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root/OpenMD/trunk/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1050 by chrisfen, Fri Sep 22 22:19:59 2006 UTC vs.
Revision 1103 by chuckv, Fri Dec 29 20:21:53 2006 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 669 | Line 671 | namespace oopse {
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;
681 >        useRF = 1;
682        } else if (myMethod == "SHIFTED_FORCE"){
683          useSF = 1;
684        } else if (myMethod == "SHIFTED_POTENTIAL"){
# Line 867 | 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 +      setNeighbors(simParams_->getNeighborListNeighbors());
877 +    }
878 +  
879 +
880    }
881  
882  
# Line 1125 | Line 1135 | namespace oopse {
1135                       "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1136              painCave.isFatal = 0;
1137              simError();
1138 +          } else {
1139 +            alphaVal = simParams_->getDampingAlpha();
1140            }
1141 +          
1142          } else {
1143            // throw error        
1144            sprintf( painCave.errMsg,
# Line 1440 | Line 1453 | namespace oopse {
1453    
1454    void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1455      IOIndexToIntegrableObject= v;
1456 +  }
1457 +
1458 +  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1459 +     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1460 +     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1461 +     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1462 +  */
1463 +  void SimInfo::getGyrationalVolume(RealType &volume){
1464 +    Mat3x3d intTensor;
1465 +    RealType det;
1466 +    Vector3d dummyAngMom;
1467 +    RealType sysconstants;
1468 +    RealType geomCnst;
1469 +
1470 +    geomCnst = 3.0/2.0;
1471 +    /* Get the inertial tensor and angular momentum for free*/
1472 +    getInertiaTensor(intTensor,dummyAngMom);
1473 +    
1474 +    det = intTensor.determinant();
1475 +    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1476 +    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1477 +    return;
1478    }
1479  
1480 +  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1481 +    Mat3x3d intTensor;
1482 +    Vector3d dummyAngMom;
1483 +    RealType sysconstants;
1484 +    RealType geomCnst;
1485 +
1486 +    geomCnst = 3.0/2.0;
1487 +    /* Get the inertial tensor and angular momentum for free*/
1488 +    getInertiaTensor(intTensor,dummyAngMom);
1489 +    
1490 +    detI = intTensor.determinant();
1491 +    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1492 +    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1493 +    return;
1494 +  }
1495   /*
1496     void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1497        assert( v.size() == nAtoms_ + nRigidBodies_);

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