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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 1275 by cli2, Fri Jul 4 20:54:29 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/BaseAtomTypesSectionParser.hpp"
51   #include "io/AtomTypesSectionParser.hpp"
52 + #include "io/BaseAtomTypesSectionParser.hpp"
53   #include "io/LennardJonesAtomTypesSectionParser.hpp"
54   #include "io/ChargeAtomTypesSectionParser.hpp"
55   #include "io/MultipoleAtomTypesSectionParser.hpp"
56   #include "io/StickyAtomTypesSectionParser.hpp"
57 + #include "io/StickyPowerAtomTypesSectionParser.hpp"
58 + #include "io/GayBerneAtomTypesSectionParser.hpp"
59   #include "io/BondTypesSectionParser.hpp"
60   #include "io/BendTypesSectionParser.hpp"
61   #include "io/TorsionTypesSectionParser.hpp"
62 + #include "io/OptionSectionParser.hpp"
63   #include "UseTheForce/ForceFieldCreator.hpp"
64  
65   namespace oopse {
66      
67 < DUFF::DUFF(){
67 >  DUFF::DUFF(){
68  
69      //set default force field filename
70      setForceFieldFileName("DUFF2.frc");
71  
72 <    //the order of adding section parsers are important
73 <    //DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
74 <    //These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
75 <    //AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
76 <    //of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the
77 <    //"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
78 <    //important. AtomTypesSectionParser should be added before other atom type section parsers.
79 <    //Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser.
80 <    //The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
81 <    //not important.
82 <    spMan_.push_back(new DirectionalAtomTypesSectionParser());
72 >    //The order of adding section parsers is important.
73 >    //OptionSectionParser must come first to set options for other parsers
74 >    //DirectionalAtomTypesSectionParser should be added before
75 >    //AtomTypesSectionParser, and these two section parsers will actually
76 >    //create "real" AtomTypes (AtomTypesSectionParser will create AtomType and
77 >    //DirectionalAtomTypesSectionParser will create DirectionalAtomType, which
78 >    //is a subclass of AtomType and should come first). Other AtomTypes Section
79 >    //Parser will not create the "real" AtomType, they only add and set some
80 >    //attribute of the AtomType. Thus their order are not important.
81 >    //AtomTypesSectionParser should be added before other atom type section
82 >    //parsers. Make sure they are added after DirectionalAtomTypesSectionParser
83 >    //and AtomTypesSectionParser. The order of BondTypesSectionParser,
84 >    //BendTypesSectionParser and TorsionTypesSectionParser are not important.
85 >    spMan_.push_back(new OptionSectionParser(forceFieldOptions_));    
86 >    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
87 >    spMan_.push_back(new BaseAtomTypesSectionParser());
88      spMan_.push_back(new AtomTypesSectionParser());
89 <    spMan_.push_back(new LennardJonesAtomTypesSectionParser());
90 <    spMan_.push_back(new ChargeAtomTypesSectionParser());
91 <    spMan_.push_back(new MultipoleAtomTypesSectionParser());
92 <    spMan_.push_back(new StickyAtomTypesSectionParser());
93 <    spMan_.push_back(new BondTypesSectionParser());
94 <    spMan_.push_back(new BendTypesSectionParser());
95 <    spMan_.push_back(new TorsionTypesSectionParser());
89 >    spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
90 >    spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
91 >    spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
92 >    spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
93 >    spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
94 >    spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
95 >    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
96 >    spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
97 >    spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
98      
99 < }
99 >  }
100  
101 < void DUFF::parse(const std::string& filename) {
101 >  void DUFF::parse(const std::string& filename) {
102      ifstrstream* ffStream;
103 +    bool hasGBtypes;
104 +
105      ffStream = openForceFieldFile(filename);
106  
107      spMan_.parse(*ffStream, *this);
# Line 93 | Line 109 | void DUFF::parse(const std::string& filename) {
109      ForceField::AtomTypeContainer::MapTypeIterator i;
110      AtomType* at;
111  
112 <    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
113 <        at->makeFortranAtomType();
112 >    for (at = atomTypeCont_.beginType(i); at != NULL;
113 >         at = atomTypeCont_.nextType(i)) {
114 >      at->makeFortranAtomType();
115      }
116  
117 <    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
118 <        at->complete();
117 >    for (at = atomTypeCont_.beginType(i); at != NULL;
118 >         at = atomTypeCont_.nextType(i)) {
119 >      at->complete();
120      }
121 +
122 +    hasGBtypes = false;
123 +    for (at = atomTypeCont_.beginType(i); at != NULL;
124 +         at = atomTypeCont_.nextType(i)) {
125 +      if (at->isGayBerne())
126 +        hasGBtypes = true;
127 +    }
128      
129 < }
129 >    int isError = 0;
130  
131 +    if (hasGBtypes) {
132 +      completeGBFF(&isError);
133 +    }
134 +
135 +    delete ffStream;
136 +    
137 +  }
138 +
139 +  DUFF::~DUFF(){
140 +    destroyLJTypes();
141 +    destroyStickyTypes();
142 +    destroyGayBerneTypes();
143 +  }
144   } //end namespace oopse

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