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Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs.
Revision 1709 by gezelter, Tue May 15 13:04:08 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 47 | Line 48
48   * @version 1.0
49   */
50  
51 +
52   #include "brains/ForceManager.hpp"
53   #include "primitives/Molecule.hpp"
54   #define __OPENMD_C
# Line 58 | Line 60
60   #include "nonbonded/NonBondedInteraction.hpp"
61   #include "parallel/ForceMatrixDecomposition.hpp"
62  
63 + #include <cstdio>
64 + #include <iostream>
65 + #include <iomanip>
66 +
67   using namespace std;
68   namespace OpenMD {
69    
70    ForceManager::ForceManager(SimInfo * info) : info_(info) {
71 <
72 < #ifdef IS_MPI
73 <    fDecomp_ = new ForceMatrixDecomposition(info_);
68 < #else
69 <    // fDecomp_ = new ForceSerialDecomposition(info);
70 < #endif
71 >    forceField_ = info_->getForceField();
72 >    interactionMan_ = new InteractionManager();
73 >    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74    }
75 +
76 +  /**
77 +   * setupCutoffs
78 +   *
79 +   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
80 +   * and cutoffPolicy
81 +   *
82 +   * cutoffRadius : realType
83 +   *  If the cutoffRadius was explicitly set, use that value.
84 +   *  If the cutoffRadius was not explicitly set:
85 +   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
86 +   *      No electrostatic atoms?  Poll the atom types present in the
87 +   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
88 +   *      Use the maximum suggested value that was found.
89 +   *
90 +   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
91 +   *                        or SHIFTED_POTENTIAL)
92 +   *      If cutoffMethod was explicitly set, use that choice.
93 +   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
94 +   *
95 +   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
96 +   *      If cutoffPolicy was explicitly set, use that choice.
97 +   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
98 +   *
99 +   * switchingRadius : realType
100 +   *  If the cutoffMethod was set to SWITCHED:
101 +   *      If the switchingRadius was explicitly set, use that value
102 +   *          (but do a sanity check first).
103 +   *      If the switchingRadius was not explicitly set: use 0.85 *
104 +   *      cutoffRadius_
105 +   *  If the cutoffMethod was not set to SWITCHED:
106 +   *      Set switchingRadius equal to cutoffRadius for safety.
107 +   */
108 +  void ForceManager::setupCutoffs() {
109 +    
110 +    Globals* simParams_ = info_->getSimParams();
111 +    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112 +    int mdFileVersion;
113 +    
114 +    if (simParams_->haveMDfileVersion())
115 +      mdFileVersion = simParams_->getMDfileVersion();
116 +    else
117 +      mdFileVersion = 0;
118 +  
119 +    if (simParams_->haveCutoffRadius()) {
120 +      rCut_ = simParams_->getCutoffRadius();
121 +    } else {      
122 +      if (info_->usesElectrostaticAtoms()) {
123 +        sprintf(painCave.errMsg,
124 +                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
125 +                "\tOpenMD will use a default value of 12.0 angstroms"
126 +                "\tfor the cutoffRadius.\n");
127 +        painCave.isFatal = 0;
128 +        painCave.severity = OPENMD_INFO;
129 +        simError();
130 +        rCut_ = 12.0;
131 +      } else {
132 +        RealType thisCut;
133 +        set<AtomType*>::iterator i;
134 +        set<AtomType*> atomTypes;
135 +        atomTypes = info_->getSimulatedAtomTypes();        
136 +        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
137 +          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
138 +          rCut_ = max(thisCut, rCut_);
139 +        }
140 +        sprintf(painCave.errMsg,
141 +                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
142 +                "\tOpenMD will use %lf angstroms.\n",
143 +                rCut_);
144 +        painCave.isFatal = 0;
145 +        painCave.severity = OPENMD_INFO;
146 +        simError();
147 +      }
148 +    }
149 +
150 +    fDecomp_->setUserCutoff(rCut_);
151 +    interactionMan_->setCutoffRadius(rCut_);
152 +
153 +    map<string, CutoffMethod> stringToCutoffMethod;
154 +    stringToCutoffMethod["HARD"] = HARD;
155 +    stringToCutoffMethod["SWITCHED"] = SWITCHED;
156 +    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
157 +    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
158    
159 <  void ForceManager::calcForces() {
159 >    if (simParams_->haveCutoffMethod()) {
160 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
161 >      map<string, CutoffMethod>::iterator i;
162 >      i = stringToCutoffMethod.find(cutMeth);
163 >      if (i == stringToCutoffMethod.end()) {
164 >        sprintf(painCave.errMsg,
165 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
166 >                "\tShould be one of: "
167 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
168 >                cutMeth.c_str());
169 >        painCave.isFatal = 1;
170 >        painCave.severity = OPENMD_ERROR;
171 >        simError();
172 >      } else {
173 >        cutoffMethod_ = i->second;
174 >      }
175 >    } else {
176 >      if (mdFileVersion > 1) {
177 >        sprintf(painCave.errMsg,
178 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
179 >                "\tOpenMD will use SHIFTED_FORCE.\n");
180 >        painCave.isFatal = 0;
181 >        painCave.severity = OPENMD_INFO;
182 >        simError();
183 >        cutoffMethod_ = SHIFTED_FORCE;        
184 >      } else {
185 >        // handle the case where the old file version was in play
186 >        // (there should be no cutoffMethod, so we have to deduce it
187 >        // from other data).        
188 >
189 >        sprintf(painCave.errMsg,
190 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
191 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
192 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
193 >                "\tbehavior of the older (version 1) code.  To remove this\n"
194 >                "\twarning, add an explicit cutoffMethod and change the top\n"
195 >                "\tof the file so that it begins with <OpenMD version=2>\n");
196 >        painCave.isFatal = 0;
197 >        painCave.severity = OPENMD_WARNING;
198 >        simError();            
199 >                
200 >        // The old file version tethered the shifting behavior to the
201 >        // electrostaticSummationMethod keyword.
202 >        
203 >        if (simParams_->haveElectrostaticSummationMethod()) {
204 >          std::string myMethod = simParams_->getElectrostaticSummationMethod();
205 >          toUpper(myMethod);
206 >        
207 >          if (myMethod == "SHIFTED_POTENTIAL") {
208 >            cutoffMethod_ = SHIFTED_POTENTIAL;
209 >          } else if (myMethod == "SHIFTED_FORCE") {
210 >            cutoffMethod_ = SHIFTED_FORCE;
211 >          }
212 >        
213 >          if (simParams_->haveSwitchingRadius())
214 >            rSwitch_ = simParams_->getSwitchingRadius();
215 >
216 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
217 >            if (simParams_->haveSwitchingRadius()){
218 >              sprintf(painCave.errMsg,
219 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
220 >                      "\tA value was set for the switchingRadius\n"
221 >                      "\teven though the electrostaticSummationMethod was\n"
222 >                      "\tset to %s\n", myMethod.c_str());
223 >              painCave.severity = OPENMD_WARNING;
224 >              painCave.isFatal = 1;
225 >              simError();            
226 >            }
227 >          }
228 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
229 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
230 >              sprintf(painCave.errMsg,
231 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
232 >                      "\tcutoffRadius and switchingRadius are set to the\n"
233 >                      "\tsame value.  OpenMD will use shifted force\n"
234 >                      "\tpotentials instead of switching functions.\n");
235 >              painCave.isFatal = 0;
236 >              painCave.severity = OPENMD_WARNING;
237 >              simError();            
238 >            } else {
239 >              cutoffMethod_ = SHIFTED_POTENTIAL;
240 >              sprintf(painCave.errMsg,
241 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
242 >                      "\tcutoffRadius and switchingRadius are set to the\n"
243 >                      "\tsame value.  OpenMD will use shifted potentials\n"
244 >                      "\tinstead of switching functions.\n");
245 >              painCave.isFatal = 0;
246 >              painCave.severity = OPENMD_WARNING;
247 >              simError();            
248 >            }
249 >          }
250 >        }
251 >      }
252 >    }
253 >
254 >    map<string, CutoffPolicy> stringToCutoffPolicy;
255 >    stringToCutoffPolicy["MIX"] = MIX;
256 >    stringToCutoffPolicy["MAX"] = MAX;
257 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
258 >
259 >    std::string cutPolicy;
260 >    if (forceFieldOptions_.haveCutoffPolicy()){
261 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
262 >    }else if (simParams_->haveCutoffPolicy()) {
263 >      cutPolicy = simParams_->getCutoffPolicy();
264 >    }
265 >
266 >    if (!cutPolicy.empty()){
267 >      toUpper(cutPolicy);
268 >      map<string, CutoffPolicy>::iterator i;
269 >      i = stringToCutoffPolicy.find(cutPolicy);
270 >
271 >      if (i == stringToCutoffPolicy.end()) {
272 >        sprintf(painCave.errMsg,
273 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
274 >                "\tShould be one of: "
275 >                "MIX, MAX, or TRADITIONAL\n",
276 >                cutPolicy.c_str());
277 >        painCave.isFatal = 1;
278 >        painCave.severity = OPENMD_ERROR;
279 >        simError();
280 >      } else {
281 >        cutoffPolicy_ = i->second;
282 >      }
283 >    } else {
284 >      sprintf(painCave.errMsg,
285 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
286 >              "\tOpenMD will use TRADITIONAL.\n");
287 >      painCave.isFatal = 0;
288 >      painCave.severity = OPENMD_INFO;
289 >      simError();
290 >      cutoffPolicy_ = TRADITIONAL;        
291 >    }
292 >
293 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
294 >        
295 >    // create the switching function object:
296 >
297 >    switcher_ = new SwitchingFunction();
298 >  
299 >    if (cutoffMethod_ == SWITCHED) {
300 >      if (simParams_->haveSwitchingRadius()) {
301 >        rSwitch_ = simParams_->getSwitchingRadius();
302 >        if (rSwitch_ > rCut_) {        
303 >          sprintf(painCave.errMsg,
304 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
305 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
306 >          painCave.isFatal = 1;
307 >          painCave.severity = OPENMD_ERROR;
308 >          simError();
309 >        }
310 >      } else {      
311 >        rSwitch_ = 0.85 * rCut_;
312 >        sprintf(painCave.errMsg,
313 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
314 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
315 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
316 >        painCave.isFatal = 0;
317 >        painCave.severity = OPENMD_WARNING;
318 >        simError();
319 >      }
320 >    } else {
321 >      if (mdFileVersion > 1) {
322 >        // throw an error if we define a switching radius and don't need one.
323 >        // older file versions should not do this.
324 >        if (simParams_->haveSwitchingRadius()) {
325 >          map<string, CutoffMethod>::const_iterator it;
326 >          string theMeth;
327 >          for (it = stringToCutoffMethod.begin();
328 >               it != stringToCutoffMethod.end(); ++it) {
329 >            if (it->second == cutoffMethod_) {
330 >              theMeth = it->first;
331 >              break;
332 >            }
333 >          }
334 >          sprintf(painCave.errMsg,
335 >                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
336 >                  "\tis not set to SWITCHED, so switchingRadius value\n"
337 >                  "\twill be ignored for this simulation\n", theMeth.c_str());
338 >          painCave.isFatal = 0;
339 >          painCave.severity = OPENMD_WARNING;
340 >          simError();
341 >        }
342 >      }
343 >      rSwitch_ = rCut_;
344 >    }
345      
346 +    // Default to cubic switching function.
347 +    sft_ = cubic;
348 +    if (simParams_->haveSwitchingFunctionType()) {
349 +      string funcType = simParams_->getSwitchingFunctionType();
350 +      toUpper(funcType);
351 +      if (funcType == "CUBIC") {
352 +        sft_ = cubic;
353 +      } else {
354 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
355 +          sft_ = fifth_order_poly;
356 +        } else {
357 +          // throw error        
358 +          sprintf( painCave.errMsg,
359 +                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
360 +                   "\tswitchingFunctionType must be one of: "
361 +                   "\"cubic\" or \"fifth_order_polynomial\".",
362 +                   funcType.c_str() );
363 +          painCave.isFatal = 1;
364 +          painCave.severity = OPENMD_ERROR;
365 +          simError();
366 +        }          
367 +      }
368 +    }
369 +    switcher_->setSwitchType(sft_);
370 +    switcher_->setSwitch(rSwitch_, rCut_);
371 +    interactionMan_->setSwitchingRadius(rSwitch_);
372 +  }
373 +
374 +
375 +
376 +  
377 +  void ForceManager::initialize() {
378 +
379      if (!info_->isTopologyDone()) {
380 +
381        info_->update();
382        interactionMan_->setSimInfo(info_);
383        interactionMan_->initialize();
384 <      swfun_ = interactionMan_->getSwitchingFunction();
385 <      fDecomp_->distributeInitialData();
386 <      info_->prepareTopology();
384 >
385 >      // We want to delay the cutoffs until after the interaction
386 >      // manager has set up the atom-atom interactions so that we can
387 >      // query them for suggested cutoff values
388 >      setupCutoffs();
389 >
390 >      info_->prepareTopology();      
391      }
392 +
393 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
394      
395 +    // Force fields can set options on how to scale van der Waals and
396 +    // electrostatic interactions for atoms connected via bonds, bends
397 +    // and torsions in this case the topological distance between
398 +    // atoms is:
399 +    // 0 = topologically unconnected
400 +    // 1 = bonded together
401 +    // 2 = connected via a bend
402 +    // 3 = connected via a torsion
403 +    
404 +    vdwScale_.reserve(4);
405 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
406 +
407 +    electrostaticScale_.reserve(4);
408 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
409 +
410 +    vdwScale_[0] = 1.0;
411 +    vdwScale_[1] = fopts.getvdw12scale();
412 +    vdwScale_[2] = fopts.getvdw13scale();
413 +    vdwScale_[3] = fopts.getvdw14scale();
414 +    
415 +    electrostaticScale_[0] = 1.0;
416 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
417 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
418 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
419 +    
420 +    fDecomp_->distributeInitialData();
421 +
422 +    initialized_ = true;
423 +
424 +  }
425 +
426 +  void ForceManager::calcForces() {
427 +    
428 +    if (!initialized_) initialize();
429 +
430      preCalculation();  
431      shortRangeInteractions();
432      longRangeInteractions();
433 <    postCalculation();
88 <    
433 >    postCalculation();    
434    }
435    
436    void ForceManager::preCalculation() {
# Line 102 | Line 447 | namespace OpenMD {
447      
448      for (mol = info_->beginMolecule(mi); mol != NULL;
449           mol = info_->nextMolecule(mi)) {
450 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
450 >      for(atom = mol->beginAtom(ai); atom != NULL;
451 >          atom = mol->nextAtom(ai)) {
452          atom->zeroForcesAndTorques();
453        }
454 <          
454 >      
455        //change the positions of atoms which belong to the rigidbodies
456        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
457             rb = mol->nextRigidBody(rbIter)) {
458          rb->zeroForcesAndTorques();
459        }        
460 <
460 >      
461        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
462          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
463              cg = mol->nextCutoffGroup(ci)) {
# Line 120 | Line 466 | namespace OpenMD {
466          }
467        }      
468      }
469 <  
469 >    
470      // Zero out the stress tensor
471      tau *= 0.0;
472      
# Line 174 | Line 520 | namespace OpenMD {
520            dataSet.prev.angle = dataSet.curr.angle = angle;
521            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
522            dataSet.deltaV = 0.0;
523 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
523 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
524 >                                                                  dataSet));
525          }else {
526            i->second.prev.angle = i->second.curr.angle;
527            i->second.prev.potential = i->second.curr.potential;
# Line 245 | Line 592 | namespace OpenMD {
592    
593    void ForceManager::longRangeInteractions() {
594  
248 –    // some of this initial stuff will go away:
595      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
596      DataStorage* config = &(curSnapshot->atomData);
597      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;    
598  
599 <    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
600 <      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
599 >    //calculate the center of mass of cutoff group
600 >
601 >    SimInfo::MoleculeIterator mi;
602 >    Molecule* mol;
603 >    Molecule::CutoffGroupIterator ci;
604 >    CutoffGroup* cg;
605 >
606 >    if(info_->getNCutoffGroups() > 0){      
607 >      for (mol = info_->beginMolecule(mi); mol != NULL;
608 >           mol = info_->nextMolecule(mi)) {
609 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
610 >            cg = mol->nextCutoffGroup(ci)) {
611 >          cg->updateCOM();
612 >        }
613 >      }      
614      } else {
615        // center of mass of the group is the same as position of the atom  
616        // if cutoff group does not exist
617 <      rc = pos;
617 >      cgConfig->position = config->position;
618      }
267 –    
268 –    //initialize data before passing to fortran
269 –    RealType longRangePotential[N_INTERACTION_FAMILIES];
270 –    RealType lrPot = 0.0;
271 –    int isError = 0;
619  
620 <    // 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 <
620 >    fDecomp_->zeroWorkArrays();
621      fDecomp_->distributeData();
622 <
623 <    int cg1, cg2, atom1, atom2;
624 <    Vector3d d_grp, dag;
625 <    RealType rgrpsq, rgrp;
622 >    
623 >    int cg1, cg2, atom1, atom2, topoDist;
624 >    Vector3d d_grp, dag, d;
625 >    RealType rgrpsq, rgrp, r2, r;
626 >    RealType electroMult, vdwMult;
627      RealType vij;
628 <    Vector3d fij, fg;
629 <    pair<int, int> gtypes;
628 >    Vector3d fij, fg, f1;
629 >    tuple3<RealType, RealType, RealType> cuts;
630      RealType rCutSq;
631      bool in_switching_region;
632      RealType sw, dswdr, swderiv;
# Line 292 | Line 634 | namespace OpenMD {
634      InteractionData idat;
635      SelfData sdat;
636      RealType mf;
637 +    RealType lrPot;
638 +    RealType vpair;
639 +    potVec longRangePotential(0.0);
640 +    potVec workPot(0.0);
641  
642      int loopStart, loopEnd;
643  
644 +    idat.vdwMult = &vdwMult;
645 +    idat.electroMult = &electroMult;
646 +    idat.pot = &workPot;
647 +    sdat.pot = fDecomp_->getEmbeddingPotential();
648 +    idat.vpair = &vpair;
649 +    idat.f1 = &f1;
650 +    idat.sw = &sw;
651 +    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
652 +    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
653 +    
654      loopEnd = PAIR_LOOP;
655      if (info_->requiresPrepair() ) {
656        loopStart = PREPAIR_LOOP;
657      } else {
658        loopStart = PAIR_LOOP;
659      }
660 <
661 <    for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
662 <      
660 >  
661 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
662 >    
663        if (iLoop == loopStart) {
664          bool update_nlist = fDecomp_->checkNeighborList();
665          if (update_nlist)
666            neighborList = fDecomp_->buildNeighborList();
667 <      }
667 >      }            
668  
669        for (vector<pair<int, int> >::iterator it = neighborList.begin();
670               it != neighborList.end(); ++it) {
671 <        
671 >                
672          cg1 = (*it).first;
673          cg2 = (*it).second;
674 +        
675 +        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
676  
319 –        gtypes = fDecomp_->getGroupTypes(cg1, cg2);
677          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
678 +
679          curSnapshot->wrapVector(d_grp);        
680          rgrpsq = d_grp.lengthSquare();
681 <        rCutSq = groupCutoffMap[gtypes].first;
681 >        rCutSq = cuts.second;
682  
683          if (rgrpsq < rCutSq) {
684 <          *(idat.rcut) = groupCutoffMap[gtypes].second;
684 >          idat.rcut = &cuts.first;
685            if (iLoop == PAIR_LOOP) {
686 <            vij *= 0.0;
686 >            vij = 0.0;
687              fij = V3Zero;
688            }
689            
690 <          in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
691 <                                                  rgrp);              
690 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
691 >                                                     rgrp);
692 >          
693            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
694            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
695  
# Line 341 | Line 700 | namespace OpenMD {
700              for (vector<int>::iterator jb = atomListColumn.begin();
701                   jb != atomListColumn.end(); ++jb) {              
702                atom2 = (*jb);
703 <              
703 >
704                if (!fDecomp_->skipAtomPair(atom1, atom2)) {
705 +                vpair = 0.0;
706 +                workPot = 0.0;
707 +                f1 = V3Zero;
708 +
709 +                fDecomp_->fillInteractionData(idat, atom1, atom2);
710                  
711 <                idat = fDecomp_->fillInteractionData(atom1, atom2);
711 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
712 >                vdwMult = vdwScale_[topoDist];
713 >                electroMult = electrostaticScale_[topoDist];
714  
715                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
716 <                  *(idat.d) = d_grp;
717 <                  *(idat.r2) = rgrpsq;
716 >                  idat.d = &d_grp;
717 >                  idat.r2 = &rgrpsq;
718                  } else {
719 <                  *(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
720 <                  curSnapshot->wrapVector( *(idat.d) );
721 <                  *(idat.r2) = idat.d->lengthSquare();
719 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
720 >                  curSnapshot->wrapVector( d );
721 >                  r2 = d.lengthSquare();
722 >                  idat.d = &d;
723 >                  idat.r2 = &r2;
724                  }
357 –                
358 –                *(idat.rij) = sqrt( *(idat.r2) );
725                
726 +                r = sqrt( *(idat.r2) );
727 +                idat.rij = &r;
728 +              
729                  if (iLoop == PREPAIR_LOOP) {
730                    interactionMan_->doPrePair(idat);
731                  } else {
732                    interactionMan_->doPair(idat);
733 <                  vij += *(idat.vpair);
734 <                  fij += *(idat.f1);
735 <                  tau -= outProduct( *(idat.d), *(idat.f1));
733 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
734 >                  vij += vpair;
735 >                  fij += f1;
736 >                  tau -= outProduct( *(idat.d), f1);
737                  }
738                }
739              }
# Line 373 | Line 743 | namespace OpenMD {
743              if (in_switching_region) {
744                swderiv = vij * dswdr / rgrp;
745                fg = swderiv * d_grp;
376 –
746                fij += fg;
747  
748                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
# Line 388 | Line 757 | namespace OpenMD {
757                  // presence in switching region
758                  fg = swderiv * d_grp * mf;
759                  fDecomp_->addForceToAtomRow(atom1, fg);
391 –
760                  if (atomListRow.size() > 1) {
761                    if (info_->usesAtomicVirial()) {
762                      // find the distance between the atom
# Line 417 | Line 785 | namespace OpenMD {
785                  }
786                }
787              }
788 <            //if (!SIM_uses_AtomicVirial) {
788 >            //if (!info_->usesAtomicVirial()) {
789              //  tau -= outProduct(d_grp, fij);
790              //}
791            }
# Line 425 | Line 793 | namespace OpenMD {
793        }
794  
795        if (iLoop == PREPAIR_LOOP) {
796 <        if (info_->requiresPrepair()) {            
796 >        if (info_->requiresPrepair()) {
797 >
798            fDecomp_->collectIntermediateData();
799 <          atomListLocal = fDecomp_->getAtomList();
800 <          for (vector<int>::iterator ia = atomListLocal.begin();
801 <               ia != atomListLocal.end(); ++ia) {              
433 <            atom1 = (*ia);            
434 <            sdat = fDecomp_->fillSelfData(atom1);
799 >
800 >          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
801 >            fDecomp_->fillSelfData(sdat, atom1);
802              interactionMan_->doPreForce(sdat);
803            }
804 <          fDecomp_->distributeIntermediateData();        
804 >
805 >          fDecomp_->distributeIntermediateData();
806 >
807          }
808        }
440 –
809      }
810      
811      fDecomp_->collectData();
812 <    
813 <    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);    
812 >        
813 >    if (info_->requiresSelfCorrection()) {
814  
815 <        if (info_->requiresSkipCorrection()) {
816 <          vector<int> skipList = fDecomp_->getSkipsForAtom(atom1);
817 <          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 <        }
815 >      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
816 >        fDecomp_->fillSelfData(sdat, atom1);
817 >        interactionMan_->doSelfCorrection(sdat);
818        }
466 –    }
819  
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
820      }
821 <        
821 >
822 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
823 >      *(fDecomp_->getPairwisePotential());
824 >
825 >    lrPot = longRangePotential.sum();
826 >
827      //store the tau and long range potential    
828      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
829      curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
# Line 500 | Line 854 | namespace OpenMD {
854      MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
855                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
856   #endif
857 <    curSnapshot->statData.setTau(tau);
857 >    curSnapshot->setTau(tau);
858    }
859  
860   } //end namespace OpenMD

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