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root/OpenMD/branches/development/src/brains/ForceManager.cpp
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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1489 by gezelter, Tue Aug 10 18:34:59 2010 UTC vs.
Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC

# Line 47 | Line 47
47   * @version 1.0
48   */
49  
50 +
51   #include "brains/ForceManager.hpp"
52   #include "primitives/Molecule.hpp"
52 – #include "UseTheForce/doForces_interface.h"
53   #define __OPENMD_C
54 – #include "UseTheForce/DarkSide/fInteractionMap.h"
54   #include "utils/simError.h"
55   #include "primitives/Bond.hpp"
56   #include "primitives/Bend.hpp"
57   #include "primitives/Torsion.hpp"
58   #include "primitives/Inversion.hpp"
59 + #include "nonbonded/NonBondedInteraction.hpp"
60 + #include "parallel/ForceMatrixDecomposition.hpp"
61  
62 + using namespace std;
63   namespace OpenMD {
64    
65 <  ForceManager::ForceManager(SimInfo * info) : info_(info),
66 <                                               NBforcesInitialized_(false) {
67 <    lj_ = LJ::Instance();
68 <    lj_->setForceField(info_->getForceField());
65 >  ForceManager::ForceManager(SimInfo * info) : info_(info) {
66 >    forceField_ = info_->getForceField();
67 >    fDecomp_ = new ForceMatrixDecomposition(info_);
68 >    interactionMan_ = new InteractionManager();
69 >  }
70  
71 <    gb_ = GB::Instance();
72 <    gb_->setForceField(info_->getForceField());
71 >  /**
72 >   * setupCutoffs
73 >   *
74 >   * Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
75 >   *
76 >   * cutoffRadius : realType
77 >   *  If the cutoffRadius was explicitly set, use that value.
78 >   *  If the cutoffRadius was not explicitly set:
79 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
80 >   *      No electrostatic atoms?  Poll the atom types present in the
81 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
82 >   *      Use the maximum suggested value that was found.
83 >   *
84 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
85 >   *      If cutoffMethod was explicitly set, use that choice.
86 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
87 >   *
88 >   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
89 >   *      If cutoffPolicy was explicitly set, use that choice.
90 >   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
91 >   */
92 >  void ForceManager::setupCutoffs() {
93 >    
94 >    Globals* simParams_ = info_->getSimParams();
95 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
96 >    
97 >    if (simParams_->haveCutoffRadius()) {
98 >      rCut_ = simParams_->getCutoffRadius();
99 >    } else {      
100 >      if (info_->usesElectrostaticAtoms()) {
101 >        sprintf(painCave.errMsg,
102 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
103 >                "\tOpenMD will use a default value of 12.0 angstroms"
104 >                "\tfor the cutoffRadius.\n");
105 >        painCave.isFatal = 0;
106 >        painCave.severity = OPENMD_INFO;
107 >        simError();
108 >        rCut_ = 12.0;
109 >      } else {
110 >        RealType thisCut;
111 >        set<AtomType*>::iterator i;
112 >        set<AtomType*> atomTypes;
113 >        atomTypes = info_->getSimulatedAtomTypes();        
114 >        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
115 >          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
116 >          rCut_ = max(thisCut, rCut_);
117 >        }
118 >        sprintf(painCave.errMsg,
119 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
120 >                "\tOpenMD will use %lf angstroms.\n",
121 >                rCut_);
122 >        painCave.isFatal = 0;
123 >        painCave.severity = OPENMD_INFO;
124 >        simError();
125 >      }            
126 >    }
127  
128 <    sticky_ = Sticky::Instance();
129 <    sticky_->setForceField(info_->getForceField());
128 >    map<string, CutoffMethod> stringToCutoffMethod;
129 >    stringToCutoffMethod["HARD"] = HARD;
130 >    stringToCutoffMethod["SWITCHED"] = SWITCHED;
131 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
132 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
133 >  
134 >    if (simParams_->haveCutoffMethod()) {
135 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
136 >      map<string, CutoffMethod>::iterator i;
137 >      i = stringToCutoffMethod.find(cutMeth);
138 >      if (i == stringToCutoffMethod.end()) {
139 >        sprintf(painCave.errMsg,
140 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
141 >                "\tShould be one of: "
142 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
143 >                cutMeth.c_str());
144 >        painCave.isFatal = 1;
145 >        painCave.severity = OPENMD_ERROR;
146 >        simError();
147 >      } else {
148 >        cutoffMethod_ = i->second;
149 >      }
150 >    } else {
151 >      sprintf(painCave.errMsg,
152 >              "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
153 >              "\tOpenMD will use SHIFTED_FORCE.\n");
154 >      painCave.isFatal = 0;
155 >      painCave.severity = OPENMD_INFO;
156 >      simError();
157 >      cutoffMethod_ = SHIFTED_FORCE;        
158 >    }
159  
160 <    eam_ = EAM::Instance();
161 <    eam_->setForceField(info_->getForceField());
160 >    map<string, CutoffPolicy> stringToCutoffPolicy;
161 >    stringToCutoffPolicy["MIX"] = MIX;
162 >    stringToCutoffPolicy["MAX"] = MAX;
163 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
164  
165 <    sc_ = SC::Instance();
166 <    sc_->setForceField(info_->getForceField());
167 <  }
168 <
169 <  void ForceManager::calcForces() {
82 <    
83 <    if (!info_->isFortranInitialized()) {
84 <      info_->update();
165 >    std::string cutPolicy;
166 >    if (forceFieldOptions_.haveCutoffPolicy()){
167 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
168 >    }else if (simParams_->haveCutoffPolicy()) {
169 >      cutPolicy = simParams_->getCutoffPolicy();
170      }
86 –    
87 –    preCalculation();
88 –    
89 –    calcShortRangeInteraction();
171  
172 <    calcLongRangeInteraction();
172 >    if (!cutPolicy.empty()){
173 >      toUpper(cutPolicy);
174 >      map<string, CutoffPolicy>::iterator i;
175 >      i = stringToCutoffPolicy.find(cutPolicy);
176  
177 <    postCalculation();
177 >      if (i == stringToCutoffPolicy.end()) {
178 >        sprintf(painCave.errMsg,
179 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
180 >                "\tShould be one of: "
181 >                "MIX, MAX, or TRADITIONAL\n",
182 >                cutPolicy.c_str());
183 >        painCave.isFatal = 1;
184 >        painCave.severity = OPENMD_ERROR;
185 >        simError();
186 >      } else {
187 >        cutoffPolicy_ = i->second;
188 >      }
189 >    } else {
190 >      sprintf(painCave.errMsg,
191 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
192 >              "\tOpenMD will use TRADITIONAL.\n");
193 >      painCave.isFatal = 0;
194 >      painCave.severity = OPENMD_INFO;
195 >      simError();
196 >      cutoffPolicy_ = TRADITIONAL;        
197 >    }
198 >  }
199 >
200 >  /**
201 >   * setupSwitching
202 >   *
203 >   * Sets the values of switchingRadius and
204 >   *  If the switchingRadius was explicitly set, use that value (but check it)
205 >   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
206 >   */
207 >  void ForceManager::setupSwitching() {
208 >    Globals* simParams_ = info_->getSimParams();
209 >
210 >    // create the switching function object:
211 >    switcher_ = new SwitchingFunction();
212      
213 +    if (simParams_->haveSwitchingRadius()) {
214 +      rSwitch_ = simParams_->getSwitchingRadius();
215 +      if (rSwitch_ > rCut_) {        
216 +        sprintf(painCave.errMsg,
217 +                "ForceManager::setupSwitching: switchingRadius (%f) is larger "
218 +                "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
219 +        painCave.isFatal = 1;
220 +        painCave.severity = OPENMD_ERROR;
221 +        simError();
222 +      }
223 +    } else {      
224 +      rSwitch_ = 0.85 * rCut_;
225 +      sprintf(painCave.errMsg,
226 +              "ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
227 +              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
228 +              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
229 +      painCave.isFatal = 0;
230 +      painCave.severity = OPENMD_WARNING;
231 +      simError();
232 +    }          
233 +    
234 +    // Default to cubic switching function.
235 +    sft_ = cubic;
236 +    if (simParams_->haveSwitchingFunctionType()) {
237 +      string funcType = simParams_->getSwitchingFunctionType();
238 +      toUpper(funcType);
239 +      if (funcType == "CUBIC") {
240 +        sft_ = cubic;
241 +      } else {
242 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
243 +          sft_ = fifth_order_poly;
244 +        } else {
245 +          // throw error        
246 +          sprintf( painCave.errMsg,
247 +                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
248 +                   "\tswitchingFunctionType must be one of: "
249 +                   "\"cubic\" or \"fifth_order_polynomial\".",
250 +                   funcType.c_str() );
251 +          painCave.isFatal = 1;
252 +          painCave.severity = OPENMD_ERROR;
253 +          simError();
254 +        }          
255 +      }
256 +    }
257 +    switcher_->setSwitchType(sft_);
258 +    switcher_->setSwitch(rSwitch_, rCut_);
259    }
260    
261 +  void ForceManager::initialize() {
262 +
263 +    if (!info_->isTopologyDone()) {
264 +      info_->update();
265 +      interactionMan_->setSimInfo(info_);
266 +      interactionMan_->initialize();
267 +
268 +      // We want to delay the cutoffs until after the interaction
269 +      // manager has set up the atom-atom interactions so that we can
270 +      // query them for suggested cutoff values
271 +
272 +      setupCutoffs();
273 +      setupSwitching();
274 +
275 +      info_->prepareTopology();      
276 +    }
277 +
278 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
279 +    
280 +    // Force fields can set options on how to scale van der Waals and electrostatic
281 +    // interactions for atoms connected via bonds, bends and torsions
282 +    // in this case the topological distance between atoms is:
283 +    // 0 = topologically unconnected
284 +    // 1 = bonded together
285 +    // 2 = connected via a bend
286 +    // 3 = connected via a torsion
287 +    
288 +    vdwScale_.reserve(4);
289 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
290 +
291 +    electrostaticScale_.reserve(4);
292 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
293 +
294 +    vdwScale_[0] = 1.0;
295 +    vdwScale_[1] = fopts.getvdw12scale();
296 +    vdwScale_[2] = fopts.getvdw13scale();
297 +    vdwScale_[3] = fopts.getvdw14scale();
298 +    
299 +    electrostaticScale_[0] = 1.0;
300 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
301 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
302 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
303 +    
304 +    fDecomp_->distributeInitialData();
305 +
306 +    initialized_ = true;
307 +
308 +  }
309 +
310 +  void ForceManager::calcForces() {
311 +    
312 +    if (!initialized_) initialize();
313 +
314 +    preCalculation();  
315 +    shortRangeInteractions();
316 +    longRangeInteractions();
317 +    postCalculation();    
318 +  }
319 +  
320    void ForceManager::preCalculation() {
321      SimInfo::MoleculeIterator mi;
322      Molecule* mol;
# Line 101 | Line 324 | namespace OpenMD {
324      Atom* atom;
325      Molecule::RigidBodyIterator rbIter;
326      RigidBody* rb;
327 +    Molecule::CutoffGroupIterator ci;
328 +    CutoffGroup* cg;
329      
330      // forces are zeroed here, before any are accumulated.
106 –    // NOTE: do not rezero the forces in Fortran.
331      
332      for (mol = info_->beginMolecule(mi); mol != NULL;
333           mol = info_->nextMolecule(mi)) {
# Line 116 | Line 340 | namespace OpenMD {
340             rb = mol->nextRigidBody(rbIter)) {
341          rb->zeroForcesAndTorques();
342        }        
343 <          
343 >
344 >      if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
345 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
346 >            cg = mol->nextCutoffGroup(ci)) {
347 >          //calculate the center of mass of cutoff group
348 >          cg->updateCOM();
349 >        }
350 >      }      
351      }
352 <    
352 >  
353      // Zero out the stress tensor
354      tau *= 0.0;
355      
356    }
357    
358 <  void ForceManager::calcShortRangeInteraction() {
358 >  void ForceManager::shortRangeInteractions() {
359      Molecule* mol;
360      RigidBody* rb;
361      Bond* bond;
# Line 166 | Line 397 | namespace OpenMD {
397          RealType currBendPot = bend->getPotential();          
398          
399          bendPotential += bend->getPotential();
400 <        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
400 >        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
401          if (i == bendDataSets.end()) {
402            BendDataSet dataSet;
403            dataSet.prev.angle = dataSet.curr.angle = angle;
404            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
405            dataSet.deltaV = 0.0;
406 <          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
406 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
407          }else {
408            i->second.prev.angle = i->second.curr.angle;
409            i->second.prev.potential = i->second.curr.potential;
# Line 189 | Line 420 | namespace OpenMD {
420          torsion->calcForce(angle);
421          RealType currTorsionPot = torsion->getPotential();
422          torsionPotential += torsion->getPotential();
423 <        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
423 >        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
424          if (i == torsionDataSets.end()) {
425            TorsionDataSet dataSet;
426            dataSet.prev.angle = dataSet.curr.angle = angle;
427            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
428            dataSet.deltaV = 0.0;
429 <          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
429 >          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
430          }else {
431            i->second.prev.angle = i->second.curr.angle;
432            i->second.prev.potential = i->second.curr.potential;
# Line 205 | Line 436 | namespace OpenMD {
436                                     i->second.prev.potential);
437          }      
438        }      
439 <
439 >      
440        for (inversion = mol->beginInversion(inversionIter);
441             inversion != NULL;
442             inversion = mol->nextInversion(inversionIter)) {
# Line 213 | Line 444 | namespace OpenMD {
444          inversion->calcForce(angle);
445          RealType currInversionPot = inversion->getPotential();
446          inversionPotential += inversion->getPotential();
447 <        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
447 >        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
448          if (i == inversionDataSets.end()) {
449            InversionDataSet dataSet;
450            dataSet.prev.angle = dataSet.curr.angle = angle;
451            dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
452            dataSet.deltaV = 0.0;
453 <          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
453 >          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
454          }else {
455            i->second.prev.angle = i->second.curr.angle;
456            i->second.prev.potential = i->second.curr.potential;
# Line 238 | Line 469 | namespace OpenMD {
469      curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
470      curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
471      curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
472 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
242 <    
472 >    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
473    }
474    
475 <  void ForceManager::calcLongRangeInteraction() {
246 <    Snapshot* curSnapshot;
247 <    DataStorage* config;
248 <    RealType* frc;
249 <    RealType* pos;
250 <    RealType* trq;
251 <    RealType* A;
252 <    RealType* electroFrame;
253 <    RealType* rc;
254 <    RealType* particlePot;
255 <    
256 <    //get current snapshot from SimInfo
257 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
258 <    
259 <    //get array pointers
260 <    config = &(curSnapshot->atomData);
261 <    frc = config->getArrayPointer(DataStorage::dslForce);
262 <    pos = config->getArrayPointer(DataStorage::dslPosition);
263 <    trq = config->getArrayPointer(DataStorage::dslTorque);
264 <    A   = config->getArrayPointer(DataStorage::dslAmat);
265 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
266 <    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
475 >  void ForceManager::longRangeInteractions() {
476  
477 <    //calculate the center of mass of cutoff group
478 <    SimInfo::MoleculeIterator mi;
479 <    Molecule* mol;
480 <    Molecule::CutoffGroupIterator ci;
481 <    CutoffGroup* cg;
482 <    Vector3d com;
483 <    std::vector<Vector3d> rcGroup;
484 <    
485 <    if(info_->getNCutoffGroups() > 0){
486 <      
487 <      for (mol = info_->beginMolecule(mi); mol != NULL;
488 <           mol = info_->nextMolecule(mi)) {
489 <        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
490 <            cg = mol->nextCutoffGroup(ci)) {
282 <          cg->getCOM(com);
283 <          rcGroup.push_back(com);
284 <        }
285 <      }// end for (mol)
286 <      
287 <      rc = rcGroup[0].getArrayPointer();
477 >    // some of this initial stuff will go away:
478 >    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
479 >    DataStorage* config = &(curSnapshot->atomData);
480 >    DataStorage* cgConfig = &(curSnapshot->cgData);
481 >    RealType* frc = config->getArrayPointer(DataStorage::dslForce);
482 >    RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
483 >    RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
484 >    RealType* A = config->getArrayPointer(DataStorage::dslAmat);
485 >    RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
486 >    RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
487 >    RealType* rc;    
488 >
489 >    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
490 >      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
491      } else {
492        // center of mass of the group is the same as position of the atom  
493        // if cutoff group does not exist
494        rc = pos;
495      }
496      
497 <    //initialize data before passing to fortran
498 <    RealType longRangePotential[LR_POT_TYPES];
499 <    RealType lrPot = 0.0;
500 <    Vector3d totalDipole;
501 <    int isError = 0;
497 >    // new stuff starts here:
498 >    fDecomp_->zeroWorkArrays();
499 >    fDecomp_->distributeData();
500 >
501 >    int cg1, cg2, atom1, atom2;
502 >    Vector3d d_grp, dag;
503 >    RealType rgrpsq, rgrp;
504 >    RealType vij;
505 >    Vector3d fij, fg;
506 >    tuple3<RealType, RealType, RealType> cuts;
507 >    RealType rCutSq;
508 >    bool in_switching_region;
509 >    RealType sw, dswdr, swderiv;
510 >    vector<int> atomListColumn, atomListRow, atomListLocal;
511 >    InteractionData idat;
512 >    SelfData sdat;
513 >    RealType mf;
514 >    potVec pot(0.0);
515 >    potVec longRangePotential(0.0);
516 >    RealType lrPot;
517  
518 <    for (int i=0; i<LR_POT_TYPES;i++){
519 <      longRangePotential[i]=0.0; //Initialize array
518 >    int loopStart, loopEnd;
519 >
520 >    loopEnd = PAIR_LOOP;
521 >    if (info_->requiresPrepair() ) {
522 >      loopStart = PREPAIR_LOOP;
523 >    } else {
524 >      loopStart = PAIR_LOOP;
525      }
526 <    
527 <    doForceLoop(pos,
528 <                rc,
529 <                A,
530 <                electroFrame,
531 <                frc,
532 <                trq,
533 <                tau.getArrayPointer(),
534 <                longRangePotential,
535 <                particlePot,
536 <                &isError );
537 <    
538 <    if( isError ){
539 <      sprintf( painCave.errMsg,
540 <               "Error returned from the fortran force calculation.\n" );
541 <      painCave.isFatal = 1;
542 <      simError();
526 >
527 >    for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
528 >      
529 >      if (iLoop == loopStart) {
530 >        bool update_nlist = fDecomp_->checkNeighborList();
531 >        if (update_nlist)
532 >          neighborList = fDecomp_->buildNeighborList();
533 >      }
534 >
535 >      for (vector<pair<int, int> >::iterator it = neighborList.begin();
536 >             it != neighborList.end(); ++it) {
537 >        
538 >        cg1 = (*it).first;
539 >        cg2 = (*it).second;
540 >        
541 >        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
542 >
543 >        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
544 >        curSnapshot->wrapVector(d_grp);        
545 >        rgrpsq = d_grp.lengthSquare();
546 >
547 >        rCutSq = cuts.second;
548 >
549 >        if (rgrpsq < rCutSq) {
550 >          *(idat.rcut) = cuts.first;
551 >          if (iLoop == PAIR_LOOP) {
552 >            vij *= 0.0;
553 >            fij = V3Zero;
554 >          }
555 >          
556 >          in_switching_region = switcher_->getSwitch(rgrpsq, *(idat.sw), dswdr,
557 >                                                     rgrp);
558 >              
559 >          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
560 >          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
561 >
562 >          for (vector<int>::iterator ia = atomListRow.begin();
563 >               ia != atomListRow.end(); ++ia) {            
564 >            atom1 = (*ia);
565 >            
566 >            for (vector<int>::iterator jb = atomListColumn.begin();
567 >                 jb != atomListColumn.end(); ++jb) {              
568 >              atom2 = (*jb);
569 >              
570 >              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
571 >                
572 >                pot *= 0.0;
573 >
574 >                idat = fDecomp_->fillInteractionData(atom1, atom2);
575 >                *(idat.pot) = pot;
576 >
577 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
578 >                  *(idat.d) = d_grp;
579 >                  *(idat.r2) = rgrpsq;
580 >                } else {
581 >                  *(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
582 >                  curSnapshot->wrapVector( *(idat.d) );
583 >                  *(idat.r2) = idat.d->lengthSquare();
584 >                }
585 >                
586 >                *(idat.rij) = sqrt( *(idat.r2) );
587 >              
588 >                if (iLoop == PREPAIR_LOOP) {
589 >                  interactionMan_->doPrePair(idat);
590 >                } else {
591 >                  interactionMan_->doPair(idat);
592 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
593 >                  vij += *(idat.vpair);
594 >                  fij += *(idat.f1);
595 >                  tau -= outProduct( *(idat.d), *(idat.f1));
596 >                }
597 >              }
598 >            }
599 >          }
600 >
601 >          if (iLoop == PAIR_LOOP) {
602 >            if (in_switching_region) {
603 >              swderiv = vij * dswdr / rgrp;
604 >              fg = swderiv * d_grp;
605 >
606 >              fij += fg;
607 >
608 >              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
609 >                tau -= outProduct( *(idat.d), fg);
610 >              }
611 >          
612 >              for (vector<int>::iterator ia = atomListRow.begin();
613 >                   ia != atomListRow.end(); ++ia) {            
614 >                atom1 = (*ia);                
615 >                mf = fDecomp_->getMassFactorRow(atom1);
616 >                // fg is the force on atom ia due to cutoff group's
617 >                // presence in switching region
618 >                fg = swderiv * d_grp * mf;
619 >                fDecomp_->addForceToAtomRow(atom1, fg);
620 >
621 >                if (atomListRow.size() > 1) {
622 >                  if (info_->usesAtomicVirial()) {
623 >                    // find the distance between the atom
624 >                    // and the center of the cutoff group:
625 >                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
626 >                    tau -= outProduct(dag, fg);
627 >                  }
628 >                }
629 >              }
630 >              for (vector<int>::iterator jb = atomListColumn.begin();
631 >                   jb != atomListColumn.end(); ++jb) {              
632 >                atom2 = (*jb);
633 >                mf = fDecomp_->getMassFactorColumn(atom2);
634 >                // fg is the force on atom jb due to cutoff group's
635 >                // presence in switching region
636 >                fg = -swderiv * d_grp * mf;
637 >                fDecomp_->addForceToAtomColumn(atom2, fg);
638 >
639 >                if (atomListColumn.size() > 1) {
640 >                  if (info_->usesAtomicVirial()) {
641 >                    // find the distance between the atom
642 >                    // and the center of the cutoff group:
643 >                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
644 >                    tau -= outProduct(dag, fg);
645 >                  }
646 >                }
647 >              }
648 >            }
649 >            //if (!SIM_uses_AtomicVirial) {
650 >            //  tau -= outProduct(d_grp, fij);
651 >            //}
652 >          }
653 >        }
654 >      }
655 >
656 >      if (iLoop == PREPAIR_LOOP) {
657 >        if (info_->requiresPrepair()) {            
658 >          fDecomp_->collectIntermediateData();
659 >
660 >          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
661 >            sdat = fDecomp_->fillSelfData(atom1);
662 >            interactionMan_->doPreForce(sdat);
663 >          }
664 >
665 >          fDecomp_->distributeIntermediateData();        
666 >        }
667 >      }
668 >
669      }
321 –    for (int i=0; i<LR_POT_TYPES;i++){
322 –      lrPot += longRangePotential[i]; //Quick hack
323 –    }
670      
671 <    // grab the simulation box dipole moment if specified
672 <    if (info_->getCalcBoxDipole()){
673 <      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
671 >    fDecomp_->collectData();
672 >    
673 >    if ( info_->requiresSkipCorrection() ) {
674        
675 <      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
676 <      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
677 <      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
675 >      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
676 >
677 >        vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
678 >        
679 >        for (vector<int>::iterator jb = skipList.begin();
680 >             jb != skipList.end(); ++jb) {        
681 >    
682 >          atom2 = (*jb);
683 >          idat = fDecomp_->fillSkipData(atom1, atom2);
684 >          interactionMan_->doSkipCorrection(idat);
685 >
686 >        }
687 >      }
688      }
689      
690 +    if (info_->requiresSelfCorrection()) {
691 +
692 +      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
693 +        sdat = fDecomp_->fillSelfData(atom1);
694 +        interactionMan_->doSelfCorrection(sdat);
695 +      }
696 +
697 +    }
698 +
699 +    longRangePotential = fDecomp_->getLongRangePotential();
700 +    lrPot = longRangePotential.sum();
701 +
702      //store the tau and long range potential    
703      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
704 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
705 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
704 >    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
705 >    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
706    }
707  
708    

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