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root/OpenMD/branches/development/src/primitives/RigidBody.hpp

Comparing:
trunk/src/primitives/RigidBody.hpp (file contents), Revision 284 by tim, Fri Feb 4 04:57:04 2005 UTC vs.
branches/development/src/primitives/RigidBody.hpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 54 | Line 54
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:
57	>	namespace OpenMD{
58	>	class RigidBody : public StuntDouble {
59	>	public:
60
61	<	typedef std::vector<Atom*>::iterator AtomIterator;
61	>	typedef std::vector<Atom*>::iterator AtomIterator;
62
63	<	RigidBody();
63	>	RigidBody();
64
65	<	virtual std::string getType() { return name_;}
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;}
67	>	/** Sets the name of this stuntRealType*/
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);
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);
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();
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);
99	>	/** Sets the internal unit frame of this stuntdouble by three euler angles */
100	>	void setElectroFrameFromEuler(RealType phi, RealType theta, RealType 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();
102	>	/**
103	>	* Returns the gradient of this stuntdouble
104	>	* @return the inertia tensor of this stuntdouble
105	>	* @see #setI
106	>	*/
107	>	virtual std::vector<RealType> getGrad();
108
109	<	virtual void accept(BaseVisitor* v);
109	>	virtual void accept(BaseVisitor* v);
110
111	<	void addAtom(Atom* at, AtomStamp* ats);
111	>	void addAtom(Atom* at, AtomStamp* ats);
112
113	<	/** calculate the reference coordinates */
114	<	void calcRefCoords();
113	>	/** calculates the reference coordinates */
114	>	void calcRefCoords();
115
116	<	/** Convert Atomic forces and torques to total forces and torques */
117	<	void calcForcesAndTorques();
116	>	/** Converts 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();
119	>	/** 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	<	Atom* beginAtom(std::vector<Atom*>::iterator& i);
122	>	/** update the positions of atoms belong to this rigidbody */
123	>	void updateAtoms();
124
125	<	Atom* nextAtom(std::vector<Atom*>::iterator& i);
125	>	void updateAtoms(int frame);
126
127	<	std::vector<Atom*>::iterator getBeginAtomIter() {
128	<	return atoms_.begin();
129	<	}
127	>	void updateAtomVel();
128	>
129	>	void updateAtomVel(int frame);
130
131	<	std::vector<Atom*>::iterator getEndAtomIter() {
132	<	return atoms_.end();
133	<	}
131	>	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
132	>	i = atoms_.begin();
133	>	return i != atoms_.end() ? *i : NULL;
134	>	}
135
136	<	/**
137	<	* Returns the atoms of this rigid body
138	<	* @return the atoms of this rigid body in a vector
139	<	* @deprecate
138	<	*/
139	<	std::vector<Atom*> getAtoms() {
140	<	return atoms_;
141	<	}
136	>	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
137	>	++i;
138	>	return i != atoms_.end() ? *i : NULL;
139	>	}
140
141	<	/**
142	<	* Returns the number of atoms in this rigid body
143	<	* @return the number of atoms in this rigid body
144	<	*/
145	<	int getNumAtoms() {
146	<	return atoms_.size();
147	<	}
141	>	std::vector<Atom*>::iterator getBeginAtomIter() {
142	>	return atoms_.begin();
143	>	}
144	>
145	>	std::vector<Atom*>::iterator getEndAtomIter() {
146	>	return atoms_.end();
147	>	}
148
149	<	/**
150	<	* Return the position of atom which belongs to this rigid body.
151	<	* @return true if index is valid otherwise return false
152	<	* @param pos the position of atom which will be set on return if index is valid
153	<	* @param index the index of the atom in rigid body's private data member atoms_
154	<	*/
155	<	bool getAtomPos(Vector3d& pos, unsigned int index);
149	>	/**
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
158	<	/**
159	<	* Return the position of atom which belongs to this rigid body.
160	<	* @return true if atom belongs to this rigid body,otherwise return false
161	<	* @param pos position of atom which will be set on return if atom belongs to this rigid body
162	<	* @param atom the pointer to an atom
163	<	*/
164	<	bool getAtomPos(Vector3d& pos, Atom* atom);
158	>	/**
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
166	<	/**
167	<	* Return the velocity of atom which belongs to this rigid body.
168	<	* @return true if index is valid otherwise return false
169	<	* @param vel the velocity 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 getAtomVel(Vector3d& vel, unsigned int index);
166	>	/**
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
174	<	/**
175	<	* Return the velocity of atom which belongs to this rigid body.
176	<	* @return true if atom belongs to this rigid body,otherwise return false
177	<	* @param vel velocity 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 getAtomVel(Vector3d& vel, Atom*);
174	>	/**
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
182	<	/**
183	<	* Return the reference coordinate of atom which belongs to this rigid body.
184	<	* @return true if index is valid otherwise return false
185	<	* @param coor the reference coordinate 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 getAtomRefCoor(Vector3d& coor, unsigned int index);
182	>	/**
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
190	<	/**
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 coor 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 getAtomRefCoor(Vector3d& coor, Atom* atom);
190	>	/**
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
198	<	private:
199	<	std::string name_;
200	<	Mat3x3d inertiaTensor_;
201	<	RotMat3x3d sU_;               /**< body fixed standard unit vector */
198	>	/**
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	>
206	>	/**
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	>
214	>	private:
215	>	std::string name_;
216	>	Mat3x3d inertiaTensor_;
217	>	RotMat3x3d sU_;               /**< body fixed standard unit vector */
218
219	<	std::vector<Atom*> atoms_;
220	<	std::vector<Vector3d> refCoords_;
221	<	std::vector<RotMat3x3d> refOrients_;
222	<	};
219	>	std::vector<Atom*> atoms_;
220	>	std::vector<Vector3d> refCoords_;
221	>	std::vector<RotMat3x3d> refOrients_;
222	>	};
223
224	<	}//namepace oopse
224	>	}//namespace OpenMD
225
226		#endif //PRIMITIVES_RIGIDBODY_HPP
227

Comparing:
trunk/src/primitives/RigidBody.hpp (property svn:keywords), Revision 284 by tim, Fri Feb 4 04:57:04 2005 UTC vs.
branches/development/src/primitives/RigidBody.hpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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