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
 * @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:	1808
Committed:	Mon Oct 22 20:42:10 2012 UTC (12 years, 6 months ago) by gezelter
File size:	7255 byte(s)
Log Message:	A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	507	/**
44			* @file ForceField.hpp
45			* @author tlin
46			* @date 11/04/2004
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	gezelter	1627	#include "io/ifstrstream.hpp"
59	tim	749	#include "io/ForceFieldOptions.hpp"
60	gezelter	1725	#include "io/SectionParserManager.hpp"
61	gezelter	246	#include "utils/TypeContainer.hpp"
62	gezelter	1269	#include "utils/Tuple.hpp"
63	gezelter	246	#include "types/AtomType.hpp"
64			#include "types/BondType.hpp"
65			#include "types/BendType.hpp"
66			#include "types/TorsionType.hpp"
67	cli2	1275	#include "types/InversionType.hpp"
68	chuckv	1151	#include "types/NonBondedInteractionType.hpp"
69	gezelter	1725
70	gezelter	1390	namespace OpenMD {
71	gezelter	206
72	gezelter	507	class ForceField{
73	gezelter	206
74	gezelter	507	public:
75			typedef TypeContainer<AtomType, 1> AtomTypeContainer;
76			typedef TypeContainer<BondType, 2> BondTypeContainer;
77			typedef TypeContainer<BendType, 3> BendTypeContainer;
78			typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
79	cli2	1275	typedef TypeContainer<InversionType, 4> InversionTypeContainer;
80			typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
81
82	gezelter	1725	ForceField(std::string ffName);
83	cli2	1275
84	gezelter	1535	virtual ~ForceField() {};
85	gezelter	206
86	gezelter	507	std::string getForceFieldFileName() {
87			return forceFieldFileName_;
88			}
89	gezelter	206
90	gezelter	507	void setForceFieldFileName(const std::string& filename) {
91			forceFieldFileName_ = filename;
92			}
93	gezelter	246
94	gezelter	1725	virtual void parse(const std::string& filename);
95	gezelter	206
96	gezelter	507	AtomType* getAtomType(const std::string &at);
97	gezelter	1535	AtomType* getAtomType(int ident);
98	gezelter	507	BondType* getBondType(const std::string &at1, const std::string &at2);
99			BendType* getBendType(const std::string &at1, const std::string &at2,
100	chrisfen	514	const std::string &at3);
101	gezelter	507	TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
102	chrisfen	514	const std::string &at3, const std::string &at4);
103	cli2	1275	InversionType* getInversionType(const std::string &at1,
104			const std::string &at2,
105			const std::string &at3,
106			const std::string &at4);
107			NonBondedInteractionType* getNonBondedInteractionType(const std::string &at1, const std::string &at2);
108
109	gezelter	507	BondType* getExactBondType(const std::string &at1, const std::string &at2);
110			BendType* getExactBendType(const std::string &at1, const std::string &at2,
111	chrisfen	514	const std::string &at3);
112			TorsionType* getExactTorsionType(const std::string &at1,
113			const std::string &at2,
114			const std::string &at3,
115			const std::string &at4);
116	cli2	1275	InversionType* getExactInversionType(const std::string &at1,
117			const std::string &at2,
118			const std::string &at3,
119			const std::string &at4);
120			NonBondedInteractionType* getExactNonBondedInteractionType(const std::string &at1, const std::string &at2);
121
122
123	gezelter	507	//avoid make virtual function public
124			//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
125	tim	963	virtual RealType getRcutFromAtomType(AtomType* at);
126	cli2	1275
127	gezelter	507	std::string getWildCard() {
128			return wildCardAtomTypeName_;
129			}
130	cli2	1275
131	gezelter	507	void setWildCard(const std::string& wildCard) {
132			wildCardAtomTypeName_ = wildCard;
133			}
134	cli2	1275
135	gezelter	507	unsigned int getNAtomType() {
136			return atomTypeCont_.size();
137			}
138	gezelter	1467
139	gezelter	1476	AtomTypeContainer* getAtomTypes() {
140			return &atomTypeCont_;
141	gezelter	1467	}
142
143	gezelter	1476	NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
144			return &nonBondedInteractionTypeCont_;
145	gezelter	1467	}
146	gezelter	246
147	gezelter	507	bool addAtomType(const std::string &at, AtomType* atomType);
148	gezelter	246
149	gezelter	1282	bool replaceAtomType(const std::string &at, AtomType* atomType);
150
151	chrisfen	514	bool addBondType(const std::string &at1, const std::string &at2,
152			BondType* bondType);
153	gezelter	246
154	gezelter	507	bool addBendType(const std::string &at1, const std::string &at2,
155			const std::string &at3, BendType* bendType);
156	gezelter	246
157	gezelter	507	bool addTorsionType(const std::string &at1, const std::string &at2,
158	cli2	1275	const std::string &at3, const std::string &at4,
159			TorsionType* torsionType);
160	gezelter	246
161	cli2	1275	bool addInversionType(const std::string &at1, const std::string &at2,
162			const std::string &at3, const std::string &at4,
163			InversionType* inversionType);
164
165			bool addNonBondedInteractionType(const std::string &at1,
166			const std::string &at2,
167			NonBondedInteractionType* nbiType);
168
169	gezelter	507	ifstrstream* openForceFieldFile(const std::string& filename);
170	cli2	1275
171	tim	749	ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
172	chuckv	821
173	gezelter	507	protected:
174	gezelter	246
175	gezelter	507	AtomTypeContainer atomTypeCont_;
176			BondTypeContainer bondTypeCont_;
177			BendTypeContainer bendTypeCont_;
178			TorsionTypeContainer torsionTypeCont_;
179	cli2	1275	InversionTypeContainer inversionTypeCont_;
180	chuckv	1151	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
181	tim	749	ForceFieldOptions forceFieldOptions_;
182	gezelter	1535	std::map<int, std::string> atypeIdentToName;
183	gezelter	1725	SectionParserManager spMan_;
184
185	tim	749
186	gezelter	507	private:
187	gezelter	1535	std::string ffPath_;
188			std::string wildCardAtomTypeName_;
189	cli2	1275	std::string forceFieldFileName_;
190
191	gezelter	507	};
192	gezelter	1390	}//end namespace OpenMD
193	gezelter	206	#endif
194