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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 1095 by chuckv, Tue Dec 5 00:17:24 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"
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 66 | 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 603 | namespace oopse {
603      /** @deprecate */    
604      int isError = 0;
605      
606 +    setupCutoff();
607 +    
608      setupElectrostaticSummationMethod( isError );
609      setupSwitchingFunction();
610      setupAccumulateBoxDipole();
# 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 +      setNeighbors(simParams_->getNeighborListNeighbors());
877 +    }
878 +  
879 +
880    }
881  
882  
# Line 1073 | Line 1068 | namespace oopse {
1068      int sm = UNDAMPED;
1069      RealType alphaVal;
1070      RealType dielectric;
1071 <
1071 >    
1072      errorOut = isError;
1078 –    alphaVal = simParams_->getDampingAlpha();
1079 –    dielectric = simParams_->getDielectric();
1073  
1074      if (simParams_->haveElectrostaticSummationMethod()) {
1075        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1093 | Line 1086 | namespace oopse {
1086              if (myMethod == "SHIFTED_FORCE") {            
1087                esm = SHIFTED_FORCE;
1088              } else {
1089 <              if (myMethod == "REACTION_FIELD") {            
1089 >              if (myMethod == "REACTION_FIELD") {
1090                  esm = REACTION_FIELD;
1091 +                dielectric = simParams_->getDielectric();
1092 +                if (!simParams_->haveDielectric()) {
1093 +                  // throw warning
1094 +                  sprintf( painCave.errMsg,
1095 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1096 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1097 +                  painCave.isFatal = 0;
1098 +                  simError();
1099 +                }
1100                } else {
1101                  // throw error        
1102                  sprintf( painCave.errMsg,
# Line 1121 | Line 1123 | namespace oopse {
1123          if (myScreen == "DAMPED") {
1124            sm = DAMPED;
1125            if (!simParams_->haveDampingAlpha()) {
1126 <            //throw error
1126 >            // first set a cutoff dependent alpha value
1127 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1128 >            alphaVal = 0.5125 - rcut_* 0.025;
1129 >            // for values rcut > 20.5, alpha is zero
1130 >            if (alphaVal < 0) alphaVal = 0;
1131 >
1132 >            // throw warning
1133              sprintf( painCave.errMsg,
1134                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1135 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1135 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1136              painCave.isFatal = 0;
1137              simError();
1138 +          } else {
1139 +            alphaVal = simParams_->getDampingAlpha();
1140            }
1141 +          
1142          } else {
1143            // throw error        
1144            sprintf( painCave.errMsg,
# Line 1436 | Line 1447 | namespace oopse {
1447        return angularMomentum;
1448     }
1449    
1450 <  
1450 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1451 >    return IOIndexToIntegrableObject.at(index);
1452 >  }
1453 >  
1454 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1455 >    IOIndexToIntegrableObject= v;
1456 >  }
1457 >
1458 > /*
1459 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1460 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1461 >      sdByGlobalIndex_ = v;
1462 >    }
1463 >
1464 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1465 >      //assert(index < nAtoms_ + nRigidBodies_);
1466 >      return sdByGlobalIndex_.at(index);
1467 >    }  
1468 > */  
1469   }//end namespace oopse
1470  

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