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Comparing trunk/src/UseTheForce/ForceField.hpp (file contents):
Revision 206 by gezelter, Thu Nov 4 20:51:23 2004 UTC vs.
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC

# Line 1 | Line 1
1 + /*
2 + * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 + *
4 + * The University of Notre Dame grants you ("Licensee") a
5 + * non-exclusive, royalty free, license to use, modify and
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
19 + *    notice, this list of conditions and the following disclaimer.
20 + *
21 + * 3. Redistributions in binary form must reproduce the above copyright
22 + *    notice, this list of conditions and the following disclaimer in the
23 + *    documentation and/or other materials provided with the
24 + *    distribution.
25 + *
26 + * This software is provided "AS IS," without a warranty of any
27 + * kind. All express or implied conditions, representations and
28 + * warranties, including any implied warranty of merchantability,
29 + * fitness for a particular purpose or non-infringement, are hereby
30 + * excluded.  The University of Notre Dame and its licensors shall not
31 + * be liable for any damages suffered by licensee as a result of
32 + * using, modifying or distributing the software or its
33 + * derivatives. In no event will the University of Notre Dame or its
34 + * licensors be liable for any lost revenue, profit or data, or for
35 + * direct, indirect, special, consequential, incidental or punitive
36 + * damages, however caused and regardless of the theory of liability,
37 + * arising out of the use of or inability to use software, even if the
38 + * University of Notre Dame has been advised of the possibility of
39 + * such damages.
40 + */
41 +
42 + /**
43 +  * @file ForceField.hpp
44 +  * @author tlin
45 +  * @date 11/04/2004
46 +  * @time 22:51am
47 +  * @version 1.0
48 +  */
49 +  
50   #ifndef USETHEFORCE_FORCEFIELD_HPP
51   #define USETHEFORCE_FORCEFIELD_HPP
52  
53   #define MK_STR(s) # s
54   #define STR_DEFINE(t, s) t = MK_STR(s)
55  
56 < #include <utilities>
56 > #include <string>
57 > #include <utility>
58  
9 – #include "utils/Tuple.hpp"
10 – #include "types/ShapeAtomType.hpp"
59   #include "io/basic_ifstrstream.hpp"
60 + #include "utils/TypeContainer.hpp"
61 + #include "types/AtomType.hpp"
62 + #include "types/BondType.hpp"
63 + #include "types/BendType.hpp"
64 + #include "types/TorsionType.hpp"
65  
66 < using namespace std;
14 < using namespace oopse;
66 > namespace oopse {
67  
68 + /**
69 + * @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
70 + * @brief
71 + */
72   class ForceField{
73  
74 < public:
74 >    public:
75  
76 <  ForceField(){
77 <    hasVariant=false;
78 <    ffPath = getenv("FORCE_PARAM_PATH");
79 <    if( ffPath.empty() ) {
80 <      STR_DEFINE(ffPath, FRC_PATH );
81 <    }  
26 <  }
76 >        typedef TypeContainer<AtomType, 1> AtomTypeContainer;
77 >        typedef TypeContainer<BondType, 2> BondTypeContainer;
78 >        typedef TypeContainer<BendType, 3> BendTypeContainer;
79 >        typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
80 >        
81 >        ForceField();
82  
83 <  virtual ~ForceFields(){}
83 >        virtual ~ForceField(){}
84  
85 <  void setVariant(const string &variant) { hasVariant = true; theVariant = variant; }
86 <  virtual void readParams( void ) = 0;  
87 <  
33 <  AtomType* getMatchingAtomType(const string &at);
34 <  BondType* getMatchingBondType(const string &at1, const string &at2);
35 <  BendType* getMatchingBendType(const string &at1, const string &at2,
36 <                                const string &at3);
37 <  TorsionType* getMatchingTorsionType(const string &at1, const string &at2,
38 <                                      const string &at3, const string &at4);
85 >        std::string getForceFieldFileName() {
86 >            return forceFieldFileName_;
87 >        }
88  
89 <  double getRcutForAtomType(AtomType* at);
90 <  
91 < protected:
92 <  
93 <  string ffPath;
45 <  ifstrstream forceFile;
46 <  bool hasVariant;
47 <  string variant;
48 <  map<string, AtomType*> atomTypeMap;
49 <  map<pair<string,string>, BondType*> bondTypeMap;
50 <  map<tuple3<string,string,string>, BendType*> bendTypeMap;
51 <  map<tuple4<string,string,string,string>, TorsionType*> torsionTypeMap;
52 <  string wildCardAtomTypeName;
89 >        void setForceFieldFileName(const std::string& filename) {
90 >            forceFieldFileName_ = filename;
91 >        }
92 >        
93 >        virtual void parse(const std::string& filename) = 0;  
94  
95 < };
95 >        AtomType* getAtomType(const std::string &at);
96 >        BondType* getBondType(const std::string &at1, const std::string &at2);
97 >        BendType* getBendType(const std::string &at1, const std::string &at2,
98 >                                    const std::string &at3);
99 >        TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
100 >                                          const std::string &at3, const std::string &at4);
101  
102 +        BondType* getExactBondType(const std::string &at1, const std::string &at2);
103 +        BendType* getExactBendType(const std::string &at1, const std::string &at2,
104 +                                    const std::string &at3);
105 +        TorsionType* getExactTorsionType(const std::string &at1, const std::string &at2,
106 +                                          const std::string &at3, const std::string &at4);
107  
108 +
109 +        //avoid make virtual function public
110 +        //Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
111 +        virtual double getRcutFromAtomType(AtomType* at);
112 +
113 +        std::string getWildCard() {
114 +            return wildCardAtomTypeName_;
115 +        }
116 +
117 +        void setWildCard(const std::string& wildCard) {
118 +            wildCardAtomTypeName_ = wildCard;
119 +        }
120 +
121 +
122 +        unsigned int getNAtomType() {
123 +            return atomTypeCont_.size();
124 +        }
125 +        
126 +        bool addAtomType(const std::string &at, AtomType* atomType);
127 +
128 +        bool addBondType(const std::string &at1, const std::string &at2, BondType* bondType);
129 +
130 +        bool addBendType(const std::string &at1, const std::string &at2,
131 +                                    const std::string &at3, BendType* bendType);
132 +
133 +        bool addTorsionType(const std::string &at1, const std::string &at2,
134 +                                          const std::string &at3, const std::string &at4, TorsionType* torsionType);
135 +
136 +        ifstrstream* openForceFieldFile(const std::string& filename);
137 +
138 +    protected:
139 +
140 +        AtomTypeContainer atomTypeCont_;    
141 +        BondTypeContainer bondTypeCont_;
142 +        BendTypeContainer bendTypeCont_;
143 +        TorsionTypeContainer torsionTypeCont_;
144 +        
145 +    private:  
146 +        std::string ffPath_;
147 +
148 +        std::string wildCardAtomTypeName_;
149 +
150 +        std::string forceFieldFileName_;
151 + };
152 +
153 +
154 + }//end namespace oopse
155   #endif
156  

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