src/primitives/RigidBody.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 RigidBody.hpp
 * @author    tlin
 * @date  10/23/2004
 * @version 1.0
 */ 

#ifndef PRIMITIVES_RIGIDBODY_HPP
#define PRIMITIVES_RIGIDBODY_HPP

#include <vector>

#include "primitives/StuntDouble.hpp"
#include "primitives/DirectionalAtom.hpp"
#include "types/AtomStamp.hpp"
namespace OpenMD{
  class RigidBody : public StuntDouble {
  public:

    typedef std::vector<Atom*>::iterator AtomIterator;        

    RigidBody();

    virtual std::string getType() { return name_;}
        
    /** Sets the name of this stuntRealType*/
    virtual void setType(const std::string& name) { name_ = name;}
    

    /**
     * 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 
     * @note setA will not change the position and rotation matrix of Directional atoms belong to
     * this rigidbody. If you want to do that, use #updateAtoms
     */         
    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);

    /**
     * Returns the inertia tensor of this stuntdouble
     * @return the inertia tensor of this stuntdouble
     */ 
    virtual Mat3x3d getI();


    /** Sets the internal unit frame of this stuntdouble by three euler angles */
    void setElectroFrameFromEuler(RealType phi, RealType theta, RealType psi);
        
    /**
     * Returns the gradient of this stuntdouble
     * @return the inertia tensor of this stuntdouble
     * @see #setI
     */ 
    virtual std::vector<RealType> getGrad();

    virtual void accept(BaseVisitor* v);

    void addAtom(Atom* at, AtomStamp* ats);

    /** calculates the reference coordinates */
    void calcRefCoords();

    /** Converts Atomic forces and torques to total forces and torques */
    void calcForcesAndTorques();

    /** Converts Atomic forces and torques to total forces and torques and computes the rigid body contribution to the virial.  Returns the rigid body contribution to the virial as a 3x3 matrix. */
    Mat3x3d calcForcesAndTorquesAndVirial();

    /** update the positions of atoms belong to this rigidbody */
    void updateAtoms();

    void updateAtoms(int frame);

    void updateAtomVel();

    void updateAtomVel(int frame);
        
    Atom* beginAtom(std::vector<Atom*>::iterator& i) {
      i = atoms_.begin();
      return i != atoms_.end() ? *i : NULL;
    }

    Atom* nextAtom(std::vector<Atom*>::iterator& i) {
      ++i;
      return i != atoms_.end() ? *i : NULL;
    }

    std::vector<Atom*>::iterator getBeginAtomIter() {
      return atoms_.begin();
    }
        
    std::vector<Atom*>::iterator getEndAtomIter() {
      return atoms_.end();
    }

    /** 
     * Returns the atoms of this rigid body
     * @return the atoms of this rigid body in a vector
     * @deprecate
     */           
    std::vector<Atom*> getAtoms() {
      return atoms_;
    }

    /** 
     * Returns the number of atoms in this rigid body
     * @return the number of atoms in this rigid body
     */
    int getNumAtoms() {
      return atoms_.size();
    }

    /**
     * Return the position of atom which belongs to this rigid body.
     * @return true if index is valid otherwise return false
     * @param pos the position of atom which will be set on return if index is valid
     * @param index the index of the atom in rigid body's private data member atoms_
     */
    bool getAtomPos(Vector3d& pos, unsigned int index);

    /**
     * Return the position of atom which belongs to this rigid body.
     * @return true if atom belongs to this rigid body,otherwise return false
     * @param pos position of atom which will be set on return if atom belongs to this rigid body
     * @param atom the pointer to an atom
     */            
    bool getAtomPos(Vector3d& pos, Atom* atom);

    /**
     * Return the velocity of atom which belongs to this rigid body.
     * @return true if index is valid otherwise return false
     * @param vel the velocity of atom which will be set on return if index is valid
     * @param index the index of the atom in rigid body's private data member atoms_
     */
    bool getAtomVel(Vector3d& vel, unsigned int index);

    /**
     * Return the velocity of atom which belongs to this rigid body.
     * @return true if atom belongs to this rigid body,otherwise return false
     * @param vel velocity of atom which will be set on return if atom belongs to this rigid body
     * @param atom the pointer to an atom
     */ 
    bool getAtomVel(Vector3d& vel, Atom*);

    /**
     * Return the reference coordinate of atom which belongs to this rigid body.
     * @return true if index is valid otherwise return false
     * @param coor the reference coordinate of atom which will be set on return if index is valid
     * @param index the index of the atom in rigid body's private data member atoms_
     */
    bool getAtomRefCoor(Vector3d& coor, unsigned int index);

    /**
     * Return the velocity of atom which belongs to this rigid body.
     * @return true if atom belongs to this rigid body,otherwise return false
     * @param coor velocity of atom which will be set on return if atom belongs to this rigid body
     * @param atom the pointer to an atom
     */ 
    bool getAtomRefCoor(Vector3d& coor, Atom* atom);

  private:
    std::string name_;        
    Mat3x3d inertiaTensor_;     
    RotMat3x3d sU_;               /**< body fixed standard unit vector */
        
    std::vector<Atom*> atoms_;
    std::vector<Vector3d> refCoords_;
    std::vector<RotMat3x3d> refOrients_;
  };

}//namespace OpenMD

#endif //PRIMITIVES_RIGIDBODY_HPP

Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	8153 byte(s)
Log Message:	updated copyright notices
#	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 RigidBody.hpp
45	* @author tlin
46	* @date 10/23/2004
47	* @version 1.0
48	*/
49
50	#ifndef PRIMITIVES_RIGIDBODY_HPP
51	#define PRIMITIVES_RIGIDBODY_HPP
52
53	#include <vector>
54
55	#include "primitives/StuntDouble.hpp"
56	#include "primitives/DirectionalAtom.hpp"
57	#include "types/AtomStamp.hpp"
58	namespace OpenMD{
59	class RigidBody : public StuntDouble {
60	public:
61
62	typedef std::vector<Atom*>::iterator AtomIterator;
63
64	RigidBody();
65
66	virtual std::string getType() { return name_;}
67
68	/** Sets the name of this stuntRealType*/
69	virtual void setType(const std::string& name) { name_ = name;}
70
71
72	/**
73	* Sets the previous rotation matrix of this stuntdouble
74	* @param a new rotation matrix
75	*/
76	virtual void setPrevA(const RotMat3x3d& a);
77
78	/**
79	* Sets the current rotation matrix of this stuntdouble
80	* @param a new rotation matrix
81	* @note setA will not change the position and rotation matrix of Directional atoms belong to
82	* this rigidbody. If you want to do that, use #updateAtoms
83	*/
84	virtual void setA(const RotMat3x3d& a);
85	/**
86	* Sets the rotation matrix of this stuntdouble in specified snapshot
87	* @param a rotation matrix to be set
88	* @param snapshotNo
89	* @see #getA
90	*/
91	virtual void setA(const RotMat3x3d& a, int snapshotNo);
92
93	/**
94	* Returns the inertia tensor of this stuntdouble
95	* @return the inertia tensor of this stuntdouble
96	*/
97	virtual Mat3x3d getI();
98
99
100	/** Sets the internal unit frame of this stuntdouble by three euler angles */
101	void setElectroFrameFromEuler(RealType phi, RealType theta, RealType psi);
102
103	/**
104	* Returns the gradient of this stuntdouble
105	* @return the inertia tensor of this stuntdouble
106	* @see #setI
107	*/
108	virtual std::vector<RealType> getGrad();
109
110	virtual void accept(BaseVisitor* v);
111
112	void addAtom(Atom* at, AtomStamp* ats);
113
114	/** calculates the reference coordinates */
115	void calcRefCoords();
116
117	/** Converts Atomic forces and torques to total forces and torques */
118	void calcForcesAndTorques();
119
120	/** Converts Atomic forces and torques to total forces and torques and computes the rigid body contribution to the virial. Returns the rigid body contribution to the virial as a 3x3 matrix. */
121	Mat3x3d calcForcesAndTorquesAndVirial();
122
123	/** update the positions of atoms belong to this rigidbody */
124	void updateAtoms();
125
126	void updateAtoms(int frame);
127
128	void updateAtomVel();
129
130	void updateAtomVel(int frame);
131
132	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
133	i = atoms_.begin();
134	return i != atoms_.end() ? *i : NULL;
135	}
136
137	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
138	++i;
139	return i != atoms_.end() ? *i : NULL;
140	}
141
142	std::vector<Atom*>::iterator getBeginAtomIter() {
143	return atoms_.begin();
144	}
145
146	std::vector<Atom*>::iterator getEndAtomIter() {
147	return atoms_.end();
148	}
149
150	/**
151	* Returns the atoms of this rigid body
152	* @return the atoms of this rigid body in a vector
153	* @deprecate
154	*/
155	std::vector<Atom*> getAtoms() {
156	return atoms_;
157	}
158
159	/**
160	* Returns the number of atoms in this rigid body
161	* @return the number of atoms in this rigid body
162	*/
163	int getNumAtoms() {
164	return atoms_.size();
165	}
166
167	/**
168	* Return the position of atom which belongs to this rigid body.
169	* @return true if index is valid otherwise return false
170	* @param pos the position of atom which will be set on return if index is valid
171	* @param index the index of the atom in rigid body's private data member atoms_
172	*/
173	bool getAtomPos(Vector3d& pos, unsigned int index);
174
175	/**
176	* Return the position of atom which belongs to this rigid body.
177	* @return true if atom belongs to this rigid body,otherwise return false
178	* @param pos position of atom which will be set on return if atom belongs to this rigid body
179	* @param atom the pointer to an atom
180	*/
181	bool getAtomPos(Vector3d& pos, Atom* atom);
182
183	/**
184	* Return the velocity of atom which belongs to this rigid body.
185	* @return true if index is valid otherwise return false
186	* @param vel the velocity of atom which will be set on return if index is valid
187	* @param index the index of the atom in rigid body's private data member atoms_
188	*/
189	bool getAtomVel(Vector3d& vel, unsigned int index);
190
191	/**
192	* Return the velocity of atom which belongs to this rigid body.
193	* @return true if atom belongs to this rigid body,otherwise return false
194	* @param vel velocity of atom which will be set on return if atom belongs to this rigid body
195	* @param atom the pointer to an atom
196	*/
197	bool getAtomVel(Vector3d& vel, Atom*);
198
199	/**
200	* Return the reference coordinate of atom which belongs to this rigid body.
201	* @return true if index is valid otherwise return false
202	* @param coor the reference coordinate of atom which will be set on return if index is valid
203	* @param index the index of the atom in rigid body's private data member atoms_
204	*/
205	bool getAtomRefCoor(Vector3d& coor, unsigned int index);
206
207	/**
208	* Return the velocity of atom which belongs to this rigid body.
209	* @return true if atom belongs to this rigid body,otherwise return false
210	* @param coor velocity of atom which will be set on return if atom belongs to this rigid body
211	* @param atom the pointer to an atom
212	*/
213	bool getAtomRefCoor(Vector3d& coor, Atom* atom);
214
215	private:
216	std::string name_;
217	Mat3x3d inertiaTensor_;
218	RotMat3x3d sU_; /*< body fixed standard unit vector /
219
220	std::vector<Atom*> atoms_;
221	std::vector<Vector3d> refCoords_;
222	std::vector<RotMat3x3d> refOrients_;
223	};
224
225	}//namespace OpenMD
226
227	#endif //PRIMITIVES_RIGIDBODY_HPP
228