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  • 1
    In: Biogeosciences, Copernicus GmbH, Vol. 20, No. 13 ( 2023-07-06), p. 2645-2669
    Abstract: Abstract. Global biogeochemical ocean models help to investigate the present and potential future state of the ocean, its productivity and cascading effects on higher trophic levels such as fish. They are often subjectively tuned against data sets of inorganic tracers and surface chlorophyll and only very rarely against organic components such as particulate organic carbon or zooplankton. The resulting uncertainty in biogeochemical model parameters (and parameterisations) associated with these components can explain some of the large spread of global model solutions with regard to the cycling of organic matter and its impacts on biogeochemical tracer distributions, such as oxygen minimum zones (OMZs). A second source of uncertainty arises from differences in the model spin-up length as, so far, there seems to be no agreement on the required simulation time that should elapse before a global model is assessed against observations. We investigated these two sources of uncertainty by optimising a global biogeochemical ocean model against the root-mean-squared error (RMSE) of six different combinations of data sets and different spin-up times. Besides nutrients and oxygen, the observational data sets also included phyto- and zooplankton, as well as dissolved and particulate organic phosphorus (DOP and POP, respectively). We further analysed the optimised model performance with regard to global biogeochemical fluxes, oxygen inventory and OMZ volume. Following the optimisation procedure, we evaluated the RMSE for all tracers located in the upper 100 m (except for POP, for which we considered the entire vertical domain), regardless of their consideration during optimisation. For the different optimal model solutions, we find a narrow range of the RMSE, between 14 % of the average RMSE after 10 years and 24 % after 3000 years of simulation. Global biogeochemical fluxes, global oxygen bias and OMZ volume showed a much stronger divergence among the models and over time than RMSE, indicating that even models that are similar with regard to local surface tracer concentrations can perform very differently when assessed against the global diagnostics for oxygen. Considering organic tracers in the optimisation had a strong impact on the particle flux exponent (Martin b) and may reduce much of the uncertainty in this parameter and the resulting deep particle flux. Independent of the optimisation setup, the OMZ volume showed a particularly sensitive response with strong trends over time, even after 3000 years of simulation time (despite the constant physical forcing); a high sensitivity to simulation time; and the highest sensitivity to model parameters arising from the tuning strategy setup (variation of almost 80 % of the ensemble mean). In conclusion, calibration against observations of organic tracers can help to improve global biogeochemical models even after short spin-up times; here especially, observations of deep particle flux could provide a powerful constraint. However, a large uncertainty remains with regard to global OMZ volume and its evolution over time, which can show very dynamic behaviour during the model spin-up, which renders temporal extrapolation to a final equilibrium state difficult if not impossible. Given that the real ocean shows variations on many timescales, the assumption of observations representing a steady-state ocean may require some reconsideration.
    Type of Medium: Online Resource
    ISSN: 1726-4189
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2023
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  • 2
    Online Resource
    Online Resource
    Copernicus GmbH ; 2020
    In:  Biogeosciences Vol. 17, No. 12 ( 2020-06-18), p. 3057-3082
    In: Biogeosciences, Copernicus GmbH, Vol. 17, No. 12 ( 2020-06-18), p. 3057-3082
    Abstract: Abstract. Global biogeochemical ocean models are often tuned to match the observed distributions and fluxes of inorganic and organic quantities. This tuning is typically carried out “by hand”. However, this rather subjective approach might not yield the best fit to observations, is closely linked to the circulation employed and is thus influenced by its specific features and even its faults. We here investigate the effect of model tuning, via objective optimisation, of one biogeochemical model of intermediate complexity when simulated in five different offline circulations. For each circulation, three of six model parameters have been adjusted to characteristic features of the respective circulation. The values of these three parameters – namely, the oxygen utilisation of remineralisation, the particle flux parameter and potential nitrogen fixation rate – correlate significantly with deep mixing and ideal age of North Atlantic Deep Water (NADW) and the outcrop area of Antarctic Intermediate Waters (AAIW) and Subantarctic Mode Water (SAMW) in the Southern Ocean. The clear relationship between these parameters and circulation characteristics, which can be easily diagnosed from global models, can provide guidance when tuning global biogeochemistry within any new circulation model. The results from 20 global cross-validation experiments show that parameter sets optimised for a specific circulation can be transferred between similar circulations without losing too much of the model's fit to observed quantities. When compared to model intercomparisons of subjectively tuned, global coupled biogeochemistry–circulation models, each with different circulation and/or biogeochemistry, our results show a much lower range of oxygen inventory, oxygen minimum zone (OMZ) volume and global biogeochemical fluxes. Export production depends to a large extent on the circulation applied, while deep particle flux is mostly determined by the particle flux parameter. Oxygen inventory, OMZ volume, primary production and fixed-nitrogen turnover depend more or less equally on both factors, with OMZ volume showing the highest sensitivity, and residual variability. These results show a beneficial effect of optimisation, even when a biogeochemical model is first optimised in a relatively coarse circulation and then transferred to a different finer-resolution circulation model.
    Type of Medium: Online Resource
    ISSN: 1726-4189
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2020
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  • 3
    Online Resource
    Online Resource
    Copernicus GmbH ; 2022
    In:  Geoscientific Model Development Vol. 15, No. 9 ( 2022-05-05), p. 3537-3554
    In: Geoscientific Model Development, Copernicus GmbH, Vol. 15, No. 9 ( 2022-05-05), p. 3537-3554
    Abstract: Abstract. The skill of global ocean biogeochemical models, and the earth system models in which they are embedded, can be improved by systematic calibration of the parameter values against observations. However, such tuning is seldom undertaken as these models are computationally very expensive. Here we investigate the performance of DFO-LS, a local, derivative-free optimisation algorithm which has been designed for computationally expensive models with irregular model–data misfit landscapes typical of biogeochemical models. We use DFO-LS to calibrate six parameters of a relatively complex global ocean biogeochemical model (MOPS) against synthetic dissolved oxygen, phosphate and nitrate “observations” from a reference run of the same model with a known parameter configuration. The performance of DFO-LS is compared with that of CMA-ES, another derivative-free algorithm that was applied in a previous study to the same model in one of the first successful attempts at calibrating a global model of this complexity. We find that DFO-LS successfully recovers five of the six parameters in approximately 40 evaluations of the misfit function (each one requiring a 3000-year run of MOPS to equilibrium), while CMA-ES needs over 1200 evaluations. Moreover, DFO-LS reached a “baseline” misfit, defined by observational noise, in just 11–14 evaluations, whereas CMA-ES required approximately 340 evaluations. We also find that the performance of DFO-LS is not significantly affected by observational sparsity, however fewer parameters were successfully optimised in the presence of observational uncertainty. The results presented here suggest that DFO-LS is sufficiently inexpensive and robust to apply to the calibration of complex, global ocean biogeochemical models.
    Type of Medium: Online Resource
    ISSN: 1991-9603
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2022
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  • 4
    Online Resource
    Online Resource
    Copernicus GmbH ; 2017
    In:  Biogeosciences Vol. 14, No. 21 ( 2017-11-08), p. 4965-4984
    In: Biogeosciences, Copernicus GmbH, Vol. 14, No. 21 ( 2017-11-08), p. 4965-4984
    Abstract: Abstract. The assessment of the ocean biota's role in climate change is often carried out with global biogeochemical ocean models that contain many components and involve a high level of parametric uncertainty. Because many data that relate to tracers included in a model are only sparsely observed, assessment of model skill is often restricted to tracers that can be easily measured and assembled. Examination of the models' fit to climatologies of inorganic tracers, after the models have been spun up to steady state, is a common but computationally expensive procedure to assess model performance and reliability. Using new tools that have become available for global model assessment and calibration in steady state, this paper examines two different model types – a complex seven-component model (MOPS) and a very simple four-component model (RetroMOPS) – for their fit to dissolved quantities. Before comparing the models, a subset of their biogeochemical parameters has been optimised against annual-mean nutrients and oxygen. Both model types fit the observations almost equally well. The simple model contains only two nutrients: oxygen and dissolved organic phosphorus (DOP). Its misfit and large-scale tracer distributions are sensitive to the parameterisation of DOP production and decay. The spatio-temporal decoupling of nitrogen and oxygen, and processes involved in their uptake and release, renders oxygen and nitrate valuable tracers for model calibration. In addition, the non-conservative nature of these tracers (with respect to their upper boundary condition) introduces the global bias (fixed nitrogen and oxygen inventory) as a useful additional constraint on model parameters. Dissolved organic phosphorus at the surface behaves antagonistically to phosphate, and suggests that observations of this tracer – although difficult to measure – may be an important asset for model calibration.
    Type of Medium: Online Resource
    ISSN: 1726-4189
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2017
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  • 5
    In: Geoscientific Model Development, Copernicus GmbH, Vol. 9, No. 8 ( 2016-08-02), p. 2589-2622
    Abstract: Abstract. Idealised and hindcast simulations performed with the stand-alone ocean carbon-cycle configuration of the Norwegian Earth System Model (NorESM-OC) are described and evaluated. We present simulation results of three different model configurations (two different model versions at different grid resolutions) using two different atmospheric forcing data sets. Model version NorESM-OC1 corresponds to the version that is included in the NorESM-ME1 fully coupled model, which participated in CMIP5. The main update between NorESM-OC1 and NorESM-OC1.2 is the addition of two new options for the treatment of sinking particles. We find that using a constant sinking speed, which has been the standard in NorESM's ocean carbon cycle module HAMOCC (HAMburg Ocean Carbon Cycle model), does not transport enough particulate organic carbon (POC) into the deep ocean below approximately 2000 m depth. The two newly implemented parameterisations, a particle aggregation scheme with prognostic sinking speed, and a simpler scheme that uses a linear increase in the sinking speed with depth, provide better agreement with observed POC fluxes. Additionally, reduced deep ocean biases of oxygen and remineralised phosphate indicate a better performance of the new parameterisations. For model version 1.2, a re-tuning of the ecosystem parameterisation has been performed, which (i) reduces previously too high primary production at high latitudes, (ii) consequently improves model results for surface nutrients, and (iii) reduces alkalinity and dissolved inorganic carbon biases at low latitudes. We use hindcast simulations with prescribed observed and constant (pre-industrial) atmospheric CO2 concentrations to derive the past and contemporary ocean carbon sink. For the period 1990–1999 we find an average ocean carbon uptake ranging from 2.01 to 2.58 Pg C yr−1 depending on model version, grid resolution, and atmospheric forcing data set.
    Type of Medium: Online Resource
    ISSN: 1991-9603
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2016
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  • 6
    Online Resource
    Online Resource
    Copernicus GmbH ; 2017
    In:  Geoscientific Model Development Vol. 10, No. 1 ( 2017-01-09), p. 127-154
    In: Geoscientific Model Development, Copernicus GmbH, Vol. 10, No. 1 ( 2017-01-09), p. 127-154
    Abstract: Abstract. Global biogeochemical ocean models contain a variety of different biogeochemical components and often much simplified representations of complex dynamical interactions, which are described by many ( ≈ 10 to  ≈ 100) parameters. The values of many of these parameters are empirically difficult to constrain, due to the fact that in the models they represent processes for a range of different groups of organisms at the same time, while even for single species parameter values are often difficult to determine in situ. Therefore, these models are subject to a high level of parametric uncertainty. This may be of consequence for their skill with respect to accurately describing the relevant features of the present ocean, as well as their sensitivity to possible environmental changes. We here present a framework for the calibration of global biogeochemical ocean models on short and long timescales. The framework combines an offline approach for transport of biogeochemical tracers with an estimation of distribution algorithm (Covariance Matrix Adaption Evolution Strategy, CMA-ES). We explore the performance and capability of this framework by five different optimizations of six biogeochemical parameters of a global biogeochemical model, simulated over 3000 years. First, a twin experiment explores the feasibility of this approach. Four optimizations against a climatology of observations of annual mean dissolved nutrients and oxygen determine the extent to which different setups of the optimization influence model fit and parameter estimates. Because the misfit function applied focuses on the large-scale distribution of inorganic biogeochemical tracers, parameters that act on large spatial and temporal scales are determined earliest, and with the least spread. Parameters more closely tied to surface biology, which act on shorter timescales, are more difficult to determine. In particular, the search for optimum zooplankton parameters can benefit from a sound knowledge of maximum and minimum parameter values, leading to a more efficient optimization. It is encouraging that, although the misfit function does not contain any direct information about biogeochemical turnover, the optimized models nevertheless provide a better fit to observed global biogeochemical fluxes.
    Type of Medium: Online Resource
    ISSN: 1991-9603
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2017
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  • 7
    Online Resource
    Online Resource
    Copernicus GmbH ; 2017
    In:  Geoscientific Model Development Vol. 10, No. 6 ( 2017-06-29), p. 2425-2445
    In: Geoscientific Model Development, Copernicus GmbH, Vol. 10, No. 6 ( 2017-06-29), p. 2425-2445
    Abstract: Abstract. Conventional integration of Earth system and ocean models can accrue considerable computational expenses, particularly for marine biogeochemical applications. Offline numerical schemes in which only the biogeochemical tracers are time stepped and transported using a pre-computed circulation field can substantially reduce the burden and are thus an attractive alternative. One such scheme is the transport matrix method (TMM), which represents tracer transport as a sequence of sparse matrix–vector products that can be performed efficiently on distributed-memory computers. While the TMM has been used for a variety of geochemical and biogeochemical studies, to date the resulting solutions have not been comprehensively assessed against their online counterparts. Here, we present a detailed comparison of the two. It is based on simulations of the state-of-the-art biogeochemical sub-model embedded within the widely used coarse-resolution University of Victoria Earth System Climate Model (UVic ESCM). The default, non-linear advection scheme was first replaced with a linear, third-order upwind-biased advection scheme to satisfy the linearity requirement of the TMM. Transport matrices were extracted from an equilibrium run of the physical model and subsequently used to integrate the biogeochemical model offline to equilibrium. The identical biogeochemical model was also run online. Our simulations show that offline integration introduces some bias to biogeochemical quantities through the omission of the polar filtering used in UVic ESCM and in the offline application of time-dependent forcing fields, with high latitudes showing the largest differences with respect to the online model. Differences in other regions and in the seasonality of nutrients and phytoplankton distributions are found to be relatively minor, giving confidence that the TMM is a reliable tool for offline integration of complex biogeochemical models. Moreover, while UVic ESCM is a serial code, the TMM can be run on a parallel machine with no change to the underlying biogeochemical code, thus providing orders of magnitude speed-up over the online model.
    Type of Medium: Online Resource
    ISSN: 1991-9603
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2017
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  • 8
    Online Resource
    Online Resource
    Copernicus GmbH ; 2019
    In:  Biogeosciences Vol. 16, No. 15 ( 2019-08-15), p. 3095-3111
    In: Biogeosciences, Copernicus GmbH, Vol. 16, No. 15 ( 2019-08-15), p. 3095-3111
    Abstract: Abstract. Particle aggregation determines the particle flux length scale and affects the marine oxygen concentration and thus the volume of oxygen minimum zones (OMZs) that are of special relevance for ocean nutrient cycles and marine ecosystems and that have been found to expand faster than can be explained by current state-of-the-art models. To investigate the impact of particle aggregation on global model performance, we carried out a sensitivity study with different parameterisations of marine aggregates and two different model resolutions. Model performance was investigated with respect to global nutrient and oxygen concentrations, as well as extent and location of OMZs. Results show that including an aggregation model improves the representation of OMZs. Moreover, we found that besides a fine spatial resolution of the model grid, the consideration of porous particles, an intermediate-to-high particle sinking speed and a moderate-to-high stickiness improve the model fit to both global distributions of dissolved inorganic tracers and regional patterns of OMZs, compared to a model without aggregation. Our model results therefore suggest that improvements not only in the model physics but also in the description of particle aggregation processes can play a substantial role in improving the representation of dissolved inorganic tracers and OMZs on a global scale. However, dissolved inorganic tracers are apparently not sufficient for a global model calibration, which could necessitate global model calibration against a global observational dataset of marine organic particles.
    Type of Medium: Online Resource
    ISSN: 1726-4189
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2019
    detail.hit.zdb_id: 2158181-2
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  • 9
    In: Geoscientific Model Development, Copernicus GmbH, Vol. 15, No. 15 ( 2022-08-02), p. 5987-6024
    Abstract: Abstract. The consideration of marine biogeochemistry is essential for simulating the carbon cycle in an Earth system model. Here we present the implementation and evaluation of a marine biogeochemical model, the Model of Oceanic Pelagic Stoichiometry (MOPS) in the Flexible Ocean and Climate Infrastructure (FOCI) climate model. FOCI-MOPS enables the simulation of marine biological processes, i.e. the marine carbon, nitrogen, and oxygen cycles with prescribed or prognostic atmospheric CO2 concentration. A series of experiments covering the historical period (1850–2014) were performed following the DECK (Diagnostic, Evaluation and Characterization of Klima) and CMIP6 (Coupled Model Intercomparison Project 6) protocols. Overall, modelled biogeochemical tracer distributions and fluxes, transient evolution in surface air temperature, air–sea CO2 fluxes, and changes in ocean carbon and heat contents are in good agreement with observations. Modelled inorganic and organic tracer distributions are quantitatively evaluated by statistically derived metrics. Results of the FOCI-MOPS model, including sea surface temperature, surface pH, oxygen (100–600 m), nitrate (0–100 m), and primary production, are within the range of other CMIP6 model results. Overall, the evaluation of FOCI-MOPS indicates its suitability for Earth climate system simulations.
    Type of Medium: Online Resource
    ISSN: 1991-9603
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2022
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  • 10
    In: Biogeosciences, Copernicus GmbH, Vol. 18, No. 9 ( 2021-05-12), p. 2891-2916
    Abstract: Abstract. Small pelagic fish off the coast of Peru in the eastern tropical South Pacific (ETSP) support around 10 % of global fish catches. Their stocks fluctuate interannually due to environmental variability which can be exacerbated by fishing pressure. Because these fish are planktivorous, any change in fish abundance may directly affect the plankton and the biogeochemical system. To investigate the potential effects of variability in small pelagic fish populations on lower trophic levels, we used a coupled physical–biogeochemical model to build scenarios for the ETSP and compare these against an already-published reference simulation. The scenarios mimic changes in fish predation by either increasing or decreasing mortality of the model's large and small zooplankton compartments. The results revealed that large zooplankton was the main driver of the response of the community. Its concentration increased under low mortality conditions, and its prey, small zooplankton and large phytoplankton, decreased. The response was opposite, but weaker, in the high mortality scenarios. This asymmetric behaviour can be explained by the different ecological roles of large, omnivorous zooplankton and small zooplankton, which in the model is strictly herbivorous. The response of small zooplankton depended on the antagonistic effects of mortality changes as well as on the grazing pressure by large zooplankton. The results of this study provide a first insight into how the plankton ecosystem might respond if variations in fish populations were modelled explicitly.
    Type of Medium: Online Resource
    ISSN: 1726-4189
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2021
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