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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 1618 by gezelter, Mon Sep 12 17:09:26 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 (mdFileVersion > 1) {
321 >        // throw an error if we define a switching radius and don't need one.
322 >        // older file versions should not do this.
323 >        if (simParams_->haveSwitchingRadius()) {
324 >          map<string, CutoffMethod>::const_iterator it;
325 >          string theMeth;
326 >          for (it = stringToCutoffMethod.begin();
327 >               it != stringToCutoffMethod.end(); ++it) {
328 >            if (it->second == cutoffMethod_) {
329 >              theMeth = it->first;
330 >              break;
331 >            }
332 >          }
333 >          sprintf(painCave.errMsg,
334 >                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
335 >                  "\tis not set to SWITCHED, so switchingRadius value\n"
336 >                  "\twill be ignored for this simulation\n", theMeth.c_str());
337 >          painCave.isFatal = 0;
338 >          painCave.severity = OPENMD_WARNING;
339 >          simError();
340 >        }
341 >      }
342 >      rSwitch_ = rCut_;
343 >    }
344      
345 +    // Default to cubic switching function.
346 +    sft_ = cubic;
347 +    if (simParams_->haveSwitchingFunctionType()) {
348 +      string funcType = simParams_->getSwitchingFunctionType();
349 +      toUpper(funcType);
350 +      if (funcType == "CUBIC") {
351 +        sft_ = cubic;
352 +      } else {
353 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
354 +          sft_ = fifth_order_poly;
355 +        } else {
356 +          // throw error        
357 +          sprintf( painCave.errMsg,
358 +                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
359 +                   "\tswitchingFunctionType must be one of: "
360 +                   "\"cubic\" or \"fifth_order_polynomial\".",
361 +                   funcType.c_str() );
362 +          painCave.isFatal = 1;
363 +          painCave.severity = OPENMD_ERROR;
364 +          simError();
365 +        }          
366 +      }
367 +    }
368 +    switcher_->setSwitchType(sft_);
369 +    switcher_->setSwitch(rSwitch_, rCut_);
370 +    interactionMan_->setSwitchingRadius(rSwitch_);
371 +  }
372 +
373 +
374 +
375 +  
376 +  void ForceManager::initialize() {
377 +
378      if (!info_->isTopologyDone()) {
379 +
380        info_->update();
381        interactionMan_->setSimInfo(info_);
382        interactionMan_->initialize();
383 <      swfun_ = interactionMan_->getSwitchingFunction();
384 <      fDecomp_->distributeInitialData();
385 <      info_->prepareTopology();
383 >
384 >      // We want to delay the cutoffs until after the interaction
385 >      // manager has set up the atom-atom interactions so that we can
386 >      // query them for suggested cutoff values
387 >      setupCutoffs();
388 >
389 >      info_->prepareTopology();      
390      }
391 +
392 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
393      
394 +    // Force fields can set options on how to scale van der Waals and
395 +    // electrostatic interactions for atoms connected via bonds, bends
396 +    // and torsions in this case the topological distance between
397 +    // atoms is:
398 +    // 0 = topologically unconnected
399 +    // 1 = bonded together
400 +    // 2 = connected via a bend
401 +    // 3 = connected via a torsion
402 +    
403 +    vdwScale_.reserve(4);
404 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
405 +
406 +    electrostaticScale_.reserve(4);
407 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
408 +
409 +    vdwScale_[0] = 1.0;
410 +    vdwScale_[1] = fopts.getvdw12scale();
411 +    vdwScale_[2] = fopts.getvdw13scale();
412 +    vdwScale_[3] = fopts.getvdw14scale();
413 +    
414 +    electrostaticScale_[0] = 1.0;
415 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
416 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
417 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
418 +    
419 +    fDecomp_->distributeInitialData();
420 +
421 +    initialized_ = true;
422 +
423 +  }
424 +
425 +  void ForceManager::calcForces() {
426 +    
427 +    if (!initialized_) initialize();
428 +
429      preCalculation();  
430      shortRangeInteractions();
431      longRangeInteractions();
432 <    postCalculation();
88 <    
432 >    postCalculation();    
433    }
434    
435    void ForceManager::preCalculation() {
# Line 102 | Line 446 | namespace OpenMD {
446      
447      for (mol = info_->beginMolecule(mi); mol != NULL;
448           mol = info_->nextMolecule(mi)) {
449 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
449 >      for(atom = mol->beginAtom(ai); atom != NULL;
450 >          atom = mol->nextAtom(ai)) {
451          atom->zeroForcesAndTorques();
452        }
453 <          
453 >      
454        //change the positions of atoms which belong to the rigidbodies
455        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
456             rb = mol->nextRigidBody(rbIter)) {
457          rb->zeroForcesAndTorques();
458        }        
459 <
459 >      
460        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
461          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
462              cg = mol->nextCutoffGroup(ci)) {
# Line 120 | Line 465 | namespace OpenMD {
465          }
466        }      
467      }
468 <  
468 >    
469      // Zero out the stress tensor
470      tau *= 0.0;
471      
# Line 174 | Line 519 | namespace OpenMD {
519            dataSet.prev.angle = dataSet.curr.angle = angle;
520            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
521            dataSet.deltaV = 0.0;
522 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
522 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
523 >                                                                  dataSet));
524          }else {
525            i->second.prev.angle = i->second.curr.angle;
526            i->second.prev.potential = i->second.curr.potential;
# Line 245 | Line 591 | namespace OpenMD {
591    
592    void ForceManager::longRangeInteractions() {
593  
248 –    // some of this initial stuff will go away:
594      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
595      DataStorage* config = &(curSnapshot->atomData);
596      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;    
597  
598 <    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
599 <      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
598 >    //calculate the center of mass of cutoff group
599 >
600 >    SimInfo::MoleculeIterator mi;
601 >    Molecule* mol;
602 >    Molecule::CutoffGroupIterator ci;
603 >    CutoffGroup* cg;
604 >
605 >    if(info_->getNCutoffGroups() > 0){      
606 >      for (mol = info_->beginMolecule(mi); mol != NULL;
607 >           mol = info_->nextMolecule(mi)) {
608 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
609 >            cg = mol->nextCutoffGroup(ci)) {
610 >          cg->updateCOM();
611 >        }
612 >      }      
613      } else {
614        // center of mass of the group is the same as position of the atom  
615        // if cutoff group does not exist
616 <      rc = pos;
616 >      cgConfig->position = config->position;
617      }
267 –    
268 –    //initialize data before passing to fortran
269 –    RealType longRangePotential[N_INTERACTION_FAMILIES];
270 –    RealType lrPot = 0.0;
271 –    int isError = 0;
618  
619 <    // 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 <
619 >    fDecomp_->zeroWorkArrays();
620      fDecomp_->distributeData();
621 <
622 <    int cg1, cg2, atom1, atom2;
623 <    Vector3d d_grp, dag;
624 <    RealType rgrpsq, rgrp;
621 >    
622 >    int cg1, cg2, atom1, atom2, topoDist;
623 >    Vector3d d_grp, dag, d;
624 >    RealType rgrpsq, rgrp, r2, r;
625 >    RealType electroMult, vdwMult;
626      RealType vij;
627 <    Vector3d fij, fg;
628 <    pair<int, int> gtypes;
627 >    Vector3d fij, fg, f1;
628 >    tuple3<RealType, RealType, RealType> cuts;
629      RealType rCutSq;
630      bool in_switching_region;
631      RealType sw, dswdr, swderiv;
# Line 292 | Line 633 | namespace OpenMD {
633      InteractionData idat;
634      SelfData sdat;
635      RealType mf;
636 +    RealType lrPot;
637 +    RealType vpair;
638 +    potVec longRangePotential(0.0);
639 +    potVec workPot(0.0);
640  
641      int loopStart, loopEnd;
642  
643 +    idat.vdwMult = &vdwMult;
644 +    idat.electroMult = &electroMult;
645 +    idat.pot = &workPot;
646 +    sdat.pot = fDecomp_->getEmbeddingPotential();
647 +    idat.vpair = &vpair;
648 +    idat.f1 = &f1;
649 +    idat.sw = &sw;
650 +    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
651 +    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
652 +    
653      loopEnd = PAIR_LOOP;
654      if (info_->requiresPrepair() ) {
655        loopStart = PREPAIR_LOOP;
656      } else {
657        loopStart = PAIR_LOOP;
658      }
659 <
660 <    for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
661 <      
659 >  
660 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
661 >    
662        if (iLoop == loopStart) {
663          bool update_nlist = fDecomp_->checkNeighborList();
664          if (update_nlist)
665            neighborList = fDecomp_->buildNeighborList();
666 <      }
666 >      }            
667  
668        for (vector<pair<int, int> >::iterator it = neighborList.begin();
669               it != neighborList.end(); ++it) {
670 <        
670 >                
671          cg1 = (*it).first;
672          cg2 = (*it).second;
673 +        
674 +        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
675  
319 –        gtypes = fDecomp_->getGroupTypes(cg1, cg2);
676          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
677 +
678          curSnapshot->wrapVector(d_grp);        
679          rgrpsq = d_grp.lengthSquare();
680 <        rCutSq = groupCutoffMap[gtypes].first;
680 >        rCutSq = cuts.second;
681  
682          if (rgrpsq < rCutSq) {
683 <          *(idat.rcut) = groupCutoffMap[gtypes].second;
683 >          idat.rcut = &cuts.first;
684            if (iLoop == PAIR_LOOP) {
685 <            vij *= 0.0;
685 >            vij = 0.0;
686              fij = V3Zero;
687            }
688            
689 <          in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
690 <                                                  rgrp);              
689 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
690 >                                                     rgrp);
691 >          
692            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
693            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
694  
# Line 341 | Line 699 | namespace OpenMD {
699              for (vector<int>::iterator jb = atomListColumn.begin();
700                   jb != atomListColumn.end(); ++jb) {              
701                atom2 = (*jb);
702 <              
702 >
703                if (!fDecomp_->skipAtomPair(atom1, atom2)) {
704 +                vpair = 0.0;
705 +                workPot = 0.0;
706 +                f1 = V3Zero;
707 +
708 +                fDecomp_->fillInteractionData(idat, atom1, atom2);
709                  
710 <                idat = fDecomp_->fillInteractionData(atom1, atom2);
710 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
711 >                vdwMult = vdwScale_[topoDist];
712 >                electroMult = electrostaticScale_[topoDist];
713  
714                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
715 <                  *(idat.d) = d_grp;
716 <                  *(idat.r2) = rgrpsq;
715 >                  idat.d = &d_grp;
716 >                  idat.r2 = &rgrpsq;
717                  } else {
718 <                  *(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
719 <                  curSnapshot->wrapVector( *(idat.d) );
720 <                  *(idat.r2) = idat.d->lengthSquare();
718 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
719 >                  curSnapshot->wrapVector( d );
720 >                  r2 = d.lengthSquare();
721 >                  idat.d = &d;
722 >                  idat.r2 = &r2;
723                  }
357 –                
358 –                *(idat.rij) = sqrt( *(idat.r2) );
724                
725 +                r = sqrt( *(idat.r2) );
726 +                idat.rij = &r;
727 +              
728                  if (iLoop == PREPAIR_LOOP) {
729                    interactionMan_->doPrePair(idat);
730                  } else {
731                    interactionMan_->doPair(idat);
732 <                  vij += *(idat.vpair);
733 <                  fij += *(idat.f1);
734 <                  tau -= outProduct( *(idat.d), *(idat.f1));
732 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
733 >                  vij += vpair;
734 >                  fij += f1;
735 >                  tau -= outProduct( *(idat.d), f1);
736                  }
737                }
738              }
# Line 373 | Line 742 | namespace OpenMD {
742              if (in_switching_region) {
743                swderiv = vij * dswdr / rgrp;
744                fg = swderiv * d_grp;
376 –
745                fij += fg;
746  
747                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
# Line 388 | Line 756 | namespace OpenMD {
756                  // presence in switching region
757                  fg = swderiv * d_grp * mf;
758                  fDecomp_->addForceToAtomRow(atom1, fg);
391 –
759                  if (atomListRow.size() > 1) {
760                    if (info_->usesAtomicVirial()) {
761                      // find the distance between the atom
# Line 417 | Line 784 | namespace OpenMD {
784                  }
785                }
786              }
787 <            //if (!SIM_uses_AtomicVirial) {
787 >            //if (!info_->usesAtomicVirial()) {
788              //  tau -= outProduct(d_grp, fij);
789              //}
790            }
# Line 425 | Line 792 | namespace OpenMD {
792        }
793  
794        if (iLoop == PREPAIR_LOOP) {
795 <        if (info_->requiresPrepair()) {            
795 >        if (info_->requiresPrepair()) {
796 >
797            fDecomp_->collectIntermediateData();
798 <          atomListLocal = fDecomp_->getAtomList();
799 <          for (vector<int>::iterator ia = atomListLocal.begin();
800 <               ia != atomListLocal.end(); ++ia) {              
433 <            atom1 = (*ia);            
434 <            sdat = fDecomp_->fillSelfData(atom1);
798 >
799 >          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
800 >            fDecomp_->fillSelfData(sdat, atom1);
801              interactionMan_->doPreForce(sdat);
802            }
803 <          fDecomp_->distributeIntermediateData();        
803 >
804 >          fDecomp_->distributeIntermediateData();
805 >
806          }
807        }
440 –
808      }
809      
810      fDecomp_->collectData();
811 <    
812 <    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);    
811 >        
812 >    if (info_->requiresSelfCorrection()) {
813  
814 <        if (info_->requiresSkipCorrection()) {
815 <          vector<int> skipList = fDecomp_->getSkipsForAtom(atom1);
816 <          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 <        }
814 >      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
815 >        fDecomp_->fillSelfData(sdat, atom1);
816 >        interactionMan_->doSelfCorrection(sdat);
817        }
466 –    }
818  
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
819      }
820 <        
820 >
821 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
822 >      *(fDecomp_->getPairwisePotential());
823 >
824 >    lrPot = longRangePotential.sum();
825 >
826      //store the tau and long range potential    
827      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
828      curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];

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