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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1570 by gezelter, Thu May 26 21:56:04 2011 UTC vs.
Revision 1616 by gezelter, Tue Aug 30 15:45:35 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 +    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 {      
121 +      if (info_->usesElectrostaticAtoms()) {
122 +        sprintf(painCave.errMsg,
123 +                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
124 +                "\tOpenMD will use a default value of 12.0 angstroms"
125 +                "\tfor the cutoffRadius.\n");
126 +        painCave.isFatal = 0;
127 +        painCave.severity = OPENMD_INFO;
128 +        simError();
129 +        rCut_ = 12.0;
130 +      } else {
131 +        RealType thisCut;
132 +        set<AtomType*>::iterator i;
133 +        set<AtomType*> atomTypes;
134 +        atomTypes = info_->getSimulatedAtomTypes();        
135 +        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
136 +          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
137 +          rCut_ = max(thisCut, rCut_);
138 +        }
139 +        sprintf(painCave.errMsg,
140 +                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
141 +                "\tOpenMD will use %lf angstroms.\n",
142 +                rCut_);
143 +        painCave.isFatal = 0;
144 +        painCave.severity = OPENMD_INFO;
145 +        simError();
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;
155 +    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
156 +    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
157    
158 <  void ForceManager::calcForces() {
158 >    if (simParams_->haveCutoffMethod()) {
159 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
160 >      map<string, CutoffMethod>::iterator i;
161 >      i = stringToCutoffMethod.find(cutMeth);
162 >      if (i == stringToCutoffMethod.end()) {
163 >        sprintf(painCave.errMsg,
164 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
165 >                "\tShould be one of: "
166 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
167 >                cutMeth.c_str());
168 >        painCave.isFatal = 1;
169 >        painCave.severity = OPENMD_ERROR;
170 >        simError();
171 >      } else {
172 >        cutoffMethod_ = i->second;
173 >      }
174 >    } else {
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;
254 >    stringToCutoffPolicy["MIX"] = MIX;
255 >    stringToCutoffPolicy["MAX"] = MAX;
256 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
257 >
258 >    std::string cutPolicy;
259 >    if (forceFieldOptions_.haveCutoffPolicy()){
260 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
261 >    }else if (simParams_->haveCutoffPolicy()) {
262 >      cutPolicy = simParams_->getCutoffPolicy();
263 >    }
264 >
265 >    if (!cutPolicy.empty()){
266 >      toUpper(cutPolicy);
267 >      map<string, CutoffPolicy>::iterator i;
268 >      i = stringToCutoffPolicy.find(cutPolicy);
269 >
270 >      if (i == stringToCutoffPolicy.end()) {
271 >        sprintf(painCave.errMsg,
272 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
273 >                "\tShould be one of: "
274 >                "MIX, MAX, or TRADITIONAL\n",
275 >                cutPolicy.c_str());
276 >        painCave.isFatal = 1;
277 >        painCave.severity = OPENMD_ERROR;
278 >        simError();
279 >      } else {
280 >        cutoffPolicy_ = i->second;
281 >      }
282 >    } else {
283 >      sprintf(painCave.errMsg,
284 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
285 >              "\tOpenMD will use TRADITIONAL.\n");
286 >      painCave.isFatal = 0;
287 >      painCave.severity = OPENMD_INFO;
288 >      simError();
289 >      cutoffPolicy_ = TRADITIONAL;        
290 >    }
291 >
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::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 >      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);
347 +      if (funcType == "CUBIC") {
348 +        sft_ = cubic;
349 +      } else {
350 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
351 +          sft_ = fifth_order_poly;
352 +        } else {
353 +          // throw error        
354 +          sprintf( painCave.errMsg,
355 +                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
356 +                   "\tswitchingFunctionType must be one of: "
357 +                   "\"cubic\" or \"fifth_order_polynomial\".",
358 +                   funcType.c_str() );
359 +          painCave.isFatal = 1;
360 +          painCave.severity = OPENMD_ERROR;
361 +          simError();
362 +        }          
363 +      }
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();
380 <      swfun_ = interactionMan_->getSwitchingFunction();
381 <      fDecomp_->distributeInitialData();
382 <      info_->prepareTopology();
380 >
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
384 >      setupCutoffs();
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
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
398 +    // 3 = connected via a torsion
399 +    
400 +    vdwScale_.reserve(4);
401 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
402 +
403 +    electrostaticScale_.reserve(4);
404 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
405 +
406 +    vdwScale_[0] = 1.0;
407 +    vdwScale_[1] = fopts.getvdw12scale();
408 +    vdwScale_[2] = fopts.getvdw13scale();
409 +    vdwScale_[3] = fopts.getvdw14scale();
410 +    
411 +    electrostaticScale_[0] = 1.0;
412 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
413 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
414 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
415 +    
416 +    fDecomp_->distributeInitialData();
417 +
418 +    initialized_ = true;
419 +
420 +  }
421 +
422 +  void ForceManager::calcForces() {
423 +    
424 +    if (!initialized_) initialize();
425 +
426      preCalculation();  
427      shortRangeInteractions();
428      longRangeInteractions();
429 <    postCalculation();
88 <    
429 >    postCalculation();    
430    }
431    
432    void ForceManager::preCalculation() {
# Line 102 | 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 120 | Line 462 | namespace OpenMD {
462          }
463        }      
464      }
465 <  
465 >    
466      // Zero out the stress tensor
467      tau *= 0.0;
468      
# Line 174 | 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 245 | Line 588 | namespace OpenMD {
588    
589    void ForceManager::longRangeInteractions() {
590  
248 –    // some of this initial stuff will go away:
591      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
592      DataStorage* config = &(curSnapshot->atomData);
593      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;    
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      }
267 –    
268 –    //initialize data before passing to fortran
269 –    RealType longRangePotential[N_INTERACTION_FAMILIES];
270 –    RealType lrPot = 0.0;
271 –    int isError = 0;
615  
616 <    // 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 <
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;
625 <    pair<int, int> gtypes;
624 >    Vector3d fij, fg, f1;
625 >    tuple3<RealType, RealType, RealType> cuts;
626      RealType rCutSq;
627      bool in_switching_region;
628      RealType sw, dswdr, swderiv;
# Line 292 | Line 630 | namespace OpenMD {
630      InteractionData idat;
631      SelfData sdat;
632      RealType mf;
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  
319 –        gtypes = fDecomp_->getGroupTypes(cg1, cg2);
673          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
674 +
675          curSnapshot->wrapVector(d_grp);        
676          rgrpsq = d_grp.lengthSquare();
677 <        rCutSq = groupCutoffMap[gtypes].first;
677 >        rCutSq = cuts.second;
678  
679          if (rgrpsq < rCutSq) {
680 <          *(idat.rcut) = groupCutoffMap[gtypes].second;
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 = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
687 <                                                  rgrp);              
686 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
687 >                                                     rgrp);
688 >          
689            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
690            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
691  
# Line 341 | 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 <                idat = fDecomp_->fillInteractionData(atom1, atom2);
707 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
708 >                vdwMult = vdwScale_[topoDist];
709 >                electroMult = electrostaticScale_[topoDist];
710  
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                  }
357 –                
358 –                *(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 <                  vij += *(idat.vpair);
730 <                  fij += *(idat.f1);
731 <                  tau -= outProduct( *(idat.d), *(idat.f1));
729 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
730 >                  vij += vpair;
731 >                  fij += f1;
732 >                  tau -= outProduct( *(idat.d), f1);
733                  }
734                }
735              }
# Line 373 | Line 739 | namespace OpenMD {
739              if (in_switching_region) {
740                swderiv = vij * dswdr / rgrp;
741                fg = swderiv * d_grp;
376 –
742                fij += fg;
743  
744                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
# Line 388 | Line 753 | namespace OpenMD {
753                  // presence in switching region
754                  fg = swderiv * d_grp * mf;
755                  fDecomp_->addForceToAtomRow(atom1, fg);
391 –
756                  if (atomListRow.size() > 1) {
757                    if (info_->usesAtomicVirial()) {
758                      // find the distance between the atom
# Line 417 | 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 425 | 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        }
439 –
805      }
806      
807      fDecomp_->collectData();
443 –    
444 –    if ( info_->requiresSkipCorrection() ) {
445 –      
446 –      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
447 –
448 –        vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
808          
450 –        for (vector<int>::iterator jb = skipList.begin();
451 –             jb != skipList.end(); ++jb) {        
452 –    
453 –          atom2 = (*jb);
454 –          idat = fDecomp_->fillSkipData(atom1, atom2);
455 –          interactionMan_->doSkipCorrection(idat);
456 –
457 –        }
458 –      }
459 –    }
460 –    
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 <    // dangerous to iterate over enums, but we'll live on the edge:
819 <    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
820 <      lrPot += longRangePotential[i]; //Quick hack
821 <    }
822 <        
818 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
819 >      *(fDecomp_->getPairwisePotential());
820 >
821 >    lrPot = longRangePotential.sum();
822 >
823      //store the tau and long range potential    
824      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
825      curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];

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