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#include <vector> |
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#include <iostream> |
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#include "constraints/ConstraintPair.hpp" |
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#include "math/Vector3.hpp" |
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#include "primitives/Atom.hpp" |
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#include "primitives/RigidBody.hpp" |
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< |
//#include "primitives/Bond.hpp" |
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< |
//#include "primitives/Bend.hpp" |
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< |
//#include "primitives/Torsion.hpp" |
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< |
#include "primitives/SRI.hpp" |
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> |
#include "primitives/Bond.hpp" |
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> |
#include "primitives/Bend.hpp" |
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> |
#include "primitives/Torsion.hpp" |
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#include "primitives/CutoffGroup.hpp" |
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namespace oopse{ |
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void addRigidBody(RigidBody *rb); |
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/** add a cutoff group into this molecule */ |
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< |
void addCutoffGroup(CutoffGroup* cp); |
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> |
void addCutoffGroup(CutoffGroup* cp); |
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void addConstraintPair(ConstraintPair* consPair); |
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/** */ |
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void complete(); |
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} |
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/** Returns the total number of constraints in this molecule */ |
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< |
unsigned int getNConstraints() { |
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return constraints_.size(); |
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> |
unsigned int getNConstraintPairs() { |
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> |
return constraintPairs_.size(); |
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} |
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Atom* getAtomAt(unsigned int i) { |
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*/ |
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CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i); |
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< |
Constraint* beginConstraint(std::vector<Constraint*>::iterator& i); |
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> |
ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i); |
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< |
Constraint* nextConstraint(std::vector<Constraint*>::iterator& i); |
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> |
ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i); |
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– |
//void setStampID( int info ) {stampID = info;} |
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void calcForces( void ); |
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void atoms2rigidBodies( void ); |
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/** return the total potential energy of short range interaction of this molecule */ |
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double getPotential(); |
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/** get total mass of this molecule */ |
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double getMass(); |
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/** return the center of mass of this molecule */ |
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Vector3d getCom(); |
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std::vector<RigidBody*> rigidBodies_; |
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std::vector<StuntDouble*> integrableObjects_; |
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std::vector<CutoffGroup*> cutoffGroups_; |
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< |
std::vector<Constraint*> constraints_; |
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> |
std::vector<ConstraintPair*> constraintPairs_; |
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int stampId_; |
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std::string moleculeName_; |
