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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 1024 by tim, Wed Aug 30 18:42:29 2006 UTC vs.
Revision 1095 by chuckv, Tue Dec 5 00:17:24 2006 UTC

# Line 59 | Line 59
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 67
67   #include "selection/SelectionManager.hpp"
68   #include "io/ForceFieldOptions.hpp"
69   #include "UseTheForce/ForceField.hpp"
70 +
71  
72   #ifdef IS_MPI
73   #include "UseTheForce/mpiComponentPlan.h"
# Line 600 | Line 602 | namespace oopse {
602      //setup fortran force field
603      /** @deprecate */    
604      int isError = 0;
605 +    
606 +    setupCutoff();
607      
608      setupElectrostaticSummationMethod( isError );
609      setupSwitchingFunction();
# Line 611 | Line 615 | namespace oopse {
615        painCave.isFatal = 1;
616        simError();
617      }
614 –  
615 –    
616 –    setupCutoff();
618  
619      calcNdf();
620      calcNdfRaw();
# Line 670 | 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 784 | Line 786 | namespace oopse {
786      fInfo_.SIM_uses_SF = useSF;
787      fInfo_.SIM_uses_SP = useSP;
788      fInfo_.SIM_uses_BoxDipole = useBoxDipole;
787 –
788 –    if( myMethod == "REACTION_FIELD") {
789 –      
790 –      if (simParams_->haveDielectric()) {
791 –        fInfo_.dielect = simParams_->getDielectric();
792 –      } else {
793 –        sprintf(painCave.errMsg,
794 –                "SimSetup Error: No Dielectric constant was set.\n"
795 –                "\tYou are trying to use Reaction Field without"
796 –                "\tsetting a dielectric constant!\n");
797 –        painCave.isFatal = 1;
798 –        simError();
799 –      }      
800 –    }
801 –
789    }
790  
791    void SimInfo::setupFortranSim() {
# Line 883 | 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 1074 | Line 1068 | namespace oopse {
1068      int sm = UNDAMPED;
1069      RealType alphaVal;
1070      RealType dielectric;
1071 <
1071 >    
1072      errorOut = isError;
1079 –    alphaVal = simParams_->getDampingAlpha();
1080 –    dielectric = simParams_->getDielectric();
1073  
1074      if (simParams_->haveElectrostaticSummationMethod()) {
1075        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1094 | 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 1122 | 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,

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