From 70473feffbfc9beda5ae921f4a500da3e181dd96 Mon Sep 17 00:00:00 2001 From: "C. Brenhin Keller" Date: Wed, 25 Dec 2024 17:11:02 -0500 Subject: [PATCH] Update example script and manifest --- examples/Manifest.toml | 94 ++++++++++++++++++++--------------------- examples/tTinversion.jl | 22 ++++++---- 2 files changed, 60 insertions(+), 56 deletions(-) diff --git a/examples/Manifest.toml b/examples/Manifest.toml index b79fd2d..f80f330 100644 --- a/examples/Manifest.toml +++ b/examples/Manifest.toml @@ -165,9 +165,9 @@ version = "1.21.6+0" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1" +git-tree-sha1 = "35abeca13bc0425cff9e59e229d971f5231323bf" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+2" +version = "1.0.8+3" [[deps.CEnum]] git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" @@ -420,9 +420,9 @@ version = "0.1.11" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e51db81749b0777b2147fbe7b783ee79045b8e99" +git-tree-sha1 = "f42a5b1e20e009a43c3646635ed81a9fcaccb287" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.6.4+1" +version = "2.6.4+2" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] @@ -450,9 +450,9 @@ version = "1.8.0" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4d81ed14783ec49ce9f2e168208a12ce1815aa25" +git-tree-sha1 = "5cf2433259aa3985046792e2afc01fcec076b549" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" -version = "3.3.10+1" +version = "3.3.10+2" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] @@ -550,15 +550,15 @@ version = "3.4.0+2" [[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 = "52adc6828958ea8a0cf923d53aa10773dbca7d5f" +git-tree-sha1 = "424c8f76017e39fdfcdbb5935a8e6742244959e8" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.9" +version = "0.73.10" [[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 = "4e9e2966af45b06f24fd952285841428f1d6e858" +git-tree-sha1 = "b90934c8cb33920a8dc66736471dc3961b42ec9f" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.9+0" +version = "0.73.10+0" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -651,9 +651,9 @@ version = "0.1.17" [[deps.Hwloc_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "50aedf345a709ab75872f80a2779568dc0bb461b" +git-tree-sha1 = "290232556f4ffb60ac3e476acf28e1a46e764742" uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" -version = "2.11.2+1" +version = "2.11.2+2" [[deps.HypergeometricFunctions]] deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] @@ -873,9 +873,9 @@ version = "0.1.9" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b" +git-tree-sha1 = "a007feb38b422fbdab534406aeca1b86823cb4d6" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.6.1" +version = "1.7.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -891,9 +891,9 @@ version = "0.1.5" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "ef10afc9f4b942bcd75f4c3bc9d9e8d802944c23" +git-tree-sha1 = "3447a92280ecaad1bd93d3fce3d408b6cfff8913" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.1.0+0" +version = "3.1.0+1" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -903,9 +903,9 @@ version = "3.100.2+0" [[deps.LERC_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "36bdbc52f13a7d1dcb0f3cd694e01677a515655b" +git-tree-sha1 = "78e0f4b5270c4ae09c7c5f78e77b904199038945" uuid = "88015f11-f218-50d7-93a8-a6af411a945d" -version = "4.0.0+0" +version = "4.0.0+2" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -915,9 +915,9 @@ version = "18.1.7+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731" +git-tree-sha1 = "16e6ec700154e8004dba90b4aec376f68905d104" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.2+1" +version = "2.10.2+2" [[deps.LaTeXStrings]] git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" @@ -1017,9 +1017,9 @@ version = "1.17.0+1" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "84eef7acd508ee5b3e956a2ae51b05024181dee0" +git-tree-sha1 = "d841749621f4dcf0ddc26a27d1f6484dfc37659a" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.40.2+0" +version = "2.40.2+1" [[deps.Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] @@ -1029,9 +1029,9 @@ version = "4.7.0+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "edbf5309f9ddf1cab25afc344b1e8150b7c832f9" +git-tree-sha1 = "9d630b7fb0be32eeb5e8da515f5e8a26deb457fe" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.40.2+0" +version = "2.40.2+1" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] @@ -1089,9 +1089,9 @@ version = "0.15.0" [[deps.Lz4_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "abf88ff67f4fd89839efcae2f4c39cbc4ecd0846" +git-tree-sha1 = "dbd00758ab9d8f454b2feadb6071eb50af62c824" uuid = "5ced341a-0733-55b8-9ab6-a4889d929147" -version = "1.10.0+1" +version = "1.10.0+2" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] @@ -1277,15 +1277,15 @@ version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10" +git-tree-sha1 = "f58782a883ecbf9fb48dcd363f9ccd65f36c23a8" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.15+1" +version = "3.0.15+2" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" +git-tree-sha1 = "418e63d434f5ca12b188bbb287dfbe10a5af1da4" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" -version = "0.5.5+0" +version = "0.5.5+1" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1720,9 +1720,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f" +git-tree-sha1 = "7c01731da8ab6d3094c4d44c9057b00932459255" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.8" +version = "1.9.9" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -1803,11 +1803,9 @@ version = "1.11.0" [[deps.Thermochron]] deps = ["BangBang", "Distributions", "LinearAlgebra", "LoopVectorization", "LsqFit", "NaNStatistics", "ProgressMeter", "Reexport", "StatGeochemBase", "Statistics"] -git-tree-sha1 = "4aac9852980be2495ace0b98808c95c491ea4c3d" -repo-rev = "main" -repo-url = "https://github.com/OpenThermochronology/Thermochron.jl.git" +git-tree-sha1 = "564963d0e54783519627be48d6c25b1635a4ba33" uuid = "b9a8379e-ee1a-4388-b7ca-7852af1cef08" -version = "0.11.0" +version = "0.11.1" weakdeps = ["Plots"] [deps.Thermochron.extensions] @@ -1903,9 +1901,9 @@ version = "1.21.0+2" [[deps.Wayland_protocols_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "93f43ab61b16ddfb2fd3bb13b3ce241cafb0e6c9" +git-tree-sha1 = "5db3e9d307d32baba7067b13fc7b5aa6edd4a19a" uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" -version = "1.31.0+0" +version = "1.36.0+0" [[deps.WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] @@ -1927,9 +1925,9 @@ version = "1.1.42+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "15e637a697345f6743674f1322beefbc5dcd5cfc" +git-tree-sha1 = "ecda72ccaf6a67c190c9adf27034ee569bccbc3a" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.6.3+0" +version = "5.6.3+1" [[deps.Xorg_libICE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2082,9 +2080,9 @@ version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b" +git-tree-sha1 = "7dc5adc3f9bfb9b091b7952f4f6048b7e37acafc" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.6+1" +version = "1.5.6+2" [[deps.eudev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] @@ -2106,9 +2104,9 @@ version = "3.1.1+1" [[deps.libaec_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "46bf7be2917b59b761247be3f317ddf75e50e997" +git-tree-sha1 = "648c439c8643710976b4c8b30dccbbe6439fb4db" uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0" -version = "1.1.2+0" +version = "1.1.2+1" [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2153,15 +2151,15 @@ version = "1.18.0+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280" +git-tree-sha1 = "9c42636e3205e555e5785e902387be0061e7efc1" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.44+0" +version = "1.6.44+1" [[deps.libsixel_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"] -git-tree-sha1 = "7dfa0fd9c783d3d0cc43ea1af53d69ba45c447df" +git-tree-sha1 = "80c5ae2c7b5163441018f4666b179f1ffca194c1" uuid = "075b6546-f08a-558a-be8f-8157d0f608a5" -version = "1.10.3+1" +version = "1.10.3+2" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] diff --git a/examples/tTinversion.jl b/examples/tTinversion.jl index 0d743dc..d832cef 100755 --- a/examples/tTinversion.jl +++ b/examples/tTinversion.jl @@ -28,25 +28,31 @@ # # # # # # # # # # Choice of regional thermochron data # # # # # # # # # # # Literature samples from Guenthner et al. 2013 (AJS), Minnesota + # (23 ZirconHe, 11 ApatiteHe) name = "Minnesota" ds = importdataset("minnesota.csv", ',', importas=:Tuple) + # # Literature samples from McDannell et al. 2022 (doi: 10.1130/G50315.1), Manitoba + # # (12 ZirconHe, 5 ApatiteHe, 47 ApatiteFT, 269 ApatiteTrackLength) + # name = "Manitoba" + # ds = importdataset("manitoba.csv", ',', importas=:Tuple) + ## --- Prepare problem model = ( - nsteps = 600000, # [n] How many steps of the Markov chain should we run? + nsteps = 1000000, # [n] How many steps of the Markov chain should we run? burnin = 350000, # [n] How long should we wait for MC to converge (become stationary) dr = 1.0, # [μm] Radius step size dt = 8.0, # [Ma] Time step size dTmax = 10.0, # [Ma/dt] Maximum reheating/burial per model timestep. If too high, may cause numerical problems in Crank-Nicholson solve Tinit = 400.0, # [C] Initial model temperature (i.e., crystallization temperature) - ΔTinit = -50.0, # [C] Tinit can vary from Tinit to Tinit+ΔTinit + ΔTinit = -100.0, # [C] Tinit can vary from Tinit to Tinit+ΔTinit Tnow = 0.0, # [C] Current surface temperature ΔTnow = 20.0, # [Ma] Tnow may vary from Tnow to Tnow+ΔTnow tnow = 0.0, # [Ma] Today minpoints = 15, # [n] Minimum allowed number of t-T points maxpoints = 50, # [n] Maximum allowed number of t-T points - dynamicsigma = true, # Update model uncertainties? + dynamicsigma = false, # Update model uncertainties? dynamicjumping = true, # Update the t and t jumping (proposal) distributions based on previously accepted jumps # Damage and annealing models for diffusivity (specify custom kinetics if desired) adm = RDAAM(), # Flowers et al. 2009 (doi: 10.1016/j.gca.2009.01.015) @@ -72,6 +78,7 @@ detail = DetailInterval() # # Uncomment this section to require greater t-T node density in some time interval + # # (typically the youngest end of the total time interval, where you may expect the data more resolving power) # detail = DetailInterval( # agemin = 0.0, # Youngest end of detail interval # agemax = 541.0, # Oldest end of detail interval @@ -210,16 +217,15 @@ ## --- Create image of paths - # Desired rsolution of tTing image + # Desired rsolution of tT image xresolution = 2000 yresolution = 1000 - burnin = model.burnin # Resize the post-burnin part of the stationary distribution - tTdist = Array{Float64}(undef, xresolution, model.nsteps-burnin) + tTdist = Array{Float64}(undef, xresolution, model.nsteps) xq = range(0, model.tinit, length=xresolution) - @time @inbounds for i = 1:model.nsteps-burnin - linterp1s!(view(tTdist,:,i), view(tT.tpointdist,:,i+burnin), view(tT.Tpointdist,:,i+burnin), xq) + @time @inbounds for i = 1:model.nsteps + linterp1s!(view(tTdist,:,i), view(tT.tpointdist,:,i), view(tT.Tpointdist,:,i), xq) end # Calculate composite image