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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 1269 by gezelter, Tue Jul 1 13:28:23 2008 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)
53 > #include "config.h"
54 > #include <string>
55 > #include <utility>
56 > #include <vector>
57  
7 – #include <utilities>
8 –
9 – #include "utils/Tuple.hpp"
10 – #include "types/ShapeAtomType.hpp"
58   #include "io/basic_ifstrstream.hpp"
59 + #include "io/ForceFieldOptions.hpp"
60 + #include "utils/TypeContainer.hpp"
61 + #include "utils/Tuple.hpp"
62 + #include "types/AtomType.hpp"
63 + #include "types/BondType.hpp"
64 + #include "types/BendType.hpp"
65 + #include "types/TorsionType.hpp"
66 + #include "types/NonBondedInteractionType.hpp"
67 + #include "UseTheForce/fForceOptions.h"
68 + namespace oopse {
69  
70 < using namespace std;
71 < using namespace oopse;
70 >  /**
71 >   * @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
72 >   * @brief
73 >   */
74 >  class ForceField{
75  
76 < class ForceField{
76 >  public:
77  
78 < public:
78 >    typedef TypeContainer<AtomType, 1> AtomTypeContainer;
79 >    typedef TypeContainer<BondType, 2> BondTypeContainer;
80 >    typedef TypeContainer<BendType, 3> BendTypeContainer;
81 >    typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
82 >                typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
83 >        
84 >    ForceField();
85  
86 <  ForceField(){
21 <    hasVariant=false;
22 <    ffPath = getenv("FORCE_PARAM_PATH");
23 <    if( ffPath.empty() ) {
24 <      STR_DEFINE(ffPath, FRC_PATH );
25 <    }  
26 <  }
86 >    virtual ~ForceField();
87  
88 <  virtual ~ForceFields(){}
88 >    std::string getForceFieldFileName() {
89 >      return forceFieldFileName_;
90 >    }
91  
92 <  void setVariant(const string &variant) { hasVariant = true; theVariant = variant; }
93 <  virtual void readParams( void ) = 0;  
94 <  
95 <  AtomType* getMatchingAtomType(const string &at);
96 <  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);
92 >    void setForceFieldFileName(const std::string& filename) {
93 >      forceFieldFileName_ = filename;
94 >    }
95 >        
96 >    virtual void parse(const std::string& filename) = 0;  
97  
98 <  double getRcutForAtomType(AtomType* at);
99 <  
100 < protected:
101 <  
102 <  string ffPath;
103 <  ifstrstream forceFile;
104 <  bool hasVariant;
105 <  string variant;
106 <  map<string, AtomType*> atomTypeMap;
107 <  map<pair<string,string>, BondType*> bondTypeMap;
108 <  map<tuple3<string,string,string>, BendType*> bendTypeMap;
109 <  map<tuple4<string,string,string,string>, TorsionType*> torsionTypeMap;
110 <  string wildCardAtomTypeName;
98 >    AtomType* getAtomType(const std::string &at);
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);
102 >    TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
103 >                                const std::string &at3, const std::string &at4);
104 >                NonBondedInteractionType* getNonBondedInteractionType(const std::string &at1, const std::string &at2);
105 >                                                                                                                        
106 >    BondType* getExactBondType(const std::string &at1, const std::string &at2);
107 >    BendType* getExactBendType(const std::string &at1, const std::string &at2,
108 >                               const std::string &at3);
109 >    TorsionType* getExactTorsionType(const std::string &at1,
110 >                                     const std::string &at2,
111 >                                     const std::string &at3,
112 >                                     const std::string &at4);
113 >                NonBondedInteractionType* getExactNonBondedInteractionType(const std::string &at1, const std::string &at2);
114  
54 – };
115  
116 +    //avoid make virtual function public
117 +    //Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
118 +    virtual RealType getRcutFromAtomType(AtomType* at);
119  
120 +    std::string getWildCard() {
121 +      return wildCardAtomTypeName_;
122 +    }
123 +
124 +    void setWildCard(const std::string& wildCard) {
125 +      wildCardAtomTypeName_ = wildCard;
126 +    }
127 +
128 +
129 +    unsigned int getNAtomType() {
130 +      return atomTypeCont_.size();
131 +    }
132 +        
133 +    bool addAtomType(const std::string &at, AtomType* atomType);
134 +
135 +    bool addBondType(const std::string &at1, const std::string &at2,
136 +                     BondType* bondType);
137 +
138 +    bool addBendType(const std::string &at1, const std::string &at2,
139 +                     const std::string &at3, BendType* bendType);
140 +
141 +    bool addTorsionType(const std::string &at1, const std::string &at2,
142 +                        const std::string &at3, const std::string &at4, TorsionType* torsionType);
143 +
144 +    bool addNonBondedInteractionType(const std::string &at1, const std::string &at2,
145 +                        NonBondedInteractionType* nbiType);
146 +
147 +    ifstrstream* openForceFieldFile(const std::string& filename);
148 +
149 +    ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
150 +
151 +    void setFortranForceOptions(void);
152 +
153 +
154 +  protected:
155 +
156 +    AtomTypeContainer atomTypeCont_;    
157 +    BondTypeContainer bondTypeCont_;
158 +    BendTypeContainer bendTypeCont_;
159 +    TorsionTypeContainer torsionTypeCont_;
160 +    NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
161 +    ForceFieldOptions forceFieldOptions_;
162 +    
163 +  private:  
164 +    std::string ffPath_;
165 +
166 +    std::string wildCardAtomTypeName_;
167 +
168 +    std::string forceFieldFileName_;
169 +
170 +
171 +  };
172 + }//end namespace oopse
173   #endif
174  

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