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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 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 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 669 | Line 669 | namespace oopse {
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;
679 >        useRF = 1;
680        } else if (myMethod == "SHIFTED_FORCE"){
681          useSF = 1;
682        } else if (myMethod == "SHIFTED_POTENTIAL"){
# Line 783 | Line 784 | namespace oopse {
784      fInfo_.SIM_uses_SF = useSF;
785      fInfo_.SIM_uses_SP = useSP;
786      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 –
787    }
788  
789    void SimInfo::setupFortranSim() {
# Line 1073 | Line 1059 | namespace oopse {
1059      int sm = UNDAMPED;
1060      RealType alphaVal;
1061      RealType dielectric;
1062 <
1062 >    
1063      errorOut = isError;
1078 –    alphaVal = simParams_->getDampingAlpha();
1079 –    dielectric = simParams_->getDielectric();
1064  
1065      if (simParams_->haveElectrostaticSummationMethod()) {
1066        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1093 | 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 1121 | 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 1436 | 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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