In this technical note we present the multi-purpose atmospheric chemistry model MECCA. Owing to its versatility and modular structure, it can be used for tropospheric as well as stratospheric chemistry calculations. Extending the code to other domains (e.g. mesospheric or oceanic chemistry) is easily possible. MECCA contains a comprehensive atmospheric reaction mechanism that currently includes: 1) the basic O3, CH4, HOx, and NOx chemistry, 2) non-methane hydrocarbon (NMHC) chemistry, 3) halogen (Cl, Br, I) chemistry, and 4) sulfur chemistry. Not only gas-phase chemistry but also aqueous-phase and heterogeneous reactions are considered. Arbitrary subsets of the comprehensive mechanism can be selected according to the research objectives. The program code resulting from the chemical mechanism can easily be used in any model, from a simple box model to a comprehensive global general circulation model

A. Kerkweg

J. Lelieveld

P. Jöckel

R. Sander

International audienceIn this technical note we present the multi-purpose atmospheric chemistry model MECCA. Owing to its versatility and modular structure, it can be used for tropospheric as well as stratospheric chemistry calculations. Extending the code to other domains (e.g. mesospheric or oceanic chemistry) is easily possible. MECCA contains a comprehensive atmospheric reaction mechanism that currently includes: 1) the basic O3, CH4, HOx, and NOx chemistry, 2) non-methane hydrocarbon (NMHC) chemistry, 3) halogen (Cl, Br, I) chemistry, and 4) sulfur chemistry. Not only gas-phase chemistry but also aqueous-phase and heterogeneous reactions are considered. Arbitrary subsets of the comprehensive mechanism can be selected according to the research objectives. The program code resulting from the chemical mechanism can easily be used in any model, from a simple box model to a comprehensive global general circulation model

Sander, R.

Kerkweg, A.

Jöckel, P.

Lelieveld, J.

HAL-INSU

Technical note: The new comprehensive atmospheric chemistry module MECCA

In this technical note we present the multi-purpose atmospheric  chemistry model MECCA. Owing to its versatility and modular structure,  it can be used for tropospheric as well as stratospheric chemistry  calculations. Extending the code to other domains (e.g. mesospheric  or oceanic chemistry) is easily possible. MECCA contains a  comprehensive atmospheric reaction mechanism that currently includes:  1) the basic O3, CH4, HOx, and NOx  chemistry, 2) non-methane hydrocarbon (NMHC) chemistry, 3) halogen  (Cl, Br, I) chemistry, and 4) sulfur chemistry.  Not only gas-phase chemistry but also aqueous-phase and heterogeneous  reactions are considered. Arbitrary subsets of the comprehensive  mechanism can be selected according to the research objectives. The  program code resulting from the chemical mechanism can easily be used  in any model, from a simple box model to a comprehensive global  general circulation model

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Atmos. Chem. Phys., 5, 445–450, 2005www.atmos-chem-phys.org/acp/5/445/SRef-ID: 1680-7324/acp/2005-5-445European Geosciences UnionAtmosphericChemistryand PhysicsTechnical note: The new comprehensive atmospheric chemistrymodule MECCAR. Sander, A. Kerkweg, P. J¨ ockel, and J. LelieveldAir Chemistry Department, Max-Planck-Institute of Chemistry, P.O. Box 3060, 55020 Mainz, GermanyReceived: 20 September 2004 – Published in Atmos. Chem. Phys. Discuss.: 5 November 2004Revised: 2 February 2005 – Accepted: 3 February 2005 – Published: 11 February 2005Abstract. In this technical note we present the multi-purposeatmosphericchemistrymodelMECCA.Owingtoitsversatil-ity and modular structure, it can be used for tropospheric aswell as stratospheric chemistry calculations. Extending thecode to other domains (e.g. mesospheric or oceanic chem-istry) is easily possible. MECCA contains a comprehen-sive atmospheric reaction mechanism that currently includes:1) the basic O3, CH4, HOx, and NOx chemistry, 2) non-methane hydrocarbon (NMHC) chemistry, 3) halogen (Cl,Br, I) chemistry, and 4) sulfur chemistry. Not only gas-phasechemistry but also aqueous-phase and heterogeneous reac-tions are considered. Arbitrary subsets of the comprehensivemechanism can be selected according to the research objec-tives. The program code resulting from the chemical mech-anism can easily be used in any model, from a simple boxmodel to a comprehensive global general circulation model.1 IntroductionMany computer models of atmospheric chemistry have beendeveloped in the past decades. Since eachwas aimed at a par-ticular goal, they vary strongly in complexity and efﬁciency.Often they encompass the basic chemistry of O3, CH4, HOx(=OH+HO2), and NOx (=NO+NO2). Some also include amoredetailedmechanismforhigherhydrocarbons, halogens,sulfur, or other species. There are box and column models aswell as two- or three-dimensional regional and global mod-els available. Chemical mechanisms have been developedfor the gas phase and also for aerosols and cloud droplets.The focus is usually on either stratospheric or troposphericchemistry. The chemistry codes are intertwined with mete-orological models that supply parameters such as radiation,temperature, pressure, humidity, and wind ﬁelds.Correspondence to: R. Sander(sander@mpch-mainz.mpg.de)Aspartofthemodeldevelopment, oneoftenneedstocom-bine several chemistry mechanisms. Another frequently oc-curing task is coupling chemical mechanisms to a meteoro-logical model, for example, for an intercomparison. Unfortu-nately, these are both time-consuming tasks due to differentapproaches and incompatibilities between the codes. Also, itis often complicated because there is no clear separation be-tween the meteorological and the chemical part of the model,and such a setup is sensitive to errors.In our implementation we apply a new approach aimed atavoiding the above mentioned problems. Here, we presentthe new comprehensive and ﬂexible atmospheric chem-istry module MECCA (Module Efﬁciently Calculating theChemistry of the Atmosphere).2 Model DescriptionThe main features of MECCA, as described in detail below,are:Chemical ﬂexibility: The chemical mechanism contains alarge number of reactions from which the user can select acustom-designed subset. It is easy to adjust the mechanism,e.g. according to the latest kinetics insights.Numerical ﬂexibility: The numerical integration method canbe chosen according to individual requirements of the stiffset of differential equations (efﬁciency, stability, accuracy,precision).Modularity: Due to its modular structure and strict adher-ence to the MESSy standard (explained below), the codecan be easily coupled to other meteorological base mod-els (e.g. box models, 1-dimensional column models, or 3-dimensional models).Portability: The Fortran95 code is written in a portable wayto allow its use on different platforms (e.g. Linux, Unix).Availability: The code is freely available to the scientiﬁccommunity.© 2005 Author(s). This work is licensed under a Creative Commons License.446 R. Sander et al.: The MECCA chemistry module2.1 Chemical ﬂexibilityIn the current version of MECCA, ﬁve previously publishedchemical mechanisms have been combined and updated.Tropospheric hydrocarbon chemistry is adopted from vonKuhlmann et al. (2003). The chemistry of the stratosphereis based on the model of Steil et al. (1998) and the MainzChemical Box Model (Meilinger, 2000). Tropospheric halo-gen chemistry is taken from Sander and Crutzen (1996) andvon Glasow et al. (2002). The current mechanism con-tains 116 species and 295 reactions in the gas phase, and 91species and 258 reactions in the aqueous phase. The ratecoefﬁcients are updated according to Sander et al. (2003),Atkinson et al. (2004), and other references. A detailed list-ing of reactions, rate coefﬁcients, and their references can befound in the electronic supplement at http://www.copernicus.org/EGU/acp/acp/5/445/acp-5-445-sp.zip. Itisbothpossibleand desirable to add reactions to the mechanism in the nearfuture. However, for computational efﬁciency, it is normallynot required to integrate the whole mechanism. Thereforewe have implemented a method by which the user can easilycreate a custom-made chemical mechanism. Each reactionhas several labels to categorize it. For example, the labelsTr and St indicate reactions relevant in the troposphere andthe stratosphere, respectively. These labels are not mutuallyexclusive. Manyreactionsneedtobeconsideredforbothlay-ers. There are also labels for the phase in which they occur(gas or aqueous phase) and for the elements that they con-tain (e.g. Cl, Br, and I for reactions of the halogen species).It is also possible to create new labels for speciﬁc purposes.For example, all reactions with the label Mbl are part of areduced mechanism for the marine boundary layer. Usinga Boolean expression based on these labels, it is possibleto create custom-made subsets of the comprehensive mecha-nism. The main advantage of maintaining a single compre-hensive mechanism is that new reactions and updates of ratecoefﬁcients need to be included only once so that they areimmediately available for all subsets.2.2 Numerical ﬂexibilityOnce a subset of the full mechanism has been selected asdescribed above, the kinetic preprocessor (KPP) software(Damian et al., 2002, Sandu and Sander, in preparation,20051) is used to transform the chemical equations into For-tran95 code. From a numerical point of view, atmosphericchemistry is a challenge due to the coexistence of very stable(e.g. CH4) and very reactive species, e.g. O(1D). To over-come the stiffness issue, associated with the large range oftimescales within a single set of differential equations, ro-bust numerical solvers are necessary. KPP provides severalsolvers with either manual or automatic time step control.1Sandu, A. and Sander, R.: Technical note: Simulating chemi-cal systems in Fortran90 and Matlab with the Kinetic PreProcessorKPP-2.0, Atmos. Chem. Phys., in preparation, 2005.Although computationally more demanding, the latter arebest suited for the most difﬁcult stiffness problems e.g. as-sociated with multiphase chemistry. For each individual ap-plication, it is necessary to balance the advantages and dis-advantages regarding efﬁciency, stability, accuracy, and pre-cision. We found that for most of our chemical mechanisms,Rosenbrock solvers of 2nd or 3rd order (Sandu et al., 1997)work best. However, we stress that it may be necessary totest other solvers as well to achieve the best performancefor a given set of equations. Fortunately, switching betweensolvers is easy with KPP and does not requireany reprogram-ming of the chemistry scheme.There are also other numerical software packages avail-able to integrate these stiff sets of differential equations, e.g.AutoChem (http://pdfcentral.shriver.umbc.edu/AutoChem/),Spack (Djouad et al., 2003), Chemkin (http://www.reactiondesign.com/products/open/chemkin.html), Odepack(http://www.llnl.gov/CASC/odepack/), and Facsimile (Cur-tis and Sweetenham, 1987). We have chosen KPP for ourMECCA model because, as far as we know, it is the onlyprogram that combines the following properties:– The generated chemistry code is suitable for integrationinto larger models.– KPP is capable of producing Fortran95 code.– KPP allows to choose between several numerical inte-grators.– The code is free.2.3 ModularityAn important feature of MECCA is its modular structure.Without any changes to the code, it is possible to linkMECCA to different meteorological base models. This isachieved by strict adherence to the MESSy standard, as de-scribed by J¨ ockel et al. (2005). A major advantage of thismodularity is that it allows extensive testing of the chemicalmechanism in a box model before starting computationallyexpensive global model runs. The box models are easy tohandle. All that is needed is to supply constant values or atime series for temperature, pressure, humidity, and J-valuesof photolysis reactions. At present, MECCA chemistry mod-ules have been coupled to three box models and a 3-D globalgeneral circulation model. Preliminary results are shown inSect. 3.2.4 PortabilityTo ensure maximum portability, the code is written in stan-dard Fortran95 (ISO/IEC-1539-1). It does not depend on anycompiler-speciﬁc language extensions. We have checked thisusing the fortran analyser forcheck (http://www.forcheck.nl/). The system requirements for the MECCA installationare:Atmos. Chem. Phys., 5, 445–450, 2005 www.atmos-chem-phys.org/acp/5/445/R. Sander et al.: The MECCA chemistry module 447Fig. 1. Comparison of the MECCA chemistry (right column) against the Facsimile code of MOCCA (left column). As an example, thetemporal evolutions of O3, OH, and H2O2 are shown.– A Unix or Linux operating system including the stan-dard tools (tcsh, gawk, sed, make, etc.)– A Fortran95 compiler (So far, we have compiledMECCA successfully with GNU, Lahey, Intel, Com-paq, IBM, and NEC compilers)– The KPP software (available in the electronic sup-plement and also at http://www.cs.vt.edu/∼asandu/Software/KPP)– Optional: The netcdf library to obtain output ﬁles innetcdf format (without it, output is made to ascii ﬁles)– Optional: LaTEX to print a table containing the rate co-efﬁcients of the current reaction mechanismwww.atmos-chem-phys.org/acp/5/445/ Atmos. Chem. Phys., 5, 445–450, 2005448 R. Sander et al.: The MECCA chemistry moduleFig. 2. Sample plot showing results of a stratospheric box modelcoupled to MECCA chemistry (J. L. Grenfell, pers. comm., 2004).2.5 AvailabilityWe believe that the scientiﬁc community will beneﬁt mostif MECCA is freely available. Therefore we have put theMECCA code under the GNU public licence (http://www.gnu.org/copyleft/gpl.html). We hope that this leads to a wideacceptance of MECCA as an addition or alternative to com-mercial software like Facsimile. We also hope for feed-back from the community to maintain state-of-the-art soft-ware and chemical kinetics information. The current versionis provided in the electronic supplement together with a usermanual which describes how to install, execute, and mod-ify MECCA on your computer. Future updates will be pro-vided through our web page http://www.mpch-mainz.mpg.de/∼sander/messy/mecca/ for download.3 Results and discussionTo illustrate its versatility, we present here some sample ap-plications of MECCA.3.1 Halogen chemistry in the marine boundary layerSince the reactions of our comprehensive multiphase chem-istry model MOCCA (Sander and Crutzen, 1996; Vogt et al.,1996) have been implemented in MECCA, a comparison ofthese two models is a good start to validate MECCA. Wehave written a box model that provides typical conditions(temperature, pressure, humidity, sea-salt aerosol, and J-values of photolysis reactions) of the marine boundary layerat mid-latitude in spring, similar to MOCCA. From the com-prehensive set of chemical reactions in MECCA, we dis-carded those that occur only in the stratosphere as well asthose of higher hydrocarbons (≥C2). Some results of bothmodel runs are shown in Fig. 1. The similarity is not sur-prising, given the similar reaction mechanisms. It shows thatFig. 3. Comparison between HCHO measured in the MINATROCcampaign and HCHO calculated with MECCA (M. de Reus, pers.comm., 2004). The solid line represents the ideal 1:1 relationship.The dashed line corresponds to a deviation of a factor of two.MECCA with its KPP integrator is capable of handling thevery stiff set of differential equations and of reproducing theresults of MOCCA. Minor differences result from updatedrate constants and slightly different boundary conditions.3.2 Stratospheric chemistryGrenfell et al. (2004)2 have coupled MECCA to a strato-spheric box model to quantify ozone loss via chemical cy-cles and pathways. Some results from a sensitivity study oftheirs, involving the effect of increased water, chlorine andbromine upon stratospheric ozone, are shown in Fig. 2. Forthese calculations, tropospheric reactions were excluded.3.3 Modeling the ﬁeld campaign MINATROCMECCA can also be used to compare ﬁeld data with modelresults. De Reus et al. (2005)3 used measured data of long-lived species from the MINATROC campaign as input forMECCA. For each set of measurements, the model was rununtil HCHO concentrations reached a steady state. The re-sults were compared to observed values of HCHO as shownin Fig. 3. Only for 4 out of 272 data points is the discrepancy2Grenfell, J. L., Lehmann, R., Mieth, P., and Langematz,U.: Chemical reaction pathways affecting stratospheric and meso-spheric ozone, J. Geophys. Res., submitted, 2004.3De Reus, M., Fischer, H., Sander, R., Gros, V., Kormann, R.,Salisbury, G., van Dingenen, R., Williams, J., Z¨ ollner, M., andLelieveld, J.: Reduced trace gas mixing ratios in a dense Saharandust plume, comparison of observations and photochemical box-model calculations, Atmos. Chem. Phys., submitted, 2005.Atmos. Chem. Phys., 5, 445–450, 2005 www.atmos-chem-phys.org/acp/5/445/R. Sander et al.: The MECCA chemistry module 449between measured and modeled data larger than a factor oftwo, which is approximately the total uncertainty of all mea-sured parameters used as input for the model calculations.Obviously, much of the measured variability in HCHO is as-sociated with irregular ambient conditions, which is difﬁcultto capture by a model. Nevertheless, the comparison in Fig. 3suggests that systematic model biases are low.3.4 Global chemistryBox models allow quick sensitivity studies of the selectedchemical mechanism. Often, however, regional or globalstudies are desired. Therefore we have coupled the MECCAmechanism via the MESSy interface to the general circula-tion model (GCM) ECHAM5 (http://www.mpimet.mpg.de/en/extra/models/echam/echam5.php). In this setup, MECCAcalculates all chemical processes, whereas the GCM inte-grates the non-chemical sources and sinks (e.g. advection,convection, dry deposition, sedimentation, ...) of thesespecies. In Fig. 4 we show results to illustrate how the tro-pospheric halogen chemistry described above can also beapplied on a global scale (Kerkweg et al., in preparation,20054). Of course, other subsets of the MECCA mechanism(e.g. stratospheric chemistry or very condensed schemes forextended climate studies) can also be selected in global ap-plications.4 ConclusionsIn this technical note, we present the versatile modelMECCA. Its chemical and numerical ﬂexibility, its modu-larity, and its portability make it an ideal tool for many ap-plications. The scheme is publicly available for atmosphericchemistry and climate research.Acknowledgements. We are grateful to A. Sandu for providing theKPP software which made the development of MECCA possible.We would also like to thank R. von Glasow and R. von Kuhlmannfor making their KPP chemistry codes available.Edited by: M. DamerisReferencesAtkinson, R., Baulch, D. L., Cox, R. A., Crowley, J. N., Hamp-son, R. F., Hynes, R. G., Jenkin, M. E., Rossi, M. J., and Troe, J.:Evaluated kinetic and photochemical data for atmospheric chem-istry: Volume I – gas phase reactions of Ox, HOx, NOx and SOxspecies, Atmos. Chem. Phys., 4, 1461–1738, 2004,SRef-ID: 1680-7324/acp/2004-4-1461.4Kerkweg, A. and Sander, R.: Global modeling ofmarine halogen chemistry with the chemistry-climate modelECHAM5/MESSy, Atmos. Chem. Phys., in preparation, 2005.Fig. 4. Sample plot showing preliminary results of chloride en-richment factors EF(Cl) in near-surface sea-salt aerosol. Thecalculations were made with the MECCA chemistry coupled toECHAM5/MESSy. Chloride deﬁcits (i.e. values of EF(Cl)<1) oc-cur where acid displacement has transformed aerosol chloride intogaseous HCl. This occurs mainly in areas where sea-salt aerosolmixes with anthropogenically produced acids such as H2SO4 andHNO3.Curtis, A. R. and Sweetenham, W. P.: Facsimile/Chekmat User’sManual, Tech. rep., Computer Science and Systems Division,Harwell Lab., Oxfordshire, Great Britain, 1987.Damian, V., Sandu, A., Damian, M., Potra, F., and Carmichael,G. R.: The kinetic preprocessor KPP – a software environmentfor solving chemical kinetics, Comput. Chem. Eng., 26, 1567–1579, 2002.Djouad, R., Sportisse, B., and Audiffren, N.: Reduction of mul-tiphase atmospheric chemistry, J. Atmos. Chem., 46, 131–157,2003.J¨ ockel, P., Sander, R., Kerkweg, A., Tost, H., and Lelieveld, J.:Technical Note: The Modular Earth Submodel System (MESSy)– a new approach towards Earth System Modeling, Atmos.Chem. Phys., 5, 433–444, 2005,SRef-ID: 1680-7324/acp/2005-5-433.Meilinger, S. K.: Heterogeneous Chemistry in the Tropopause Re-gion: Impact of Aircraft Emissions, Ph.D. Thesis, ETH Z¨ urich,Switzerland, http://www.mpch-mainz.mpg.de/∼smeili/diss/dissnew.ps.gz, 2000.Sander, R. and Crutzen, P. J.: Model study indicating halogen ac-tivation and ozone destruction in polluted air masses transportedto the sea, J. Geophys. Res., 101D, 9121–9138, 1996.Sander, S. P., Finlayson-Pitts, B. J., Friedl, R. R., Golden, D. M.,Huie, R. E., Kolb, C. E., Kurylo, M. J., Molina, M. J., Moortgat,G. K., Orkin, V. L., and Ravishankara, A. R.: Chemical Kineticsand Photochemical Data for Use in Atmospheric Studies, Evalu-ation Number 14, JPL Publication 02-25, Jet Propulsion Labora-tory, Pasadena, CA, 2003.Sandu, A., Verwer, J. G., Blom, J. G., Spee, E. J., Carmichael,G. R., and Potra, F. A.: Benchmarking stiff ODE solvers for at-mospheric chemistry problems II: Rosenbrock solvers, Atmos.Environ., 31, 3459–3472, 1997.www.atmos-chem-phys.org/acp/5/445/ Atmos. Chem. Phys., 5, 445–450, 2005450 R. Sander et al.: The MECCA chemistry moduleSteil, B., Dameris, M., Br¨ uhl, C., Crutzen, P. J., Grewe, V., Ponater,M., and Sausen, R.: Development of a chemistry module forGCMs: First results of a multiannual integration, Ann. Geophys.,16, 205–228, 1998,SRef-ID: 1432-0576/ag/1998-16-205.Vogt, R., Crutzen, P. J., and Sander, R.: A mechanism for halo-gen release from sea-salt aerosol in the remote marine boundarylayer, Nature, 383, 327–330, 1996.von Glasow, R., Sander, R., Bott, A., and Crutzen, P. J.: Mod-eling halogen chemistry in the marine boundary layer, 1.Cloud-free MBL, J. Geophys. Res., 107D, 4341, doi:10.1029/2001JD000942, 2002.von Kuhlmann, R., Lawrence, M. G., Crutzen, P. J., and Rasch,P. J.: A model for studies of tropospheric ozone and nonmethanehydrocarbons: Model description and ozone results, J. Geophys.Res., 108D, doi:10.1029/2002JD002893, 2003.Atmos. Chem. Phys., 5, 445–450, 2005 www.atmos-chem-phys.org/acp/5/445/

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