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

Comparing:
trunk/src/primitives/RigidBody.hpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 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	<	#ifndef __RIGIDBODY_HPP__
2	<	#define __RIGIDBODY_HPP__
1	>	/*
2	>	* 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. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
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	>	*
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	>	/**
44	>	* @file RigidBody.hpp
45	>	* @author    tlin
46	>	* @date  10/23/2004
47	>	* @version 1.0
48	>	*/
49
50	+	#ifndef PRIMITIVES_RIGIDBODY_HPP
51	+	#define PRIMITIVES_RIGIDBODY_HPP
52	+
53		#include <vector>
54	<	//#include "primitives/Atom.hpp"
6	<	//#include "types/AtomStamp.hpp"
7	<	#include "types/RigidBodyStamp.hpp"
54	>
55		#include "primitives/StuntDouble.hpp"
56	<	using namespace std;
56	>	#include "primitives/DirectionalAtom.hpp"
57	>	#include "types/AtomStamp.hpp"
58	>	namespace OpenMD{
59	>	class RigidBody : public StuntDouble {
60	>	public:
61
62	<	class Atom;
12	<	class AtomStamp;
62	>	typedef std::vector<Atom*>::iterator AtomIterator;
63
64	<	typedef struct {
15	<	double vec[3];
16	<	double& operator[](int index) {return vec[index];}
17	<	} vec3;
64	>	RigidBody();
65
66	<	typedef struct {
67	<	double mat[3][3];
68	<	double* operator[](int index) {return mat[index];}
69	<	} mat3x3;
66	>	virtual std::string getType() { return name_;}
67	>
68	>	/** Sets the name of this stuntRealType*/
69	>	virtual void setType(const std::string& name) { name_ = name;}
70	>
71
72	<	class RigidBody : public StuntDouble {
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);
92
93	<	public:
94	<
95	<	RigidBody();
96	<	//RigidBody(const RigidBody& rb);
97	<
31	<	virtual ~RigidBody();
32	<
33	<	void addAtom(Atom* at, AtomStamp* ats);
93	>	/**
94	>	* Returns the inertia tensor of this stuntdouble
95	>	* @return the inertia tensor of this stuntdouble
96	>	*/
97	>	virtual Mat3x3d getI();
98
99	<	void getPos( double theP[3] );
100	<	void setPos( double theP[3] );
99	>	/**
100	>	* Returns the gradient of this stuntdouble
101	>	* @return the gradient of this stuntdouble
102	>	*/
103	>	virtual std::vector<RealType> getGrad();
104
105	<	void getVel( double theV[3] );
39	<	void setVel( double theV[3] );
105	>	virtual void accept(BaseVisitor* v);
106
107	<	void getFrc( double theF[3] );
42	<	void addFrc( double theF[3] );
43	<	void zeroForces();
44	<
45	<	virtual bool isLinear() {return is_linear;}
46	<	virtual int linearAxis() {return linear_axis;}
107	>	void addAtom(Atom* at, AtomStamp* ats);
108
109	<	double getMass( void ) { return mass; }
109	>	/** calculates the reference coordinates */
110	>	void calcRefCoords();
111
112	<	void printAmatIndex( void );
113	<	void setEuler( double phi, double theta, double psi );
52	<	void getQ( double the_q[4] ); // get the quanternions
53	<	void setQ( double the_q[4] );
112	>	/** Converts Atomic forces and torques to total forces and torques */
113	>	void calcForcesAndTorques();
114
115	<	void getA( double the_A[3][3] ); // get the full rotation matrix
116	<	void setA( double the_A[3][3] );
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	<	void getJ( double theJ[3] );
59	<	void setJ( double theJ[3] );
126	>	void updateAtoms(int frame);
127
128	<	virtual void setType(char* type) {strcpy(rbName, type);}
62	<	virtual char* getType() { return rbName;}
128	>	void updateAtomVel();
129
130	<	void getTrq( double theT[3] );
131	<	void addTrq( double theT[3] );
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	<	void getI( double the_I[3][3] );
138	<	void lab2Body( double r[3] );
139	<	void body2Lab( double r[3] );
137	>	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
138	>	++i;
139	>	return i != atoms_.end() ? *i : NULL;
140	>	}
141
142	<	double getZangle( );
143	<	void setZangle( double zAng );
144	<	void addZangle( double zAng );
142	>	std::vector<Atom*>::iterator getBeginAtomIter() {
143	>	return atoms_.begin();
144	>	}
145	>
146	>	std::vector<Atom*>::iterator getEndAtomIter() {
147	>	return atoms_.end();
148	>	}
149
150	<	void calcRefCoords( void );
151	<	void doEulerToRotMat(vec3 &euler, mat3x3 &myA );
152	<	void calcForcesAndTorques( void );
153	<	void updateAtoms( void );
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	<	//void yourAtomsHaveMoved( void );
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	<	// Four functions added for derivatives with respect to Euler Angles:
168	<	// (Needed for minimization routines):
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	<	void getGrad(double gradient[6] );
176	<	void getEulerAngles( double myEuler[3] );
177	<
178	<	double max(double x, double y);
179	<	double min(double x, double y);
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);
190
191	<	// utility routines
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	<	void findCOM( void );
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	<	virtual void accept(BaseVisitor* v);
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	<	vector<Atom*> getAtoms() { return myAtoms;}
216	<	int getNumAtoms() {return myAtoms.size();}
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	>	};
224
225	<	void getAtomPos(double theP[3], int index);
102	<	void getAtomVel(double theV[3], int index);
103	<	void getAtomRefCoor(double pos[3], int index);
104	<	protected:
225	>	}//namespace OpenMD
226
227	<	double mass;     // the total mass
107	<	double pos[3];   // the position array (center of mass)
108	<	double vel[3];   // the velocity array (center of mass)
109	<	double frc[3];   // the force array    (center of mass)
110	<	double trq[3];   // the torque vector  ( space fixed )
111	<	double ji[3];    // the angular momentum vector (body fixed)
112	<	double A[3][3];  // the rotation matrix
113	<	double I[3][3];  // the inertial tensor (body fixed)
114	<	double sU[3][3]; // the standard unit vectors (body fixed)
115	<	double zAngle;   // the rotation about the z-axis (body fixed)
227	>	#endif //PRIMITIVES_RIGIDBODY_HPP
228
117	–	bool is_linear;
118	–	int linear_axis;
119	–	double momIntTol;
120	–
121	–	vector<Atom*> myAtoms;  // the vector of atoms
122	–	vector<vec3> refCoords;
123	–	vector<mat3x3> refOrients;
124	–
125	–	char rbName[100]; //it will eventually be converted into string
126	–	};
127	–
128	–	#endif

Comparing:
trunk/src/primitives/RigidBody.hpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 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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