scholarly journals AtChem, an open source box-model for the Master Chemical Mechanism

2019 ◽  
Author(s):  
Roberto Sommariva ◽  
Sam Cox ◽  
Chris Martin ◽  
Kasia Borońska ◽  
Jenny Young ◽  
...  
Keyword(s):  
Open Source ◽  
Atmospheric Chemistry ◽  
Web Application ◽  
Box Model ◽  
Chemical Mechanism ◽  
Control Software ◽  
Sensitivity Studies ◽  
Master Chemical Mechanism ◽  
Field Campaigns ◽  
Set Up

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.

scholarly journals AtChem (version 1), an open-source box model for the Master Chemical Mechanism

2020 ◽  
Vol 13 (1) ◽  
pp. 169-183 ◽  
Author(s):  
Roberto Sommariva ◽  
Sam Cox ◽  
Chris Martin ◽  
Kasia Borońska ◽  
Jenny Young ◽  
...  
Keyword(s):  
Open Source ◽  
Atmospheric Chemistry ◽  
Web Application ◽  
Box Model ◽  
Chemical Mechanism ◽  
Code Base ◽  
Sensitivity Studies ◽  
Master Chemical Mechanism ◽  
Field Campaigns ◽  
Set Up

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.

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

2019 ◽  
Vol 12 (4) ◽  
pp. 1365-1385 ◽  
Author(s):  
Rolf Sander ◽  
Andreas Baumgaertner ◽  
David Cabrera-Perez ◽  
Franziska Frank ◽  
Sergey Gromov ◽  
...  
Keyword(s):  
Atmospheric Chemistry ◽  
Box Model ◽  
Chemical Mechanism ◽  
Chemical Mechanisms ◽  
Community Model ◽  
Volatile Organic ◽  
Master Chemical Mechanism ◽  
New Feature ◽  
User Friendly ◽  
Skeletal Mechanism

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.

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 ◽  
...  
Keyword(s):  
Atmospheric Chemistry ◽  
Box Model ◽  
Chemical Mechanism ◽  
Chemical Mechanisms ◽  
Community Model ◽  
Volatile Organic ◽  
Master Chemical Mechanism ◽  
New Feature ◽  
User Friendly ◽  
Skeletal Mechanism

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.

scholarly journals Hydroxyl radicals in the tropical troposphere over the Suriname rainforest: comparison of measurements with the box model MECCA

2008 ◽  
Vol 8 (4) ◽  
pp. 15239-15289 ◽  
Author(s):  
D. Kubistin ◽  
H. Harder ◽  
M. Martinez ◽  
M. Rudolf ◽  
R. Sander ◽  
...  
Keyword(s):  
Atmospheric Chemistry ◽  
Tropical Rainforest ◽  
Source Region ◽  
Degradation Process ◽  
Reaction Scheme ◽  
Box Model ◽  
Chemical Mechanism ◽  
Similar Amount ◽  
Oxidation Capacity ◽  
Mixing Ratios

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.

scholarly journals Development of a chlorine chemistry module for the Master Chemical Mechanism

2015 ◽  
Vol 8 (6) ◽  
pp. 4823-4849
Author(s):  
L. K. Xue ◽  
S. M. Saunders ◽  
T. Wang ◽  
R. Gao ◽  
X. F. Wang ◽  
...  
Keyword(s):  
Atmospheric Chemistry ◽  
Southern China ◽  
Oxidative Capacity ◽  
Early Morning ◽  
Chemical Mechanism ◽  
Atmospheric Photochemistry ◽  
Nitryl Chloride ◽  
Chemistry Research ◽  
Master Chemical Mechanism ◽  
Chemistry Module

Abstract. The chlorine atom (Cl·) has a high potential to perturb atmospheric photochemistry by oxidizing volatile organic compounds (VOCs), but the exact role it plays in the polluted troposphere remains unclear. The Master Chemical Mechanism (MCM) is a near explicit mechanism that has been widely applied in the atmospheric chemistry research. While it addresses comprehensively the chemistry initiated by the OH, O3 and NO3 radicals, its representation of the Cl· chemistry is incomplete as it only considers the reactions for alkanes. In this paper, we develop a more comprehensive Cl· chemistry module that can be directly incorporated within the MCM framework. A suite of 199 chemical reactions describes the Cl·-initiated degradation of alkenes, aromatics, aldehydes, ketones, alcohols, and some organic acids and nitrates, along with the inorganic chemistry involving Cl· and its precursors. To demonstrate the potential influence of the new chemistry module, it was incorporated into a MCM box model to evaluate the impacts of nitryl chloride (ClNO2), a product of nocturnal halogen activation by nitrogen oxides (NOx), on the following-day's atmospheric photochemistry. With constraints of recent observations collected at a coastal site in Hong Kong, southern China, the modeling analyses suggest that the Cl· produced from ClNO2 photolysis may substantially enhance the atmospheric oxidative capacity, VOC oxidation, and O3 formation, particularly in the early morning period. The results demonstrate the critical need for photochemical models to include more fully chlorine chemistry in order to better understand the atmospheric photochemistry in polluted environments subject to intense emissions of NOx, VOCs and chlorine-containing constituents.

scholarly journals ROOOH: a missing piece of the puzzle for OH measurements in low-NO environments?

2019 ◽  
Vol 19 (1) ◽  
pp. 349-362 ◽  
Author(s):  
Christa Fittschen ◽  
Mohamad Al Ajami ◽  
Sebastien Batut ◽  
Valerio Ferracci ◽  
Scott Archer-Nicholls ◽  
...  
Keyword(s):  
Atmospheric Chemistry ◽  
Unknown Origin ◽  
Oh Radicals ◽  
New Class ◽  
Expansion Technique ◽  
Field Campaigns ◽  
Reliable Quantification ◽  
Set Up ◽  
Gas Expansion ◽  
The University

Abstract. Field campaigns have been carried out with the FAGE (fluorescence assay by gas expansion) technique in remote biogenic environments in the last decade to quantify the in situ concentrations of OH, the main oxidant in the atmosphere. These data have revealed concentrations of OH radicals up to a factor of 10 higher than predicted by models, whereby the disagreement increases with decreasing NO concentration. This was interpreted as a major lack in our understanding of the chemistry of biogenic VOCs (volatile organic compounds), particularly isoprene, which are dominant in remote pristine conditions. But interferences in these measurements of unknown origin have also been discovered for some FAGE instruments: using a pre-injector, all ambient OH is removed by fast reaction before entering the FAGE cell, and any remaining OH signal can be attributed to an interference. This technique is now systematically used for FAGE measurements, allowing the reliable quantification of ambient OH concentrations along with the signal due to interference OH. However, the disagreement between modelled and measured high OH concentrations of earlier field campaigns as well as the origin of the now-quantifiable background OH is still not understood. We present in this paper the compelling idea that this interference, and thus the disagreement between model and measurement in earlier field campaigns, might be at least partially due to the unexpected decomposition of a new class of molecule, ROOOH, within the FAGE instruments. This idea is based on experiments, obtained with the FAGE set-up of the University of Lille, and supported by a modelling study. Even though the occurrence of this interference will be highly dependent on the design and measurement conditions of different FAGE instruments, including ROOOH in atmospheric chemistry models might reflect a missing piece of the puzzle in our understanding of OH in clean atmospheres.

scholarly journals A fast stratospheric chemistry solver: the E4CHEM submodel for the atmospheric chemistry global circulation model EMAC

2010 ◽  
Vol 3 (1) ◽  
pp. 321-328 ◽  
Author(s):  
A. J. G. Baumgaertner ◽  
P. Jöckel ◽  
B. Steil ◽  
H. Tost ◽  
R. Sander
Keyword(s):  
Atmospheric Chemistry ◽  
General Circulation ◽  
Circulation Model ◽  
Reaction Rates ◽  
Heterogeneous Reactions ◽  
Tropospheric Chemistry ◽  
Box Model ◽  
Chemical Mechanism ◽  
Global Circulation Model ◽  
Stratospheric Chemistry

Abstract. The atmospheric chemistry general circulation model ECHAM5/MESSy (EMAC) and the atmospheric chemistry box model CAABA are extended by a computationally very efficient submodel for atmospheric chemistry, E4CHEM. It focuses on stratospheric chemistry but also includes background tropospheric chemistry. It is based on the chemistry of MAECHAM4-CHEM and is intended to serve as a simple and fast alternative to the flexible but also computationally more demanding submodel MECCA. In a model setup with E4CHEM, EMAC is now also suitable for simulations of longer time scales. The reaction mechanism contains basic O3, CH4, CO, HOx, NOx, and ClOx gas phase chemistry. In addition, E4CHEM includes optional fast routines for heterogeneous reactions on sulphate aerosols and polar stratospheric clouds (substituting the existing submodels PSC and HETCHEM), and scavenging (substituting the existing submodel SCAV). We describe the implementation of E4CHEM into the MESSy structure of CAABA and EMAC. For some species the steady state in the box model differs by up to 100% when compared to results from CAABA/MECCA due to different reaction rates. After an update of the reaction rates in E4CHEM the mixing ratios in both boxmodel and 3-D model simulations are in satisfactory agreement with the results from a simulation where MECCA with a similar chemistry scheme was employed. Finally, a comparison against a simulation with a more complex and already evaluated chemical mechanism is presented in order to discuss shortcomings associated with the simplification of the chemical mechanism.

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