src/nonbonded/EAM.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_EAM_HPP
#define NONBONDED_EAM_HPP

#include "nonbonded/NonBondedInteraction.hpp"
#include "types/EAMAdapter.hpp"
#include "brains/ForceField.hpp"
#include "math/Vector3.hpp"
#include "math/CubicSpline.hpp"

namespace OpenMD {

  struct EAMAtomData {
    CubicSpline* rho;
    CubicSpline* F;
    CubicSpline* Z;
    RealType rcut;
    bool isFluctuating;
    RealType qToRhoScaling;
  };
  
  struct EAMInteractionData {
    CubicSpline* phi;
    RealType rcut;
    bool explicitlySet;
  };
  
  enum EAMMixingMethod{
    eamJohnson,
    eamDaw,
    eamUnknown
  };
  
  class EAM : public MetallicInteraction {
    
  public:    
    EAM();
    void setForceField(ForceField *ff) {forceField_ = ff;};
    void setSimulatedAtomTypes(set<AtomType*> &simtypes) {simTypes_ = simtypes;};
    void addType(AtomType* atomType);
    void addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType dr, int nr, std::vector<RealType> phiAB);
    void calcDensity(InteractionData &idat);
    void calcFunctional(SelfData &sdat);
    void calcForce(InteractionData &idat);
    virtual string getName() { return name_; }
    virtual int getHash() { return EAM_INTERACTION; }
    virtual RealType getSuggestedCutoffRadius(pair<AtomType*,AtomType*> atypes);
    void setCutoffRadius( RealType rCut );


  private:
    void initialize();  
    CubicSpline* getPhi(AtomType* atomType1, AtomType* atomType2);
    
    bool initialized_;
    bool haveCutoffRadius_;
    set<int> EAMtypes;         /**< The set of AtomType idents that are EAM types */
    vector<int> EAMtids;       /**< The mapping from AtomType ident -> EAM type ident */
    vector<EAMAtomData> EAMdata; /**< The EAM atomic data indexed by EAM type ident */
    vector<vector<EAMInteractionData> > MixingMap;  /**< The mixing parameters between two EAM types */
    int nEAM_;

    ForceField* forceField_;
    set<AtomType*> simTypes_;
    RealType pre11_;
    RealType eamRcut_;
    EAMMixingMethod mixMeth_;    
    string name_;
    
  };
}

                               
#endif
Revision:	1928
Committed:	Sat Aug 17 13:03:17 2013 UTC (11 years, 11 months ago) by gezelter
File size:	4246 byte(s)
Log Message:	Fixed a few bugs in EAM and Electrostatic.
#	User	Rev	Content
1	gezelter	1478	/*
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	1478	*/
42
43			#ifndef NONBONDED_EAM_HPP
44			#define NONBONDED_EAM_HPP
45
46	gezelter	1502	#include "nonbonded/NonBondedInteraction.hpp"
47	gezelter	1710	#include "types/EAMAdapter.hpp"
48	gezelter	1725	#include "brains/ForceField.hpp"
49	gezelter	1478	#include "math/Vector3.hpp"
50			#include "math/CubicSpline.hpp"
51
52			namespace OpenMD {
53
54			struct EAMAtomData {
55	gezelter	1479	CubicSpline* rho;
56			CubicSpline* F;
57			CubicSpline* Z;
58	gezelter	1478	RealType rcut;
59	gezelter	1927	bool isFluctuating;
60			RealType qToRhoScaling;
61	gezelter	1478	};
62
63			struct EAMInteractionData {
64	gezelter	1479	CubicSpline* phi;
65	gezelter	1928	RealType rcut;
66	gezelter	1478	bool explicitlySet;
67			};
68
69			enum EAMMixingMethod{
70			eamJohnson,
71			eamDaw,
72			eamUnknown
73			};
74
75	gezelter	1502	class EAM : public MetallicInteraction {
76	gezelter	1478
77			public:
78	gezelter	1502	EAM();
79			void setForceField(ForceField *ff) {forceField_ = ff;};
80	gezelter	1895	void setSimulatedAtomTypes(set<AtomType*> &simtypes) {simTypes_ = simtypes;};
81	gezelter	1502	void addType(AtomType* atomType);
82			void addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType dr, int nr, std::vector<RealType> phiAB);
83	gezelter	1545	void calcDensity(InteractionData &idat);
84			void calcFunctional(SelfData &sdat);
85	gezelter	1536	void calcForce(InteractionData &idat);
86	gezelter	1502	virtual string getName() { return name_; }
87	gezelter	1927	virtual int getHash() { return EAM_INTERACTION; }
88	gezelter	1545	virtual RealType getSuggestedCutoffRadius(pair<AtomType,AtomType> atypes);
89	gezelter	1586	void setCutoffRadius( RealType rCut );
90	gezelter	1478
91	gezelter	1586
92	gezelter	1478	private:
93	gezelter	1502	void initialize();
94			CubicSpline* getPhi(AtomType* atomType1, AtomType* atomType2);
95	gezelter	1478
96	gezelter	1502	bool initialized_;
97	gezelter	1586	bool haveCutoffRadius_;
98	gezelter	1895	set<int> EAMtypes; /*< The set of AtomType idents that are EAM types /
99			vector<int> EAMtids; /*< The mapping from AtomType ident -> EAM type ident /
100			vector<EAMAtomData> EAMdata; /*< The EAM atomic data indexed by EAM type ident /
101			vector<vector<EAMInteractionData> > MixingMap; /*< The mixing parameters between two EAM types /
102			int nEAM_;
103
104	gezelter	1502	ForceField* forceField_;
105	gezelter	1895	set<AtomType*> simTypes_;
106	gezelter	1927	RealType pre11_;
107	gezelter	1502	RealType eamRcut_;
108			EAMMixingMethod mixMeth_;
109			string name_;
110	gezelter	1478
111			};
112			}
113
114
115			#endif