ALBERT

Description: Towards a regional ocean forecasting system for the IBI (Iberia-Biscay-Ireland area): developments and improvements within the ECOOP project framework Ocean Science, 8, 143-159, 2012 Author(s): S. Cailleau, J. Chanut, J.-M. Lellouche, B. Levier, C. Maraldi, G. Reffray, and M. G. Sotillo The regional ocean operational system remains a key element in downscaling from large scale (global or basin scale) systems to coastal ones. It enables the transition between systems in which the resolution and the resolved physics are quite different. Indeed, coastal applications need a system to predict local high frequency events (inferior to the day) such as storm surges, while deep sea applications need a system to predict large scale lower frequency ocean features. In the framework of the ECOOP project, a regional system for the Iberia-Biscay-Ireland area has been upgraded from an existing V0 version to a V2. This paper focuses on the improvements from the V1 system, for which the physics are close to a large scale basin system, to the V2 for which the physics are more adapted to shelf and coastal issues. Strong developments such as higher regional physics resolution in the NEMO Ocean General Circulation Model for tides, non linear free surface and adapted vertical mixing schemes among others have been implemented in the V2 version. Thus, regional thermal fronts due to tidal mixing now appear in the latest version solution and are quite well positioned. Moreover, simulation of the stratification in shelf areas is also improved in the V2.

Description: The Nexus Land-Use model version 1.0, an approach articulating biophysical potentials and economic dynamics to model competition for land-use Geoscientific Model Development Discussions, 5, 571-638, 2012 Author(s): F. Souty, T. Brunelle, P. Dumas, B. Dorin, P. Ciais, R. Crassous, C. Müller, and A. Bondeau Interactions between food demand, biomass energy and forest preservation are driving both food prices and land-use changes, regionally and globally. This study presents a new model called Nexus Land-Use version 1.0 which describes these interactions through a generic representation of agricultural intensification mechanisms. The Nexus Land-Use model equations combine biophysics and economics into a single coherent framework to calculate crop yields, food prices, and resulting pasture and cropland areas within 12 regions inter-connected with each other by international trade. The representation of cropland and livestock production systems in each region relies on three components: (i) a biomass production function derived from the crop yield response function to inputs such as industrial fertilisers; (ii) a detailed representation of the livestock production system subdivided into an intensive and an extensive component, and (iii) a spatially explicit distribution of potential (maximal) crop yields prescribed from the Lund-Postdam-Jena global vegetation model for managed Land (LPJmL). The economic principles governing decisions about land-use and intensification are adapted from the Ricardian rent theory, assuming cost minimisation for farmers. The land-use modelling approach described in this paper entails several advantages. Firstly, it makes it possible to explore interactions among different types of biomass demand for food and animal feed, in a consistent approach, including indirect effects on land-use change resulting from international trade. Secondly, yield variations induced by the possible expansion of croplands on less suitable marginal lands are modelled by using regional land area distributions of potential yields, and a calculated boundary between intensive and extensive production. The model equations and parameter values are first described in details. Then, idealised scenarios exploring the impact of forest preservation policies or rising energy price on agricultural intensification are described, and their impacts on pasture and cropland areas are investigated.

Description: Modelling sub-grid wetland in the ORCHIDEE global land surface model: evaluation against river discharges and remotely sensed data Geoscientific Model Development Discussions, 5, 683-735, 2012 Author(s): B. Ringeval, B. Decharme, S. L. Piao, P. Ciais, F. Papa, N. de Noblet-Ducoudré, C. Prigent, P. Friedlingstein, I. Gouttevin, C. Koven, and A. Ducharne The quality of the global hydrological simulations performed by Land Surface Models (LSMs) strongly depends on processes that occur at unresolved spatial scales. Approaches such as TOPMODEL have been developed, which allow soil moisture redistribution within each grid-cell, based upon sub-grid scale topography. Moreover, the coupling between TOPMODEL and a LSM appears as a potential way to simulate wetland extent dynamic and its sensitivity to climate, a recently identified research problem for biogeochemical modelling, including methane emissions. Global evaluation of the coupling between TOPMODEL and an LSM is difficult, and prior attempts have been indirect, based on the evaluation of the simulated river flow. This study presents a new way to evaluate this coupling, within the ORCHIDEE LSM, using remote sensing data of inundated areas. Because of differences in nature between the satellite derived information – inundation extent – and the variable diagnosed by TOPMODEL/ORCHIDEE – area at maximum soil water content –, the evaluation focuses on the spatial distribution of these two quantities as well as on their temporal variation. Despite some difficulties in exactly matching observed localized inundated events, we obtain a rather good agreement in the distribution of these two quantities at a global scale. Floodplains are not accounted for in the model, and this is a major limitation. The difficulty of reproducing the year-to-year variability of the observed inundated area (for instance, the decreasing trend by the end of 90s) is also underlined. Classical indirect evaluation based on comparison between simulated and observed riverflow is also performed and underlines difficulties to simulate riverflow after coupling with TOPMODEL. The relationship between inundation and river flow at the basin scale in the model is analyzed, using both methods (evaluation against remote sensing data and riverflow). Finally, we discuss the potential of the TOPMODEL/LSM coupling to simulate wetland areas. A major limitation of the coupling for this purpose is linked to its ability to simulate a global wetland coverage consistent with the commonly used datasets. However, it seems to be a good opportunity to account for the wetland areas sensitivity to the climate and thus to simulate its temporal variability.

Description: Technical Note: Detection of gas bubble leakage via correlation of water column multibeam images Ocean Science, 8, 175-181, 2012 Author(s): J. Schneider von Deimling and C. Papenberg Hydroacoustic detection of natural gas release from the seafloor has been conducted in the past by using singlebeam echosounders. In contrast, modern multibeam swath mapping systems allow much wider coverage, higher resolution, and offer 3-D spatial correlation. Up to the present, the extremely high data rate hampers water column backscatter investigations and more sophisticated visualization and processing techniques are needed. Here, we present water column backscatter data acquired with a 50 kHz prototype multibeam system over a period of 75 seconds. Display types are of swath-images as well as of a "re-sorted" singlebeam presentation. Thus, individual and/or groups of gas bubbles rising from the 24 m deep seafloor clearly emerge in the acoustic images, making it possible to estimate rise velocities. A sophisticated processing scheme is introduced to identify those rising gas bubbles in the hydroacoustic data. We apply a cross-correlation technique adapted from particle imaging velocimetry (PIV) to the acoustic backscatter images. Temporal and spatial drift patterns of the bubbles are assessed and are shown to match very well to measured and theoretical rise patterns. The application of this processing to our field data gives clear results with respect to unambiguous bubble detection and remote bubble rise velocimetry. The method can identify and exclude the main source of misinterpretations, i.e. fish-mediated echoes. Although image-based cross-correlation techniques are well known in the field of fluid mechanics for high resolution and non-inversive current flow field analysis, we present the first application of this technique as an acoustic bubble detector.

Description: Black Sea coastal forecasting system Ocean Science, 8, 183-196, 2012 Author(s): A. I. Kubryakov, G. K. Korotaev, V. L. Dorofeev, Y. B. Ratner, A. Palazov, N. Valchev, V. Malciu, R. Matescu, and T. Oguz The Black Sea coastal nowcasting and forecasting system was built within the framework of EU FP6 ECOOP (European COastalshelf sea OPerational observing and forecasting system) project for five regions: the south-western basin along the coasts of Bulgaria and Turkey, the north-western shelf along the Romanian and Ukrainian coasts, coastal zone around of the Crimea peninsula, the north-eastern Russian coastal zone and the coastal zone of Georgia. The system operates in the real-time mode during the ECOOP project and afterwards. The forecasts include temperature, salinity and current velocity fields. Ecosystem model operates in the off-line mode near the Crimea coast.

Description: Sea surface temperature anomalies, seasonal cycle and trend regimes in the Eastern Pacific coast Ocean Science, 8, 81-90, 2012 Author(s): A. Ramos-Rodríguez, D. B. Lluch-Cota, S. E. Lluch-Cota, and A. Trasviña-Castro We used the extended reconstruction of sea surface temperature (ERSST) to analyze the variation of surface temperature and the seasonal cycle along the coast of the eastern Pacific (60° N–60° S, 61 pixels alongshore) from 1950 to 2010 (732 months). First, we analyzed the monthly anomalies and looked for a relationship of such anomalies with total solar irradiance (TSI) and then the Regime Shift Detector (RSD) was applied to detect possible temperature regimes in the series. Afterwards, we calculated a yearly temperature range per pixel (amplitude of seasonal cycle) and through the subtraction of a latitudinal theoretical curve of temperature based on solar irradiance, the residuals of the seasonal cycle were obtained. The results showed an almost complete spatial synchrony and dominance of negative anomalies from 1950 to mid-late 1970's, with a switch to near-zero and positive anomalies that lasted up to late 1990's when a new shift to negative values was detected. Such a shift lasted until the early 2000's when positive anomalies appeared again but there was a change to negative anomalies in the late 2000's. These results were supported by the RSD. The TSI variability shows a clear relationship with that of sea surface temperature anomalies and with the regime changes. This is probably due to a difference in the amount of energy received from the sun. Comparing the "cool regime" versus the "warm regime", the second one received 0.39% more energy (approximately 3 × 10 8 J m −2 ) from the sun. Seasonal cycles show larger ranges at northern latitudes (〉40° N), northern tropical-temperate transition zone (20°–26° N) and in the tropical-equatorial band (0°–30° S). The smallest ranges occur at 0°–16° N and 50°–60° S. The residuals (seasonal minus the theoretical curve) indicated a clear modulation due to advection by ocean currents.

Description: Evaluation of a near-global eddy-resolving ocean model Geoscientific Model Development Discussions, 5, 4305-4354, 2012 Author(s): P. R. Oke, D. A. Griffin, A. Schiller, R. J. Matear, R. Fiedler, J. Mansbridge, A. Lenton, M. Cahill, M. A. Chamberlain, and K. Ridgway Analysis of the variability in an 18-yr run of a near-global, eddy-resolving ocean general circulation model coupled with biogeochemistry is presented. Comparisons between modelled and observed mean sea level (MSL), mixed-layer depth (MLD), sea-level anomaly (SLA), sea-surface temperature (SST), and Chlorophyll a indicate that the model variability is realistic. We find some systematic errors in the modelled MLD, with the model generally deeper than observations, that results in errors in the Chlorophyll a , owing to the strong biophysical coupling. We evaluate several other metrics in the model, including the zonally-averaged seasonal cycle of SST, meridional overturning, volume transports through key Straits and passages, zonal averaged temperature and salinity, and El Nino-related SST indices. We find that the modelled seasonal cycle in SST is 0.5–1.5 °C weaker than observed; volume transports of the Antarctic Circumpolar Current, the East Australian Current, and Indonesian Throughflow are in good agreement with observational estimates; and the correlation between the modelled and observed NINO SST indices exceed 0.91. Most aspects of the model circulation are realistic. We conclude that the model output is suitable for broader analysis to better understand ocean dynamics and ocean variability.

Description: Evaluating a lightning parameterization based on cloud-top height for mesoscale numerical model simulations Geoscientific Model Development Discussions, 5, 3493-3531, 2012 Author(s): J. Wong, M. C. Barth, and D. Noone The Price and Rind lightning parameterization based on cloud-top height is a commonly used method for predicting flash rate in global chemistry models. As mesoscale simulations begin to implement flash rate predictions at resolutions that partially resolve convection, it is necessary to validate and understand the behavior of this method within such regime. In this study, we tested the flash rate parameterization, intra-cloud/cloud-to-ground (IC:CG) partitioning parameterization, and the associated resolution dependency "calibration factor" by Price and Rind using the Weather Research and Forecasting (WRF) model running at 36 km, 12 km, and 4 km grid spacings within the continental United States. Our results show that while the integrated flash count is consistent with observation when model biases in convection are taken into account, an erroneous frequency distribution is simulated. When the spectral characteristics of lightning flash rate is a concern, we recommend the use of prescribed IC:CG values. In addition, using cloud-top from convective parameterization, the "calibration factor" is also shown to be insufficient in reconciling the resolution dependency at the tested grid spacing used in this study. We recommend scaling by areal ratio relative to a base-case grid spacing determined by convective core density.

Description: Using model reduction to predict the soil-surface C 18 OO flux: an example of representing complex biogeochemical dynamics in a computationally efficient manner Geoscientific Model Development Discussions, 5, 3469-3491, 2012 Author(s): W. J. Riley Earth System Models (ESMs) must calculate large-scale interactions between the land and atmosphere while accurately characterizing fine-scale spatial heterogeneity in water, carbon, and nutrient dynamics. We present here a high-dimensional model representation (HDMR) approach that allows detailed process representation of a coupled carbon and water tracer (the δ 18 O value of the soil-surface CO 2 flux (δ F s )) in a computationally tractable manner. δ F s depends on the δ 18 O value of soil water, soil moisture, soil temperature, and soil CO 2 production (all of which are depth-dependent), and the δ 18 O value of above-surface CO 2 . We tested the HDMR approach over a growing season in a C 4 -dominated pasture using two vertical soil discretizations. The difference between the HDMR approach and the full model solution in the three-month integrated isoflux was less than 0.2% (0.5 mol m −2 ‰), and the approach is up to 100 times faster than the full numerical solution. This type of model reduction approach allows representation of complex coupled biogeochemical processes in regional and global climate models and can be extended to characterize subgrid-scale spatial heterogeneity.

Description: ECOCLIMAP-II/Europe: a twofold database of ecosystems and surface parameters at 1-km resolution based on satellite information for use in land surface, meteorological and climate models Geoscientific Model Development Discussions, 5, 3573-3620, 2012 Author(s): S. Faroux, A. T. Kaptué Tchuenté, J.-L. Roujean, V. Masson, E. Martin, and P. Le Moigne The overall objective of the present study is to introduce the new ECOCLIMAP-II database for Europe, which is an upgrade for this region of the former initiative, ECOCLIMAP-I, already implemented at global scale. The ECOCLIMAP programme is a dual database at 1-km resolution that includes an ecosystem classification and a coherent set of land surface parameters that are primarily mandatory in meteorological modelling (notably leaf area index and albedo). Hence, the aim of this innovative physiography is to enhance the quality of initialisation and impose some surface attributes within the scope of weather forecasting and climate related studies. The strategy for implementing ECOCLIMAP-II is to depart from prevalent land cover products such as CLC2000 (Corine Land Cover) and GLC2000 (Global Land Cover) by splitting existing classes into new classes that possess a better regional character by virtue of the climatic environment (latitude, proximity to the sea, topography). The leaf area index (LAI) from MODIS and NDVI from SPOT/Vegetation yield the two proxy variables that were considered here in order to perform a multi-year trimmed analysis between 1999 and 2005 using the K-means method. Further, meteorological applications require each land cover type to appear as a partition of fractions of 4 main surface types or tiles (nature, water bodies, sea, urban areas) and, inside the nature tile, fractions of 12 Plant Functional Types (PFTs) representing generic vegetation types – principally broadleaf forest, needleleaf forest, C3 and C4 crops, grassland and bare land – as incorporated by the SVAT model ISBA developed at Météo France. This landscape division also forms the cornerstone of a validation exercise. The new ECOCLIMAP-II can be verified with auxiliary land cover products at very fine and coarse resolutions by means of versatile land occupation nomenclatures.

Description: Microstructure observations during the spring 2011 STRATIPHYT-II cruise in the northeast Atlantic Ocean Science, 8, 945-957, 2012 Author(s): E. Jurado, H. A. Dijkstra, and H. J. van der Woerd Small-scale temperature and conductivity variations have been measured in the upper 100 m of the northeast Atlantic during the STRATIPHYT-II cruise (Las Palmas–Reykjavik, 6 April–3 May 2011). The measurements were done at midday and comprised 2 to 15 vertical profiles at each station. The derived turbulent quantities show a transition between weakly-stratified (mixed layer depth, MLD, 100), which was centered at about 48° N. The temperature eddy diffusivities, K T , range from 10 −5 to 10 0 m 2 s −1 in the weakly-stratified stations, and range from 3 × 10 −4 to 2 × 10 0 m 2 s −1 in the well-mixed stations. The turbulent kinetic energy dissipation rates, ε, range from 3 × 10 −8 to 2 × 10 −6 m 2 s −3 south of the transition zone, and from 10 −7 to 10 −5 m 2 s −3 north of the transition zone. The station-averaged K T values throughout the mixed layer increase exponentially with the wind speed. The station-averaged ε values throughout the mixed layer scale with the wind stress similarity variable with a scaling factor of about 1.8 in the wind-dominated stations (ε ≈ 1.8 u ☆ 3 /(−κ z )). The values of K T and ε are on average 10 times higher compared to the values measured at the same stations in July 2009. The results presented here constitute a unique data set giving large spatial coverage of upper ocean spring turbulence quantities.

Description: Intercomparison of temperature trends in IPCC CMIP5 simulations with observations, reanalyses and CMIP3 models Geoscientific Model Development Discussions, 5, 3621-3645, 2012 Author(s): J. Xu and A. M. Powell Jr. On the basis of the fifth Coupled Model Intercomparison Project (CMIP5) and the climate model simulations covering 1979 through 2005, the temperature trends and their uncertainties have been examined to note the similarities or differences compared to the radiosonde observations, reanalyses and the third Coupled Model Intercomparison Project (CMIP3) simulations. The results show noticeable discrepancies for the estimated temperature trends in the four data groups (Radiosonde, Reanalysis, CMIP3 and CMIP5) although similarities can be observed. Compared to the CMIP3 model simulations, the simulation in some of CMIP5 models were improved. The CMIP5 models displayed a negative temperature trend in the stratosphere closer to the strong negative trend seen in the observations. However, the positive tropospheric trend in the tropics is overestimated by the CMIP5 models relative to CMIP3 models. While some of the models produce temperature trend patterns more highly correlated with the observed patterns in CMIP5, the other models (such as CCSM4 and IPSL_CM5A-LR) exhibit the reverse tendency. The CMIP5 temperature trend uncertainty was significantly reduced in most areas, especially in the Arctic and Antarctic stratosphere, compared to the CMIP3 simulations. Similar to the CMIP3, the CMIP5 simulations overestimated the tropospheric warming in the tropics and Southern Hemisphere and underestimated the stratospheric cooling. The crossover point where tropospheric warming changes into stratospheric cooling occurred near 100 hPa in the tropics, which is higher than in the radiosonde and reanalysis data. The result is likely related to the overestimation of convective activity over the tropical areas in both the CMIP3 and CMIP5 models. Generally, for the temperature trend estimates associated with the numerical models including the reanalyses and global climate models, the uncertainty in the stratosphere is much larger than that in the troposphere, and the uncertainty in the Antarctic is the largest. In addition, note that the reanalyses show the largest uncertainty in the lower tropical stratosphere, and the CMIP3 simulations show the largest uncertainty in both the south and north polar regions.

Description: Present state of global wetland extent and wetland methane modelling: methodology of a model intercomparison project (WETCHIMP) Geoscientific Model Development Discussions, 5, 4071-4136, 2012 Author(s): R. Wania, J. R. Melton, E. L. Hodson, B. Poulter, B. Ringeval, R. Spahni, T. Bohn, C. A. Avis, G. Chen, A. V. Eliseev, P. O. Hopcroft, W. J. Riley, Z. M. Subin, H. Tian, V. Brovkin, P. M. van Bodegom, T. Kleinen, Z. C. Yu, J. S. Singarayer, S. Zürcher, D. P. Lettenmaier, D. J. Beerling, S. N. Denisov, C. Prigent, F. Papa, and J. O. Kaplan The Wetland and Wetland CH 4 Intercomparison of Models Project (WETCHIMP) was created to evaluate our present ability to simulate large-scale wetland characteristics and corresponding methane (CH 4 ) emissions. A multi-model comparison is essential to evaluate the key uncertainties in the mechanisms and parameters leading to methane emissions. Ten modelling groups joined WETCHIMP to run eight global and two regional models with a common experimental protocol using the same climate and atmospheric carbon dioxide (CO 2 ) forcing datasets. We reported the main conclusions from the intercomparison effort in a companion paper (Melton et al., 2012). Here we provide technical details for the six experiments, which included an equilibrium, a transient, and an optimized run plus three sensitivity experiments (temperature, precipitation, and atmospheric CO 2 concentration). The diversity of approaches used by the models is summarized through a series of conceptual figures, and is used to evaluate the wide range of wetland extents and CH 4 fluxes predicted by the models in the equilibrium run. We discuss relationships among the various approaches and patterns in consistencies of these model predictions. Within this group of models, there are three broad classes of methods used to estimate wetland extent: prescribed based on wetland distribution maps, prognostic relationships between hydrological states based on satellite observations, and explicit hydrological mass balances. A larger variety of approaches was used to estimate the net CH 4 fluxes from wetland systems. Even though modelling of wetland extents and CH 4 emissions has progressed significantly over recent decades, large uncertainties still exist when estimating CH 4 emissions: there is little consensus on model structure or complexity due to knowledge gaps, different aims of the models, and the range of temporal and spatial resolutions of the models.

Description: Improving the representation of secondary organic aerosol (SOA) in the MOZART-4 global chemical transport model Geoscientific Model Development Discussions, 5, 4187-4232, 2012 Author(s): A. Mahmud and K. C. Barsanti The secondary organic aerosol (SOA) module in the Model for Ozone and Related chemical Tracers, version 4 (MOZART-4) has been updated by replacing existing two-product (2p) parameters with those obtained from two-product volatility basis set (2p-VBS) fits, and by treating SOA formation from the following volatile organic compounds (VOCs): isoprene, propene and lumped alkenes. Strong seasonal and spatial variations in global SOA distributions were demonstrated, with significant differences in the predicted concentrations between the base-case and updated model versions. The base-case MOZART-4 predicted annual average SOA of 0.36 ± 0.50 μg m −3 in South America, 0.31 ± 0.38 μg m −3 in Indonesia, 0.09 ± 0.05 μg m −3 in the USA, and 0.12 ± 0.07 μg m −3 in Europe. Concentrations from the updated versions of the model showed a~marked increase in annual average SOA. Using the updated set of parameters alone (MZ4-v1) increased annual average SOA by ~8%, ~16%, ~56%, and ~108% from the base-case in South America, Indonesia, USA, and Europe, respectively. Treatment of additional parent VOCs (MZ4-v2) resulted in an even more dramatic increase of ~178–406% in annual average SOA for these regions over the base-case. The increases in predicted SOA concentrations further resulted in increases in corresponding SOA contributions to annual average total aerosol optical depth (AOD) by

Description: Modeling agriculture in the Community Land Model Geoscientific Model Development Discussions, 5, 4137-4185, 2012 Author(s): B. Drewniak, J. Song, J. Prell, V. R. Kotamarthi, and R. Jacob The potential impact of climate change on agriculture is uncertain. In addition, agriculture could influence above- and below-ground carbon storage. Development of models that represent agriculture is necessary to address these impacts. We have developed an approach to integrate agriculture representations for three crop types – maize, soybean, and spring wheat – into the coupled carbon-nitrogen version of the Community Land Model (CLM), to help address these questions. Here we present the new model, CLM-Crop, validated against observations from two AmeriFlux sites in the United States, planted with maize and soybean. Seasonal carbon fluxes compared well with field measurements. CLM-Crop yields were comparable with observations in some regions, although the generality of the crop model and its lack of technology and irrigation made direct comparison difficult. CLM-Crop was compared against the standard CLM3.5, which simulates crops as grass. The comparison showed improvement in gross primary productivity in regions where crops are the dominant vegetation cover. Crop yields and productivity were negatively correlated with temperature and positively correlated with precipitation. In case studies with the new crop model looking at impacts of residue management and planting date on crop yield, we found that increased residue returned to the litter pool increased crop yield, while reduced residue returns resulted in yield decreases. Using climate controls to signal planting date caused different responses in different crops. Maize and soybean had opposite reactions: when low temperature threshold resulted in early planting, maize responded with a loss of yield, but soybean yields increased. Our improvements in CLM demonstrate a new capability in the model – simulating agriculture in a realistic way, complete with fertilizer and residue management practices. Results are encouraging, with improved representation of human influences on the land surface and the potentially resulting climate impacts.

Description: A test of numerical instability and stiffness in the parametrizations of the ARPÉGE and ALADIN models Geoscientific Model Development Discussions, 5, 4233-4268, 2012 Author(s): M. Tudor Meteorological numerical weather prediction (NWP) models solve a system of partial differential equations in time and space. Semi-lagrangian advection scheme in the model dynamics allows for long time-steps. These longer time-steps can result in instabilities occurring in the model physics. A system of differential equations in which some solution components decay more rapidly than others is stiff. In this case it is stability rather than accuracy that restricts the time-step. The vertical diffusion parametrization can cause fast non-meteorological oscillations around the slowly evolving true solution (fibrillations). These are treated with an anti-fibrillation scheme. But small oscillations remain in an operational weather forecasts using ARPÉGE and ALADIN models. It is needed to test of the complete model formulation, as implemented in the operational forecast. In this paper, a simple test is designed. The test reveals if the formulation of particular physical parametrization is a stiff problem or potentially numerically unstable in combination with any other part of the model. When the test is applied to a stable scheme, the solution remains stable. But, applying the test to a potentially unstable scheme yields a solution with fibrillations of substantial amplitude. The parametrizations of a NWP model ARPÉGE were tested one by one to see which one may be the source of unstable model behaviour. The test has identified the stratiform precipitation scheme (a diagnostic Kessler type scheme) as a stiff problem, particularly the term that describes the evaporation of snow.

Description: Impact of the sea surface temperature forcing on hindcasts of Madden-Julian Oscillation events using the ECMWF model Ocean Science, 8, 1071-1084, 2012 Author(s): E. de Boisséson, M. A. Balmaseda, F. Vitart, and K. Mogensen This paper explores the sensitivity of hindcasts of the Madden Julian Oscillation (MJO) to the use of different sea surface temperture (SST) products as lower boundary conditions in the European Centre for Medium-range Weather Forecasts (ECMWF) atmospheric model. Three sets of monthly hindcast experiments are conducted, starting from initial conditions from the ERA interim reanalysis. First, as a reference, the atmosphere is forced by the SST used to produce ERA interim. In the second and third experiments, the SST is switched to the OSTIA (Operational Sea Surface Temperature and Sea-Ice Analysis) and the AVHRR-only (Advanced Very High Resolution Radiometer) reanalyses, respectively. Tests on the temporal resolution of the SST show that monthly fields are not optimal, while weekly and daily resolutions provide similar MJO scores. When using either OSTIA or AVHRR, the propagation of the MJO is degraded and the resulting scores are lower than in the reference experiment. Further experiments show that this loss of skill cannot be attributed to either the difference in mean state or temporal variability between the SST products. Additional diagnostics show that the phase relationship between either OSTIA or AVHRR SST and the MJO convection is distorted with respect to satellite observations and the ERA interim reanalysis. This distortion is expected to impact the MJO hindcasts, leading to a relative loss of forecast skill. A realistic representation of ocean–atmosphere interactions is thus needed for MJO hindcasts, but not all SST products – though accurate for other purposes – fulfill this requirement.

Description: Imbalance of energy and momentum source terms of the sea wave transfer equation for fully developed seas Ocean Science, 8, 1085-1098, 2012 Author(s): G. V. Caudal In the concept of full development, the sea wave spectrum is regarded as a nearly stationary solution of the wave transfer equation, where source and sink terms should be in balance with respect to both energy and momentum. Using a two-dimensional empirical sea wave spectral model at full development, this paper performs an assessment of the compatibility of the energy and momentum budgets of sea waves over the whole spectral range. Among the various combinations of model functions for wave breaking and wind source terms tested, not one is found to fulfill simultaneously the energy and momentum balance of the transfer equation. Based on experimental and theoretical grounds, wave breaking is known to contribute to frequency downshift of a narrow-banded wave spectrum when the modulational instability is combined with wave breaking. On those grounds, it is assumed that, in addition to dissipation, wave breaking produces a spectral energy flux directed toward low wavenumbers. I show that it is then possible to remove the energy and momentum budget inconsistency, and correspondingly the required strength of this spectral flux is estimated. Introducing such a downward spectral flux permits fulfilling both energy and momentum balance conditions. Meanwhile, the consistency between the transfer equation and empirical spectra, estimated by means of a cost function K, is either improved or slightly reduced, depending upon the wave breaking and wind source terms chosen. Other tests are performed in which it is further assumed that wave breaking would also be associated with azimuthal diffusion of the spectral energy. This would correspondingly reduce the required downward spectral flux by a factor of up to 5, although it would not be able to remove it entirely.

Description: MESMO 2: a mechanistic marine silica cycle and coupling to a simple terrestrial scheme Geoscientific Model Development Discussions, 5, 2999-3033, 2012 Author(s): K. Matsumoto, K. S. Tokos, A. Huston, and H. Joy-Warren Here we describe the second version of Minnesota Earth System Model for Ocean biogeochemistry (MESMO 2), an earth system model of intermediate complexity, which consists of a dynamical ocean, dynamic-thermodynamic sea ice, and energy moisture balanced atmosphere. The new version has more realistic land ice masks and is driven by seasonal winds. A major aim in version 2 is representing the marine silica cycle mechanistically in order to investigate climate-carbon feedbacks involving diatoms, a critically important class of phytoplankton in terms of carbon export production. This is achieved in part by including iron, on which phytoplankton uptake of silicic acid depends. Also, MESMO 2 is coupled to an existing terrestrial model, which allows for the exchange of carbon, water, and energy between land and the atmosphere. The coupled model, called MESMO 2E, is appropriate for more complete earth system simulations. The new version was calibrated with the goal of preserving reasonable interior ocean ventilation and various biological production rates in the ocean and land, while simulating key features of the marine silica cycle.

Description: High frequency fluctuations in the heat content of an ocean general circulation model Ocean Science, 8, 813-825, 2012 Author(s): A. M. Huerta-Casas and D. J. Webb The transport and storage of heat by the ocean is of crucial importance because of its effect on ocean dynamics and its impact on the atmosphere, climate and climate change. Unfortunately, limits to the amount of data that can be collected and stored mean that many experimental and modelling studies of the heat budget have to make use of mean datasets where the effects of short term fluctuations are lost. In this paper we investigate the magnitude of the resulting errors by making use of data from OCCAM, a high resolution global ocean model. The model carries out a proper heat balance every time step so any imbalances that are found in the analysis must result from the use of mean fields. The study concentrates on two areas of the ocean affecting the El Nino. The first is the region of tropical instability waves north of the Equator. The second is in the upwelling region along the Equator. It is shown that in both cases, processes with a period of less than five days can have a significant impact on the heat budget. Thus, analyses using data averaged over five days or more are likely to have significant errors. It is also shown that if a series of instantaneous values is available, reasonable estimates can be made of the size of the errors. In model studies, such values are available in the form of the datasets used to restart the model. In experimental studies they may be in the form of individual unaveraged observations.

Description: A 20-year reanalysis experiment in the Baltic Sea using three-dimensional variational (3DVAR) method Ocean Science, 8, 827-844, 2012 Author(s): W. Fu, J. She, and M. Dobrynin A 20-year retrospective reanalysis of the ocean state in the Baltic Sea is constructed by assimilating available historical temperature and salinity profiles into an operational numerical model with three-dimensional variational (3DVAR) method. To determine the accuracy of the reanalysis, the authors present a series of comparisons to independent observations on a monthly mean basis. In the reanalysis, temperature (T) and salinity (S) fit better with independent measurements than the free run at different depths. Overall, the mean biases of temperature and salinity for the 20 year period are reduced by 0.32 °C and 0.34 psu, respectively. Similarly, the mean root mean square error (RMSE) is decreased by 0.35 °C for temperature and 0.3 psu for salinity compared to the free run. The modeled sea surface temperature, which is mainly controlled by the weather forcing, shows the least improvements due to sparse in situ observations. Deep layers, on the other hand, witness significant and stable model error improvements. In particular, the salinity related to saline water intrusions into the Baltic Proper is largely improved in the reanalysis. The major inflow events such as in 1993 and 2003 are captured more accurately as the model salinity in the bottom layer is increased by 2–3 psu. Compared to independent sea level at 14 tide gauge stations, the correlation between model and observation is increased by 2%–5%, while the RMSE is generally reduced by 10 cm. It is found that the reduction of RMSE comes mainly from the reduction of mean bias. In addition, the changes in density induced by the assimilation of T/S contribute little to the barotropic transport in the shallow Danish Transition zone. The mixed layer depth exhibits strong seasonal variations in the Baltic Sea. The basin-averaged value is about 10 m in summer and 30 m in winter. By comparison, the assimilation induces a change of 20 m to the mixed layer depth in deep waters and wintertime, whereas small changes of about 2 m occur in summer and shallow waters. It is related to the strong heating in summer and the dominant role of the surface forcing in shallow water, which largely offset the effect of the assimilation.

Description: A new method to diagnose the contribution of anthropogenic activities to temperature: temperature tagging Geoscientific Model Development Discussions, 5, 3183-3215, 2012 Author(s): V. Grewe This study presents a new methodology, called temperature tagging. It keeps track of the contributions of individual processes to temperature within a climate model simulation. As a first step and as a test bed a simple box climate model is regarded. The model consists of an atmosphere, which absorbs and emits radiation and of a surface, which reflects, absorbs and emits radiation. The tagging methodology is used to investigate the impact of the atmosphere on surface temperature. Four processes are investigated in more detail and their contribution to the surface temperature quantified: (i) shortwave influx and shortwave atmospheric absorption ("sw"), (ii) longwave atmospheric absorption due to non-CO 2 greenhouse gases ("nC"), (iii) due to a base case CO 2 concentration ("bC"), and (iv) due to an enhanced CO 2 concentration ("eC"). The differential equation for the temperature in the box climate model is decomposed into four equations for the tagged temperatures. This method is applied to investigate the contribution of longwave absorption to the surface temperature (greenhouse effect), which is calculated to be 68 K. This estimate contrasts an alternative calculation of the greenhouse effect of slightly more than 30 K based on the difference of the surface temperature with and without an atmosphere. The difference of the two estimates is due to a shortwave cooling effect and a reduced contribution of the shortwave to the total downward flux: The shortwave absorption of the atmosphere results in a reduced net shortwave flux at the surface of 192 W m −2 , leading to a cooling of the surface by 14 K. Introducing an atmosphere results in a downward longwave flux at the surface due to atmospheric absorption of 189 W m −2 , which roughly equals the net shortwave flux of 192 W m −2 . This longwave flux is a result of both, the radiation due to atmospheric temperatures and its longwave absorption. Hence the longwave absorption roughly accounts for 91 W m −2 out of a total of 381 W m −2 (roughly 25%) and therefore accounts for a temperature of 68 K. In a second experiment, the CO 2 concentration is doubled, which leads to an increase in surface temperature of 1.2 K, resulting from an temperature increase due to CO 2 of 1.9 K, due to non-CO 2 greenhouse gases of 0.6 K and a cooling of 1.3 K due to a reduced importance of the solar heating for the surface and atmospheric temperatures. These two experiments show the feasibility of temperature tagging and its potential as a diagnostic for climate simulations.

Description: Evaluation of Release-05 GRACE time-variable gravity coefficients over the ocean Ocean Science, 8, 859-868, 2012 Author(s): D. P. Chambers and J. A. Bonin The latest release of GRACE (Gravity Recovery and Climate Experiment) gravity field coefficients (Release-05, or RL05) are evaluated for ocean applications. Data have been processed using the current methodology for Release-04 (RL04) coefficients, and have been compared to output from two different ocean models. Results indicate that RL05 data from the three Science Data Centers – the Center for Space Research (CSR), GeoForschungsZentrum (GFZ), and Jet Propulsion Laboratory (JPL) – are more consistent among themselves than the previous RL04 data. Moreover, the variance of residuals with the output of an ocean model is 50–60% lower for RL05 data than for RL04 data. A more optimized destriping algorithm is also tested, which improves the results slightly. By comparing the GRACE maps with two different ocean models, we can better estimate the uncertainty in the RL05 maps. We find the standard error to be about 1 cm (equivalent water thickness) in the low- and mid-latitudes, and between 1.5 and 2 cm in the polar and subpolar oceans, which is comparable to estimated uncertainty for the output from the ocean models.

Description: The Mediterranean Ocean Colour Observing System – system development and product validation Ocean Science, 8, 869-883, 2012 Author(s): G. Volpe, S. Colella, V. Forneris, C. Tronconi, and R. Santoleri This paper presents the Mediterranean Ocean Colour Observing System in the framework of the growing demand of near real-time data emerging within the operational oceanography international context. The main issues related to the satellite operational oceanography are tied to the following: (1) the near real-time ability to track data flow uncertainty sources; (2) in case of failure, to provide backup solutions to end-users; and (3) to scientifically assess the product quality. We describe the major scientific and technological steps made to develop, maintain and improve the operational system and its products. A method for assessing the near real-time product quality is developed and its limitation discussed. Main results are concerned with the degradation, starting from mid-2010, of the MODIS Aqua channel at 443 nm with its successive recovery thanks to the new calibration scheme implemented in the recently released SeaDAS version 6.4. The product validation analysis highlights that SeaWiFS chlorophyll product over the Mediterranean Sea is the best performing in comparison with those of MODIS and MERIS. Despite their general good agreement with in situ observations, MODIS- and MERIS-derived chlorophyll present a slight and systematic underestimation of the in situ counter part. The most relevant implications induced by these results are discussed from an operational point of view.

Description: Implementation of the Fast-JX Photolysis scheme into the UKCA component of the MetUM chemistry climate model Geoscientific Model Development Discussions, 5, 3217-3260, 2012 Author(s): P. J. Telford, N. L. Abraham, A. T. Archibald, P. Braesicke, M. Dalvi, O. Morgenstern, F. M. O'Connor, N. A. D. Richards, and J. A. Pyle Atmospheric chemistry is driven by photolytic reactions, making their modelling a crucial component of atmospheric models. We describe the implementation and validation of Fast-JX, a state of the art model of interactive photolysis, into the MetUM chemistry climate model. This allows for interactive photolysis frequencies to be calculated in the troposphere and augments the calculation of the frequencies in the stratosphere by accounting for clouds and aerosols in addition to ozone. In order to demonstrate the effectiveness of this new photolysis scheme we employ new methods of validating the model, including techniques for sampling the model to compare to flight track and satellite data.

Description: COSTRICE – three model online coupling using OASIS: problems and solutions Geoscientific Model Development Discussions, 5, 3261-3310, 2012 Author(s): H. T. M. Ho, B. Rockel, H. Kapitza, B. Geyer, and E. Meyer The coupled system COSTRICE is developed for the first time in order to reproduce the interactions and feedbacks between atmosphere, ocean and sea-ice in a two-way online coupled model system containing three component models for regional climate simulations over Baltic Sea and North Sea regions. The regional climate model CCLM 1 is coupled to the regional ocean model TRIMNP 1 and the sea ice model CICE 1 via the coupler OASIS3. In this study, CCLM is setup with a horizontal grid mesh size of 50 km and 32 vertical atmosphere layers and driven by the 6-h ERA-interim reanalysis data as initial and boundary conditions. TRIMNP is setup with a horizontal grid mesh size of 12.8 km and 50 vertical ocean levels. CICE calculates ice in 5 categories and runs with the same horizontal resolution as TRIMNP but only over the Baltic Sea and the Kattegat Bay of the North Sea. In a two-way online coupling process, CCLM is linked to TRIMNP through sea surface temperature (SST) as lower boundary condition every 3 h and TRIMNP is driven by 1-h atmospheric state variables and fluxes of CCLM. The data exchange processes between TRIMNP and CICE as well as from CCLM to CICE take place with an interval of 3 h. The coupled model is applied in a study for climate simulations over Baltic Sea and North Sea regions in 1997. The coupled system is set up to run in parallel on the super computing system IBM-power 6 at the German Climate Computing Center (DKRZ). 1 See Table A1.

Description: A generalized tagging method Geoscientific Model Development Discussions, 5, 3311-3324, 2012 Author(s): V. Grewe The understanding of causes of changes in climate-chemistry simulations is an important, but often challenging task. In atmospheric chemistry, one approach is to tag species according to their origin (e.g. emission categories) and to inherit these tags to other species during subsequent reactions. This concept was recently employed to calculate the contribution of atmospheric processes to temperature. Here a new concept for tagging any state variable is presented. This generalized tagging method results from a sensitivity analysis of the forcing terms of the right hand side of the governing differential equations. In a couple of examples, the consistency with previous approaches is shown. Since the method is based on a ratio describing relative sensitivities, singularities occur where the method is not applicable. For some applications, like in atmospheric chemistry, these singularities can easily be removed. However, one theoretical example is given, where this method is not applicable at all.

Description: Technical Note: Improving computational efficiency in large linear inverse problems: an example from carbon dioxide flux estimation Geoscientific Model Development Discussions, 5, 3325-3342, 2012 Author(s): V. Yadav and A. M. Michalak Addressing a variety of questions within Earth science disciplines entails the inference of the spatio-temporal distribution of parameters of interest based on observations of related quantities. Such estimation problems often represent inverse problems that are formulated as linear optimization problems. Computational limitations arise when the number of observations and/or the size of the discretized state space become large, especially if the inverse problem is formulated in a probabilistic framework and therefore aims to assess the uncertainty associated with the estimates. This work proposes two approaches to lower the computational costs and memory requirements for large linear space-time inverse problems, taking the Bayesian approach for estimating carbon dioxide (CO 2 ) emissions and uptake (a.k.a. fluxes) as a prototypical example. The first algorithm can be used to efficiently multiply two matrices, as long as one can be expressed as a Kronecker product of two smaller matrices, a condition that is typical when multiplying a sensitivity matrix by a covariance matrix in the solution of inverse problems. The second algorithm can be used to compute a posteriori uncertainties directly at aggregated spatio-temporal scales, which are the scales of most interest in many inverse problems. Both algorithms have significantly lower memory requirements and computational complexity relative to direct computation of the same quantities (O( n 2.5 ) vs. O( n 3 )). For an examined benchmark problem, the two algorithms yielded a three and six order of magnitude increase in computational efficiency, respectively, relative to direct computation of the same quantities. Sample computer code is provided for assessing the computational and memory efficiency of the proposed algorithms for matrices of different dimensions.

Description: Quality assessment concept of the World Data Center for Climate and its application to CMIP5 data Geoscientific Model Development Discussions, 5, 781-802, 2012 Author(s): M. Stockhause, H. Höck, F. Toussaint, and M. Lautenschlager The preservation of data in a high state of quality and suitable for interdisciplinary use is one of the most pressing and challenging current issues in long-term archiving. For high volume data such as climate model data, the data and data replica are no longer stored centrally but distributed over several local data repositories, e.g. the data of the Climate Model Intercomparison Project No. 5 (CMIP5). The most important part of the data is to be published as DOI according to the World Data Center for Climate's (WDCC) application of the DataCite regulations. The integrated part of WDCC's data publication process, the data quality assessment, was adapted to the requirements of a federated data infrastructure. A concept of a distributed and federated quality assessment procedure was developed, in which the work load and responsibility for quality control is shared between the three primary CMIP5 data centers: Program for Climate Model Diagnosis and Intercomparison (PCMDI), British Atmospheric Data Centre (BADC), and WDCC. This distributed quality control concept, its pilot implementation for CMIP5, and first experiences are presented.

Description: SPITFIRE-2: an improved fire module for Dynamic Global Vegetation Models Geoscientific Model Development Discussions, 5, 2347-2443, 2012 Author(s): M. Pfeiffer and J. O. Kaplan Fire is the primary disturbance factor in many terrestrial ecosystems. Wildfire alters vegetation structure and composition, affects carbon storage and biogeochemical cycling, and results in the release of climatically relevant trace gases, including CO 2 , CO, CH 4 , NO x , and aerosols. Assessing the impacts of global wildfire on centennial to multi-millennial timescales requires the linkage of process-based fire modeling with vegetation modeling using Dynamic Global Vegetation Models (DGVMs). Here we present a new fire module, SPITFIRE-2, and an update to the LPJ-DGVM that includes major improvements to the way in which fire occurrence, behavior, and the effect of fire on vegetation is simulated. The new fire module includes explicit calculation of natural ignitions, the representation of multi-day burning and coalescence of fires and the calculation of rates of spread in different vegetation types, as well as a simple scheme to model crown fires. We describe a new representation of anthropogenic biomass burning under preindustrial conditions that distinguishes the way in which the relationship between humans and fire are different between hunter-gatherers, obligate pastoralists, and farmers. Where and when available, we evaluate our model simulations against remote-sensing based estimates of burned area. While wildfire in much of the modern world is largely influenced by anthropogenic suppression and ignitions, in those parts of the world where natural fire is still the dominant process, e.g. in remote areas of the boreal forest, our results demonstrate a significant improvement in simulated burned area over previous models. With its unique properties of being able to simulate preindustrial fire, the new module we present here is particularly well suited for the investigation of climate-human-fire relationships on multi-millennial timescales.

Description: The Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP): overview and description of models, simulations and climate diagnostics Geoscientific Model Development Discussions, 5, 2445-2502, 2012 Author(s): J.-F. Lamarque, D. T. Shindell, B. Josse, P. J. Young, I. Cionni, V. Eyring, D. Bergmann, P. Cameron-Smith, W. J. Collins, R. Doherty, S. Dalsoren, G. Faluvegi, G. Folberth, S. J. Ghan, L. W. Horowitz, Y. H. Lee, I. A. MacKenzie, T. Nagashima, V. Naik, D. Plummer, M. Righi, S. Rumbold, M. Schulz, R. B. Skeie, D. S. Stevenson, S. Strode, K. Sudo, S. Szopa, A. Voulgarakis, and G. Zeng The Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP) consists of a series of timeslice experiments targeting the long-term changes in atmospheric composition between 1850 and 2100, with the goal of documenting radiative forcing and the associated composition changes. Here we introduce the various simulations performed under ACCMIP and the associated model output. The ACCMIP models have a wide range of horizontal and vertical resolutions, vertical extent, chemistry schemes and interaction with radiation and clouds. While anthropogenic and biomass burning emissions were specified for all time slices in the ACCMIP protocol, it is found that the natural emissions lead to a significant range in emissions, mostly for ozone precursors. The analysis of selected present-day climate diagnostics (precipitation, temperature, specific humidity and zonal wind) reveals biases consistent with state-of-the-art climate models. The model-to-model comparison of changes in temperature, specific humidity and zonal wind between 1850 and 2000 and between 2000 and 2100 indicates mostly consistent results, but with outliers different enough to possibly affect their representation of climate impact on chemistry.

Description: Setup of the PMIP3 paleoclimate experiments conducted using an Earth System Model, MIROC-ESM Geoscientific Model Development Discussions, 5, 2527-2569, 2012 Author(s): T. Sueyoshi, R. Ohgaito, A. Yamamoto, M. O. Chikamoto, T. Hajima, H. Okajima, M. Yoshimori, M. Abe, R. O'ishi, F. Saito, S. Watanabe, M. Kawamiya, and A. Abe-Ouchi The importance of climate model evaluation using paleoclimate simulations for better future climate projections has been recognized by the Intergovernmental Panel on Climate Change. In recent years, Earth System Models (ESMs) were developed to investigate carbon-cycle climate feedback, as well as to project the future climate. Paleoclimate events, especially those associated with the variations in atmospheric CO 2 level or land vegetation, provide suitable benchmarks to evaluate ESMs. Here we present implementations of the paleoclimate experiments proposed by the Coupled Model Intercomparison Project phase 5/Paleoclimate Modelling Intercomparison Project phase 3 (CMIP5/PMIP3) using an Earth System Model, MIROC-ESM. In this paper, experimental settings and procedures of the mid-Holocene, the Last Glacial Maximum, and the Last Millennium experiments are explained. The first two experiments are time slice experiments and the last one is a transient experiment. The complexity of the model requires various steps to correctly configure the experiments. Several basic outputs are also shown.

Description: Aerosol-climate interactions in the Norwegian Earth System Model – NorESM Geoscientific Model Development Discussions, 5, 2599-2685, 2012 Author(s): A. Kirkevåg, T. Iversen, Ø. Seland, C. Hoose, J. E. Kristjánsson, H. Struthers, A. M. L. Ekman, S. Ghan, J. Griesfeller, E. D. Nilsson, and M. Schulz The objective of this study is to document and evaluate recent changes and updates to the module for aerosols and aerosol-cloud-radiation interactions in the atmospheric module CAM4-Oslo of the Norwegian Earth System Model (NorESM). Particular attention is paid to the role of natural organics, sea salt, and mineral dust in determining the gross aerosol properties as well as the anthropogenic contribution to these properties and the associated direct and indirect radiative forcing. The aerosol module is extended from earlier versions that have been published, and includes life-cycling of sea-salt, mineral dust, particulate sulphate, black carbon, and primary and secondary organics. The impacts of most of the numerous changes since previous versions are thoroughly explored by sensitivity experiments. The most important changes are: modified prognostic sea salt emissions; updated treatment of precipitation scavenging and gravitational settling; inclusion of biogenic primary organics and methane sulphonic acid (MSA) from oceans; almost doubled production of land-based biogenic secondary organic aerosols (SOA); and increased ratio of organic matter to organic carbon (OM / OC) for biomass burning aerosols from 1.4 to 2.6. Compared with in-situ measurements and remotely sensed data, the new treatments of sea salt and dust aerosols give smaller biases in near surface mass concentrations and aerosol optical depth than in the earlier model version. The model biases for mass concentrations are approximately unchanged for sulphate and BC. The enhanced levels of modeled OM yield improved overall statistics, even though OM is still underestimated in Europe and over-estimated in North America. The global direct radiative forcing (DRF) at the top of the atmosphere has changed from a small positive value to −0.08 W m −2 in CAM4-Oslo. The sensitivity tests suggest that this change can be attributed to the new treatment of biomass burning aerosols and gravitational settling. Although it has not been a goal in this study, the new DRF estimate is closer both to the median model estimate from the AeroCom inter-comparison and the best estimate in IPCC AR4. Estimated DRF at the ground surface has increased by ca. 60%, to −1.89 W m −2 . We show that this can be explained by new emission data and omitted mixing of constituents between updrafts and downdrafts in convective clouds. The increased abundance of natural OM and the introduction of a cloud droplet spectral dispersion formulation are the most important contributions to a considerably decreased estimate of the indirect radiative forcing (IndRF). The IndRF is also found to be sensitive to assumptions about the coating of insoluble aerosols by sulphate and OM. The IndRF of −1.2 W m −2 , which is closer to the IPCC AR4 estimates than the previous estimate of −1.9 W m −2 , has thus been obtained without imposing unrealistic artificial lower bounds on cloud droplet number concentrations.

Description: Inclusion of Ash and SO 2 emissions from volcanic eruptions in WRF-CHEM: development and some applications Geoscientific Model Development Discussions, 5, 2571-2597, 2012 Author(s): M. Stuefer, S. R. Freitas, G. Grell, P. Webley, S. Peckham, and S. A. McKeen We describe a new functionality within the Weather Research and Forecasting model with coupled Chemistry (WRF-Chem) that allows simulating emission, transport, dispersion, transformation and sedimentation of pollutants released during volcanic activities. Emissions from both an explosive eruption case and relatively calm degassing situation are considered using the most recent volcanic emission databases. A preprocessor tool provides emission fields and additional information needed to establish the initial three-dimensional cloud umbrella/vertical distribution within the transport model grid, as well as the timing and duration of an eruption. From this source condition, the transport, dispersion and sedimentation of the ash-cloud can be realistically simulated by WRF-Chem using its own dynamics, physical parameterization as well as data assimilation. Examples of model validation include a comparison of tephra fall deposits from the 1989 eruption of Mount Redoubt (Alaska), and the dispersion of ash from the 2010 Eyjafjallajökull eruption in Iceland. Both model applications show good coincidence between WRF-Chem and observations.

Description: Net primary productivity, upwelling and coastal currents in the Gulf of Ulloa, Baja California, México Ocean Science, 8, 703-711, 2012 Author(s): E. González-Rodríguez, A. Trasviña-Castro, G. Gaxiola-Castro, L. Zamudio, and R. Cervantes-Duarte The Gulf of Ulloa, a highly productive area off the western coast of the Baja California Peninsula, is examined for five successive years (2003–2007) by using satellite data and seasonal net primary productivity (NPP) estimates obtained from a vertical generalised production model. The results identify that northwestern winds blow parallel to the coast throughout the year. However, highest NPP occurs from March to June. During this period, an equatorward coastal current transports water from neighbouring upwelling areas to the northern Gulf of Ulloa and in combination with local upwelling, which injects nutrients into the euphotic zone, produce the observed increase in NPP. The opposite situation occurs in late summer when a warm poleward current of tropical characteristics arrives and inhibits the productivity in the whole region and generates the yearly lowest NPP levels. Our findings reveal the importance of lateral advection in the modulation of the primary productivity in this subtropical upwelling region.

Description: Assessment of a physical-biogeochemical coupled model system for operational service in the Baltic Sea Ocean Science, 8, 683-701, 2012 Author(s): Z. Wan, J. She, M. Maar, L. Jonasson, and J. Baasch-Larsen Thanks to the abundant observation data, we are able to deploy the traditional point-to-point comparison and statistical measures in combination with a comprehensive model validation scheme to assess the skills of the biogeochemical model ERGOM in providing an operational service for the Baltic Sea. The model assessment concludes that the operational products can resolve the main observed seasonal features for phytoplankton biomass, dissolved inorganic nitrogen, dissolved inorganic phosphorus and dissolved oxygen in euphotic layers as well as their vertical profiles. This assessment reflects that the model errors of the operational system at the current stage are mainly caused by insufficient light penetration, excessive organic particle export downward, insufficient regional adaptation and some from improper initialization. This study highlights the importance of applying multiple schemes in order to assess model skills rigidly and identify main causes for major model errors.

Description: A web-based software tool to estimate unregulated daily streamflow at ungauged rivers Geoscientific Model Development Discussions, 5, 2503-2526, 2012 Author(s): S. A. Archfield, P. A. Steeves, J. D. Guthrie, and K. G. Ries III Streamflow information is critical for solving any number of hydrologic problems. Often times, streamflow information is needed at locations which are ungauged and, therefore, have no observations on which to base water management decisions. Furthermore, there has been increasing need for daily streamflow time series to manage rivers for both human and ecological functions. To facilitate negotiation between human and ecological demands for water, this paper presents the first publically-available, map-based, regional software tool to interactively estimate daily streamflow time series at any user-selected ungauged river location. The map interface allows users to locate and click on a river location, which then returns estimates of daily streamflow for the location selected. For the demonstration region in the northeast United States, daily streamflow was shown to be reliably estimated by the software tool, with efficiency values computed from observed and estimated streamflows ranging from 0.69 to 0.92. The software tool provides a general framework that can be applied to other regions for which daily streamflow estimates are needed.

Description: An operational model for the West Iberian coast: products and services Ocean Science, 8, 713-732, 2012 Author(s): M. Mateus, G. Riflet, P. Chambel, L. Fernandes, R. Fernandes, M. Juliano, F. Campuzano, H. de Pablo, and R. Neves This paper presents the structure and application of a regional scale operational modelling tool for the West Iberian coast, and discusses its potential for products and services for both scientific and coastal management activities. The forecasting suite includes nested hydrodynamic models forced with up-to-date meteorological forecast data and large-scale model results. The present status of the system and its recent upgrades are reviewed, offering a general description of the main components of the system: the forcing data, the circulation model, the model outputs and the validation methodology of model results. Seasonal differences in temperature, salinity and current velocity fields are illustrated and show satisfactory reproduction of the top and deep layer thermodynamics. The system provides boundary forcing for a number of local-scale model applications via downscaling of the solution and enables potential products and services from which civil society will benefit.

Description: On the shelf resonances of the Gulf of Carpentaria and the Arafura Sea Ocean Science, 8, 733-750, 2012 Author(s): D. J. Webb A numerical model is used to investigate the resonances of the Gulf of Carpentaria and the Arafura Sea, and the additional insights that come from extending the analysis into the complex angular velocity plane. When the model is forced at the shelf edge with physically realistic real values of the angular velocity, the response functions at points within the region show maxima and other behaviour which imply that resonances are involved but provide little additional information. The study is then extended to complex angular velocities, and the results then show a clear pattern of gravity wave and Rossby wave like resonances. The properties of the resonances are investigated and used to reinterpret the response at real values of angular velocity. It is found that in some regions the response is dominated by modes trapped between the shelf edge and the coast or between opposing coastlines. In other regions the resonances show cooperative behaviour, possibly indicating the importance of other physical processes.

Description: The analysis of large-scale turbulence characteristics in the Indonesian seas derived from a regional model based on the Princeton Ocean Model Ocean Science, 8, 615-631, 2012 Author(s): K. O'Driscoll and V. Kamenkovich Turbulence characteristics in the Indonesian seas on the horizontal scale of order of 100 km were calculated with a regional model of the Indonesian seas circulation in the area based on the Princeton Ocean Model (POM). As is well known, the POM incorporates the Mellor–Yamada turbulence closure scheme. The calculated characteristics are: twice the turbulence kinetic energy per unit mass, q 2 ; the turbulence master scale, ℓ; mixing coefficients of momentum, K M ; and temperature and salinity, K H ; etc. The analyzed turbulence has been generated essentially by the shear of large-scale ocean currents and by the large-scale wind turbulence. We focused on the analysis of turbulence around important topographic features, such as the Lifamatola Sill, the North Sangihe Ridge, the Dewakang Sill, and the North and South Halmahera Sea Sills. In general, the structure of turbulence characteristics in these regions turned out to be similar. For this reason, we have carried out a detailed analysis of the Lifamatola Sill region because dynamically this region is very important and some estimates of mixing coefficients in this area are available. Briefly, the main results are as follows. The distribution of q 2 is quite adequately reproduced by the model. To the north of the Lifamatola Sill (in the Maluku Sea) and to the south of the Sill (in the Seram Sea), large values of q 2 occur in the deep layer extending several hundred meters above the bottom. The observed increase of q 2 near the very bottom is probably due to the increase of velocity shear and the corresponding shear production of q 2 very close to the bottom. The turbulence master scale, ℓ, was found to be constant in the main depth of the ocean, while ℓ rapidly decreases close to the bottom, as one would expect. However, in deep profiles away from the sill, the effect of topography results in the ℓ structure being unreasonably complicated as one moves towards the bottom. Values of 15 to 20 × 10 −4 m 2 s −1 were obtained for K M and K H in deep water in the vicinity of the Lifamatola Sill. These estimates agree well with basin-scale averaged values of 13.3 × 10 −4 m 2 s −1 found diagnostically for K H in the deep Banda and Seram Seas (Gordon et al., 2003) and a value of 9.0 × 10 −4 m 2 s −1 found diagnostically for K H for the deep Banda Sea system (van Aken et al., 1988). The somewhat higher simulated values can be explained by the presence of steep topography around the sill.

Description: TOPAZ4: an ocean-sea ice data assimilation system for the North Atlantic and Arctic Ocean Science, 8, 633-656, 2012 Author(s): P. Sakov, F. Counillon, L. Bertino, K. A. Lisæter, P. R. Oke, and A. Korablev We present a detailed description of TOPAZ4, the latest version of TOPAZ – a coupled ocean-sea ice data assimilation system for the North Atlantic Ocean and Arctic. It is the only operational, large-scale ocean data assimilation system that uses the ensemble Kalman filter. This means that TOPAZ features a time-evolving, state-dependent estimate of the state error covariance. Based on results from the pilot MyOcean reanalysis for 2003–2008, we demonstrate that TOPAZ4 produces a realistic estimate of the ocean circulation in the North Atlantic and the sea-ice variability in the Arctic. We find that the ensemble spread for temperature and sea-level remains fairly constant throughout the reanalysis demonstrating that the data assimilation system is robust to ensemble collapse. Moreover, the ensemble spread for ice concentration is well correlated with the actual errors. This indicates that the ensemble statistics provide reliable state-dependent error estimates – a feature that is unique to ensemble-based data assimilation systems. We demonstrate that the quality of the reanalysis changes when different sea surface temperature products are assimilated, or when in-situ profiles below the ice in the Arctic Ocean are assimilated. We find that data assimilation improves the match to independent observations compared to a free model. Improvements are particularly noticeable for ice thickness, salinity in the Arctic, and temperature in the Fram Strait, but not for transport estimates or underwater temperature. At the same time, the pilot reanalysis has revealed several flaws in the system that have degraded its performance. Finally, we show that a simple bias estimation scheme can effectively detect the seasonal or constant bias in temperature and sea-level.

Description: Using multi-model averaging to improve the reliability of catchment scale nitrogen predictions Geoscientific Model Development Discussions, 5, 2289-2310, 2012 Author(s): J.-F. Exbrayat, N. R. Viney, H.-G. Frede, and L. Breuer Hydro-biogeochemical models are used to foresee the impact of mitigation measures on water quality. Usually, scenario-based studies rely on single model applications. This is done in spite of the widely acknowledged advantage of ensemble approaches to cope with structural model uncertainty issues. As an attempt to demonstrate the reliability of such multi-model efforts in the hydro-biogeochemical context, this methodological contribution proposes an adaptation of the Reliability Ensemble Averaging (REA) philosophy to nitrogen losses predictions. A total of 4 models are used to predict the total nitrogen (TN) losses from the well-monitored Ellen Brook catchment in Western Australia. Simulations include re-predictions of current conditions and a set of straightforward management changes targeting fertilization scenarios. Results show that, in spite of good calibration metrics, one of the models provides a very different response to management changes. This behaviour leads the simple average of the ensemble members to also predict reductions in TN export that are not in agreement with the other models. However, considering the convergence of model predictions in the more sophisticated REA approach assigns more weight to previously less well calibrated models that are more in agreement with each other. This method also avoids having to disqualify any of the ensemble members, which is always sensible.

Description: Atlantic transport variability at 25° N in six hydrographic sections Ocean Science, 8, 497-523, 2012 Author(s): C. P. Atkinson, H. L. Bryden, S. A. Cunningham, and B. A. King In January and February 2010, a sixth transatlantic hydrographic section was completed across 25° N, extending the hydrographic record at this latitude to over half a century. In combination with continuous transport measurements made since 2004 at 26.5° N by the Rapid-WATCH project, we reassess transport variability in the 25° N hydrographic record. Past studies of transport variability at this latitude have assumed transport estimates from each hydrographic section to represent annual average conditions. In this study the uncertainty in this assumption is assessed through use of Rapid-WATCH observations to quantify sub-seasonal and seasonal transport variability. Whilst in the upper-ocean no significant interannual or decadal transport variability are identified in the hydrographic record, in the deep ocean transport variability in both depth and potential temperature classes suggests some interannual or decadal variability may have occurred. This is particularly striking in the lower North Atlantic Deep Water where southward transports prior to 1998 were greater than recent transports by several Sverdrups. Whilst a cooling and freshening of Denmark Straits Overflow Water has occurred which is coincident with these transport changes, these water mass changes appear to be density compensated. Transport changes are the result of changing velocity shear in the vicinity of the Deep Western Boundary Current.

Description: Propagation and dissipation of internal tides in the Oslofjord Ocean Science, 8, 525-543, 2012 Author(s): A. Staalstrøm, E. Aas, and B. Liljebladh Observations of velocity, pressure, temperature and salinity in the inner Oslofjord have been analysed to provide new information about the relationships between internal tides generated by tidal currents across the Drøbak Sill and dissipation and diffusivity in the fjord. The most energetic vertical displacement of density surfaces inside the sill is associated with the first internal mode that has maximum amplitude around sill depth. The amplitude of the vertical displacement around sill depth correlates with the amplitude of the surface elevation, and, at a distance of 1 km inside the sill, the ratio between the amplitudes is 38, decreasing to 11 at a distance of 10 km. The greatest vertical displacements inside the sill, however, are found at 40 m depth. These latter internal waves are not associated with a first-mode internal tide, but are rather associated with higher internal modes controlled by stratification. The energy flux of the internal wave propagating from the Drøbak Sill into the inner fjord on the east side of the Håøya Island is estimated to vary in the range 155–430 kW. This is the same order of magnitude as the estimated barotropic energy loss over the Drøbak Sill (250 kW), but only 4–10% of the total barotropic flux. Approximately 40–70% of the internal energy flux is lost within a distance of 10 km from the sill. The mean diffusivity below 90 m depth in this area (~20 cm 2 s −1 ) is more than four times higher than in the rest of the fjord (~5 cm 2 s −1 or less).

Description: Development of high resolution land surface parameters for the Community Land Model Geoscientific Model Development Discussions, 5, 1435-1481, 2012 Author(s): Y. Ke, L. R. Leung, M. Huang, A. M. Coleman, H. Li, and M. S. Wigmosta There is a growing need for high-resolution land surface parameters as land surface models are being applied at increasingly higher spatial resolution offline as well as in regional and global models. The default land surface parameters for the most recent version of the Community Land Model (i.e. CLM 4.0) are at 0.5° or coarser resolutions, released with the model from the National Center for Atmospheric Research (NCAR). Plant Functional Types (PFTs), vegetation properties such as Leaf Area Index (LAI), Stem Area Index (SAI), and non-vegetated land covers were developed using remotely-sensed datasets retrieved in late 1990's and the beginning of this century. In this study, we developed new land surface parameters for CLM 4.0, specifically PFTs, LAI, SAI and non-vegetated land cover composition, at 0.05° resolution globally based on the most recent MODIS land cover and improved MODIS LAI products. Compared to the current CLM 4.0 parameters, the new parameters produced a decreased coverage by bare soil and trees, but an increased coverage by shrub, grass, and cropland. The new parameters result in a decrease in global seasonal LAI, with the biggest decrease in boreal forests; however, the new parameters also show a large increase in LAI in tropical forest. Differences between the new and the current parameters are mainly caused by changes in the sources of remotely sensed data and the representation of land cover in the source data. The new high-resolution land surface parameters have been used in a coupled land-atmosphere model (WRF-CLM) applied to the western US to demonstrate their use in high-resolution modeling. Future work will include global offline CLMsimulations to examine the impacts of source data resolution and subsequent land parameter changes on simulated land surface processes.

Description: The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions Geoscientific Model Development Discussions, 5, 1503-1560, 2012 Author(s): A. B. Guenther, X. Jiang, C. L. Heald, T. Sakulyanontvittaya, T. Duhl, L. K. Emmons, and X. Wang The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1) is a modeling framework for estimating fluxes of 147 biogenic compounds between terrestrial ecosystems and the atmosphere using simple mechanistic algorithms to account for the major known processes controlling biogenic emissions. It is available as an offline code and has also been coupled into land surface models and atmospheric chemistry models. MEGAN2.1 is an update from the previous versions including MEGAN2.0 for isoprene emissions and MEGAN2.04, which estimates emissions of 138 compounds. Isoprene comprises about half of the estimated total global biogenic volatile organic compound (BVOC) emission of 1 Pg (1000 Tg or 10 15 g). Another 10 compounds including methanol, ethanol, acetaldehyde, acetone, α-pinene, β-pinene, t −β-ocimene, limonene, ethene, and propene together contribute another 30% of the estimated emission. An additional 20 compounds (mostly terpenoids) are associated with another 17% of the total emission with the remaining 3% distributed among 125 compounds. Emissions of 41 monoterpenes and 32 sesquiterpenes together comprise about 15% and 3%, respectively, of the total global BVOC emission. Tropical trees cover about 18% of the global land surface and are estimated to be responsible for 60% of terpenoid emissions and 48% of other VOC emissions. Other trees cover about the same area but are estimated to contribute only about 10% of total emissions. The magnitude of the emissions estimated with MEGAN2.1 are within the range of estimates reported using other approaches and much of the differences between reported values can be attributed to landcover and meteorological driving variables. The offline version of MEGAN2.1 source code and driving variables is available from http://acd.ucar.edu/~guenther/MEGAN/MEGAN.htm and the version integrated into the Community Land Model version 4 (CLM4) can be downloaded from http://www.cesm.ucar.edu/ .

Description: A simulation study of the ensemble-based data assimilation of satellite-borne lidar aerosol observations Geoscientific Model Development Discussions, 5, 1877-1947, 2012 Author(s): T. T. Sekiyama, T. Y. Tanaka, and T. Miyoshi A four-dimensional ensemble-based data assimilation system was assessed by observing system simulation experiments (OSSEs), in which the CALIPSO satellite was emulated via simulated satellite-borne lidar aerosol observations. Its performance over athree-month period was validated according to the Method for Object-based Diagnostic Evaluation (MODE), using aerosol optical thickness (AOT) distributions in East Asia as the objects of analysis. Consequently, this data assimilation system demonstrated the ability to produce better analyses of sulfate and dust aerosols in comparison to a free-running simulation model. For example, the mean centroid distance (from the truth) over a three-month collection period of aerosol plumes was improved from 2.15 grids (≈ 600 km) to 1.45 grids (≈ 400 km) for sulfate aerosols and from 2.59 grids (≈ 750 km) to 1.14 grids (≈ 330 km) for dust aerosols; the mean area ratio (to the truth) over a three-month collection period of aerosol plumes was improved from 0.49 to 0.76 for sulfate aerosols and from 0.51 to 0.72 for dust aerosols. The satellite-borne lidar data assimilation successfully improved the aerosol plume analysis and the dust emission estimation in the OSSEs. These results present great possibilities for the beneficial use of lidar data, whose distribution is vertically/temporally dense but horizontally sparse, when coupled with a four-dimensional data assimilation system. In addition, sensitivity tests were conducted, and their results indicated that the degree of freedom to control the aerosol variables was probably limited in the data assimilation because the meteorological field in the system was constrained to weather reanalysis using Newtonian relaxation. Further improvements to the aerosol analysis can be performed through the simultaneous assimilation of aerosol observations with meteorological observations. The OSSE results strongly suggest that the use of real CALIPSO data will have a beneficial effect on obtaining more accurate sulfate and dust aerosol analyses. Furthermore, the use of the same OSSE technique will allow us to perform a prior assessment of the next-generation lidar satellite EarthCARE, which will be launched in 2015.

Description: Sensitivity analysis and calibration of a soil carbon model (SoilGen2) in two contrasting loess forest soils Geoscientific Model Development Discussions, 5, 1817-1849, 2012 Author(s): Y. Y. Yu, P. A. Finke, H. B. Wu, and Z. T. Guo To accurately estimate past terrestrial carbon pools is the key to understand the global carbon cycle and its relationship with the climate system. SoilGen2 is a useful tool to obtain aspects of soil properties (including carbon content) by simulating soil formation processes; thus it offers an opportunity for past soil carbon pool reconstruction. In order to apply it to various environmental conditions, parameters related to carbon cycle process in SoilGen2 are calibrated based on 6 soil pedons from two typical loess deposition regions (Belgium and China). Sensitivity analysis using Morris' method shows that decomposition rate of humus ( k HUM ), fraction of incoming plant material as leaf litter (fr ecto ) and decomposition rate of resistant plant material ( k RPM ) are 3 most sensitive parameters that would cause the greatest uncertainty in simulated change of soil organic carbon in both regions. According to the principle of minimizing the difference between simulated and measured organic carbon by comparing quality indices, the suited values of k HUM , fr ecto and k RPM in the model are deduced step by step. The difference of calibrated parameters between Belgium and China may be attributed to their different vegetation types and climate conditions. This calibrated model is improved for better simulation of carbon change in the whole pedon and has potential for future modeling of carbon cycle in paleosols.

Description: Activation of the operational ecohydrodynamic model (3-D CEMBS) – the hydrodynamic part Geoscientific Model Development Discussions, 5, 1851-1875, 2012 Author(s): L. Dzierzbicka-Głowacka, J. Jakacki, M. Janecki, and A. Nowicki The paper presents a description of the hydrodynamic part of the coupled ice-ocean model that also includes ecosystem predictive model for evaluation of the condition of the marine environment and the Baltic ecosystem, as well as a preliminary empirical verification of the operational hydrodynamic model based on the POP code in order to determine the consistence between the results obtained from the model and experimental results for the sea surface temperature. The current Baltic Sea model is based on the Community Earth System Model (CESM from NCAR – National Center for Atmospheric Research). CESM was adopted for the Baltic Sea as a coupled sea-ice model. It consists of the Community Ice Code (CICE model, version 4.0) and the Parallel Ocean Program (POP, version 2.1). The models are coupled through the coupler (CPL7), which is based on the Model Coupling Toolkit (MCT) routines. The current horizontal resolution is about 2 km (1/48 degrees). The ocean model has 21 vertical levels. The driver time step is 1440 s and it is also coupling the time step. The ocean model time step is about 480 s (8 min). Currently, the model is forced by fields from the European Center for Medium Weather Forecast. In the operational mode, 48-h atmospheric forecasts are used, which are supplied by the UM model of the Interdisciplinary Centre for Mathematical and Computational Modelling of the Warsaw University. The model of the marine ecosystem is the right tool for monitoring the state and bioproductivity of the marine ecosystem and forecasting the physical and ecological changes in the studied basin.

Description: Operational SAR-based sea ice drift monitoring over the Baltic Sea Ocean Science, 8, 473-483, 2012 Author(s): J. Karvonen An algorithm for computing ice drift from pairs of synthetic aperture radar (SAR) images covering a common area has been developed at FMI. The algorithm has been developed based on the C-band SAR data over the Baltic Sea. It is based on phase correlation in two scales (coarse and fine) with some additional constraints. The algorithm has been running operationally in the Baltic Sea from the beginning of 2011, using Radarsat-1 ScanSAR wide mode and Envisat ASAR wide swath mode data. The resulting ice drift fields are publicly available as part of the MyOcean EC project. The SAR-based ice drift vectors have been compared to the drift vectors from drifter buoys in the Baltic Sea during the first operational season, and also these validation results are shown in this paper. Also some navigationally useful sea ice quantities, which can be derived from ice drift vector fields, are presented.

Description: Tagged ozone mechanism for MOZART-4, CAM-chem, and other chemical transport models Geoscientific Model Development Discussions, 5, 1949-1985, 2012 Author(s): L. K. Emmons, P. G. Hess, J.-F. Lamarque, and G. G. Pfister A procedure for tagging ozone produced from NO sources through updates to an existing chemical mechanism is described, and results from its implementation in the Model for Ozone and Related chemical Tracers (MOZART-4), a global chemical transport model, are presented. Artificial tracers are added to the mechanism, thus not affecting the standard chemistry. The results are linear in the troposphere, i.e., the sum of ozone from individual tagged sources equals the ozone from all sources to within 3% in zonal mean monthly averages. The stratospheric ozone contribution to the troposphere determined from the difference between total ozone and ozone from all tagged sources is significantly less than estimates using a traditional stratospheric ozone tracer (8 vs 20 ppbv at the surface). The commonly used technique of perturbing NO emissions by 20% in a region to determine its ozone contribution is compared to the tagging technique, showing that the tagged ozone is 2–4 times the ozone contribution that was deduced from perturbing emissions.

Description: Coupling technologies for Earth System Modelling Geoscientific Model Development Discussions, 5, 1987-2006, 2012 Author(s): S. Valcke, V. Balaji, A. Craig, C. DeLuca, R. Dunlap, R. W. Ford, R. Jacob, J. Larson, R. O'Kuinghttons, G. D. Riley, and M. Vertenstein This paper presents a review of the software currently used in climate modelling in general and in CMIP5 in particular to couple the numerical codes representing the different components of the Earth system. The coupling technologies presented show common features, such as the ability to communicate and regrid data, but also offer different functions and implementations. Design characteristics of the different approaches are discussed as well as future challenges arising from the increasing complexity of scientific problems and computing platforms.

Description: Downscale cascades in tracer transport test cases: an intercomparison of the dynamical cores in the Community Atmosphere Model CAM5 Geoscientific Model Development Discussions, 5, 1781-1816, 2012 Author(s): J. Kent, C. Jablonowski, J. P. Whitehead, and R. B. Rood The accurate modelling of cascades to unresolved scales is an important part of the tracer transport component of dynamical cores of weather and climate models. This paper aims to investigate the ability of the advection schemes in the National Center for Atmospheric Research's Community Atmosphere Model version 5 (CAM5) to model this cascade. In order to quantify the effects of the different advection schemes in CAM5, four two-dimensional tracer transport test cases are presented. Three of the tests stretch the tracer below the scale of coarse resolution grids to ensure the downscale cascade of tracer variance. These results are compared with a high resolution reference solution, which is simulated on a resolution fine enough to resolve the tracer during the test. The fourth test has two separate flow cells, and is designed so that any tracer in the Western Hemisphere should not pass into the Eastern Hemisphere. This is to test whether the diffusion in transport schemes, often in the form of explicit hyper-diffusion terms or implicit through monotonic limiters, contains unphysical mixing. An intercomparison of three of the dynamical cores of the National Center for Atmospheric Research's Community Atmosphere Model version 5 is performed. The results show that the finite-volume (CAM-FV) and spectral element (CAM-SE) dynamical cores model the downscale cascade of tracer variance better than the semi-Lagrangian transport scheme of the Eulerian spectral transform core (CAM-EUL). Each scheme tested produces unphysical mass in the Eastern Hemisphere of the separate cells test.

Description: Impact of SLA assimilation in the Sicily Channel Regional Model: model skills and mesoscale features Ocean Science, 8, 485-496, 2012 Author(s): A. Olita, S. Dobricic, A. Ribotti, L. Fazioli, A. Cucco, C. Dufau, and R. Sorgente The impact of the assimilation of MyOcean sea level anomalies along-track data on the analyses of the Sicily Channel Regional Model was studied. The numerical model has a resolution of 1/32° degrees and is capable to reproduce mesoscale and sub-mesoscale features. The impact of the SLA assimilation is studied by comparing a simulation (SIM, which does not assimilate data) with an analysis (AN) assimilating SLA along-track multi-mission data produced in the framework of MyOcean project. The quality of the analysis was evaluated by computing RMSE of the misfits between analysis background and observations (sea level) before assimilation. A qualitative evaluation of the ability of the analyses to reproduce mesoscale structures is accomplished by comparing model results with ocean colour and SST satellite data, able to detect such features on the ocean surface. CTD profiles allowed to evaluate the impact of the SLA assimilation along the water column. We found a significant improvement for AN solution in terms of SLA RMSE with respect to SIM (the averaged RMSE of AN SLA misfits over 2 years is about 0.5 cm smaller than SIM). Comparison with CTD data shows a questionable improvement produced by the assimilation process in terms of vertical features: AN is better in temperature while for salinity it gets worse than SIM at the surface. This suggests that a better a-priori description of the vertical error covariances would be desirable. The qualitative comparison of simulation and analyses with synoptic satellite independent data proves that SLA assimilation allows to correctly reproduce some dynamical features (above all the circulation in the Ionian portion of the domain) and mesoscale structures otherwise misplaced or neglected by SIM. Such mesoscale changes also infer that the eddy momentum fluxes (i.e. Reynolds stresses) show major changes in the Ionian area. Changes in Reynolds stresses reflect a different pumping of eastward momentum from the eddy to the mean flow, in turn influencing transports through the channel.

Description: CLM4-BeTR, a generic biogeochemical transport and reaction module for CLM4: model development, evaluation, and application Geoscientific Model Development Discussions, 5, 2705-2744, 2012 Author(s): J. Tang, W. J. Riley, C. D. Koven, and Z. M. Subin To improve regional and global biogeochemistry modeling and climate predictability, we have developed a generic reactive transport module for the land model CLM4 (called CLM4-BeTR (Biogeochemical Transport and Reactions)). CLM4-BeTR represents the transport, interactions, and biotic and abiotic transformations of an arbitrary number of tracers (aka chemical species) in an arbitrary number of phases (e.g. dissolved, gaseous, sorbed, aggregate). An operator splitting approach was employed and consistent boundary conditions were derived for each modeled sub-process. Tracer fluxes, associated with hydrological processes such as surface run-on and run-off, belowground drainage, and ice to liquid conversion were also computed consistently with the bulk water fluxes calculated by the soil physics module in CLM4. The transport code was evaluated and found be in good agreement with several analytical test cases. The model was then applied at the Harvard Forest site with a representation of depth-dependent belowground biogeochemistry. The results indicated that, at this site, (1) CLM4-BeTR was able to simulate soil-surface CO 2 effluxes and soil CO 2 profiles accurately; (2) the transient surface CO 2 effluxes calculated based on the tracer transport mechanism were in general not equal to the belowground CO 2 production rates and that their differences varied according to the seasonal cycle of soil physics and biogeochemistry; (3) losses of CO 2 through processes other than surface gas efflux were less than 1% of the overall soil respiration; and (4) the contributions of root respiration and heterotrophic respiration have distinct temporal signals in surface CO 2 effluxes and soil CO 2 concentrations. The development of CLM4-BeTR will allow detailed comparisons between ecosystem observations and predictions and insights to the modeling of terrestrial biogeochemistry.

Description: The Norwegian Earth System Model, NorESM1-M – Part 2: Climate response and scenario projections Geoscientific Model Development Discussions, 5, 2933-2998, 2012 Author(s): T. Iversen, M. Bentsen, I. Bethke, J. B. Debernard, A. Kirkevåg, Ø. Seland, H. Drange, J. E. Kristjánsson, I. Medhaug, M. Sand, and I. A. Seierstad The NorESM1-M simulation results for CMIP5 ( http://cmip-pcmdi.llnl.gov/cmip5/index.html ) are described and discussed. Together with the accompanying paper by Bentsen et al. (2012), this paper documents that NorESM1-M is a valuable global climate model for research and for providing complementary results to the evaluation of possible man made climate change. NorESM is based on the model CCSM4 operated at NCAR on behalf of many contributors in USA. The ocean model is replaced by a developed version of MICOM and the atmospheric model is extended with on-line calculations of aerosols, their direct effect, and their indirect effect on warm clouds. Model validation is presented in a companion paper (Bentsen et al., 2012). NorESM1-M is estimated to have equilibrium climate sensitivity slightly smaller than 2.9 K, a transient climate response just below 1.4 K, and is less sensitive than most other models. Cloud feedbacks damp the response, and a strong AMOC reduces the heat fraction available for increasing near surface temperatures, for evaporation, and for melting ice. The future projections based on RCP scenarios yield global surface air temperature increase almost one standard deviation lower than a 15-model average. Summer sea-ice is projected to decrease considerably by 2100, and completely for RCP8.5. The AMOC is projected to reduce by 12%, 15–17%, and 32% for the RCP2.6, 4.5, 6.0 and 8.5 respectively. Precipitation is projected to increase in the tropics, decrease in the subtropics and in southern parts of the northern extra-tropics during summer, and otherwise increase in most of the extra-tropics. Changes in the atmospheric water cycle indicate that precipitation events over continents will become more intense and dry spells more frequent. Extra-tropical storminess in the Northern Hemisphere is projected to shift northwards. There are indications of more frequent spring and summer blocking in the Euro-Atlantic sectors and that ENSO events weaken but appear more frequent. These indications are uncertain because of biases in the model's representation of present-day conditions. There are indications that positive phase PNA and negative phase NAO become less frequent under the RCP8.5 scenario, but also this result is considered uncertain. Single-forcing experiments indicate that aerosols and greenhouse gases produce similar geographical patterns of response for near surface temperature and precipitation. These patterns tend to have opposite sign, with important exceptions for precipitation at low latitudes. The asymmetric aerosol effects between the two hemispheres leads to a southward displacement of ITCZ. Both forcing agents thus tend to reduce northern hemispheric subtropical precipitation.

Description: The Norwegian Earth System Model, NorESM1-M – Part 1: Description and basic evaluation Geoscientific Model Development Discussions, 5, 2843-2931, 2012 Author(s): M. Bentsen, I. Bethke, J. B. Debernard, T. Iversen, A. Kirkevåg, Ø. Seland, H. Drange, C. Roelandt, I. A. Seierstad, C. Hoose, and J. E. Kristjánsson The core version of the Norwegian Climate Center's Earth System Model, named NorESM1-M, is presented. The NorESM-family of models are based on the Community Climate System Model version 4 (CCSM4) of the University Corporation for Atmospheric Research, but differs from the latter by, in particular, an isopycnic coordinate ocean model and advanced chemistry-aerosol-cloud-radiation interaction schemes. NorESM1-M has a horizontal resolution of approximately 2° for the atmosphere and land components and 1° for the ocean and ice components. NorESM is also available in a lower resolution version (NorESM1-L) and a version that includes prognostic biogeochemical cycling (NorESM1-ME). The latter two model configurations are not part of this paper. Here, a first-order assessment of the model stability, the mean model state and the internal variability based on the model experiments made available to CMIP5 are presented. Further analysis of the model performance is provided in an accompanying paper (Iversen et al., 2012), presenting the corresponding climate response and scenario projections made with NorESM1-M.

Description: Simulations of the Mid-Pliocene Warm Period using the NASA/GISS ModelE2-R Earth System Model Geoscientific Model Development Discussions, 5, 2811-2842, 2012 Author(s): M. A. Chandler, L. E. Sohl, J. A. Jonas, and H. J. Dowsett Climate reconstructions of the mid-Pliocene Warm Period (mPWP) bear many similarities to aspects of future global warming as projected by the Intergovernmental Panel on Climate Change. In particular, marine and terrestrial paleoclimate data point to high latitude temperature amplification, with associated decreases in sea ice and land ice and altered vegetation distributions that show expansion of warmer climate biomes into higher latitudes. NASA GISS climate models have been used to study the Pliocene climate since the USGS PRISM project first identified that the mid-Pliocene North Atlantic sea surface temperatures were anomalously warm. Here we present the most recent simulations of the Pliocene using the AR5/CMIP5 version of the GISS Earth System Model known as ModelE2-R. These simulations constitute the NASA contribution to the Pliocene Model Intercomparison Project (PlioMIP) Experiment 2. Many findings presented here corroborate results from other PlioMIP multi-model ensemble papers, but we also emphasize features in the ModelE2-R simulations that are unlike the ensemble means. We provide discussion of features that show considerable improvement compared with simulations from previous versions of the NASA GISS models, improvement defined here as simulation results that more closely resemble the ocean core data as well as the PRISM3D reconstructions of the mid-Pliocene climate. In some regions even qualitative agreement between model results and paleodata are an improvement over past studies, but the dramatic warming in the North Atlantic and Greenland-Iceland-Norwegian Sea in these new simulations is by far the most accurate portrayal ever of this key geographic region by the GISS climate model. Our belief is that continued development of key physical routines in the atmospheric model, along with higher resolution and recent corrections to mixing parameterizations in the ocean model, have led to an Earth System Model that will produce more accurate projections of future climate.

Description: PORT, a CESM tool for the diagnosis of radiative forcing Geoscientific Model Development Discussions, 5, 2687-2704, 2012 Author(s): A. J. Conley, J.-F. Lamarque, F. Vitt, W. D. Collins, and J. Kiehl The Parallel Offline Radiative Transfer (PORT) model is a tool for diagnosing radiative forcing. It isolates the radiation code from the Community Atmosphere Model (CAM4) in the Community Earth System Model (CESM1). The computation of radiative forcing from doubling of carbon dioxide and from the change of ozone concentration from year 1850 to 2000 illustrates the use of PORT.

Description: A methodology for estimating seasonal cycles of atmospheric CO 2 resulting from terrestrial net ecosystem exchange (NEE) fluxes using the Transcom T3L2 pulse-response functions Geoscientific Model Development Discussions, 5, 2789-2809, 2012 Author(s): C. D. Nevison, D. F. Baker, and K. R. Gurney We present a method for translating modeled terrestrial net ecosystem exchange (NEE) fluxes of carbon into the corresponding seasonal cycles in atmospheric CO 2 . The method is based on the pulse-response functions from the Transcom 3 Level 2 (T3L2) atmospheric tracer transport model (ATM) intercomparison. The new pulse-response method is considerably faster than a full forward ATM simulation, allowing CO 2 seasonal cycles to be computed in seconds, rather than the days or weeks required for a forward simulation. Further, the results provide an estimate of the range of transport uncertainty across 13 different ATMs associated with the translation of surface NEE fluxes into an atmospheric signal. We evaluate the method against the results of archived forward ATM simulations from T3L2. The latter are also used to estimate the uncertainties associated with oceanic and fossil fuel influences. We present a regional breakdown at selected monitoring sites of the contribution to the atmospheric CO 2 cycle from the 11 different T3L2 land regions. A test case of the pulse-response code, forced by NEE fluxes from the Community Land Model, suggests that for many terrestrial models, discrepancies between model results and observed atmospheric CO 2 cycles will be large enough to clearly transcend ATM uncertainties.

Description: Modeling atmospheric ammonia and ammonium using a backward-in-time stochastic Lagrangian air quality model (STILT-Chem v0.7) Geoscientific Model Development Discussions, 5, 2745-2788, 2012 Author(s): D. Wen, J. C. Lin, L. Zhang, R. Vet, and M. D. Moran A new chemistry module of atmospheric ammonia (NH 3 ) and ammonium (NH 4 + ) was incorporated into a backward-in-time stochastic Lagrangian air quality model (STILT-Chem) that was originally developed to simulate the concentrations of a variety of gas-phase species at receptors. STILT-Chem simulates the transport of air parcels backward in time using ensembles of fictitious particles with stochastic motions, while simulating emissions, deposition and chemical transformation forward in time along trajectories identified by the backward-in-time simulations. The incorporation of the new chemistry module allows the model to simulate not only gaseous species, but also multi-phase species involving NH 3 and NH 4 + . The model was applied to simulate concentrations of NH 3 and particulate NH 4 + at six sites in the Canadian province of Ontario for a six-month period in 2006. The model-predicted concentrations of NH 3 and particulate NH 4 + were compared with observations, which show broad agreement between simulated concentrations and observations. Since the model is based on back trajectories, the influence of each major process such as emission, deposition and chemical conversion on the concentration of a modeled species at a receptor can be determined for every upstream location at each time step. This makes it possible to quantitatively investigate the upstream processes affecting receptor concentrations. The modeled results suggest that the concentrations of NH 3 at those sites were significantly and frequently affected by southwestern Ontario, northern Ohio, and nearby areas. NH 3 is mainly contributed by emission sources whereas particulate NH 4 + is mainly contributed by the gas-to-aerosol chemical conversion of NH 3 . Dry deposition is the largest removal process for both NH 3 and particulate NH 4 + . This study revealed the contrast between agricultural versus forest sites. Not only were emissions of NH 3 higher, but removal mechanisms (especially chemical loss for NH 3 and dry deposition for NH 4 + ) were less efficient for agricultural sites. This combination explains the significantly higher concentrations of NH 3 and particulate NH 4 + observed at agricultural sites.

Description: Three-dimensional modelling of wave-induced current from the surf zone to the inner shelf Ocean Science, 8, 657-681, 2012 Author(s): H. Michaud, P. Marsaleix, Y. Leredde, C. Estournel, F. Bourrin, F. Lyard, C. Mayet, and F. Ardhuin We develop and implement a new method to take into account the impact of waves into the 3-D circulation model SYMPHONIE (Marsaleix et al., 2008, 2009a) following the simplified equations of Bennis et al. (2011) which use glm2z-RANS theory (Ardhuin et al., 2008c). These adiabatic equations are completed by additional parameterizations of wave breaking, bottom friction and wave-enhanced vertical mixing, making the forcing valid from the surf zone through to the open ocean. The wave forcing is performed by wave generation and propagation models WAVEWATCH III® (Tolman, 2008, 2009; Ardhuin et al., 2010) and SWAN (Booij et al., 1999). The model is tested and compared with other models for a plane beach test case, previously tested by Haas and Warner (2009)and Uchiyama et al. (2010). A comparison is also made with the laboratory measurements of Haller et al. (2002) of a barred beach with channels. Results fit with previous simulations performed by other models and with available observational data. Finally, a realistic case is simulated with energetic waves travelling over a coast of the Gulf of Lion (in the northwest of the Mediterranean Sea) for which currents are available at different depths as well as an accurate bathymetric database of the 0–10 m depth range. A grid nesting approach is used to account for the different forcings acting at different spatial scales. The simulation coupling the effects of waves and currents is successful to reproduce the powerful northward littoral drift in the 0–15 m depth zone. More precisely, two distinct cases are identified: When waves have a normal angle of incidence with the coast, they are responsible for complex circulation cells and rip currents in the surf zone, and when they travel obliquely, they generate a northward littoral drift. These features are more complicated than in the test cases, due to the complex bathymetry and the consideration of wind and non-stationary processes. Wave impacts in the inner shelf are less visible since wind and regional circulation seem to be the predominant forcings. Besides, a discrepancy between model and observations is noted at that scale, possibly linked to an underestimation of the wind stress. This three-dimensional method allows a good representation of vertical current profiles and permits the calculation of the shear stress associated with waves and currents. Future work will focus on the combination with a sediment transport model.

Description: How should sparse in situ measurements be compared to continuous model data? Geoscientific Model Development Discussions, 5, 2311-2345, 2012 Author(s): L. de Mora, M. Butenschön, and J. I. Allen This work demonstrates the importance of an adequate method to sub-sample model results when comparing with in situ measurements. A test of model skill was performed by comparing a multi-decadal hindcast against a sparse, unevenly distributed historic in situ dataset. The comparison was performed using a point-to-point method. The point-to-point method masked out all hindcast cells that did not have a corresponding in situ measurement in order to compare each in situ measurement against its most similar cell from the model. The application of the point-to-point method showed that the model was successful at reproducing many inter-annual trends. Furthermore, this success was not immediately apparent using the previous comparison methods, which compared model and measurements aggregated to regional averages. Time series, data density and target diagrams were employed to illustrate the impact of switching from the previous method to the point-to-point method. The comparison based on regional averages gave significantly different and sometimes contradicting results that could lead to erroneous conclusions on the model performance. We therefore recommend that researchers take into account for the limitations of the in situ datasets, process the model to resemble the data as much as possible, and we advocate greater transparency in the publication of methodology.

Description: Particle aggregation at the edges of anticyclonic eddies and implications for distribution of biomass Ocean Science, 8, 389-400, 2012 Author(s): A. Samuelsen, S. S. Hjøllo, J. A. Johannessen, and R. Patel Acoustic measurements show that the biomass of zooplankton and mesopelagic fish is redistributed by mesoscale variability and that the signal extends over several hundred meters depth. The mechanisms governing this distribution are not well understood, but influences from both physical (i.e. redistribution) and biological processes (i.e. nutrient transport, primary production, active swimming, etc.) are likely. This study examines how hydrodynamic conditions and basic vertical swimming behavior act to distribute biomass in an anticyclonic eddy. Using an eddy-resolving 2.3 km-resolution physical ocean model as forcing for a particle-tracking module, particles representing passively floating organisms and organisms with vertical swimming behavior are released within an eddy and monitored for 20 to 30 days. The role of hydrodynamic conditions on the distribution of biomass is discussed in relation to the acoustic measurements. Particles released close to the surface tend, in agreement with the observations, to accumulate around the edge of the eddy, whereas particles released at depth gradually become distributed along the isopycnals. After a month they are displaced several hundreds meters in the vertical with the deepest particles found close to the eddy center and the shallowest close to the edge. There is no evidence of aggregation of particles along the eddy rim in the last simulation. The model results points towards a physical mechanism for aggregation at the surface, however biological processes cannot be ruled out using the current modeling tool.

Description: The chemical transport model Oslo CTM3 Geoscientific Model Development Discussions, 5, 1561-1626, 2012 Author(s): O. A. Søvde, M. J. Prather, I. S. A. Isaksen, T. K. Berntsen, F. Stordal, X. Zhu, C. D. Holmes, and J. Hsu We present here the global chemical transport model Oslo CTM3, an update of the Oslo CTM2. The update comprises a faster transport scheme, an improved wet scavenging scheme for large scale rain, updated photolysis rates and a new lightning parameterization. Oslo CTM3 is better parallelized and allows for stable, large time steps for advection, enabling more complex or high resolution simulations. Thorough comparisons between the Oslo CTM3, Oslo CTM2 and measurements are performed, and in general the Oslo CTM3 is found to reproduce measurements well. Inclusion of tropospheric sulfur chemistry and nitrate aerosols in CTM3 is shown to be important to reproduce tropospheric O 3 , OH and the CH 4 lifetime well. Using the same meteorology to drive the two models, shows that some features related to transport are better resolved by the CTM3, such as polar cap transport, while features like transport close to the vortex edge are resolved better in the Oslo CTM2 due to its required shorter transport time step. The longer transport time steps in CTM3 result in larger errors e.g. near the jets, and when necessary, this can be remedied by using a shorter time step. An additional, more accurate and time consuming, treatment of polar cap transport is presented, however, both perform acceptably. A new treatment of the horizontal distribution of lightning is presented and found to compare well with measurements. Vertical distributions of lighting are updated, and tested against the old vertical distribution. The new profiles are found to produce more NO x in the tropical middle troposphere, and less at the surface and at high altitudes.

Description: Influence of Ross Sea Bottom Water changes on the warming and freshening of the Antarctic Bottom Water in the Australian-Antarctic Basin Ocean Science, 8, 419-432, 2012 Author(s): K. Shimada, S. Aoki, K. I. Ohshima, and S. R. Rintoul Changes to the properties of Antarctic Bottom Water in the Australian-Antarctic Basin (AA-AABW) between the 1990s and 2000s are documented using data from the WOCE Hydrographic Program (WHP) and repeated hydrographic surveys. Strong cooling and freshening are observed on isopycnal layers denser than γ n = 28.30 kg m −3 . Changes in the average salinity and potential temperature below this isopycnal correspond to a basin-wide warming of 1300 ± 200 GW and freshening of 24 ± 3 Gt year −1 . Recent changes to dense shelf water in the source regions in the Ross Sea and George V Land can explain the freshening of AA-AABW but not its extensive warming. An alternative mechanism for this warming is a decrease in the supply of AABW from the Ross Sea (RSBW). Hydrographic profiles between the western Ross Sea and George V Land (171–158° E) were analyzed with a simple advective-diffusive model to assess the causes of the observed changes. The model suggests that the warming of RSBW observed between the 1970s and 2000s can be explained by a 21 ± 23% reduction in RSBW transport and the enhancement of the vertical diffusion of heat resulting from a 30 ± 7% weakening of the abyssal stratification. The documented freshening of Ross Sea dense shelf water leads to a reduction in both salinity and density stratification. Therefore the direct freshening of RSBW at its source also produces an indirect warming of the RSBW. A simple box model suggests that the changes in RSBW properties and volume transport (a decrease of 6.7% is assumed between the year 1995 and 2005) can explain 51 ± 6% of the warming and 84 ± 10% of the freshening observed in AA-AABW.

Description: Support to oil spill emergencies in the Bonifacio Strait, western Mediterranean Ocean Science, 8, 443-454, 2012 Author(s): A. Cucco, A. Ribotti, A. Olita, L. Fazioli, B. Sorgente, M. Sinerchia, A. Satta, A. Perilli, M. Borghini, K. Schroeder, and R. Sorgente An innovative forecasting system of the coastal marine circulation has been implemented in the Bonifacio Strait area, between Corsica and Sardinia, using a numerical approach to facilitate the rapid planning and coordination of remedial actions for oil spill emergencies at sea by local authorities. Downscaling and nesting techniques from regional to coastal scale and a 3-D hydrodynamic numerical model, coupled with a wind wave model, are the core of the integrated Bonifacio Strait system. Such a system is capable of predicting operationally the dispersion of hydrocarbon spills in the area, both in forward and backward mode, through an easy-to-use graphical user interface. A set of applications are described and discussed including both operational applications aimed at providing rapid responses to local oil spill emergences and managing applications aimed at mitigating the risk of oil spill impacts on the coast.

Description: Unified parameterization of the planetary boundary layer and shallow convection with a higher-order turbulence closure in the community atmosphere model: single column experiments Geoscientific Model Development Discussions, 5, 1743-1780, 2012 Author(s): P. A. Bogenschutz, A. Gettelman, H. Morrison, V. E. Larson, D. P. Schanen, N. R. Meyer, and C. Craig This paper describes the coupling of the Community Atmosphere Model (CAM) version 5 with a unified multi-variate probability density function (PDF) parameterization, Cloud Layers Unified by Binormals (CLUBB). CLUBB replaces the planetary boundary layer (PBL), shallow convection, and cloud macrophysics schemes in CAM5 with a higher-order turbulence closure based on an assumed PDF. Comparisons of single-column versions of CAM5 and CAM-CLUBB are provided in this paper for several boundary layer regimes. As compared to Large Eddy Simulations (LES), CAM-CLUBB and CAM5 simulate marine stratocumulus regimes with similar accuracy. For shallow convective regimes, CAM-CLUBB improves the representation of cloud cover and liquid water path (LWP). In addition, for shallow convection CAM-CLUBB offers better fidelity for sub-grid scale vertical velocity, which is an important input for aerosol activation. Finally, CAM-CLUBB results are more robust to changes in vertical and temporal resolution when compared to CAM5.

Description: On the chemical dynamics of extracellular polysaccharides in the high Arctic surface microlayer Ocean Science, 8, 401-418, 2012 Author(s): Q. Gao, C. Leck, C. Rauschenberg, and P. A. Matrai The surface microlayer (SML) represents a unique system of which the physicochemical characteristics may differ from those of the underlying subsurface seawater (SSW). Within the Arctic pack ice area, the SML has been characterized as enriched in small colloids of biological origin, resulting from extracellular polymeric secretions (EPS). During the Arctic Summer Cloud Ocean Study (ASCOS) in August 2008, particulate organic matter (POM, with size range 〉 0.22 μm) and dissolved organic matter (DOM, 〈 0.22 μm, obtained after filtration) samples were collected and chemically characterized from the SML and the corresponding SSW at an open lead centered at 87.5° N and 5° E. Total organic carbon was persistently enriched in the SML with a mean enrichment factor (EF) of 1.45 ± 0.41, whereas sporadic depletions of dissolved carbohydrates and amino acids were observed. Monosaccharide compositional analysis reveals that EPS in the Arctic lead was formed mainly of distinctive heteropolysaccharides, enriched in xylose, fucose and glucose. The mean concentrations of total hydrolysable neutral sugars in SSW were 94.9 ± 37.5 nM in high molecular weight (HMW) DOM (〉 5 kDa) and 64.4 ± 14.5 nM in POM. The enrichment of polysaccharides in the SML appeared to be a common feature, with EFs ranging from 1.7 to 7.0 for particulate polysaccharides and 3.5 to 12.1 for polysaccharides in the HMW DOM fraction. A calculated monosaccharide yield suggests that polymers in the HMW DOM fraction were scavenged, without substantial degradation, into the SML. Bubble scavenging experiments showed that newly aggregated particles could be formed abiotically by coagulation of low molecular weight nanometer-sized gels. Aerosol particles, artificially generated by bubbling experiments, were enriched in polysaccharides by factors of 22–70, relative to the source seawater. We propose that bubble scavenging of surface-active polysaccharides could be one of the possible mechanisms for the enrichment of polysaccharides in the high Arctic open lead SML.

Description: On the influence of wind and waves on underwater irradiance fluctuations Ocean Science, 8, 455-471, 2012 Author(s): M. Hieronymi and A. Macke The influence of various wind and wave conditions on the variability of downwelling irradiance E d (490 nm) in water is subject of this study. The work is based on a two-dimensional Monte Carlo radiative transfer model with high spatial resolution. The model assumes conditions that are ideal for wave focusing, thus simulation results reveal the upper limit for light fluctuations. Local wind primarily determines the steepness of capillary-gravity waves which in turn dominate the irradiance variability near the surface. Down to 3 m depth, maximum irradiance peaks that exceed the mean irradiance E d by a factor of more than 7 can be observed at low wind speeds up to 5 m s −1 . The strength of irradiance fluctuations can be even amplified under the influence of higher ultra-gravity waves; thereby peaks can exceed 11 E d . Sea states influence the light field much deeper; gravity waves can cause considerable irradiance variability even at 100 m depth. The simulation results show that under realistic conditions 50% radiative enhancements compared to the mean can still occur at 30 m depth. At greater depths, the underwater light variability depends on the wave steepness of the characteristic wave of a sea state; steeper waves cause stronger light fluctuations.

Description: Transport of warm Upper Circumpolar Deep Water onto the western Antarctic Peninsula continental shelf Ocean Science, 8, 433-442, 2012 Author(s): D. G. Martinson and D. C. McKee Five thermistor moorings were placed on the continental shelf of the western Antarctic Peninsula (between 2007 and 2010) in an effort to identify the mechanism(s) responsible for delivering warm Upper Circumpolar Deep Water (UCDW) onto the broad continental shelf from the Antarctic Circumpolar Current (ACC) flowing over the adjacent continental slope. Historically, four mechanisms have been suggested: (1) eddies shed from the ACC, (2) flow into the cross-shelf-cutting canyons with overflow onto the nominal shelf, (3) general upwelling, and (4) episodic advective diversions of the ACC onto the shelf. The mooring array showed that for the years of deployment, the dominant mechanism is eddies; upwelling may also contribute but to an unknown extent. Mechanism 2 played no role, though the canyons have been shown previously to channel UCDW across the shelf into Marguerite Bay. Mechanism 4 played no role independently, though eddies may be advected within a greater intrusion of the background flow.

Description: Implementation of the chemistry module MECCA (v2.5) in the modal aerosol version of the Community Atmosphere Model component (v3.6.33) of the Community Earth System Model Geoscientific Model Development Discussions, 5, 1483-1501, 2012 Author(s): M. S. Long, W. C. Keene, R. Easter, R. Sander, A. Kerkweg, D. Erickson, X. Liu, and S. Ghan A coupled atmospheric chemistry and climate system model was developed using the modal aerosol version of the National Center for Atmospheric Research Community Atmosphere Model (modal-CAM) and the Max Planck Institute for Chemistry's Module Efficiently Calculating the Chemistry of the Atmosphere (MECCA) to provide enhanced resolution of multiphase processes, particularly those involving inorganic halogens, and associated impacts on atmospheric composition and climate. Three Rosenbrock solvers (Ros-2, Ros-3, RODAS-3) were tested in conjunction with the basic load balancing options available to modal CAM (1) to establish an optimal configuration of the implicitly-solved multiphase chemistry module that maximizes both computational speed and repeatability of Ros-2 and RODAS-3 results versus Ros-3, and (2) to identify potential implementation strategies for future versions of this and similar coupled systems. RODAS-3 was faster than Ros-2 and Ros-3 with good reproduction of Ros-3 results, while Ros-2 was both slower and substantially less reproducible relative to Ros-3 results. Modal-CAM with MECCA chemistry was a factor of 15 slower than modal-CAM using standard chemistry. MECCA chemistry integration times demonstrated a systematic frequency distribution for all three solvers, and revealed that the change in run-time performance was due to a change in the frequency distribution chemical integration times; the peak frequency was similar for all solvers. This suggests that efficient chemistry-focused load-balancing schemes can be developed that rely on the parameters of this frequency distribution.

Description: Describing Earth System Simulations with the Metafor CIM Geoscientific Model Development Discussions, 5, 1669-1689, 2012 Author(s): B. N. Lawrence, V. Balaji, P. Bentley, S. Callaghan, C. DeLuca, S. Denvil, G. Devine, M. Elkington, R. W. Ford, E. Guilyardi, M. Lautenschlager, M. Morgan, M.-P. Moine, S. Murphy, C. Pascoe, H. Ramthun, P. Slavin, L. Steenman-Clark, F. Toussaint, A. Treshansky, and S. Valcke The Metafor project has developed a Common Information Model (CIM) using the ISO1900 series formalism to describe the sorts of numerical experiments carried out by the earth system modelling community, the models they use, and the simulations that result. Here we describe the mechanism by which the CIM was developed, and its key properties. We introduce the conceptual and application versions and the controlled vocabularies developed in the context of supporting the fifth Coupled Model Intercomparison Project (CMIP5). We describe how the CIM has been used in experiments to describe model coupling properties and describe the near term expected evolution of the CIM.

Description: Lidar signal simulation for the evaluation of aerosols in chemistry-transport models Geoscientific Model Development Discussions, 5, 1691-1741, 2012 Author(s): S. Stromatas, S. Turquety, L. Menut, H. Chepfer, J. C. Péré, G. Cesana, and B. Bessagnet We present an adaptable tool, the OPTSIM (OPTical properties SIMulation) software, for the simulation of optical properties and lidar attenuated backscattered profiles (β ' ) from aerosol concentrations calculated by chemistry-transport models (CTM). It was developed to support model evaluation using an original approach based on the lidar Level 1 observations (β ' ), avoiding the use of Level 2 aerosol retrievals which include specific assumptions on aerosol types that may not be in agreement with the CTM. In addition to an evaluation of the aerosol loading and optical properties, active remote sensing allows the analysis of aerosols' vertical structures. An academic case study for two different species (black carbon and dust) is presented and shows the consistency of the simulator. Illustrations are then given through the analysis of dust events in the Mediterranean region during the summer 2007. These are based on simulations by the CHIMERE regional CTM and observations from the CALIOP space-based lidar, and highlight the potential of this approach to evaluate the concentration, size and vertical structure of the aerosol plumes.

Description: On the outflow of dense water from the Weddell and Ross Seas in OCCAM model Ocean Science, 8, 369-388, 2012 Author(s): R. Kerr, K. J. Heywood, M. M. Mata, and C. A. E. Garcia We describe the seasonal and interannual variability of volume transports in the Weddell and Ross Seas using the 1/12° 20-yr simulation of the OCCAM global ocean general circulation model. The average simulated full-depth cumulative volume transports were 28.5 ± 2.9 Sv (1 Sv ≡ 10 6 m 3 s −1 ) and 13.4 ± 5.2 Sv, across the main export regions of the Weddell and Ross Seas, respectively. The values of mean outflow of Antarctic Bottom Water (AABW) (defined by neutral density γ n ≥ 28.27 kg m −3 ) from the Weddell and Ross Seas of 10.6 ± 3.1 Sv and 0.5 ± 0.7 Sv, respectively, agree with the range reported in historical observational studies. The export of Weddell Sea dense water in OCCAM is primarily determined by the strength of the Weddell Gyre. Variability in AABW export is predominantly at periods of ~1 yr and 2–4 yr.

Description: Better constraints on the sea-ice state using global sea-ice data assimilation Geoscientific Model Development Discussions, 5, 1627-1667, 2012 Author(s): P. Mathiot, C. König Beatty, T. Fichefet, H. Goosse, F. Massonnet, and M. Vancoppenolle Short-term and decadal sea-ice prediction systems need a realistic initial state, generally obtained using ice-ocean model simulations with data assimilation. However, only sea-ice concentration and velocity data are currently assimilated. In this work, an Ensemble Kalman Filter system is used to assimilate observed ice concentration and freeboard (i.e. thickness of emerged sea ice) data into a global coupled ocean–sea-ice model. The impact and effectiveness of our data assimilation system is assessed in two steps: firstly, through the assimilation of synthetic data (i.e., model-generated data) and, secondly, through the assimilation of satellite data. While ice concentrations are available daily, freeboard data used in this study are only available during six one-month periods spread over 2005–2007. Our results show that the simulated Arctic and Antarctic sea-ice extents are improved by the assimilation of synthetic ice concentration data. Assimilation of synthetic ice freeboard data improves the simulated sea-ice thickness field. Using real ice concentration data enhances the model realism in both hemispheres. Assimilation of ice concentration data significantly improves the total hemispheric sea-ice extent all year long, especially in summer. Combining the assimilation of ice freeboard and concentration data leads to better ice thickness, but does not further improve the ice extent. Moreover, the improvements in sea-ice thickness due to the assimilation of ice freeboard remain visible well beyond the assimilation periods.

Description: Modeling wet deposition of inorganics over Northeast Asia with MRI-PM/c and the effects of super large sea salt droplets at near-the-coast stations Geoscientific Model Development Discussions, 5, 1341-1379, 2012 Author(s): M. Kajino, M. Deushi, T. Maki, N. Oshima, Y. Inomata, K. Sato, T. Ohizumi, and H. Ueda We conducted a regional-scale simulation (with grid spacing = 60 km) over Northeast Asia for the entire year of 2006 by using an aerosol chemical transport model, the lateral and upper boundary concentrations of which we predicted with a global stratospheric and tropospheric chemistry-climate model, with a horizontal resolution of T42 (grid spacing ~300 km) and a time resolution of 1 h. The present one-way nested global-through-regional-scale model is called the Meteorological Research Institute – Passive-tracers Model system for atmospheric Chemistry (MRI-PM/c). We evaluated the model performance with respect to the major inorganic components in rain and snow measured by stations of the Acid Deposition Monitoring Network in East Asia (EANET). Through statistical analysis, we show that the model successfully reproduced the regional-scale processes of emission, transport, transformation, and wet deposition of major inorganic species derived from anthropogenic and natural sources, including SO 4 2− , NH 4 + , NO 3 − , Na + and Ca 2+ . Interestingly, the only exception was Na + in precipitation at near-coastal stations (where the distance from the coast was from 150 to 700 m), concentrations of which were significantly underestimated by the model, by up to a factor of 30. This result suggested that the contribution of short-lived, super-large sea salt droplets (SLSD; D 〉 10–100 μm) was substantial in precipitation samples at stations near the coast of Japan; thus samples were horizontally representative only within the traveling distances of SLSD (from 1 to 10 km). Nevertheless, the calculated effect of SLSD on precipitation pH was very low, a change of about +0.014 on average, even if the ratio of SLSD to all sea salt in precipitation was assumed to be 90%.

Description: Transports and budgets in a 1/4 ° global ocean reanalysis 1989–2010 Ocean Science, 8, 333-344, 2012 Author(s): K. Haines, M. Valdivieso, H. Zuo, and V. N. Stepanov Large-scale ocean transports of heat and freshwater have not been well monitored, and yet the regional budgets of these quantities are important to understanding the role of the oceans in climate and climate change. In contrast, atmospheric heat and freshwater transports are commonly assessed from atmospheric reanalysis products, despite the presence of non-conserving data assimilation based on the wealth of distributed atmospheric observations as constraints. The ability to carry out ocean reanalyses globally at eddy-permitting resolutions of 1/4 ° or better, along with new global ocean observation programs, now makes a similar approach viable for the ocean. In this paper we examine the budgets and transports within a global high resolution ocean model constrained by ocean data assimilation, and compare them with independent oceanic and atmospheric estimates.

Description: Mid-Pliocene climate modelled using the UK Hadley Centre Model: PlioMIP Experiments 1 and 2 Geoscientific Model Development Discussions, 5, 837-871, 2012 Author(s): F. J. Bragg, D. J. Lunt, and A. M. Haywood The Pliocene Model Intercomparison Project (PlioMIP) project is a sub-project of the Paleoclimate Modelling Intercomparison Project (PMIP) whose objective is to compare predictions of the mid-Pliocene climate from the widest possible range of general circulation models. The mid-Pliocene (3.3–3.0 Ma) is the most recent sustained period of greater warmth and atmospheric carbon dioxide concentration than the pre-industrial times and as such has potential to inform predictions of our warming climate in the coming century. This paper describes the UK contribution to PlioMIP using the Hadley Centre Model both in atmosphere-only mode (HadAM3, PlioMIP Experiment 1) and atmosphere-ocean coupled mode (HadCM3, PlioMIP Experiment 2). The coupled model predicts a greater overall warming (3.3 °C) relative to the control than the atmosphere-only (2.5 °C). The Northern Hemisphere latitudinal temperature gradient is greater in the coupled model with a warmer equator and colder Arctic than the atmosphere-only model, which is constrained by sea surface temperatures from Pliocene proxy reconstructions. The atmosphere-only model predicts a reduction in equatorial precipitation and south Asian monsoon intensity whereas the coupled models shows and increase in the intensity of these systems. Sensitivity studies using alternative boundary conditions for both the Pliocene and the control simulations are presented, which indicate the sensitivity of the mid-Pliocene warming to uncertainties in both pre-industrial and mid-Pliocene climate.

Description: Performance of McRAS-AC in the GEOS-5 AGCM: aerosol-cloud-microphysics, precipitation, cloud radiative effects, and circulation Geoscientific Model Development Discussions, 5, 1381-1434, 2012 Author(s): Y. C. Sud, D. Lee, L. Oreopoulos, D. Barahona, A. Nenes, and M. J. Suarez A revised version of the Microphysics of clouds with Relaxed Arakawa-Schubert and Aerosol-Cloud interaction scheme (McRAS-AC) including, among others, the Barahona and Nenes ice nucleation parameterization, is implemented in the GEOS-5 AGCM. Various fields from a 10-yr long integration of the AGCM with McRAS-AC were compared with their counterparts from an integration of the baseline GEOS-5 AGCM using satellite data as observations. Generally McRAS-AC simulations have smaller biases in cloud fields and cloud radiative effects over most of the regions of the Earth than the baseline GEOS-5 AGCM. Two systematic biases are identified in the McRAS-AC runs: one under-prediction of cloud particles around 40° S–60° S, and one over-prediction of cloud water path during Northern Hemisphere summer over the Gulf Stream and North Pacific. Sensitivity analyses show that these biases potentially originate from biases in the aerosol input. The first bias is largely eliminated in a sensitivity test using 50% smaller sea-salt aerosol particles, while the second bias is much reduced when interactive aerosol chemistry was turned on. The main drawback of McRAS-AC is dearth of low-level marine stratus clouds, probably due to lack of boundary-layer clouds that is an outcome of explicit dry-convection not yet implemented into the cloud model. Nevertheless, McRAS-AC simulates realistic clouds and their optical properties that can further improve with better aerosol-input. Thereby, McRAS-AC has the potential to be a valuable tool for climate modeling research because of its superior simulation capabilities that physically couple aerosols, cloud microphysics, cloud macrophysics, and cloud-radiation interaction for all clouds.

Description: 137 Cs off Fukushima Dai-ichi, Japan – model based estimates of dilution and fate Ocean Science, 8, 319-332, 2012 Author(s): H. Dietze and I. Kriest In the aftermath of an earthquake and tsunami on 11 March 2011 radioactive 137 Cs was discharged from a damaged nuclear power plant to the sea off Fukushima Dai-ichi, Japan. Here we explore its dilution and fate with a state-of-the-art global ocean general circulation model, which is eddy-resolving in the region of interest. We find apparent consistency between our simulated circulation, estimates of 137 Cs discharged ranging from 0.94 p Bq (Japanese Government, 2011) to 3.5 ± 0.7 p Bq (Tsumune et al., 2012), and measurements by Japanese authorities and the power plant operator. In contrast, our simulations are apparently inconsistent with the high 27 ± 15 p Bq discharge estimate of Bailly du Bois et al. (2012). Expressed in terms of a diffusivity we diagnose, from our simulations, an initial dilution on the shelf of 60 to 100 m 2 s −1 . The cross-shelf diffusivity is at 500 ± 300 m 2 s −1 significantly higher and variable in time as indicated by its uncertainty. Expressed as an effective residence time of surface water on the shelf, the latter estimate transfers to 43 ± 16 days. As regards the fate of 137 Cs, our simulations suggest that activities up to 4 mBq l −1 prevail in the Kuroshio-Oyashio Interfrontal Zone one year after the accident. This allows for low but detectable 0.1 to 0.3 m Bq l −1 entering the North Pacific Intermediate Water before the 137 Cs signal is flushed away. The latter estimates concern the direct release to the sea only.

Description: A vertical-mode decomposition to investigate low-frequency internal motion across the Atlantic at 26° N Ocean Science, 8, 345-367, 2012 Author(s): Z. B. Szuts, J. R. Blundell, M. P. Chidichimo, and J. Marotzke Hydrographic data from full-depth moorings maintained by the Rapid/\-MOCHA project and spanning the Atlantic at 26° N are decomposed into vertical modes in order to give a dynamical framework for interpreting the observed fluctuations. Vertical modes at each mooring are fit to pressure perturbations using a Gauss-Markov inversion. Away from boundaries, the vertical structure is almost entirely described by the first baroclinic mode, as confirmed by high correlation between the original signal and reconstructions using only the first baroclinic mode. These first baroclinic motions are also highly coherent with altimetric sea surface height (SSH). Within a Rossby radius (45 km) of the western and eastern boundaries, however, the decomposition contains significant variance at higher modes, and there is a corresponding decrease in the agreement between SSH and either the original signal or the first baroclinic mode reconstruction. Compared to the full transport signal, transport fluctuations described by the first baroclinic mode represent

Description: Modelling mid-Pliocene climate with COSMOS Geoscientific Model Development Discussions, 5, 917-966, 2012 Author(s): C. Stepanek and G. Lohmann In this manuscript we describe the experimental procedure employed at the Alfred Wegener Institute in Germany in the preparation of the simulations for the Pliocene Model Intercomparison Project (PlioMIP). We present a description of the utilized community earth system models (COSMOS) and document the procedures which we applied to transfer the Pliocene Research, Interpretation and Synoptic Mapping Project (PRISM) mid-Pliocene reconstruction into model forcing fields. The model setup and spin-up procedure are described for both the paleo and preindustrial (PI) time-slices of PlioMIP experiments 1 and 2, and general results that depict the performance of our model setup for mid-Pliocene conditions are presented. The mid-Pliocene as simulated with our COSMOS-setup and PRISM boundary conditions is both warmer and wetter than the PI. The globally averaged annual mean surface air temperature in the mid-Pliocene standalone atmosphere (fully coupled atmosphere-ocean) simulation is 17.35 °C (17.82 °C), which implies a warming of 2.23 °C (3.40 °C) relative to the respective PI control simulation.

Description: TopoSUB: a tool for efficient large area numerical modelling in complex topography at sub-grid scales Geoscientific Model Development Discussions, 5, 1041-1076, 2012 Author(s): J. Fiddes and S. Gruber Mountain regions are highly sensitive to global climate change. However, large scale assessments of mountain environments remain problematic due to the high resolution required of model grids to capture strong lateral variability. To alleviate this, tools are required to bridge the scale gap between gridded climate datasets (climate models and re-analyses) and unresolved (by coarse grids) sub-grid mountain topography. We address this problem with a sub-grid method. It relies on sampling the most important aspects of land surface heterogeneity through a lumped scheme, allowing for the application of numerical land surface models (LSM) over large areas in mountain regions. This is achieved by including the effect of mountain topography on these processes at the sub-grid scale using a multidimensional informed sampling procedure together with a 1-D lumped model that can be driven by gridded climate datasets. This paper provides a description of this sub-grid scheme, TopoSUB, as well as assessing its performance against a distributed model. We demonstrate the ability of TopoSUB to approximate results simulated by a distributed numerical LSM at around 10 4 less computations. These significant gains in computing resources allow for: (1) numerical modelling of processes at fine grid resolutions over large areas; (2) extremely efficient statistical descriptions of sub-grid behaviour; (3) a "sub-grid aware" aggregation of simulated variables to course grids; and (4) freeing of resources for treatment of uncertainty in the modelling process.

Description: Impact of a time-dependent background error covariance matrix on air quality analysis Geoscientific Model Development Discussions, 5, 873-916, 2012 Author(s): E. Jaumouillé, S. Massart, A. Piacentini, D. Cariolle, and V.-H. Peuch In this article we study the influence of different characteristics of our assimilation system on the surface ozone analyses over Europe. Emphasis is placed on the evaluation of the background error covariance matrix (BECM). Data assimilation systems require a BECM in order to obtain an optimal representation of the physical state. A posteriori diagnostics are an efficient way to check the consistency of the used BECM. In this study we derived a diagnostic to estimate the BECM. On the other hand an increasingly used approach to obtain such a covariance matrix is to estimate it from an ensemble of perturbed assimilation experiments. We applied this method, combined with variational assimilation, while analysing the surface ozone distribution over Europe. We first show that the resulting covariance matrix is strongly time (hourly and seasonally) and space dependent. We then built several configurations of the background error covariance matrix with none, one or two of its components derived from the ensemble estimation. We used each of these configurations to produce surface ozone analyses. All the analyses are compared between themselves and compared to assimilated data or data from independent validation stations. The configurations are very well correlated with the validation stations, but with varying regional and seasonal characteristics. The largest correlation is obtained with the experiments using time and space dependent correlation of the background errors. Results show that our assimilation process is efficient in bringing the model assimilations closer to the observations than the direct simulation, but we cannot conclude which BECM configuration is the best. The impact of the background error covariances configuration on four-days forecasts is also studied. Although mostly positive, the impact depends on the season and lasts longer during the winter season.

Description: Numerical uncertainty at mesoscale in a Lagrangian model in complex terrain Geoscientific Model Development Discussions, 5, 967-991, 2012 Author(s): J. Brioude, W. M. Angevine, S. A. McKeen, and E.-Y. Hsie Recently, it has been shown that mass conservation in Lagrangian models is improved by using time-average winds out of Eulerian models. In this study, we evaluate the mass conservation and trajectory uncertainties in complex terrain at mesoscale using the FLEXPART Lagrangian particle dispersion model coupled with the WRF mesoscale model. The specific form of vertical wind used is found to have a large effect. Time average wind with time average sigma dot (σ · ), instantaneous wind with geometric cartesian vertical wind ( w ) and instantaneous wind with σ · are used to simulate mixing ratios of a passive tracer in forward and backward runs using different time interval outputs and horizontal resolutions in California. Mass conservation in the FLEXPART model was not an issue when using time-average wind or instantaneous wind with σ · . However, mass was poorly conserved using instantaneous wind with w , with a typical variation of 25% within 24 h. Uncertainties in surface residence time (a backtrajectory product commonly used in source receptor studies or inverse modeling) calculated for each backtrajectory run were also analyzed. The smallest uncertainties were systematically found when using time-average wind. Uncertainties using instantaneous wind with σ · were slightly larger, as long as the time interval of output was sufficiently small. The largest uncertainties were found when using instantaneous wind with w . Those uncertainties were found to be linearly correlated with the local average gradient of orography. Differences in uncertainty were much smaller when trajectories were calculated over flat terrain. For a typical run at mesoscale in complex terrain, 4 km horizontal resolution and 1 h time interval output, the average uncertainty and bias in surface residence time is, respectively 8.4% and −2.5% using time-average wind, and 13% and −3.7% using instantaneous wind with σ · in complex terrain. The corresponding values for instantaneous wind with cartesian w were 24% and −11%. While the use of time-average wind systematically improves uncertainty in FLEXPART, the improvements are small, and therfore a systematic use of time-average wind in Lagrangian models is not necessarily required. Use of cartesian vertical wind in complex terrain, however, should be avoided.

Description: Models of soil organic matter decomposition: the SOILR package, version 1.0 Geoscientific Model Development Discussions, 5, 993-1039, 2012 Author(s): C. A. Sierra, M. Müller, and S. E. Trumbore Organic matter decomposition is a very important process within the Earth System because it controls the rates of mineralization of carbon and other biogeochemical elements, determining their flux to the atmosphere and the hydrosphere. SOILR is a modeling framework that contains a library of functions and tools for modeling soil organic matter decomposition under the R environment for computing. It implements a variety of model structures and tools to represent carbon storage and release from soil organic matter. In SOILR organic matter decomposition is represented as a linear system of ordinary differential equations that generalizes the structure of most compartment-based decomposition models. A variety of functions is also available to represent environmental effects on decomposition rates. This document presents the conceptual basis for the functions implemented in the package. It is complementary to the help pages released with the software.

Description: A semi-analytical solution to accelerate spin-up of a coupled carbon and nitrogen land model to steady state Geoscientific Model Development Discussions, 5, 803-836, 2012 Author(s): J. Xia, Y. Luo, Y.-P. Wang, E. Weng, and O. Hararuk The spin-up of land models to steady state of coupled carbon-nitrogen processes is computationally so costly that it becomes a~bottleneck issue for global analysis. In this study, we introduced a semi-analytical solution (SAS) for the spin-up issue. SAS is fundamentally based on the analytic solution to a set of equations that describe carbon transfers within ecosystems over time. SAS is implemented by three steps: (1) having an initial spin-up with prior pool-size values until net primary productivity (NPP) reaches steady state, (2) calculating quasi steady-state pool sizes by letting fluxes of the equations equal zero, and (3) having a final spin-up to meet the criterion of steady state. Step 2 is enabled by averaged time-varying variables over one period of repeated driving forcings. SAS was applied to both site-level and global scale spin-up of the Australian Community Atmosphere Biosphere Land Exchange (CABLE) model. For the carbon-cycle-only simulations, SAS saved 95.7% and 92.4% of computational time for site-level and global spin-up, respectively, in comparison with the traditional method. For the carbon-nitrogen-coupled simulations, SAS reduced computational cost by 84.5% and 86.6% for site-level and global spin-up, respectively. The estimated steady-state pool sizes represent the ecosystem carbon storage capacity, which was 12.1 kg C m −2 with the coupled carbon-nitrogen global model, 14.6% lower than that with the carbon-only model. The nitrogen down-regulation in modeled carbon storage is partly due to the 4.6% decrease in carbon influx (i.e., net primary productivity) and partly due to the 10.5% reduction in residence times. This steady-state analysis accelerated by the SAS method can facilitate comparative studies of structural differences in determining the ecosystem carbon storage capacity among biogeochemical models. Overall, the computational efficiency of SAS potentially permits many global analyses that are impossible with the traditional spin-up methods, such as ensemble analysis of land models against parameter variations.

Description: Wave climate in the Arkona Basin, the Baltic Sea Ocean Science, 8, 287-300, 2012 Author(s): T. Soomere, R. Weisse, and A. Behrens The basic features of the wave climate in the Southwestern Baltic Sea (such as the average and typical wave conditions, frequency of occurrence of different wave parameters, variations in wave heights from weekly to decadal scales) are established based on waverider measurements at the Darss Sill in 1991–2010. The measured climate is compared with two numerical simulations with the WAM wave model driven by downscaled reanalysis of wind fields for 1958–2002 and by adjusted geostrophic winds for 1970–2007. The wave climate in this region is typical for semi-enclosed basins of the Baltic Sea. The maximum wave heights are about half of those in the Baltic Proper. The maximum recorded significant wave height H S =4.46 m occurred on 3 November 1995. The wave height exhibits no long-term trend but reveals modest interannual (about 12 % of the long-term mean of 0.76 m) and substantial seasonal variation. The wave periods are mostly concentrated in a narrow range of 2.6–4 s. Their distribution is almost constant over decades. The role of remote swell is very small.

Description: Laminar and weakly turbulent oceanic gravity currents performing inertial oscillations Ocean Science, 8, 301-317, 2012 Author(s): A. Wirth The small scale dynamics of a weakly turbulent oceanic gravity current is determined. The gravity current considered is initially at rest and adjusts by performing inertial oscillations to a geostrophic mean flow. The dynamics is explored with a hierarchy of mathematical models. The most involved are the fully 3-D Navier-Stokes equations subject to the Boussinesq approximation. A 1-D and 0-D mathematical model of the same gravity current dynamics are systematically derived. Using this hierarchy and the numerical solutions of the mathematical models, the turbulent dynamics at the bottom and the interface is explored and their interaction investigated. Three different regimes of the small scale dynamics of the gravity current are identified, they are characterised by laminar flow, coherent roll vortices and turbulent dynamics with coherent streaks and bursts. The problem of the rectification of the turbulent fluxes, that is, how to average out the fluctuations and calculate their average influence on the flow, is considered. It is shown that two different regimes of friction are superposed, an Ekman friction applies to the average geostrophic flow and a linear friction, not influenced by rotation, to the inertial oscillations. The combination of the two makes the bulk friction non-local in time for the 0-D model. The implications of the results for parametrisations of the Ekman dynamics and the small scale turbulent fluxes in the planetary boundary layer are discussed.

Description: A community diagnostic tool for Chemistry Climate Model Validation Geoscientific Model Development Discussions, 5, 1229-1261, 2012 Author(s): A. Gettelman, V. Eyring, C. Fischer, H. Shiona, I. Cionni, M. Neish, O. Morgenstern, S. W. Wood, and Z. Li This technical note presents an overview of the Chemistry-Climate Model Validation Diagnostic (CCMVal-Diag) tool for model evaluation. The CCMVal-Diag tool is a flexible and extensible open source package that facilitates the complex evaluation of global models. Models can be compared to other models, ensemble members (simulations with the same model), and/or many types of observations. The tool can also compute quantitative performance metrics. The initial construction and application is to coupled Chemistry-Climate Models (CCMs) participating in CCMVal, but the evaluation of climate models that submitted output to the Coupled Model Intercomparison Project (CMIP) is also possible. The package has been used to assist with analysis of simulations for the 2010 WMO/UNEP Scientific Ozone Assessment and the SPARC Report on the Evaluation of CCMs. The CCMVal-Diag tool is described and examples of how it functions are presented, along with links to detailed descriptions, instructions and source code. The CCMVal-Diag tool is supporting model development as well as quantifying model improvements, both for different versions of individual models and for different generations of community-wide collections of models used in international assessments. The code allows further extensions by different users for different applications and types, e.g. to other components of the Earth System. User modifications are encouraged and easy to perform with a minimum of coding.

Description: Description of a hybrid ice sheet-shelf model, and application to Antarctica Geoscientific Model Development Discussions, 5, 1077-1134, 2012 Author(s): D. Pollard and R. M. DeConto The formulation of a 3-D ice sheet-shelf model is described. The model is designed for long-term continental-scale applications, and has been used mostly in paleoclimatic studies. It uses a hybrid combination of the scaled Shallow Ice and Shallow Shelf Approximations for ice flow. Floating ice shelves and grounding-line migration are included, with parameterized ice fluxes at grounding lines that allows relatively coarse resolutions to be used. All significant components and parameterizations of the model are described in some detail. Basic results for modern Antarctica are compared with observations, and simulations over the last 5 million yr are shown to be similar to previously published results using an earlier model version. The sensitivity of ice retreat during the last deglaciation to basal sliding coefficients is discussed.

Description: A new marine ecosystem model for the University of Victoria Earth system climate model Geoscientific Model Development Discussions, 5, 1135-1201, 2012 Author(s): D. P. Keller, A. Oschlies, and M. Eby Earth system climate models (ESCMs) are valuable tools that can be used to gain a better understanding of the climate system, global biogeochemical cycles, and how anthropogenically-driven changes may affect them. Here we describe improvements made to the marine biogeochemical ecosystem component of the University of Victoria's ESCM (version 2.9). Major changes include corrections to the code and equations describing phytoplankton light limitation and zooplankton grazing, the implementation of a more realistic zooplankton growth and grazing model, and the implementation of an iron limitation scheme to constrain phytoplankton growth. The new model is evaluated after a 10 000-yr spin-up and compared to both the previous version and observations. For the majority of biogeochemical tracers and ecosystem processes the new model shows significant improvements when compared to the previous version and evaluated against observations. Many of the improvements are due to better simulation of seasonal changes in higher latitude ecosystems and the effect that this has on ocean biogeochemistry. This improved model is intended to provide a basic new ESCM model component, which can be used as is or expanded upon (i.e., the addition of new tracers), for climate change and biogeochemical cycling research.

Description: Development of a parameterization of black carbon aging for use in general circulation models Geoscientific Model Development Discussions, 5, 1263-1293, 2012 Author(s): N. Oshima and M. Koike A parameterization of black carbon (BC) aging in the atmosphere is developed for use in general circulation models (GCMs) that separately treats size distributions of hydrophobic BC and hydrophilic BC using lognormal modes. The rate of BC aging is expressed as the conversion rate from hydrophobic BC to hydrophilic BC modes (i.e., inverse of the e-folding time of the conversion, 1/ τ BC ). In this study, the conversion rates are estimated using results of detailed calculations by a size and mixing state resolved aerosol box model with numerous initial conditions. We introduce a new concept, the hydrophobic-BC-mass-normalized coating rate ( V BC ), defined as the rate of increase of the mass concentration of condensed materials on hydrophobic BC normalized by the hydrophobic BC mass concentration. Although the conversion rate largely varies depending on the atmospheric conditions and the concentrations of chemical species, we find that the variations of the conversion rate are generally expressed well by a unique function of V BC for given lognormal size distributions of hydrophobic BC. The parameterized conversion rate is expressed as a function of V BC , which enables the representation of diurnal and seasonal variations of the BC aging rate and its spatial differences in polluted and clean air, while other widely used constant conversion rates cannot. Application of our newly developed parameterization to GCMs will provide more reliable estimates of the spatial distribution of BC and its radiative effects at regional and global scales.

Description: Pre-industrial and mid-Pliocene simulations with NorESM-L – AGCM simulations Geoscientific Model Development Discussions, 5, 1203-1227, 2012 Author(s): Z. Zhang and Q. Yan In the Pliocene Model Intercomparison Project (PlioMIP), two sets of experiments are suggested. One includes a reference and a mid-Pliocene experiment run with atmosphere general circulation models (AGCM experiments, referred to as Experiments I), the other includes a pre-industrial and a mid-Pliocene experiment run with coupled ocean-atmosphere general circulation models (AOGCM experiments, referred to as Experiment II). In this paper, we describe the AGCM experiments with the atmosphere model in the low resolution version of the Norwegian Earth System Model (NorESM-L), and also assess the potential uncertainties in analyzing mid-Pliocene climate anomalies, due to choosing SST fields for the reference experiment. We carry out a mid-Pliocene experiment, a control experiment forced by the modern SST fields, and a pre-industrial experiment forced by the monthly SST fields from HadISST averaged between 1879 and 1900. Our experiments illustrate that the simulated mid-Pliocene global annual mean SAT is 17.1 °C. It is 2.5 °C warmer than the control experiment, but 2.7 °C warmer than the pre-industrial experiment. We find that the uncertainties in analyses of mid-Pliocene climate anomalies are small on a global scale, but still large on a regional scale. On the regional scale, these uncertainties should be noticed and assessed in future PlioMIP studies.

Description: Modeling of wave-induced irradiance variability in the upper ocean mixed layer Ocean Science, 8, 103-120, 2012 Author(s): M. Hieronymi, A. Macke, and O. Zielinski A Monte Carlo based radiative transfer model has been developed for calculating the availability of solar radiation within the top 100 m of the ocean. The model is optimized for simulations of spatial high resolution downwelling irradiance E d fluctuations that arise from the lensing effect of waves at the water surface. In a first step the accuracy of simulation results has been verified by measurements of the oceanic underwater light field and through intercomparison with an established radiative transfer model. Secondly the potential depth-impact of nonlinear shaped single waves, from capillary to swell waves, is assessed by considering the most favorable conditions for light focusing, i.e. monochromatic light at 490 nm, very clear oceanic water with a low chlorophyll a content of 0.1 mg m −3 and high sun elevation. Finally light fields below irregular wave profiles accounting for realistic sea states were simulated. Our simulation results suggest that under open ocean conditions light flashes with 50% irradiance enhancements can appear down to 35 m depth, and light variability in the range of ±10% compared to the mean E d is still possible in 100 m depth.

Description: Towards an improved description of ocean uncertainties: effect of local anamorphic transformations on spatial correlations Ocean Science, 8, 121-142, 2012 Author(s): J.-M. Brankart, C.-E. Testut, D. Béal, M. Doron, C. Fontana, M. Meinvielle, P. Brasseur, and J. Verron The objective of this paper is to investigate if the description of ocean uncertainties can be significantly improved by applying a local anamorphic transformation to each model variable, and by making the assumption of joint Gaussianity for the transformed variables, rather than for the original variables. For that purpose, it is first argued that a significant improvement can already be obtained by deriving the local transformations from a simple histogram description of the marginal distributions. Two distinctive advantages of this solution for large size applications are the conciseness and the numerical efficiency of the description. Second, various oceanographic examples are used to evaluate the effect of the resulting piecewise linear local anamorphic transformations on the spatial correlation structure. These examples include (i) stochastic ensemble descriptions of the effect of atmospheric uncertainties on the ocean mixed layer, and of wind uncertainties or parameter uncertainties on the ecosystem, and (ii) non-stochastic ensemble descriptions of forecast uncertainties in current sea ice and ecosystem pre-operational developments. The results indicate that (i) the transformation is accurate enough to faithfully preserve the correlation structure if the joint distribution is already close to Gaussian, and (ii) the transformation has the general tendency of increasing the correlation radius as soon as the spatial dependence between random variables becomes nonlinear, with the important consequence of reducing the number of degrees of freedom in the uncertainties, and thus increasing the benefit that can be expected from a given observation network.

Description: Seasonal leaf dynamics for tropical evergreen forests in a process based global ecosystem model Geoscientific Model Development Discussions, 5, 639-681, 2012 Author(s): M. De Weirdt, H. Verbeeck, F. Maignan, P. Peylin, B. Poulter, D. Bonal, P. Ciais, and K. Steppe The influence of seasonal phenology in tropical humid forests on canopy photosynthesis remains poorly understood and its representation in global vegetation models highly simplified, typically with no seasonal variability of canopy leaf area properties taken into account. However, recent flux tower and remote sensing studies suggest that seasonal phenology in tropical rainforests exerts a large influence over carbon and water fluxes, with feedbacks that can significantly influence climate dynamics. A more realistic description of the underlying mechanisms that drive seasonal tropical forest photosynthesis and phenology could improve the correspondence of global vegetation model outputs with the wet-dry season biogeochemical patterns measured at flux tower sites. Here, we introduce a leaf Net Primary Production (NPP) based canopy dynamics scheme for evergreen tropical forests in the global terrestrial ecosystem model ORCHIDEE and validated the new scheme against in-situ carbon flux measurements. Modelled Gross Primary Productivity (GPP) patterns are analyzed in details for a flux tower site in French Guiana, in a forest where the dry season is short and where the vegetation is considered to have developed adaptive mechanisms against drought stress. By including leaf litterfall seasonality and a coincident light driven leaf flush and seasonal change in photosynthetic capacity in ORCHIDEE, modelled carbon and water fluxes more accurately represent the observations. The fit to GPP flux data was substantially improved and the results confirmed that by modifying canopy dynamics to benefit from increased light conditions, a better representation of the seasonal carbon flux patterns was made.

Description: Mesoscale variability of water masses in the Arabian Sea as revealed by ARGO floats Ocean Science, 8, 227-248, 2012 Author(s): X. Carton, P. L'Hegaret, and R. Baraille By analysing ARGO float data over the last four years, a few aspects of the mesoscale variability of water masses in the Arabian Sea are described. The Red Sea Outflow Water (RSOW) is concentrated in the Southwestern Gulf of Aden, in particular when a cyclonic gyre predominates in this region. Salinities of 36.5 and temperatures of 16 °C are found in this area at depths between 600 and 1000 m. RSOW is more dilute in the eastern part of the Gulf, where intense and relatively barotropic gyres mix it with Indian ocean Central Water. RSOW is also detected along the northeastern coast of Socotra, and fragments of RSOW are found between one and three degrees of latitude north of this island. In the whole Gulf of Aden, the correlation between the deep motions of the floats and the sea-level anomaly measured by altimetry is strong, at regional scale. The finer scale details of the float trajectories are not sampled by altimetry and are often related to the anomalous water masses that the floats encounter. The Persian Gulf Water (PGW) is found in the float profiles near Ras ash Sharbatat (near 57° E, 18° N), again with 36.5 in salinity and about 18–19 °C in temperature. These observations were achieved in winter when the southwestward monsoon currents can advect PGW along the South Arabian coast. Fragments of PGW were also observed in the Arabian Sea between 18 and 20° N and 63 and 65° E in summer, showing that this water mass can escape the Gulf of Oman southeastward, during that season. Kinetic energy distributions of floats with respect to distance or angle share common features between the two regions (Gulf of Aden and Arabian Sea), in particular peaks at 30, 50 and 150 km scales and along the axis of monsoon currents. Hydrological measurements by floats are also influenced by the seasonal variations of PGW and RSOW in these regions.

Description: Variational assimilation of Lagrangian trajectories in the Mediterranean ocean Forecasting System Ocean Science, 8, 249-259, 2012 Author(s): J. A. U. Nilsson, S. Dobricic, N. Pinardi, P.-M. Poulain, and D. Pettenuzzo A novel method for three-dimensional variational assimilation of Lagrangian data with a primitive-equation ocean model is proposed. The assimilation scheme was implemented in the Mediterranean ocean Forecasting System and evaluated for a 4-month period. Four experiments were designed to assess the impact of trajectory assimilation on the model output, i.e. the sea-surface height, velocity, temperature and salinity fields. It was found from the drifter and Argo trajectory assimilation experiment that the forecast skill of surface-drifter trajectories improved by 15 %, that of intermediate-depth float trajectories by 20 %, and moreover, that the forecasted sea-surface height fields improved locally by 5 % compared to satellite data, while the quality of the temperature and salinity fields remained at previous levels. In conclusion, the addition of Lagrangian trajectory assimilation proved to reduce the uncertainties in the model fields, thus yielding a higher accuracy of the ocean forecasts.