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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#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();

    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:	1782
Committed:	Wed Aug 22 02:28:28 2012 UTC (12 years, 8 months ago) by gezelter
File size:	4292 byte(s)
Log Message:	MERGE OpenMD development branch 1465:1781 into trunk
#	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, 24107 (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 CONSTRAINTS_ZCONSTRAINTFORCEMANAGER_HPP
44	#define CONSTRAINTS_ZCONSTRAINTFORCEMANAGER_HPP
45	#include <list>
46	#include <string>
47	#include <vector>
48	#include "brains/ForceManager.hpp"
49	#include "constraints/ZconsStruct.hpp"
50	#include "io/ZConsWriter.hpp"
51	namespace OpenMD {
52
53	class ZconstraintForceManager : public ForceManager {
54	public:
55	ZconstraintForceManager(SimInfo* info);
56	~ZconstraintForceManager();
57
58	virtual void calcForces();
59
60	RealType getZConsTime() { return zconsTime_; }
61	std::string getZConsOutput() { return zconsOutput_; }
62
63	void update();
64	virtual void init();
65	private:
66
67	bool isZMol(Molecule* mol);
68	void thermalize(void);
69
70	void zeroVelocity();
71	void doZconstraintForce();
72	void doHarmonic();
73	bool checkZConsState();
74	void updateZPos();
75	void updateCantPos();
76	void calcTotalMassMovingZMols();
77	bool haveMovingZMols();
78	bool haveFixedZMols();
79	RealType getZTargetPos(int index);
80	RealType getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce) ;
81	RealType getZFOfMovingMols(Molecule* mol, RealType totalForce) ;
82	RealType getHFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce);
83	RealType getHFOfUnconsMols(Molecule* mol, RealType totalForce);
84
85	std::list<ZconstraintMol> movingZMols_; /*< moving zconstraint molecules/
86	std::list<ZconstraintMol> fixedZMols_; /*< fixed zconstraint molecules/
87	std::vector<Molecule> unzconsMols_; /< free molecules/
88
89	RealType zconsTime_;
90	std::string zconsOutput_;
91	RealType zconsTol_;
92	bool usingSMD_;
93	RealType zconsFixingTime_;
94	RealType zconsGap_;
95	bool usingZconsGap_;
96	RealType dt_;
97
98	const static int whichDirection = 2;
99
100	std::map<int, ZconstraintParam> allZMolIndices_;
101
102	Snapshot* currSnapshot_;
103	RealType currZconsTime_;
104
105	RealType totMassMovingZMols_;
106	RealType totMassUnconsMols_; /*< mass of unconstraint molecules in the whole system (never change) /
107
108	ZConsWriter* fzOut;
109	const RealType infiniteTime;
110	};
111
112	}
113	#endif