OAT external force utilities documentation

Forces

Python data structures for all forces defined by oxDNA

oxDNA_analysis_tools.external_force_utils.forces.mutual_trap	A spring force that pulls a particle towards the position of another particle
oxDNA_analysis_tools.external_force_utils.forces.string	A linear force along a vector
oxDNA_analysis_tools.external_force_utils.forces.harmonic_trap	A linear potential well that traps a particle
oxDNA_analysis_tools.external_force_utils.forces.rotating_harmonic_trap	A harmonic trap that rotates in space with constant angular velocity
oxDNA_analysis_tools.external_force_utils.forces.repulsion_plane	A plane that forces the affected particle to stay on one side.
oxDNA_analysis_tools.external_force_utils.forces.attraction_plane	A plane that pulls the affected particle towards it while staying on one side.
oxDNA_analysis_tools.external_force_utils.forces.repulsion_sphere	A sphere that encloses the particle

oxDNA_analysis_tools.external_force_utils.forces.mutual_trap(particle: int, ref_particle: int, stiff: float, r0: float, PBC: bool, rate: float = 0, stiff_rate: float = 0) → Dict

A spring force that pulls a particle towards the position of another particle

Parameters:

• particle (int) – the particle that the force acts upon

• ref_particle (int) – the particle that the particle will be pulled towards

• stiff (float) – the force constant of the spring (in simulation units)

• r0 (float) – the equlibrium distance of the spring

• PBC (0 or 1) – does the force calculation take PBC into account (almost always 1)

• rate (float) – changes r0 by this much every time step

• stiff_rate (float) – changes stiff by this much every time step

oxDNA_analysis_tools.external_force_utils.forces.string(particle: int, f0: float, rate: float, direction: List[float]) → Dict

A linear force along a vector

Parameters:

• particle (int) – the particle that the force acts upon

• f0 (float) – the initial strength of the force at t=0 (in simulation units)

• rate (float) – growing rate of the force (simulation units/timestep)

• direction ([float, float, float]) – the direction of the force

oxDNA_analysis_tools.external_force_utils.forces.harmonic_trap(particle: int, pos0: List[float], stiff: float, rate: float, direction: List[float]) → Dict

A linear potential well that traps a particle

Parameters:

• particle (int) – the particle that the force acts upon

• pos0 ([float, float, float]) – the position of the trap at t=0

• stiff (float) – the stiffness of the trap (force = stiff * dx)

• rate (float) – the velocity of the trap (simulation units/time step)

• direction ([float, float, float]) – the direction of movement of the trap

oxDNA_analysis_tools.external_force_utils.forces.rotating_harmonic_trap(particle: int, pos0: List[float], stiff: float, rate: float, base: float, center: List[float], axis: List[float], mask: List[float]) → Dict

A harmonic trap that rotates in space with constant angular velocity

Parameters:

• particle (int) – the particle that the force acts upon

• pos0 ([float, float, float]) – the position of the trap at t=0

• stiff (float) – the stiffness of the trap (force = stiff * dx)

• rate (float) – the angular velocity of the trap (simulation units/time step)

• base (float) – initial phase of the trap

• center ([float, float, float]) – the center of the circle

• axis ([float, float, float]) – the rotation axis of the trap

• mask ([float, float, float]) – the masking vector of the trap (force vector is element-wise multiplied by mask)

oxDNA_analysis_tools.external_force_utils.forces.repulsion_plane(particle: int, stiff: float, direction: List[float], position: List[float]) → Dict

A plane that forces the affected particle to stay on one side.

Parameters:

• particle (int) – the particle that the force acts upon. -1 will act on whole system.

• stiff (float) – the stiffness of the trap (force = stiff * distance below plane)

• direction ([float, float, float]) – the normal vecor to the plane

• position ([float, float, float]) – position of the plane (plane is d0*x + d1*y + d2*z + position = 0)

oxDNA_analysis_tools.external_force_utils.forces.attraction_plane(particle: int, stiff: float, direction: List[float], position: List[float]) → Dict

A plane that pulls the affected particle towards it while staying on one side.

Parameters:

• particle (int) – the particle that the force acts upon. -1 will act on whole system.

• stiff (float) – the stiffness of the trap (force = stiff * distance below plane)

• direction ([float, float, float]) – the normal vector to the plane

• position ([float, float, float]) – position of the plane (plane is d0*x + d1*y + d2*z + position = 0)

oxDNA_analysis_tools.external_force_utils.forces.repulsion_sphere(particle: int, center: List[float], stiff: float, r0: float, rate: float) → Dict

A sphere that encloses the particle

Parameters:

• particle (int) – the particle that the force acts upon

• center ([float, float, float]) – the center of the sphere

• stiff (float) – stiffness of trap

• r0 (float) – radius of sphere at t=0

• rate (float) – the sphere’s radius changes to r = r0 + rate*t

Reader/Writer

Read and write oxDNA external force files

oxDNA_analysis_tools.external_force_utils.force_reader.read_force_file	Read a force file into a list of force dictionaries.
oxDNA_analysis_tools.external_force_utils.force_reader.write_force_file	Write a list of forces out to a file.

oxDNA_analysis_tools.external_force_utils.force_reader.read_force_file(file: str) → List[Dict]

Read a force file into a list of force dictionaries.

Parameters:

file (str) – file to read from

Returns:

a list of force dictionaries

Return type:

force_list (list)

oxDNA_analysis_tools.external_force_utils.force_reader.write_force_file(force_list, filename, mode='w+')

Write a list of forces out to a file.

Parameters:

• force_list (list) – a list of force dictionaries

• filename (str) – file to write out to

• mode (<optional>) – the mode of the python open funciton. Defaults to ‘w’ change mode to ‘a’ if you want to append instead of overwrite.