src/primitives/Bend.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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @file Bend.hpp
 * @author    tlin
 * @date  11/01/2004
 * @version 1.0
 */ 


#ifndef PRIMITIVES_BEND_HPP
#define PRIMITIVES_BEND_HPP

#include "primitives/ShortRangeInteraction.hpp"
#include "primitives/Atom.hpp"
#include "types/BendType.hpp"

namespace OpenMD {
  struct BendData {
    RealType angle;
    RealType potential;
  };
  
  struct BendDataSet {
    RealType deltaV;
    BendData prev;
    BendData curr;
  };
  
  class Bend : public ShortRangeInteraction {
  public:
    Bend(Atom* atom1, Atom* atom2, Atom* atom3, BendType* bt)
      : ShortRangeInteraction(), bendType_(bt) {
      atoms_.resize(3);
      atoms_[0] = atom1;
      atoms_[1] = atom2;
      atoms_[2] = atom3;
    }
    
    virtual ~Bend() {}
    virtual void calcForce(RealType& angle, bool doParticlePot);
    
    RealType getValue(int snapshotNo) {
      Vector3d pos1 = atoms_[0]->getPos(snapshotNo);
      Vector3d pos2 = atoms_[1]->getPos(snapshotNo);
      Vector3d pos3 = atoms_[2]->getPos(snapshotNo);
      
      Vector3d r21 = pos1 - pos2;
      RealType d21 = r21.length();
      
      RealType d21inv = 1.0 / d21;
    
      Vector3d r23 = pos3 - pos2;
      RealType d23 = r23.length();
      
      RealType d23inv = 1.0 / d23;
      
      RealType cosTheta = dot(r21, r23) / (d21 * d23);
      
      //check roundoff     
      if (cosTheta > 1.0) {
        cosTheta = 1.0;
      } else if (cosTheta < -1.0) {
        cosTheta = -1.0;
      }
      
      return acos(cosTheta);
    }


    RealType getPotential() {
      return potential_;
    }
    
    Atom* getAtomA() {
      return atoms_[0];
    }
    
    Atom* getAtomB() {
      return atoms_[1];
    }
    
    Atom* getAtomC() {
      return atoms_[2];
    }
    
    BendType * getBendType() {
      return bendType_;
    }
    
    virtual std::string getName() { return name_;}        
    /** Sets the name of this bend for selections */
    virtual void setName(const std::string& name) { name_ = name;}

    void accept(BaseVisitor* v) {
      v->visit(this);
    }    

  protected:
    
    RealType potential_;
    BendType* bendType_; /**< bend type */
    std::string name_;        

  };    
} //end namespace OpenMD
#endif //PRIMITIVES_BEND_HPP

Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 5 months ago) by gezelter
File size:	4417 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			/**
44			* @file Bend.hpp
45			* @author tlin
46			* @date 11/01/2004
47			* @version 1.0
48			*/
49
50
51			#ifndef PRIMITIVES_BEND_HPP
52			#define PRIMITIVES_BEND_HPP
53	gezelter	1953
54			#include "primitives/ShortRangeInteraction.hpp"
55	gezelter	246	#include "primitives/Atom.hpp"
56			#include "types/BendType.hpp"
57	gezelter	1953
58	gezelter	1390	namespace OpenMD {
59	gezelter	1211	struct BendData {
60	tim	963	RealType angle;
61			RealType potential;
62	gezelter	1211	};
63
64			struct BendDataSet {
65	tim	963	RealType deltaV;
66	tim	749	BendData prev;
67			BendData curr;
68	gezelter	1211	};
69
70	gezelter	1953	class Bend : public ShortRangeInteraction {
71	gezelter	507	public:
72			Bend(Atom* atom1, Atom* atom2, Atom* atom3, BendType* bt)
73	gezelter	1953	: ShortRangeInteraction(), bendType_(bt) {
74			atoms_.resize(3);
75			atoms_[0] = atom1;
76			atoms_[1] = atom2;
77			atoms_[2] = atom3;
78			}
79	gezelter	1211
80	gezelter	507	virtual ~Bend() {}
81	gezelter	1782	virtual void calcForce(RealType& angle, bool doParticlePot);
82	gezelter	1211
83	gezelter	1953	RealType getValue(int snapshotNo) {
84			Vector3d pos1 = atoms_[0]->getPos(snapshotNo);
85			Vector3d pos2 = atoms_[1]->getPos(snapshotNo);
86			Vector3d pos3 = atoms_[2]->getPos(snapshotNo);
87
88			Vector3d r21 = pos1 - pos2;
89			RealType d21 = r21.length();
90
91			RealType d21inv = 1.0 / d21;
92
93			Vector3d r23 = pos3 - pos2;
94			RealType d23 = r23.length();
95
96			RealType d23inv = 1.0 / d23;
97
98			RealType cosTheta = dot(r21, r23) / (d21 * d23);
99
100			//check roundoff
101			if (cosTheta > 1.0) {
102			cosTheta = 1.0;
103			} else if (cosTheta < -1.0) {
104			cosTheta = -1.0;
105			}
106
107			return acos(cosTheta);
108			}
109
110
111	tim	963	RealType getPotential() {
112	gezelter	507	return potential_;
113			}
114	gezelter	1211
115	gezelter	507	Atom* getAtomA() {
116	gezelter	1953	return atoms_[0];
117	gezelter	507	}
118	gezelter	1211
119	gezelter	507	Atom* getAtomB() {
120	gezelter	1953	return atoms_[1];
121	gezelter	507	}
122	gezelter	1211
123	gezelter	507	Atom* getAtomC() {
124	gezelter	1953	return atoms_[2];
125	gezelter	507	}
126	gezelter	1211
127	gezelter	507	BendType * getBendType() {
128			return bendType_;
129			}
130	gezelter	1211
131	gezelter	1953	virtual std::string getName() { return name_;}
132			/** Sets the name of this bend for selections */
133			virtual void setName(const std::string& name) { name_ = name;}
134
135			void accept(BaseVisitor* v) {
136			v->visit(this);
137			}
138
139	gezelter	507	protected:
140	gezelter	1211
141	tim	963	RealType potential_;
142	gezelter	507	BendType* bendType_; /*< bend type /
143	gezelter	1953	std::string name_;
144
145	gezelter	507	};
146	gezelter	1390	} //end namespace OpenMD
147	gezelter	246	#endif //PRIMITIVES_BEND_HPP
148