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
#	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	* @version 1.0
48	*/
49
50	#ifndef USETHEFORCE_FORCEFIELD_HPP
51	#define USETHEFORCE_FORCEFIELD_HPP
52
53	#include "config.h"
54	#include <string>
55	#include <utility>
56	#include <vector>
57
58	#include "io/ifstrstream.hpp"
59	#include "io/ForceFieldOptions.hpp"
60	#include "io/SectionParserManager.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
70	namespace OpenMD {
71
72	class ForceField{
73
74	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	typedef TypeContainer<InversionType, 4> InversionTypeContainer;
80	typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
81
82	ForceField(std::string ffName);
83
84	virtual ~ForceField() {};
85
86	std::string getForceFieldFileName() {
87	return forceFieldFileName_;
88	}
89
90	void setForceFieldFileName(const std::string& filename) {
91	forceFieldFileName_ = filename;
92	}
93
94	virtual void parse(const std::string& filename);
95
96	AtomType* getAtomType(const std::string &at);
97	AtomType* getAtomType(int ident);
98	BondType* getBondType(const std::string &at1, const std::string &at2);
99	BendType* getBendType(const std::string &at1, const std::string &at2,
100	const std::string &at3);
101	TorsionType* getTorsionType(const std::string &at1, const std::string &at2,
102	const std::string &at3, const std::string &at4);
103	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	BondType* getExactBondType(const std::string &at1, const std::string &at2);
110	BendType* getExactBendType(const std::string &at1, const std::string &at2,
111	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	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	//avoid make virtual function public
124	//Herb Sutter and Andrei Alexandrescu, C++ coding Standards, Addision-Wesley
125	virtual RealType getRcutFromAtomType(AtomType* at);
126
127	std::string getWildCard() {
128	return wildCardAtomTypeName_;
129	}
130
131	void setWildCard(const std::string& wildCard) {
132	wildCardAtomTypeName_ = wildCard;
133	}
134
135	unsigned int getNAtomType() {
136	return atomTypeCont_.size();
137	}
138
139	AtomTypeContainer* getAtomTypes() {
140	return &atomTypeCont_;
141	}
142
143	NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
144	return &nonBondedInteractionTypeCont_;
145	}
146
147	bool addAtomType(const std::string &at, AtomType* atomType);
148
149	bool replaceAtomType(const std::string &at, AtomType* atomType);
150
151	bool addBondType(const std::string &at1, const std::string &at2,
152	BondType* bondType);
153
154	bool addBendType(const std::string &at1, const std::string &at2,
155	const std::string &at3, BendType* bendType);
156
157	bool addTorsionType(const std::string &at1, const std::string &at2,
158	const std::string &at3, const std::string &at4,
159	TorsionType* torsionType);
160
161	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	ifstrstream* openForceFieldFile(const std::string& filename);
170
171	ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
172
173	protected:
174
175	AtomTypeContainer atomTypeCont_;
176	BondTypeContainer bondTypeCont_;
177	BendTypeContainer bendTypeCont_;
178	TorsionTypeContainer torsionTypeCont_;
179	InversionTypeContainer inversionTypeCont_;
180	NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
181	ForceFieldOptions forceFieldOptions_;
182	std::map<int, std::string> atypeIdentToName;
183	SectionParserManager spMan_;
184
185
186	private:
187	std::string ffPath_;
188	std::string wildCardAtomTypeName_;
189	std::string forceFieldFileName_;
190
191	};
192	}//end namespace OpenMD
193	#endif
194