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Fix method ambiguities in spatial massaction jump #392

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Fix method ambiguities in spatial massaction jump #392

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984a350
Fix the method ambiguities in `spatial_massaction_jump.jl`.
Vilin97 Jan 6, 2024
c621810
Fix flattening.
Vilin97 Jan 7, 2024
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6 changes: 1 addition & 5 deletions src/spatial/flatten.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -18,11 +18,7 @@ function flatten(ma_jump, prob::DiscreteProblem, spatial_system, hopping_constan
rx_rates = ma_jump.scaled_rates
elseif isa(ma_jump, SpatialMassActionJump)
num_nodes = num_sites(spatial_system)
if isnothing(ma_jump.uniform_rates) && isnothing(ma_jump.spatial_rates)
rx_rates = zeros(0, num_nodes)
elseif isnothing(ma_jump.uniform_rates)
rx_rates = ma_jump.spatial_rates
elseif isnothing(ma_jump.spatial_rates)
if isempty(ma_jump.spatial_rates)
rx_rates = reshape(repeat(ma_jump.uniform_rates, num_nodes),
length(ma_jump.uniform_rates), num_nodes)
else
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90 changes: 19 additions & 71 deletions src/spatial/spatial_massaction_jump.jl
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Original file line number Diff line number Diff line change
@@ -1,7 +1,4 @@
const AVecOrNothing = Union{AbstractVector, Nothing}
const AMatOrNothing = Union{AbstractMatrix, Nothing}

struct SpatialMassActionJump{A <: AVecOrNothing, B <: AMatOrNothing, S, U, V} <:
struct SpatialMassActionJump{A <: AbstractVector, B <: AbstractMatrix, S, U, V} <:
AbstractMassActionJump
uniform_rates::A # reactions that are uniform in space
spatial_rates::B # reactions whose rate depends on the site
Expand All @@ -16,25 +13,24 @@ struct SpatialMassActionJump{A <: AVecOrNothing, B <: AMatOrNothing, S, U, V} <:
reactant_stoch::S, net_stoch::U,
param_mapper::V, scale_rates::Bool,
useiszero::Bool,
nocopy::Bool) where {A <: AVecOrNothing,
B <: AMatOrNothing,
nocopy::Bool) where {A <: AbstractVector,
B <: AbstractMatrix,
S, U, V}
uniform_rates = (nocopy || isnothing(uniform_rates)) ? uniform_rates :
copy(uniform_rates)
spatial_rates = (nocopy || isnothing(spatial_rates)) ? spatial_rates :
copy(spatial_rates)
uniform_rates = nocopy ? uniform_rates : copy(uniform_rates)
spatial_rates = nocopy ? spatial_rates : copy(spatial_rates)

reactant_stoch = nocopy ? reactant_stoch : copy(reactant_stoch)
for i in eachindex(reactant_stoch)
if useiszero && (length(reactant_stoch[i]) == 1) &&
iszero(reactant_stoch[i][1][1])
reactant_stoch[i] = typeof(reactant_stoch[i])()
end
end
num_unif_rates = isnothing(uniform_rates) ? 0 : length(uniform_rates)
num_unif_rates = length(uniform_rates)
if scale_rates && num_unif_rates > 0
scalerates!(uniform_rates, reactant_stoch)
end
if scale_rates && !isnothing(spatial_rates) && !isempty(spatial_rates)
if scale_rates && !isempty(spatial_rates)
scalerates!(spatial_rates, reactant_stoch[(num_unif_rates + 1):end])
end
new(uniform_rates, spatial_rates, reactant_stoch, net_stoch, param_mapper)
Expand All @@ -43,83 +39,35 @@ end

################ Constructors ##################

function SpatialMassActionJump(urates::A, srates::B, rs::S, ns::U, pmapper::V;
function SpatialMassActionJump(urates::A, srates::B, rs, ns, pmapper = nothing;
scale_rates = true, useiszero = true,
nocopy = false) where {A <: AVecOrNothing,
B <: AMatOrNothing, S, U, V}
SpatialMassActionJump{A, B, S, U, V}(urates, srates, rs, ns, pmapper, scale_rates,
nocopy = false) where {A <: AbstractVector,
B <: AbstractMatrix}
SpatialMassActionJump{A, B, typeof(rs), typeof(ns), typeof(pmapper)}(urates, srates, rs, ns, pmapper, scale_rates,
useiszero, nocopy)
end
function SpatialMassActionJump(urates::A, srates::B, rs, ns; scale_rates = true,
useiszero = true,
nocopy = false) where {A <: AVecOrNothing,
B <: AMatOrNothing}
SpatialMassActionJump(urates, srates, rs, ns, nothing; scale_rates = scale_rates,
useiszero = useiszero, nocopy = nocopy)
end

function SpatialMassActionJump(srates::B, rs, ns, pmapper; scale_rates = true,
useiszero = true,
nocopy = false) where {B <: AMatOrNothing}
SpatialMassActionJump(nothing, srates, rs, ns, pmapper; scale_rates = scale_rates,
useiszero = useiszero, nocopy = nocopy)
end
function SpatialMassActionJump(srates::B, rs, ns; scale_rates = true, useiszero = true,
nocopy = false) where {B <: AMatOrNothing}
SpatialMassActionJump(nothing, srates, rs, ns, nothing; scale_rates = scale_rates,
useiszero = useiszero, nocopy = nocopy)
function SpatialMassActionJump(srates::AbstractMatrix, rs, ns, pmapper = nothing; kwargs...)
SpatialMassActionJump(Vector{eltype(srates)}(undef, 0), srates, rs, ns, pmapper; kwargs...)
end

function SpatialMassActionJump(urates::A, rs, ns, pmapper; scale_rates = true,
useiszero = true,
nocopy = false) where {A <: AVecOrNothing}
SpatialMassActionJump(urates, nothing, rs, ns, pmapper; scale_rates = scale_rates,
useiszero = useiszero, nocopy = nocopy)
end
function SpatialMassActionJump(urates::A, rs, ns; scale_rates = true, useiszero = true,
nocopy = false) where {A <: AVecOrNothing}
SpatialMassActionJump(urates, nothing, rs, ns, nothing; scale_rates = scale_rates,
useiszero = useiszero, nocopy = nocopy)
function SpatialMassActionJump(urates::AbstractVector, rs::AbstractVector, ns, pmapper = nothing; kwargs...)
SpatialMassActionJump(urates, Matrix{eltype(urates)}(undef, 0, 0), rs, ns, pmapper; kwargs...)
end

function SpatialMassActionJump(ma_jumps::MassActionJump{T, S, U, V}; scale_rates = true,
useiszero = true, nocopy = false) where {T, S, U, V}
function SpatialMassActionJump(ma_jumps::M; kwargs...) where {M <: MassActionJump}
SpatialMassActionJump(ma_jumps.scaled_rates, ma_jumps.reactant_stoch,
ma_jumps.net_stoch, ma_jumps.param_mapper;
scale_rates = scale_rates, useiszero = useiszero, nocopy = nocopy)
kwargs...)
end

##############################################

function get_num_majumps(smaj::SpatialMassActionJump{Nothing, Nothing, S, U, V}) where
{S, U, V}
0
end
function get_num_majumps(smaj::SpatialMassActionJump{Nothing, B, S, U, V}) where
{B, S, U, V}
size(smaj.spatial_rates, 1)
end
function get_num_majumps(smaj::SpatialMassActionJump{A, Nothing, S, U, V}) where
{A, S, U, V}
length(smaj.uniform_rates)
end
function get_num_majumps(smaj::SpatialMassActionJump{A, B, S, U, V}) where
{A <: AbstractVector, B <: AbstractMatrix, S, U, V}
length(smaj.uniform_rates) + size(smaj.spatial_rates, 1)
end
using_params(smaj::SpatialMassActionJump) = false

function rate_at_site(rx, site,
smaj::SpatialMassActionJump{Nothing, B, S, U, V}) where {B, S, U, V}
smaj.spatial_rates[rx, site]
end
function rate_at_site(rx, site,
smaj::SpatialMassActionJump{A, Nothing, S, U, V}) where {A, S, U, V}
smaj.uniform_rates[rx]
end
function rate_at_site(rx, site,
smaj::SpatialMassActionJump{A, B, S, U, V}) where
{A <: AbstractVector, B <: AbstractMatrix, S, U, V}
smaj::SpatialMassActionJump)
num_unif_rxs = length(smaj.uniform_rates)
rx <= num_unif_rxs ? smaj.uniform_rates[rx] :
smaj.spatial_rates[rx - num_unif_rxs, site]
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