From 2b8fa0a7227a5f7934d9602885f081c0b3dc634c Mon Sep 17 00:00:00 2001 From: Ninadlt <166744945+nnd389@users.noreply.github.com> Date: Fri, 25 Oct 2024 10:44:10 -0500 Subject: [PATCH 01/18] Updated the nelson ODE function, (made it nicer to look at) and added parameters --- benchmarks/AstroChem/nelson.jmd | 302 ++++++++++++++++++-------------- 1 file changed, 166 insertions(+), 136 deletions(-) diff --git a/benchmarks/AstroChem/nelson.jmd b/benchmarks/AstroChem/nelson.jmd index 8b2226157..16f43e326 100644 --- a/benchmarks/AstroChem/nelson.jmd +++ b/benchmarks/AstroChem/nelson.jmd @@ -1,6 +1,6 @@ --- title: Nelson Work-Precision Diagrams -author: Stella Offner and Chris Rackauckas +author: Nina De La Torre (Advised by Stella Offner) and Chris Rackauckas --- ```julia @@ -11,144 +11,176 @@ using ODEInterface, ODEInterfaceDiffEq ``` ```julia -T = 10 -Av = 2 # This is what depotic uses for visual extinction -Go = 1.7 # I think despotic uses 1.7 -n_H = 611 -shield = 1 - -function Nelson_ODE(du,u,p,t) - # 1: H2 - #= du[1] = -1.2e-17 * u[1] + - n_H * (1.9e-6 * u[2] * u[3]) / (T^0.54) - - n_H * 4e-16 * u[1] * u[12] - - n_H * 7e-15 * u[1] * u[5] + - n_H * 1.7e-9 * u[10] * u[2] + - n_H * 2e-9 * u[2] * u[6] + - n_H * 2e-9 * u[2] * u[14] + - n_H * 8e-10 * u[2] * u[8] =# - du[1] = 0 - - # 2: H3+ - du[2] = 1.2e-17 * u[1] + - n_H * (-1.9e-6 * u[3] * u[2]) / (T^0.54) - - n_H * 1.7e-9 * u[10] * u[2] - - n_H * 2e-9 * u[2] * u[6] - - n_H * 2e-9 * u[2] * u[14] - - n_H * 8e-10 * u[2] * u[8] - - # 3: e - du[3] = n_H * (-1.4e-10 * u[3] * u[12]) / (T^0.61) - - n_H * (3.8e-10 * u[13] * u[3]) / (T^0.65) - - n_H * (3.3e-5 * u[11] * u[3]) / T + - 1.2e-17 * u[1] - - n_H * (1.9e-6 * u[3] * u[2]) / (T^0.54) + - 6.8e-18 * u[4] - - n_H * (9e-11 * u[3] * u[5]) / (T^0.64) + - 3e-10 * Go * exp(-3 * Av) * u[6] + - n_H * 2e-9 * u[2] * u[13] ## CHECK I added this extra term from a CR ionization reaction - + 2.0e-10 * Go * exp(-1.9 * Av) * u[14] # this term was added as part of the skipped photoreaction - - - # 4: He - du[4] = n_H * (9e-11 * u[3] * u[5]) / (T^0.64) - - 6.8e-18 * u[4] + - n_H * 7e-15 * u[1] * u[5] + - n_H * 1.6e-9 * u[10] * u[5] - #du[4] = 0 - - # 5: He+ 6.8e-18 or 1.1 - du[5] = 6.8e-18 * u[4] - - n_H * (9e-11 * u[3] * u[5]) / (T^0.64) - - n_H * 7e-15 * u[1] * u[5] - - n_H * 1.6e-9 * u[10] * u[5] - #u[5] = 0 - - # 6: C - du[6] = n_H * (1.4e-10 * u[3] * u[12]) / (T^0.61) - - n_H * 2e-9 * u[2] * u[6] - - n_H * 5.8e-12 * (T^0.5) * u[9] * u[6] + - 1e-9 * Go * exp(-1.5 * Av) * u[7] - - 3e-10 * Go * exp(-3 * Av) * u[6] + - 1e-10 * Go * exp(-3 * Av) * u[10] * shield - - # 7: CHx - du[7] = n_H * (-2e-10) * u[7] * u[8] + - n_H * 4e-16 * u[1] * u[12] + - n_H * 2e-9 * u[2] * u[6] - - 1e-9 * Go * u[7] * exp(-1.5 * Av) - - # 8: O - du[8] = n_H * (-2e-10) * u[7] * u[8] + - n_H * 1.6e-9 * u[10] * u[5] - - n_H * 8e-10 * u[2] * u[8] + - 5e-10 * Go * exp(-1.7 * Av) * u[9] + - 1e-10 * Go * exp(-3 * Av) * u[10] * shield - - # 9: OHx - du[9] = n_H * (-1e-9) * u[9] * u[12] + - n_H * 8e-10 * u[2] * u[8] - - n_H * 5.8e-12 * (T^0.5) * u[9] * u[6] - - 5e-10 * Go * exp(-1.7 * Av) * u[9] - - # 10: CO - du[10] = n_H * (3.3e-5 * u[11] * u[3]) / T + - n_H * 2e-10 * u[7] * u[8] - - n_H * 1.7e-9 * u[10] * u[2] - - n_H * 1.6e-9 * u[10] * u[5] + - n_H * 5.8e-12 * (T^0.5) * u[9] * u[6] - - 1e-10 * Go * exp(-3 * Av) * u[10] + - 1.5e-10 * Go * exp(-2.5 * Av) * u[11] * shield - - # 11: HCO+ - du[11] = n_H * (-3.3e-5 * u[11] * u[3]) / T + - n_H * 1e-9 * u[9] * u[12] + - n_H * 1.7e-9 * u[10] * u[2] - - 1.5e-10 * Go * exp(-2.5 * Av) * u[11] - - # 12: C+ - du[12] = n_H * (-1.4e-10 * u[3] * u[12]) / (T^0.61) - - n_H * 4e-16 * u[1] * u[12] - - n_H * 1e-9 * u[9] * u[12] + - n_H * 1.6e-9 * u[10] * u[5] + - 3e-10 * Go * exp(-3 * Av) * u[6] - - # 13: M+ - du[13] = n_H * (-3.8e-10 * u[13] * u[3]) / (T^0.65) + - n_H * 2e-9 * u[2] * u[14] - + 2.0e-10 * Go * exp(-1.9 * Av) * u[14] # this term was added as part of the skipped photoreaction - - # 14: M - du[14] = n_H * (3.8e-10 * u[13] * u[3]) / (T^0.65) - - n_H * 2e-9 * u[2] * u[14] - - 2.0e-10 * Go * exp(-1.9 * Av) * u[14] # this term was added as part of the skipped photoreaction +#= +The ODE function defined below models the reduced carbon-oxygen +chemistry network of Nelson & Langer (1999, ApJ, 524, 923). + +This Julia ODE function was written by Nina De La Torre advised by Stella Offner. +The solution was compared with results derived by DESPOTIC, (Mark Krumholz, 2013) +a code to Derive the Energetics and Spectra of Optically Thick Insterstellar Clouds. +DESPOTIC has pre-defined networks, one of them coming from the Nelson & Langer paper, +so the initial conditions and parameters were meant to mimic those from DESPOTIC. + +Note: The composite hydrocarbon radical CHx represents both CH and CH2, +the composite oxygen species OHx represents OH, H2O, O2 and their ions, +and M represents the low ionization potential metals Mg, Fe, Ca, and Na. + + Parameter definitions: + T = 10 --> Tempurature (Kelvin) + Av = 2 --> V-Band Extinction + G₀ = 1.7 --> Go; "a factor that determines the flux of FUV radiation relative to the standard interstellar value (G₀ = 1) as reported by Habing (1968)." + n_H = 611 --> Hydrogen Number Density + shield = 1 --> "CO self-shielding factor of van Dishoeck & Black (1988), taken from Bergin et al. (1995)" +=# + +function Nelson!(du,u,p,t) + T, Av, Go, n_H, shield = p + + # 1: H2 + du[1] = -1.2e-17 * u[1] + + n_H * (1.9e-6 * u[2] * u[3]) / (T^0.54) - + n_H * 4e-16 * u[1] * u[12] - + n_H * 7e-15 * u[1] * u[5] + + n_H * 1.7e-9 * u[10] * u[2] + + n_H * 2e-9 * u[2] * u[6] + + n_H * 2e-9 * u[2] * u[14] + + n_H * 8e-10 * u[2] * u[8] + + # 2: H3+ + du[2] = 1.2e-17 * u[1] + + n_H * (-1.9e-6 * u[3] * u[2]) / (T^0.54) - + n_H * 1.7e-9 * u[10] * u[2] - + n_H * 2e-9 * u[2] * u[6] - + n_H * 2e-9 * u[2] * u[14] - + n_H * 8e-10 * u[2] * u[8] + + # 3: e + du[3] = n_H * (-1.4e-10 * u[3] * u[12]) / (T^0.61) - + n_H * (3.8e-10 * u[13] * u[3]) / (T^0.65) - + n_H * (3.3e-5 * u[11] * u[3]) / T + + 1.2e-17 * u[1] - + n_H * (1.9e-6 * u[3] * u[2]) / (T^0.54) + + 6.8e-18 * u[4] - + n_H * (9e-11 * u[3] * u[5]) / (T^0.64) + + 3e-10 * Go * exp(-3 * Av) * u[6] + + n_H * 2e-9 * u[2] * u[13] + + 2.0e-10 * Go * exp(-1.9 * Av) * u[14] + + # 4: He + du[4] = n_H * (9e-11 * u[3] * u[5]) / (T^0.64) - + 6.8e-18 * u[4] + + n_H * 7e-15 * u[1] * u[5] + + n_H * 1.6e-9 * u[10] * u[5] + + # 5: He+ + du[5] = 6.8e-18 * u[4] - + n_H * (9e-11 * u[3] * u[5]) / (T^0.64) - + n_H * 7e-15 * u[1] * u[5] - + n_H * 1.6e-9 * u[10] * u[5] + + # 6: C + du[6] = n_H * (1.4e-10 * u[3] * u[12]) / (T^0.61) - + n_H * 2e-9 * u[2] * u[6] - + n_H * 5.8e-12 * (T^0.5) * u[9] * u[6] + + 1e-9 * Go * exp(-1.5 * Av) * u[7] - + 3e-10 * Go * exp(-3 * Av) * u[6] + + 1e-10 * Go * exp(-3 * Av) * u[10] * shield + + # 7: CHx + du[7] = n_H * (-2e-10) * u[7] * u[8] + + n_H * 4e-16 * u[1] * u[12] + + n_H * 2e-9 * u[2] * u[6] - + 1e-9 * Go * u[7] * exp(-1.5 * Av) + + # 8: O + du[8] = n_H * (-2e-10) * u[7] * u[8] + + n_H * 1.6e-9 * u[10] * u[5] - + n_H * 8e-10 * u[2] * u[8] + + 5e-10 * Go * exp(-1.7 * Av) * u[9] + + 1e-10 * Go * exp(-3 * Av) * u[10] * shield + + # 9: OHx + du[9] = n_H * (-1e-9) * u[9] * u[12] + + n_H * 8e-10 * u[2] * u[8] - + n_H * 5.8e-12 * (T^0.5) * u[9] * u[6] - + 5e-10 * Go * exp(-1.7 * Av) * u[9] + + # 10: CO + du[10] = n_H * (3.3e-5 * u[11] * u[3]) / T + + n_H * 2e-10 * u[7] * u[8] - + n_H * 1.7e-9 * u[10] * u[2] - + n_H * 1.6e-9 * u[10] * u[5] + + n_H * 5.8e-12 * (T^0.5) * u[9] * u[6] - + 1e-10 * Go * exp(-3 * Av) * u[10] + + 1.5e-10 * Go * exp(-2.5 * Av) * u[11] * shield + + # 11: HCO+ + du[11] = n_H * (-3.3e-5 * u[11] * u[3]) / T + + n_H * 1e-9 * u[9] * u[12] + + n_H * 1.7e-9 * u[10] * u[2] - + 1.5e-10 * Go * exp(-2.5 * Av) * u[11] + + # 12: C+ + du[12] = n_H * (-1.4e-10 * u[3] * u[12]) / (T^0.61) - + n_H * 4e-16 * u[1] * u[12] - + n_H * 1e-9 * u[9] * u[12] + + n_H * 1.6e-9 * u[10] * u[5] + + 3e-10 * Go * exp(-3 * Av) * u[6] + + # 13: M+ + du[13] = n_H * (-3.8e-10 * u[13] * u[3]) / (T^0.65) + + n_H * 2e-9 * u[2] * u[14] + + 2.0e-10 * Go * exp(-1.9 * Av) * u[14] + + # 14: M + du[14] = n_H * (3.8e-10 * u[13] * u[3]) / (T^0.65) - + n_H * 2e-9 * u[2] * u[14] - + 2.0e-10 * Go * exp(-1.9 * Av) * u[14] end - -u0 = [0.5 ; # 1: H2 yep? - 9.059e-9 ; # 2: H3+ yep - 2.0e-4 ; # 3: e yep - 0.1 ; # 4: He SEE lines 535 NL99 - 7.866e-7 ; # 5: He+ yep? should be 2.622e-5 - 0.0 ; # 6: C yep - 0.0 ; # 7: CHx yep - 0.0004 ; # 8: O yep - 0.0 ; # 9: OHx yep - 0.0 ; # 10: CO yep - 0.0 ; # 11: HCO+ yep - 0.0002 ; # 12: C+ yep - 2.0e-7 ; # 13: M+ yep - 2.0e-7 ] # 14: M yep - - -tspan = (0.0, 30 * 3.16e10) # ~30 thousand yrs - -prob = ODEProblem(Nelson_ODE, u0, tspan) +# Set the Timespan, Parameters, and Initial Conditions +seconds_per_year = 3600 * 24 * 365 +tspan = (0.0, 30000 * seconds_per_year) # ~30 thousand yrs + +params = (10, # T + 2, # Av + 1.7, # Go + 611, # n_H + 1) # shield + +u0 = [0.5, # 1: H2 + 9.059e-9, # 2: H3+ + 2.0e-4, # 3: e + 0.1, # 4: He + 7.866e-7, # 5: He+ + 0.0, # 6: C + 0.0, # 7: CHx + 0.0004, # 8: O + 0.0, # 9: OHx + 0.0, # 10: CO + 0.0, # 11: HCO+ + 0.0002, # 12: C+ + 2.0e-7, # 13: M+ + 2.0e-7] # 14: M + + +prob = ODEProblem(Nelson!, u0, tspan, params) refsol = solve(prob, Vern9(), abstol=1e-14, reltol=1e-14) +sol1 = solve(prob, Rodas5P()) +sol2 = solve(prob, FBDF()) +sol3 = solve(prob, QNDF()) +sol4 = solve(prob, CVODE_BDF()) + using Plots -plot(sol; yscale=:log10, idxs = (0,5)) +colors = palette(:acton, 5) +p1 = plot(sol1, vars = (0,11), lc=colors[1], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using Rodas5 (correct solution)") +p2 = plot(sol2, vars = (0,11), lc=colors[2], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using FBDF") +p3 = plot(sol3, vars = (0,11), lc=colors[3], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using QNDF") +p4 = plot(sol4, vars = (0,11), lc=colors[4], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using CVODE FBDF") +combined_plot = plot(p1, p2, p3, p4, layout=(4, 1), dpi = 600, pallete=:acton) +display(combined_plot) ``` ## Run Benchmark @@ -157,8 +189,6 @@ plot(sol; yscale=:log10, idxs = (0,5)) abstols = 1.0 ./ 10.0 .^ (8:10) reltols = 1.0 ./ 10.0 .^ (8:10) -sol = solve(prob, CVODE_BDF(), abstol=1e-14, reltol=1e-14) - setups = [ Dict(:alg=>FBDF()), Dict(:alg=>QNDF()), @@ -182,4 +212,4 @@ setups = [ wp = WorkPrecisionSet(prob,abstols,reltols,setups;appxsol=refsol,save_everystep=false, print_names = true) plot(wp) -``` \ No newline at end of file +``` From 17c3c5597e861740f39a0de82a5a4f9bd0195edb Mon Sep 17 00:00:00 2001 From: Ninadlt <166744945+nnd389@users.noreply.github.com> Date: Fri, 25 Oct 2024 10:54:07 -0500 Subject: [PATCH 02/18] Updated the nelson ODE function, (made it nicer to look at) and added parameters --- benchmarks/AstroChem/nelson.jmd | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/benchmarks/AstroChem/nelson.jmd b/benchmarks/AstroChem/nelson.jmd index 16f43e326..44fa995ec 100644 --- a/benchmarks/AstroChem/nelson.jmd +++ b/benchmarks/AstroChem/nelson.jmd @@ -15,7 +15,7 @@ using ODEInterface, ODEInterfaceDiffEq The ODE function defined below models the reduced carbon-oxygen chemistry network of Nelson & Langer (1999, ApJ, 524, 923). -This Julia ODE function was written by Nina De La Torre advised by Stella Offner. +This Julia ODE function was written by Nina De La Torre advised by Dr. Stella Offner. The solution was compared with results derived by DESPOTIC, (Mark Krumholz, 2013) a code to Derive the Energetics and Spectra of Optically Thick Insterstellar Clouds. DESPOTIC has pre-defined networks, one of them coming from the Nelson & Langer paper, @@ -167,18 +167,18 @@ u0 = [0.5, # 1: H2 prob = ODEProblem(Nelson!, u0, tspan, params) refsol = solve(prob, Vern9(), abstol=1e-14, reltol=1e-14) - sol1 = solve(prob, Rodas5P()) sol2 = solve(prob, FBDF()) -sol3 = solve(prob, QNDF()) -sol4 = solve(prob, CVODE_BDF()) +sol3 = solve(prob, lsoda()) +sol4 = solve(prob, lsoda(), saveat = 1e10) + using Plots colors = palette(:acton, 5) p1 = plot(sol1, vars = (0,11), lc=colors[1], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using Rodas5 (correct solution)") p2 = plot(sol2, vars = (0,11), lc=colors[2], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using FBDF") -p3 = plot(sol3, vars = (0,11), lc=colors[3], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using QNDF") -p4 = plot(sol4, vars = (0,11), lc=colors[4], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using CVODE FBDF") +p3 = plot(sol3, vars = (0,11), lc=colors[3], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using lsoda") +p4 = plot(sol4, vars = (0,11), lc=colors[4], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using lsoda with saveat") combined_plot = plot(p1, p2, p3, p4, layout=(4, 1), dpi = 600, pallete=:acton) display(combined_plot) ``` From f4ab04406d4b23d0199842dba664ea4229c4a3af Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Fri, 25 Oct 2024 16:16:10 +0000 Subject: [PATCH 03/18] Update nelson.jmd --- benchmarks/AstroChem/nelson.jmd | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/benchmarks/AstroChem/nelson.jmd b/benchmarks/AstroChem/nelson.jmd index 44fa995ec..f33c0fb4e 100644 --- a/benchmarks/AstroChem/nelson.jmd +++ b/benchmarks/AstroChem/nelson.jmd @@ -10,8 +10,6 @@ using Sundials, LSODA using ODEInterface, ODEInterfaceDiffEq ``` -```julia -#= The ODE function defined below models the reduced carbon-oxygen chemistry network of Nelson & Langer (1999, ApJ, 524, 923). @@ -31,8 +29,8 @@ and M represents the low ionization potential metals Mg, Fe, Ca, and Na. G₀ = 1.7 --> Go; "a factor that determines the flux of FUV radiation relative to the standard interstellar value (G₀ = 1) as reported by Habing (1968)." n_H = 611 --> Hydrogen Number Density shield = 1 --> "CO self-shielding factor of van Dishoeck & Black (1988), taken from Bergin et al. (1995)" -=# +```julia function Nelson!(du,u,p,t) T, Av, Go, n_H, shield = p @@ -164,7 +162,6 @@ u0 = [0.5, # 1: H2 2.0e-7, # 13: M+ 2.0e-7] # 14: M - prob = ODEProblem(Nelson!, u0, tspan, params) refsol = solve(prob, Vern9(), abstol=1e-14, reltol=1e-14) sol1 = solve(prob, Rodas5P()) @@ -172,7 +169,9 @@ sol2 = solve(prob, FBDF()) sol3 = solve(prob, lsoda()) sol4 = solve(prob, lsoda(), saveat = 1e10) +## Validation Plot +```julia using Plots colors = palette(:acton, 5) p1 = plot(sol1, vars = (0,11), lc=colors[1], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using Rodas5 (correct solution)") From 238089b94a783a9300a9016bc51a489a7e681dd4 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Sun, 27 Oct 2024 14:09:46 -0100 Subject: [PATCH 04/18] bump astrochem manifest --- benchmarks/AstroChem/Manifest.toml | 444 +++++++++++++++++------------ 1 file changed, 269 insertions(+), 175 deletions(-) diff --git a/benchmarks/AstroChem/Manifest.toml b/benchmarks/AstroChem/Manifest.toml index 71c54843a..6d535c7fc 100644 --- a/benchmarks/AstroChem/Manifest.toml +++ b/benchmarks/AstroChem/Manifest.toml @@ -2,12 +2,12 @@ julia_version = "1.10.5" manifest_format = "2.0" -project_hash = "8702bd396dbf00bab17774defca37a9a55f9bfee" +project_hash = "c8f3f46aa53e8a8350ecf2bd2339388769308b5d" [[deps.ADTypes]] -git-tree-sha1 = "99a6f5d0ce1c7c6afdb759daa30226f71c54f6b0" +git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.7.1" +version = "1.9.0" weakdeps = ["ChainRulesCore", "EnzymeCore"] [deps.ADTypes.extensions] @@ -20,31 +20,35 @@ uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.5" [[deps.Accessors]] -deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] -git-tree-sha1 = "f61b15be1d76846c0ce31d3fcfac5380ae53db6a" +deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"] +git-tree-sha1 = "b392ede862e506d451fc1616e79aa6f4c673dab8" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.37" +version = "0.1.38" [deps.Accessors.extensions] AccessorsAxisKeysExt = "AxisKeys" + AccessorsDatesExt = "Dates" AccessorsIntervalSetsExt = "IntervalSets" AccessorsStaticArraysExt = "StaticArrays" AccessorsStructArraysExt = "StructArrays" + AccessorsTestExt = "Test" AccessorsUnitfulExt = "Unitful" [deps.Accessors.weakdeps] AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" Requires = "ae029012-a4dd-5104-9daa-d747884805df" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099" +git-tree-sha1 = "d80af0733c99ea80575f612813fa6aa71022d33a" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "4.0.4" +version = "4.1.0" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] @@ -98,9 +102,9 @@ version = "7.16.0" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "0dd7edaff278e346eb0ca07a7e75c9438408a3ce" +git-tree-sha1 = "492681bc44fac86804706ddb37da10880a2bd528" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.10.3" +version = "1.10.4" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -136,9 +140,9 @@ version = "0.1.6" [[deps.BlockArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra"] -git-tree-sha1 = "5c0ffe1dff8cb7112de075f1b1cb32191675fcba" +git-tree-sha1 = "d434647f798823bcae510aee0bc0401927f64391" uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" -version = "1.1.0" +version = "1.1.1" [deps.BlockArrays.extensions] BlockArraysBandedMatricesExt = "BandedMatrices" @@ -148,9 +152,9 @@ version = "1.1.0" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" +git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+1" +version = "1.0.8+2" [[deps.CEnum]] git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" @@ -171,9 +175,9 @@ version = "3.4.3" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "a2f1c8c668c8e3cb4cca4e57a8efdb09067bb3fd" +git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.0+2" +version = "1.18.2+1" [[deps.Catalyst]] deps = ["Combinatorics", "DataStructures", "DiffEqBase", "DocStringExtensions", "DynamicPolynomials", "DynamicQuantities", "Graphs", "JumpProcesses", "LaTeXStrings", "Latexify", "LinearAlgebra", "MacroTools", "ModelingToolkit", "Parameters", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SymbolicUtils", "Symbolics", "Unitful"] @@ -197,9 +201,9 @@ version = "14.4.1" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "71acdbf594aab5bbb2cec89b208c41b4c411e49f" +git-tree-sha1 = "3e4b134270b372f2ed4d4d0e936aabaefc1802bc" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.24.0" +version = "1.25.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -219,9 +223,9 @@ version = "0.7.6" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "b5278586822443594ff615963b0c09755771b3e0" +git-tree-sha1 = "13951eb68769ad1cd460cdb2e64e5e95f1bf123d" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.26.0" +version = "3.27.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -251,10 +255,10 @@ uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" version = "1.0.2" [[deps.CommonMark]] -deps = ["Crayons", "JSON", "PrecompileTools", "URIs"] -git-tree-sha1 = "532c4185d3c9037c0237546d817858b23cf9e071" +deps = ["Crayons", "PrecompileTools"] +git-tree-sha1 = "3faae67b8899797592335832fccf4b3c80bb04fa" uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6" -version = "0.8.12" +version = "0.8.15" [[deps.CommonSolve]] git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" @@ -372,10 +376,10 @@ uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" version = "1.9.1" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] -git-tree-sha1 = "d7d43a1cc11dc4e4e5378816ae720fccd75a77c8" +deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "TruncatedStacktraces"] +git-tree-sha1 = "f8eefbb7e910f59087c4bb09ce670f235758ee4a" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.155.0" +version = "6.158.3" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -406,17 +410,16 @@ version = "6.155.0" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.DiffEqCallbacks]] -deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NonlinearSolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "19dbd44d18bbfdfcf5e56c99cea9b0ed23df350a" +deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "7f700fa4fb6e55f4672f8218ef228107245a2e9d" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "3.9.1" -weakdeps = ["OrdinaryDiffEq", "OrdinaryDiffEqCore", "Sundials"] +version = "4.0.0" [[deps.DiffEqDevTools]] deps = ["DiffEqBase", "DiffEqNoiseProcess", "Distributed", "LinearAlgebra", "Logging", "NLsolve", "RecipesBase", "RecursiveArrayTools", "RootedTrees", "SciMLBase", "Statistics", "StructArrays"] -git-tree-sha1 = "35f51dc83977ca2cc45f9a0abd55ed9efd54eff7" +git-tree-sha1 = "167a3a413b954aca9e64d785f8ea096e23e5afb8" uuid = "f3b72e0c-5b89-59e1-b016-84e28bfd966d" -version = "2.45.0" +version = "2.45.1" [[deps.DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] @@ -443,10 +446,10 @@ uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" version = "1.15.1" [[deps.DifferentiationInterface]] -deps = ["ADTypes", "Compat", "DocStringExtensions", "FillArrays", "LinearAlgebra", "PackageExtensionCompat", "SparseArrays", "SparseMatrixColorings"] -git-tree-sha1 = "9b23f9a816790b8ab9914c3c86321a546e92cbe7" +deps = ["ADTypes", "LinearAlgebra"] +git-tree-sha1 = "16611777adf4a818f18c33210895947814180964" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.5.17" +version = "0.6.16" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -456,10 +459,13 @@ version = "0.5.17" DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" DifferentiationInterfaceForwardDiffExt = "ForwardDiff" + DifferentiationInterfaceMooncakeExt = "Mooncake" DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff" DifferentiationInterfaceReverseDiffExt = "ReverseDiff" + DifferentiationInterfaceSparseArraysExt = "SparseArrays" + DifferentiationInterfaceSparseMatrixColoringsExt = "SparseMatrixColorings" + DifferentiationInterfaceStaticArraysExt = "StaticArrays" DifferentiationInterfaceSymbolicsExt = "Symbolics" - DifferentiationInterfaceTapirExt = "Tapir" DifferentiationInterfaceTrackerExt = "Tracker" DifferentiationInterfaceZygoteExt = ["Zygote", "ForwardDiff"] @@ -471,18 +477,21 @@ version = "0.5.17" FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" - Tapir = "07d77754-e150-4737-8c94-cd238a1fb45b" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.DispatchDoctor]] deps = ["MacroTools", "Preferences"] -git-tree-sha1 = "c2acd1de2c4c357928f9fb6b60b402d914621378" +git-tree-sha1 = "810cae95ca4db1c563be2d7d38fa9b7289d302db" uuid = "8d63f2c5-f18a-4cf2-ba9d-b3f60fc568c8" -version = "0.4.14" +version = "0.4.16" weakdeps = ["ChainRulesCore", "EnzymeCore"] [deps.DispatchDoctor.extensions] @@ -491,9 +500,9 @@ weakdeps = ["ChainRulesCore", "EnzymeCore"] [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" +git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.11" +version = "0.10.12" weakdeps = ["ChainRulesCore", "SparseArrays"] [deps.Distances.extensions] @@ -506,9 +515,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "e6c693a0e4394f8fda0e51a5bdf5aef26f8235e9" +git-tree-sha1 = "d7477ecdafb813ddee2ae727afa94e9dcb5f3fb0" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.111" +version = "0.25.112" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -551,9 +560,9 @@ version = "0.6.0" [[deps.DynamicQuantities]] deps = ["Compat", "DispatchDoctor", "PackageExtensionCompat", "TestItems", "Tricks"] -git-tree-sha1 = "317430fb3dcfb17831eb0e4bcd852358a48a4e7a" +git-tree-sha1 = "82b3ab10e1d14cd79d813d30005d52ac3ef9ea97" uuid = "06fc5a27-2a28-4c7c-a15d-362465fb6821" -version = "1.0.0" +version = "1.1.0" [deps.DynamicQuantities.extensions] DynamicQuantitiesLinearAlgebraExt = "LinearAlgebra" @@ -573,9 +582,9 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.EnzymeCore]] -git-tree-sha1 = "8f205a601760f4798a10f138c3940f0451d95188" +git-tree-sha1 = "9c3a42611e525352e9ad5e4134ddca5c692ff209" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.7.8" +version = "0.8.4" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -618,9 +627,9 @@ version = "0.8.5" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] -git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" +git-tree-sha1 = "53ebe7511fa11d33bec688a9178fac4e49eeee00" uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.1" +version = "0.4.2" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] @@ -645,6 +654,27 @@ git-tree-sha1 = "cbf5edddb61a43669710cbc2241bc08b36d9e660" uuid = "29a986be-02c6-4525-aec4-84b980013641" version = "2.0.4" +[[deps.FastPower]] +git-tree-sha1 = "46aee43f62bc2bc06a74e2d668ffeea0a2689c93" +uuid = "a4df4552-cc26-4903-aec0-212e50a0e84b" +version = "1.1.0" + + [deps.FastPower.extensions] + FastPowerEnzymeExt = "Enzyme" + FastPowerForwardDiffExt = "ForwardDiff" + FastPowerMeasurementsExt = "Measurements" + FastPowerMonteCarloMeasurementsExt = "MonteCarloMeasurements" + FastPowerReverseDiffExt = "ReverseDiff" + FastPowerTrackerExt = "Tracker" + + [deps.FastPower.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" @@ -666,19 +696,21 @@ uuid = "64ca27bc-2ba2-4a57-88aa-44e436879224" version = "1.4.1" [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Setfield", "SparseArrays"] -git-tree-sha1 = "f9219347ebf700e77ca1d48ef84e4a82a6701882" +deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] +git-tree-sha1 = "b10bdafd1647f57ace3885143936749d61638c3b" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.24.0" +version = "2.26.0" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices" + FiniteDiffSparseArraysExt = "SparseArrays" FiniteDiffStaticArraysExt = "StaticArrays" [deps.FiniteDiff.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.FixedPointNumbers]] @@ -755,15 +787,21 @@ version = "0.1.6" [[deps.GR]] deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] -git-tree-sha1 = "629693584cef594c3f6f99e76e7a7ad17e60e8d5" +git-tree-sha1 = "ee28ddcd5517d54e417182fec3886e7412d3926f" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.7" +version = "0.73.8" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "a8863b69c2a0859f2c2c87ebdc4c6712e88bdf0d" +git-tree-sha1 = "f31929b9e67066bee48eec8b03c0df47d31a74b3" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.7+0" +version = "0.73.8+0" + +[[deps.GenericLinearAlgebra]] +deps = ["LinearAlgebra", "Printf", "Random", "libblastrampoline_jll"] +git-tree-sha1 = "f47136cac29a9b7a8a88dbce1195394978091edb" +uuid = "14197337-ba66-59df-a3e3-ca00e7dcff7a" +version = "0.3.13" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -779,9 +817,9 @@ version = "0.21.0+0" [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba" +git-tree-sha1 = "674ff0db93fffcd11a3573986e550d66cd4fd71f" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.80.2+0" +version = "2.80.5+0" [[deps.Glob]] git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" @@ -796,9 +834,9 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "ebd18c326fa6cee1efb7da9a3b45cf69da2ed4d9" +git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.11.2" +version = "1.12.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -866,9 +904,9 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] IntervalSetsStatisticsExt = "Statistics" [[deps.InverseFunctions]] -git-tree-sha1 = "2787db24f4e03daf859c6509ff87764e4182f7d1" +git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.16" +version = "0.1.17" weakdeps = ["Dates", "Test"] [deps.InverseFunctions.extensions] @@ -893,9 +931,9 @@ version = "0.1.8" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "f389674c99bfcde17dc57454011aa44d5a260a40" +git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.6.0" +version = "1.6.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -905,21 +943,21 @@ version = "0.21.4" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637" +git-tree-sha1 = "25ee0be4d43d0269027024d75a24c24d6c6e590c" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.0.3+0" +version = "3.0.4+0" [[deps.JuliaFormatter]] deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "PrecompileTools", "TOML", "Tokenize"] -git-tree-sha1 = "bb4696471330275adfd6c78c6173f276e8c067aa" +git-tree-sha1 = "59cf7ad64f1b0708a4fa4369879d33bad3239b56" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.60" +version = "1.0.62" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] -git-tree-sha1 = "6e0fb267f2c869df59b6bf9f8cb0f2794f2d85e9" +git-tree-sha1 = "c3a2cb6f968404ed3b1d5382bbdd7b7d83966598" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.13.7" +version = "9.14.0" weakdeps = ["FastBroadcast"] [[deps.KLU]] @@ -930,9 +968,9 @@ version = "0.6.0" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "267dad6b4b7b5d529c76d40ff48d33f7e94cb834" +git-tree-sha1 = "4f20a2df85a9e5d55c9e84634bbf808ed038cabd" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.6" +version = "0.9.8" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -941,16 +979,16 @@ uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" version = "3.100.2+0" [[deps.LERC_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "36bdbc52f13a7d1dcb0f3cd694e01677a515655b" uuid = "88015f11-f218-50d7-93a8-a6af411a945d" -version = "3.0.0+1" +version = "4.0.0+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e16271d212accd09d52ee0ae98956b8a05c4b626" +git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "17.0.6+0" +version = "18.1.7+0" [[deps.LSODA]] deps = ["Compat", "DiffEqBase", "LSODA_jll", "LinearAlgebra", "Parameters", "Printf", "SciMLBase"] @@ -966,19 +1004,14 @@ version = "0.1.2+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d" +git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.2+0" +version = "2.10.2+1" [[deps.LaTeXStrings]] -git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" +git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.1" - -[[deps.LambertW]] -git-tree-sha1 = "c5ffc834de5d61d00d2b0e18c96267cffc21f648" -uuid = "984bce1d-4616-540c-a9ee-88d1112d94c9" -version = "0.4.6" +version = "1.4.0" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] @@ -1059,9 +1092,9 @@ version = "3.2.2+1" [[deps.Libgcrypt_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] -git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673" +git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.11+0" +version = "1.11.0+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] @@ -1071,15 +1104,15 @@ version = "1.6.0+0" [[deps.Libgpg_error_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed" +git-tree-sha1 = "c6ce1e19f3aec9b59186bdf06cdf3c4fc5f5f3e6" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.49.0+0" +version = "1.50.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" +git-tree-sha1 = "61dfdba58e585066d8bce214c5a51eaa0539f269" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.17.0+0" +version = "1.17.0+1" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1089,9 +1122,9 @@ version = "2.40.1+0" [[deps.Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "2da088d113af58221c52828a80378e16be7d037a" +git-tree-sha1 = "b404131d06f7886402758c9ce2214b636eb4d54a" uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.5.1+1" +version = "4.7.0+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1099,6 +1132,16 @@ git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" version = "2.40.1+0" +[[deps.LineSearch]] +deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"] +git-tree-sha1 = "97d502765cc5cf3a722120f50da03c2474efce04" +uuid = "87fe0de2-c867-4266-b59a-2f0a94fc965b" +version = "0.1.4" +weakdeps = ["LineSearches"] + + [deps.LineSearch.extensions] + LineSearchLineSearchesExt = "LineSearches" + [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] git-tree-sha1 = "e4c3be53733db1051cc15ecf573b1042b3a712a1" @@ -1111,17 +1154,17 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "6c5e4555ac2bc449a28604e184f759d18fc08420" +git-tree-sha1 = "ddb60aabc5efb0670c7ddde5fedf7ab44520a3e6" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.34.0" +version = "2.36.1" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" LinearSolveCUDSSExt = "CUDSS" - LinearSolveEnzymeExt = ["Enzyme", "EnzymeCore"] - LinearSolveFastAlmostBandedMatricesExt = ["FastAlmostBandedMatrices"] + LinearSolveEnzymeExt = "EnzymeCore" + LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKernelAbstractionsExt = "KernelAbstractions" @@ -1135,7 +1178,6 @@ version = "2.34.0" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" - Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" @@ -1167,9 +1209,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075" +git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.3" +version = "1.1.0" [[deps.LoopVectorization]] deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] @@ -1244,21 +1286,23 @@ version = "1.2.0" uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.ModelingToolkit]] -deps = ["AbstractTrees", "ArrayInterface", "BlockArrays", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "DynamicQuantities", "ExprTools", "Expronicon", "FindFirstFunctions", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "NaNMath", "NonlinearSolve", "OrderedCollections", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] -git-tree-sha1 = "f87f07e0471323694ff5d9f52ff763e2e4ffacfe" +deps = ["AbstractTrees", "ArrayInterface", "BlockArrays", "Combinatorics", "CommonSolve", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "DynamicQuantities", "ExprTools", "Expronicon", "FindFirstFunctions", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "Graphs", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "NaNMath", "NonlinearSolve", "OffsetArrays", "OrderedCollections", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] +git-tree-sha1 = "4e18caba05cb1a32469c15edb634341a246a533d" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "9.39.0" +version = "9.48.0" [deps.ModelingToolkit.extensions] MTKBifurcationKitExt = "BifurcationKit" MTKChainRulesCoreExt = "ChainRulesCore" MTKDeepDiffsExt = "DeepDiffs" + MTKHomotopyContinuationExt = "HomotopyContinuation" MTKLabelledArraysExt = "LabelledArrays" [deps.ModelingToolkit.weakdeps] BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6" + HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327" LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" [[deps.MozillaCACerts_jll]] @@ -1272,15 +1316,15 @@ version = "0.2.4" [[deps.MultivariatePolynomials]] deps = ["ChainRulesCore", "DataStructures", "LinearAlgebra", "MutableArithmetics"] -git-tree-sha1 = "5c1d1d9361e1417e5a065e1f84dc3686cbdaea21" +git-tree-sha1 = "8d39779e29f80aa6c071e7ac17101c6e31f075d7" uuid = "102ac46a-7ee4-5c85-9060-abc95bfdeaa3" -version = "0.5.6" +version = "0.5.7" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "d0a6b1096b584a2b88efb70a92f8cb8c881eb38a" +git-tree-sha1 = "90077f1e79de8c9c7c8a90644494411111f4e07b" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.4.6" +version = "1.5.2" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1305,10 +1349,10 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "bcd8812e751326ff1d4b2dd50764b93df51f143b" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] +git-tree-sha1 = "4d8944f32db2b07a2bdf8477e878bcb9c9ea2308" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "3.14.0" +version = "3.15.1" [deps.NonlinearSolve.extensions] NonlinearSolveBandedMatricesExt = "BandedMatrices" @@ -1320,8 +1364,6 @@ version = "3.14.0" NonlinearSolveNLsolveExt = "NLsolve" NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations" NonlinearSolveSpeedMappingExt = "SpeedMapping" - NonlinearSolveSymbolicsExt = "Symbolics" - NonlinearSolveZygoteExt = "Zygote" [deps.NonlinearSolve.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" @@ -1333,8 +1375,6 @@ version = "3.14.0" NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" SIAMFANLEquations = "084e46ad-d928-497d-ad5e-07fa361a48c4" SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412" - Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.ODEInterface]] deps = ["Dates", "Libdl", "LinearAlgebra", "Markdown", "ODEInterface_jll", "Unicode"] @@ -1387,9 +1427,9 @@ version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1b35263570443fdd9e76c76b7062116e2f374ab8" +git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.15+0" +version = "3.0.15+1" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1439,10 +1479,10 @@ uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" version = "1.1.2" [[deps.OrdinaryDiffEqCore]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "TruncatedStacktraces"] -git-tree-sha1 = "35fdf60f6b5e283ea2292d3f1c57abce6175c406" +deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "TruncatedStacktraces"] +git-tree-sha1 = "1175717a62ab21736a8f5d0d2531d2a6ad3b9e74" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "1.5.1" +version = "1.9.0" weakdeps = ["EnzymeCore"] [deps.OrdinaryDiffEqCore.extensions] @@ -1473,16 +1513,16 @@ uuid = "e0540318-69ee-4070-8777-9e2de6de23de" version = "1.1.0" [[deps.OrdinaryDiffEqExtrapolation]] -deps = ["DiffEqBase", "FastBroadcast", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "fea595528a160ed5cade9eee217a9691b1d97714" +deps = ["DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport"] +git-tree-sha1 = "0260b1657069608f2a2f26f58f65019d8a9070ab" uuid = "becaefa8-8ca2-5cf9-886d-c06f3d2bd2c4" -version = "1.1.0" +version = "1.2.0" [[deps.OrdinaryDiffEqFIRK]] -deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLOperators"] -git-tree-sha1 = "795221c662698851328cb7787965ab4a180d9468" +deps = ["DiffEqBase", "FastBroadcast", "FastPower", "GenericLinearAlgebra", "GenericSchur", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polynomials", "RecursiveArrayTools", "Reexport", "RootedTrees", "SciMLOperators", "Symbolics"] +git-tree-sha1 = "5735f4c094dff311f5064d1a351da9669e4647e3" uuid = "5960d6e9-dd7a-4743-88e7-cf307b64f125" -version = "1.1.1" +version = "1.2.0" [[deps.OrdinaryDiffEqFeagin]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -1668,10 +1708,10 @@ uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" version = "3.2.0" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "7b1a9df27f072ac4c9c7cbe5efb198489258d1f5" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"] +git-tree-sha1 = "650a022b2ce86c7dcfbdecf00f78afeeb20e5655" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.4.1" +version = "1.4.2" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] @@ -1711,6 +1751,24 @@ git-tree-sha1 = "645bed98cd47f72f67316fd42fc47dee771aefcd" uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" version = "0.2.2" +[[deps.Polynomials]] +deps = ["LinearAlgebra", "RecipesBase", "Requires", "Setfield", "SparseArrays"] +git-tree-sha1 = "1a9cfb2dc2c2f1bd63f1906d72af39a79b49b736" +uuid = "f27b6e38-b328-58d1-80ce-0feddd5e7a45" +version = "4.0.11" + + [deps.Polynomials.extensions] + PolynomialsChainRulesCoreExt = "ChainRulesCore" + PolynomialsFFTWExt = "FFTW" + PolynomialsMakieCoreExt = "MakieCore" + PolynomialsMutableArithmeticsExt = "MutableArithmetics" + + [deps.Polynomials.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" + MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b" + MutableArithmetics = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" + [[deps.PositiveFactorizations]] deps = ["LinearAlgebra"] git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20" @@ -1786,9 +1844,9 @@ version = "6.7.1+1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "1d587203cf851a51bf1ea31ad7ff89eff8d625ea" +git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.11.0" +version = "2.11.1" [deps.QuadGK.extensions] QuadGKEnzymeExt = "Enzyme" @@ -1885,15 +1943,15 @@ version = "1.1.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +git-tree-sha1 = "852bd0f55565a9e973fcfee83a84413270224dc4" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.1" +version = "0.8.0" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e60724fd3beea548353984dc61c943ecddb0e29a" +git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.3+0" +version = "0.5.1+0" [[deps.RootedTrees]] deps = ["LaTeXStrings", "Latexify", "LinearAlgebra", "Preferences", "RecipesBase", "Requires"] @@ -1927,10 +1985,10 @@ uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" version = "0.6.43" [[deps.SciMLBase]] -deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "952e09c65264fe2a8155dd6aad60c188a0b83f69" +deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "328dd8738fad35cfe53c427a30e711ed45a1d900" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.53.0" +version = "2.57.1" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -1951,11 +2009,17 @@ version = "2.53.0" RCall = "6f49c342-dc21-5d91-9882-a32aef131414" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" +[[deps.SciMLJacobianOperators]] +deps = ["ADTypes", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] +git-tree-sha1 = "991d2a8900e687e2c693d587daa739c8fda01366" +uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" +version = "0.1.0" + [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] -git-tree-sha1 = "e39c5f217f9aca640c8e27ab21acf557a3967db5" +git-tree-sha1 = "ef388ca9e4921ec5614ce714f8aa59a5cd33d867" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.10" +version = "0.3.11" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -1994,15 +2058,15 @@ uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" version = "1.0.3" [[deps.SimpleBufferStream]] -git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" -version = "1.1.0" +version = "1.2.0" [[deps.SimpleNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "4d7a7c177bcb4c6dc465f09db91bfdb28c578919" +git-tree-sha1 = "44021f3efc023be3871195d8ad98b865001a2fa1" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.12.0" +version = "1.12.3" [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" @@ -2041,11 +2105,31 @@ deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" version = "1.10.0" +[[deps.SparseConnectivityTracer]] +deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "6914df6005bab9940e2a96879a97a43e1fb1ce78" +uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" +version = "0.6.8" + + [deps.SparseConnectivityTracer.extensions] + SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" + SparseConnectivityTracerLogExpFunctionsExt = "LogExpFunctions" + SparseConnectivityTracerNNlibExt = "NNlib" + SparseConnectivityTracerNaNMathExt = "NaNMath" + SparseConnectivityTracerSpecialFunctionsExt = "SpecialFunctions" + + [deps.SparseConnectivityTracer.weakdeps] + DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0" + LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" + NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" + NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + [[deps.SparseDiffTools]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "c9e5d7ee75cf6a1ca3a22c9a6a4ef451792cf62b" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "UnPack", "VertexSafeGraphs"] +git-tree-sha1 = "b906758c107b049b6b71599b9f928d9b14e5554a" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.20.0" +version = "2.23.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" @@ -2062,10 +2146,14 @@ version = "2.20.0" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SparseMatrixColorings]] -deps = ["ADTypes", "Compat", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "996dff77d814c45c3f2342fa0113e4ad31e712e8" +deps = ["ADTypes", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "f37f046636f8dc353a39279abfefe296db212171" uuid = "0a514795-09f3-496d-8182-132a7b665d35" -version = "0.4.0" +version = "0.4.8" +weakdeps = ["Colors"] + + [deps.SparseMatrixColorings.extensions] + SparseMatrixColoringsColorsExt = "Colors" [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] @@ -2083,6 +2171,12 @@ weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" +[[deps.StableRNGs]] +deps = ["Random"] +git-tree-sha1 = "83e6cce8324d49dfaf9ef059227f91ed4441a8e5" +uuid = "860ef19b-820b-49d6-a774-d7a799459cd3" +version = "1.0.2" + [[deps.Static]] deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" @@ -2102,9 +2196,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50" +git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.7" +version = "1.9.8" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -2135,9 +2229,9 @@ version = "0.34.3" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a" +git-tree-sha1 = "b423576adc27097764a90e163157bcfc9acf0f46" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.1" +version = "1.3.2" weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] @@ -2174,9 +2268,9 @@ version = "7.2.1+1" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "82304990120934137261aa085e0d05a412fe0825" +git-tree-sha1 = "e87efb31e5360cb223a151c2398903dc2faeb32b" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.25.0" +version = "4.26.0" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"] @@ -2186,9 +2280,9 @@ version = "5.2.2+0" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "988e04b34a4c3b824fb656f542473df99a4f610d" +git-tree-sha1 = "4bc96df5d71515b1cb86dd626915f06f4c0d46f5" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.30" +version = "0.3.33" [[deps.SymbolicLimits]] deps = ["SymbolicUtils"] @@ -2198,9 +2292,9 @@ version = "0.2.2" [[deps.SymbolicUtils]] deps = ["AbstractTrees", "ArrayInterface", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "TermInterface", "TimerOutputs", "Unityper"] -git-tree-sha1 = "9d983078d9e99421fcca44c373e4304b8421fdde" +git-tree-sha1 = "04e9157537ba51dad58336976f8d04b9ab7122f0" uuid = "d1185830-fcd6-423d-90d6-eec64667417b" -version = "3.6.0" +version = "3.7.2" [deps.SymbolicUtils.extensions] SymbolicUtilsLabelledArraysExt = "LabelledArrays" @@ -2211,10 +2305,10 @@ version = "3.6.0" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" [[deps.Symbolics]] -deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "Primes", "RecipesBase", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] -git-tree-sha1 = "2226d810512c678d2ec9c2a9b2e227c2ebc43573" +deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "IfElse", "LaTeXStrings", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "Primes", "RecipesBase", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] +git-tree-sha1 = "ef7532b95fbd529e1252cabb36bba64803020840" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "6.11.0" +version = "6.16.0" [deps.Symbolics.extensions] SymbolicsForwardDiffExt = "ForwardDiff" @@ -2282,9 +2376,9 @@ version = "0.5.2" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "5a13ae8a41237cff5ecf34f73eb1b8f42fff6531" +git-tree-sha1 = "3a6f063d690135f5c1ba351412c82bae4d1402bf" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.24" +version = "0.5.25" [[deps.Tokenize]] git-tree-sha1 = "468b4685af4abe0e9fd4d7bf495a6554a6276e75" @@ -2292,9 +2386,9 @@ uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624" version = "0.5.29" [[deps.TranscodingStreams]] -git-tree-sha1 = "e84b3a11b9bece70d14cce63406bbc79ed3464d2" +git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.11.2" +version = "0.11.3" [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] @@ -2396,9 +2490,9 @@ version = "1.31.0+0" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "1165b0443d0eca63ac1e32b8c0eb69ed2f4f8127" +git-tree-sha1 = "6a451c6f33a176150f315726eba8b92fbfdb9ae7" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.13.3+0" +version = "2.13.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] @@ -2408,9 +2502,9 @@ version = "1.1.41+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632" +git-tree-sha1 = "15e637a697345f6743674f1322beefbc5dcd5cfc" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.4.6+0" +version = "5.6.3+0" [[deps.Xorg_libICE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2563,9 +2657,9 @@ version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b" +git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.6+0" +version = "1.5.6+1" [[deps.eudev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] @@ -2628,9 +2722,9 @@ version = "1.18.0+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" +git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.43+1" +version = "1.6.44+0" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] From 08882e588854dbd5e1d1ef736473b2da3a1afb3c Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Mon, 28 Oct 2024 14:55:20 -0100 Subject: [PATCH 05/18] update manifest --- benchmarks/AstroChem/Manifest.toml | 22 +++++++++++----------- benchmarks/AstroChem/Project.toml | 4 ++-- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/benchmarks/AstroChem/Manifest.toml b/benchmarks/AstroChem/Manifest.toml index 6d535c7fc..7ecdb92ea 100644 --- a/benchmarks/AstroChem/Manifest.toml +++ b/benchmarks/AstroChem/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.5" manifest_format = "2.0" -project_hash = "c8f3f46aa53e8a8350ecf2bd2339388769308b5d" +project_hash = "81a84463ee3fb40ec2e360f288f69699605fb501" [[deps.ADTypes]] git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081" @@ -447,9 +447,9 @@ version = "1.15.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "16611777adf4a818f18c33210895947814180964" +git-tree-sha1 = "89d7cfcd1c4d9137497148e44e87ed4866ed6730" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.6.16" +version = "0.6.17" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -489,9 +489,9 @@ version = "0.6.16" [[deps.DispatchDoctor]] deps = ["MacroTools", "Preferences"] -git-tree-sha1 = "810cae95ca4db1c563be2d7d38fa9b7289d302db" +git-tree-sha1 = "453df2ce2aef7de59c69a56d31dcd2ec3384dd77" uuid = "8d63f2c5-f18a-4cf2-ba9d-b3f60fc568c8" -version = "0.4.16" +version = "0.4.17" weakdeps = ["ChainRulesCore", "EnzymeCore"] [deps.DispatchDoctor.extensions] @@ -655,9 +655,9 @@ uuid = "29a986be-02c6-4525-aec4-84b980013641" version = "2.0.4" [[deps.FastPower]] -git-tree-sha1 = "46aee43f62bc2bc06a74e2d668ffeea0a2689c93" +git-tree-sha1 = "58c3431137131577a7c379d00fea00be524338fb" uuid = "a4df4552-cc26-4903-aec0-212e50a0e84b" -version = "1.1.0" +version = "1.1.1" [deps.FastPower.extensions] FastPowerEnzymeExt = "Enzyme" @@ -799,9 +799,9 @@ version = "0.73.8+0" [[deps.GenericLinearAlgebra]] deps = ["LinearAlgebra", "Printf", "Random", "libblastrampoline_jll"] -git-tree-sha1 = "f47136cac29a9b7a8a88dbce1195394978091edb" +git-tree-sha1 = "c4f9c87b74aedf20920034bd4db81d0bffc527d2" uuid = "14197337-ba66-59df-a3e3-ca00e7dcff7a" -version = "0.3.13" +version = "0.3.14" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -1514,9 +1514,9 @@ version = "1.1.0" [[deps.OrdinaryDiffEqExtrapolation]] deps = ["DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "0260b1657069608f2a2f26f58f65019d8a9070ab" +git-tree-sha1 = "048bcccc8f59c20d5b4ad268eef4d7d21c005a94" uuid = "becaefa8-8ca2-5cf9-886d-c06f3d2bd2c4" -version = "1.2.0" +version = "1.2.1" [[deps.OrdinaryDiffEqFIRK]] deps = ["DiffEqBase", "FastBroadcast", "FastPower", "GenericLinearAlgebra", "GenericSchur", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polynomials", "RecursiveArrayTools", "Reexport", "RootedTrees", "SciMLOperators", "Symbolics"] diff --git a/benchmarks/AstroChem/Project.toml b/benchmarks/AstroChem/Project.toml index 8b36869f8..ae007082e 100644 --- a/benchmarks/AstroChem/Project.toml +++ b/benchmarks/AstroChem/Project.toml @@ -21,8 +21,8 @@ LinearSolve = "2" LSODA = "0.7" NaNMath = "1" ODEInterface = "0.5" -OrdinaryDiffEq = "6" -OrdinaryDiffEqCore = "1" +OrdinaryDiffEq = "6.89" +OrdinaryDiffEqCore = "1.9" ODEInterfaceDiffEq = "3" Plots = "1" Sundials = "4" From 8d5e757a31d1d7dbb473d6c69fb063922254b3f5 Mon Sep 17 00:00:00 2001 From: Oscar Smith Date: Mon, 28 Oct 2024 16:13:03 -0400 Subject: [PATCH 06/18] typo --- benchmarks/AstroChem/nelson.jmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/benchmarks/AstroChem/nelson.jmd b/benchmarks/AstroChem/nelson.jmd index f33c0fb4e..9d6789542 100644 --- a/benchmarks/AstroChem/nelson.jmd +++ b/benchmarks/AstroChem/nelson.jmd @@ -24,7 +24,7 @@ the composite oxygen species OHx represents OH, H2O, O2 and their ions, and M represents the low ionization potential metals Mg, Fe, Ca, and Na. Parameter definitions: - T = 10 --> Tempurature (Kelvin) + T = 10 --> Temperature (Kelvin) Av = 2 --> V-Band Extinction G₀ = 1.7 --> Go; "a factor that determines the flux of FUV radiation relative to the standard interstellar value (G₀ = 1) as reported by Habing (1968)." n_H = 611 --> Hydrogen Number Density From 1525c7753803998429ee0e05f6e03cd95c7bceb2 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Sun, 10 Nov 2024 10:03:07 -0100 Subject: [PATCH 07/18] bump manifest --- benchmarks/AstroChem/Manifest.toml | 132 +++++++++++++++-------------- 1 file changed, 70 insertions(+), 62 deletions(-) diff --git a/benchmarks/AstroChem/Manifest.toml b/benchmarks/AstroChem/Manifest.toml index 7ecdb92ea..ed6140ed6 100644 --- a/benchmarks/AstroChem/Manifest.toml +++ b/benchmarks/AstroChem/Manifest.toml @@ -1,6 +1,6 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.10.5" +julia_version = "1.10.6" manifest_format = "2.0" project_hash = "81a84463ee3fb40ec2e360f288f69699605fb501" @@ -46,9 +46,9 @@ version = "0.1.38" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "d80af0733c99ea80575f612813fa6aa71022d33a" +git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "4.1.0" +version = "4.1.1" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] @@ -72,15 +72,16 @@ version = "0.4.0" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra"] -git-tree-sha1 = "3640d077b6dafd64ceb8fd5c1ec76f7ca53bcf76" +git-tree-sha1 = "d60a1922358aa203019b7857a2c8c37329b8736c" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.16.0" +version = "7.17.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" ArrayInterfaceCUDSSExt = "CUDSS" + ArrayInterfaceChainRulesCoreExt = "ChainRulesCore" ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" ArrayInterfaceReverseDiffExt = "ReverseDiff" @@ -94,6 +95,7 @@ version = "7.16.0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" @@ -223,21 +225,27 @@ version = "0.7.6" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "13951eb68769ad1cd460cdb2e64e5e95f1bf123d" +git-tree-sha1 = "c785dfb1b3bfddd1da557e861b919819b82bbe5b" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.27.0" +version = "3.27.1" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "b10d0b65641d57b8b4d5e234446582de5047050d" +git-tree-sha1 = "c7acce7a7e1078a20a285211dd73cd3941a871d6" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.11.5" +version = "0.12.0" + + [deps.ColorTypes.extensions] + StyledStringsExt = "StyledStrings" + + [deps.ColorTypes.weakdeps] + StyledStrings = "f489334b-da3d-4c2e-b8f0-e476e12c162b" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "Requires", "Statistics", "TensorCore"] -git-tree-sha1 = "a1f44953f2382ebb937d60dafbe2deea4bd23249" +git-tree-sha1 = "8b3b6f87ce8f65a2b4f857528fd8d70086cd72b1" uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.10.0" +version = "0.11.0" weakdeps = ["SpecialFunctions"] [deps.ColorVectorSpace.extensions] @@ -245,9 +253,9 @@ weakdeps = ["SpecialFunctions"] [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0" +git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.11" +version = "0.13.0" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -411,9 +419,9 @@ version = "6.158.3" [[deps.DiffEqCallbacks]] deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "7f700fa4fb6e55f4672f8218ef228107245a2e9d" +git-tree-sha1 = "b1f970a2873a2cf76ce35fb0ed2b755a11b31052" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "4.0.0" +version = "4.1.0" [[deps.DiffEqDevTools]] deps = ["DiffEqBase", "DiffEqNoiseProcess", "Distributed", "LinearAlgebra", "Logging", "NLsolve", "RecipesBase", "RecursiveArrayTools", "RootedTrees", "SciMLBase", "Statistics", "StructArrays"] @@ -447,9 +455,9 @@ version = "1.15.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "89d7cfcd1c4d9137497148e44e87ed4866ed6730" +git-tree-sha1 = "0c99576d0b93df0aff1bed9d9adddef14e4e658f" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.6.17" +version = "0.6.22" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -515,9 +523,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d7477ecdafb813ddee2ae727afa94e9dcb5f3fb0" +git-tree-sha1 = "3101c32aab536e7a27b1763c0797dba151b899ad" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.112" +version = "0.25.113" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -559,10 +567,10 @@ uuid = "7c1d4256-1411-5781-91ec-d7bc3513ac07" version = "0.6.0" [[deps.DynamicQuantities]] -deps = ["Compat", "DispatchDoctor", "PackageExtensionCompat", "TestItems", "Tricks"] -git-tree-sha1 = "82b3ab10e1d14cd79d813d30005d52ac3ef9ea97" +deps = ["DispatchDoctor", "TestItems", "Tricks"] +git-tree-sha1 = "192f34efd3912f4020b225e01d896f567f5f03e8" uuid = "06fc5a27-2a28-4c7c-a15d-362465fb6821" -version = "1.1.0" +version = "1.3.0" [deps.DynamicQuantities.extensions] DynamicQuantitiesLinearAlgebraExt = "LinearAlgebra" @@ -582,9 +590,9 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.EnzymeCore]] -git-tree-sha1 = "9c3a42611e525352e9ad5e4134ddca5c692ff209" +git-tree-sha1 = "04c777af6ef65530a96ab68f0a81a4608113aa1d" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.8.4" +version = "0.8.5" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -732,9 +740,9 @@ version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" +git-tree-sha1 = "a2df1b776752e3f344e5116c06d75a10436ab853" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.36" +version = "0.10.38" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] @@ -845,9 +853,9 @@ version = "1.0.2" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed" +git-tree-sha1 = "1336e07ba2eb75614c99496501a8f4b233e9fafe" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.8" +version = "1.10.10" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] @@ -1154,9 +1162,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "ddb60aabc5efb0670c7ddde5fedf7ab44520a3e6" +git-tree-sha1 = "591de175461afd8323aa24b7686062574527aa3a" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.36.1" +version = "2.36.2" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" @@ -1287,9 +1295,9 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.ModelingToolkit]] deps = ["AbstractTrees", "ArrayInterface", "BlockArrays", "Combinatorics", "CommonSolve", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "DynamicQuantities", "ExprTools", "Expronicon", "FindFirstFunctions", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "Graphs", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "NaNMath", "NonlinearSolve", "OffsetArrays", "OrderedCollections", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] -git-tree-sha1 = "4e18caba05cb1a32469c15edb634341a246a533d" +git-tree-sha1 = "b96b0749d6d9c8d6480641dcfcc02a265cf6d9e7" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "9.48.0" +version = "9.50.0" [deps.ModelingToolkit.extensions] MTKBifurcationKitExt = "BifurcationKit" @@ -1384,9 +1392,9 @@ version = "0.5.0" [[deps.ODEInterfaceDiffEq]] deps = ["Compat", "DataStructures", "DiffEqBase", "FunctionWrappers", "LinearAlgebra", "ODEInterface", "Reexport", "SciMLBase"] -git-tree-sha1 = "a4816454042d72e4bae37d13e592591381356a17" +git-tree-sha1 = "598df5118c036a8ac8a53c5d158921eba5fc0d32" uuid = "09606e27-ecf5-54fc-bb29-004bd9f985bf" -version = "3.13.3" +version = "3.13.4" [[deps.ODEInterface_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1479,10 +1487,10 @@ uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" version = "1.1.2" [[deps.OrdinaryDiffEqCore]] -deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "TruncatedStacktraces"] -git-tree-sha1 = "1175717a62ab21736a8f5d0d2531d2a6ad3b9e74" +deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"] +git-tree-sha1 = "5e8c500a80674850543394ce3c745b73ad51fea0" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "1.9.0" +version = "1.10.0" weakdeps = ["EnzymeCore"] [deps.OrdinaryDiffEqCore.extensions] @@ -1568,9 +1576,9 @@ version = "1.2.1" [[deps.OrdinaryDiffEqNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "PreallocationTools", "RecursiveArrayTools", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "StaticArrays"] -git-tree-sha1 = "a2a4119f3e35f7982f78e17beea7b12485d179e9" +git-tree-sha1 = "e4be6539f4aaae8db1f29fcfdf6ef817df1f25cf" uuid = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8" -version = "1.2.1" +version = "1.2.2" [[deps.OrdinaryDiffEqNordsieck]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -1703,15 +1711,15 @@ version = "1.10.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = "6e55c6841ce3411ccb3457ee52fc48cb698d6fb0" +git-tree-sha1 = "41031ef3a1be6f5bbbf3e8073f210556daeae5ca" uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" -version = "3.2.0" +version = "3.3.0" [[deps.PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"] -git-tree-sha1 = "650a022b2ce86c7dcfbdecf00f78afeeb20e5655" +git-tree-sha1 = "3ca9a356cd2e113c420f2c13bea19f8d3fb1cb18" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.4.2" +version = "1.4.3" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] @@ -1888,9 +1896,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "b034171b93aebc81b3e1890a036d13a9c4a9e3e0" +git-tree-sha1 = "6f4dca5fd8e97087a76b7ab8384d1c3086ace0b7" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.27.0" +version = "3.27.3" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -1986,9 +1994,9 @@ version = "0.6.43" [[deps.SciMLBase]] deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] -git-tree-sha1 = "328dd8738fad35cfe53c427a30e711ed45a1d900" +git-tree-sha1 = "7527b9adb22904f0f51d8ab85d826f81ebb6f78d" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.57.1" +version = "2.59.2" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -2010,16 +2018,16 @@ version = "2.57.1" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLJacobianOperators]] -deps = ["ADTypes", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] -git-tree-sha1 = "991d2a8900e687e2c693d587daa739c8fda01366" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] +git-tree-sha1 = "f66048bb969e67bd7d1bdd03cd0b81219642bbd0" uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" -version = "0.1.0" +version = "0.1.1" [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] -git-tree-sha1 = "ef388ca9e4921ec5614ce714f8aa59a5cd33d867" +git-tree-sha1 = "6149620767866d4b0f0f7028639b6e661b6a1e44" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.11" +version = "0.3.12" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -2147,9 +2155,9 @@ version = "2.23.0" [[deps.SparseMatrixColorings]] deps = ["ADTypes", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "f37f046636f8dc353a39279abfefe296db212171" +git-tree-sha1 = "670f2c8109e87d79788baef47880b946e529f1a2" uuid = "0a514795-09f3-496d-8182-132a7b665d35" -version = "0.4.8" +version = "0.4.9" weakdeps = ["Colors"] [deps.SparseMatrixColorings.extensions] @@ -2268,9 +2276,9 @@ version = "7.2.1+1" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "e87efb31e5360cb223a151c2398903dc2faeb32b" +git-tree-sha1 = "56661ac133ea6df96fea8d6bb4eb18875b002206" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.26.0" +version = "4.26.1" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"] @@ -2280,9 +2288,9 @@ version = "5.2.2+0" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "4bc96df5d71515b1cb86dd626915f06f4c0d46f5" +git-tree-sha1 = "20cf607cafb31f922bce84d60379203e7a126911" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.33" +version = "0.3.34" [[deps.SymbolicLimits]] deps = ["SymbolicUtils"] @@ -2306,9 +2314,9 @@ version = "3.7.2" [[deps.Symbolics]] deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "IfElse", "LaTeXStrings", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "Primes", "RecipesBase", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] -git-tree-sha1 = "ef7532b95fbd529e1252cabb36bba64803020840" +git-tree-sha1 = "0caef7687abf7094132fa3112bf5514c36a99226" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "6.16.0" +version = "6.18.3" [deps.Symbolics.extensions] SymbolicsForwardDiffExt = "ForwardDiff" @@ -2460,9 +2468,9 @@ version = "0.2.0" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "e7f5b81c65eb858bed630fe006837b935518aca5" +git-tree-sha1 = "4ab62a49f1d8d9548a1c8d1a75e5f55cf196f64e" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.70" +version = "0.21.71" [[deps.VertexSafeGraphs]] deps = ["Graphs"] From 4f741fd581ebe240dc7d6fd19b0024f514bd1091 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Mon, 11 Nov 2024 04:11:47 -0100 Subject: [PATCH 08/18] bump OrdinaryDiffEqDifferentiation --- benchmarks/AstroChem/Manifest.toml | 10 +++++----- benchmarks/AstroChem/Project.toml | 4 ++-- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/benchmarks/AstroChem/Manifest.toml b/benchmarks/AstroChem/Manifest.toml index ed6140ed6..131bd41ac 100644 --- a/benchmarks/AstroChem/Manifest.toml +++ b/benchmarks/AstroChem/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.6" manifest_format = "2.0" -project_hash = "81a84463ee3fb40ec2e360f288f69699605fb501" +project_hash = "1c364e7a636297027abcbe8c90ea8c3fdb811c84" [[deps.ADTypes]] git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081" @@ -871,9 +871,9 @@ version = "0.1.17" [[deps.HypergeometricFunctions]] deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb" +git-tree-sha1 = "b1c2585431c382e3fe5805874bda6aea90a95de9" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.24" +version = "0.3.25" [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -1504,9 +1504,9 @@ version = "1.1.0" [[deps.OrdinaryDiffEqDifferentiation]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays"] -git-tree-sha1 = "e63ec633b1efa99e3caa2e26a01faaa88ba6cef9" +git-tree-sha1 = "8977f283a7d89c5d5c06c933467ed4af0a99f2f7" uuid = "4302a76b-040a-498a-8c04-15b101fed76b" -version = "1.1.0" +version = "1.2.0" [[deps.OrdinaryDiffEqExplicitRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "TruncatedStacktraces"] diff --git a/benchmarks/AstroChem/Project.toml b/benchmarks/AstroChem/Project.toml index ae007082e..62e4e2e02 100644 --- a/benchmarks/AstroChem/Project.toml +++ b/benchmarks/AstroChem/Project.toml @@ -17,13 +17,13 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" BenchmarkTools = "1" Catalyst = "14" DiffEqDevTools = "2" -LinearSolve = "2" LSODA = "0.7" +LinearSolve = "2" NaNMath = "1" ODEInterface = "0.5" +ODEInterfaceDiffEq = "3" OrdinaryDiffEq = "6.89" OrdinaryDiffEqCore = "1.9" -ODEInterfaceDiffEq = "3" Plots = "1" Sundials = "4" Symbolics = "6" From f64834be9b782f02c69bbd145a33d9b8a5f3e9d1 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Mon, 11 Nov 2024 04:48:55 -0100 Subject: [PATCH 09/18] more bump --- benchmarks/AstroChem/Manifest.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/benchmarks/AstroChem/Manifest.toml b/benchmarks/AstroChem/Manifest.toml index 131bd41ac..674fd82d9 100644 --- a/benchmarks/AstroChem/Manifest.toml +++ b/benchmarks/AstroChem/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.6" manifest_format = "2.0" -project_hash = "1c364e7a636297027abcbe8c90ea8c3fdb811c84" +project_hash = "81a84463ee3fb40ec2e360f288f69699605fb501" [[deps.ADTypes]] git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081" @@ -1612,9 +1612,9 @@ version = "1.1.0" [[deps.OrdinaryDiffEqRosenbrock]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "96b47cdd12cb4ce8f70d701b49f855271a462bd4" +git-tree-sha1 = "56cbbdc43bd0e88083fcef3efa296501b5a435da" uuid = "43230ef6-c299-4910-a778-202eb28ce4ce" -version = "1.2.0" +version = "1.3.0" [[deps.OrdinaryDiffEqSDIRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] From e7ab6c5cc315fce84f1eae142996b65eed003f8d Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Mon, 11 Nov 2024 12:58:56 -0100 Subject: [PATCH 10/18] final bump? --- benchmarks/AstroChem/Manifest.toml | 117 ++++++++++++++++++++--------- 1 file changed, 82 insertions(+), 35 deletions(-) diff --git a/benchmarks/AstroChem/Manifest.toml b/benchmarks/AstroChem/Manifest.toml index 674fd82d9..692170702 100644 --- a/benchmarks/AstroChem/Manifest.toml +++ b/benchmarks/AstroChem/Manifest.toml @@ -152,6 +152,16 @@ version = "1.1.1" [deps.BlockArrays.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" +[[deps.BracketingNonlinearSolve]] +deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "95cb19c37ea427617e9795655667712f03058d98" +uuid = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e" +version = "1.1.0" +weakdeps = ["ForwardDiff"] + + [deps.BracketingNonlinearSolve.extensions] + BracketingNonlinearSolveForwardDiffExt = "ForwardDiff" + [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1" @@ -181,6 +191,11 @@ git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.18.2+1" +[[deps.Cassette]] +git-tree-sha1 = "f8764df8d9d2aec2812f009a1ac39e46c33354b8" +uuid = "7057c7e9-c182-5462-911a-8362d720325c" +version = "0.3.14" + [[deps.Catalyst]] deps = ["Combinatorics", "DataStructures", "DiffEqBase", "DocStringExtensions", "DynamicPolynomials", "DynamicQuantities", "Graphs", "JumpProcesses", "LaTeXStrings", "Latexify", "LinearAlgebra", "MacroTools", "ModelingToolkit", "Parameters", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SymbolicUtils", "Symbolics", "Unitful"] git-tree-sha1 = "dafd059c1d80ba02006978cd05ea7264ff1f362e" @@ -760,6 +775,12 @@ git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2" uuid = "559328eb-81f9-559d-9380-de523a88c83c" version = "1.0.14+0" +[[deps.FunctionProperties]] +deps = ["Cassette", "DiffRules"] +git-tree-sha1 = "bf7c740307eb0ee80e05d8aafbd0c5a901578398" +uuid = "f62d2435-5019-4c03-9749-2d4c77af0cbc" +version = "0.1.2" + [[deps.FunctionWrappers]] git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" @@ -1357,32 +1378,78 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "4d8944f32db2b07a2bdf8477e878bcb9c9ea2308" +deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface"] +git-tree-sha1 = "22f3efdd47bd18d8a26bd559fff254e6b21000fd" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "3.15.1" +version = "4.1.0" [deps.NonlinearSolve.extensions] - NonlinearSolveBandedMatricesExt = "BandedMatrices" NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" NonlinearSolveFixedPointAccelerationExt = "FixedPointAcceleration" NonlinearSolveLeastSquaresOptimExt = "LeastSquaresOptim" NonlinearSolveMINPACKExt = "MINPACK" NonlinearSolveNLSolversExt = "NLSolvers" - NonlinearSolveNLsolveExt = "NLsolve" + NonlinearSolveNLsolveExt = ["NLsolve", "LineSearches"] + NonlinearSolvePETScExt = ["PETSc", "MPI"] NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations" NonlinearSolveSpeedMappingExt = "SpeedMapping" + NonlinearSolveSundialsExt = "Sundials" [deps.NonlinearSolve.weakdeps] - BandedMatrices = "aae01518-5342-5314-be14-df237901396f" FastLevenbergMarquardt = "7a0df574-e128-4d35-8cbd-3d84502bf7ce" FixedPointAcceleration = "817d07cb-a79a-5c30-9a31-890123675176" LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891" + LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" MINPACK = "4854310b-de5a-5eb6-a2a5-c1dee2bd17f9" + MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" NLSolvers = "337daf1e-9722-11e9-073e-8b9effe078ba" NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" + PETSc = "ace2c81b-2b5f-4b1e-a30d-d662738edfe0" SIAMFANLEquations = "084e46ad-d928-497d-ad5e-07fa361a48c4" SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412" + Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" + +[[deps.NonlinearSolveBase]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "FunctionProperties", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] +git-tree-sha1 = "1589ef8aac99a21d132adf1ec5cbe6ef651760ff" +uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" +version = "1.3.1" + + [deps.NonlinearSolveBase.extensions] + NonlinearSolveBaseBandedMatricesExt = "BandedMatrices" + NonlinearSolveBaseDiffEqBaseExt = "DiffEqBase" + NonlinearSolveBaseForwardDiffExt = "ForwardDiff" + NonlinearSolveBaseLineSearchExt = "LineSearch" + NonlinearSolveBaseLinearSolveExt = "LinearSolve" + NonlinearSolveBaseSparseArraysExt = "SparseArrays" + NonlinearSolveBaseSparseMatrixColoringsExt = "SparseMatrixColorings" + + [deps.NonlinearSolveBase.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + LineSearch = "87fe0de2-c867-4266-b59a-2f0a94fc965b" + LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" + +[[deps.NonlinearSolveFirstOrder]] +deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "dc8535cecb0f9d978019e44b7144b9e84ab85424" +uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" +version = "1.0.0" + +[[deps.NonlinearSolveQuasiNewton]] +deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] +git-tree-sha1 = "066d4940938f4bb5fd1ce146e61a373f40b89d31" +uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" +version = "1.0.0" + +[[deps.NonlinearSolveSpectralMethods]] +deps = ["CommonSolve", "ConcreteStructs", "DiffEqBase", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "cc97c44e396ab820401c8c404bc1fd18d4c884bd" +uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2" +version = "1.0.0" [[deps.ODEInterface]] deps = ["Dates", "Libdl", "LinearAlgebra", "Markdown", "ODEInterface_jll", "Unicode"] @@ -1470,9 +1537,9 @@ version = "1.6.3" [[deps.OrdinaryDiffEq]] deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqAdamsBashforthMoulton", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqExplicitRK", "OrdinaryDiffEqExponentialRK", "OrdinaryDiffEqExtrapolation", "OrdinaryDiffEqFIRK", "OrdinaryDiffEqFeagin", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqHighOrderRK", "OrdinaryDiffEqIMEXMultistep", "OrdinaryDiffEqLinear", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqLowStorageRK", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqNordsieck", "OrdinaryDiffEqPDIRK", "OrdinaryDiffEqPRK", "OrdinaryDiffEqQPRK", "OrdinaryDiffEqRKN", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqSSPRK", "OrdinaryDiffEqStabilizedIRK", "OrdinaryDiffEqStabilizedRK", "OrdinaryDiffEqSymplecticRK", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "cd892f12371c287dc50d6ad3af075b088b6f2d48" +git-tree-sha1 = "aa3897f89be34bdfd86472f5345d5f1f6576bcc5" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.89.0" +version = "6.90.0" [[deps.OrdinaryDiffEqAdamsBashforthMoulton]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -1576,9 +1643,9 @@ version = "1.2.1" [[deps.OrdinaryDiffEqNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "PreallocationTools", "RecursiveArrayTools", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "StaticArrays"] -git-tree-sha1 = "e4be6539f4aaae8db1f29fcfdf6ef817df1f25cf" +git-tree-sha1 = "5e1b316555fa95892edc13f6a429ac784d0be4dd" uuid = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8" -version = "1.2.2" +version = "1.2.4" [[deps.OrdinaryDiffEqNordsieck]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -2071,22 +2138,22 @@ uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" version = "1.2.0" [[deps.SimpleNonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "44021f3efc023be3871195d8ad98b865001a2fa1" +deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "f7e2042e0b68c6bb19a0a1594839792737f51d84" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.12.3" +version = "2.0.0" [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" + SimpleNonlinearSolveDiffEqBaseExt = "DiffEqBase" SimpleNonlinearSolveReverseDiffExt = "ReverseDiff" SimpleNonlinearSolveTrackerExt = "Tracker" - SimpleNonlinearSolveZygoteExt = "Zygote" [deps.SimpleNonlinearSolve.weakdeps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -2113,26 +2180,6 @@ deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" version = "1.10.0" -[[deps.SparseConnectivityTracer]] -deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "6914df6005bab9940e2a96879a97a43e1fb1ce78" -uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" -version = "0.6.8" - - [deps.SparseConnectivityTracer.extensions] - SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" - SparseConnectivityTracerLogExpFunctionsExt = "LogExpFunctions" - SparseConnectivityTracerNNlibExt = "NNlib" - SparseConnectivityTracerNaNMathExt = "NaNMath" - SparseConnectivityTracerSpecialFunctionsExt = "SpecialFunctions" - - [deps.SparseConnectivityTracer.weakdeps] - DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0" - LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" - NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" - NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" - SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" - [[deps.SparseDiffTools]] deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "UnPack", "VertexSafeGraphs"] git-tree-sha1 = "b906758c107b049b6b71599b9f928d9b14e5554a" From 5082383ac3e47aac2658472aa2eab7a7027be313 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Tue, 12 Nov 2024 12:05:02 -0100 Subject: [PATCH 11/18] simplify a bit --- benchmarks/AstroChem/astrochem.jmd | 7 +++---- benchmarks/AstroChem/nelson.jmd | 9 ++++----- 2 files changed, 7 insertions(+), 9 deletions(-) diff --git a/benchmarks/AstroChem/astrochem.jmd b/benchmarks/AstroChem/astrochem.jmd index f2180def2..4c8cdf664 100644 --- a/benchmarks/AstroChem/astrochem.jmd +++ b/benchmarks/AstroChem/astrochem.jmd @@ -392,14 +392,13 @@ reltols = 1.0 ./ 10.0 .^ (9:10) setups = [ Dict(:alg=>FBDF()), - Dict(:alg=>QNDF()), - #Dict(:alg=>Rodas4P()), + #Dict(:alg=>QNDF()), Dict(:alg=>CVODE_BDF()), #Dict(:alg=>ddebdf()), #Dict(:alg=>Rodas4()), Dict(:alg=>Rodas5P()), - Dict(:alg=>KenCarp4()), - Dict(:alg=>KenCarp47()), + #Dict(:alg=>KenCarp4()), + #Dict(:alg=>KenCarp47()), Dict(:alg=>RadauIIA9()), #Dict(:alg=>rodas()), #Dict(:alg=>radau()), diff --git a/benchmarks/AstroChem/nelson.jmd b/benchmarks/AstroChem/nelson.jmd index 9d6789542..a34aec2d4 100644 --- a/benchmarks/AstroChem/nelson.jmd +++ b/benchmarks/AstroChem/nelson.jmd @@ -174,12 +174,11 @@ sol4 = solve(prob, lsoda(), saveat = 1e10) ```julia using Plots colors = palette(:acton, 5) -p1 = plot(sol1, vars = (0,11), lc=colors[1], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using Rodas5 (correct solution)") -p2 = plot(sol2, vars = (0,11), lc=colors[2], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using FBDF") -p3 = plot(sol3, vars = (0,11), lc=colors[3], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using lsoda") -p4 = plot(sol4, vars = (0,11), lc=colors[4], legend = false, titlefontsize = 12, lw = 3, xlabel = "", title = "HCO+ solved using lsoda with saveat") +p1 = plot(sol1, vars = (0,11), lc=colors[1], legend = false, titlefontsize = 12, lw = 3, title = "HCO+ solved using Rodas5 (correct solution)") +p2 = plot(sol2, vars = (0,11), lc=colors[2], legend = false, titlefontsize = 12, lw = 3, title = "HCO+ solved using FBDF") +p3 = plot(sol3, vars = (0,11), lc=colors[3], legend = false, titlefontsize = 12, lw = 3, title = "HCO+ solved using lsoda") +p4 = plot(sol4, vars = (0,11), lc=colors[4], legend = false, titlefontsize = 12, lw = 3, title = "HCO+ solved using lsoda with saveat") combined_plot = plot(p1, p2, p3, p4, layout=(4, 1), dpi = 600, pallete=:acton) -display(combined_plot) ``` ## Run Benchmark From 5eda15ccc770301d0e5c20456cff999799878c99 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Wed, 13 Nov 2024 08:49:14 -0100 Subject: [PATCH 12/18] Update benchmarks/AstroChem/astrochem.jmd --- benchmarks/AstroChem/astrochem.jmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/benchmarks/AstroChem/astrochem.jmd b/benchmarks/AstroChem/astrochem.jmd index 4c8cdf664..927819ec6 100644 --- a/benchmarks/AstroChem/astrochem.jmd +++ b/benchmarks/AstroChem/astrochem.jmd @@ -399,7 +399,7 @@ setups = [ Dict(:alg=>Rodas5P()), #Dict(:alg=>KenCarp4()), #Dict(:alg=>KenCarp47()), - Dict(:alg=>RadauIIA9()), + #Dict(:alg=>RadauIIA9()), #Dict(:alg=>rodas()), #Dict(:alg=>radau()), #Dict(:alg=>lsoda()), From efbedc9db7e33ca29a574474db226e5633be5055 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Wed, 13 Nov 2024 08:49:59 -0100 Subject: [PATCH 13/18] Update nelson.jmd --- benchmarks/AstroChem/nelson.jmd | 3 +++ 1 file changed, 3 insertions(+) diff --git a/benchmarks/AstroChem/nelson.jmd b/benchmarks/AstroChem/nelson.jmd index a34aec2d4..a1a24912f 100644 --- a/benchmarks/AstroChem/nelson.jmd +++ b/benchmarks/AstroChem/nelson.jmd @@ -178,6 +178,9 @@ p1 = plot(sol1, vars = (0,11), lc=colors[1], legend = false, titlefontsize = 12, p2 = plot(sol2, vars = (0,11), lc=colors[2], legend = false, titlefontsize = 12, lw = 3, title = "HCO+ solved using FBDF") p3 = plot(sol3, vars = (0,11), lc=colors[3], legend = false, titlefontsize = 12, lw = 3, title = "HCO+ solved using lsoda") p4 = plot(sol4, vars = (0,11), lc=colors[4], legend = false, titlefontsize = 12, lw = 3, title = "HCO+ solved using lsoda with saveat") +``` + +```julia combined_plot = plot(p1, p2, p3, p4, layout=(4, 1), dpi = 600, pallete=:acton) ``` From 6d1db035cf158ac3640140cb94793d16a26a6cdd Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Wed, 13 Nov 2024 23:22:54 -0100 Subject: [PATCH 14/18] simplify a bit --- benchmarks/AstroChem/astrochem.jmd | 15 ++++++--------- benchmarks/AstroChem/nelson.jmd | 8 ++++---- 2 files changed, 10 insertions(+), 13 deletions(-) diff --git a/benchmarks/AstroChem/astrochem.jmd b/benchmarks/AstroChem/astrochem.jmd index 927819ec6..5b9c351fd 100644 --- a/benchmarks/AstroChem/astrochem.jmd +++ b/benchmarks/AstroChem/astrochem.jmd @@ -381,9 +381,7 @@ refsol = solve(oprob, Rodas5P(), abstol=1e-14, reltol=1e-14) ``` ```julia -refsol = solve(oprob, Rodas5P(), abstol=1e-13, reltol=1e-13) - -solve(oprob, RadauIIA9(), abstol=1e-9, reltol=1e-9) +refsol = solve(oprob, Rodas5P(), abstol=1e-13, reltol=1e-13)) # Run Benchmark @@ -392,17 +390,16 @@ reltols = 1.0 ./ 10.0 .^ (9:10) setups = [ Dict(:alg=>FBDF()), - #Dict(:alg=>QNDF()), + Dict(:alg=>QNDF()), Dict(:alg=>CVODE_BDF()), #Dict(:alg=>ddebdf()), - #Dict(:alg=>Rodas4()), Dict(:alg=>Rodas5P()), - #Dict(:alg=>KenCarp4()), - #Dict(:alg=>KenCarp47()), - #Dict(:alg=>RadauIIA9()), + Dict(:alg=>KenCarp4()), + Dict(:alg=>KenCarp47()), + Dict(:alg=>RadauIIA9()), #Dict(:alg=>rodas()), #Dict(:alg=>radau()), - #Dict(:alg=>lsoda()), + Dict(:alg=>lsoda()), #Dict(:alg=>ImplicitEulerExtrapolation(min_order = 5, init_order = 3,threading = OrdinaryDiffEqCore.PolyesterThreads())), #Dict(:alg=>ImplicitEulerExtrapolation(min_order = 5, init_order = 3,threading = false)), #Dict(:alg=>ImplicitEulerBarycentricExtrapolation(min_order = 5, threading = OrdinaryDiffEqCore.PolyesterThreads())), diff --git a/benchmarks/AstroChem/nelson.jmd b/benchmarks/AstroChem/nelson.jmd index a1a24912f..367c44c25 100644 --- a/benchmarks/AstroChem/nelson.jmd +++ b/benchmarks/AstroChem/nelson.jmd @@ -174,10 +174,10 @@ sol4 = solve(prob, lsoda(), saveat = 1e10) ```julia using Plots colors = palette(:acton, 5) -p1 = plot(sol1, vars = (0,11), lc=colors[1], legend = false, titlefontsize = 12, lw = 3, title = "HCO+ solved using Rodas5 (correct solution)") -p2 = plot(sol2, vars = (0,11), lc=colors[2], legend = false, titlefontsize = 12, lw = 3, title = "HCO+ solved using FBDF") -p3 = plot(sol3, vars = (0,11), lc=colors[3], legend = false, titlefontsize = 12, lw = 3, title = "HCO+ solved using lsoda") -p4 = plot(sol4, vars = (0,11), lc=colors[4], legend = false, titlefontsize = 12, lw = 3, title = "HCO+ solved using lsoda with saveat") +p1 = plot(sol1, vars = (0,11), lc=colors[1], legend = false, titlefontsize = 12, lw = 3, title = "Rodas5") +p2 = plot(sol2, vars = (0,11), lc=colors[2], legend = false, titlefontsize = 12, lw = 3, title = "FBDF") +p3 = plot(sol3, vars = (0,11), lc=colors[3], legend = false, titlefontsize = 12, lw = 3, title = "lsoda") +p4 = plot(sol4, vars = (0,11), lc=colors[4], legend = false, titlefontsize = 12, lw = 3, title = "lsoda with saveat") ``` ```julia From db7f53f59ccb6801fd5a2b4a91d1e1bdbf758a70 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Thu, 14 Nov 2024 18:24:53 -0100 Subject: [PATCH 15/18] Update benchmarks/AstroChem/astrochem.jmd --- benchmarks/AstroChem/astrochem.jmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/benchmarks/AstroChem/astrochem.jmd b/benchmarks/AstroChem/astrochem.jmd index 5b9c351fd..ec734f4e2 100644 --- a/benchmarks/AstroChem/astrochem.jmd +++ b/benchmarks/AstroChem/astrochem.jmd @@ -381,7 +381,7 @@ refsol = solve(oprob, Rodas5P(), abstol=1e-14, reltol=1e-14) ``` ```julia -refsol = solve(oprob, Rodas5P(), abstol=1e-13, reltol=1e-13)) +refsol = solve(oprob, Rodas5P(), abstol=1e-13, reltol=1e-13) # Run Benchmark From 29517b92cc6248ad97027dedf71f8904c262e759 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Thu, 14 Nov 2024 18:26:00 -0100 Subject: [PATCH 16/18] Update nelson.jmd --- benchmarks/AstroChem/nelson.jmd | 1 + 1 file changed, 1 insertion(+) diff --git a/benchmarks/AstroChem/nelson.jmd b/benchmarks/AstroChem/nelson.jmd index 367c44c25..3adb3992a 100644 --- a/benchmarks/AstroChem/nelson.jmd +++ b/benchmarks/AstroChem/nelson.jmd @@ -168,6 +168,7 @@ sol1 = solve(prob, Rodas5P()) sol2 = solve(prob, FBDF()) sol3 = solve(prob, lsoda()) sol4 = solve(prob, lsoda(), saveat = 1e10) +``` ## Validation Plot From bf4f81c4e7098025cebc46d7965723c9ec2550dd Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Thu, 14 Nov 2024 23:48:24 -0100 Subject: [PATCH 17/18] Update nelson.jmd --- benchmarks/AstroChem/nelson.jmd | 2 -- 1 file changed, 2 deletions(-) diff --git a/benchmarks/AstroChem/nelson.jmd b/benchmarks/AstroChem/nelson.jmd index 3adb3992a..bbe7f9924 100644 --- a/benchmarks/AstroChem/nelson.jmd +++ b/benchmarks/AstroChem/nelson.jmd @@ -179,9 +179,7 @@ p1 = plot(sol1, vars = (0,11), lc=colors[1], legend = false, titlefontsize = 12, p2 = plot(sol2, vars = (0,11), lc=colors[2], legend = false, titlefontsize = 12, lw = 3, title = "FBDF") p3 = plot(sol3, vars = (0,11), lc=colors[3], legend = false, titlefontsize = 12, lw = 3, title = "lsoda") p4 = plot(sol4, vars = (0,11), lc=colors[4], legend = false, titlefontsize = 12, lw = 3, title = "lsoda with saveat") -``` -```julia combined_plot = plot(p1, p2, p3, p4, layout=(4, 1), dpi = 600, pallete=:acton) ``` From d290772d4b7b896d810c2a3890a556c77f683691 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Thu, 14 Nov 2024 23:48:44 -0100 Subject: [PATCH 18/18] Update benchmarks/AstroChem/astrochem.jmd --- benchmarks/AstroChem/astrochem.jmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/benchmarks/AstroChem/astrochem.jmd b/benchmarks/AstroChem/astrochem.jmd index ec734f4e2..5bfe913b6 100644 --- a/benchmarks/AstroChem/astrochem.jmd +++ b/benchmarks/AstroChem/astrochem.jmd @@ -396,7 +396,7 @@ setups = [ Dict(:alg=>Rodas5P()), Dict(:alg=>KenCarp4()), Dict(:alg=>KenCarp47()), - Dict(:alg=>RadauIIA9()), + #Dict(:alg=>RadauIIA9()), #Dict(:alg=>rodas()), #Dict(:alg=>radau()), Dict(:alg=>lsoda()),