narupatools.imd.interactions

Shorthand methods for creating various IMD interactions.

Functions

constant_interaction

Interaction that applies a constant force to a set of particles.

gaussian_interaction

Interaction that applies a gaussian force to a set of particles.

spring_interaction

Interaction that applies a spring force to a set of particles.
narupatools.imd.interactions.constant_interaction(*, force: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], particles: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], scale: float = 1.0, **kwargs: Any) → narupa.imd.particle_interaction.ParticleInteraction

Interaction that applies a constant force to a set of particles.

This applies a force \(F_C\) on the center of mass equal to:

\[F_C = k F\]

where \(F\) is the force to apply to the center of mass and \(k\) is a scaling factor.

The force \(F_i\) experienced by each particle is given by a mass weighting of this force:

\[F_i = \frac{m_i}{M} F_C\]

where \(m_i\) is the mass of the i-th particle and \(M\) is the total mass of the set of particles the interaction is applied to.

Parameters

  • force – Force \(F\) to apply to the set of particles, in kilojoules per mole per nanometer.

  • particles – Set of particles to apply the interaction to.

  • scale – Dimensionless scaling factor \(k\) to scale the energy and force applied.

  • kwargs – Arbitrary values to add to the interaction.

Returns

A particle interaction that represents the given interactive force.

narupatools.imd.interactions.gaussian_interaction(*, particles: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], scale: float = 1.0, position: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], **kwargs: Any) → narupa.imd.particle_interaction.ParticleInteraction

Interaction that applies a gaussian force to a set of particles.

This applies a force \(F_C\) on the center of mass equal to:

\[F_C = - k (r_C - r_0) \exp(-\frac{(r_C - r_0)^2}{2}))\]

where \(r_C\) is the center of mass of the particles, r_0 is the position of the interaction and \(k\) is a scaling factor.

The force \(F_i\) experienced by each particle is given by a mass weighting of this force:

\[F_i = \frac{m_i}{M} F_C\]

where \(m_i\) is the mass of the i-th particle and \(M\) is the total mass of the set of particles the interaction is applied to.

Parameters

  • position – Position that the gaussian well is centered, in nanometers.

  • particles – Set of particles to apply the interaction to.

  • scale – Dimensionless scaling factor \(k\) to scale the energy and force applied.

  • kwargs – Arbitrary arguments for the interaction.

Returns

A particle interaction that represents the given interactive force.

narupatools.imd.interactions.spring_interaction(*, particles: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], scale: float = 1.0, position: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], **kwargs: Any) → narupa.imd.particle_interaction.ParticleInteraction

Interaction that applies a spring force to a set of particles.

This applies a force \(F_C\) on the center of mass equal to:

\[F_C = - k (r_C - r_0)\]

where \(r_C\) is the center of mass of the particles, r_0 is the position of the interaction and \(k\) is a scaling factor.

The force \(F_i\) experienced by each particle is given by a mass weighting of this force:

\[F_i = \frac{m_i}{M} F_C\]

where \(m_i\) is the mass of the i-th particle and \(M\) is the total mass of the set of particles the interaction is applied to.

Parameters

  • position – Position that the spring is anchored to, in nanometers.

  • particles – Set of particles to apply the interaction to.

  • scale – Dimensionless scaling factor \(k\) to scale the energy and force applied.

  • kwargs – Arbitrary arguments for the interaction.

Returns

A particle interaction that represents the given interactive force.