fix jerome

CondaPkg.toml

@@ -0,0 +1,2 @@
+[deps]
+tikzplotlib = ""

Project.toml

@@ -7,6 +7,8 @@ year = 2024
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
+Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
+CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"

examples/analysis_pedestal_sim.jl

@@ -0,0 +1,30 @@
+#=
+Author: Jerome Guterl ([email protected])
+ Company: General Atomics
+ impurity_iz_rec_timescale.jl (c) 2024=#
+
+using ADAS, Plots
+gr()
+impurities = [:C, :Ne, :Si, :Ar, :Kr, :Xe, :W]
+Lz = Dict(imp => ADAS.get_cooling_rates(imp) for imp in impurities);
+Rrad = [ADAS.get_radiation_rates(imp) for imp in impurities];
+Zeff = [ADAS.get_Zeff(imp) for imp in impurities];
+Zmean = Dict(imp => ADAS.get_Zmean(imp) for imp in impurities);
+Rrec = Dict(imp => ADAS.get_recombination_rate(imp) for imp in impurities);
+Riz = Dict(imp => ADAS.get_ionization_rate(imp) for imp in impurities)
+# Zmean = Dict(Lz_.imp => [ADAS.get_Zmean(Lz_.imp)(ne_, Te_) for (Te_, ne_) in zip(Te, ne)] for Lz_ in Lz)
+using Format
+using LaTeXStrings
+R_ = [-18.3921, -15.1886, -12.2722, -9.6468, -7.3198, -5.2925, -3.5710, -2.164, -1.0753, -0.3050]
+Prad_sim = [5.1086, 4.5802, 4.0441, 3.5318, 3.0742, 2.7724, 2.6058, 2.4659, 2.2395, 1.7829]
+ne_sim = [9.1732, 8.7446, 8.3351, 7.8059, 6.9740, 6.2106, 5.5308, 4.9412, 4.4436, 4.0410] * 1e19
+c_z_sim = [0.1944, 0.2034, 0.2127, 0.2271, 0.2583, 0.2992, 0.3524, 0.4204, 0.5046, 0.6109] *0.01
+Te_sim = [1538.9561, 1359.4824, 1193.0386, 1038.3017, 891.58594, 750.65806, 617.58147, 496.69831, 393.1432, 312.39886]
+
+Lz_Kr_sim = [Lz[:Kr].Lz_tot(ne_,Te_) for (ne_,Te_) in zip(ne_sim,Te_sim)]
+plot(R_, Lz_Kr_sim)
+plot(R_, Lz_Kr_sim .* c_z_sim .* ne_sim .^2 )
+
+
+
+# plot(title="Average charge s

examples/aurora_validations/plot_cooling_rates.jl

@@ -0,0 +1,58 @@
+
+using ADAS, Plots, OrderedCollections, Format
+gr()
+
+using PyCall
+aurora = pyimport("aurora")
+np =pyimport("numpy")
+Te_eV = np.logspace(np.log10(1), np.log10(1e4), 1000)
+ne_cm3 = 10e13 * np.ones_like(Te_eV)
+imp = "Kr"
+line_rad_tot, cont_rad_tot = aurora.get_cooling_factors(imp, ne_cm3, Te_eV, plot=true, ion_resolved=false)
+files = ["scd", "acd"]
+atom_data_eq = aurora.get_atom_data(imp, files)
+_Te, fz = aurora.get_frac_abundances(atom_data_eq, ne_cm3, Te_eV)
+#=
+import aurora
+import numpy as np
+import matplotlib.pyplot as plt
+
+plt.ion()
+
+
+# scan Te and fix a value of ne
+Te_eV = np.logspace(np.log10(1), np.log10(1e4), 1000)
+ne_cm3 = 10e13 * np.ones_like(Te_eV)
+
+imp = "Kr"
+
+# basic cooling curve, considering ionization equilibrium between charge states
+line_rad_tot, cont_rad_tot = aurora.get_cooling_factors(
+    imp, ne_cm3, Te_eV, plot=True, ion_resolved=False
+)
+
+
+aurora.get_frac_abundances(imp, ne_cm3, Te_eV, plot=True)
+files = ["scd", "acd"]
+atom_data_eq = aurora.get_atom_data(imp, files)
+
+
+_Te, fz = aurora.get_frac_abundances(atom_data_eq, ne_cm3, Te_eV)
+=#
+impurities = [:Kr]
+color_ = [:orange, :gray, :blue, :black, :cyan, :red]
+
+Lz = OrderedDict(imp => ADAS.get_cooling_rates(imp; plt_year="41") for imp in impurities);
+using Plots
+Log10Range(args...; kw...) = 10 .^ LinRange(args...; kw...)
+p = plot(layout=1, framestyle=:box, palette=:darktest, size=(400, 400))
+for (i, Lz_) in enumerate(values(Lz))
+    plot!(Lz_, Te=Log10Range(0, 4, 1000), xlim=[5.0, 2e4], ylim=[1e-34, 5e-31], xscale=:log10, yscale=:log10, layout=1, color=color_[i])
+end
+plot!(Te_aurora, Lz_aurora, label="aurora Kr")
+plot!()
+y = Log10Range(-34, -31, 4)
+x = Log10Range(1, 4, 4)
+yticks!(p, y)
+xticks!(p, x)
+plot!(legendposition=:bottomright, legendfontsize=12, legendcolumns=2)

examples/cr_vapor_pressure.txt

@@ -0,0 +1,223 @@
+# from https://www2.iap.tuwien.ac.at/www/surface/vapor_pressure
+# T(K)	T(°C)	p(bar)
+300.0	26.85	0
+310.0	36.85	2.47e-57
+320.0	46.85	2.38e-55
+330.0	56.85	1.74e-53
+340.0	66.85	9.87e-52
+350.0	76.85	4.45e-50
+360.0	86.85	1.62e-48
+370.0	96.85	4.88e-47
+380.0	106.9	1.23e-45
+390.0	116.9	2.61e-44
+400.0	126.9	4.77e-43
+410.0	136.9	7.57e-42
+420.0	146.9	1.05e-40
+430.0	156.9	1.29e-39
+440.0	166.9	1.42e-38
+450.0	176.9	1.40e-37
+460.0	186.9	1.25e-36
+470.0	196.9	1.02e-35
+480.0	206.9	7.59e-35
+490.0	216.9	5.21e-34
+500.0	226.9	3.32e-33
+510.0	236.9	1.96e-32
+520.0	246.9	1.08e-31
+530.0	256.9	5.61e-31
+540.0	266.9	2.73e-30
+550.0	276.9	1.26e-29
+560.0	286.9	5.48e-29
+570.0	296.9	2.27e-28
+580.0	306.9	8.93e-28
+590.0	316.9	3.36e-27
+600.0	326.9	1.21e-26
+610.0	336.9	4.17e-26
+620.0	346.9	1.38e-25
+630.0	356.9	4.41e-25
+640.0	366.9	1.36e-24
+650.0	376.9	4.03e-24
+660.0	386.9	1.16e-23
+670.0	396.9	3.23e-23
+680.0	406.9	8.74e-23
+690.0	416.9	2.30e-22
+700.0	426.9	5.87e-22
+710.0	436.9	1.46e-21
+720.0	446.9	3.55e-21
+730.0	456.9	8.40e-21
+740.0	466.9	1.94e-20
+750.0	476.9	4.40e-20
+760.0	486.9	9.74e-20
+770.0	496.9	2.11e-19
+780.0	506.9	4.49e-19
+790.0	516.9	9.38e-19
+800.0	526.9	1.92e-18
+810.0	536.9	3.87e-18
+820.0	546.9	7.65e-18
+830.0	556.9	1.49e-17
+840.0	566.9	2.85e-17
+850.0	576.9	5.38e-17
+860.0	586.9	1.00e-16
+870.0	596.9	1.83e-16
+880.0	606.9	3.31e-16
+890.0	616.9	5.91e-16
+900.0	626.9	1.04e-15
+910.0	636.9	1.81e-15
+920.0	646.9	3.11e-15
+930.0	656.9	5.28e-15
+940.0	666.9	8.88e-15
+950.0	676.9	1.47e-14
+960.0	686.9	2.42e-14
+970.0	696.9	3.94e-14
+980.0	706.9	6.35e-14
+990.0	716.9	1.01e-13
+1000	726.9	1.60e-13
+1010	736.9	2.51e-13
+1020	746.9	3.90e-13
+1030	756.9	6.00e-13
+1040	766.9	9.16e-13
+1050	776.9	1.39e-12
+1060	786.9	2.08e-12
+1070	796.9	3.11e-12
+1080	806.9	4.60e-12
+1090	816.9	6.76e-12
+1100	826.9	9.86e-12
+1110	836.9	1.43e-11
+1120	846.9	2.06e-11
+1130	856.9	2.95e-11
+1140	866.9	4.19e-11
+1150	876.9	5.92e-11
+1160	886.9	8.31e-11
+1170	896.9	1.16e-10
+1180	906.9	1.61e-10
+1190	916.9	2.23e-10
+1200	926.9	3.06e-10
+1210	936.9	4.18e-10
+1220	946.9	5.68e-10
+1230	956.9	7.68e-10
+1240	966.9	1.03e-9
+1250	976.9	1.38e-9
+1260	986.9	1.85e-9
+1270	996.9	2.45e-9
+1280	1007	3.24e-9
+1290	1017	4.26e-9
+1300	1027	5.59e-9
+1310	1037	7.29e-9
+1320	1047	9.47e-9
+1330	1057	1.23e-8
+1340	1067	1.58e-8
+1350	1077	2.03e-8
+1360	1087	2.60e-8
+1370	1097	3.32e-8
+1380	1107	4.22e-8
+1390	1117	5.34e-8
+1400	1127	6.74e-8
+1410	1137	8.48e-8
+1420	1147	1.06e-7
+1430	1157	1.33e-7
+1440	1167	1.66e-7
+1450	1177	2.06e-7
+1460	1187	2.55e-7
+1470	1197	3.15e-7
+1480	1207	3.88e-7
+1490	1217	4.76e-7
+1500	1227	5.83e-7
+1510	1237	7.13e-7
+1520	1247	8.68e-7
+1530	1257	1.05e-6
+1540	1267	1.28e-6
+1550	1277	1.55e-6
+1560	1287	1.86e-6
+1570	1297	2.24e-6
+1580	1307	2.69e-6
+1590	1317	3.23e-6
+1600	1327	3.86e-6
+1610	1337	4.60e-6
+1620	1347	5.47e-6
+1630	1357	6.49e-6
+1640	1367	7.69e-6
+1650	1377	9.10e-6
+1660	1387	1.07e-5
+1670	1397	1.26e-5
+1680	1407	1.49e-5
+1690	1417	1.74e-5
+1700	1427	2.04e-5
+1710	1437	2.39e-5
+1720	1447	2.78e-5
+1730	1457	3.24e-5
+1740	1467	3.77e-5
+1750	1477	4.37e-5
+1760	1487	5.06e-5
+1770	1497	5.86e-5
+1780	1507	6.76e-5
+1790	1517	7.80e-5
+1800	1527	8.98e-5
+1810	1537	1.03e-4
+1820	1547	1.18e-4
+1830	1557	1.36e-4
+1840	1567	1.55e-4
+1850	1577	1.77e-4
+1860	1587	2.02e-4
+1870	1597	2.30e-4
+1880	1607	2.62e-4
+1890	1617	2.98e-4
+1900	1627	3.38e-4
+1910	1637	3.83e-4
+1920	1647	4.33e-4
+1930	1657	4.89e-4
+1940	1667	5.52e-4
+1950	1677	6.23e-4
+1960	1687	7.01e-4
+1970	1697	7.88e-4
+1980	1707	8.85e-4
+1990	1717	9.93e-4
+2000	1727	1.11e-3
+2010	1737	1.25e-3
+2020	1747	1.39e-3
+2030	1757	1.56e-3
+2040	1767	1.74e-3
+2050	1777	1.93e-3
+2060	1787	2.15e-3
+2070	1797	2.40e-3
+2080	1807	2.66e-3
+2090	1817	2.95e-3
+2100	1827	3.28e-3
+2110	1837	3.63e-3
+2120	1847	4.02e-3
+2130	1857	4.42e-3
+2140	1867	4.84e-3
+2150	1877	5.30e-3
+2160	1887	5.80e-3
+2170	1897	6.34e-3
+2180	1907	6.93e-3
+2190	1917	7.57e-3
+2200	1927	8.25e-3
+2210	1937	9.00e-3
+2220	1947	9.80e-3
+2230	1957	0.0107
+2240	1967	0.0116
+2250	1977	0.0126
+2260	1987	0.0137
+2270	1997	0.0148
+2280	2007	0.0161
+2290	2017	0.0174
+2300	2027	0.0189
+2310	2037	0.0204
+2320	2047	0.0221
+2330	2057	0.0239
+2340	2067	0.0258
+2350	2077	0.0278
+2360	2087	0.0300
+2370	2097	0.0323
+2380	2107	0.0348
+2390	2117	0.0375
+2400	2127	0.0403
+2410	2137	0.0434
+2420	2147	0.0466
+2430	2157	0.0500
+2440	2167	0.0537
+2450	2177	0.0576
+2460	2187	0.0618
+2470	2197	0.0662
+2480	2207	0.0708
+2490	2217	0.0758
+2500	2227	0.0811

examples/plot_Zeff_export_tex.jl

@@ -0,0 +1,40 @@
+
+using ADAS, Plots, OrderedCollections, Format, PGFPlotsX
+
+impurities = [:Ne, :Ar, :Cr, :Kr, :W]
+color_ = [:blue, :green, :red, :black, :cyan, :red]
+Lz = OrderedDict(imp => ADAS.get_cooling_rates(imp) for imp in impurities);
+Zeff = Dict(imp => ADAS.get_Zeff(imp) for imp in impurities)
+pgfplotsx()
+Log10Range(args...; kw...) = 10 .^ LinRange(args...; kw...)
+p = plot(layout=1, framestyle=:box, palette=:darktest, size=(400, 400))
+for (i, Lz_) in enumerate(values(Lz))
+    plot!(Lz_, Te=Log10Range(0.5, 4.5, 1000), xlim=[5.0, 2e4], ylim=[1e-34, 5e-31], xscale=:log10, yscale=:log10, layout=1, color=color_[i])
+end
+# y = Log10Range(-34, -31, 4)
+# x = Log10Range(1, 4, 4)
+# yticks!(p, y)
+# xticks!(p, x)
+# plot!(legendposition=:bottomright, legendfontsize=12, legendcolumns=2)
+# #%%
+# using NumericalIntegration
+# Prad_tot = Dict(k => NumericalIntegration.integrate(r_omp, v) for (k, v) in Pvol_rad)
+# fraction_imp = 0.0:0.001:0.005
+# Zeff_ped = Dict(imp => [ADAS.get_Zeff(imp)(f, ne_ped, Te_ped) for f in fraction_imp] for imp in impurities)
+using LaTeXStrings
+p = plot()
+Te = Log10Range(1, 4, 100)
+ne = 1e19
+fraction = [0.001, 0.01]
+color_ = [:blue, :green, :red, :black, :cyan, :red]
+linestyle_ = [:solid,:dash]
+plot!(xlabel="Te[eV]", ylabel=L"$Z_{eff} = \frac{\sum n_a Z_a^2}{n_e}")
+plot!(title="Zeff in C-R equilibrium\n", titlefontsize=8)
+for (i,imp) in enumerate([:Ne,:Ar,:Kr])
+    for (j,f) in enumerate(fraction)
+        plot!(Te, [Zeff[imp](f, ne, Te_) for Te_ in Te], label="$imp : $(f*100)%", lw=1.0, color=color_[i],linestyle=linestyle_[j])
+    end
+end
+fs =12
+plot!(framestyle=:box, ylims=(0, 5.0), xtickfontsize=fs, ytickfontsize=fs, xguidefontsize=fs, yguidefontsize=fs, legendfontsize=fs)
+#save("zeff.tikz", p)