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

Comparing:
trunk/src/primitives/RigidBody.hpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/primitives/RigidBody.hpp (file contents), Revision 1794 by gezelter, Thu Sep 6 19:44:06 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:
60	<	RigidBody();
58	>	namespace OpenMD{
59	>	class RigidBody : public StuntDouble {
60	>	public:
61
62	<	virtual std::string getType() { return name_;}
62	>	typedef std::vector<Atom*>::iterator AtomIterator;
63	>
64	>	RigidBody();
65	>
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 inertia tensor of this stuntdouble
102	+	* @see #setI
103	+	*/
104	+	virtual std::vector<RealType> getGrad();
105
106	<	/** Sets the internal unit frame of this stuntdouble by three euler angles */
97	<	void setElectroFrameFromEuler(double phi, double theta, double psi);
98	<
99	<	/**
100	<	* Returns the gradient of this stuntdouble
101	<	* @return the inertia tensor of this stuntdouble
102	<	* @see #setI
103	<	*/
104	<	virtual std::vector<double> getGrad();
106	>	virtual void accept(BaseVisitor* v);
107
108	<	virtual void accept(BaseVisitor* v);
108	>	void addAtom(Atom* at, AtomStamp* ats);
109
110	<	void addAtom(Atom* at, AtomStamp* ats);
110	>	/** calculates the reference coordinates */
111	>	void calcRefCoords();
112
113	<	/** calculate the reference coordinates */
114	<	void calcRefCoords();
113	>	/** Converts Atomic forces and torques to total forces and torques */
114	>	void calcForcesAndTorques();
115
116	<	/** Convert Atomic forces and torques to total forces and torques */
117	<	void calcForcesAndTorques();
116	>	/**
117	>	Converts Atomic forces and torques to total forces and torques
118	>	and computes the rigid body contribution to the virial.
119	>	Returns the rigid body contribution to the virial as a 3x3
120	>	matrix.
121	>	*/
122	>	Mat3x3d calcForcesAndTorquesAndVirial();
123	>
124	>	/** update the positions of atoms belong to this rigidbody */
125	>	void updateAtoms();
126
127	<	/** update the positions of atoms belong to this rigidbody */
117	<	void updateAtoms();
127	>	void updateAtoms(int frame);
128
129	<	Atom* beginAtom(std::vector<Atom*>::iterator& i);
129	>	void updateAtomVel();
130
131	<	Atom* nextAtom(std::vector<Atom*>::iterator& i);
131	>	void updateAtomVel(int frame);
132	>
133	>	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
134	>	i = atoms_.begin();
135	>	return i != atoms_.end() ? *i : NULL;
136	>	}
137
138	<	std::vector<Atom*>::iterator getBeginAtomIter() {
139	<	return atoms_.begin();
140	<	}
138	>	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
139	>	++i;
140	>	return i != atoms_.end() ? *i : NULL;
141	>	}
142	>
143	>	std::vector<Atom*>::iterator getBeginAtomIter() {
144	>	return atoms_.begin();
145	>	}
146
147	<	std::vector<Atom*>::iterator getEndAtomIter() {
148	<	return atoms_.end();
149	<	}
147	>	std::vector<Atom*>::iterator getEndAtomIter() {
148	>	return atoms_.end();
149	>	}
150
151	<	/**
152	<	* Returns the atoms of this rigid body
153	<	* @return the atoms of this rigid body in a vector
154	<	* @deprecate
155	<	*/
156	<	std::vector<Atom*> getAtoms() {
157	<	return atoms_;
158	<	}
151	>	/**
152	>	* Returns the atoms of this rigid body
153	>	* @return the atoms of this rigid body in a vector
154	>	* @deprecate
155	>	*/
156	>	std::vector<Atom*> getAtoms() {
157	>	return atoms_;
158	>	}
159
160	<	/**
161	<	* Returns the number of atoms in this rigid body
162	<	* @return the number of atoms in this rigid body
163	<	*/
164	<	int getNumAtoms() {
165	<	return atoms_.size();
166	<	}
160	>	/**
161	>	* Returns the number of atoms in this rigid body
162	>	* @return the number of atoms in this rigid body
163	>	*/
164	>	int getNumAtoms() {
165	>	return atoms_.size();
166	>	}
167
168	<	/**
169	<	* Return the position of atom which belongs to this rigid body.
170	<	* @return true if index is valid otherwise return false
171	<	* @param pos the position of atom which will be set on return if index is valid
172	<	* @param index the index of the atom in rigid body's private data member atoms_
173	<	*/
174	<	bool getAtomPos(Vector3d& pos, unsigned int index);
168	>	/**
169	>	* Return the position of atom which belongs to this rigid body.
170	>	* @return true if index is valid otherwise return false
171	>	* @param pos the position of atom which will be set on return if index is valid
172	>	* @param index the index of the atom in rigid body's private data member atoms_
173	>	*/
174	>	bool getAtomPos(Vector3d& pos, unsigned int index);
175
176	<	/**
177	<	* Return the position of atom which belongs to this rigid body.
178	<	* @return true if atom belongs to this rigid body,otherwise return false
179	<	* @param pos position of atom which will be set on return if atom belongs to this rigid body
180	<	* @param atom the pointer to an atom
181	<	*/
182	<	bool getAtomPos(Vector3d& pos, Atom* atom);
176	>	/**
177	>	* Return the position of atom which belongs to this rigid body.
178	>	* @return true if atom belongs to this rigid body,otherwise return false
179	>	* @param pos position of atom which will be set on return if atom belongs to this rigid body
180	>	* @param atom the pointer to an atom
181	>	*/
182	>	bool getAtomPos(Vector3d& pos, Atom* atom);
183
184	<	/**
185	<	* Return the velocity of atom which belongs to this rigid body.
186	<	* @return true if index is valid otherwise return false
187	<	* @param vel the velocity of atom which will be set on return if index is valid
188	<	* @param index the index of the atom in rigid body's private data member atoms_
189	<	*/
190	<	bool getAtomVel(Vector3d& vel, unsigned int index);
184	>	/**
185	>	* Return the velocity of atom which belongs to this rigid body.
186	>	* @return true if index is valid otherwise return false
187	>	* @param vel the velocity of atom which will be set on return if index is valid
188	>	* @param index the index of the atom in rigid body's private data member atoms_
189	>	*/
190	>	bool getAtomVel(Vector3d& vel, unsigned int index);
191
192	<	/**
193	<	* Return the velocity of atom which belongs to this rigid body.
194	<	* @return true if atom belongs to this rigid body,otherwise return false
195	<	* @param vel velocity of atom which will be set on return if atom belongs to this rigid body
196	<	* @param atom the pointer to an atom
197	<	*/
198	<	bool getAtomVel(Vector3d& vel, Atom*);
192	>	/**
193	>	* Return the velocity of atom which belongs to this rigid body.
194	>	* @return true if atom belongs to this rigid body,otherwise return false
195	>	* @param vel velocity of atom which will be set on return if atom belongs to this rigid body
196	>	* @param atom the pointer to an atom
197	>	*/
198	>	bool getAtomVel(Vector3d& vel, Atom*);
199
200	<	/**
201	<	* Return the reference coordinate of atom which belongs to this rigid body.
202	<	* @return true if index is valid otherwise return false
203	<	* @param coor the reference coordinate of atom which will be set on return if index is valid
204	<	* @param index the index of the atom in rigid body's private data member atoms_
205	<	*/
206	<	bool getAtomRefCoor(Vector3d& coor, unsigned int index);
200	>	/**
201	>	* Return the reference coordinate of atom which belongs to this rigid body.
202	>	* @return true if index is valid otherwise return false
203	>	* @param coor the reference coordinate of atom which will be set on return if index is valid
204	>	* @param index the index of the atom in rigid body's private data member atoms_
205	>	*/
206	>	bool getAtomRefCoor(Vector3d& coor, unsigned int index);
207
208	<	/**
209	<	* Return the velocity of atom which belongs to this rigid body.
210	<	* @return true if atom belongs to this rigid body,otherwise return false
211	<	* @param coor velocity of atom which will be set on return if atom belongs to this rigid body
212	<	* @param atom the pointer to an atom
213	<	*/
214	<	bool getAtomRefCoor(Vector3d& coor, Atom* atom);
208	>	/**
209	>	* Return the velocity of atom which belongs to this rigid body.
210	>	* @return true if atom belongs to this rigid body,otherwise return false
211	>	* @param coor velocity of atom which will be set on return if atom belongs to this rigid body
212	>	* @param atom the pointer to an atom
213	>	*/
214	>	bool getAtomRefCoor(Vector3d& coor, Atom* atom);
215
216	<	private:
217	<	std::string name_;
218	<	Mat3x3d inertiaTensor_;
219	<	RotMat3x3d sU_;               /**< body fixed standard unit vector */
216	>	private:
217	>	std::string name_;
218	>	Mat3x3d inertiaTensor_;
219	>	RotMat3x3d sU_;               /**< body fixed standard unit vector */
220
221	<	std::vector<Atom*> atoms_;
222	<	std::vector<Vector3d> refCoords_;
223	<	std::vector<RotMat3x3d> refOrients_;
224	<	};
221	>	std::vector<Atom*> atoms_;
222	>	std::vector<Vector3d> refCoords_;
223	>	std::vector<RotMat3x3d> refOrients_;
224	>	};
225
226	<	}//namepace oopse
226	>	}//namespace OpenMD
227
228		#endif //PRIMITIVES_RIGIDBODY_HPP
229

Comparing:
trunk/src/primitives/RigidBody.hpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/primitives/RigidBody.hpp (property svn:keywords), Revision 1794 by gezelter, Thu Sep 6 19:44:06 2012 UTC

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