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 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_;
  };

}//namepace oopse

#endif //PRIMITIVES_RIGIDBODY_HPP

Revision:	1126
Committed:	Fri Apr 6 21:53:43 2007 UTC (18 years, 1 month ago) by gezelter
Original Path:	*trunk/src/primitives/RigidBody.hpp*
File size:	8043 byte(s)
Log Message:	Massive update to do virials (both atomic and cutoff-group) correctly. The rigid body constraint contributions had been missing and this was masked by the use of cutoff groups...
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	2
49	gezelter	246	#ifndef PRIMITIVES_RIGIDBODY_HPP
50			#define PRIMITIVES_RIGIDBODY_HPP
51
52	gezelter	2	#include <vector>
53	gezelter	246
54	tim	3	#include "primitives/StuntDouble.hpp"
55	gezelter	246	#include "primitives/DirectionalAtom.hpp"
56			#include "types/AtomStamp.hpp"
57			namespace oopse{
58	gezelter	507	class RigidBody : public StuntDouble {
59			public:
60	tim	284
61	gezelter	507	typedef std::vector<Atom*>::iterator AtomIterator;
62	tim	284
63	gezelter	507	RigidBody();
64	gezelter	2
65	gezelter	507	virtual std::string getType() { return name_;}
66	gezelter	246
67	tim	963	/** Sets the name of this stuntRealType*/
68	gezelter	507	virtual void setType(const std::string& name) { name_ = name;}
69	gezelter	246
70	gezelter	2
71	gezelter	507	/**
72			* Sets the previous rotation matrix of this stuntdouble
73			* @param a new rotation matrix
74			*/
75			virtual void setPrevA(const RotMat3x3d& a);
76	gezelter	246
77	gezelter	507	/**
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	2
92	gezelter	507	/**
93			* Returns the inertia tensor of this stuntdouble
94			* @return the inertia tensor of this stuntdouble
95			*/
96			virtual Mat3x3d getI();
97	gezelter	2
98
99	gezelter	507	/** Sets the internal unit frame of this stuntdouble by three euler angles */
100	tim	963	void setElectroFrameFromEuler(RealType phi, RealType theta, RealType psi);
101	gezelter	246
102	gezelter	507	/**
103			* Returns the gradient of this stuntdouble
104			* @return the inertia tensor of this stuntdouble
105			* @see #setI
106			*/
107	tim	963	virtual std::vector<RealType> getGrad();
108	gezelter	2
109	gezelter	507	virtual void accept(BaseVisitor* v);
110	gezelter	2
111	gezelter	507	void addAtom(Atom* at, AtomStamp* ats);
112	gezelter	2
113	gezelter	1126	/** calculates the reference coordinates */
114	gezelter	507	void calcRefCoords();
115	gezelter	2
116	gezelter	1126	/** Converts Atomic forces and torques to total forces and torques */
117	gezelter	507	void calcForcesAndTorques();
118	gezelter	2
119	gezelter	1126	/** 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. */
120			Mat3x3d calcForcesAndTorquesAndVirial();
121
122	gezelter	507	/** update the positions of atoms belong to this rigidbody */
123			void updateAtoms();
124	gezelter	2
125	gezelter	507	void updateAtoms(int frame);
126	tim	318
127	gezelter	507	void updateAtomVel();
128	tim	318
129	gezelter	507	void updateAtomVel(int frame);
130	tim	318
131	gezelter	507	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
132			i = atoms_.begin();
133			return i != atoms_.end() ? *i : NULL;
134			}
135	gezelter	2
136	gezelter	507	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
137			++i;
138			return i != atoms_.end() ? *i : NULL;
139			}
140	gezelter	2
141	gezelter	507	std::vector<Atom*>::iterator getBeginAtomIter() {
142			return atoms_.begin();
143			}
144	gezelter	246
145	gezelter	507	std::vector<Atom*>::iterator getEndAtomIter() {
146			return atoms_.end();
147			}
148	gezelter	2
149	gezelter	507	/**
150			* Returns the atoms of this rigid body
151			* @return the atoms of this rigid body in a vector
152			* @deprecate
153			*/
154			std::vector<Atom*> getAtoms() {
155			return atoms_;
156			}
157	gezelter	2
158	gezelter	507	/**
159			* Returns the number of atoms in this rigid body
160			* @return the number of atoms in this rigid body
161			*/
162			int getNumAtoms() {
163			return atoms_.size();
164			}
165	gezelter	2
166	gezelter	507	/**
167			* Return the position of atom which belongs to this rigid body.
168			* @return true if index is valid otherwise return false
169			* @param pos the position of atom which will be set on return if index is valid
170			* @param index the index of the atom in rigid body's private data member atoms_
171			*/
172			bool getAtomPos(Vector3d& pos, unsigned int index);
173	gezelter	2
174	gezelter	507	/**
175			* Return the position of atom which belongs to this rigid body.
176			* @return true if atom belongs to this rigid body,otherwise return false
177			* @param pos position of atom which will be set on return if atom belongs to this rigid body
178			* @param atom the pointer to an atom
179			*/
180			bool getAtomPos(Vector3d& pos, Atom* atom);
181	gezelter	2
182	gezelter	507	/**
183			* Return the velocity of atom which belongs to this rigid body.
184			* @return true if index is valid otherwise return false
185			* @param vel the velocity of atom which will be set on return if index is valid
186			* @param index the index of the atom in rigid body's private data member atoms_
187			*/
188			bool getAtomVel(Vector3d& vel, unsigned int index);
189	gezelter	2
190	gezelter	507	/**
191			* Return the velocity of atom which belongs to this rigid body.
192			* @return true if atom belongs to this rigid body,otherwise return false
193			* @param vel velocity of atom which will be set on return if atom belongs to this rigid body
194			* @param atom the pointer to an atom
195			*/
196			bool getAtomVel(Vector3d& vel, Atom*);
197	gezelter	2
198	gezelter	507	/**
199			* Return the reference coordinate of atom which belongs to this rigid body.
200			* @return true if index is valid otherwise return false
201			* @param coor the reference coordinate of atom which will be set on return if index is valid
202			* @param index the index of the atom in rigid body's private data member atoms_
203			*/
204			bool getAtomRefCoor(Vector3d& coor, unsigned int index);
205	gezelter	2
206	gezelter	507	/**
207			* Return the velocity of atom which belongs to this rigid body.
208			* @return true if atom belongs to this rigid body,otherwise return false
209			* @param coor velocity of atom which will be set on return if atom belongs to this rigid body
210			* @param atom the pointer to an atom
211			*/
212			bool getAtomRefCoor(Vector3d& coor, Atom* atom);
213	gezelter	2
214	gezelter	507	private:
215			std::string name_;
216			Mat3x3d inertiaTensor_;
217			RotMat3x3d sU_; /*< body fixed standard unit vector /
218	gezelter	246
219	gezelter	507	std::vector<Atom*> atoms_;
220			std::vector<Vector3d> refCoords_;
221			std::vector<RotMat3x3d> refOrients_;
222			};
223	gezelter	2
224	gezelter	246	}//namepace oopse
225	gezelter	2
226	gezelter	246	#endif //PRIMITIVES_RIGIDBODY_HPP
227	gezelter	2