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 = 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
  };

  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 */
    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) */
    RealType* vdwMult;        /**< multiplier for van der Waals interactions */
    RealType* electroMult;    /**< multiplier for electrostatic interactions */
    potVec* pot;              /**< total potential */
    RealType* vpair;          /**< pair potential */
    RealType* particlePot1;   /**< pointer to particle potential for atom1 */
    RealType* particlePot2;   /**< pointer to particle potential for atom2 */
    Vector3d* f1;             /**< force between the two atoms */
    Mat3x3d* eFrame1;         /**< pointer to electrostatic frame for atom 1 */
    Mat3x3d* eFrame2;         /**< pointer to electrostatic frame for atom 2 */
    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;           /**< 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* skippedCharge1; /**< charge skipped on atom1 in pairwise interaction loop with atom2 */
    RealType* skippedCharge2; /**< charge skipped on atom2 in pairwise interaction loop with atom1 */
  };

  /* Read and write values */
  struct InteractionDataPrv {
        bool shiftedPot;          /**< shift the potential up inside the cutoff? */
                bool shiftedForce;        /**< shifted forces smoothly inside the cutoff? */

        /* Write values */
        RealType sw;             /**< switching function value at rij */
    potVec pot;              /**< total potential */
    RealType vpair;          /**< pair potential */
    Vector3d f1;             /**< force between the two atoms */

    bool excluded;            /**< is this excluded from *direct* pairwise interactions? (some indirect interactions may still apply) */
    pair<AtomType*, AtomType*> atypes; /**< pair of atom types interacting */
    RotMat3x3d* A1;           /**< pointer to rotation matrix of first atom */
                RotMat3x3d* A2;           /**< pointer to rotation matrix of second atom */
                Mat3x3d* eFrame1;         /**< pointer to electrostatic frame for atom 1 */
                Mat3x3d* eFrame2;         /**< pointer to electrostatic frame for atom 2 */
                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* particlePot1;   /**< pointer to particle potential for atom1 */
                RealType* particlePot2;   /**< pointer to particle potential for atom2 */
    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 vdwMult;        /**< multiplier for van der Waals interactions */
                RealType electroMult;    /**< multiplier for electrostatic interactions */
                Vector3d d;              /**< interatomic vector (already wrapped into box) */
                RealType r2;             /**< square of rij */
                RealType rij;            /**< interatomic separation */

    /* Read values */
    RealType rcut;           /**< cutoff radius for this interaction */
    int* topoDist;            /**< topological distance between atoms */
  };

  /** 
   * 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 */
    Mat3x3d* eFrame;        /**< pointer to electrostatic frame for atom */
    RealType* skippedCharge;/**< charge skipped in pairwise interaction loop */
    potVec* pot;            /**< total potential */
    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 */
  };
  
    
  /**
   * The basic interface for non-bonded interactions.  
   */
  class NonBondedInteraction {
  public:
    NonBondedInteraction() {}
    virtual ~NonBondedInteraction() {}
    virtual void initForce() = 0;
    virtual void calcForce(InteractionData &idat) = 0;
    virtual InteractionFamily getFamily() = 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;}    
  };    

  /**
   * 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:	1614
Committed:	Tue Aug 23 20:55:51 2011 UTC (13 years, 11 months ago) by mciznick
File size:	11307 byte(s)
Log Message:	Updated scalability of OpenMP threads.
#	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 = 0, /*< No family defined /
60	VANDERWAALS_FAMILY = 1, /*< Long-range dispersion and short-range pauli repulsion /
61	ELECTROSTATIC_FAMILY = 2, /*< Coulombic and point-multipole interactions /
62	METALLIC_FAMILY = 3, /*< Transition metal interactions involving electron density /
63	HYDROGENBONDING_FAMILY = 4,/*< Short-range directional interactions /
64	N_INTERACTION_FAMILIES = 5
65	};
66
67	typedef Vector<RealType, N_INTERACTION_FAMILIES> potVec;
68
69	/**
70	* The InteractionData struct.
71	*
72	* This is used to pass pointers to data to specific non-bonded
73	* interactions for force calculations. Not all of the struct
74	* members are utilized by any given interaction.
75	*/
76	struct InteractionData {
77	pair<AtomType, AtomType> atypes; /*< pair of atom types interacting /
78	Vector3d* d; /*< interatomic vector (already wrapped into box) /
79	RealType* rij; /*< interatomic separation /
80	RealType* r2; /*< square of rij /
81	RealType* rcut; /*< cutoff radius for this interaction /
82	bool shiftedPot; /*< shift the potential up inside the cutoff? /
83	bool shiftedForce; /*< shifted forces smoothly inside the cutoff? /
84	RealType* sw; /*< switching function value at rij /
85	int* topoDist; /*< topological distance between atoms /
86	bool excluded; /*< is this excluded from direct* pairwise interactions? (some indirect interactions may still apply) */
87	RealType* vdwMult; /*< multiplier for van der Waals interactions /
88	RealType* electroMult; /*< multiplier for electrostatic interactions /
89	potVec* pot; /*< total potential /
90	RealType* vpair; /*< pair potential /
91	RealType* particlePot1; /*< pointer to particle potential for atom1 /
92	RealType* particlePot2; /*< pointer to particle potential for atom2 /
93	Vector3d* f1; /*< force between the two atoms /
94	Mat3x3d* eFrame1; /*< pointer to electrostatic frame for atom 1 /
95	Mat3x3d* eFrame2; /*< pointer to electrostatic frame for atom 2 /
96	RotMat3x3d* A1; /*< pointer to rotation matrix of first atom /
97	RotMat3x3d* A2; /*< pointer to rotation matrix of second atom /
98	Vector3d* t1; /*< pointer to torque on first atom /
99	Vector3d* t2; /*< pointer to torque on second atom /
100	RealType* rho1; /*< total electron density at first atom /
101	RealType* rho2; /*< total electron density at second atom /
102	RealType* frho1; /*< density functional at first atom /
103	RealType* frho2; /*< density functional at second atom /
104	RealType* dfrho1; /*< derivative of functional for atom 1 /
105	RealType* dfrho2; /*< derivative of functional for atom 2 /
106	RealType* skippedCharge1; /*< charge skipped on atom1 in pairwise interaction loop with atom2 /
107	RealType* skippedCharge2; /*< charge skipped on atom2 in pairwise interaction loop with atom1 /
108	};
109
110	/* Read and write values */
111	struct InteractionDataPrv {
112	bool shiftedPot; /*< shift the potential up inside the cutoff? /
113	bool shiftedForce; /*< shifted forces smoothly inside the cutoff? /
114
115	/* Write values */
116	RealType sw; /*< switching function value at rij /
117	potVec pot; /*< total potential /
118	RealType vpair; /*< pair potential /
119	Vector3d f1; /*< force between the two atoms /
120
121	bool excluded; /*< is this excluded from direct* pairwise interactions? (some indirect interactions may still apply) */
122	pair<AtomType, AtomType> atypes; /*< pair of atom types interacting /
123	RotMat3x3d* A1; /*< pointer to rotation matrix of first atom /
124	RotMat3x3d* A2; /*< pointer to rotation matrix of second atom /
125	Mat3x3d* eFrame1; /*< pointer to electrostatic frame for atom 1 /
126	Mat3x3d* eFrame2; /*< pointer to electrostatic frame for atom 2 /
127	Vector3d* t1; /*< pointer to torque on first atom /
128	Vector3d* t2; /*< pointer to torque on second atom /
129	RealType* rho1; /*< total electron density at first atom /
130	RealType* rho2; /*< total electron density at second atom /
131	RealType* frho1; /*< density functional at first atom /
132	RealType* frho2; /*< density functional at second atom /
133	RealType* dfrho1; /*< derivative of functional for atom 1 /
134	RealType* dfrho2; /*< derivative of functional for atom 2 /
135	RealType* particlePot1; /*< pointer to particle potential for atom1 /
136	RealType* particlePot2; /*< pointer to particle potential for atom2 /
137	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
140	RealType vdwMult; /*< multiplier for van der Waals interactions /
141	RealType electroMult; /*< multiplier for electrostatic interactions /
142	Vector3d d; /*< interatomic vector (already wrapped into box) /
143	RealType r2; /*< square of rij /
144	RealType rij; /*< interatomic separation /
145
146	/* Read values */
147	RealType rcut; /*< cutoff radius for this interaction /
148	int* topoDist; /*< topological distance between atoms /
149	};
150
151	/**
152	* The SelfData struct.
153	*
154	* This is used to pass pointers to data for the self-interaction or
155	* derived information on a single atom after a pass through all
156	* other interactions. This is used by electrostatic methods that
157	* have long-range corrections involving interactions with a medium
158	* or a boundary and also by specific metal interactions for
159	* electron density functional calculations. Not all of the struct
160	* members are utilized by any given self interaction.
161	*/
162	struct SelfData {
163	AtomType* atype; /*< pointer to AtomType of the atom /
164	Mat3x3d* eFrame; /*< pointer to electrostatic frame for atom /
165	RealType* skippedCharge;/*< charge skipped in pairwise interaction loop /
166	potVec* pot; /*< total potential /
167	RealType* particlePot; /*< contribution to potential from this particle /
168	Vector3d* t; /*< pointer to resultant torque on atom /
169	RealType* rho; /*< electron density /
170	RealType* frho; /*< value of density functional for atom /
171	RealType* dfrhodrho; /*< derivative of density functional for atom /
172	};
173
174
175	/**
176	* The basic interface for non-bonded interactions.
177	*/
178	class NonBondedInteraction {
179	public:
180	NonBondedInteraction() {}
181	virtual ~NonBondedInteraction() {}
182	virtual void initForce() = 0;
183	virtual void calcForce(InteractionData &idat) = 0;
184	virtual InteractionFamily getFamily() = 0;
185	virtual RealType getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) = 0;
186	virtual string getName() = 0;
187	};
188
189	/**
190	* The basic interface for van der Waals interactions.
191	*/
192	class VanDerWaalsInteraction : public NonBondedInteraction {
193	public:
194	VanDerWaalsInteraction() : NonBondedInteraction() { }
195	virtual ~VanDerWaalsInteraction() {}
196	virtual InteractionFamily getFamily() {return VANDERWAALS_FAMILY;}
197	};
198
199	/**
200	* The basic interface for electrostatic interactions.
201	*/
202	class ElectrostaticInteraction : public NonBondedInteraction {
203	public:
204	ElectrostaticInteraction() : NonBondedInteraction() { }
205	virtual ~ElectrostaticInteraction() {}
206	virtual void calcSelfCorrection(SelfData &sdat) = 0;
207	virtual InteractionFamily getFamily() {return ELECTROSTATIC_FAMILY;}
208	};
209
210	/**
211	* The basic interface for metallic interactions.
212	*/
213	class MetallicInteraction : public NonBondedInteraction {
214	public:
215	MetallicInteraction() : NonBondedInteraction() { }
216	virtual ~MetallicInteraction() {}
217	virtual void calcDensity(InteractionData &idat) = 0;
218	virtual void calcFunctional(SelfData &sdat) = 0;
219	virtual InteractionFamily getFamily() {return METALLIC_FAMILY;}
220	};
221
222	/**
223	* The basic interface for hydrogen bonding interactions.
224	*/
225	class HydrogenBondingInteraction : public NonBondedInteraction {
226	public:
227	HydrogenBondingInteraction() : NonBondedInteraction() { }
228	virtual ~HydrogenBondingInteraction() {}
229	virtual InteractionFamily getFamily() {return HYDROGENBONDING_FAMILY;}
230	};
231
232	} //end namespace OpenMD
233	#endif