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"

namespace OpenMD {

  struct ElectrostaticAtomData {
    bool is_Charge;
    bool is_Dipole;
    bool is_Quadrupole;
    bool is_Fluctuating;
    RealType fixedCharge;
    RealType hardness;
    RealType electronegativity;
    int slaterN;
    RealType slaterZeta;
    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) {forceField_ = ff;};
    void setSimulatedAtomTypes(set<AtomType*> &simtypes) {simTypes_ = 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_;
    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 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;
    
    // 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:	1925
Committed:	Wed Aug 7 15:24:16 2013 UTC (11 years, 11 months ago) by gezelter
File size:	8217 byte(s)
Log Message:	More ewald fixes, reporting reciprocal potential in stats.
#	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	1502
53			namespace OpenMD {
54
55			struct ElectrostaticAtomData {
56			bool is_Charge;
57			bool is_Dipole;
58			bool is_Quadrupole;
59	gezelter	1718	bool is_Fluctuating;
60			RealType fixedCharge;
61			RealType hardness;
62			RealType electronegativity;
63	gezelter	1767	int slaterN;
64	gezelter	1718	RealType slaterZeta;
65	gezelter	1879	Vector3d dipole;
66			Mat3x3d quadrupole;
67	gezelter	1502	};
68	gezelter	1718
69	gezelter	1502	enum ElectrostaticSummationMethod{
70	gezelter	1528	esm_HARD,
71			esm_SWITCHING_FUNCTION,
72			esm_SHIFTED_POTENTIAL,
73			esm_SHIFTED_FORCE,
74	gezelter	1879	esm_TAYLOR_SHIFTED,
75	gezelter	1528	esm_REACTION_FIELD,
76	gezelter	1915	esm_EWALD_FULL,
77			esm_EWALD_PME, /*< PME Ewald methods aren't supported yet /
78			esm_EWALD_SPME /*< SPME Ewald methods aren't supported yet /
79	gezelter	1502	};
80
81			enum ElectrostaticScreeningMethod{
82			UNDAMPED,
83			DAMPED
84			};
85
86			class Electrostatic : public ElectrostaticInteraction {
87
88			public:
89			Electrostatic();
90			void setForceField(ForceField *ff) {forceField_ = ff;};
91	gezelter	1895	void setSimulatedAtomTypes(set<AtomType*> &simtypes) {simTypes_ = simtypes;};
92	gezelter	1584	void setSimInfo(SimInfo* info) {info_ = info;};
93	gezelter	1502	void addType(AtomType* atomType);
94	gezelter	1536	virtual void calcForce(InteractionData &idat);
95	gezelter	1545	virtual void calcSelfCorrection(SelfData &sdat);
96	gezelter	1502	virtual string getName() {return name_;}
97	gezelter	1545	virtual RealType getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes);
98	gezelter	1584	void setCutoffRadius( RealType rCut );
99	gezelter	1502	void setElectrostaticSummationMethod( ElectrostaticSummationMethod esm );
100			void setElectrostaticScreeningMethod( ElectrostaticScreeningMethod sm );
101			void setDampingAlpha( RealType alpha );
102			void setReactionFieldDielectric( RealType dielectric );
103	gezelter	1925	void ReciprocalSpaceSum(RealType &pot);
104	gezelter	1502
105			private:
106			void initialize();
107			string name_;
108			bool initialized_;
109	gezelter	1528	bool haveCutoffRadius_;
110	gezelter	1502	bool haveDampingAlpha_;
111			bool haveDielectric_;
112	gezelter	1879	bool haveElectroSplines_;
113	gezelter	1895
114			int nElectro_;
115			int nFlucq_;
116
117			set<int> Etypes; /*< The set of AtomType idents that are Electrostatic types /
118			vector<int> Etids; /*< The mapping from AtomType ident -> Electrostatic ident /
119			set<int> FQtypes; /*< The set of AtomType idents that are fluctuating types /
120			vector<int> FQtids; /*< The mapping from AtomType ident -> fluctuating ident /
121			vector<ElectrostaticAtomData> ElectrostaticMap; /*< data about Electrostatic types /
122			vector<vector<CubicSpline> > Jij; /< Coulomb integral for two fq types /
123
124
125	gezelter	1584	SimInfo* info_;
126	gezelter	1502	ForceField* forceField_;
127	gezelter	1895	set<AtomType*> simTypes_;
128	gezelter	1528	RealType cutoffRadius_;
129	gezelter	1502	RealType pre11_;
130			RealType pre12_;
131			RealType pre22_;
132			RealType pre14_;
133	gezelter	1879	RealType pre24_;
134			RealType pre44_;
135			RealType v01, v11, v21, v22, v31, v32, v41, v42, v43;
136			RealType dv01, dv11, dv21, dv22, dv31, dv32, dv41, dv42, dv43;
137			RealType v01or, v11or, v21or, v22or, v31or, v32or, v41or, v42or, v43or;
138	gezelter	1502	RealType chargeToC_;
139			RealType angstromToM_;
140			RealType debyeToCm_;
141			int np_;
142			ElectrostaticSummationMethod summationMethod_;
143			ElectrostaticScreeningMethod screeningMethod_;
144	gezelter	1528	map<string, ElectrostaticSummationMethod> summationMap_;
145			map<string, ElectrostaticScreeningMethod> screeningMap_;
146	gezelter	1502	RealType dampingAlpha_;
147			RealType dielectric_;
148			RealType preRF_;
149	gezelter	1900	RealType selfMult1_;
150			RealType selfMult2_;
151			RealType selfMult4_;
152	gezelter	1879
153			CubicSpline* v01s;
154			CubicSpline* v11s;
155			CubicSpline* v21s;
156			CubicSpline* v22s;
157			CubicSpline* v31s;
158			CubicSpline* v32s;
159			CubicSpline* v41s;
160			CubicSpline* v42s;
161			CubicSpline* v43s;
162
163	gezelter	1893	ElectrostaticAtomData data1;
164			ElectrostaticAtomData data2;
165			RealType C_a, C_b; // Charges
166			Vector3d D_a, D_b; // Dipoles (space-fixed)
167			Mat3x3d Q_a, Q_b; // Quadrupoles (space-fixed)
168
169			RealType ri; // Distance utility scalar
170			RealType rdDa, rdDb; // Dipole utility scalars
171			Vector3d rxDa, rxDb; // Dipole utility vectors
172			RealType rdQar, rdQbr, trQa, trQb; // Quadrupole utility scalars
173			Vector3d Qar, Qbr, rQa, rQb, rxQar, rxQbr; // Quadrupole utility vectors
174			RealType pref;
175
176			RealType DadDb, trQaQb, DadQbr, DbdQar; // Cross-interaction scalars
177			RealType rQaQbr;
178			Vector3d DaxDb, DadQb, DbdQa, DaxQbr, DbxQar; // Cross-interaction vectors
179			Vector3d rQaQb, QaQbr, QaxQb, rQaxQbr;
180			Mat3x3d QaQb; // Cross-interaction matrices
181
182			RealType U; // Potential
183			Vector3d F; // Force
184			Vector3d Ta; // Torque on site a
185			Vector3d Tb; // Torque on site b
186			Vector3d Ea; // Electric field at site a
187			Vector3d Eb; // Electric field at site b
188			RealType dUdCa; // fluctuating charge force at site a
189			RealType dUdCb; // fluctuating charge force at site a
190
191			// Indirect interactions mediated by the reaction field.
192			RealType indirect_Pot; // Potential
193			Vector3d indirect_F; // Force
194			Vector3d indirect_Ta; // Torque on site a
195			Vector3d indirect_Tb; // Torque on site b
196
197			// Excluded potential that is still computed for fluctuating charges
198			RealType excluded_Pot;
199
200			RealType rfContrib, coulInt;
201
202			// spline for coulomb integral
203			CubicSpline* J;
204			Vector3d rhat;
205
206			// logicals
207
208			bool a_is_Charge;
209			bool a_is_Dipole;
210			bool a_is_Quadrupole;
211			bool a_is_Fluctuating;
212
213			bool b_is_Charge;
214			bool b_is_Dipole;
215			bool b_is_Quadrupole;
216			bool b_is_Fluctuating;
217
218
219	gezelter	1879	/*
220			CubicSpline* dv01s;
221			CubicSpline* dv11s;
222			CubicSpline* dv21s;
223			CubicSpline* dv22s;
224			CubicSpline* dv31s;
225			CubicSpline* dv32s;
226			CubicSpline* dv41s;
227			CubicSpline* dv42s;
228			CubicSpline* dv43s;
229			*/
230	gezelter	1502	};
231			}
232
233
234			#endif