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Revision 1579 by gezelter, Thu Jun 9 20:26:29 2011 UTC vs.
Revision 1794 by gezelter, Thu Sep 6 19:44:06 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 57 | Line 58
58   #include "primitives/Torsion.hpp"
59   #include "primitives/Inversion.hpp"
60   #include "nonbonded/NonBondedInteraction.hpp"
61 + #include "perturbations/ElectricField.hpp"
62   #include "parallel/ForceMatrixDecomposition.hpp"
63  
64 + #include <cstdio>
65 + #include <iostream>
66 + #include <iomanip>
67 +
68   using namespace std;
69   namespace OpenMD {
70    
# Line 71 | Line 77 | namespace OpenMD {
77    /**
78     * setupCutoffs
79     *
80 <   * Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
80 >   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
81 >   * and cutoffPolicy
82     *
83     * cutoffRadius : realType
84     *  If the cutoffRadius was explicitly set, use that value.
# Line 81 | Line 88 | namespace OpenMD {
88     *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
89     *      Use the maximum suggested value that was found.
90     *
91 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
91 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
92 >   *                        or SHIFTED_POTENTIAL)
93     *      If cutoffMethod was explicitly set, use that choice.
94     *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
95     *
96     * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
97     *      If cutoffPolicy was explicitly set, use that choice.
98     *      If cutoffPolicy was not explicitly set, use TRADITIONAL
99 +   *
100 +   * switchingRadius : realType
101 +   *  If the cutoffMethod was set to SWITCHED:
102 +   *      If the switchingRadius was explicitly set, use that value
103 +   *          (but do a sanity check first).
104 +   *      If the switchingRadius was not explicitly set: use 0.85 *
105 +   *      cutoffRadius_
106 +   *  If the cutoffMethod was not set to SWITCHED:
107 +   *      Set switchingRadius equal to cutoffRadius for safety.
108     */
109    void ForceManager::setupCutoffs() {
110      
111      Globals* simParams_ = info_->getSimParams();
112      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
113 +    int mdFileVersion;
114 +    rCut_ = 0.0; //Needs a value for a later max() call;  
115      
116 +    if (simParams_->haveMDfileVersion())
117 +      mdFileVersion = simParams_->getMDfileVersion();
118 +    else
119 +      mdFileVersion = 0;
120 +  
121      if (simParams_->haveCutoffRadius()) {
122        rCut_ = simParams_->getCutoffRadius();
123      } else {      
# Line 123 | Line 147 | namespace OpenMD {
147          painCave.severity = OPENMD_INFO;
148          simError();
149        }
126 –      fDecomp_->setUserCutoff(rCut_);
150      }
151  
152 +    fDecomp_->setUserCutoff(rCut_);
153 +    interactionMan_->setCutoffRadius(rCut_);
154 +
155      map<string, CutoffMethod> stringToCutoffMethod;
156      stringToCutoffMethod["HARD"] = HARD;
157      stringToCutoffMethod["SWITCHED"] = SWITCHED;
# Line 149 | Line 175 | namespace OpenMD {
175          cutoffMethod_ = i->second;
176        }
177      } else {
178 <      sprintf(painCave.errMsg,
179 <              "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
180 <              "\tOpenMD will use SHIFTED_FORCE.\n");
181 <      painCave.isFatal = 0;
182 <      painCave.severity = OPENMD_INFO;
183 <      simError();
184 <      cutoffMethod_ = SHIFTED_FORCE;        
178 >      if (mdFileVersion > 1) {
179 >        sprintf(painCave.errMsg,
180 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
181 >                "\tOpenMD will use SHIFTED_FORCE.\n");
182 >        painCave.isFatal = 0;
183 >        painCave.severity = OPENMD_INFO;
184 >        simError();
185 >        cutoffMethod_ = SHIFTED_FORCE;        
186 >      } else {
187 >        // handle the case where the old file version was in play
188 >        // (there should be no cutoffMethod, so we have to deduce it
189 >        // from other data).        
190 >
191 >        sprintf(painCave.errMsg,
192 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
193 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
194 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
195 >                "\tbehavior of the older (version 1) code.  To remove this\n"
196 >                "\twarning, add an explicit cutoffMethod and change the top\n"
197 >                "\tof the file so that it begins with <OpenMD version=2>\n");
198 >        painCave.isFatal = 0;
199 >        painCave.severity = OPENMD_WARNING;
200 >        simError();            
201 >                
202 >        // The old file version tethered the shifting behavior to the
203 >        // electrostaticSummationMethod keyword.
204 >        
205 >        if (simParams_->haveElectrostaticSummationMethod()) {
206 >          string myMethod = simParams_->getElectrostaticSummationMethod();
207 >          toUpper(myMethod);
208 >        
209 >          if (myMethod == "SHIFTED_POTENTIAL") {
210 >            cutoffMethod_ = SHIFTED_POTENTIAL;
211 >          } else if (myMethod == "SHIFTED_FORCE") {
212 >            cutoffMethod_ = SHIFTED_FORCE;
213 >          }
214 >        
215 >          if (simParams_->haveSwitchingRadius())
216 >            rSwitch_ = simParams_->getSwitchingRadius();
217 >
218 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
219 >            if (simParams_->haveSwitchingRadius()){
220 >              sprintf(painCave.errMsg,
221 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
222 >                      "\tA value was set for the switchingRadius\n"
223 >                      "\teven though the electrostaticSummationMethod was\n"
224 >                      "\tset to %s\n", myMethod.c_str());
225 >              painCave.severity = OPENMD_WARNING;
226 >              painCave.isFatal = 1;
227 >              simError();            
228 >            }
229 >          }
230 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
231 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
232 >              sprintf(painCave.errMsg,
233 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
234 >                      "\tcutoffRadius and switchingRadius are set to the\n"
235 >                      "\tsame value.  OpenMD will use shifted force\n"
236 >                      "\tpotentials instead of switching functions.\n");
237 >              painCave.isFatal = 0;
238 >              painCave.severity = OPENMD_WARNING;
239 >              simError();            
240 >            } else {
241 >              cutoffMethod_ = SHIFTED_POTENTIAL;
242 >              sprintf(painCave.errMsg,
243 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
244 >                      "\tcutoffRadius and switchingRadius are set to the\n"
245 >                      "\tsame value.  OpenMD will use shifted potentials\n"
246 >                      "\tinstead of switching functions.\n");
247 >              painCave.isFatal = 0;
248 >              painCave.severity = OPENMD_WARNING;
249 >              simError();            
250 >            }
251 >          }
252 >        }
253 >      }
254      }
255  
256      map<string, CutoffPolicy> stringToCutoffPolicy;
# Line 163 | Line 258 | namespace OpenMD {
258      stringToCutoffPolicy["MAX"] = MAX;
259      stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
260  
261 <    std::string cutPolicy;
261 >    string cutPolicy;
262      if (forceFieldOptions_.haveCutoffPolicy()){
263        cutPolicy = forceFieldOptions_.getCutoffPolicy();
264      }else if (simParams_->haveCutoffPolicy()) {
# Line 196 | Line 291 | namespace OpenMD {
291        simError();
292        cutoffPolicy_ = TRADITIONAL;        
293      }
199 –    fDecomp_->setCutoffPolicy(cutoffPolicy_);
200 –  }
294  
295 <  /**
296 <   * setupSwitching
204 <   *
205 <   * Sets the values of switchingRadius and
206 <   *  If the switchingRadius was explicitly set, use that value (but check it)
207 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
208 <   */
209 <  void ForceManager::setupSwitching() {
210 <    Globals* simParams_ = info_->getSimParams();
211 <
295 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
296 >        
297      // create the switching function object:
298 +
299      switcher_ = new SwitchingFunction();
300 <    
301 <    if (simParams_->haveSwitchingRadius()) {
302 <      rSwitch_ = simParams_->getSwitchingRadius();
303 <      if (rSwitch_ > rCut_) {        
300 >  
301 >    if (cutoffMethod_ == SWITCHED) {
302 >      if (simParams_->haveSwitchingRadius()) {
303 >        rSwitch_ = simParams_->getSwitchingRadius();
304 >        if (rSwitch_ > rCut_) {        
305 >          sprintf(painCave.errMsg,
306 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
307 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
308 >          painCave.isFatal = 1;
309 >          painCave.severity = OPENMD_ERROR;
310 >          simError();
311 >        }
312 >      } else {      
313 >        rSwitch_ = 0.85 * rCut_;
314          sprintf(painCave.errMsg,
315 <                "ForceManager::setupSwitching: switchingRadius (%f) is larger "
316 <                "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
317 <        painCave.isFatal = 1;
318 <        painCave.severity = OPENMD_ERROR;
315 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
316 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
317 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
318 >        painCave.isFatal = 0;
319 >        painCave.severity = OPENMD_WARNING;
320          simError();
321        }
322 <    } else {      
323 <      rSwitch_ = 0.85 * rCut_;
324 <      sprintf(painCave.errMsg,
325 <              "ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
326 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
327 <              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
328 <      painCave.isFatal = 0;
329 <      painCave.severity = OPENMD_WARNING;
330 <      simError();
331 <    }          
322 >    } else {
323 >      if (mdFileVersion > 1) {
324 >        // throw an error if we define a switching radius and don't need one.
325 >        // older file versions should not do this.
326 >        if (simParams_->haveSwitchingRadius()) {
327 >          map<string, CutoffMethod>::const_iterator it;
328 >          string theMeth;
329 >          for (it = stringToCutoffMethod.begin();
330 >               it != stringToCutoffMethod.end(); ++it) {
331 >            if (it->second == cutoffMethod_) {
332 >              theMeth = it->first;
333 >              break;
334 >            }
335 >          }
336 >          sprintf(painCave.errMsg,
337 >                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
338 >                  "\tis not set to SWITCHED, so switchingRadius value\n"
339 >                  "\twill be ignored for this simulation\n", theMeth.c_str());
340 >          painCave.isFatal = 0;
341 >          painCave.severity = OPENMD_WARNING;
342 >          simError();
343 >        }
344 >      }
345 >      rSwitch_ = rCut_;
346 >    }
347      
348      // Default to cubic switching function.
349      sft_ = cubic;
# Line 259 | Line 371 | namespace OpenMD {
371      switcher_->setSwitchType(sft_);
372      switcher_->setSwitch(rSwitch_, rCut_);
373    }
374 +
375 +
376 +
377    
378    void ForceManager::initialize() {
379  
380      if (!info_->isTopologyDone()) {
381 +
382        info_->update();
383        interactionMan_->setSimInfo(info_);
384        interactionMan_->initialize();
# Line 270 | Line 386 | namespace OpenMD {
386        // We want to delay the cutoffs until after the interaction
387        // manager has set up the atom-atom interactions so that we can
388        // query them for suggested cutoff values
273 –
389        setupCutoffs();
275 –      setupSwitching();
390  
391        info_->prepareTopology();      
392 +
393 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
394 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
395 +      if (doHeatFlux_) doParticlePot_ = true;
396 +
397 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
398 +  
399      }
400  
401      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
402      
403 <    // Force fields can set options on how to scale van der Waals and electrostatic
404 <    // interactions for atoms connected via bonds, bends and torsions
405 <    // in this case the topological distance between atoms is:
403 >    // Force fields can set options on how to scale van der Waals and
404 >    // electrostatic interactions for atoms connected via bonds, bends
405 >    // and torsions in this case the topological distance between
406 >    // atoms is:
407      // 0 = topologically unconnected
408      // 1 = bonded together
409      // 2 = connected via a bend
# Line 303 | Line 425 | namespace OpenMD {
425      electrostaticScale_[2] = fopts.getelectrostatic13scale();
426      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
427      
428 +    if (info_->getSimParams()->haveElectricField()) {
429 +      ElectricField* eField = new ElectricField(info_);
430 +      perturbations_.push_back(eField);
431 +    }
432 +
433      fDecomp_->distributeInitialData();
434  
435      initialized_ = true;
# Line 329 | Line 456 | namespace OpenMD {
456      Molecule::CutoffGroupIterator ci;
457      CutoffGroup* cg;
458      
459 <    // forces are zeroed here, before any are accumulated.
459 >    // forces and potentials are zeroed here, before any are
460 >    // accumulated.
461      
462 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
463 +
464 +    snap->setBondPotential(0.0);
465 +    snap->setBendPotential(0.0);
466 +    snap->setTorsionPotential(0.0);
467 +    snap->setInversionPotential(0.0);
468 +
469 +    potVec zeroPot(0.0);
470 +    snap->setLongRangePotential(zeroPot);
471 +    snap->setExcludedPotentials(zeroPot);
472 +
473 +    snap->setRestraintPotential(0.0);
474 +    snap->setRawPotential(0.0);
475 +
476      for (mol = info_->beginMolecule(mi); mol != NULL;
477           mol = info_->nextMolecule(mi)) {
478 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
478 >      for(atom = mol->beginAtom(ai); atom != NULL;
479 >          atom = mol->nextAtom(ai)) {
480          atom->zeroForcesAndTorques();
481        }
482 <          
482 >      
483        //change the positions of atoms which belong to the rigidbodies
484        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
485             rb = mol->nextRigidBody(rbIter)) {
486          rb->zeroForcesAndTorques();
487        }        
488 <
488 >      
489        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
490          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
491              cg = mol->nextCutoffGroup(ci)) {
# Line 351 | Line 494 | namespace OpenMD {
494          }
495        }      
496      }
354 –  
355 –    // Zero out the stress tensor
356 –    tau *= 0.0;
497      
498 +    // Zero out the stress tensor
499 +    stressTensor *= 0.0;
500 +    // Zero out the heatFlux
501 +    fDecomp_->setHeatFlux( Vector3d(0.0) );    
502    }
503    
504    void ForceManager::shortRangeInteractions() {
# Line 387 | Line 531 | namespace OpenMD {
531  
532        for (bond = mol->beginBond(bondIter); bond != NULL;
533             bond = mol->nextBond(bondIter)) {
534 <        bond->calcForce();
534 >        bond->calcForce(doParticlePot_);
535          bondPotential += bond->getPotential();
536        }
537  
# Line 395 | Line 539 | namespace OpenMD {
539             bend = mol->nextBend(bendIter)) {
540          
541          RealType angle;
542 <        bend->calcForce(angle);
542 >        bend->calcForce(angle, doParticlePot_);
543          RealType currBendPot = bend->getPotential();          
544          
545          bendPotential += bend->getPotential();
# Line 405 | Line 549 | namespace OpenMD {
549            dataSet.prev.angle = dataSet.curr.angle = angle;
550            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
551            dataSet.deltaV = 0.0;
552 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
552 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
553 >                                                                  dataSet));
554          }else {
555            i->second.prev.angle = i->second.curr.angle;
556            i->second.prev.potential = i->second.curr.potential;
# Line 419 | Line 564 | namespace OpenMD {
564        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
565             torsion = mol->nextTorsion(torsionIter)) {
566          RealType angle;
567 <        torsion->calcForce(angle);
567 >        torsion->calcForce(angle, doParticlePot_);
568          RealType currTorsionPot = torsion->getPotential();
569          torsionPotential += torsion->getPotential();
570          map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
# Line 443 | Line 588 | namespace OpenMD {
588             inversion != NULL;
589             inversion = mol->nextInversion(inversionIter)) {
590          RealType angle;
591 <        inversion->calcForce(angle);
591 >        inversion->calcForce(angle, doParticlePot_);
592          RealType currInversionPot = inversion->getPotential();
593          inversionPotential += inversion->getPotential();
594          map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
# Line 463 | Line 608 | namespace OpenMD {
608          }      
609        }      
610      }
611 <    
612 <    RealType  shortRangePotential = bondPotential + bendPotential +
613 <      torsionPotential +  inversionPotential;    
611 >
612 > #ifdef IS_MPI
613 >    // Collect from all nodes.  This should eventually be moved into a
614 >    // SystemDecomposition, but this is a better place than in
615 >    // Thermo to do the collection.
616 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
617 >                              MPI::SUM);
618 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
619 >                              MPI::SUM);
620 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
621 >                              MPI::REALTYPE, MPI::SUM);
622 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
623 >                              MPI::REALTYPE, MPI::SUM);
624 > #endif
625 >
626      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
627 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
628 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
629 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
630 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
631 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
627 >
628 >    curSnapshot->setBondPotential(bondPotential);
629 >    curSnapshot->setBendPotential(bendPotential);
630 >    curSnapshot->setTorsionPotential(torsionPotential);
631 >    curSnapshot->setInversionPotential(inversionPotential);
632 >    
633 >    // RealType shortRangePotential = bondPotential + bendPotential +
634 >    //   torsionPotential +  inversionPotential;    
635 >
636 >    // curSnapshot->setShortRangePotential(shortRangePotential);
637    }
638    
639    void ForceManager::longRangeInteractions() {
640 <    // some of this initial stuff will go away:
640 >
641 >
642      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
643      DataStorage* config = &(curSnapshot->atomData);
644      DataStorage* cgConfig = &(curSnapshot->cgData);
482 –    RealType* frc = config->getArrayPointer(DataStorage::dslForce);
483 –    RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
484 –    RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
485 –    RealType* A = config->getArrayPointer(DataStorage::dslAmat);
486 –    RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
487 –    RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
645  
646 <    // new stuff starts here:
647 <    
646 >    //calculate the center of mass of cutoff group
647 >
648 >    SimInfo::MoleculeIterator mi;
649 >    Molecule* mol;
650 >    Molecule::CutoffGroupIterator ci;
651 >    CutoffGroup* cg;
652 >
653 >    if(info_->getNCutoffGroups() > 0){      
654 >      for (mol = info_->beginMolecule(mi); mol != NULL;
655 >           mol = info_->nextMolecule(mi)) {
656 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
657 >            cg = mol->nextCutoffGroup(ci)) {
658 >          cg->updateCOM();
659 >        }
660 >      }      
661 >    } else {
662 >      // center of mass of the group is the same as position of the atom  
663 >      // if cutoff group does not exist
664 >      cgConfig->position = config->position;
665 >      cgConfig->velocity = config->velocity;
666 >    }
667 >
668      fDecomp_->zeroWorkArrays();
669      fDecomp_->distributeData();
670      
671      int cg1, cg2, atom1, atom2, topoDist;
672 <    Vector3d d_grp, dag, d;
672 >    Vector3d d_grp, dag, d, gvel2, vel2;
673      RealType rgrpsq, rgrp, r2, r;
674      RealType electroMult, vdwMult;
675      RealType vij;
676 <    Vector3d fij, fg;
676 >    Vector3d fij, fg, f1;
677      tuple3<RealType, RealType, RealType> cuts;
678      RealType rCutSq;
679      bool in_switching_region;
# Line 505 | Line 682 | namespace OpenMD {
682      InteractionData idat;
683      SelfData sdat;
684      RealType mf;
508 –    potVec pot(0.0);
509 –    potVec longRangePotential(0.0);
510 –    RealType lrPot;
685      RealType vpair;
686 +    RealType dVdFQ1(0.0);
687 +    RealType dVdFQ2(0.0);
688 +    potVec longRangePotential(0.0);
689 +    potVec workPot(0.0);
690 +    potVec exPot(0.0);
691 +    Vector3d eField1(0.0);
692 +    Vector3d eField2(0.0);
693 +    vector<int>::iterator ia, jb;
694  
695      int loopStart, loopEnd;
696  
697 +    idat.vdwMult = &vdwMult;
698 +    idat.electroMult = &electroMult;
699 +    idat.pot = &workPot;
700 +    idat.excludedPot = &exPot;
701 +    sdat.pot = fDecomp_->getEmbeddingPotential();
702 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
703 +    idat.vpair = &vpair;
704 +    idat.dVdFQ1 = &dVdFQ1;
705 +    idat.dVdFQ2 = &dVdFQ2;
706 +    idat.eField1 = &eField1;
707 +    idat.eField2 = &eField2;  
708 +    idat.f1 = &f1;
709 +    idat.sw = &sw;
710 +    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
711 +    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
712 +    idat.doParticlePot = doParticlePot_;
713 +    idat.doElectricField = doElectricField_;
714 +    sdat.doParticlePot = doParticlePot_;
715 +    
716      loopEnd = PAIR_LOOP;
717      if (info_->requiresPrepair() ) {
718        loopStart = PREPAIR_LOOP;
719      } else {
720        loopStart = PAIR_LOOP;
721      }
521 –    
522 –
722      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
723      
724        if (iLoop == loopStart) {
725          bool update_nlist = fDecomp_->checkNeighborList();
726          if (update_nlist)
727            neighborList = fDecomp_->buildNeighborList();
728 <      }      
729 <        
728 >      }            
729 >
730        for (vector<pair<int, int> >::iterator it = neighborList.begin();
731               it != neighborList.end(); ++it) {
732                  
# Line 537 | Line 736 | namespace OpenMD {
736          cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
737  
738          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
739 +
740          curSnapshot->wrapVector(d_grp);        
741          rgrpsq = d_grp.lengthSquare();
542 –
742          rCutSq = cuts.second;
743  
744          if (rgrpsq < rCutSq) {
745            idat.rcut = &cuts.first;
746            if (iLoop == PAIR_LOOP) {
747 <            vij *= 0.0;
747 >            vij = 0.0;
748              fij = V3Zero;
749            }
750            
751            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
752                                                       rgrp);
753  
555 –          idat.sw = &sw;
556 –              
754            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
755            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
756  
757 <          for (vector<int>::iterator ia = atomListRow.begin();
757 >          if (doHeatFlux_)
758 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
759 >
760 >          for (ia = atomListRow.begin();
761                 ia != atomListRow.end(); ++ia) {            
762              atom1 = (*ia);
763 <            
764 <            for (vector<int>::iterator jb = atomListColumn.begin();
763 >
764 >            for (jb = atomListColumn.begin();
765                   jb != atomListColumn.end(); ++jb) {              
766                atom2 = (*jb);
767 <              
768 <              cerr << "doing atoms " << atom1 << " " << atom2 << "\n";
769 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
570 <                
767 >
768 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
769 >
770                  vpair = 0.0;
771 +                workPot = 0.0;
772 +                exPot = 0.0;
773 +                f1 = V3Zero;
774 +                dVdFQ1 = 0.0;
775 +                dVdFQ2 = 0.0;
776  
777 <                cerr << "filling idat atoms " << atom1 << " " << atom2 << "\n";
778 <                idat = fDecomp_->fillInteractionData(atom1, atom2);
575 <                cerr << "done with idat\n";
576 <                
777 >                fDecomp_->fillInteractionData(idat, atom1, atom2);
778 >
779                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
780                  vdwMult = vdwScale_[topoDist];
781                  electroMult = electrostaticScale_[topoDist];
782  
581 –                idat.vdwMult = &vdwMult;
582 –                idat.electroMult = &electroMult;
583 –                idat.pot = &pot;
584 –                idat.vpair = &vpair;
585 –
783                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
784                    idat.d = &d_grp;
785                    idat.r2 = &rgrpsq;
786 +                  if (doHeatFlux_)
787 +                    vel2 = gvel2;
788                  } else {
789                    d = fDecomp_->getInteratomicVector(atom1, atom2);
790                    curSnapshot->wrapVector( d );
791                    r2 = d.lengthSquare();
792                    idat.d = &d;
793                    idat.r2 = &r2;
794 +                  if (doHeatFlux_)
795 +                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
796                  }
797 <                
798 <                cerr << "d = " << d << "\n";
598 <                cerr << "r2 = " << r2 << "\n";
599 <                r = sqrt( r2 );
797 >              
798 >                r = sqrt( *(idat.r2) );
799                  idat.rij = &r;
800                
801                  if (iLoop == PREPAIR_LOOP) {
802                    interactionMan_->doPrePair(idat);
803                  } else {
605 –                  cerr << "doing doPair " << atom1 << " " << atom2 << " " << r << "\n";
804                    interactionMan_->doPair(idat);
805                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
806 <                  vij += *(idat.vpair);
807 <                  fij += *(idat.f1);
808 <                  tau -= outProduct( *(idat.d), *(idat.f1));
806 >                  vij += vpair;
807 >                  fij += f1;
808 >                  stressTensor -= outProduct( *(idat.d), f1);
809 >                  if (doHeatFlux_)
810 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
811                  }
812                }
813              }
# Line 617 | Line 817 | namespace OpenMD {
817              if (in_switching_region) {
818                swderiv = vij * dswdr / rgrp;
819                fg = swderiv * d_grp;
620 –
820                fij += fg;
821  
822                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
823 <                tau -= outProduct( *(idat.d), fg);
823 >                stressTensor -= outProduct( *(idat.d), fg);
824 >                if (doHeatFlux_)
825 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
826 >                
827                }
828            
829 <              for (vector<int>::iterator ia = atomListRow.begin();
829 >              for (ia = atomListRow.begin();
830                     ia != atomListRow.end(); ++ia) {            
831                  atom1 = (*ia);                
832                  mf = fDecomp_->getMassFactorRow(atom1);
# Line 632 | Line 834 | namespace OpenMD {
834                  // presence in switching region
835                  fg = swderiv * d_grp * mf;
836                  fDecomp_->addForceToAtomRow(atom1, fg);
635 –
837                  if (atomListRow.size() > 1) {
838                    if (info_->usesAtomicVirial()) {
839                      // find the distance between the atom
840                      // and the center of the cutoff group:
841                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
842 <                    tau -= outProduct(dag, fg);
842 >                    stressTensor -= outProduct(dag, fg);
843 >                    if (doHeatFlux_)
844 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
845                    }
846                  }
847                }
848 <              for (vector<int>::iterator jb = atomListColumn.begin();
848 >              for (jb = atomListColumn.begin();
849                     jb != atomListColumn.end(); ++jb) {              
850                  atom2 = (*jb);
851                  mf = fDecomp_->getMassFactorColumn(atom2);
# Line 656 | Line 859 | namespace OpenMD {
859                      // find the distance between the atom
860                      // and the center of the cutoff group:
861                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
862 <                    tau -= outProduct(dag, fg);
862 >                    stressTensor -= outProduct(dag, fg);
863 >                    if (doHeatFlux_)
864 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
865                    }
866                  }
867                }
868              }
869 <            //if (!SIM_uses_AtomicVirial) {
870 <            //  tau -= outProduct(d_grp, fij);
869 >            //if (!info_->usesAtomicVirial()) {
870 >            //  stressTensor -= outProduct(d_grp, fij);
871 >            //  if (doHeatFlux_)
872 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
873              //}
874            }
875          }
876        }
877  
878        if (iLoop == PREPAIR_LOOP) {
879 <        if (info_->requiresPrepair()) {            
879 >        if (info_->requiresPrepair()) {
880 >
881            fDecomp_->collectIntermediateData();
882  
883 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
884 <            sdat = fDecomp_->fillSelfData(atom1);
883 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
884 >            fDecomp_->fillSelfData(sdat, atom1);
885              interactionMan_->doPreForce(sdat);
886            }
887  
888 <          fDecomp_->distributeIntermediateData();        
888 >          fDecomp_->distributeIntermediateData();
889 >
890          }
891        }
683 –
892      }
893      
894 +    // collects pairwise information
895      fDecomp_->collectData();
687 –    
688 –    if ( info_->requiresSkipCorrection() ) {
689 –      
690 –      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
691 –
692 –        vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 );
896          
694 –        for (vector<int>::iterator jb = skipList.begin();
695 –             jb != skipList.end(); ++jb) {        
696 –    
697 –          atom2 = (*jb);
698 –          idat = fDecomp_->fillSkipData(atom1, atom2);
699 –          interactionMan_->doSkipCorrection(idat);
700 –
701 –        }
702 –      }
703 –    }
704 –    
897      if (info_->requiresSelfCorrection()) {
898 <
899 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
708 <        sdat = fDecomp_->fillSelfData(atom1);
898 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
899 >        fDecomp_->fillSelfData(sdat, atom1);
900          interactionMan_->doSelfCorrection(sdat);
901        }
711 –
902      }
903  
904 <    longRangePotential = fDecomp_->getLongRangePotential();
905 <    lrPot = longRangePotential.sum();
904 >    // collects single-atom information
905 >    fDecomp_->collectSelfData();
906  
907 <    //store the tau and long range potential    
908 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
909 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
910 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
907 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
908 >      *(fDecomp_->getPairwisePotential());
909 >
910 >    curSnapshot->setLongRangePotential(longRangePotential);
911 >
912 >    // collects single-atom information
913 >    fDecomp_->collectSelfData();
914 >
915 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
916 >      *(fDecomp_->getPairwisePotential());
917 >
918 >    curSnapshot->setLongRangePotential(longRangePotential);
919 >    
920 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
921 >                                         *(fDecomp_->getExcludedPotential()));
922 >
923    }
924  
925    
926    void ForceManager::postCalculation() {
927 +
928 +    vector<Perturbation*>::iterator pi;
929 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
930 +      (*pi)->applyPerturbation();
931 +    }
932 +
933      SimInfo::MoleculeIterator mi;
934      Molecule* mol;
935      Molecule::RigidBodyIterator rbIter;
936      RigidBody* rb;
937      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
938 <    
938 >  
939      // collect the atomic forces onto rigid bodies
940      
941      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 735 | Line 943 | namespace OpenMD {
943        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
944             rb = mol->nextRigidBody(rbIter)) {
945          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
946 <        tau += rbTau;
946 >        stressTensor += rbTau;
947        }
948      }
949      
950   #ifdef IS_MPI
951 <    Mat3x3d tmpTau(tau);
952 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
745 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
951 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
952 >                              MPI::REALTYPE, MPI::SUM);
953   #endif
954 <    curSnapshot->statData.setTau(tau);
954 >    curSnapshot->setStressTensor(stressTensor);
955 >    
956    }
749 –
957   } //end namespace OpenMD

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