ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/trunk/src/brains/ForceManager.hpp

Comparing trunk/src/brains/ForceManager.hpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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	<	/**
44	<	* @file ForceManager.hpp
45	<	* @author tlin
46	<	* @date 11/09/2004
47	<	* @time 10:36am
48	<	* @version 1.0
48	<	*/
43	>	/**
44	>	* @file ForceManager.hpp
45	>	* @author tlin
46	>	* @date 11/09/2004
47	>	* @version 1.0
48	>	*/
49
50		#ifndef BRAINS_FORCEMANAGER_HPP
51		#define BRAINS_FORCEMANAGER_HPP
52
53		#include "brains/SimInfo.hpp"
54	+	#include "primitives/Molecule.hpp"
55	+	#include "nonbonded/Cutoffs.hpp"
56	+	#include "nonbonded/SwitchingFunction.hpp"
57	+	#include "nonbonded/InteractionManager.hpp"
58	+	#include "perturbations/Perturbation.hpp"
59	+	#include "parallel/ForceDecomposition.hpp"
60	+	#include "brains/Thermo.hpp"
61
62	<	namespace oopse {
62	>	#define PREPAIR_LOOP 0
63	>	#define PAIR_LOOP 1
64
65	<	/**
66	<	* @class ForceManager ForceManager.hpp "brains/ForceManager.hpp"
67	<	* ForceManager is responsible for calculating the short range interactions (c++) and
68	<	* long range interactions(fortran). If fortran side is not setup before the force calculation,
69	<	* call SimInfo's update function to settle it down.
70	<	* @note the reason we delay fortran side's setup is that some applications (Dump2XYZ etc.)
71	<	* may not need force calculation, why bother?
72	<	*/
73	<	class ForceManager {
65	>	using namespace std;
66	>	namespace OpenMD {
67	>	/**
68	>	* @class ForceManager ForceManager.hpp "brains/ForceManager.hpp"
69	>	* ForceManager is responsible for calculating both the short range
70	>	* (bonded) interactions and long range (non-bonded) interactions.
71	>	*
72	>	* @note the reason we delay some of the setup is that
73	>	* initialization must wait until after the force field has been
74	>	* parsed so that the atom types are known.
75	>	*/
76	>	class ForceManager {
77
78	<	public:
79	<	ForceManager(SimInfo * info) : info_(info) {}
80	<
81	<	virtual ~ForceManager() {}
78	>	public:
79	>	ForceManager(SimInfo * info);
80	>	virtual ~ForceManager();
81	>	virtual void calcForces();
82	>	void initialize();
83
84	<	//public virtual function should be avoided
85	<	/**@todo need refactory */
86	<	virtual void calcForces(bool needPotential, bool needStress);
84	>	protected:
85	>	bool initialized_;
86	>	bool doParticlePot_;
87	>	bool doElectricField_;
88	>	bool doSitePotential_;
89	>	bool doHeatFlux_;
90	>	bool doLongRangeCorrections_;
91	>	bool usePeriodicBoundaryConditions_;
92
93	<	virtual void init() {}
94	<	protected:
93	>	virtual void setupCutoffs();
94	>	virtual void preCalculation();
95	>	virtual void shortRangeInteractions();
96	>	virtual void longRangeInteractions();
97	>	virtual void postCalculation();
98
99	<	virtual void preCalculation();
100	<
101	<	virtual void calcShortRangeInteraction();
99	>	SimInfo* info_;
100	>	ForceField* forceField_;
101	>	InteractionManager* interactionMan_;
102	>	ForceDecomposition* fDecomp_;
103	>	SwitchingFunction* switcher_;
104	>	Thermo* thermo;
105
106	<	virtual void calcLongRangeInteraction(bool needPotential, bool needStress);
106	>	SwitchingFunctionType sft_;/**< Type of switching function in use */
107	>	RealType rCut_;            /**< cutoff radius for non-bonded interactions */
108	>	RealType rSwitch_;         /**< inner radius of switching function */
109	>	CutoffMethod cutoffMethod_;/**< Cutoff Method for most non-bonded interactions */
110	>	CutoffPolicy cutoffPolicy_;/**< Cutoff Policy for non-bonded interactions */
111
112	<	virtual void postCalculation();
113	<
114	<	SimInfo * info_;
112	>	set<AtomType*> atomTypes_;
113	>	vector<pair<AtomType*, AtomType*> > interactions_;
114	>	map<Bend*, BendDataSet> bendDataSets;
115	>	map<Torsion*, TorsionDataSet> torsionDataSets;
116	>	map<Inversion*, InversionDataSet> inversionDataSets;
117	>	vector<pair<int, int> > neighborList_;
118
119	<	};
119	>	vector<RealType> vdwScale_;
120	>	vector<RealType> electrostaticScale_;
121
122	<	} //end namespace oopse
122	>	Mat3x3d stressTensor;
123	>
124	>	vector<Perturbation*> perturbations_;
125	>	};
126	>	}
127		#endif //BRAINS_FORCEMANAGER_HPP

Comparing trunk/src/brains/ForceManager.hpp (property svn:keywords):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines