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root/group/trunk/OOPSE-2.0/src/brains/SimInfo.cpp
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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 2252 by chuckv, Mon May 30 14:01:52 2005 UTC vs.
Revision 2310 by chrisfen, Mon Sep 19 23:21:46 2005 UTC

# Line 52 | Line 52
52   #include "brains/SimInfo.hpp"
53   #include "math/Vector3.hpp"
54   #include "primitives/Molecule.hpp"
55 + #include "UseTheForce/fCutoffPolicy.h"
56 + #include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
57   #include "UseTheForce/doForces_interface.h"
58 + #include "UseTheForce/DarkSide/electrostatic_interface.h"
59   #include "UseTheForce/notifyCutoffs_interface.h"
60   #include "utils/MemoryUtils.hpp"
61   #include "utils/simError.h"
# Line 462 | Line 465 | namespace oopse {
465      //setup fortran force field
466      /** @deprecate */    
467      int isError = 0;
468 <    initFortranFF( &fInfo_.SIM_uses_RF , &isError );
468 >    
469 >    setupElectrostaticSummationMethod( isError );
470 >
471      if(isError){
472        sprintf( painCave.errMsg,
473                 "ForceField error: There was an error initializing the forceField in fortran.\n" );
# Line 518 | Line 523 | namespace oopse {
523      int useElectrostatics = 0;
524      //usePBC and useRF are from simParams
525      int usePBC = simParams_->getPBC();
526 <    int useRF = simParams_->getUseRF();
526 >    int useRF;
527 >
528 >    // set the useRF logical
529 >    std::string myMethod = simParams_->getElectrostaticSummationMethod();
530 >    if (myMethod == "REACTION_FIELD")
531 >      useRF = 1;
532 >    else
533 >      useRF = 0;
534  
535      //loop over all of the atom types
536      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
# Line 583 | Line 595 | namespace oopse {
595  
596      temp = useRF;
597      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
598 <    
598 >
599   #endif
600  
601      fInfo_.SIM_uses_PBC = usePBC;    
# Line 600 | Line 612 | namespace oopse {
612      fInfo_.SIM_uses_FLARB = useFLARB;
613      fInfo_.SIM_uses_RF = useRF;
614  
615 <    if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
615 >    if( fInfo_.SIM_uses_Dipoles && myMethod == "REACTION_FIELD") {
616  
617        if (simParams_->haveDielectric()) {
618          fInfo_.dielect = simParams_->getDielectric();
# Line 830 | Line 842 | namespace oopse {
842      }
843    }
844  
845 <  void SimInfo::setupCutoff() {
845 >  void SimInfo::setupCutoff() {    
846      getCutoff(rcut_, rsw_);    
847      double rnblist = rcut_ + 1; // skin of neighbor list
848  
849      //Pass these cutoff radius etc. to fortran. This function should be called once and only once
850 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
850 >    
851 >    int cp =  TRADITIONAL_CUTOFF_POLICY;
852 >    if (simParams_->haveCutoffPolicy()) {
853 >      std::string myPolicy = simParams_->getCutoffPolicy();
854 >      if (myPolicy == "MIX") {
855 >        cp = MIX_CUTOFF_POLICY;
856 >      } else {
857 >        if (myPolicy == "MAX") {
858 >          cp = MAX_CUTOFF_POLICY;
859 >        } else {
860 >          if (myPolicy == "TRADITIONAL") {            
861 >            cp = TRADITIONAL_CUTOFF_POLICY;
862 >          } else {
863 >            // throw error        
864 >            sprintf( painCave.errMsg,
865 >                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
866 >            painCave.isFatal = 1;
867 >            simError();
868 >          }    
869 >        }          
870 >      }
871 >    }
872 >    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
873 >    // also send cutoff notification to electrostatics
874 >    setElectrostaticCutoffRadius(&rcut_);
875    }
876  
877 +  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
878 +    
879 +    int errorOut;
880 +    int esm =  NONE;
881 +    double alphaVal;
882 +    double dielectric;
883 +
884 +    errorOut = isError;
885 +    alphaVal = simParams_->getDampingAlpha();
886 +    dielectric = simParams_->getDielectric();
887 +
888 +    if (simParams_->haveElectrostaticSummationMethod()) {
889 +      std::string myMethod = simParams_->getElectrostaticSummationMethod();
890 +      if (myMethod == "NONE") {
891 +        esm = NONE;
892 +      } else {
893 +        if (myMethod == "UNDAMPED_WOLF") {
894 +          esm = UNDAMPED_WOLF;
895 +        } else {
896 +          if (myMethod == "DAMPED_WOLF") {            
897 +            esm = DAMPED_WOLF;
898 +            if (!simParams_->haveDampingAlpha()) {
899 +              //throw error
900 +              sprintf( painCave.errMsg,
901 +                       "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal);
902 +              painCave.isFatal = 0;
903 +              simError();
904 +            }
905 +          } else {
906 +            if (myMethod == "REACTION_FIELD") {
907 +              esm = REACTION_FIELD;
908 +            } else {
909 +              // throw error        
910 +              sprintf( painCave.errMsg,
911 +                       "SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
912 +              painCave.isFatal = 1;
913 +              simError();
914 +            }    
915 +          }          
916 +        }
917 +      }
918 +    }
919 +    // let's pass some summation method variables to fortran
920 +    setElectrostaticSummationMethod( &esm );
921 +    setDampedWolfAlpha( &alphaVal );
922 +    setReactionFieldDielectric( &dielectric );
923 +    initFortranFF( &esm, &errorOut );
924 +  }
925 +
926    void SimInfo::addProperty(GenericData* genData) {
927      properties_.addProperty(genData);  
928    }
# Line 981 | Line 1066 | namespace oopse {
1066    
1067     /*
1068     Return intertia tensor for entire system and angular momentum Vector.
1069 +
1070 +
1071 +       [  Ixx -Ixy  -Ixz ]
1072 +  J =| -Iyx  Iyy  -Iyz |
1073 +       [ -Izx -Iyz   Izz ]
1074      */
1075  
1076     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
# Line 1032 | Line 1122 | namespace oopse {
1122        inertiaTensor(0,1) = -xy;
1123        inertiaTensor(0,2) = -xz;
1124        inertiaTensor(1,0) = -xy;
1125 <      inertiaTensor(2,0) = xx + zz;
1125 >      inertiaTensor(1,1) = xx + zz;
1126        inertiaTensor(1,2) = -yz;
1127        inertiaTensor(2,0) = -xz;
1128        inertiaTensor(2,1) = -yz;
# Line 1060 | Line 1150 | namespace oopse {
1150        SimInfo::MoleculeIterator i;
1151        Molecule* mol;
1152        
1153 <      Vector3d thisq(0.0);
1154 <      Vector3d thisv(0.0);
1153 >      Vector3d thisr(0.0);
1154 >      Vector3d thisp(0.0);
1155        
1156 <      double thisMass = 0.0;
1156 >      double thisMass;
1157        
1158        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1159 <         thisq = mol->getCom()-com;
1160 <         thisv = mol->getComVel()-comVel;
1161 <         thisMass = mol->getMass();
1072 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1159 >        thisMass = mol->getMass();
1160 >        thisr = mol->getCom()-com;
1161 >        thisp = (mol->getComVel()-comVel)*thisMass;
1162          
1163 +        angularMomentum += cross( thisr, thisp );
1164 +        
1165        }  
1166        
1167   #ifdef IS_MPI

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