build based on a8ec9f4

Author: Documenter.jl

julia-docs/dev/docstrings.html

@@ -222,6 +222,7 @@ <h2 class="anchored" data-anchor-id="union---b2cfd89fb0d1b9c6"><code data-shortc
 <li><p><code>min_compartment_volume_ratio::Float64</code>: Smallest volume a compartment can have before being deactivated as a ratio to a full compartment volume.</p></li>
 <li><p><code>chemistryengine::MEDYAN.RDMESampler</code>: The reaction diffusion master equation sampler, contains the diffusing and regular fixed species state</p></li>
 <li><p><code>chem_cylinders::Vector{MEDYAN.ChemCylinders}</code>: Data about filament cylinders, indexed by filament type id</p></li>
+<li><p><code>balls::StructArrays.StructVector{MEDYAN.Ball, @NamedTuple{position::Vector{StaticArraysCore.SVector{3, Float64}}, radius::Vector{Float32}, stiffness::Vector{Float32}, state::Vector{StaticArraysCore.SVector{3, Int64}}}, Int64}</code></p></li>
 <li><p><code>membranes::Vector</code>: All membrane meshes.</p></li>
 <li><p><code>link_manager::MEDYAN.LinkManager</code></p></li>
 <li><p><code>decimated_2mon_site_managers::Vector{MEDYAN.AbstractDecimated2MonSiteManager}</code>: Site managers, indexed by site id</p></li>
@@ -244,17 +245,15 @@ <h2 class="anchored" data-anchor-id="union---b2cfd89fb0d1b9c6"><code data-shortc
 <li><p><code>shake_before_minimization::Float64</code>: Standard deviation of noise added to coordinates before starting minimization.</p></li>
 <li><p><code>iter_max_cg_minimization::Int64</code>: Max number of steps in conjugate gradient minimization.</p></li>
 <li><p><code>maxstep::Float64</code>: max step to take during line search (nm)</p></li>
-<li><p><code>max_cylinder_force::Float64</code>: max cylinder force when two cylinders are at zero distance (pN)</p></li>
 <li><p><code>check_neighborlist_error::Bool</code>: If true neighborlists are checked for errors on every force calc. This is extremely slow, but useful for testing neighborlist errors.</p></li>
 <li><p><code>nthreads::Int64</code>: Experimental Set to more than 1 to enable multi threading. This is currently may result in non bitwise reproducable simulations. Results should be statistcally identical, but this is currently not well tested.</p></li>
-<li><p><code>enable_cylinder_volume_exclusion::Ref{Bool}</code>: Are cylinder volume exclusion forces calculated</p></li>
-<li><p><code>enable_triangle_bead_volume_exclusion::Bool</code>: Are triangle-bead volume exclusion forces calculated.</p></li>
-<li><p><code>cylinder_skin_radius::Float64</code>: Extra cell list cutoff radius in nm. The cell lists are reset after a bead moves over this amount</p></li>
+<li><p><code>enable_collision::Ref{Bool}</code>: Are collision forces calculated</p></li>
+<li><p><code>collision_skin::Float64</code>: Extra collision neighbor list cutoff radius in nm. The neighbor lists are reset after something moves over this amount</p></li>
+<li><p><code>collision_switchover_scale_unitless::Float32</code>: Smoothing scale to avoid sharp forces when two cylinders are collinear</p></li>
 <li><p><code>filamentmechparams::Vector{MEDYAN.FilamentMechParams}</code>: The filament mechanical parameters, indexed by filament type id</p></li>
 <li><p><code>membranemechparams::Vector{MEDYAN.MembraneMechParams}</code>: Membrane mechanical parameters, indexed by membrane type id.</p></li>
 <li><p><code>func_membranespeciespotentialenergy::Any</code>: Membrane species potential energy function. See docs on default function for more info.</p></li>
-<li><p><code>membranefilamentmechparams::MEDYAN.MembraneFilamentMechParams</code>: Membrane-filament mechanical interaction parameters.</p></li>
-<li><p><code>external_energy_forces!::Any</code>: External energy/force expressions. This should be a mutating function taking a <code>(fc::MEDYAN.ForceContext)</code>, which adds to <code>fc.forces, fc.energies, and fc.energy</code>. The energy and force must be consistent, and this is not checked. This can be used as ad-hoc solutions to experiment with uncommon forces, such as specifically designed attachments, etc. If this variable is used often, consider moving it into MEDYAN.</p></li>
+<li><p><code>external_energy_forces!::Any</code>: External energy/force expressions. This should be a mutating function taking a <code>(fc::MEDYAN.ForceContext, vectorized_x)</code>, which adds to <code>fc.forces, fc.energies, and fc.energy</code>. The energy and force must be consistent, and this is not checked. This can be used as ad-hoc solutions to experiment with uncommon forces, such as specifically designed attachments, etc. If this variable is used often, consider moving it into MEDYAN.</p></li>
 <li><p><code>chemboundary::MEDYAN.Boundary</code>: chemical boundary, updates compartment volumes and diffusion rates</p></li>
 <li><p><code>meshindex_as_chemboundary::Ref{Int64}</code>: The membrane index used as chemical boundary. If values other than 0 is used, the actual interior region of the chemical boundary is the intersection between</p>
 <ul>