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();

        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:	1973
Committed:	Fri Feb 4 22:41:23 2005 UTC (19 years, 5 months ago) by tim
File size:	8183 byte(s)
Log Message:	adding missing implementation
#	User	Rev	Content
1	gezelter	1930	/*
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	gezelter	1490
49	gezelter	1930	#ifndef PRIMITIVES_RIGIDBODY_HPP
50			#define PRIMITIVES_RIGIDBODY_HPP
51
52	gezelter	1490	#include <vector>
53	gezelter	1930
54	tim	1492	#include "primitives/StuntDouble.hpp"
55	gezelter	1930	#include "primitives/DirectionalAtom.hpp"
56			#include "types/AtomStamp.hpp"
57			namespace oopse{
58	gezelter	1490	class RigidBody : public StuntDouble {
59	gezelter	1930	public:
60	tim	1968
61			typedef std::vector<Atom*>::iterator AtomIterator;
62
63	gezelter	1930	RigidBody();
64	gezelter	1490
65	gezelter	1930	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	gezelter	1490
71	gezelter	1930	/**
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	gezelter	1490
92	gezelter	1930	/**
93			* Returns the inertia tensor of this stuntdouble
94			* @return the inertia tensor of this stuntdouble
95			*/
96			virtual Mat3x3d getI();
97	gezelter	1490
98
99	gezelter	1930	/** 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	gezelter	1490
109	gezelter	1930	virtual void accept(BaseVisitor* v);
110	gezelter	1490
111	gezelter	1930	void addAtom(Atom* at, AtomStamp* ats);
112	gezelter	1490
113	gezelter	1930	/** calculate the reference coordinates */
114			void calcRefCoords();
115	gezelter	1490
116	gezelter	1930	/** Convert Atomic forces and torques to total forces and torques */
117			void calcForcesAndTorques();
118	gezelter	1490
119	gezelter	1930	/** update the positions of atoms belong to this rigidbody */
120			void updateAtoms();
121	gezelter	1490
122	tim	1973	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
123			i = atoms_.begin();
124			return i != atoms_.end() ? *i : NULL;
125			}
126	gezelter	1490
127	tim	1973	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
128			++i;
129			return i != atoms_.end() ? *i : NULL;
130			}
131	gezelter	1490
132	gezelter	1930	std::vector<Atom*>::iterator getBeginAtomIter() {
133			return atoms_.begin();
134			}
135
136			std::vector<Atom*>::iterator getEndAtomIter() {
137			return atoms_.end();
138			}
139	gezelter	1490
140	gezelter	1930	/**
141			* Returns the atoms of this rigid body
142			* @return the atoms of this rigid body in a vector
143			* @deprecate
144			*/
145			std::vector<Atom*> getAtoms() {
146			return atoms_;
147			}
148	gezelter	1490
149	gezelter	1930	/**
150			* Returns the number of atoms in this rigid body
151			* @return the number of atoms in this rigid body
152			*/
153			int getNumAtoms() {
154			return atoms_.size();
155			}
156	gezelter	1490
157	gezelter	1930	/**
158			* Return the position of atom which belongs to this rigid body.
159			* @return true if index is valid otherwise return false
160			* @param pos the position of atom which will be set on return if index is valid
161			* @param index the index of the atom in rigid body's private data member atoms_
162			*/
163			bool getAtomPos(Vector3d& pos, unsigned int index);
164	gezelter	1490
165	gezelter	1930	/**
166			* Return the position of atom which belongs to this rigid body.
167			* @return true if atom belongs to this rigid body,otherwise return false
168			* @param pos position of atom which will be set on return if atom belongs to this rigid body
169			* @param atom the pointer to an atom
170			*/
171			bool getAtomPos(Vector3d& pos, Atom* atom);
172	gezelter	1490
173	gezelter	1930	/**
174			* Return the velocity of atom which belongs to this rigid body.
175			* @return true if index is valid otherwise return false
176			* @param vel the velocity of atom which will be set on return if index is valid
177			* @param index the index of the atom in rigid body's private data member atoms_
178			*/
179			bool getAtomVel(Vector3d& vel, unsigned int index);
180	gezelter	1490
181	gezelter	1930	/**
182			* Return the velocity of atom which belongs to this rigid body.
183			* @return true if atom belongs to this rigid body,otherwise return false
184			* @param vel velocity of atom which will be set on return if atom belongs to this rigid body
185			* @param atom the pointer to an atom
186			*/
187			bool getAtomVel(Vector3d& vel, Atom*);
188	gezelter	1490
189	gezelter	1930	/**
190			* Return the reference coordinate of atom which belongs to this rigid body.
191			* @return true if index is valid otherwise return false
192			* @param coor the reference coordinate of atom which will be set on return if index is valid
193			* @param index the index of the atom in rigid body's private data member atoms_
194			*/
195			bool getAtomRefCoor(Vector3d& coor, unsigned int index);
196	gezelter	1490
197	gezelter	1930	/**
198			* Return the velocity of atom which belongs to this rigid body.
199			* @return true if atom belongs to this rigid body,otherwise return false
200			* @param coor velocity of atom which will be set on return if atom belongs to this rigid body
201			* @param atom the pointer to an atom
202			*/
203			bool getAtomRefCoor(Vector3d& coor, Atom* atom);
204	gezelter	1490
205	gezelter	1930	private:
206			std::string name_;
207			Mat3x3d inertiaTensor_;
208			RotMat3x3d sU_; /*< body fixed standard unit vector /
209
210			std::vector<Atom*> atoms_;
211			std::vector<Vector3d> refCoords_;
212			std::vector<RotMat3x3d> refOrients_;
213			};
214	gezelter	1490
215	gezelter	1930	}//namepace oopse
216	gezelter	1490
217	gezelter	1930	#endif //PRIMITIVES_RIGIDBODY_HPP
218	gezelter	1490