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root/OpenMD/trunk/src/brains/ForceField.hpp
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Comparing:
branches/development/src/UseTheForce/ForceField.hpp (file contents), Revision 1467 by gezelter, Sat Jul 17 15:33:03 2010 UTC vs.
branches/development/src/brains/ForceField.hpp (file contents), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 55 | Line 56
56   #include <utility>
57   #include <vector>
58  
59 < #include "io/basic_ifstrstream.hpp"
59 > #include "io/ifstrstream.hpp"
60   #include "io/ForceFieldOptions.hpp"
61 + #include "io/SectionParserManager.hpp"
62   #include "utils/TypeContainer.hpp"
63   #include "utils/Tuple.hpp"
64   #include "types/AtomType.hpp"
# Line 65 | Line 67
67   #include "types/TorsionType.hpp"
68   #include "types/InversionType.hpp"
69   #include "types/NonBondedInteractionType.hpp"
70 < #include "UseTheForce/fForceOptions.h"
70 >
71   namespace OpenMD {
72  
71 –  /**
72 –   * @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
73 –   * @brief
74 –   */
73    class ForceField{
74  
75    public:
78 –
76      typedef TypeContainer<AtomType, 1> AtomTypeContainer;
77      typedef TypeContainer<BondType, 2> BondTypeContainer;
78      typedef TypeContainer<BendType, 3> BendTypeContainer;
# Line 83 | Line 80 | namespace OpenMD {
80      typedef TypeContainer<InversionType, 4> InversionTypeContainer;
81      typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
82      
83 <    ForceField();
83 >    ForceField(std::string ffName);
84      
85 <    virtual ~ForceField();
85 >    virtual ~ForceField() {};
86  
87      std::string getForceFieldFileName() {
88        return forceFieldFileName_;
# Line 95 | Line 92 | namespace OpenMD {
92        forceFieldFileName_ = filename;
93      }
94          
95 <    virtual void parse(const std::string& filename) = 0;  
95 >    virtual void parse(const std::string& filename);  
96  
97      AtomType* getAtomType(const std::string &at);
98 +    AtomType* getAtomType(int ident);
99      BondType* getBondType(const std::string &at1, const std::string &at2);
100      BendType* getBendType(const std::string &at1, const std::string &at2,
101                            const std::string &at3);
# Line 139 | Line 137 | namespace OpenMD {
137        return atomTypeCont_.size();
138      }
139  
140 <    AtomTypeContainer getAtomTypes() {
141 <      return atomTypeCont_;
140 >    AtomTypeContainer* getAtomTypes() {
141 >      return &atomTypeCont_;
142      }
143      
144 <    NonBondedInteractionTypeContainer getNonBondedInteractionTypes() {
145 <      return nonBondedInteractionTypeCont_;
144 >    NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
145 >      return &nonBondedInteractionTypeCont_;
146      }
147          
148      bool addAtomType(const std::string &at, AtomType* atomType);
# Line 173 | Line 171 | namespace OpenMD {
171      
172      ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
173  
176 –    void setFortranForceOptions(void);
177 –
178 –
174    protected:
175  
176      AtomTypeContainer atomTypeCont_;    
# Line 185 | Line 180 | namespace OpenMD {
180      InversionTypeContainer inversionTypeCont_;
181      NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
182      ForceFieldOptions forceFieldOptions_;
183 +    std::map<int, std::string> atypeIdentToName;
184 +    SectionParserManager spMan_;
185 +
186      
187    private:  
188 <    std::string ffPath_;
189 <    
192 <    std::string wildCardAtomTypeName_;
193 <    
188 >    std::string ffPath_;    
189 >    std::string wildCardAtomTypeName_;    
190      std::string forceFieldFileName_;    
191      
192    };

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