DOI: 10.5281/zenodo.7402614
title: Atmospheric clumped O2 isotope composition simulation data and analysis scripts from EMAC/aMC models

description: This publication contains source code, data and analysis scripts/results of the simulations presented in the following manuscript: Laskar, A.H., G.A. Adnew, S.S. Gromov, R. Peethambaran, B. Steil, J. Lelieveld, T. Blunier and T. Röckmann (2022). "Large variations in atmospheric oxidants and temperature during the Holocene" (in review) <strong>EMAC simulations analysis</strong> The analysis contains integrals of species burdens and other atmospheric physicochemical parameters obtained with the clumped isotopes of oxygen (CIO)-enabled ECHAM/MESSy Atmospheric Chemistry model (EMAC, see MESSy consortium website for more information) model in various climate states. Simulations were performed in 2021–2022 at the German Climate Computing Centre (DKRZ) with the support of the PalMod project. Analysis data is stored in human/machine-readable file <code>D36-EMAC-analysis.dat</code>, please refer to its header for variables description, etc. Additional (to those presented in the manuscript) analysis plots from EMAC data analysis are available in <code>D36-EMAC-analysis.vsz</code> (see the hardcopy in <code>D36-EMAC-analysis.pdf</code>) prepared using the Veusz software. <strong>2BM/MC (two-box Monte-Carlo) model code, simulation data and analysis</strong> 2BM/MC code/simulation setup is implemented within the advanced Monte-Carlo framework (aMC) and is available in the respective repository. A copy of the source code used to perform simulations is provided here (see <code>aMC-vpCIO.tar.gz</code> archive). 2BM/MC output is stored in the netCDF format (ver. 4) and can be read in by any compatible software. The output contains probe statistics (reference <em>probed</em> distributions of the variables) in <code>vpCIO-probe_stat-*.nc</code> and resulting statistics (distributions <em>matching</em> given criteria, i.e. changes to the Δ36 signature vs. PD conditions) in <code>vpCIO-delta-*.nc</code> files, respectively. We use NOAA Ferret software to derive additional statistics of the third parameter (viz. average STE (<em>S</em>) changes) over the obtained 2D frequency histograms of other parameters (viz. changes to equilibration rate (<em>Req)</em> and temperature (<em>Teq</em>)). The scripts exemplifying this calculation are presented in <code>D36-vpCIO-analysis__proc*</code> files, which output results/overview plots in <code>vpCIO-delta-*__proc.nc</code> and <code>vpCIO-delta-*.gif</code> files. The analysis of the 2BM/MC simulation is available in <code>D36-vpCIO-analysis.vsz</code> script (see the hardcopy in <code>D36-vpCIO-analysis.pdf</code>) prepared using the Veusz software. Note that some plots require the abovementioned third-parameter statistics as input. <strong>Performing simulations with 2BM/MC</strong> In order to perform simulations (e.g. with altered parameters), please follow the respective guide for and build the <code>aMC-vpCIO</code> model. A typical sequence of shell commands to build and run 2BM/MC (which is referred to as <code>vpCIO</code> generic model within the <code>aMC</code>) is: <pre><code># clone the distribution and check-out `vpCIO` branch or particular commit referenced in the repository history [user@pc]/~&gt; git clone https://gitlab.com/sergey.gromov/amc.git [user@pc]/~&gt; cd amc [user@pc]/~/amc&gt; git checkout vpCIO # or unpack the source code available in this publication: [user@pc]/~&gt; tar -xvf `aMC-vpCIO.tar.gz` [user@pc]/~&gt; cd amc # build the aMC/vpCIO model executable # (note that you need at least a GCC or Intel compiler suite and respective netCDF v.4 library Fortran interface available in your environment): [user@pc]/~/amc&gt; make vpCIO # adjust model setup (see the `vpCIO/amc.nml` namelist) ... # perform simulation [user@pc]/~/amc&gt; cd vpCIO [user@pc]/~/amc/vpCIO&gt; ./xamc # calculate additional statistics/produce overview with NOAA Ferret: [user@pc]/~/amc/vpCIO&gt; ferret -gif -script D36-vpCIO-analysis__proc.jnl MH [user@pc]/~/amc/vpCIO&gt; ./D36-vpCIO-analysis__proc</code></pre> Note that output files contain the build timestamp and repository commit hash for the code used in the simulation, e.g.: <pre><code>[user@pc]/~/amc/vpCIO&gt; ncdump -h ./vpCIO-delta-dMH.nc | grep 'build' :build = "vpCIO@https://gitlab.com/sergey.gromov/amc__aMC_v1.9-110-g2566229@2022-12-09T16:43:12+01:00__built@2022-12-09T16:48:03+01:00__&lt;user&gt;@&lt;email.com&gt;" ;</code></pre> Please contact Sergey Gromov ( sergey.gromov (at) mpic.de ) for additional information and access to the original experiment data.
description: {"references": ["https://veusz.github.io/", "https://ferret.pmel.noaa.gov/", "https://www.unidata.ucar.edu/software/netcdf/"]}