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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs.
Revision 1592 by gezelter, Tue Jul 12 20:33:14 2011 UTC

# Line 47 | Line 47
47   * @version 1.0
48   */
49  
50 +
51   #include "brains/ForceManager.hpp"
52   #include "primitives/Molecule.hpp"
53   #define __OPENMD_C
# Line 58 | 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 <
71 < #ifdef IS_MPI
72 <    fDecomp_ = new ForceMatrixDecomposition(info_);
68 < #else
69 <    // fDecomp_ = new ForceSerialDecomposition(info);
70 < #endif
70 >    forceField_ = info_->getForceField();
71 >    interactionMan_ = new InteractionManager();
72 >    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
73    }
74 +
75 +  /**
76 +   * setupCutoffs
77 +   *
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.
83 +   *  If the cutoffRadius was not explicitly set:
84 +   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
85 +   *      No electrostatic atoms?  Poll the atom types present in the
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,
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 +    
112 +    if (simParams_->haveCutoffRadius()) {
113 +      rCut_ = simParams_->getCutoffRadius();
114 +    } else {      
115 +      if (info_->usesElectrostaticAtoms()) {
116 +        sprintf(painCave.errMsg,
117 +                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
118 +                "\tOpenMD will use a default value of 12.0 angstroms"
119 +                "\tfor the cutoffRadius.\n");
120 +        painCave.isFatal = 0;
121 +        painCave.severity = OPENMD_INFO;
122 +        simError();
123 +        rCut_ = 12.0;
124 +      } else {
125 +        RealType thisCut;
126 +        set<AtomType*>::iterator i;
127 +        set<AtomType*> atomTypes;
128 +        atomTypes = info_->getSimulatedAtomTypes();        
129 +        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
130 +          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
131 +          rCut_ = max(thisCut, rCut_);
132 +        }
133 +        sprintf(painCave.errMsg,
134 +                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
135 +                "\tOpenMD will use %lf angstroms.\n",
136 +                rCut_);
137 +        painCave.isFatal = 0;
138 +        painCave.severity = OPENMD_INFO;
139 +        simError();
140 +      }
141 +    }
142 +
143 +    fDecomp_->setUserCutoff(rCut_);
144 +    interactionMan_->setCutoffRadius(rCut_);
145 +
146 +    map<string, CutoffMethod> stringToCutoffMethod;
147 +    stringToCutoffMethod["HARD"] = HARD;
148 +    stringToCutoffMethod["SWITCHED"] = SWITCHED;
149 +    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
150 +    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
151    
152 <  void ForceManager::calcForces() {
152 >    if (simParams_->haveCutoffMethod()) {
153 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
154 >      map<string, CutoffMethod>::iterator i;
155 >      i = stringToCutoffMethod.find(cutMeth);
156 >      if (i == stringToCutoffMethod.end()) {
157 >        sprintf(painCave.errMsg,
158 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
159 >                "\tShould be one of: "
160 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
161 >                cutMeth.c_str());
162 >        painCave.isFatal = 1;
163 >        painCave.severity = OPENMD_ERROR;
164 >        simError();
165 >      } else {
166 >        cutoffMethod_ = i->second;
167 >      }
168 >    } else {
169 >      sprintf(painCave.errMsg,
170 >              "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
171 >              "\tOpenMD will use SHIFTED_FORCE.\n");
172 >      painCave.isFatal = 0;
173 >      painCave.severity = OPENMD_INFO;
174 >      simError();
175 >      cutoffMethod_ = SHIFTED_FORCE;        
176 >    }
177 >
178 >    map<string, CutoffPolicy> stringToCutoffPolicy;
179 >    stringToCutoffPolicy["MIX"] = MIX;
180 >    stringToCutoffPolicy["MAX"] = MAX;
181 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
182 >
183 >    std::string cutPolicy;
184 >    if (forceFieldOptions_.haveCutoffPolicy()){
185 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
186 >    }else if (simParams_->haveCutoffPolicy()) {
187 >      cutPolicy = simParams_->getCutoffPolicy();
188 >    }
189 >
190 >    if (!cutPolicy.empty()){
191 >      toUpper(cutPolicy);
192 >      map<string, CutoffPolicy>::iterator i;
193 >      i = stringToCutoffPolicy.find(cutPolicy);
194 >
195 >      if (i == stringToCutoffPolicy.end()) {
196 >        sprintf(painCave.errMsg,
197 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
198 >                "\tShould be one of: "
199 >                "MIX, MAX, or TRADITIONAL\n",
200 >                cutPolicy.c_str());
201 >        painCave.isFatal = 1;
202 >        painCave.severity = OPENMD_ERROR;
203 >        simError();
204 >      } else {
205 >        cutoffPolicy_ = i->second;
206 >      }
207 >    } else {
208 >      sprintf(painCave.errMsg,
209 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
210 >              "\tOpenMD will use TRADITIONAL.\n");
211 >      painCave.isFatal = 0;
212 >      painCave.severity = OPENMD_INFO;
213 >      simError();
214 >      cutoffPolicy_ = TRADITIONAL;        
215 >    }
216 >
217 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
218 >        
219 >    // create the switching function object:
220 >
221 >    switcher_ = new SwitchingFunction();
222 >  
223 >    if (cutoffMethod_ == SWITCHED) {
224 >      if (simParams_->haveSwitchingRadius()) {
225 >        rSwitch_ = simParams_->getSwitchingRadius();
226 >        if (rSwitch_ > rCut_) {        
227 >          sprintf(painCave.errMsg,
228 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
229 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
230 >          painCave.isFatal = 1;
231 >          painCave.severity = OPENMD_ERROR;
232 >          simError();
233 >        }
234 >      } else {      
235 >        rSwitch_ = 0.85 * rCut_;
236 >        sprintf(painCave.errMsg,
237 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
238 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
239 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
240 >        painCave.isFatal = 0;
241 >        painCave.severity = OPENMD_WARNING;
242 >        simError();
243 >      }
244 >    } else {
245 >      if (simParams_->haveSwitchingRadius()) {
246 >        map<string, CutoffMethod>::const_iterator it;
247 >        string theMeth;
248 >        for (it = stringToCutoffMethod.begin();
249 >             it != stringToCutoffMethod.end(); ++it) {
250 >          if (it->second == cutoffMethod_) {
251 >            theMeth = it->first;
252 >            break;
253 >          }
254 >        }
255 >        sprintf(painCave.errMsg,
256 >                "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
257 >                "\tis not set to SWITCHED, so switchingRadius value\n"
258 >                "\twill be ignored for this simulation\n", theMeth.c_str());
259 >        painCave.isFatal = 0;
260 >        painCave.severity = OPENMD_WARNING;
261 >        simError();
262 >      }
263 >
264 >      rSwitch_ = rCut_;
265 >    }
266      
267 +    // Default to cubic switching function.
268 +    sft_ = cubic;
269 +    if (simParams_->haveSwitchingFunctionType()) {
270 +      string funcType = simParams_->getSwitchingFunctionType();
271 +      toUpper(funcType);
272 +      if (funcType == "CUBIC") {
273 +        sft_ = cubic;
274 +      } else {
275 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
276 +          sft_ = fifth_order_poly;
277 +        } else {
278 +          // throw error        
279 +          sprintf( painCave.errMsg,
280 +                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
281 +                   "\tswitchingFunctionType must be one of: "
282 +                   "\"cubic\" or \"fifth_order_polynomial\".",
283 +                   funcType.c_str() );
284 +          painCave.isFatal = 1;
285 +          painCave.severity = OPENMD_ERROR;
286 +          simError();
287 +        }          
288 +      }
289 +    }
290 +    switcher_->setSwitchType(sft_);
291 +    switcher_->setSwitch(rSwitch_, rCut_);
292 +    interactionMan_->setSwitchingRadius(rSwitch_);
293 +  }
294 +  
295 +  void ForceManager::initialize() {
296 +
297      if (!info_->isTopologyDone()) {
298 +
299        info_->update();
300        interactionMan_->setSimInfo(info_);
301        interactionMan_->initialize();
302 <      swfun_ = interactionMan_->getSwitchingFunction();
303 <      fDecomp_->distributeInitialData();
304 <      info_->prepareTopology();
302 >
303 >      // We want to delay the cutoffs until after the interaction
304 >      // manager has set up the atom-atom interactions so that we can
305 >      // query them for suggested cutoff values
306 >      setupCutoffs();
307 >
308 >      info_->prepareTopology();      
309      }
310 +
311 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
312      
313 +    // Force fields can set options on how to scale van der Waals and
314 +    // electrostatic interactions for atoms connected via bonds, bends
315 +    // and torsions in this case the topological distance between
316 +    // atoms is:
317 +    // 0 = topologically unconnected
318 +    // 1 = bonded together
319 +    // 2 = connected via a bend
320 +    // 3 = connected via a torsion
321 +    
322 +    vdwScale_.reserve(4);
323 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
324 +
325 +    electrostaticScale_.reserve(4);
326 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
327 +
328 +    vdwScale_[0] = 1.0;
329 +    vdwScale_[1] = fopts.getvdw12scale();
330 +    vdwScale_[2] = fopts.getvdw13scale();
331 +    vdwScale_[3] = fopts.getvdw14scale();
332 +    
333 +    electrostaticScale_[0] = 1.0;
334 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
335 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
336 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
337 +    
338 +    fDecomp_->distributeInitialData();
339 +
340 +    initialized_ = true;
341 +
342 +  }
343 +
344 +  void ForceManager::calcForces() {
345 +    
346 +    if (!initialized_) initialize();
347 +
348      preCalculation();  
349      shortRangeInteractions();
350      longRangeInteractions();
351 <    postCalculation();
88 <    
351 >    postCalculation();    
352    }
353    
354    void ForceManager::preCalculation() {
# Line 102 | Line 365 | namespace OpenMD {
365      
366      for (mol = info_->beginMolecule(mi); mol != NULL;
367           mol = info_->nextMolecule(mi)) {
368 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
368 >      for(atom = mol->beginAtom(ai); atom != NULL;
369 >          atom = mol->nextAtom(ai)) {
370          atom->zeroForcesAndTorques();
371        }
372 <          
372 >      
373        //change the positions of atoms which belong to the rigidbodies
374        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
375             rb = mol->nextRigidBody(rbIter)) {
376          rb->zeroForcesAndTorques();
377        }        
378 <
378 >      
379        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
380          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
381              cg = mol->nextCutoffGroup(ci)) {
# Line 120 | Line 384 | namespace OpenMD {
384          }
385        }      
386      }
387 <  
387 >    
388      // Zero out the stress tensor
389      tau *= 0.0;
390      
# Line 174 | Line 438 | namespace OpenMD {
438            dataSet.prev.angle = dataSet.curr.angle = angle;
439            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
440            dataSet.deltaV = 0.0;
441 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
441 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
442 >                                                                  dataSet));
443          }else {
444            i->second.prev.angle = i->second.curr.angle;
445            i->second.prev.potential = i->second.curr.potential;
# Line 245 | Line 510 | namespace OpenMD {
510    
511    void ForceManager::longRangeInteractions() {
512  
248 –    // some of this initial stuff will go away:
513      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
514      DataStorage* config = &(curSnapshot->atomData);
515      DataStorage* cgConfig = &(curSnapshot->cgData);
252 –    RealType* frc = config->getArrayPointer(DataStorage::dslForce);
253 –    RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
254 –    RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
255 –    RealType* A = config->getArrayPointer(DataStorage::dslAmat);
256 –    RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
257 –    RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
258 –    RealType* rc;    
516  
517 <    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
518 <      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
517 >    //calculate the center of mass of cutoff group
518 >
519 >    SimInfo::MoleculeIterator mi;
520 >    Molecule* mol;
521 >    Molecule::CutoffGroupIterator ci;
522 >    CutoffGroup* cg;
523 >
524 >    if(info_->getNCutoffGroups() > 0){      
525 >      for (mol = info_->beginMolecule(mi); mol != NULL;
526 >           mol = info_->nextMolecule(mi)) {
527 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
528 >            cg = mol->nextCutoffGroup(ci)) {
529 >          cg->updateCOM();
530 >        }
531 >      }      
532      } else {
533        // center of mass of the group is the same as position of the atom  
534        // if cutoff group does not exist
535 <      rc = pos;
535 >      cgConfig->position = config->position;
536      }
267 –    
268 –    //initialize data before passing to fortran
269 –    RealType longRangePotential[N_INTERACTION_FAMILIES];
270 –    RealType lrPot = 0.0;
271 –    int isError = 0;
537  
538 <    // dangerous to iterate over enums, but we'll live on the edge:
274 <    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
275 <      longRangePotential[i]=0.0; //Initialize array
276 <    }
277 <
278 <    // new stuff starts here:
279 <
538 >    fDecomp_->zeroWorkArrays();
539      fDecomp_->distributeData();
540 <
541 <    int cg1, cg2, atom1, atom2;
542 <    Vector3d d_grp, dag;
543 <    RealType rgrpsq, rgrp;
540 >    
541 >    int cg1, cg2, atom1, atom2, topoDist;
542 >    Vector3d d_grp, dag, d;
543 >    RealType rgrpsq, rgrp, r2, r;
544 >    RealType electroMult, vdwMult;
545      RealType vij;
546 <    Vector3d fij, fg;
547 <    pair<int, int> gtypes;
546 >    Vector3d fij, fg, f1;
547 >    tuple3<RealType, RealType, RealType> cuts;
548      RealType rCutSq;
549      bool in_switching_region;
550      RealType sw, dswdr, swderiv;
# Line 292 | Line 552 | namespace OpenMD {
552      InteractionData idat;
553      SelfData sdat;
554      RealType mf;
555 +    RealType lrPot;
556 +    RealType vpair;
557 +    potVec longRangePotential(0.0);
558 +    potVec workPot(0.0);
559  
560      int loopStart, loopEnd;
561  
562 +    idat.vdwMult = &vdwMult;
563 +    idat.electroMult = &electroMult;
564 +    idat.pot = &workPot;
565 +    sdat.pot = fDecomp_->getEmbeddingPotential();
566 +    idat.vpair = &vpair;
567 +    idat.f1 = &f1;
568 +    idat.sw = &sw;
569 +    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
570 +    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
571 +    
572      loopEnd = PAIR_LOOP;
573      if (info_->requiresPrepair() ) {
574        loopStart = PREPAIR_LOOP;
575      } else {
576        loopStart = PAIR_LOOP;
577      }
578 <
579 <    for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
580 <      
578 >  
579 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
580 >    
581        if (iLoop == loopStart) {
582          bool update_nlist = fDecomp_->checkNeighborList();
583          if (update_nlist)
584            neighborList = fDecomp_->buildNeighborList();
585 <      }
586 <
585 >      }      
586 >        
587        for (vector<pair<int, int> >::iterator it = neighborList.begin();
588               it != neighborList.end(); ++it) {
589 <        
589 >                
590          cg1 = (*it).first;
591          cg2 = (*it).second;
592 +        
593 +        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
594  
319 –        gtypes = fDecomp_->getGroupTypes(cg1, cg2);
595          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
596          curSnapshot->wrapVector(d_grp);        
597          rgrpsq = d_grp.lengthSquare();
323 –        rCutSq = groupCutoffMap[gtypes].first;
598  
599 +        rCutSq = cuts.second;
600 +
601          if (rgrpsq < rCutSq) {
602 <          *(idat.rcut) = groupCutoffMap[gtypes].second;
602 >          idat.rcut = &cuts.first;
603            if (iLoop == PAIR_LOOP) {
604 <            vij *= 0.0;
604 >            vij = 0.0;
605              fij = V3Zero;
606            }
607            
608 <          in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
609 <                                                  rgrp);              
608 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
609 >                                                     rgrp);
610 >              
611            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
612            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
613  
# Line 341 | Line 618 | namespace OpenMD {
618              for (vector<int>::iterator jb = atomListColumn.begin();
619                   jb != atomListColumn.end(); ++jb) {              
620                atom2 = (*jb);
621 <              
621 >            
622                if (!fDecomp_->skipAtomPair(atom1, atom2)) {
623 +                vpair = 0.0;
624 +                workPot = 0.0;
625 +                f1 = V3Zero;
626 +
627 +                fDecomp_->fillInteractionData(idat, atom1, atom2);
628                  
629 <                idat = fDecomp_->fillInteractionData(atom1, atom2);
629 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
630 >                vdwMult = vdwScale_[topoDist];
631 >                electroMult = electrostaticScale_[topoDist];
632  
633                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
634 <                  *(idat.d) = d_grp;
635 <                  *(idat.r2) = rgrpsq;
634 >                  idat.d = &d_grp;
635 >                  idat.r2 = &rgrpsq;
636                  } else {
637 <                  *(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
638 <                  curSnapshot->wrapVector( *(idat.d) );
639 <                  *(idat.r2) = idat.d->lengthSquare();
637 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
638 >                  curSnapshot->wrapVector( d );
639 >                  r2 = d.lengthSquare();
640 >                  idat.d = &d;
641 >                  idat.r2 = &r2;
642                  }
643                  
644 <                *(idat.rij) = sqrt( *(idat.r2) );
644 >                r = sqrt( *(idat.r2) );
645 >                idat.rij = &r;
646                
647                  if (iLoop == PREPAIR_LOOP) {
648                    interactionMan_->doPrePair(idat);
649                  } else {
650                    interactionMan_->doPair(idat);
651 <                  vij += *(idat.vpair);
652 <                  fij += *(idat.f1);
653 <                  tau -= outProduct( *(idat.d), *(idat.f1));
651 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
652 >                  vij += vpair;
653 >                  fij += f1;
654 >                  cerr << "ats = " << atom1 << " " << atom2 << "d = " << *(idat.d) << " f1 = " << f1 << "\n";
655 >                  tau -= outProduct( *(idat.d), f1);
656                  }
657                }
658              }
# Line 373 | Line 662 | namespace OpenMD {
662              if (in_switching_region) {
663                swderiv = vij * dswdr / rgrp;
664                fg = swderiv * d_grp;
376 –
665                fij += fg;
666  
667                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
# Line 425 | Line 713 | namespace OpenMD {
713        }
714  
715        if (iLoop == PREPAIR_LOOP) {
716 <        if (info_->requiresPrepair()) {            
716 >        if (info_->requiresPrepair()) {
717 >
718            fDecomp_->collectIntermediateData();
719 <          atomListLocal = fDecomp_->getAtomList();
720 <          for (vector<int>::iterator ia = atomListLocal.begin();
721 <               ia != atomListLocal.end(); ++ia) {              
433 <            atom1 = (*ia);            
434 <            sdat = fDecomp_->fillSelfData(atom1);
719 >
720 >          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
721 >            fDecomp_->fillSelfData(sdat, atom1);
722              interactionMan_->doPreForce(sdat);
723            }
724 <          fDecomp_->distributeIntermediateData();        
724 >
725 >          fDecomp_->distributeIntermediateData();
726 >
727          }
728        }
729  
730      }
731      
732      fDecomp_->collectData();
733 <    
734 <    if (info_->requiresSkipCorrection() || info_->requiresSelfCorrection()) {
446 <      atomListLocal = fDecomp_->getAtomList();
447 <      for (vector<int>::iterator ia = atomListLocal.begin();
448 <           ia != atomListLocal.end(); ++ia) {              
449 <        atom1 = (*ia);    
733 >        
734 >    if (info_->requiresSelfCorrection()) {
735  
736 <        if (info_->requiresSkipCorrection()) {
737 <          vector<int> skipList = fDecomp_->getSkipsForAtom(atom1);
738 <          for (vector<int>::iterator jb = skipList.begin();
454 <               jb != skipList.end(); ++jb) {              
455 <            atom2 = (*jb);
456 <            idat = fDecomp_->fillSkipData(atom1, atom2);
457 <            interactionMan_->doSkipCorrection(idat);
458 <          }
459 <        }
460 <          
461 <        if (info_->requiresSelfCorrection()) {
462 <          sdat = fDecomp_->fillSelfData(atom1);
463 <          interactionMan_->doSelfCorrection(sdat);
464 <        }
736 >      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
737 >        fDecomp_->fillSelfData(sdat, atom1);
738 >        interactionMan_->doSelfCorrection(sdat);
739        }
466 –    }
740  
468 –    // dangerous to iterate over enums, but we'll live on the edge:
469 –    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
470 –      lrPot += longRangePotential[i]; //Quick hack
741      }
742 <        
742 >
743 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
744 >      *(fDecomp_->getPairwisePotential());
745 >
746 >    lrPot = longRangePotential.sum();
747 >
748      //store the tau and long range potential    
749      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
750      curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];

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