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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 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"
# Line 65 | Line 67
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"
# Line 599 | Line 602 | namespace oopse {
602      //setup fortran force field
603      /** @deprecate */    
604      int isError = 0;
605 +    
606 +    setupCutoff();
607      
608      setupElectrostaticSummationMethod( isError );
609      setupSwitchingFunction();
# Line 610 | Line 615 | namespace oopse {
615        painCave.isFatal = 1;
616        simError();
617      }
613 –  
614 –    
615 –    setupCutoff();
618  
619      calcNdf();
620      calcNdfRaw();
# 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 783 | Line 786 | namespace oopse {
786      fInfo_.SIM_uses_SF = useSF;
787      fInfo_.SIM_uses_SP = useSP;
788      fInfo_.SIM_uses_BoxDipole = useBoxDipole;
786 –
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 –
789    }
790  
791    void SimInfo::setupFortranSim() {
# Line 882 | 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 1073 | Line 1069 | namespace oopse {
1069      int sm = UNDAMPED;
1070      RealType alphaVal;
1071      RealType dielectric;
1072 <
1072 >    
1073      errorOut = isError;
1078 –    alphaVal = simParams_->getDampingAlpha();
1079 –    dielectric = simParams_->getDielectric();
1074  
1075      if (simParams_->haveElectrostaticSummationMethod()) {
1076        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1093 | 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 1121 | 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 1436 | Line 1448 | namespace oopse {
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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