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

#include "config.h"
#include <string>
#include <utility>
#include <vector>

#include "io/basic_ifstrstream.hpp"
#include "io/ForceFieldOptions.hpp"
#include "utils/TypeContainer.hpp"
#include "utils/Tuple.hpp"
#include "types/AtomType.hpp"
#include "types/BondType.hpp"
#include "types/BendType.hpp"
#include "types/TorsionType.hpp"
#include "types/InversionType.hpp"
#include "types/NonBondedInteractionType.hpp"
#include "UseTheForce/fForceOptions.h"
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;
    typedef TypeContainer<InversionType, 4> InversionTypeContainer;
    typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
    
    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);
    InversionType* getInversionType(const std::string &at1, 
                                    const std::string &at2,
                                    const std::string &at3, 
                                    const std::string &at4);
    NonBondedInteractionType* getNonBondedInteractionType(const std::string &at1, const std::string &at2);
    
    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);
    InversionType* getExactInversionType(const std::string &at1, 
                                         const std::string &at2,
                                         const std::string &at3, 
                                         const std::string &at4);
    NonBondedInteractionType* getExactNonBondedInteractionType(const std::string &at1, const std::string &at2);
    
    
    //avoid make virtual function public
    //Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
    virtual RealType 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 replaceAtomType(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);

    bool addInversionType(const std::string &at1, const std::string &at2,
                          const std::string &at3, const std::string &at4,
                          InversionType* inversionType);
    
    bool addNonBondedInteractionType(const std::string &at1, 
                                     const std::string &at2, 
                                     NonBondedInteractionType* nbiType);
    
    ifstrstream* openForceFieldFile(const std::string& filename);
    
    ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}

    void setFortranForceOptions(void);

 
  protected:

    AtomTypeContainer atomTypeCont_;    
    BondTypeContainer bondTypeCont_;
    BendTypeContainer bendTypeCont_;
    TorsionTypeContainer torsionTypeCont_;
    InversionTypeContainer inversionTypeCont_;
    NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
    ForceFieldOptions forceFieldOptions_;
    
  private:  
    std::string ffPath_;
    
    std::string wildCardAtomTypeName_;
    
    std::string forceFieldFileName_;    
    
  };
}//end namespace oopse
#endif

Revision:	1282
Committed:	Wed Jul 30 18:11:19 2008 UTC (16 years, 9 months ago) by gezelter
Original Path:	*trunk/src/UseTheForce/ForceField.hpp*
File size:	6964 byte(s)
Log Message:	Many fixes
#	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	gezelter	762	#include "config.h"
54	gezelter	246	#include <string>
55			#include <utility>
56	gezelter	1269	#include <vector>
57	gezelter	206
58			#include "io/basic_ifstrstream.hpp"
59	tim	749	#include "io/ForceFieldOptions.hpp"
60	gezelter	246	#include "utils/TypeContainer.hpp"
61	gezelter	1269	#include "utils/Tuple.hpp"
62	gezelter	246	#include "types/AtomType.hpp"
63			#include "types/BondType.hpp"
64			#include "types/BendType.hpp"
65			#include "types/TorsionType.hpp"
66	cli2	1275	#include "types/InversionType.hpp"
67	chuckv	1151	#include "types/NonBondedInteractionType.hpp"
68	chuckv	821	#include "UseTheForce/fForceOptions.h"
69	gezelter	246	namespace oopse {
70	gezelter	206
71	gezelter	507	/**
72			* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
73			* @brief
74			*/
75			class ForceField{
76	gezelter	206
77	gezelter	507	public:
78	gezelter	206
79	gezelter	507	typedef TypeContainer<AtomType, 1> AtomTypeContainer;
80			typedef TypeContainer<BondType, 2> BondTypeContainer;
81			typedef TypeContainer<BendType, 3> BendTypeContainer;
82			typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
83	cli2	1275	typedef TypeContainer<InversionType, 4> InversionTypeContainer;
84			typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
85
86	gezelter	507	ForceField();
87	cli2	1275
88	gezelter	507	virtual ~ForceField();
89	gezelter	206
90	gezelter	507	std::string getForceFieldFileName() {
91			return forceFieldFileName_;
92			}
93	gezelter	206
94	gezelter	507	void setForceFieldFileName(const std::string& filename) {
95			forceFieldFileName_ = filename;
96			}
97	gezelter	246
98	gezelter	507	virtual void parse(const std::string& filename) = 0;
99	gezelter	206
100	gezelter	507	AtomType* getAtomType(const std::string &at);
101			BondType* getBondType(const std::string &at1, const std::string &at2);
102			BendType* getBendType(const std::string &at1, const std::string &at2,
103	chrisfen	514	const std::string &at3);
104	gezelter	507	TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
105	chrisfen	514	const std::string &at3, const std::string &at4);
106	cli2	1275	InversionType* getInversionType(const std::string &at1,
107			const std::string &at2,
108			const std::string &at3,
109			const std::string &at4);
110			NonBondedInteractionType* getNonBondedInteractionType(const std::string &at1, const std::string &at2);
111
112	gezelter	507	BondType* getExactBondType(const std::string &at1, const std::string &at2);
113			BendType* getExactBendType(const std::string &at1, const std::string &at2,
114	chrisfen	514	const std::string &at3);
115			TorsionType* getExactTorsionType(const std::string &at1,
116			const std::string &at2,
117			const std::string &at3,
118			const std::string &at4);
119	cli2	1275	InversionType* getExactInversionType(const std::string &at1,
120			const std::string &at2,
121			const std::string &at3,
122			const std::string &at4);
123			NonBondedInteractionType* getExactNonBondedInteractionType(const std::string &at1, const std::string &at2);
124
125
126	gezelter	507	//avoid make virtual function public
127			//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
128	tim	963	virtual RealType getRcutFromAtomType(AtomType* at);
129	cli2	1275
130	gezelter	507	std::string getWildCard() {
131			return wildCardAtomTypeName_;
132			}
133	cli2	1275
134	gezelter	507	void setWildCard(const std::string& wildCard) {
135			wildCardAtomTypeName_ = wildCard;
136			}
137	cli2	1275
138	gezelter	507	unsigned int getNAtomType() {
139			return atomTypeCont_.size();
140			}
141	gezelter	246
142	gezelter	507	bool addAtomType(const std::string &at, AtomType* atomType);
143	gezelter	246
144	gezelter	1282	bool replaceAtomType(const std::string &at, AtomType* atomType);
145
146	chrisfen	514	bool addBondType(const std::string &at1, const std::string &at2,
147			BondType* bondType);
148	gezelter	246
149	gezelter	507	bool addBendType(const std::string &at1, const std::string &at2,
150			const std::string &at3, BendType* bendType);
151	gezelter	246
152	gezelter	507	bool addTorsionType(const std::string &at1, const std::string &at2,
153	cli2	1275	const std::string &at3, const std::string &at4,
154			TorsionType* torsionType);
155	gezelter	246
156	cli2	1275	bool addInversionType(const std::string &at1, const std::string &at2,
157			const std::string &at3, const std::string &at4,
158			InversionType* inversionType);
159
160			bool addNonBondedInteractionType(const std::string &at1,
161			const std::string &at2,
162			NonBondedInteractionType* nbiType);
163
164	gezelter	507	ifstrstream* openForceFieldFile(const std::string& filename);
165	cli2	1275
166	tim	749	ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
167	chuckv	821
168			void setFortranForceOptions(void);
169	gezelter	1269
170
171	gezelter	507	protected:
172	gezelter	246
173	gezelter	507	AtomTypeContainer atomTypeCont_;
174			BondTypeContainer bondTypeCont_;
175			BendTypeContainer bendTypeCont_;
176			TorsionTypeContainer torsionTypeCont_;
177	cli2	1275	InversionTypeContainer inversionTypeCont_;
178	chuckv	1151	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
179	tim	749	ForceFieldOptions forceFieldOptions_;
180
181	gezelter	507	private:
182			std::string ffPath_;
183	cli2	1275
184	gezelter	507	std::string wildCardAtomTypeName_;
185	cli2	1275
186			std::string forceFieldFileName_;
187
188	gezelter	507	};
189	gezelter	246	}//end namespace oopse
190	gezelter	206	#endif
191