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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1798 by gezelter, Thu Sep 13 14:10:11 2012 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 781 | Line 781 | namespace OpenMD {
781  
782      return atomTypes;        
783    }
784 +
785 +
786 +  int getGlobalCountOfType(AtomType* atype) {
787 +    /*
788 +    set<AtomType*> atypes = getSimulatedAtomTypes();
789 +    map<AtomType*, int> counts_;
790  
791 +    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
792 +      for(atom = mol->beginAtom(ai); atom != NULL;
793 +          atom = mol->nextAtom(ai)) {
794 +        atom->getAtomType();
795 +      }      
796 +    }    
797 +    */
798 +    return 0;
799 +  }
800 +
801    void SimInfo::setupSimVariables() {
802      useAtomicVirial_ = simParams_->getUseAtomicVirial();
803      // we only call setAccumulateBoxDipole if the accumulateBoxDipole
# Line 879 | Line 895 | namespace OpenMD {
895  
896  
897    void SimInfo::prepareTopology() {
882 –    int nExclude, nOneTwo, nOneThree, nOneFour;
898  
899      //calculate mass ratio of cutoff group
900      SimInfo::MoleculeIterator mi;
# Line 926 | Line 941 | namespace OpenMD {
941        }
942      }    
943      
929 –    //scan topology
930 –
931 –    nExclude = excludedInteractions_.getSize();
932 –    nOneTwo = oneTwoInteractions_.getSize();
933 –    nOneThree = oneThreeInteractions_.getSize();
934 –    nOneFour = oneFourInteractions_.getSize();
935 –
936 –    int* excludeList = excludedInteractions_.getPairList();
937 –    int* oneTwoList = oneTwoInteractions_.getPairList();
938 –    int* oneThreeList = oneThreeInteractions_.getPairList();
939 –    int* oneFourList = oneFourInteractions_.getPairList();
940 –
944      topologyDone_ = true;
945    }
946  
# Line 1009 | Line 1012 | namespace OpenMD {
1012    
1013    
1014    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1015 <    if (index >= IOIndexToIntegrableObject.size()) {
1015 >    if (index >= int(IOIndexToIntegrableObject.size())) {
1016        sprintf(painCave.errMsg,
1017                "SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1018                "\tindex exceeds number of known objects!\n");

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