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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 604 by chrisfen, Fri Sep 16 19:00:12 2005 UTC vs.
Revision 645 by chrisfen, Tue Oct 4 19:34:03 2005 UTC

# Line 53 | Line 53
53   #include "math/Vector3.hpp"
54   #include "primitives/Molecule.hpp"
55   #include "UseTheForce/fCutoffPolicy.h"
56 < #include "UseTheForce/Darkside/fElectrostaticSummationMethod.h"
56 > #include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
57   #include "UseTheForce/doForces_interface.h"
58 + #include "UseTheForce/DarkSide/electrostatic_interface.h"
59   #include "UseTheForce/notifyCutoffs_interface.h"
60   #include "utils/MemoryUtils.hpp"
61   #include "utils/simError.h"
# Line 82 | Line 83 | namespace oopse {
83        MoleculeStamp* molStamp;
84        int nMolWithSameStamp;
85        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86 <      int nGroups = 0;          //total cutoff groups defined in meta-data file
86 >      int nGroups = 0;      //total cutoff groups defined in meta-data file
87        CutoffGroupStamp* cgStamp;    
88        RigidBodyStamp* rbStamp;
89        int nRigidAtoms = 0;
# Line 107 | Line 108 | namespace oopse {
108          }
109  
110          nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
111 +
112          nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
113  
114          //calculate atoms in rigid bodies
# Line 123 | Line 125 | namespace oopse {
125          
126        }
127  
128 <      //every free atom (atom does not belong to cutoff groups) is a cutoff group
129 <      //therefore the total number of cutoff groups in the system is equal to
130 <      //the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
131 <      //file plus the number of cutoff groups defined in meta-data file
128 >      //every free atom (atom does not belong to cutoff groups) is a cutoff
129 >      //group therefore the total number of cutoff groups in the system is
130 >      //equal to the total number of atoms minus number of atoms belong to
131 >      //cutoff group defined in meta-data file plus the number of cutoff
132 >      //groups defined in meta-data file
133        nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134  
135 <      //every free atom (atom does not belong to rigid bodies) is an integrable object
136 <      //therefore the total number of  integrable objects in the system is equal to
137 <      //the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
138 <      //file plus the number of  rigid bodies defined in meta-data file
139 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
140 <
135 >      //every free atom (atom does not belong to rigid bodies) is an
136 >      //integrable object therefore the total number of integrable objects
137 >      //in the system is equal to the total number of atoms minus number of
138 >      //atoms belong to rigid body defined in meta-data file plus the number
139 >      //of rigid bodies defined in meta-data file
140 >      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141 >                                                + nGlobalRigidBodies_;
142 >  
143        nGlobalMols_ = molStampIds_.size();
144  
145   #ifdef IS_MPI    
# Line 522 | Line 527 | namespace oopse {
527      int useElectrostatics = 0;
528      //usePBC and useRF are from simParams
529      int usePBC = simParams_->getPBC();
530 +    int useRF;
531  
532 +    // set the useRF logical
533 +    std::string myMethod = simParams_->getElectrostaticSummationMethod();
534 +    if (myMethod == "REACTION_FIELD")
535 +      useRF = 1;
536 +    else
537 +      useRF = 0;
538 +
539      //loop over all of the atom types
540      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
541        useLennardJones |= (*i)->isLennardJones();
# Line 584 | Line 597 | namespace oopse {
597      temp = useFLARB;
598      MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
599  
600 +    temp = useRF;
601 +    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
602 +
603   #endif
604  
605      fInfo_.SIM_uses_PBC = usePBC;    
# Line 598 | Line 614 | namespace oopse {
614      fInfo_.SIM_uses_EAM = useEAM;
615      fInfo_.SIM_uses_Shapes = useShape;
616      fInfo_.SIM_uses_FLARB = useFLARB;
617 +    fInfo_.SIM_uses_RF = useRF;
618  
619 <    if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
619 >    if( fInfo_.SIM_uses_Dipoles && myMethod == "REACTION_FIELD") {
620  
621        if (simParams_->haveDielectric()) {
622          fInfo_.dielect = simParams_->getDielectric();
# Line 649 | Line 666 | namespace oopse {
666  
667          totalMass = cg->getMass();
668          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
669 <          mfact.push_back(atom->getMass()/totalMass);
669 >          // Check for massless groups - set mfact to 1 if true
670 >          if (totalMass != 0)
671 >            mfact.push_back(atom->getMass()/totalMass);
672 >          else
673 >            mfact.push_back( 1.0 );
674          }
675  
676        }      
# Line 855 | Line 876 | namespace oopse {
876            }    
877          }          
878        }
879 +    }
880 +
881 +
882 +    if (simParams_->haveSkinThickness()) {
883 +      double skinThickness = simParams_->getSkinThickness();
884      }
885 +
886      notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
887 +    // also send cutoff notification to electrostatics
888 +    setElectrostaticCutoffRadius(&rcut_);
889    }
890  
891    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
# Line 864 | Line 893 | namespace oopse {
893      int errorOut;
894      int esm =  NONE;
895      double alphaVal;
896 +    double dielectric;
897  
898      errorOut = isError;
899 +    alphaVal = simParams_->getDampingAlpha();
900 +    dielectric = simParams_->getDielectric();
901  
902      if (simParams_->haveElectrostaticSummationMethod()) {
903        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 880 | Line 912 | namespace oopse {
912              if (!simParams_->haveDampingAlpha()) {
913                //throw error
914                sprintf( painCave.errMsg,
915 <                       "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", simParams_->getDampingAlpha());
915 >                       "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal);
916                painCave.isFatal = 0;
917                simError();
918              }
887 –            alphaVal = simParams_->getDampingAlpha();
919            } else {
920              if (myMethod == "REACTION_FIELD") {
921                esm = REACTION_FIELD;
# Line 899 | Line 930 | namespace oopse {
930          }
931        }
932      }
933 <    initFortranFF( &fInfo_.SIM_uses_RF, &esm, &alphaVal, &errorOut );
933 >    // let's pass some summation method variables to fortran
934 >    setElectrostaticSummationMethod( &esm );
935 >    setDampedWolfAlpha( &alphaVal );
936 >    setReactionFieldDielectric( &dielectric );
937 >    initFortranFF( &esm, &errorOut );
938    }
939  
940    void SimInfo::addProperty(GenericData* genData) {

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