src/nonbonded/Electrostatic.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_ELECTROSTATIC_HPP
#define NONBONDED_ELECTROSTATIC_HPP

#include "nonbonded/NonBondedInteraction.hpp"
#include "types/AtomType.hpp"
#include "brains/ForceField.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/CubicSpline.hpp"
#include "brains/SimInfo.hpp"
#include "flucq/FluctuatingChargeForces.hpp"

namespace OpenMD {

  struct ElectrostaticAtomData {
    bool is_Charge;
    bool is_Dipole;
    bool is_Quadrupole;
    bool is_Fluctuating;
    bool has_MultipleMinima;
    RealType fixedCharge;
    RealType hardness;
    RealType electronegativity;
    int slaterN;
    RealType slaterZeta;
    RealType curvature;
    RealType coupling;
    vector<pair<int, RealType> > diabats;
    Vector3d dipole;
    Mat3x3d  quadrupole;
  };
      
  enum ElectrostaticSummationMethod{
    esm_HARD,
    esm_SWITCHING_FUNCTION,
    esm_SHIFTED_POTENTIAL,
    esm_SHIFTED_FORCE,
    esm_TAYLOR_SHIFTED,
    esm_REACTION_FIELD,
    esm_EWALD_FULL,  
    esm_EWALD_PME,   /**< PME  Ewald methods aren't supported yet */
    esm_EWALD_SPME   /**< SPME Ewald methods aren't supported yet */
  };

  enum ElectrostaticScreeningMethod{
    UNDAMPED,
    DAMPED
  };
  
  class Electrostatic : public ElectrostaticInteraction {
    
  public:    
    Electrostatic();
    void setForceField(ForceField *ff);
    void setSimulatedAtomTypes(set<AtomType*> &simtypes);
    void setSimInfo(SimInfo* info) {info_ = info;};
    void addType(AtomType* atomType);
    virtual void calcForce(InteractionData &idat);
    virtual void calcSelfCorrection(SelfData &sdat);
    virtual string getName() {return name_;}
    virtual RealType getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes);
    void setCutoffRadius( RealType rCut );
    void setElectrostaticSummationMethod( ElectrostaticSummationMethod esm );
    void setElectrostaticScreeningMethod( ElectrostaticScreeningMethod sm );
    void setDampingAlpha( RealType alpha );
    void setReactionFieldDielectric( RealType dielectric );
    void ReciprocalSpaceSum(RealType &pot);

  private:
    void initialize();
    string name_;
    bool initialized_;
    bool haveCutoffRadius_;
    bool haveDampingAlpha_;
    bool haveDielectric_;
    bool haveElectroSplines_;

    int nElectro_;
    int nFlucq_;

    set<int> Etypes;             /**< The set of AtomType idents that are Electrostatic types */
    vector<int> Etids;           /**< The mapping from AtomType ident -> Electrostatic ident */
    set<int> FQtypes;            /**< The set of AtomType idents that are fluctuating types */
    vector<int> FQtids;          /**< The mapping from AtomType ident -> fluctuating ident */
    vector<ElectrostaticAtomData> ElectrostaticMap; /**< data about Electrostatic types */
    vector<vector<CubicSpline*> > Jij;              /**< Coulomb integral for two fq types */
    

    SimInfo* info_;
    ForceField* forceField_;
    FluctuatingChargeForces* flucQ_;
    set<AtomType*> simTypes_;
    RealType cutoffRadius_;
    RealType pre11_;
    RealType pre12_;
    RealType pre22_;
    RealType pre14_;
    RealType pre24_;
    RealType pre44_;
    RealType v01, v11, v21, v22, v31, v32, v41, v42, v43;
    RealType dv01, dv11, dv21, dv22, dv31, dv32, dv41, dv42, dv43;
    RealType v01or, v11or, v21or, v22or, v31or, v32or, v41or, v42or, v43or;
    RealType chargeToC_;
    RealType angstromToM_;
    RealType debyeToCm_;
    int np_;
    ElectrostaticSummationMethod summationMethod_;    
    ElectrostaticScreeningMethod screeningMethod_;
    map<string, ElectrostaticSummationMethod> summationMap_;
    map<string, ElectrostaticScreeningMethod> screeningMap_;
    RealType dampingAlpha_;
    RealType dielectric_;
    RealType preRF_;
    RealType selfMult1_; 
    RealType selfMult2_;
    RealType selfMult4_;

    CubicSpline* v01s;
    CubicSpline* v11s;
    CubicSpline* v21s;
    CubicSpline* v22s;
    CubicSpline* v31s;
    CubicSpline* v32s;
    CubicSpline* v41s;
    CubicSpline* v42s;
    CubicSpline* v43s;

    ElectrostaticAtomData data1;
    ElectrostaticAtomData data2;
    RealType C_a, C_b;  // Charges 
    Vector3d D_a, D_b;  // Dipoles (space-fixed)
    Mat3x3d  Q_a, Q_b;  // Quadrupoles (space-fixed)

    RealType ri;                                 // Distance utility scalar
    RealType rdDa, rdDb;                         // Dipole utility scalars
    Vector3d rxDa, rxDb;                         // Dipole utility vectors
    RealType rdQar, rdQbr, trQa, trQb;           // Quadrupole utility scalars
    Vector3d Qar, Qbr, rQa, rQb, rxQar, rxQbr;   // Quadrupole utility vectors
    RealType pref;

    RealType DadDb, trQaQb, DadQbr, DbdQar;       // Cross-interaction scalars
    RealType rQaQbr;
    Vector3d DaxDb, DadQb, DbdQa, DaxQbr, DbxQar; // Cross-interaction vectors
    Vector3d rQaQb, QaQbr, QaxQb, rQaxQbr;
    Mat3x3d  QaQb;                                // Cross-interaction matrices

    RealType U;  // Potential
    Vector3d F;  // Force
    Vector3d Ta; // Torque on site a
    Vector3d Tb; // Torque on site b
    Vector3d Ea; // Electric field at site a
    Vector3d Eb; // Electric field at site b
    RealType Pa; // Site potential at site a
    RealType Pb; // Site potential at site b
    RealType dUdCa; // fluctuating charge force at site a
    RealType dUdCb; // fluctuating charge force at site a
    
    // Indirect interactions mediated by the reaction field.
    RealType indirect_Pot;  // Potential
    Vector3d indirect_F;    // Force
    Vector3d indirect_Ta;   // Torque on site a
    Vector3d indirect_Tb;   // Torque on site b

    // Excluded potential that is still computed for fluctuating charges
    RealType excluded_Pot;

    RealType rfContrib, coulInt, dJdr;
    
    // spline for coulomb integral
    CubicSpline* J;
    Vector3d rhat;
      
    // logicals

    bool a_is_Charge;
    bool a_is_Dipole;
    bool a_is_Quadrupole;
    bool a_is_Fluctuating;

    bool b_is_Charge;
    bool b_is_Dipole;
    bool b_is_Quadrupole;
    bool b_is_Fluctuating;


    /*
    CubicSpline* dv01s;
    CubicSpline* dv11s;
    CubicSpline* dv21s;
    CubicSpline* dv22s;
    CubicSpline* dv31s;
    CubicSpline* dv32s;
    CubicSpline* dv41s;
    CubicSpline* dv42s;
    CubicSpline* dv43s;
    */
  };
}

                               
#endif
Revision:	1993
Committed:	Tue Apr 29 17:32:31 2014 UTC (11 years, 3 months ago) by gezelter
File size:	8469 byte(s)
Log Message:	Added sitePotentials for the Choi et al. potential-frequency maps for nitriles
#	User	Rev	Content
1	gezelter	1502	/*
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	1502	*/
42
43			#ifndef NONBONDED_ELECTROSTATIC_HPP
44			#define NONBONDED_ELECTROSTATIC_HPP
45
46			#include "nonbonded/NonBondedInteraction.hpp"
47			#include "types/AtomType.hpp"
48	gezelter	1725	#include "brains/ForceField.hpp"
49	gezelter	1502	#include "math/SquareMatrix3.hpp"
50			#include "math/CubicSpline.hpp"
51	gezelter	1584	#include "brains/SimInfo.hpp"
52	gezelter	1969	#include "flucq/FluctuatingChargeForces.hpp"
53	gezelter	1502
54			namespace OpenMD {
55
56			struct ElectrostaticAtomData {
57			bool is_Charge;
58			bool is_Dipole;
59			bool is_Quadrupole;
60	gezelter	1718	bool is_Fluctuating;
61	gezelter	1969	bool has_MultipleMinima;
62	gezelter	1718	RealType fixedCharge;
63			RealType hardness;
64			RealType electronegativity;
65	gezelter	1767	int slaterN;
66	gezelter	1718	RealType slaterZeta;
67	gezelter	1969	RealType curvature;
68			RealType coupling;
69			vector<pair<int, RealType> > diabats;
70	gezelter	1879	Vector3d dipole;
71			Mat3x3d quadrupole;
72	gezelter	1502	};
73	gezelter	1718
74	gezelter	1502	enum ElectrostaticSummationMethod{
75	gezelter	1528	esm_HARD,
76			esm_SWITCHING_FUNCTION,
77			esm_SHIFTED_POTENTIAL,
78			esm_SHIFTED_FORCE,
79	gezelter	1879	esm_TAYLOR_SHIFTED,
80	gezelter	1528	esm_REACTION_FIELD,
81	gezelter	1915	esm_EWALD_FULL,
82			esm_EWALD_PME, /*< PME Ewald methods aren't supported yet /
83			esm_EWALD_SPME /*< SPME Ewald methods aren't supported yet /
84	gezelter	1502	};
85
86			enum ElectrostaticScreeningMethod{
87			UNDAMPED,
88			DAMPED
89			};
90
91			class Electrostatic : public ElectrostaticInteraction {
92
93			public:
94			Electrostatic();
95	gezelter	1969	void setForceField(ForceField *ff);
96			void setSimulatedAtomTypes(set<AtomType*> &simtypes);
97	gezelter	1584	void setSimInfo(SimInfo* info) {info_ = info;};
98	gezelter	1502	void addType(AtomType* atomType);
99	gezelter	1536	virtual void calcForce(InteractionData &idat);
100	gezelter	1545	virtual void calcSelfCorrection(SelfData &sdat);
101	gezelter	1502	virtual string getName() {return name_;}
102	gezelter	1545	virtual RealType getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes);
103	gezelter	1584	void setCutoffRadius( RealType rCut );
104	gezelter	1502	void setElectrostaticSummationMethod( ElectrostaticSummationMethod esm );
105			void setElectrostaticScreeningMethod( ElectrostaticScreeningMethod sm );
106			void setDampingAlpha( RealType alpha );
107			void setReactionFieldDielectric( RealType dielectric );
108	gezelter	1925	void ReciprocalSpaceSum(RealType &pot);
109	gezelter	1502
110			private:
111			void initialize();
112			string name_;
113			bool initialized_;
114	gezelter	1528	bool haveCutoffRadius_;
115	gezelter	1502	bool haveDampingAlpha_;
116			bool haveDielectric_;
117	gezelter	1879	bool haveElectroSplines_;
118	gezelter	1895
119			int nElectro_;
120			int nFlucq_;
121
122			set<int> Etypes; /*< The set of AtomType idents that are Electrostatic types /
123			vector<int> Etids; /*< The mapping from AtomType ident -> Electrostatic ident /
124			set<int> FQtypes; /*< The set of AtomType idents that are fluctuating types /
125			vector<int> FQtids; /*< The mapping from AtomType ident -> fluctuating ident /
126			vector<ElectrostaticAtomData> ElectrostaticMap; /*< data about Electrostatic types /
127			vector<vector<CubicSpline> > Jij; /< Coulomb integral for two fq types /
128
129
130	gezelter	1584	SimInfo* info_;
131	gezelter	1502	ForceField* forceField_;
132	gezelter	1969	FluctuatingChargeForces* flucQ_;
133	gezelter	1895	set<AtomType*> simTypes_;
134	gezelter	1528	RealType cutoffRadius_;
135	gezelter	1502	RealType pre11_;
136			RealType pre12_;
137			RealType pre22_;
138			RealType pre14_;
139	gezelter	1879	RealType pre24_;
140			RealType pre44_;
141			RealType v01, v11, v21, v22, v31, v32, v41, v42, v43;
142			RealType dv01, dv11, dv21, dv22, dv31, dv32, dv41, dv42, dv43;
143			RealType v01or, v11or, v21or, v22or, v31or, v32or, v41or, v42or, v43or;
144	gezelter	1502	RealType chargeToC_;
145			RealType angstromToM_;
146			RealType debyeToCm_;
147			int np_;
148			ElectrostaticSummationMethod summationMethod_;
149			ElectrostaticScreeningMethod screeningMethod_;
150	gezelter	1528	map<string, ElectrostaticSummationMethod> summationMap_;
151			map<string, ElectrostaticScreeningMethod> screeningMap_;
152	gezelter	1502	RealType dampingAlpha_;
153			RealType dielectric_;
154			RealType preRF_;
155	gezelter	1900	RealType selfMult1_;
156			RealType selfMult2_;
157			RealType selfMult4_;
158	gezelter	1879
159			CubicSpline* v01s;
160			CubicSpline* v11s;
161			CubicSpline* v21s;
162			CubicSpline* v22s;
163			CubicSpline* v31s;
164			CubicSpline* v32s;
165			CubicSpline* v41s;
166			CubicSpline* v42s;
167			CubicSpline* v43s;
168
169	gezelter	1893	ElectrostaticAtomData data1;
170			ElectrostaticAtomData data2;
171			RealType C_a, C_b; // Charges
172			Vector3d D_a, D_b; // Dipoles (space-fixed)
173			Mat3x3d Q_a, Q_b; // Quadrupoles (space-fixed)
174
175			RealType ri; // Distance utility scalar
176			RealType rdDa, rdDb; // Dipole utility scalars
177			Vector3d rxDa, rxDb; // Dipole utility vectors
178			RealType rdQar, rdQbr, trQa, trQb; // Quadrupole utility scalars
179			Vector3d Qar, Qbr, rQa, rQb, rxQar, rxQbr; // Quadrupole utility vectors
180			RealType pref;
181
182			RealType DadDb, trQaQb, DadQbr, DbdQar; // Cross-interaction scalars
183			RealType rQaQbr;
184			Vector3d DaxDb, DadQb, DbdQa, DaxQbr, DbxQar; // Cross-interaction vectors
185			Vector3d rQaQb, QaQbr, QaxQb, rQaxQbr;
186			Mat3x3d QaQb; // Cross-interaction matrices
187
188			RealType U; // Potential
189			Vector3d F; // Force
190			Vector3d Ta; // Torque on site a
191			Vector3d Tb; // Torque on site b
192			Vector3d Ea; // Electric field at site a
193			Vector3d Eb; // Electric field at site b
194	gezelter	1993	RealType Pa; // Site potential at site a
195			RealType Pb; // Site potential at site b
196	gezelter	1893	RealType dUdCa; // fluctuating charge force at site a
197			RealType dUdCb; // fluctuating charge force at site a
198
199			// Indirect interactions mediated by the reaction field.
200			RealType indirect_Pot; // Potential
201			Vector3d indirect_F; // Force
202			Vector3d indirect_Ta; // Torque on site a
203			Vector3d indirect_Tb; // Torque on site b
204
205			// Excluded potential that is still computed for fluctuating charges
206			RealType excluded_Pot;
207
208	gezelter	1932	RealType rfContrib, coulInt, dJdr;
209	gezelter	1893
210			// spline for coulomb integral
211			CubicSpline* J;
212			Vector3d rhat;
213
214			// logicals
215
216			bool a_is_Charge;
217			bool a_is_Dipole;
218			bool a_is_Quadrupole;
219			bool a_is_Fluctuating;
220
221			bool b_is_Charge;
222			bool b_is_Dipole;
223			bool b_is_Quadrupole;
224			bool b_is_Fluctuating;
225
226
227	gezelter	1879	/*
228			CubicSpline* dv01s;
229			CubicSpline* dv11s;
230			CubicSpline* dv21s;
231			CubicSpline* dv22s;
232			CubicSpline* dv31s;
233			CubicSpline* dv32s;
234			CubicSpline* dv41s;
235			CubicSpline* dv42s;
236			CubicSpline* dv43s;
237			*/
238	gezelter	1502	};
239			}
240
241
242			#endif