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root/OpenMD/trunk/src/UseTheForce/DUFF.cpp
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Comparing trunk/src/UseTheForce/DUFF.cpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1269 by gezelter, Tue Jul 1 13:28:23 2008 UTC

# Line 43 | Line 43
43   #include "UseTheForce/DUFF.hpp"
44   #include "UseTheForce/DarkSide/lj_interface.h"
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/LennardJonesAtomTypesSectionParser.hpp"
52   #include "io/ChargeAtomTypesSectionParser.hpp"
53   #include "io/MultipoleAtomTypesSectionParser.hpp"
54   #include "io/StickyAtomTypesSectionParser.hpp"
55 + #include "io/StickyPowerAtomTypesSectionParser.hpp"
56 + #include "io/GayBerneAtomTypesSectionParser.hpp"
57   #include "io/BondTypesSectionParser.hpp"
58   #include "io/BendTypesSectionParser.hpp"
59   #include "io/TorsionTypesSectionParser.hpp"
60 + #include "io/OptionSectionParser.hpp"
61   #include "UseTheForce/ForceFieldCreator.hpp"
62  
63   namespace oopse {
64      
65 < DUFF::DUFF(){
65 >  DUFF::DUFF(){
66  
67      //set default force field filename
68      setForceFieldFileName("DUFF2.frc");
69  
70 <    //the order of adding section parsers are important
71 <    //DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
72 <    //These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
73 <    //AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
74 <    //of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the
75 <    //"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
76 <    //important. AtomTypesSectionParser should be added before other atom type section parsers.
77 <    //Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser.
78 <    //The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
79 <    //not important.
80 <    spMan_.push_back(new DirectionalAtomTypesSectionParser());
70 >    //The order of adding section parsers is important.
71 >    //OptionSectionParser must come first to set options for other parsers
72 >    //DirectionalAtomTypesSectionParser should be added before
73 >    //AtomTypesSectionParser, and these two section parsers will actually
74 >    //create "real" AtomTypes (AtomTypesSectionParser will create AtomType and
75 >    //DirectionalAtomTypesSectionParser will create DirectionalAtomType, which
76 >    //is a subclass of AtomType and should come first). Other AtomTypes Section
77 >    //Parser will not create the "real" AtomType, they only add and set some
78 >    //attribute of the AtomType. Thus their order are not important.
79 >    //AtomTypesSectionParser should be added before other atom type section
80 >    //parsers. Make sure they are added after DirectionalAtomTypesSectionParser
81 >    //and AtomTypesSectionParser. The order of BondTypesSectionParser,
82 >    //BendTypesSectionParser and TorsionTypesSectionParser are not important.
83 >    spMan_.push_back(new OptionSectionParser(forceFieldOptions_));    
84 >    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
85 >    spMan_.push_back(new BaseAtomTypesSectionParser());
86      spMan_.push_back(new AtomTypesSectionParser());
87 <    spMan_.push_back(new LennardJonesAtomTypesSectionParser());
88 <    spMan_.push_back(new ChargeAtomTypesSectionParser());
89 <    spMan_.push_back(new MultipoleAtomTypesSectionParser());
90 <    spMan_.push_back(new StickyAtomTypesSectionParser());
91 <    spMan_.push_back(new BondTypesSectionParser());
92 <    spMan_.push_back(new BendTypesSectionParser());
93 <    spMan_.push_back(new TorsionTypesSectionParser());
87 >    spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
88 >    spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
89 >    spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
90 >    spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
91 >    spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
92 >    spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
93 >    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
94 >    spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
95 >    spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
96      
97 < }
97 >  }
98  
99 < void DUFF::parse(const std::string& filename) {
99 >  void DUFF::parse(const std::string& filename) {
100      ifstrstream* ffStream;
101 +    bool hasGBtypes;
102 +
103      ffStream = openForceFieldFile(filename);
104  
105      spMan_.parse(*ffStream, *this);
# Line 93 | Line 107 | void DUFF::parse(const std::string& filename) {
107      ForceField::AtomTypeContainer::MapTypeIterator i;
108      AtomType* at;
109  
110 <    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
111 <        at->makeFortranAtomType();
110 >    for (at = atomTypeCont_.beginType(i); at != NULL;
111 >         at = atomTypeCont_.nextType(i)) {
112 >      at->makeFortranAtomType();
113      }
114  
115 <    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
116 <        at->complete();
115 >    for (at = atomTypeCont_.beginType(i); at != NULL;
116 >         at = atomTypeCont_.nextType(i)) {
117 >      at->complete();
118      }
119 +
120 +    hasGBtypes = false;
121 +    for (at = atomTypeCont_.beginType(i); at != NULL;
122 +         at = atomTypeCont_.nextType(i)) {
123 +      if (at->isGayBerne())
124 +        hasGBtypes = true;
125 +    }
126      
127 < }
127 >    int isError = 0;
128  
129 +    if (hasGBtypes) {
130 +      completeGBFF(&isError);
131 +    }
132 +
133 +    delete ffStream;
134 +    
135 +  }
136 +
137 +  DUFF::~DUFF(){
138 +    destroyLJTypes();
139 +    destroyStickyTypes();
140 +    destroyGayBerneTypes();
141 +  }
142   } //end namespace oopse

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