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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 3 months ago) by gezelter
File size:	4181 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	2204	class ZconstraintForceManager : public ForceManager {
53			public:
54			ZconstraintForceManager(SimInfo* info);
55			~ZconstraintForceManager();
56	gezelter	1930
57	gezelter	2204	virtual void calcForces(bool needPotential, bool needStress);
58	gezelter	1930
59	gezelter	2204	double getZConsTime() { return zconsTime_; }
60			std::string getZConsOutput() { return zconsOutput_; }
61	gezelter	1930
62	gezelter	2204	void update();
63			virtual void init();
64			private:
65	gezelter	1930
66	gezelter	2204	bool isZMol(Molecule* mol);
67			void thermalize(void);
68	gezelter	1930
69	gezelter	2204	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	gezelter	1930
84	gezelter	2204	std::list<ZconstraintMol> movingZMols_; /*< moving zconstraint molecules/
85			std::list<ZconstraintMol> fixedZMols_; /*< fixed zconstraint molecules/
86			std::vector<Molecule> unzconsMols_; /< free molecules/
87	gezelter	1930
88	gezelter	2204	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	gezelter	1930
97	gezelter	2204	const static int whichDirection = 2;
98	gezelter	1930
99	gezelter	2204	std::map<int, ZconstraintParam> allZMolIndices_;
100	gezelter	1930
101	gezelter	2204	Snapshot* currSnapshot_;
102			double currZconsTime_;
103	gezelter	1930
104	gezelter	2204	double totMassMovingZMols_;
105			double totMassUnconsMols_; /*< mass of unconstraint molecules in the whole system (never change) /
106	gezelter	1930
107	gezelter	2204	ZConsWriter* fzOut;
108			const double infiniteTime;
109			};
110	gezelter	1930
111			}
112			#endif