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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 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC vs.
Revision 1583 by gezelter, Thu Jun 16 22:00:08 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 "parallel/ForceDecomposition.hpp"
60 < //#include "parallel/SerialDecomposition.hpp"
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 <                                               NBforcesInitialized_(false) {
71 < #ifdef IS_MPI
72 <    decomp_ = new ForceDecomposition(info_);
69 < #else
70 <    //  decomp_ = new SerialDecomposition(info);
71 < #endif
69 >  ForceManager::ForceManager(SimInfo * info) : info_(info) {
70 >    forceField_ = info_->getForceField();
71 >    interactionMan_ = new InteractionManager();
72 >    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
73    }
74 <
75 <  void ForceManager::calcForces() {
74 >
75 >  /**
76 >   * setupCutoffs
77 >   *
78 >   * Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
79 >   *
80 >   * cutoffRadius : realType
81 >   *  If the cutoffRadius was explicitly set, use that value.
82 >   *  If the cutoffRadius was not explicitly set:
83 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
84 >   *      No electrostatic atoms?  Poll the atom types present in the
85 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
86 >   *      Use the maximum suggested value that was found.
87 >   *
88 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
89 >   *      If cutoffMethod was explicitly set, use that choice.
90 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
91 >   *
92 >   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
93 >   *      If cutoffPolicy was explicitly set, use that choice.
94 >   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
95 >   */
96 >  void ForceManager::setupCutoffs() {
97      
98 +    Globals* simParams_ = info_->getSimParams();
99 +    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
100 +    
101 +    if (simParams_->haveCutoffRadius()) {
102 +      rCut_ = simParams_->getCutoffRadius();
103 +    } else {      
104 +      if (info_->usesElectrostaticAtoms()) {
105 +        sprintf(painCave.errMsg,
106 +                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
107 +                "\tOpenMD will use a default value of 12.0 angstroms"
108 +                "\tfor the cutoffRadius.\n");
109 +        painCave.isFatal = 0;
110 +        painCave.severity = OPENMD_INFO;
111 +        simError();
112 +        rCut_ = 12.0;
113 +      } else {
114 +        RealType thisCut;
115 +        set<AtomType*>::iterator i;
116 +        set<AtomType*> atomTypes;
117 +        atomTypes = info_->getSimulatedAtomTypes();        
118 +        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
119 +          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
120 +          rCut_ = max(thisCut, rCut_);
121 +        }
122 +        sprintf(painCave.errMsg,
123 +                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
124 +                "\tOpenMD will use %lf angstroms.\n",
125 +                rCut_);
126 +        painCave.isFatal = 0;
127 +        painCave.severity = OPENMD_INFO;
128 +        simError();
129 +      }
130 +    }
131  
132 <    if (!info_->isFortranInitialized()) {
133 <      info_->update();
134 <      nbiMan_->setSimInfo(info_);
135 <      nbiMan_->initialize();
136 <      decomp_->distributeInitialData();
137 <      info_->setupFortran();
132 >    fDecomp_->setUserCutoff(rCut_);
133 >
134 >    map<string, CutoffMethod> stringToCutoffMethod;
135 >    stringToCutoffMethod["HARD"] = HARD;
136 >    stringToCutoffMethod["SWITCHED"] = SWITCHED;
137 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
138 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
139 >  
140 >    if (simParams_->haveCutoffMethod()) {
141 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
142 >      map<string, CutoffMethod>::iterator i;
143 >      i = stringToCutoffMethod.find(cutMeth);
144 >      if (i == stringToCutoffMethod.end()) {
145 >        sprintf(painCave.errMsg,
146 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
147 >                "\tShould be one of: "
148 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
149 >                cutMeth.c_str());
150 >        painCave.isFatal = 1;
151 >        painCave.severity = OPENMD_ERROR;
152 >        simError();
153 >      } else {
154 >        cutoffMethod_ = i->second;
155 >      }
156 >    } else {
157 >      sprintf(painCave.errMsg,
158 >              "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
159 >              "\tOpenMD will use SHIFTED_FORCE.\n");
160 >      painCave.isFatal = 0;
161 >      painCave.severity = OPENMD_INFO;
162 >      simError();
163 >      cutoffMethod_ = SHIFTED_FORCE;        
164      }
165 +
166 +    map<string, CutoffPolicy> stringToCutoffPolicy;
167 +    stringToCutoffPolicy["MIX"] = MIX;
168 +    stringToCutoffPolicy["MAX"] = MAX;
169 +    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
170 +
171 +    std::string cutPolicy;
172 +    if (forceFieldOptions_.haveCutoffPolicy()){
173 +      cutPolicy = forceFieldOptions_.getCutoffPolicy();
174 +    }else if (simParams_->haveCutoffPolicy()) {
175 +      cutPolicy = simParams_->getCutoffPolicy();
176 +    }
177 +
178 +    if (!cutPolicy.empty()){
179 +      toUpper(cutPolicy);
180 +      map<string, CutoffPolicy>::iterator i;
181 +      i = stringToCutoffPolicy.find(cutPolicy);
182 +
183 +      if (i == stringToCutoffPolicy.end()) {
184 +        sprintf(painCave.errMsg,
185 +                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
186 +                "\tShould be one of: "
187 +                "MIX, MAX, or TRADITIONAL\n",
188 +                cutPolicy.c_str());
189 +        painCave.isFatal = 1;
190 +        painCave.severity = OPENMD_ERROR;
191 +        simError();
192 +      } else {
193 +        cutoffPolicy_ = i->second;
194 +      }
195 +    } else {
196 +      sprintf(painCave.errMsg,
197 +              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
198 +              "\tOpenMD will use TRADITIONAL.\n");
199 +      painCave.isFatal = 0;
200 +      painCave.severity = OPENMD_INFO;
201 +      simError();
202 +      cutoffPolicy_ = TRADITIONAL;        
203 +    }
204 +    fDecomp_->setCutoffPolicy(cutoffPolicy_);
205 +  }
206 +
207 +  /**
208 +   * setupSwitching
209 +   *
210 +   * Sets the values of switchingRadius and
211 +   *  If the switchingRadius was explicitly set, use that value (but check it)
212 +   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
213 +   */
214 +  void ForceManager::setupSwitching() {
215 +    Globals* simParams_ = info_->getSimParams();
216 +
217 +    // create the switching function object:
218 +    switcher_ = new SwitchingFunction();
219      
220 <    preCalculation();  
221 <    calcShortRangeInteraction();
222 <    calcLongRangeInteraction();
223 <    postCalculation();
220 >    if (simParams_->haveSwitchingRadius()) {
221 >      rSwitch_ = simParams_->getSwitchingRadius();
222 >      if (rSwitch_ > rCut_) {        
223 >        sprintf(painCave.errMsg,
224 >                "ForceManager::setupSwitching: switchingRadius (%f) is larger "
225 >                "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
226 >        painCave.isFatal = 1;
227 >        painCave.severity = OPENMD_ERROR;
228 >        simError();
229 >      }
230 >    } else {      
231 >      rSwitch_ = 0.85 * rCut_;
232 >      sprintf(painCave.errMsg,
233 >              "ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
234 >              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
235 >              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
236 >      painCave.isFatal = 0;
237 >      painCave.severity = OPENMD_WARNING;
238 >      simError();
239 >    }          
240      
241 +    // Default to cubic switching function.
242 +    sft_ = cubic;
243 +    if (simParams_->haveSwitchingFunctionType()) {
244 +      string funcType = simParams_->getSwitchingFunctionType();
245 +      toUpper(funcType);
246 +      if (funcType == "CUBIC") {
247 +        sft_ = cubic;
248 +      } else {
249 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
250 +          sft_ = fifth_order_poly;
251 +        } else {
252 +          // throw error        
253 +          sprintf( painCave.errMsg,
254 +                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
255 +                   "\tswitchingFunctionType must be one of: "
256 +                   "\"cubic\" or \"fifth_order_polynomial\".",
257 +                   funcType.c_str() );
258 +          painCave.isFatal = 1;
259 +          painCave.severity = OPENMD_ERROR;
260 +          simError();
261 +        }          
262 +      }
263 +    }
264 +    switcher_->setSwitchType(sft_);
265 +    switcher_->setSwitch(rSwitch_, rCut_);
266    }
267    
268 +  void ForceManager::initialize() {
269 +
270 +    if (!info_->isTopologyDone()) {
271 +      info_->update();
272 +      interactionMan_->setSimInfo(info_);
273 +      interactionMan_->initialize();
274 +
275 +      // We want to delay the cutoffs until after the interaction
276 +      // manager has set up the atom-atom interactions so that we can
277 +      // query them for suggested cutoff values
278 +
279 +      setupCutoffs();
280 +      setupSwitching();
281 +
282 +      info_->prepareTopology();      
283 +    }
284 +
285 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
286 +    
287 +    // Force fields can set options on how to scale van der Waals and electrostatic
288 +    // interactions for atoms connected via bonds, bends and torsions
289 +    // in this case the topological distance between atoms is:
290 +    // 0 = topologically unconnected
291 +    // 1 = bonded together
292 +    // 2 = connected via a bend
293 +    // 3 = connected via a torsion
294 +    
295 +    vdwScale_.reserve(4);
296 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
297 +
298 +    electrostaticScale_.reserve(4);
299 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
300 +
301 +    vdwScale_[0] = 1.0;
302 +    vdwScale_[1] = fopts.getvdw12scale();
303 +    vdwScale_[2] = fopts.getvdw13scale();
304 +    vdwScale_[3] = fopts.getvdw14scale();
305 +    
306 +    electrostaticScale_[0] = 1.0;
307 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
308 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
309 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
310 +    
311 +    fDecomp_->distributeInitialData();
312 +
313 +    initialized_ = true;
314 +
315 +  }
316 +
317 +  void ForceManager::calcForces() {
318 +    
319 +    if (!initialized_) initialize();
320 +
321 +    preCalculation();  
322 +    shortRangeInteractions();
323 +    longRangeInteractions();
324 +    postCalculation();    
325 +  }
326 +  
327    void ForceManager::preCalculation() {
328      SimInfo::MoleculeIterator mi;
329      Molecule* mol;
# Line 100 | Line 335 | namespace OpenMD {
335      CutoffGroup* cg;
336      
337      // forces are zeroed here, before any are accumulated.
103 –    // NOTE: do not rezero the forces in Fortran.
338      
339      for (mol = info_->beginMolecule(mi); mol != NULL;
340           mol = info_->nextMolecule(mi)) {
# Line 115 | Line 349 | namespace OpenMD {
349        }        
350  
351        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
118 –        std::cerr << "should not see me \n";
352          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
353              cg = mol->nextCutoffGroup(ci)) {
354            //calculate the center of mass of cutoff group
# Line 129 | Line 362 | namespace OpenMD {
362      
363    }
364    
365 <  void ForceManager::calcShortRangeInteraction() {
365 >  void ForceManager::shortRangeInteractions() {
366      Molecule* mol;
367      RigidBody* rb;
368      Bond* bond;
# Line 171 | Line 404 | namespace OpenMD {
404          RealType currBendPot = bend->getPotential();          
405          
406          bendPotential += bend->getPotential();
407 <        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
407 >        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
408          if (i == bendDataSets.end()) {
409            BendDataSet dataSet;
410            dataSet.prev.angle = dataSet.curr.angle = angle;
411            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
412            dataSet.deltaV = 0.0;
413 <          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
413 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
414          }else {
415            i->second.prev.angle = i->second.curr.angle;
416            i->second.prev.potential = i->second.curr.potential;
# Line 194 | Line 427 | namespace OpenMD {
427          torsion->calcForce(angle);
428          RealType currTorsionPot = torsion->getPotential();
429          torsionPotential += torsion->getPotential();
430 <        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
430 >        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
431          if (i == torsionDataSets.end()) {
432            TorsionDataSet dataSet;
433            dataSet.prev.angle = dataSet.curr.angle = angle;
434            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
435            dataSet.deltaV = 0.0;
436 <          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
436 >          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
437          }else {
438            i->second.prev.angle = i->second.curr.angle;
439            i->second.prev.potential = i->second.curr.potential;
# Line 210 | Line 443 | namespace OpenMD {
443                                     i->second.prev.potential);
444          }      
445        }      
446 <
446 >      
447        for (inversion = mol->beginInversion(inversionIter);
448             inversion != NULL;
449             inversion = mol->nextInversion(inversionIter)) {
# Line 218 | Line 451 | namespace OpenMD {
451          inversion->calcForce(angle);
452          RealType currInversionPot = inversion->getPotential();
453          inversionPotential += inversion->getPotential();
454 <        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
454 >        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
455          if (i == inversionDataSets.end()) {
456            InversionDataSet dataSet;
457            dataSet.prev.angle = dataSet.curr.angle = angle;
458            dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
459            dataSet.deltaV = 0.0;
460 <          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
460 >          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
461          }else {
462            i->second.prev.angle = i->second.curr.angle;
463            i->second.prev.potential = i->second.curr.potential;
# Line 243 | Line 476 | namespace OpenMD {
476      curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
477      curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
478      curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
479 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
247 <    
479 >    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
480    }
481    
482 <  void ForceManager::calcLongRangeInteraction() {
251 <    Snapshot* curSnapshot;
252 <    DataStorage* config;
253 <    DataStorage* cgConfig;
254 <    RealType* frc;
255 <    RealType* pos;
256 <    RealType* trq;
257 <    RealType* A;
258 <    RealType* electroFrame;
259 <    RealType* rc;
260 <    RealType* particlePot;
261 <    
262 <    //get current snapshot from SimInfo
263 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
264 <    
265 <    //get array pointers
266 <    config = &(curSnapshot->atomData);
267 <    cgConfig = &(curSnapshot->cgData);
268 <    frc = config->getArrayPointer(DataStorage::dslForce);
269 <    pos = config->getArrayPointer(DataStorage::dslPosition);
270 <    trq = config->getArrayPointer(DataStorage::dslTorque);
271 <    A   = config->getArrayPointer(DataStorage::dslAmat);
272 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
273 <    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
482 >  void ForceManager::longRangeInteractions() {
483  
484 <    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
485 <      std::cerr << "should not see me \n";
486 <      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
484 >    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
485 >    DataStorage* config = &(curSnapshot->atomData);
486 >    DataStorage* cgConfig = &(curSnapshot->cgData);
487 >
488 >    //calculate the center of mass of cutoff group
489 >
490 >    SimInfo::MoleculeIterator mi;
491 >    Molecule* mol;
492 >    Molecule::CutoffGroupIterator ci;
493 >    CutoffGroup* cg;
494 >
495 >    if(info_->getNCutoffGroups() > 0){      
496 >      for (mol = info_->beginMolecule(mi); mol != NULL;
497 >           mol = info_->nextMolecule(mi)) {
498 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
499 >            cg = mol->nextCutoffGroup(ci)) {
500 >          cg->updateCOM();
501 >        }
502 >      }      
503      } else {
504        // center of mass of the group is the same as position of the atom  
505        // if cutoff group does not exist
506 <      rc = pos;
506 >      cgConfig->position = config->position;
507      }
508 +
509 +    fDecomp_->zeroWorkArrays();
510 +    fDecomp_->distributeData();
511      
512 <    //initialize data before passing to fortran
513 <    RealType longRangePotential[LR_POT_TYPES];
514 <    RealType lrPot = 0.0;
515 <    int isError = 0;
512 >    int cg1, cg2, atom1, atom2, topoDist;
513 >    Vector3d d_grp, dag, d;
514 >    RealType rgrpsq, rgrp, r2, r;
515 >    RealType electroMult, vdwMult;
516 >    RealType vij;
517 >    Vector3d fij, fg, f1;
518 >    tuple3<RealType, RealType, RealType> cuts;
519 >    RealType rCutSq;
520 >    bool in_switching_region;
521 >    RealType sw, dswdr, swderiv;
522 >    vector<int> atomListColumn, atomListRow, atomListLocal;
523 >    InteractionData idat;
524 >    SelfData sdat;
525 >    RealType mf;
526 >    RealType lrPot;
527 >    RealType vpair;
528 >    potVec longRangePotential(0.0);
529 >    potVec workPot(0.0);
530  
531 <    for (int i=0; i<LR_POT_TYPES;i++){
532 <      longRangePotential[i]=0.0; //Initialize array
531 >    int loopStart, loopEnd;
532 >
533 >    idat.vdwMult = &vdwMult;
534 >    idat.electroMult = &electroMult;
535 >    idat.pot = &workPot;
536 >    sdat.pot = fDecomp_->getEmbeddingPotential();
537 >    idat.vpair = &vpair;
538 >    idat.f1 = &f1;
539 >    idat.sw = &sw;
540 >    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
541 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
542 >    
543 >    loopEnd = PAIR_LOOP;
544 >    if (info_->requiresPrepair() ) {
545 >      loopStart = PREPAIR_LOOP;
546 >    } else {
547 >      loopStart = PAIR_LOOP;
548      }
549 +  
550 +    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
551      
552 <    decomp_->distributeData();
552 >      if (iLoop == loopStart) {
553 >        bool update_nlist = fDecomp_->checkNeighborList();
554 >        if (update_nlist)
555 >          neighborList = fDecomp_->buildNeighborList();
556 >      }      
557 >        
558 >      for (vector<pair<int, int> >::iterator it = neighborList.begin();
559 >             it != neighborList.end(); ++it) {
560 >                
561 >        cg1 = (*it).first;
562 >        cg2 = (*it).second;
563 >        
564 >        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
565  
566 <    int nLoops = 1;
567 <    for (int iLoop = 0; iLoop < nLoops; iLoop++) {
568 <      doForceLoop(pos,
298 <                  rc,
299 <                  A,
300 <                  electroFrame,
301 <                  frc,
302 <                  trq,
303 <                  tau.getArrayPointer(),
304 <                  longRangePotential,
305 <                  particlePot,
306 <                  &isError );  
566 >        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
567 >        curSnapshot->wrapVector(d_grp);        
568 >        rgrpsq = d_grp.lengthSquare();
569  
570 <      if (nLoops > 1) {
571 <        decomp_->collectIntermediateData();
572 <        decomp_->distributeIntermediateData();
570 >        rCutSq = cuts.second;
571 >
572 >        if (rgrpsq < rCutSq) {
573 >          idat.rcut = &cuts.first;
574 >          if (iLoop == PAIR_LOOP) {
575 >            vij *= 0.0;
576 >            fij = V3Zero;
577 >          }
578 >          
579 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
580 >                                                     rgrp);
581 >              
582 >          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
583 >          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
584 >
585 >          for (vector<int>::iterator ia = atomListRow.begin();
586 >               ia != atomListRow.end(); ++ia) {            
587 >            atom1 = (*ia);
588 >            
589 >            for (vector<int>::iterator jb = atomListColumn.begin();
590 >                 jb != atomListColumn.end(); ++jb) {              
591 >              atom2 = (*jb);
592 >            
593 >              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
594 >                vpair = 0.0;
595 >                workPot = 0.0;
596 >                f1 = V3Zero;
597 >
598 >                fDecomp_->fillInteractionData(idat, atom1, atom2);
599 >                
600 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
601 >                vdwMult = vdwScale_[topoDist];
602 >                electroMult = electrostaticScale_[topoDist];
603 >
604 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
605 >                  idat.d = &d_grp;
606 >                  idat.r2 = &rgrpsq;
607 >                } else {
608 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
609 >                  curSnapshot->wrapVector( d );
610 >                  r2 = d.lengthSquare();
611 >                  idat.d = &d;
612 >                  idat.r2 = &r2;
613 >                }
614 >                
615 >                r = sqrt( *(idat.r2) );
616 >                idat.rij = &r;
617 >              
618 >                if (iLoop == PREPAIR_LOOP) {
619 >                  interactionMan_->doPrePair(idat);
620 >                } else {
621 >                  interactionMan_->doPair(idat);
622 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
623 >                  vij += vpair;
624 >                  fij += f1;
625 >                  tau -= outProduct( *(idat.d), f1);
626 >                }
627 >              }
628 >            }
629 >          }
630 >
631 >          if (iLoop == PAIR_LOOP) {
632 >            if (in_switching_region) {
633 >              swderiv = vij * dswdr / rgrp;
634 >              fg = swderiv * d_grp;
635 >
636 >              fij += fg;
637 >
638 >              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
639 >                tau -= outProduct( *(idat.d), fg);
640 >              }
641 >          
642 >              for (vector<int>::iterator ia = atomListRow.begin();
643 >                   ia != atomListRow.end(); ++ia) {            
644 >                atom1 = (*ia);                
645 >                mf = fDecomp_->getMassFactorRow(atom1);
646 >                // fg is the force on atom ia due to cutoff group's
647 >                // presence in switching region
648 >                fg = swderiv * d_grp * mf;
649 >                fDecomp_->addForceToAtomRow(atom1, fg);
650 >
651 >                if (atomListRow.size() > 1) {
652 >                  if (info_->usesAtomicVirial()) {
653 >                    // find the distance between the atom
654 >                    // and the center of the cutoff group:
655 >                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
656 >                    tau -= outProduct(dag, fg);
657 >                  }
658 >                }
659 >              }
660 >              for (vector<int>::iterator jb = atomListColumn.begin();
661 >                   jb != atomListColumn.end(); ++jb) {              
662 >                atom2 = (*jb);
663 >                mf = fDecomp_->getMassFactorColumn(atom2);
664 >                // fg is the force on atom jb due to cutoff group's
665 >                // presence in switching region
666 >                fg = -swderiv * d_grp * mf;
667 >                fDecomp_->addForceToAtomColumn(atom2, fg);
668 >
669 >                if (atomListColumn.size() > 1) {
670 >                  if (info_->usesAtomicVirial()) {
671 >                    // find the distance between the atom
672 >                    // and the center of the cutoff group:
673 >                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
674 >                    tau -= outProduct(dag, fg);
675 >                  }
676 >                }
677 >              }
678 >            }
679 >            //if (!SIM_uses_AtomicVirial) {
680 >            //  tau -= outProduct(d_grp, fij);
681 >            //}
682 >          }
683 >        }
684        }
685 +
686 +      if (iLoop == PREPAIR_LOOP) {
687 +        if (info_->requiresPrepair()) {            
688 +          fDecomp_->collectIntermediateData();
689 +
690 +          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
691 +            fDecomp_->fillSelfData(sdat, atom1);
692 +            interactionMan_->doPreForce(sdat);
693 +          }
694 +          
695 +          
696 +          fDecomp_->distributeIntermediateData();        
697 +        }
698 +      }
699 +
700      }
701 <  
702 <    decomp_->collectData();
701 >    
702 >    fDecomp_->collectData();
703 >    
704 >    if ( info_->requiresSkipCorrection() ) {
705 >      
706 >      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
707  
708 <    if( isError ){
709 <      sprintf( painCave.errMsg,
710 <               "Error returned from the fortran force calculation.\n" );
711 <      painCave.isFatal = 1;
712 <      simError();
708 >        vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 );
709 >        
710 >        for (vector<int>::iterator jb = skipList.begin();
711 >             jb != skipList.end(); ++jb) {        
712 >    
713 >          atom2 = (*jb);
714 >          fDecomp_->fillSkipData(idat, atom1, atom2);
715 >          interactionMan_->doSkipCorrection(idat);
716 >          fDecomp_->unpackSkipData(idat, atom1, atom2);
717 >
718 >        }
719 >      }
720      }
721 <    for (int i=0; i<LR_POT_TYPES;i++){
722 <      lrPot += longRangePotential[i]; //Quick hack
721 >    
722 >    if (info_->requiresSelfCorrection()) {
723 >
724 >      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
725 >        fDecomp_->fillSelfData(sdat, atom1);
726 >        interactionMan_->doSelfCorrection(sdat);
727 >      }
728 >
729      }
730 <        
730 >
731 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
732 >      *(fDecomp_->getPairwisePotential());
733 >
734 >    lrPot = longRangePotential.sum();
735 >
736      //store the tau and long range potential    
737      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
738 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
739 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
738 >    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
739 >    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
740    }
741  
742    

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