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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1570 by gezelter, Thu May 26 21:56:04 2011 UTC vs.
Revision 1711 by gezelter, Sat May 19 02:58:35 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 >          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 >    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 >      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
393 >      cerr << "dPP = " << doParticlePot_ << "\n";
394 >  
395      }
396 +
397 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
398      
399 +    // Force fields can set options on how to scale van der Waals and
400 +    // electrostatic interactions for atoms connected via bonds, bends
401 +    // and torsions in this case the topological distance between
402 +    // atoms is:
403 +    // 0 = topologically unconnected
404 +    // 1 = bonded together
405 +    // 2 = connected via a bend
406 +    // 3 = connected via a torsion
407 +    
408 +    vdwScale_.reserve(4);
409 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
410 +
411 +    electrostaticScale_.reserve(4);
412 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
413 +
414 +    vdwScale_[0] = 1.0;
415 +    vdwScale_[1] = fopts.getvdw12scale();
416 +    vdwScale_[2] = fopts.getvdw13scale();
417 +    vdwScale_[3] = fopts.getvdw14scale();
418 +    
419 +    electrostaticScale_[0] = 1.0;
420 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
421 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
422 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
423 +    
424 +    fDecomp_->distributeInitialData();
425 +
426 +    initialized_ = true;
427 +
428 +  }
429 +
430 +  void ForceManager::calcForces() {
431 +    
432 +    if (!initialized_) initialize();
433 +
434      preCalculation();  
435      shortRangeInteractions();
436      longRangeInteractions();
437 <    postCalculation();
88 <    
437 >    postCalculation();    
438    }
439    
440    void ForceManager::preCalculation() {
# Line 102 | Line 451 | namespace OpenMD {
451      
452      for (mol = info_->beginMolecule(mi); mol != NULL;
453           mol = info_->nextMolecule(mi)) {
454 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
454 >      for(atom = mol->beginAtom(ai); atom != NULL;
455 >          atom = mol->nextAtom(ai)) {
456          atom->zeroForcesAndTorques();
457        }
458 <          
458 >      
459        //change the positions of atoms which belong to the rigidbodies
460        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
461             rb = mol->nextRigidBody(rbIter)) {
462          rb->zeroForcesAndTorques();
463        }        
464 <
464 >      
465        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
466          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
467              cg = mol->nextCutoffGroup(ci)) {
# Line 120 | Line 470 | namespace OpenMD {
470          }
471        }      
472      }
473 <  
473 >    
474      // Zero out the stress tensor
475      tau *= 0.0;
476      
# Line 174 | Line 524 | namespace OpenMD {
524            dataSet.prev.angle = dataSet.curr.angle = angle;
525            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
526            dataSet.deltaV = 0.0;
527 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
527 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
528 >                                                                  dataSet));
529          }else {
530            i->second.prev.angle = i->second.curr.angle;
531            i->second.prev.potential = i->second.curr.potential;
# Line 245 | Line 596 | namespace OpenMD {
596    
597    void ForceManager::longRangeInteractions() {
598  
248 –    // some of this initial stuff will go away:
599      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
600      DataStorage* config = &(curSnapshot->atomData);
601      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;    
602  
603 <    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
604 <      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
603 >    //calculate the center of mass of cutoff group
604 >
605 >    SimInfo::MoleculeIterator mi;
606 >    Molecule* mol;
607 >    Molecule::CutoffGroupIterator ci;
608 >    CutoffGroup* cg;
609 >
610 >    if(info_->getNCutoffGroups() > 0){      
611 >      for (mol = info_->beginMolecule(mi); mol != NULL;
612 >           mol = info_->nextMolecule(mi)) {
613 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
614 >            cg = mol->nextCutoffGroup(ci)) {
615 >          cg->updateCOM();
616 >        }
617 >      }      
618      } else {
619        // center of mass of the group is the same as position of the atom  
620        // if cutoff group does not exist
621 <      rc = pos;
621 >      cgConfig->position = config->position;
622      }
267 –    
268 –    //initialize data before passing to fortran
269 –    RealType longRangePotential[N_INTERACTION_FAMILIES];
270 –    RealType lrPot = 0.0;
271 –    int isError = 0;
623  
624 <    // 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 <
624 >    fDecomp_->zeroWorkArrays();
625      fDecomp_->distributeData();
626 <
627 <    int cg1, cg2, atom1, atom2;
628 <    Vector3d d_grp, dag;
629 <    RealType rgrpsq, rgrp;
626 >    
627 >    int cg1, cg2, atom1, atom2, topoDist;
628 >    Vector3d d_grp, dag, d;
629 >    RealType rgrpsq, rgrp, r2, r;
630 >    RealType electroMult, vdwMult;
631      RealType vij;
632 <    Vector3d fij, fg;
633 <    pair<int, int> gtypes;
632 >    Vector3d fij, fg, f1;
633 >    tuple3<RealType, RealType, RealType> cuts;
634      RealType rCutSq;
635      bool in_switching_region;
636      RealType sw, dswdr, swderiv;
# Line 292 | Line 638 | namespace OpenMD {
638      InteractionData idat;
639      SelfData sdat;
640      RealType mf;
641 +    RealType lrPot;
642 +    RealType vpair;
643 +    potVec longRangePotential(0.0);
644 +    potVec workPot(0.0);
645  
646      int loopStart, loopEnd;
647  
648 +    idat.vdwMult = &vdwMult;
649 +    idat.electroMult = &electroMult;
650 +    idat.pot = &workPot;
651 +    sdat.pot = fDecomp_->getEmbeddingPotential();
652 +    idat.vpair = &vpair;
653 +    idat.f1 = &f1;
654 +    idat.sw = &sw;
655 +    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
656 +    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
657 +    idat.doParticlePot = doParticlePot_;
658 +    sdat.doParticlePot = doParticlePot_;
659 +    
660      loopEnd = PAIR_LOOP;
661      if (info_->requiresPrepair() ) {
662        loopStart = PREPAIR_LOOP;
663      } else {
664        loopStart = PAIR_LOOP;
665      }
666 <
667 <    for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
668 <      
666 >  
667 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
668 >    
669        if (iLoop == loopStart) {
670          bool update_nlist = fDecomp_->checkNeighborList();
671          if (update_nlist)
672            neighborList = fDecomp_->buildNeighborList();
673 <      }
673 >      }            
674  
675        for (vector<pair<int, int> >::iterator it = neighborList.begin();
676               it != neighborList.end(); ++it) {
677 <        
677 >                
678          cg1 = (*it).first;
679          cg2 = (*it).second;
680 +        
681 +        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
682  
319 –        gtypes = fDecomp_->getGroupTypes(cg1, cg2);
683          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
684 +
685          curSnapshot->wrapVector(d_grp);        
686          rgrpsq = d_grp.lengthSquare();
687 <        rCutSq = groupCutoffMap[gtypes].first;
687 >        rCutSq = cuts.second;
688  
689          if (rgrpsq < rCutSq) {
690 <          *(idat.rcut) = groupCutoffMap[gtypes].second;
690 >          idat.rcut = &cuts.first;
691            if (iLoop == PAIR_LOOP) {
692 <            vij *= 0.0;
692 >            vij = 0.0;
693              fij = V3Zero;
694            }
695            
696 <          in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
697 <                                                  rgrp);              
696 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
697 >                                                     rgrp);
698 >          
699            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
700            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
701  
# Line 341 | Line 706 | namespace OpenMD {
706              for (vector<int>::iterator jb = atomListColumn.begin();
707                   jb != atomListColumn.end(); ++jb) {              
708                atom2 = (*jb);
709 <              
709 >
710                if (!fDecomp_->skipAtomPair(atom1, atom2)) {
711 +                vpair = 0.0;
712 +                workPot = 0.0;
713 +                f1 = V3Zero;
714 +
715 +                fDecomp_->fillInteractionData(idat, atom1, atom2);
716                  
717 <                idat = fDecomp_->fillInteractionData(atom1, atom2);
717 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
718 >                vdwMult = vdwScale_[topoDist];
719 >                electroMult = electrostaticScale_[topoDist];
720  
721                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
722 <                  *(idat.d) = d_grp;
723 <                  *(idat.r2) = rgrpsq;
722 >                  idat.d = &d_grp;
723 >                  idat.r2 = &rgrpsq;
724                  } else {
725 <                  *(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
726 <                  curSnapshot->wrapVector( *(idat.d) );
727 <                  *(idat.r2) = idat.d->lengthSquare();
725 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
726 >                  curSnapshot->wrapVector( d );
727 >                  r2 = d.lengthSquare();
728 >                  idat.d = &d;
729 >                  idat.r2 = &r2;
730                  }
357 –                
358 –                *(idat.rij) = sqrt( *(idat.r2) );
731                
732 +                r = sqrt( *(idat.r2) );
733 +                idat.rij = &r;
734 +              
735                  if (iLoop == PREPAIR_LOOP) {
736                    interactionMan_->doPrePair(idat);
737                  } else {
738                    interactionMan_->doPair(idat);
739 <                  vij += *(idat.vpair);
740 <                  fij += *(idat.f1);
741 <                  tau -= outProduct( *(idat.d), *(idat.f1));
739 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
740 >                  vij += vpair;
741 >                  fij += f1;
742 >                  tau -= outProduct( *(idat.d), f1);
743                  }
744                }
745              }
# Line 373 | Line 749 | namespace OpenMD {
749              if (in_switching_region) {
750                swderiv = vij * dswdr / rgrp;
751                fg = swderiv * d_grp;
376 –
752                fij += fg;
753  
754                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
# Line 388 | Line 763 | namespace OpenMD {
763                  // presence in switching region
764                  fg = swderiv * d_grp * mf;
765                  fDecomp_->addForceToAtomRow(atom1, fg);
391 –
766                  if (atomListRow.size() > 1) {
767                    if (info_->usesAtomicVirial()) {
768                      // find the distance between the atom
# Line 417 | Line 791 | namespace OpenMD {
791                  }
792                }
793              }
794 <            //if (!SIM_uses_AtomicVirial) {
794 >            //if (!info_->usesAtomicVirial()) {
795              //  tau -= outProduct(d_grp, fij);
796              //}
797            }
# Line 425 | Line 799 | namespace OpenMD {
799        }
800  
801        if (iLoop == PREPAIR_LOOP) {
802 <        if (info_->requiresPrepair()) {            
802 >        if (info_->requiresPrepair()) {
803 >
804            fDecomp_->collectIntermediateData();
805  
806            for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
807 <            sdat = fDecomp_->fillSelfData(atom1);
807 >            fDecomp_->fillSelfData(sdat, atom1);
808              interactionMan_->doPreForce(sdat);
809            }
810  
811 <          fDecomp_->distributeIntermediateData();        
811 >          fDecomp_->distributeIntermediateData();
812 >
813          }
814        }
439 –
815      }
816      
817      fDecomp_->collectData();
443 –    
444 –    if ( info_->requiresSkipCorrection() ) {
445 –      
446 –      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
447 –
448 –        vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
818          
450 –        for (vector<int>::iterator jb = skipList.begin();
451 –             jb != skipList.end(); ++jb) {        
452 –    
453 –          atom2 = (*jb);
454 –          idat = fDecomp_->fillSkipData(atom1, atom2);
455 –          interactionMan_->doSkipCorrection(idat);
456 –
457 –        }
458 –      }
459 –    }
460 –    
819      if (info_->requiresSelfCorrection()) {
820  
821        for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
822 <        sdat = fDecomp_->fillSelfData(atom1);
822 >        fDecomp_->fillSelfData(sdat, atom1);
823          interactionMan_->doSelfCorrection(sdat);
824        }
825  
826      }
827  
828 <    // dangerous to iterate over enums, but we'll live on the edge:
829 <    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
830 <      lrPot += longRangePotential[i]; //Quick hack
831 <    }
832 <        
828 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
829 >      *(fDecomp_->getPairwisePotential());
830 >
831 >    lrPot = longRangePotential.sum();
832 >
833      //store the tau and long range potential    
834      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
835      curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
# Line 502 | Line 860 | namespace OpenMD {
860      MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
861                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
862   #endif
863 <    curSnapshot->statData.setTau(tau);
863 >    curSnapshot->setTau(tau);
864    }
865  
866   } //end namespace OpenMD

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