| 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. 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> |
| 5 |
– |
//#include "Atom.hpp" |
| 6 |
– |
//#include "AtomStamp.hpp" |
| 7 |
– |
#include "RigidBodyStamp.hpp" |
| 8 |
– |
#include "StuntDouble.hpp" |
| 9 |
– |
using namespace std; |
| 53 |
|
|
| 54 |
< |
class Atom; |
| 55 |
< |
class AtomStamp; |
| 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 |
|
|
| 61 |
< |
typedef struct { |
| 15 |
< |
double vec[3]; |
| 16 |
< |
double& operator[](int index) {return vec[index];} |
| 17 |
< |
} vec3; |
| 61 |
> |
typedef std::vector<Atom*>::iterator AtomIterator; |
| 62 |
|
|
| 63 |
< |
typedef struct { |
| 20 |
< |
double mat[3][3]; |
| 21 |
< |
double* operator[](int index) {return mat[index];} |
| 22 |
< |
} mat3x3; |
| 63 |
> |
RigidBody(); |
| 64 |
|
|
| 65 |
< |
class RigidBody : public StuntDouble { |
| 65 |
> |
virtual std::string getType() { return name_;} |
| 66 |
> |
|
| 67 |
> |
/** Sets the name of this stuntRealType*/ |
| 68 |
> |
virtual void setType(const std::string& name) { name_ = name;} |
| 69 |
> |
|
| 70 |
|
|
| 71 |
< |
public: |
| 72 |
< |
|
| 73 |
< |
RigidBody(); |
| 74 |
< |
//RigidBody(const RigidBody& rb); |
| 75 |
< |
|
| 76 |
< |
virtual ~RigidBody(); |
| 77 |
< |
|
| 78 |
< |
void addAtom(Atom* at, AtomStamp* ats); |
| 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); |
| 91 |
|
|
| 92 |
< |
void getPos( double theP[3] ); |
| 93 |
< |
void setPos( double theP[3] ); |
| 92 |
> |
/** |
| 93 |
> |
* Returns the inertia tensor of this stuntdouble |
| 94 |
> |
* @return the inertia tensor of this stuntdouble |
| 95 |
> |
*/ |
| 96 |
> |
virtual Mat3x3d getI(); |
| 97 |
|
|
| 38 |
– |
void getVel( double theV[3] ); |
| 39 |
– |
void setVel( double theV[3] ); |
| 98 |
|
|
| 99 |
< |
void getFrc( double theF[3] ); |
| 100 |
< |
void addFrc( double theF[3] ); |
| 101 |
< |
void zeroForces(); |
| 102 |
< |
|
| 103 |
< |
virtual bool isLinear() {return is_linear;} |
| 104 |
< |
virtual int linearAxis() {return linear_axis;} |
| 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<RealType> getGrad(); |
| 108 |
|
|
| 109 |
< |
double getMass( void ) { return mass; } |
| 109 |
> |
virtual void accept(BaseVisitor* v); |
| 110 |
|
|
| 111 |
< |
void printAmatIndex( void ); |
| 51 |
< |
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] ); |
| 111 |
> |
void addAtom(Atom* at, AtomStamp* ats); |
| 112 |
|
|
| 113 |
< |
void getA( double the_A[3][3] ); // get the full rotation matrix |
| 114 |
< |
void setA( double the_A[3][3] ); |
| 113 |
> |
/** calculate the reference coordinates */ |
| 114 |
> |
void calcRefCoords(); |
| 115 |
|
|
| 116 |
< |
void getJ( double theJ[3] ); |
| 117 |
< |
void setJ( double theJ[3] ); |
| 116 |
> |
/** Convert Atomic forces and torques to total forces and torques */ |
| 117 |
> |
void calcForcesAndTorques(); |
| 118 |
|
|
| 119 |
< |
virtual void setType(char* type) {strcpy(rbName, type);} |
| 120 |
< |
virtual char* getType() { return rbName;} |
| 119 |
> |
/** update the positions of atoms belong to this rigidbody */ |
| 120 |
> |
void updateAtoms(); |
| 121 |
|
|
| 122 |
< |
void getTrq( double theT[3] ); |
| 65 |
< |
void addTrq( double theT[3] ); |
| 122 |
> |
void updateAtoms(int frame); |
| 123 |
|
|
| 124 |
< |
void getI( double the_I[3][3] ); |
| 68 |
< |
void lab2Body( double r[3] ); |
| 69 |
< |
void body2Lab( double r[3] ); |
| 124 |
> |
void updateAtomVel(); |
| 125 |
|
|
| 126 |
< |
double getZangle( ); |
| 127 |
< |
void setZangle( double zAng ); |
| 128 |
< |
void addZangle( double zAng ); |
| 126 |
> |
void updateAtomVel(int frame); |
| 127 |
> |
|
| 128 |
> |
Atom* beginAtom(std::vector<Atom*>::iterator& i) { |
| 129 |
> |
i = atoms_.begin(); |
| 130 |
> |
return i != atoms_.end() ? *i : NULL; |
| 131 |
> |
} |
| 132 |
|
|
| 133 |
< |
void calcRefCoords( void ); |
| 134 |
< |
void doEulerToRotMat(vec3 &euler, mat3x3 &myA ); |
| 135 |
< |
void calcForcesAndTorques( void ); |
| 136 |
< |
void updateAtoms( void ); |
| 133 |
> |
Atom* nextAtom(std::vector<Atom*>::iterator& i) { |
| 134 |
> |
++i; |
| 135 |
> |
return i != atoms_.end() ? *i : NULL; |
| 136 |
> |
} |
| 137 |
|
|
| 138 |
< |
//void yourAtomsHaveMoved( void ); |
| 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 |
< |
// Four functions added for derivatives with respect to Euler Angles: |
| 147 |
< |
// (Needed for minimization routines): |
| 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 |
< |
void getGrad(double gradient[6] ); |
| 156 |
< |
void getEulerAngles( double myEuler[3] ); |
| 157 |
< |
|
| 158 |
< |
double max(double x, double y); |
| 159 |
< |
double min(double x, double y); |
| 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 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 |
< |
// utility routines |
| 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 |
< |
void findCOM( void ); |
| 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 |
< |
virtual void accept(BaseVisitor* v); |
| 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 |
< |
vector<Atom*> getAtoms() { return myAtoms;} |
| 196 |
< |
int getNumAtoms() {return myAtoms.size();} |
| 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 |
< |
void getAtomPos(double theP[3], int index); |
| 204 |
< |
void getAtomVel(double theV[3], int index); |
| 205 |
< |
void getAtomRefCoor(double pos[3], int index); |
| 206 |
< |
protected: |
| 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 |
< |
double mass; // the total mass |
| 212 |
< |
double pos[3]; // the position array (center of mass) |
| 213 |
< |
double vel[3]; // the velocity array (center of mass) |
| 214 |
< |
double frc[3]; // the force array (center of mass) |
| 215 |
< |
double trq[3]; // the torque vector ( space fixed ) |
| 216 |
< |
double ji[3]; // the angular momentum vector (body fixed) |
| 217 |
< |
double A[3][3]; // the rotation matrix |
| 218 |
< |
double I[3][3]; // the inertial tensor (body fixed) |
| 219 |
< |
double sU[3][3]; // the standard unit vectors (body fixed) |
| 115 |
< |
double zAngle; // the rotation about the z-axis (body fixed) |
| 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 |
> |
}; |
| 220 |
|
|
| 221 |
< |
bool is_linear; |
| 118 |
< |
int linear_axis; |
| 119 |
< |
double momIntTol; |
| 221 |
> |
}//namepace oopse |
| 222 |
|
|
| 223 |
< |
vector<Atom*> myAtoms; // the vector of atoms |
| 122 |
< |
vector<vec3> refCoords; |
| 123 |
< |
vector<mat3x3> refOrients; |
| 223 |
> |
#endif //PRIMITIVES_RIGIDBODY_HPP |
| 224 |
|
|
| 125 |
– |
char rbName[100]; //it will eventually be converted into string |
| 126 |
– |
}; |
| 127 |
– |
|
| 128 |
– |
#endif |
