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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 1078 by gezelter, Wed Oct 18 21:58:48 2006 UTC vs.
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 UTC

# Line 59 | Line 59
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"
# Line 67 | Line 68
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 90 | Line 92 | namespace oopse {
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), calcBoxDipole_(false) {
95 >    sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
96 >    useAtomicVirial_(true) {
97  
98        MoleculeStamp* molStamp;
99        int nMolWithSameStamp;
# Line 664 | Line 667 | namespace oopse {
667      int useSF;
668      int useSP;
669      int useBoxDipole;
670 +
671      std::string myMethod;
672  
673      // set the useRF logical
# Line 688 | Line 692 | namespace oopse {
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 765 | Line 771 | namespace oopse {
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 784 | Line 793 | namespace oopse {
793      fInfo_.SIM_uses_SF = useSF;
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 868 | 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 936 | Line 954 | namespace oopse {
954  
955      // Check the cutoff policy
956      int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
957 +
958 +    // Set LJ shifting bools to false
959 +    ljsp_ = false;
960 +    ljsf_ = false;
961  
962      std::string myPolicy;
963      if (forceFieldOptions_.haveCutoffPolicy()){
# Line 1000 | Line 1022 | namespace oopse {
1022            simError();
1023          }
1024        }
1025 +
1026 +      if (simParams_->haveElectrostaticSummationMethod()) {
1027 +        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1028 +        toUpper(myMethod);
1029 +        
1030 +        if (myMethod == "SHIFTED_POTENTIAL") {
1031 +          ljsp_ = true;
1032 +        } else if (myMethod == "SHIFTED_FORCE") {
1033 +          ljsf_ = true;
1034 +        }
1035 +      }
1036 +      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1037        
1004 –      notifyFortranCutoffs(&rcut_, &rsw_);
1005 –      
1038      } else {
1039        
1040        // For electrostatic atoms, we'll assume a large safe value:
# Line 1018 | Line 1050 | namespace oopse {
1050          if (simParams_->haveElectrostaticSummationMethod()) {
1051            std::string myMethod = simParams_->getElectrostaticSummationMethod();
1052            toUpper(myMethod);
1053 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1053 >      
1054 >      // For the time being, we're tethering the LJ shifted behavior to the
1055 >      // electrostaticSummationMethod keyword options
1056 >          if (myMethod == "SHIFTED_POTENTIAL") {
1057 >            ljsp_ = true;
1058 >          } else if (myMethod == "SHIFTED_FORCE") {
1059 >            ljsf_ = true;
1060 >          }
1061 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1062              if (simParams_->haveSwitchingRadius()){
1063                sprintf(painCave.errMsg,
1064                        "SimInfo Warning: A value was set for the switchingRadius\n"
# Line 1041 | Line 1081 | namespace oopse {
1081            simError();
1082            rsw_ = 0.85 * rcut_;
1083          }
1084 <        notifyFortranCutoffs(&rcut_, &rsw_);
1084 >
1085 >        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1086 >
1087        } else {
1088          // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1089          // We'll punt and let fortran figure out the cutoffs later.
# Line 1126 | Line 1168 | namespace oopse {
1168                       "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1169              painCave.isFatal = 0;
1170              simError();
1171 +          } else {
1172 +            alphaVal = simParams_->getDampingAlpha();
1173            }
1174 +          
1175          } else {
1176            // throw error        
1177            sprintf( painCave.errMsg,
# Line 1442 | Line 1487 | namespace oopse {
1487    void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1488      IOIndexToIntegrableObject= v;
1489    }
1490 +
1491 +  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1492 +     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1493 +     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1494 +     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1495 +  */
1496 +  void SimInfo::getGyrationalVolume(RealType &volume){
1497 +    Mat3x3d intTensor;
1498 +    RealType det;
1499 +    Vector3d dummyAngMom;
1500 +    RealType sysconstants;
1501 +    RealType geomCnst;
1502  
1503 +    geomCnst = 3.0/2.0;
1504 +    /* Get the inertial tensor and angular momentum for free*/
1505 +    getInertiaTensor(intTensor,dummyAngMom);
1506 +    
1507 +    det = intTensor.determinant();
1508 +    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1509 +    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1510 +    return;
1511 +  }
1512 +
1513 +  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1514 +    Mat3x3d intTensor;
1515 +    Vector3d dummyAngMom;
1516 +    RealType sysconstants;
1517 +    RealType geomCnst;
1518 +
1519 +    geomCnst = 3.0/2.0;
1520 +    /* Get the inertial tensor and angular momentum for free*/
1521 +    getInertiaTensor(intTensor,dummyAngMom);
1522 +    
1523 +    detI = intTensor.determinant();
1524 +    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1525 +    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1526 +    return;
1527 +  }
1528   /*
1529     void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1530        assert( v.size() == nAtoms_ + nRigidBodies_);

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