src/primitives/DirectionalAtom.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).
 */
 
/**
 * @file DirectionalAtom.hpp
 * @author    tlin
 * @date  10/23/2004
 * @version 1.0
 */ 

#ifndef PRIMITIVES_DIRECTIONALATOM_HPP
#define PRIMITIVES_DIRECTIONALATOM_HPP

#include "primitives/Atom.hpp"
#include "types/AtomType.hpp"
namespace OpenMD{
  class DirectionalAtom : public Atom {
  public:
    DirectionalAtom(AtomType* dAtomType);
    /**
     * Returns the inertia tensor of this stuntdouble
     * @return the inertia tensor of this stuntdouble
     */ 
    virtual Mat3x3d getI();            
    
    /**
     * Sets  the previous rotation matrix of this stuntdouble
     * @param a  new rotation matrix 
     */         
    virtual void setPrevA(const RotMat3x3d& a);
    
    /**
     * Sets  the current rotation matrix of this stuntdouble
     * @param a  new rotation matrix 
     */         
    virtual void setA(const RotMat3x3d& a);
    
    /**
     * Sets  the rotation matrix of this stuntdouble in specified snapshot
     * @param a rotation matrix to be set 
     * @param snapshotNo 
     * @see #getA
     */         
    virtual void setA(const RotMat3x3d& a, int snapshotNo);
    
    /** 
     * Left multiple rotation matrix by another rotation matrix 
     * @param m a rotation matrix
     */
    void rotateBy(const RotMat3x3d& m);
        
    /**
     * Returns the gradient of this stuntdouble
     * @return the gradient of this stuntdouble
     */ 
    virtual std::vector<RealType> getGrad();
    
    virtual void accept(BaseVisitor* v);
   
  private:
    Mat3x3d I_;
    RotMat3x3d electroBodyFrame_; // body fixed standard eletrostatic frame
  };  
}//namespace OpenMD
#endif //PRIMITIVES_DIRECTIONALATOM_HPP
Revision:	1710
Committed:	Fri May 18 21:44:02 2012 UTC (12 years, 11 months ago) by gezelter
File size:	3844 byte(s)
Log Message:	Added an adapter layer between the AtomType and the rest of the code to handle the bolt-on capabilities of new types. Fixed a long-standing bug in how storageLayout was being set to the maximum possible value. Started to add infrastructure for Polarizable and fluc-Q calculations.
#	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	/**
44	* @file DirectionalAtom.hpp
45	* @author tlin
46	* @date 10/23/2004
47	* @version 1.0
48	*/
49
50	#ifndef PRIMITIVES_DIRECTIONALATOM_HPP
51	#define PRIMITIVES_DIRECTIONALATOM_HPP
52
53	#include "primitives/Atom.hpp"
54	#include "types/AtomType.hpp"
55	namespace OpenMD{
56	class DirectionalAtom : public Atom {
57	public:
58	DirectionalAtom(AtomType* dAtomType);
59	/**
60	* Returns the inertia tensor of this stuntdouble
61	* @return the inertia tensor of this stuntdouble
62	*/
63	virtual Mat3x3d getI();
64
65	/**
66	* Sets the previous rotation matrix of this stuntdouble
67	* @param a new rotation matrix
68	*/
69	virtual void setPrevA(const RotMat3x3d& a);
70
71	/**
72	* Sets the current rotation matrix of this stuntdouble
73	* @param a new rotation matrix
74	*/
75	virtual void setA(const RotMat3x3d& a);
76
77	/**
78	* Sets the rotation matrix of this stuntdouble in specified snapshot
79	* @param a rotation matrix to be set
80	* @param snapshotNo
81	* @see #getA
82	*/
83	virtual void setA(const RotMat3x3d& a, int snapshotNo);
84
85	/**
86	* Left multiple rotation matrix by another rotation matrix
87	* @param m a rotation matrix
88	*/
89	void rotateBy(const RotMat3x3d& m);
90
91	/**
92	* Returns the gradient of this stuntdouble
93	* @return the gradient of this stuntdouble
94	*/
95	virtual std::vector<RealType> getGrad();
96
97	virtual void accept(BaseVisitor* v);
98
99	private:
100	Mat3x3d I_;
101	RotMat3x3d electroBodyFrame_; // body fixed standard eletrostatic frame
102	};
103	}//namespace OpenMD
104	#endif //PRIMITIVES_DIRECTIONALATOM_HPP