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Comparing:
trunk/src/UseTheForce/ForceField.hpp (file contents), Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
branches/development/src/UseTheForce/ForceField.hpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
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).                        
40   */
41  
42   /**
# Line 55 | Line 55
55   #include <utility>
56   #include <vector>
57  
58 < #include "io/basic_ifstrstream.hpp"
58 > #include "io/ifstrstream.hpp"
59   #include "io/ForceFieldOptions.hpp"
60   #include "utils/TypeContainer.hpp"
61   #include "utils/Tuple.hpp"
# Line 65 | Line 65
65   #include "types/TorsionType.hpp"
66   #include "types/InversionType.hpp"
67   #include "types/NonBondedInteractionType.hpp"
68 < #include "UseTheForce/fForceOptions.h"
69 < namespace oopse {
68 > namespace OpenMD {
69  
70    /**
71     * @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
# Line 83 | Line 82 | namespace oopse {
82      typedef TypeContainer<InversionType, 4> InversionTypeContainer;
83      typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
84      
85 <    ForceField();
85 >    ForceField();
86      
87 <    virtual ~ForceField();
87 >    virtual ~ForceField() {};
88  
89      std::string getForceFieldFileName() {
90        return forceFieldFileName_;
# Line 98 | Line 97 | namespace oopse {
97      virtual void parse(const std::string& filename) = 0;  
98  
99      AtomType* getAtomType(const std::string &at);
100 +    AtomType* getAtomType(int ident);
101      BondType* getBondType(const std::string &at1, const std::string &at2);
102      BendType* getBendType(const std::string &at1, const std::string &at2,
103                            const std::string &at3);
# Line 138 | Line 138 | namespace oopse {
138      unsigned int getNAtomType() {
139        return atomTypeCont_.size();
140      }
141 +
142 +    AtomTypeContainer* getAtomTypes() {
143 +      return &atomTypeCont_;
144 +    }
145 +    
146 +    NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
147 +      return &nonBondedInteractionTypeCont_;
148 +    }
149          
150      bool addAtomType(const std::string &at, AtomType* atomType);
151  
152 +    bool replaceAtomType(const std::string &at, AtomType* atomType);
153 +
154      bool addBondType(const std::string &at1, const std::string &at2,
155                       BondType* bondType);
156  
# Line 163 | Line 173 | namespace oopse {
173      
174      ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
175  
166 –    void setFortranForceOptions(void);
167 –
168 –
176    protected:
177  
178      AtomTypeContainer atomTypeCont_;    
# Line 175 | Line 182 | namespace oopse {
182      InversionTypeContainer inversionTypeCont_;
183      NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
184      ForceFieldOptions forceFieldOptions_;
185 +    std::map<int, std::string> atypeIdentToName;
186      
187    private:  
188 <    std::string ffPath_;
189 <    
182 <    std::string wildCardAtomTypeName_;
183 <    
188 >    std::string ffPath_;    
189 >    std::string wildCardAtomTypeName_;    
190      std::string forceFieldFileName_;    
191      
192    };
193 < }//end namespace oopse
193 > }//end namespace OpenMD
194   #endif
195  

Comparing:
trunk/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
branches/development/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

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