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root/OpenMD/trunk/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 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 599 | Line 600 | namespace oopse {
600      //setup fortran force field
601      /** @deprecate */    
602      int isError = 0;
603 +    
604 +    setupCutoff();
605      
606      setupElectrostaticSummationMethod( isError );
607      setupSwitchingFunction();
# Line 610 | Line 613 | namespace oopse {
613        painCave.isFatal = 1;
614        simError();
615      }
613 –  
614 –    
615 –    setupCutoff();
616  
617      calcNdf();
618      calcNdfRaw();
# Line 783 | Line 783 | namespace oopse {
783      fInfo_.SIM_uses_SF = useSF;
784      fInfo_.SIM_uses_SP = useSP;
785      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 –
786    }
787  
788    void SimInfo::setupFortranSim() {
# Line 1073 | Line 1058 | namespace oopse {
1058      int sm = UNDAMPED;
1059      RealType alphaVal;
1060      RealType dielectric;
1061 <
1061 >    
1062      errorOut = isError;
1078 –    alphaVal = simParams_->getDampingAlpha();
1079 –    dielectric = simParams_->getDielectric();
1063  
1064      if (simParams_->haveElectrostaticSummationMethod()) {
1065        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1093 | 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 1121 | 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 1436 | Line 1434 | namespace oopse {
1434        return angularMomentum;
1435     }
1436    
1437 <  
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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