Bond angle potential

namespace mdk
class BondAngles : public mdk::Force
#include <BondAngles.hpp>

A force field for bond angles (both heurestic and native variants, depending on whether a triple has an associated native bond angle (in such cases the native variant supercedes the heurestic variant).

Public Functions

virtual void bind(Simulation &simulation) override

Bind the force field to a simulation.

Parameters

simulation – Simulation to bind to.

virtual void asyncPart(Dynamics &dynamics) override

“Asynchronous” part of the potential. Here it’s the only part.

Parameters

dynamics – Dynamics object to add potential energy and forces to.

Private Members

HeuresticBA *heurBA = nullptr

The “heurestic” part of the potential.

NativeBA *natBA = nullptr

The “native” part of the potential.

Bytes inRange

Whether a triple (i-1, i, i+1) is connected, i.e. in one chain.

Friends

friend class HeuresticBA
friend class NativeBA
namespace mdk
class HeuresticBA : public mdk::SimulVar
#include <HeuresticBA.hpp>

“Heurestic” part of the bond angle potential, applied when a triple has no associated native bond angle.

Public Functions

virtual void bind(Simulation &simulation) override

Bind the part to the simulation - in particular, find (and possibly create) BondAngles force field and add itself to it.

Parameters

simulation – Simulation to bind to.

inline void term(int i, double theta, double &V, double &dV_dth) const

Term of the formula for bond angle potential. Note: it’s inline in order for the compiler to inline it in BondAngles.cpp file.

Parameters

  • i – The index i in the triple (i-1, i, i+1).

  • theta – Value of the bond angle between i-1, i and i+1.

  • V – Potential energy reference to add to.

  • dV_dth – Derivative of potential energy wrt the angle theta to add to.

Private Members

double coeff[numOfPTs][D + 1]

Polynomial coefficients.

Bytes angleTypes

List of “types of triples”, or rather pair types for (i, i+1) for a triple (i-1, i, i+1).

Private Static Attributes

static constexpr const int D = 6

Degree of the polynomial.

Friends

friend class BondAngles
namespace mdk
class NativeBA : public mdk::SimulVar
#include <NativeBA.hpp>

“Native” part of the bond angle potential, applied when a triple has an associated native bond angle.

Public Functions

virtual void bind(Simulation &simulation) override

Bind the part to the simulation - in particular, find (and possibly create) BondAngles force field and add itself to it.

Parameters

simulation – Simulation to bind to.

inline void term(int i, double theta, double &V, double &dV_dth) const

Term of the formula for bond angle potential. Note: it’s inline in order for the compiler to inline it in BondAngles.cpp file.

Parameters

  • i – The index i in the triple (i-1, i, i+1).

  • theta – Value of the bond angle between i-1, i and i+1.

  • V – Potential energy reference to add to.

  • dV_dth – Derivative of potential energy wrt the angle theta to add to.

Private Members

Bytes isNative

isNative[i] is 1 if (i-1, i, i+1) has an associated native bond angle, 0 otherwise.

Scalars theta0

theta0[i] contains the native bond angle whenever such is defined. For triples (i-1, i, i+1) which have no such associated angle, the value is undefined.

double CBA = 30.0 * eps / pow(rad, 2)

Value of $k_\theta$.

Friends

friend class BondAngles