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#ifndef __RIGIDBODY_HPP__ |
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#define __RIGIDBODY_HPP__ |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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/** |
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* @file RigidBody.hpp |
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* @author tlin |
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* @date 10/23/2004 |
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* @version 1.0 |
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*/ |
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#ifndef PRIMITIVES_RIGIDBODY_HPP |
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#define PRIMITIVES_RIGIDBODY_HPP |
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|
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#include <vector> |
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//#include "primitives/Atom.hpp" |
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//#include "types/AtomStamp.hpp" |
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#include "types/RigidBodyStamp.hpp" |
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|
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#include "primitives/StuntDouble.hpp" |
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using namespace std; |
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#include "primitives/DirectionalAtom.hpp" |
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#include "types/AtomStamp.hpp" |
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namespace oopse{ |
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class RigidBody : public StuntDouble { |
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public: |
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class Atom; |
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class AtomStamp; |
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typedef std::vector<Atom*>::iterator AtomIterator; |
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typedef struct { |
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double vec[3]; |
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double& operator[](int index) {return vec[index];} |
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} vec3; |
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RigidBody(); |
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typedef struct { |
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double mat[3][3]; |
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double* operator[](int index) {return mat[index];} |
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} mat3x3; |
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virtual std::string getType() { return name_;} |
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|
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/** Sets the name of this stuntRealType*/ |
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virtual void setType(const std::string& name) { name_ = name;} |
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class RigidBody : public StuntDouble { |
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/** |
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* Sets the previous rotation matrix of this stuntdouble |
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* @param a new rotation matrix |
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*/ |
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virtual void setPrevA(const RotMat3x3d& a); |
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|
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/** |
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* Sets the current rotation matrix of this stuntdouble |
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* @param a new rotation matrix |
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* @note setA will not change the position and rotation matrix of Directional atoms belong to |
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* this rigidbody. If you want to do that, use #updateAtoms |
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*/ |
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virtual void setA(const RotMat3x3d& a); |
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/** |
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* Sets the rotation matrix of this stuntdouble in specified snapshot |
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* @param a rotation matrix to be set |
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* @param snapshotNo |
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* @see #getA |
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*/ |
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virtual void setA(const RotMat3x3d& a, int snapshotNo); |
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public: |
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RigidBody(); |
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//RigidBody(const RigidBody& rb); |
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virtual ~RigidBody(); |
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void addAtom(Atom* at, AtomStamp* ats); |
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/** |
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* Returns the inertia tensor of this stuntdouble |
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* @return the inertia tensor of this stuntdouble |
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*/ |
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virtual Mat3x3d getI(); |
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void getPos( double theP[3] ); |
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void setPos( double theP[3] ); |
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void getVel( double theV[3] ); |
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void setVel( double theV[3] ); |
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/** Sets the internal unit frame of this stuntdouble by three euler angles */ |
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void setElectroFrameFromEuler(RealType phi, RealType theta, RealType psi); |
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|
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/** |
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* Returns the gradient of this stuntdouble |
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* @return the inertia tensor of this stuntdouble |
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* @see #setI |
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*/ |
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virtual std::vector<RealType> getGrad(); |
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void getFrc( double theF[3] ); |
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void addFrc( double theF[3] ); |
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void zeroForces(); |
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virtual bool isLinear() {return is_linear;} |
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virtual int linearAxis() {return linear_axis;} |
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virtual void accept(BaseVisitor* v); |
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double getMass( void ) { return mass; } |
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void addAtom(Atom* at, AtomStamp* ats); |
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void printAmatIndex( void ); |
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void setEuler( double phi, double theta, double psi ); |
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void getQ( double the_q[4] ); // get the quanternions |
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void setQ( double the_q[4] ); |
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/** calculates the reference coordinates */ |
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void calcRefCoords(); |
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void getA( double the_A[3][3] ); // get the full rotation matrix |
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void setA( double the_A[3][3] ); |
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/** Converts Atomic forces and torques to total forces and torques */ |
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void calcForcesAndTorques(); |
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void getJ( double theJ[3] ); |
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void setJ( double theJ[3] ); |
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/** Converts Atomic forces and torques to total forces and torques and computes the rigid body contribution to the virial. Returns the rigid body contribution to the virial as a 3x3 matrix. */ |
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Mat3x3d calcForcesAndTorquesAndVirial(); |
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virtual void setType(char* type) {strcpy(rbName, type);} |
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virtual char* getType() { return rbName;} |
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/** update the positions of atoms belong to this rigidbody */ |
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void updateAtoms(); |
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void getTrq( double theT[3] ); |
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void addTrq( double theT[3] ); |
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void updateAtoms(int frame); |
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void getI( double the_I[3][3] ); |
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void lab2Body( double r[3] ); |
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void body2Lab( double r[3] ); |
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void updateAtomVel(); |
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double getZangle( ); |
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void setZangle( double zAng ); |
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void addZangle( double zAng ); |
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void updateAtomVel(int frame); |
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Atom* beginAtom(std::vector<Atom*>::iterator& i) { |
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i = atoms_.begin(); |
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return i != atoms_.end() ? *i : NULL; |
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} |
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void calcRefCoords( void ); |
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void doEulerToRotMat(vec3 &euler, mat3x3 &myA ); |
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void calcForcesAndTorques( void ); |
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void updateAtoms( void ); |
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Atom* nextAtom(std::vector<Atom*>::iterator& i) { |
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++i; |
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return i != atoms_.end() ? *i : NULL; |
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} |
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//void yourAtomsHaveMoved( void ); |
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std::vector<Atom*>::iterator getBeginAtomIter() { |
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return atoms_.begin(); |
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} |
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std::vector<Atom*>::iterator getEndAtomIter() { |
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return atoms_.end(); |
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} |
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// Four functions added for derivatives with respect to Euler Angles: |
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// (Needed for minimization routines): |
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/** |
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* Returns the atoms of this rigid body |
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* @return the atoms of this rigid body in a vector |
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* @deprecate |
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*/ |
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std::vector<Atom*> getAtoms() { |
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return atoms_; |
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} |
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void getGrad(double gradient[6] ); |
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void getEulerAngles( double myEuler[3] ); |
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double max(double x, double y); |
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double min(double x, double y); |
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/** |
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* Returns the number of atoms in this rigid body |
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* @return the number of atoms in this rigid body |
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*/ |
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int getNumAtoms() { |
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return atoms_.size(); |
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} |
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/** |
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* Return the position of atom which belongs to this rigid body. |
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* @return true if index is valid otherwise return false |
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* @param pos the position of atom which will be set on return if index is valid |
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* @param index the index of the atom in rigid body's private data member atoms_ |
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*/ |
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bool getAtomPos(Vector3d& pos, unsigned int index); |
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// utility routines |
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/** |
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* Return the position of atom which belongs to this rigid body. |
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* @return true if atom belongs to this rigid body,otherwise return false |
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* @param pos position of atom which will be set on return if atom belongs to this rigid body |
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* @param atom the pointer to an atom |
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*/ |
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bool getAtomPos(Vector3d& pos, Atom* atom); |
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void findCOM( void ); |
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/** |
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* Return the velocity of atom which belongs to this rigid body. |
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* @return true if index is valid otherwise return false |
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* @param vel the velocity of atom which will be set on return if index is valid |
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* @param index the index of the atom in rigid body's private data member atoms_ |
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*/ |
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bool getAtomVel(Vector3d& vel, unsigned int index); |
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virtual void accept(BaseVisitor* v); |
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/** |
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* Return the velocity of atom which belongs to this rigid body. |
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* @return true if atom belongs to this rigid body,otherwise return false |
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* @param vel velocity of atom which will be set on return if atom belongs to this rigid body |
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* @param atom the pointer to an atom |
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*/ |
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bool getAtomVel(Vector3d& vel, Atom*); |
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vector<Atom*> getAtoms() { return myAtoms;} |
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int getNumAtoms() {return myAtoms.size();} |
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/** |
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* Return the reference coordinate of atom which belongs to this rigid body. |
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* @return true if index is valid otherwise return false |
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* @param coor the reference coordinate of atom which will be set on return if index is valid |
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* @param index the index of the atom in rigid body's private data member atoms_ |
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*/ |
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bool getAtomRefCoor(Vector3d& coor, unsigned int index); |
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void getAtomPos(double theP[3], int index); |
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void getAtomVel(double theV[3], int index); |
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void getAtomRefCoor(double pos[3], int index); |
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protected: |
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/** |
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* Return the velocity of atom which belongs to this rigid body. |
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* @return true if atom belongs to this rigid body,otherwise return false |
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* @param coor velocity of atom which will be set on return if atom belongs to this rigid body |
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* @param atom the pointer to an atom |
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*/ |
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bool getAtomRefCoor(Vector3d& coor, Atom* atom); |
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double mass; // the total mass |
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double pos[3]; // the position array (center of mass) |
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double vel[3]; // the velocity array (center of mass) |
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double frc[3]; // the force array (center of mass) |
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double trq[3]; // the torque vector ( space fixed ) |
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double ji[3]; // the angular momentum vector (body fixed) |
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double A[3][3]; // the rotation matrix |
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double I[3][3]; // the inertial tensor (body fixed) |
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double sU[3][3]; // the standard unit vectors (body fixed) |
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double zAngle; // the rotation about the z-axis (body fixed) |
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private: |
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std::string name_; |
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Mat3x3d inertiaTensor_; |
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RotMat3x3d sU_; /**< body fixed standard unit vector */ |
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std::vector<Atom*> atoms_; |
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std::vector<Vector3d> refCoords_; |
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std::vector<RotMat3x3d> refOrients_; |
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}; |
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bool is_linear; |
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int linear_axis; |
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double momIntTol; |
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}//namepace oopse |
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vector<Atom*> myAtoms; // the vector of atoms |
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vector<vec3> refCoords; |
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vector<mat3x3> refOrients; |
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#endif //PRIMITIVES_RIGIDBODY_HPP |
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char rbName[100]; //it will eventually be converted into string |
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}; |
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|
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#endif |
