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#ifndef _SRI_H_ |
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#define _SRI_H_ |
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|
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#include <iostream> |
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|
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#include "primitives/Atom.hpp" |
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#include "primitives/DirectionalAtom.hpp" |
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#include "primitives/AbstractClasses.hpp" |
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|
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// a little home-made vector structure |
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|
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struct vect{ |
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double x; |
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double y; |
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double z; |
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double length; |
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}; |
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|
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/************************************************************************ |
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* |
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* This section describes the base bond, bend, and torsion |
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* classes. later these classes will be extended to good/evil ends. |
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* |
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************************************************************************/ |
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|
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class Bond : public SRI{ |
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|
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public: |
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Bond(); |
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virtual ~Bond(); |
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|
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void calc_forces(); |
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int is_constrained() {return c_is_constrained;} |
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Constraint *get_constraint() {return c_constraint;} |
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void constrain(double bond_distance); |
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|
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protected: |
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virtual double bond_force(double r_ab) = 0; |
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void set_atoms( Atom &, Atom & ); |
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|
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int c_is_constrained; |
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Constraint *c_constraint; |
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Atom * c_p_a; /* atom a */ |
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Atom * c_p_b; /* atom b */ |
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}; |
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|
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|
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class Bend : public SRI{ |
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|
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public: |
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Bend() {} |
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virtual ~Bend() {} |
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|
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virtual void calc_forces(); |
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int is_constrained() {return 0;} |
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Constraint *get_constraint() {return NULL;} |
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void constrain(double bond_distance){} /*meaningless for bends */ |
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|
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protected: |
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virtual double bend_force(double theta) = 0; |
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void set_atoms( Atom &, Atom &, Atom & ); |
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|
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Atom * c_p_a; /* atom a */ |
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Atom * c_p_b; /* atom b */ |
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Atom * c_p_c; /* atom c */ |
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}; |
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|
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class Torsion : public SRI{ |
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|
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public: |
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Torsion() {} |
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virtual ~Torsion() {} |
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|
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void calc_forces(); |
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int is_constrained() {return 0;} |
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Constraint *get_constraint() {return NULL;} |
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void constrain(double bond_distance){} /*meaningless for torsions */ |
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|
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|
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|
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protected: |
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|
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void set_atoms(Atom &, Atom &, Atom &, Atom &); |
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virtual double torsion_force(double cos_phi) = 0; |
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|
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Atom * c_p_a; |
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Atom * c_p_b; |
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Atom * c_p_c; |
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Atom * c_p_d; |
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}; |
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|
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/********************************************************************** |
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* |
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* These next classes are extensions of the base classes. These are |
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* the actual objects which will be used in the simulation. |
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* |
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**********************************************************************/ |
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|
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class ConstrainedBond : public Bond{ |
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|
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public: |
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ConstrainedBond( Atom &a, Atom &b, double constraint ); |
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~ConstrainedBond() {} |
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|
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void printMe( void ){ |
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std::cerr << c_p_a->getType() << " - " << c_p_b->getType() |
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<< ": " << c_p_a->getIndex() << " - " |
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<< c_p_b->getIndex() |
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<< ", d0 = " << d0 << "\n"; |
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} |
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|
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private: |
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double bond_force( double r_ab ){ return 0.0; } |
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double d0; |
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}; |
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|
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class HarmonicBond : public Bond{ |
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|
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public: |
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HarmonicBond(Atom &a, Atom &b, double theR0, double theK0 ); |
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~HarmonicBond(){} |
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|
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void printMe( void ){ |
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std::cerr << c_p_a->getType() << " - " << c_p_b->getType() |
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<< ": " << c_p_a->getIndex() << " - " |
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<< c_p_b->getIndex() |
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<< ", d0 = " << d0 << ", k0 = " << k0 <<"\n"; |
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} |
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|
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private: |
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double bond_force( double r_ab ); |
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double d0; |
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double k0; |
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|
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}; |
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|
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class QuadraticBend : public Bend{ |
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|
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public: |
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QuadraticBend( Atom &a, Atom &b, Atom &c ); |
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~QuadraticBend(){} |
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|
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void setConstants( double the_c1, double the_c2, double the_c3, |
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double the_Th0 ); |
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void printMe( void ){ |
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std::cerr << c_p_a->getType() << " - " << c_p_b->getType() << " - " |
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<< c_p_c->getType() << " : " |
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<< c_p_a->getIndex() << " - " << c_p_b->getIndex() << " - " |
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<< c_p_c->getIndex() |
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<<", k1 = " << c1 << "; k2 = " << c2 |
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<< "; k3 = " << c3 << "; theta0 =" << theta0 << "\n"; |
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} |
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|
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private: |
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double bend_force( double theta ); |
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|
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double c1, c2, c3; |
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double theta0; |
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}; |
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|
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class GhostBend : public Bend{ |
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|
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public: |
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GhostBend( Atom &a, Atom &b ); |
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~GhostBend(){} |
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|
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void calc_forces( void ); |
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|
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void setConstants( double the_c1, double the_c2, double the_c3, |
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double the_Th0 ); |
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void printMe( void ){ |
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std::cerr << c_p_a->getType() << " - " << c_p_b->getType() |
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<< " : " |
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<< c_p_a->getIndex() << " - " << c_p_b->getIndex() << " - " |
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<<", k1 = " << c1 << "; k2 = " << c2 |
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<< "; k3 = " << c3 << "; theta0 =" << theta0 << "\n"; |
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} |
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|
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private: |
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double bend_force( double theta ); |
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|
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double c1, c2, c3; |
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double theta0; |
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|
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DirectionalAtom* atomB; |
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}; |
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|
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class CubicTorsion : public Torsion{ |
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|
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public: |
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CubicTorsion( Atom &a, Atom &b, Atom &c, Atom &d ); |
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~CubicTorsion() {} |
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void setConstants( double the_k1, double the_k2, double the_k3, |
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double the_k4 ); |
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void printMe( void ){ |
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std::cerr << c_p_a->getType() << " - " << c_p_b->getType() << " - " |
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<< c_p_c->getType() << " - " << c_p_d->getType() << ": " |
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<< c_p_a->getIndex() << " - " << c_p_b->getIndex() << " - " |
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<< c_p_c->getIndex() << " - " << c_p_d->getIndex() |
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<< ", k1 = " << k1 << "; k2 = " << k2 |
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<< "; k3 = " << k3 << "; k4 =" << k4 << "\n"; |
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} |
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|
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private: |
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|
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double torsion_force( double cos_phi ); |
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|
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double k1, k2, k3, k4; |
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}; |
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#endif |
