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root/group/trunk/OOPSE-2.0/src/brains/SimInfo.cpp
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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 2344 by chrisfen, Tue Oct 4 19:34:03 2005 UTC vs.
Revision 2400 by chrisfen, Wed Oct 26 23:32:25 2005 UTC

# Line 526 | Line 526 | namespace oopse {
526      int useDirectionalAtom = 0;    
527      int useElectrostatics = 0;
528      //usePBC and useRF are from simParams
529 <    int usePBC = simParams_->getPBC();
529 >    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
530      int useRF;
531 +    std::string myMethod;
532  
533      // set the useRF logical
534 <    std::string myMethod = simParams_->getElectrostaticSummationMethod();
535 <    if (myMethod == "REACTION_FIELD")
536 <      useRF = 1;
537 <    else
538 <      useRF = 0;
534 >    useRF = 0;
535 >
536 >
537 >    if (simParams_->haveElectrostaticSummationMethod()) {
538 >      std::string myMethod = simParams_->getElectrostaticSummationMethod();
539 >      toUpper(myMethod);
540 >      if (myMethod == "REACTION_FIELD") {
541 >        useRF=1;
542 >      }
543 >    }
544  
545      //loop over all of the atom types
546      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
# Line 616 | Line 622 | namespace oopse {
622      fInfo_.SIM_uses_FLARB = useFLARB;
623      fInfo_.SIM_uses_RF = useRF;
624  
625 <    if( fInfo_.SIM_uses_Dipoles && myMethod == "REACTION_FIELD") {
626 <
625 >    if( myMethod == "REACTION_FIELD") {
626 >      
627        if (simParams_->haveDielectric()) {
628          fInfo_.dielect = simParams_->getDielectric();
629        } else {
# Line 627 | Line 633 | namespace oopse {
633                  "\tsetting a dielectric constant!\n");
634          painCave.isFatal = 1;
635          simError();
636 <      }
631 <        
632 <    } else {
633 <      fInfo_.dielect = 0.0;
636 >      }      
637      }
635 –
638    }
639  
640    void SimInfo::setupFortranSim() {
# Line 806 | Line 808 | namespace oopse {
808      
809      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
810          
811 <      if (!simParams_->haveRcut()){
811 >      if (!simParams_->haveCutoffRadius()){
812          sprintf(painCave.errMsg,
813                  "SimCreator Warning: No value was set for the cutoffRadius.\n"
814                  "\tOOPSE will use a default value of 15.0 angstroms"
# Line 815 | Line 817 | namespace oopse {
817          simError();
818          rcut = 15.0;
819        } else{
820 <        rcut = simParams_->getRcut();
820 >        rcut = simParams_->getCutoffRadius();
821        }
822  
823 <      if (!simParams_->haveRsw()){
823 >      if (!simParams_->haveSwitchingRadius()){
824          sprintf(painCave.errMsg,
825                  "SimCreator Warning: No value was set for switchingRadius.\n"
826                  "\tOOPSE will use a default value of\n"
827 <                "\t0.95 * cutoffRadius for the switchingRadius\n");
827 >                "\t0.85 * cutoffRadius for the switchingRadius\n");
828          painCave.isFatal = 0;
829          simError();
830 <        rsw = 0.95 * rcut;
830 >        rsw = 0.85 * rcut;
831        } else{
832 <        rsw = simParams_->getRsw();
832 >        rsw = simParams_->getSwitchingRadius();
833        }
834  
835      } else {
836        // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
837        //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
838          
839 <      if (simParams_->haveRcut()) {
840 <        rcut = simParams_->getRcut();
839 >      if (simParams_->haveCutoffRadius()) {
840 >        rcut = simParams_->getCutoffRadius();
841        } else {
842          //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
843          rcut = calcMaxCutoffRadius();
844        }
845  
846 <      if (simParams_->haveRsw()) {
847 <        rsw  = simParams_->getRsw();
846 >      if (simParams_->haveSwitchingRadius()) {
847 >        rsw  = simParams_->getSwitchingRadius();
848        } else {
849          rsw = rcut;
850        }
# Line 859 | Line 861 | namespace oopse {
861      int cp =  TRADITIONAL_CUTOFF_POLICY;
862      if (simParams_->haveCutoffPolicy()) {
863        std::string myPolicy = simParams_->getCutoffPolicy();
864 +      toUpper(myPolicy);
865        if (myPolicy == "MIX") {
866          cp = MIX_CUTOFF_POLICY;
867        } else {
# Line 885 | Line 888 | namespace oopse {
888  
889      notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
890      // also send cutoff notification to electrostatics
891 <    setElectrostaticCutoffRadius(&rcut_);
891 >    setElectrostaticCutoffRadius(&rcut_, &rsw_);
892    }
893  
894    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
# Line 901 | Line 904 | namespace oopse {
904  
905      if (simParams_->haveElectrostaticSummationMethod()) {
906        std::string myMethod = simParams_->getElectrostaticSummationMethod();
907 +      toUpper(myMethod);
908        if (myMethod == "NONE") {
909          esm = NONE;
910        } else {
# Line 917 | Line 921 | namespace oopse {
921                simError();
922              }
923            } else {
924 <            if (myMethod == "REACTION_FIELD") {
924 >            if (myMethod == "REACTION_FIELD") {      
925                esm = REACTION_FIELD;
926              } else {
927                // throw error        

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