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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 1121 by chuckv, Mon Feb 26 04:45:42 2007 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) {
95 >    sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
96  
97        MoleculeStamp* molStamp;
98        int nMolWithSameStamp;
# Line 288 | Line 293 | namespace oopse {
293  
294    }
295  
296 +  int SimInfo::getFdf() {
297 + #ifdef IS_MPI
298 +    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
299 + #else
300 +    fdf_ = fdf_local;
301 + #endif
302 +    return fdf_;
303 +  }
304 +    
305    void SimInfo::calcNdfRaw() {
306      int ndfRaw_local;
307  
# Line 589 | Line 603 | namespace oopse {
603      /** @deprecate */    
604      int isError = 0;
605      
606 +    setupCutoff();
607 +    
608      setupElectrostaticSummationMethod( isError );
609      setupSwitchingFunction();
610 +    setupAccumulateBoxDipole();
611  
612      if(isError){
613        sprintf( painCave.errMsg,
# Line 598 | Line 615 | namespace oopse {
615        painCave.isFatal = 1;
616        simError();
617      }
601 –  
602 –    
603 –    setupCutoff();
618  
619      calcNdf();
620      calcNdfRaw();
# Line 650 | Line 664 | namespace oopse {
664      int usePBC = simParams_->getUsePeriodicBoundaryConditions();
665      int useRF;
666      int useSF;
667 +    int useSP;
668 +    int useBoxDipole;
669      std::string myMethod;
670  
671      // set the useRF logical
672      useRF = 0;
673      useSF = 0;
674 +    useSP = 0;
675  
676  
677      if (simParams_->haveElectrostaticSummationMethod()) {
678        std::string myMethod = simParams_->getElectrostaticSummationMethod();
679        toUpper(myMethod);
680 <      if (myMethod == "REACTION_FIELD") {
681 <        useRF=1;
682 <      } else {
683 <        if (myMethod == "SHIFTED_FORCE") {
684 <          useSF = 1;
685 <        }
680 >      if (myMethod == "REACTION_FIELD"){
681 >        useRF = 1;
682 >      } else if (myMethod == "SHIFTED_FORCE"){
683 >        useSF = 1;
684 >      } else if (myMethod == "SHIFTED_POTENTIAL"){
685 >        useSP = 1;
686        }
687      }
688 +    
689 +    if (simParams_->haveAccumulateBoxDipole())
690 +      if (simParams_->getAccumulateBoxDipole())
691 +        useBoxDipole = 1;
692  
693      //loop over all of the atom types
694      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
# Line 738 | Line 759 | namespace oopse {
759      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
760  
761      temp = useSF;
762 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
762 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
763  
764 +    temp = useSP;
765 +    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766 +
767 +    temp = useBoxDipole;
768 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769 +
770   #endif
771  
772      fInfo_.SIM_uses_PBC = usePBC;    
# Line 757 | Line 784 | namespace oopse {
784      fInfo_.SIM_uses_FLARB = useFLARB;
785      fInfo_.SIM_uses_RF = useRF;
786      fInfo_.SIM_uses_SF = useSF;
787 <
788 <    if( myMethod == "REACTION_FIELD") {
762 <      
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 <
787 >    fInfo_.SIM_uses_SP = useSP;
788 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
789    }
790  
791    void SimInfo::setupFortranSim() {
# Line 788 | Line 802 | namespace oopse {
802      }
803  
804      //calculate mass ratio of cutoff group
805 <    std::vector<double> mfact;
805 >    std::vector<RealType> mfact;
806      SimInfo::MoleculeIterator mi;
807      Molecule* mol;
808      Molecule::CutoffGroupIterator ci;
809      CutoffGroup* cg;
810      Molecule::AtomIterator ai;
811      Atom* atom;
812 <    double totalMass;
812 >    RealType totalMass;
813  
814      //to avoid memory reallocation, reserve enough space for mfact
815      mfact.reserve(getNCutoffGroups());
# Line 856 | Line 870 | namespace oopse {
870               "succesfully sent the simulation information to fortran.\n");
871      MPIcheckPoint();
872   #endif // is_mpi
873 +
874 +    // Setup number of neighbors in neighbor list if present
875 +    if (simParams_->haveNeighborListNeighbors()) {
876 +      int nlistNeighbors = simParams_->getNeighborListNeighbors();
877 +      setNeighbors(&nlistNeighbors);
878 +    }
879 +  
880 +
881    }
882  
883  
# Line 920 | Line 942 | namespace oopse {
942  
943    void SimInfo::setupCutoff() {          
944      
945 +    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
946 +
947      // Check the cutoff policy
948 <    int cp =  TRADITIONAL_CUTOFF_POLICY;
949 <    if (simParams_->haveCutoffPolicy()) {
950 <      std::string myPolicy = simParams_->getCutoffPolicy();
948 >    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
949 >
950 >    std::string myPolicy;
951 >    if (forceFieldOptions_.haveCutoffPolicy()){
952 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
953 >    }else if (simParams_->haveCutoffPolicy()) {
954 >      myPolicy = simParams_->getCutoffPolicy();
955 >    }
956 >
957 >    if (!myPolicy.empty()){
958        toUpper(myPolicy);
959        if (myPolicy == "MIX") {
960          cp = MIX_CUTOFF_POLICY;
# Line 946 | Line 977 | namespace oopse {
977      notifyFortranCutoffPolicy(&cp);
978  
979      // Check the Skin Thickness for neighborlists
980 <    double skin;
980 >    RealType skin;
981      if (simParams_->haveSkinThickness()) {
982        skin = simParams_->getSkinThickness();
983        notifyFortranSkinThickness(&skin);
# Line 958 | Line 989 | namespace oopse {
989        if (simParams_->haveSwitchingRadius()) {
990          rsw_  = simParams_->getSwitchingRadius();
991        } else {
992 <        rsw_ = rcut_;
992 >        if (fInfo_.SIM_uses_Charges |
993 >            fInfo_.SIM_uses_Dipoles |
994 >            fInfo_.SIM_uses_RF) {
995 >          
996 >          rsw_ = 0.85 * rcut_;
997 >          sprintf(painCave.errMsg,
998 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
999 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1000 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1001 >        painCave.isFatal = 0;
1002 >        simError();
1003 >        } else {
1004 >          rsw_ = rcut_;
1005 >          sprintf(painCave.errMsg,
1006 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1007 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1008 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1009 >          painCave.isFatal = 0;
1010 >          simError();
1011 >        }
1012        }
1013 +      
1014        notifyFortranCutoffs(&rcut_, &rsw_);
1015        
1016      } else {
# Line 1016 | Line 1067 | namespace oopse {
1067      int errorOut;
1068      int esm =  NONE;
1069      int sm = UNDAMPED;
1070 <    double alphaVal;
1071 <    double dielectric;
1072 <
1070 >    RealType alphaVal;
1071 >    RealType dielectric;
1072 >    
1073      errorOut = isError;
1023 –    alphaVal = simParams_->getDampingAlpha();
1024 –    dielectric = simParams_->getDielectric();
1074  
1075      if (simParams_->haveElectrostaticSummationMethod()) {
1076        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1038 | Line 1087 | namespace oopse {
1087              if (myMethod == "SHIFTED_FORCE") {            
1088                esm = SHIFTED_FORCE;
1089              } else {
1090 <              if (myMethod == "REACTION_FIELD") {            
1090 >              if (myMethod == "REACTION_FIELD") {
1091                  esm = REACTION_FIELD;
1092 +                dielectric = simParams_->getDielectric();
1093 +                if (!simParams_->haveDielectric()) {
1094 +                  // throw warning
1095 +                  sprintf( painCave.errMsg,
1096 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1097 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1098 +                  painCave.isFatal = 0;
1099 +                  simError();
1100 +                }
1101                } else {
1102                  // throw error        
1103                  sprintf( painCave.errMsg,
# Line 1066 | Line 1124 | namespace oopse {
1124          if (myScreen == "DAMPED") {
1125            sm = DAMPED;
1126            if (!simParams_->haveDampingAlpha()) {
1127 <            //throw error
1127 >            // first set a cutoff dependent alpha value
1128 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1129 >            alphaVal = 0.5125 - rcut_* 0.025;
1130 >            // for values rcut > 20.5, alpha is zero
1131 >            if (alphaVal < 0) alphaVal = 0;
1132 >
1133 >            // throw warning
1134              sprintf( painCave.errMsg,
1135                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1136 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1136 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1137              painCave.isFatal = 0;
1138              simError();
1139 +          } else {
1140 +            alphaVal = simParams_->getDampingAlpha();
1141            }
1142 +          
1143          } else {
1144            // throw error        
1145            sprintf( painCave.errMsg,
# Line 1088 | Line 1155 | namespace oopse {
1155      
1156      // let's pass some summation method variables to fortran
1157      setElectrostaticSummationMethod( &esm );
1158 <    notifyFortranElectrostaticMethod( &esm );
1158 >    setFortranElectrostaticMethod( &esm );
1159      setScreeningMethod( &sm );
1160      setDampingAlpha( &alphaVal );
1161      setReactionFieldDielectric( &dielectric );
# Line 1121 | Line 1188 | namespace oopse {
1188  
1189    }
1190  
1191 +  void SimInfo::setupAccumulateBoxDipole() {    
1192 +
1193 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1194 +    if ( simParams_->haveAccumulateBoxDipole() )
1195 +      if ( simParams_->getAccumulateBoxDipole() ) {
1196 +        setAccumulateBoxDipole();
1197 +        calcBoxDipole_ = true;
1198 +      }
1199 +
1200 +  }
1201 +
1202    void SimInfo::addProperty(GenericData* genData) {
1203      properties_.addProperty(genData);  
1204    }
# Line 1177 | Line 1255 | namespace oopse {
1255      Molecule* mol;
1256  
1257      Vector3d comVel(0.0);
1258 <    double totalMass = 0.0;
1258 >    RealType totalMass = 0.0;
1259      
1260  
1261      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1262 <      double mass = mol->getMass();
1262 >      RealType mass = mol->getMass();
1263        totalMass += mass;
1264        comVel += mass * mol->getComVel();
1265      }  
1266  
1267   #ifdef IS_MPI
1268 <    double tmpMass = totalMass;
1268 >    RealType tmpMass = totalMass;
1269      Vector3d tmpComVel(comVel);    
1270 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1271 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1270 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1271 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1272   #endif
1273  
1274      comVel /= totalMass;
# Line 1203 | Line 1281 | namespace oopse {
1281      Molecule* mol;
1282  
1283      Vector3d com(0.0);
1284 <    double totalMass = 0.0;
1284 >    RealType totalMass = 0.0;
1285      
1286      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1287 <      double mass = mol->getMass();
1287 >      RealType mass = mol->getMass();
1288        totalMass += mass;
1289        com += mass * mol->getCom();
1290      }  
1291  
1292   #ifdef IS_MPI
1293 <    double tmpMass = totalMass;
1293 >    RealType tmpMass = totalMass;
1294      Vector3d tmpCom(com);    
1295 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1296 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1295 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1296 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1297   #endif
1298  
1299      com /= totalMass;
# Line 1239 | Line 1317 | namespace oopse {
1317        Molecule* mol;
1318        
1319      
1320 <      double totalMass = 0.0;
1320 >      RealType totalMass = 0.0;
1321      
1322  
1323        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1324 <         double mass = mol->getMass();
1324 >         RealType mass = mol->getMass();
1325           totalMass += mass;
1326           com += mass * mol->getCom();
1327           comVel += mass * mol->getComVel();          
1328        }  
1329        
1330   #ifdef IS_MPI
1331 <      double tmpMass = totalMass;
1331 >      RealType tmpMass = totalMass;
1332        Vector3d tmpCom(com);  
1333        Vector3d tmpComVel(comVel);
1334 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1335 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1336 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1334 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1335 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1336 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1337   #endif
1338        
1339        com /= totalMass;
# Line 1274 | Line 1352 | namespace oopse {
1352     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1353        
1354  
1355 <      double xx = 0.0;
1356 <      double yy = 0.0;
1357 <      double zz = 0.0;
1358 <      double xy = 0.0;
1359 <      double xz = 0.0;
1360 <      double yz = 0.0;
1355 >      RealType xx = 0.0;
1356 >      RealType yy = 0.0;
1357 >      RealType zz = 0.0;
1358 >      RealType xy = 0.0;
1359 >      RealType xz = 0.0;
1360 >      RealType yz = 0.0;
1361        Vector3d com(0.0);
1362        Vector3d comVel(0.0);
1363        
# Line 1291 | Line 1369 | namespace oopse {
1369        Vector3d thisq(0.0);
1370        Vector3d thisv(0.0);
1371  
1372 <      double thisMass = 0.0;
1372 >      RealType thisMass = 0.0;
1373      
1374        
1375        
# Line 1329 | Line 1407 | namespace oopse {
1407   #ifdef IS_MPI
1408        Mat3x3d tmpI(inertiaTensor);
1409        Vector3d tmpAngMom;
1410 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1411 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1410 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1411 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1412   #endif
1413                
1414        return;
# Line 1351 | Line 1429 | namespace oopse {
1429        Vector3d thisr(0.0);
1430        Vector3d thisp(0.0);
1431        
1432 <      double thisMass;
1432 >      RealType thisMass;
1433        
1434        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1435          thisMass = mol->getMass();
# Line 1364 | Line 1442 | namespace oopse {
1442        
1443   #ifdef IS_MPI
1444        Vector3d tmpAngMom;
1445 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1445 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1446   #endif
1447        
1448        return angularMomentum;
1449     }
1450    
1451 <  
1451 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1452 >    return IOIndexToIntegrableObject.at(index);
1453 >  }
1454 >  
1455 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1456 >    IOIndexToIntegrableObject= v;
1457 >  }
1458 >
1459 >  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1460 >     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1461 >     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1462 >     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1463 >  */
1464 >  void SimInfo::getGyrationalVolume(RealType &volume){
1465 >    Mat3x3d intTensor;
1466 >    RealType det;
1467 >    Vector3d dummyAngMom;
1468 >    RealType sysconstants;
1469 >    RealType geomCnst;
1470 >
1471 >    geomCnst = 3.0/2.0;
1472 >    /* Get the inertial tensor and angular momentum for free*/
1473 >    getInertiaTensor(intTensor,dummyAngMom);
1474 >    
1475 >    det = intTensor.determinant();
1476 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1477 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1478 >    return;
1479 >  }
1480 >
1481 >  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1482 >    Mat3x3d intTensor;
1483 >    Vector3d dummyAngMom;
1484 >    RealType sysconstants;
1485 >    RealType geomCnst;
1486 >
1487 >    geomCnst = 3.0/2.0;
1488 >    /* Get the inertial tensor and angular momentum for free*/
1489 >    getInertiaTensor(intTensor,dummyAngMom);
1490 >    
1491 >    detI = intTensor.determinant();
1492 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1493 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1494 >    return;
1495 >  }
1496 > /*
1497 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1498 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1499 >      sdByGlobalIndex_ = v;
1500 >    }
1501 >
1502 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1503 >      //assert(index < nAtoms_ + nRigidBodies_);
1504 >      return sdByGlobalIndex_.at(index);
1505 >    }  
1506 > */  
1507   }//end namespace oopse
1508  

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