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Fix Adjoint Sensitivities #237

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merged 5 commits into from
Feb 8, 2024
Merged

Fix Adjoint Sensitivities #237

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29f6718
replace DiffEqSensitivity with SciMLSensitivity
mjohnson541 Oct 2, 2023
97cbe16
adapt adjoint_sensitivity syntax
mjohnson541 Oct 2, 2023
0cd3601
increase absolute tolerances for test runs in adjoint sensitivities
mjohnson541 Feb 7, 2024
f0aa710
Remove parametrized typing from getadjointsensitivities
mjohnson541 Feb 7, 2024
e80bb70
Fix type stability in getadjointsensitivities
mjohnson541 Feb 7, 2024
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4 changes: 2 additions & 2 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@ Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
DiffEqSensitivity = "41bf760c-e81c-5289-8e54-58b1f1f8abe2"
FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
Expand All @@ -28,6 +27,7 @@ QuartzImageIO = "dca85d43-d64c-5e67-8c65-017450d5d020"
RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1"
SmoothingSplines = "102930c3-cf33-599f-b3b1-9a29a5acab30"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
Expand All @@ -47,7 +47,7 @@ Colors = "0.11,0.12"
Conda = "1"
CSV = "0"
DataFrames = "1"
DiffEqSensitivity = "6"
SciMLSensitivity = "^7"
ForwardDiff = "0.10"
Images = "0.24"
IncompleteLU = "0.2"
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28 changes: 17 additions & 11 deletions src/Simulation.jl
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
using SciMLBase
import SciMLBase: AbstractODESolution, HermiteInterpolation
using DiffEqSensitivity
import SciMLBase: AbstractODESolution, HermiteInterpolation, AbstractDiffEqInterpolation
using SciMLSensitivity
using ForwardDiff
using PreallocationTools
using LinearAlgebra

abstract type AbstractSimulation end
export AbstractSimulation
Expand Down Expand Up @@ -319,7 +320,7 @@
function rops(ssys::SystemSimulation, name, t)
domains = getfield.(ssys.sims, :domain)
ind = findfirst(isequal(name), ssys.names)
Nrxns = sum([length(sim.domain.phase.reactions) for sim in ssys.sims]) + sum(Vector{Int}([length(inter.reactions) for inter in ssys.interfaces if hasproperty(inter, :reactions)]))

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Nspcs = sum([length(getphasespecies(sim.domain.phase)) for sim in ssys.sims])
cstot = zeros(Nspcs)
vns = Array{Any,1}(undef, length(domains))
Expand Down Expand Up @@ -459,8 +460,8 @@
this assumes no changes in code branching during simulation, if that were to become no longer true, the Tracker
based alternative algorithm is slower, but avoids this concern.
"""
function getadjointsensitivities(bsol::Q, target::String, solver::W; sensalg::W2=InterpolatingAdjoint(autojacvec=ReverseDiffVJP(false)),
abstol::Float64=1e-6, reltol::Float64=1e-3, normalize=true, kwargs...) where {Q,W,W2}
function getadjointsensitivities(bsol::Simulation, target::String, solver; sensalg=InterpolatingAdjoint(autojacvec=ReverseDiffVJP(false)),
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Why do we remove typing for W and W2?

abstol::Float64=1e-6, reltol::Float64=1e-3, normalize=true, kwargs...)
@assert target in bsol.names || target in ["T", "V", "P", "mass"]

pethane = 160
Expand Down Expand Up @@ -538,15 +539,19 @@

if length(bsol.domain.p) <= pethane
if target in ["T", "V", "P", "mass"] || !isempty(bsol.interfaces)
du0, dpadj = adjoint_sensitivities(bsol.sol, solver, g, nothing, (dgdu, dgdp); sensealg=sensalg, abstol=abstol, reltol=reltol, kwargs...)
du0, dpadj = adjoint_sensitivities(bsol.sol, solver; g=g, dgdu_continuous=dgdu,
dgdp_continuous=dgdp, sensealg=sensalg, abstol=abstol, reltol=reltol, kwargs...)
else
du0, dpadj = adjoint_sensitivities(bsol.sol, solver, sensg, nothing, (dsensgdu, dsensgdp); sensealg=sensalg, abstol=abstol, reltol=reltol, kwargs...)
du0, dpadj = adjoint_sensitivities(bsol.sol, solver; g=sensg, dgdu_continuous=dsensgdu,
dgdp_continuous=dsensgdp, sensealg=sensalg, abstol=abstol, reltol=reltol, kwargs...)
end
else
if target in ["T", "V", "P", "mass"] || !isempty(bsol.interfaces)
du0, dpadj = adjoint_sensitivities(bsol.sol, solver, g, nothing, (dgdurevdiff, dgdprevdiff); sensealg=sensalg, abstol=abstol, reltol=reltol, kwargs...)
du0, dpadj = adjoint_sensitivities(bsol.sol, solver; g=g, dgdu_continuous=gdurevdiff,

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dgdp_continuous=dgdprevdiff, sensealg=sensalg, abstol=abstol, reltol=reltol, kwargs...)
else
du0, dpadj = adjoint_sensitivities(bsol.sol, solver, sensg, nothing, (dsensgdurevdiff, dsensgdprevdiff); sensealg=sensalg, abstol=abstol, reltol=reltol, kwargs...)
du0, dpadj = adjoint_sensitivities(bsol.sol, solver; g=sensg, dgdu_continuous=dsensgdurevdiff,

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dgdp_continuous=dsensgdprevdiff, sensealg=sensalg, abstol=abstol, reltol=reltol, kwargs...)
end
end
if normalize
Expand All @@ -557,7 +562,7 @@
dpadj ./= bsol.sol(bsol.sol.t[end])[ind]
end
end
return dpadj
return dpadj::LinearAlgebra.Adjoint{Float64, Vector{Float64}}
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I'm surprised that this is needed

end

function getadjointsensitivities(syssim::Q, bsol::W3, target::String, solver::W; sensalg::W2=InterpolatingAdjoint(autojacvec=ReverseDiffVJP(false)),
Expand Down Expand Up @@ -591,7 +596,8 @@
end
dgdu(out, y, p, t) = ForwardDiff.gradient!(out, y -> g(y, p, t), y)
dgdp(out, y, p, t) = ForwardDiff.gradient!(out, p -> g(y, p, t), p)
du0, dpadj = adjoint_sensitivities(syssim.sol, solver, g, nothing, (dgdu, dgdp); sensealg=sensalg, abstol=abstol, reltol=reltol, kwargs...)
du0, dpadj = adjoint_sensitivities(syssim.sol, solver; g=g, dgdu_continuous=dgdu, dgdp_continuous=dgdp,
sensealg=sensalg, abstol=abstol, reltol=reltol, kwargs...)
if normalize
for domain in domains
dpadj[domain.parameterindexes[1]+length(domain.phase.species):domain.parameterindexes[2]] .*= syssim.p[domain.parameterindexes[1]+length(domain.phase.species):domain.parameterindexes[2]]
Expand All @@ -600,7 +606,7 @@
dpadj ./= bsol.sol(bsol.sol.t[end])[ind]
end
end
return dpadj
return dpadj::LinearAlgebra.Adjoint{Float64, Vector{Float64}}
end
export getadjointsensitivities

Expand Down Expand Up @@ -777,15 +783,15 @@
CSV.write(save_name, df)
end

function save(syss::T, save_name::String) where {T<:SystemSimulation}
df = DataFrame(syss.sol)
for sim in syss.sims
rename!(df, names(df)[sim.domain.indexes[1]:sim.domain.indexes[2]] .=> sim.names .* "($(sim.domain.phase.name))")
for (thermovariable, index) in sim.domain.thermovariabledict
rename!(df, names(df)[index] => thermovariable)
end
end
CSV.write(save_name, df)

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end
export save

10 changes: 5 additions & 5 deletions src/TestReactors.jl
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Expand Up @@ -220,7 +220,7 @@ jp=jacobianpforwarddiff(y,p,t,domain,[],nothing);
@test all((abs.(jpa.-jp) .> 1e-4.*abs.(jp).+1e-16).==false)

#sensitivities
dps = getadjointsensitivities(sim,"H2",CVODE_BDF(linear_solver=:GMRES);sensealg=InterpolatingAdjoint(autojacvec=ReverseDiffVJP(true)),abstol=1e-16,reltol=1e-6)
dps = getadjointsensitivities(sim,"H2",CVODE_BDF(linear_solver=:GMRES);sensealg=InterpolatingAdjoint(autojacvec=ReverseDiffVJP(true)),abstol=1e-12,reltol=1e-6)
react2 = Reactor(domain,y0,(0.0,150.11094);p=p,forwardsensitivities=true)
sol2 = solve(react2.ode,CVODE_BDF(linear_solver=:GMRES),abstol=1e-21,reltol=1e-7); #solve the ode associated with the reactor
sim2 = Simulation(sol2,domain)
Expand Down Expand Up @@ -272,7 +272,7 @@ end;
@test all((abs.(jpa.-jp) .> 1e-4.*abs.(jp).+1e-16).==false)

#sensitivities
dps = getadjointsensitivities(sim,"H2",CVODE_BDF(linear_solver=:GMRES);sensealg=InterpolatingAdjoint(autojacvec=ReverseDiffVJP(true)),abstol=1e-16,reltol=1e-6)
dps = getadjointsensitivities(sim,"H2",CVODE_BDF(linear_solver=:GMRES);sensealg=InterpolatingAdjoint(autojacvec=ReverseDiffVJP(true)),abstol=1e-12,reltol=1e-6)
react2 = Reactor(domain,y0,(0.0,150.11094),interfaces;p=p,forwardsensitivities=true)
sol2 = solve(react2.ode,CVODE_BDF(linear_solver=:GMRES),abstol=1e-21,reltol=1e-7); #solve the ode associated with the reactor
sim2 = Simulation(sol2,domain,interfaces)
Expand Down Expand Up @@ -316,7 +316,7 @@ jp=jacobianpforwarddiff(y,p,t,domain,[],nothing);
react = Reactor(domain,y0,(0.0,0.02),p=p) #Create the reactor object
sol = solve(react.ode,CVODE_BDF(),abstol=1e-20,reltol=1e-12); #solve the ode associated with the reactor
sim = Simulation(sol,domain)
dps = getadjointsensitivities(sim,"H2",CVODE_BDF();sensealg=InterpolatingAdjoint(autojacvec=ReverseDiffVJP(false)),abstol=1e-16,reltol=1e-6)
dps = getadjointsensitivities(sim,"H2",CVODE_BDF();sensealg=InterpolatingAdjoint(autojacvec=ReverseDiffVJP(false)),abstol=1e-12,reltol=1e-6)
react2 = Reactor(domain,y0,(0.0,0.02);p=p,forwardsensitivities=true)
sol2 = solve(react2.ode,CVODE_BDF(),abstol=1e-16,reltol=1e-6); #solve the ode associated with the reactor
sim2 = Simulation(sol2,domain)
Expand Down Expand Up @@ -488,8 +488,8 @@ end;
@test sol(t)[1:length(spcs)] ≈ solV(t)[1:end-2] rtol=1e-5
@test sol(t)[length(spcs)+1:end-4] ≈ solV(t)[1:end-2] rtol=1e-5

dpsV = getadjointsensitivities(simV,"H2",CVODE_BDF();sensealg=InterpolatingAdjoint(autojacvec=ReverseDiffVJP(false)),abstol=1e-16,reltol=1e-6)
dps = getadjointsensitivities(sysim,sysim.sims[1],"H2",CVODE_BDF();sensealg=InterpolatingAdjoint(autojacvec=ReverseDiffVJP(false)),abstol=1e-16,reltol=1e-6)
dpsV = getadjointsensitivities(simV,"H2",CVODE_BDF();sensealg=InterpolatingAdjoint(autojacvec=ReverseDiffVJP(false)),abstol=1e-12,reltol=1e-6)
dps = getadjointsensitivities(sysim,sysim.sims[1],"H2",CVODE_BDF();sensealg=InterpolatingAdjoint(autojacvec=ReverseDiffVJP(false)),abstol=1e-12,reltol=1e-6)
@test dpsV ≈ dps rtol=1e-4
end;

Expand Down
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