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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 1808 by gezelter, Mon Oct 22 20:42:10 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 54 | Line 55
55		#include "primitives/StuntDouble.hpp"
56		#include "primitives/DirectionalAtom.hpp"
57		#include "types/AtomStamp.hpp"
58	<	namespace oopse{
59	<	class RigidBody : public StuntDouble {
60	<	public:
58	>	namespace OpenMD{
59	>	class RigidBody : public StuntDouble {
60	>	public:
61
62	<	typedef std::vector<Atom*>::iterator AtomIterator;
62	>	typedef std::vector<Atom*>::iterator AtomIterator;
63
64	<	RigidBody();
64	>	RigidBody();
65
66	<	virtual std::string getType() { return name_;}
66	>	virtual std::string getType() { return name_;}
67
68	<	/** Sets the name of this stuntdouble*/
69	<	virtual void setType(const std::string& name) { name_ = name;}
68	>	/** Sets the name of this stuntRealType*/
69	>	virtual void setType(const std::string& name) { name_ = name;}
70
71
72	<	/**
73	<	* Sets  the previous rotation matrix of this stuntdouble
74	<	* @param a  new rotation matrix
75	<	*/
76	<	virtual void setPrevA(const RotMat3x3d& a);
72	>	/**
73	>	* Sets  the previous rotation matrix of this stuntdouble
74	>	* @param a  new rotation matrix
75	>	*/
76	>	virtual void setPrevA(const RotMat3x3d& a);
77
78	<	/**
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);
78	>	/**
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
93	<	/**
94	<	* Returns the inertia tensor of this stuntdouble
95	<	* @return the inertia tensor of this stuntdouble
96	<	*/
97	<	virtual Mat3x3d getI();
93	>	/**
94	>	* Returns the inertia tensor of this stuntdouble
95	>	* @return the inertia tensor of this stuntdouble
96	>	*/
97	>	virtual Mat3x3d getI();
98
99	+	/**
100	+	* Returns the gradient of this stuntdouble
101	+	* @return the gradient of this stuntdouble
102	+	*/
103	+	virtual std::vector<RealType> getGrad();
104
105	<	/** 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();
105	>	virtual void accept(BaseVisitor* v);
106
107	<	virtual void accept(BaseVisitor* v);
107	>	void addAtom(Atom* at, AtomStamp* ats);
108
109	<	void addAtom(Atom* at, AtomStamp* ats);
109	>	/** calculates the reference coordinates */
110	>	void calcRefCoords();
111
112	<	/** calculate the reference coordinates */
113	<	void calcRefCoords();
112	>	/** Converts Atomic forces and torques to total forces and torques */
113	>	void calcForcesAndTorques();
114
115	<	/** Convert Atomic forces and torques to total forces and torques */
116	<	void calcForcesAndTorques();
115	>	/**
116	>	Converts Atomic forces and torques to total forces and torques
117	>	and computes the rigid body contribution to the virial.
118	>	Returns the rigid body contribution to the virial as a 3x3
119	>	matrix.
120	>	*/
121	>	Mat3x3d calcForcesAndTorquesAndVirial();
122	>
123	>	/** update the positions of atoms belong to this rigidbody */
124	>	void updateAtoms();
125
126	<	/** update the positions of atoms belong to this rigidbody */
120	<	void updateAtoms();
126	>	void updateAtoms(int frame);
127
128	<	Atom* beginAtom(std::vector<Atom*>::iterator& i);
128	>	void updateAtomVel();
129
130	<	Atom* nextAtom(std::vector<Atom*>::iterator& i);
130	>	void updateAtomVel(int frame);
131	>
132	>	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
133	>	i = atoms_.begin();
134	>	return i != atoms_.end() ? *i : NULL;
135	>	}
136
137	<	std::vector<Atom*>::iterator getBeginAtomIter() {
138	<	return atoms_.begin();
139	<	}
137	>	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
138	>	++i;
139	>	return i != atoms_.end() ? *i : NULL;
140	>	}
141	>
142	>	std::vector<Atom*>::iterator getBeginAtomIter() {
143	>	return atoms_.begin();
144	>	}
145
146	<	std::vector<Atom*>::iterator getEndAtomIter() {
147	<	return atoms_.end();
148	<	}
146	>	std::vector<Atom*>::iterator getEndAtomIter() {
147	>	return atoms_.end();
148	>	}
149
150	<	/**
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	<	}
150	>	/**
151	>	* Returns the atoms of this rigid body
152	>	* @return the atoms of this rigid body in a vector
153	>	* @deprecated
154	>	*/
155	>	std::vector<Atom*> getAtoms() {
156	>	return atoms_;
157	>	}
158
159	<	/**
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	<	}
159	>	/**
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
167	<	/**
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);
167	>	/**
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
175	<	/**
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);
175	>	/**
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
183	<	/**
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);
183	>	/**
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
191	<	/**
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*);
191	>	/**
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
199	<	/**
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);
199	>	/**
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
207	<	/**
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);
207	>	/**
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
215	<	private:
216	<	std::string name_;
217	<	Mat3x3d inertiaTensor_;
218	<	RotMat3x3d sU_;               /**< body fixed standard unit vector */
215	>	private:
216	>	std::string name_;
217	>	Mat3x3d inertiaTensor_;
218	>	RotMat3x3d sU_;               /**< body fixed standard unit vector */
219
220	<	std::vector<Atom*> atoms_;
221	<	std::vector<Vector3d> refCoords_;
222	<	std::vector<RotMat3x3d> refOrients_;
223	<	};
220	>	std::vector<Atom*> atoms_;
221	>	std::vector<Vector3d> refCoords_;
222	>	std::vector<RotMat3x3d> refOrients_;
223	>	};
224
225	<	}//namepace oopse
225	>	}//namespace OpenMD
226
227		#endif //PRIMITIVES_RIGIDBODY_HPP
228

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 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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