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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1616 by gezelter, Tue Aug 30 15:45:35 2011 UTC vs.
Revision 1715 by gezelter, Tue May 22 21:55:31 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 200 | Line 201 | namespace OpenMD {
201          // electrostaticSummationMethod keyword.
202          
203          if (simParams_->haveElectrostaticSummationMethod()) {
204 <          std::string myMethod = simParams_->getElectrostaticSummationMethod();
204 >          string myMethod = simParams_->getElectrostaticSummationMethod();
205            toUpper(myMethod);
206          
207            if (myMethod == "SHIFTED_POTENTIAL") {
# Line 255 | Line 256 | namespace OpenMD {
256      stringToCutoffPolicy["MAX"] = MAX;
257      stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
258  
259 <    std::string cutPolicy;
259 >    string cutPolicy;
260      if (forceFieldOptions_.haveCutoffPolicy()){
261        cutPolicy = forceFieldOptions_.getCutoffPolicy();
262      }else if (simParams_->haveCutoffPolicy()) {
# Line 317 | Line 318 | namespace OpenMD {
318          simError();
319        }
320      } else {
321 <      if (simParams_->haveSwitchingRadius()) {
322 <        map<string, CutoffMethod>::const_iterator it;
323 <        string theMeth;
324 <        for (it = stringToCutoffMethod.begin();
325 <             it != stringToCutoffMethod.end(); ++it) {
326 <          if (it->second == cutoffMethod_) {
327 <            theMeth = it->first;
328 <            break;
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          }
330 –        sprintf(painCave.errMsg,
331 –                "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
332 –                "\tis not set to SWITCHED, so switchingRadius value\n"
333 –                "\twill be ignored for this simulation\n", theMeth.c_str());
334 –        painCave.isFatal = 0;
335 –        painCave.severity = OPENMD_WARNING;
336 –        simError();
342        }
338 –
343        rSwitch_ = rCut_;
344      }
345      
# Line 384 | Line 388 | namespace OpenMD {
388        setupCutoffs();
389  
390        info_->prepareTopology();      
391 +
392 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
393 +  
394      }
395  
396      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
# Line 498 | Line 505 | namespace OpenMD {
505  
506        for (bond = mol->beginBond(bondIter); bond != NULL;
507             bond = mol->nextBond(bondIter)) {
508 <        bond->calcForce();
508 >        bond->calcForce(doParticlePot_);
509          bondPotential += bond->getPotential();
510        }
511  
# Line 506 | Line 513 | namespace OpenMD {
513             bend = mol->nextBend(bendIter)) {
514          
515          RealType angle;
516 <        bend->calcForce(angle);
516 >        bend->calcForce(angle, doParticlePot_);
517          RealType currBendPot = bend->getPotential();          
518          
519          bendPotential += bend->getPotential();
# Line 531 | Line 538 | namespace OpenMD {
538        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
539             torsion = mol->nextTorsion(torsionIter)) {
540          RealType angle;
541 <        torsion->calcForce(angle);
541 >        torsion->calcForce(angle, doParticlePot_);
542          RealType currTorsionPot = torsion->getPotential();
543          torsionPotential += torsion->getPotential();
544          map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
# Line 555 | Line 562 | namespace OpenMD {
562             inversion != NULL;
563             inversion = mol->nextInversion(inversionIter)) {
564          RealType angle;
565 <        inversion->calcForce(angle);
565 >        inversion->calcForce(angle, doParticlePot_);
566          RealType currInversionPot = inversion->getPotential();
567          inversionPotential += inversion->getPotential();
568          map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
# Line 634 | Line 641 | namespace OpenMD {
641      RealType vpair;
642      potVec longRangePotential(0.0);
643      potVec workPot(0.0);
644 +    vector<int>::iterator ia, jb;
645  
646      int loopStart, loopEnd;
647  
# Line 646 | Line 654 | namespace OpenMD {
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() ) {
# Line 689 | Line 699 | namespace OpenMD {
699            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
700            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
701  
702 <          for (vector<int>::iterator ia = atomListRow.begin();
702 >          for (ia = atomListRow.begin();
703                 ia != atomListRow.end(); ++ia) {            
704              atom1 = (*ia);
705              
706 <            for (vector<int>::iterator jb = atomListColumn.begin();
706 >            for (jb = atomListColumn.begin();
707                   jb != atomListColumn.end(); ++jb) {              
708                atom2 = (*jb);
709  
# Line 745 | Line 755 | namespace OpenMD {
755                  tau -= outProduct( *(idat.d), fg);
756                }
757            
758 <              for (vector<int>::iterator ia = atomListRow.begin();
758 >              for (ia = atomListRow.begin();
759                     ia != atomListRow.end(); ++ia) {            
760                  atom1 = (*ia);                
761                  mf = fDecomp_->getMassFactorRow(atom1);
# Line 762 | Line 772 | namespace OpenMD {
772                    }
773                  }
774                }
775 <              for (vector<int>::iterator jb = atomListColumn.begin();
775 >              for (jb = atomListColumn.begin();
776                     jb != atomListColumn.end(); ++jb) {              
777                  atom2 = (*jb);
778                  mf = fDecomp_->getMassFactorColumn(atom2);
# Line 850 | 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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