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Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

JuliaFormatter

[JuliaFormatter] reported by reviewdog 🐶


[JuliaFormatter] reported by reviewdog 🐶

@testset "TC: $(nameof(typeof(termination_condition)))" for termination_condition in
TERMINATION_CONDITIONS


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u0=[-10.0, -1.0, 1.0, 2.0, 3.0, 4.0, 10.0]
p=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
sol=solve_oop(newton_fails, u0, p; solver = TrustRegion())


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max_trust_radius=[10.0, 100.0, 1000.0]
initial_trust_radius=[10.0, 1.0, 0.1]
step_threshold=[0.0, 0.01, 0.25]
shrink_threshold=[0.25, 0.3, 0.5]
expand_threshold=[0.5, 0.8, 0.9]
shrink_factor=[0.1, 0.3, 0.5]
expand_factor=[1.5, 2.0, 3.0]
max_shrink_times=[10, 20, 30]
list_of_options=zip(


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sol=solve_oop(quadratic_f, [1.0, 1.0], 2.0; solver = alg)


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err=maximum(abs, quadratic_f(sol.u, 2.0))


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maxiterations=[2, 3, 4, 5]
u0=[1.0, 1.0]


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@testset "TC: $(nameof(typeof(termination_condition)))" for termination_condition in
TERMINATION_CONDITIONS


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u0=[-10.0, -1.0, 1.0, 2.0, 3.0, 4.0, 10.0]
p=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
sol=solve_oop(newton_fails, u0, p; solver = LevenbergMarquardt())


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@testset "TC: $(nameof(typeof(termination_condition)))" for termination_condition in
TERMINATION_CONDITIONS


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damping_initial=[0.5, 2.0, 5.0]
damping_increase_factor=[1.5, 3.0, 10.0]
damping_decrease_factor=Float64[2, 5, 10.0]
finite_diff_step_geodesic=[0.02, 0.2, 0.3]
α_geodesic=[0.6, 0.8, 0.9]
b_uphill=Float64[0, 1, 2]
min_damping_D=[1e-12, 1e-9, 1e-4]
list_of_options=zip(


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sol=solve_oop(quadratic_f, [1.0, 1.0], 2.0; solver = alg, maxiters = 10000)


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err=maximum(abs, quadratic_f(sol.u, 2.0))


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Δ=Tridiagonal(-ones(99), 2*ones(100), -ones(99))
return u+0.1*u .* Δ*u-p


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Δ=Tridiagonal(-ones(99), 2*ones(100), -ones(99))
du.=u+0.1*u .* Δ*u-p


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Δ=Tridiagonal(-ones(99), 2*ones(100), -ones(99))
return v+0.1*(u .* Δ*v+v .* Δ*u)


[JuliaFormatter] reported by reviewdog 🐶

Δ=Tridiagonal(-ones(99), 2*ones(100), -ones(99))
du.=v+0.1*(u .* Δ*v+v .* Δ*u)


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prob=NonlinearProblem(NonlinearFunction{false}(F; jvp = JVP), u0, u0)
sol=solve(prob, NewtonRaphson(; linsolve = KrylovJL_GMRES()); abstol = 1e-13)
err=maximum(abs, sol.resid)


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prob=NonlinearProblem(NonlinearFunction{true}(F!; jvp = JVP!), u0, u0)
sol=solve(prob, NewtonRaphson(; linsolve = KrylovJL_GMRES()); abstol = 1e-13)
err=maximum(abs, sol.resid)


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j,
1] = alpha *
(u[im1, j, 1] + u[ip1, j, 1] + u[i, jp1, 1] + u[i, jm1, 1] -
4u[i, j, 1]) +
B +
u[i, j, 1]^2 * u[i, j, 2] - (A + 1) * u[i, j, 1] +
brusselator_f(x, y)


[JuliaFormatter] reported by reviewdog 🐶

j,
2] = alpha *
(u[im1, j, 2] + u[ip1, j, 2] + u[i, jp1, 2] + u[i, jm1, 2] -
4u[i, j, 2]) + A * u[i, j, 1] - u[i, j, 1]^2 * u[i, j, 2]


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u0s=([1.0, 1.0], @SVector[1.0, 1.0], 1.0)


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@testset "TC: $(nameof(typeof(termination_condition)))" for termination_condition in
TERMINATION_CONDITIONS


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[JuliaFormatter] reported by reviewdog 🐶

@testset "TC: $(nameof(typeof(termination_condition)))" for termination_condition in
TERMINATION_CONDITIONS


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[JuliaFormatter] reported by reviewdog 🐶

@testset "TC: $(nameof(typeof(termination_condition)))" for termination_condition in
TERMINATION_CONDITIONS


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u0s=([1.0, 1.0], @SVector[1.0, 1.0], 1.0)


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u0=[-10.0, -1.0, 1.0, 2.0, 3.0, 4.0, 10.0]
p=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
sol=solve_oop(newton_fails, u0, p; solver = DFSane())


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σ_min=[1e-10, 1e-5, 1e-4]
σ_max=[1e10, 1e5, 1e4]
σ_1=[1.0, 0.5, 2.0]
M=[10, 1, 100]
γ=[1e-4, 1e-3, 1e-5]
τ_min=[0.1, 0.2, 0.3]
τ_max=[0.5, 0.8, 0.9]
nexp=[2, 1, 2]
η_strategy=[
(f_1, k, x, F)->f_1/k^2, (f_1, k, x, F)->f_1/k^3,
(f_1, k, x, F)->f_1/k^4


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list_of_options=zip(σ_min, σ_max, σ_1, M, γ, τ_min, τ_max, nexp, η_strategy)


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probN=NonlinearProblem{false}(quadratic_f, [1.0, 1.0], 2.0)
sol=solve(probN, alg, abstol = 1e-11)


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@testset "TC: $(nameof(typeof(termination_condition)))" for termination_condition in
TERMINATION_CONDITIONS


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du[1]=cos(u[2])-u[1]
du[2]=sin(u[1]+u[2])+u[2]
du[3]=2u[4]+u[3]+1.0
du[4]=u[5]^2+u[4]
du[5]=u[3]^2+u[5]
du[6]=u[1]+u[2]+u[3]+u[4]+u[5]+2.0u[6]+2.5u[7]+1.5u[8]
du[7]=u[1]+u[2]+u[3]+2.0u[4]+u[5]+4.0u[6]-1.5u[7]+1.5u[8]
du[8]=u[1]+2.0u[2]+3.0u[3]+5.0u[4]+6.0u[5]+u[6]-u[7]-u[8]


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prob=NonlinearProblem(f, zeros(8))
sol=solve(prob, NewtonRaphson())


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u0=zeros(2)
p=zeros(3)


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du[1]=cos(u[2])-u[1]
du[2]=sin(u[1]+u[2])+u[2]


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explicitfun1(p, sols)=nothing
prob1=NonlinearProblem(


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sol1=solve(prob1, NewtonRaphson())


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du[1]=2u[2]+u[1]+1.0
du[2]=u[3]^2+u[2]
du[3]=u[1]^2+u[3]


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explicitfun2(p, sols)=nothing
prob2=NonlinearProblem(


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sol2=solve(prob2, NewtonRaphson())


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du[1]=p[1]+2.0u[1]+2.5u[2]+1.5u[3]
du[2]=p[2]+4.0u[1]-1.5u[2]+1.5u[3]
du[3]=p[3]++u[1]-u[2]-u[3]


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p[1]=sols[1][1]+sols[1][2]+sols[2][1]+sols[2][2]+sols[2][3]
p[2]=sols[1][1]+sols[1][2]+sols[2][1]+2.0sols[2][2]+sols[2][3]
p[3]=sols[1][1]+2.0sols[1][2]+3.0sols[2][1]+5.0sols[2][2]+
6.0sols[2][3]


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sol3=solve(prob3, NewtonRaphson())
manualscc=[sol1; sol2; sol3]


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sccprob=SciMLBase.SCCNonlinearProblem([prob1, prob2, prob3],


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scc_sol=solve(sccprob, NewtonRaphson())


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@testset "Termination Condition: $(nameof(typeof(termination_condition))) u0: $(nameof(typeof(u0)))" for termination_condition in
TERMINATION_CONDITIONS,


[JuliaFormatter] reported by reviewdog 🐶

@testset "Termination Condition: $(nameof(typeof(termination_condition))) u0: $(nameof(typeof(u0)))" for termination_condition in
TERMINATION_CONDITIONS,


[JuliaFormatter] reported by reviewdog 🐶

@testset "Termination Condition: $(nameof(typeof(termination_condition))) u0: $(nameof(typeof(u0)))" for termination_condition in
TERMINATION_CONDITIONS,


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u0=[-10.0, -1.0, 1.0, 2.0, 3.0, 4.0, 10.0]
p=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]


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prob=NonlinearProblem(quadratic_f, ones(4), 2.0; maxiters = 2)
sol=solve(prob, SimpleNewtonRaphson())


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u, p) -> vcat(u .* u .- p, u .* u .- p)),


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@testset "$idx: $(dict["title"]) | alg #$(alg_id)" for (alg_id, alg) in
enumerate(alg_ops)


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alg_ops=(RobustMultiNewton(), FastShortcutNonlinearPolyalg())


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broken_tests=Dict(alg=>Int[] for alg in alg_ops)
broken_tests[alg_ops[1]]=[]
broken_tests[alg_ops[2]]=[]


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broken_tests=Dict(alg=>Int[] for alg in alg_ops)
broken_tests[alg_ops[1]]=[1]


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alg_ops=(SimpleHalley(; autodiff = AutoForwardDiff()),)


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broken_tests=Dict(alg=>Int[] for alg in alg_ops)
broken_tests[alg_ops[1]]=[1, 5, 15, 16, 18]


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broken_tests=Dict(alg=>Int[] for alg in alg_ops)
broken_tests[alg_ops[1]]=[11, 21]
broken_tests[alg_ops[2]]=[11, 21]
broken_tests[alg_ops[3]]=[11, 21]
broken_tests[alg_ops[4]]=[8, 11, 21]
broken_tests[alg_ops[5]]=[21]
broken_tests[alg_ops[6]]=[11, 21]
broken_tests[alg_ops[7]]=[3, 15, 16, 21]
broken_tests[alg_ops[8]]=[15, 16]


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broken_tests=Dict(alg=>Int[] for alg in alg_ops)
broken_tests[alg_ops[1]]=[11, 21]
broken_tests[alg_ops[2]]=[11, 21]
broken_tests[alg_ops[3]]=[11, 21]


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broken_tests=Dict(alg=>Int[] for alg in alg_ops)
broken_tests[alg_ops[1]]=[1, 2, 3, 5, 21]


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if VERSIONv"1.11-"
broken_tests[alg_ops[2]]=[1, 2, 3, 5, 6, 11, 21]


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broken_tests[alg_ops[2]]=[1, 2, 3, 5, 6, 21]


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broken_tests[alg_ops[2]]=[1, 2, 3, 5, 6, 11, 21]


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broken_tests=Dict(alg=>Int[] for alg in alg_ops)
broken_tests[alg_ops[2]]=[1, 5, 8, 11, 18]
broken_tests[alg_ops[4]]=[5, 6, 8, 11]


[JuliaFormatter] reported by reviewdog 🐶

broken_tests[alg_ops[1]]=[1, 5, 11]
broken_tests[alg_ops[3]]=[1, 5, 6, 9, 11]
if VERSIONv"1.11-"
broken_tests[alg_ops[5]]=[1, 4, 5, 11]


[JuliaFormatter] reported by reviewdog 🐶

broken_tests[alg_ops[5]]=[1, 5, 11]


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broken_tests[alg_ops[1]]=[1, 5, 11, 15]
broken_tests[alg_ops[3]]=[1, 5, 6, 9, 11, 16]
broken_tests[alg_ops[5]]=[1, 5, 11]


[JuliaFormatter] reported by reviewdog 🐶


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broken_tests=Dict(alg=>Int[] for alg in alg_ops)
broken_tests[alg_ops[1]]=[1, 2, 4, 5, 11, 18, 22]
broken_tests[alg_ops[2]]=[2, 4, 5, 7, 18, 22]
broken_tests[alg_ops[3]]=[1, 2, 4, 5, 11, 22]


[JuliaFormatter] reported by reviewdog 🐶

alg_ops=(PseudoTransient(),)


[JuliaFormatter] reported by reviewdog 🐶

broken_tests=Dict(alg=>Int[] for alg in alg_ops)
broken_tests[alg_ops[1]]=[1, 2, 3, 11, 15, 16]


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for nfn in
(Base.Fix1(maximum, abs), Base.Fix2(norm, 2), Base.Fix2(norm, Inf))


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compatible(u0, p) || continue


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nlls_problems=[prob_oop, prob_iip]


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sol=solve(prob, solver; maxiters = 10000, abstol = 1e-8)


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resid=zeros(length(p))
ForwardDiff.jacobian!(J, (resid, θ)->loss_function(resid, θ, p), resid, θ)


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jac(θ, p)=ForwardDiff.jacobian->loss_function(θ, p), θ)


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solvers=Any[FastLevenbergMarquardtJL(linsolve) for linsolve in (:cholesky, :qr)]
Sys.isapple()||push!(solvers, CMINPACK())


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sol=solve(prob, solver; maxiters = 10000, abstol = 1e-8)


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sol=solve(prob, solver; maxiters = 10000, abstol = 1e-8)


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x_sa=SA[-1.0, -0.5, 0.0, 0.5, 1.0]


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const y_target_sa=true_function(x_sa, θ_true)


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θ_init_sa=SVector{4}(θ_init)
prob_sa=NonlinearLeastSquaresProblem{false}(loss_function_sa, θ_init_sa, x)


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sol=solve(prob_sa, FastLevenbergMarquardtJL())


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du[1]=2-2u[1]
du[2]=u[1]-4u[2]


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u0=zeros(2)
prob_iip=SteadyStateProblem(f_iip, u0)


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f_oop(u, p, t)=[2-2u[1], u[1]-4u[2]]
u0=zeros(2)
prob_oop=SteadyStateProblem(f_oop, u0)


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du[1]=2-2u[1]
du[2]=u[1]-4u[2]


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u0=zeros(2)
prob_iip=NonlinearProblem{true}(f_iip, u0)


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f_oop(u, p)=[2-2u[1], u[1]-4u[2]]
u0=zeros(2)
prob_oop=NonlinearProblem{false}(f_oop, u0)


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f_tol(u, p)=u^2-2
prob_tol=NonlinearProblem(f_tol, 1.0)


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alg isa CMINPACK&&Sys.isapple()&&continue
alg isa PETScSNES&&Sys.iswindows()&&continue
sol=solve(prob_tol, alg, abstol = tol)


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f_jfnk(u, p)=u^2-2
prob_jfnk=NonlinearProblem(f_jfnk, 1.0)


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sol=solve(prob_jfnk, SIAMFANLEquationsJL(linsolve = :gmres), abstol = tol)


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fvec[1]=(x[1]+3)*(x[2]^3-7)+18
fvec[2]=sin(x[2]*exp(x[1])-1)


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prob=NonlinearProblem{true}(f!, [0.1; 1.2])
sol=solve(prob, NLsolveJL(autodiff = :central))


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sol=solve(prob, SIAMFANLEquationsJL())


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sol=solve(prob, NLsolveJL(autodiff = :forward))


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f_custom_jac!(F, u, p)=(F[1:152]=u .^ 2 .- p)
j_custom_jac!(J, u, p)=(J[1:152, 1:152]=diagm(2 .* u))


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init=ones(152)
A=ones(152)
A[6]=0.8


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f=NonlinearFunction(f_custom_jac!; jac = j_custom_jac!)
p=A


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ProbN=NonlinearProblem(f, init, p)


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sol=solve(ProbN, NLsolveJL(); abstol = 1e-8)


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sol=solve(ProbN, SIAMFANLEquationsJL(; method = :newton); abstol = 1e-8)


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sol=solve(ProbN, SIAMFANLEquationsJL(; method = :pseudotransient); abstol = 1e-8)


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sol=solve(ProbN, PETScSNES(); abstol = 1e-8)


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u0=[1.0, 1.0]
probN=NonlinearProblem{false}(f, u0)


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sol=solve(probN, PETScSNES(); abstol = 1e-8)


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u0=[1.0f0, 1.0f0]
probN=NonlinearProblem{false}(f, u0)


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sol=solve(probN, PETScSNES(); abstol = 1e-5)


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u0=Float16[1.0, 1.0]
probN=NonlinearProblem{false}(f, u0)

Comment on lines +81 to +85
j,
1] = alpha * (u[im1, j, 1] + u[ip1, j, 1] + u[i, jp1, 1] + u[i, jm1, 1] -
4u[i, j, 1]) +
B +
u[i, j, 1]^2 * u[i, j, 2] - (A + 1) * u[i, j, 1] + brusselator_f(x, y)
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[JuliaFormatter] reported by reviewdog 🐶

Suggested change
j,
1] = alpha * (u[im1, j, 1] + u[ip1, j, 1] + u[i, jp1, 1] + u[i, jm1, 1] -
4u[i, j, 1]) +
B +
u[i, j, 1]^2 * u[i, j, 2] - (A + 1) * u[i, j, 1] + brusselator_f(x, y)
j,
1] = alpha * (u[im1, j, 1] + u[ip1, j, 1] + u[i, jp1, 1] + u[i, jm1, 1] -
4u[i, j, 1]) +
B +
u[i, j, 1]^2 * u[i, j, 2] - (A + 1) * u[i, j, 1] + brusselator_f(x, y)

Comment on lines +87 to +89
j,
2] = alpha * (u[im1, j, 2] + u[ip1, j, 2] + u[i, jp1, 2] + u[i, jm1, 2] -
4u[i, j, 2]) + A * u[i, j, 1] - u[i, j, 1]^2 * u[i, j, 2]
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[JuliaFormatter] reported by reviewdog 🐶

Suggested change
j,
2] = alpha * (u[im1, j, 2] + u[ip1, j, 2] + u[i, jp1, 2] + u[i, jm1, 2] -
4u[i, j, 2]) + A * u[i, j, 1] - u[i, j, 1]^2 * u[i, j, 2]
j,
2] = alpha * (u[im1, j, 2] + u[ip1, j, 2] + u[i, jp1, 2] + u[i, jm1, 2] -
4u[i, j, 2]) + A * u[i, j, 1] - u[i, j, 1]^2 * u[i, j, 2]


fj_scalar = @closure (Jx, x) -> begin
fj_scalar = @closure (Jx,
x) -> begin
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[JuliaFormatter] reported by reviewdog 🐶

Suggested change
x) -> begin
x) -> begin

Comment on lines +53 to +54
cx,
user_ctx) -> begin
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[JuliaFormatter] reported by reviewdog 🐶

Suggested change
cx,
user_ctx) -> begin
cx,
user_ctx) -> begin

Comment on lines +93 to +95
J,
_,
user_ctx) -> begin
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[JuliaFormatter] reported by reviewdog 🐶

Suggested change
J,
_,
user_ctx) -> begin
J,
_,
user_ctx) -> begin

Comment on lines +49 to +50
Diagonal(randn!(similar(A, size(A, 1)))), LinearAlgebra.I
)
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[JuliaFormatter] reported by reviewdog 🐶

Suggested change
Diagonal(randn!(similar(A, size(A, 1)))), LinearAlgebra.I
)
Diagonal(randn!(similar(A, size(A, 1)))), LinearAlgebra.I
)


@testitem "NewtonRaphson: Iterator Interface" setup=[CoreRootfindTesting] tags=[:core] begin
p = range(0.01, 2, length = 200)
p=range(0.01, 2, length = 200)
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[JuliaFormatter] reported by reviewdog 🐶

Suggested change
p=range(0.01, 2, length = 200)
p = range(0.01, 2, length = 200)

Comment on lines +83 to +85
@testset "TC: $(nameof(typeof(termination_condition)))" for termination_condition in
TERMINATION_CONDITIONS

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[JuliaFormatter] reported by reviewdog 🐶

Suggested change
@testset "TC: $(nameof(typeof(termination_condition)))" for termination_condition in
TERMINATION_CONDITIONS
@testset "TC: $(nameof(typeof(termination_condition)))" for termination_condition in TERMINATION_CONDITIONS

Comment on lines +101 to +103
preconditioners=[
(u0)->nothing,
u0->((args...)->(Diagonal(rand!(similar(u0))), nothing))
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[JuliaFormatter] reported by reviewdog 🐶

Suggested change
preconditioners=[
(u0)->nothing,
u0->((args...)->(Diagonal(rand!(similar(u0))), nothing))
preconditioners = [
(u0) -> nothing,
u0 -> ((args...) -> (Diagonal(rand!(similar(u0))), nothing))

Comment on lines +133 to +134
Diagonal(randn!(similar(A, size(A, 1)))), LinearAlgebra.I
)
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[JuliaFormatter] reported by reviewdog 🐶

Suggested change
Diagonal(randn!(similar(A, size(A, 1)))), LinearAlgebra.I
)
Diagonal(randn!(similar(A, size(A, 1)))), LinearAlgebra.I
)

@ChrisRackauckas ChrisRackauckas deleted the format branch May 13, 2025 02:50
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2 participants