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Comparing:
trunk/src/UseTheForce/ForceField.hpp (file contents), Revision 1282 by gezelter, Wed Jul 30 18:11:19 2008 UTC vs.
branches/development/src/UseTheForce/ForceField.hpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 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]  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"
69 < #include "UseTheForce/fForceOptions.h"
69 < namespace oopse {
69 > namespace OpenMD {
70  
71    /**
72     * @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
# Line 83 | Line 83 | namespace oopse {
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 oopse {
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 138 | Line 139 | namespace oopse {
139      unsigned int getNAtomType() {
140        return atomTypeCont_.size();
141      }
142 +
143 +    AtomTypeContainer* getAtomTypes() {
144 +      return &atomTypeCont_;
145 +    }
146 +    
147 +    NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
148 +      return &nonBondedInteractionTypeCont_;
149 +    }
150          
151      bool addAtomType(const std::string &at, AtomType* atomType);
152  
# Line 165 | Line 174 | namespace oopse {
174      
175      ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
176  
168 –    void setFortranForceOptions(void);
169 –
170 –
177    protected:
178  
179      AtomTypeContainer atomTypeCont_;    
# Line 177 | Line 183 | namespace oopse {
183      InversionTypeContainer inversionTypeCont_;
184      NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
185      ForceFieldOptions forceFieldOptions_;
186 +    std::map<int, std::string> atypeIdentToName;
187      
188    private:  
189 <    std::string ffPath_;
190 <    
184 <    std::string wildCardAtomTypeName_;
185 <    
189 >    std::string ffPath_;    
190 >    std::string wildCardAtomTypeName_;    
191      std::string forceFieldFileName_;    
192      
193    };
194 < }//end namespace oopse
194 > }//end namespace OpenMD
195   #endif
196  

Comparing:
trunk/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 1282 by gezelter, Wed Jul 30 18:11:19 2008 UTC vs.
branches/development/src/UseTheForce/ForceField.hpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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