src/UseTheForce/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:	2211
Committed:	Thu Apr 21 14:12:19 2005 UTC (19 years, 2 months ago) by chrisfen
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...
#	Content
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 <string>
57	#include <utility>
58
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	namespace oopse {
67
68	/**
69	* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
70	* @brief
71	*/
72	class ForceField{
73
74	public:
75
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 ~ForceField();
84
85	std::string getForceFieldFileName() {
86	return forceFieldFileName_;
87	}
88
89	void setForceFieldFileName(const std::string& filename) {
90	forceFieldFileName_ = filename;
91	}
92
93	virtual void parse(const std::string& filename) = 0;
94
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,
106	const std::string &at2,
107	const std::string &at3,
108	const std::string &at4);
109
110
111	//avoid make virtual function public
112	//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
113	virtual double getRcutFromAtomType(AtomType* at);
114
115	std::string getWildCard() {
116	return wildCardAtomTypeName_;
117	}
118
119	void setWildCard(const std::string& wildCard) {
120	wildCardAtomTypeName_ = wildCard;
121	}
122
123
124	unsigned int getNAtomType() {
125	return atomTypeCont_.size();
126	}
127
128	bool addAtomType(const std::string &at, AtomType* atomType);
129
130	bool addBondType(const std::string &at1, const std::string &at2,
131	BondType* bondType);
132
133	bool addBendType(const std::string &at1, const std::string &at2,
134	const std::string &at3, BendType* bendType);
135
136	bool addTorsionType(const std::string &at1, const std::string &at2,
137	const std::string &at3, const std::string &at4, TorsionType* torsionType);
138
139	ifstrstream* openForceFieldFile(const std::string& filename);
140
141	protected:
142
143	AtomTypeContainer atomTypeCont_;
144	BondTypeContainer bondTypeCont_;
145	BendTypeContainer bendTypeCont_;
146	TorsionTypeContainer torsionTypeCont_;
147
148	private:
149	std::string ffPath_;
150
151	std::string wildCardAtomTypeName_;
152
153	std::string forceFieldFileName_;
154	};
155
156
157	}//end namespace oopse
158	#endif
159