src/nonbonded/Sticky.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_STICKY_HPP
#define NONBONDED_STICKY_HPP

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

using namespace std;
namespace OpenMD {

  struct StickyInteractionData {
    RealType rl;
    RealType ru;
    RealType rlp;
    RealType rup;
    RealType rbig;
    RealType w0;
    RealType v0;
    RealType v0p;
    CubicSpline* s;
    CubicSpline* sp;
    bool isPower;
  };

  class Sticky : public HydrogenBondingInteraction {
    
  public:    
    Sticky();
    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 STICKY_INTERACTION; }
    virtual RealType getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes);
    
  private:
    void initialize();
    bool initialized_;
    set<int> Stypes;              /**< The set of AtomType idents that are Sticky types */
    vector<int> Stids;            /**< The mapping from AtomType ident -> Sticky type ident */
    vector<vector<StickyInteractionData> > MixingMap;  /**< The mixing parameters between 
                                                          two Sticky types */
    int nSticky_;
    ForceField* forceField_;    
    set<AtomType*> simTypes_;
    string name_;
  };
}

                               
#endif
Revision:	1927
Committed:	Wed Aug 14 20:19:19 2013 UTC (11 years, 11 months ago) by gezelter
File size:	3770 byte(s)
Log Message:	FlucRho/EAM initial commit
#	Content
1	/*
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	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	#ifndef NONBONDED_STICKY_HPP
44	#define NONBONDED_STICKY_HPP
45
46	#include "nonbonded/NonBondedInteraction.hpp"
47	#include "types/StickyAdapter.hpp"
48	#include "brains/ForceField.hpp"
49	#include "math/SquareMatrix3.hpp"
50	#include "math/CubicSpline.hpp"
51
52	using namespace std;
53	namespace OpenMD {
54
55	struct StickyInteractionData {
56	RealType rl;
57	RealType ru;
58	RealType rlp;
59	RealType rup;
60	RealType rbig;
61	RealType w0;
62	RealType v0;
63	RealType v0p;
64	CubicSpline* s;
65	CubicSpline* sp;
66	bool isPower;
67	};
68
69	class Sticky : public HydrogenBondingInteraction {
70
71	public:
72	Sticky();
73	void setForceField(ForceField *ff) {forceField_ = ff;};
74	void setSimulatedAtomTypes(set<AtomType*> &simtypes) {simTypes_ = simtypes;};
75	void addType(AtomType* atomType);
76	virtual void calcForce(InteractionData &idat);
77	virtual string getName() { return name_; }
78	virtual int getHash() { return STICKY_INTERACTION; }
79	virtual RealType getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes);
80
81	private:
82	void initialize();
83	bool initialized_;
84	set<int> Stypes; /*< The set of AtomType idents that are Sticky types /
85	vector<int> Stids; /*< The mapping from AtomType ident -> Sticky type ident /
86	vector<vector<StickyInteractionData> > MixingMap; /**< The mixing parameters between
87	two Sticky types */
88	int nSticky_;
89	ForceField* forceField_;
90	set<AtomType*> simTypes_;
91	string name_;
92	};
93	}
94
95
96	#endif