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. 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 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 oopse{
  class RigidBody : public StuntDouble {
  public:

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

    RigidBody();

    virtual std::string getType() { return name_;}
        
    /** Sets the name of this stuntdouble*/
    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(double phi, double theta, double psi);
        
    /**
     * Returns the gradient of this stuntdouble
     * @return the inertia tensor of this stuntdouble
     * @see #setI
     */ 
    virtual std::vector<double> getGrad();

    virtual void accept(BaseVisitor* v);

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

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

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

    /** 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_;
  };

}//namepace oopse

#endif //PRIMITIVES_RIGIDBODY_HPP

Revision:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	7787 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	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. 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 RigidBody.hpp
44	* @author tlin
45	* @date 10/23/2004
46	* @version 1.0
47	*/
48
49	#ifndef PRIMITIVES_RIGIDBODY_HPP
50	#define PRIMITIVES_RIGIDBODY_HPP
51
52	#include <vector>
53
54	#include "primitives/StuntDouble.hpp"
55	#include "primitives/DirectionalAtom.hpp"
56	#include "types/AtomStamp.hpp"
57	namespace oopse{
58	class RigidBody : public StuntDouble {
59	public:
60
61	typedef std::vector<Atom*>::iterator AtomIterator;
62
63	RigidBody();
64
65	virtual std::string getType() { return name_;}
66
67	/** Sets the name of this stuntdouble*/
68	virtual void setType(const std::string& name) { name_ = name;}
69
70
71	/**
72	* Sets the previous rotation matrix of this stuntdouble
73	* @param a new rotation matrix
74	*/
75	virtual void setPrevA(const RotMat3x3d& a);
76
77	/**
78	* Sets the current rotation matrix of this stuntdouble
79	* @param a new rotation matrix
80	* @note setA will not change the position and rotation matrix of Directional atoms belong to
81	* this rigidbody. If you want to do that, use #updateAtoms
82	*/
83	virtual void setA(const RotMat3x3d& a);
84	/**
85	* Sets the rotation matrix of this stuntdouble in specified snapshot
86	* @param a rotation matrix to be set
87	* @param snapshotNo
88	* @see #getA
89	*/
90	virtual void setA(const RotMat3x3d& a, int snapshotNo);
91
92	/**
93	* Returns the inertia tensor of this stuntdouble
94	* @return the inertia tensor of this stuntdouble
95	*/
96	virtual Mat3x3d getI();
97
98
99	/** Sets the internal unit frame of this stuntdouble by three euler angles */
100	void setElectroFrameFromEuler(double phi, double theta, double psi);
101
102	/**
103	* Returns the gradient of this stuntdouble
104	* @return the inertia tensor of this stuntdouble
105	* @see #setI
106	*/
107	virtual std::vector<double> getGrad();
108
109	virtual void accept(BaseVisitor* v);
110
111	void addAtom(Atom* at, AtomStamp* ats);
112
113	/** calculate the reference coordinates */
114	void calcRefCoords();
115
116	/** Convert Atomic forces and torques to total forces and torques */
117	void calcForcesAndTorques();
118
119	/** update the positions of atoms belong to this rigidbody */
120	void updateAtoms();
121
122	void updateAtoms(int frame);
123
124	void updateAtomVel();
125
126	void updateAtomVel(int frame);
127
128	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
129	i = atoms_.begin();
130	return i != atoms_.end() ? *i : NULL;
131	}
132
133	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
134	++i;
135	return i != atoms_.end() ? *i : NULL;
136	}
137
138	std::vector<Atom*>::iterator getBeginAtomIter() {
139	return atoms_.begin();
140	}
141
142	std::vector<Atom*>::iterator getEndAtomIter() {
143	return atoms_.end();
144	}
145
146	/**
147	* Returns the atoms of this rigid body
148	* @return the atoms of this rigid body in a vector
149	* @deprecate
150	*/
151	std::vector<Atom*> getAtoms() {
152	return atoms_;
153	}
154
155	/**
156	* Returns the number of atoms in this rigid body
157	* @return the number of atoms in this rigid body
158	*/
159	int getNumAtoms() {
160	return atoms_.size();
161	}
162
163	/**
164	* Return the position of atom which belongs to this rigid body.
165	* @return true if index is valid otherwise return false
166	* @param pos the position of atom which will be set on return if index is valid
167	* @param index the index of the atom in rigid body's private data member atoms_
168	*/
169	bool getAtomPos(Vector3d& pos, unsigned int index);
170
171	/**
172	* Return the position of atom which belongs to this rigid body.
173	* @return true if atom belongs to this rigid body,otherwise return false
174	* @param pos position of atom which will be set on return if atom belongs to this rigid body
175	* @param atom the pointer to an atom
176	*/
177	bool getAtomPos(Vector3d& pos, Atom* atom);
178
179	/**
180	* Return the velocity of atom which belongs to this rigid body.
181	* @return true if index is valid otherwise return false
182	* @param vel the velocity of atom which will be set on return if index is valid
183	* @param index the index of the atom in rigid body's private data member atoms_
184	*/
185	bool getAtomVel(Vector3d& vel, unsigned int index);
186
187	/**
188	* Return the velocity of atom which belongs to this rigid body.
189	* @return true if atom belongs to this rigid body,otherwise return false
190	* @param vel velocity of atom which will be set on return if atom belongs to this rigid body
191	* @param atom the pointer to an atom
192	*/
193	bool getAtomVel(Vector3d& vel, Atom*);
194
195	/**
196	* Return the reference coordinate of atom which belongs to this rigid body.
197	* @return true if index is valid otherwise return false
198	* @param coor the reference coordinate of atom which will be set on return if index is valid
199	* @param index the index of the atom in rigid body's private data member atoms_
200	*/
201	bool getAtomRefCoor(Vector3d& coor, unsigned int index);
202
203	/**
204	* Return the velocity of atom which belongs to this rigid body.
205	* @return true if atom belongs to this rigid body,otherwise return false
206	* @param coor velocity of atom which will be set on return if atom belongs to this rigid body
207	* @param atom the pointer to an atom
208	*/
209	bool getAtomRefCoor(Vector3d& coor, Atom* atom);
210
211	private:
212	std::string name_;
213	Mat3x3d inertiaTensor_;
214	RotMat3x3d sU_; /*< body fixed standard unit vector /
215
216	std::vector<Atom*> atoms_;
217	std::vector<Vector3d> refCoords_;
218	std::vector<RotMat3x3d> refOrients_;
219	};
220
221	}//namepace oopse
222
223	#endif //PRIMITIVES_RIGIDBODY_HPP
224