Accelerating simulations using REDCHEM_v0.0 for atmospheric chemistry mechanism reduction

Abstract. Chemical mechanism reduction is common practice in combustion research for accelerating numerical simulations, however there have been limited applications 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, and its performance is evaluated both a priori against the model scenario results, but also 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 speedup for both cases, with a minimal loss of accuracy with regards to the spatio-temporal mixing ratio of the target species, which was selected to be ozone.

Download Full-text

Validation of nine years of MOPITT V5 NIR using MOZAIC/IAGOS measurements: biases and long-term stability

Atmospheric Measurement Techniques ◽

10.5194/amt-7-3783-2014 ◽

2014 ◽

Vol 7 (11) ◽

pp. 3783-3799 ◽

Cited By ~ 8

Author(s):

A. T. J. de Laat ◽

I. Aben ◽

M. Deeter ◽

P. Nédélec ◽

H. Eskes ◽

...

Keyword(s):

Near Infrared ◽

Transport Model ◽

A Priori ◽

Validation Data ◽

Chemistry Transport Model ◽

Large Variability ◽

Long Term Stability ◽

Spatio Temporal ◽

Good Agreement

Abstract. Validation results from a comparison between Measurement Of Pollution In The Troposphere (MOPITT) V5 Near InfraRed (NIR) carbon monoxide (CO) total column measurements and Measurement of Ozone and Water Vapour on Airbus in-service Aircraft (MOZAIC)/In-Service Aircraft for a Global Observing System (IAGOS) aircraft measurements are presented. A good agreement is found between MOPITT and MOZAIC/IAGOS measurements, consistent with results from earlier studies using different validation data and despite large variability in MOPITT CO total columns along the spatial footprint of the MOZAIC/IAGOS measurements. Validation results improve when taking the large spatial footprint of the MOZAIC/IAGOS data into account. No statistically significant drift was detected in the validation results over the period 2002–2010 at global, continental and local (airport) scales. Furthermore, for those situations where MOZAIC/IAGOS measurements differed from the MOPITT a priori, the MOPITT measurements clearly outperformed the MOPITT a priori data, indicating that MOPITT NIR retrievals add value to the MOPITT a priori. Results from a high spatial resolution simulation of the chemistry-transport model MOCAGE (MOdèle de Chimie Atmosphérique à Grande Echelle) showed that the most likely explanation for the large MOPITT variability along the MOZAIC-IAGOS profile flight path is related to spatio-temporal CO variability, which should be kept in mind when using MOZAIC/IAGOS profile measurements for validating satellite nadir observations.

Download Full-text

Ethane, ethyne and carbon monoxide concentrations in the upper troposphere and lower stratosphere from ACE and GEOS-Chem: a comparison study

Atmospheric Chemistry and Physics Discussions ◽

10.5194/acpd-11-13099-2011 ◽

2011 ◽

Vol 11 (4) ◽

pp. 13099-13139 ◽

Cited By ~ 1

Author(s):

G. González Abad ◽

N. D. C. Allen ◽

P. F. Bernath ◽

C. D. Boone ◽

S. D. McLeod ◽

...

Keyword(s):

Carbon Monoxide ◽

Atmospheric Chemistry ◽

Transport Model ◽

Chemical Mechanism ◽

Chemical Transport Model ◽

Spectrometer Data ◽

Chemistry Experiment ◽

Global Mean ◽

Tropospheric Concentrations ◽

Good Agreement

Abstract. Near global upper tropospheric concentrations of carbon monoxide (CO), ethane (C2H6) and ethyne (C2H2) from ACE (Atmospheric Chemistry Experiment) Fourier transform spectrometer on board the Canadian satellite SCISAT-1 are presented and compared with the output from the Chemical Transport Model (CTM) GEOS-Chem. The retrievals of ethane and ethyne from ACE have been improved for this paper by using new sets of microwindows compared with those for previous versions of ACE data. With the improved ethyne retrieval we have been able to produce a near global upper tropospheric distribution of C2H2 from space. Carbon monoxide, ethane and ethyne concentrations retrieved using ACE spectra show the expected seasonality linked to variations in the anthropogenic emissions and destruction rates as well as seasonal biomass burning activity. The GEOS-Chem model was run using the dicarbonyl chemistry suite, an extended chemical mechanism in which ethyne is treated explicitly. Seasonal cycles observed from satellite data are well reproduced by the model output, however the simulated CO concentrations are found to be systematically biased low over the Northern Hemisphere. An average negative global mean bias of 12% and 7% of the model relative to the satellite observations has been found for CO and C2H6 respectively and a positive global mean bias of 1% has been found for C2H2. ACE data are compared for validation purposes with MkIV spectrometer data and Global Tropospheric Experiment (GTE) TRACE-A campaign data showing good agreement with all of them.

Download Full-text

The community atmospheric chemistry box model CAABA/MECCA-4.0

Geoscientific Model Development ◽

10.5194/gmd-12-1365-2019 ◽

2019 ◽

Vol 12 (4) ◽

pp. 1365-1385 ◽

Cited By ~ 11

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.

Download Full-text

The added value of satellite observations of methane forunderstanding the contemporary methane budget

Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences ◽

10.1098/rsta.2021.0106 ◽

2021 ◽

Vol 379 (2210) ◽

pp. 20210106

Author(s):

Paul I. Palmer ◽

Liang Feng ◽

Mark F. Lunt ◽

Robert J. Parker ◽

Hartmut Bösch ◽

...

Keyword(s):

Atmospheric Chemistry ◽

Transport Model ◽

A Priori ◽

Added Value ◽

Atmospheric Methane ◽

Sources And Sinks ◽

Methane Budget ◽

Spatial Coverage ◽

New Research ◽

The Tropics

Surface observations have recorded large and incompletely understood changes to atmospheric methane (CH 4 ) this century. However, their ability to reveal the responsible surface sources and sinks is limited by their geographical distribution, which is biased towards the northern midlatitudes. Data from Earth-orbiting satellites designed specifically to measure atmospheric CH 4 have been available since 2009 with the launch of the Japanese Greenhouse gases Observing SATellite (GOSAT). We assess the added value of GOSAT to data collected by the US National Oceanic and Atmospheric Administration (NOAA), which have been the lynchpin for knowledge about atmospheric CH 4 since the 1980s. To achieve that we use the GEOS-Chem atmospheric chemistry transport model and an inverse method to infer a posteriori flux estimates from the NOAA and GOSAT data using common a priori emission inventories. We find the main benefit of GOSAT data is from its additional coverage over the tropics where we report large increases since the 2014/2016 El Niño, driven by biomass burning, biogenic emissions and energy production. We use data from the European TROPOspheric Monitoring Instrument to show how better spatial coverage and resolution measurements allow us to quantify previously unattainable diffuse sources of CH 4 , thereby opening up a new research frontier. This article is part of a discussion meeting issue ‘Rising methane: is warming feeding warming? (part 1)’.

Download Full-text

Constraints on OH in a global 3D inversion of methyl chloroform

10.5194/egusphere-egu2020-18458 ◽

2020 ◽

Author(s):

Stijn Naus ◽

Stephen Montzka ◽

Prabir Patra ◽

Maarten Krol

Keyword(s):

Interannual Variability ◽

Atmospheric Chemistry ◽

Transport Model ◽

Spatial Scales ◽

Atmospheric Pollutants ◽

Box Model ◽

Latitudinal Gradients ◽

Model Studies ◽

Methyl Chloroform ◽

Spatio Temporal

The hydroxyl radical (OH) is the primary atmospheric oxidant. In this role, OH is involved in the removal of a wide variety of atmospheric pollutants and greenhouse gases. Despite the central role of OH in atmospheric chemistry, important metrics such as interannual variability and trends in OH on large spatial scales remain poorly constrained. This is mainly due to its low abundance and short lifetime of seconds.Over the past decades, the anthropogenically emitted methyl chloroform (MCF) has been uniquely qualified as a tracer to indirectly constrain OH on large spatio-temporal scales. However, recent box model studies have shown that OH, as estimated from MCF observations, is still very uncertain 1,2,3. This translates for example to large uncertainties in global methane (CH4) emissions, even if changes in the global CH4 burden are well-defined. Box model studies however, do not fully capitalize on the MCF measurement network and the gradients therein. Moreover, they may introduce biases due to incorrect or incomplete representation of atmospheric transport.Here, we present results from a 4DVAR inversion of MCF over the 1998-2018 period, performed in the 3D chemistry-transport model TM5. Starting from typical OH priors, we find adjustments in the OH spatio-temporal distribution that bring the simulated MCF mole fractions closer to observations. Large uncertainties in this improved estimate remain, but we find that no large interannual variability (>2%) and no significant trend in global mean OH are needed to match MCF observations. We do find significant adjustments in the latitudinal gradients of OH (e.g. an increase in tropical OH).1&#160;Rigby, M., et al. PNAS (2017), 114.21: 5373-53772 Turner, A.J., et al. PNAS (2017), 114.21: 5367-53723 Naus, S et al. ACP (2019), 19.1: 407-424

Download Full-text

The chemistry CATT–BRAMS model (CCATT–BRAMS 4.5): a regional atmospheric model system for integrated air quality and weather forecasting and research

Geoscientific Model Development Discussions ◽

10.5194/gmdd-6-1173-2013 ◽

2013 ◽

Vol 6 (1) ◽

pp. 1173-1222 ◽

Cited By ~ 9

Author(s):

K. M. Longo ◽

S. R. Freitas ◽

M. Pirre ◽

V. Marécal ◽

L. F. Rodrigues ◽

...

Keyword(s):

Atmospheric Chemistry ◽

Amazon Basin ◽

Weather Forecasting ◽

Transport Model ◽

Atmospheric Model ◽

Atmospheric Modeling ◽

Chemical Mechanism ◽

Model Description ◽

Tracer Transport ◽

Chemical Transport Model

Abstract. The Coupled Chemistry Aerosol-Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CCATT–BRAMS, version 4.5) is an online regional chemical transport model designed for local and regional studies of atmospheric chemistry from surface to the lower stratosphere suitable both for operational and research purposes. It includes gaseous/aqueous chemistry, photochemistry, scavenging and dry deposition. The CCATT–BRAMS model takes advantages of the BRAMS specific development for the tropics/subtropics and of the recent availability of preprocessing tools for chemical mechanisms and of fast codes for photolysis rates. BRAMS includes state-of-the-art physical parameterizations and dynamic formulations to simulate atmospheric circulations of scales down to meters. The online coupling between meteorology and chemistry allows the system to be used for simultaneous atmospheric weather and chemical composition forecasts as well as potential feedbacks between them. The entire system comprises three preprocessing software tools for chemical mechanism (which are user defined), aerosol and trace gases emission fields and atmospheric and chemistry fields for initial and boundary conditions. In this paper, the model description is provided along evaluations performed using observational data obtained from ground-based stations, instruments aboard of aircrafts and retrieval from space remote sensing. The evaluation takes into account model application on different scales from megacities and Amazon Basin up to intercontinental region of the Southern Hemisphere.

Download Full-text

Ethane, ethyne and carbon monoxide concentrations in the upper troposphere and lower stratosphere from ACE and GEOS-Chem: a comparison study

Atmospheric Chemistry and Physics ◽

10.5194/acp-11-9927-2011 ◽

2011 ◽

Vol 11 (18) ◽

pp. 9927-9941 ◽

Cited By ~ 22

Author(s):

G. González Abad ◽

N. D. C. Allen ◽

P. F. Bernath ◽

C. D. Boone ◽

S. D. McLeod ◽

...

Keyword(s):

Carbon Monoxide ◽

Atmospheric Chemistry ◽

Transport Model ◽

Chemical Mechanism ◽

Chemical Transport Model ◽

Spectrometer Data ◽

Chemistry Experiment ◽

Global Mean ◽

Tropospheric Concentrations ◽

Good Agreement

Abstract. Near global upper tropospheric concentrations of carbon monoxide (CO), ethane (C2H6) and ethyne (C2H2) from ACE (Atmospheric Chemistry Experiment) Fourier transform spectrometer on board the Canadian satellite SCISAT-1 are presented and compared with the output from the Chemical Transport Model (CTM) GEOS-Chem. The retrievals of ethane and ethyne from ACE have been improved for this paper by using new sets of microwindows compared with those for previous versions of ACE data. With the improved ethyne retrieval we have been able to produce a near global upper tropospheric distribution of C2H2 from space. Carbon monoxide, ethane and ethyne concentrations retrieved using ACE spectra show the expected seasonality linked to variations in the anthropogenic emissions and destruction rates as well as seasonal biomass burning activity. The GEOS-Chem model was run using the dicarbonyl chemistry suite, an extended chemical mechanism in which ethyne is treated explicitly. Seasonal cycles observed from satellite data are well reproduced by the model output, however the simulated CO concentrations are found to be systematically biased low over the Northern Hemisphere. An average negative global mean bias of 12% and 7% of the model relative to the satellite observations has been found for CO and C2H6 respectively and a positive global mean bias of 1% has been found for C2H2. ACE data are compared for validation purposes with MkIV spectrometer data and Global Tropospheric Experiment (GTE) TRACE-A campaign data showing good agreement with all of them.

Download Full-text

Tropospheric chemistry in the integrated forecasting system of ECMWF

Geoscientific Model Development Discussions ◽

10.5194/gmdd-7-7733-2014 ◽

2014 ◽

Vol 7 (6) ◽

pp. 7733-7803 ◽

Cited By ~ 6

Author(s):

J. Flemming ◽

V. Huijnen ◽

J. Arteta ◽

P. Bechtold ◽

A. Beljaars ◽

...

Keyword(s):

Atmospheric Chemistry ◽

Transport Model ◽

Nitrogen Monoxide ◽

Coupled System ◽

Tropospheric Chemistry ◽

Chemical Mechanism ◽

Atmospheric Composition ◽

Chemical Transport Model ◽

Data Set ◽

Forecasting System

Abstract. A representation of atmospheric chemistry has been included in the Integrated Forecasting System (IFS) of the European Centre for Medium-range Weather Forecasts (ECMWF). The new chemistry modules complement the aerosol modules of the IFS for atmospheric composition, which is named C-IFS. C-IFS for chemistry supersedes a coupled system, in which the Chemical Transport Model (CTM) Model for OZone and Related chemical Tracers 3 was two-way coupled to the IFS (IFS-MOZART). This paper contains a description of the new on-line implementation, an evaluation with observations and a comparison of the performance of C-IFS with MOZART and with a re-analysis of atmospheric composition produced by IFS-MOZART within the Monitoring Atmospheric Composition and Climate (MACC) project. The chemical mechanism of C-IFS is an extended version of the Carbon Bond 2005 (CB05) chemical mechanism as implemented in the CTM Transport Model 5 (TM5). CB05 describes tropospheric chemistry with 54 species and 126 reactions. Wet deposition and lightning nitrogen monoxide (NO) emissions are modelled in C-IFS using the detailed input of the IFS physics package. A one-year simulation by C-IFS, MOZART and the MACC re-analysis is evaluated against ozonesondes, carbon monoxide (CO) aircraft profiles, European surface observations of ozone (O3), CO, sulphur dioxide (SO2) and nitrogen dioxide (NO2) as well as satellite retrievals of CO, tropospheric NO2 and formaldehyde. Anthropogenic emissions from the MACC/CityZen (MACCity) inventory and biomass burning emissions from the Global Fire Assimilation System (GFAS) data set were used in the simulations by both C-IFS and MOZART. C-IFS (CB05) showed an improved performance with respect to MOZART for CO, upper tropospheric O3, winter time SO2 and was of a similar accuracy for other evaluated species. C-IFS (CB05) is about ten times more computationally efficient than IFS-MOZART.

Download Full-text

Global emissions of non-methane hydrocarbons deduced from SCIAMACHY formaldehyde columns through 2003–2006

Atmospheric Chemistry and Physics ◽

10.5194/acp-9-3663-2009 ◽

2009 ◽

Vol 9 (11) ◽

pp. 3663-3679 ◽

Cited By ~ 123

Author(s):

T. Stavrakou ◽

J.-F. Müller ◽

I. De Smedt ◽

M. Van Roozendael ◽

G. R. van der Werf ◽

...

Keyword(s):

Biomass Burning ◽

Amazon Basin ◽

A Priori Estimates ◽

Transport Model ◽

A Priori ◽

Chemical Mechanism ◽

Strong Increase ◽

High Signal ◽

Fire Emissions ◽

The Impact

Abstract. Formaldehyde columns retrieved from the Scanning Imaging Absorption Spectrometer for Atmospheric Chartography/Chemistry (SCIAMACHY) instrument onboard ENVISAT satellite through 2003 to 2006 are used as top-down constraints to derive updated global biogenic and biomass burning flux estimates for the non-methane volatile organic compounds (NMVOCs) precursors of formaldehyde. Our interest is centered over regions experiencing strong emissions, and hence exhibiting a high signal-to-noise ratio and lower measurement uncertainties. The formaldehyde dataset used in this study has been recently made available to the community and complements the long record of formaldehyde measurements from the Global Ozone Monitoring Experiment (GOME). We use the IMAGESv2 global chemistry-transport model driven by the Global Fire Emissions Database (GFED) version 1 or 2 for biomass burning, and from the newly developed MEGAN-ECMWF isoprene emission database. The adjoint of the model is implemented in a grid-based framework within which emission fluxes are derived at the model resolution, together with a differentiation of the sources in a grid cell. Two inversion studies are conducted using either the GFEDv1 or GFEDv2 as a priori for the pyrogenic fluxes. Although on the global scale the inferred emissions from the two categories exhibit only weak deviations from the corresponding a priori estimates, the regional updates often present large departures from their a priori values. The posterior isoprene emissions over North America, amounting to about 34 Tg C/yr, are estimated to be on average by 25% lower than the a priori over 2003–2006, whereas a strong increase (55%) is deduced over the south African continent, the optimized emission being estimated at 57 Tg C/yr. Over Indonesia the biogenic emissions appear to be overestimated by 20–30%, whereas over Indochina and the Amazon basin during the wet season the a priori inventory captures both the seasonality and the magnitude of the observed columns. Although neither biomass burning inventory seems to be consistent with the data over all regions, pyrogenic estimates inferred from the two inversions are reasonably similar, despite their a priori deviations. A number of sensitivity experiments are conducted in order to assess the impact of uncertainties related to the inversion setup and the chemical mechanism. Whereas changes in the background error covariance matrix have only a limited impact on the posterior fluxes, the use of an alternative isoprene mechanism characterized by lower HCHO yields (the GEOS-Chem mechanism) increases the posterior isoprene source estimate by 11% over northern America, and by up to 40% in tropical regions.

Download Full-text