ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/UseTheForce/DUFF.cpp
(Generate patch)

Comparing trunk/src/UseTheForce/DUFF.cpp (file contents):
Revision 532 by chrisfen, Tue May 17 22:35:01 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"
# Line 55 | Line 58
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 {
# Line 65 | Line 69 | namespace oopse {
69      setForceFieldFileName("DUFF2.frc");
70  
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
# Line 76 | Line 81 | namespace oopse {
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 DirectionalAtomTypesSectionParser());
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 StickyPowerAtomTypesSectionParser());
93 <    spMan_.push_back(new GayBerneAtomTypesSectionParser());
94 <    spMan_.push_back(new BondTypesSectionParser());
95 <    spMan_.push_back(new BendTypesSectionParser());
96 <    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    }
99  
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 101 | Line 110 | namespace oopse {
110  
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  
# Line 109 | Line 129 | namespace oopse {
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 +    int isError = 0;
140 +
141 +    if (hasGBtypes) {
142 +      completeGBFF(&isError);
143 +    }
144 +
145      delete ffStream;
146      
147    }
# Line 116 | Line 149 | namespace oopse {
149    DUFF::~DUFF(){
150      destroyLJTypes();
151      destroyStickyTypes();
152 +    destroyGayBerneTypes();
153    }
154   } //end namespace oopse

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines