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Comparing trunk/src/primitives/RigidBody.hpp (file contents):
Revision 284 by tim, Fri Feb 4 04:57:04 2005 UTC vs.
Revision 963 by tim, Wed May 17 21:51:42 2006 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 55 | Line 55 | namespace oopse{
55   #include "primitives/DirectionalAtom.hpp"
56   #include "types/AtomStamp.hpp"
57   namespace oopse{
58 < class RigidBody : public StuntDouble {
59 <    public:
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 >    /** calculate the reference coordinates */
114 >    void calcRefCoords();
115  
116 <        /** Convert Atomic forces and torques to total forces and torques */
117 <        void calcForcesAndTorques();
116 >    /** Convert 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 >    /** update the positions of atoms belong to this rigidbody */
120 >    void updateAtoms();
121  
122 <        Atom* beginAtom(std::vector<Atom*>::iterator& i);
122 >    void updateAtoms(int frame);
123  
124 <        Atom* nextAtom(std::vector<Atom*>::iterator& i);
124 >    void updateAtomVel();
125  
126 <        std::vector<Atom*>::iterator getBeginAtomIter() {
127 <            return atoms_.begin();
128 <        }
126 >    void updateAtomVel(int frame);
127          
128 <        std::vector<Atom*>::iterator getEndAtomIter() {
129 <            return atoms_.end();
130 <        }
128 >    Atom* beginAtom(std::vector<Atom*>::iterator& i) {
129 >      i = atoms_.begin();
130 >      return i != atoms_.end() ? *i : NULL;
131 >    }
132  
133 <        /**
134 <         * Returns the atoms of this rigid body
135 <         * @return the atoms of this rigid body in a vector
136 <         * @deprecate
138 <         */          
139 <        std::vector<Atom*> getAtoms() {
140 <            return atoms_;
141 <        }
133 >    Atom* nextAtom(std::vector<Atom*>::iterator& i) {
134 >      ++i;
135 >      return i != atoms_.end() ? *i : NULL;
136 >    }
137  
138 <        /**
139 <         * Returns the number of atoms in this rigid body
140 <         * @return the number of atoms in this rigid body
141 <         */
142 <        int getNumAtoms() {
143 <            return atoms_.size();
144 <        }
138 >    std::vector<Atom*>::iterator getBeginAtomIter() {
139 >      return atoms_.begin();
140 >    }
141 >        
142 >    std::vector<Atom*>::iterator getEndAtomIter() {
143 >      return atoms_.end();
144 >    }
145  
146 <        /**
147 <         * Return the position of atom which belongs to this rigid body.
148 <         * @return true if index is valid otherwise return false
149 <         * @param pos the position of atom which will be set on return if index is valid
150 <         * @param index the index of the atom in rigid body's private data member atoms_
151 <         */
152 <        bool getAtomPos(Vector3d& pos, unsigned int index);
146 >    /**
147 >     * Returns the atoms of this rigid body
148 >     * @return the atoms of this rigid body in a vector
149 >     * @deprecate
150 >     */          
151 >    std::vector<Atom*> getAtoms() {
152 >      return atoms_;
153 >    }
154  
155 <        /**
156 <         * Return the position of atom which belongs to this rigid body.
157 <         * @return true if atom belongs to this rigid body,otherwise return false
158 <         * @param pos position of atom which will be set on return if atom belongs to this rigid body
159 <         * @param atom the pointer to an atom
160 <         */            
161 <        bool getAtomPos(Vector3d& pos, Atom* atom);
155 >    /**
156 >     * Returns the number of atoms in this rigid body
157 >     * @return the number of atoms in this rigid body
158 >     */
159 >    int getNumAtoms() {
160 >      return atoms_.size();
161 >    }
162  
163 <        /**
164 <         * Return the velocity of atom which belongs to this rigid body.
165 <         * @return true if index is valid otherwise return false
166 <         * @param vel the velocity of atom which will be set on return if index is valid
167 <         * @param index the index of the atom in rigid body's private data member atoms_
168 <         */
169 <        bool getAtomVel(Vector3d& vel, unsigned int index);
163 >    /**
164 >     * Return the position of atom which belongs to this rigid body.
165 >     * @return true if index is valid otherwise return false
166 >     * @param pos the position of atom which will be set on return if index is valid
167 >     * @param index the index of the atom in rigid body's private data member atoms_
168 >     */
169 >    bool getAtomPos(Vector3d& pos, unsigned int index);
170  
171 <        /**
172 <         * Return the velocity of atom which belongs to this rigid body.
173 <         * @return true if atom belongs to this rigid body,otherwise return false
174 <         * @param vel velocity of atom which will be set on return if atom belongs to this rigid body
175 <         * @param atom the pointer to an atom
176 <         */
177 <        bool getAtomVel(Vector3d& vel, Atom*);
171 >    /**
172 >     * Return the position of atom which belongs to this rigid body.
173 >     * @return true if atom belongs to this rigid body,otherwise return false
174 >     * @param pos position of atom which will be set on return if atom belongs to this rigid body
175 >     * @param atom the pointer to an atom
176 >     */            
177 >    bool getAtomPos(Vector3d& pos, Atom* atom);
178  
179 <        /**
180 <         * Return the reference coordinate of atom which belongs to this rigid body.
181 <         * @return true if index is valid otherwise return false
182 <         * @param coor the reference coordinate of atom which will be set on return if index is valid
183 <         * @param index the index of the atom in rigid body's private data member atoms_
184 <         */
185 <        bool getAtomRefCoor(Vector3d& coor, unsigned int index);
179 >    /**
180 >     * Return the velocity of atom which belongs to this rigid body.
181 >     * @return true if index is valid otherwise return false
182 >     * @param vel the velocity of atom which will be set on return if index is valid
183 >     * @param index the index of the atom in rigid body's private data member atoms_
184 >     */
185 >    bool getAtomVel(Vector3d& vel, unsigned int index);
186  
187 <        /**
188 <         * Return the velocity of atom which belongs to this rigid body.
189 <         * @return true if atom belongs to this rigid body,otherwise return false
190 <         * @param coor velocity of atom which will be set on return if atom belongs to this rigid body
191 <         * @param atom the pointer to an atom
192 <         */
193 <        bool getAtomRefCoor(Vector3d& coor, Atom* atom);
187 >    /**
188 >     * Return the velocity of atom which belongs to this rigid body.
189 >     * @return true if atom belongs to this rigid body,otherwise return false
190 >     * @param vel velocity of atom which will be set on return if atom belongs to this rigid body
191 >     * @param atom the pointer to an atom
192 >     */
193 >    bool getAtomVel(Vector3d& vel, Atom*);
194  
195 <    private:
196 <        std::string name_;        
197 <        Mat3x3d inertiaTensor_;    
198 <        RotMat3x3d sU_;               /**< body fixed standard unit vector */
195 >    /**
196 >     * Return the reference coordinate of atom which belongs to this rigid body.
197 >     * @return true if index is valid otherwise return false
198 >     * @param coor the reference coordinate of atom which will be set on return if index is valid
199 >     * @param index the index of the atom in rigid body's private data member atoms_
200 >     */
201 >    bool getAtomRefCoor(Vector3d& coor, unsigned int index);
202 >
203 >    /**
204 >     * Return the velocity of atom which belongs to this rigid body.
205 >     * @return true if atom belongs to this rigid body,otherwise return false
206 >     * @param coor velocity of atom which will be set on return if atom belongs to this rigid body
207 >     * @param atom the pointer to an atom
208 >     */
209 >    bool getAtomRefCoor(Vector3d& coor, Atom* atom);
210 >
211 >  private:
212 >    std::string name_;        
213 >    Mat3x3d inertiaTensor_;    
214 >    RotMat3x3d sU_;               /**< body fixed standard unit vector */
215          
216 <        std::vector<Atom*> atoms_;
217 <        std::vector<Vector3d> refCoords_;
218 <        std::vector<RotMat3x3d> refOrients_;
219 < };
216 >    std::vector<Atom*> atoms_;
217 >    std::vector<Vector3d> refCoords_;
218 >    std::vector<RotMat3x3d> refOrients_;
219 >  };
220  
221   }//namepace oopse
222  

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