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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 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1089 by chrisfen, Wed Nov 1 22:22:44 2006 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"
# Line 89 | Line 90 | namespace oopse {
90      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
91      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
92      nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
93 <    sman_(NULL), fortranInitialized_(false) {
93 >    sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
94  
95        MoleculeStamp* molStamp;
96        int nMolWithSameStamp;
# Line 600 | Line 601 | namespace oopse {
601      /** @deprecate */    
602      int isError = 0;
603      
604 +    setupCutoff();
605 +    
606      setupElectrostaticSummationMethod( isError );
607      setupSwitchingFunction();
608 +    setupAccumulateBoxDipole();
609  
610      if(isError){
611        sprintf( painCave.errMsg,
# Line 609 | Line 613 | namespace oopse {
613        painCave.isFatal = 1;
614        simError();
615      }
612 –  
613 –    
614 –    setupCutoff();
616  
617      calcNdf();
618      calcNdfRaw();
# Line 661 | Line 662 | namespace oopse {
662      int usePBC = simParams_->getUsePeriodicBoundaryConditions();
663      int useRF;
664      int useSF;
665 +    int useSP;
666 +    int useBoxDipole;
667      std::string myMethod;
668  
669      // set the useRF logical
670      useRF = 0;
671      useSF = 0;
672 +    useSP = 0;
673  
674  
675      if (simParams_->haveElectrostaticSummationMethod()) {
676        std::string myMethod = simParams_->getElectrostaticSummationMethod();
677        toUpper(myMethod);
678 <      if (myMethod == "REACTION_FIELD") {
679 <        useRF=1;
680 <      } else {
681 <        if (myMethod == "SHIFTED_FORCE") {
682 <          useSF = 1;
683 <        }
678 >      if (myMethod == "REACTION_FIELD"){
679 >        useRF = 1;
680 >      } else if (myMethod == "SHIFTED_FORCE"){
681 >        useSF = 1;
682 >      } else if (myMethod == "SHIFTED_POTENTIAL"){
683 >        useSP = 1;
684        }
685      }
686 +    
687 +    if (simParams_->haveAccumulateBoxDipole())
688 +      if (simParams_->getAccumulateBoxDipole())
689 +        useBoxDipole = 1;
690  
691      //loop over all of the atom types
692      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
# Line 749 | Line 757 | namespace oopse {
757      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
758  
759      temp = useSF;
760 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
760 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
761  
762 +    temp = useSP;
763 +    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764 +
765 +    temp = useBoxDipole;
766 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767 +
768   #endif
769  
770      fInfo_.SIM_uses_PBC = usePBC;    
# Line 768 | Line 782 | namespace oopse {
782      fInfo_.SIM_uses_FLARB = useFLARB;
783      fInfo_.SIM_uses_RF = useRF;
784      fInfo_.SIM_uses_SF = useSF;
785 <
786 <    if( myMethod == "REACTION_FIELD") {
773 <      
774 <      if (simParams_->haveDielectric()) {
775 <        fInfo_.dielect = simParams_->getDielectric();
776 <      } else {
777 <        sprintf(painCave.errMsg,
778 <                "SimSetup Error: No Dielectric constant was set.\n"
779 <                "\tYou are trying to use Reaction Field without"
780 <                "\tsetting a dielectric constant!\n");
781 <        painCave.isFatal = 1;
782 <        simError();
783 <      }      
784 <    }
785 <
785 >    fInfo_.SIM_uses_SP = useSP;
786 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
787    }
788  
789    void SimInfo::setupFortranSim() {
# Line 1058 | Line 1059 | namespace oopse {
1059      int sm = UNDAMPED;
1060      RealType alphaVal;
1061      RealType dielectric;
1062 <
1062 >    
1063      errorOut = isError;
1063 –    alphaVal = simParams_->getDampingAlpha();
1064 –    dielectric = simParams_->getDielectric();
1064  
1065      if (simParams_->haveElectrostaticSummationMethod()) {
1066        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1078 | Line 1077 | namespace oopse {
1077              if (myMethod == "SHIFTED_FORCE") {            
1078                esm = SHIFTED_FORCE;
1079              } else {
1080 <              if (myMethod == "REACTION_FIELD") {            
1080 >              if (myMethod == "REACTION_FIELD") {
1081                  esm = REACTION_FIELD;
1082 +                dielectric = simParams_->getDielectric();
1083 +                if (!simParams_->haveDielectric()) {
1084 +                  // throw warning
1085 +                  sprintf( painCave.errMsg,
1086 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1087 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1088 +                  painCave.isFatal = 0;
1089 +                  simError();
1090 +                }
1091                } else {
1092                  // throw error        
1093                  sprintf( painCave.errMsg,
# Line 1106 | Line 1114 | namespace oopse {
1114          if (myScreen == "DAMPED") {
1115            sm = DAMPED;
1116            if (!simParams_->haveDampingAlpha()) {
1117 <            //throw error
1117 >            // first set a cutoff dependent alpha value
1118 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1119 >            alphaVal = 0.5125 - rcut_* 0.025;
1120 >            // for values rcut > 20.5, alpha is zero
1121 >            if (alphaVal < 0) alphaVal = 0;
1122 >
1123 >            // throw warning
1124              sprintf( painCave.errMsg,
1125                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1126 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1126 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1127              painCave.isFatal = 0;
1128              simError();
1129 +          } else {
1130 +            alphaVal = simParams_->getDampingAlpha();
1131            }
1132 +          
1133          } else {
1134            // throw error        
1135            sprintf( painCave.errMsg,
# Line 1161 | Line 1178 | namespace oopse {
1178  
1179    }
1180  
1181 +  void SimInfo::setupAccumulateBoxDipole() {    
1182 +
1183 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1184 +    if ( simParams_->haveAccumulateBoxDipole() )
1185 +      if ( simParams_->getAccumulateBoxDipole() ) {
1186 +        setAccumulateBoxDipole();
1187 +        calcBoxDipole_ = true;
1188 +      }
1189 +
1190 +  }
1191 +
1192    void SimInfo::addProperty(GenericData* genData) {
1193      properties_.addProperty(genData);  
1194    }
# Line 1410 | Line 1438 | namespace oopse {
1438        return angularMomentum;
1439     }
1440    
1441 <  
1441 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1442 >    return IOIndexToIntegrableObject.at(index);
1443 >  }
1444 >  
1445 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1446 >    IOIndexToIntegrableObject= v;
1447 >  }
1448 >
1449 > /*
1450 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1451 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1452 >      sdByGlobalIndex_ = v;
1453 >    }
1454 >
1455 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1456 >      //assert(index < nAtoms_ + nRigidBodies_);
1457 >      return sdByGlobalIndex_.at(index);
1458 >    }  
1459 > */  
1460   }//end namespace oopse
1461  

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