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.
Introduction
MECCA (Module Efficiently Calculating the Chemistry of the Atmosphere) is an atmospheric chemistry module
that contains a comprehensive chemical mechanism with tropospheric and stratospheric
chemistry of both the gas and the aqueous phases. For the numerical integration, MECCA
uses the KPP (Kinetic PreProcessor) software
.
To apply the MECCA chemistry to atmospheric conditions, MECCA must be connected to a base
model via the MESSy (Modular Earth Submodel System) interface . This
base model can be a complex 3-dimensional model but it can also be a simple box model.
CAABA (Chemistry As A Boxmodel Application) is such a box model, simulating the
atmospheric environment in which the MECCA chemistry takes place.
A full description of CAABA/MECCA has already been published elsewhere .
Here, we only present new features that have been implemented after version 3.0.
Section describes all changes related to the chemical mechanism of MECCA.
In Sect. we show several new options for calculating photolysis rate
coefficients in the model. Section presents new features that are only
useful when MECCA is coupled to a global (3-dimensional) base model.
The chemical mechanism MECCA
MECCA is a chemistry submodel that contains a comprehensive atmospheric reaction
mechanism. In addition to the basic HOx (OH+HO2),
NOx (NO+NO2), and CH4 chemistry, it also includes
nonmethane volatile organic compounds (NMVOCs), halogens (Cl, Br,
I), sulfur (S), and mercury (Hg) chemistry. Recent extensions of
MECCA are presented in the following sections.
The Mainz Organic Mechanism (MOM)
The MOM is the default oxidation mechanism for volatile organic compounds (VOCs) in
MECCA. The current MOM mechanism is a further development of the versions used by
and . It includes developments from , ,
and . MOM chemistry has been used by to study oxidation
processes in the Mediterranean atmosphere. Figure shows all 43 emitted
species that are treated by MOM. These species are alkanes and alkenes up to four carbon
atoms, ethyne (acetylene), two nitriles, isoprene, 2-methyl-3-buten-2-ol (MBO), five
monoterpenes, and nine aromatics. Most of the oxidation scheme is explicit. Lumping is
used for some isomers with similar properties, e.g., the MOM species “LXYL” presents
the sum of o-, m-, and p-xylene. All lumped species are marked by the prefix “L”
in their names. The full mechanism includes about 600 species and 1600 reactions. A list
of all chemical reactions, including rate coefficients and references, is available in
the Supplement
().
Emitted VOCs treated by MOM.
The mechanism for the isoprene oxidation was developed starting from MIM2 ,
which is a reduction of MCM v3.1 (Master Chemical Mechanism; ). The
major mechanisms that regenerate OH under low-NOx conditions are
included. OH addition to the unsaturated isoprene hydroperoxides has been implemented
yielding, entirely, epoxydiols and OH according to . The Z-1,4- and
Z-4,1-ISOPO2 isomers undergo 1,6-H-shifts as originally proposed by . In
MOM, the corresponding rate coefficients are those computed by , and the
66 % yields of isoprene-derived hydroperoxyenals (HPALDs) are according to
. For the non-HPALD-yielding channel, the corresponding mechanisms proposed
by and have been included but in a simplified manner. The
estimated photo-induced cascade of reactions produces substantial amounts of OH
(see Sect. ). Finally, methacrolein (MACR) oxidation has been implemented
according to , except for the fate of the methylvinyl radical. The rate of
the 1,4-H-shift for the MACRO2 radical is now calculated using the expression reported by
.
Oxidation of the two important terpenes, α-pinene and
β-pinene, is based on MCM . However, important
modifications following the theoretical work of L. Vereecken have been
implemented with some simplifications . For
instance, minor channels of the OH- and O3-initiated
oxidation are neglected.
Aromatics (benzene, toluene, xylenes) are oxidized in the mechanism by ,
which is to a large extent a reduction of the corresponding MCM .
Photolysis of ortho-nitrophenols yielding HONO has been added according to
and . Finally, reactions of phenyl peroxy radicals with
NO2 yielding NO3 have been added, consistent with .
Oxidation of VOCs by O3 and NO3 is similar to that in
MCM. The oxidation by OH, however, significantly differs from MCM
treatment and therefore is detailed in the next section.
VOC reactions with OH
Reactions of OH with organic molecules can be either H abstraction or
OH addition. If available, experimental rate coefficients are preferred and taken
mostly from the IUPAC kinetic data evaluation . Unmeasured rate
coefficients for the C1 to C5 species are estimated with a site-specific
structure–activity relationship (SAR) similar to MCM, based on the work of
and . The base rate coefficients for OH addition to double bonds are
taken from the more recent SAR by . For the C6 to C11
closed-shell species, the MCM rate coefficients are retained. It is worth noting that the
SAR-estimated ones have no temperature dependence and are only given at 298 K. The
effect of neighboring groups is expressed by substituent factors and is differentiated by
functional group. Most substituent factors by are updated or calculated ex
novo by computing the relative rate coefficient of OH with the simplest VOC
bearing the substituent relative to the one of its parent compound
(Table ). A clear limitation of this approach is that for OH
addition, no substituent effect on the branching ratios is considered. No rigorous
evaluation of the SAR has been conducted and the estimation uncertainty is expected to be
in the same range as for the SAR used by MCM.
Structure–activity relationship (SAR) parameters and substituent factors in MOM, largely based on
for H abstraction and on for OH addition,
unless noted otherwise. Most base rate constants and substituent
factors are updated with data from . Original values for
the substituent factors given by are listed in
parentheses. All rate constants refer to reactions with OH.
k for H abstraction by OH in cm-3s-1kp (primary)4.49×10-18×(T/K)2×exp(-320K/T)ks (secondary)4.50×10-18×(T/K)2×exp(253K/T)kt (tertiary)a2.12×10-18×(T/K)2×exp(696K/T)k (hydroxylic)2.1×10-18×(T/K)2×exp(-85K/T)k (carboxylic)0.7×4.0×10-14×exp(850K/T)=0.7×kCH3CO2Hk (hydroperoxidic)0.6×5.3×10-12×exp(190K/T)=0.6×kCH3OOHSubstituent factors F(X)F(-CH2-)1.23 (1.23)F(>CH-)1.23 (1.23)F(>C<)1.23 (1.23)Fsec(-OH)3.44 (3.50)(kCH3CH2OH→CH3CHOH)/ksFtert(-OH)2.68 (3.50)k2-propanol-2kp-kROH→ROk2-methylpropane-3kpFsec(-OOH)8.00 (-)(kCH3OOH→CH2OOH)/kpFtert(-OOH)8.00 (-)(kCH3OOH→CH2OOH)/kpF(-ONO2)0.04 (0.04)F(-CH2ONO2)0.20 (0.20)F(-C(O)OONO2)0.25 (-)(kCH3C(O)OONO2)/kpFsec(-allyl)3.6b (1.00)kCH2CHCH3→CH2CHCH2kCH3CH2CH3→CH3CH2CH2F(-CHO)0.55 (0.75)kHOCH2CHO→HOCHCHOkpFsec(-OH)F(-COOH)1.67 (0.74)(kCH3COOH→CH2COOH)/kpF(-C(=O)R)0.73 (0.75)(kCH3CHO→CH3CO)/ktF(=O)8.15 (8.70)(kCH3CHO→CH3CO)/ktFprim(-CH2OH)1.29 (1.23)(kCH3CH2OH→CH2CH2OH)/kpFtert(-CH2OH)0.53 (-)(kHOCH2CHO→HOCH2CO)/(ktF(=O))k for OH addition to double bonds in cm-3s-1kadp (primary)4.5×10-12×(T/300K)-0.850.5kC2H4 (high-pressure limit)kads (secondary)1/4×(1.1×10-11×exp(485K/T)0.5kcis/trans-2-butene+1.0×10-11×exp(553K/T))kadt (tertiary)1.922×10-11×exp(450K/T)-kadsk2-methyl-2-butene-kads3.0×10-110.5(k1,3-butadiene-2kadp)5.7×10-110.5(k2,3-dimethyl-1,3-butadiene-2kadp)Substituent factors Fa(X)Fa(-C(O)OONO2)0.56 (-)kMPAN/k2-methylpropeneFa(-CHO)0.31 (0.34)kmethacroleinadd/k2-methylpropeneFa(-C(O)CH3)0.76 (0.90)kMVK/kpropeneFa(-CH2OH)1.7 (1.6)k2-propene-1-ol/kpropeneFa(-CH2OOH)1.7 (-)k2-propene-1-ol/kpropeneFa(>CHOH)2.2 (1.6)k1-pentene-3-ol/k1-penteneFa(>CHOOH)2.2 (1.6)k1-pentene-3-ol/k1-penteneFa(-C(O)OH)0.25 (0.25)Fa(-CH2ONO2)0.64 (0.47)kO2NOCH2C(CH3)=CHCH2OHFa(-CH2OH)k2-methyl-2-butene
a There is a sign error in who present the value
exp(-696K/T) instead of exp(696K/T).
b Median value from the range calculated by .
The general formulae for H abstraction by OH are
1k(CH3X)=kp⋅F(X),2k(CH2XY)=ks⋅F(X)⋅F(Y),3k(CHXYZ)=kt⋅F(X)⋅F(Y)⋅F(Z),
where kp, ks, and kt are the group rate
coefficients for the hydrogens on the primary, secondary, and tertiary carbon atoms,
respectively, and F(X) is the factor for the substituent X.
The SAR for OH addition to (poly)alkenes is based on the hypothesis that the
site-specific rate coefficient depends solely on the stability of the radical product
. Thus, rate coefficients for the formation of primary, secondary, and
tertiary radicals are derived from the high-pressure limits for ethene, 2-butene, and
2,3-dimethyl-2-butene, respectively. It is worth noting that for the tertiary radical
formation, solely used the rate coefficient for 2,3-dimethyl-2-butene and
not that for 2-methyl-2-butene minus that for the secondary radical.
RO2 reactions with NOx and NO3
Reactions with NO are the dominant sink for RO2 under polluted conditions.
The RO2-size independent MCM rate coefficient is used with the exception of
CH3O2 and CH3CH2O2, for which the IUPAC recommendations are followed
. In general, the two possible reaction channels are considered:
R1RO2+NO→(1-α)×(RO+NO2)R2→α×RONO2
with α being the yield for the formation of
alkyl nitrates, which curb tropospheric ozone production. Acyl RO2 do not form
nitrates. The CH3ONO2 yield is calculated according to with a
reduction according to . The CH3CH2ONO2 yield is calculated
according to . For all other peroxy radicals, the corresponding alkyl nitrate
yields are calculated with the relationship by , which depends on
temperature, pressure, and molecular size. However, the latter is not represented by the
number of carbon atoms but by the number of heavy atoms (excluding the -OO moiety)
according to . The oxygen atom in β-carbonyl RO2 is not
counted. Due to disagreement in the literature, no dependence of α on the degree
of RO2 substitution (primary, secondary, and tertiary) is considered. Reduction
factors for β- and γ-carbonyl RO2 are derived from and
for bicyclic RO2 from aromatics are derived from . As an example,
Fig. shows the predicted variable yield for the nitrate of the
secondary hydroxy butyl peroxy radical.
Temperature- and pressure-dependent nitrate yield for the
secondary hydroxybutyl peroxy radical obtained and calculated by MOM. A
constant yield of about 10 % (“Old model”) is used by MCM.
Formation and decomposition of many peroxy nitrates is considered. The equilibria of acyl
peroxy nitrates with their parent RO2 are represented as in MCM but the
JPL (Jet Propulsion Laboratory) kinetic data are used. Only
three alkyl peroxy nitrates – CH3O2NO2, CH3CH2O2NO2, and
CH3COCH2O2NO2 – are represented. The equilibrium reactions for the latter are
taken from , , and . Reactions of peroxy radicals
with NO3 all produce the corresponding alkoxy radical and NO2:
RO2+NO3→RO+NO2+O2.
The temperature-independent rate coefficient of
k(C2H5O2+NO3)=2.3×10-12cm-3s-1 is used for all RCH2O2. For acyl
peroxy radicals, an enhancement factor of k(CH3C(O)OO+NO3)/k(C2H5O2+NO3)=1.74 is calculated based on the peroxy
acetyl radical.
RO2 reactions with HOx
HO2 reactions are often competitive with NO reactions of peroxy radicals.
The former reactions are known to proceed via three channels:
R4RO2+HO2→RO+OH+O2,R5→ROOH+O2,R6→ROH+O3,
of which only the first is a radical-propagating channel. Alkyl peroxy radicals cannot
have the O3 channel and their rate coefficient is calculated as a function of the
number of carbons according to the fitting formula provided by and
. The branching ratios of the OH channel for β-carbonyl, alkoxy,
and bicyclic peroxy radicals are taken from , , and ,
respectively. A 10 % OH yield for reactions of β-hydroxyl peroxy radicals
is taken from the isoprene oxidation study of , which is consistent with the
results of and . The HO2 reaction of the simplest acyl
peroxy radical (CH3CO3) has unique branching ratios as determined by direct
OH and O3 measurements . For all other acyl peroxy radicals,
the kinetic data for β-hydroxy acyl peroxy radicals, e.g., HOCH2CO3, are
taken from with the rate coefficient having the temperature dependence as
recommended by IUPAC.
There is laboratory evidence for a non-negligible reaction of
CH3O2 with OH:
CH3O2+OH→CH3O+HO2.
The lower limit of the rate coefficient 1.4×10-10cm-3s-1
reported by is used in MOM. This is consistent with the revised experimental
value by the same laboratory . The major reaction channel involving
HO2 elimination represents (80±20) % and is set as the only channel
. The other possible channels are very uncertain and are therefore not
included.
RO2 permutation reactions
Second-order rate constants k2nd for permutation
reactions (in cm-3s-1). Here, kCH3O2=1.03E-13×exp(365K/T)cm-3s-1 is
for the self reaction of CH3O2.
Variablek2nd=2×kRO2×kCH3O2based onreferencek_RO2RCO32×2E-12×exp(500K/T)CH3CO3+CH3O2Alkyl radicals (unsubstituted, >C3) k_RO2pRO22×1E-12×kCH3O2RO2=(CH3)2CHCH2O2k_RO2sRO22×1.6E-12×exp(-2200K/T)×kCH3O2RO2=i-C3H7O2k_RO2tRO22×3.8E-13×exp(-1430K/T)t-C4H9O2+CH3O2Alkyl radical with either O or Cl in βk_RO2pORO22×7.5E-13×exp(500K/T)CH3COCH2O2+CH3O2k_RO2sORO22×7.7E-15×exp(1330K/T)×kCH3O2RO2=CH3CH(OH)CH(O2)CH3k_RO2tORO22×4.7E-13×exp(-1420K/T)×kCH3O2RO2=(CH3)2C(OH)CO2(CH3)2Allyl- and β-hydroxy alkyl radicals k_RO2LISOPACO22×(2.8E-12+3.9E-12)/2×kCH3O2RO2= ISOPAO2 and ISOPCO2k_RO2ISOPBO22×6.9E-14×kCH3O2RO2= ISOPBO2k_RO2ISOPDO22×4.8E-12×kCH3O2RO2= ISOPDO2
The self and cross reactions of organic peroxy radicals are treated according
to the permutation reaction formalism in MCM . Every organic
peroxy radical reacts in a pseudo-first-order reaction with a rate
coefficient that is expressed as
k1st=2×kRO2×kCH3O2×[RO2],
where kRO2 is the second-order rate coefficient of the self reaction of the
organic peroxy radical, kCH3O2 is the second-order rate coefficient of the
self reaction of CH3O2, and [RO2] is the sum of the concentrations of
all organic peroxy radicals. The formalism is a simplification of the approach by
under the assumption that the dominant co-reactant of RO2 is
CH3O2. The value of kCH3O2 is taken from the IUPAC
recommendations. Expressions for kRO2 distinguish acyl from alkyl peroxy
radicals. The latter are differentiated by the degree and kind of substituents close to
the -OO moiety. The rate expressions (Table ) are not from MCM, except for
β-hydroxyl radicals, and have a temperature dependence.
Photo-induced reactions
The enhanced photolysis of carbonyl nitrates from isoprene is implemented according to
and . The enhancement is applied to the photolysis rate
coefficients (j values) of nitrooxyacetone (NOA), nitrooxyacetaldehyde
(NO3CH2CHO), lumped nitrates of methyl ethyl
ketone (LMEKNO3), nitrates of MVK (methyl vinyl ketone) and MACR, and
unsaturated C5-nitrooxyaldehyde from the isoprene +NO3 reaction.
Keto–enol tautomerization of aldehydes induced by light absorption is implemented based
on data for acetaldehyde . The enols are in equilibrium with the
corresponding aldehydes by HCOOH catalysis . Formic acid is then
produced upon reaction of the enols with OH similarly to the simplest enol
. Vinyl alcohol is also produced in the photolysis of propanal.
Photolysis of HPALDs is according to and and
the subsequent photolysis of the resulting carbonyl enols HVMK
(hydroxy vinyl methyl ketone) and HMAC (3-hydroxy-2-methyl-acrolein) is
treated according to and .
Nitrophenols undergo photolysis yielding HONO, according to
and , and assumed co-products being cyclic
ketenes. However, the OH-formation channel is not
implemented.
Conjugated unsaturated dialdehydes (like butenedial and
2-methyl-butenedial resulting from the oxidation of isoprene and
aromatics) undergo photolysis based on and MCM. Only the
major channel, CO loss, is considered, and the j values are
scaled with j(NO2). The ketenes from photolysis of
hydroperoxyacetyl-conjugated unsaturated aldehydes from isoprene,
conjugated unsaturated dialdehydes and nitrophenols undergo
photodissociation yielding CO and an excited Criegee intermediate. The
j value is assumed to be the same as that for MVK with a unity quantum
yield.
Other chemical mechanisms
In addition to the native chemistry mechanism of MECCA (available in the file
), several other independent mechanisms are now provided as well. The
chemical mechanisms CB05BASCOE and MOZART from the Copernicus Atmosphere Monitoring
Service project (CAMS 42) and the Jülich Atmospheric Mechanism (JAM002) have been
converted to KPP format and introduced into MECCA. It is also possible to use our
previous simple mechanism MIM1 . In addition, chemical mechanisms extracted
and downloaded from the MCM web page can be converted with a script that makes them
compatible with CAABA/MECCA. All mechanisms are suitable for stratospheric as well as
tropospheric calculations. They all include the chemistry of chlorine, bromine, and
isoprene. They differ in the treatment of terpenes. MIM1 has no terpenes at all.
CB05BASCOE and MOZART include terpenes as a lumped species. Only MCM, MOM, and JAM002
treat some terpenes individually, e.g., pinene. The JAM002 mechanism is larger than
CB05BASCOE and MOZART but small compared to MECCA with MOM. The very detailed MCM is the
largest of all. More information about the chemical mechanisms is provided in the
following sections.
Intercomparison of the MOM (black),
CB05BASCOE (red), MOZART
(green), MIM1 (blue), MCM
(magenta), and JAM002 (cyan) mechanisms. The
simulations represent the boundary layer over the Amazon forest.
They start on 1 August at midnight and last for 5 days. Temperature,
pressure, and relative humidity are set to 301 K, 101 325 Pa, and
70 %, respectively. The model is initialized with 2 nmol mol-1
isoprene (C5H8), 500 pmol mol-1 of terpenes (MOM: 100 pmol mol-1 of α-pinene, β-pinene, camphene, carene, and
sabinene each; CB05BASCOE and MOZART: lumped terpenes; MIM1: no
terpenes; MCM and JAM002: 200 pmol mol-1α-pinene and 300 pmol mol-1β-pinene), and 100 pmol mol-1 PAN. During the
model simulation, emissions of NO are set to
3.3×10-9cm-2s-1.
CB05BASCOE
The CB05BASCOE scheme is a merge of a tropospheric and stratospheric
chemistry scheme. The tropospheric chemistry is based on the Carbon Bond mechanism 2005
CB05,. Here, a lumping approach is adopted for organic species by
defining a separate tracer species for specific types of functional groups. The scheme
has been modified and extended to include an explicit treatment of C1 to
C3 species , SO2, dimethyl sulfide (DMS), methyl sulfonic
acid (MSA), and ammonia (NH3), as described by . The reaction rates
follow the recommendations given in either the JPL or IUPAC evaluation .
The stratospheric chemistry is based on that from the BASCOE (Belgian Assimilation System
for Chemical ObsErvations) system and is labeled “sb15b”. This chemical
scheme merges the reaction lists developed by to produce short-term
analyses, with the list included in the SOCRATES 2-D model for long-term studies of the
middle atmosphere . The list of species includes all the ozone-depleting
substances and greenhouse gases necessary for multidecadal simulations of the couplings
between dynamics and chemistry in the stratosphere, as well as the reservoir and
short-lived species necessary for a complete description of stratospheric ozone
photochemistry. Gas-phase and heterogeneous reaction rates are taken from the JPL
evaluations 17 and 18 . The merged reaction mechanism includes 99
species interacting through 211 gas-phase and 10 heterogeneous reactions. Details
regarding its implementation and evaluation within the ECMWF Integrated Forecasting
System (IFS) are given by . The complete mechanism of CB05BASCOE (species and
equations) can be found in the directory in the Supplement.
MOZART
The tropospheric chemistry in MOZART (Model of OZone And Related Tracers) is based on the
MOZART-3 mechanism by . It includes additional species and reactions from
MOZART-4 and further updates from the Community Atmosphere Model with
interactive chemistry, referred to as CAM4-chem . The chemical mechanism
includes an updated isoprene oxidation scheme and a better treatment of volatile organic
compounds, with lumped species to represent large alkanes, alkenes, and aromatic
compounds as well as their oxidation products. Overall, it includes the degradation of
C1, C2, C3, C4, C5, C7, and C10
species. The heterogeneous chemistry in the troposphere is implemented according to the
corresponding module from CB05BASCOE. MOZART includes the extended stratospheric
chemistry discussed by with further updates from CAM4-chem . This includes detailed gas-phase halogen chemistry of chlorine and bromine. The
stratospheric chemistry accounts for heterogeneous processes on liquid sulfate aerosols
and polar stratospheric clouds, following the approach of . The complete
mechanism of MOZART (species and equations) can be found in the directory
in the Supplement. Overall, the MOZART mechanism includes 117
gas-phase species, 65 photolysis reactions, and 247 gas-phase reactions. Rate
coefficients are taken from the JPL recommendations .
JAM002
Version 2 of the Jülich Atmospheric Mechanism (JAM002) has been implemented in the
ECHAM-HAMMOZ chemistry–climate model . It is a blend of the stratospheric
chemistry scheme of the Whole Atmosphere Chemistry Climate Model WACCM;
and version 4 of the tropospheric MOZART model . The combined chemistry
scheme of WACCM and MOZART has been enhanced with a detailed representation of the
oxidation of isoprene following the Mainz Isoprene Mechanism 2 MIM2; ,
and by adding a few primary volatile organic compounds and their oxidation chains. The
isoprene oxidation scheme includes recent discoveries of 1,6 H-shift reactions
, the formation of epoxide , and the photolysis of HPALDs
. Some of the reaction products and rates were taken from MCM .
Radical–radical reactions have been substantially revised since . In
contrast to MCM, JAM002 does not use a radical pool but instead follows the pathways of
peroxy radical reactions with HO2, CH3O2, and CH3COO2 (peroxy
acetyl) as explicitly as possible. Inorganic tropospheric chemistry considers ozone,
NO, NO2, NO3, N2O5, HONO, HNO3,
HNO4, HCN, CO, H2, OH, HO2, H2O2,
NH3, chlorine and bromine species, SO2, and oxygen atoms. The complete
mechanism of JAM002 (species and equations) can be found in the directory
in the Supplement. In total, JAM002 contains 246 species and 733
reactions, including 142 photolysis reactions. Detailed information can be found in
.
Master Chemical Mechanism (MCM)
The MCM describes in detail the tropospheric degradation of more than a
hundred VOCs . It is widely used as the reference mechanism
for modeling studies of atmospheric processes. Although the standard organic
chemistry mechanism in MECCA (MOM, described above) is sufficient for many
model applications, a more explicit mechanism can be necessary when studying
specific VOCs. For example, the fate of limonene (C10H16)
emitted from boreal forests is not included in the standard MECCA mechanism.
To use MCM reactions inside MECCA, the new tool has been
added. It converts a subset extracted from the MCM web page
(http://mcm.leeds.ac.uk/MCM; last access: 26 March 2019) to a KPP
equation file that is compatible with MECCA. The user manual provides a
detailed description of this new tool.
Simplified example list of species with overall interaction
coefficients (OICs). The full mechanism includes all species; the
skeletal mechanisms s1, s2, and s3 only include species above a
certain OIC threshold. Targets with OIC =1 are always
included. The color coding of the skeletal mechanism (used also in
Fig. ) shows in which mechanism a species
occurs. For example, orange is used for species that are included
in the full mechanism and in s1 but not in s2 and s3.
Skeletal reduction of terpene chemistry in the MOM reaction
scheme (only C10 species are shown here). Vertex colors
and OIC values correspond to those in Table ; only the
green and yellow species are kept in the reduced mechanism.
Mechanism intercomparison
Having several mechanisms implemented in the same modeling system enables mechanism
intercomparison studies under exactly the same conditions. This approach ensures that any
resulting differences come from the chemical mechanism, not from any other parts of the
model. We have performed such an intercomparison for MOM, CB05BASCOE, MOZART, MIM1,
JAM002, and a comparable subset of MCM. Details about these model runs and the results
for all species are available in the directory in the Supplement.
Some representative results are shown in Fig. . All mechanisms show a very
similar decay of the initial isoprene because they all use similar rate constants for the
main reactions of isoprene with ozone, OH and NO3. In contrast, the results for
the terpenes differ. In CB05BASCOE and MOZART, the rate constants for the lumped terpenes
are taken from α-pinene. In the other mechanisms, β-pinene (and other
terpenes) are considered individually. Since β-pinene reacts with ozone much slower
than α-pinene, the explicit treatment of β-pinene in the mechanism leads to
a slower decay of the terpenes than in the lumped mechanisms. With respect to
peroxyacetyl nitrate (PAN), CB05BASCOE especially shows very different values during the
first day of the simulation. The calculated diurnal cycles of ozone, OH, and
NO2 are similar for all mechanisms but their absolute values vary; highest
concentrations are produced by MIM1 and MCM, and the lowest by CB05BASCOE and JAM002. MOM
and MOZART are in between.
It is interesting to compare our results to a mechanism intercomparison study
conducted about 10 years ago by , who partially used predecessors
of the mechanisms in our code. They found significant differences for both
PAN and isoprene. Using the present-day versions of the mechanisms, we still
see differences for PAN but very similar results for isoprene.
Skeletal mechanism reduction
In the area of fuel combustion research, chemical models require highly complex
mechanisms to describe ignition, flame propagation, and other properties. In order to
save computing time, several methods have been developed to create a simplified chemical
mechanism (called skeletal mechanism), which still produce similar results as the full
mechanism e.g.,. One of these methods is DRGEP (Directed Relation Graph
with Error Propagation), which was introduced by and implemented into the
MARS (Mechanism Automatic Reduction Software) model by and . The
DRGEP code from MARS has been implemented in CAABA/MECCA, making the skeletal reduction
method available for atmospheric chemistry mechanisms. The most important quantities of
DRGEP are briefly explained below; full details can be found in .
Targets:
Important chemical species, for which the skeletal
mechanism has to produce similar results as the full mechanism.
Sample points:
A set of environmental conditions (temperature,
pressure, concentrations of chemical species) simulated by the
chemistry model.
Interaction coefficients (DIC, PIC, OIC):
The importance of
chemical species in a mechanism is defined in terms of several
interaction coefficients. The direct interaction coefficient (DIC)
describes the importance of one species for another, based on its
normalized contribution to production/consumption rates through
reactions involving both species. Then, a graph search calculates a
path interaction coefficient (PIC) based on the product of direct
interaction coefficients along the path from target to species, where
nodes represent species and weighted directed edges represent DICs.
Finally, the overall interaction coefficient (OIC) is the maximum of
all PICs between target and species. It is calculated for all sample
points and expressed as a value between 0 (unimportant) and 1
(important). For targets, OIC =1 by definition. OIC values are only
calculated for the full mechanism.
Error δskel:
A normalized value describing the
error when using a skeletal mechanism instead of the full mechanism. A
skeletal mechanism is suitable if δskel<1 for all
targets and sample points. To allow individual weighting, the
calculation of δskel depends on a target threshold
AbsTol and a maximum acceptable relative tolerance
RelTol, which are defined for all targets:
δskel=max(xskel,AbsTol)max(xfull,AbsTol)-1/RelTol,
where xfull and xskel are the mixing ratios
calculated with the full and the skeletal mechanism, respectively.
OIC threshold εep:
A chemical species is
considered important if OIC(species) >εep. The
final εep calculated by DRGEP is the maximum value
for which δskel<1 still holds.
To test the skeletal mechanism generation, we chose HCHO, HO2,
NO, O3, and OH as targets, allowing a relative
tolerance of RelTol=20 % for mixing ratios above a threshold
of AbsTol=1 pmol mol-1. Sample points were extracted from
a global atmospheric chemistry simulation with a setup similar to that
presented by . The chemical compositions were taken from several
boxes at two altitudes (at the surface and at about 1 km). As we want the
skeletal mechanism to perform well not only at typical concentrations of the
targets but also when they are very high or very low, we picked boxes where
the targets reach their minimum, average, or maximum concentrations,
respectively. This resulted in the generation of 30 sample points (5 targets
times (min/ave/max) times 2 altitudes), covering a wide range of values. The
full mechanism contained the complete set of species from MOM
(Sect. ). To illustrate the mechanism, the subset describing
terpene chemistry is shown in Fig. . The importance
(OIC values) of a few selected species is shown in Table . Three
skeletal mechanisms (s1, s2, s3) were generated, reducing the number of
species from 663 in the full mechanism to 462, 429, and 411, respectively.
The number of reactions was reduced from 2091 to 1444, 1320, and 1262,
respectively. The third skeletal mechanism (s3) was rejected because it did
not fulfill the criterion δskel<1. Results obtained with
the full mechanism and with s2 were compared in a global simulation, as
described below in Sect. .
Kinetic and isotope tagging
We have updated the sub-submodel MECCA-TAG , which had been introduced in
version 3.0 of CAABA. Several improvements to the kinetic tagging technique were
implemented. These new features include the following.
Selectable composition transfer mode. Depending on the research
question, prescribed-, molecular-, or element-weighted composition
transfer may be selected. These modes determine the shares with which
each reactant contributes to the products in the tagged chemical
reactions: according to user-specified weightings, proportional to the
reacting molecules count, or following the given element (e.g., C or
H) content, respectively. Whilst the latter mode is intrinsic to
isotope tagging, the others may be used for custom tagging
configurations, e.g., product yield calculations.
Diagnostics for unaccounted production or loss of elemental composition. MECCA-TAG optionally adds passive diagnostic species to
the tagged reactions with unbalanced transfer of the element of
interest. This helps to quantify the amount of atoms the chemical
mechanism receives from or loses to “nothing”, including the isotope
composition of such mass-balance violations.
The new “class shifting” tagging mode. This mode allows for
migration of molecules between the tagging classes in specified
reactions, which allows for quantifying various exchange processes in the
mechanism. For instance, one can distinguish oxidation generations: in
reactions with given oxidants the products become “promoted” to the
tagging class of the next oxidation generation. Another application of
“class shifting” is quantifying the efficiency of recycling chains.
In essence, such is the “online” implementation of the approach
similar to that of , with the number of tagging classes
defining the maximum of the recycling sequences it is possible to
follow.
The range of MECCA-TAG applications was extended with new tagging
configurations.
Radiocarbon configurations. These facilitate simulating the
14C content in a desired set of species, including the
routines for calculating abundances using conventional units like pMC
(percent Modern Carbon).
Hydrogen isotope chemistry. Now MECCA-TAG allows for tracing pathways
of H transfer between the species in the mechanism. Furthermore, D/H
isotope chemistry (including relevant kinetic isotope effects for
HOx and C1–C2 chemistry) are included. The
configuration and calculations of the composition transfer were
extended with the possibility to specify isotope branching ratios
necessary for the consistent D/H kinetics simulations. Both H transfer
and D/H chemistry are currently evaluated in stratospheric setups of
CAABA .
O2clumped isotope chemistry. Simulation of nonstochastic
distributions of 18O18O and 17O18O
isotopologues (Δ36 and Δ35 signatures) resulting
from O(3P)-mediated temperature-dependent isotope exchange
kinetics.
There are also some changes in the implementation and software requirements.
There is no “doubling” mode anymore for evaluating the results of the
optimized tagging. Performing kinetic tagging of the chemical mechanism with
MECCA-TAG requires the Free Pascal Compiler (fpc,
https://www.freepascal.org/, last access: 26 March 2019, version ≥2.6) at the time the script is run. The sub-submodel files are
located in the directory of the distribution. The directory
contains tagging configuration control files
(). The option to tag a newly created chemical mechanism is
available in the script (also via batch files). Further details
about the MECCA-TAG code development can be found in the file
within the CAABA distribution.
Photolysis
CAABA contains several submodels that provide photolysis rate coefficients j, also
called “j values”. The simple submodels READJ and SAPPHO have already been described
by . READJ has not changed since version 3.0. SAPPHO photolysis rates can now
be scaled using a common enhancement factor “efact” for all photolysis rates. This has,
for instance, been used to simulate the very bright conditions within a cloud top
. The updated and new photolysis submodels JVAL and RADJIMT are described in
the sections below.
JVAL
The submodel JVAL inside the CAABA/MECCA model calculates j values using the method of
. It was first updated to the version described by and then
additional changes were made. Many new photolysis reactions have been added, most of them
related to either species from the MOM mechanism (CH3NO3, CH3O2NO2, CH3ONO, CH3O2, HCOOH,
C2H5NO3, NOA, MEKNO3, BENZAL, HOC6H4NO2, CH3COCO2H, IPRCHO2HCO, C2H5CHO2HCO, C3H7CHO2HCO,
PeDIONE24, PINAL2HCO) or organic halogen compounds (CF2ClCFCl2, CH3CFCl2, CF3CF2Cl,
CF2ClCF2Cl, CHF2Cl, CHCl3, CH2Cl2). Besides, bug fixes were necessary regarding incorrect
temperature dependencies of the ozone and OCS
cross sections in the input data.
RADJIMT
RADJIMT is a new submodel that provides dissociation and ionization rates due
to absorption of light and energetic photoelectrons in the mesosphere and
thermosphere (see Table ). It is part of the upper
atmosphere extension of MESSy initially described by , which was
partly based on the implementations from the middle and upper atmosphere
model CMAT2 . For upper atmosphere simulations with
CAABA, MECCA was extended by the relevant chemical species (electrons and
ions) and reactions (labeled
in ). For the respective literature sources,
see in the Supplement.
New upper atmosphere reactions for which RADJIMT provides j values.
Photodissociation and photoionization due to the absorption of solar X-ray,
EUV (extreme ultraviolet), and UV radiation are calculated using fluxes
from the SOLAR2000 empirical model , the GLOW model , and data
presented by and . Relative partitioning between the possible
products of the ionization process are based on the model of and
.
For solar zenith angles larger than 75∘, the atmospheric column of
each absorbing species is calculated using an approximation of the Chapman
grazing incidence function .
Reaction enthalpies in kJ mol-1 (exothermic chemical heating) are
provided as a product of the relevant chemical reactions when “” is defined in the MECCA batch file. Radiative heating
and cooling is also calculated by the submodel (variable
“”).
As an example, we have performed simulations with CAABA using the MECCA
and RADJIMT submodels. The mechanism was created using the batch file
, which selects reactions of the upper atmosphere
labeled . The model setup in was
used: the temperature was kept constant at 195 K and the pressure was set to 0.5 Pa
(approximately 85 km). The model starts on 1 January. Chemical species were initialized
using the values provided by in their Tables A.6.1 and A.6.2. The default
time step length of 20 min was used. For MECCA and RADJIMT, the default settings were
used. Model-calculated mixing ratios for a few selected species are shown in
Fig. . A comprehensive set of plots is available in
and in the Supplement.
Model-calculated mixing ratios from an upper atmosphere
simulation with MECCA and RADJIMT: diurnal cycles for 4 January
(after 3 days of spinup) for the Equator (black) and a latitude of
50∘ N (red). Time is in hours with local noon at 12.
See Sect. for further details.
DISSOC
The new MESSy submodel DISSOC is based on the photolysis scheme by . Briefly,
it calculates a table of the so-called enhancement factor, which is basically the ratio
of the actinic flux at a specific location to the solar irradiance at the top of the
atmosphere. The enhancement factor depends on the pressure level, solar zenith angle, and
wavelength. Input data are the solar irradiance at the top of the atmosphere, absorption
cross sections, and ozone and oxygen profiles. For the implementation into global models,
the input profiles are allowed to be latitude dependent, which increases the dimensions
of the enhancement factor table from 3 to 4. Photolysis rates are calculated from the
tabulated enhancement factor as a wavelength integral over the product with the
absorption cross sections. The calculation is formulated in spherical geometry, such that
it can be also applied to zenith angles above 90∘. Rayleigh scattering is
calculated based on . Absorption cross sections are taken from the current
JPL recommendations .
The code was first implemented by and coupled to a stratospheric
chemistry-box model . improved the treatment of the diffuse
actinic flux and corrected an implementation error of . The extension to the
use of multiple latitudes was introduced within the development of the model CLaMS
. The possibility to calculate diurnally averaged photolysis rates was
introduced for the simplified fast chemistry setup used in multi-annual CLaMS simulations
.
In the current configuration, DISSOC determines the photolysis rates for 38
photolysis reactions that are primarily of relevance in stratospheric
chemistry. A standard setup contains 36 pressure levels, 18 latitude bins,
and 28 solar zenith angle bins (of which 8 are above 90∘). Of the 203
standard wavelength intervals between 116 and 850 nm, typically only
the 159 intervals above 175 nm are used for tropospheric and
stratospheric applications.
MECCA in the MESSy modeling system
Apart from using MECCA inside the CAABA box model, it is also possible to connect MECCA
chemistry to a trajectory or global 3-dimensional model via the MESSy infrastructure
. Recent developments of MECCA shown in this section are related to its
implementation inside MESSy.
TRAJECT
The TRAJECT submodel by allows for simulations of atmospheric chemistry
along precalculated Lagrangian trajectories. For this purpose, the air parcel simulated
by CAABA is moved through space and time along a trajectory taken from an external input
file, while simulating atmospheric photochemistry with MECCA and JVAL. More generally,
TRAJECT allows us to prescribe physical boundary conditions for CAABA box model
simulations. A typical application is the simulation of atmospheric trajectories (balloon
measurements or backward trajectories). However, laboratory conditions (e.g., in a flow
reactor) can also be prescribed. The previous TRAJECT version, described by ,
has been updated. The output is now more consistent with the trajectory input file, as
physical information is now written out beginning with the first time step instead of the
second. In general, an integration time step of chemical kinetics is always performed
with the physical parameters given for the end of the time step. In that way, the mixing
ratios written out at the end of a time step are consistent with the physical conditions
at that point. Also, solar zenith angle and local time at the end of a time step are now
consistent with the given longitude and latitude for that trajectory point.
In addition to the trajectory input file, an external input file with j values for
NO2 can be used to scale all j values with the factor
jfac=j(NO2,external)j(NO2,JVAL).
To facilitate the analysis of the scaling impact, jfac is now
written to output. Scaling thresholds have been implemented to prevent
artifacts that would occur when j(NO2,JVAL) is very small
and the calculation of jfac approaches a division by zero.
PolyMECCA/CHEMGLUE
In a standard global model simulation, the MESSy submodel MECCA contains
one chemical mechanism that is used for all grid boxes. This ensures a
consistent chemistry simulation from the surface to the upper
atmosphere. However, in some cases, it may be preferable to allow
different mechanisms in different boxes, e.g., terpene chemistry only in
the troposphere and ion chemistry only in the mesosphere.
With the script , several independent chemical MECCA
mechanisms can be produced. The first mechanism has the name
“”, as usual. Additional mechanisms are labeled with a
three-digit suffix. For example, the code of mechanism 2 is contained in
and related files.
To select an appropriate mechanism at each point in space and time, the MESSy submodel
CHEMGLUE has been written. The name of the submodel was chosen because CHEMGLUE can also
glue together different chemical mechanisms at the border where a chemical species is
included in one mechanism but not in the other. CHEMGLUE defines the new channel object
“”, which contains the mechanism number for each grid point. These
values can either be selected statically, e.g., depending on the model level number or
the sea–land fraction mask. Alternatively, a dynamic (time-dependent) selection based on
chemical or meteorological variables is possible, e.g., pressure, temperature, or the
concentrations of ozone or isoprene.
Note that even when different boxes of a global model simulation use
different chemistry mechanisms, the set of tracers contains all species
from all mechanisms for all boxes.
The implementation ensures binary identical results when one chemical
mechanism (“”) is replaced by two identical copies of it
(“” and “”).
Results of the global comparison between the FULL, POLY, and
SKEL mechanisms (see Sect. for details). Shown
are surface mixing ratios of ozone (a, c, e) and isoprene (b, d, f) at the end of the simulation,
i.e., after one month.
Panels (a) and (b) show results obtained with the FULL chemistry mechanism.
Panels (c) and (d) compare POLY to FULL, and panels (e) and (f) compare SKEL
to FULL.
For a more realistic test, we created two different chemical mechanisms for
organics. In the first mechanism, only the oxidation of methane is considered, and all
nonmethane hydrocarbons are neglected. The second (FULL) contains the full set of MOM
(Sect. ) reactions. CHEMGLUE selects the second mechanism whenever the
mixing ratios of organics are above a threshold (isoprene >100 pmol mol-1,
α-pinene >100 pmol mol-1, or toluene >10 pmol mol-1). To
investigate how much CPU time can be saved and how much the simplification affects the
results, we have performed global test simulations based on the ECHAM5/MESSy atmospheric
chemistry (EMAC) model by . The horizontal resolution was T42
(2.8∘×2.8∘), with 47 vertical levels. Starting on 1 January 2009,
1 month was simulated. To facilitate the intercomparison between the simulations, the
feedback of chemistry on the meteorology was switched off. Three different chemical
schemes were tested.
FULL. Full MOM chemistry was activated throughout the atmosphere.
POLY. PolyMECCA/CHEMGLUE switches between the full MOM chemistry
and the methane-only chemistry as described above.
SKEL. The skeletal mechanism s2 as described in
Sect. was activated throughout the atmosphere.
The CPU usage for the POLY and SKEL simulations are 62 % and 65 % of
the FULL simulation, respectively. Results are shown in
Fig. . Overall, the agreement between the
simulations is quite good, considering that the simplified mechanisms
neglect many reactions.
CHEMPROP
Chemical properties of the species in the reaction mechanism are needed at
many locations in the model, e.g., molar masses (M), Henry's law constants
(H), accommodation coefficients (α), acidity constants
(KA), and ion charge numbers (z). These values have so far been
stored at different locations in the code (,
, and elsewhere). Because maintaining data that are
spread over several source files is tedious and error-prone, the new CHEMPROP
database has been created, which stores all values centrally in the ASCII
table . MECCA (and other submodels) can
access these chemical property data via MESSy tracer containers, as described
by .
Further changes
The new subroutines and dilute
the concentrations of chemicals in an air parcel by mixing it with
unperturbed air. This can, for example, be used for modeling chemistry
in an expanding volcanic plume or smog plume. An alternative usage for these
subroutines is the simulation of the flow in and out of a reaction
chamber e.g.,.
A new functionality has been implemented for the external
initialization of chemical species from a netCDF file: if the time
axis of the input file contains more than one point, the time values
are used to interpolate mixing ratios at model start time. This is
convenient for bundling several initializations into one file, for
instance to initialize several CAABA simulations from different points
along a trajectory with recorded mixing ratios (see also
Sect. ). If the time axis of the input file contains
only one point, the mixing ratios are read into CAABA, regardless of
the time value.
We extended CAABA with parameters to optionally control the output
step frequency () and the output
synchronization frequency (). The first
variable sets the frequency at which values are written to the output.
A value of =α skips α-1
time steps and writes only every αth time step to the output
file. The second variable controls the output synchronization. Data
are buffered for time steps before they are
written to the output files. Both parameters enable the user to carry
out very long box model simulations without being constrained by
machine I/O performance, and they can individually regulate the output
file size. A high value of has a positive
effect on performance. However, in case of machine failure, buffered
output steps are lost.
The treatment of humidity has been improved. Now specific as well
as relative humidity (RH) is available throughout CAABA, and can be
interconverted with generic conversion functions. Of the two, specific
humidity is the more robust variable for humidity because the
definition of RH can be based on either partial pressure or on
specific humidity . There are various parameterizations
for saturation water vapor pressure, and RH can be defined over liquid
surface even below 0 ∘C if supercooling is allowed. Functions
that use humidity as input (concentration of air, conversion between
humidity, and water vapor concentration) now use the unambiguous
specific humidity. If necessary, it is derived from relative humidity
taking all of the above considerations into account.
For better model time control, two boolean namelist parameters
have been introduced: repeats a diurnal cycle
while repeats a certain point in time,
effectively freezing the solar zenith angle.
The selection of various chemical species to define steady state
has been simplified to allow for more flexibility in the criteria. The
progress towards the defined steady state is now logged during CAABA
runtime. Artifacts by species' concentrations close to zero are now
prevented.
Several shell scripts have been converted to python
(, , ). They use
the netcdf4 interface and don't depend on the availability of the
NetCDF operators (e.g., ) anymore. Currently, the python
scripts are in beta testing. In future versions, they will replace the
current tcsh scripts.
Model results can now be visualized with the python script
using matplotlib. The previously used ferret
scripts are still included but not actively supported anymore.
Complex reaction mechanisms can be interpreted as graphs, with
species representing vertices and reactions representing edges. To
visualize and analyze these graphs, the “graph-tool” software by
can now be used. For example,
Fig. was created with graph-tool.
Rate coefficients have been updated to the latest JPL
recommendations and recent laboratory studies. A complete
list of chemical reactions, rate coefficients, and references is
available in the Supplement ().
The kinetic preprocessor KPP performs the numerical
integration of the chemical reaction mechanism. It has been updated to
the latest version 2.2.3, which contains a number of small fixes
throughout the
code (http://people.cs.vt.edu/~asandu/Software/Kpp, last access: 26 March 2019).
The python scripts and check
the internal consistency of the chemical mechanism.
Details of all new features have been added to the updated user
manual, which now also includes an index. Additional minor bug fixes
can be found in the file.
Summary and outlook
We have presented the current version of the atmospheric chemistry module
MECCA-4.0, which includes several new
features: skeletal mechanism reduction, the MOM chemical mechanism for organic compounds,
optional inclusion of reactions from MCM and other chemical mechanisms, updated isotope
tagging, and improved and new photolysis modules. When MECCA is connected to a global
model, PolyMECCA and CHEMGLUE allow coexisting multiple chemistry mechanisms. CAABA/MECCA
is now available to the research community.
Based on the model development described in this paper, our current and upcoming goals
are the following. (For work in progress, initials of the principal investigators are
shown in parentheses.)
reduce complex mechanisms to a size suitable for global model
simulations (RS, KEN),
perform a chemistry module intercomparison including CB05BASCOE
and MOZART within a global chemistry modeling framework ,
evaluate MOM chemistry and its effect on secondary aerosol
formation (AP),
compare MOM chemistry to measurements obtained during the recent
AQABA field campaign (HH),
advance our understanding of the role of organic compounds on the
tropospheric ozone and HOx budgets (DT),
compare model results with studies at the SAPHIR chamber (DT),
investigate the multiphase chemical pathways leading to organic
acids and aerosols (DT),
simulate stratospheric isotope H exchanges between
CH4 and H2O (SG),
implement additional photolysis modules (e.g., CLOUDJ, TUV) and
compare the resulting j values (HH),
parallelize to distribute independent (e.g., Monte Carlo or
sensitivity) box model simulations on multiple cores (HH),
study the impact of aromatic compounds on atmospheric chemistry
(RS, manuscript in preparation).
Code and data availability
The CAABA/MECCA model code is available as a community
model published under the GNU General Public License
(http://www.gnu.org/copyleft/gpl.html, last access: 26 March 2019). The
model code can be found in the Supplement. In addition to the complete code,
a list of chemical reactions – including rate coefficients and references
(meccanism.pdf) – and a user manual
(caaba_mecca_manual.pdf) are available in the manual
directory of the Supplement. For further information and updates, the MECCA
web page at http://www.mecca.messy-interface.org (last access: 26 March
2019) can be consulted.
The supplement related to this article is available online at: https://doi.org/10.5194/gmd-12-1365-2019-supplement.
Author contributions
RS develops and maintains the CAABA/MECCA software. AB provided RADJIMT.
DCP provided the aromatic chemistry mechanism of MOM. FF added code to
control the model output. JUG provided DISSOC and helped with its
implementation in MESSy. SG provided the MECCA-TAG sub-submodel. HH and ST
provided code for the inclusion of the MCM reaction schemes. PJ contributed
to several model development projects (MESSy modeling system, PolyMECCA,
CHEMPROP, CHEMGLUE) and maintains the interfaces to ensure that the modules
are not only compatible with the box model but also with the 3-D models. VH
contributed through initiating the provision of CAMS chemistry models for
inclusion in MECCA, and for generation of the CB05BASCOE merged chemical
mechanism. VAK integrated CB05BASCOE and MOZART into MECCA. KEN provided code
for the skeletal mechanism generation. AP contributed to several model
development projects (MESSy modeling system, scenarios for skeletal mechanism
generation, MOM, CAMS, PolyMECCA testing). HR provided an update of the
TRAJECT submodel. MGS provided JAM002, and DT provided MOM.
Competing interests
The authors declare that they have no conflict of
interest.
Acknowledgements
We thank Simon Chabrillat and Idir Bouarar for provision of the
mechanisms BASCOE and MOZART, respectively. We also thank Tim Butler
for contributing the diagnostic tool . Duy Cai
added some photolysis reactions to JVAL. Tilo Fytterer and Stefan
Versick discovered and reported the temperature dependence bug of the
ozone and OCS photolyses in JVAL. Vincent Huijnen acknowledges funding from the
Copernicus Atmosphere Monitoring Service (CAMS). Model results were
plotted using the open-source software
matplotlib (https://matplotlib.org, last access: 26 March 2019) and
ferret (http://ferret.pmel.noaa.gov, last access: 26 March 2019).The article processing charges for this open-access
publication were covered by the Max Planck Society.
Review statement
This paper was edited by Slimane Bekki and reviewed by two
anonymous referees.
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