DOI: 10.5281/zenodo.3550951
title: Simulation data and software scripts used in calculus of ∆36 signature from EMAC clumped O2 isotope-inclusive model

description: This publication contains simulation data and software scripts for calculating quantities related to clumped oxygen isotope signature (∆<sub>36</sub>) derivation, as described in the "static" framework of (Yeung<em>‍ et‍ al.</em>, 2016, hereinafter "Y16") and subsequently used in Yeung<em>‍ et‍ al.</em>‍ (2019) analysis. We provide the output of the 1950–2011 transient simulation with EMAC model (Gromov<em>‍ et‍ al.</em>, 2019) with explicit "dynamic" simulation of ∆<sub>36</sub> (<em>i.e.</em> <sup>18</sup>O<sup>18</sup>O isotopologues undergoing transport, mixing and O(<sup>3</sup>P)-mediated isotope equilibration) to demonstrate the importance of several assumptions/simplifications involved in the Y16 calculus. <strong>Background</strong> Y16 framework employs stratosphere-troposphere mixing model which operates with the following variables regarded as tropospheric averages (see Eq.(2) in Y16): E<sub>trop</sub> : O<sub>2</sub> isotope exchange (equilibration) rate mediated by O(<sup>3</sup>P) T<sub>equil</sub> : temperature at whish exchange (equilibration) occurs ∆<sub>36</sub>,<sub>Tequil</sub> : tropospherix mixing end-member (corresponds T<sub>equil</sub>, i.e. equilibration in the troposphere) ∆<sub>36</sub><sub>,strat</sub> : end-member composition of stratospheric O<sub>2</sub> entering the troposphere ∆<sub>36</sub><sub>,trop</sub> : resulting tropospheric isotope composition (under assumption that tropospheric O<sub>2</sub> is well mixed on annual timescales) Using the EMAC data, we check several assumptions/simplifications involved in the Y16 calculus, which appear to underrepresent important processes in the atmosphere. These are, <em>viz.</em>: - calculation of ∆<sub>36</sub>,<sub>Tequil</sub> value is calculated by merely projecting the whole-troposphere T<sub>equil</sub> value onto Wang<em>‍ et‍ al.</em>‍ (2004) ∆<sub>36</sub>–T<sub>equil</sub> curve (<em>i.e. </em>disregarding atmospheric mixing effects), - use of annual instead of monthly averages of temperature and species concentrations (renders effectively lower T<sub>equil</sub>, as O(<sup>3</sup>P) is mostly present in warmer seasons), - use of additional "residence time" τ<sub>box</sub> (density weighting) for tropospheric integrals. <strong>Performing calculations</strong> Two scripts are used to calculate/retrieve "static" and "dynamic" data, which require Ferret NOAA PMEL (http://ferretop.pmel.noaa.gov/Ferret/, v7.4 or later) software. In order to perform all operations yourself, please download all files to the same directory and run the following scripts using Ferret, e.g.: <pre><code class="language-json">[user@pc]/home&gt; cd /home/user/path_where_files_are [user@pc]/home/user/path_where_files_are&gt; ferret NOAA/PMEL TMAP FERRET v7.4 (optimized) Linux 2.6.32-696.18.7.el6.x86_64 64-bit - 04/17/18 &lt;date&gt; &lt;time&gt; yes? go dynamic_calc-EMAC.jnl [start_year] [end_year] yes? go static_calc-Y16.jnl [diag_year] [start_year] [end_year] </code></pre> with optional parameters: [start_year] and [end_year]: the span for which time series calculated [diag_year]: output diagnostic plots of major terms for a given year The scripts produce several files, of which the following ones are used in subsequent analysis: dynamic_calc-EMAC__ATom_TR-pr4b__1950-2011_am.dat static_calc-Y16__ATom_TR-pr4b__1950-2011_am.nc The naming of indicates which assumptions were kept/discarded in the below calculation of a variable &lt;var&gt;, <em>viz.</em>: &lt;var&gt;_Y16 – implies using Y16 calculus "as is", &lt;var&gt;_MW – using only mass-weighting for tropospheric integrals (without additional density weighting) and molar (as opposed to volumetric) exchange rates, &lt;var&gt;_*_aa – using annual instead of monthly averages of temperature, O(<sup>3</sup>P) and O<sub>2</sub> concentrations. The trend analysis of the calculated time series is done in spreadsheet software (see static_calc-Y16_am-trends.xlsx). Extended figures and analysis are made using Veusz (https://veusz.github.io, v3.0.1.1 or later) software (see static_calc-Y16_am.vsz), the results are presented here as well (see static_calc-Y16_am.pdf). <strong>Results / discussion</strong> Note the diagnostic plots highlighting differences in the calculated tropospheric integrals. One of the largest effects on the result has the choice of additional “residence time” weighting in Y16, which is assumed proportional to air density (see relative contribution of different areas in troposphere to the final averages in figure below, also in diag-rel_cont_to_trop_ave-2005.gif plot). Our analysis of the obtained time series highlight the following critical points on the Y16 calculus: Use of annual average temperatures and O(<sup>3</sup>P) concentrations leads to effectively lower exchange temperatures – because higher O(<sup>3</sup>P) concentrations usually coincide with higher temperatures in warmer seasons. The amount of the effect is 1.5−2 K expressed in T<sub>equil</sub>. In Eqs. (3) and (4): Use of V<sub>trop</sub> outside the integral is inappropriate, as the rate is assumed to be volumetric ([molec/cm<sup>3</sup>/s], it is followed by dV under the integral). This disregards volumetric weighting of the rate, in favour of other weightings under the integral. Use of “residence time weighting” (τ<sub>box</sub>) is not justified – the model in Eq. (2) assumes tropospheric O<sub>2</sub> is well-mixed (Y16). Any additional (to mass) weighting automatically implies the troposphere is not well-mixed. Irrespective of 3), use of air density as the proxy for τ<sub>box</sub> is not justified – simply regard two boxes with very different air densities and temperatures of 0°C and 10°C, respectively. It happens that the same amount of O<sub>2</sub> molecules underwent isotope exchange in each gridbox. What is the average equilibration temperature of molecules over both boxes? It should be 5°C, however density weighting will inappropriately shift this value towards that of the denser box. In Eqs. (4) and (5): k<sub>exch</sub> is used in volumetric units (i.e. [molec/cm<sup>3</sup>/s], as it is multiplied by [O(<sup>3</sup>P)][O<sub>2</sub>] to obtain the exchange rate) but inappropriately weighted by air mass and density (via τ<sub>box</sub>). This is another inconsistency in weighting. Eq. (2) is used to derive ∆<sub>36,strat</sub> that fits observed Δ<sub>36</sub> and calculated E<sub>trop</sub> and ∆<sub>36</sub>,<sub>Tequil</sub>. Why the same (as for troposphere) calculus is not used for the stratospheric end-member signature? Note, Eq. (2) implies that stratosphere is a well-mixed reservoir as well (and it is so on annual timescales). Y16 calculus disregards atmospheric mixing effects. Tropospheric average of gridcell temperatures and ∆<sub>36</sub>,<sub>Tequil</sub> (calculated per cell) will not be located on Wang curve – the average ∆<sub>36</sub>,<sub>Tequil</sub> value will always be higher (about (0.065–0.067)‰ for present-day conditions) than that expected from the average T<sub>equil</sub>. To recap, inconsistencies in 1), 2), 3) and 5) lead to erroneous estimates of E<sub>trop</sub>, T<sub>equil</sub>, ∆<sub>36</sub>,<sub>Tequil</sub> and therefore implicitly ∆<sub>36,strat</sub>, which was derived as the value fitting observed ∆<sub>36</sub> in Eq. (2) or Y16. The major consequence is that temperatures and rates in lower-tropospheric gridcells have very high weight in the resulting averages. The correct weighting results in much larger sensitivity of ∆<sub>36,trop</sub> to upper-tropospheric O<sub>3</sub>, as shown in figure below for 2005. Typical underestimated and correct values are listed below (based on EMAC output): <pre><code>Parameter Y16 (erroneous) MW (correct) static/with mixing Difference (MW−Y16) ------------------------------------------------------------------------------------ Etrop 1.05–1.30 1.45–1.7 ~30% [10^19 mol/a] Tequil −(15–13) −(38–35) ~3K [°C] ∆36,Tequil 1.99–1.96 2.34–2.29 / 2.41–2.36 ~0.06‰ / ~0.12 [‰] ∆36,strat 2.3‰ 2.8‰ ~0.5‰ T(∆36,strat) −35.7 T(O3=150 ppbv) −67.5 ~30K [°C] (Ranges denote change throughout 1950–2011 period)</code></pre> To note, ∆<sub>36</sub>,<sub>Tequil</sub> values estimated in Y16 are (1.93–1.90)‰, which suggests even higher tropospheric equilibration temperatures (–(10.6−8.4)°C, respectively) than listed above. ∆<sub>36,strat</sub> value estimated in Y16 corresponds temperature of −35.7°C, which is ~30K higher than typical temperatures at O<sub>3</sub>=150 nmol/mol height (EMAC output). Furthermore, this value does not fit the presented observational data, when substituted into Eq. (2) of Y16. Regarding the analysis Yeung<em>‍ et‍ al.</em>‍ (2019) based on Y16 calculus, we outline further critical points: Absolute ∆<sub>36,trop</sub> value estimated using erroneous terms from Y16 calculus and inconsistent ∆<sub>36,strat</sub> is likely wrong. Use of constant ∆<sub>36,strat</sub> (estimated for present-day conditions) implies stratospheric O<sub>3</sub> does not change, which is not justified. It can be shown with Eq. (2) of Y16 that different ∆<sub>36,strat</sub> values lead to different temporal trends in ∆<sub>36,trop</sub>. Hence derived ∆<sub>36,trop</sub> temporal changes are not correct as well. If mixing is regarded, higher ∆<sub>36</sub>,<sub>Tequil</sub> will result in less strong temporal trend in estimated ∆<sub>36,trop</sub> (about ~1/2 of the static calculus value for 1950–2011, based on EMAC data). <strong>References:</strong> Gromov,‍ S., Röckmann,‍ T., Laskar,‍ A.‍ H.,‍ and Peethambaran,‍ R.: Modelling the abundance of <sup>18</sup>O<sup>18</sup>O in the atmosphere and its sensitivity to temperature and O<sub>3</sub> photochemistry, <em>Geophys. Res. Abstr.</em>,<strong> 21</strong>, EGU2019‑16938, doi:‍ 10.5281/zenodo.3545956, 2019. Wang,‍ Z., Schauble,‍ E.‍ A.,‍ and Eiler,‍ J.‍ M.: Equilibrium thermodynamics of multiply substituted isotopologues of molecular gases, <em>Geochim. Cosmochim. Acta</em>,<strong> 68</strong>, 4779−4797, doi:‍ 10.1016/j.gca.2004.05.039, 2004. Yeung,‍ L.‍ Y., Murray,‍ L.‍ T., Ash,‍ J.‍ L., Young,‍ E.‍ D., Boering,‍ K.‍ A., Atlas,‍ E.‍ L., Schauffler,‍ S.‍ M., Lueb,‍ R.‍ A., Langenfelds,‍ R.‍ L., Krummel,‍ P.‍ B., Steele,‍ L.‍ P.,‍ and Eastham,‍ S.‍ D.: Isotopic ordering in atmospheric O<sub>2</sub> as a tracer of ozone photochemistry and the tropical atmosphere,‍ <em>J. Geophys. Res. Atm.</em>,<strong> 121</strong>, 12,541−512,559, doi:‍ 10.1002/2016JD025455, 2016. Yeung,‍ L.‍ Y., Murray,‍ L.‍ T., Martinerie,‍ P., Witrant,‍ E., Hu,‍ H., Banerjee,‍ A., Orsi,‍ A.,‍ and Chappellaz,‍ J.: Isotopic constraint on the twentieth‑century increase in tropospheric ozone, <em>Nature</em>,<strong> 570</strong>, 224−227, doi:‍ 10.1038/s41586‑019‑1277‑1, 2019.
description: {"references": ["NOAA PMEL Ferret (https://ferretop.pmel.noaa.gov/Ferret/)", "Veusz (https://veusz.github.io)", "netCDF (https://www.unidata.ucar.edu/software/netcdf/)"]}