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 "io/ForceFieldOptions.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);

    ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
  protected:

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

    std::string wildCardAtomTypeName_;

    std::string forceFieldFileName_;
  };

 
}//end namespace oopse
#endif

Revision:	2448
Committed:	Wed Nov 16 23:10:02 2005 UTC (18 years, 8 months ago) by tim
File size:	5558 byte(s)
Log Message:	OptionSectionParser get compiled
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	2204	/**
43			* @file ForceField.hpp
44			* @author tlin
45			* @date 11/04/2004
46			* @time 22:51am
47			* @version 1.0
48			*/
49	gezelter	1930
50	gezelter	1711	#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	1930	#include <string>
57			#include <utility>
58	gezelter	1711
59			#include "io/basic_ifstrstream.hpp"
60	tim	2448	#include "io/ForceFieldOptions.hpp"
61	gezelter	1930	#include "utils/TypeContainer.hpp"
62			#include "types/AtomType.hpp"
63			#include "types/BondType.hpp"
64			#include "types/BendType.hpp"
65			#include "types/TorsionType.hpp"
66	gezelter	1711
67	gezelter	1930	namespace oopse {
68	gezelter	1711
69	gezelter	2204	/**
70			* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
71			* @brief
72			*/
73			class ForceField{
74	gezelter	1711
75	gezelter	2204	public:
76	gezelter	1711
77	gezelter	2204	typedef TypeContainer<AtomType, 1> AtomTypeContainer;
78			typedef TypeContainer<BondType, 2> BondTypeContainer;
79			typedef TypeContainer<BendType, 3> BendTypeContainer;
80			typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
81	gezelter	1930
82	gezelter	2204	ForceField();
83	gezelter	1711
84	gezelter	2204	virtual ~ForceField();
85	gezelter	1711
86	gezelter	2204	std::string getForceFieldFileName() {
87			return forceFieldFileName_;
88			}
89	gezelter	1711
90	gezelter	2204	void setForceFieldFileName(const std::string& filename) {
91			forceFieldFileName_ = filename;
92			}
93	gezelter	1930
94	gezelter	2204	virtual void parse(const std::string& filename) = 0;
95	gezelter	1711
96	gezelter	2204	AtomType* getAtomType(const std::string &at);
97			BondType* getBondType(const std::string &at1, const std::string &at2);
98			BendType* getBendType(const std::string &at1, const std::string &at2,
99	chrisfen	2211	const std::string &at3);
100	gezelter	2204	TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
101	chrisfen	2211	const std::string &at3, const std::string &at4);
102	gezelter	1930
103	gezelter	2204	BondType* getExactBondType(const std::string &at1, const std::string &at2);
104			BendType* getExactBendType(const std::string &at1, const std::string &at2,
105	chrisfen	2211	const std::string &at3);
106			TorsionType* getExactTorsionType(const std::string &at1,
107			const std::string &at2,
108			const std::string &at3,
109			const std::string &at4);
110	gezelter	1930
111
112	gezelter	2204	//avoid make virtual function public
113			//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
114			virtual double getRcutFromAtomType(AtomType* at);
115	gezelter	1930
116	gezelter	2204	std::string getWildCard() {
117			return wildCardAtomTypeName_;
118			}
119	gezelter	1930
120	gezelter	2204	void setWildCard(const std::string& wildCard) {
121			wildCardAtomTypeName_ = wildCard;
122			}
123	gezelter	1930
124
125	gezelter	2204	unsigned int getNAtomType() {
126			return atomTypeCont_.size();
127			}
128	gezelter	1930
129	gezelter	2204	bool addAtomType(const std::string &at, AtomType* atomType);
130	gezelter	1930
131	chrisfen	2211	bool addBondType(const std::string &at1, const std::string &at2,
132			BondType* bondType);
133	gezelter	1930
134	gezelter	2204	bool addBendType(const std::string &at1, const std::string &at2,
135			const std::string &at3, BendType* bendType);
136	gezelter	1930
137	gezelter	2204	bool addTorsionType(const std::string &at1, const std::string &at2,
138			const std::string &at3, const std::string &at4, TorsionType* torsionType);
139	gezelter	1930
140	gezelter	2204	ifstrstream* openForceFieldFile(const std::string& filename);
141	gezelter	1930
142	tim	2448	ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
143	gezelter	2204	protected:
144	gezelter	1930
145	gezelter	2204	AtomTypeContainer atomTypeCont_;
146			BondTypeContainer bondTypeCont_;
147			BendTypeContainer bendTypeCont_;
148			TorsionTypeContainer torsionTypeCont_;
149	tim	2448	ForceFieldOptions forceFieldOptions_;
150
151	gezelter	2204	private:
152			std::string ffPath_;
153	gezelter	1930
154	gezelter	2204	std::string wildCardAtomTypeName_;
155	gezelter	1930
156	gezelter	2204	std::string forceFieldFileName_;
157			};
158	gezelter	1711
159	gezelter	1930
160			}//end namespace oopse
161	gezelter	1711	#endif
162