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Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
Revision 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
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   /**
44   * @file ForceManager.cpp
45   * @author tlin
46   * @date 11/09/2004
46 – * @time 10:39am
47   * @version 1.0
48   */
49  
# Line 57 | Line 57
57   #include "primitives/Torsion.hpp"
58   #include "primitives/Inversion.hpp"
59   #include "nonbonded/NonBondedInteraction.hpp"
60 + #include "perturbations/ElectricField.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      forceField_ = info_->getForceField();
72 <    fDecomp_ = new ForceMatrixDecomposition(info_);
72 >    interactionMan_ = new InteractionManager();
73 >    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74    }
75  
76    /**
77     * setupCutoffs
78     *
79 <   * Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
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.
# Line 80 | Line 87 | namespace OpenMD {
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, SHIFTED_POTENTIAL)
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 +    rCut_ = 0.0; //Needs a value for a later max() call;  
114      
115 +    if (simParams_->haveMDfileVersion())
116 +      mdFileVersion = simParams_->getMDfileVersion();
117 +    else
118 +      mdFileVersion = 0;
119 +  
120 +    // We need the list of simulated atom types to figure out cutoffs
121 +    // as well as long range corrections.
122 +
123 +    set<AtomType*>::iterator i;
124 +    set<AtomType*> atomTypes_;
125 +    atomTypes_ = info_->getSimulatedAtomTypes();
126 +
127      if (simParams_->haveCutoffRadius()) {
128        rCut_ = simParams_->getCutoffRadius();
129      } else {      
# Line 107 | Line 138 | namespace OpenMD {
138          rCut_ = 12.0;
139        } else {
140          RealType thisCut;
141 <        set<AtomType*>::iterator i;
111 <        set<AtomType*> atomTypes;
112 <        atomTypes = info_->getSimulatedAtomTypes();        
113 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
141 >        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
142            thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
143            rCut_ = max(thisCut, rCut_);
144          }
# Line 121 | Line 149 | namespace OpenMD {
149          painCave.isFatal = 0;
150          painCave.severity = OPENMD_INFO;
151          simError();
152 <      }            
152 >      }
153      }
154  
155 +    fDecomp_->setUserCutoff(rCut_);
156 +    interactionMan_->setCutoffRadius(rCut_);
157 +
158      map<string, CutoffMethod> stringToCutoffMethod;
159      stringToCutoffMethod["HARD"] = HARD;
160      stringToCutoffMethod["SWITCHED"] = SWITCHED;
# Line 147 | Line 178 | namespace OpenMD {
178          cutoffMethod_ = i->second;
179        }
180      } else {
181 <      sprintf(painCave.errMsg,
182 <              "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
183 <              "\tOpenMD will use SHIFTED_FORCE.\n");
184 <      painCave.isFatal = 0;
185 <      painCave.severity = OPENMD_INFO;
186 <      simError();
187 <      cutoffMethod_ = SHIFTED_FORCE;        
181 >      if (mdFileVersion > 1) {
182 >        sprintf(painCave.errMsg,
183 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
184 >                "\tOpenMD will use SHIFTED_FORCE.\n");
185 >        painCave.isFatal = 0;
186 >        painCave.severity = OPENMD_INFO;
187 >        simError();
188 >        cutoffMethod_ = SHIFTED_FORCE;        
189 >      } else {
190 >        // handle the case where the old file version was in play
191 >        // (there should be no cutoffMethod, so we have to deduce it
192 >        // from other data).        
193 >
194 >        sprintf(painCave.errMsg,
195 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
196 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
197 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
198 >                "\tbehavior of the older (version 1) code.  To remove this\n"
199 >                "\twarning, add an explicit cutoffMethod and change the top\n"
200 >                "\tof the file so that it begins with <OpenMD version=2>\n");
201 >        painCave.isFatal = 0;
202 >        painCave.severity = OPENMD_WARNING;
203 >        simError();            
204 >                
205 >        // The old file version tethered the shifting behavior to the
206 >        // electrostaticSummationMethod keyword.
207 >        
208 >        if (simParams_->haveElectrostaticSummationMethod()) {
209 >          string myMethod = simParams_->getElectrostaticSummationMethod();
210 >          toUpper(myMethod);
211 >        
212 >          if (myMethod == "SHIFTED_POTENTIAL") {
213 >            cutoffMethod_ = SHIFTED_POTENTIAL;
214 >          } else if (myMethod == "SHIFTED_FORCE") {
215 >            cutoffMethod_ = SHIFTED_FORCE;
216 >          }
217 >        
218 >          if (simParams_->haveSwitchingRadius())
219 >            rSwitch_ = simParams_->getSwitchingRadius();
220 >
221 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
222 >            if (simParams_->haveSwitchingRadius()){
223 >              sprintf(painCave.errMsg,
224 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
225 >                      "\tA value was set for the switchingRadius\n"
226 >                      "\teven though the electrostaticSummationMethod was\n"
227 >                      "\tset to %s\n", myMethod.c_str());
228 >              painCave.severity = OPENMD_WARNING;
229 >              painCave.isFatal = 1;
230 >              simError();            
231 >            }
232 >          }
233 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
234 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
235 >              sprintf(painCave.errMsg,
236 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
237 >                      "\tcutoffRadius and switchingRadius are set to the\n"
238 >                      "\tsame value.  OpenMD will use shifted force\n"
239 >                      "\tpotentials instead of switching functions.\n");
240 >              painCave.isFatal = 0;
241 >              painCave.severity = OPENMD_WARNING;
242 >              simError();            
243 >            } else {
244 >              cutoffMethod_ = SHIFTED_POTENTIAL;
245 >              sprintf(painCave.errMsg,
246 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
247 >                      "\tcutoffRadius and switchingRadius are set to the\n"
248 >                      "\tsame value.  OpenMD will use shifted potentials\n"
249 >                      "\tinstead of switching functions.\n");
250 >              painCave.isFatal = 0;
251 >              painCave.severity = OPENMD_WARNING;
252 >              simError();            
253 >            }
254 >          }
255 >        }
256 >      }
257      }
258  
259      map<string, CutoffPolicy> stringToCutoffPolicy;
# Line 161 | Line 261 | namespace OpenMD {
261      stringToCutoffPolicy["MAX"] = MAX;
262      stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
263  
264 <    std::string cutPolicy;
264 >    string cutPolicy;
265      if (forceFieldOptions_.haveCutoffPolicy()){
266        cutPolicy = forceFieldOptions_.getCutoffPolicy();
267      }else if (simParams_->haveCutoffPolicy()) {
# Line 194 | Line 294 | namespace OpenMD {
294        simError();
295        cutoffPolicy_ = TRADITIONAL;        
296      }
197 –  }
297  
298 <  /**
299 <   * setupSwitching
300 <   *
301 <   * Sets the values of switchingRadius and
302 <   *  If the switchingRadius was explicitly set, use that value (but check it)
303 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
304 <   */
305 <  void ForceManager::setupSwitching() {
306 <    Globals* simParams_ = info_->getSimParams();
307 <    
308 <    if (simParams_->haveSwitchingRadius()) {
309 <      rSwitch_ = simParams_->getSwitchingRadius();
310 <      if (rSwitch_ > rCut_) {        
298 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
299 >        
300 >    // create the switching function object:
301 >
302 >    switcher_ = new SwitchingFunction();
303 >  
304 >    if (cutoffMethod_ == SWITCHED) {
305 >      if (simParams_->haveSwitchingRadius()) {
306 >        rSwitch_ = simParams_->getSwitchingRadius();
307 >        if (rSwitch_ > rCut_) {        
308 >          sprintf(painCave.errMsg,
309 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
310 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
311 >          painCave.isFatal = 1;
312 >          painCave.severity = OPENMD_ERROR;
313 >          simError();
314 >        }
315 >      } else {      
316 >        rSwitch_ = 0.85 * rCut_;
317          sprintf(painCave.errMsg,
318 <                "ForceManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
319 <                rSwitch_, rCut_);
320 <        painCave.isFatal = 1;
321 <        painCave.severity = OPENMD_ERROR;
318 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
319 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
320 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
321 >        painCave.isFatal = 0;
322 >        painCave.severity = OPENMD_WARNING;
323          simError();
324        }
325 <    } else {      
326 <      rSwitch_ = 0.85 * rCut_;
327 <      sprintf(painCave.errMsg,
328 <              "ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
329 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
330 <              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
331 <      painCave.isFatal = 0;
332 <      painCave.severity = OPENMD_WARNING;
333 <      simError();
334 <    }          
325 >    } else {
326 >      if (mdFileVersion > 1) {
327 >        // throw an error if we define a switching radius and don't need one.
328 >        // older file versions should not do this.
329 >        if (simParams_->haveSwitchingRadius()) {
330 >          map<string, CutoffMethod>::const_iterator it;
331 >          string theMeth;
332 >          for (it = stringToCutoffMethod.begin();
333 >               it != stringToCutoffMethod.end(); ++it) {
334 >            if (it->second == cutoffMethod_) {
335 >              theMeth = it->first;
336 >              break;
337 >            }
338 >          }
339 >          sprintf(painCave.errMsg,
340 >                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
341 >                  "\tis not set to SWITCHED, so switchingRadius value\n"
342 >                  "\twill be ignored for this simulation\n", theMeth.c_str());
343 >          painCave.isFatal = 0;
344 >          painCave.severity = OPENMD_WARNING;
345 >          simError();
346 >        }
347 >      }
348 >      rSwitch_ = rCut_;
349 >    }
350      
351 +    // Default to cubic switching function.
352 +    sft_ = cubic;
353      if (simParams_->haveSwitchingFunctionType()) {
354        string funcType = simParams_->getSwitchingFunctionType();
355        toUpper(funcType);
# Line 251 | Line 374 | namespace OpenMD {
374      switcher_->setSwitchType(sft_);
375      switcher_->setSwitch(rSwitch_, rCut_);
376    }
377 +
378 +
379 +
380    
381    void ForceManager::initialize() {
382  
383      if (!info_->isTopologyDone()) {
384 +
385        info_->update();
386        interactionMan_->setSimInfo(info_);
387        interactionMan_->initialize();
# Line 262 | Line 389 | namespace OpenMD {
389        // We want to delay the cutoffs until after the interaction
390        // manager has set up the atom-atom interactions so that we can
391        // query them for suggested cutoff values
265 –
392        setupCutoffs();
267 –      setupSwitching();
393  
394        info_->prepareTopology();      
395 +
396 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
397 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
398 +      if (doHeatFlux_) doParticlePot_ = true;
399 +
400 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
401 +  
402      }
403  
404      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
405      
406 <    // Force fields can set options on how to scale van der Waals and electrostatic
407 <    // interactions for atoms connected via bonds, bends and torsions
408 <    // in this case the topological distance between atoms is:
406 >    // Force fields can set options on how to scale van der Waals and
407 >    // electrostatic interactions for atoms connected via bonds, bends
408 >    // and torsions in this case the topological distance between
409 >    // atoms is:
410      // 0 = topologically unconnected
411      // 1 = bonded together
412      // 2 = connected via a bend
# Line 295 | Line 428 | namespace OpenMD {
428      electrostaticScale_[2] = fopts.getelectrostatic13scale();
429      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
430      
431 +    if (info_->getSimParams()->haveElectricField()) {
432 +      ElectricField* eField = new ElectricField(info_);
433 +      perturbations_.push_back(eField);
434 +    }
435 +
436      fDecomp_->distributeInitialData();
437  
438      initialized_ = true;
# Line 321 | Line 459 | namespace OpenMD {
459      Molecule::CutoffGroupIterator ci;
460      CutoffGroup* cg;
461      
462 <    // forces are zeroed here, before any are accumulated.
462 >    // forces and potentials are zeroed here, before any are
463 >    // accumulated.
464      
465 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
466 +
467 +    snap->setBondPotential(0.0);
468 +    snap->setBendPotential(0.0);
469 +    snap->setTorsionPotential(0.0);
470 +    snap->setInversionPotential(0.0);
471 +
472 +    potVec zeroPot(0.0);
473 +    snap->setLongRangePotential(zeroPot);
474 +    snap->setExcludedPotentials(zeroPot);
475 +
476 +    snap->setRestraintPotential(0.0);
477 +    snap->setRawPotential(0.0);
478 +
479      for (mol = info_->beginMolecule(mi); mol != NULL;
480           mol = info_->nextMolecule(mi)) {
481 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
481 >      for(atom = mol->beginAtom(ai); atom != NULL;
482 >          atom = mol->nextAtom(ai)) {
483          atom->zeroForcesAndTorques();
484        }
485 <          
485 >      
486        //change the positions of atoms which belong to the rigidbodies
487        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
488             rb = mol->nextRigidBody(rbIter)) {
489          rb->zeroForcesAndTorques();
490        }        
491 <
491 >      
492        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
493          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
494              cg = mol->nextCutoffGroup(ci)) {
# Line 343 | Line 497 | namespace OpenMD {
497          }
498        }      
499      }
346 –  
347 –    // Zero out the stress tensor
348 –    tau *= 0.0;
500      
501 +    // Zero out the stress tensor
502 +    stressTensor *= 0.0;
503 +    // Zero out the heatFlux
504 +    fDecomp_->setHeatFlux( Vector3d(0.0) );    
505    }
506    
507    void ForceManager::shortRangeInteractions() {
# Line 379 | Line 534 | namespace OpenMD {
534  
535        for (bond = mol->beginBond(bondIter); bond != NULL;
536             bond = mol->nextBond(bondIter)) {
537 <        bond->calcForce();
537 >        bond->calcForce(doParticlePot_);
538          bondPotential += bond->getPotential();
539        }
540  
# Line 387 | Line 542 | namespace OpenMD {
542             bend = mol->nextBend(bendIter)) {
543          
544          RealType angle;
545 <        bend->calcForce(angle);
545 >        bend->calcForce(angle, doParticlePot_);
546          RealType currBendPot = bend->getPotential();          
547          
548          bendPotential += bend->getPotential();
# Line 397 | Line 552 | namespace OpenMD {
552            dataSet.prev.angle = dataSet.curr.angle = angle;
553            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
554            dataSet.deltaV = 0.0;
555 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
555 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
556 >                                                                  dataSet));
557          }else {
558            i->second.prev.angle = i->second.curr.angle;
559            i->second.prev.potential = i->second.curr.potential;
# Line 411 | Line 567 | namespace OpenMD {
567        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
568             torsion = mol->nextTorsion(torsionIter)) {
569          RealType angle;
570 <        torsion->calcForce(angle);
570 >        torsion->calcForce(angle, doParticlePot_);
571          RealType currTorsionPot = torsion->getPotential();
572          torsionPotential += torsion->getPotential();
573          map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
# Line 435 | Line 591 | namespace OpenMD {
591             inversion != NULL;
592             inversion = mol->nextInversion(inversionIter)) {
593          RealType angle;
594 <        inversion->calcForce(angle);
594 >        inversion->calcForce(angle, doParticlePot_);
595          RealType currInversionPot = inversion->getPotential();
596          inversionPotential += inversion->getPotential();
597          map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
# Line 455 | Line 611 | namespace OpenMD {
611          }      
612        }      
613      }
614 <    
615 <    RealType  shortRangePotential = bondPotential + bendPotential +
616 <      torsionPotential +  inversionPotential;    
614 >
615 > #ifdef IS_MPI
616 >    // Collect from all nodes.  This should eventually be moved into a
617 >    // SystemDecomposition, but this is a better place than in
618 >    // Thermo to do the collection.
619 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
620 >                              MPI::SUM);
621 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
622 >                              MPI::SUM);
623 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
624 >                              MPI::REALTYPE, MPI::SUM);
625 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
626 >                              MPI::REALTYPE, MPI::SUM);
627 > #endif
628 >
629      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
630 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
631 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
632 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
633 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
634 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
630 >
631 >    curSnapshot->setBondPotential(bondPotential);
632 >    curSnapshot->setBendPotential(bendPotential);
633 >    curSnapshot->setTorsionPotential(torsionPotential);
634 >    curSnapshot->setInversionPotential(inversionPotential);
635 >    
636 >    // RealType shortRangePotential = bondPotential + bendPotential +
637 >    //   torsionPotential +  inversionPotential;    
638 >
639 >    // curSnapshot->setShortRangePotential(shortRangePotential);
640    }
641    
642    void ForceManager::longRangeInteractions() {
643  
644 <    // some of this initial stuff will go away:
644 >
645      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
646      DataStorage* config = &(curSnapshot->atomData);
647      DataStorage* cgConfig = &(curSnapshot->cgData);
475 –    RealType* frc = config->getArrayPointer(DataStorage::dslForce);
476 –    RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
477 –    RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
478 –    RealType* A = config->getArrayPointer(DataStorage::dslAmat);
479 –    RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
480 –    RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
481 –    RealType* rc;    
648  
649 <    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
650 <      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
649 >    //calculate the center of mass of cutoff group
650 >
651 >    SimInfo::MoleculeIterator mi;
652 >    Molecule* mol;
653 >    Molecule::CutoffGroupIterator ci;
654 >    CutoffGroup* cg;
655 >
656 >    if(info_->getNCutoffGroups() > 0){      
657 >      for (mol = info_->beginMolecule(mi); mol != NULL;
658 >           mol = info_->nextMolecule(mi)) {
659 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
660 >            cg = mol->nextCutoffGroup(ci)) {
661 >          cg->updateCOM();
662 >        }
663 >      }      
664      } else {
665        // center of mass of the group is the same as position of the atom  
666        // if cutoff group does not exist
667 <      rc = pos;
667 >      cgConfig->position = config->position;
668 >      cgConfig->velocity = config->velocity;
669      }
670 <    
491 <    // new stuff starts here:
670 >
671      fDecomp_->zeroWorkArrays();
672      fDecomp_->distributeData();
673 <
674 <    int cg1, cg2, atom1, atom2;
675 <    Vector3d d_grp, dag;
676 <    RealType rgrpsq, rgrp;
673 >    
674 >    int cg1, cg2, atom1, atom2, topoDist;
675 >    Vector3d d_grp, dag, d, gvel2, vel2;
676 >    RealType rgrpsq, rgrp, r2, r;
677 >    RealType electroMult, vdwMult;
678      RealType vij;
679 <    Vector3d fij, fg;
679 >    Vector3d fij, fg, f1;
680      tuple3<RealType, RealType, RealType> cuts;
681      RealType rCutSq;
682      bool in_switching_region;
# Line 505 | Line 685 | namespace OpenMD {
685      InteractionData idat;
686      SelfData sdat;
687      RealType mf;
688 <    potVec pot(0.0);
688 >    RealType vpair;
689 >    RealType dVdFQ1(0.0);
690 >    RealType dVdFQ2(0.0);
691      potVec longRangePotential(0.0);
692 <    RealType lrPot;
692 >    potVec workPot(0.0);
693 >    potVec exPot(0.0);
694 >    Vector3d eField1(0.0);
695 >    Vector3d eField2(0.0);
696 >    vector<int>::iterator ia, jb;
697  
698      int loopStart, loopEnd;
699  
700 +    idat.vdwMult = &vdwMult;
701 +    idat.electroMult = &electroMult;
702 +    idat.pot = &workPot;
703 +    idat.excludedPot = &exPot;
704 +    sdat.pot = fDecomp_->getEmbeddingPotential();
705 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
706 +    idat.vpair = &vpair;
707 +    idat.dVdFQ1 = &dVdFQ1;
708 +    idat.dVdFQ2 = &dVdFQ2;
709 +    idat.eField1 = &eField1;
710 +    idat.eField2 = &eField2;  
711 +    idat.f1 = &f1;
712 +    idat.sw = &sw;
713 +    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
714 +    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
715 +    idat.doParticlePot = doParticlePot_;
716 +    idat.doElectricField = doElectricField_;
717 +    sdat.doParticlePot = doParticlePot_;
718 +    
719      loopEnd = PAIR_LOOP;
720      if (info_->requiresPrepair() ) {
721        loopStart = PREPAIR_LOOP;
722      } else {
723        loopStart = PAIR_LOOP;
724      }
725 <
726 <    for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
522 <      
725 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
726 >    
727        if (iLoop == loopStart) {
728          bool update_nlist = fDecomp_->checkNeighborList();
729          if (update_nlist)
730            neighborList = fDecomp_->buildNeighborList();
731 <      }
731 >      }            
732  
733        for (vector<pair<int, int> >::iterator it = neighborList.begin();
734               it != neighborList.end(); ++it) {
735 <        
735 >                
736          cg1 = (*it).first;
737          cg2 = (*it).second;
738          
739          cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
740  
741          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
742 +
743          curSnapshot->wrapVector(d_grp);        
744          rgrpsq = d_grp.lengthSquare();
540 –
745          rCutSq = cuts.second;
746  
747          if (rgrpsq < rCutSq) {
748 <          *(idat.rcut) = cuts.first;
748 >          idat.rcut = &cuts.first;
749            if (iLoop == PAIR_LOOP) {
750 <            vij *= 0.0;
750 >            vij = 0.0;
751              fij = V3Zero;
752 +            eField1 = V3Zero;
753 +            eField2 = V3Zero;
754            }
755            
756 <          in_switching_region = switcher_->getSwitch(rgrpsq, *(idat.sw), dswdr,
756 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
757                                                       rgrp);
758 <              
758 >
759            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
760            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
761  
762 <          for (vector<int>::iterator ia = atomListRow.begin();
762 >          if (doHeatFlux_)
763 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
764 >
765 >          for (ia = atomListRow.begin();
766                 ia != atomListRow.end(); ++ia) {            
767              atom1 = (*ia);
768 <            
769 <            for (vector<int>::iterator jb = atomListColumn.begin();
768 >
769 >            for (jb = atomListColumn.begin();
770                   jb != atomListColumn.end(); ++jb) {              
771                atom2 = (*jb);
563 –              
564 –              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
565 –                
566 –                pot *= 0.0;
772  
773 <                idat = fDecomp_->fillInteractionData(atom1, atom2);
569 <                *(idat.pot) = pot;
773 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
774  
775 +                vpair = 0.0;
776 +                workPot = 0.0;
777 +                exPot = 0.0;
778 +                f1 = V3Zero;
779 +                dVdFQ1 = 0.0;
780 +                dVdFQ2 = 0.0;
781 +
782 +                fDecomp_->fillInteractionData(idat, atom1, atom2);
783 +
784 +                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
785 +                vdwMult = vdwScale_[topoDist];
786 +                electroMult = electrostaticScale_[topoDist];
787 +
788                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
789 <                  *(idat.d) = d_grp;
790 <                  *(idat.r2) = rgrpsq;
789 >                  idat.d = &d_grp;
790 >                  idat.r2 = &rgrpsq;
791 >                  if (doHeatFlux_)
792 >                    vel2 = gvel2;
793                  } else {
794 <                  *(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
795 <                  curSnapshot->wrapVector( *(idat.d) );
796 <                  *(idat.r2) = idat.d->lengthSquare();
794 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
795 >                  curSnapshot->wrapVector( d );
796 >                  r2 = d.lengthSquare();
797 >                  idat.d = &d;
798 >                  idat.r2 = &r2;
799 >                  if (doHeatFlux_)
800 >                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
801                  }
579 –                
580 –                *(idat.rij) = sqrt( *(idat.r2) );
802                
803 +                r = sqrt( *(idat.r2) );
804 +                idat.rij = &r;
805 +              
806                  if (iLoop == PREPAIR_LOOP) {
807                    interactionMan_->doPrePair(idat);
808                  } else {
809                    interactionMan_->doPair(idat);
810                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
811 <                  vij += *(idat.vpair);
812 <                  fij += *(idat.f1);
813 <                  tau -= outProduct( *(idat.d), *(idat.f1));
811 >                  vij += vpair;
812 >                  fij += f1;
813 >                  stressTensor -= outProduct( *(idat.d), f1);
814 >                  if (doHeatFlux_)
815 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
816                  }
817                }
818              }
# Line 596 | Line 822 | namespace OpenMD {
822              if (in_switching_region) {
823                swderiv = vij * dswdr / rgrp;
824                fg = swderiv * d_grp;
599 –
825                fij += fg;
826  
827                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
828 <                tau -= outProduct( *(idat.d), fg);
828 >                if (!fDecomp_->skipAtomPair(atomListRow[0],
829 >                                            atomListColumn[0],
830 >                                            cg1, cg2)) {
831 >                  stressTensor -= outProduct( *(idat.d), fg);
832 >                  if (doHeatFlux_)
833 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
834 >                }                
835                }
836            
837 <              for (vector<int>::iterator ia = atomListRow.begin();
837 >              for (ia = atomListRow.begin();
838                     ia != atomListRow.end(); ++ia) {            
839                  atom1 = (*ia);                
840                  mf = fDecomp_->getMassFactorRow(atom1);
# Line 611 | Line 842 | namespace OpenMD {
842                  // presence in switching region
843                  fg = swderiv * d_grp * mf;
844                  fDecomp_->addForceToAtomRow(atom1, fg);
614 –
845                  if (atomListRow.size() > 1) {
846                    if (info_->usesAtomicVirial()) {
847                      // find the distance between the atom
848                      // and the center of the cutoff group:
849                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
850 <                    tau -= outProduct(dag, fg);
850 >                    stressTensor -= outProduct(dag, fg);
851 >                    if (doHeatFlux_)
852 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
853                    }
854                  }
855                }
856 <              for (vector<int>::iterator jb = atomListColumn.begin();
856 >              for (jb = atomListColumn.begin();
857                     jb != atomListColumn.end(); ++jb) {              
858                  atom2 = (*jb);
859                  mf = fDecomp_->getMassFactorColumn(atom2);
# Line 635 | Line 867 | namespace OpenMD {
867                      // find the distance between the atom
868                      // and the center of the cutoff group:
869                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
870 <                    tau -= outProduct(dag, fg);
870 >                    stressTensor -= outProduct(dag, fg);
871 >                    if (doHeatFlux_)
872 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
873                    }
874                  }
875                }
876              }
877 <            //if (!SIM_uses_AtomicVirial) {
878 <            //  tau -= outProduct(d_grp, fij);
877 >            //if (!info_->usesAtomicVirial()) {
878 >            //  stressTensor -= outProduct(d_grp, fij);
879 >            //  if (doHeatFlux_)
880 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
881              //}
882            }
883          }
884        }
885  
886        if (iLoop == PREPAIR_LOOP) {
887 <        if (info_->requiresPrepair()) {            
887 >        if (info_->requiresPrepair()) {
888 >
889            fDecomp_->collectIntermediateData();
890  
891 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
892 <            sdat = fDecomp_->fillSelfData(atom1);
891 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
892 >            fDecomp_->fillSelfData(sdat, atom1);
893              interactionMan_->doPreForce(sdat);
894            }
895  
896 <          fDecomp_->distributeIntermediateData();        
896 >          fDecomp_->distributeIntermediateData();
897 >
898          }
899        }
662 –
900      }
901      
902 +    // collects pairwise information
903      fDecomp_->collectData();
666 –    
667 –    if ( info_->requiresSkipCorrection() ) {
668 –      
669 –      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
670 –
671 –        vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
904          
673 –        for (vector<int>::iterator jb = skipList.begin();
674 –             jb != skipList.end(); ++jb) {        
675 –    
676 –          atom2 = (*jb);
677 –          idat = fDecomp_->fillSkipData(atom1, atom2);
678 –          interactionMan_->doSkipCorrection(idat);
679 –
680 –        }
681 –      }
682 –    }
683 –    
905      if (info_->requiresSelfCorrection()) {
906 <
907 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
687 <        sdat = fDecomp_->fillSelfData(atom1);
906 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
907 >        fDecomp_->fillSelfData(sdat, atom1);
908          interactionMan_->doSelfCorrection(sdat);
909        }
690 –
910      }
911  
912 <    longRangePotential = fDecomp_->getLongRangePotential();
913 <    lrPot = longRangePotential.sum();
912 >    // collects single-atom information
913 >    fDecomp_->collectSelfData();
914  
915 <    //store the tau and long range potential    
916 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
917 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
918 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
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 714 | 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(),
724 <                  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);
955 <  }
954 >    curSnapshot->setStressTensor(stressTensor);
955 >    
956 >    if (info_->getSimParams()->getUseLongRangeCorrections()) {
957 >      /*
958 >      RealType vol = curSnapshot->getVolume();
959 >      RealType Elrc(0.0);
960 >      RealType Wlrc(0.0);
961  
962 < } //end namespace OpenMD
962 >      set<AtomType*>::iterator i;
963 >      set<AtomType*>::iterator j;
964 >    
965 >      RealType n_i, n_j;
966 >      RealType rho_i, rho_j;
967 >      pair<RealType, RealType> LRI;
968 >      
969 >      for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
970 >        n_i = RealType(info_->getGlobalCountOfType(*i));
971 >        rho_i = n_i /  vol;
972 >        for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
973 >          n_j = RealType(info_->getGlobalCountOfType(*j));
974 >          rho_j = n_j / vol;
975 >          
976 >          LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
977 >
978 >          Elrc += n_i   * rho_j * LRI.first;
979 >          Wlrc -= rho_i * rho_j * LRI.second;
980 >        }
981 >      }
982 >      Elrc *= 2.0 * NumericConstant::PI;
983 >      Wlrc *= 2.0 * NumericConstant::PI;
984 >
985 >      RealType lrp = curSnapshot->getLongRangePotential();
986 >      curSnapshot->setLongRangePotential(lrp + Elrc);
987 >      stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
988 >      curSnapshot->setStressTensor(stressTensor);
989 >      */
990 >    
991 >    }
992 >  }
993 > }

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