DirectCR-RSSA

src/JumpProcesses.jl

@@ -63,6 +63,7 @@ include("spatial/bracketing.jl")
 
 include("spatial/nsm.jl")
 include("spatial/directcrdirect.jl")
+include("spatial/directcrrssa.jl")
 
 include("aggregators/aggregated_api.jl")
 
@@ -99,6 +100,6 @@ export ExtendedJumpArray
 export CartesianGrid, CartesianGridRej
 export SpatialMassActionJump
 export outdegree, num_sites, neighbors
-export NSM, DirectCRDirect
+export NSM, DirectCRDirect, DirectCRRSSA
 
 end # module

src/aggregators/aggregators.jl

@@ -163,6 +163,8 @@ algorithm with optimal binning,  Journal of Chemical Physics 143, 074108
 """
 struct DirectCRDirect <: AbstractAggregatorAlgorithm end
 
+struct DirectCRRSSA <: AbstractAggregatorAlgorithm end
+
 const JUMP_AGGREGATORS = (Direct(), DirectFW(), DirectCR(), SortingDirect(), RSSA(), FRM(),
     FRMFW(), NRM(), RSSACR(), RDirect(), Coevolve())
 
@@ -192,6 +194,7 @@ supports_variablerates(aggregator::Coevolve) = true
 is_spatial(aggregator::AbstractAggregatorAlgorithm) = false
 is_spatial(aggregator::NSM) = true
 is_spatial(aggregator::DirectCRDirect) = true
+is_spatial(aggregator::DirectCRRSSA) = true
 
 # return the fastest aggregator out of the available ones
 function select_aggregator(jumps::JumpSet; vartojumps_map = nothing,

src/spatial/bracketing.jl

@@ -5,9 +5,15 @@ struct LowHigh{T}
     low::T
     high::T
 
-    LowHigh(low::T, high::T) where {T} = new{T}(deepcopy(low), deepcopy(high))
-    LowHigh(pair::Tuple{T, T}) where {T} = new{T}(pair[1], pair[2])
-    LowHigh(low_and_high::T) where {T} = new{T}(low_and_high, deepcopy(low_and_high))
+    function LowHigh(low::T, high::T; do_copy = true) where {T} 
+        if do_copy
+            return new{T}(deepcopy(low), deepcopy(high))
+        else
+            return new{T}(low, high)
+        end
+    end
+    LowHigh(pair::Tuple{T,T}; kwargs...) where {T} = LowHigh(pair[1], pair[2]; kwargs...)
+    LowHigh(low_and_high::T; kwargs...) where {T} = LowHigh(low_and_high, low_and_high; kwargs...)
 end
 
 function Base.show(io::IO, ::MIME"text/plain", low_high::LowHigh)
@@ -16,22 +22,32 @@ function Base.show(io::IO, ::MIME"text/plain", low_high::LowHigh)
 end
 
 @inline function update_u_brackets!(u_low_high::LowHigh, bracket_data, u::AbstractMatrix)
-    @inbounds for (i, uval) in enumerate(u)
-        u_low_high[i] = LowHigh(get_spec_brackets(bracket_data, i, uval))
+    num_species, num_sites = size(u)
+    update_u_brackets!(u_low_high, bracket_data, u, 1:num_species, 1:num_sites)
+end
+
+@inline function update_u_brackets!(u_low_high::LowHigh, bracket_data, u::AbstractMatrix, species_vec, sites)
+    @inbounds for site in sites
+        for species in species_vec
+            u_low_high[species, site] = LowHigh(get_spec_brackets(bracket_data, species, u[species, site]))
+        end
     end
     nothing
 end
 
+function is_inside_brackets(u_low_high::LowHigh{M}, u::M, species, site) where {M}
+    return u_low_high.low[species, site] < u[species, site] < u_low_high.high[species, site]
+end
+
 ### convenience functions for LowHigh ###
-function setindex!(low_high::LowHigh, val::LowHigh, i)
-    low_high.low[i] = val.low
-    low_high.high[i] = val.high
+function setindex!(low_high::LowHigh{A}, val::LowHigh, i...) where {A <: AbstractArray}
+    low_high.low[i...] = val.low
+    low_high.high[i...] = val.high
     val
 end
+getindex(low_high::LowHigh{A}, i) where {A <: AbstractArray} = LowHigh(low_high.low[i], low_high.high[i])
 
-function getindex(low_high::LowHigh, i)
-    return LowHigh(low_high.low[i], low_high.high[i])
-end
+get_majumps(rx_rates::LowHigh{R}) where {R <: RxRates} = get_majumps(rx_rates.low)
 
 function total_site_rate(rx_rates::LowHigh, hop_rates::LowHigh, site)
     return LowHigh(
@@ -48,3 +64,8 @@ function update_hop_rates!(hop_rates::LowHigh, species, u_low_high, site, spatia
     update_hop_rates!(hop_rates.low, species, u_low_high.low, site, spatial_system)
     update_hop_rates!(hop_rates.high, species, u_low_high.high, site, spatial_system)
 end
+
+function reset!(low_high::LowHigh) 
+    reset!(low_high.low)
+    reset!(low_high.high)
+end

src/spatial/directcrdirect.jl

@@ -4,7 +4,6 @@
 const MINJUMPRATE = 2.0^exponent(1e-12)
 
 #NOTE state vector u is a matrix. u[i,j] is species i, site j
-#NOTE hopping_constants is a matrix. hopping_constants[i,j] is species i, site j
 mutable struct DirectCRDirectJumpAggregation{T, S, F1, F2, RNG, J, RX, HOP, DEPGR,
     VJMAP, JVMAP, SS, U <: PriorityTable,
     W <: Function} <:
@@ -107,12 +106,12 @@ end
 function initialize!(p::DirectCRDirectJumpAggregation, integrator, u, params, t)
     p.end_time = integrator.sol.prob.tspan[2]
     fill_rates_and_get_times!(p, integrator, t)
-    generate_jumps!(p, integrator, params, u, t)
+    generate_jumps!(p, integrator, u, params, t)
     nothing
 end
 
 # calculate the next jump / jump time
-function generate_jumps!(p::DirectCRDirectJumpAggregation, integrator, params, u, t)
+function generate_jumps!(p::DirectCRDirectJumpAggregation, integrator, u, params, t)
     p.next_jump_time = t + randexp(p.rng) / p.rt.gsum
     p.next_jump_time >= p.end_time && return nothing
     site = sample(p.rt, p.site_rates, p.rng)

src/spatial/directcrrssa.jl

@@ -0,0 +1,260 @@
+# site chosen with DirectCR, rx or hop chosen with RSSA
+
+############################ DirectCRRSSA ###################################
+const MINJUMPRATE = 2.0^exponent(1e-12)
+
+#NOTE state vector u is a matrix. u[i,j] is species i, site j
+mutable struct DirectCRRSSAJumpAggregation{T, BD, M, RNG, J, RX, HOP, DEPGR,
+    VJMAP, JVMAP, SS, U <: PriorityTable, S, F1, F2} <:
+               AbstractSSAJumpAggregator{T, S, F1, F2, RNG}
+    next_jump::SpatialJump{J}
+    prev_jump::SpatialJump{J}
+    next_jump_time::T
+    end_time::T
+    bracket_data::BD
+    u_low_high::LowHigh{M} # species bracketing
+    rx_rates::LowHigh{RX}
+    hop_rates::LowHigh{HOP}
+    site_rates_high::Vector{T} # we do not need site_rates_low
+    save_positions::Tuple{Bool, Bool}
+    rng::RNG
+    dep_gr::DEPGR #dep graph is same for each site
+    vartojumps_map::VJMAP #vartojumps_map is same for each site
+    jumptovars_map::JVMAP #jumptovars_map is same for each site
+    spatial_system::SS
+    numspecies::Int #number of species
+    rt::U
+    rates::F1 # legacy, not used
+    affects!::F2 # legacy, not used
+end
+
+function DirectCRRSSAJumpAggregation(nj::SpatialJump{J}, njt::T, et::T, bd::BD,
+    u_low_high::LowHigh{M}, rx_rates::LowHigh{RX},
+    hop_rates::LowHigh{HOP}, site_rates_high::Vector{T},
+    sps::Tuple{Bool, Bool}, rng::RNG, spatial_system::SS;
+    num_specs, minrate = convert(T, MINJUMPRATE),
+    vartojumps_map = nothing, jumptovars_map = nothing,
+    dep_graph = nothing,
+    kwargs...) where {J, T, BD, RX, HOP, RNG, SS, M}
+
+    # a dependency graph is needed
+    if dep_graph === nothing
+        dg = make_dependency_graph(num_specs, get_majumps(rx_rates))
+    else
+        dg = dep_graph
+        # make sure each jump depends on itself
+        add_self_dependencies!(dg)
+    end
+
+    # a species-to-reactions graph is needed
+    if vartojumps_map === nothing
+        vtoj_map = var_to_jumps_map(num_specs, get_majumps(rx_rates))
+    else
+        vtoj_map = vartojumps_map
+    end
+
+    if jumptovars_map === nothing
+        jtov_map = jump_to_vars_map(get_majumps(rx_rates))
+    else
+        jtov_map = jumptovars_map
+    end
+
+    # mapping from jump rate to group id
+    minexponent = exponent(minrate)
+
+    # use the largest power of two that is <= the passed in minrate
+    minrate = 2.0^minexponent
+    ratetogroup = rate -> priortogid(rate, minexponent)
+
+    # construct an empty initial priority table -- we'll reset this in init
+    rt = PriorityTable(ratetogroup, zeros(T, 1), minrate, 2 * minrate)
+
+    DirectCRRSSAJumpAggregation{
+        T,
+        BD,
+        M,
+        RNG,
+        J,
+        RX,
+        HOP,
+        typeof(dg),
+        typeof(vtoj_map),
+        typeof(jtov_map),
+        SS,
+        typeof(rt),
+        Nothing,
+        Nothing,
+        Nothing,
+    }(nj, nj, njt, et, bd, u_low_high, rx_rates, hop_rates, site_rates_high, sps, rng, dg,
+        vtoj_map, jtov_map, spatial_system, num_specs, rt, nothing, nothing)
+end
+
+############################# Required Functions ##############################
+# creating the JumpAggregation structure (function wrapper-based constant jumps)
+function aggregate(aggregator::DirectCRRSSA, starting_state, p, t, end_time,
+    constant_jumps, ma_jumps, save_positions, rng; hopping_constants,
+    spatial_system, bracket_data = nothing, kwargs...)
+    T = typeof(end_time)
+    num_species = size(starting_state, 1)
+    majumps = ma_jumps
+    if majumps === nothing
+        majumps = MassActionJump(Vector{T}(),
+            Vector{Vector{Pair{Int, Int}}}(),
+            Vector{Vector{Pair{Int, Int}}}())
+    end
+
+    next_jump = SpatialJump{Int}(typemax(Int), typemax(Int), typemax(Int)) #a placeholder
+    next_jump_time = typemax(T)
+    rx_rates = LowHigh(RxRates(num_sites(spatial_system), majumps),
+        RxRates(num_sites(spatial_system), majumps);
+        do_copy = false) # do not copy ma_jumps
+    hop_rates = LowHigh(HopRates(hopping_constants, spatial_system),
+        HopRates(hopping_constants, spatial_system);
+        do_copy = false) # do not copy hopping_constants
+    site_rates_high = zeros(T, num_sites(spatial_system))
+    bd = (bracket_data === nothing) ? BracketData{T, eltype(starting_state)}() :
+         bracket_data
+    u_low_high = LowHigh(starting_state)
+
+    DirectCRRSSAJumpAggregation(next_jump, next_jump_time, end_time, bd, u_low_high,
+        rx_rates, hop_rates,
+        site_rates_high, save_positions, rng, spatial_system;
+        num_specs = num_species, kwargs...)
+end
+
+# set up a new simulation and calculate the first jump / jump time
+function initialize!(p::DirectCRRSSAJumpAggregation, integrator, u, params, t)
+    p.end_time = integrator.sol.prob.tspan[2]
+    fill_rates_and_get_times!(p, integrator, t)
+    generate_jumps!(p, integrator, u, params, t)
+    nothing
+end
+
+# calculate the next jump / jump time
+function generate_jumps!(p::DirectCRRSSAJumpAggregation, integrator, u, params, t)
+    @unpack rng, rt, site_rates_high, rx_rates, hop_rates, spatial_system = p
+    time_delta = zero(t)
+    while true
+        site = sample(rt, site_rates_high, rng)
+        jump = sample_jump_direct(rx_rates.high, hop_rates.high, site, spatial_system, rng)
+        time_delta += randexp(rng)
+        if accept_jump(p, u, jump)
+            p.next_jump_time = t + time_delta / groupsum(rt)
+            p.next_jump = jump
+            break
+        end
+    end
+    nothing
+end
+
+# execute one jump, changing the system state
+function execute_jumps!(p::DirectCRRSSAJumpAggregation, integrator, u, params, t,
+    affects!)
+    update_state!(p, integrator)
+    update_dependent_rates!(p, integrator, t)
+    nothing
+end
+
+######################## SSA specific helper routines ########################
+# Return true if site is accepted.
+@inline accept_jump(p, u, jump) = is_hop(p, jump) ? accept_hop(p, u, jump) : accept_rx(p, u, jump)  
+
+
+function accept_hop(p, u, jump)
+    @unpack hop_rates, spatial_system, rng = p
+    species, site = jump.jidx, jump.src
+    acceptance_threshold = rand(rng) * hop_rate(hop_rates.high, species, site)
+    if hop_rate(hop_rates.low, species, site) > acceptance_threshold
+        return true
+    else
+        # compute the real rate. Could have used hop_rates.high as well.
+        real_rate = evalhoprate(hop_rates.low, u, species, site, spatial_system)
+        return real_rate > acceptance_threshold
+    end
+end
+
+function accept_rx(p, u, jump)
+    @unpack rx_rates, rng = p
+    rx, site = reaction_id_from_jump(p, jump), jump.src
+    acceptance_threshold = rand(rng) * rx_rate(rx_rates.high, rx, site)
+    if rx_rate(rx_rates.low, rx, site) > acceptance_threshold
+        return true
+    else
+        # compute the real rate. Could have used rx_rates.high as well.
+        real_rate = evalrxrate(rx_rates.low, u, rx, site)
+        return real_rate > acceptance_threshold
+    end
+end
+
+"""
+    fill_rates_and_get_times!(aggregation::DirectCRRSSAJumpAggregation, u, t)
+
+reset all stucts, reevaluate all rates, repopulate the priority table
+"""
+function fill_rates_and_get_times!(aggregation::DirectCRRSSAJumpAggregation, integrator, t)
+    @unpack bracket_data, u_low_high, spatial_system, rx_rates, hop_rates, site_rates_high, rt = aggregation
+    u = integrator.u
+    update_u_brackets!(u_low_high::LowHigh, bracket_data, u::AbstractMatrix)
+
+    reset!(rx_rates)
+    reset!(hop_rates)
+    fill!(site_rates_high, zero(eltype(site_rates_high)))
+
+    rxs = 1:num_rxs(rx_rates.low)
+    species = 1:(aggregation.numspecies)
+
+    for site in 1:num_sites(spatial_system)
+        update_rx_rates!(rx_rates, rxs, u_low_high, integrator, site)
+        update_hop_rates!(hop_rates, species, u_low_high, site, spatial_system)
+        site_rates_high[site] = total_site_rate(rx_rates.high, hop_rates.high, site)
+    end
+
+    # setup PriorityTable
+    reset!(rt)
+    for (pid, priority) in enumerate(site_rates_high)
+        insert!(rt, pid, priority)
+    end
+    nothing
+end
+
+"""
+    update_dependent_rates!(p, integrator, t)
+
+recalculate jump rates for jumps that depend on the just executed jump (p.prev_jump)
+"""
+function update_dependent_rates!(p::DirectCRRSSAJumpAggregation, integrator, t)
+    jump = p.prev_jump
+    if is_hop(p, jump)
+        update_brackets!(p, integrator, jump.jidx, (jump.src, jump.dst))
+    else
+        update_brackets!(p, integrator, p.jumptovars_map[reaction_id_from_jump(p, jump)], jump.src)
+    end
+end
+
+function update_brackets!(p, integrator, species_to_update, sites_to_update)
+    @unpack rx_rates, hop_rates, site_rates_high, u_low_high, bracket_data, vartojumps_map, spatial_system = p
+    u = integrator.u
+    for site in sites_to_update, species in species_to_update
+        if !is_inside_brackets(u_low_high, u, species, site)
+            update_u_brackets!(u_low_high, bracket_data, u, species, site)
+            update_rx_rates!(rx_rates,
+                vartojumps_map[species],
+                u_low_high,
+                integrator,
+                site)
+            update_hop_rates!(hop_rates, species, u_low_high, site, spatial_system)
+
+            oldrate = site_rates_high[site]
+            site_rates_high[site] = total_site_rate(rx_rates.high, hop_rates.high, site)
+            update!(p.rt, site, oldrate, site_rates_high[site])
+        end
+    end
+    nothing
+end
+
+"""
+    num_constant_rate_jumps(aggregator::DirectCRRSSAJumpAggregation)
+
+number of constant rate jumps
+"""
+num_constant_rate_jumps(aggregator::DirectCRRSSAJumpAggregation) = 0

src/spatial/hop_rates.jl

@@ -68,6 +68,8 @@ function update_hop_rates!(hop_rates::AbstractHopRates, species::AbstractArray,
     end
 end
 
+hop_rate(hop_rates, species, site) = @inbounds hop_rates.rates[species, site]
+
 """
     update_hop_rate!(hop_rates::HopRatesGraphDsi, species, u, site, spatial_system)