src/constraints/ZconstraintForceManager.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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#ifndef CONSTRAINTS_ZCONSTRAINTFORCEMANAGER_HPP
#define CONSTRAINTS_ZCONSTRAINTFORCEMANAGER_HPP
#include <list>
#include <string>
#include <vector>
#include "brains/ForceManager.hpp"
#include "constraints/ZconsStruct.hpp"
#include "io/ZConsWriter.hpp"
namespace oopse {

class ZconstraintForceManager : public ForceManager {
    public:
        ZconstraintForceManager(SimInfo* info);
        ~ZconstraintForceManager();
        
        virtual void calcForces(bool needPotential, bool needStress);

        double getZConsTime() { return zconsTime_; }
        std::string getZConsOutput() { return zconsOutput_; }    

        void update();
        virtual void init();
    private:

        bool isZMol(Molecule* mol);
        void thermalize(void);

        void zeroVelocity();
        void doZconstraintForce();
        void doHarmonic();
        bool checkZConsState();        
        void updateZPos();
        void updateCantPos();
        void calcTotalMassMovingZMols();
        bool haveMovingZMols();
        bool haveFixedZMols();
        double getZTargetPos(int index);        
        double getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce) ;
        double getZFOfMovingMols(Molecule* mol, double totalForce) ;
        double getHFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce);
        double getHFOfUnconsMols(Molecule* mol, double totalForce);        

        std::list<ZconstraintMol> movingZMols_;  /**<   moving zconstraint molecules*/
        std::list<ZconstraintMol> fixedZMols_;      /**< fixed zconstraint molecules*/
        std::vector<Molecule*> unzconsMols_;    /**< free molecules*/

        double zconsTime_;
        std::string zconsOutput_;
        double zconsTol_;
        bool usingSMD_;
        double zconsFixingTime_;  
        double zconsGap_;
        bool usingZconsGap_;
        double dt_;

        const static int whichDirection = 2;

        std::map<int, ZconstraintParam> allZMolIndices_;

        Snapshot* currSnapshot_;
        double currZconsTime_;

        double totMassMovingZMols_;
        double totMassUnconsMols_;  /**< mass of unconstraint molecules in the whole system (never change) */

        ZConsWriter* fzOut;
        const double infiniteTime;
};

}
#endif 
Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	4350 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	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. 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
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	#ifndef CONSTRAINTS_ZCONSTRAINTFORCEMANAGER_HPP
43	#define CONSTRAINTS_ZCONSTRAINTFORCEMANAGER_HPP
44	#include <list>
45	#include <string>
46	#include <vector>
47	#include "brains/ForceManager.hpp"
48	#include "constraints/ZconsStruct.hpp"
49	#include "io/ZConsWriter.hpp"
50	namespace oopse {
51
52	class ZconstraintForceManager : public ForceManager {
53	public:
54	ZconstraintForceManager(SimInfo* info);
55	~ZconstraintForceManager();
56
57	virtual void calcForces(bool needPotential, bool needStress);
58
59	double getZConsTime() { return zconsTime_; }
60	std::string getZConsOutput() { return zconsOutput_; }
61
62	void update();
63	virtual void init();
64	private:
65
66	bool isZMol(Molecule* mol);
67	void thermalize(void);
68
69	void zeroVelocity();
70	void doZconstraintForce();
71	void doHarmonic();
72	bool checkZConsState();
73	void updateZPos();
74	void updateCantPos();
75	void calcTotalMassMovingZMols();
76	bool haveMovingZMols();
77	bool haveFixedZMols();
78	double getZTargetPos(int index);
79	double getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce) ;
80	double getZFOfMovingMols(Molecule* mol, double totalForce) ;
81	double getHFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce);
82	double getHFOfUnconsMols(Molecule* mol, double totalForce);
83
84	std::list<ZconstraintMol> movingZMols_; /*< moving zconstraint molecules/
85	std::list<ZconstraintMol> fixedZMols_; /*< fixed zconstraint molecules/
86	std::vector<Molecule> unzconsMols_; /< free molecules/
87
88	double zconsTime_;
89	std::string zconsOutput_;
90	double zconsTol_;
91	bool usingSMD_;
92	double zconsFixingTime_;
93	double zconsGap_;
94	bool usingZconsGap_;
95	double dt_;
96
97	const static int whichDirection = 2;
98
99	std::map<int, ZconstraintParam> allZMolIndices_;
100
101	Snapshot* currSnapshot_;
102	double currZconsTime_;
103
104	double totMassMovingZMols_;
105	double totMassUnconsMols_; /*< mass of unconstraint molecules in the whole system (never change) /
106
107	ZConsWriter* fzOut;
108	const double infiniteTime;
109	};
110
111	}
112	#endif