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;
  };
  
  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:	1929
Committed:	Mon Aug 19 13:12:00 2013 UTC (11 years, 11 months ago) by gezelter
File size:	4193 byte(s)
Log Message:	Backing out fluc-rho and putting back the Electrostatic fluctuating charge with coulomb integrals for atoms within a region.
#	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_EAM_HPP
44	#define NONBONDED_EAM_HPP
45
46	#include "nonbonded/NonBondedInteraction.hpp"
47	#include "types/EAMAdapter.hpp"
48	#include "brains/ForceField.hpp"
49	#include "math/Vector3.hpp"
50	#include "math/CubicSpline.hpp"
51
52	namespace OpenMD {
53
54	struct EAMAtomData {
55	CubicSpline* rho;
56	CubicSpline* F;
57	CubicSpline* Z;
58	RealType rcut;
59	};
60
61	struct EAMInteractionData {
62	CubicSpline* phi;
63	RealType rcut;
64	bool explicitlySet;
65	};
66
67	enum EAMMixingMethod{
68	eamJohnson,
69	eamDaw,
70	eamUnknown
71	};
72
73	class EAM : public MetallicInteraction {
74
75	public:
76	EAM();
77	void setForceField(ForceField *ff) {forceField_ = ff;};
78	void setSimulatedAtomTypes(set<AtomType*> &simtypes) {simTypes_ = simtypes;};
79	void addType(AtomType* atomType);
80	void addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType dr, int nr, std::vector<RealType> phiAB);
81	void calcDensity(InteractionData &idat);
82	void calcFunctional(SelfData &sdat);
83	void calcForce(InteractionData &idat);
84	virtual string getName() { return name_; }
85	virtual int getHash() { return EAM_INTERACTION; }
86	virtual RealType getSuggestedCutoffRadius(pair<AtomType,AtomType> atypes);
87	void setCutoffRadius( RealType rCut );
88
89	private:
90	void initialize();
91	CubicSpline* getPhi(AtomType* atomType1, AtomType* atomType2);
92
93	bool initialized_;
94	bool haveCutoffRadius_;
95	set<int> EAMtypes; /*< The set of AtomType idents that are EAM types /
96	vector<int> EAMtids; /*< The mapping from AtomType ident -> EAM type ident /
97	vector<EAMAtomData> EAMdata; /*< The EAM atomic data indexed by EAM type ident /
98	vector<vector<EAMInteractionData> > MixingMap; /*< The mixing parameters between two EAM types /
99	int nEAM_;
100
101	ForceField* forceField_;
102	set<AtomType*> simTypes_;
103	RealType pre11_;
104	RealType eamRcut_;
105	EAMMixingMethod mixMeth_;
106	string name_;
107
108	};
109	}
110
111
112	#endif