src/restraints/Restraint.hpp

/*
 * Copyright (c) 2009 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.
 */
 
/**
 * @file Restraint.hpp
 * @author   cli2
 * @date  06/17/2009
 * @version 1.0
 */ 

#ifndef RESTRAINTS_RESTRAINT_HPP
#define RESTRAINTS_RESTRAINT_HPP

#include "config.h"
#include "utils/GenericData.hpp"
#include "math/Vector3.hpp"
#include <map>

namespace oopse {
  
  class Restraint {
  public:

    enum {
      rtDisplacement = 1,
      rtTwist = 2,
      rtSwingX = 4,
      rtSwingY = 8
    };

    typedef std::pair<RealType, RealType> RealPair;

    Restraint() : twist0_(0.0), swingX0_(0.0), swingY0_(0.0), restType_(0) {
    }
    
    virtual ~Restraint() {}

    // these are place-holders.  The subclasses will have different arguments
    // to the two functions.
    void calcForce() {}
    void setReferenceStructure() {}

    RealType getUnscaledPotential() { return pot_; }
    RealType getPotential() { return scaleFactor_ * pot_; }

    void setRestraintName(std::string name) { restName_ = name; }
    std::string getRestraintName() { return restName_; }

    /** Returns the restraint type  */
    int getRestraintType(){ return restType_; }
    /** Sets the restraint type  */
    void setRestraintType(int restType) { restType_ = restType; }

    void setScaleFactor(RealType sf) { scaleFactor_ = sf;}

    void setDisplacementForceConstant(RealType kDisp) { 
      kDisp_ = kDisp; 
      restType_ |= rtDisplacement;
      restInfo_[rtDisplacement] = std::make_pair(0.0, 0.0);
    }
    
    void setTwistForceConstant(RealType kTwist) { 
      kTwist_ = kTwist/4;
      restType_ |= rtTwist; 
      restInfo_[rtTwist] = std::make_pair(0.0, 0.0);
    }
    
    void setSwingXForceConstant(RealType kSwingX) { 
      kSwingX_ = kSwingX; 
      restType_ |= rtSwingX; 
      restInfo_[rtSwingX] = std::make_pair(0.0, 0.0);
    }

    void setSwingYForceConstant(RealType kSwingY) { 
      kSwingY_ = kSwingY; 
      restType_ |= rtSwingY; 
      restInfo_[rtSwingY] = std::make_pair(0.0, 0.0);
    }
    
    /* restraint angles are measured relative to the ideal structure, 
       and are measured in radians.  If you want to restrain to the 
       same structure as the ideal structure, these do not need to be set.
    */    
    void setRestrainedTwistAngle(RealType twist0) { 
      twist0_ = twist0; 
      restType_ |= rtTwist; 
      restInfo_[rtTwist] = std::make_pair(0.0, 0.0);
    }
    
    void setRestrainedSwingXAngle(RealType swingX0) { 
      swingX0_ = swingX0; 
      restType_ |= rtSwingX; 
      restInfo_[rtSwingX] = std::make_pair(0.0, 0.0);
    }

    void setRestrainedSwingYAngle(RealType swingY0) { 
      swingY0_ = swingY0; 
      restType_ |= rtSwingY; 
      restInfo_[rtSwingY] = std::make_pair(0.0, 0.0);
    }
    
    RealType getDisplacementForceConstant() { return kDisp_; }
    RealType getTwistForceConstant() { return kTwist_; }
    RealType getSwingXForceConstant() { return kSwingX_; }
    RealType getSwingYForceConstant() { return kSwingY_; }
    RealType getRestrainedTwistAngle() { return twist0_; }
    RealType getRestrainedSwingXAngle() { return swingX0_; }
    RealType getRestrainedSwingYAngle() { return swingY0_; }
    std::map<int, RealPair> getRestraintInfo() { return restInfo_; }

  protected:

    RealType scaleFactor_;
    RealType kDisp_;
    RealType kTwist_;
    RealType kSwingX_;
    RealType kSwingY_;
    RealType pot_;    
    RealType twist0_;
    RealType swingX0_;
    RealType swingY0_;
    
    int restType_;
    std::string restName_;
    std::map<int, RealPair> restInfo_;
  };    
 
  typedef SimpleTypeData<Restraint*> RestraintData;   

  
}
#endif
Revision:	3521
Committed:	Tue Sep 8 13:45:27 2009 UTC (14 years, 9 months ago) by cli2
File size:	5637 byte(s)
Log Message:	Added missing restraint file
#	Content
1	/*
2	* Copyright (c) 2009 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	/**
43	* @file Restraint.hpp
44	* @author cli2
45	* @date 06/17/2009
46	* @version 1.0
47	*/
48
49	#ifndef RESTRAINTS_RESTRAINT_HPP
50	#define RESTRAINTS_RESTRAINT_HPP
51
52	#include "config.h"
53	#include "utils/GenericData.hpp"
54	#include "math/Vector3.hpp"
55	#include <map>
56
57	namespace oopse {
58
59	class Restraint {
60	public:
61
62	enum {
63	rtDisplacement = 1,
64	rtTwist = 2,
65	rtSwingX = 4,
66	rtSwingY = 8
67	};
68
69	typedef std::pair<RealType, RealType> RealPair;
70
71	Restraint() : twist0_(0.0), swingX0_(0.0), swingY0_(0.0), restType_(0) {
72	}
73
74	virtual ~Restraint() {}
75
76	// these are place-holders. The subclasses will have different arguments
77	// to the two functions.
78	void calcForce() {}
79	void setReferenceStructure() {}
80
81	RealType getUnscaledPotential() { return pot_; }
82	RealType getPotential() { return scaleFactor_ * pot_; }
83
84	void setRestraintName(std::string name) { restName_ = name; }
85	std::string getRestraintName() { return restName_; }
86
87	/** Returns the restraint type */
88	int getRestraintType(){ return restType_; }
89	/** Sets the restraint type */
90	void setRestraintType(int restType) { restType_ = restType; }
91
92	void setScaleFactor(RealType sf) { scaleFactor_ = sf;}
93
94	void setDisplacementForceConstant(RealType kDisp) {
95	kDisp_ = kDisp;
96	restType_ \|= rtDisplacement;
97	restInfo_[rtDisplacement] = std::make_pair(0.0, 0.0);
98	}
99
100	void setTwistForceConstant(RealType kTwist) {
101	kTwist_ = kTwist/4;
102	restType_ \|= rtTwist;
103	restInfo_[rtTwist] = std::make_pair(0.0, 0.0);
104	}
105
106	void setSwingXForceConstant(RealType kSwingX) {
107	kSwingX_ = kSwingX;
108	restType_ \|= rtSwingX;
109	restInfo_[rtSwingX] = std::make_pair(0.0, 0.0);
110	}
111
112	void setSwingYForceConstant(RealType kSwingY) {
113	kSwingY_ = kSwingY;
114	restType_ \|= rtSwingY;
115	restInfo_[rtSwingY] = std::make_pair(0.0, 0.0);
116	}
117
118	/* restraint angles are measured relative to the ideal structure,
119	and are measured in radians. If you want to restrain to the
120	same structure as the ideal structure, these do not need to be set.
121	*/
122	void setRestrainedTwistAngle(RealType twist0) {
123	twist0_ = twist0;
124	restType_ \|= rtTwist;
125	restInfo_[rtTwist] = std::make_pair(0.0, 0.0);
126	}
127
128	void setRestrainedSwingXAngle(RealType swingX0) {
129	swingX0_ = swingX0;
130	restType_ \|= rtSwingX;
131	restInfo_[rtSwingX] = std::make_pair(0.0, 0.0);
132	}
133
134	void setRestrainedSwingYAngle(RealType swingY0) {
135	swingY0_ = swingY0;
136	restType_ \|= rtSwingY;
137	restInfo_[rtSwingY] = std::make_pair(0.0, 0.0);
138	}
139
140	RealType getDisplacementForceConstant() { return kDisp_; }
141	RealType getTwistForceConstant() { return kTwist_; }
142	RealType getSwingXForceConstant() { return kSwingX_; }
143	RealType getSwingYForceConstant() { return kSwingY_; }
144	RealType getRestrainedTwistAngle() { return twist0_; }
145	RealType getRestrainedSwingXAngle() { return swingX0_; }
146	RealType getRestrainedSwingYAngle() { return swingY0_; }
147	std::map<int, RealPair> getRestraintInfo() { return restInfo_; }
148
149	protected:
150
151	RealType scaleFactor_;
152	RealType kDisp_;
153	RealType kTwist_;
154	RealType kSwingX_;
155	RealType kSwingY_;
156	RealType pot_;
157	RealType twist0_;
158	RealType swingX0_;
159	RealType swingY0_;
160
161	int restType_;
162	std::string restName_;
163	std::map<int, RealPair> restInfo_;
164	};
165
166	typedef SimpleTypeData<Restraint*> RestraintData;
167
168
169	}
170	#endif