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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 1280 by gezelter, Wed Jul 16 02:07:09 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/BaseAtomTypesSectionParser.hpp"
52   #include "io/LennardJonesAtomTypesSectionParser.hpp"
53   #include "io/ChargeAtomTypesSectionParser.hpp"
54   #include "io/MultipoleAtomTypesSectionParser.hpp"
55   #include "io/StickyAtomTypesSectionParser.hpp"
56 + #include "io/StickyPowerAtomTypesSectionParser.hpp"
57 + #include "io/GayBerneAtomTypesSectionParser.hpp"
58   #include "io/BondTypesSectionParser.hpp"
59   #include "io/BendTypesSectionParser.hpp"
60   #include "io/TorsionTypesSectionParser.hpp"
61 + #include "io/OptionSectionParser.hpp"
62   #include "UseTheForce/ForceFieldCreator.hpp"
63  
64   namespace oopse {
65      
66 < DUFF::DUFF(){
66 >  DUFF::DUFF(){
67  
68      //set default force field filename
69      setForceFieldFileName("DUFF2.frc");
70  
71 <    //the order of adding section parsers are important
72 <    //DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
73 <    //These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
74 <    //AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
75 <    //of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the
76 <    //"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
77 <    //important. AtomTypesSectionParser should be added before other atom type section parsers.
78 <    //Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser.
79 <    //The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
80 <    //not important.
81 <    spMan_.push_back(new DirectionalAtomTypesSectionParser());
71 >    //The order of adding section parsers is important.
72 >    //OptionSectionParser must come first to set options for other parsers
73 >    //DirectionalAtomTypesSectionParser should be added before
74 >    //AtomTypesSectionParser, and these two section parsers will actually
75 >    //create "real" AtomTypes (AtomTypesSectionParser will create AtomType and
76 >    //DirectionalAtomTypesSectionParser will create DirectionalAtomType, which
77 >    //is a subclass of AtomType and should come first). Other AtomTypes Section
78 >    //Parser will not create the "real" AtomType, they only add and set some
79 >    //attribute of the AtomType. Thus their order are not important.
80 >    //AtomTypesSectionParser should be added before other atom type section
81 >    //parsers. Make sure they are added after DirectionalAtomTypesSectionParser
82 >    //and AtomTypesSectionParser. The order of BondTypesSectionParser,
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());
89 <    spMan_.push_back(new ChargeAtomTypesSectionParser());
90 <    spMan_.push_back(new MultipoleAtomTypesSectionParser());
91 <    spMan_.push_back(new StickyAtomTypesSectionParser());
92 <    spMan_.push_back(new BondTypesSectionParser());
93 <    spMan_.push_back(new BendTypesSectionParser());
94 <    spMan_.push_back(new TorsionTypesSectionParser());
88 >    spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
89 >    spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
90 >    spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
91 >    spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
92 >    spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
93 >    spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
94 >    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
95 >    spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
96 >    spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
97      
98 < }
98 >  }
99  
100 < void DUFF::parse(const std::string& filename) {
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 93 | Line 108 | void DUFF::parse(const std::string& filename) {
108      ForceField::AtomTypeContainer::MapTypeIterator i;
109      AtomType* at;
110  
111 <    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
112 <        at->makeFortranAtomType();
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  
127 <    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
128 <        at->complete();
127 >    for (at = atomTypeCont_.beginType(i); at != NULL;
128 >         at = atomTypeCont_.nextType(i)) {
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 < }
139 >    int isError = 0;
140  
141 +    if (hasGBtypes) {
142 +      completeGBFF(&isError);
143 +    }
144 +
145 +    delete ffStream;
146 +    
147 +  }
148 +
149 +  DUFF::~DUFF(){
150 +    destroyLJTypes();
151 +    destroyStickyTypes();
152 +    destroyGayBerneTypes();
153 +  }
154   } //end namespace oopse

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