agent_names::MEDYAN.AgentNames
sys_def::MEDYAN.SysDef
compartments::Vector{MEDYAN.Compartment}
grid::MEDYAN.CubicGrid
time::Float64: time (s)
stats::MEDYAN.PerformanceStats
β::Float64: inverse kT (1/(nm*pN))
base_diffusion_coeffs::Vector{Float64}: Diffusion coefficients indexed by diffusing species id (nm²/s)
membrane_species_params::StaticArraysCore.SVector{NUM_MEMBRANEDIFFUSINGSPECIES, MEDYAN.MembraneSpeciesParams} where NUM_MEMBRANEDIFFUSINGSPECIES: Membrane species parameters indexed by membrane diffusing species id.
min_chem_voxel_volume_ratio::Float64: Smallest volume a chem voxel can have before being deactivated as a ratio to a full chem voxel volume.
chemistryengine::MEDYAN.RDMESampler: The reaction diffusion master equation sampler, contains the diffusing and regular fixed species state
chem_voxel_volumes::Array{Float64, 3}: Volume of each chemical voxel
chem_voxel_areas::Array{Float64, 4}: Areas of (-x, -y, -z) faces of each chemical voxel
chem_cylinders::Vector{MEDYAN.ChemCylinders}: Data about filament cylinders, indexed by filament type id
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}
membranes::Vector: All membrane meshes.
next_membid::Ref{MEDYAN.MembId}: Next memb id
membid2membidx::Dict{MEDYAN.MembId, UInt32}: map from memb id to index memb indexes can change whenever a memb is removed, but id’s are stable
membidx2membid::Vector{MEDYAN.MembId}: map from memb index to id
link_manager::MEDYAN.LinkManager
decimated_2mon_site_managers::Vector{MEDYAN.AbstractDecimated2MonSiteManager}: Site managers, indexed by site id
filamentsites::Tuple{Vararg{Tuple{Vararg{MEDYAN.SiteData}}}}: The filament site definitions, indexed by filament type id, filament site id to get a SiteData with fields of id, site, fxsid
filamentendsites::Tuple{Vararg{Tuple{Vararg{MEDYAN.SiteData}}}}: The filamentend site definitions, indexed by filament type id, filamentend site id to get a SiteData with fields of id, site, fxsid
maxfilsite_plusrange::Vector{Int64}: The maximum plus range in monomers that any filament site or end site can see. Indexed by filament type id
maxfilsite_minusrange::Vector{Int64}: The maximum minus range in monomers that any filament site or end site can see. Indexed by filament type id
membranesites::Tuple{Vararg{MEDYAN.SiteData}}: Maps membrane site id to a SiteData with fields of id, site, fxsid.
map_membranediffusingspeciesindex_membranesiteindices::Tuple{Vararg{Vector{Int64}}}: Maps membrane diffusing species index to a list of membrane sites using this species as reactant. This is initialized during context init and should not be changed.
decimated_2mon_sites::Vector{MEDYAN.SiteData}: Site definitions, indexed by site id to get a SiteData with fields of id, site, fxsid
possiblecadherinsite_managers::Tuple{Vararg{MEDYAN.AbstractPossibleCadherinSiteManager}}: Site managers, indexed by site id
check_sitecount_error::Bool: If true site counts are checked for errors on every chem update. This is extremely slow, but useful for testing chem update errors.
compartmentreactioncallbacks::Any
bulkreactioncallbacks::Any
memdiff_bulks_index::Int64: Mock bulk species index for membrane diffusion.
viscosity::Float64: viscosity (pNs/nm² or MPas) water is about 1E-9
g_tol::Float64: maximum force magnitude after minimization (pN)
nforce_fractbit::Int64: number of fractional bits used to scale force values into Int64
nenergy_fractbit::Int64: number of fractional bits used to scale energy values into Int64
shake_before_minimization::Float64: Standard deviation of noise added to coordinates before starting minimization.
iter_max_cg_minimization::Int64: Max number of steps in conjugate gradient minimization.
maxstep::Float64: max step to take during line search (nm)
check_neighborlist_error::Bool: If true neighborlists are checked for errors on every force calc. This is extremely slow, but useful for testing neighborlist errors.
nthreads::Int64: 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.
enable_collision::Ref{Bool}: Are collision forces calculated
collision_skin::Float64: Extra collision neighbor list cutoff radius in nm. The neighbor lists are reset after something moves over this amount
collision_switchover_scale_unitless::Float32: Smoothing scale to avoid sharp forces when two cylinders are collinear
filamentmechparams::Vector{MEDYAN.FilamentMechParams}: The filament mechanical parameters, indexed by filament type id
func_membranespeciespotentialenergy::Any: Membrane species potential energy function. See docs on default function for more info.
external_energy_forces!::Any: External energy/force expressions. This should be a mutating function taking a (fc::MEDYAN.ForceContext, vectorized_x), which adds to fc.forces, fc.energies, and fc.energy. 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.
chemboundary::MEDYAN.Boundary: chemical boundary, updates compartment volumes and diffusion rates
chem_boundary_oversampling_factor::Int64: Oversampling factor for chem boundary TSDF computation. Default is 4.
chem_boundary_tsdf_max_distance::Float64: Maximum distance for TSDF truncation (nm). Actual max is max(this, 2.5*grid_spacing). Default is 312.5 nm.
chem_boundary_tsdf_cache::Union{Nothing, Array{Float64, 3}}: Cached truncated signed distance field for chem boundary. nothing means cache is invalid.
mechboundary::MEDYAN.Boundary: mechanical boundary
sharedtypedconfigs::MEDYAN.SharedTypedConfigs: Shared configurations stored in type parameters.
validflags::MEDYAN.ValidFlags: Interval system consistency validation flags.
profiler::ZoneProfilers.Profiler