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. 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 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 OpenMD {

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

    RealType 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();
    RealType getZTargetPos(int index);        
    RealType getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce) ;
    RealType getZFOfMovingMols(Molecule* mol, RealType totalForce) ;
    RealType getHFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce);
    RealType getHFOfUnconsMols(Molecule* mol, RealType totalForce);        

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

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

    const static int whichDirection = 2;

    std::map<int, ZconstraintParam> allZMolIndices_;

    Snapshot* currSnapshot_;
    RealType currZconsTime_;

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

    ZConsWriter* fzOut;
    const RealType infiniteTime;
  };

}
#endif 
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/constraints/ZconstraintForceManager.hpp*
File size:	4261 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	246	*/
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	gezelter	1390	namespace OpenMD {
51	gezelter	246
52	gezelter	507	class ZconstraintForceManager : public ForceManager {
53			public:
54			ZconstraintForceManager(SimInfo* info);
55			~ZconstraintForceManager();
56	gezelter	246
57	gezelter	507	virtual void calcForces(bool needPotential, bool needStress);
58	gezelter	246
59	tim	963	RealType getZConsTime() { return zconsTime_; }
60	gezelter	507	std::string getZConsOutput() { return zconsOutput_; }
61	gezelter	246
62	gezelter	507	void update();
63			virtual void init();
64			private:
65	gezelter	246
66	gezelter	507	bool isZMol(Molecule* mol);
67			void thermalize(void);
68	gezelter	246
69	gezelter	507	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	tim	963	RealType getZTargetPos(int index);
79			RealType getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce) ;
80			RealType getZFOfMovingMols(Molecule* mol, RealType totalForce) ;
81			RealType getHFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce);
82			RealType getHFOfUnconsMols(Molecule* mol, RealType totalForce);
83	gezelter	246
84	gezelter	507	std::list<ZconstraintMol> movingZMols_; /*< moving zconstraint molecules/
85			std::list<ZconstraintMol> fixedZMols_; /*< fixed zconstraint molecules/
86			std::vector<Molecule> unzconsMols_; /< free molecules/
87	gezelter	246
88	tim	963	RealType zconsTime_;
89	gezelter	507	std::string zconsOutput_;
90	tim	963	RealType zconsTol_;
91	gezelter	507	bool usingSMD_;
92	tim	963	RealType zconsFixingTime_;
93			RealType zconsGap_;
94	gezelter	507	bool usingZconsGap_;
95	tim	963	RealType dt_;
96	gezelter	246
97	gezelter	507	const static int whichDirection = 2;
98	gezelter	246
99	gezelter	507	std::map<int, ZconstraintParam> allZMolIndices_;
100	gezelter	246
101	gezelter	507	Snapshot* currSnapshot_;
102	tim	963	RealType currZconsTime_;
103	gezelter	246
104	tim	963	RealType totMassMovingZMols_;
105			RealType totMassUnconsMols_; /*< mass of unconstraint molecules in the whole system (never change) /
106	gezelter	246
107	gezelter	507	ZConsWriter* fzOut;
108	tim	963	const RealType infiniteTime;
109	gezelter	507	};
110	gezelter	246
111			}
112			#endif