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root/OpenMD/branches/development/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC

# Line 53 | Line 53
53   #include "brains/SimInfo.hpp"
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56 + #include "primitives/StuntDouble.hpp"
57   #include "UseTheForce/fCutoffPolicy.h"
58   #include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59   #include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60   #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61   #include "UseTheForce/doForces_interface.h"
62 + #include "UseTheForce/DarkSide/neighborLists_interface.h"
63   #include "UseTheForce/DarkSide/electrostatic_interface.h"
64   #include "UseTheForce/DarkSide/switcheroo_interface.h"
65   #include "utils/MemoryUtils.hpp"
66   #include "utils/simError.h"
67   #include "selection/SelectionManager.hpp"
68 + #include "io/ForceFieldOptions.hpp"
69 + #include "UseTheForce/ForceField.hpp"
70  
71 +
72   #ifdef IS_MPI
73   #include "UseTheForce/mpiComponentPlan.h"
74   #include "UseTheForce/DarkSide/simParallel_interface.h"
# Line 82 | Line 87 | namespace oopse {
87    
88    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89      forceField_(ff), simParams_(simParams),
90 <    ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
90 >    ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93 <    nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
94 <    nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
95 <    sman_(NULL), fortranInitialized_(false) {
93 >    nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
94 >    nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
95 >    nConstraints_(0), sman_(NULL), fortranInitialized_(false),
96 >    calcBoxDipole_(false), useAtomicVirial_(true) {
97 >
98  
99        MoleculeStamp* molStamp;
100        int nMolWithSameStamp;
# Line 96 | Line 103 | namespace oopse {
103        CutoffGroupStamp* cgStamp;    
104        RigidBodyStamp* rbStamp;
105        int nRigidAtoms = 0;
106 +
107        std::vector<Component*> components = simParams->getComponents();
108        
109        for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
# Line 150 | Line 158 | namespace oopse {
158                                                  + nGlobalRigidBodies_;
159    
160        nGlobalMols_ = molStampIds_.size();
153 –
154 – #ifdef IS_MPI    
161        molToProcMap_.resize(nGlobalMols_);
156 – #endif
157 –
162      }
163  
164    SimInfo::~SimInfo() {
# Line 192 | Line 196 | namespace oopse {
196        nBonds_ += mol->getNBonds();
197        nBends_ += mol->getNBends();
198        nTorsions_ += mol->getNTorsions();
199 +      nInversions_ += mol->getNInversions();
200        nRigidBodies_ += mol->getNRigidBodies();
201        nIntegrableObjects_ += mol->getNIntegrableObjects();
202        nCutoffGroups_ += mol->getNCutoffGroups();
# Line 217 | Line 222 | namespace oopse {
222        nBonds_ -= mol->getNBonds();
223        nBends_ -= mol->getNBends();
224        nTorsions_ -= mol->getNTorsions();
225 +      nInversions_ -= mol->getNInversions();
226        nRigidBodies_ -= mol->getNRigidBodies();
227        nIntegrableObjects_ -= mol->getNIntegrableObjects();
228        nCutoffGroups_ -= mol->getNCutoffGroups();
# Line 288 | Line 294 | namespace oopse {
294  
295    }
296  
297 +  int SimInfo::getFdf() {
298 + #ifdef IS_MPI
299 +    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
300 + #else
301 +    fdf_ = fdf_local;
302 + #endif
303 +    return fdf_;
304 +  }
305 +    
306    void SimInfo::calcNdfRaw() {
307      int ndfRaw_local;
308  
# Line 343 | Line 358 | namespace oopse {
358      std::vector<Bond*>::iterator bondIter;
359      std::vector<Bend*>::iterator bendIter;
360      std::vector<Torsion*>::iterator torsionIter;
361 +    std::vector<Inversion*>::iterator inversionIter;
362      Bond* bond;
363      Bend* bend;
364      Torsion* torsion;
365 +    Inversion* inversion;
366      int a;
367      int b;
368      int c;
# Line 408 | Line 425 | namespace oopse {
425        b = torsion->getAtomB()->getGlobalIndex();        
426        c = torsion->getAtomC()->getGlobalIndex();        
427        d = torsion->getAtomD()->getGlobalIndex();        
428 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
429 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
430 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
431 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
432 +
433 +      exclude_.addPairs(rigidSetA, rigidSetB);
434 +      exclude_.addPairs(rigidSetA, rigidSetC);
435 +      exclude_.addPairs(rigidSetA, rigidSetD);
436 +      exclude_.addPairs(rigidSetB, rigidSetC);
437 +      exclude_.addPairs(rigidSetB, rigidSetD);
438 +      exclude_.addPairs(rigidSetC, rigidSetD);
439 +
440 +      /*
441 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
442 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
443 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
444 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
445 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
446 +      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
447 +        
448 +      
449 +      exclude_.addPair(a, b);
450 +      exclude_.addPair(a, c);
451 +      exclude_.addPair(a, d);
452 +      exclude_.addPair(b, c);
453 +      exclude_.addPair(b, d);
454 +      exclude_.addPair(c, d);        
455 +      */
456 +    }
457 +
458 +    for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
459 +         inversion = mol->nextInversion(inversionIter)) {
460 +      a = inversion->getAtomA()->getGlobalIndex();
461 +      b = inversion->getAtomB()->getGlobalIndex();        
462 +      c = inversion->getAtomC()->getGlobalIndex();        
463 +      d = inversion->getAtomD()->getGlobalIndex();        
464        std::set<int> rigidSetA = getRigidSet(a, atomGroups);
465        std::set<int> rigidSetB = getRigidSet(b, atomGroups);
466        std::set<int> rigidSetC = getRigidSet(c, atomGroups);
# Line 455 | Line 508 | namespace oopse {
508      std::vector<Bond*>::iterator bondIter;
509      std::vector<Bend*>::iterator bendIter;
510      std::vector<Torsion*>::iterator torsionIter;
511 +    std::vector<Inversion*>::iterator inversionIter;
512      Bond* bond;
513      Bend* bend;
514      Torsion* torsion;
515 +    Inversion* inversion;
516      int a;
517      int b;
518      int c;
# Line 551 | Line 606 | namespace oopse {
606        */
607      }
608  
609 +    for (inversion= mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(inversionIter)) {
610 +      a = inversion->getAtomA()->getGlobalIndex();
611 +      b = inversion->getAtomB()->getGlobalIndex();        
612 +      c = inversion->getAtomC()->getGlobalIndex();        
613 +      d = inversion->getAtomD()->getGlobalIndex();        
614 +
615 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
616 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
617 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
618 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
619 +
620 +      exclude_.removePairs(rigidSetA, rigidSetB);
621 +      exclude_.removePairs(rigidSetA, rigidSetC);
622 +      exclude_.removePairs(rigidSetA, rigidSetD);
623 +      exclude_.removePairs(rigidSetB, rigidSetC);
624 +      exclude_.removePairs(rigidSetB, rigidSetD);
625 +      exclude_.removePairs(rigidSetC, rigidSetD);
626 +
627 +      /*
628 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
629 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
630 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
631 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
632 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
633 +      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
634 +
635 +      
636 +      exclude_.removePair(a, b);
637 +      exclude_.removePair(a, c);
638 +      exclude_.removePair(a, d);
639 +      exclude_.removePair(b, c);
640 +      exclude_.removePair(b, d);
641 +      exclude_.removePair(c, d);        
642 +      */
643 +    }
644 +
645      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
646        std::vector<Atom*> atoms = rb->getAtoms();
647        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 589 | Line 680 | namespace oopse {
680      /** @deprecate */    
681      int isError = 0;
682      
683 +    setupCutoff();
684 +    
685      setupElectrostaticSummationMethod( isError );
686      setupSwitchingFunction();
687 +    setupAccumulateBoxDipole();
688  
689      if(isError){
690        sprintf( painCave.errMsg,
# Line 598 | Line 692 | namespace oopse {
692        painCave.isFatal = 1;
693        simError();
694      }
601 –  
602 –    
603 –    setupCutoff();
695  
696      calcNdf();
697      calcNdfRaw();
# Line 650 | Line 741 | namespace oopse {
741      int usePBC = simParams_->getUsePeriodicBoundaryConditions();
742      int useRF;
743      int useSF;
744 +    int useSP;
745 +    int useBoxDipole;
746 +
747      std::string myMethod;
748  
749      // set the useRF logical
750      useRF = 0;
751      useSF = 0;
752 +    useSP = 0;
753  
754  
755      if (simParams_->haveElectrostaticSummationMethod()) {
756        std::string myMethod = simParams_->getElectrostaticSummationMethod();
757        toUpper(myMethod);
758 <      if (myMethod == "REACTION_FIELD") {
759 <        useRF=1;
760 <      } else {
761 <        if (myMethod == "SHIFTED_FORCE") {
762 <          useSF = 1;
763 <        }
758 >      if (myMethod == "REACTION_FIELD"){
759 >        useRF = 1;
760 >      } else if (myMethod == "SHIFTED_FORCE"){
761 >        useSF = 1;
762 >      } else if (myMethod == "SHIFTED_POTENTIAL"){
763 >        useSP = 1;
764        }
765      }
766 +    
767 +    if (simParams_->haveAccumulateBoxDipole())
768 +      if (simParams_->getAccumulateBoxDipole())
769 +        useBoxDipole = 1;
770  
771 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
772 +
773      //loop over all of the atom types
774      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
775        useLennardJones |= (*i)->isLennardJones();
# Line 738 | Line 839 | namespace oopse {
839      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
840  
841      temp = useSF;
842 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
842 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
843  
844 +    temp = useSP;
845 +    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
846 +
847 +    temp = useBoxDipole;
848 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
849 +
850 +    temp = useAtomicVirial_;
851 +    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852 +
853   #endif
854  
855      fInfo_.SIM_uses_PBC = usePBC;    
# Line 757 | Line 867 | namespace oopse {
867      fInfo_.SIM_uses_FLARB = useFLARB;
868      fInfo_.SIM_uses_RF = useRF;
869      fInfo_.SIM_uses_SF = useSF;
870 <
871 <    if( myMethod == "REACTION_FIELD") {
872 <      
763 <      if (simParams_->haveDielectric()) {
764 <        fInfo_.dielect = simParams_->getDielectric();
765 <      } else {
766 <        sprintf(painCave.errMsg,
767 <                "SimSetup Error: No Dielectric constant was set.\n"
768 <                "\tYou are trying to use Reaction Field without"
769 <                "\tsetting a dielectric constant!\n");
770 <        painCave.isFatal = 1;
771 <        simError();
772 <      }      
773 <    }
774 <
870 >    fInfo_.SIM_uses_SP = useSP;
871 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
872 >    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
873    }
874  
875    void SimInfo::setupFortranSim() {
# Line 788 | Line 886 | namespace oopse {
886      }
887  
888      //calculate mass ratio of cutoff group
889 <    std::vector<double> mfact;
889 >    std::vector<RealType> mfact;
890      SimInfo::MoleculeIterator mi;
891      Molecule* mol;
892      Molecule::CutoffGroupIterator ci;
893      CutoffGroup* cg;
894      Molecule::AtomIterator ai;
895      Atom* atom;
896 <    double totalMass;
896 >    RealType totalMass;
897  
898      //to avoid memory reallocation, reserve enough space for mfact
899      mfact.reserve(getNCutoffGroups());
# Line 838 | Line 936 | namespace oopse {
936      int nGlobalExcludes = 0;
937      int* globalExcludes = NULL;
938      int* excludeList = exclude_.getExcludeList();
939 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
940 <                   &nGlobalExcludes, globalExcludes, &molMembershipArray[0],
941 <                   &mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
942 <
939 >    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
940 >                   &nExclude, excludeList , &nGlobalExcludes, globalExcludes,
941 >                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
942 >                   &fortranGlobalGroupMembership[0], &isError);
943 >    
944      if( isError ){
945 <
945 >      
946        sprintf( painCave.errMsg,
947                 "There was an error setting the simulation information in fortran.\n" );
948        painCave.isFatal = 1;
949        painCave.severity = OOPSE_ERROR;
950        simError();
951      }
952 <
953 < #ifdef IS_MPI
952 >    
953 >    
954      sprintf( checkPointMsg,
955               "succesfully sent the simulation information to fortran.\n");
956 <    MPIcheckPoint();
957 < #endif // is_mpi
956 >    
957 >    errorCheckPoint();
958 >    
959 >    // Setup number of neighbors in neighbor list if present
960 >    if (simParams_->haveNeighborListNeighbors()) {
961 >      int nlistNeighbors = simParams_->getNeighborListNeighbors();
962 >      setNeighbors(&nlistNeighbors);
963 >    }
964 >  
965 >
966    }
967  
968  
862 – #ifdef IS_MPI
969    void SimInfo::setupFortranParallel() {
970 <    
970 > #ifdef IS_MPI    
971      //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
972      std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
973      std::vector<int> localToGlobalCutoffGroupIndex;
# Line 911 | Line 1017 | namespace oopse {
1017      }
1018  
1019      sprintf(checkPointMsg, " mpiRefresh successful.\n");
1020 <    MPIcheckPoint();
1020 >    errorCheckPoint();
1021  
1022 <
1022 > #endif
1023    }
1024  
919 – #endif
920 –
1025    void SimInfo::setupCutoff() {          
1026      
1027 +    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1028 +
1029      // Check the cutoff policy
1030 <    int cp =  TRADITIONAL_CUTOFF_POLICY;
1031 <    if (simParams_->haveCutoffPolicy()) {
1032 <      std::string myPolicy = simParams_->getCutoffPolicy();
1030 >    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1031 >
1032 >    // Set LJ shifting bools to false
1033 >    ljsp_ = false;
1034 >    ljsf_ = false;
1035 >
1036 >    std::string myPolicy;
1037 >    if (forceFieldOptions_.haveCutoffPolicy()){
1038 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
1039 >    }else if (simParams_->haveCutoffPolicy()) {
1040 >      myPolicy = simParams_->getCutoffPolicy();
1041 >    }
1042 >
1043 >    if (!myPolicy.empty()){
1044        toUpper(myPolicy);
1045        if (myPolicy == "MIX") {
1046          cp = MIX_CUTOFF_POLICY;
# Line 946 | Line 1063 | namespace oopse {
1063      notifyFortranCutoffPolicy(&cp);
1064  
1065      // Check the Skin Thickness for neighborlists
1066 <    double skin;
1066 >    RealType skin;
1067      if (simParams_->haveSkinThickness()) {
1068        skin = simParams_->getSkinThickness();
1069        notifyFortranSkinThickness(&skin);
# Line 958 | Line 1075 | namespace oopse {
1075        if (simParams_->haveSwitchingRadius()) {
1076          rsw_  = simParams_->getSwitchingRadius();
1077        } else {
1078 <        rsw_ = rcut_;
1078 >        if (fInfo_.SIM_uses_Charges |
1079 >            fInfo_.SIM_uses_Dipoles |
1080 >            fInfo_.SIM_uses_RF) {
1081 >          
1082 >          rsw_ = 0.85 * rcut_;
1083 >          sprintf(painCave.errMsg,
1084 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1085 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1086 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1087 >        painCave.isFatal = 0;
1088 >        simError();
1089 >        } else {
1090 >          rsw_ = rcut_;
1091 >          sprintf(painCave.errMsg,
1092 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1093 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1094 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1095 >          painCave.isFatal = 0;
1096 >          simError();
1097 >        }
1098        }
1099 <      notifyFortranCutoffs(&rcut_, &rsw_);
1099 >
1100 >      if (simParams_->haveElectrostaticSummationMethod()) {
1101 >        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1102 >        toUpper(myMethod);
1103 >        
1104 >        if (myMethod == "SHIFTED_POTENTIAL") {
1105 >          ljsp_ = true;
1106 >        } else if (myMethod == "SHIFTED_FORCE") {
1107 >          ljsf_ = true;
1108 >        }
1109 >      }
1110 >      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1111        
1112      } else {
1113        
# Line 977 | Line 1124 | namespace oopse {
1124          if (simParams_->haveElectrostaticSummationMethod()) {
1125            std::string myMethod = simParams_->getElectrostaticSummationMethod();
1126            toUpper(myMethod);
1127 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1127 >      
1128 >      // For the time being, we're tethering the LJ shifted behavior to the
1129 >      // electrostaticSummationMethod keyword options
1130 >          if (myMethod == "SHIFTED_POTENTIAL") {
1131 >            ljsp_ = true;
1132 >          } else if (myMethod == "SHIFTED_FORCE") {
1133 >            ljsf_ = true;
1134 >          }
1135 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1136              if (simParams_->haveSwitchingRadius()){
1137                sprintf(painCave.errMsg,
1138                        "SimInfo Warning: A value was set for the switchingRadius\n"
# Line 1000 | Line 1155 | namespace oopse {
1155            simError();
1156            rsw_ = 0.85 * rcut_;
1157          }
1158 <        notifyFortranCutoffs(&rcut_, &rsw_);
1158 >
1159 >        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1160 >
1161        } else {
1162          // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1163          // We'll punt and let fortran figure out the cutoffs later.
# Line 1016 | Line 1173 | namespace oopse {
1173      int errorOut;
1174      int esm =  NONE;
1175      int sm = UNDAMPED;
1176 <    double alphaVal;
1177 <    double dielectric;
1178 <
1176 >    RealType alphaVal;
1177 >    RealType dielectric;
1178 >    
1179      errorOut = isError;
1023 –    alphaVal = simParams_->getDampingAlpha();
1024 –    dielectric = simParams_->getDielectric();
1180  
1181      if (simParams_->haveElectrostaticSummationMethod()) {
1182        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1038 | Line 1193 | namespace oopse {
1193              if (myMethod == "SHIFTED_FORCE") {            
1194                esm = SHIFTED_FORCE;
1195              } else {
1196 <              if (myMethod == "REACTION_FIELD") {            
1196 >              if (myMethod == "REACTION_FIELD") {
1197                  esm = REACTION_FIELD;
1198 +                dielectric = simParams_->getDielectric();
1199 +                if (!simParams_->haveDielectric()) {
1200 +                  // throw warning
1201 +                  sprintf( painCave.errMsg,
1202 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1203 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1204 +                  painCave.isFatal = 0;
1205 +                  simError();
1206 +                }
1207                } else {
1208                  // throw error        
1209                  sprintf( painCave.errMsg,
# Line 1066 | Line 1230 | namespace oopse {
1230          if (myScreen == "DAMPED") {
1231            sm = DAMPED;
1232            if (!simParams_->haveDampingAlpha()) {
1233 <            //throw error
1233 >            // first set a cutoff dependent alpha value
1234 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1235 >            alphaVal = 0.5125 - rcut_* 0.025;
1236 >            // for values rcut > 20.5, alpha is zero
1237 >            if (alphaVal < 0) alphaVal = 0;
1238 >
1239 >            // throw warning
1240              sprintf( painCave.errMsg,
1241                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1242 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1242 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1243              painCave.isFatal = 0;
1244              simError();
1245 +          } else {
1246 +            alphaVal = simParams_->getDampingAlpha();
1247            }
1248 +          
1249          } else {
1250            // throw error        
1251            sprintf( painCave.errMsg,
# Line 1088 | Line 1261 | namespace oopse {
1261      
1262      // let's pass some summation method variables to fortran
1263      setElectrostaticSummationMethod( &esm );
1264 <    notifyFortranElectrostaticMethod( &esm );
1264 >    setFortranElectrostaticMethod( &esm );
1265      setScreeningMethod( &sm );
1266      setDampingAlpha( &alphaVal );
1267      setReactionFieldDielectric( &dielectric );
# Line 1121 | Line 1294 | namespace oopse {
1294  
1295    }
1296  
1297 +  void SimInfo::setupAccumulateBoxDipole() {    
1298 +
1299 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1300 +    if ( simParams_->haveAccumulateBoxDipole() )
1301 +      if ( simParams_->getAccumulateBoxDipole() ) {
1302 +        setAccumulateBoxDipole();
1303 +        calcBoxDipole_ = true;
1304 +      }
1305 +
1306 +  }
1307 +
1308    void SimInfo::addProperty(GenericData* genData) {
1309      properties_.addProperty(genData);  
1310    }
# Line 1177 | Line 1361 | namespace oopse {
1361      Molecule* mol;
1362  
1363      Vector3d comVel(0.0);
1364 <    double totalMass = 0.0;
1364 >    RealType totalMass = 0.0;
1365      
1366  
1367      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1368 <      double mass = mol->getMass();
1368 >      RealType mass = mol->getMass();
1369        totalMass += mass;
1370        comVel += mass * mol->getComVel();
1371      }  
1372  
1373   #ifdef IS_MPI
1374 <    double tmpMass = totalMass;
1374 >    RealType tmpMass = totalMass;
1375      Vector3d tmpComVel(comVel);    
1376 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1377 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1376 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1377 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1378   #endif
1379  
1380      comVel /= totalMass;
# Line 1203 | Line 1387 | namespace oopse {
1387      Molecule* mol;
1388  
1389      Vector3d com(0.0);
1390 <    double totalMass = 0.0;
1390 >    RealType totalMass = 0.0;
1391      
1392      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1393 <      double mass = mol->getMass();
1393 >      RealType mass = mol->getMass();
1394        totalMass += mass;
1395        com += mass * mol->getCom();
1396      }  
1397  
1398   #ifdef IS_MPI
1399 <    double tmpMass = totalMass;
1399 >    RealType tmpMass = totalMass;
1400      Vector3d tmpCom(com);    
1401 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1402 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1401 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1402 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1403   #endif
1404  
1405      com /= totalMass;
# Line 1239 | Line 1423 | namespace oopse {
1423        Molecule* mol;
1424        
1425      
1426 <      double totalMass = 0.0;
1426 >      RealType totalMass = 0.0;
1427      
1428  
1429        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1430 <         double mass = mol->getMass();
1430 >         RealType mass = mol->getMass();
1431           totalMass += mass;
1432           com += mass * mol->getCom();
1433           comVel += mass * mol->getComVel();          
1434        }  
1435        
1436   #ifdef IS_MPI
1437 <      double tmpMass = totalMass;
1437 >      RealType tmpMass = totalMass;
1438        Vector3d tmpCom(com);  
1439        Vector3d tmpComVel(comVel);
1440 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1441 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1442 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1440 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1441 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1442 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1443   #endif
1444        
1445        com /= totalMass;
# Line 1274 | Line 1458 | namespace oopse {
1458     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1459        
1460  
1461 <      double xx = 0.0;
1462 <      double yy = 0.0;
1463 <      double zz = 0.0;
1464 <      double xy = 0.0;
1465 <      double xz = 0.0;
1466 <      double yz = 0.0;
1461 >      RealType xx = 0.0;
1462 >      RealType yy = 0.0;
1463 >      RealType zz = 0.0;
1464 >      RealType xy = 0.0;
1465 >      RealType xz = 0.0;
1466 >      RealType yz = 0.0;
1467        Vector3d com(0.0);
1468        Vector3d comVel(0.0);
1469        
# Line 1291 | Line 1475 | namespace oopse {
1475        Vector3d thisq(0.0);
1476        Vector3d thisv(0.0);
1477  
1478 <      double thisMass = 0.0;
1478 >      RealType thisMass = 0.0;
1479      
1480        
1481        
# Line 1329 | Line 1513 | namespace oopse {
1513   #ifdef IS_MPI
1514        Mat3x3d tmpI(inertiaTensor);
1515        Vector3d tmpAngMom;
1516 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1517 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1516 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1517 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1518   #endif
1519                
1520        return;
# Line 1351 | Line 1535 | namespace oopse {
1535        Vector3d thisr(0.0);
1536        Vector3d thisp(0.0);
1537        
1538 <      double thisMass;
1538 >      RealType thisMass;
1539        
1540        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1541          thisMass = mol->getMass();
# Line 1364 | Line 1548 | namespace oopse {
1548        
1549   #ifdef IS_MPI
1550        Vector3d tmpAngMom;
1551 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1551 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1552   #endif
1553        
1554        return angularMomentum;
1555     }
1556    
1557 <  
1557 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1558 >    return IOIndexToIntegrableObject.at(index);
1559 >  }
1560 >  
1561 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1562 >    IOIndexToIntegrableObject= v;
1563 >  }
1564 >
1565 >  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1566 >     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1567 >     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1568 >     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1569 >  */
1570 >  void SimInfo::getGyrationalVolume(RealType &volume){
1571 >    Mat3x3d intTensor;
1572 >    RealType det;
1573 >    Vector3d dummyAngMom;
1574 >    RealType sysconstants;
1575 >    RealType geomCnst;
1576 >
1577 >    geomCnst = 3.0/2.0;
1578 >    /* Get the inertial tensor and angular momentum for free*/
1579 >    getInertiaTensor(intTensor,dummyAngMom);
1580 >    
1581 >    det = intTensor.determinant();
1582 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1583 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1584 >    return;
1585 >  }
1586 >
1587 >  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1588 >    Mat3x3d intTensor;
1589 >    Vector3d dummyAngMom;
1590 >    RealType sysconstants;
1591 >    RealType geomCnst;
1592 >
1593 >    geomCnst = 3.0/2.0;
1594 >    /* Get the inertial tensor and angular momentum for free*/
1595 >    getInertiaTensor(intTensor,dummyAngMom);
1596 >    
1597 >    detI = intTensor.determinant();
1598 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1599 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1600 >    return;
1601 >  }
1602 > /*
1603 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1604 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1605 >      sdByGlobalIndex_ = v;
1606 >    }
1607 >
1608 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1609 >      //assert(index < nAtoms_ + nRigidBodies_);
1610 >      return sdByGlobalIndex_.at(index);
1611 >    }  
1612 > */  
1613   }//end namespace oopse
1614  

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