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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @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/ifstrstream.hpp"
#include "io/ForceFieldOptions.hpp"
#include "io/SectionParserManager.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"

namespace OpenMD {

  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(std::string ffName);
    
    virtual ~ForceField() {};

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

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

    AtomType* getAtomType(const std::string &at);
    AtomType* getAtomType(int ident);
    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();
    }

    AtomTypeContainer* getAtomTypes() {
      return &atomTypeCont_;
    }
    
    NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
      return &nonBondedInteractionTypeCont_;
    }
        
    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_;}

  protected:

    AtomTypeContainer atomTypeCont_;    
    BondTypeContainer bondTypeCont_;
    BendTypeContainer bendTypeCont_;
    TorsionTypeContainer torsionTypeCont_;
    InversionTypeContainer inversionTypeCont_;
    NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
    ForceFieldOptions forceFieldOptions_;
    std::map<int, std::string> atypeIdentToName;
    SectionParserManager spMan_;

    
  private:  
    std::string ffPath_;    
    std::string wildCardAtomTypeName_;    
    std::string forceFieldFileName_;    
    
  };
}//end namespace OpenMD
#endif

Revision:	1725
Committed:	Sat May 26 18:13:43 2012 UTC (12 years, 11 months ago) by gezelter
Original Path:	*branches/development/src/brains/ForceField.hpp*
File size:	7272 byte(s)
Log Message:	Individual ForceField classes have been removed (they were essentially all duplicates anyway). ForceField has moved to brains, and since only one force field is in play at any time, the ForceFieldFactory and Register methods have been removed.
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	/**
44	* @file ForceField.hpp
45	* @author tlin
46	* @date 11/04/2004
47	* @time 22:51am
48	* @version 1.0
49	*/
50
51	#ifndef USETHEFORCE_FORCEFIELD_HPP
52	#define USETHEFORCE_FORCEFIELD_HPP
53
54	#include "config.h"
55	#include <string>
56	#include <utility>
57	#include <vector>
58
59	#include "io/ifstrstream.hpp"
60	#include "io/ForceFieldOptions.hpp"
61	#include "io/SectionParserManager.hpp"
62	#include "utils/TypeContainer.hpp"
63	#include "utils/Tuple.hpp"
64	#include "types/AtomType.hpp"
65	#include "types/BondType.hpp"
66	#include "types/BendType.hpp"
67	#include "types/TorsionType.hpp"
68	#include "types/InversionType.hpp"
69	#include "types/NonBondedInteractionType.hpp"
70
71	namespace OpenMD {
72
73	class ForceField{
74
75	public:
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	typedef TypeContainer<InversionType, 4> InversionTypeContainer;
81	typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
82
83	ForceField(std::string ffName);
84
85	virtual ~ForceField() {};
86
87	std::string getForceFieldFileName() {
88	return forceFieldFileName_;
89	}
90
91	void setForceFieldFileName(const std::string& filename) {
92	forceFieldFileName_ = filename;
93	}
94
95	virtual void parse(const std::string& filename);
96
97	AtomType* getAtomType(const std::string &at);
98	AtomType* getAtomType(int ident);
99	BondType* getBondType(const std::string &at1, const std::string &at2);
100	BendType* getBendType(const std::string &at1, const std::string &at2,
101	const std::string &at3);
102	TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
103	const std::string &at3, const std::string &at4);
104	InversionType* getInversionType(const std::string &at1,
105	const std::string &at2,
106	const std::string &at3,
107	const std::string &at4);
108	NonBondedInteractionType* getNonBondedInteractionType(const std::string &at1, const std::string &at2);
109
110	BondType* getExactBondType(const std::string &at1, const std::string &at2);
111	BendType* getExactBendType(const std::string &at1, const std::string &at2,
112	const std::string &at3);
113	TorsionType* getExactTorsionType(const std::string &at1,
114	const std::string &at2,
115	const std::string &at3,
116	const std::string &at4);
117	InversionType* getExactInversionType(const std::string &at1,
118	const std::string &at2,
119	const std::string &at3,
120	const std::string &at4);
121	NonBondedInteractionType* getExactNonBondedInteractionType(const std::string &at1, const std::string &at2);
122
123
124	//avoid make virtual function public
125	//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
126	virtual RealType getRcutFromAtomType(AtomType* at);
127
128	std::string getWildCard() {
129	return wildCardAtomTypeName_;
130	}
131
132	void setWildCard(const std::string& wildCard) {
133	wildCardAtomTypeName_ = wildCard;
134	}
135
136	unsigned int getNAtomType() {
137	return atomTypeCont_.size();
138	}
139
140	AtomTypeContainer* getAtomTypes() {
141	return &atomTypeCont_;
142	}
143
144	NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
145	return &nonBondedInteractionTypeCont_;
146	}
147
148	bool addAtomType(const std::string &at, AtomType* atomType);
149
150	bool replaceAtomType(const std::string &at, AtomType* atomType);
151
152	bool addBondType(const std::string &at1, const std::string &at2,
153	BondType* bondType);
154
155	bool addBendType(const std::string &at1, const std::string &at2,
156	const std::string &at3, BendType* bendType);
157
158	bool addTorsionType(const std::string &at1, const std::string &at2,
159	const std::string &at3, const std::string &at4,
160	TorsionType* torsionType);
161
162	bool addInversionType(const std::string &at1, const std::string &at2,
163	const std::string &at3, const std::string &at4,
164	InversionType* inversionType);
165
166	bool addNonBondedInteractionType(const std::string &at1,
167	const std::string &at2,
168	NonBondedInteractionType* nbiType);
169
170	ifstrstream* openForceFieldFile(const std::string& filename);
171
172	ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
173
174	protected:
175
176	AtomTypeContainer atomTypeCont_;
177	BondTypeContainer bondTypeCont_;
178	BendTypeContainer bendTypeCont_;
179	TorsionTypeContainer torsionTypeCont_;
180	InversionTypeContainer inversionTypeCont_;
181	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
182	ForceFieldOptions forceFieldOptions_;
183	std::map<int, std::string> atypeIdentToName;
184	SectionParserManager spMan_;
185
186
187	private:
188	std::string ffPath_;
189	std::string wildCardAtomTypeName_;
190	std::string forceFieldFileName_;
191
192	};
193	}//end namespace OpenMD
194	#endif
195