src/nonbonded/NonBondedInteraction.hpp

/*
 * Copyright (c) 2005 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_NONBONDEDINTERACTION_HPP
#define NONBONDED_NONBONDEDINTERACTION_HPP

#include "types/AtomType.hpp"
#include "math/SquareMatrix3.hpp"

using namespace std;
namespace OpenMD {

  /** 
   * The InteractionFamily enum.
   *
   * This is used to sort different types of non-bonded interaction
   * and to prevent multiple interactions in the same family from
   * being applied to any given pair of atom types.
   */
  enum InteractionFamily {
    NO_FAMILY = 0,             /**< No family defined */
    VANDERWAALS_FAMILY = 1,    /**< Long-range dispersion and short-range pauli repulsion */
    ELECTROSTATIC_FAMILY = 2,  /**< Coulombic and point-multipole interactions */
    METALLIC_FAMILY = 3,       /**< Transition metal interactions involving electron density */
    HYDROGENBONDING_FAMILY = 4,/**< Short-range directional interactions */
    N_INTERACTION_FAMILIES = 5
  };

  /**
   * Boolean flags for the iHash_ and sHash_ data structures. These
   * are used to greatly increase the speed of looking up the
   * low-level interaction for any given pair:
   */
  const static int ELECTROSTATIC_INTERACTION  = (1 << 0);  
  const static int LJ_INTERACTION             = (1 << 1);
  const static int EAM_INTERACTION            = (1 << 2);
  const static int SC_INTERACTION             = (1 << 3);
  const static int STICKY_INTERACTION         = (1 << 4);
  const static int GB_INTERACTION             = (1 << 5);
  const static int MORSE_INTERACTION          = (1 << 6);
  const static int REPULSIVEPOWER_INTERACTION = (1 << 7);
  const static int MAW_INTERACTION            = (1 << 8);

  typedef Vector<RealType, N_INTERACTION_FAMILIES> potVec;

  /**
   * The InteractionData struct.  
   *
   * This is used to pass pointers to data to specific non-bonded
   * interactions for force calculations.  Not all of the struct
   * members are utilized by any given interaction.
   */
  struct InteractionData {
    //pair<AtomType*, AtomType*> atypes; /**< pair of atom types interacting */
    int atid1;                /**< atomType ident for atom 1 */
    int atid2;                /**< atomType ident for atom 2 */
    Vector3d* d;              /**< interatomic vector (already wrapped into box) */
    RealType* rij;            /**< interatomic separation */
    RealType* r2;             /**< square of rij */
    RealType* rcut;           /**< cutoff radius for this interaction */
    bool shiftedPot;          /**< shift the potential up inside the cutoff? */
    bool shiftedForce;        /**< shifted forces smoothly inside the cutoff? */
    RealType* sw;             /**< switching function value at rij */
    int* topoDist;            /**< topological distance between atoms */
    bool excluded;            /**< is this excluded from *direct* pairwise interactions? (some indirect interactions may still apply) */
    bool sameRegion;          /**< are these atoms specified to be in the same region? */ 
    RealType* vdwMult;        /**< multiplier for van der Waals interactions */
    RealType* electroMult;    /**< multiplier for electrostatic interactions */
    potVec* pot;              /**< total potential */
    potVec* excludedPot;      /**< potential energy excluded from the overall calculation */
    RealType* vpair;          /**< pair potential */
    bool doParticlePot;       /**< should we bother with the particle pot? */
    bool doElectricField;     /**< should we bother with the electric field? */
    bool doSitePotential;     /**< should we bother with electrostatic site potential */
    RealType* particlePot1;   /**< pointer to particle potential for atom1 */
    RealType* particlePot2;   /**< pointer to particle potential for atom2 */
    Vector3d* f1;             /**< force between the two atoms */
    RotMat3x3d* A1;           /**< pointer to rotation matrix of first atom */
    RotMat3x3d* A2;           /**< pointer to rotation matrix of second atom */
    Vector3d* dipole1;        /**< pointer to dipole vector of first atom */
    Vector3d* dipole2;        /**< pointer to dipole vector of first atom */
    Mat3x3d* quadrupole1;     /**< pointer to quadrupole tensor of first atom */
    Mat3x3d* quadrupole2;     /**< pointer to quadrupole tensor of first atom */
    Vector3d* t1;             /**< pointer to torque on first atom */
    Vector3d* t2;             /**< pointer to torque on second atom */
    RealType* rho1;           /**< total electron density at first atom */
    RealType* rho2;           /**< total electron density at second atom */
    RealType* frho1;          /**< density functional at first atom */
    RealType* frho2;          /**< density functional at second atom */
    RealType* dfrho1;         /**< derivative of functional for atom 1 */
    RealType* dfrho2;         /**< derivative of functional for atom 2 */
    RealType* flucQ1;         /**< fluctuating charge on atom1 */
    RealType* flucQ2;         /**< fluctuating charge on atom2 */
    RealType* dVdFQ1;         /**< fluctuating charge force on atom1 */
    RealType* dVdFQ2;         /**< fluctuating charge force on atom2 */
    Vector3d* eField1;        /**< pointer to electric field on first atom */
    Vector3d* eField2;        /**< pointer to electric field on second atom */
    RealType* skippedCharge1; /**< charge skipped on atom1 in pairwise interaction loop with atom2 */
    RealType* skippedCharge2; /**< charge skipped on atom2 in pairwise interaction loop with atom1 */
    RealType* sPot1;           /**< site potential on first atom */
    RealType* sPot2;           /**< site potential on second atom */
  };
  
  /** 
   * The SelfData struct.
   * 
   * This is used to pass pointers to data for the self-interaction or
   * derived information on a single atom after a pass through all
   * other interactions.  This is used by electrostatic methods that
   * have long-range corrections involving interactions with a medium
   * or a boundary and also by specific metal interactions for
   * electron density functional calculations.  Not all of the struct
   * members are utilized by any given self interaction.
   */
  struct SelfData {
    //AtomType* atype;        /**< pointer to AtomType of the atom */
    int atid;               /**< atomType ident for the atom */
    Vector3d* dipole;       /**< pointer to dipole vector of the atom */
    Mat3x3d* quadrupole;    /**< pointer to quadrupole tensor of the atom */
    RealType* skippedCharge;/**< charge skipped in pairwise interaction loop */
    potVec* pot;            /**< total potential */
    potVec* excludedPot;    /**< potential energy excluded from the overall calculation */
    bool doParticlePot;     /**< should we bother with the particle pot? */
    RealType* particlePot;  /**< contribution to potential from this particle */
    Vector3d* t;            /**< pointer to resultant torque on atom */
    RealType* rho;          /**< electron density */
    RealType* frho;         /**< value of density functional for atom */
    RealType* dfrhodrho;    /**< derivative of density functional for atom */
    RealType* flucQ;        /**< current value of atom's fluctuating charge */
    RealType* flucQfrc;     /**< fluctuating charge derivative */
  };
  
    
  /**
   * The basic interface for non-bonded interactions.  
   */
  class NonBondedInteraction {
  public:
    NonBondedInteraction() {}
    virtual ~NonBondedInteraction() {}
    virtual void calcForce(InteractionData &idat) = 0;
    virtual InteractionFamily getFamily() = 0;
    virtual int getHash() = 0;
    virtual RealType getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) = 0;
    virtual string getName() =  0;
  };    

  /**
   * The basic interface for van der Waals interactions.
   */
  class VanDerWaalsInteraction : public NonBondedInteraction {
  public:
    VanDerWaalsInteraction() : NonBondedInteraction() { }
    virtual ~VanDerWaalsInteraction() {}
    virtual InteractionFamily getFamily() {return VANDERWAALS_FAMILY;}
  };    

  /**
   * The basic interface for electrostatic interactions.
   */
  class ElectrostaticInteraction : public NonBondedInteraction {
  public:
    ElectrostaticInteraction() : NonBondedInteraction() { }
    virtual ~ElectrostaticInteraction() {}
    virtual void calcSelfCorrection(SelfData &sdat) = 0;
    virtual InteractionFamily getFamily() {return ELECTROSTATIC_FAMILY;}   
    virtual int getHash() {return ELECTROSTATIC_INTERACTION;}
  };    

  /**
   * The basic interface for metallic interactions.
   */
  class MetallicInteraction : public NonBondedInteraction {
  public:
    MetallicInteraction() : NonBondedInteraction() { }
    virtual ~MetallicInteraction() {}
    virtual void calcDensity(InteractionData &idat) = 0;
    virtual void calcFunctional(SelfData &sdat) = 0;
    virtual InteractionFamily getFamily() {return METALLIC_FAMILY;}
  };
          
  /**
   * The basic interface for hydrogen bonding interactions.
   */
  class HydrogenBondingInteraction : public NonBondedInteraction {
  public:
    HydrogenBondingInteraction() : NonBondedInteraction() { }
    virtual ~HydrogenBondingInteraction() {}
    virtual InteractionFamily getFamily() {return HYDROGENBONDING_FAMILY;}
  };    

} //end namespace OpenMD
#endif
Revision:	1993
Committed:	Tue Apr 29 17:32:31 2014 UTC (11 years, 3 months ago) by gezelter
File size:	11434 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) 2005 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_NONBONDEDINTERACTION_HPP
44			#define NONBONDED_NONBONDEDINTERACTION_HPP
45
46			#include "types/AtomType.hpp"
47			#include "math/SquareMatrix3.hpp"
48
49			using namespace std;
50			namespace OpenMD {
51
52			/**
53			* The InteractionFamily enum.
54			*
55			* This is used to sort different types of non-bonded interaction
56			* and to prevent multiple interactions in the same family from
57			* being applied to any given pair of atom types.
58			*/
59			enum InteractionFamily {
60	gezelter	1582	NO_FAMILY = 0, /*< No family defined /
61			VANDERWAALS_FAMILY = 1, /*< Long-range dispersion and short-range pauli repulsion /
62			ELECTROSTATIC_FAMILY = 2, /*< Coulombic and point-multipole interactions /
63			METALLIC_FAMILY = 3, /*< Transition metal interactions involving electron density /
64			HYDROGENBONDING_FAMILY = 4,/*< Short-range directional interactions /
65			N_INTERACTION_FAMILIES = 5
66	gezelter	1502	};
67
68	gezelter	1895	/**
69	gezelter	1927	* Boolean flags for the iHash_ and sHash_ data structures. These
70			* are used to greatly increase the speed of looking up the
71			* low-level interaction for any given pair:
72	gezelter	1895	*/
73	gezelter	1927	const static int ELECTROSTATIC_INTERACTION = (1 << 0);
74			const static int LJ_INTERACTION = (1 << 1);
75			const static int EAM_INTERACTION = (1 << 2);
76			const static int SC_INTERACTION = (1 << 3);
77			const static int STICKY_INTERACTION = (1 << 4);
78			const static int GB_INTERACTION = (1 << 5);
79			const static int MORSE_INTERACTION = (1 << 6);
80			const static int REPULSIVEPOWER_INTERACTION = (1 << 7);
81			const static int MAW_INTERACTION = (1 << 8);
82	gezelter	1895
83	gezelter	1554	typedef Vector<RealType, N_INTERACTION_FAMILIES> potVec;
84
85	gezelter	1502	/**
86			* The InteractionData struct.
87			*
88	gezelter	1554	* This is used to pass pointers to data to specific non-bonded
89			* interactions for force calculations. Not all of the struct
90			* members are utilized by any given interaction.
91	gezelter	1502	*/
92			struct InteractionData {
93	gezelter	1930	//pair<AtomType, AtomType> atypes; /*< pair of atom types interacting /
94	gezelter	1895	int atid1; /*< atomType ident for atom 1 /
95			int atid2; /*< atomType ident for atom 2 /
96	gezelter	1554	Vector3d* d; /*< interatomic vector (already wrapped into box) /
97			RealType* rij; /*< interatomic separation /
98			RealType* r2; /*< square of rij /
99			RealType* rcut; /*< cutoff radius for this interaction /
100	gezelter	1583	bool shiftedPot; /*< shift the potential up inside the cutoff? /
101			bool shiftedForce; /*< shifted forces smoothly inside the cutoff? /
102	gezelter	1554	RealType* sw; /*< switching function value at rij /
103			int* topoDist; /*< topological distance between atoms /
104	gezelter	1587	bool excluded; /*< is this excluded from direct* pairwise interactions? (some indirect interactions may still apply) */
105	gezelter	1929	bool sameRegion; /*< are these atoms specified to be in the same region? /
106	gezelter	1554	RealType* vdwMult; /*< multiplier for van der Waals interactions /
107			RealType* electroMult; /*< multiplier for electrostatic interactions /
108			potVec* pot; /*< total potential /
109	gezelter	1760	potVec* excludedPot; /*< potential energy excluded from the overall calculation /
110	gezelter	1554	RealType* vpair; /*< pair potential /
111	gezelter	1711	bool doParticlePot; /*< should we bother with the particle pot? /
112	gezelter	1879	bool doElectricField; /*< should we bother with the electric field? /
113	gezelter	1993	bool doSitePotential; /*< should we bother with electrostatic site potential /
114	gezelter	1575	RealType* particlePot1; /*< pointer to particle potential for atom1 /
115			RealType* particlePot2; /*< pointer to particle potential for atom2 /
116	gezelter	1554	Vector3d* f1; /*< force between the two atoms /
117			RotMat3x3d* A1; /*< pointer to rotation matrix of first atom /
118			RotMat3x3d* A2; /*< pointer to rotation matrix of second atom /
119	gezelter	1879	Vector3d* dipole1; /*< pointer to dipole vector of first atom /
120			Vector3d* dipole2; /*< pointer to dipole vector of first atom /
121			Mat3x3d* quadrupole1; /*< pointer to quadrupole tensor of first atom /
122			Mat3x3d* quadrupole2; /*< pointer to quadrupole tensor of first atom /
123	gezelter	1554	Vector3d* t1; /*< pointer to torque on first atom /
124			Vector3d* t2; /*< pointer to torque on second atom /
125			RealType* rho1; /*< total electron density at first atom /
126			RealType* rho2; /*< total electron density at second atom /
127	gezelter	1575	RealType* frho1; /*< density functional at first atom /
128			RealType* frho2; /*< density functional at second atom /
129			RealType* dfrho1; /*< derivative of functional for atom 1 /
130			RealType* dfrho2; /*< derivative of functional for atom 2 /
131	gezelter	1721	RealType* flucQ1; /*< fluctuating charge on atom1 /
132			RealType* flucQ2; /*< fluctuating charge on atom2 /
133			RealType* dVdFQ1; /*< fluctuating charge force on atom1 /
134			RealType* dVdFQ2; /*< fluctuating charge force on atom2 /
135			Vector3d* eField1; /*< pointer to electric field on first atom /
136			Vector3d* eField2; /*< pointer to electric field on second atom /
137	gezelter	1587	RealType* skippedCharge1; /*< charge skipped on atom1 in pairwise interaction loop with atom2 /
138			RealType* skippedCharge2; /*< charge skipped on atom2 in pairwise interaction loop with atom1 /
139	gezelter	1993	RealType* sPot1; /*< site potential on first atom /
140			RealType* sPot2; /*< site potential on second atom /
141	gezelter	1502	};
142	gezelter	1545
143	gezelter	1502	/**
144	gezelter	1545	* The SelfData struct.
145	gezelter	1502	*
146	gezelter	1554	* This is used to pass pointers to data for the self-interaction or
147			* derived information on a single atom after a pass through all
148			* other interactions. This is used by electrostatic methods that
149			* have long-range corrections involving interactions with a medium
150			* or a boundary and also by specific metal interactions for
151			* electron density functional calculations. Not all of the struct
152			* members are utilized by any given self interaction.
153	gezelter	1502	*/
154	gezelter	1545	struct SelfData {
155	gezelter	1930	//AtomType* atype; /*< pointer to AtomType of the atom /
156	gezelter	1895	int atid; /*< atomType ident for the atom /
157	gezelter	1879	Vector3d* dipole; /*< pointer to dipole vector of the atom /
158			Mat3x3d* quadrupole; /*< pointer to quadrupole tensor of the atom /
159	gezelter	1575	RealType* skippedCharge;/*< charge skipped in pairwise interaction loop /
160			potVec* pot; /*< total potential /
161	gezelter	1761	potVec* excludedPot; /*< potential energy excluded from the overall calculation /
162	gezelter	1711	bool doParticlePot; /*< should we bother with the particle pot? /
163	gezelter	1575	RealType* particlePot; /*< contribution to potential from this particle /
164			Vector3d* t; /*< pointer to resultant torque on atom /
165			RealType* rho; /*< electron density /
166			RealType* frho; /*< value of density functional for atom /
167			RealType* dfrhodrho; /*< derivative of density functional for atom /
168	jmichalk	1734	RealType* flucQ; /*< current value of atom's fluctuating charge /
169	gezelter	1929	RealType* flucQfrc; /*< fluctuating charge derivative /
170	gezelter	1502	};
171
172
173			/**
174			* The basic interface for non-bonded interactions.
175			*/
176			class NonBondedInteraction {
177			public:
178			NonBondedInteraction() {}
179			virtual ~NonBondedInteraction() {}
180	gezelter	1536	virtual void calcForce(InteractionData &idat) = 0;
181	gezelter	1502	virtual InteractionFamily getFamily() = 0;
182	gezelter	1895	virtual int getHash() = 0;
183	gezelter	1545	virtual RealType getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) = 0;
184	gezelter	1502	virtual string getName() = 0;
185			};
186
187			/**
188			* The basic interface for van der Waals interactions.
189			*/
190			class VanDerWaalsInteraction : public NonBondedInteraction {
191			public:
192			VanDerWaalsInteraction() : NonBondedInteraction() { }
193			virtual ~VanDerWaalsInteraction() {}
194			virtual InteractionFamily getFamily() {return VANDERWAALS_FAMILY;}
195			};
196
197			/**
198			* The basic interface for electrostatic interactions.
199			*/
200			class ElectrostaticInteraction : public NonBondedInteraction {
201			public:
202			ElectrostaticInteraction() : NonBondedInteraction() { }
203			virtual ~ElectrostaticInteraction() {}
204	gezelter	1545	virtual void calcSelfCorrection(SelfData &sdat) = 0;
205	gezelter	1895	virtual InteractionFamily getFamily() {return ELECTROSTATIC_FAMILY;}
206	gezelter	1927	virtual int getHash() {return ELECTROSTATIC_INTERACTION;}
207	gezelter	1502	};
208
209			/**
210			* The basic interface for metallic interactions.
211			*/
212			class MetallicInteraction : public NonBondedInteraction {
213			public:
214			MetallicInteraction() : NonBondedInteraction() { }
215			virtual ~MetallicInteraction() {}
216	gezelter	1545	virtual void calcDensity(InteractionData &idat) = 0;
217			virtual void calcFunctional(SelfData &sdat) = 0;
218	gezelter	1502	virtual InteractionFamily getFamily() {return METALLIC_FAMILY;}
219			};
220
221			/**
222			* The basic interface for hydrogen bonding interactions.
223			*/
224			class HydrogenBondingInteraction : public NonBondedInteraction {
225			public:
226			HydrogenBondingInteraction() : NonBondedInteraction() { }
227			virtual ~HydrogenBondingInteraction() {}
228			virtual InteractionFamily getFamily() {return HYDROGENBONDING_FAMILY;}
229			};
230
231			} //end namespace OpenMD
232			#endif