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/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<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);
                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);
                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 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 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_;
    NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
    ForceFieldOptions forceFieldOptions_;
    
  private:  
    std::string ffPath_;

    std::string wildCardAtomTypeName_;

    std::string forceFieldFileName_;


  };
}//end namespace oopse
#endif

Revision:	1269
Committed:	Tue Jul 1 13:28:23 2008 UTC (17 years, 4 months ago) by gezelter
Original Path:	*trunk/src/UseTheForce/ForceField.hpp*
File size:	6221 byte(s)
Log Message:	Adding infrastructure for Amber force field.
#	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	chuckv	1151	#include "types/NonBondedInteractionType.hpp"
67	chuckv	821	#include "UseTheForce/fForceOptions.h"
68	gezelter	246	namespace oopse {
69	gezelter	206
70	gezelter	507	/**
71			* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
72			* @brief
73			*/
74			class ForceField{
75	gezelter	206
76	gezelter	507	public:
77	gezelter	206
78	gezelter	507	typedef TypeContainer<AtomType, 1> AtomTypeContainer;
79			typedef TypeContainer<BondType, 2> BondTypeContainer;
80			typedef TypeContainer<BendType, 3> BendTypeContainer;
81			typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
82	chuckv	1151	typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
83	gezelter	246
84	gezelter	507	ForceField();
85	gezelter	206
86	gezelter	507	virtual ~ForceField();
87	gezelter	206
88	gezelter	507	std::string getForceFieldFileName() {
89			return forceFieldFileName_;
90			}
91	gezelter	206
92	gezelter	507	void setForceFieldFileName(const std::string& filename) {
93			forceFieldFileName_ = filename;
94			}
95	gezelter	246
96	gezelter	507	virtual void parse(const std::string& filename) = 0;
97	gezelter	206
98	gezelter	507	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	chrisfen	514	const std::string &at3);
102	gezelter	507	TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
103	chrisfen	514	const std::string &at3, const std::string &at4);
104	chuckv	1151	NonBondedInteractionType* getNonBondedInteractionType(const std::string &at1, const std::string &at2);
105
106	gezelter	507	BondType* getExactBondType(const std::string &at1, const std::string &at2);
107			BendType* getExactBendType(const std::string &at1, const std::string &at2,
108	chrisfen	514	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	chuckv	1151	NonBondedInteractionType* getExactNonBondedInteractionType(const std::string &at1, const std::string &at2);
114	gezelter	246
115
116	gezelter	507	//avoid make virtual function public
117			//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
118	tim	963	virtual RealType getRcutFromAtomType(AtomType* at);
119	gezelter	246
120	gezelter	507	std::string getWildCard() {
121			return wildCardAtomTypeName_;
122			}
123	gezelter	246
124	gezelter	507	void setWildCard(const std::string& wildCard) {
125			wildCardAtomTypeName_ = wildCard;
126			}
127	gezelter	246
128
129	gezelter	507	unsigned int getNAtomType() {
130			return atomTypeCont_.size();
131			}
132	gezelter	246
133	gezelter	507	bool addAtomType(const std::string &at, AtomType* atomType);
134	gezelter	246
135	chrisfen	514	bool addBondType(const std::string &at1, const std::string &at2,
136			BondType* bondType);
137	gezelter	246
138	gezelter	507	bool addBendType(const std::string &at1, const std::string &at2,
139			const std::string &at3, BendType* bendType);
140	gezelter	246
141	gezelter	507	bool addTorsionType(const std::string &at1, const std::string &at2,
142			const std::string &at3, const std::string &at4, TorsionType* torsionType);
143	gezelter	246
144	chuckv	1151	bool addNonBondedInteractionType(const std::string &at1, const std::string &at2,
145			NonBondedInteractionType* nbiType);
146
147	gezelter	507	ifstrstream* openForceFieldFile(const std::string& filename);
148	gezelter	246
149	tim	749	ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
150	chuckv	821
151			void setFortranForceOptions(void);
152	gezelter	1269
153
154	gezelter	507	protected:
155	gezelter	246
156	gezelter	507	AtomTypeContainer atomTypeCont_;
157			BondTypeContainer bondTypeCont_;
158			BendTypeContainer bendTypeCont_;
159			TorsionTypeContainer torsionTypeCont_;
160	chuckv	1151	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
161	tim	749	ForceFieldOptions forceFieldOptions_;
162
163	gezelter	507	private:
164			std::string ffPath_;
165	gezelter	246
166	gezelter	507	std::string wildCardAtomTypeName_;
167	gezelter	246
168	gezelter	507	std::string forceFieldFileName_;
169	gezelter	1269
170
171	gezelter	507	};
172	gezelter	246	}//end namespace oopse
173	gezelter	206	#endif
174