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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 764 by gezelter, Mon Nov 21 22:59:21 2005 UTC vs.
Revision 809 by gezelter, Mon Dec 12 19:32:50 2005 UTC

# Line 80 | Line 80 | namespace oopse {
80      return result;
81    }
82    
83 <  SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
84 <                   ForceField* ff, Globals* simParams) :
85 <    stamps_(stamps), forceField_(ff), simParams_(simParams),
83 >  SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
84 >    forceField_(ff), simParams_(simParams),
85      ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
86      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
87      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
# Line 90 | Line 89 | namespace oopse {
89      nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
90      sman_(NULL), fortranInitialized_(false) {
91  
93 –            
94 –      std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
92        MoleculeStamp* molStamp;
93        int nMolWithSameStamp;
94        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
# Line 99 | Line 96 | namespace oopse {
96        CutoffGroupStamp* cgStamp;    
97        RigidBodyStamp* rbStamp;
98        int nRigidAtoms = 0;
99 <    
100 <      for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
101 <        molStamp = i->first;
102 <        nMolWithSameStamp = i->second;
99 >      std::vector<Component*> components = simParams->getComponents();
100 >      
101 >      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
102 >        molStamp = (*i)->getMoleculeStamp();
103 >        nMolWithSameStamp = (*i)->getNMol();
104          
105          addMoleculeStamp(molStamp, nMolWithSameStamp);
106  
107          //calculate atoms in molecules
108          nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
109  
112 –
110          //calculate atoms in cutoff groups
111          int nAtomsInGroups = 0;
112          int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
113          
114          for (int j=0; j < nCutoffGroupsInStamp; j++) {
115 <          cgStamp = molStamp->getCutoffGroup(j);
115 >          cgStamp = molStamp->getCutoffGroupStamp(j);
116            nAtomsInGroups += cgStamp->getNMembers();
117          }
118  
# Line 128 | Line 125 | namespace oopse {
125          int nRigidBodiesInStamp = molStamp->getNRigidBodies();
126          
127          for (int j=0; j < nRigidBodiesInStamp; j++) {
128 <          rbStamp = molStamp->getRigidBody(j);
128 >          rbStamp = molStamp->getRigidBodyStamp(j);
129            nAtomsInRigidBodies += rbStamp->getNMembers();
130          }
131  
# Line 167 | Line 164 | namespace oopse {
164      }
165      molecules_.clear();
166        
170 –    delete stamps_;
167      delete sman_;
168      delete simParams_;
169      delete forceField_;
# Line 274 | Line 270 | namespace oopse {
270            }
271          }
272              
273 <      }//end for (integrableObject)
274 <    }// end for (mol)
273 >      }
274 >    }
275      
276      // n_constraints is local, so subtract them on each processor
277      ndf_local -= nConstraints_;
# Line 1091 | Line 1087 | namespace oopse {
1087      }
1088      
1089      // let's pass some summation method variables to fortran
1090 <    setElectrostaticSummationMethod( &esm );
1091 <    notifyFortranElectrostaticMethod( &esm );
1090 >    setElectrostaticSumMethod( &esm );
1091 >    setFortranElectrostaticMethod( &esm );
1092      setScreeningMethod( &sm );
1093      setDampingAlpha( &alphaVal );
1094      setReactionFieldDielectric( &dielectric );

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