src/brains/ForceField.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @file ForceField.hpp
 * @author tlin
 * @date 11/04/2004
 * @time 22:51am
 * @version 1.0
 */
  
#ifndef USETHEFORCE_FORCEFIELD_HPP
#define USETHEFORCE_FORCEFIELD_HPP

#define MK_STR(s) # s
#define STR_DEFINE(t, s) t = MK_STR(s)

#include <string>
#include <utility>

#include "io/basic_ifstrstream.hpp"
#include "utils/TypeContainer.hpp"
#include "types/AtomType.hpp"
#include "types/BondType.hpp"
#include "types/BendType.hpp"
#include "types/TorsionType.hpp"

namespace oopse {

  /**
   * @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
   * @brief
   */
  class ForceField{

  public:

    typedef TypeContainer<AtomType, 1> AtomTypeContainer;
    typedef TypeContainer<BondType, 2> BondTypeContainer;
    typedef TypeContainer<BendType, 3> BendTypeContainer;
    typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
        
    ForceField(); 

    virtual ~ForceField();

    std::string getForceFieldFileName() {
      return forceFieldFileName_;
    }

    void setForceFieldFileName(const std::string& filename) {
      forceFieldFileName_ = filename;
    }
        
    virtual void parse(const std::string& filename) = 0;  

    AtomType* getAtomType(const std::string &at);
    BondType* getBondType(const std::string &at1, const std::string &at2);
    BendType* getBendType(const std::string &at1, const std::string &at2,
                          const std::string &at3);
    TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
                                const std::string &at3, const std::string &at4);

    BondType* getExactBondType(const std::string &at1, const std::string &at2);
    BendType* getExactBendType(const std::string &at1, const std::string &at2,
                               const std::string &at3);
    TorsionType* getExactTorsionType(const std::string &at1, 
                                     const std::string &at2,
                                     const std::string &at3, 
                                     const std::string &at4);


    //avoid make virtual function public
    //Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
    virtual double getRcutFromAtomType(AtomType* at);

    std::string getWildCard() {
      return wildCardAtomTypeName_;
    }

    void setWildCard(const std::string& wildCard) {
      wildCardAtomTypeName_ = wildCard;
    }


    unsigned int getNAtomType() {
      return atomTypeCont_.size();
    }
        
    bool addAtomType(const std::string &at, AtomType* atomType);

    bool addBondType(const std::string &at1, const std::string &at2, 
                     BondType* bondType);

    bool addBendType(const std::string &at1, const std::string &at2,
                     const std::string &at3, BendType* bendType);

    bool addTorsionType(const std::string &at1, const std::string &at2,
                        const std::string &at3, const std::string &at4, TorsionType* torsionType);

    ifstrstream* openForceFieldFile(const std::string& filename);

  protected:

    AtomTypeContainer atomTypeCont_;    
    BondTypeContainer bondTypeCont_;
    BendTypeContainer bendTypeCont_;
    TorsionTypeContainer torsionTypeCont_;
        
  private:  
    std::string ffPath_;

    std::string wildCardAtomTypeName_;

    std::string forceFieldFileName_;
  };

 
}//end namespace oopse
#endif

Revision:	514
Committed:	Thu Apr 21 14:12:19 2005 UTC (20 years ago) by chrisfen
Original Path:	*trunk/src/UseTheForce/ForceField.hpp*
File size:	5409 byte(s)
Log Message:	Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	507	/**
43			* @file ForceField.hpp
44			* @author tlin
45			* @date 11/04/2004
46			* @time 22:51am
47			* @version 1.0
48			*/
49	gezelter	246
50	gezelter	206	#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	gezelter	246	#include <string>
57			#include <utility>
58	gezelter	206
59			#include "io/basic_ifstrstream.hpp"
60	gezelter	246	#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	gezelter	206
66	gezelter	246	namespace oopse {
67	gezelter	206
68	gezelter	507	/**
69			* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
70			* @brief
71			*/
72			class ForceField{
73	gezelter	206
74	gezelter	507	public:
75	gezelter	206
76	gezelter	507	typedef TypeContainer<AtomType, 1> AtomTypeContainer;
77			typedef TypeContainer<BondType, 2> BondTypeContainer;
78			typedef TypeContainer<BendType, 3> BendTypeContainer;
79			typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
80	gezelter	246
81	gezelter	507	ForceField();
82	gezelter	206
83	gezelter	507	virtual ~ForceField();
84	gezelter	206
85	gezelter	507	std::string getForceFieldFileName() {
86			return forceFieldFileName_;
87			}
88	gezelter	206
89	gezelter	507	void setForceFieldFileName(const std::string& filename) {
90			forceFieldFileName_ = filename;
91			}
92	gezelter	246
93	gezelter	507	virtual void parse(const std::string& filename) = 0;
94	gezelter	206
95	gezelter	507	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	chrisfen	514	const std::string &at3);
99	gezelter	507	TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
100	chrisfen	514	const std::string &at3, const std::string &at4);
101	gezelter	246
102	gezelter	507	BondType* getExactBondType(const std::string &at1, const std::string &at2);
103			BendType* getExactBendType(const std::string &at1, const std::string &at2,
104	chrisfen	514	const std::string &at3);
105			TorsionType* getExactTorsionType(const std::string &at1,
106			const std::string &at2,
107			const std::string &at3,
108			const std::string &at4);
109	gezelter	246
110
111	gezelter	507	//avoid make virtual function public
112			//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
113			virtual double getRcutFromAtomType(AtomType* at);
114	gezelter	246
115	gezelter	507	std::string getWildCard() {
116			return wildCardAtomTypeName_;
117			}
118	gezelter	246
119	gezelter	507	void setWildCard(const std::string& wildCard) {
120			wildCardAtomTypeName_ = wildCard;
121			}
122	gezelter	246
123
124	gezelter	507	unsigned int getNAtomType() {
125			return atomTypeCont_.size();
126			}
127	gezelter	246
128	gezelter	507	bool addAtomType(const std::string &at, AtomType* atomType);
129	gezelter	246
130	chrisfen	514	bool addBondType(const std::string &at1, const std::string &at2,
131			BondType* bondType);
132	gezelter	246
133	gezelter	507	bool addBendType(const std::string &at1, const std::string &at2,
134			const std::string &at3, BendType* bendType);
135	gezelter	246
136	gezelter	507	bool addTorsionType(const std::string &at1, const std::string &at2,
137			const std::string &at3, const std::string &at4, TorsionType* torsionType);
138	gezelter	246
139	gezelter	507	ifstrstream* openForceFieldFile(const std::string& filename);
140	gezelter	246
141	gezelter	507	protected:
142	gezelter	246
143	gezelter	507	AtomTypeContainer atomTypeCont_;
144			BondTypeContainer bondTypeCont_;
145			BendTypeContainer bendTypeCont_;
146			TorsionTypeContainer torsionTypeCont_;
147	gezelter	246
148	gezelter	507	private:
149			std::string ffPath_;
150	gezelter	246
151	gezelter	507	std::string wildCardAtomTypeName_;
152	gezelter	246
153	gezelter	507	std::string forceFieldFileName_;
154			};
155	gezelter	206
156	gezelter	246
157			}//end namespace oopse
158	gezelter	206	#endif
159