ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/brains/SimInfo.cpp
(Generate patch)

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 764 by gezelter, Mon Nov 21 22:59:21 2005 UTC vs.
Revision 1126 by gezelter, Fri Apr 6 21:53:43 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 80 | Line 85 | namespace oopse {
85      return result;
86    }
87    
88 <  SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
89 <                   ForceField* ff, Globals* simParams) :
90 <    stamps_(stamps), forceField_(ff), simParams_(simParams),
86 <    ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88 >  SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89 >    forceField_(ff), simParams_(simParams),
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 >    useAtomicVirial_(true) {
97  
93 –            
94 –      std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
98        MoleculeStamp* molStamp;
99        int nMolWithSameStamp;
100        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
# Line 99 | Line 102 | namespace oopse {
102        CutoffGroupStamp* cgStamp;    
103        RigidBodyStamp* rbStamp;
104        int nRigidAtoms = 0;
105 <    
106 <      for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
107 <        molStamp = i->first;
108 <        nMolWithSameStamp = i->second;
105 >      std::vector<Component*> components = simParams->getComponents();
106 >      
107 >      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
108 >        molStamp = (*i)->getMoleculeStamp();
109 >        nMolWithSameStamp = (*i)->getNMol();
110          
111          addMoleculeStamp(molStamp, nMolWithSameStamp);
112  
113          //calculate atoms in molecules
114          nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
115  
112 –
116          //calculate atoms in cutoff groups
117          int nAtomsInGroups = 0;
118          int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119          
120          for (int j=0; j < nCutoffGroupsInStamp; j++) {
121 <          cgStamp = molStamp->getCutoffGroup(j);
121 >          cgStamp = molStamp->getCutoffGroupStamp(j);
122            nAtomsInGroups += cgStamp->getNMembers();
123          }
124  
# Line 128 | Line 131 | namespace oopse {
131          int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132          
133          for (int j=0; j < nRigidBodiesInStamp; j++) {
134 <          rbStamp = molStamp->getRigidBody(j);
134 >          rbStamp = molStamp->getRigidBodyStamp(j);
135            nAtomsInRigidBodies += rbStamp->getNMembers();
136          }
137  
# Line 167 | Line 170 | namespace oopse {
170      }
171      molecules_.clear();
172        
170 –    delete stamps_;
173      delete sman_;
174      delete simParams_;
175      delete forceField_;
# Line 274 | Line 276 | namespace oopse {
276            }
277          }
278              
279 <      }//end for (integrableObject)
280 <    }// end for (mol)
279 >      }
280 >    }
281      
282      // n_constraints is local, so subtract them on each processor
283      ndf_local -= nConstraints_;
# Line 292 | 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 592 | Line 603 | namespace oopse {
603      //setup fortran force field
604      /** @deprecate */    
605      int isError = 0;
606 +    
607 +    setupCutoff();
608      
609      setupElectrostaticSummationMethod( isError );
610      setupSwitchingFunction();
611 +    setupAccumulateBoxDipole();
612  
613      if(isError){
614        sprintf( painCave.errMsg,
# Line 602 | Line 616 | namespace oopse {
616        painCave.isFatal = 1;
617        simError();
618      }
605 –  
606 –    
607 –    setupCutoff();
619  
620      calcNdf();
621      calcNdfRaw();
# Line 654 | Line 665 | namespace oopse {
665      int usePBC = simParams_->getUsePeriodicBoundaryConditions();
666      int useRF;
667      int useSF;
668 +    int useSP;
669 +    int useBoxDipole;
670 +
671      std::string myMethod;
672  
673      // set the useRF logical
674      useRF = 0;
675      useSF = 0;
676 +    useSP = 0;
677  
678  
679      if (simParams_->haveElectrostaticSummationMethod()) {
680        std::string myMethod = simParams_->getElectrostaticSummationMethod();
681        toUpper(myMethod);
682 <      if (myMethod == "REACTION_FIELD") {
683 <        useRF=1;
684 <      } else {
685 <        if (myMethod == "SHIFTED_FORCE") {
686 <          useSF = 1;
687 <        }
682 >      if (myMethod == "REACTION_FIELD"){
683 >        useRF = 1;
684 >      } else if (myMethod == "SHIFTED_FORCE"){
685 >        useSF = 1;
686 >      } else if (myMethod == "SHIFTED_POTENTIAL"){
687 >        useSP = 1;
688        }
689      }
690 +    
691 +    if (simParams_->haveAccumulateBoxDipole())
692 +      if (simParams_->getAccumulateBoxDipole())
693 +        useBoxDipole = 1;
694  
695 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
696 +
697      //loop over all of the atom types
698      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
699        useLennardJones |= (*i)->isLennardJones();
# Line 742 | Line 763 | namespace oopse {
763      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
764  
765      temp = useSF;
766 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
766 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
767  
768 +    temp = useSP;
769 +    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770 +
771 +    temp = useBoxDipole;
772 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773 +
774 +    temp = useAtomicVirial_;
775 +    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776 +
777   #endif
778  
779      fInfo_.SIM_uses_PBC = usePBC;    
# Line 761 | Line 791 | namespace oopse {
791      fInfo_.SIM_uses_FLARB = useFLARB;
792      fInfo_.SIM_uses_RF = useRF;
793      fInfo_.SIM_uses_SF = useSF;
794 <
795 <    if( myMethod == "REACTION_FIELD") {
796 <      
767 <      if (simParams_->haveDielectric()) {
768 <        fInfo_.dielect = simParams_->getDielectric();
769 <      } else {
770 <        sprintf(painCave.errMsg,
771 <                "SimSetup Error: No Dielectric constant was set.\n"
772 <                "\tYou are trying to use Reaction Field without"
773 <                "\tsetting a dielectric constant!\n");
774 <        painCave.isFatal = 1;
775 <        simError();
776 <      }      
777 <    }
778 <
794 >    fInfo_.SIM_uses_SP = useSP;
795 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
796 >    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
797    }
798  
799    void SimInfo::setupFortranSim() {
# Line 792 | Line 810 | namespace oopse {
810      }
811  
812      //calculate mass ratio of cutoff group
813 <    std::vector<double> mfact;
813 >    std::vector<RealType> mfact;
814      SimInfo::MoleculeIterator mi;
815      Molecule* mol;
816      Molecule::CutoffGroupIterator ci;
817      CutoffGroup* cg;
818      Molecule::AtomIterator ai;
819      Atom* atom;
820 <    double totalMass;
820 >    RealType totalMass;
821  
822      //to avoid memory reallocation, reserve enough space for mfact
823      mfact.reserve(getNCutoffGroups());
# Line 860 | Line 878 | namespace oopse {
878               "succesfully sent the simulation information to fortran.\n");
879      MPIcheckPoint();
880   #endif // is_mpi
881 +
882 +    // Setup number of neighbors in neighbor list if present
883 +    if (simParams_->haveNeighborListNeighbors()) {
884 +      int nlistNeighbors = simParams_->getNeighborListNeighbors();
885 +      setNeighbors(&nlistNeighbors);
886 +    }
887 +  
888 +
889    }
890  
891  
# Line 924 | Line 950 | namespace oopse {
950  
951    void SimInfo::setupCutoff() {          
952      
953 +    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
954 +
955      // Check the cutoff policy
956 <    int cp =  TRADITIONAL_CUTOFF_POLICY;
957 <    if (simParams_->haveCutoffPolicy()) {
958 <      std::string myPolicy = simParams_->getCutoffPolicy();
956 >    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
957 >
958 >    std::string myPolicy;
959 >    if (forceFieldOptions_.haveCutoffPolicy()){
960 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
961 >    }else if (simParams_->haveCutoffPolicy()) {
962 >      myPolicy = simParams_->getCutoffPolicy();
963 >    }
964 >
965 >    if (!myPolicy.empty()){
966        toUpper(myPolicy);
967        if (myPolicy == "MIX") {
968          cp = MIX_CUTOFF_POLICY;
# Line 950 | Line 985 | namespace oopse {
985      notifyFortranCutoffPolicy(&cp);
986  
987      // Check the Skin Thickness for neighborlists
988 <    double skin;
988 >    RealType skin;
989      if (simParams_->haveSkinThickness()) {
990        skin = simParams_->getSkinThickness();
991        notifyFortranSkinThickness(&skin);
# Line 962 | Line 997 | namespace oopse {
997        if (simParams_->haveSwitchingRadius()) {
998          rsw_  = simParams_->getSwitchingRadius();
999        } else {
1000 <        rsw_ = rcut_;
1000 >        if (fInfo_.SIM_uses_Charges |
1001 >            fInfo_.SIM_uses_Dipoles |
1002 >            fInfo_.SIM_uses_RF) {
1003 >          
1004 >          rsw_ = 0.85 * rcut_;
1005 >          sprintf(painCave.errMsg,
1006 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1007 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1008 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1009 >        painCave.isFatal = 0;
1010 >        simError();
1011 >        } else {
1012 >          rsw_ = rcut_;
1013 >          sprintf(painCave.errMsg,
1014 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1015 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1016 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1017 >          painCave.isFatal = 0;
1018 >          simError();
1019 >        }
1020        }
1021 +      
1022        notifyFortranCutoffs(&rcut_, &rsw_);
1023        
1024      } else {
# Line 1020 | Line 1075 | namespace oopse {
1075      int errorOut;
1076      int esm =  NONE;
1077      int sm = UNDAMPED;
1078 <    double alphaVal;
1079 <    double dielectric;
1080 <
1078 >    RealType alphaVal;
1079 >    RealType dielectric;
1080 >    
1081      errorOut = isError;
1027 –    alphaVal = simParams_->getDampingAlpha();
1028 –    dielectric = simParams_->getDielectric();
1082  
1083      if (simParams_->haveElectrostaticSummationMethod()) {
1084        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1042 | Line 1095 | namespace oopse {
1095              if (myMethod == "SHIFTED_FORCE") {            
1096                esm = SHIFTED_FORCE;
1097              } else {
1098 <              if (myMethod == "REACTION_FIELD") {            
1098 >              if (myMethod == "REACTION_FIELD") {
1099                  esm = REACTION_FIELD;
1100 +                dielectric = simParams_->getDielectric();
1101 +                if (!simParams_->haveDielectric()) {
1102 +                  // throw warning
1103 +                  sprintf( painCave.errMsg,
1104 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1105 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1106 +                  painCave.isFatal = 0;
1107 +                  simError();
1108 +                }
1109                } else {
1110                  // throw error        
1111                  sprintf( painCave.errMsg,
# Line 1070 | Line 1132 | namespace oopse {
1132          if (myScreen == "DAMPED") {
1133            sm = DAMPED;
1134            if (!simParams_->haveDampingAlpha()) {
1135 <            //throw error
1135 >            // first set a cutoff dependent alpha value
1136 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1137 >            alphaVal = 0.5125 - rcut_* 0.025;
1138 >            // for values rcut > 20.5, alpha is zero
1139 >            if (alphaVal < 0) alphaVal = 0;
1140 >
1141 >            // throw warning
1142              sprintf( painCave.errMsg,
1143                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1144 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1144 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1145              painCave.isFatal = 0;
1146              simError();
1147 +          } else {
1148 +            alphaVal = simParams_->getDampingAlpha();
1149            }
1150 +          
1151          } else {
1152            // throw error        
1153            sprintf( painCave.errMsg,
# Line 1092 | Line 1163 | namespace oopse {
1163      
1164      // let's pass some summation method variables to fortran
1165      setElectrostaticSummationMethod( &esm );
1166 <    notifyFortranElectrostaticMethod( &esm );
1166 >    setFortranElectrostaticMethod( &esm );
1167      setScreeningMethod( &sm );
1168      setDampingAlpha( &alphaVal );
1169      setReactionFieldDielectric( &dielectric );
# Line 1125 | Line 1196 | namespace oopse {
1196  
1197    }
1198  
1199 +  void SimInfo::setupAccumulateBoxDipole() {    
1200 +
1201 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1202 +    if ( simParams_->haveAccumulateBoxDipole() )
1203 +      if ( simParams_->getAccumulateBoxDipole() ) {
1204 +        setAccumulateBoxDipole();
1205 +        calcBoxDipole_ = true;
1206 +      }
1207 +
1208 +  }
1209 +
1210    void SimInfo::addProperty(GenericData* genData) {
1211      properties_.addProperty(genData);  
1212    }
# Line 1181 | Line 1263 | namespace oopse {
1263      Molecule* mol;
1264  
1265      Vector3d comVel(0.0);
1266 <    double totalMass = 0.0;
1266 >    RealType totalMass = 0.0;
1267      
1268  
1269      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1270 <      double mass = mol->getMass();
1270 >      RealType mass = mol->getMass();
1271        totalMass += mass;
1272        comVel += mass * mol->getComVel();
1273      }  
1274  
1275   #ifdef IS_MPI
1276 <    double tmpMass = totalMass;
1276 >    RealType tmpMass = totalMass;
1277      Vector3d tmpComVel(comVel);    
1278 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1279 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1278 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1279 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1280   #endif
1281  
1282      comVel /= totalMass;
# Line 1207 | Line 1289 | namespace oopse {
1289      Molecule* mol;
1290  
1291      Vector3d com(0.0);
1292 <    double totalMass = 0.0;
1292 >    RealType totalMass = 0.0;
1293      
1294      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1295 <      double mass = mol->getMass();
1295 >      RealType mass = mol->getMass();
1296        totalMass += mass;
1297        com += mass * mol->getCom();
1298      }  
1299  
1300   #ifdef IS_MPI
1301 <    double tmpMass = totalMass;
1301 >    RealType tmpMass = totalMass;
1302      Vector3d tmpCom(com);    
1303 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1304 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1303 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1304 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1305   #endif
1306  
1307      com /= totalMass;
# Line 1243 | Line 1325 | namespace oopse {
1325        Molecule* mol;
1326        
1327      
1328 <      double totalMass = 0.0;
1328 >      RealType totalMass = 0.0;
1329      
1330  
1331        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1332 <         double mass = mol->getMass();
1332 >         RealType mass = mol->getMass();
1333           totalMass += mass;
1334           com += mass * mol->getCom();
1335           comVel += mass * mol->getComVel();          
1336        }  
1337        
1338   #ifdef IS_MPI
1339 <      double tmpMass = totalMass;
1339 >      RealType tmpMass = totalMass;
1340        Vector3d tmpCom(com);  
1341        Vector3d tmpComVel(comVel);
1342 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1343 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1344 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1342 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1343 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1344 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1345   #endif
1346        
1347        com /= totalMass;
# Line 1278 | Line 1360 | namespace oopse {
1360     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1361        
1362  
1363 <      double xx = 0.0;
1364 <      double yy = 0.0;
1365 <      double zz = 0.0;
1366 <      double xy = 0.0;
1367 <      double xz = 0.0;
1368 <      double yz = 0.0;
1363 >      RealType xx = 0.0;
1364 >      RealType yy = 0.0;
1365 >      RealType zz = 0.0;
1366 >      RealType xy = 0.0;
1367 >      RealType xz = 0.0;
1368 >      RealType yz = 0.0;
1369        Vector3d com(0.0);
1370        Vector3d comVel(0.0);
1371        
# Line 1295 | Line 1377 | namespace oopse {
1377        Vector3d thisq(0.0);
1378        Vector3d thisv(0.0);
1379  
1380 <      double thisMass = 0.0;
1380 >      RealType thisMass = 0.0;
1381      
1382        
1383        
# Line 1333 | Line 1415 | namespace oopse {
1415   #ifdef IS_MPI
1416        Mat3x3d tmpI(inertiaTensor);
1417        Vector3d tmpAngMom;
1418 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1419 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1418 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1419 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1420   #endif
1421                
1422        return;
# Line 1355 | Line 1437 | namespace oopse {
1437        Vector3d thisr(0.0);
1438        Vector3d thisp(0.0);
1439        
1440 <      double thisMass;
1440 >      RealType thisMass;
1441        
1442        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1443          thisMass = mol->getMass();
# Line 1368 | Line 1450 | namespace oopse {
1450        
1451   #ifdef IS_MPI
1452        Vector3d tmpAngMom;
1453 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1453 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1454   #endif
1455        
1456        return angularMomentum;
1457     }
1458    
1459 <  
1459 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1460 >    return IOIndexToIntegrableObject.at(index);
1461 >  }
1462 >  
1463 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1464 >    IOIndexToIntegrableObject= v;
1465 >  }
1466 >
1467 >  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1468 >     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1469 >     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1470 >     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1471 >  */
1472 >  void SimInfo::getGyrationalVolume(RealType &volume){
1473 >    Mat3x3d intTensor;
1474 >    RealType det;
1475 >    Vector3d dummyAngMom;
1476 >    RealType sysconstants;
1477 >    RealType geomCnst;
1478 >
1479 >    geomCnst = 3.0/2.0;
1480 >    /* Get the inertial tensor and angular momentum for free*/
1481 >    getInertiaTensor(intTensor,dummyAngMom);
1482 >    
1483 >    det = intTensor.determinant();
1484 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1485 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1486 >    return;
1487 >  }
1488 >
1489 >  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1490 >    Mat3x3d intTensor;
1491 >    Vector3d dummyAngMom;
1492 >    RealType sysconstants;
1493 >    RealType geomCnst;
1494 >
1495 >    geomCnst = 3.0/2.0;
1496 >    /* Get the inertial tensor and angular momentum for free*/
1497 >    getInertiaTensor(intTensor,dummyAngMom);
1498 >    
1499 >    detI = intTensor.determinant();
1500 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1501 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1502 >    return;
1503 >  }
1504 > /*
1505 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1506 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1507 >      sdByGlobalIndex_ = v;
1508 >    }
1509 >
1510 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1511 >      //assert(index < nAtoms_ + nRigidBodies_);
1512 >      return sdByGlobalIndex_.at(index);
1513 >    }  
1514 > */  
1515   }//end namespace oopse
1516  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines