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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 1024 by tim, Wed Aug 30 18:42:29 2006 UTC vs.
Revision 1121 by chuckv, Mon Feb 26 04:45:42 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 600 | 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 611 | Line 615 | namespace oopse {
615        painCave.isFatal = 1;
616        simError();
617      }
614 –  
615 –    
616 –    setupCutoff();
618  
619      calcNdf();
620      calcNdfRaw();
# Line 670 | 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 784 | Line 786 | namespace oopse {
786      fInfo_.SIM_uses_SF = useSF;
787      fInfo_.SIM_uses_SP = useSP;
788      fInfo_.SIM_uses_BoxDipole = useBoxDipole;
787 –
788 –    if( myMethod == "REACTION_FIELD") {
789 –      
790 –      if (simParams_->haveDielectric()) {
791 –        fInfo_.dielect = simParams_->getDielectric();
792 –      } else {
793 –        sprintf(painCave.errMsg,
794 –                "SimSetup Error: No Dielectric constant was set.\n"
795 –                "\tYou are trying to use Reaction Field without"
796 –                "\tsetting a dielectric constant!\n");
797 –        painCave.isFatal = 1;
798 –        simError();
799 –      }      
800 –    }
801 –
789    }
790  
791    void SimInfo::setupFortranSim() {
# Line 883 | 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 1074 | Line 1069 | namespace oopse {
1069      int sm = UNDAMPED;
1070      RealType alphaVal;
1071      RealType dielectric;
1072 <
1072 >    
1073      errorOut = isError;
1079 –    alphaVal = simParams_->getDampingAlpha();
1080 –    dielectric = simParams_->getDielectric();
1074  
1075      if (simParams_->haveElectrostaticSummationMethod()) {
1076        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1094 | 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 1122 | 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 1443 | Line 1454 | namespace oopse {
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_);

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