src/nonbonded/InteractionManager.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_INTERACTIONMANAGER_HPP
#define NONBONDED_INTERACTIONMANAGER_HPP

#include "brains/SimInfo.hpp"
#include "types/AtomType.hpp"
#include "nonbonded/LJ.hpp"
#include "nonbonded/GB.hpp"
#include "nonbonded/Sticky.hpp"
#include "nonbonded/EAM.hpp"
#include "nonbonded/SC.hpp"
#include "nonbonded/Morse.hpp"
#include "nonbonded/Electrostatic.hpp"
#include "nonbonded/MAW.hpp"
#include "nonbonded/RepulsivePower.hpp"
#include "nonbonded/SwitchingFunction.hpp"
#include "flucq/FluctuatingChargeForces.hpp"

using namespace std;

namespace OpenMD {

  /**
   * @class InteractionManager 
   * InteractionManager is responsible for
   * keeping track of the non-bonded interactions (C++)
   */
  class InteractionManager {

  public:
    InteractionManager();
    virtual ~InteractionManager();
    void setSimInfo(SimInfo* info) {info_ = info;} 
    void initialize();

    // Fortran support routines

    void doPrePair(InteractionData &idat);
    void doPreForce(SelfData &sdat);
    void doPair(InteractionData &idat);    
    void doSkipCorrection(InteractionData &idat);
    void doSelfCorrection(SelfData &sdat);
    void doReciprocalSpaceSum(RealType &recipPot);
    void setCutoffRadius(RealType rCut);
    RealType getSuggestedCutoffRadius(int *atid1);   
    RealType getSuggestedCutoffRadius(AtomType *atype);
    
  private:
    bool initialized_;

    void setupElectrostatics();

    SimInfo* info_;
    LJ* lj_;
    GB* gb_;
    Sticky* sticky_;
    EAM* eam_;
    SC* sc_;
    Morse* morse_;
    Electrostatic* electrostatic_;
    RepulsivePower* repulsivePower_;
    MAW* maw_;
    FluctuatingChargeForces* flucq_;
    
    map<int, AtomType*> typeMap_;
    /**
     * Each pair of atom types can have multiple interactions, so the
     * natural data structures are a map between the pair, and a set
     * of non-bonded interactions:
     *
     *  map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > interactions_;
     *
     * Pair creation turns out to be inefficient, and map searching
     * isn't necessary.  Instead of AtomType* sort keys, we now use
     * the AtomType idents (atids) which are ints to access the vector
     * locations.  iHash_ contains largely the same information as
     * interactions_, but in a way that doesn't require a set iterator
     * inside the main pair loop.
     */
    vector<vector<set<NonBondedInteraction*> > > interactions_;
    vector<vector<int> > iHash_;

    /* sHash_ contains the self-interaction version of iHash_ */
    vector<int> sHash_;
  };
}
#endif
Revision:	1969
Committed:	Wed Feb 26 14:14:50 2014 UTC (11 years, 3 months ago) by gezelter
File size:	4732 byte(s)
Log Message:	Fixes to deal with deprecation of MPI C++ bindings. We've reverted back to the C calls.
#	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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#ifndef NONBONDED_INTERACTIONMANAGER_HPP
44	#define NONBONDED_INTERACTIONMANAGER_HPP
45
46	#include "brains/SimInfo.hpp"
47	#include "types/AtomType.hpp"
48	#include "nonbonded/LJ.hpp"
49	#include "nonbonded/GB.hpp"
50	#include "nonbonded/Sticky.hpp"
51	#include "nonbonded/EAM.hpp"
52	#include "nonbonded/SC.hpp"
53	#include "nonbonded/Morse.hpp"
54	#include "nonbonded/Electrostatic.hpp"
55	#include "nonbonded/MAW.hpp"
56	#include "nonbonded/RepulsivePower.hpp"
57	#include "nonbonded/SwitchingFunction.hpp"
58	#include "flucq/FluctuatingChargeForces.hpp"
59
60	using namespace std;
61
62	namespace OpenMD {
63
64	/**
65	* @class InteractionManager
66	* InteractionManager is responsible for
67	* keeping track of the non-bonded interactions (C++)
68	*/
69	class InteractionManager {
70
71	public:
72	InteractionManager();
73	virtual ~InteractionManager();
74	void setSimInfo(SimInfo* info) {info_ = info;}
75	void initialize();
76
77	// Fortran support routines
78
79	void doPrePair(InteractionData &idat);
80	void doPreForce(SelfData &sdat);
81	void doPair(InteractionData &idat);
82	void doSkipCorrection(InteractionData &idat);
83	void doSelfCorrection(SelfData &sdat);
84	void doReciprocalSpaceSum(RealType &recipPot);
85	void setCutoffRadius(RealType rCut);
86	RealType getSuggestedCutoffRadius(int *atid1);
87	RealType getSuggestedCutoffRadius(AtomType *atype);
88
89	private:
90	bool initialized_;
91
92	void setupElectrostatics();
93
94	SimInfo* info_;
95	LJ* lj_;
96	GB* gb_;
97	Sticky* sticky_;
98	EAM* eam_;
99	SC* sc_;
100	Morse* morse_;
101	Electrostatic* electrostatic_;
102	RepulsivePower* repulsivePower_;
103	MAW* maw_;
104	FluctuatingChargeForces* flucq_;
105
106	map<int, AtomType*> typeMap_;
107	/**
108	* Each pair of atom types can have multiple interactions, so the
109	* natural data structures are a map between the pair, and a set
110	* of non-bonded interactions:
111	*
112	* map<pair<AtomType, AtomType>, set<NonBondedInteraction*> > interactions_;
113	*
114	* Pair creation turns out to be inefficient, and map searching
115	* isn't necessary. Instead of AtomType* sort keys, we now use
116	* the AtomType idents (atids) which are ints to access the vector
117	* locations. iHash_ contains largely the same information as
118	* interactions_, but in a way that doesn't require a set iterator
119	* inside the main pair loop.
120	*/
121	vector<vector<set<NonBondedInteraction*> > > interactions_;
122	vector<vector<int> > iHash_;
123
124	/* sHash_ contains the self-interaction version of iHash_ */
125	vector<int> sHash_;
126	};
127	}
128	#endif