src/nonbonded/GB.hpp

/*
 * Copyright (c) 2009 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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#ifndef NONBONDED_GB_HPP
#define NONBONDED_GB_HPP

#include "nonbonded/NonBondedInteraction.hpp"
#include "brains/ForceField.hpp"
#include "math/SquareMatrix3.hpp"

using namespace std;
namespace OpenMD {

  struct GBInteractionData {
    RealType sigma0;
    RealType eps0;
    RealType dw;
    RealType x2;
    RealType xa2;
    RealType xai2;
    RealType xp2;
    RealType xpap2;
    RealType xpapi2;
    bool i_is_LJ;
    bool j_is_LJ;
  };

  class GB : public VanDerWaalsInteraction {
    
  public:    
    GB();
    void setForceField(ForceField *ff) {forceField_ = ff;};
    void setSimulatedAtomTypes(set<AtomType*> &simtypes) {simTypes_ = simtypes;};
    void addType(AtomType* atomType);
    virtual void calcForce(InteractionData &idat);
    virtual string getName() {return name_;}
    virtual int getHash() { return GB_INTERACTION; }
    virtual RealType getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes);
    
  private:
    void initialize();

    bool initialized_;
    string name_;
    set<int> GBtypes;               /**< The set of AtomType idents that are GB types */
    vector<int> GBtids;             /**< The mapping from AtomType ident -> GB type ident */
    vector<vector<GBInteractionData> > MixingMap;  /**< The mixing parameters between two 
                                                      GB types */
    int nGB_;

    ForceField* forceField_;
    set<AtomType*> simTypes_;
    RealType mu_;
    RealType nu_;
    
  };
}

                               
#endif
Revision:	1930
Committed:	Mon Aug 19 13:51:04 2013 UTC (11 years, 11 months ago) by gezelter
File size:	3698 byte(s)
Log Message:	region fixes, performance boosts
#	User	Rev	Content
1	gezelter	1483	/*
2			* Copyright (c) 2009 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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	1483	*/
42
43			#ifndef NONBONDED_GB_HPP
44			#define NONBONDED_GB_HPP
45
46	gezelter	1502	#include "nonbonded/NonBondedInteraction.hpp"
47	gezelter	1725	#include "brains/ForceField.hpp"
48	gezelter	1483	#include "math/SquareMatrix3.hpp"
49
50			using namespace std;
51			namespace OpenMD {
52
53			struct GBInteractionData {
54			RealType sigma0;
55			RealType eps0;
56			RealType dw;
57			RealType x2;
58			RealType xa2;
59			RealType xai2;
60			RealType xp2;
61			RealType xpap2;
62			RealType xpapi2;
63	gezelter	1930	bool i_is_LJ;
64			bool j_is_LJ;
65	gezelter	1483	};
66
67	gezelter	1502	class GB : public VanDerWaalsInteraction {
68	gezelter	1483
69			public:
70	gezelter	1502	GB();
71			void setForceField(ForceField *ff) {forceField_ = ff;};
72	gezelter	1895	void setSimulatedAtomTypes(set<AtomType*> &simtypes) {simTypes_ = simtypes;};
73	gezelter	1502	void addType(AtomType* atomType);
74	gezelter	1536	virtual void calcForce(InteractionData &idat);
75	gezelter	1502	virtual string getName() {return name_;}
76	gezelter	1927	virtual int getHash() { return GB_INTERACTION; }
77	gezelter	1545	virtual RealType getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes);
78	gezelter	1483
79			private:
80	gezelter	1502	void initialize();
81	gezelter	1483
82	gezelter	1502	bool initialized_;
83			string name_;
84	gezelter	1895	set<int> GBtypes; /*< The set of AtomType idents that are GB types /
85			vector<int> GBtids; /*< The mapping from AtomType ident -> GB type ident /
86			vector<vector<GBInteractionData> > MixingMap; /**< The mixing parameters between two
87			GB types */
88			int nGB_;
89
90	gezelter	1502	ForceField* forceField_;
91	gezelter	1895	set<AtomType*> simTypes_;
92	gezelter	1502	RealType mu_;
93			RealType nu_;
94	gezelter	1483
95			};
96			}
97
98
99			#endif