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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#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,             /**< No family defined */
    VANDERWAALS_FAMILY,    /**< Long-range dispersion and short-range pauli repulsion */
    ELECTROSTATIC_FAMILY,  /**< Coulombic and point-multipole interactions */
    METALLIC_FAMILY,       /**< Transition metal interactions involving electron density */
    HYDROGENBONDING_FAMILY /**< Short-range directional interactions */
  };

  /**
   * The InteractionData struct.  
   *
   * This is used to pass data to specific non-bonded interactions for
   * force calculations.  Not all of the struct members are utilized
   * by any given interaction.
   */
  struct InteractionData {
    AtomType* atype1;     /**< pointer to AtomType of first atom */
    AtomType* atype2;     /**< pointer to AtomType of second atom */
    Vector3d d;           /**< interatomic vector (already wrapped into box) */
    RealType rij;         /**< interatomic separation (precomputed) */
    RealType r2;          /**< square of rij (precomputed) */
    RealType rcut;        /**< cutoff radius for this interaction */
    RealType sw;          /**< switching function value at rij (precomputed) */
    RealType vdwMult;     /**< multiplier for van der Waals interactions */
    RealType electroMult; /**< multiplier for electrostatic interactions */
    RealType pot;         /**< total potential */
    RealType vpair;       /**< pair potential */
    Vector3d f1;         /**< force between the two atoms */
    Mat3x3d eFrame1;     /**< pointer to electrostatic frame for first atom */
    Mat3x3d eFrame2;     /**< pointer to electrostatic frame for second atom*/
    RotMat3x3d A1;       /**< pointer to rotation matrix of first atom */
    RotMat3x3d A2;       /**< pointer to rotation matrix of second atom */
    Vector3d t1;         /**< pointer to torque on first atom */
    Vector3d t2;         /**< pointer to torque on second atom */
    RealType rho1;        /**< electron density at first atom */
    RealType rho2;        /**< electron density at second atom */
    RealType dfrho1;      /**< derivative of density functional for atom 1 */
    RealType dfrho2;      /**< derivative of density functional for atom 2 */
    RealType fshift1;     /**< indirect potential contribution from atom 1 */
    RealType fshift2;     /**< indirect potential contribution from atom 2 */
  };
  
  /** 
   * The SkipCorrectionData struct.
   *
   * This is used to pass data for corrections due to "skipped" pairs
   * of atoms.  These are atoms that are topologically bonded to each
   * other, but which have indirect effects by way of long range
   * interactions.  In the normal pair interaction loop, these atoms
   * are skipped entirely, so a second pass must be made to compute
   * their indirect interactions on each other.
   */
  struct SkipCorrectionData {
    AtomType* atype1;         /**< pointer to AtomType of first atom */
    AtomType* atype2;         /**< pointer to AtomType of second atom */
    Vector3d d;               /**< interatomic vector (already wrapped into box) */
    RealType rij;             /**< interatomic separation (precomputed) */
    RealType skippedCharge1;  /**< charge skipped in normal pairwise interaction loop */
    RealType skippedCharge2;  /**< charge skipped in normal pairwise interaction loop */
    RealType sw;              /**< switching function value at rij (precomputed) */
    RealType electroMult;     /**< multiplier for electrostatic interactions */
    RealType pot;             /**< total potential */
    RealType vpair;           /**< pair potential */
    Vector3d f1;              /**< force correction */
    Mat3x3d eFrame1;         /**< pointer to electrostatic frame for first atom */
    Mat3x3d eFrame2;         /**< pointer to electrostatic frame for second atom*/
    Vector3d t1;             /**< pointer to torque on first atom */
    Vector3d t2;             /**< pointer to torque on second atom */
  };

  /** 
   * The SelfCorrectionData struct.
   * 
   * This is used to pass data for the self-interaction (used by
   * electrostatic methods) that have long-range corrections involving
   * interactions with a medium or a boundary.
   */
  struct SelfCorrectionData {
    AtomType* atype;        /**< pointer to AtomType of the atom */
    Mat3x3d eFrame;        /**< pointer to electrostatic frame for first atom */
    RealType skippedCharge; /**< charge skipped in normal pairwise interaction loop */
    RealType pot;           /**< total potential contribution */
    Vector3d t;            /**< pointer to resultant torque on atom */
  };


  /**
   * The DensityData struct.  
   *
   * This is used to pass data to specific metallic interactions for
   * electron density calculations.  
   */
  
  struct DensityData {
    AtomType* atype1;     /**< pointer to AtomType of first atom */
    AtomType* atype2;     /**< pointer to AtomType of second atom */
    RealType rij;         /**< interatomic separation (precomputed) */
    RealType rho_i_at_j;  /**< electron density at second atom due to first */
    RealType rho_j_at_i;  /**< electron density at first atom due to second */
  };
  
  /**
   * The FunctionalData struct.  
   *
   * This is used to pass data to specific metallic interactions for
   * electron density functional calculations.  
   */
  
  struct FunctionalData {
    AtomType* atype;     /**< pointer to AtomType of the atom */
    RealType rho;        /**< electron density (precomputed) */
    RealType frho;       /**< value of density functional for the atom */
    RealType dfrhodrho;  /**< derivative of density functional for the atom */
  };
    
  /**
   * The basic interface for non-bonded interactions.  
   */
  class NonBondedInteraction {
  public:
    NonBondedInteraction() {}
    virtual ~NonBondedInteraction() {}
    virtual void calcForce(InteractionData idat) = 0;
    virtual InteractionFamily getFamily() = 0;
    virtual RealType getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) = 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 calcSkipCorrection(SkipCorrectionData skdat) = 0;
    virtual void calcSelfCorrection(SelfCorrectionData scdat) = 0;
    virtual InteractionFamily getFamily() {return ELECTROSTATIC_FAMILY;}
  };    

  /**
   * The basic interface for metallic interactions.
   */
  class MetallicInteraction : public NonBondedInteraction {
  public:
    MetallicInteraction() : NonBondedInteraction() { }
    virtual ~MetallicInteraction() {}
    virtual void calcDensity(DensityData ddat) = 0;
    virtual void calcFunctional(FunctionalData fdat) = 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:	1505
Committed:	Sun Oct 3 22:18:59 2010 UTC (14 years, 9 months ago) by gezelter
File size:	10185 byte(s)
Log Message:	Less busted than it was on last check-in, but still won't completely build.
#	Content
1	/*
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	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#ifndef NONBONDED_NONBONDEDINTERACTION_HPP
43	#define NONBONDED_NONBONDEDINTERACTION_HPP
44
45	#include "types/AtomType.hpp"
46	#include "math/SquareMatrix3.hpp"
47
48	using namespace std;
49	namespace OpenMD {
50
51	/**
52	* The InteractionFamily enum.
53	*
54	* This is used to sort different types of non-bonded interaction
55	* and to prevent multiple interactions in the same family from
56	* being applied to any given pair of atom types.
57	*/
58	enum InteractionFamily {
59	NO_FAMILY, /*< No family defined /
60	VANDERWAALS_FAMILY, /*< Long-range dispersion and short-range pauli repulsion /
61	ELECTROSTATIC_FAMILY, /*< Coulombic and point-multipole interactions /
62	METALLIC_FAMILY, /*< Transition metal interactions involving electron density /
63	HYDROGENBONDING_FAMILY /*< Short-range directional interactions /
64	};
65
66	/**
67	* The InteractionData struct.
68	*
69	* This is used to pass data to specific non-bonded interactions for
70	* force calculations. Not all of the struct members are utilized
71	* by any given interaction.
72	*/
73	struct InteractionData {
74	AtomType* atype1; /*< pointer to AtomType of first atom /
75	AtomType* atype2; /*< pointer to AtomType of second atom /
76	Vector3d d; /*< interatomic vector (already wrapped into box) /
77	RealType rij; /*< interatomic separation (precomputed) /
78	RealType r2; /*< square of rij (precomputed) /
79	RealType rcut; /*< cutoff radius for this interaction /
80	RealType sw; /*< switching function value at rij (precomputed) /
81	RealType vdwMult; /*< multiplier for van der Waals interactions /
82	RealType electroMult; /*< multiplier for electrostatic interactions /
83	RealType pot; /*< total potential /
84	RealType vpair; /*< pair potential /
85	Vector3d f1; /*< force between the two atoms /
86	Mat3x3d eFrame1; /*< pointer to electrostatic frame for first atom /
87	Mat3x3d eFrame2; /*< pointer to electrostatic frame for second atom/
88	RotMat3x3d A1; /*< pointer to rotation matrix of first atom /
89	RotMat3x3d A2; /*< pointer to rotation matrix of second atom /
90	Vector3d t1; /*< pointer to torque on first atom /
91	Vector3d t2; /*< pointer to torque on second atom /
92	RealType rho1; /*< electron density at first atom /
93	RealType rho2; /*< electron density at second atom /
94	RealType dfrho1; /*< derivative of density functional for atom 1 /
95	RealType dfrho2; /*< derivative of density functional for atom 2 /
96	RealType fshift1; /*< indirect potential contribution from atom 1 /
97	RealType fshift2; /*< indirect potential contribution from atom 2 /
98	};
99
100	/**
101	* The SkipCorrectionData struct.
102	*
103	* This is used to pass data for corrections due to "skipped" pairs
104	* of atoms. These are atoms that are topologically bonded to each
105	* other, but which have indirect effects by way of long range
106	* interactions. In the normal pair interaction loop, these atoms
107	* are skipped entirely, so a second pass must be made to compute
108	* their indirect interactions on each other.
109	*/
110	struct SkipCorrectionData {
111	AtomType* atype1; /*< pointer to AtomType of first atom /
112	AtomType* atype2; /*< pointer to AtomType of second atom /
113	Vector3d d; /*< interatomic vector (already wrapped into box) /
114	RealType rij; /*< interatomic separation (precomputed) /
115	RealType skippedCharge1; /*< charge skipped in normal pairwise interaction loop /
116	RealType skippedCharge2; /*< charge skipped in normal pairwise interaction loop /
117	RealType sw; /*< switching function value at rij (precomputed) /
118	RealType electroMult; /*< multiplier for electrostatic interactions /
119	RealType pot; /*< total potential /
120	RealType vpair; /*< pair potential /
121	Vector3d f1; /*< force correction /
122	Mat3x3d eFrame1; /*< pointer to electrostatic frame for first atom /
123	Mat3x3d eFrame2; /*< pointer to electrostatic frame for second atom/
124	Vector3d t1; /*< pointer to torque on first atom /
125	Vector3d t2; /*< pointer to torque on second atom /
126	};
127
128	/**
129	* The SelfCorrectionData struct.
130	*
131	* This is used to pass data for the self-interaction (used by
132	* electrostatic methods) that have long-range corrections involving
133	* interactions with a medium or a boundary.
134	*/
135	struct SelfCorrectionData {
136	AtomType* atype; /*< pointer to AtomType of the atom /
137	Mat3x3d eFrame; /*< pointer to electrostatic frame for first atom /
138	RealType skippedCharge; /*< charge skipped in normal pairwise interaction loop /
139	RealType pot; /*< total potential contribution /
140	Vector3d t; /*< pointer to resultant torque on atom /
141	};
142
143
144
145	/**
146	* The DensityData struct.
147	*
148	* This is used to pass data to specific metallic interactions for
149	* electron density calculations.
150	*/
151
152	struct DensityData {
153	AtomType* atype1; /*< pointer to AtomType of first atom /
154	AtomType* atype2; /*< pointer to AtomType of second atom /
155	RealType rij; /*< interatomic separation (precomputed) /
156	RealType rho_i_at_j; /*< electron density at second atom due to first /
157	RealType rho_j_at_i; /*< electron density at first atom due to second /
158	};
159
160	/**
161	* The FunctionalData struct.
162	*
163	* This is used to pass data to specific metallic interactions for
164	* electron density functional calculations.
165	*/
166
167	struct FunctionalData {
168	AtomType* atype; /*< pointer to AtomType of the atom /
169	RealType rho; /*< electron density (precomputed) /
170	RealType frho; /*< value of density functional for the atom /
171	RealType dfrhodrho; /*< derivative of density functional for the atom /
172	};
173
174	/**
175	* The basic interface for non-bonded interactions.
176	*/
177	class NonBondedInteraction {
178	public:
179	NonBondedInteraction() {}
180	virtual ~NonBondedInteraction() {}
181	virtual void calcForce(InteractionData idat) = 0;
182	virtual InteractionFamily getFamily() = 0;
183	virtual RealType getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) = 0;
184	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	virtual void calcSkipCorrection(SkipCorrectionData skdat) = 0;
205	virtual void calcSelfCorrection(SelfCorrectionData scdat) = 0;
206	virtual InteractionFamily getFamily() {return ELECTROSTATIC_FAMILY;}
207	};
208
209	/**
210	* The basic interface for metallic interactions.
211	*/
212	class MetallicInteraction : public NonBondedInteraction {
213	public:
214	MetallicInteraction() : NonBondedInteraction() { }
215	virtual ~MetallicInteraction() {}
216	virtual void calcDensity(DensityData ddat) = 0;
217	virtual void calcFunctional(FunctionalData fdat) = 0;
218	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