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root/OpenMD/trunk/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 1050 by chrisfen, Fri Sep 22 22:19:59 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
# Line 671 | Line 674 | namespace oopse {
674      if (simParams_->haveElectrostaticSummationMethod()) {
675        std::string myMethod = simParams_->getElectrostaticSummationMethod();
676        toUpper(myMethod);
677 <      if (myMethod == "REACTION_FIELD") {
677 >      if (myMethod == "REACTION_FIELD"){
678          useRF=1;
679 <      } else {
680 <        if (myMethod == "SHIFTED_FORCE") {
681 <          useSF = 1;
682 <        }
679 >      } else if (myMethod == "SHIFTED_FORCE"){
680 >        useSF = 1;
681 >      } else if (myMethod == "SHIFTED_POTENTIAL"){
682 >        useSP = 1;
683        }
684      }
685 +    
686 +    if (simParams_->haveAccumulateBoxDipole())
687 +      if (simParams_->getAccumulateBoxDipole())
688 +        useBoxDipole = 1;
689  
690      //loop over all of the atom types
691      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
# Line 749 | Line 756 | namespace oopse {
756      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
757  
758      temp = useSF;
759 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
759 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
760 >
761 >    temp = useSP;
762 >    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763  
764 +    temp = useBoxDipole;
765 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766 +
767   #endif
768  
769      fInfo_.SIM_uses_PBC = usePBC;    
# Line 768 | Line 781 | namespace oopse {
781      fInfo_.SIM_uses_FLARB = useFLARB;
782      fInfo_.SIM_uses_RF = useRF;
783      fInfo_.SIM_uses_SF = useSF;
784 <
785 <    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 <
784 >    fInfo_.SIM_uses_SP = useSP;
785 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
786    }
787  
788    void SimInfo::setupFortranSim() {
# Line 1058 | Line 1058 | namespace oopse {
1058      int sm = UNDAMPED;
1059      RealType alphaVal;
1060      RealType dielectric;
1061 <
1061 >    
1062      errorOut = isError;
1063 –    alphaVal = simParams_->getDampingAlpha();
1064 –    dielectric = simParams_->getDielectric();
1063  
1064      if (simParams_->haveElectrostaticSummationMethod()) {
1065        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1078 | Line 1076 | namespace oopse {
1076              if (myMethod == "SHIFTED_FORCE") {            
1077                esm = SHIFTED_FORCE;
1078              } else {
1079 <              if (myMethod == "REACTION_FIELD") {            
1079 >              if (myMethod == "REACTION_FIELD") {
1080                  esm = REACTION_FIELD;
1081 +                dielectric = simParams_->getDielectric();
1082 +                if (!simParams_->haveDielectric()) {
1083 +                  // throw warning
1084 +                  sprintf( painCave.errMsg,
1085 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1086 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1087 +                  painCave.isFatal = 0;
1088 +                  simError();
1089 +                }
1090                } else {
1091                  // throw error        
1092                  sprintf( painCave.errMsg,
# Line 1106 | Line 1113 | namespace oopse {
1113          if (myScreen == "DAMPED") {
1114            sm = DAMPED;
1115            if (!simParams_->haveDampingAlpha()) {
1116 <            //throw error
1116 >            // first set a cutoff dependent alpha value
1117 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1118 >            alphaVal = 0.5125 - rcut_* 0.025;
1119 >            // for values rcut > 20.5, alpha is zero
1120 >            if (alphaVal < 0) alphaVal = 0;
1121 >
1122 >            // throw warning
1123              sprintf( painCave.errMsg,
1124                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1125 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1125 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1126              painCave.isFatal = 0;
1127              simError();
1128            }
# Line 1158 | Line 1171 | namespace oopse {
1171  
1172      // send switching function notification to switcheroo
1173      setFunctionType(&ft);
1174 +
1175 +  }
1176 +
1177 +  void SimInfo::setupAccumulateBoxDipole() {    
1178 +
1179 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1180 +    if ( simParams_->haveAccumulateBoxDipole() )
1181 +      if ( simParams_->getAccumulateBoxDipole() ) {
1182 +        setAccumulateBoxDipole();
1183 +        calcBoxDipole_ = true;
1184 +      }
1185  
1186    }
1187  
# Line 1409 | Line 1433 | namespace oopse {
1433        
1434        return angularMomentum;
1435     }
1412 –  
1436    
1437 +  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1438 +    return IOIndexToIntegrableObject.at(index);
1439 +  }
1440 +  
1441 +  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1442 +    IOIndexToIntegrableObject= v;
1443 +  }
1444 +
1445 + /*
1446 +   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1447 +      assert( v.size() == nAtoms_ + nRigidBodies_);
1448 +      sdByGlobalIndex_ = v;
1449 +    }
1450 +
1451 +    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1452 +      //assert(index < nAtoms_ + nRigidBodies_);
1453 +      return sdByGlobalIndex_.at(index);
1454 +    }  
1455 + */  
1456   }//end namespace oopse
1457  

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