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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1809 by gezelter, Mon Nov 5 19:41:28 2012 UTC vs.
Revision 2047 by gezelter, Thu Dec 11 16:16:43 2014 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).          
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   */
# Line 44 | Line 44
44   * @file ForceManager.cpp
45   * @author tlin
46   * @date 11/09/2004
47 – * @time 10:39am
47   * @version 1.0
48   */
49  
# Line 58 | Line 57
57   #include "primitives/Torsion.hpp"
58   #include "primitives/Inversion.hpp"
59   #include "nonbonded/NonBondedInteraction.hpp"
60 < #include "perturbations/ElectricField.hpp"
60 > #include "perturbations/UniformField.hpp"
61 > #include "perturbations/UniformGradient.hpp"
62   #include "parallel/ForceMatrixDecomposition.hpp"
63  
64   #include <cstdio>
# Line 68 | Line 68 | namespace OpenMD {
68   using namespace std;
69   namespace OpenMD {
70    
71 <  ForceManager::ForceManager(SimInfo * info) : info_(info) {
71 >  ForceManager::ForceManager(SimInfo * info) : info_(info), switcher_(NULL),
72 >                                               initialized_(false) {
73      forceField_ = info_->getForceField();
74      interactionMan_ = new InteractionManager();
75      fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
76 +    thermo = new Thermo(info_);
77    }
78  
79 +  ForceManager::~ForceManager() {
80 +    perturbations_.clear();
81 +    
82 +    delete switcher_;
83 +    delete interactionMan_;
84 +    delete fDecomp_;
85 +    delete thermo;
86 +  }
87 +  
88    /**
89     * setupCutoffs
90     *
# Line 88 | Line 99 | namespace OpenMD {
99     *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
100     *      Use the maximum suggested value that was found.
101     *
102 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
103 <   *                        or SHIFTED_POTENTIAL)
102 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
103 >   *                        SHIFTED_POTENTIAL, or EWALD_FULL)
104     *      If cutoffMethod was explicitly set, use that choice.
105     *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
106     *
# Line 118 | Line 129 | namespace OpenMD {
129      else
130        mdFileVersion = 0;
131    
132 +    // We need the list of simulated atom types to figure out cutoffs
133 +    // as well as long range corrections.
134 +
135 +    set<AtomType*>::iterator i;
136 +    set<AtomType*> atomTypes_;
137 +    atomTypes_ = info_->getSimulatedAtomTypes();
138 +
139      if (simParams_->haveCutoffRadius()) {
140        rCut_ = simParams_->getCutoffRadius();
141      } else {      
# Line 132 | Line 150 | namespace OpenMD {
150          rCut_ = 12.0;
151        } else {
152          RealType thisCut;
153 <        set<AtomType*>::iterator i;
136 <        set<AtomType*> atomTypes;
137 <        atomTypes = info_->getSimulatedAtomTypes();        
138 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
153 >        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
154            thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
155            rCut_ = max(thisCut, rCut_);
156          }
# Line 157 | Line 172 | namespace OpenMD {
172      stringToCutoffMethod["SWITCHED"] = SWITCHED;
173      stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
174      stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
175 +    stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
176 +    stringToCutoffMethod["EWALD_FULL"] = EWALD_FULL;
177    
178      if (simParams_->haveCutoffMethod()) {
179        string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
# Line 166 | Line 183 | namespace OpenMD {
183          sprintf(painCave.errMsg,
184                  "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
185                  "\tShould be one of: "
186 <                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
186 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
187 >                "\tSHIFTED_FORCE, or EWALD_FULL\n",
188                  cutMeth.c_str());
189          painCave.isFatal = 1;
190          painCave.severity = OPENMD_ERROR;
# Line 210 | Line 228 | namespace OpenMD {
228              cutoffMethod_ = SHIFTED_POTENTIAL;
229            } else if (myMethod == "SHIFTED_FORCE") {
230              cutoffMethod_ = SHIFTED_FORCE;
231 +          } else if (myMethod == "TAYLOR_SHIFTED") {
232 +            cutoffMethod_ = TAYLOR_SHIFTED;
233 +          } else if (myMethod == "EWALD_FULL") {
234 +            cutoffMethod_ = EWALD_FULL;
235            }
236          
237            if (simParams_->haveSwitchingRadius())
238              rSwitch_ = simParams_->getSwitchingRadius();
239  
240 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
240 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
241 >              myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") {
242              if (simParams_->haveSwitchingRadius()){
243                sprintf(painCave.errMsg,
244                        "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
# Line 370 | Line 393 | namespace OpenMD {
393      }
394      switcher_->setSwitchType(sft_);
395      switcher_->setSwitch(rSwitch_, rCut_);
373 –    interactionMan_->setSwitchingRadius(rSwitch_);
396    }
397  
376 –
377 –
378 –  
398    void ForceManager::initialize() {
399  
400      if (!info_->isTopologyDone()) {
# Line 384 | Line 403 | namespace OpenMD {
403        interactionMan_->setSimInfo(info_);
404        interactionMan_->initialize();
405  
406 <      // We want to delay the cutoffs until after the interaction
407 <      // manager has set up the atom-atom interactions so that we can
408 <      // query them for suggested cutoff values
406 >      //! We want to delay the cutoffs until after the interaction
407 >      //! manager has set up the atom-atom interactions so that we can
408 >      //! query them for suggested cutoff values
409        setupCutoffs();
410  
411        info_->prepareTopology();      
# Line 394 | Line 413 | namespace OpenMD {
413        doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
414        doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
415        if (doHeatFlux_) doParticlePot_ = true;
416 +
417 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
418 +      doSitePotential_ = info_->getSimParams()->getOutputSitePotential();
419    
420      }
421  
422      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
423      
424 <    // Force fields can set options on how to scale van der Waals and
425 <    // electrostatic interactions for atoms connected via bonds, bends
426 <    // and torsions in this case the topological distance between
427 <    // atoms is:
428 <    // 0 = topologically unconnected
429 <    // 1 = bonded together
430 <    // 2 = connected via a bend
431 <    // 3 = connected via a torsion
424 >    //! Force fields can set options on how to scale van der Waals and
425 >    //! electrostatic interactions for atoms connected via bonds, bends
426 >    //! and torsions in this case the topological distance between
427 >    //! atoms is:
428 >    //! 0 = topologically unconnected
429 >    //! 1 = bonded together
430 >    //! 2 = connected via a bend
431 >    //! 3 = connected via a torsion
432      
433      vdwScale_.reserve(4);
434      fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
# Line 424 | Line 446 | namespace OpenMD {
446      electrostaticScale_[2] = fopts.getelectrostatic13scale();
447      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
448      
449 <    if (info_->getSimParams()->haveElectricField()) {
450 <      ElectricField* eField = new ElectricField(info_);
449 >    if (info_->getSimParams()->haveUniformField()) {
450 >      UniformField* eField = new UniformField(info_);
451        perturbations_.push_back(eField);
452      }
453 <
453 >    if (info_->getSimParams()->haveUniformGradientStrength() ||
454 >        info_->getSimParams()->haveUniformGradientDirection1() ||
455 >        info_->getSimParams()->haveUniformGradientDirection2() ) {
456 >      UniformGradient* eGrad = new UniformGradient(info_);
457 >      perturbations_.push_back(eGrad);
458 >    }
459 >    
460 >    usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
461 >    
462      fDecomp_->distributeInitialData();
463 <
463 >    
464      initialized_ = true;
465 <
465 >    
466    }
467 <
467 >  
468    void ForceManager::calcForces() {
469      
470      if (!initialized_) initialize();
471 <
471 >    
472      preCalculation();  
473      shortRangeInteractions();
474      longRangeInteractions();
# Line 612 | Line 642 | namespace OpenMD {
642      // Collect from all nodes.  This should eventually be moved into a
643      // SystemDecomposition, but this is a better place than in
644      // Thermo to do the collection.
645 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
646 <                              MPI::SUM);
647 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
648 <                              MPI::SUM);
649 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
650 <                              MPI::REALTYPE, MPI::SUM);
651 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
652 <                              MPI::REALTYPE, MPI::SUM);
645 >
646 >    MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE,
647 >                  MPI_SUM, MPI_COMM_WORLD);
648 >    MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE,
649 >                  MPI_SUM, MPI_COMM_WORLD);
650 >    MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1,
651 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
652 >    MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1,
653 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
654   #endif
655  
656      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
# Line 637 | Line 668 | namespace OpenMD {
668    
669    void ForceManager::longRangeInteractions() {
670  
640 –
671      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
672      DataStorage* config = &(curSnapshot->atomData);
673      DataStorage* cgConfig = &(curSnapshot->cgData);
674  
675 +
676      //calculate the center of mass of cutoff group
677  
678      SimInfo::MoleculeIterator mi;
# Line 674 | Line 705 | namespace OpenMD {
705      RealType vij;
706      Vector3d fij, fg, f1;
707      tuple3<RealType, RealType, RealType> cuts;
708 <    RealType rCutSq;
708 >    RealType rCut, rCutSq, rListSq;
709      bool in_switching_region;
710      RealType sw, dswdr, swderiv;
711 <    vector<int> atomListColumn, atomListRow, atomListLocal;
711 >    vector<int> atomListColumn, atomListRow;
712      InteractionData idat;
713      SelfData sdat;
714      RealType mf;
715      RealType vpair;
716      RealType dVdFQ1(0.0);
717      RealType dVdFQ2(0.0);
687 –    Vector3d eField1(0.0);
688 –    Vector3d eField2(0.0);
718      potVec longRangePotential(0.0);
719 +    RealType reciprocalPotential(0.0);
720      potVec workPot(0.0);
721      potVec exPot(0.0);
722 +    Vector3d eField1(0.0);
723 +    Vector3d eField2(0.0);
724 +    RealType sPot1(0.0);
725 +    RealType sPot2(0.0);
726 +                  
727      vector<int>::iterator ia, jb;
728  
729      int loopStart, loopEnd;
730 <
730 >    
731 >    idat.rcut = &rCut;
732      idat.vdwMult = &vdwMult;
733      idat.electroMult = &electroMult;
734      idat.pot = &workPot;
# Line 703 | Line 739 | namespace OpenMD {
739      idat.dVdFQ1 = &dVdFQ1;
740      idat.dVdFQ2 = &dVdFQ2;
741      idat.eField1 = &eField1;
742 <    idat.eField2 = &eField2;
742 >    idat.eField2 = &eField2;
743 >    idat.sPot1 = &sPot1;
744 >    idat.sPot2 = &sPot2;
745      idat.f1 = &f1;
746      idat.sw = &sw;
747      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
748 <    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
748 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE ||
749 >                         cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
750      idat.doParticlePot = doParticlePot_;
751 +    idat.doElectricField = doElectricField_;
752 +    idat.doSitePotential = doSitePotential_;
753      sdat.doParticlePot = doParticlePot_;
754      
755      loopEnd = PAIR_LOOP;
# Line 721 | Line 762 | namespace OpenMD {
762      
763        if (iLoop == loopStart) {
764          bool update_nlist = fDecomp_->checkNeighborList();
765 <        if (update_nlist)
766 <          neighborList = fDecomp_->buildNeighborList();
767 <      }            
765 >        if (update_nlist) {
766 >          if (!usePeriodicBoundaryConditions_)
767 >            Mat3x3d bbox = thermo->getBoundingBox();
768 >          fDecomp_->buildNeighborList(neighborList_);
769 >        }
770 >      }
771  
772 <      for (vector<pair<int, int> >::iterator it = neighborList.begin();
773 <             it != neighborList.end(); ++it) {
772 >      for (vector<pair<int, int> >::iterator it = neighborList_.begin();
773 >           it != neighborList_.end(); ++it) {
774                  
775          cg1 = (*it).first;
776          cg2 = (*it).second;
777          
778 <        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
778 >        fDecomp_->getGroupCutoffs(cg1, cg2, rCut, rCutSq, rListSq);
779  
780          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
781  
782 <        curSnapshot->wrapVector(d_grp);        
782 >        // already wrapped in the getIntergroupVector call:
783 >        // curSnapshot->wrapVector(d_grp);        
784          rgrpsq = d_grp.lengthSquare();
740 –        rCutSq = cuts.second;
785  
786          if (rgrpsq < rCutSq) {
743 –          idat.rcut = &cuts.first;
787            if (iLoop == PAIR_LOOP) {
788              vij = 0.0;
789 <            fij = V3Zero;
789 >            fij.zero();
790 >            eField1.zero();
791 >            eField2.zero();
792 >            sPot1 = 0.0;
793 >            sPot2 = 0.0;
794            }
795            
796            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
# Line 768 | Line 815 | namespace OpenMD {
815                  vpair = 0.0;
816                  workPot = 0.0;
817                  exPot = 0.0;
818 <                f1 = V3Zero;
818 >                f1.zero();
819                  dVdFQ1 = 0.0;
820                  dVdFQ2 = 0.0;
821  
# Line 795 | Line 842 | namespace OpenMD {
842                
843                  r = sqrt( *(idat.r2) );
844                  idat.rij = &r;
845 <              
845 >
846                  if (iLoop == PREPAIR_LOOP) {
847                    interactionMan_->doPrePair(idat);
848                  } else {
# Line 891 | Line 938 | namespace OpenMD {
938          }
939        }
940      }
941 <  
941 >    
942      // collects pairwise information
943      fDecomp_->collectData();
944 +    if (cutoffMethod_ == EWALD_FULL) {
945 +      interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
946 +
947 +      curSnapshot->setReciprocalPotential(reciprocalPotential);
948 +    }
949          
950      if (info_->requiresSelfCorrection()) {
951        for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
# Line 911 | Line 963 | namespace OpenMD {
963      curSnapshot->setLongRangePotential(longRangePotential);
964      
965      curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
966 <                                         *(fDecomp_->getExcludedPotential()));
966 >                                       *(fDecomp_->getExcludedPotential()));
967  
968    }
969  
918 –  
970    void ForceManager::postCalculation() {
971  
972      vector<Perturbation*>::iterator pi;
# Line 941 | Line 992 | namespace OpenMD {
992      }
993      
994   #ifdef IS_MPI
995 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
996 <                              MPI::REALTYPE, MPI::SUM);
995 >    MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9,
996 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
997   #endif
998      curSnapshot->setStressTensor(stressTensor);
999      
1000 +    if (info_->getSimParams()->getUseLongRangeCorrections()) {
1001 +      /*
1002 +        RealType vol = curSnapshot->getVolume();
1003 +        RealType Elrc(0.0);
1004 +        RealType Wlrc(0.0);
1005 +
1006 +        set<AtomType*>::iterator i;
1007 +        set<AtomType*>::iterator j;
1008 +    
1009 +        RealType n_i, n_j;
1010 +        RealType rho_i, rho_j;
1011 +        pair<RealType, RealType> LRI;
1012 +      
1013 +        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
1014 +        n_i = RealType(info_->getGlobalCountOfType(*i));
1015 +        rho_i = n_i /  vol;
1016 +        for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
1017 +        n_j = RealType(info_->getGlobalCountOfType(*j));
1018 +        rho_j = n_j / vol;
1019 +          
1020 +        LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
1021 +
1022 +        Elrc += n_i   * rho_j * LRI.first;
1023 +        Wlrc -= rho_i * rho_j * LRI.second;
1024 +        }
1025 +        }
1026 +        Elrc *= 2.0 * NumericConstant::PI;
1027 +        Wlrc *= 2.0 * NumericConstant::PI;
1028 +
1029 +        RealType lrp = curSnapshot->getLongRangePotential();
1030 +        curSnapshot->setLongRangePotential(lrp + Elrc);
1031 +        stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1032 +        curSnapshot->setStressTensor(stressTensor);
1033 +      */
1034 +    
1035 +    }
1036    }
1037 < } //end namespace OpenMD
1037 > }

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