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root/group/trunk/OOPSE-4/src/UseTheForce/DUFF.cpp
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Comparing trunk/OOPSE-4/src/UseTheForce/DUFF.cpp (file contents):
Revision 1930 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 2787 by gezelter, Mon Jun 5 18:24:45 2006 UTC

# Line 42 | Line 42
42  
43   #include "UseTheForce/DUFF.hpp"
44   #include "UseTheForce/DarkSide/lj_interface.h"
45 – #include "UseTheForce/DarkSide/charge_interface.h"
46 – #include "UseTheForce/DarkSide/dipole_interface.h"
45   #include "UseTheForce/DarkSide/sticky_interface.h"
46 + #include "UseTheForce/DarkSide/gb_interface.h"
47   #include "UseTheForce/ForceFieldFactory.hpp"
48   #include "io/DirectionalAtomTypesSectionParser.hpp"
49   #include "io/AtomTypesSectionParser.hpp"
50   #include "io/LennardJonesAtomTypesSectionParser.hpp"
51 < #include "io/ElectrostaticAtomTypesSectionParser.hpp"
51 > #include "io/ChargeAtomTypesSectionParser.hpp"
52 > #include "io/MultipoleAtomTypesSectionParser.hpp"
53   #include "io/StickyAtomTypesSectionParser.hpp"
54 + #include "io/StickyPowerAtomTypesSectionParser.hpp"
55 + #include "io/GayBerneAtomTypesSectionParser.hpp"
56   #include "io/BondTypesSectionParser.hpp"
57   #include "io/BendTypesSectionParser.hpp"
58   #include "io/TorsionTypesSectionParser.hpp"
59 + #include "io/OptionSectionParser.hpp"
60   #include "UseTheForce/ForceFieldCreator.hpp"
61  
62   namespace oopse {
63      
64 < DUFF::DUFF(){
64 >  DUFF::DUFF(){
65  
66      //set default force field filename
67      setForceFieldFileName("DUFF2.frc");
68  
69 <    //the order of adding section parsers are important
70 <    //DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
71 <    //These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
72 <    //AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
73 <    //of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the
74 <    //"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
75 <    //important. AtomTypesSectionParser should be added before other atom type section parsers.
76 <    //Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser.
77 <    //The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
78 <    //not important.
79 <    spMan_.push_back(new DirectionalAtomTypesSectionParser());
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.
82 >    spMan_.push_back(new OptionSectionParser(forceFieldOptions_));    
83 >    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
84      spMan_.push_back(new AtomTypesSectionParser());
85 <    spMan_.push_back(new LennardJonesAtomTypesSectionParser());
86 <    spMan_.push_back(new ElectrostaticAtomTypesSectionParser());
87 <    spMan_.push_back(new StickyAtomTypesSectionParser());
88 <    spMan_.push_back(new BondTypesSectionParser());
89 <    spMan_.push_back(new BendTypesSectionParser());
90 <    spMan_.push_back(new TorsionTypesSectionParser());
85 >    spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
86 >    spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
87 >    spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
88 >    spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
89 >    spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
90 >    spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
91 >    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
92 >    spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
93 >    spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
94      
95 < }
95 >  }
96  
97 < void DUFF::parse(const std::string& filename) {
97 >  void DUFF::parse(const std::string& filename) {
98      ifstrstream* ffStream;
99 +    bool hasGBtypes;
100 +
101      ffStream = openForceFieldFile(filename);
102  
103      spMan_.parse(*ffStream, *this);
# Line 93 | Line 105 | void DUFF::parse(const std::string& filename) {
105      ForceField::AtomTypeContainer::MapTypeIterator i;
106      AtomType* at;
107  
108 <    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
109 <        at->makeFortranAtomType();
108 >    for (at = atomTypeCont_.beginType(i); at != NULL;
109 >         at = atomTypeCont_.nextType(i)) {
110 >      at->makeFortranAtomType();
111      }
112  
113 <    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
114 <        at->complete();
113 >    for (at = atomTypeCont_.beginType(i); at != NULL;
114 >         at = atomTypeCont_.nextType(i)) {
115 >      at->complete();
116      }
117 +
118 +    hasGBtypes = false;
119 +    for (at = atomTypeCont_.beginType(i); at != NULL;
120 +         at = atomTypeCont_.nextType(i)) {
121 +      if (at->isGayBerne())
122 +        hasGBtypes = true;
123 +    }
124      
125 < }
125 >    int isError = 0;
126  
127 +    if (hasGBtypes) {
128 +      completeGBFF(&isError);
129 +    }
130 +
131 +    delete ffStream;
132 +    
133 +  }
134 +
135 +  DUFF::~DUFF(){
136 +    destroyLJTypes();
137 +    destroyStickyTypes();
138 +    destroyGayBerneTypes();
139 +  }
140   } //end namespace oopse

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