test/brains/RigidBody.hpp

/*
 * Copyright (C) 2000-2009  The Open Molecular Dynamics Engine (OpenMD) project
 * 
 * Contact: gezelter@openscience.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */

/**
 * @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"
namespace OpenMD{
    class RigidBody : public StuntDouble {
        public:
            RigidBody();

           /**
             * 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 
             */         
            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 setUnitFrameFromEuler(double phi, double theta, double psi);
            
            /**
             * Returns the gradient of this stuntdouble
             * @return the inertia tensor of this stuntdouble
             * @see #setI
             */ 
            virtual std::vector<double> getGrad();

            virtual void accept(BaseVisitor* v);

            void addAtom(Atom* atom);

            /** calculate the reference coordinates */
            void calcRefCoords();

            /** Convert Atomic forces and torques to total forces and torques */
            void calcForcesAndTorques();

            /** update the positions of atoms belong to this rigidbody */
            void updateAtoms();

            /** 
             * Returns the atoms of this rigid body
             * @return the atoms of this rigid body in a vector
             */           
            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:
            
            Mat3x3d inertiaTensor_;     
            RotMat3x3d sU_;               /**< body fixed standard unit vector */
            
            std::vector<Atom*> atoms_;
            std::vector<Vector3d> refCoords_;
    };

}//namepace OpenMD

#endif //PRIMITIVES_RIGIDBODY_HPP

Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	6616 byte(s)
Log Message:	Creating busticated version of OpenMD
#	User	Rev	Content
1	tim	147	/*
2	gezelter	1390	* Copyright (C) 2000-2009 The Open Molecular Dynamics Engine (OpenMD) project
3	tim	147	*
4	gezelter	1390	* Contact: gezelter@openscience.org
5	tim	147	*
6			* This program is free software; you can redistribute it and/or
7			* modify it under the terms of the GNU Lesser General Public License
8			* as published by the Free Software Foundation; either version 2.1
9			* of the License, or (at your option) any later version.
10			* All we ask is that proper credit is given for our work, which includes
11			* - but is not limited to - adding the above copyright notice to the beginning
12			* of your source code files, and to any copyright notice that you may distribute
13			* with programs based on this work.
14			*
15			* This program is distributed in the hope that it will be useful,
16			* but WITHOUT ANY WARRANTY; without even the implied warranty of
17			* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18			* GNU Lesser General Public License for more details.
19			*
20			* You should have received a copy of the GNU Lesser General Public License
21			* along with this program; if not, write to the Free Software
22			* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23			*
24			*/
25
26			/**
27			* @file RigidBody.hpp
28			* @author tlin
29			* @date 10/23/2004
30			* @version 1.0
31			*/
32
33			#ifndef PRIMITIVES_RIGIDBODY_HPP
34			#define PRIMITIVES_RIGIDBODY_HPP
35
36	tim	190	#include <vector>
37	tim	147
38	tim	190	#include "primitives/StuntDouble.hpp"
39	tim	197	#include "primitives/DirectionalAtom.hpp"
40	gezelter	1390	namespace OpenMD{
41	tim	190	class RigidBody : public StuntDouble {
42	tim	147	public:
43			RigidBody();
44	tim	189
45			/**
46			* Sets the previous rotation matrix of this stuntdouble
47			* @param a new rotation matrix
48			*/
49			virtual void setPrevA(const RotMat3x3d& a);
50
51			/**
52			* Sets the current rotation matrix of this stuntdouble
53			* @param a new rotation matrix
54			*/
55			virtual void setA(const RotMat3x3d& a);
56			/**
57			* Sets the rotation matrix of this stuntdouble in specified snapshot
58			* @param a rotation matrix to be set
59			* @param snapshotNo
60			* @see #getA
61			*/
62			virtual void setA(const RotMat3x3d& a, int snapshotNo);
63
64	tim	147	/**
65			* Returns the inertia tensor of this stuntdouble
66			* @return the inertia tensor of this stuntdouble
67			*/
68			virtual Mat3x3d getI();
69
70
71	tim	190	/** Sets the internal unit frame of this stuntdouble by three euler angles */
72			void setUnitFrameFromEuler(double phi, double theta, double psi);
73
74	tim	147	/**
75			* Returns the gradient of this stuntdouble
76			* @return the inertia tensor of this stuntdouble
77			* @see #setI
78			*/
79			virtual std::vector<double> getGrad();
80
81			virtual void accept(BaseVisitor* v);
82
83	tim	152	void addAtom(Atom* atom);
84
85			/** calculate the reference coordinates */
86	tim	147	void calcRefCoords();
87
88			/** Convert Atomic forces and torques to total forces and torques */
89			void calcForcesAndTorques();
90
91			/** update the positions of atoms belong to this rigidbody */
92			void updateAtoms();
93
94			/**
95			* Returns the atoms of this rigid body
96			* @return the atoms of this rigid body in a vector
97			*/
98	tim	190	std::vector<Atom*> getAtoms() {
99			return atoms_;
100			}
101	tim	147
102			/**
103			* Returns the number of atoms in this rigid body
104			* @return the number of atoms in this rigid body
105			*/
106	tim	190	int getNumAtoms() {
107			return atoms_.size();
108			}
109	tim	147
110	tim	190	/**
111			* Return the position of atom which belongs to this rigid body.
112			* @return true if index is valid otherwise return false
113			* @param pos the position of atom which will be set on return if index is valid
114			* @param index the index of the atom in rigid body's private data member atoms_
115			*/
116			bool getAtomPos(Vector3d& pos, unsigned int index);
117
118			/**
119			* Return the position of atom which belongs to this rigid body.
120			* @return true if atom belongs to this rigid body,otherwise return false
121			* @param pos position of atom which will be set on return if atom belongs to this rigid body
122			* @param atom the pointer to an atom
123			*/
124	tim	147	bool getAtomPos(Vector3d& pos, Atom* atom);
125
126	tim	190	/**
127			* Return the velocity of atom which belongs to this rigid body.
128			* @return true if index is valid otherwise return false
129			* @param vel the velocity of atom which will be set on return if index is valid
130			* @param index the index of the atom in rigid body's private data member atoms_
131			*/
132			bool getAtomVel(Vector3d& vel, unsigned int index);
133
134			/**
135			* Return the velocity of atom which belongs to this rigid body.
136			* @return true if atom belongs to this rigid body,otherwise return false
137			* @param vel velocity of atom which will be set on return if atom belongs to this rigid body
138			* @param atom the pointer to an atom
139			*/
140	tim	147	bool getAtomVel(Vector3d& vel, Atom*);
141
142	tim	190	/**
143			* Return the reference coordinate of atom which belongs to this rigid body.
144			* @return true if index is valid otherwise return false
145			* @param coor the reference coordinate of atom which will be set on return if index is valid
146			* @param index the index of the atom in rigid body's private data member atoms_
147			*/
148			bool getAtomRefCoor(Vector3d& coor, unsigned int index);
149
150			/**
151			* Return the velocity of atom which belongs to this rigid body.
152			* @return true if atom belongs to this rigid body,otherwise return false
153			* @param coor velocity of atom which will be set on return if atom belongs to this rigid body
154			* @param atom the pointer to an atom
155			*/
156	tim	147	bool getAtomRefCoor(Vector3d& coor, Atom* atom);
157
158			private:
159
160	tim	189	Mat3x3d inertiaTensor_;
161			RotMat3x3d sU_; /*< body fixed standard unit vector /
162
163	tim	190	std::vector<Atom*> atoms_;
164			std::vector<Vector3d> refCoords_;
165	tim	147	};
166
167	gezelter	1390	}//namepace OpenMD
168	tim	147
169			#endif //PRIMITIVES_RIGIDBODY_HPP
170