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root/OpenMD/trunk/src/UseTheForce/DUFF.cpp
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Comparing trunk/src/UseTheForce/DUFF.cpp (file contents):
Revision 802 by chuckv, Thu Dec 8 15:38:49 2005 UTC vs.
Revision 1280 by gezelter, Wed Jul 16 02:07:09 2008 UTC

# Line 45 | Line 45
45   #include "UseTheForce/DarkSide/sticky_interface.h"
46   #include "UseTheForce/DarkSide/gb_interface.h"
47   #include "UseTheForce/ForceFieldFactory.hpp"
48 + #include "io/BaseAtomTypesSectionParser.hpp"
49   #include "io/DirectionalAtomTypesSectionParser.hpp"
50   #include "io/AtomTypesSectionParser.hpp"
51 + #include "io/BaseAtomTypesSectionParser.hpp"
52   #include "io/LennardJonesAtomTypesSectionParser.hpp"
53   #include "io/ChargeAtomTypesSectionParser.hpp"
54   #include "io/MultipoleAtomTypesSectionParser.hpp"
# Line 81 | Line 83 | namespace oopse {
83      //BendTypesSectionParser and TorsionTypesSectionParser are not important.
84      spMan_.push_back(new OptionSectionParser(forceFieldOptions_));    
85      spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
86 +    spMan_.push_back(new BaseAtomTypesSectionParser());
87      spMan_.push_back(new AtomTypesSectionParser());
88      spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
89      spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
# Line 96 | Line 99 | namespace oopse {
99  
100    void DUFF::parse(const std::string& filename) {
101      ifstrstream* ffStream;
102 +    bool hasGBtypes;
103 +
104      ffStream = openForceFieldFile(filename);
105  
106      spMan_.parse(*ffStream, *this);
# Line 105 | Line 110 | namespace oopse {
110  
111      for (at = atomTypeCont_.beginType(i); at != NULL;
112           at = atomTypeCont_.nextType(i)) {
113 +      // useBase sets the responsibilities, and these have to be done
114 +      // after the atomTypes and Base types have all been scanned:
115 +
116 +      std::vector<AtomType*> ayb = at->allYourBase();      
117 +      if (ayb.size() > 1) {
118 +        for (int j = ayb.size()-1; j > 0; j--) {
119 +          
120 +          ayb[j-1]->useBase(ayb[j]);
121 +
122 +        }
123 +      }
124        at->makeFortranAtomType();
125      }
126  
# Line 113 | Line 129 | namespace oopse {
129        at->complete();
130      }
131  
132 +    hasGBtypes = false;
133 +    for (at = atomTypeCont_.beginType(i); at != NULL;
134 +         at = atomTypeCont_.nextType(i)) {
135 +      if (at->isGayBerne())
136 +        hasGBtypes = true;
137 +    }
138 +    
139      int isError = 0;
140  
141 +    if (hasGBtypes) {
142 +      completeGBFF(&isError);
143 +    }
144 +
145      delete ffStream;
146      
147    }

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