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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.
Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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 "utils/TypeContainer.hpp"
62   #include "utils/Tuple.hpp"
# Line 65 | Line 66
66   #include "types/TorsionType.hpp"
67   #include "types/InversionType.hpp"
68   #include "types/NonBondedInteractionType.hpp"
68 – #include "UseTheForce/fForceOptions.h"
69   namespace OpenMD {
70  
71    /**
# Line 83 | Line 83 | namespace OpenMD {
83      typedef TypeContainer<InversionType, 4> InversionTypeContainer;
84      typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
85      
86 <    ForceField();
86 >    ForceField();
87      
88 <    virtual ~ForceField();
88 >    virtual ~ForceField() {};
89  
90      std::string getForceFieldFileName() {
91        return forceFieldFileName_;
# Line 98 | Line 98 | namespace OpenMD {
98      virtual void parse(const std::string& filename) = 0;  
99  
100      AtomType* getAtomType(const std::string &at);
101 +    AtomType* getAtomType(int ident);
102      BondType* getBondType(const std::string &at1, const std::string &at2);
103      BendType* getBendType(const std::string &at1, const std::string &at2,
104                            const std::string &at3);
# Line 139 | Line 140 | namespace OpenMD {
140        return atomTypeCont_.size();
141      }
142  
143 <    AtomTypeContainer getAtomTypes() {
144 <      return atomTypeCont_;
143 >    AtomTypeContainer* getAtomTypes() {
144 >      return &atomTypeCont_;
145      }
146      
147 <    NonBondedInteractionTypeContainer getNonBondedInteractionTypes() {
148 <      return nonBondedInteractionTypeCont_;
147 >    NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
148 >      return &nonBondedInteractionTypeCont_;
149      }
150          
151      bool addAtomType(const std::string &at, AtomType* atomType);
# Line 173 | Line 174 | namespace OpenMD {
174      
175      ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
176  
176 –    void setFortranForceOptions(void);
177 –
178 –
177    protected:
178  
179      AtomTypeContainer atomTypeCont_;    
# Line 185 | Line 183 | namespace OpenMD {
183      InversionTypeContainer inversionTypeCont_;
184      NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
185      ForceFieldOptions forceFieldOptions_;
186 +    std::map<int, std::string> atypeIdentToName;
187      
188    private:  
189 <    std::string ffPath_;
190 <    
192 <    std::string wildCardAtomTypeName_;
193 <    
189 >    std::string ffPath_;    
190 >    std::string wildCardAtomTypeName_;    
191      std::string forceFieldFileName_;    
192      
193    };

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