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
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			/**
44			* @file RigidBody.hpp
45			* @author tlin
46			* @date 10/23/2004
47			* @version 1.0
48			*/
49	gezelter	2
50	gezelter	246	#ifndef PRIMITIVES_RIGIDBODY_HPP
51			#define PRIMITIVES_RIGIDBODY_HPP
52
53	gezelter	2	#include <vector>
54	gezelter	246
55	tim	3	#include "primitives/StuntDouble.hpp"
56	gezelter	246	#include "primitives/DirectionalAtom.hpp"
57			#include "types/AtomStamp.hpp"
58	gezelter	1390	namespace OpenMD{
59	gezelter	507	class RigidBody : public StuntDouble {
60			public:
61	tim	284
62	gezelter	507	typedef std::vector<Atom*>::iterator AtomIterator;
63	tim	284
64	gezelter	507	RigidBody();
65	gezelter	2
66	gezelter	507	virtual std::string getType() { return name_;}
67	gezelter	246
68	tim	963	/** Sets the name of this stuntRealType*/
69	gezelter	507	virtual void setType(const std::string& name) { name_ = name;}
70	gezelter	246
71	gezelter	2
72	gezelter	507	/**
73			* Sets the previous rotation matrix of this stuntdouble
74			* @param a new rotation matrix
75			*/
76			virtual void setPrevA(const RotMat3x3d& a);
77	gezelter	246
78	gezelter	507	/**
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	gezelter	2
93	gezelter	507	/**
94			* Returns the inertia tensor of this stuntdouble
95			* @return the inertia tensor of this stuntdouble
96			*/
97			virtual Mat3x3d getI();
98	gezelter	2
99
100	gezelter	507	/** Sets the internal unit frame of this stuntdouble by three euler angles */
101	tim	963	void setElectroFrameFromEuler(RealType phi, RealType theta, RealType psi);
102	gezelter	246
103	gezelter	507	/**
104			* Returns the gradient of this stuntdouble
105			* @return the inertia tensor of this stuntdouble
106			* @see #setI
107			*/
108	tim	963	virtual std::vector<RealType> getGrad();
109	gezelter	2
110	gezelter	507	virtual void accept(BaseVisitor* v);
111	gezelter	2
112	gezelter	507	void addAtom(Atom* at, AtomStamp* ats);
113	gezelter	2
114	gezelter	1126	/** calculates the reference coordinates */
115	gezelter	507	void calcRefCoords();
116	gezelter	2
117	gezelter	1126	/** Converts Atomic forces and torques to total forces and torques */
118	gezelter	507	void calcForcesAndTorques();
119	gezelter	2
120	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. */
121			Mat3x3d calcForcesAndTorquesAndVirial();
122
123	gezelter	507	/** update the positions of atoms belong to this rigidbody */
124			void updateAtoms();
125	gezelter	2
126	gezelter	507	void updateAtoms(int frame);
127	tim	318
128	gezelter	507	void updateAtomVel();
129	tim	318
130	gezelter	507	void updateAtomVel(int frame);
131	tim	318
132	gezelter	507	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
133			i = atoms_.begin();
134			return i != atoms_.end() ? *i : NULL;
135			}
136	gezelter	2
137	gezelter	507	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
138			++i;
139			return i != atoms_.end() ? *i : NULL;
140			}
141	gezelter	2
142	gezelter	507	std::vector<Atom*>::iterator getBeginAtomIter() {
143			return atoms_.begin();
144			}
145	gezelter	246
146	gezelter	507	std::vector<Atom*>::iterator getEndAtomIter() {
147			return atoms_.end();
148			}
149	gezelter	2
150	gezelter	507	/**
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	gezelter	2
159	gezelter	507	/**
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	gezelter	2
167	gezelter	507	/**
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	gezelter	2
175	gezelter	507	/**
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	gezelter	2
183	gezelter	507	/**
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	gezelter	2
191	gezelter	507	/**
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	gezelter	2
199	gezelter	507	/**
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	gezelter	2
207	gezelter	507	/**
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	gezelter	2
215	gezelter	507	private:
216			std::string name_;
217			Mat3x3d inertiaTensor_;
218			RotMat3x3d sU_; /*< body fixed standard unit vector /
219	gezelter	246
220	gezelter	507	std::vector<Atom*> atoms_;
221			std::vector<Vector3d> refCoords_;
222			std::vector<RotMat3x3d> refOrients_;
223			};
224	gezelter	2
225	gezelter	1390	}//namespace OpenMD
226	gezelter	2
227	gezelter	246	#endif //PRIMITIVES_RIGIDBODY_HPP
228	gezelter	2