| 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. 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 |
| 19 |
* notice, this list of conditions and the following disclaimer. |
| 20 |
* |
| 21 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
* documentation and/or other materials provided with the |
| 24 |
* distribution. |
| 25 |
* |
| 26 |
* This software is provided "AS IS," without a warranty of any |
| 27 |
* kind. All express or implied conditions, representations and |
| 28 |
* warranties, including any implied warranty of merchantability, |
| 29 |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
* be liable for any damages suffered by licensee as a result of |
| 32 |
* using, modifying or distributing the software or its |
| 33 |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
* damages, however caused and regardless of the theory of liability, |
| 37 |
* arising out of the use of or inability to use software, even if the |
| 38 |
* University of Notre Dame has been advised of the possibility of |
| 39 |
* such damages. |
| 40 |
*/ |
| 41 |
|
| 42 |
/** |
| 43 |
* @file RigidBody.hpp |
| 44 |
* @author tlin |
| 45 |
* @date 10/23/2004 |
| 46 |
* @version 1.0 |
| 47 |
*/ |
| 48 |
|
| 49 |
#ifndef PRIMITIVES_RIGIDBODY_HPP |
| 50 |
#define PRIMITIVES_RIGIDBODY_HPP |
| 51 |
|
| 52 |
#include <vector> |
| 53 |
|
| 54 |
#include "primitives/StuntDouble.hpp" |
| 55 |
#include "primitives/DirectionalAtom.hpp" |
| 56 |
#include "types/AtomStamp.hpp" |
| 57 |
namespace oopse{ |
| 58 |
class RigidBody : public StuntDouble { |
| 59 |
public: |
| 60 |
RigidBody(); |
| 61 |
|
| 62 |
virtual std::string getType() { return name_;} |
| 63 |
|
| 64 |
/** Sets the name of this stuntdouble*/ |
| 65 |
virtual void setType(const std::string& name) { name_ = name;} |
| 66 |
|
| 67 |
|
| 68 |
/** |
| 69 |
* Sets the previous rotation matrix of this stuntdouble |
| 70 |
* @param a new rotation matrix |
| 71 |
*/ |
| 72 |
virtual void setPrevA(const RotMat3x3d& a); |
| 73 |
|
| 74 |
/** |
| 75 |
* Sets the current rotation matrix of this stuntdouble |
| 76 |
* @param a new rotation matrix |
| 77 |
* @note setA will not change the position and rotation matrix of Directional atoms belong to |
| 78 |
* this rigidbody. If you want to do that, use #updateAtoms |
| 79 |
*/ |
| 80 |
virtual void setA(const RotMat3x3d& a); |
| 81 |
/** |
| 82 |
* Sets the rotation matrix of this stuntdouble in specified snapshot |
| 83 |
* @param a rotation matrix to be set |
| 84 |
* @param snapshotNo |
| 85 |
* @see #getA |
| 86 |
*/ |
| 87 |
virtual void setA(const RotMat3x3d& a, int snapshotNo); |
| 88 |
|
| 89 |
/** |
| 90 |
* Returns the inertia tensor of this stuntdouble |
| 91 |
* @return the inertia tensor of this stuntdouble |
| 92 |
*/ |
| 93 |
virtual Mat3x3d getI(); |
| 94 |
|
| 95 |
|
| 96 |
/** 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(); |
| 105 |
|
| 106 |
virtual void accept(BaseVisitor* v); |
| 107 |
|
| 108 |
void addAtom(Atom* at, AtomStamp* ats); |
| 109 |
|
| 110 |
/** calculate the reference coordinates */ |
| 111 |
void calcRefCoords(); |
| 112 |
|
| 113 |
/** Convert Atomic forces and torques to total forces and torques */ |
| 114 |
void calcForcesAndTorques(); |
| 115 |
|
| 116 |
/** update the positions of atoms belong to this rigidbody */ |
| 117 |
void updateAtoms(); |
| 118 |
|
| 119 |
Atom* beginAtom(std::vector<Atom*>::iterator& i); |
| 120 |
|
| 121 |
Atom* nextAtom(std::vector<Atom*>::iterator& i); |
| 122 |
|
| 123 |
std::vector<Atom*>::iterator getBeginAtomIter() { |
| 124 |
return atoms_.begin(); |
| 125 |
} |
| 126 |
|
| 127 |
std::vector<Atom*>::iterator getEndAtomIter() { |
| 128 |
return atoms_.end(); |
| 129 |
} |
| 130 |
|
| 131 |
/** |
| 132 |
* Returns the atoms of this rigid body |
| 133 |
* @return the atoms of this rigid body in a vector |
| 134 |
* @deprecate |
| 135 |
*/ |
| 136 |
std::vector<Atom*> getAtoms() { |
| 137 |
return atoms_; |
| 138 |
} |
| 139 |
|
| 140 |
/** |
| 141 |
* Returns the number of atoms in this rigid body |
| 142 |
* @return the number of atoms in this rigid body |
| 143 |
*/ |
| 144 |
int getNumAtoms() { |
| 145 |
return atoms_.size(); |
| 146 |
} |
| 147 |
|
| 148 |
/** |
| 149 |
* Return the position of atom which belongs to this rigid body. |
| 150 |
* @return true if index is valid otherwise return false |
| 151 |
* @param pos the position of atom which will be set on return if index is valid |
| 152 |
* @param index the index of the atom in rigid body's private data member atoms_ |
| 153 |
*/ |
| 154 |
bool getAtomPos(Vector3d& pos, unsigned int index); |
| 155 |
|
| 156 |
/** |
| 157 |
* Return the position of atom which belongs to this rigid body. |
| 158 |
* @return true if atom belongs to this rigid body,otherwise return false |
| 159 |
* @param pos position of atom which will be set on return if atom belongs to this rigid body |
| 160 |
* @param atom the pointer to an atom |
| 161 |
*/ |
| 162 |
bool getAtomPos(Vector3d& pos, Atom* atom); |
| 163 |
|
| 164 |
/** |
| 165 |
* Return the velocity of atom which belongs to this rigid body. |
| 166 |
* @return true if index is valid otherwise return false |
| 167 |
* @param vel the velocity of atom which will be set on return if index is valid |
| 168 |
* @param index the index of the atom in rigid body's private data member atoms_ |
| 169 |
*/ |
| 170 |
bool getAtomVel(Vector3d& vel, unsigned int index); |
| 171 |
|
| 172 |
/** |
| 173 |
* Return the velocity of atom which belongs to this rigid body. |
| 174 |
* @return true if atom belongs to this rigid body,otherwise return false |
| 175 |
* @param vel velocity of atom which will be set on return if atom belongs to this rigid body |
| 176 |
* @param atom the pointer to an atom |
| 177 |
*/ |
| 178 |
bool getAtomVel(Vector3d& vel, Atom*); |
| 179 |
|
| 180 |
/** |
| 181 |
* Return the reference coordinate of atom which belongs to this rigid body. |
| 182 |
* @return true if index is valid otherwise return false |
| 183 |
* @param coor the reference coordinate of atom which will be set on return if index is valid |
| 184 |
* @param index the index of the atom in rigid body's private data member atoms_ |
| 185 |
*/ |
| 186 |
bool getAtomRefCoor(Vector3d& coor, unsigned int index); |
| 187 |
|
| 188 |
/** |
| 189 |
* Return the velocity of atom which belongs to this rigid body. |
| 190 |
* @return true if atom belongs to this rigid body,otherwise return false |
| 191 |
* @param coor velocity of atom which will be set on return if atom belongs to this rigid body |
| 192 |
* @param atom the pointer to an atom |
| 193 |
*/ |
| 194 |
bool getAtomRefCoor(Vector3d& coor, Atom* atom); |
| 195 |
|
| 196 |
private: |
| 197 |
std::string name_; |
| 198 |
Mat3x3d inertiaTensor_; |
| 199 |
RotMat3x3d sU_; /**< body fixed standard unit vector */ |
| 200 |
|
| 201 |
std::vector<Atom*> atoms_; |
| 202 |
std::vector<Vector3d> refCoords_; |
| 203 |
std::vector<RotMat3x3d> refOrients_; |
| 204 |
}; |
| 205 |
|
| 206 |
}//namepace oopse |
| 207 |
|
| 208 |
#endif //PRIMITIVES_RIGIDBODY_HPP |
| 209 |
|
