src/primitives/Inversion.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 Inversion.hpp
 * @author    tlin
 * @date  11/01/2004
 * @version 1.0
 */

#ifndef PRIMITIVES_INVERSION_HPP
#define PRIMITIVES_INVERSION_HPP

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

namespace OpenMD {
  struct InversionData {
    RealType angle;
    RealType potential;
  };

  struct InversionDataSet {
    RealType deltaV;
    InversionData prev;
    InversionData curr;
  };

  /**
   * @class Inversion Inversion.hpp "primitives/Inversion.hpp"
   */
  class Inversion : public ShortRangeInteraction {
  public:
    Inversion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, InversionType* it);
    virtual ~Inversion() {}
    virtual void calcForce(RealType& angle, bool doParticlePot);
        
    RealType getValue(int snapshotNo) {
      // In OpenMD's version of an inversion, the central atom
      // comes first.  However, to get the planarity in a typical cosine
      // version of this potential (i.e. Amber-style), the central atom
      // is treated as atom *3* in a standard torsion form:
      
      Vector3d pos1 = atoms_[1]->getPos(snapshotNo);
      Vector3d pos2 = atoms_[2]->getPos(snapshotNo);
      Vector3d pos3 = atoms_[0]->getPos(snapshotNo);
      Vector3d pos4 = atoms_[3]->getPos(snapshotNo);
      
      Vector3d r31 = pos1 - pos3;
      Vector3d r23 = pos3 - pos2;
      Vector3d r43 = pos3 - pos4;
      
      //  Calculate the cross products and distances
      Vector3d A = cross(r31, r43);
      RealType rA = A.length();
      Vector3d B = cross(r43, r23);
      RealType rB = B.length();
      //Vector3d C = cross(r23, A);
      //RealType rC = C.length();
      
      A.normalize();
      B.normalize();
      //C.normalize();
      
      //  Calculate the sin and cos
      RealType cos_phi = dot(A, B) ;
      if (cos_phi > 1.0) cos_phi = 1.0;
      if (cos_phi < -1.0) cos_phi = -1.0;
      return acos(cos_phi);
    }


    RealType getPotential() {
      return potential_;
    }

    Atom* getAtomA() {
      return atoms_[0];
    }

    Atom* getAtomB() {
      return atoms_[1];
    }

    Atom* getAtomC() {
      return atoms_[2];
    }

    Atom* getAtomD() {
      return atoms_[3];
    }

    InversionType * getInversionType() {
      return inversionType_;
    }
    virtual std::string getName() { return name_;}        
    /** Sets the name of this inversion for selections */
    virtual void setName(const std::string& name) { name_ = name;}

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

  protected:
    InversionType* inversionType_;
    InversionKey inversionKey_;
    std::string name_;        

    RealType potential_;
  };    

}
#endif //PRIMITIVES_INVERSION_HPP
Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 5 months ago) by gezelter
File size:	4936 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	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, 234107 (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	/**
44	* @file Inversion.hpp
45	* @author tlin
46	* @date 11/01/2004
47	* @version 1.0
48	*/
49
50	#ifndef PRIMITIVES_INVERSION_HPP
51	#define PRIMITIVES_INVERSION_HPP
52
53	#include "primitives/ShortRangeInteraction.hpp"
54	#include "primitives/Atom.hpp"
55	#include "types/InversionType.hpp"
56
57	namespace OpenMD {
58	struct InversionData {
59	RealType angle;
60	RealType potential;
61	};
62
63	struct InversionDataSet {
64	RealType deltaV;
65	InversionData prev;
66	InversionData curr;
67	};
68
69	/**
70	* @class Inversion Inversion.hpp "primitives/Inversion.hpp"
71	*/
72	class Inversion : public ShortRangeInteraction {
73	public:
74	Inversion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, InversionType* it);
75	virtual ~Inversion() {}
76	virtual void calcForce(RealType& angle, bool doParticlePot);
77
78	RealType getValue(int snapshotNo) {
79	// In OpenMD's version of an inversion, the central atom
80	// comes first. However, to get the planarity in a typical cosine
81	// version of this potential (i.e. Amber-style), the central atom
82	// is treated as atom 3 in a standard torsion form:
83
84	Vector3d pos1 = atoms_[1]->getPos(snapshotNo);
85	Vector3d pos2 = atoms_[2]->getPos(snapshotNo);
86	Vector3d pos3 = atoms_[0]->getPos(snapshotNo);
87	Vector3d pos4 = atoms_[3]->getPos(snapshotNo);
88
89	Vector3d r31 = pos1 - pos3;
90	Vector3d r23 = pos3 - pos2;
91	Vector3d r43 = pos3 - pos4;
92
93	// Calculate the cross products and distances
94	Vector3d A = cross(r31, r43);
95	RealType rA = A.length();
96	Vector3d B = cross(r43, r23);
97	RealType rB = B.length();
98	//Vector3d C = cross(r23, A);
99	//RealType rC = C.length();
100
101	A.normalize();
102	B.normalize();
103	//C.normalize();
104
105	// Calculate the sin and cos
106	RealType cos_phi = dot(A, B) ;
107	if (cos_phi > 1.0) cos_phi = 1.0;
108	if (cos_phi < -1.0) cos_phi = -1.0;
109	return acos(cos_phi);
110	}
111
112
113	RealType getPotential() {
114	return potential_;
115	}
116
117	Atom* getAtomA() {
118	return atoms_[0];
119	}
120
121	Atom* getAtomB() {
122	return atoms_[1];
123	}
124
125	Atom* getAtomC() {
126	return atoms_[2];
127	}
128
129	Atom* getAtomD() {
130	return atoms_[3];
131	}
132
133	InversionType * getInversionType() {
134	return inversionType_;
135	}
136	virtual std::string getName() { return name_;}
137	/** Sets the name of this inversion for selections */
138	virtual void setName(const std::string& name) { name_ = name;}
139
140	void accept(BaseVisitor* v) {
141	v->visit(this);
142	}
143
144	protected:
145	InversionType* inversionType_;
146	InversionKey inversionKey_;
147	std::string name_;
148
149	RealType potential_;
150	};
151
152	}
153	#endif //PRIMITIVES_INVERSION_HPP