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:	1782
Committed:	Wed Aug 22 02:28:28 2012 UTC (12 years, 8 months ago) by gezelter
File size:	7272 byte(s)
Log Message:	MERGE OpenMD development branch 1465:1781 into trunk
#	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