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

Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	7277 byte(s)
Log Message:	updated copyright notices
#	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 "utils/TypeContainer.hpp"
62	#include "utils/Tuple.hpp"
63	#include "types/AtomType.hpp"
64	#include "types/BondType.hpp"
65	#include "types/BendType.hpp"
66	#include "types/TorsionType.hpp"
67	#include "types/InversionType.hpp"
68	#include "types/NonBondedInteractionType.hpp"
69	namespace OpenMD {
70
71	/**
72	* @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
73	* @brief
74	*/
75	class ForceField{
76
77	public:
78
79	typedef TypeContainer<AtomType, 1> AtomTypeContainer;
80	typedef TypeContainer<BondType, 2> BondTypeContainer;
81	typedef TypeContainer<BendType, 3> BendTypeContainer;
82	typedef TypeContainer<TorsionType, 4> TorsionTypeContainer;
83	typedef TypeContainer<InversionType, 4> InversionTypeContainer;
84	typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
85
86	ForceField();
87
88	virtual ~ForceField() {};
89
90	std::string getForceFieldFileName() {
91	return forceFieldFileName_;
92	}
93
94	void setForceFieldFileName(const std::string& filename) {
95	forceFieldFileName_ = filename;
96	}
97
98	virtual void parse(const std::string& filename) = 0;
99
100	AtomType* getAtomType(const std::string &at);
101	AtomType* getAtomType(int ident);
102	BondType* getBondType(const std::string &at1, const std::string &at2);
103	BendType* getBendType(const std::string &at1, const std::string &at2,
104	const std::string &at3);
105	TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
106	const std::string &at3, const std::string &at4);
107	InversionType* getInversionType(const std::string &at1,
108	const std::string &at2,
109	const std::string &at3,
110	const std::string &at4);
111	NonBondedInteractionType* getNonBondedInteractionType(const std::string &at1, const std::string &at2);
112
113	BondType* getExactBondType(const std::string &at1, const std::string &at2);
114	BendType* getExactBendType(const std::string &at1, const std::string &at2,
115	const std::string &at3);
116	TorsionType* getExactTorsionType(const std::string &at1,
117	const std::string &at2,
118	const std::string &at3,
119	const std::string &at4);
120	InversionType* getExactInversionType(const std::string &at1,
121	const std::string &at2,
122	const std::string &at3,
123	const std::string &at4);
124	NonBondedInteractionType* getExactNonBondedInteractionType(const std::string &at1, const std::string &at2);
125
126
127	//avoid make virtual function public
128	//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
129	virtual RealType getRcutFromAtomType(AtomType* at);
130
131	std::string getWildCard() {
132	return wildCardAtomTypeName_;
133	}
134
135	void setWildCard(const std::string& wildCard) {
136	wildCardAtomTypeName_ = wildCard;
137	}
138
139	unsigned int getNAtomType() {
140	return atomTypeCont_.size();
141	}
142
143	AtomTypeContainer* getAtomTypes() {
144	return &atomTypeCont_;
145	}
146
147	NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
148	return &nonBondedInteractionTypeCont_;
149	}
150
151	bool addAtomType(const std::string &at, AtomType* atomType);
152
153	bool replaceAtomType(const std::string &at, AtomType* atomType);
154
155	bool addBondType(const std::string &at1, const std::string &at2,
156	BondType* bondType);
157
158	bool addBendType(const std::string &at1, const std::string &at2,
159	const std::string &at3, BendType* bendType);
160
161	bool addTorsionType(const std::string &at1, const std::string &at2,
162	const std::string &at3, const std::string &at4,
163	TorsionType* torsionType);
164
165	bool addInversionType(const std::string &at1, const std::string &at2,
166	const std::string &at3, const std::string &at4,
167	InversionType* inversionType);
168
169	bool addNonBondedInteractionType(const std::string &at1,
170	const std::string &at2,
171	NonBondedInteractionType* nbiType);
172
173	ifstrstream* openForceFieldFile(const std::string& filename);
174
175	ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
176
177	protected:
178
179	AtomTypeContainer atomTypeCont_;
180	BondTypeContainer bondTypeCont_;
181	BendTypeContainer bendTypeCont_;
182	TorsionTypeContainer torsionTypeCont_;
183	InversionTypeContainer inversionTypeCont_;
184	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
185	ForceFieldOptions forceFieldOptions_;
186	std::map<int, std::string> atypeIdentToName;
187
188	private:
189	std::string ffPath_;
190	std::string wildCardAtomTypeName_;
191	std::string forceFieldFileName_;
192
193	};
194	}//end namespace OpenMD
195	#endif
196