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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 1282 by gezelter, Wed Jul 30 18:11:19 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 66 | Line 68 | namespace oopse {
68      //set default force field filename
69      setForceFieldFileName("DUFF2.frc");
70  
69 –    //The order of adding section parsers is important.
70 –    //OptionSectionParser must come first to set options for other parsers
71 –    //DirectionalAtomTypesSectionParser should be added before
72 –    //AtomTypesSectionParser, and these two section parsers will actually
73 –    //create "real" AtomTypes (AtomTypesSectionParser will create AtomType and
74 –    //DirectionalAtomTypesSectionParser will create DirectionalAtomType, which
75 –    //is a subclass of AtomType and should come first). Other AtomTypes Section
76 –    //Parser will not create the "real" AtomType, they only add and set some
77 –    //attribute of the AtomType. Thus their order are not important.
78 –    //AtomTypesSectionParser should be added before other atom type section
79 –    //parsers. Make sure they are added after DirectionalAtomTypesSectionParser
80 –    //and AtomTypesSectionParser. The order of BondTypesSectionParser,
81 –    //BendTypesSectionParser and TorsionTypesSectionParser are not important.
71      spMan_.push_back(new OptionSectionParser(forceFieldOptions_));    
72 <    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
72 >    spMan_.push_back(new BaseAtomTypesSectionParser());
73      spMan_.push_back(new AtomTypesSectionParser());
74 +    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
75      spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
76      spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
77      spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
# Line 96 | Line 86 | namespace oopse {
86  
87    void DUFF::parse(const std::string& filename) {
88      ifstrstream* ffStream;
89 +    bool hasGBtypes;
90 +
91      ffStream = openForceFieldFile(filename);
92  
93      spMan_.parse(*ffStream, *this);
# Line 105 | Line 97 | namespace oopse {
97  
98      for (at = atomTypeCont_.beginType(i); at != NULL;
99           at = atomTypeCont_.nextType(i)) {
100 +      // useBase sets the responsibilities, and these have to be done
101 +      // after the atomTypes and Base types have all been scanned:
102 +
103 +      std::vector<AtomType*> ayb = at->allYourBase();      
104 +      if (ayb.size() > 1) {
105 +        for (int j = ayb.size()-1; j > 0; j--) {
106 +          
107 +          ayb[j-1]->useBase(ayb[j]);
108 +
109 +        }
110 +      }
111        at->makeFortranAtomType();
112      }
113  
# Line 113 | Line 116 | namespace oopse {
116        at->complete();
117      }
118  
119 +    hasGBtypes = false;
120 +    for (at = atomTypeCont_.beginType(i); at != NULL;
121 +         at = atomTypeCont_.nextType(i)) {
122 +      if (at->isGayBerne())
123 +        hasGBtypes = true;
124 +    }
125 +    
126      int isError = 0;
127  
128 +    if (hasGBtypes) {
129 +      completeGBFF(&isError);
130 +    }
131 +
132      delete ffStream;
133      
134    }

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