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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 998 by chrisfen, Mon Jul 3 13:18:43 2006 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"
# Line 66 | 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 89 | 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 600 | Line 604 | namespace oopse {
604      /** @deprecate */    
605      int isError = 0;
606      
607 +    setupCutoff();
608 +    
609      setupElectrostaticSummationMethod( isError );
610      setupSwitchingFunction();
611      setupAccumulateBoxDipole();
# Line 610 | Line 616 | namespace oopse {
616        painCave.isFatal = 1;
617        simError();
618      }
613 –  
614 –    
615 –    setupCutoff();
619  
620      calcNdf();
621      calcNdfRaw();
# 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
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;
683 >        useRF = 1;
684        } else if (myMethod == "SHIFTED_FORCE"){
685          useSF = 1;
686        } else if (myMethod == "SHIFTED_POTENTIAL"){
# Line 687 | 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 764 | 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 783 | Line 793 | namespace oopse {
793      fInfo_.SIM_uses_SF = useSF;
794      fInfo_.SIM_uses_SP = useSP;
795      fInfo_.SIM_uses_BoxDipole = useBoxDipole;
796 <
787 <    if( myMethod == "REACTION_FIELD") {
788 <      
789 <      if (simParams_->haveDielectric()) {
790 <        fInfo_.dielect = simParams_->getDielectric();
791 <      } else {
792 <        sprintf(painCave.errMsg,
793 <                "SimSetup Error: No Dielectric constant was set.\n"
794 <                "\tYou are trying to use Reaction Field without"
795 <                "\tsetting a dielectric constant!\n");
796 <        painCave.isFatal = 1;
797 <        simError();
798 <      }      
799 <    }
800 <
796 >    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
797    }
798  
799    void SimInfo::setupFortranSim() {
# Line 882 | 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 1073 | Line 1077 | namespace oopse {
1077      int sm = UNDAMPED;
1078      RealType alphaVal;
1079      RealType dielectric;
1080 <
1080 >    
1081      errorOut = isError;
1078 –    alphaVal = simParams_->getDampingAlpha();
1079 –    dielectric = simParams_->getDielectric();
1082  
1083      if (simParams_->haveElectrostaticSummationMethod()) {
1084        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1093 | 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 1121 | 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 1435 | Line 1455 | namespace oopse {
1455        
1456        return angularMomentum;
1457     }
1438 –  
1458    
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  

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