Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
78 >   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
79 >   * and cutoffPolicy
80     *
81     * cutoffRadius : realType
82     *  If the cutoffRadius was explicitly set, use that value.
# Line 80 | Line 86 | namespace OpenMD {
86     *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
87     *      Use the maximum suggested value that was found.
88     *
89 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
89 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
90 >   *                        or SHIFTED_POTENTIAL)
91     *      If cutoffMethod was explicitly set, use that choice.
92     *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
93     *
94     * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
95     *      If cutoffPolicy was explicitly set, use that choice.
96     *      If cutoffPolicy was not explicitly set, use TRADITIONAL
97 +   *
98 +   * switchingRadius : realType
99 +   *  If the cutoffMethod was set to SWITCHED:
100 +   *      If the switchingRadius was explicitly set, use that value
101 +   *          (but do a sanity check first).
102 +   *      If the switchingRadius was not explicitly set: use 0.85 *
103 +   *      cutoffRadius_
104 +   *  If the cutoffMethod was not set to SWITCHED:
105 +   *      Set switchingRadius equal to cutoffRadius for safety.
106     */
107    void ForceManager::setupCutoffs() {
108      
109      Globals* simParams_ = info_->getSimParams();
110      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
111 +    int mdFileVersion;
112      
113 +    if (simParams_->haveMDfileVersion())
114 +      mdFileVersion = simParams_->getMDfileVersion();
115 +    else
116 +      mdFileVersion = 0;
117 +  
118      if (simParams_->haveCutoffRadius()) {
119        rCut_ = simParams_->getCutoffRadius();
120      } else {      
# Line 121 | Line 143 | namespace OpenMD {
143          painCave.isFatal = 0;
144          painCave.severity = OPENMD_INFO;
145          simError();
146 <      }            
146 >      }
147      }
148  
149 +    fDecomp_->setUserCutoff(rCut_);
150 +    interactionMan_->setCutoffRadius(rCut_);
151 +
152      map<string, CutoffMethod> stringToCutoffMethod;
153      stringToCutoffMethod["HARD"] = HARD;
154      stringToCutoffMethod["SWITCHED"] = SWITCHED;
# Line 147 | Line 172 | namespace OpenMD {
172          cutoffMethod_ = i->second;
173        }
174      } else {
175 <      sprintf(painCave.errMsg,
176 <              "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
177 <              "\tOpenMD will use SHIFTED_FORCE.\n");
178 <      painCave.isFatal = 0;
179 <      painCave.severity = OPENMD_INFO;
180 <      simError();
181 <      cutoffMethod_ = SHIFTED_FORCE;        
175 >      if (mdFileVersion > 1) {
176 >        sprintf(painCave.errMsg,
177 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
178 >                "\tOpenMD will use SHIFTED_FORCE.\n");
179 >        painCave.isFatal = 0;
180 >        painCave.severity = OPENMD_INFO;
181 >        simError();
182 >        cutoffMethod_ = SHIFTED_FORCE;        
183 >      } else {
184 >        // handle the case where the old file version was in play
185 >        // (there should be no cutoffMethod, so we have to deduce it
186 >        // from other data).        
187 >
188 >        sprintf(painCave.errMsg,
189 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
190 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
191 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
192 >                "\tbehavior of the older (version 1) code.  To remove this\n"
193 >                "\twarning, add an explicit cutoffMethod and change the top\n"
194 >                "\tof the file so that it begins with <OpenMD version=2>\n");
195 >        painCave.isFatal = 0;
196 >        painCave.severity = OPENMD_WARNING;
197 >        simError();            
198 >                
199 >        // The old file version tethered the shifting behavior to the
200 >        // electrostaticSummationMethod keyword.
201 >        
202 >        if (simParams_->haveElectrostaticSummationMethod()) {
203 >          std::string myMethod = simParams_->getElectrostaticSummationMethod();
204 >          toUpper(myMethod);
205 >        
206 >          if (myMethod == "SHIFTED_POTENTIAL") {
207 >            cutoffMethod_ = SHIFTED_POTENTIAL;
208 >          } else if (myMethod == "SHIFTED_FORCE") {
209 >            cutoffMethod_ = SHIFTED_FORCE;
210 >          }
211 >        
212 >          if (simParams_->haveSwitchingRadius())
213 >            rSwitch_ = simParams_->getSwitchingRadius();
214 >
215 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
216 >            if (simParams_->haveSwitchingRadius()){
217 >              sprintf(painCave.errMsg,
218 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
219 >                      "\tA value was set for the switchingRadius\n"
220 >                      "\teven though the electrostaticSummationMethod was\n"
221 >                      "\tset to %s\n", myMethod.c_str());
222 >              painCave.severity = OPENMD_WARNING;
223 >              painCave.isFatal = 1;
224 >              simError();            
225 >            }
226 >          }
227 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
228 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
229 >              sprintf(painCave.errMsg,
230 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
231 >                      "\tcutoffRadius and switchingRadius are set to the\n"
232 >                      "\tsame value.  OpenMD will use shifted force\n"
233 >                      "\tpotentials instead of switching functions.\n");
234 >              painCave.isFatal = 0;
235 >              painCave.severity = OPENMD_WARNING;
236 >              simError();            
237 >            } else {
238 >              cutoffMethod_ = SHIFTED_POTENTIAL;
239 >              sprintf(painCave.errMsg,
240 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
241 >                      "\tcutoffRadius and switchingRadius are set to the\n"
242 >                      "\tsame value.  OpenMD will use shifted potentials\n"
243 >                      "\tinstead of switching functions.\n");
244 >              painCave.isFatal = 0;
245 >              painCave.severity = OPENMD_WARNING;
246 >              simError();            
247 >            }
248 >          }
249 >        }
250 >      }
251      }
252  
253      map<string, CutoffPolicy> stringToCutoffPolicy;
# Line 194 | Line 288 | namespace OpenMD {
288        simError();
289        cutoffPolicy_ = TRADITIONAL;        
290      }
197 –  }
291  
292 <  /**
293 <   * setupSwitching
294 <   *
295 <   * Sets the values of switchingRadius and
296 <   *  If the switchingRadius was explicitly set, use that value (but check it)
297 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
298 <   */
299 <  void ForceManager::setupSwitching() {
300 <    Globals* simParams_ = info_->getSimParams();
301 <    
302 <    if (simParams_->haveSwitchingRadius()) {
303 <      rSwitch_ = simParams_->getSwitchingRadius();
304 <      if (rSwitch_ > rCut_) {        
292 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
293 >        
294 >    // create the switching function object:
295 >
296 >    switcher_ = new SwitchingFunction();
297 >  
298 >    if (cutoffMethod_ == SWITCHED) {
299 >      if (simParams_->haveSwitchingRadius()) {
300 >        rSwitch_ = simParams_->getSwitchingRadius();
301 >        if (rSwitch_ > rCut_) {        
302 >          sprintf(painCave.errMsg,
303 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
304 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
305 >          painCave.isFatal = 1;
306 >          painCave.severity = OPENMD_ERROR;
307 >          simError();
308 >        }
309 >      } else {      
310 >        rSwitch_ = 0.85 * rCut_;
311          sprintf(painCave.errMsg,
312 <                "ForceManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
313 <                rSwitch_, rCut_);
314 <        painCave.isFatal = 1;
315 <        painCave.severity = OPENMD_ERROR;
312 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
313 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
314 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
315 >        painCave.isFatal = 0;
316 >        painCave.severity = OPENMD_WARNING;
317          simError();
318        }
319 <    } else {      
320 <      rSwitch_ = 0.85 * rCut_;
321 <      sprintf(painCave.errMsg,
322 <              "ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
323 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
324 <              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
325 <      painCave.isFatal = 0;
326 <      painCave.severity = OPENMD_WARNING;
327 <      simError();
328 <    }          
319 >    } else {
320 >      if (simParams_->haveSwitchingRadius()) {
321 >        map<string, CutoffMethod>::const_iterator it;
322 >        string theMeth;
323 >        for (it = stringToCutoffMethod.begin();
324 >             it != stringToCutoffMethod.end(); ++it) {
325 >          if (it->second == cutoffMethod_) {
326 >            theMeth = it->first;
327 >            break;
328 >          }
329 >        }
330 >        sprintf(painCave.errMsg,
331 >                "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
332 >                "\tis not set to SWITCHED, so switchingRadius value\n"
333 >                "\twill be ignored for this simulation\n", theMeth.c_str());
334 >        painCave.isFatal = 0;
335 >        painCave.severity = OPENMD_WARNING;
336 >        simError();
337 >      }
338 >
339 >      rSwitch_ = rCut_;
340 >    }
341      
342 +    // Default to cubic switching function.
343 +    sft_ = cubic;
344      if (simParams_->haveSwitchingFunctionType()) {
345        string funcType = simParams_->getSwitchingFunctionType();
346        toUpper(funcType);
# Line 250 | Line 364 | namespace OpenMD {
364      }
365      switcher_->setSwitchType(sft_);
366      switcher_->setSwitch(rSwitch_, rCut_);
367 +    interactionMan_->setSwitchingRadius(rSwitch_);
368    }
369 +
370 +
371 +
372    
373    void ForceManager::initialize() {
374  
375      if (!info_->isTopologyDone()) {
376 +
377        info_->update();
378        interactionMan_->setSimInfo(info_);
379        interactionMan_->initialize();
# Line 262 | Line 381 | namespace OpenMD {
381        // We want to delay the cutoffs until after the interaction
382        // manager has set up the atom-atom interactions so that we can
383        // query them for suggested cutoff values
265 –
384        setupCutoffs();
267 –      setupSwitching();
385  
386        info_->prepareTopology();      
387      }
388  
389      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
390      
391 <    // Force fields can set options on how to scale van der Waals and electrostatic
392 <    // interactions for atoms connected via bonds, bends and torsions
393 <    // in this case the topological distance between atoms is:
391 >    // Force fields can set options on how to scale van der Waals and
392 >    // electrostatic interactions for atoms connected via bonds, bends
393 >    // and torsions in this case the topological distance between
394 >    // atoms is:
395      // 0 = topologically unconnected
396      // 1 = bonded together
397      // 2 = connected via a bend
# Line 325 | Line 443 | namespace OpenMD {
443      
444      for (mol = info_->beginMolecule(mi); mol != NULL;
445           mol = info_->nextMolecule(mi)) {
446 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
446 >      for(atom = mol->beginAtom(ai); atom != NULL;
447 >          atom = mol->nextAtom(ai)) {
448          atom->zeroForcesAndTorques();
449        }
450 <          
450 >      
451        //change the positions of atoms which belong to the rigidbodies
452        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
453             rb = mol->nextRigidBody(rbIter)) {
454          rb->zeroForcesAndTorques();
455        }        
456 <
456 >      
457        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
458          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
459              cg = mol->nextCutoffGroup(ci)) {
# Line 343 | Line 462 | namespace OpenMD {
462          }
463        }      
464      }
465 <  
465 >    
466      // Zero out the stress tensor
467      tau *= 0.0;
468      
# Line 397 | Line 516 | namespace OpenMD {
516            dataSet.prev.angle = dataSet.curr.angle = angle;
517            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
518            dataSet.deltaV = 0.0;
519 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
519 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
520 >                                                                  dataSet));
521          }else {
522            i->second.prev.angle = i->second.curr.angle;
523            i->second.prev.potential = i->second.curr.potential;
# Line 468 | Line 588 | namespace OpenMD {
588    
589    void ForceManager::longRangeInteractions() {
590  
471 –    // some of this initial stuff will go away:
591      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
592      DataStorage* config = &(curSnapshot->atomData);
593      DataStorage* cgConfig = &(curSnapshot->cgData);
475 –    RealType* frc = config->getArrayPointer(DataStorage::dslForce);
476 –    RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
477 –    RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
478 –    RealType* A = config->getArrayPointer(DataStorage::dslAmat);
479 –    RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
480 –    RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
481 –    RealType* rc;    
594  
595 <    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
596 <      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
595 >    //calculate the center of mass of cutoff group
596 >
597 >    SimInfo::MoleculeIterator mi;
598 >    Molecule* mol;
599 >    Molecule::CutoffGroupIterator ci;
600 >    CutoffGroup* cg;
601 >
602 >    if(info_->getNCutoffGroups() > 0){      
603 >      for (mol = info_->beginMolecule(mi); mol != NULL;
604 >           mol = info_->nextMolecule(mi)) {
605 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
606 >            cg = mol->nextCutoffGroup(ci)) {
607 >          cg->updateCOM();
608 >        }
609 >      }      
610      } else {
611        // center of mass of the group is the same as position of the atom  
612        // if cutoff group does not exist
613 <      rc = pos;
613 >      cgConfig->position = config->position;
614      }
615 <    
491 <    // new stuff starts here:
615 >
616      fDecomp_->zeroWorkArrays();
617      fDecomp_->distributeData();
618 <
619 <    int cg1, cg2, atom1, atom2;
620 <    Vector3d d_grp, dag;
621 <    RealType rgrpsq, rgrp;
618 >    
619 >    int cg1, cg2, atom1, atom2, topoDist;
620 >    Vector3d d_grp, dag, d;
621 >    RealType rgrpsq, rgrp, r2, r;
622 >    RealType electroMult, vdwMult;
623      RealType vij;
624 <    Vector3d fij, fg;
624 >    Vector3d fij, fg, f1;
625      tuple3<RealType, RealType, RealType> cuts;
626      RealType rCutSq;
627      bool in_switching_region;
# Line 505 | Line 630 | namespace OpenMD {
630      InteractionData idat;
631      SelfData sdat;
632      RealType mf;
508 –    potVec pot(0.0);
509 –    potVec longRangePotential(0.0);
633      RealType lrPot;
634 +    RealType vpair;
635 +    potVec longRangePotential(0.0);
636 +    potVec workPot(0.0);
637  
638      int loopStart, loopEnd;
639  
640 +    idat.vdwMult = &vdwMult;
641 +    idat.electroMult = &electroMult;
642 +    idat.pot = &workPot;
643 +    sdat.pot = fDecomp_->getEmbeddingPotential();
644 +    idat.vpair = &vpair;
645 +    idat.f1 = &f1;
646 +    idat.sw = &sw;
647 +    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
648 +    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
649 +    
650      loopEnd = PAIR_LOOP;
651      if (info_->requiresPrepair() ) {
652        loopStart = PREPAIR_LOOP;
653      } else {
654        loopStart = PAIR_LOOP;
655      }
656 <
657 <    for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
658 <      
656 >  
657 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
658 >    
659        if (iLoop == loopStart) {
660          bool update_nlist = fDecomp_->checkNeighborList();
661          if (update_nlist)
662            neighborList = fDecomp_->buildNeighborList();
663 <      }
663 >      }            
664  
665        for (vector<pair<int, int> >::iterator it = neighborList.begin();
666               it != neighborList.end(); ++it) {
667 <        
667 >                
668          cg1 = (*it).first;
669          cg2 = (*it).second;
670          
671          cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
672  
673          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
674 +
675          curSnapshot->wrapVector(d_grp);        
676          rgrpsq = d_grp.lengthSquare();
540 –
677          rCutSq = cuts.second;
678  
679          if (rgrpsq < rCutSq) {
680 <          *(idat.rcut) = cuts.first;
680 >          idat.rcut = &cuts.first;
681            if (iLoop == PAIR_LOOP) {
682 <            vij *= 0.0;
682 >            vij = 0.0;
683              fij = V3Zero;
684            }
685            
686 <          in_switching_region = switcher_->getSwitch(rgrpsq, *(idat.sw), dswdr,
686 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
687                                                       rgrp);
688 <              
688 >          
689            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
690            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
691  
# Line 560 | Line 696 | namespace OpenMD {
696              for (vector<int>::iterator jb = atomListColumn.begin();
697                   jb != atomListColumn.end(); ++jb) {              
698                atom2 = (*jb);
699 <              
699 >
700                if (!fDecomp_->skipAtomPair(atom1, atom2)) {
701 +                vpair = 0.0;
702 +                workPot = 0.0;
703 +                f1 = V3Zero;
704 +
705 +                fDecomp_->fillInteractionData(idat, atom1, atom2);
706                  
707 <                pot *= 0.0;
707 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
708 >                vdwMult = vdwScale_[topoDist];
709 >                electroMult = electrostaticScale_[topoDist];
710  
568 –                idat = fDecomp_->fillInteractionData(atom1, atom2);
569 –                *(idat.pot) = pot;
570 –
711                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
712 <                  *(idat.d) = d_grp;
713 <                  *(idat.r2) = rgrpsq;
712 >                  idat.d = &d_grp;
713 >                  idat.r2 = &rgrpsq;
714                  } else {
715 <                  *(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
716 <                  curSnapshot->wrapVector( *(idat.d) );
717 <                  *(idat.r2) = idat.d->lengthSquare();
715 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
716 >                  curSnapshot->wrapVector( d );
717 >                  r2 = d.lengthSquare();
718 >                  idat.d = &d;
719 >                  idat.r2 = &r2;
720                  }
579 –                
580 –                *(idat.rij) = sqrt( *(idat.r2) );
721                
722 +                r = sqrt( *(idat.r2) );
723 +                idat.rij = &r;
724 +              
725                  if (iLoop == PREPAIR_LOOP) {
726                    interactionMan_->doPrePair(idat);
727                  } else {
728                    interactionMan_->doPair(idat);
729                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
730 <                  vij += *(idat.vpair);
731 <                  fij += *(idat.f1);
732 <                  tau -= outProduct( *(idat.d), *(idat.f1));
730 >                  vij += vpair;
731 >                  fij += f1;
732 >                  tau -= outProduct( *(idat.d), f1);
733                  }
734                }
735              }
# Line 596 | Line 739 | namespace OpenMD {
739              if (in_switching_region) {
740                swderiv = vij * dswdr / rgrp;
741                fg = swderiv * d_grp;
599 –
742                fij += fg;
743  
744                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
# Line 611 | Line 753 | namespace OpenMD {
753                  // presence in switching region
754                  fg = swderiv * d_grp * mf;
755                  fDecomp_->addForceToAtomRow(atom1, fg);
614 –
756                  if (atomListRow.size() > 1) {
757                    if (info_->usesAtomicVirial()) {
758                      // find the distance between the atom
# Line 640 | Line 781 | namespace OpenMD {
781                  }
782                }
783              }
784 <            //if (!SIM_uses_AtomicVirial) {
784 >            //if (!info_->usesAtomicVirial()) {
785              //  tau -= outProduct(d_grp, fij);
786              //}
787            }
# Line 648 | Line 789 | namespace OpenMD {
789        }
790  
791        if (iLoop == PREPAIR_LOOP) {
792 <        if (info_->requiresPrepair()) {            
792 >        if (info_->requiresPrepair()) {
793 >
794            fDecomp_->collectIntermediateData();
795  
796            for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
797 <            sdat = fDecomp_->fillSelfData(atom1);
797 >            fDecomp_->fillSelfData(sdat, atom1);
798              interactionMan_->doPreForce(sdat);
799            }
800  
801 <          fDecomp_->distributeIntermediateData();        
801 >          fDecomp_->distributeIntermediateData();
802 >
803          }
804        }
662 –
805      }
806      
807      fDecomp_->collectData();
666 –    
667 –    if ( info_->requiresSkipCorrection() ) {
668 –      
669 –      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
670 –
671 –        vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
808          
673 –        for (vector<int>::iterator jb = skipList.begin();
674 –             jb != skipList.end(); ++jb) {        
675 –    
676 –          atom2 = (*jb);
677 –          idat = fDecomp_->fillSkipData(atom1, atom2);
678 –          interactionMan_->doSkipCorrection(idat);
679 –
680 –        }
681 –      }
682 –    }
683 –    
809      if (info_->requiresSelfCorrection()) {
810  
811        for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
812 <        sdat = fDecomp_->fillSelfData(atom1);
812 >        fDecomp_->fillSelfData(sdat, atom1);
813          interactionMan_->doSelfCorrection(sdat);
814        }
815  
816      }
817  
818 <    longRangePotential = fDecomp_->getLongRangePotential();
818 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
819 >      *(fDecomp_->getPairwisePotential());
820 >
821      lrPot = longRangePotential.sum();
822  
823      //store the tau and long range potential    

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines