MEDYAN.Boundary

Union{}

Mechanical boundary

A set of soft planes and capsules that push beads back inside the domain. Apply it with set_mech_boundary!.

Rather than filling in the fields by hand, use one of the constructors:

• boundary_box: planes at the edges of a CubicGrid.
• boundary_plane: a single plane.
• boundary_capsule: a sphere or capsule, inside or outside.
• boundary_cylinder: a cylinder with flat ends.

Combine boundaries with ∩. Boundary() is the empty boundary, which applies no forces.

• planes::Vector{StaticArraysCore.SVector{4, Float64}}: Planes that make up the mechanical boundary of the simulation.

  E = 1//2 * relu(pos ⋅ planes[bi][1:3] - planes[bi][4])^2

  For example, a mech bounding plane [1,0,0,3] would try and make x < 3 nm with a spring constant of 1 pN/nm.

  2.0*[1,0,0,3] would try and make x < 3 nm with a spring constant of 4 pN/nm.

• plane_layers::Vector{UInt32}: Collision layers for each plane. Empty for chemical boundaries.

• plane_ncmask::Vector{UInt32}: No-collide mask for each plane. Empty for chemical boundaries.

• capsules::Vector{StaticArraysCore.SVector{8, Float64}}: Capsules that make up the mechanical boundary of the simulation.

  capsules[bi][1:3] is the starting point of the spine line segment (nm). capsules[bi][4:6] is the axis of the spine line segment (nm). capsules[bi][7] is the radius (nm). If the radius is negative, the domain is the outside of the capsule, if the radius is positive the domain is inside the capsule. capsules[bi][8] is the spring constant (pN/nm).

  if capsules[bi][4:6] is zero then the capsule is a sphere. Capsule boundaries can be combined with plane boundaries to create cylinder boundaries.

  E = 1//2*k*relu(sign(r0)*d - r0)^2 where:

  • d is the distance of the point to the spine line segment described by capsules[bi][1:6].
  • r0 is capsules[bi][7]
  • k is capsules[bi][8]

• capsule_layers::Vector{UInt32}: Collision layers for each capsule. Empty for chemical boundaries.

• capsule_ncmask::Vector{UInt32}: No-collide mask for each capsule. Empty for chemical boundaries.