scholarly journals The atmospheric chemistry box model CAABA/MECCA-4.0gmdd

2018 ◽  
Author(s):  
Rolf Sander ◽  
Andreas Baumgaertner ◽  
David Cabrera ◽  
Franziska Frank ◽  
Jens-Uwe Grooß ◽  
...  

Abstract. We present version 4.0gmdd of the atmospheric chemistry box model CAABA/MECCA which now includes a number of new features: (i) skeletal mechanism reduction, (ii) the MOM chemical mechanism for volatile organic compounds, (iii) an option to include reactions from the Master Chemical Mechanism (MCM) and other chemical mechanisms, (iv) updated isotope tagging, and (v) improved and new photolysis modules (JVAL, RADJIMT, DISSOC). Further, when MECCA is connected to a global model, the new feature of coexisting multiple chemistry mechanisms (PolyMECCA/CHEMGLUE) can be used. Additional changes have been implemented to make the code more user-friendly and to facilitate the analysis of the model results. Like earlier versions, CAABA/MECCA-4.0gmdd is a community model published under the GNU General Public License.

2019 ◽  
Vol 12 (4) ◽  
pp. 1365-1385 ◽  
Author(s):  
Rolf Sander ◽  
Andreas Baumgaertner ◽  
David Cabrera-Perez ◽  
Franziska Frank ◽  
Sergey Gromov ◽  
...  

Abstract. We present version 4.0 of the atmospheric chemistry box model CAABA/MECCA that now includes a number of new features: (i) skeletal mechanism reduction, (ii) the Mainz Organic Mechanism (MOM) chemical mechanism for volatile organic compounds, (iii) an option to include reactions from the Master Chemical Mechanism (MCM) and other chemical mechanisms, (iv) updated isotope tagging, and (v) improved and new photolysis modules (JVAL, RADJIMT, DISSOC). Further, when MECCA is connected to a global model, the new feature of coexisting multiple chemistry mechanisms (PolyMECCA/CHEMGLUE) can be used. Additional changes have been implemented to make the code more user-friendly and to facilitate the analysis of the model results. Like earlier versions, CAABA/MECCA-4.0 is a community model published under the GNU General Public License.


2019 ◽  
Author(s):  
Roberto Sommariva ◽  
Sam Cox ◽  
Chris Martin ◽  
Kasia Borońska ◽  
Jenny Young ◽  
...  

Abstract. AtChem is an open source zero-dimensional box-model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism (MCM, http://mcm.york.ac.uk/). AtChem was initially developed within the EUROCHAMP project as a web application (AtChem-online, https://atchem.leeds.ac.uk/webapp/) for modelling environmental chamber experiments; it was recently upgraded and further developed into a standalone offline version (AtChem2) which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies. AtChem is installed, set up and configured using semi-automated scripts and simple text configuration files, making it easy to use even for non-experienced users. A key feature of AtChem is that it can easily be constrained to observational data which may have different timescales, thus retaining all the information contained in the observations. Implementation of a continuous integration workflow, coupled with a comprehensive suite of tests and version control software, makes the AtChem codebase robust, reliable and traceable. The AtChem2 code and documentation are available at https://github.com/AtChem/, under the open source MIT license.


2011 ◽  
Vol 4 (2) ◽  
pp. 373-380 ◽  
Author(s):  
R. Sander ◽  
A. Baumgaertner ◽  
S. Gromov ◽  
H. Harder ◽  
P. Jöckel ◽  
...  

Abstract. We present version 3.0 of the atmospheric chemistry box model CAABA/MECCA. In addition to a complete update of the rate coefficients to the most recent recommendations, a number of new features have been added: chemistry in multiple aerosol size bins; automatic multiple simulations reaching steady-state conditions; Monte-Carlo simulations with randomly varied rate coefficients within their experimental uncertainties; calculations along Lagrangian trajectories; mercury chemistry; more detailed isoprene chemistry; tagging of isotopically labeled species. Further changes have been implemented to make the code more user-friendly and to facilitate the analysis of the model results. Like earlier versions, CAABA/MECCA-3.0 is a community model published under the GNU General Public License.


2020 ◽  
Vol 13 (1) ◽  
pp. 169-183 ◽  
Author(s):  
Roberto Sommariva ◽  
Sam Cox ◽  
Chris Martin ◽  
Kasia Borońska ◽  
Jenny Young ◽  
...  

Abstract. AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism (MCM, http://mcm.york.ac.uk/, last access: 16 January 2020). AtChem was initially developed within the EUROCHAMP project as a web application (AtChem-online, https://atchem.leeds.ac.uk/webapp/, last access: 16 January 2020) for modelling environmental chamber experiments; it was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies. AtChem is installed, set up and configured using semi-automated scripts and simple text configuration files, making it easy to use even for inexperienced users. A key feature of AtChem is that it can easily be constrained to observational data which may have different timescales, thus retaining all the information contained in the observations. Implementation of a continuous integration workflow, coupled with a comprehensive suite of tests and version control software, makes the AtChem code base robust, reliable and traceable. The AtChem2 code and documentation are available at https://github.com/AtChem/ (last access: 16 January 2020) under the open-source MIT License.


2011 ◽  
Vol 4 (1) ◽  
pp. 197-217 ◽  
Author(s):  
R. Sander ◽  
A. Baumgaertner ◽  
S. Gromov ◽  
H. Harder ◽  
P. Jöckel ◽  
...  

Abstract. We present version 3.0gmdd of the atmospheric chemistry box model CAABA/MECCA. In addition to a complete update of the rate coefficients to the most recent recommendations, a number of new features have been added: chemistry in multiple aerosol size bins; automatic multiple simulations reaching steady-state conditions; Monte-Carlo simulations with randomly varied rate coefficients within their experimental uncertainties; calculations along Lagrangian trajectories; mercury chemistry; more detailed isoprene chemistry; tagging of isotopically labeled species. Further changes have been implemented to make the code more user-friendly and to facilitate the analysis of the model results. Like earlier versions, CAABA/MECCA-3.0gmdd is a community model published under the GNU General Public License (GPL).


2016 ◽  
Vol 73 (12) ◽  
pp. 4699-4710 ◽  
Author(s):  
Philip A. Feiner ◽  
William H. Brune ◽  
David O. Miller ◽  
Li Zhang ◽  
Ronald C. Cohen ◽  
...  

Abstract The chemical species emitted by forests create complex atmospheric oxidation chemistry and influence global atmospheric oxidation capacity and climate. The Southern Oxidant and Aerosol Study (SOAS) provided an opportunity to test the oxidation chemistry in a forest where isoprene is the dominant biogenic volatile organic compound. Hydroxyl (OH) and hydroperoxyl (HO2) radicals were two of the hundreds of atmospheric chemical species measured, as was OH reactivity (the inverse of the OH lifetime). OH was measured by laser-induced fluorescence (LIF) and by taking the difference in signals without and with an OH scavenger that was added just outside the instrument’s pinhole inlet. To test whether the chemistry at SOAS can be simulated by current model mechanisms, OH and HO2 were evaluated with a box model using two chemical mechanisms: Master Chemical Mechanism, version 3.2 (MCMv3.2), augmented with explicit isoprene chemistry and MCMv3.3.1. Measured and modeled OH peak at about 106 cm−3 and agree well within combined uncertainties. Measured and modeled HO2 peak at about 27 pptv and also agree well within combined uncertainties. Median OH reactivity cycled between about 11 s−1 at dawn and about 26 s−1 during midafternoon. A good test of the oxidation chemistry is the balance between OH production and loss rates using measurements; this balance was observed to within uncertainties. These SOAS results provide strong evidence that the current isoprene mechanisms are consistent with measured OH and HO2 and, thus, capture significant aspects of the atmospheric oxidation chemistry in this isoprene-rich forest.


2018 ◽  
Vol 11 (8) ◽  
pp. 3391-3407 ◽  
Author(s):  
Zacharias Marinou Nikolaou ◽  
Jyh-Yuan Chen ◽  
Yiannis Proestos ◽  
Jos Lelieveld ◽  
Rolf Sander

Abstract. Chemical mechanism reduction is common practice in combustion research for accelerating numerical simulations; however, there have been limited applications of this practice in atmospheric chemistry. In this study, we employ a powerful reduction method in order to produce a skeletal mechanism of an atmospheric chemistry code that is commonly used in air quality and climate modelling. The skeletal mechanism is developed using input data from a model scenario. Its performance is then evaluated both a priori against the model scenario results and a posteriori by implementing the skeletal mechanism in a chemistry transport model, namely the Weather Research and Forecasting code with Chemistry. Preliminary results, indicate a substantial increase in computational speed-up for both cases, with a minimal loss of accuracy with regards to the simulated spatio-temporal mixing ratio of the target species, which was selected to be ozone.


2008 ◽  
Vol 8 (4) ◽  
pp. 15239-15289 ◽  
Author(s):  
D. Kubistin ◽  
H. Harder ◽  
M. Martinez ◽  
M. Rudolf ◽  
R. Sander ◽  
...  

Abstract. As a major source region of the hydroxyl radical OH, the Tropics largely control the oxidation capacity of the atmosphere on a global scale. However, emissions of hydrocarbons from the tropical rainforest that react rapidly with OH can potentially deplete the amount of OH and thereby reduce the oxidation capacity. The airborne GABRIEL field campaign in equatorial South America (Suriname) in October 2005 investigated the influence of the tropical rainforest on the HOx budget (HOx=OH+HO2). The first observations of OH and HO2 over a tropical rainforest are compared to steady state concentrations calculated with the atmospheric chemistry box model MECCA. The important precursors and sinks for HOx chemistry, measured during the campaign, are used as constraining parameters for the simulation of OH and HO2. Significant underestimations of HOx are found by the model over land during the afternoon, with mean ratios of observation to model of 12.2±3.5 and 4.1±1.4 for OH and HO2, respectively. The discrepancy between measurements and simulation results is correlated to the abundance of isoprene. While for low isoprene mixing ratios (above ocean or at altitudes >3 km), observation and simulation agree fairly well, for mixing ratios >200 pptV (<3 km over the rainforest) the model tends to underestimate the HOx observations as a function of isoprene. Box model simulations have been performed with the condensed chemical mechanism of MECCA and with the detailed isoprene reaction scheme of MCM, resulting in similar results for HOx concentrations. Simulations with constrained HO2 concentrations show that the conversion from HO2 to OH in the model is too low. However, by neglecting the isoprene chemistry in the model, observations and simulations agree much better. An OH source similar to the strength of the OH sink via isoprene chemistry is needed in the model to resolve the discrepancy. A possible explanation is that the oxidation of isoprene by OH not only dominates the removal of OH but also produces it in a similar amount. Several additional reactions which directly produce OH have been implemented into the box model, suggesting that upper limits in producing OH are still not able to reproduce the observations (improvement by factors of ≈2.4 and ≈2 for OH and HO2, respectively). We determine that OH has to be recycled to 94% instead of the simulated 38% to match the observations, which is most likely to happen in the isoprene degradation process, otherwise additional sources are required.


2018 ◽  
Author(s):  
Benjamin Brown-Steiner ◽  
Noelle E. Selin ◽  
Ronald Prinn ◽  
Simone Tilmes ◽  
Louisa Emmons ◽  
...  

Abstract. While state-of-the-art complex chemical mechanisms expand our understanding of atmospheric chemistry, their sheer size and computational requirements often limit simulations to short length, or ensembles to only a few members. Here we present and compare three 25-year offline simulations with chemical mechanisms of different levels of complexity using CESM Version 1.2 CAM-chem (CAM4): the MOZART-4 mechanism, the Reduced Hydrocarbon mechanism, and the Super-Fast mechanism. We show that, for most regions and time periods, differences in simulated ozone chemistry between these three mechanisms is smaller than the model-observation differences themselves. The MOZART-4 mechanism and the Reduced Hydrocarbon are in close agreement in their representation of ozone throughout the troposphere during all time periods (annual, seasonal and diurnal). While the Super-Fast mechanism tends to have higher simulated ozone variability and differs from the MOZART-4 mechanism over regions of high biogenic emissions, it is surprisingly capable of simulating ozone adequately given its simplicity. We explore the trade-offs between chemical mechanism complexity and computational cost by identifying regions where the simpler mechanisms are comparable to the MOZART-4 mechanism, and regions where they are not. The Super-Fast mechanism is three times as fast as the MOZART-4 mechanism, which allows for longer simulations, or ensembles with more members, that may not be feasible with the MOZART-4 mechanism given limited computational resources.


2011 ◽  
Vol 11 (21) ◽  
pp. 10779-10790 ◽  
Author(s):  
M. M. Galloway ◽  
A. J. Huisman ◽  
L. D. Yee ◽  
A. W. H. Chan ◽  
C. L. Loza ◽  
...  

Abstract. We present first-generation and total production yields of glyoxal, methylglyoxal, glycolaldehyde, and hydroxyacetone from the oxidation of isoprene, methyl vinyl ketone (MVK), and methacrolein (MACR) with OH under high NOx conditions. Several of these first-generation yields are not included in commonly used chemical mechanisms, such as the Leeds Master Chemical Mechanism (MCM) v. 3.2. The first-generation yield of glyoxal from isoprene was determined to be 2.1 (±0.6)%. Inclusion of first-generation production of glyoxal, glycolaldehyde and hydroxyacetone from isoprene greatly improves performance of an MCM based model during the initial part of the experiments. In order to further improve performance of the MCM based model, higher generation glyoxal production was reduced by lowering the first-generation yield of glyoxal from C5 hydroxycarbonyls. The results suggest that glyoxal production from reaction of OH with isoprene under high NOx conditions can be approximated by inclusion of a first-generation production term together with secondary production only via glycolaldehyde. Analogously, methylglyoxal production can be approximated by a first-generation production term from isoprene, and secondary production via MVK, MACR and hydroxyacetone. The first-generation yields reported here correspond to less than 5% of the total oxidized yield from isoprene and thus only have a small effect on the fate of isoprene. However, due to the abundance of isoprene, the combination of first-generation yields and reduced higher generation production of glyoxal from C5 hydroxycarbonyls is important for models that include the production of the small organic molecules from isoprene.


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